Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold115
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: 1475684
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
File 10 of 10
Found at i:1446405 original size:31 final size:31
Alignment explanation
Indices: 1446362--1446438 Score: 95
Period size: 31 Copynumber: 2.5 Consensus size: 31
1446352 TAGGTTGGAA
*
1446362 CAAAAA-TCACTATTCTTATCCAG-TGGCACGG
1 CAAAAACT-ACTATTCTTAT-CAGATGACACGG
*
1446393 CAAAAACTACTATTTTTATCAGATGACACGG
1 CAAAAACTACTATTCTTATCAGATGACACGG
*
1446424 AAAAAACTACTATTC
1 CAAAAACTACTATTC
1446439 CTAACTGGTG
Statistics
Matches: 40, Mismatches: 4, Indels: 4
0.83 0.08 0.08
Matches are distributed among these distances:
30 3 0.08
31 36 0.90
32 1 0.03
ACGTcount: A:0.39, C:0.22, G:0.12, T:0.27
Consensus pattern (31 bp):
CAAAAACTACTATTCTTATCAGATGACACGG
Found at i:1446454 original size:31 final size:31
Alignment explanation
Indices: 1446384--1446454 Score: 79
Period size: 31 Copynumber: 2.3 Consensus size: 31
1446374 TTCTTATCCA
* ** *
1446384 GTGGCACGGCAAAAACTACTATTTTTATCAG
1 GTGGCACGGAAAAAACTACTATTCCTAACAG
* * *
1446415 ATGACACGGAAAAAACTACTATTCCTAACTG
1 GTGGCACGGAAAAAACTACTATTCCTAACAG
1446446 GTGGCACGG
1 GTGGCACGG
1446455 TTTAAAACCG
Statistics
Matches: 31, Mismatches: 9, Indels: 0
0.77 0.22 0.00
Matches are distributed among these distances:
31 31 1.00
ACGTcount: A:0.34, C:0.21, G:0.21, T:0.24
Consensus pattern (31 bp):
GTGGCACGGAAAAAACTACTATTCCTAACAG
Found at i:1450319 original size:13 final size:13
Alignment explanation
Indices: 1450301--1450325 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1450291 CATAAAATGT
1450301 TGTATCGATACAA
1 TGTATCGATACAA
1450314 TGTATCGATACA
1 TGTATCGATACA
1450326 TATTTTTTTG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:1450323 original size:33 final size:33
Alignment explanation
Indices: 1450281--1450350 Score: 104
Period size: 33 Copynumber: 2.1 Consensus size: 33
1450271 TTCAACGATT
1450281 TGTATCGATACATAAAATGTTGTATCGATACAA
1 TGTATCGATACATAAAATGTTGTATCGATACAA
*** *
1450314 TGTATCGATACATATTTTTTTGTATCGATACAA
1 TGTATCGATACATAAAATGTTGTATCGATACAA
1450347 TGTA
1 TGTA
1450351 AGCTACTGCC
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
33 33 1.00
ACGTcount: A:0.34, C:0.11, G:0.14, T:0.40
Consensus pattern (33 bp):
TGTATCGATACATAAAATGTTGTATCGATACAA
Found at i:1450408 original size:13 final size:13
Alignment explanation
Indices: 1450390--1450414 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1450380 ATTACTCACA
1450390 TGTATCGATACAT
1 TGTATCGATACAT
1450403 TGTATCGATACA
1 TGTATCGATACA
1450415 CTGATCTTTG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:1450479 original size:52 final size:52
Alignment explanation
Indices: 1450423--1450543 Score: 224
Period size: 52 Copynumber: 2.3 Consensus size: 52
1450413 CACTGATCTT
*
1450423 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACATTATAAAA
1 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATAAAA
*
1450475 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATTAAA
1 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATAAAA
1450527 TGTATCGATACATGCAG
1 TGTATCGATACATGCAG
1450544 TAACTTTTCA
Statistics
Matches: 67, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
52 67 1.00
ACGTcount: A:0.35, C:0.18, G:0.18, T:0.29
Consensus pattern (52 bp):
TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATAAAA
Found at i:1454394 original size:13 final size:13
Alignment explanation
Indices: 1454376--1454401 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1454366 ACAAAGATCC
1454376 ATGTATCGATACA
1 ATGTATCGATACA
1454389 ATGTATCGATACA
1 ATGTATCGATACA
1454402 TTGATTAATG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:1454401 original size:33 final size:33
Alignment explanation
Indices: 1454359--1454421 Score: 90
Period size: 33 Copynumber: 1.9 Consensus size: 33
1454349 TTCCCAGATA
*
1454359 TATCGATACAAAGATCCATGTATCGATACAATG
1 TATCGATACAAAGATCAATGTATCGATACAATG
** *
1454392 TATCGATACATTGATTAATGTATCGATACA
1 TATCGATACAAAGATCAATGTATCGATACA
1454422 TTTCCTTGGC
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
33 26 1.00
ACGTcount: A:0.38, C:0.16, G:0.14, T:0.32
Consensus pattern (33 bp):
TATCGATACAAAGATCAATGTATCGATACAATG
Found at i:1455325 original size:49 final size:49
Alignment explanation
Indices: 1455110--1456330 Score: 767
Period size: 49 Copynumber: 25.9 Consensus size: 49
1455100 GTGATAAAGA
* * * * *
1455110 TGCCAATATGCTGATTCACGGCCAACAATATTGGGCTTAAAGTTGAGAAAAAGG
1 TGCCAATATGCTGATTCAAGGCCAACGACATTGGACTTAAAGAT--G---AAGG
* * * * * * *
1455164 ATGTCAATGTGCTGATTCACA-GTCAGCGACATTAGACTTGAAGAAGAA--
1 -TGCCAATATGCTGATTCA-AGGCCAACGACATTGGACTTAAAGATGAAGG
* ** * * * * *
1455212 TGCCAATGTGCTGAGACAAGGCCAGCGACATTGGGCTTAGGAATGTTAAAGA
1 TGCCAATATGCTGATTCAAGGCCAACGACATTGGACTTA--AA-GATGAAGG
* * * * *
1455264 TGCCAATATGTTGATTCAAGGCCAATGATATCGGACTTAAGGATGAAGG
1 TGCCAATATGCTGATTCAAGGCCAACGACATTGGACTTAAAGATGAAGG
* * * * *
1455313 TGCCAATGTGTTGATTCAAGGCCAACGACATTAGACTTGAAGAAGAA--
1 TGCCAATATGCTGATTCAAGGCCAACGACATTGGACTTAAAGATGAAGG
* * * **
1455360 TGCCAATGTGTTGATTCAAGGCCAATGACATTGGGTTTTAAAGATGACGAAGG
1 TGCCAATATGCTGATTCAAGGCCAACGACATT-GGACTTAAAGAT---GAAGG
* *
1455413 CGCCAATATGCTGATTCAAGGCCAACGATATTGGACTTAAAGATGAAGG
1 TGCCAATATGCTGATTCAAGGCCAACGACATTGGACTTAAAGATGAAGG
* * *
1455462 TGCCAATGTGCTGATTCAAGACCAACGACATTGGACTTGAAGATGAAGG
1 TGCCAATATGCTGATTCAAGGCCAACGACATTGGACTTAAAGATGAAGG
* * * *
1455511 TGCCAATATGCTGATTCAAGGCCAGCGATATTGGGCTTAAAGATGGTTGAGG
1 TGCCAATATGCTGATTCAAGGCCAACGACATTGGACTTAAAGAT-G--AAGG
* * * * * * *
1455563 TGCCGATGTGCTGATTCAAGGCCCACGGCATCGGTCTTAAAGATAAAGG
1 TGCCAATATGCTGATTCAAGGCCAACGACATTGGACTTAAAGATGAAGG
* * *
1455612 TGCCAATATGCTTATTCAAGGCCAACGATATCGGACTTAAAGATGAAGG
1 TGCCAATATGCTGATTCAAGGCCAACGACATTGGACTTAAAGATGAAGG
* ** *
1455661 TGCCAATGTGCTGATTCAAGGCCAGTGACATTAGACTTAAAGATGAAGG
1 TGCCAATATGCTGATTCAAGGCCAACGACATTGGACTTAAAGATGAAGG
* * * * *
1455710 TGCCACTATGCTGATTCAAGGCTAGCGATATTGGGC-T-----T--A--
1 TGCCAATATGCTGATTCAAGGCCAACGACATTGGACTTAAAGATGAAGG
* * * *
1455749 TGCCAATGTGTTGATTCAAGGCCAACGACATTGGTCTTAAAGATAAAGG
1 TGCCAATATGCTGATTCAAGGCCAACGACATTGGACTTAAAGATGAAGG
* * * *
1455798 TGCCAATATGCTGATTCAAGGCCAGCGATACTGGGC-T-----T----G
1 TGCCAATATGCTGATTCAAGGCCAACGACATTGGACTTAAAGATGAAGG
* * * * *
1455837 TGCCAATGTGCTGATTCAAGGCCAGCGACAATGGTCTTAAAGA-CAAGG
1 TGCCAATATGCTGATTCAAGGCCAACGACATTGGACTTAAAGATGAAGG
* *
1455885 TGCCAATATGCTGATTCAAGGCCAACGATATTGGGC-T-----T--A--
1 TGCCAATATGCTGATTCAAGGCCAACGACATTGGACTTAAAGATGAAGG
* * * *
1455924 TGCCAATGTGCTGATTCAAGGCCAGCGACATTGGTCTTAAAGA-CAAGG
1 TGCCAATATGCTGATTCAAGGCCAACGACATTGGACTTAAAGATGAAGG
* * *
1455972 TGCCAATATGCCGATTCAAGGCCAACGATATTGGGC-T-----T--A--
1 TGCCAATATGCTGATTCAAGGCCAACGACATTGGACTTAAAGATGAAGG
* * * *
1456011 TGCCAATGTGCTGATTCAAGGCCAGCGACATTGGTCTTAAAGA-CAAGG
1 TGCCAATATGCTGATTCAAGGCCAACGACATTGGACTTAAAGATGAAGG
* * *
1456059 TGCCAATATGCTGATTCAAGGCCAGCGATATTGGGC-T-----T--A--
1 TGCCAATATGCTGATTCAAGGCCAACGACATTGGACTTAAAGATGAAGG
* * * * *
1456098 TGCCAATGTGCTGATTCAAGGTCAGCGACATTGGTCTTAAAGA-CAAGG
1 TGCCAATATGCTGATTCAAGGCCAACGACATTGGACTTAAAGATGAAGG
* * *
1456146 TGCCAATATGCTCATTCAAGGCCAACGATATTGGAC-TCAAGATGGAAATGG
1 TGCCAATATGCTGATTCAAGGCCAACGACATTGGACTTAAAGAT-G-AA-GG
** * * * *
1456197 TGCCAATATGCTGATTCAAGGTTAGCAATATTGGA-TT-----TAAAGG
1 TGCCAATATGCTGATTCAAGGCCAACGACATTGGACTTAAAGATGAAGG
* * * * *
1456240 TGCTAATGTGCTGATTCAAGGCCAGCGACATCGG-TTTCAAAGATGAAGG
1 TGCCAATATGCTGATTCAAGGCCAACGACATTGGACTT-AAAGATGAAGG
* *
1456289 TGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAG
1 TGCCAATATGCTGATTCAAGGCCAACGACATTGGACTTAAAG
1456331 GTGCCACGGA
Statistics
Matches: 914, Mismatches: 170, Indels: 170
0.73 0.14 0.14
Matches are distributed among these distances:
39 157 0.17
40 5 0.01
41 4 0.00
43 33 0.04
44 2 0.00
45 1 0.00
46 5 0.01
47 70 0.08
48 135 0.15
49 317 0.35
50 11 0.01
51 36 0.04
52 79 0.09
53 28 0.03
55 31 0.03
ACGTcount: A:0.31, C:0.18, G:0.26, T:0.25
Consensus pattern (49 bp):
TGCCAATATGCTGATTCAAGGCCAACGACATTGGACTTAAAGATGAAGG
Found at i:1455629 original size:150 final size:149
Alignment explanation
Indices: 1455110--1456097 Score: 740
Period size: 150 Copynumber: 6.9 Consensus size: 149
1455100 GTGATAAAGA
* * * * * *
1455110 TGCCAATATGCTGATTCACGGCCAACAATATTGGGCTTAAAGTTGAGAAAAAGGATGTCAATGTG
1 TGCCAATATGCTGATTCAAGGCCAACGATATCGGACTTAAAGAT--G---AAGG-TGCCAATGTG
* * * * * **
1455175 CTGATTCACA-GTCAGCGACATTAGACTTGAAGAAGAA--TGCCAATGTGCTGAGACAAGGCCAG
60 TTGATTCA-AGGCCAACGACATTGGACTTGAAGATGAAGGTGCCAATGTGCTGATTCAAGGCCAG
* *
1455237 CGACATTGGGCTT-AGGAATGTTAAAGA
124 CGACATTGGGCTTAAAG-ATGTT-AAGG
* * *
1455264 TGCCAATATGTTGATTCAAGGCCAATGATATCGGACTTAAGGATGAAGGTGCCAATGTGTTGATT
1 TGCCAATATGCTGATTCAAGGCCAACGATATCGGACTTAAAGATGAAGGTGCCAATGTGTTGATT
* * * **
1455329 CAAGGCCAACGACATTAGACTTGAAGAAGAA--TGCCAATGTGTTGATTCAAGGCCAATGACATT
66 CAAGGCCAACGACATTGGACTTGAAGATGAAGGTGCCAATGTGCTGATTCAAGGCCAGCGACATT
* **
1455392 GGGTTTTAAAGATGACGAAGG
131 GGG-CTTAAAGATG-TTAAGG
* * *
1455413 CGCCAATATGCTGATTCAAGGCCAACGATATTGGACTTAAAGATGAAGGTGCCAATGTGCTGATT
1 TGCCAATATGCTGATTCAAGGCCAACGATATCGGACTTAAAGATGAAGGTGCCAATGTGTTGATT
* * *
1455478 CAAGACCAACGACATTGGACTTGAAGATGAAGGTGCCAATATGCTGATTCAAGGCCAGCGATATT
66 CAAGGCCAACGACATTGGACTTGAAGATGAAGGTGCCAATGTGCTGATTCAAGGCCAGCGACATT
*
1455543 GGGCTTAAAGATGGTTGAGG
131 GGGCTTAAAGAT-GTTAAGG
* * * ** * * *
1455563 TGCCGATGTGCTGATTCAAGGCCCACGGCATCGGTCTTAAAGATAAAGGTGCCAATATGCTT-AT
1 TGCCAATATGCTGATTCAAGGCCAACGATATCGGACTTAAAGATGAAGGTGCCAATGTG-TTGAT
* * * *
1455627 TCAAGGCCAACGATATCGGACTTAAAGATGAAGGTGCCAATGTGCTGATTCAAGGCCAGTGACAT
65 TCAAGGCCAACGACATTGGACTTGAAGATGAAGGTGCCAATGTGCTGATTCAAGGCCAGCGACAT
* *
1455692 TAGACTTAAAGATG--AAGG
130 TGGGCTTAAAGATGTTAAGG
* * * * *
1455710 TGCCACTATGCTGATTCAAGGCTAGCGATATTGGGC-T-----T--A--TGCCAATGTGTTGATT
1 TGCCAATATGCTGATTCAAGGCCAACGATATCGGACTTAAAGATGAAGGTGCCAATGTGTTGATT
* * * * * *
1455765 CAAGGCCAACGACATTGGTCTTAAAGATAAAGGTGCCAATATGCTGATTCAAGGCCAGCGATACT
66 CAAGGCCAACGACATTGGACTTGAAGATGAAGGTGCCAATGTGCTGATTCAAGGCCAGCGACATT
1455830 GGGC---------TT---G
131 GGGCTTAAAGATGTTAAGG
* * * * * * *
1455837 TGCCAATGTGCTGATTCAAGGCCAGCGACAAT-GGTCTTAAAGA-CAAGGTGCCAATATGCTGAT
1 TGCCAATATGCTGATTCAAGGCCAACGA-TATCGGACTTAAAGATGAAGGTGCCAATGTGTTGAT
* *
1455900 TCAAGGCCAACGATATTGGGC-T-----T--A--TGCCAATGTGCTGATTCAAGGCCAGCGACAT
65 TCAAGGCCAACGACATTGGACTTGAAGATGAAGGTGCCAATGTGCTGATTCAAGGCCAGCGACAT
* *
1455955 TGGTCTTAAAGA---CAAGG
130 TGGGCTTAAAGATGTTAAGG
* * * *
1455972 TGCCAATATGCCGATTCAAGGCCAACGATATTGGGC-T-----T--A--TGCCAATGTGCTGATT
1 TGCCAATATGCTGATTCAAGGCCAACGATATCGGACTTAAAGATGAAGGTGCCAATGTGTTGATT
* * * * * *
1456027 CAAGGCCAGCGACATTGGTCTTAAAGA-CAAGGTGCCAATATGCTGATTCAAGGCCAGCGATATT
66 CAAGGCCAACGACATTGGACTTGAAGATGAAGGTGCCAATGTGCTGATTCAAGGCCAGCGACATT
1456091 GGGCTTA
131 GGGCTTA
1456098 TGCCAATGTG
Statistics
Matches: 682, Mismatches: 108, Indels: 107
0.76 0.12 0.12
Matches are distributed among these distances:
126 64 0.09
127 30 0.04
128 5 0.01
130 1 0.00
133 1 0.00
134 4 0.01
135 66 0.10
136 34 0.05
137 71 0.10
139 1 0.00
141 1 0.00
146 1 0.00
147 30 0.04
148 71 0.10
149 100 0.15
150 133 0.20
151 32 0.05
152 1 0.00
154 36 0.05
ACGTcount: A:0.31, C:0.18, G:0.26, T:0.25
Consensus pattern (149 bp):
TGCCAATATGCTGATTCAAGGCCAACGATATCGGACTTAAAGATGAAGGTGCCAATGTGTTGATT
CAAGGCCAACGACATTGGACTTGAAGATGAAGGTGCCAATGTGCTGATTCAAGGCCAGCGACATT
GGGCTTAAAGATGTTAAGG
Found at i:1455658 original size:199 final size:179
Alignment explanation
Indices: 1455563--1456182 Score: 807
Period size: 174 Copynumber: 3.5 Consensus size: 179
1455553 ATGGTTGAGG
* * * * *
1455563 TGCCGATGTGCTGATTCAAGGCCCACGGCATCGGTCTTAAAGATAAAGGTGCCAATATGCTTATT
1 TGCCAATGTGCTGATTCAAGGCCAACGACATTGGTCTTAAAGATAAAGGTGCCAATATGCTGATT
*
1455628 CAAGGCCAACGATATCGGACTTAAAGATGAAGGTGCCAATGTGCTGATTCAAGGCCAGTGACATT
66 CAAGGCCAACGATATCGGAC-T-----T--A-GTGCCAATGTGCTGATTCAAGGCCAGCGACATT
* * *
1455693 AGACTTAAAGATGAAGGTGCCACTATGCTGATTCAAGGCTAGCGATATTGGGC--TTA
122 GGACTTAAAGATGAAGGTGCCAATATGCTGATTCAAGGCCAGCGATATTGGGCTTTTA
*
1455749 TGCCAATGTGTTGATTCAAGGCCAACGACATTGGTCTTAAAGATAAAGGTGCCAATATGCTGATT
1 TGCCAATGTGCTGATTCAAGGCCAACGACATTGGTCTTAAAGATAAAGGTGCCAATATGCTGATT
* * * *
1455814 CAAGGCCAGCGATA-CTGGGCTT-GTGCCAATGTGCTGATTCAAGGCCAGCGACAATGGTCTTAA
66 CAAGGCCAACGATATC-GGACTTAGTGCCAATGTGCTGATTCAAGGCCAGCGACATTGGACTTAA
* *
1455877 AGA-CAAGGTGCCAATATGCTGATTCAAGGCCAACGATATTGGGC--TTA
130 AGATGAAGGTGCCAATATGCTGATTCAAGGCCAGCGATATTGGGCTTTTA
* * *
1455924 TGCCAATGTGCTGATTCAAGGCCAGCGACATTGGTCTTAAAGA-CAAGGTGCCAATATGCCGATT
1 TGCCAATGTGCTGATTCAAGGCCAACGACATTGGTCTTAAAGATAAAGGTGCCAATATGCTGATT
* * *
1455988 CAAGGCCAACGATATTGGGCTTA-TGCCAATGTGCTGATTCAAGGCCAGCGACATTGGTCTTAAA
66 CAAGGCCAACGATATCGGACTTAGTGCCAATGTGCTGATTCAAGGCCAGCGACATTGGACTTAAA
*
1456052 GA-CAAGGTGCCAATATGCTGATTCAAGGCCAGCGATATTGGGC--TTA
131 GATGAAGGTGCCAATATGCTGATTCAAGGCCAGCGATATTGGGCTTTTA
* * * *
1456098 TGCCAATGTGCTGATTCAAGGTCAGCGACATTGGTCTTAAAGA-CAAGGTGCCAATATGCTCATT
1 TGCCAATGTGCTGATTCAAGGCCAACGACATTGGTCTTAAAGATAAAGGTGCCAATATGCTGATT
*
1456162 CAAGGCCAACGATATTGGACT
66 CAAGGCCAACGATATCGGACT
1456183 CAAGATGGAA
Statistics
Matches: 403, Mismatches: 28, Indels: 18
0.90 0.06 0.04
Matches are distributed among these distances:
174 204 0.51
175 81 0.20
176 40 0.10
180 1 0.00
185 2 0.00
186 75 0.19
ACGTcount: A:0.29, C:0.20, G:0.25, T:0.25
Consensus pattern (179 bp):
TGCCAATGTGCTGATTCAAGGCCAACGACATTGGTCTTAAAGATAAAGGTGCCAATATGCTGATT
CAAGGCCAACGATATCGGACTTAGTGCCAATGTGCTGATTCAAGGCCAGCGACATTGGACTTAAA
GATGAAGGTGCCAATATGCTGATTCAAGGCCAGCGATATTGGGCTTTTA
Found at i:1455764 original size:39 final size:39
Alignment explanation
Indices: 1455718--1456136 Score: 289
Period size: 39 Copynumber: 9.8 Consensus size: 39
1455708 GGTGCCACTA
* *
1455718 TGCTGATTCAAGGCTAGCGATATTGGGCTTATGCCAATG
1 TGCTGATTCAAGGCCAGCGACATTGGGCTTATGCCAATG
* * * *
1455757 TGTTGATTCAAGGCCAACGACATTGGTCTTAAAGATAAAGGTGCCAATA
1 TGCTGATTCAAGGCCAGCGACATTGGGC-T-----T--A--TGCCAATG
* * *
1455806 TGCTGATTCAAGGCCAGCGATACTGGGCTTGTGCCAATG
1 TGCTGATTCAAGGCCAGCGACATTGGGCTTATGCCAATG
* * *
1455845 TGCTGATTCAAGGCCAGCGACAATGGTCTTAAAGACAAGGTGCCAATA
1 TGCTGATTCAAGGCCAGCGACATTGGGCTT-------A--TGCCAATG
* *
1455893 TGCTGATTCAAGGCCAACGATATTGGGCTTATGCCAATG
1 TGCTGATTCAAGGCCAGCGACATTGGGCTTATGCCAATG
* *
1455932 TGCTGATTCAAGGCCAGCGACATTGGTCTTAAAGACAAGGTGCCAATA
1 TGCTGATTCAAGGCCAGCGACATTGGGCTT-------A--TGCCAATG
* * *
1455980 TGCCGATTCAAGGCCAACGATATTGGGCTTATGCCAATG
1 TGCTGATTCAAGGCCAGCGACATTGGGCTTATGCCAATG
* *
1456019 TGCTGATTCAAGGCCAGCGACATTGGTCTTAAAGACAAGGTGCCAATA
1 TGCTGATTCAAGGCCAGCGACATTGGGCTT-------A--TGCCAATG
*
1456067 TGCTGATTCAAGGCCAGCGATATTGGGCTTATGCCAATG
1 TGCTGATTCAAGGCCAGCGACATTGGGCTTATGCCAATG
* *
1456106 TGCTGATTCAAGGTCAGCGACATTGGTCTTA
1 TGCTGATTCAAGGCCAGCGACATTGGGCTTA
1456137 AAGACAAGGT
Statistics
Matches: 300, Mismatches: 43, Indels: 74
0.72 0.10 0.18
Matches are distributed among these distances:
39 159 0.53
40 1 0.00
41 3 0.01
43 1 0.00
45 1 0.00
46 2 0.01
47 1 0.00
48 102 0.34
49 30 0.10
ACGTcount: A:0.28, C:0.20, G:0.26, T:0.26
Consensus pattern (39 bp):
TGCTGATTCAAGGCCAGCGACATTGGGCTTATGCCAATG
Found at i:1455907 original size:48 final size:47
Alignment explanation
Indices: 1455836--1456330 Score: 420
Period size: 48 Copynumber: 10.9 Consensus size: 47
1455826 TACTGGGCTT
* * *
1455836 GTGCCAATGTGCTGATTCAAGGCCAGCGACAATGGTCTTAAAGACAAG
1 GTGCCAATATGCTGATTCAAGGCCAGCGATATTGGTCTTAAAGA-AAG
* *
1455884 GTGCCAATATGCTGATTCAAGGCCAACGATATTGGGCTT------A-
1 GTGCCAATATGCTGATTCAAGGCCAGCGATATTGGTCTTAAAGAAAG
* *
1455924 -TGCCAATGTGCTGATTCAAGGCCAGCGACATTGGTCTTAAAGACAAG
1 GTGCCAATATGCTGATTCAAGGCCAGCGATATTGGTCTTAAAGA-AAG
* * *
1455971 GTGCCAATATGCCGATTCAAGGCCAACGATATTGGGCTT------A-
1 GTGCCAATATGCTGATTCAAGGCCAGCGATATTGGTCTTAAAGAAAG
* *
1456011 -TGCCAATGTGCTGATTCAAGGCCAGCGACATTGGTCTTAAAGACAAG
1 GTGCCAATATGCTGATTCAAGGCCAGCGATATTGGTCTTAAAGA-AAG
*
1456058 GTGCCAATATGCTGATTCAAGGCCAGCGATATTGGGCTT------A-
1 GTGCCAATATGCTGATTCAAGGCCAGCGATATTGGTCTTAAAGAAAG
* * *
1456098 -TGCCAATGTGCTGATTCAAGGTCAGCGACATTGGTCTTAAAGACAAG
1 GTGCCAATATGCTGATTCAAGGCCAGCGATATTGGTCTTAAAGA-AAG
* * * *
1456145 GTGCCAATATGCTCATTCAAGGCCAACGATATTGGACTCAAGATGGAAATG
1 GTGCCAATATGCTGATTCAAGGCCAGCGATATTGGTCTTAA-A--GAAA-G
** *
1456196 GTGCCAATATGCTGATTCAAGGTTAGCAATATTGGAT-TT----AAAG
1 GTGCCAATATGCTGATTCAAGGCCAGCGATATTGG-TCTTAAAGAAAG
* * * *
1456239 GTGCTAATGTGCTGATTCAAGGCCAGCGACATCGGT-TTCAAAGATGAAG
1 GTGCCAATATGCTGATTCAAGGCCAGCGATATTGGTCTT-AAAGA--AAG
*
1456288 GTGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAG
1 GTGCCAATATGCTGATTCAAGGCCAGCGATATTGGTCTTAAAG
1456331 GTGCCACGGA
Statistics
Matches: 355, Mismatches: 52, Indels: 79
0.73 0.11 0.16
Matches are distributed among these distances:
39 101 0.28
41 3 0.01
42 3 0.01
43 29 0.08
44 3 0.01
46 3 0.01
47 1 0.00
48 135 0.38
49 39 0.11
50 4 0.01
51 34 0.10
ACGTcount: A:0.30, C:0.19, G:0.26, T:0.25
Consensus pattern (47 bp):
GTGCCAATATGCTGATTCAAGGCCAGCGATATTGGTCTTAAAGAAAG
Found at i:1455928 original size:87 final size:87
Alignment explanation
Indices: 1455661--1456179 Score: 858
Period size: 87 Copynumber: 5.9 Consensus size: 87
1455651 AAGATGAAGG
* * * * *
1455661 TGCCAATGTGCTGATTCAAGGCCAGTGACATTAGACTTAAAGATGAAGGTGCCACTATGCTGATT
1 TGCCAATGTGCTGATTCAAGGCCAGCGACATTGGTCTTAAAGA-CAAGGTGCCAATATGCTGATT
* *
1455726 CAAGGCTAGCGATATTGGGCTTA
65 CAAGGCCAACGATATTGGGCTTA
* * *
1455749 TGCCAATGTGTTGATTCAAGGCCAACGACATTGGTCTTAAAGATAAAGGTGCCAATATGCTGATT
1 TGCCAATGTGCTGATTCAAGGCCAGCGACATTGGTCTTAAAGA-CAAGGTGCCAATATGCTGATT
* * *
1455814 CAAGGCCAGCGATACTGGGCTTG
65 CAAGGCCAACGATATTGGGCTTA
*
1455837 TGCCAATGTGCTGATTCAAGGCCAGCGACAATGGTCTTAAAGACAAGGTGCCAATATGCTGATTC
1 TGCCAATGTGCTGATTCAAGGCCAGCGACATTGGTCTTAAAGACAAGGTGCCAATATGCTGATTC
1455902 AAGGCCAACGATATTGGGCTTA
66 AAGGCCAACGATATTGGGCTTA
*
1455924 TGCCAATGTGCTGATTCAAGGCCAGCGACATTGGTCTTAAAGACAAGGTGCCAATATGCCGATTC
1 TGCCAATGTGCTGATTCAAGGCCAGCGACATTGGTCTTAAAGACAAGGTGCCAATATGCTGATTC
1455989 AAGGCCAACGATATTGGGCTTA
66 AAGGCCAACGATATTGGGCTTA
1456011 TGCCAATGTGCTGATTCAAGGCCAGCGACATTGGTCTTAAAGACAAGGTGCCAATATGCTGATTC
1 TGCCAATGTGCTGATTCAAGGCCAGCGACATTGGTCTTAAAGACAAGGTGCCAATATGCTGATTC
*
1456076 AAGGCCAGCGATATTGGGCTTA
66 AAGGCCAACGATATTGGGCTTA
* *
1456098 TGCCAATGTGCTGATTCAAGGTCAGCGACATTGGTCTTAAAGACAAGGTGCCAATATGCTCATTC
1 TGCCAATGTGCTGATTCAAGGCCAGCGACATTGGTCTTAAAGACAAGGTGCCAATATGCTGATTC
1456163 AAGGCCAACGATATTGG
66 AAGGCCAACGATATTGG
1456180 ACTCAAGATG
Statistics
Matches: 407, Mismatches: 24, Indels: 1
0.94 0.06 0.00
Matches are distributed among these distances:
87 289 0.71
88 118 0.29
ACGTcount: A:0.29, C:0.20, G:0.26, T:0.25
Consensus pattern (87 bp):
TGCCAATGTGCTGATTCAAGGCCAGCGACATTGGTCTTAAAGACAAGGTGCCAATATGCTGATTC
AAGGCCAACGATATTGGGCTTA
Found at i:1456304 original size:92 final size:94
Alignment explanation
Indices: 1456142--1456336 Score: 252
Period size: 92 Copynumber: 2.1 Consensus size: 94
1456132 TCTTAAAGAC
* *
1456142 AAGGTGCCAATATGCTCATTCAAGGCCAACGATATTGGACTCAAGATGGAAATGGTGCCAATATG
1 AAGGTGCCAATATGCTCATTCAAGGCCAACGACATCGGACTCAAGATGGAAATGGTGCCAATATG
** *
1456207 CTGATTCAAGGTTAGCAATATTGGATTTA
66 CTGATTCAAGGCCAGCAATATTGGACTTA
* * * * **
1456236 AAGGTGCTAATGTGCTGATTCAAGGCCAGCGACATCGGTTTCAAAGAT-G-AA-GGTGCCAATAT
1 AAGGTGCCAATATGCTCATTCAAGGCCAACGACATCGGACTC-AAGATGGAAATGGTGCCAATAT
*
1456298 GCTGATTCAAGGCCAGCGATATTGGACTTA
65 GCTGATTCAAGGCCAGCAATATTGGACTTA
1456328 AAGGTGCCA
1 AAGGTGCCA
1456337 CGGAGTTGTG
Statistics
Matches: 87, Mismatches: 13, Indels: 4
0.84 0.12 0.04
Matches are distributed among these distances:
92 45 0.52
93 2 0.02
94 35 0.40
95 5 0.06
ACGTcount: A:0.31, C:0.17, G:0.26, T:0.26
Consensus pattern (94 bp):
AAGGTGCCAATATGCTCATTCAAGGCCAACGACATCGGACTCAAGATGGAAATGGTGCCAATATG
CTGATTCAAGGCCAGCAATATTGGACTTA
Found at i:1456375 original size:34 final size:33
Alignment explanation
Indices: 1456327--1456480 Score: 194
Period size: 34 Copynumber: 4.8 Consensus size: 33
1456317 TATTGGACTT
* *
1456327 AAAGGTGCCACGGAGTTGTGGACTTAAAAGAAAA
1 AAAGATGCCACGGAGTTGTGGACTTAAAAG-GAA
1456361 AAAGATGCCACGGAGTTGTGGACTTAAAAGGAA
1 AAAGATGCCACGGAGTTGTGGACTTAAAAGGAA
*
1456394 AAAGAGTGCCACGGAGTCGTGGACTTAAAAGG--
1 AAAGA-TGCCACGGAGTTGTGGACTTAAAAGGAA
*
1456426 ---G-TGTCACGGAGTTGTGGACTTAAAAGGAA
1 AAAGATGCCACGGAGTTGTGGACTTAAAAGGAA
*
1456455 AAAGAGTGCCACGGAGTCGTGGACTT
1 AAAGA-TGCCACGGAGTTGTGGACTT
1456481 TTGGAAAAGA
Statistics
Matches: 105, Mismatches: 7, Indels: 16
0.82 0.05 0.12
Matches are distributed among these distances:
27 24 0.23
29 1 0.01
32 1 0.01
33 7 0.07
34 72 0.69
ACGTcount: A:0.35, C:0.14, G:0.32, T:0.19
Consensus pattern (33 bp):
AAAGATGCCACGGAGTTGTGGACTTAAAAGGAA
Found at i:1456452 original size:27 final size:27
Alignment explanation
Indices: 1456393--1456452 Score: 93
Period size: 27 Copynumber: 2.2 Consensus size: 27
1456383 CTTAAAAGGA
*
1456393 AAAAGAGTGCCACGGAGTCGTGGACTT
1 AAAAGGGTGCCACGGAGTCGTGGACTT
* *
1456420 AAAAGGGTGTCACGGAGTTGTGGACTT
1 AAAAGGGTGCCACGGAGTCGTGGACTT
1456447 AAAAGG
1 AAAAGG
1456453 AAAAAGAGTG
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
27 30 1.00
ACGTcount: A:0.32, C:0.13, G:0.35, T:0.20
Consensus pattern (27 bp):
AAAAGGGTGCCACGGAGTCGTGGACTT
Found at i:1456591 original size:31 final size:31
Alignment explanation
Indices: 1456360--1456933 Score: 561
Period size: 31 Copynumber: 18.1 Consensus size: 31
1456350 TTAAAAGAAA
* * **
1456360 AAAAGATGCCACGGAGTTGTGGACTTAAAAGG
1 AAAAGATGCCACTGAGTCGTGGACTTTGAA-G
*
1456392 AAAAAGAGTGCCACGGAGTCGTGGAC-TT--A-
1 -AAAAGA-TGCCACTGAGTCGTGGACTTTGAAG
* * * * * **
1456421 AAAGGGTGTCACGGAGTTGTGGACTTAAAAGG
1 AAAAGATGCCACTGAGTCGTGGACTTTGAA-G
*
1456453 AAAAAGAGTGCCACGGAGTCGTGGACTTTTG--G
1 -AAAAGA-TGCCACTGAGTCGTGGAC-TTTGAAG
** *
1456485 AAAAGATGCTGCTGAGTCGTGGATTTTTGAAG
1 AAAAGATGCCACTGAGTCGTGGA-CTTTGAAG
1456517 AAAAAAGATGCCACTGAGTCGTGGACTTTGAAG
1 --AAAAGATGCCACTGAGTCGTGGACTTTGAAG
* * *
1456550 AAAAAAAGATGCCACTGTGTCATGGACGTTGAAG
1 ---AAAAGATGCCACTGAGTCGTGGACTTTGAAG
* * *
1456584 AAAAGATGTCACTGTGTCGTGGACTTTAAAG
1 AAAAGATGCCACTGAGTCGTGGACTTTGAAG
*
1456615 AAAAGATGCCACTGAGTCATGGACTTTGGGAA-
1 AAAAGATGCCACTGAGTCGTGGACTTT--GAAG
* * * *
1456647 AAAAGACGCCACTGGGTCATGGACTTGGAAG
1 AAAAGATGCCACTGAGTCGTGGACTTTGAAG
*
1456678 AAAAGATGTCACTGAGTCGTGGACTTTGAAG
1 AAAAGATGCCACTGAGTCGTGGACTTTGAAG
* *
1456709 AAGAGATGCCACTGAGTCGTGGATTTTGGGGAA-
1 AAAAGATGCCACTGAGTCGTGGACTTT---GAAG
* *
1456742 AAAAGATGCCACTGGGTCGTGGACTTGGAAG
1 AAAAGATGCCACTGAGTCGTGGACTTTGAAG
1456773 AAAAGATGCCACTGAGTCGTGGACTTTGAAG
1 AAAAGATGCCACTGAGTCGTGGACTTTGAAG
* *
1456804 AAGAGATGCCACTGAGTCGTGGACTTTGAGGAA
1 AAAAGATGCCACTGAGTCGTGGACTTTGA--AG
* * *
1456837 AAAAGACGCCACTAAGTCGTGGACTTGGAAG
1 AAAAGATGCCACTGAGTCGTGGACTTTGAAG
*
1456868 AAAAGATGCCACTGAGTCATGGACTTTGAAG
1 AAAAGATGCCACTGAGTCGTGGACTTTGAAG
*
1456899 AAGAGATGCCACTGAGTCGTGGACTTTGAAG
1 AAAAGATGCCACTGAGTCGTGGACTTTGAAG
1456930 AAAA
1 AAAA
1456934 AAGATTTGAT
Statistics
Matches: 455, Mismatches: 62, Indels: 50
0.80 0.11 0.09
Matches are distributed among these distances:
27 16 0.04
28 5 0.01
30 25 0.05
31 225 0.49
32 26 0.06
33 69 0.15
34 87 0.19
35 2 0.00
ACGTcount: A:0.33, C:0.15, G:0.31, T:0.22
Consensus pattern (31 bp):
AAAAGATGCCACTGAGTCGTGGACTTTGAAG
Found at i:1456786 original size:95 final size:95
Alignment explanation
Indices: 1456358--1456938 Score: 671
Period size: 95 Copynumber: 6.1 Consensus size: 95
1456348 ACTTAAAAGA
* ** *
1456358 AAAAAAGATGCCAC-GGAGTTGTGGACTTAAAAGGAAAAAGAGTGCCACGGAGTCGTGGAC-TT-
1 AAAAAAGATGCCACTGG-GTCGTGGACTTGGAA-G-AAAAGA-TGCCACTGAGTCGTGGACTTTG
* * * * **
1456420 AA-AAG-GGTGTCACGGAGTTGTGGACTTAAAAGG
62 AAGAAGAGATGCCACTGAGTCGTGGACTT-TGAGG
* ** *
1456453 -AAAAAGAGTGCCAC-GGAGTCGTGGACTTTTG--GAAAAGATGCTGCTGAGTCGTGGATTTTTG
1 AAAAAAGA-TGCCACTGG-GTCGTGGAC-TTGGAAGAAAAGATGCCACTGAGTCGTGGA-CTTTG
* *
1456514 AAGAAAAAAGATGCCACTGAGTCGTGGACTTTGAAGA
62 AAG--AAGAGATGCCACTGAGTCGTGGACTTTG-AGG
* * * * *
1456551 AAAAAAGATGCCACTGTGTCATGGACGTT-GAAGAAAAGATGTCACTGTGTCGTGGACTTTAAAG
1 AAAAAAGATGCCACTGGGTCGTGGAC-TTGGAAGAAAAGATGCCACTGAGTCGTGGACTTTGAAG
* *
1456615 AAAAGATGCCACTGAGTCATGGACTTTG-GG
65 AAGAGATGCCACTGAGTCGTGGACTTTGAGG
* * *
1456645 AAAAAAGACGCCACTGGGTCATGGACTTGGAAGAAAAGATGTCACTGAGTCGTGGACTTTGAAGA
1 AAAAAAGATGCCACTGGGTCGTGGACTTGGAAGAAAAGATGCCACTGAGTCGTGGACTTTGAAGA
* *
1456710 AGAGATGCCACTGAGTCGTGGATTTTGGGG
66 AGAGATGCCACTGAGTCGTGGACTTTGAGG
1456740 AAAAAAGATGCCACTGGGTCGTGGACTTGGAAGAAAAGATGCCACTGAGTCGTGGACTTTGAAGA
1 AAAAAAGATGCCACTGGGTCGTGGACTTGGAAGAAAAGATGCCACTGAGTCGTGGACTTTGAAGA
1456805 AGAGATGCCACTGAGTCGTGGACTTTGAGG
66 AGAGATGCCACTGAGTCGTGGACTTTGAGG
* ** *
1456835 AAAAAAGACGCCACTAAGTCGTGGACTTGGAAGAAAAGATGCCACTGAGTCATGGACTTTGAAGA
1 AAAAAAGATGCCACTGGGTCGTGGACTTGGAAGAAAAGATGCCACTGAGTCGTGGACTTTGAAGA
*
1456900 AGAGATGCCACTGAGTCGTGGACTTTGAAG
66 AGAGATGCCACTGAGTCGTGGACTTTGAGG
1456930 AAAAAAGAT
1 AAAAAAGAT
1456939 TTGATGAATT
Statistics
Matches: 426, Mismatches: 44, Indels: 32
0.85 0.09 0.06
Matches are distributed among these distances:
91 14 0.03
92 6 0.01
93 5 0.01
94 92 0.22
95 207 0.49
96 29 0.07
97 3 0.01
98 42 0.10
99 28 0.07
ACGTcount: A:0.33, C:0.14, G:0.30, T:0.22
Consensus pattern (95 bp):
AAAAAAGATGCCACTGGGTCGTGGACTTGGAAGAAAAGATGCCACTGAGTCGTGGACTTTGAAGA
AGAGATGCCACTGAGTCGTGGACTTTGAGG
Found at i:1456938 original size:64 final size:62
Alignment explanation
Indices: 1456360--1456933 Score: 561
Period size: 64 Copynumber: 9.1 Consensus size: 62
1456350 TTAAAAGAAA
* * ** *
1456360 AAAAGATGCCACGGAGTTGTGGACTTAAAAGGAAAAAGAGTGCCACGGAGTCGTGGAC-TT--A-
1 AAAAGATGCCACTGAGTCGTGGACTTTGAA-G-AAAAGA-TGCCACTGAGTCGTGGACTTTGAAG
* * * * * ** *
1456421 AAAGGGTGTCACGGAGTTGTGGACTTAAAAGGAAAAAGAGTGCCACGGAGTCGTGGACTTTTG--
1 AAAAGATGCCACTGAGTCGTGGACTTTGAA-G-AAAAGA-TGCCACTGAGTCGTGGAC-TTTGAA
1456484 G
62 G
** *
1456485 AAAAGATGCTGCTGAGTCGTGGATTTTTGAAGAAAAAAGATGCCACTGAGTCGTGGACTTTGAAG
1 AAAAGATGCCACTGAGTCGTGGA-CTTTGAAG--AAAAGATGCCACTGAGTCGTGGACTTTGAAG
* * * * * *
1456550 AAAAAAAGATGCCACTGTGTCATGGACGTTGAAGAAAAGATGTCACTGTGTCGTGGACTTTAAAG
1 ---AAAAGATGCCACTGAGTCGTGGACTTTGAAGAAAAGATGCCACTGAGTCGTGGACTTTGAAG
* * * * *
1456615 AAAAGATGCCACTGAGTCATGGACTTTGGGAA-AAAAGACGCCACTGGGTCATGGACTTGGAAG
1 AAAAGATGCCACTGAGTCGTGGACTTT--GAAGAAAAGATGCCACTGAGTCGTGGACTTTGAAG
* * *
1456678 AAAAGATGTCACTGAGTCGTGGACTTTGAAGAAGAGATGCCACTGAGTCGTGGATTTTGGGGAA-
1 AAAAGATGCCACTGAGTCGTGGACTTTGAAGAAAAGATGCCACTGAGTCGTGGACTTT---GAAG
* *
1456742 AAAAGATGCCACTGGGTCGTGGACTTGGAAGAAAAGATGCCACTGAGTCGTGGACTTTGAAG
1 AAAAGATGCCACTGAGTCGTGGACTTTGAAGAAAAGATGCCACTGAGTCGTGGACTTTGAAG
* * * * *
1456804 AAGAGATGCCACTGAGTCGTGGACTTTGAGGAAAAAAGACGCCACTAAGTCGTGGACTTGGAAG
1 AAAAGATGCCACTGAGTCGTGGACTTTGA--AGAAAAGATGCCACTGAGTCGTGGACTTTGAAG
* *
1456868 AAAAGATGCCACTGAGTCATGGACTTTGAAGAAGAGATGCCACTGAGTCGTGGACTTTGAAG
1 AAAAGATGCCACTGAGTCGTGGACTTTGAAGAAAAGATGCCACTGAGTCGTGGACTTTGAAG
1456930 AAAA
1 AAAA
1456934 AAGATTTGAT
Statistics
Matches: 435, Mismatches: 58, Indels: 39
0.82 0.11 0.07
Matches are distributed among these distances:
61 61 0.14
62 104 0.24
63 56 0.13
64 146 0.34
65 43 0.10
67 6 0.01
68 19 0.04
ACGTcount: A:0.33, C:0.15, G:0.31, T:0.22
Consensus pattern (62 bp):
AAAAGATGCCACTGAGTCGTGGACTTTGAAGAAAAGATGCCACTGAGTCGTGGACTTTGAAG
Found at i:1458167 original size:15 final size:15
Alignment explanation
Indices: 1458140--1458172 Score: 50
Period size: 15 Copynumber: 2.2 Consensus size: 15
1458130 GCACTCTCTC
1458140 TTTTTTTTGTTTTTG
1 TTTTTTTTGTTTTTG
1458155 TTTTTGTTT-TTTTTG
1 TTTTT-TTTGTTTTTG
1458170 TTT
1 TTT
1458173 GTGTGTTTAC
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 14 0.82
16 3 0.18
ACGTcount: A:0.00, C:0.00, G:0.12, T:0.88
Consensus pattern (15 bp):
TTTTTTTTGTTTTTG
Found at i:1458186 original size:21 final size:21
Alignment explanation
Indices: 1458141--1458186 Score: 56
Period size: 21 Copynumber: 2.2 Consensus size: 21
1458131 CACTCTCTCT
* * **
1458141 TTTTTTTGTTTTTGTTTTTGT
1 TTTTTTTGTTTGTGTGTTTAC
1458162 TTTTTTTGTTTGTGTGTTTAC
1 TTTTTTTGTTTGTGTGTTTAC
1458183 TTTT
1 TTTT
1458187 GACTTTTTCA
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.02, C:0.02, G:0.15, T:0.80
Consensus pattern (21 bp):
TTTTTTTGTTTGTGTGTTTAC
Found at i:1466128 original size:17 final size:18
Alignment explanation
Indices: 1466101--1466135 Score: 63
Period size: 17 Copynumber: 2.0 Consensus size: 18
1466091 AATGACCAAG
1466101 AAAACATTTATTGTACAT
1 AAAACATTTATTGTACAT
1466119 AAAA-ATTTATTGTACAT
1 AAAACATTTATTGTACAT
1466136 GTATTATTTT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 13 0.76
18 4 0.24
ACGTcount: A:0.46, C:0.09, G:0.06, T:0.40
Consensus pattern (18 bp):
AAAACATTTATTGTACAT
Found at i:1466201 original size:11 final size:11
Alignment explanation
Indices: 1466185--1466221 Score: 56
Period size: 11 Copynumber: 3.4 Consensus size: 11
1466175 TTATCTCTTT
1466185 TTATTTATAAA
1 TTATTTATAAA
* *
1466196 TTATTTTTAAT
1 TTATTTATAAA
1466207 TTATTTATAAA
1 TTATTTATAAA
1466218 TTAT
1 TTAT
1466222 ACAAATTTAT
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
11 22 1.00
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (11 bp):
TTATTTATAAA
Found at i:1466408 original size:314 final size:315
Alignment explanation
Indices: 1465803--1466422 Score: 1039
Period size: 314 Copynumber: 2.0 Consensus size: 315
1465793 AATGACCAAG
*
1465803 AAAATATTTATTGTATATGTATTATTTTTATTAAAATTAATTAATATTGTGCATGTATTATTACT
1 AAAATATTTATTGTACATGTATTATTTTTATTAAAATTAATTAATATTGTGCATGTATTATTACT
1465868 TTTTATTTAGAAATTATTTTTAATTTATTTATAAATTATACAAATTTATTTTTATTAAAATTAAT
66 TTTTATTTAGAAATTATTTTTAATTTATTTATAAATTATACAAATTTATTTTTATTAAAATTAAT
* **
1465933 TAATATTATACATGTATTATTTTTATAATTGATAGAACTTAAATTTATGTTAACCAACAATATTT
131 TAATATTATACATGTATGATTTTTATAATTGATAGAACTTAAATTTATGTTAACCAACAATAAAT
* ** * *
1465998 TACTTTTTTCGATAACGGCTTATTTCGGATTTACAGATGCACATATTTTATTTTTCGGTAACGAC
196 TACTTTTTTCGATAACGACTTATTTCGGATTTACAGAAACACACATTTTATTTTTCAGTAACGAC
1466063 TTAAATACGAGCTTTCCTTTATCTATAAAATGACCAAGAAAACATTTATTGTACAT
261 TTAAATACGAGCTTTCCTTTATCTATAAAATGACCAAGAAAA-ATTTATTGTACAT
1466119 AAAA-ATTTATTGTACATGTATTATTTTTATTAAAATTAATTAATATTGTGCATGTATTATCT-C
1 AAAATATTTATTGTACATGTATTATTTTTATTAAAATTAATTAATATTGTGCATGTATTAT-TAC
*
1466182 TTTTTATTTATAAATTATTTTTAATTTATTTATAAATTATACAAATTTATTTTTATTAAAATTAA
65 TTTTTATTTAGAAATTATTTTTAATTTATTTATAAATTATACAAATTTATTTTTATTAAAATTAA
* *
1466247 TTAATATT-TACATGTATGATTTTTATAATTGATAGAACTTAAATTTATGTTAGCTAACAATAAA
130 TTAATATTATACATGTATGATTTTTATAATTGATAGAACTTAAATTTATGTTAACCAACAATAAA
* *
1466311 TTACTTTTTTTGATAACGACTTATTTCGGATTTACAGAAATACACATTTTATTTTTCAGTAACGA
195 TTACTTTTTTCGATAACGACTTATTTCGGATTTACAGAAACACACATTTTATTTTTCAGTAACGA
* * * *
1466376 TTTAAATATGAGCTTTCTTTTATCTGTAAAATGACCAAGAAAAATTT
260 CTTAAATACGAGCTTTCCTTTATCTATAAAATGACCAAGAAAAATTT
1466423 TCCTCAACTT
Statistics
Matches: 285, Mismatches: 18, Indels: 5
0.93 0.06 0.02
Matches are distributed among these distances:
313 4 0.01
314 148 0.52
315 128 0.45
316 5 0.02
ACGTcount: A:0.37, C:0.08, G:0.08, T:0.47
Consensus pattern (315 bp):
AAAATATTTATTGTACATGTATTATTTTTATTAAAATTAATTAATATTGTGCATGTATTATTACT
TTTTATTTAGAAATTATTTTTAATTTATTTATAAATTATACAAATTTATTTTTATTAAAATTAAT
TAATATTATACATGTATGATTTTTATAATTGATAGAACTTAAATTTATGTTAACCAACAATAAAT
TACTTTTTTCGATAACGACTTATTTCGGATTTACAGAAACACACATTTTATTTTTCAGTAACGAC
TTAAATACGAGCTTTCCTTTATCTATAAAATGACCAAGAAAAATTTATTGTACAT
Found at i:1467453 original size:89 final size:89
Alignment explanation
Indices: 1467228--1468141 Score: 810
Period size: 86 Copynumber: 10.4 Consensus size: 89
1467218 GCAGTCTTTC
* * ** **
1467228 TTTTTTCTTATTAAAAAGAATTTTCTTCTCAGATATAATT-ATGCATTAGTCTAATCCTTGTAGT
1 TTTTTTC-TATAAAAAAGAATCTGATTCTCAGATATAATTCATGCATTAGTCTAATCCTTACAGT
1467292 CTGACATTTACAATCAATTAGTC-T
65 CTGACATTTACAATCAATTAGTCTT
* * *
1467316 TTTTTTCTATAAAAAAGAAT-TCGATTCTCAAATATAATTCATGCATTAATCTAATCCTTGCAGT
1 TTTTTTCTATAAAAAAGAATCT-GATTCTCAGATATAATTCATGCATTAGTCTAATCCTTACAGT
* *
1467380 CTAATATTTACAATCAATTAGTCTT
65 CTGACATTTACAATCAATTAGTCTT
* * *
1467405 TTTTTTCTACAAAAAAGAATCTGATTCTCAGATATAATTCATGCATTAATCTTATCCTTACAGTC
1 TTTTTTCTATAAAAAAGAATCTGATTCTCAGATATAATTCATGCATTAGTCTAATCCTTACAGTC
1467470 TGACATTTACAATCAATTAGTCTT
66 TGACATTTACAATCAATTAGTCTT
**** * * *
1467494 TCTTTTT-T-T-CTGTA-ATTCTGATTTTTAGATATAATTC-T-C-----T-T-ATCCTTACAGT
1 T-TTTTTCTATAAAAAAGAATCTGATTCTCAGATATAATTCATGCATTAGTCTAATCCTTACAGT
1467546 CTGACATTTACAATCAATTAGTCTT
65 CTGACATTTACAATCAATTAGTCTT
**** * * * * *
1467571 TCTTTTT-T-T-CTGTA-ATTCTAATTTTCAGATATAATTCATGCATTAGTCTAATCATTGCAGT
1 T-TTTTTCTATAAAAAAGAATCTGATTCTCAGATATAATTCATGCATTAGTCTAATCCTTACAGT
1467632 CTGACATTTACAATCAATTAGTCTGTCTTT
65 CTGACATTTACAATCAATTA----GTC-TT
* * * **
1467662 TTTTTTCTATAAAAAAGAATCCT-ATTTTCATATATAATTCATGCATTAGTATAATTTTTACAGT
1 TTTTTTCTATAAAAAAGAAT-CTGATTCTCAGATATAATTCATGCATTAGTCTAATCCTTACAGT
* * *
1467726 CTAACATTTACAATTAATTA-AC-T
65 CTGACATTTACAATCAATTAGTCTT
* * * *
1467749 TTTTTTCTATAAAAAA-AATTTAATTCTCAGATATCATCCATGCATTAGTCTAATCCTTACAGTC
1 TTTTTTCTATAAAAAAGAATCTGATTCTCAGATATAATTCATGCATTAGTCTAATCCTTACAGTC
* * * * * *
1467813 TAAAATTTACAATTAGTCA-AC-T
66 TGACATTTACAATCAATTAGTCTT
* * * * *
1467835 TTTTTTCTATAAAAAA-AATTTGATTCTCAAATATTATTAATGCATTAGTCTAATCCTTATAGTC
1 TTTTTTCTATAAAAAAGAATCTGATTCTCAGATATAATTCATGCATTAGTCTAATCCTTACAGTC
* * * *
1467899 TAACATTTACAATCACTCA-ACTTT
66 TGACATTTACAATCAATTAGTC-TT
* * * *
1467923 TTTTTTCTATAAAAAAGAATCCGATTCTCAAATATAATTCATACATTAGTCTAATCTTTACAGGT
1 TTTTTTCTATAAAAAAGAATCTGATTCTCAGATATAATTCATGCATTAGTCTAATCCTTACA-GT
* * *
1467988 -TGACATTTACAATTAATTAACTTTTCT
65 CTGACATTTACAATCAATT-A-GTCT-T
* * * *
1468015 TTTTTTCTATAAAAAAGAAT-TGATTCTTAGACATAATTCATGCATTAGACTAATCCTTGCAGTC
1 TTTTTTCTATAAAAAAGAATCTGATTCTCAGATATAATTCATGCATTAGTCTAATCCTTACAGTC
* *
1468079 TGACATTTACAATCAATCA-ACTT
66 TGACATTTACAATCAATTAGTCTT
* *
1468102 TTCTTTTTTCATAAAAAAGAATCTGATTCTTAGATATAAT
1 TT-TTTTCT-ATAAAAAAGAATCTGATTCTCAGATATAAT
1468142 CGCATTTATT
Statistics
Matches: 703, Mismatches: 86, Indels: 72
0.82 0.10 0.08
Matches are distributed among these distances:
77 71 0.10
78 2 0.00
79 2 0.00
84 2 0.00
85 3 0.00
86 183 0.26
87 47 0.07
88 73 0.10
89 149 0.21
90 36 0.05
91 54 0.08
92 22 0.03
93 1 0.00
94 56 0.08
95 2 0.00
ACGTcount: A:0.34, C:0.16, G:0.07, T:0.43
Consensus pattern (89 bp):
TTTTTTCTATAAAAAAGAATCTGATTCTCAGATATAATTCATGCATTAGTCTAATCCTTACAGTC
TGACATTTACAATCAATTAGTCTT
Found at i:1467581 original size:77 final size:78
Alignment explanation
Indices: 1467453--1467665 Score: 311
Period size: 77 Copynumber: 2.6 Consensus size: 78
1467443 TCATGCATTA
*
1467453 ATCTTATCCTTACAGTCTGACATTTACAATCAATTAGTCTTTCTTTTTTTCTGTAATTCTGATTT
1 ATCTTATCCTTACAGTCTGACATTTACAATCAATTAGTCTTTCTTTTTTTCTGTAATTCTAATTT
*
1467518 TTAGATATAATTC
66 TCAGATATAATTC
1467531 -TCTTATCCTTACAGTCTGACATTTACAATCAATTAGTCTTTCTTTTTTTCTGTAATTCTAATTT
1 ATCTTATCCTTACAGTCTGACATTTACAATCAATTAGTCTTTCTTTTTTTCTGTAATTCTAATTT
1467595 TCAGATATAATTC
66 TCAGATATAATTC
* *
1467608 ATGCATTAGTCTAATCATTGCAGTCTGACATTTACAATCAATTAGTCTGTCTTTTTTT
1 AT-C-TTA-TC----C-TTACAGTCTGACATTTACAATCAATTAGTCTTTCTTTTTTT
1467666 TTCTATAAAA
Statistics
Matches: 122, Mismatches: 4, Indels: 10
0.90 0.03 0.07
Matches are distributed among these distances:
77 75 0.61
78 1 0.01
79 1 0.01
80 3 0.02
81 2 0.02
85 1 0.01
86 39 0.32
ACGTcount: A:0.26, C:0.17, G:0.08, T:0.48
Consensus pattern (78 bp):
ATCTTATCCTTACAGTCTGACATTTACAATCAATTAGTCTTTCTTTTTTTCTGTAATTCTAATTT
TCAGATATAATTC
Found at i:1468070 original size:180 final size:179
Alignment explanation
Indices: 1467223--1468141 Score: 811
Period size: 180 Copynumber: 5.2 Consensus size: 179
1467213 TCTTTGCAGT
* * **
1467223 CTTTCTTTTTTCTTATTAAAAAGAATTTTCTTCTCAGATATAATT-ATGCATTAGTCTAATCCTT
1 CTTT-TTTTTTC-TATAAAAAAGAATCTGATTCTCAGATATAATTCATGCATTAGTCTAATCCTT
** * *
1467287 GTAGTCTGACATTTACAATCAATT-A--GTCTTTTTTTCTATAAAAAAGAATTCGATTCTCAAAT
64 ACAGTCTGACATTTACAATCAATTAATTTTCTTTTTTTCTATAAAAAAGAATT-GATTCTTAAAT
* * *
1467349 ATAATTCATGCATTA-ATCTAATCCTTGCAGTCTAATATTTACAATCAAT-TA
128 ATAATTCATGCATTAGA-CTAATCCTTACAGTCTAACATTTACAATCAATCAA
* * * *
1467400 GTCTTTTTTTTCTACAAAAAAGAATCTGATTCTCAGATATAATTCATGCATTAATCTTATCCTTA
1 CT-TTTTTTTTCTATAAAAAAGAATCTGATTCTCAGATATAATTCATGCATTAGTCTAATCCTTA
* * * * *
1467465 CAGTCTGACATTTACAATCAATTAGTCTTTCTTTTTTTCTGT-----A-ATTCTGATTTTTAGAT
65 CAGTCTGACATTTACAATCAATTAAT-TTTCTTTTTTTCTATAAAAAAGAAT-TGATTCTTAAAT
* * *
1467524 ATAATTC-T-C--T----T-ATCCTTACAGTCTGACATTTACAATCAATTAGT
128 ATAATTCATGCATTAGACTAATCCTTACAGTCTAACATTTACAATCAATCA-A
* * * * *
1467568 CTTTCTTTTTTTCTGT-----A-ATTCTAATTTTCAGATATAATTCATGCATTAGTCTAATCATT
1 C-TT-TTTTTTTCTATAAAAAAGAATCTGATTCTCAGATATAATTCATGCATTAGTCTAATCCTT
* * *
1467627 GCAGTCTGACATTTACAATCAATTAGTCTGTCTTTTTTTTTCTATAAAAAAGAATCCT-ATT-TT
64 ACAGTCTGACATTTACAATCAATTAAT-T-T-TCTTTTTTTCTATAAAAAAGAAT--TGATTCTT
* ** * *
1467690 CATATATAATTCATGCATTAGTA-TAATTTTTACAGTCTAACATTTACAATTAATTAA
124 -AAATATAATTCATGCATTAG-ACTAATCCTTACAGTCTAACATTTACAATCAATCAA
* * * *
1467747 C--TTTTTTTCTATAAAAAA-AATTTAATTCTCAGATATCATCCATGCATTAGTCTAATCCTTAC
1 CTTTTTTTTTCTATAAAAAAGAATCTGATTCTCAGATATAATTCATGCATTAGTCTAATCCTTAC
* * * * * *
1467809 AGTCTAAAATTTACAATTAGTCAA----CTTTTTTTCTATAAAAAA-AATTTGATTCTCAAATAT
66 AGTCTGACATTTACAATCAATTAATTTTCTTTTTTTCTATAAAAAAGAA-TTGATTCTTAAATAT
* * * * *
1467869 TATTAATGCATTAGTCTAATCCTTATAGTCTAACATTTACAATCACTCAA
130 AATTCATGCATTAGACTAATCCTTACAGTCTAACATTTACAATCAATCAA
* * * *
1467919 CTTTTTTTTTCTATAAAAAAGAATCCGATTCTCAAATATAATTCATACATTAGTCTAATCTTTAC
1 CTTTTTTTTTCTATAAAAAAGAATCTGATTCTCAGATATAATTCATGCATTAGTCTAATCCTTAC
* * *
1467984 AGGT-TGACATTTACAATTAATTAACTTTTCTTTTTTTCTATAAAAAAGAATTGATTCTTAGACA
66 A-GTCTGACATTTACAATCAATTAA-TTTTCTTTTTTTCTATAAAAAAGAATTGATTCTTAAATA
* *
1468048 TAATTCATGCATTAGACTAATCCTTGCAGTCTGACATTTACAATCAATCAA
129 TAATTCATGCATTAGACTAATCCTTACAGTCTAACATTTACAATCAATCAA
*
1468099 CTTTTCTTTTT-TCATAAAAAAGAATCTGATTCTTAGATATAAT
1 CTTTT-TTTTTCT-ATAAAAAAGAATCTGATTCTCAGATATAAT
1468142 CGCATTTATT
Statistics
Matches: 599, Mismatches: 92, Indels: 98
0.76 0.12 0.12
Matches are distributed among these distances:
163 64 0.11
164 2 0.00
165 11 0.02
166 26 0.04
167 1 0.00
168 1 0.00
169 10 0.02
170 3 0.01
171 17 0.03
172 54 0.09
173 21 0.04
174 18 0.03
175 81 0.14
176 31 0.05
177 47 0.08
178 2 0.00
179 2 0.00
180 162 0.27
181 46 0.08
ACGTcount: A:0.34, C:0.16, G:0.07, T:0.43
Consensus pattern (179 bp):
CTTTTTTTTTCTATAAAAAAGAATCTGATTCTCAGATATAATTCATGCATTAGTCTAATCCTTAC
AGTCTGACATTTACAATCAATTAATTTTCTTTTTTTCTATAAAAAAGAATTGATTCTTAAATATA
ATTCATGCATTAGACTAATCCTTACAGTCTAACATTTACAATCAATCAA
Found at i:1469043 original size:118 final size:118
Alignment explanation
Indices: 1468724--1469074 Score: 437
Period size: 121 Copynumber: 2.9 Consensus size: 118
1468714 TATTATTTTT
* * * * *
1468724 AATAAAAATAATATTTAATTAACTTAAAAAAATTTATAGTAATAAATTAAAA-TATTAATT-T-T
1 AATAAAAATAATATTTAATTAAGTTTAAAAAATTTACATTAACAAATTAAAATTATT-ATTATAT
* ** * *
1468786 TTTTAAAATAAAAATTTAAATAAAAATAAAAAAGTTTTATTATTATTATTTTTAATAA
65 TTTTAAAATAAAAA---AATTTTAAATAAAAAGGTTTT-TTATTATAATTTTTAATAA
1468844 AATTAAAAATAATATTTAATTAAGTTTAAAAAA-TTACATTAACAAATTAAAATTTATTATTATA
1 AA-TAAAAATAATATTTAATTAAGTTTAAAAAATTTACATTAACAAATTAAAA-TTATTATTATA
* *
1468908 TTTTTATAAAAATAAAAAATTTTAAATAAAAAGGTTTTTTATTATAATTTTTACTAA
64 TTTTTA-AAATA-AAAAAATTTTAAATAAAAAGGTTTTTTATTATAATTTTTAATAA
1468965 AATAAAAATAATA-TTAA-TAAGTTTAAAAAATTTACATTAACAAATTAAATATTAATTATTATA
1 AATAAAAATAATATTTAATTAAGTTTAAAAAATTTACATTAACAAATTAAA-ATT-ATTATTATA
1469028 TTTTTAAAAT-AAAAAATTTTAAATTAAAAAGGTTTTTTATTATAATT
64 TTTTTAAAATAAAAAAATTTTAAA-TAAAAAGGTTTTTTATTATAATT
1469075 ATATTTTTAT
Statistics
Matches: 207, Mismatches: 13, Indels: 24
0.85 0.05 0.10
Matches are distributed among these distances:
117 13 0.06
118 36 0.17
119 27 0.13
120 45 0.22
121 50 0.24
122 22 0.11
123 6 0.03
124 4 0.02
125 4 0.02
ACGTcount: A:0.53, C:0.02, G:0.02, T:0.43
Consensus pattern (118 bp):
AATAAAAATAATATTTAATTAAGTTTAAAAAATTTACATTAACAAATTAAAATTATTATTATATT
TTTAAAATAAAAAAATTTTAAATAAAAAGGTTTTTTATTATAATTTTTAATAA
Found at i:1469347 original size:22 final size:22
Alignment explanation
Indices: 1469322--1469405 Score: 82
Period size: 22 Copynumber: 3.8 Consensus size: 22
1469312 AATGATAATT
1469322 TTTTTTAATTCT-TTAAATGTTA
1 TTTTTTAATT-TATTAAATGTTA
* *
1469344 TTTTTTAATTTGTT-AATGTAAA
1 TTTTTTAATTTATTAAATGT-TA
* *
1469366 TTTTTAAATTTAATTAAATATTA
1 TTTTTTAATTT-ATTAAATGTTA
*
1469389 TTTTTTATTTTATTAAA
1 TTTTTTAATTTATTAAA
1469406 AAAGAATAAT
Statistics
Matches: 51, Mismatches: 7, Indels: 8
0.77 0.11 0.12
Matches are distributed among these distances:
21 6 0.12
22 29 0.57
23 12 0.24
24 4 0.08
ACGTcount: A:0.33, C:0.01, G:0.04, T:0.62
Consensus pattern (22 bp):
TTTTTTAATTTATTAAATGTTA
Found at i:1469370 original size:45 final size:45
Alignment explanation
Indices: 1469311--1469404 Score: 102
Period size: 45 Copynumber: 2.1 Consensus size: 45
1469301 TTTTATTGAA
* * * *
1469311 TAATGATAATTTTTTTTAATTCT-TTAAATGTTATTTTTTAATTTGT
1 TAATGATAA-ATTTTTAAATT-TATTAAATATTATTTTTTAATTTAT
*
1469357 TAATG-TAAATTTTTAAATTTAATTAAATATTATTTTTTATTTTAT
1 TAATGATAAATTTTTAAATTT-ATTAAATATTATTTTTTAATTTAT
1469402 TAA
1 TAA
1469405 AAAAGAATAA
Statistics
Matches: 41, Mismatches: 5, Indels: 5
0.80 0.10 0.10
Matches are distributed among these distances:
43 1 0.02
44 9 0.22
45 26 0.63
46 5 0.12
ACGTcount: A:0.34, C:0.01, G:0.04, T:0.61
Consensus pattern (45 bp):
TAATGATAAATTTTTAAATTTATTAAATATTATTTTTTAATTTAT
Found at i:1469423 original size:32 final size:32
Alignment explanation
Indices: 1469391--1469457 Score: 84
Period size: 32 Copynumber: 2.2 Consensus size: 32
1469381 AAATATTATT
*
1469391 TTTTATTTTAT-TAAAAA-AGAATAATAAATA
1 TTTTATTTTTTATAAAAACAGAATAATAAATA
** *
1469421 TTTTATTTTTTATAAAAACTTAATAATTAATA
1 TTTTATTTTTTATAAAAACAGAATAATAAATA
1469453 TTTTA
1 TTTTA
1469458 ATTTGTAATA
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
30 10 0.32
31 6 0.19
32 15 0.48
ACGTcount: A:0.46, C:0.01, G:0.01, T:0.51
Consensus pattern (32 bp):
TTTTATTTTTTATAAAAACAGAATAATAAATA
Found at i:1469586 original size:108 final size:104
Alignment explanation
Indices: 1469346--1469609 Score: 302
Period size: 108 Copynumber: 2.5 Consensus size: 104
1469336 AAATGTTATT
*
1469346 TTTTAATTTGTTAATGTAAATTTTTAAATTTAATTAAATATTATTTTTTATTTTATTAAAAAAGA
1 TTTTAATTT-TTAATGTAAATTTTTAAAATTAATTAAATATTATTTTTTATTTTATTAAAAAAGA
1469411 ATAATAAATATTTTATTTTTTATAAAAACTTAATAATTAATA
65 ATAATAAATATTTTATTTTTTATAAAAA--TAATAATTAATA
* * * *
1469453 TTTTAATTTGTAATATAATTTTTTTTAAACTTAATTAAATA-TATTTTTTAATTTTATTAAAATA
1 TTTTAATTTTTAATGTAA--ATTTTTAAAATTAATTAAATATTATTTTTT-ATTTTATTAAAA-A
* * **
1469517 ATAATAAT-AATCCTTTTAATTTAATTTTATTTTAAA-AATAATTAATA
62 AGAATAATAAAT-ATTTT-A-TT--TTTTA-TAAAAATAATAATTAATA
1469564 TTTT-ATTTTTAATGTAAATTTTTAAAATTAATTAAATATTATTTTT
1 TTTTAATTTTTAATGTAAATTTTTAAAATTAATTAAATATTATTTTT
1469610 ATTAAAAAAT
Statistics
Matches: 134, Mismatches: 12, Indels: 20
0.81 0.07 0.12
Matches are distributed among these distances:
106 7 0.05
107 17 0.13
108 53 0.40
109 19 0.14
110 12 0.09
111 17 0.13
113 5 0.04
114 4 0.03
ACGTcount: A:0.42, C:0.02, G:0.02, T:0.55
Consensus pattern (104 bp):
TTTTAATTTTTAATGTAAATTTTTAAAATTAATTAAATATTATTTTTTATTTTATTAAAAAAGAA
TAATAAATATTTTATTTTTTATAAAAATAATAATTAATA
Found at i:1469658 original size:31 final size:31
Alignment explanation
Indices: 1469589--1469658 Score: 81
Period size: 31 Copynumber: 2.3 Consensus size: 31
1469579 AAATTTTTAA
*
1469589 AATTAATTAAATATTATTTTTATTAAAAAAT
1 AATTAATTAAACATTATTTTTATTAAAAAAT
* *
1469620 AAATAATTAAGACATTATTATTTA-T-AAAATT
1 AATTAATTAA-ACATTATT-TTTATTAAAAAAT
1469651 AATTAATT
1 AATTAATT
1469659 TATAAAAAAT
Statistics
Matches: 33, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
31 21 0.64
32 8 0.24
33 4 0.12
ACGTcount: A:0.51, C:0.01, G:0.01, T:0.46
Consensus pattern (31 bp):
AATTAATTAAACATTATTTTTATTAAAAAAT
Found at i:1469729 original size:15 final size:16
Alignment explanation
Indices: 1469699--1469730 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
1469689 TTGATATGAT
1469699 TGATTTTTTAACTGTA
1 TGATTTTTTAACTGTA
1469715 TGATTTTTTAA-TGTA
1 TGATTTTTTAACTGTA
1469730 T
1 T
1469731 TTATTAAAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 5 0.31
16 11 0.69
ACGTcount: A:0.25, C:0.03, G:0.12, T:0.59
Consensus pattern (16 bp):
TGATTTTTTAACTGTA
Found at i:1469783 original size:28 final size:29
Alignment explanation
Indices: 1469730--1469784 Score: 76
Period size: 28 Copynumber: 1.9 Consensus size: 29
1469720 TTTTAATGTA
* *
1469730 TTTATTAAAAAACTTATTTTTCAAAATAT
1 TTTATTAAAAAACTTATTTATAAAAATAT
*
1469759 TTTA-TAAAAAATTTATTTATAAAAAT
1 TTTATTAAAAAACTTATTTATAAAAAT
1469785 TAAAAAAATT
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
28 19 0.83
29 4 0.17
ACGTcount: A:0.49, C:0.04, G:0.00, T:0.47
Consensus pattern (29 bp):
TTTATTAAAAAACTTATTTATAAAAATAT
Found at i:1470019 original size:8 final size:7
Alignment explanation
Indices: 1470002--1470034 Score: 57
Period size: 7 Copynumber: 4.7 Consensus size: 7
1469992 TTTTATTTGT
1470002 ATTTAAA
1 ATTTAAA
*
1470009 TTTTAAA
1 ATTTAAA
1470016 ATTTAAA
1 ATTTAAA
1470023 ATTTAAA
1 ATTTAAA
1470030 ATTTA
1 ATTTA
1470035 TGATTTTTAA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
7 24 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (7 bp):
ATTTAAA
Found at i:1470161 original size:33 final size:31
Alignment explanation
Indices: 1470082--1470186 Score: 108
Period size: 33 Copynumber: 3.3 Consensus size: 31
1470072 ATTTATATTT
* *
1470082 ATTTT-ATTAATTTATT-TTTAAAATAAATATA
1 ATTTTAATT-ATTTATTATTTAATAT-AACATA
*
1470113 ATTTTAATTA-CTATTATTTAATATAACATA
1 ATTTTAATTATTTATTATTTAATATAACATA
1470143 ATTTTAATATATTTTATTATTTAATATAACTATA
1 ATTTTAAT-TA-TTTATTATTTAATATAAC-ATA
*
1470177 ATTTCAATTA
1 ATTTTAATTA
1470187 CTTACTTTTT
Statistics
Matches: 63, Mismatches: 5, Indels: 10
0.81 0.06 0.13
Matches are distributed among these distances:
30 17 0.27
31 15 0.24
32 3 0.05
33 18 0.29
34 10 0.16
ACGTcount: A:0.43, C:0.04, G:0.00, T:0.53
Consensus pattern (31 bp):
ATTTTAATTATTTATTATTTAATATAACATA
Found at i:1470369 original size:23 final size:22
Alignment explanation
Indices: 1470343--1470420 Score: 61
Period size: 21 Copynumber: 3.5 Consensus size: 22
1470333 TTATCATTAC
1470343 TATTATGATTAAAATTAAATATT
1 TATTATGATTAAAATTAAAT-TT
* *
1470366 TATTTTATGATT-AATTTTAATTT
1 TA--TTATGATTAAAATTAAATTT
* *
1470389 TATTATGATCATAATT-AATTT
1 TATTATGATTAAAATTAAATTT
* *
1470410 TAATATTATTA
1 TATTATGATTA
1470421 CTCTTTTTGA
Statistics
Matches: 44, Mismatches: 8, Indels: 8
0.73 0.13 0.13
Matches are distributed among these distances:
21 20 0.45
22 3 0.07
23 6 0.14
24 7 0.16
25 8 0.18
ACGTcount: A:0.40, C:0.01, G:0.04, T:0.55
Consensus pattern (22 bp):
TATTATGATTAAAATTAAATTT
Found at i:1470385 original size:25 final size:23
Alignment explanation
Indices: 1470345--1470411 Score: 66
Period size: 21 Copynumber: 2.9 Consensus size: 23
1470335 ATCATTACTA
1470345 TTATGATTAAAATTAAATATTTATT
1 TTATGATTAAAATT-AAT-TTTATT
**
1470370 TTATGATTAATTTTAATTTTA--
1 TTATGATTAAAATTAATTTTATT
* *
1470391 TTATGATCATAATTAATTTTA
1 TTATGATTAAAATTAATTTTA
1470412 ATATTATTAC
Statistics
Matches: 36, Mismatches: 6, Indels: 4
0.78 0.13 0.09
Matches are distributed among these distances:
21 17 0.47
23 4 0.11
24 3 0.08
25 12 0.33
ACGTcount: A:0.39, C:0.01, G:0.04, T:0.55
Consensus pattern (23 bp):
TTATGATTAAAATTAATTTTATT
Found at i:1475087 original size:4 final size:4
Alignment explanation
Indices: 1475078--1475121 Score: 61
Period size: 4 Copynumber: 11.0 Consensus size: 4
1475068 GTGCCTGTAA
* * *
1475078 ACAT ACAT ACTT AAAT ACAT ACAT ACAT AAAT ACAT ACAT ACAT
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
1475122 GTGCATACAT
Statistics
Matches: 34, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
4 34 1.00
ACGTcount: A:0.52, C:0.20, G:0.00, T:0.27
Consensus pattern (4 bp):
ACAT
Found at i:1475099 original size:16 final size:16
Alignment explanation
Indices: 1475078--1475121 Score: 79
Period size: 16 Copynumber: 2.8 Consensus size: 16
1475068 GTGCCTGTAA
*
1475078 ACATACATACTTAAAT
1 ACATACATACATAAAT
1475094 ACATACATACATAAAT
1 ACATACATACATAAAT
1475110 ACATACATACAT
1 ACATACATACAT
1475122 GTGCATACAT
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
16 27 1.00
ACGTcount: A:0.52, C:0.20, G:0.00, T:0.27
Consensus pattern (16 bp):
ACATACATACATAAAT
Done.