Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold119
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: 3173904
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 8 of 20
Found at i:1233179 original size:52 final size:51
Alignment explanation
Indices: 1232868--1233256 Score: 241
Period size: 52 Copynumber: 7.4 Consensus size: 51
1232858 CTCAATTCTC
* * * * * *
1232868 CACAATCGGGGATATTCCAACTCCGATTTTATTTTCAAAACACTAA-TTTT
1 CACAATCGGGGATACTCCAACCCCGGTTTTATTTCCAAAATACCAATTTTT
* * * *
1232918 CTATAATCGGGGATACTCCAACTCCGATTTTATTTCCAAAAAACACCAATTTCTT
1 C-ACAATCGGGGATACTCCAACCCCGGTTTTATTTCC--AAAATACCAATTT-TT
* * ****
1232973 CACAATCGGGGATACTCCAACCCC-G-TTGATCATCGGGGATACTCCAACCCCGTTATTT
1 CACAATCGGGGATACTCCAACCCCGGTTTTAT-TTCCAAAATA--CCAA-----TT-TTT
* * ** ***
1233031 C-CGA--GGGGATACTCCAACCTCGACTTTATTTCCAAAATATTGATTTTT
1 CACAATCGGGGATACTCCAACCCCGGTTTTATTTCCAAAATACCAATTTTT
* * * * * *
1233079 CATAATTGGGGATACTCCAACCCCGGTTTTATTGCTAAAACACTAATTTTT
1 CACAATCGGGGATACTCCAACCCCGGTTTTATTTCCAAAATACCAATTTTT
* * * *
1233130 CCACAATCGGGGATACTTCAACCCCGGTTTTATTTTCGAAATACCAATTTTC
1 -CACAATCGGGGATACTCCAACCCCGGTTTTATTTCCAAAATACCAATTTTT
** * *
1233182 CTTTAATCGGGGATACTCCAACTCCGATTTTATTTCCAAAAATACCAATTTTT
1 C-ACAATCGGGGATACTCCAACCCCGGTTTTATTTCC-AAAATACCAATTTTT
* *
1233235 CACAGTCGAGGATACTCCAACC
1 CACAATCGGGGATACTCCAACC
1233257 TCGTTATTTC
Statistics
Matches: 258, Mismatches: 59, Indels: 42
0.72 0.16 0.12
Matches are distributed among these distances:
48 4 0.02
49 3 0.01
50 1 0.00
51 71 0.28
52 90 0.35
53 29 0.11
54 24 0.09
55 19 0.07
56 5 0.02
57 6 0.02
58 5 0.02
59 1 0.00
ACGTcount: A:0.29, C:0.26, G:0.13, T:0.32
Consensus pattern (51 bp):
CACAATCGGGGATACTCCAACCCCGGTTTTATTTCCAAAATACCAATTTTT
Found at i:1233276 original size:28 final size:28
Alignment explanation
Indices: 1233244--1233315 Score: 99
Period size: 28 Copynumber: 2.6 Consensus size: 28
1233234 TCACAGTCGA
* * **
1233244 GGATACTCCAACCTCGTTATTTCATCGG
1 GGATACTCCAACCCCGTTACTTCAGAGG
*
1233272 GGATACTCCAACCCCGTTACTTCCGAGG
1 GGATACTCCAACCCCGTTACTTCAGAGG
1233300 GGATACTCCAACCCCG
1 GGATACTCCAACCCCG
1233316 GCTTTATTCC
Statistics
Matches: 39, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
28 39 1.00
ACGTcount: A:0.22, C:0.35, G:0.19, T:0.24
Consensus pattern (28 bp):
GGATACTCCAACCCCGTTACTTCAGAGG
Found at i:1233333 original size:263 final size:263
Alignment explanation
Indices: 1232866--1233366 Score: 794
Period size: 263 Copynumber: 1.9 Consensus size: 263
1232856 TTCTCAATTC
* *
1232866 TCCACAATCGGGGATATTCCAACTCCGATTTTATTTTCAAAACACTAATTTTCTATAATCGGGGA
1 TCCACAATCGGGGATATTCCAACCCCGATTTTATTTTCAAAACACCAATTTTCTATAATCGGGGA
*
1232931 TACTCCAACTCCGATTTTATTTCCAAAAAACACCAATTTCTTCACAATCGGGGATACTCCAACCC
66 TACTCCAACTCCGATTTTATTTCCAAAAAACACCAATTTCTTCACAATCGAGGATACTCCAACCC
* *
1232996 CGTTGATCATCGGGGATACTCCAACCCCGTTATTTCCGAGGGGATACTCCAACCTCGACTTTATT
131 CGTTGATCATCGGGGATACTCCAACCCCGTTACTTCCGAGGGGATACTCCAACCCCGACTTTATT
* * *
1233061 TCCAAAATATTGATTTTTCATAATTGGGGATACTCCAACCCCGGTTTTATTGCTAAAACACTAAT
196 CCCAAAATATTGATTTCTCATAATTGGGAATACTCCAACCCCGGTTTTATTGCTAAAACACTAAT
1233126 TTT
261 TTT
* * * *
1233129 TCCACAATCGGGGATACTT-CAACCCCGGTTTTATTTTCGAAATACCAATTTTCCTTTAATCGGG
1 TCCACAATCGGGGATA-TTCCAACCCCGATTTTATTTTCAAAACACCAATTTT-CTATAATCGGG
* *
1233193 GATACTCCAACTCCGATTTTATTTCC-AAAAATACCAATTT-TTCACAGTCGAGGATACTCCAAC
64 GATACTCCAACTCCGATTTTATTTCCAAAAAACACCAATTTCTTCACAATCGAGGATACTCCAAC
* *
1233256 CTCGTT-ATTTCATCGGGGATACTCCAACCCCGTTACTTCCGAGGGGATACTCCAACCCCGGCTT
129 CCCGTTGA--TCATCGGGGATACTCCAACCCCGTTACTTCCGAGGGGATACTCCAACCCCGACTT
1233320 TATTCCCAAAATATTGATTTCTCATAATTGGGAATACTCCAACCCCG
192 TATTCCCAAAATATTGATTTCTCATAATTGGGAATACTCCAACCCCG
1233367 TTATTTTCGA
Statistics
Matches: 218, Mismatches: 16, Indels: 8
0.90 0.07 0.03
Matches are distributed among these distances:
261 1 0.00
262 26 0.12
263 153 0.70
264 38 0.17
ACGTcount: A:0.28, C:0.27, G:0.14, T:0.32
Consensus pattern (263 bp):
TCCACAATCGGGGATATTCCAACCCCGATTTTATTTTCAAAACACCAATTTTCTATAATCGGGGA
TACTCCAACTCCGATTTTATTTCCAAAAAACACCAATTTCTTCACAATCGAGGATACTCCAACCC
CGTTGATCATCGGGGATACTCCAACCCCGTTACTTCCGAGGGGATACTCCAACCCCGACTTTATT
CCCAAAATATTGATTTCTCATAATTGGGAATACTCCAACCCCGGTTTTATTGCTAAAACACTAAT
TTT
Found at i:1245868 original size:13 final size:12
Alignment explanation
Indices: 1245849--1245882 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
1245839 ACCTTCTCTT
*
1245849 CAAAAAAAAAAG
1 CAAAAAAAAAAA
1245861 CAAAAAAAAAAA
1 CAAAAAAAAAAA
1245873 CAAAGAAAAA
1 CAAA-AAAAA
1245883 GGAGAGAAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
12 15 0.75
13 5 0.25
ACGTcount: A:0.85, C:0.09, G:0.06, T:0.00
Consensus pattern (12 bp):
CAAAAAAAAAAA
Found at i:1247042 original size:55 final size:55
Alignment explanation
Indices: 1246862--1247554 Score: 911
Period size: 55 Copynumber: 12.4 Consensus size: 55
1246852 CTCCTTCCGC
*
1246862 TTTCCAGTCCTCAAAGAGCAGGACGCCTTTTCTTTTAAAGCCCACACAAGTTGGTGGCAT
1 TTTCCAGTCCTCAAAGAGCAGGACACC-TTTC----AAAGCCCACACAAGTTGGTGGCAT
*
1246922 TTTCCAGTCCTCAAAGAGCGGGACACCTTTTCTTTTAAAGCCCACACAAGTTGGTGGCAT
1 TTTCCAGTCCTCAAAGAGCAGGACACC-TTTC----AAAGCCCACACAAGTTGGTGGCAT
* *
1246982 TTTCCAGTCCTCAAAGAGTAGAACACCTTTCAAAGCCCACACAAGTTGGTGGCAT
1 TTTCCAGTCCTCAAAGAGCAGGACACCTTTCAAAGCCCACACAAGTTGGTGGCAT
*
1247037 TTTCCAGTCCTCAAAGAGCAGGACACCTCTT-AAAGCCCACACAAGTTGGTGGCACC
1 TTTCCAGTCCTCAAAGAGCAGGACACCT-TTCAAAGCCCACACAAGTTGGTGGCA-T
* *
1247093 TTT-CAGTCCCCAAAGAGCAGGACACCTTTCAAAACCCAGC-CAAGTTGGTGGCAT
1 TTTCCAGTCCTCAAAGAGCAGGACACCTTTCAAAGCCCA-CACAAGTTGGTGGCAT
1247147 TTTCCAGTCCTCAAAGAGCAGGACACCTTTCAAAGCCCACACAAGTTGGTGGCAT
1 TTTCCAGTCCTCAAAGAGCAGGACACCTTTCAAAGCCCACACAAGTTGGTGGCAT
* * *
1247202 TTTCCAATCCTCAAAGAGCAGGACACCTCTT-AAAGCCTACACAAGTTGGTGGCACC
1 TTTCCAGTCCTCAAAGAGCAGGACACCT-TTCAAAGCCCACACAAGTTGGTGGCA-T
*
1247258 TTT-CAGTCCCCAAAGAGCAGGACACCTTTCAAAGCCCAC-CAAAGTTGGTGGCAT
1 TTTCCAGTCCTCAAAGAGCAGGACACCTTTCAAAGCCCACAC-AAGTTGGTGGCAT
* * *
1247312 TTTCAAGTCCTCAAAGAGCAGGACACCTTTTAAAGCCCACACAAGTTGGTGGCACC
1 TTTCCAGTCCTCAAAGAGCAGGACACCTTTCAAAGCCCACACAAGTTGGTGGCA-T
*
1247368 TTT-CAGTCCCCAAAGAGCAGGACACCTTTCAAAGCCCACACAAGTTGGTGGCAT
1 TTTCCAGTCCTCAAAGAGCAGGACACCTTTCAAAGCCCACACAAGTTGGTGGCAT
* * *
1247422 TTTCCAATCCTCAAAGAGCAGGACACCTCTT-AAAGCCCATACAAGTTGGTGGCACC
1 TTTCCAGTCCTCAAAGAGCAGGACACCT-TTCAAAGCCCACACAAGTTGGTGGCA-T
* * * *
1247478 TTT-CAATCCTTAAAGAGCAGGACGCCTTTCAAAGCCCACACGAGTTGGTGGCACT
1 TTTCCAGTCCTCAAAGAGCAGGACACCTTTCAAAGCCCACACAAGTTGGTGGCA-T
* * *
1247533 TTT-TACTCCTCAATGAGCAGGA
1 TTTCCAGTCCTCAAAGAGCAGGA
1247555 TACACTTTAT
Statistics
Matches: 575, Mismatches: 41, Indels: 39
0.88 0.06 0.06
Matches are distributed among these distances:
54 17 0.03
55 452 0.79
56 20 0.03
59 4 0.01
60 82 0.14
ACGTcount: A:0.29, C:0.29, G:0.20, T:0.23
Consensus pattern (55 bp):
TTTCCAGTCCTCAAAGAGCAGGACACCTTTCAAAGCCCACACAAGTTGGTGGCAT
Found at i:1247284 original size:26 final size:26
Alignment explanation
Indices: 1247254--1247398 Score: 82
Period size: 26 Copynumber: 5.3 Consensus size: 26
1247244 AAGTTGGTGG
1247254 CACCTTTCAGTCCCCAAAGAGCAGGA
1 CACCTTTCAGTCCCCAAAGAGCAGGA
* * **
1247280 CACCTTTCAAAGCCCACCAAAGTTGGTGG-
1 CACCTTTC--AGTCC-CCAAAG-AGCAGGA
* *
1247309 CA-TTTTCAAGTCCTCAAAGAGCAGGA
1 CACCTTTC-AGTCCCCAAAGAGCAGGA
* * **
1247335 CACCTTTTAAAG-CCCACACAAGTTGGTGG-
1 CACC-TTT-CAGTCCC-CA-AAG-AGCAGGA
1247364 CACCTTTCAGTCCCCAAAGAGCAGGA
1 CACCTTTCAGTCCCCAAAGAGCAGGA
1247390 CACCTTTCA
1 CACCTTTCA
1247399 AAGCCCACAC
Statistics
Matches: 86, Mismatches: 20, Indels: 26
0.65 0.15 0.20
Matches are distributed among these distances:
25 6 0.07
26 27 0.31
27 11 0.13
28 21 0.24
29 15 0.17
30 6 0.07
ACGTcount: A:0.30, C:0.31, G:0.19, T:0.21
Consensus pattern (26 bp):
CACCTTTCAGTCCCCAAAGAGCAGGA
Found at i:1247368 original size:29 final size:29
Alignment explanation
Indices: 1247335--1247420 Score: 74
Period size: 28 Copynumber: 3.1 Consensus size: 29
1247325 AAGAGCAGGA
1247335 CACCTTTTAAAGCCCACACAAGTTGGTGG
1 CACCTTTTAAAGCCCACACAAGTTGGTGG
* * **
1247364 CACC-TTT-CAGTCCC-CA-AAG-AGCAGG
1 CACCTTTTAAAG-CCCACACAAGTTGGTGG
*
1247389 ACACCTTTCAAAGCCCACACAAGTTGGTGG
1 -CACCTTTTAAAGCCCACACAAGTTGGTGG
1247419 CA
1 CA
1247421 TTTTCCAATC
Statistics
Matches: 41, Mismatches: 9, Indels: 14
0.64 0.14 0.22
Matches are distributed among these distances:
25 3 0.07
26 7 0.17
27 9 0.22
28 10 0.24
29 9 0.22
30 3 0.07
ACGTcount: A:0.29, C:0.31, G:0.20, T:0.20
Consensus pattern (29 bp):
CACCTTTTAAAGCCCACACAAGTTGGTGG
Found at i:1249834 original size:52 final size:51
Alignment explanation
Indices: 1249545--1249933 Score: 261
Period size: 52 Copynumber: 7.4 Consensus size: 51
1249535 CTCAATTCTC
* * * *
1249545 CACAATCGAGGATATTCCAACTCCGATTTTATTT-TCAAAACACTAA-TTTT
1 CACAATCGGGGATACTCCAACCCCGATTTTATTTCT-AAAACACCAATTTTT
* * *
1249595 CTATAATCGGGGATACTCCAACTCCGATTTTATTTCCAAAAAACACCAATTTCTT
1 C-ACAATCGGGGATACTCCAACCCCGATTTTATTT-C-TAAAACACCAATTT-TT
* * ** **
1249650 CACAATCGGGGATACTCCAACCCCG-TTGATCATCGGGGATACTCCAAC-CCCGTTATTT
1 CACAATCGGGGATACTCCAACCCCGATT--TTAT------TTCTAAAACACCAATT-TTT
* * * * * * ***
1249708 CA-GA--GAGGATACTCCAACCGCGACTTTATTTCCAAAATATTGATTTTT
1 CACAATCGGGGATACTCCAACCCCGATTTTATTTCTAAAACACCAATTTTT
* * *
1249756 CACAATCGGGGATACTCCAACCCCGGTTTTATTGCTAAAACACTAATTTTT
1 CACAATCGGGGATACTCCAACCCCGATTTTATTTCTAAAACACCAATTTTT
* * *
1249807 CCACAATCGGGGATACTCCAACCCCGGTTTTATTTTTGAAACACCAATTTTT
1 -CACAATCGGGGATACTCCAACCCCGATTTTATTTCTAAAACACCAATTTTT
** * * *
1249859 CTTTAATCGGGGATACTCCAACTCCGATTTTATTTCCAAAAATACCAATTTTT
1 C-ACAATCGGGGATACTCCAACCCCGATTTTATTT-CTAAAACACCAATTTTT
* *
1249912 CACAGTCGAGGATACTCCAACC
1 CACAATCGGGGATACTCCAACC
1249934 TCGTTATTTC
Statistics
Matches: 261, Mismatches: 55, Indels: 44
0.73 0.15 0.12
Matches are distributed among these distances:
48 9 0.03
49 3 0.01
50 1 0.00
51 66 0.25
52 92 0.35
53 25 0.10
54 27 0.10
55 22 0.08
56 1 0.00
57 1 0.00
58 8 0.03
59 4 0.02
60 1 0.00
61 1 0.00
ACGTcount: A:0.30, C:0.26, G:0.13, T:0.31
Consensus pattern (51 bp):
CACAATCGGGGATACTCCAACCCCGATTTTATTTCTAAAACACCAATTTTT
Found at i:1249978 original size:28 final size:28
Alignment explanation
Indices: 1249921--1249980 Score: 75
Period size: 28 Copynumber: 2.1 Consensus size: 28
1249911 TCACAGTCGA
* * **
1249921 GGATACTCCAACCTCGTTATTTCATCGG
1 GGATACTCCAACCCCGTTACTTCAGAGG
*
1249949 GGATACTCCAACCCCGTTACTTCCGAGG
1 GGATACTCCAACCCCGTTACTTCAGAGG
1249977 GGAT
1 GGAT
1249981 GCTCTAGCCC
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
28 27 1.00
ACGTcount: A:0.22, C:0.30, G:0.22, T:0.27
Consensus pattern (28 bp):
GGATACTCCAACCCCGTTACTTCAGAGG
Found at i:1250010 original size:263 final size:263
Alignment explanation
Indices: 1249543--1250043 Score: 722
Period size: 263 Copynumber: 1.9 Consensus size: 263
1249533 TTCTCAATTC
* * *
1249543 TCCACAATCGAGGATATTCCAACTCCGATTTTATTTTCAAAACACTAATTTTCTATAATCGGGGA
1 TCCACAATCGAGGATACTCCAACCCCGATTTTATTTTCAAAACACCAATTTTCTATAATCGGGGA
*
1249608 TACTCCAACTCCGATTTTATTTCCAAAAAACACCAATTTCTTCACAATCGGGGATACTCCAACCC
66 TACTCCAACTCCGATTTTATTTCCAAAAAACACCAATTTCTTCACAATCGAGGATACTCCAACCC
*
1249673 CGTTGATCATCGGGGATACTCCAACCCCGTTATTTCAGAGAGGATACTCCAACCGCGACTTTATT
131 CGTTGATCATCGGGGATACTCCAACCCCGTTACTTCAGAGAGGATACTCCAACCGCGACTTTATT
* * *
1249738 TCCAAAATATTGATTTTTCACAATCGGGGATACTCCAACCCCGGTTTTATTGCTAAAACACTAAT
196 CCCAAAATATTGATTTCTCACAATCGGGAATACTCCAACCCCGGTTTTATTGCTAAAACACTAAT
1249803 TTT
261 TTT
* * ** *
1249806 TCCACAATCGGGGATACTCCAACCCCGGTTTTATTTTTGAAACACCAATTTTTCTTTAATCGGGG
1 TCCACAATCGAGGATACTCCAACCCCGATTTTATTTTCAAAACACCAA-TTTTCTATAATCGGGG
* *
1249871 ATACTCCAACTCCGATTTTATTTCC-AAAAATACCAATTT-TTCACAGTCGAGGATACTCCAACC
65 ATACTCCAACTCCGATTTTATTTCCAAAAAACACCAATTTCTTCACAATCGAGGATACTCCAACC
* * * * * * *
1249934 TCGTT-ATTTCATCGGGGATACTCCAACCCCGTTACTTCCGAGGGGATGCTCTAGCC-CTAGCTT
130 CCGTTGA--TCATCGGGGATACTCCAACCCCGTTACTTCAGAGAGGATACTCCAACCGCGA-CTT
* *
1249997 TATTCCCAAAATATTGATTTCTCATAATTGGGAATACTCCAACCCCG
192 TATTCCCAAAATATTGATTTCTCACAATCGGGAATACTCCAACCCCG
1250044 TTATTTTCGA
Statistics
Matches: 210, Mismatches: 24, Indels: 8
0.87 0.10 0.03
Matches are distributed among these distances:
261 1 0.00
262 28 0.13
263 141 0.67
264 40 0.19
ACGTcount: A:0.28, C:0.27, G:0.14, T:0.31
Consensus pattern (263 bp):
TCCACAATCGAGGATACTCCAACCCCGATTTTATTTTCAAAACACCAATTTTCTATAATCGGGGA
TACTCCAACTCCGATTTTATTTCCAAAAAACACCAATTTCTTCACAATCGAGGATACTCCAACCC
CGTTGATCATCGGGGATACTCCAACCCCGTTACTTCAGAGAGGATACTCCAACCGCGACTTTATT
CCCAAAATATTGATTTCTCACAATCGGGAATACTCCAACCCCGGTTTTATTGCTAAAACACTAAT
TTT
Found at i:1251322 original size:52 final size:52
Alignment explanation
Indices: 1251232--1251388 Score: 215
Period size: 52 Copynumber: 3.0 Consensus size: 52
1251222 AAAACCATTT
* * ** *
1251232 ACTAAAAAGTTACTGAACTTTAAAAAAATGATTTTATGATTTGTGTATACCA
1 ACTAAAAAGTTACTAAACTTTAAAAAAACGATACTATGATTTGCGTATACCA
*
1251284 ACTAAAAAGTTACTAAACTTTAAAAGAACGATACTATGATTTGCGTATACCA
1 ACTAAAAAGTTACTAAACTTTAAAAAAACGATACTATGATTTGCGTATACCA
* ** * *
1251336 ACTAAAAAGTTACTAAACTTTAAAAAAATGATTTTACGATTTGCATATACCA
1 ACTAAAAAGTTACTAAACTTTAAAAAAACGATACTATGATTTGCGTATACCA
1251388 A
1 A
1251389 AGATCTATAA
Statistics
Matches: 93, Mismatches: 12, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
52 93 1.00
ACGTcount: A:0.45, C:0.13, G:0.10, T:0.32
Consensus pattern (52 bp):
ACTAAAAAGTTACTAAACTTTAAAAAAACGATACTATGATTTGCGTATACCA
Found at i:1255056 original size:13 final size:13
Alignment explanation
Indices: 1255038--1255063 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1255028 CAATTTTTTG
1255038 TGTATCGATACAT
1 TGTATCGATACAT
1255051 TGTATCGATACAT
1 TGTATCGATACAT
1255064 ACTTGTTGTA
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:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:1257645 original size:20 final size:20
Alignment explanation
Indices: 1257620--1257698 Score: 77
Period size: 20 Copynumber: 3.7 Consensus size: 20
1257610 TATCGGATAC
1257620 AATGTATCGATACAAAGAAA
1 AATGTATCGATACAAAGAAA
**
1257640 AATGTATCGATACATTGAAA
1 AATGTATCGATACAAAGAAA
*
1257660 TTCCAGATGTATCGATACACAGAAA
1 ----A-ATGTATCGATACAAAGAAA
*
1257685 CATGTATCGATACA
1 AATGTATCGATACA
1257699 TTTTGGACAT
Statistics
Matches: 49, Mismatches: 5, Indels: 10
0.77 0.08 0.16
Matches are distributed among these distances:
20 31 0.63
24 1 0.02
25 17 0.35
ACGTcount: A:0.44, C:0.15, G:0.15, T:0.25
Consensus pattern (20 bp):
AATGTATCGATACAAAGAAA
Found at i:1259734 original size:15 final size:15
Alignment explanation
Indices: 1259714--1259744 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
1259704 ATTTCGTTTG
*
1259714 GAGCTTCTTCATTTT
1 GAGCTTCCTCATTTT
1259729 GAGCTTCCTCATTTT
1 GAGCTTCCTCATTTT
1259744 G
1 G
1259745 GACATTTTTA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.13, C:0.23, G:0.16, T:0.48
Consensus pattern (15 bp):
GAGCTTCCTCATTTT
Found at i:1261549 original size:21 final size:21
Alignment explanation
Indices: 1261520--1261564 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 21
1261510 AAGTTTTTAT
*
1261520 TTTTCTTAGCTAAC-TCATTA
1 TTTTCTTAGCCAACTTCATTA
*
1261540 TTTTCATTAGCCAACTTCTTTA
1 TTTTC-TTAGCCAACTTCATTA
1261562 TTT
1 TTT
1261565 CAACTTGCAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 5 0.24
21 8 0.38
22 8 0.38
ACGTcount: A:0.22, C:0.20, G:0.04, T:0.53
Consensus pattern (21 bp):
TTTTCTTAGCCAACTTCATTA
Found at i:1263803 original size:13 final size:13
Alignment explanation
Indices: 1263785--1263810 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1263775 CAATTTTTTG
1263785 TGTATCGATACAT
1 TGTATCGATACAT
1263798 TGTATCGATACAT
1 TGTATCGATACAT
1263811 ACTTGCTGTA
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:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:1265662 original size:16 final size:17
Alignment explanation
Indices: 1265641--1265694 Score: 67
Period size: 16 Copynumber: 3.3 Consensus size: 17
1265631 TTACCTAATA
1265641 AAATTTAAAA-TAAAAT
1 AAATTTAAAATTAAAAT
*
1265657 AAATTTAAAATTAAGA-
1 AAATTTAAAATTAAAAT
*
1265673 AAAGTTAAAATTAAAAT
1 AAATTTAAAATTAAAAT
*
1265690 CAATT
1 AAATT
1265695 CTTAGCAATA
Statistics
Matches: 31, Mismatches: 5, Indels: 3
0.79 0.13 0.08
Matches are distributed among these distances:
16 24 0.77
17 7 0.23
ACGTcount: A:0.63, C:0.02, G:0.04, T:0.31
Consensus pattern (17 bp):
AAATTTAAAATTAAAAT
Found at i:1266275 original size:152 final size:153
Alignment explanation
Indices: 1265944--1266601 Score: 814
Period size: 152 Copynumber: 4.3 Consensus size: 153
1265934 CATATTTTGG
* * * * * * * * *
1265944 AAAAAAAATCTAAAACTTATAAAATAAATTTAATTTTTTAAAATTGATTTAATATGAATCAAAAA
1 AAAAAAATTCTAAAACTCATAAAATAAATTGAATTTGTCAAAAATGATTTAATATCAATTAAACA
*
1266009 ATAATATTTGAAGAATTTTAAAAATTATAAACTTTAGAAAAATCCTACTAAAAAATTTATG-GAG
66 ATAATATTTGAAGAATTTTAAAAATTATAAAC-TTAGAAAAATCCTACTAAAAAATTTACGAGAG
*
1266073 TAGAAAACTCTGTATTTCGATAAT
130 TAGAAAACTCTGTATTTTGATAAT
** * * * * *
1266097 AGGAAAATTCTAAAGCTCATACAATAAATTGAATTTATTAAAAATGATATAATATCAATTAAACA
1 AAAAAAATTCTAAAACTCATAAAATAAATTGAATTTGTCAAAAATGATTTAATATCAATTAAACA
* * * *
1266162 ATAATATTTGAAGAAATTTGAAAATTATAAACTTAGAAGAATCTTA-TCAAAAAATTTACGA-AG
66 ATAATATTTGAAGAATTTTAAAAATTATAAACTTAGAAAAATCCTACT-AAAAAATTTACGAGAG
* *
1266225 TAGAAAACTCAGTATTTTGATAAC
130 TAGAAAACTCTGTATTTTGATAAT
*
1266249 AAAAAAATTCTAAAACTCATAAAATAAATTGAATTTGTCAAAAATAATTTAATATCAATTAAA-A
1 AAAAAAATTCTAAAACTCATAAAATAAATTGAATTTGTCAAAAATGATTTAATATCAATTAAACA
* * * *
1266313 ATAATATTTGAATAATTTTGAAAATTATAAACTTAGAAAAATCCTACTAAAAAATTTA-TAGAGA
66 ATAATATTTGAAGAATTTTAAAAATTATAAACTTAGAAAAATCCTACTAAAAAATTTACGAGAGT
*
1266377 AGAAAA-TTTCGTATTTTGATAAT
131 AGAAAACTCT-GTATTTTGATAAT
* * *
1266400 AAGAAAAATTCTAAAATTCATAAAATAAGTTGAATTTGTCAACAATGATTTAATATCAATTAAAC
1 AA-AAAAATTCTAAAACTCATAAAATAAATTGAATTTGTCAAAAATGATTTAATATCAATTAAAC
* *
1266465 AATAATATTTGAAGAATTTTAAAAATTGTAAACTTATAAAAAT-CTGAC-AATAAAATTTAC-AG
65 AATAATATTTGAAGAATTTTAAAAATTATAAACTTAGAAAAATCCT-ACTAA-AAAATTTACGAG
*
1266527 GGTAGAAAACTCTGTATTTTGATAAT
128 AGTAGAAAACTCTGTATTTTGATAAT
* * * * *
1266553 AGATAAATTCTAAAACTCATAAAATAAGTTAAAATTT-TCAAAACTGATT
1 AAAAAAATTCTAAAACTCATAAAATAAATT-GAATTTGTCAAAAATGATT
1266602 CTATGGTGAT
Statistics
Matches: 438, Mismatches: 55, Indels: 25
0.85 0.11 0.05
Matches are distributed among these distances:
150 2 0.00
151 76 0.17
152 199 0.45
153 159 0.36
154 2 0.00
ACGTcount: A:0.50, C:0.08, G:0.08, T:0.34
Consensus pattern (153 bp):
AAAAAAATTCTAAAACTCATAAAATAAATTGAATTTGTCAAAAATGATTTAATATCAATTAAACA
ATAATATTTGAAGAATTTTAAAAATTATAAACTTAGAAAAATCCTACTAAAAAATTTACGAGAGT
AGAAAACTCTGTATTTTGATAAT
Found at i:1269114 original size:13 final size:13
Alignment explanation
Indices: 1269096--1269120 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1269086 CATAAAATGT
1269096 TGTATCGATACAA
1 TGTATCGATACAA
1269109 TGTATCGATACA
1 TGTATCGATACA
1269121 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:1269118 original size:33 final size:33
Alignment explanation
Indices: 1269076--1269145 Score: 104
Period size: 33 Copynumber: 2.1 Consensus size: 33
1269066 TTCAACGATT
1269076 TGTATCGATACATAAAATGTTGTATCGATACAA
1 TGTATCGATACATAAAATGTTGTATCGATACAA
*** *
1269109 TGTATCGATACATATTTTTTTGTATCGATACAA
1 TGTATCGATACATAAAATGTTGTATCGATACAA
1269142 TGTA
1 TGTA
1269146 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:1269203 original size:13 final size:13
Alignment explanation
Indices: 1269185--1269209 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1269175 ATTACTCACA
1269185 TGTATCGATACAT
1 TGTATCGATACAT
1269198 TGTATCGATACA
1 TGTATCGATACA
1269210 CTAATCTTTG
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:1269346 original size:52 final size:52
Alignment explanation
Indices: 1269198--1269338 Score: 228
Period size: 52 Copynumber: 2.7 Consensus size: 52
1269188 ATCGATACAT
* ***
1269198 TGTATCGATACACTAATCTTTGTATCGATACATGCAGGCAAATTTGCCCAGA
1 TGTATCGATACACTATTAAATGTATCGATACATGCAGGCAAATTTGCCCAGA
* *
1269250 TGTATCGATACATTATAAAATGTATCGATACATGCAGGCAAATTTGCCCAGA
1 TGTATCGATACACTATTAAATGTATCGATACATGCAGGCAAATTTGCCCAGA
1269302 TGTATCGATACACTATTAAATGTATCGATACATGCAG
1 TGTATCGATACACTATTAAATGTATCGATACATGCAG
1269339 ATAAATTTTC
Statistics
Matches: 81, Mismatches: 8, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
52 81 1.00
ACGTcount: A:0.34, C:0.18, G:0.17, T:0.30
Consensus pattern (52 bp):
TGTATCGATACACTATTAAATGTATCGATACATGCAGGCAAATTTGCCCAGA
Found at i:1277112 original size:50 final size:51
Alignment explanation
Indices: 1277053--1277148 Score: 140
Period size: 51 Copynumber: 1.9 Consensus size: 51
1277043 TGAACAATAC
1277053 ATGTATCGATACATTAT-TTTTTTTATCCAGATGTATCGATACATTTTTCA
1 ATGTATCGATACATTATGTTTTTTTATCCAGATGTATCGATACATTTTTCA
* ** * *
1277103 ATGTATCGATACATTCTGTTTTTTTATCTTGTTGTATCTATACATT
1 ATGTATCGATACATTATGTTTTTTTATCCAGATGTATCGATACATT
1277149 GAAAAATGTA
Statistics
Matches: 40, Mismatches: 5, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
50 16 0.40
51 24 0.60
ACGTcount: A:0.25, C:0.14, G:0.10, T:0.51
Consensus pattern (51 bp):
ATGTATCGATACATTATGTTTTTTTATCCAGATGTATCGATACATTTTTCA
Found at i:1277157 original size:51 final size:50
Alignment explanation
Indices: 1277053--1277167 Score: 131
Period size: 51 Copynumber: 2.3 Consensus size: 50
1277043 TGAACAATAC
****
1277053 ATGTATCGATACATTATTTTTTTTATCCAGATGTATCGATACATTTTTCA
1 ATGTATCGATACATTATTTTTTTTATCCAGATGTATCGATACATTGAAAA
* ** * *
1277103 ATGTATCGATACATTCTGTTTTTTTATCTTGTTGTATCTATACATTGAAAA
1 ATGTATCGATACATTAT-TTTTTTTATCCAGATGTATCGATACATTGAAAA
*
1277154 ATGTATCGACACAT
1 ATGTATCGATACAT
1277168 CTAGTTTATT
Statistics
Matches: 54, Mismatches: 10, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
50 16 0.30
51 38 0.70
ACGTcount: A:0.29, C:0.14, G:0.11, T:0.46
Consensus pattern (50 bp):
ATGTATCGATACATTATTTTTTTTATCCAGATGTATCGATACATTGAAAA
Found at i:1278095 original size:20 final size:20
Alignment explanation
Indices: 1278057--1278096 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
1278047 TAGCCTTTGA
*
1278057 TCATACATTTTCAATATGTT
1 TCATACATTTTCAACATGTT
* *
1278077 TCATGCATTTTTAACATGTT
1 TCATACATTTTCAACATGTT
1278097 CGGCATCTCA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.28, C:0.15, G:0.07, T:0.50
Consensus pattern (20 bp):
TCATACATTTTCAACATGTT
Found at i:1292334 original size:28 final size:28
Alignment explanation
Indices: 1292290--1292980 Score: 792
Period size: 28 Copynumber: 24.5 Consensus size: 28
1292280 TAATACGACC
*
1292290 TCTTTTCAAAGCCCACAAGTTAGTGGCA
1 TCTTTTCAAAGCCCACAAGTCAGTGGCA
*
1292318 TCTTTTCAAAGCTCACAAGTCAGTGGCA
1 TCTTTTCAAAGCCCACAAGTCAGTGGCA
* * *
1292346 CCTTCTT-AAAGCCCATATGTCAGTGGCA
1 TCTT-TTCAAAGCCCACAAGTCAGTGGCA
* ** *
1292374 CCTCCTCAAAGCCCACATGTCAGTGGCA
1 TCTTTTCAAAGCCCACAAGTCAGTGGCA
* *
1292402 TCCTTTCAAAGCCCATAAGTCAGTGGCA
1 TCTTTTCAAAGCCCACAAGTCAGTGGCA
* *
1292430 TCTTTTCAAAACCCATAAGTCAGTGGCA
1 TCTTTTCAAAGCCCACAAGTCAGTGGCA
* * *
1292458 TCTTTTCTAAGCCCATAAGTTAGTGGCA
1 TCTTTTCAAAGCCCACAAGTCAGTGGCA
* * *
1292486 CCTTCTCAAAGCCCACAAATCAGTGGCA
1 TCTTTTCAAAGCCCACAAGTCAGTGGCA
* * * *
1292514 TCTTTTCAAAGCCCATAACTTAATGGCA
1 TCTTTTCAAAGCCCACAAGTCAGTGGCA
* * *
1292542 TCCTTTCAAAGCCCACAAGTTAATGGCA
1 TCTTTTCAAAGCCCACAAGTCAGTGGCA
* * * * *
1292570 TCCTTTCAAAGCCCATAAGTTACTAGCA
1 TCTTTTCAAAGCCCACAAGTCAGTGGCA
* *
1292598 TCCTTTCAAAGCCCACAAGTCAATGGCA
1 TCTTTTCAAAGCCCACAAGTCAGTGGCA
*
1292626 TCCTTTCAAAGCCCACAAGTCAGTGGCA
1 TCTTTTCAAAGCCCACAAGTCAGTGGCA
* * *
1292654 CCTTTTTAAAGCCCACAAGTCAGTGCCA
1 TCTTTTCAAAGCCCACAAGTCAGTGGCA
1292682 -CATTTTCAAAGCCCACAAGTCAGTGGCA
1 TC-TTTTCAAAGCCCACAAGTCAGTGGCA
* *
1292710 TCTTTTTAAAGCCCATAAGTCAGTGGCA
1 TCTTTTCAAAGCCCACAAGTCAGTGGCA
* * *
1292738 CCTTCTCAAAGCCCACATGTCAGTGGCA
1 TCTTTTCAAAGCCCACAAGTCAGTGGCA
* * *
1292766 TCCTTTCAAAGCCCATAAGTCAGTGGTA
1 TCTTTTCAAAGCCCACAAGTCAGTGGCA
*
1292794 TCTTCTCAAAGCCCACAAGTCAGTGGCA
1 TCTTTTCAAAGCCCACAAGTCAGTGGCA
* * *
1292822 CCTTCTCAAAGCCCACAAGTCAGCGGCA
1 TCTTTTCAAAGCCCACAAGTCAGTGGCA
* *
1292850 TCCTTTCAAAACCCACAAGTCAGTGGCA
1 TCTTTTCAAAGCCCACAAGTCAGTGGCA
*
1292878 TCTTTTCAAAGCCCACAAGTCAGTGGTA
1 TCTTTTCAAAGCCCACAAGTCAGTGGCA
*
1292906 TCTTTTCAAAGCCCACATAAGTCGGTGGCA
1 TCTTTTCAAAGCCCAC--AAGTCAGTGGCA
* *
1292936 TATTTTCAAAGCCCACACAAGTCGGTGGCA
1 TCTTTTCAAAG-CC-CACAAGTCAGTGGCA
*
1292966 ACTTTCTCTAAAGCC
1 TCTTT-TC-AAAGCC
1292981 GTACAAGTTG
Statistics
Matches: 572, Mismatches: 81, Indels: 17
0.85 0.12 0.03
Matches are distributed among these distances:
27 2 0.00
28 519 0.91
29 3 0.01
30 35 0.06
31 6 0.01
32 7 0.01
ACGTcount: A:0.29, C:0.29, G:0.16, T:0.25
Consensus pattern (28 bp):
TCTTTTCAAAGCCCACAAGTCAGTGGCA
Found at i:1293609 original size:20 final size:21
Alignment explanation
Indices: 1293584--1293638 Score: 76
Period size: 22 Copynumber: 2.6 Consensus size: 21
1293574 AAAGAAAGGG
1293584 TACAATTACAATT-TGACAAT
1 TACAATTACAATTGTGACAAT
*
1293604 TACAATTGCAATTTGTGACAAT
1 TACAATTACAA-TTGTGACAAT
*
1293626 TACAATGACAATT
1 TACAATTACAATT
1293639 AAAATTTGGA
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
20 10 0.33
21 4 0.13
22 16 0.53
ACGTcount: A:0.42, C:0.15, G:0.09, T:0.35
Consensus pattern (21 bp):
TACAATTACAATTGTGACAAT
Found at i:1294122 original size:20 final size:20
Alignment explanation
Indices: 1294097--1294143 Score: 67
Period size: 20 Copynumber: 2.4 Consensus size: 20
1294087 TAAATTTTGA
*
1294097 GATACATGTATGAATGTATC
1 GATACATGTATCAATGTATC
* *
1294117 GATACATTTTTCAATGTATC
1 GATACATGTATCAATGTATC
1294137 GATACAT
1 GATACAT
1294144 TCTGTTTTTC
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.34, C:0.13, G:0.15, T:0.38
Consensus pattern (20 bp):
GATACATGTATCAATGTATC
Found at i:1294617 original size:13 final size:12
Alignment explanation
Indices: 1294585--1294619 Score: 52
Period size: 12 Copynumber: 2.8 Consensus size: 12
1294575 AAAGAATCCT
*
1294585 TTTTCAACCATA
1 TTTTCAGCCATA
1294597 TTTTCAGCCATA
1 TTTTCAGCCATA
1294609 TTTTCCAGCCA
1 TTTT-CAGCCA
1294620 CATTACCACT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
12 15 0.71
13 6 0.29
ACGTcount: A:0.26, C:0.29, G:0.06, T:0.40
Consensus pattern (12 bp):
TTTTCAGCCATA
Found at i:1303825 original size:17 final size:16
Alignment explanation
Indices: 1303803--1303879 Score: 55
Period size: 17 Copynumber: 4.6 Consensus size: 16
1303793 CATGAATGTC
1303803 ATTATGAATATTCATAA
1 ATTATGAA-ATTCATAA
* *
1303820 ATTATGAAAGTTAATGA
1 ATTATGAAA-TTCATAA
* *
1303837 ATTATGAAAATTTATGA
1 ATTATG-AAATTCATAA
**
1303854 GCTATGAACATTCATAA
1 ATTATGAA-ATTCATAA
*
1303871 ACTATGAAA
1 ATTATGAAA
1303880 ATTTATGAGC
Statistics
Matches: 49, Mismatches: 8, Indels: 7
0.77 0.12 0.11
Matches are distributed among these distances:
16 4 0.08
17 42 0.86
18 3 0.06
ACGTcount: A:0.47, C:0.06, G:0.12, T:0.35
Consensus pattern (16 bp):
ATTATGAAATTCATAA
Found at i:1303860 original size:34 final size:34
Alignment explanation
Indices: 1303822--1303899 Score: 104
Period size: 34 Copynumber: 2.3 Consensus size: 34
1303812 ATTCATAAAT
* *
1303822 TATGAA-AGTTAATGAATTATGAAAATTTATGAGC
1 TATGAACA-TTAATAAACTATGAAAATTTATGAGC
*
1303856 TATGAACATTCATAAACTATGAAAATTTATGAGC
1 TATGAACATTAATAAACTATGAAAATTTATGAGC
*
1303890 TATAAACATT
1 TATGAACATT
1303900 CTTGTCTTAT
Statistics
Matches: 39, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
34 38 0.97
35 1 0.03
ACGTcount: A:0.45, C:0.08, G:0.13, T:0.35
Consensus pattern (34 bp):
TATGAACATTAATAAACTATGAAAATTTATGAGC
Found at i:1303892 original size:17 final size:17
Alignment explanation
Indices: 1303839--1303892 Score: 72
Period size: 17 Copynumber: 3.2 Consensus size: 17
1303829 GTTAATGAAT
1303839 TATGAAAATTTATGAGC
1 TATGAAAATTTATGAGC
* * * *
1303856 TATGAACATTCATAAAC
1 TATGAAAATTTATGAGC
1303873 TATGAAAATTTATGAGC
1 TATGAAAATTTATGAGC
1303890 TAT
1 TAT
1303893 AAACATTCTT
Statistics
Matches: 29, Mismatches: 8, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
17 29 1.00
ACGTcount: A:0.43, C:0.09, G:0.13, T:0.35
Consensus pattern (17 bp):
TATGAAAATTTATGAGC
Found at i:1305057 original size:20 final size:20
Alignment explanation
Indices: 1305034--1305080 Score: 69
Period size: 20 Copynumber: 2.4 Consensus size: 20
1305024 AATAATACTT
1305034 ATATTTTAAATATT-TATAAA
1 ATATTTTAAATATTAT-TAAA
*
1305054 ATATTTTATATATTATTAAA
1 ATATTTTAAATATTATTAAA
1305074 ATATTTT
1 ATATTTT
1305081 TAAAATAATA
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
20 24 0.96
21 1 0.04
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (20 bp):
ATATTTTAAATATTATTAAA
Found at i:1305194 original size:24 final size:24
Alignment explanation
Indices: 1305167--1305223 Score: 87
Period size: 24 Copynumber: 2.4 Consensus size: 24
1305157 TAATAATATT
*
1305167 TAATTATATATGAAAATACTTTAA
1 TAATAATATATGAAAATACTTTAA
* *
1305191 TAATAATATATTAAAATATTTTAA
1 TAATAATATATGAAAATACTTTAA
1305215 TAATAATAT
1 TAATAATAT
1305224 TTAATAATAT
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 30 1.00
ACGTcount: A:0.53, C:0.02, G:0.02, T:0.44
Consensus pattern (24 bp):
TAATAATATATGAAAATACTTTAA
Found at i:1305205 original size:74 final size:71
Alignment explanation
Indices: 1305043--1305232 Score: 187
Period size: 74 Copynumber: 2.7 Consensus size: 71
1305033 TATATTTTAA
* * * *
1305043 ATATTTATAA-AATATTTTATATATTATTAA-AAT-ATTTTTAA-AATAATATTTAATTAAATAC
1 ATATTAATAATAATATTTAAAATATT-TTAATAATAATATTTAATAATAATATTTAATTAAATAC
1305104 TAAATAT
65 TAAATAT
* * * * *
1305111 ATATTAGTAATAATCTTTAAAACTATATTTAATAATTTATCTTTAATAATAATATTTAATTATAT
1 ATATTAATAATAATATTTAAAA-TAT-TTTAATAA-TAATATTTAATAATAATATTTAATTAAAT
1305176 A-TGAAA-AT
63 ACT-AAATAT
1305184 ACT-TTAATAATAATATATTAAAATATTTTAATAATAATATTTAATAATA
1 A-TATTAATAATAATAT-TTAAAATATTTTAATAATAATATTTAATAATA
1305233 TATGAAAGTA
Statistics
Matches: 101, Mismatches: 11, Indels: 17
0.78 0.09 0.13
Matches are distributed among these distances:
68 8 0.08
69 8 0.08
70 7 0.07
71 16 0.16
72 9 0.09
73 25 0.25
74 28 0.28
ACGTcount: A:0.49, C:0.03, G:0.01, T:0.47
Consensus pattern (71 bp):
ATATTAATAATAATATTTAAAATATTTTAATAATAATATTTAATAATAATATTTAATTAAATACT
AAATAT
Found at i:1305214 original size:10 final size:11
Alignment explanation
Indices: 1304986--1305368 Score: 89
Period size: 11 Copynumber: 33.5 Consensus size: 11
1304976 GCAATATAAC
1304986 TAATGATTTTAA
1 TAAT-ATTTTAA
*
1304998 TAATATTTAAA
1 TAATATTTTAA
1305009 TATATATATTTAA
1 TA-ATAT-TTTAA
* ** *
1305022 -AAAATAATAC
1 TAATATTTTAA
*
1305032 TTATATTTT-A
1 TAATATTTTAA
1305042 -AATATTTATAA
1 TAATATTT-TAA
1305053 -AATATTTT-A
1 TAATATTTTAA
1305062 T-ATATTATTAA
1 TAATATT-TTAA
1305073 -AATATTTTTAA
1 TAATA-TTTTAA
1305084 -AATAATATTTAA
1 TAAT-AT-TTTAA
* *
1305096 TTAA-ATACTAAA
1 -TAATAT-TTTAA
*
1305108 TATATATTAGTAA
1 TA-ATATT-TTAA
*
1305121 TAAT-CTTTAA
1 TAATATTTTAA
1305131 -AACTATATTTAA
1 TAA-TAT-TTTAA
1305143 TAATTTATCTTTAA
1 TAA--TAT-TTTAA
1305157 TAATAATATTTAA
1 TAAT-AT-TTTAA
* * *
1305170 TTATATATGAA
1 TAATATTTTAA
1305181 -AATACTTTAATAA
1 TAATA-TTT--TAA
*
1305194 TAATATATTAA
1 TAATATTTTAA
1305205 -AATATTTTAA
1 TAATATTTTAA
1305215 TAATAATATTTAA
1 TAAT-AT-TTTAA
* *
1305228 TAATATATGAA
1 TAATATTTTAA
*
1305239 -AGTATTTTAA
1 TAATATTTTAA
* *
1305249 TAAAAATATTAAA
1 T-AATAT-TTTAA
*
1305262 TAAT-TATTAA
1 TAATATTTTAA
* *
1305272 AAATACTTTAA
1 TAATATTTTAA
* * *
1305283 TAATAATATAC
1 TAATATTTTAA
*
1305294 TAAATTTTTTTAA
1 T-AA-TATTTTAA
* *
1305307 TAAAAATATTTAG
1 T-AATAT-TTTAA
1305320 TAATATATTTAA
1 TAATAT-TTTAA
*
1305332 TTATA-TTTAA
1 TAATATTTTAA
**
1305342 TAATATACTAA
1 TAATATTTTAA
1305353 -AATATTTTAA
1 TAATATTTTAA
1305363 TAATAT
1 TAATAT
1305369 ATTTGAAAAT
Statistics
Matches: 268, Mismatches: 64, Indels: 79
0.65 0.16 0.19
Matches are distributed among these distances:
9 14 0.05
10 52 0.19
11 73 0.27
12 59 0.22
13 53 0.20
14 17 0.06
ACGTcount: A:0.50, C:0.02, G:0.02, T:0.46
Consensus pattern (11 bp):
TAATATTTTAA
Found at i:1305229 original size:34 final size:34
Alignment explanation
Indices: 1305191--1305291 Score: 141
Period size: 34 Copynumber: 3.0 Consensus size: 34
1305181 AATACTTTAA
1305191 TAATAATATATTAAAATATTTTAATAATAATATT
1 TAATAATATATTAAAATATTTTAATAATAATATT
* * *
1305225 TAATAATATATGAAAGTATTTTAATAAAAATATT
1 TAATAATATATTAAAATATTTTAATAATAATATT
* *
1305259 AAATAAT-TATTAAAAATACTTTAATAATAATAT
1 TAATAATATATT-AAAATATTTTAATAATAATAT
1305292 ACTAAATTTT
Statistics
Matches: 58, Mismatches: 8, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
33 3 0.05
34 55 0.95
ACGTcount: A:0.54, C:0.01, G:0.02, T:0.43
Consensus pattern (34 bp):
TAATAATATATTAAAATATTTTAATAATAATATT
Found at i:1305279 original size:92 final size:92
Alignment explanation
Indices: 1305152--1305327 Score: 255
Period size: 92 Copynumber: 1.9 Consensus size: 92
1305142 ATAATTTATC
* * * * *
1305152 TTTAATAATAATATTTAATTATATATGAAAATACTTTAATAATAATATATTAAAATATTTTAATA
1 TTTAATAAAAATATTAAATAATATATAAAAATACTTTAATAATAATATACTAAAATATTTTAATA
*
1305217 ATAATATTTAATAATATATGAAAGTAT
66 AAAATATTTAATAATATATGAAAGTAT
* *
1305244 TTTAATAAAAATATTAAATAAT-TATTAAAAATACTTTAATAATAATATACTAAATTTTTTTAAT
1 TTTAATAAAAATATTAAATAATATA-TAAAAATACTTTAATAATAATATACTAAAATATTTTAAT
*
1305308 AAAAATATTTAGTAATATAT
65 AAAAATATTTAATAATATAT
1305328 TTAATTATAT
Statistics
Matches: 74, Mismatches: 9, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
91 2 0.03
92 72 0.97
ACGTcount: A:0.52, C:0.02, G:0.02, T:0.44
Consensus pattern (92 bp):
TTTAATAAAAATATTAAATAATATATAAAAATACTTTAATAATAATATACTAAAATATTTTAATA
AAAATATTTAATAATATATGAAAGTAT
Found at i:1305339 original size:22 final size:22
Alignment explanation
Indices: 1305307--1305380 Score: 80
Period size: 22 Copynumber: 3.4 Consensus size: 22
1305297 ATTTTTTTAA
* *
1305307 TAAAAATATTTAGTAATATATT
1 TAAATATATTTAATAATATATT
* *
1305329 TAATTATATTTAATAATATACT
1 TAAATATATTTAATAATATATT
*
1305351 AAAATAT-TTTAATAATATATT
1 TAAATATATTTAATAATATATT
1305372 TGAAA-ATAT
1 T-AAATATAT
1305381 GAATATTTAA
Statistics
Matches: 42, Mismatches: 8, Indels: 4
0.78 0.15 0.07
Matches are distributed among these distances:
21 15 0.36
22 27 0.64
ACGTcount: A:0.50, C:0.01, G:0.03, T:0.46
Consensus pattern (22 bp):
TAAATATATTTAATAATATATT
Found at i:1305387 original size:59 final size:57
Alignment explanation
Indices: 1305158--1305400 Score: 200
Period size: 58 Copynumber: 4.2 Consensus size: 57
1305148 TATCTTTAAT
* * *
1305158 AATAATATTTAATTATATA-TGAAAATACTTTAATAATAATATATT-AAAATAT-TTTAA
1 AATAATATTTAATAATATACT-AAAATATTTTAATAAAAATAT-TTAAAAATATATTT-A
*
1305215 TAATAATATTTAATAATATA-TGAAAGTATTTTAATAAAAATA-TTAAATAAT-TA-TTA
1 -AATAATATTTAATAATATACT-AAAATATTTTAATAAAAATATTTAAA-AATATATTTA
* * **
1305271 AA-AATACTTTAATAATAATATACTAAATTTTTTTAATAAAAATATTTAGTAATATATTT-
1 AATAATA--TT--TAATAATATACTAAAATATTTTAATAAAAATATTTAAAAATATATTTA
* *
1305330 AATTATATTTAATAATATACTAAAATATTTTAAT-AATATATTTGAAAATATGAATATTTA
1 AATAATATTTAATAATATACTAAAATATTTTAATAAAAATATTT-AAAA-AT--ATATTTA
1305390 AATAATATTTA
1 AATAATATTTA
1305401 GTAGTTTAAT
Statistics
Matches: 153, Mismatches: 15, Indels: 32
0.76 0.08 0.16
Matches are distributed among these distances:
54 4 0.03
55 10 0.07
56 30 0.20
57 7 0.05
58 73 0.48
59 14 0.09
60 15 0.10
ACGTcount: A:0.51, C:0.02, G:0.02, T:0.44
Consensus pattern (57 bp):
AATAATATTTAATAATATACTAAAATATTTTAATAAAAATATTTAAAAATATATTTA
Found at i:1306710 original size:17 final size:17
Alignment explanation
Indices: 1306655--1306725 Score: 65
Period size: 17 Copynumber: 4.2 Consensus size: 17
1306645 TCACAATACA
*
1306655 TGAACAGTGATGAACAG
1 TGAATAGTGATGAACAG
* *
1306672 T-AATGAATGGTGATAC-G
1 TGAAT-AGTGATGA-ACAG
* *
1306689 TGAATAGTTATGAATAG
1 TGAATAGTGATGAACAG
1306706 TGAATAGTGATGAACAG
1 TGAATAGTGATGAACAG
1306723 TGA
1 TGA
1306726 TACATCGATA
Statistics
Matches: 41, Mismatches: 9, Indels: 8
0.71 0.16 0.14
Matches are distributed among these distances:
16 3 0.07
17 33 0.80
18 5 0.12
ACGTcount: A:0.39, C:0.06, G:0.28, T:0.27
Consensus pattern (17 bp):
TGAATAGTGATGAACAG
Found at i:1306822 original size:13 final size:13
Alignment explanation
Indices: 1306804--1306828 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1306794 CTACCAGTTT
1306804 ATGTATCGATACA
1 ATGTATCGATACA
1306817 ATGTATCGATAC
1 ATGTATCGATAC
1306829 TAAGCAAAAT
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):
ATGTATCGATACA
Found at i:1306863 original size:21 final size:21
Alignment explanation
Indices: 1306837--1306877 Score: 73
Period size: 21 Copynumber: 2.0 Consensus size: 21
1306827 ACTAAGCAAA
1306837 ATGTATCAATACAATTAAGGT
1 ATGTATCAATACAATTAAGGT
*
1306858 ATGTATCGATACAATTAAGG
1 ATGTATCAATACAATTAAGG
1306878 GTTTCGACCC
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.41, C:0.10, G:0.17, T:0.32
Consensus pattern (21 bp):
ATGTATCAATACAATTAAGGT
Found at i:1310293 original size:20 final size:20
Alignment explanation
Indices: 1310268--1310310 Score: 68
Period size: 20 Copynumber: 2.1 Consensus size: 20
1310258 TTTTCTCCTC
* *
1310268 TAATTCATTTATTTTCTTTT
1 TAATTCACTTAATTTCTTTT
1310288 TAATTCACTTAATTTCTTTT
1 TAATTCACTTAATTTCTTTT
1310308 TAA
1 TAA
1310311 GAATATTATT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.26, C:0.12, G:0.00, T:0.63
Consensus pattern (20 bp):
TAATTCACTTAATTTCTTTT
Found at i:1310762 original size:21 final size:21
Alignment explanation
Indices: 1310721--1310762 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
1310711 AGCCATTTCT
*
1310721 TCATTTTCATCAACCTCTTGA
1 TCATTTTCATCAACATCTTGA
* *
1310742 TCATTTTCATCATCATTTTGA
1 TCATTTTCATCAACATCTTGA
1310763 ACGGTTGATT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.24, C:0.24, G:0.05, T:0.48
Consensus pattern (21 bp):
TCATTTTCATCAACATCTTGA
Found at i:1312378 original size:13 final size:13
Alignment explanation
Indices: 1312360--1312384 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1312350 CTATTCATAA
1312360 TGTATCGATACAC
1 TGTATCGATACAC
1312373 TGTATCGATACA
1 TGTATCGATACA
1312385 ATACATGAAC
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:0.20, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAC
Found at i:1312876 original size:26 final size:27
Alignment explanation
Indices: 1312848--1312919 Score: 76
Period size: 27 Copynumber: 2.7 Consensus size: 27
1312838 TATAATTGTA
*
1312848 TTTAAAATATTATATATTTATATTAAT
1 TTTAAAATATTATATATTTATATAAAT
* * *
1312875 TTTGACATATTA-ATATTTTTTATAAAT
1 TTTAAAATATTATATA-TTTATATAAAT
1312902 TTTAAATATATT-TATATT
1 TTTAAA-ATATTATATATT
1312920 GTATTTGTAT
Statistics
Matches: 36, Mismatches: 6, Indels: 6
0.75 0.12 0.12
Matches are distributed among these distances:
26 3 0.08
27 25 0.69
28 8 0.22
ACGTcount: A:0.40, C:0.01, G:0.01, T:0.57
Consensus pattern (27 bp):
TTTAAAATATTATATATTTATATAAAT
Found at i:1313334 original size:20 final size:20
Alignment explanation
Indices: 1313306--1313362 Score: 78
Period size: 20 Copynumber: 2.9 Consensus size: 20
1313296 TTTTCACAAT
*
1313306 TTGTATCGATACATTGTCCA
1 TTGTATCGATACATTATCCA
* *
1313326 TTGTGTCGATACATTATTCA
1 TTGTATCGATACATTATCCA
*
1313346 TTGTATCAATACATTAT
1 TTGTATCGATACATTAT
1313363 GGGTTTTACC
Statistics
Matches: 32, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 32 1.00
ACGTcount: A:0.28, C:0.16, G:0.12, T:0.44
Consensus pattern (20 bp):
TTGTATCGATACATTATCCA
Found at i:1314671 original size:20 final size:21
Alignment explanation
Indices: 1314646--1314708 Score: 85
Period size: 20 Copynumber: 3.1 Consensus size: 21
1314636 TGCCAAGGAA
1314646 ATGTATCGATACATT-TATCG
1 ATGTATCGATACATTGTATCG
1314666 ATGTATCGATACATTGTATCG
1 ATGTATCGATACATTGTATCG
** *
1314687 ATACATCGAT-CTTTGTATCG
1 ATGTATCGATACATTGTATCG
1314707 AT
1 AT
1314709 ACATCTAGGA
Statistics
Matches: 39, Mismatches: 3, Indels: 2
0.89 0.07 0.05
Matches are distributed among these distances:
20 26 0.67
21 13 0.33
ACGTcount: A:0.29, C:0.16, G:0.16, T:0.40
Consensus pattern (21 bp):
ATGTATCGATACATTGTATCG
Found at i:1314685 original size:13 final size:13
Alignment explanation
Indices: 1314667--1314692 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1314657 CATTTATCGA
1314667 TGTATCGATACAT
1 TGTATCGATACAT
1314680 TGTATCGATACAT
1 TGTATCGATACAT
1314693 CGATCTTTGT
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:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:1314689 original size:33 final size:33
Alignment explanation
Indices: 1314647--1314712 Score: 96
Period size: 33 Copynumber: 2.0 Consensus size: 33
1314637 GCCAAGGAAA
**
1314647 TGTATCGATACATTTATCGATGTATCGATACAT
1 TGTATCGATACATCGATCGATGTATCGATACAT
**
1314680 TGTATCGATACATCGATCTTTGTATCGATACAT
1 TGTATCGATACATCGATCGATGTATCGATACAT
1314713 CTAGGAAGTT
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 29 1.00
ACGTcount: A:0.29, C:0.17, G:0.15, T:0.39
Consensus pattern (33 bp):
TGTATCGATACATCGATCGATGTATCGATACAT
Found at i:1317126 original size:51 final size:51
Alignment explanation
Indices: 1317061--1317174 Score: 169
Period size: 51 Copynumber: 2.2 Consensus size: 51
1317051 ATTTTTCATC
*
1317061 TCGGGGATACTCCAA-TCCCGATTTCATTTCCAAAACA-TCAATTTTTCTCAA
1 TCGGGGATACTCCAACT-CCGATTTCATTTCCAAAACACT-AATTTTTCACAA
* *
1317112 TCGGGGATACTCCAACTTCGATTTTATTTCCAAAACACTAATTTTTCACAA
1 TCGGGGATACTCCAACTCCGATTTCATTTCCAAAACACTAATTTTTCACAA
1317163 TCGGGGATACTC
1 TCGGGGATACTC
1317175 TAACCTCGTT
Statistics
Matches: 58, Mismatches: 3, Indels: 4
0.89 0.05 0.06
Matches are distributed among these distances:
51 56 0.97
52 2 0.03
ACGTcount: A:0.29, C:0.25, G:0.12, T:0.33
Consensus pattern (51 bp):
TCGGGGATACTCCAACTCCGATTTCATTTCCAAAACACTAATTTTTCACAA
Found at i:1317194 original size:28 final size:28
Alignment explanation
Indices: 1317162--1317234 Score: 87
Period size: 28 Copynumber: 2.6 Consensus size: 28
1317152 ATTTTTCACA
* *
1317162 ATCGGGGATACTCTAACCTCGTTATTTC
1 ATCGGGGATACTCCAACCCCGTTATTTC
*
1317190 ATCGGGGATACTCCCACCCCGTTATTT-
1 ATCGGGGATACTCCAACCCCGTTATTTC
1317217 -TCGAGGGGATACTCCAAC
1 ATC--GGGGATACTCCAAC
1317235 TCCGGCTTTA
Statistics
Matches: 39, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
26 2 0.05
28 37 0.95
ACGTcount: A:0.22, C:0.29, G:0.21, T:0.29
Consensus pattern (28 bp):
ATCGGGGATACTCCAACCCCGTTATTTC
Found at i:1317273 original size:79 final size:79
Alignment explanation
Indices: 1317190--1317364 Score: 228
Period size: 79 Copynumber: 2.2 Consensus size: 79
1317180 TCGTTATTTC
* * *
1317190 ATCGGGGATACTCCCACCCCGTTATTTTCGAGGGGATACTCCAACTCC-GGCTTTATTTCTAAAA
1 ATCGGGGATACTCCAACCCCATTATTTTCGAGGGGATACTCCAAC-CCTAGCTTTATTTCTAAAA
* ** *
1317254 TATTAATT-TCTCATA
65 CACCAATTCTC-CACA
* * *
1317269 ATCGGGGATACTCCAATCCCATTATTTTCGAGGGGATACTCCAACCCTAGTTTTATTTCTGAAAC
1 ATCGGGGATACTCCAACCCCATTATTTTCGAGGGGATACTCCAACCCTAGCTTTATTTCTAAAAC
1317334 ACCAATTCTCCACA
66 ACCAATTCTCCACA
1317348 ATCGGGGATACTCCAAC
1 ATCGGGGATACTCCAAC
1317365 TCCGATTTTA
Statistics
Matches: 83, Mismatches: 11, Indels: 4
0.85 0.11 0.04
Matches are distributed among these distances:
78 2 0.02
79 79 0.95
80 2 0.02
ACGTcount: A:0.27, C:0.27, G:0.15, T:0.31
Consensus pattern (79 bp):
ATCGGGGATACTCCAACCCCATTATTTTCGAGGGGATACTCCAACCCTAGCTTTATTTCTAAAAC
ACCAATTCTCCACA
Found at i:1317304 original size:107 final size:106
Alignment explanation
Indices: 1317114--1317315 Score: 255
Period size: 107 Copynumber: 1.9 Consensus size: 106
1317104 TTTCTCAATC
* * * *
1317114 GGGGATACTCCAACTTCGATTTTATTTCCAAAACACTAATTTTTCACAATCGGGGATACTCTAAC
1 GGGGATACTCCAACTCCGACTTTATTTCCAAAACACTAATTTCTCACAATCGGGGATACTCCAAC
* *
1317179 CTCGTTATTTCATCGGGGATACTCCCACCCCGTTATTTTCGA
66 CTCATTATTTCA-CGGGGATACTCCAACCCCGTTATTTTCGA
* * * * *
1317221 GGGGATACTCCAACTCCGGCTTTATTTCTAAAATATTAATTTCTCATAATCGGGGATACTCCAAT
1 GGGGATACTCCAACTCCGACTTTATTTCCAAAACACTAATTTCTCACAATCGGGGATACTCCAA-
1317286 CC-CATTATTTTCGA-GGGGATACTCCAACCC
65 CCTCATTA-TTTC-ACGGGGATACTCCAACCC
1317316 TAGTTTTATT
Statistics
Matches: 81, Mismatches: 11, Indels: 6
0.83 0.11 0.06
Matches are distributed among these distances:
107 74 0.91
108 6 0.07
109 1 0.01
ACGTcount: A:0.26, C:0.26, G:0.15, T:0.33
Consensus pattern (106 bp):
GGGGATACTCCAACTCCGACTTTATTTCCAAAACACTAATTTCTCACAATCGGGGATACTCCAAC
CTCATTATTTCACGGGGATACTCCAACCCCGTTATTTTCGA
Found at i:1317360 original size:51 final size:51
Alignment explanation
Indices: 1317300--1317411 Score: 145
Period size: 51 Copynumber: 2.2 Consensus size: 51
1317290 TTATTTTCGA
* **
1317300 GGGGATACTCCAAC-CCTAGTTTTATTTCTGAAACACCAATTCTCCACAATC
1 GGGGATACTCCAACTCCGA-TTTTATTTCCAAAACACCAATTCTCCACAATC
* * * *
1317351 GGGGATACTCCAACTCCGATTTTATTTCCAAAACACTAATTTTTCACAATT
1 GGGGATACTCCAACTCCGATTTTATTTCCAAAACACCAATTCTCCACAATC
1317402 GGGGATACTC
1 GGGGATACTC
1317412 TAGCCCTGTT
Statistics
Matches: 53, Mismatches: 7, Indels: 2
0.85 0.11 0.03
Matches are distributed among these distances:
51 50 0.94
52 3 0.06
ACGTcount: A:0.29, C:0.26, G:0.13, T:0.31
Consensus pattern (51 bp):
GGGGATACTCCAACTCCGATTTTATTTCCAAAACACCAATTCTCCACAATC
Found at i:1317483 original size:237 final size:237
Alignment explanation
Indices: 1317063--1317530 Score: 699
Period size: 237 Copynumber: 2.0 Consensus size: 237
1317053 TTTTCATCTC
* * * *
1317063 GGGGATACTCCAATCCCGATTTCATTTCCAAAACATCAATTTTTCTCAATCGGGGATACTCCAAC
1 GGGGATACTCCAATCCCGATTTCATTTCCAAAACACCAATTCTCCACAATCGGGGATACTCCAAC
*
1317128 TTCGATTTTATTTCCAAAACACTAATTTTTCACAATCGGGGATACTCTAACCTCGTTATTTCATC
66 TCCGATTTTATTTCCAAAACACTAATTTTTCACAATCGGGGATACTCTAACCTCGTTATTTCATC
* * ** *
1317193 GGGGATACTCCCACCCCGTTATTTTCGAGGGGATACTCCAACTCCGGCTTTATTTCTAAAATATT
131 GGGGATACTCCAACCCCGTTATTTTCGAGGGGATACTCCAACCCCAACTTTATTTCTAAAATACT
* *
1317258 AATTTCTCATAATCGGGGATACTCCAATCCCATTATTTTCGA
196 AATTTCTCACAATCGGGGATACTCCAACCCCATTATTTTCGA
* * **
1317300 GGGGATACTCCAA-CCCTAGTTTTATTTCTGAAACACCAATTCTCCACAATCGGGGATACTCCAA
1 GGGGATACTCCAATCCCGA-TTTCATTTCCAAAACACCAATTCTCCACAATCGGGGATACTCCAA
* *
1317364 CTCCGATTTTATTTCCAAAACACTAATTTTTCACAATTGGGGATACTCTAGCC-CTGTTATTTCA
65 CTCCGATTTTATTTCCAAAACACTAATTTTTCACAATCGGGGATACTCTAACCTC-GTTATTTCA
1317428 TCGGGGATACTCCAACCCCGTTA-TTTCTGAGGGGATACTCCAACCCCAACTTTATTTCTAAAAT
129 TCGGGGATACTCCAACCCCGTTATTTTC-GAGGGGATACTCCAACCCCAACTTTATTTCTAAAAT
* * *
1317492 ACTGATTTTTCACAATCGGGGATACTCCAACCCCGTTAT
193 ACTAATTTCTCACAATCGGGGATACTCCAACCCCATTAT
1317531 GATCTCCAAA
Statistics
Matches: 207, Mismatches: 21, Indels: 6
0.88 0.09 0.03
Matches are distributed among these distances:
236 9 0.04
237 198 0.96
ACGTcount: A:0.27, C:0.26, G:0.14, T:0.33
Consensus pattern (237 bp):
GGGGATACTCCAATCCCGATTTCATTTCCAAAACACCAATTCTCCACAATCGGGGATACTCCAAC
TCCGATTTTATTTCCAAAACACTAATTTTTCACAATCGGGGATACTCTAACCTCGTTATTTCATC
GGGGATACTCCAACCCCGTTATTTTCGAGGGGATACTCCAACCCCAACTTTATTTCTAAAATACT
AATTTCTCACAATCGGGGATACTCCAACCCCATTATTTTCGA
Found at i:1317486 original size:31 final size:28
Alignment explanation
Indices: 1317402--1317474 Score: 94
Period size: 28 Copynumber: 2.6 Consensus size: 28
1317392 TTTCACAATT
* * * *
1317402 GGGGATACTCTAGCCCTGTTATTTCAT-C
1 GGGGATACTCCAACCCCGTTATTTC-TGA
1317430 GGGGATACTCCAACCCCGTTATTTCTGA
1 GGGGATACTCCAACCCCGTTATTTCTGA
1317458 GGGGATACTCCAACCCC
1 GGGGATACTCCAACCCC
1317475 AACTTTATTT
Statistics
Matches: 40, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
27 1 0.03
28 39 0.98
ACGTcount: A:0.21, C:0.30, G:0.22, T:0.27
Consensus pattern (28 bp):
GGGGATACTCCAACCCCGTTATTTCTGA
Found at i:1318708 original size:5 final size:5
Alignment explanation
Indices: 1318698--1318733 Score: 72
Period size: 5 Copynumber: 7.2 Consensus size: 5
1318688 GCATTTGTTC
1318698 TTTCT TTTCT TTTCT TTTCT TTTCT TTTCT TTTCT T
1 TTTCT TTTCT TTTCT TTTCT TTTCT TTTCT TTTCT T
1318734 CCCATAAACA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 31 1.00
ACGTcount: A:0.00, C:0.19, G:0.00, T:0.81
Consensus pattern (5 bp):
TTTCT
Found at i:1320142 original size:79 final size:78
Alignment explanation
Indices: 1319961--1320352 Score: 484
Period size: 79 Copynumber: 5.0 Consensus size: 78
1319951 ATTCATGTTT
* * * * *
1319961 TTATTTCCGAGAGGATATTCCAACCCC-AGTTTTATTTCCAAAACACCAATTTTTCACAATCTGG
1 TTATTTTCGAGGGGATACTCCAACCCCGA-TTTTATTTTCAAAACACCAATTTTTCACAATCGGG
* **
1320025 ATACTCCAACCCTG
65 ATACTCTAACCCCA
* * *
1320039 TTA-TTTCTGGGGGGATACTCCAACCCTGATTTTATTTCCAAAACACCAATTTTTCACAATCGGA
1 TTATTTTC-GAGGGGATACTCCAACCCCGATTTTATTTTCAAAACACCAATTTTTCACAATCGG-
* **
1320103 GATACTCTAATCCTG
64 GATACTCTAACCCCA
* ** *
1320118 TTATTTTCGAGGGGATACTCCAACCCCGGTTTTATTTTTGAAACACCAATTTTTCACAATTGGGG
1 TTATTTTCGAGGGGATACTCCAACCCCGATTTTATTTTCAAAACACCAATTTTTCACAA-TCGGG
1320183 ATACTCTAACCCCA
65 ATACTCTAACCCCA
* * *
1320197 TTATTTTCGAGGGGATATTCCAACCCTGGTTTTATTTTCAAAACACCAATTTTTCACAATCAGGG
1 TTATTTTCGAGGGGATACTCCAACCCCGATTTTATTTTCAAAACACCAATTTTTCACAATC-GGG
*
1320262 ATACTCCAACCCCA
65 ATACTCTAACCCCA
* *
1320276 TTATCTTT-GAGGGGATACTCCAACCCCGATTTTATTTTCAAAACACTAATTTTCCACAATCGGG
1 TTAT-TTTCGAGGGGATACTCCAACCCCGATTTTATTTTCAAAACACCAATTTTTCACAATC-GG
1320340 GATACTCTAACCC
64 GATACTCTAACCC
1320353 TAGTTTTATT
Statistics
Matches: 276, Mismatches: 31, Indels: 13
0.86 0.10 0.04
Matches are distributed among these distances:
77 3 0.01
78 52 0.19
79 211 0.76
80 10 0.04
ACGTcount: A:0.28, C:0.26, G:0.13, T:0.33
Consensus pattern (78 bp):
TTATTTTCGAGGGGATACTCCAACCCCGATTTTATTTTCAAAACACCAATTTTTCACAATCGGGA
TACTCTAACCCCA
Found at i:1320359 original size:130 final size:130
Alignment explanation
Indices: 1320207--1320482 Score: 401
Period size: 130 Copynumber: 2.1 Consensus size: 130
1320197 TTATTTTCGA
* *
1320207 GGGGATATTCCAACCCTGGTTTTATTTTCAAAACACCAATTTTTCACAATCAGG-GATACTCCAA
1 GGGGATACTCCAACCCTAGTTTTATTTTCAAAACACCAATTTTTCACAATC-GGAGATACTCCAA
* * *
1320271 CCCCATTATCTTTGAGGGGATACTCCAACCCCGATTTTATTTTCAAAACACTAATTTTCCACAAT
65 CCCCATTATCTTTGAGGAGATACTCCAACCCCAATATTATTTTCAAAACACTAATTTTCCACAAT
1320336 C
130 C
* * *
1320337 GGGGATACTCTAACCCTAGTTTTATTTTCAAAACACCAATTTTTCACACTCGGAGATACTCTAAC
1 GGGGATACTCCAACCCTAGTTTTATTTTCAAAACACCAATTTTTCACAATCGGAGATACTCCAAC
* * * * * * *
1320402 CCCGTTATTTTTGAGGAGATACTCCAACCCCAATATTATTTTTAAAACATTAATTTTTCACTATT
66 CCCATTATCTTTGAGGAGATACTCCAACCCCAATATTATTTTCAAAACACTAATTTTCCACAATC
1320467 GGGGATACTCCAACCC
1 GGGGATACTCCAACCC
1320483 CGTTATTTTT
Statistics
Matches: 129, Mismatches: 16, Indels: 2
0.88 0.11 0.01
Matches are distributed among these distances:
129 2 0.02
130 127 0.98
ACGTcount: A:0.30, C:0.25, G:0.12, T:0.33
Consensus pattern (130 bp):
GGGGATACTCCAACCCTAGTTTTATTTTCAAAACACCAATTTTTCACAATCGGAGATACTCCAAC
CCCATTATCTTTGAGGAGATACTCCAACCCCAATATTATTTTCAAAACACTAATTTTCCACAATC
Found at i:1320362 original size:51 final size:51
Alignment explanation
Indices: 1320286--1320403 Score: 166
Period size: 51 Copynumber: 2.3 Consensus size: 51
1320276 TTATCTTTGA
* * *
1320286 GGGGATACTCCAACCCCGATTTTATTTTCAAAACACTAATTTTCCACAATC
1 GGGGATACTCTAACCCAGATTTTATTTTCAAAACACCAATTTTCCACAATC
* *
1320337 GGGGATACTCTAACCCTAG-TTTTATTTTCAAAACACCAATTTTTCACACTC
1 GGGGATACTCTAACCC-AGATTTTATTTTCAAAACACCAATTTTCCACAATC
*
1320388 GGAGATACTCTAACCC
1 GGGGATACTCTAACCC
1320404 CGTTATTTTT
Statistics
Matches: 60, Mismatches: 6, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
51 59 0.98
52 1 0.02
ACGTcount: A:0.31, C:0.27, G:0.11, T:0.31
Consensus pattern (51 bp):
GGGGATACTCTAACCCAGATTTTATTTTCAAAACACCAATTTTCCACAATC
Found at i:1320412 original size:209 final size:209
Alignment explanation
Indices: 1320128--1320519 Score: 523
Period size: 209 Copynumber: 1.9 Consensus size: 209
1320118 TTATTTTCGA
* ** * *
1320128 GGGGATACTCCAACCCCGGTTTTATTTTTGAAACACCAATTTTTCACAATTGGGGATACTCTAAC
1 GGGGATACTCCAACCCCAGTTTTATTTTCAAAACACCAATTTTTCACAATCGGAGATACTCTAAC
* * *** *
1320193 CCCATTATTTTCGAGGGGATATTCCAACCCTGGTTTTATTTTCAAAACACCAATTTTTCACAATC
66 CCCATTATTTTCGAGGAGATACTCCAACCCCAATATTATTTTCAAAACACCAATTTTTCACAATC
*
1320258 AGGGATACTCCAACCCCATTATCTTTGAGGGGATACTCCAACCCCGATTTTATTTTCAAAACACT
131 AGGGATACTCCAACCCCATTATCTTTAAGGGGATACTCCAACCCCGATTTTATTTTCAAAACACT
1320323 AATTTTCCACAATC
196 AATTTTCCACAATC
* * *
1320337 GGGGATACTCTAACCCTAGTTTTATTTTCAAAACACCAATTTTTCACACTCGGAGATACTCTAAC
1 GGGGATACTCCAACCCCAGTTTTATTTTCAAAACACCAATTTTTCACAATCGGAGATACTCTAAC
* * * ** * *
1320402 CCCGTTATTTTTGAGGAGATACTCCAACCCCAATATTATTTTTAAAACATTAATTTTTCACTATT
66 CCCATTATTTTCGAGGAGATACTCCAACCCCAATATTATTTTCAAAACACCAATTTTTCACAATC
* * * * * * *
1320467 GGGGATACTCCAACCCCGTTATTTTTAAGGGGGTACTCCGACCTCGTTTTTAT
131 AGGGATACTCCAACCCCATTATCTTTAAGGGGATACTCCAACCCCGATTTTAT
1320520 CTCCAAAATA
Statistics
Matches: 154, Mismatches: 29, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
209 154 1.00
ACGTcount: A:0.28, C:0.24, G:0.13, T:0.34
Consensus pattern (209 bp):
GGGGATACTCCAACCCCAGTTTTATTTTCAAAACACCAATTTTTCACAATCGGAGATACTCTAAC
CCCATTATTTTCGAGGAGATACTCCAACCCCAATATTATTTTCAAAACACCAATTTTTCACAATC
AGGGATACTCCAACCCCATTATCTTTAAGGGGATACTCCAACCCCGATTTTATTTTCAAAACACT
AATTTTCCACAATC
Found at i:1320474 original size:79 final size:79
Alignment explanation
Indices: 1320340--1320492 Score: 200
Period size: 79 Copynumber: 1.9 Consensus size: 79
1320330 CACAATCGGG
* * * * *
1320340 GATACTCTAACCCTAGTTTTATTTTCAAAACACCAATTTTTCACACTCGGAGATACTCTAACCCC
1 GATACTCCAACCCCAATATTATTTTCAAAACACCAATTTTTCACACTCGGAGATACTCCAACCCC
1320405 GTTATTTTTGAGGA
66 GTTATTTTTGAGGA
* ** * *
1320419 GATACTCCAACCCCAATATTATTTTTAAAACATTAATTTTTCACTA-TTGGGGATACTCCAACCC
1 GATACTCCAACCCCAATATTATTTTCAAAACACCAATTTTTCAC-ACTCGGAGATACTCCAACCC
1320483 CGTTATTTTT
65 CGTTATTTTT
1320493 AAGGGGGTAC
Statistics
Matches: 63, Mismatches: 10, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
79 62 0.98
80 1 0.02
ACGTcount: A:0.29, C:0.24, G:0.10, T:0.37
Consensus pattern (79 bp):
GATACTCCAACCCCAATATTATTTTCAAAACACCAATTTTTCACACTCGGAGATACTCCAACCCC
GTTATTTTTGAGGA
Found at i:1320533 original size:79 final size:80
Alignment explanation
Indices: 1320374--1320541 Score: 178
Period size: 79 Copynumber: 2.1 Consensus size: 80
1320364 TCAAAACACC
* *
1320374 AATTTTTCACACTCGGAGATACTCTAACCCCGTTATTTTTGAGGAGATACTCCAACCCCAATATT
1 AATTTTTCACACTCGGAGATACTCCAACCCCGTTATTTTTAAGGAGATACTCCAACCCCAATATT
* **
1320439 ATTTTTAAAACATT-
66 ATCTCCAAAACATTA
* * * * * * ** *
1320453 AATTTTTCACTA-TTGGGGATACTCCAACCCCGTTATTTTTAAGGGGGTACTCCGACCTCGTTTT
1 AATTTTTCAC-ACTCGGAGATACTCCAACCCCGTTATTTTTAAGGAGATACTCCAACCCCAATAT
*
1320517 TATCTCCAAAATATTA
65 TATCTCCAAAACATTA
1320533 AATTTTTCA
1 AATTTTTCA
1320542 TCGGAAGATG
Statistics
Matches: 72, Mismatches: 15, Indels: 3
0.80 0.17 0.03
Matches are distributed among these distances:
79 62 0.86
80 10 0.14
ACGTcount: A:0.29, C:0.22, G:0.12, T:0.38
Consensus pattern (80 bp):
AATTTTTCACACTCGGAGATACTCCAACCCCGTTATTTTTAAGGAGATACTCCAACCCCAATATT
ATCTCCAAAACATTA
Found at i:1331687 original size:39 final size:38
Alignment explanation
Indices: 1331644--1331827 Score: 133
Period size: 36 Copynumber: 4.9 Consensus size: 38
1331634 ATTTCACAGT
* *
1331644 ACTACTATTAACAACTAATTCTAGATAATCTGCATGATA
1 ACTACTATCAACAACTAATTCTAGATAATCTGCA-CATA
* * ** * * *
1331683 ACTACAATCAACAAATGTTTCTACAT-AT-TTCACATT
1 ACTACTATCAACAACTAATTCTAGATAATCTGCACATA
* * *
1331719 GCTACTATCAACAACTAATCCGAGATAATCTGCACGATA
1 ACTACTATCAACAACTAATTCTAGATAATCTGCAC-ATA
* * ** * * *
1331758 ACTACAATCAACAAATGTTTCTACAT-AT-TTCACATT
1 ACTACTATCAACAACTAATTCTAGATAATCTGCACATA
* *
1331794 ACTACTATCAACAACTAATCCGAGATAATCTGCA
1 ACTACTATCAACAACTAATTCTAGATAATCTGCA
1331828 TATTTCACAT
Statistics
Matches: 103, Mismatches: 37, Indels: 11
0.68 0.25 0.07
Matches are distributed among these distances:
36 41 0.40
37 11 0.11
38 11 0.11
39 40 0.39
ACGTcount: A:0.40, C:0.23, G:0.07, T:0.30
Consensus pattern (38 bp):
ACTACTATCAACAACTAATTCTAGATAATCTGCACATA
Found at i:1331714 original size:75 final size:75
Alignment explanation
Indices: 1331584--1331828 Score: 393
Period size: 75 Copynumber: 3.3 Consensus size: 75
1331574 GATGAAATGA
* * * *
1331584 TAATCCAAGATAATGTGCATGATAATTACAATCAACAAATGTTT-TAGCATATTTCACAGTACTA
1 TAATCCGAGATAATCTGCATGATAACTACAATCAACAAATGTTTCTA-CATATTTCACATTACTA
*
1331648 CTATTAACAAC
65 CTATCAACAAC
* * *
1331659 TAATTCTAGATAATCTGCATGATAACTACAATCAACAAATGTTTCTACATATTTCACATTGCTAC
1 TAATCCGAGATAATCTGCATGATAACTACAATCAACAAATGTTTCTACATATTTCACATTACTAC
1331724 TATCAACAAC
66 TATCAACAAC
*
1331734 TAATCCGAGATAATCTGCACGATAACTACAATCAACAAATGTTTCTACATATTTCACATTACTAC
1 TAATCCGAGATAATCTGCATGATAACTACAATCAACAAATGTTTCTACATATTTCACATTACTAC
1331799 TATCAACAAC
66 TATCAACAAC
1331809 TAATCCGAGATAATCTGCAT
1 TAATCCGAGATAATCTGCAT
1331829 ATTTCACATT
Statistics
Matches: 157, Mismatches: 12, Indels: 2
0.92 0.07 0.01
Matches are distributed among these distances:
75 155 0.99
76 2 0.01
ACGTcount: A:0.40, C:0.21, G:0.08, T:0.31
Consensus pattern (75 bp):
TAATCCGAGATAATCTGCATGATAACTACAATCAACAAATGTTTCTACATATTTCACATTACTAC
TATCAACAAC
Found at i:1331804 original size:36 final size:36
Alignment explanation
Indices: 1331614--1331807 Score: 138
Period size: 36 Copynumber: 5.2 Consensus size: 36
1331604 GATAATTACA
*
1331614 ATCAACAAATGTTT-TAGCATATTTCACAGTACTACT
1 ATCAACAAATGTTTCTA-CATATTTCACATTACTACT
* * ** * * * * *
1331650 ATTAACAACTAATTCTAGATAATCTGCATGATAACTACA
1 ATCAACAAATGTTTCTACAT-AT-TTCA-CATTACTACT
*
1331689 ATCAACAAATGTTTCTACATATTTCACATTGCTACT
1 ATCAACAAATGTTTCTACATATTTCACATTACTACT
* ** * * * * * *
1331725 ATCAACAACTAATCCGAGATAATCTGCACGATAACTACA
1 ATCAACAAATGTTTCTACAT-AT-TTCAC-ATTACTACT
1331764 ATCAACAAATGTTTCTACATATTTCACATTACTACT
1 ATCAACAAATGTTTCTACATATTTCACATTACTACT
1331800 ATCAACAA
1 ATCAACAA
1331808 CTAATCCGAG
Statistics
Matches: 112, Mismatches: 39, Indels: 14
0.68 0.24 0.08
Matches are distributed among these distances:
36 47 0.42
37 13 0.12
38 11 0.10
39 41 0.37
ACGTcount: A:0.40, C:0.22, G:0.07, T:0.32
Consensus pattern (36 bp):
ATCAACAAATGTTTCTACATATTTCACATTACTACT
Found at i:1332307 original size:15 final size:15
Alignment explanation
Indices: 1332285--1332325 Score: 64
Period size: 15 Copynumber: 2.7 Consensus size: 15
1332275 TGGGTAAACA
1332285 AGTGGTGGATGCACG
1 AGTGGTGGATGCACG
*
1332300 AGTTGTGGATGCACG
1 AGTGGTGGATGCACG
*
1332315 GGTGGTGGATG
1 AGTGGTGGATG
1332326 GACAGGATTA
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
15 23 1.00
ACGTcount: A:0.17, C:0.10, G:0.49, T:0.24
Consensus pattern (15 bp):
AGTGGTGGATGCACG
Found at i:1333464 original size:75 final size:75
Alignment explanation
Indices: 1333334--1333550 Score: 301
Period size: 75 Copynumber: 2.9 Consensus size: 75
1333324 ATGTAAAATA
* * *
1333334 TGCAGATTATCTCAGATTAGTTGTTGATAGTAGTAATGTGAAATATGCAGTAACATTTATTGATT
1 TGCAGATTATCTCGGATTAGTTGTTGATAGTAGTAATGTGAAATATGTAGAAACATTTATTGATT
*
1333399 GTAGTTGTCG
66 GTAGTTATCG
* * * *
1333409 TGCAGATTATCTCGGATTAATTGTTGATAGTAGCAATATGAAATATGTAGAAACATTTGTTGATT
1 TGCAGATTATCTCGGATTAGTTGTTGATAGTAGTAATGTGAAATATGTAGAAACATTTATTGATT
* *
1333474 ATAGTTATTG
66 GTAGTTATCG
* * *
1333484 TGCAGATTATCTCGGAATAGTTGTTGATAGTAGTACTGTGAAATATGCT-GAAACAATTATTGAT
1 TGCAGATTATCTCGGATTAGTTGTTGATAGTAGTAATGTGAAATATG-TAGAAACATTTATTGAT
1333548 TGT
65 TGT
1333551 GTGAGCTCAA
Statistics
Matches: 123, Mismatches: 18, Indels: 2
0.86 0.13 0.01
Matches are distributed among these distances:
75 122 0.99
76 1 0.01
ACGTcount: A:0.31, C:0.08, G:0.22, T:0.39
Consensus pattern (75 bp):
TGCAGATTATCTCGGATTAGTTGTTGATAGTAGTAATGTGAAATATGTAGAAACATTTATTGATT
GTAGTTATCG
Found at i:1333838 original size:34 final size:35
Alignment explanation
Indices: 1333800--1333866 Score: 102
Period size: 37 Copynumber: 1.9 Consensus size: 35
1333790 CCTTACAACA
1333800 CTATC-TTTC-AAGGCTAAGATAGAAACCTCTCTCT
1 CTATCTTTTCAAAGGCTAAGATAG-AACCTCTCTCT
1333834 CTATCTTTTTCAAAGGCTAAGATAGAACCTCTC
1 CTATC-TTTTCAAAGGCTAAGATAGAACCTCTC
1333867 AATCACTTAG
Statistics
Matches: 30, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
34 5 0.17
36 12 0.40
37 13 0.43
ACGTcount: A:0.30, C:0.25, G:0.12, T:0.33
Consensus pattern (35 bp):
CTATCTTTTCAAAGGCTAAGATAGAACCTCTCTCT
Found at i:1334329 original size:20 final size:20
Alignment explanation
Indices: 1334304--1334355 Score: 70
Period size: 19 Copynumber: 2.6 Consensus size: 20
1334294 TACAAGCCAA
** *
1334304 TGTATCGATACAATTTTTTG
1 TGTATCGATACAATACTTGG
1334324 TGTATCGATAC-ATACTTGG
1 TGTATCGATACAATACTTGG
1334343 TGTATCGATACAA
1 TGTATCGATACAA
1334356 GTTTGGCTAC
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
19 16 0.57
20 12 0.43
ACGTcount: A:0.29, C:0.13, G:0.17, T:0.40
Consensus pattern (20 bp):
TGTATCGATACAATACTTGG
Found at i:1334361 original size:19 final size:18
Alignment explanation
Indices: 1334304--1334361 Score: 62
Period size: 19 Copynumber: 3.0 Consensus size: 18
1334294 TACAAGCCAA
*
1334304 TGTATCGATACAATTTTTTG
1 TGTATCGATACAA--TTTGG
*
1334324 TGTATCGATACATACTTGG
1 TGTATCGATACA-ATTTGG
1334343 TGTATCGATACAAGTTTGG
1 TGTATCGATACAA-TTTGG
1334362 CTACTGCCAA
Statistics
Matches: 33, Mismatches: 3, Indels: 5
0.80 0.07 0.12
Matches are distributed among these distances:
18 1 0.03
19 19 0.58
20 12 0.36
21 1 0.03
ACGTcount: A:0.26, C:0.12, G:0.21, T:0.41
Consensus pattern (18 bp):
TGTATCGATACAATTTGG
Found at i:1334417 original size:20 final size:20
Alignment explanation
Indices: 1334375--1334426 Score: 68
Period size: 20 Copynumber: 2.6 Consensus size: 20
1334365 CTGCCAAGAA
****
1334375 ATGTATCGATACATTTTTTC
1 ATGTATCGATACATTGCAAC
1334395 ATGTATCGATACATTGCAAC
1 ATGTATCGATACATTGCAAC
1334415 ATGTATCGATAC
1 ATGTATCGATAC
1334427 TTTGAATTGT
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 28 1.00
ACGTcount: A:0.31, C:0.17, G:0.13, T:0.38
Consensus pattern (20 bp):
ATGTATCGATACATTGCAAC
Found at i:1335099 original size:12 final size:12
Alignment explanation
Indices: 1335082--1335107 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
1335072 TAATTCACAC
1335082 ATATCAAAATTT
1 ATATCAAAATTT
1335094 ATATCAAAATTT
1 ATATCAAAATTT
1335106 AT
1 AT
1335108 TTGCATATAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.50, C:0.08, G:0.00, T:0.42
Consensus pattern (12 bp):
ATATCAAAATTT
Found at i:1336166 original size:13 final size:13
Alignment explanation
Indices: 1336148--1336172 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1336138 ACTGAAGTAA
1336148 TGTATCGATACAT
1 TGTATCGATACAT
1336161 TGTATCGATACA
1 TGTATCGATACA
1336173 ATCTGGAAAA
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:1336772 original size:23 final size:24
Alignment explanation
Indices: 1336727--1336773 Score: 62
Period size: 23 Copynumber: 2.0 Consensus size: 24
1336717 CAAAGAATTG
*
1336727 AACACAAATTCAATTAAGCACAAA
1 AACACAAATTCAATTAAGAACAAA
1336751 AACACAAA-TCAATTGAA-AACAAA
1 AACACAAATTCAATT-AAGAACAAA
1336774 TTTTCAACAA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
23 11 0.52
24 10 0.48
ACGTcount: A:0.62, C:0.19, G:0.04, T:0.15
Consensus pattern (24 bp):
AACACAAATTCAATTAAGAACAAA
Found at i:1339370 original size:34 final size:35
Alignment explanation
Indices: 1339332--1339398 Score: 102
Period size: 37 Copynumber: 1.9 Consensus size: 35
1339322 CCTTACAACA
1339332 CTATC-TTTC-AAGGCTAAGATAGAAACCTCTCTCT
1 CTATCTTTTCAAAGGCTAAGATAG-AACCTCTCTCT
1339366 CTATCTTTTTCAAAGGCTAAGATAGAACCTCTC
1 CTATC-TTTTCAAAGGCTAAGATAGAACCTCTC
1339399 AATCACTTAG
Statistics
Matches: 30, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
34 5 0.17
36 12 0.40
37 13 0.43
ACGTcount: A:0.30, C:0.25, G:0.12, T:0.33
Consensus pattern (35 bp):
CTATCTTTTCAAAGGCTAAGATAGAACCTCTCTCT
Found at i:1339874 original size:13 final size:13
Alignment explanation
Indices: 1339856--1339881 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1339846 TAATTTTTTG
1339856 TGTATCGATACAT
1 TGTATCGATACAT
1339869 TGTATCGATACAT
1 TGTATCGATACAT
1339882 ACTTGGTGTA
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:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:1343430 original size:61 final size:61
Alignment explanation
Indices: 1343341--1343840 Score: 543
Period size: 61 Copynumber: 8.3 Consensus size: 61
1343331 ATCCTTTCAA
* * *
1343341 TCCTCGAAA-AGCATGACGCCTTTTCCTTTTAAAGCCCGCACAAGTTGGTGGCA-CTTTTCAG
1 TCCTC-AAAGAGCAGGACGCCTTTTCCTTTTAAAGCCCACACAAGTTGGTGGCACCTTCT-AG
* * **
1343402 TCCTCAAAGAGCAAGACGCCTTTTCCTTTTTAAGCTGACACAAGTTGGTGGCACCTTCTAG
1 TCCTCAAAGAGCAGGACGCCTTTTCCTTTTAAAGCCCACACAAGTTGGTGGCACCTTCTAG
* * * *
1343463 TCC-CTAAAGAGTAGGATGCCCTTTTCCTTTTAAAGCCTACACAAGTTGGTGGCATCTTCTAG
1 TCCTC-AAAGAGCAGGACG-CCTTTTCCTTTTAAAGCCCACACAAGTTGGTGGCACCTTCTAG
* * * *
1343525 TCCCCAAAGAGCAGGACGCCTTTTCCTTTTAAAGCCCACACAAGTTGGCGACACCTTCCAG
1 TCCTCAAAGAGCAGGACGCCTTTTCCTTTTAAAGCCCACACAAGTTGGTGGCACCTTCTAG
* * *
1343586 TTCTCAAAGAGCAAGAC-AC-TTT-CTTTTCAAAGCCCACACAAGTTGGTGGCACCTTCTAG
1 TCCTCAAAGAGCAGGACGCCTTTTCCTTTT-AAAGCCCACACAAGTTGGTGGCACCTTCTAG
* * ** *
1343645 TCCTCAAGGAGTAGGACTTCTTTTCCTTTTAAAGCTCACACAAGTTGGTGGCACCTTCTAG
1 TCCTCAAAGAGCAGGACGCCTTTTCCTTTTAAAGCCCACACAAGTTGGTGGCACCTTCTAG
* ** * **
1343706 TTCTCAAAGAGCAGGA-AAC-TTTCCTTTCAAAGCTGACACAAGTTGGTGGCA-CTTCTAG
1 TCCTCAAAGAGCAGGACGCCTTTTCCTTTTAAAGCCCACACAAGTTGGTGGCACCTTCTAG
* * * * * * *
1343764 TTCTCAAAGAGCAAGACACCTTCTCCTTTTAAAACCCACATAAGTTGGTGGCAACTTCTAG
1 TCCTCAAAGAGCAGGACGCCTTTTCCTTTTAAAGCCCACACAAGTTGGTGGCACCTTCTAG
*
1343825 T-CTCCAACGAGCAGGA
1 TCCT-CAAAGAGCAGGA
1343841 TGCGTTTCCT
Statistics
Matches: 376, Mismatches: 50, Indels: 26
0.83 0.11 0.06
Matches are distributed among these distances:
58 27 0.07
59 76 0.20
60 35 0.09
61 175 0.47
62 62 0.16
63 1 0.00
ACGTcount: A:0.26, C:0.27, G:0.19, T:0.28
Consensus pattern (61 bp):
TCCTCAAAGAGCAGGACGCCTTTTCCTTTTAAAGCCCACACAAGTTGGTGGCACCTTCTAG
Found at i:1343548 original size:123 final size:119
Alignment explanation
Indices: 1343362--1343840 Score: 559
Period size: 120 Copynumber: 4.0 Consensus size: 119
1343352 CATGACGCCT
* *
1343362 TTTCCTTTTAAAGCCCGCACAAGTTGGTGGCACTTTTCAGTCCTCAAAGAGCAAGACGCCTTTTC
1 TTTCCTTTTAAAGCCCACACAAGTTGGTGGCACTTCT-AGTCCTCAAAGAGCAAGACGCCTTTTC
* ** * *
1343427 CTTTTTAAGCTGACACAAGTTGGTGGCACCTTCTAGTCC-CTAAAGAGTAGGATGCCC
65 CTTTTAAAGCCCACACAAGTTGGTGGCACCTTCTAGTCCTC-AAAGAGCAGGA--CAC
* * *
1343484 TTTTCCTTTTAAAGCCTACACAAGTTGGTGGCATCTTCTAGTCCCCAAAGAGCAGGACGCCTTTT
1 -TTTCCTTTTAAAGCCCACACAAGTTGGTGGCA-CTTCTAGTCCTCAAAGAGCAAGACGCCTTTT
* * * * *
1343549 CCTTTTAAAGCCCACACAAGTTGGCGACACCTTCCAGTTCTCAAAGAGCAAGACAC
64 CCTTTTAAAGCCCACACAAGTTGGTGGCACCTTCTAGTCCTCAAAGAGCAGGACAC
* * * **
1343605 TTT-CTTTTCAAAGCCCACACAAGTTGGTGGCACCTTCTAGTCCTCAAGGAGTAGGACTTCTTTT
1 TTTCCTTTT-AAAGCCCACACAAGTTGGTGGCA-CTTCTAGTCCTCAAAGAGCAAGACGCCTTTT
* * *
1343669 CCTTTTAAAGCTCACACAAGTTGGTGGCACCTTCTAGTTCTCAAAGAGCAGGAAAC
64 CCTTTTAAAGCCCACACAAGTTGGTGGCACCTTCTAGTCCTCAAAGAGCAGGACAC
* ** * * *
1343725 TTTCCTTTCAAAGCTGACACAAGTTGGTGGCACTTCTAGTTCTCAAAGAGCAAGACACCTTCTCC
1 TTTCCTTTTAAAGCCCACACAAGTTGGTGGCACTTCTAGTCCTCAAAGAGCAAGACGCCTTTTCC
* * * *
1343790 TTTTAAAACCCACATAAGTTGGTGGCAACTTCTAGT-CTCCAACGAGCAGGA
66 TTTTAAAGCCCACACAAGTTGGTGGCACCTTCTAGTCCT-CAAAGAGCAGGA
1343841 TGCGTTTCCT
Statistics
Matches: 308, Mismatches: 43, Indels: 14
0.84 0.12 0.04
Matches are distributed among these distances:
118 2 0.01
119 74 0.24
120 125 0.41
121 6 0.02
123 96 0.31
124 5 0.02
ACGTcount: A:0.26, C:0.27, G:0.19, T:0.28
Consensus pattern (119 bp):
TTTCCTTTTAAAGCCCACACAAGTTGGTGGCACTTCTAGTCCTCAAAGAGCAAGACGCCTTTTCC
TTTTAAAGCCCACACAAGTTGGTGGCACCTTCTAGTCCTCAAAGAGCAGGACAC
Found at i:1344180 original size:3 final size:3
Alignment explanation
Indices: 1344174--1344235 Score: 99
Period size: 3 Copynumber: 20.7 Consensus size: 3
1344164 TACCTAAAAA
*
1344174 AAT AAT AAT AAT AAT AA- AAGT AAC AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AA-T AAT AAT AAT AAT AAT AAT AAT AAT
1344219 AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AA
1344236 ATCGAATGCC
Statistics
Matches: 55, Mismatches: 2, Indels: 4
0.90 0.03 0.07
Matches are distributed among these distances:
2 2 0.04
3 51 0.93
4 2 0.04
ACGTcount: A:0.68, C:0.02, G:0.02, T:0.29
Consensus pattern (3 bp):
AAT
Found at i:1344740 original size:50 final size:50
Alignment explanation
Indices: 1344660--1344788 Score: 177
Period size: 50 Copynumber: 2.6 Consensus size: 50
1344650 AATTTGTATT
* *
1344660 GATAAATTGTTTATTGTATCAATACATTCTGGGTTTTACCTAGATATATC
1 GATAAATTGTTCATTGTATCGATACATTCTGGGTTTTACCTAGATATATC
* * *
1344710 GATACATTGTTCATTGTATCGATACATTCTGGGTTTTACCTGGATGTATC
1 GATAAATTGTTCATTGTATCGATACATTCTGGGTTTTACCTAGATATATC
* * * *
1344760 AATATATTTTTCAATGTATCGATACATTC
1 GATAAATTGTTCATTGTATCGATACATTC
1344789 GGGCATTTTT
Statistics
Matches: 70, Mismatches: 9, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
50 70 1.00
ACGTcount: A:0.28, C:0.14, G:0.15, T:0.43
Consensus pattern (50 bp):
GATAAATTGTTCATTGTATCGATACATTCTGGGTTTTACCTAGATATATC
Found at i:1347276 original size:79 final size:79
Alignment explanation
Indices: 1347094--1347704 Score: 613
Period size: 79 Copynumber: 7.7 Consensus size: 79
1347084 ATTCATGTTT
* * * * *
1347094 TTATTTCTGAGGGGATACTCCAACCCCGGTTTTGTTTGCAAAACA-CTAATTTTTTACAATCGGG
1 TTATTTCCGAGGGGATACTCCAACCCCGGTTTTATTTCCAAAACATC-AATTTTTCACAATC-AG
*
1347158 GGATACT-TCAACCCCG
64 GGATACTCT-AACCCCA
* * * *
1347174 TTATTTCTGAAGGGATACCCCAACCCCGGTTTTATTTTCAAAACA-CTAATTTTTCACAATCAGG
1 TTATTTCCGAGGGGATACTCCAACCCCGGTTTTATTTCCAAAACATC-AATTTTTCACAATCAGG
* *
1347238 AATACTCTAATCCCA
65 GATACTCTAACCCCA
* * * *
1347253 TTATTTCCGAGGGGATACTCCAACCTCGGTTTTATTTCCAAAATATCAATTTTTCATAATTAGGG
1 TTATTTCCGAGGGGATACTCCAACCCCGGTTTTATTTCCAAAACATCAATTTTTCACAATCAGGG
*
1347318 ATACTCTAACCCTA
66 ATACTCTAACCCCA
*** * *
1347332 TTATTTTAAAGGGGATACTCCAACCTCGGTTTTATTTCCAAAACATCAATTTTTCACAAT-TGAG
1 TTATTTCCGAGGGGATACTCCAACCCCGGTTTTATTTCCAAAACATCAATTTTTCACAATCAG-G
* *
1347396 GATACTCCAACCCCG
65 GATACTCTAACCCCA
* * * **
1347411 TTATTTCTGAGGGGATACTCTAACCCCGATTTTATTTCCAAAACATCAATTTTTCACAATTGGGG
1 TTATTTCCGAGGGGATACTCCAACCCCGGTTTTATTTCCAAAACATCAATTTTTCACAATCAGGG
* *
1347476 ATACTCTAAGCCCG
66 ATACTCTAACCCCA
* * * * * *
1347490 TTATTTTCGAGGGGATACTCCAACTCCGATTTTATTTTCAAAACACCAATTTTTCACAATCGGGG
1 TTATTTCCGAGGGGATACTCCAACCCCGGTTTTATTTCCAAAACATCAATTTTTCACAATCAGGG
*
1347555 ACACTCTAACCCCA
66 ATACTCTAACCCCA
* * * * * *
1347569 TTATTTCCGAGGGGATACTCCAATCCCGATTTTATTTTCAAAACATCGATTTTTCACCAT-TGGT
1 TTATTTCCGAGGGGATACTCCAACCCCGGTTTTATTTCCAAAACATCAATTTTTCACAATCAGG-
* **
1347633 GATACTCCAACCCTG
65 GATACTCTAACCCCA
** * * * * * *
1347648 TTATTTCTAATGGGG-TACTCCGACCTCGTTTTTATCTCCAAAATATTAAATTTTTCA
1 TTATTTCCGA-GGGGATACTCCAACCCCGGTTTTATTTCCAAAACA-TCAATTTTTCA
1347705 TCCGGAGATG
Statistics
Matches: 454, Mismatches: 70, Indels: 14
0.84 0.13 0.03
Matches are distributed among these distances:
78 3 0.01
79 379 0.83
80 72 0.16
ACGTcount: A:0.28, C:0.24, G:0.13, T:0.35
Consensus pattern (79 bp):
TTATTTCCGAGGGGATACTCCAACCCCGGTTTTATTTCCAAAACATCAATTTTTCACAATCAGGG
ATACTCTAACCCCA
Found at i:1347374 original size:158 final size:159
Alignment explanation
Indices: 1347094--1347704 Score: 686
Period size: 158 Copynumber: 3.9 Consensus size: 159
1347084 ATTCATGTTT
* * * * * *
1347094 TTATTTCTGAGGGGATACTCCAACCCCGGTTTTGTTTGCAAAACA-CTAATTTTTTACAATCGGG
1 TTATTTCCGAGGGGATACTCCAACCCCGATTTTATTTCCAAAACATC-AATTTTTCACAAT-TGG
* * * * *
1347158 GGATACT-TCAACCCCGTTATTTCTGAA-GGGATACCCCAACCCCGGTTTTATTTTCAAAACACT
64 GGATACTCT-AACCCTGTTATTTCTAAAGGGGATACTCCAACCTCGGTTTTATTTCCAAAACACT
*
1347221 -AATTTTTCACAATCAGGAATACTCTAATCCCA
128 AAATTTTTCACAATCAGG-ATACTCTAACCCCA
* * * * *
1347253 TTATTTCCGAGGGGATACTCCAACCTCGGTTTTATTTCCAAAATATCAATTTTTCATAATTAGGG
1 TTATTTCCGAGGGGATACTCCAACCCCGATTTTATTTCCAAAACATCAATTTTTCACAATTGGGG
* *
1347318 ATACTCTAACCCTATTATTT-TAAAGGGGATACTCCAACCTCGGTTTTATTTCCAAAACA-TCAA
66 ATACTCTAACCCTGTTATTTCTAAAGGGGATACTCCAACCTCGGTTTTATTTCCAAAACACTAAA
* * *
1347381 TTTTTCACAATTGAGGATACTCCAACCCCG
131 TTTTTCACAA-TCAGGATACTCTAACCCCA
* *
1347411 TTATTTCTGAGGGGATACTCTAACCCCGATTTTATTTCCAAAACATCAATTTTTCACAATTGGGG
1 TTATTTCCGAGGGGATACTCCAACCCCGATTTTATTTCCAAAACATCAATTTTTCACAATTGGGG
** * * *
1347476 ATACTCTAAGCCC-GTTATTT-TCGAGGGGATACTCCAA-CTCCGATTTTATTTTCAAAACAC-C
66 ATACTCTAA-CCCTGTTATTTCTAAAGGGGATACTCCAACCT-CGGTTTTATTTCCAAAACACTA
* *
1347537 AATTTTTCACAATCGGGGACACTCTAACCCCA
129 AATTTTTCACAATC-AGGATACTCTAACCCCA
* * * * *
1347569 TTATTTCCGAGGGGATACTCCAATCCCGATTTTATTTTCAAAACATCGATTTTTCACCATTGGTG
1 TTATTTCCGAGGGGATACTCCAACCCCGATTTTATTTCCAAAACATCAATTTTTCACAATTGGGG
* * * * * * *
1347634 ATACTCCAACCCTGTTATTTCTAATGGGG-TACTCCGACCTCGTTTTTATCTCCAAAATATTAAA
66 ATACTCTAACCCTGTTATTTCTAAAGGGGATACTCCAACCTCGGTTTTATTTCCAAAACACTAAA
1347698 TTTTTCA
131 TTTTTCA
1347705 TCCGGAGATG
Statistics
Matches: 385, Mismatches: 54, Indels: 26
0.83 0.12 0.06
Matches are distributed among these distances:
157 10 0.03
158 299 0.78
159 75 0.19
160 1 0.00
ACGTcount: A:0.28, C:0.24, G:0.13, T:0.35
Consensus pattern (159 bp):
TTATTTCCGAGGGGATACTCCAACCCCGATTTTATTTCCAAAACATCAATTTTTCACAATTGGGG
ATACTCTAACCCTGTTATTTCTAAAGGGGATACTCCAACCTCGGTTTTATTTCCAAAACACTAAA
TTTTTCACAATCAGGATACTCTAACCCCA
Found at i:1347482 original size:237 final size:235
Alignment explanation
Indices: 1347094--1347704 Score: 708
Period size: 237 Copynumber: 2.6 Consensus size: 235
1347084 ATTCATGTTT
** * * * *
1347094 TTATTTCTGAGGGGATACTCCAACCCCGGTTTTGTTTGCAAAACA-CTAATTTTTTACAATCGGG
1 TTATTTCAAAGGGGATACTCCAA-CCCGGTTTTATTTCCAAAACATC-AATTTTTCACAAT--TG
* * * * *
1347158 GGATACTTCAACCCCGTTATTTCTGAAGGGATACCCCAACCCCGGTTTTATTTTCAAAACA-CTA
62 GGATACTCCAACCCCGTTATTTCTGAGGGGATACTCCAACCCCGATTTTATTTCCAAAACATC-A
* *
1347222 ATTTTTCACAATCAGGAATACTCTAATCCCATTATTTCCGAGGGGATACTCCAAC-CTCGGTTTT
126 ATTTTTCACAATCAGGAATACTCTAAGCCCATTATTTCCGAGGGGATACTCCAACTC-CGATTTT
* * * * * *
1347286 ATTTCCAAAATATCAATTTTTCATAATTAGGGATACTCTAACCCTA
190 ATTTCCAAAACACCAATTTTTCACAATCAGGGACACTCTAACCCCA
*
1347332 TTATTTTAAAGGGGATACTCCAACCTCGGTTTTATTTCCAAAACATCAATTTTTCACAATTGAGG
1 TTATTTCAAAGGGGATACTCCAACC-CGGTTTTATTTCCAAAACATCAATTTTTCACAATTG-GG
*
1347397 ATACTCCAACCCCGTTATTTCTGAGGGGATACTCTAACCCCGATTTTATTTCCAAAACATCAATT
64 ATACTCCAACCCCGTTATTTCTGAGGGGATACTCCAACCCCGATTTTATTTCCAAAACATCAATT
** * * *
1347462 TTTCACAATTGGGGATACTCTAAGCCCGTTATTTTCGAGGGGATACTCCAACTCCGATTTTATTT
129 TTTCACAATCAGGAATACTCTAAGCCCATTATTTCCGAGGGGATACTCCAACTCCGATTTTATTT
* *
1347527 TCAAAACACCAATTTTTCACAATCGGGGACACTCTAACCCCA
194 CCAAAACACCAATTTTTCACAATCAGGGACACTCTAACCCCA
** * * * *
1347569 TTATTTCCGAGGGGATACTCCAATCCCGATTTTATTTTCAAAACATCGATTTTTCACCATTGGTG
1 TTATTTCAAAGGGGATACTCCAA-CCCGGTTTTATTTCCAAAACATCAATTTTTCACAATTGG-G
* * * * * * * *
1347634 ATACTCCAACCCTGTTATTTCTAATGGGG-TACTCCGACCTCGTTTTTATCTCCAAAATATTAAA
64 ATACTCCAACCCCGTTATTTCTGA-GGGGATACTCCAACCCCGATTTTATTTCCAAAACA-TCAA
1347698 TTTTTCA
127 TTTTTCA
1347705 TCCGGAGATG
Statistics
Matches: 320, Mismatches: 44, Indels: 18
0.84 0.12 0.05
Matches are distributed among these distances:
236 2 0.01
237 250 0.78
238 67 0.21
239 1 0.00
ACGTcount: A:0.28, C:0.24, G:0.13, T:0.35
Consensus pattern (235 bp):
TTATTTCAAAGGGGATACTCCAACCCGGTTTTATTTCCAAAACATCAATTTTTCACAATTGGGAT
ACTCCAACCCCGTTATTTCTGAGGGGATACTCCAACCCCGATTTTATTTCCAAAACATCAATTTT
TCACAATCAGGAATACTCTAAGCCCATTATTTCCGAGGGGATACTCCAACTCCGATTTTATTTCC
AAAACACCAATTTTTCACAATCAGGGACACTCTAACCCCA
Found at i:1351053 original size:15 final size:16
Alignment explanation
Indices: 1351019--1351056 Score: 51
Period size: 16 Copynumber: 2.4 Consensus size: 16
1351009 CAATATTAAA
* *
1351019 AAATAAAAAAAATTGT
1 AAATATAAAAAATCGT
1351035 AAATATAAAAAATCG-
1 AAATATAAAAAATCGT
1351050 AAATATA
1 AAATATA
1351057 GATTTATTAA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
15 7 0.35
16 13 0.65
ACGTcount: A:0.68, C:0.03, G:0.05, T:0.24
Consensus pattern (16 bp):
AAATATAAAAAATCGT
Found at i:1351181 original size:7 final size:7
Alignment explanation
Indices: 1351166--1351203 Score: 67
Period size: 7 Copynumber: 5.3 Consensus size: 7
1351156 TTTTTATATC
1351166 TAATATAA
1 TAAT-TAA
1351174 TAATTAA
1 TAATTAA
1351181 TAATTAA
1 TAATTAA
1351188 TAATTAA
1 TAATTAA
1351195 TAATTAA
1 TAATTAA
1351202 TA
1 TA
1351204 TAAAAAATTT
Statistics
Matches: 30, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
7 26 0.87
8 4 0.13
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (7 bp):
TAATTAA
Found at i:1351488 original size:30 final size:29
Alignment explanation
Indices: 1351452--1351508 Score: 80
Period size: 30 Copynumber: 1.9 Consensus size: 29
1351442 TATTTTTAAA
1351452 AATTTATATTTATATTT-TTATAATTAAAAT
1 AATTTATATTTA-ATTTATTA-AATTAAAAT
*
1351482 AATTTATTTTTAATTTATTAAATTAAA
1 AATTTATATTTAATTTATTAAATTAAA
1351509 TTTATATTTT
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
29 11 0.44
30 14 0.56
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (29 bp):
AATTTATATTTAATTTATTAAATTAAAAT
Found at i:1352610 original size:80 final size:80
Alignment explanation
Indices: 1352468--1352627 Score: 250
Period size: 80 Copynumber: 2.0 Consensus size: 80
1352458 TTCCCTCCTC
* *
1352468 CCTCATTGTAAGTATTTCCTTTCTTTAAAACAGAATATTAACGCTGATAGTTCACTTAACATGTT
1 CCTCATTGTAAGCATTTCCTTTCTTTAAAACA-AATATTAACGCTGATAGTCCACTTAACATGTT
*
1352533 GTTCCTAACATTATAT
65 GTTCCCAACATTATAT
* *
1352549 CCTCATTGTTAGCATTTCCTTTCTTTAAATAC-AATATTAACGCTGATAGTCCACTTGACATGTT
1 CCTCATTGTAAGCATTTCCTTTCTTTAAA-ACAAATATTAACGCTGATAGTCCACTTAACATGTT
1352613 GTTCCCAACATTATA
65 GTTCCCAACATTATA
1352628 GGAAAAAGGA
Statistics
Matches: 73, Mismatches: 5, Indels: 3
0.90 0.06 0.04
Matches are distributed among these distances:
80 44 0.60
81 27 0.37
82 2 0.03
ACGTcount: A:0.29, C:0.21, G:0.10, T:0.40
Consensus pattern (80 bp):
CCTCATTGTAAGCATTTCCTTTCTTTAAAACAAATATTAACGCTGATAGTCCACTTAACATGTTG
TTCCCAACATTATAT
Found at i:1352670 original size:15 final size:15
Alignment explanation
Indices: 1352622--1352670 Score: 55
Period size: 15 Copynumber: 3.3 Consensus size: 15
1352612 TGTTCCCAAC
1352622 ATTATAGGAAAAAGG
1 ATTATAGGAAAAAGG
* * *
1352637 ATTATTAGCATAAA-C
1 ATTA-TAGGAAAAAGG
1352652 ATTATAGGAAAAAGG
1 ATTATAGGAAAAAGG
1352667 ATTA
1 ATTA
1352671 ATGGCATAAC
Statistics
Matches: 26, Mismatches: 6, Indels: 4
0.72 0.17 0.11
Matches are distributed among these distances:
14 7 0.27
15 12 0.46
16 7 0.27
ACGTcount: A:0.51, C:0.04, G:0.18, T:0.27
Consensus pattern (15 bp):
ATTATAGGAAAAAGG
Found at i:1352682 original size:29 final size:30
Alignment explanation
Indices: 1352619--1352679 Score: 104
Period size: 30 Copynumber: 2.0 Consensus size: 30
1352609 TGTTGTTCCC
*
1352619 AACATTATAGGAAAAAGGATTATTAGCATA
1 AACATTATAGGAAAAAGGATTAATAGCATA
*
1352649 AACATTATAGGAAAAAGGATTAATGGCATA
1 AACATTATAGGAAAAAGGATTAATAGCATA
1352679 A
1 A
1352680 CATATTTTCA
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
30 29 1.00
ACGTcount: A:0.51, C:0.07, G:0.18, T:0.25
Consensus pattern (30 bp):
AACATTATAGGAAAAAGGATTAATAGCATA
Found at i:1362390 original size:22 final size:22
Alignment explanation
Indices: 1362347--1362391 Score: 72
Period size: 22 Copynumber: 2.0 Consensus size: 22
1362337 ATTCATCTTG
* *
1362347 AAATTTTAGGAATTTGATTCCT
1 AAATTTTAGGAATTTCACTCCT
1362369 AAATTTTAGGAATTTCACTCCT
1 AAATTTTAGGAATTTCACTCCT
1362391 A
1 A
1362392 CTAGAAAACT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.33, C:0.13, G:0.11, T:0.42
Consensus pattern (22 bp):
AAATTTTAGGAATTTCACTCCT
Found at i:1367519 original size:13 final size:13
Alignment explanation
Indices: 1367501--1367526 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1367491 AATTTTTTGG
1367501 TGTATCGATACAT
1 TGTATCGATACAT
1367514 TGTATCGATACAT
1 TGTATCGATACAT
1367527 ACTTGGTGTA
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:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:1369959 original size:21 final size:21
Alignment explanation
Indices: 1369935--1369981 Score: 62
Period size: 21 Copynumber: 2.3 Consensus size: 21
1369925 TTTGAAGCTG
1369935 ATTTTG-A-TGAAAAACGAAGT
1 ATTTTGAAGTGAAAAAC-AAGT
*
1369955 AATTTGAAGTGAAAAACAAGT
1 ATTTTGAAGTGAAAAACAAGT
1369976 ATTTTG
1 ATTTTG
1369982 TAAAAGATTT
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
20 5 0.22
21 10 0.43
22 8 0.35
ACGTcount: A:0.45, C:0.04, G:0.19, T:0.32
Consensus pattern (21 bp):
ATTTTGAAGTGAAAAACAAGT
Found at i:1370120 original size:13 final size:13
Alignment explanation
Indices: 1370102--1370140 Score: 60
Period size: 13 Copynumber: 3.0 Consensus size: 13
1370092 ATAATCCCCC
*
1370102 TGTATCGATACAG
1 TGTATCGATACAA
1370115 TGTATCGATACAA
1 TGTATCGATACAA
*
1370128 TGTTTCGATACAA
1 TGTATCGATACAA
1370141 AGAAAGATGT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
13 24 1.00
ACGTcount: A:0.33, C:0.15, G:0.18, T:0.33
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:1370155 original size:20 final size:20
Alignment explanation
Indices: 1370127--1370224 Score: 115
Period size: 20 Copynumber: 4.7 Consensus size: 20
1370117 TATCGATACA
*
1370127 ATGTTTCGATACAAAGAAAG
1 ATGTATCGATACAAAGAAAG
1370147 ATGTATCGATACAAAGAAAG
1 ATGTATCGATACAAAGAAAG
*
1370167 ATGTATCGATACAATGAATTTCCAG
1 ATGTATCGATACAAAGAA-----AG
* *
1370192 ATGTATCGATACACAGAAAC
1 ATGTATCGATACAAAGAAAG
1370212 ATGTATCGATACA
1 ATGTATCGATACA
1370225 TTTTGGACAT
Statistics
Matches: 68, Mismatches: 5, Indels: 10
0.82 0.06 0.12
Matches are distributed among these distances:
20 50 0.74
25 18 0.26
ACGTcount: A:0.43, C:0.14, G:0.17, T:0.26
Consensus pattern (20 bp):
ATGTATCGATACAAAGAAAG
Found at i:1376339 original size:13 final size:13
Alignment explanation
Indices: 1376321--1376346 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1376311 AATTTTTTGG
1376321 TGTATCGATACAT
1 TGTATCGATACAT
1376334 TGTATCGATACAT
1 TGTATCGATACAT
1376347 ACTTGGTGTA
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:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:1381466 original size:20 final size:19
Alignment explanation
Indices: 1381441--1381622 Score: 145
Period size: 20 Copynumber: 9.8 Consensus size: 19
1381431 TTTTCACAAT
1381441 TTGTATCGATACATTGTTCA
1 TTGTATCGATACATT-TTCA
1381461 TTGTATCGATACATTATTCA
1 TTGTATCGATACATT-TTCA
1381481 TTGTATCGATACATTATTCA
1 TTGTATCGATACATT-TTCA
1381501 TTGTATCGATACA--TT-A
1 TTGTATCGATACATTTTCA
*
1381517 ---TATCGATACATTGCTCA
1 TTGTATCGATACATT-TTCA
1381534 TTGTATCGAT--A----CA
1 TTGTATCGATACATTTTCA
*
1381547 TTGTATCGATACATTGCTCA
1 TTGTATCGATACATT-TTCA
**
1381567 TTGTATCGATACATTACCCA
1 TTGTATCGATACATT-TTCA
*
1381587 GATGTATCGATACATTTTACA
1 -TTGTATCGATACATTTT-CA
* *
1381608 ATGCATCGATACATT
1 TTGTATCGATACATT
1381623 CAAGCATTTT
Statistics
Matches: 138, Mismatches: 8, Indels: 32
0.78 0.04 0.18
Matches are distributed among these distances:
13 22 0.16
15 1 0.01
16 2 0.01
17 3 0.02
18 1 0.01
20 93 0.67
21 16 0.12
ACGTcount: A:0.30, C:0.18, G:0.13, T:0.40
Consensus pattern (19 bp):
TTGTATCGATACATTTTCA
Found at i:1381526 original size:33 final size:33
Alignment explanation
Indices: 1381479--1381582 Score: 172
Period size: 33 Copynumber: 3.2 Consensus size: 33
1381469 ATACATTATT
* **
1381479 CATTGTATCGATACATTATTCATTGTATCGATA
1 CATTATATCGATACATTGCTCATTGTATCGATA
1381512 CATTATATCGATACATTGCTCATTGTATCGATA
1 CATTATATCGATACATTGCTCATTGTATCGATA
*
1381545 CATTGTATCGATACATTGCTCATTGTATCGATA
1 CATTATATCGATACATTGCTCATTGTATCGATA
1381578 CATTA
1 CATTA
1381583 CCCAGATGTA
Statistics
Matches: 66, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
33 66 1.00
ACGTcount: A:0.30, C:0.17, G:0.12, T:0.40
Consensus pattern (33 bp):
CATTATATCGATACATTGCTCATTGTATCGATA
Found at i:1381574 original size:53 final size:53
Alignment explanation
Indices: 1381441--1381602 Score: 184
Period size: 53 Copynumber: 3.0 Consensus size: 53
1381431 TTTTCACAAT
* *
1381441 TTGTATCGATACATTGTTCATTGTATCGATACATTATTCATTGTATCGATACA
1 TTGTATCGATACATTGATCATTGTATCGATACATTACTCATTGTATCGATACA
* ** * * *
1381494 TTAT-TC-ATTGTATCGATACATTATATCGATACATTGCTCATTGTATCGATACA
1 TTGTATCGA-TACATTGAT-CATTGTATCGATACATTACTCATTGTATCGATACA
* * *
1381547 TTGTATCGATACATTGCTCATTGTATCGATACATTACCCAGATGTATCGATACA
1 TTGTATCGATACATTGATCATTGTATCGATACATTACTCA-TTGTATCGATACA
1381601 TT
1 TT
1381603 TTACAATGCA
Statistics
Matches: 87, Mismatches: 17, Indels: 9
0.77 0.15 0.08
Matches are distributed among these distances:
51 1 0.01
52 7 0.08
53 57 0.66
54 21 0.24
55 1 0.01
ACGTcount: A:0.29, C:0.17, G:0.13, T:0.41
Consensus pattern (53 bp):
TTGTATCGATACATTGATCATTGTATCGATACATTACTCATTGTATCGATACA
Found at i:1381581 original size:13 final size:13
Alignment explanation
Indices: 1381499--1381562 Score: 77
Period size: 13 Copynumber: 5.4 Consensus size: 13
1381489 ATACATTATT
1381499 CATTGTATCGATA
1 CATTGTATCGATA
*
1381512 CATTATATCGATA
1 CATTGTATCGATA
1381525 CATTG---C--T-
1 CATTGTATCGATA
1381532 CATTGTATCGATA
1 CATTGTATCGATA
1381545 CATTGTATCGATA
1 CATTGTATCGATA
1381558 CATTG
1 CATTG
1381563 CTCATTGTAT
Statistics
Matches: 43, Mismatches: 2, Indels: 12
0.75 0.04 0.21
Matches are distributed among these distances:
7 5 0.12
8 1 0.02
10 2 0.05
12 1 0.02
13 34 0.79
ACGTcount: A:0.30, C:0.17, G:0.14, T:0.39
Consensus pattern (13 bp):
CATTGTATCGATA
Found at i:1384068 original size:51 final size:50
Alignment explanation
Indices: 1383895--1384071 Score: 171
Period size: 51 Copynumber: 3.5 Consensus size: 50
1383885 ATTTCTAGAT
* * * *
1383895 TTTTCAT-CTCGGGGATACTCC-ATTCCCGGTTTCATTTCCAAAACA-TCAA
1 TTTTCATAATCGGGGATACTCCAACT-CCGATTTTATTTCCAAAACACT-AA
* * * **
1383944 TTTTTCTTAATCGGGGATGCTCCAACTCCGATTTTATTTCTAAAACACCCA
1 -TTTTCATAATCGGGGATACTCCAACTCCGATTTTATTTCCAAAACACTAA
* * *
1383995 TTTTCCATAATCAGGGACACTCCAACTCCGATTTTATTTCCAAAACACTGAC
1 TTTT-CATAATCGGGGATACTCCAACTCCGATTTTATTTCCAAAACACT-AA
*
1384047 TTTTCACAATCGGGGATACTCCAAC
1 TTTTCATAATCGGGGATACTCCAAC
1384072 CCCATTATTT
Statistics
Matches: 102, Mismatches: 20, Indels: 9
0.78 0.15 0.07
Matches are distributed among these distances:
50 10 0.10
51 86 0.84
52 6 0.06
ACGTcount: A:0.27, C:0.28, G:0.12, T:0.33
Consensus pattern (50 bp):
TTTTCATAATCGGGGATACTCCAACTCCGATTTTATTTCCAAAACACTAA
Found at i:1384317 original size:28 final size:28
Alignment explanation
Indices: 1384286--1384358 Score: 119
Period size: 28 Copynumber: 2.6 Consensus size: 28
1384276 ATTTTTTATC
* *
1384286 GGGATACTCCAACCCTGTTATTTTCGAG
1 GGGATACTCCAACCCCGTTATTTCCGAG
*
1384314 GGGATACCCCAACCCCGTTATTTCCGAG
1 GGGATACTCCAACCCCGTTATTTCCGAG
1384342 GGGATACTCCAACCCCG
1 GGGATACTCCAACCCCG
1384359 GTTTTATTTC
Statistics
Matches: 41, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
28 41 1.00
ACGTcount: A:0.22, C:0.33, G:0.22, T:0.23
Consensus pattern (28 bp):
GGGATACTCCAACCCCGTTATTTCCGAG
Found at i:1384328 original size:75 final size:76
Alignment explanation
Indices: 1384008--1384330 Score: 353
Period size: 76 Copynumber: 4.2 Consensus size: 76
1383998 TCCATAATCA
* * * * * * * *
1384008 GGGACACTCCAACTCCGATTTTATTTCCAAAACACTGACTTTTCACAATCGGGGATACTCCAACC
1 GGGACACCCCAACCCCGGTTTTATTTCTAAAACA-TCAATTTT-TC-ATCAGGGATACTCCAACC
*
1384073 CCATTA-TTTCTGAG
63 CCGTTATTTTC-GAG
* * ** * *
1384087 GGGACACTCTAACCCCCATTTTATTTTTAAAACATCAATTTTTCATCAGGGATACTCTAACCCCG
1 GGGACACCCCAACCCCGGTTTTATTTCTAAAACATCAATTTTTCATCAGGGATACTCCAACCCCG
*
1384152 TTATTTCCGAG
66 TTATTTTCGAG
* * * * * *
1384163 GGAACACTCCAACCCCAGTTTTATTTCTAAAACATCAATTTTTCATCGGGGATACTCTAACCCAG
1 GGGACACCCCAACCCCGGTTTTATTTCTAAAACATCAATTTTTCATCAGGGATACTCCAACCCCG
*
1384228 TTATTTTCAAG
66 TTATTTTCGAG
* * *
1384239 GGGATACCCCAACCCCGGTTTTATTTCTAAAACATCAATTTTTTATC-GGGATACTCCAACCCTG
1 GGGACACCCCAACCCCGGTTTTATTTCTAAAACATCAATTTTTCATCAGGGATACTCCAACCCCG
1384303 TTATTTTCGAG
66 TTATTTTCGAG
*
1384314 GGGATACCCCAACCCCG
1 GGGACACCCCAACCCCG
1384331 TTATTTCCGA
Statistics
Matches: 214, Mismatches: 29, Indels: 6
0.86 0.12 0.02
Matches are distributed among these distances:
75 42 0.20
76 133 0.62
77 4 0.02
78 6 0.03
79 29 0.14
ACGTcount: A:0.28, C:0.28, G:0.14, T:0.31
Consensus pattern (76 bp):
GGGACACCCCAACCCCGGTTTTATTTCTAAAACATCAATTTTTCATCAGGGATACTCCAACCCCG
TTATTTTCGAG
Found at i:1384335 original size:103 final size:106
Alignment explanation
Indices: 1384210--1384437 Score: 329
Period size: 103 Copynumber: 2.2 Consensus size: 106
1384200 ATTTTTCATC
* * *
1384210 GGGGATACTCTAACCCAGTTATTTTCAAGGGGATACCCCAACCCCGGTTTTATTTCTAAAACATC
1 GGGGATACTCCAACCCCGTTATTTCCAAGGGGATACCCCAACCCCGGTTTTATTTCTAAAACATC
**
1384275 AATTTTT-TA-TC-GGGATACTCCAACCCTGTTATTT-TCGA
66 AATTTTTATAGTCGGGGATACTCCAACCCCCTTATTTCT-GA
* * *
1384313 GGGGATACCCCAACCCCGTTATTTCCGAGGGGATACTCCAACCCCGGTTTTATTTCTAAAACATC
1 GGGGATACTCCAACCCCGTTATTTCCAAGGGGATACCCCAACCCCGGTTTTATTTCTAAAACATC
1384378 AATTTTTCATAGTCGGGGATACTCCAACCCCCTTATTTCTGA
66 AATTTTT-ATAGTCGGGGATACTCCAACCCCCTTATTTCTGA
1384420 GGGGATACTCCAATCCCC
1 GGGGATACTCCAA-CCCC
1384438 ATTTTATTTC
Statistics
Matches: 110, Mismatches: 9, Indels: 7
0.87 0.07 0.06
Matches are distributed among these distances:
103 66 0.60
105 2 0.02
106 2 0.02
107 35 0.32
108 5 0.05
ACGTcount: A:0.25, C:0.28, G:0.17, T:0.31
Consensus pattern (106 bp):
GGGGATACTCCAACCCCGTTATTTCCAAGGGGATACCCCAACCCCGGTTTTATTTCTAAAACATC
AATTTTTATAGTCGGGGATACTCCAACCCCCTTATTTCTGA
Found at i:1384405 original size:79 final size:79
Alignment explanation
Indices: 1384313--1384516 Score: 320
Period size: 79 Copynumber: 2.6 Consensus size: 79
1384303 TTATTTTCGA
* * *
1384313 GGGGATACCCCAACCCCGTTATTTCCGAGGGGATACTCCAACCCCGGTTTTATTTCTAAAACATC
1 GGGGATACTCCAACCCCGTTATTTCTGAGGGGATACTCCAACCCCGATTTTATTTCTAAAACATC
* *
1384378 AATTTTTCATAGTC
66 AATTTTTCACAATC
* *
1384392 GGGGATACTCCAACCCCCTTATTTCTGAGGGGATACTCCAATCCCC-ATTTTATTTCTAAATCAT
1 GGGGATACTCCAACCCCGTTATTTCTGAGGGGATACTCCAA-CCCCGATTTTATTTCTAAAACAT
1384456 CAATTTTTCACAATC
65 CAATTTTTCACAATC
*
1384471 GGGGATACTCCAACCCCGTTATTTTTGAGGGGATACTCCAACCCCG
1 GGGGATACTCCAACCCCGTTATTTCTGAGGGGATACTCCAACCCCG
1384517 TTATTATCTC
Statistics
Matches: 114, Mismatches: 9, Indels: 4
0.90 0.07 0.03
Matches are distributed among these distances:
78 4 0.04
79 106 0.93
80 4 0.04
ACGTcount: A:0.25, C:0.28, G:0.16, T:0.30
Consensus pattern (79 bp):
GGGGATACTCCAACCCCGTTATTTCTGAGGGGATACTCCAACCCCGATTTTATTTCTAAAACATC
AATTTTTCACAATC
Found at i:1387920 original size:17 final size:16
Alignment explanation
Indices: 1387877--1387926 Score: 66
Period size: 17 Copynumber: 3.1 Consensus size: 16
1387867 GTCAGGCGGA
1387877 AAGAAAATTAGAAAGAT
1 AAGAAAATT-GAAAGAT
*
1387894 AA-AAAATTGAAGGAT
1 AAGAAAATTGAAAGAT
1387909 AAGAAAAGTTGAAAGAT
1 AAGAAAA-TTGAAAGAT
1387926 A
1 A
1387927 GACAATATAT
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
15 8 0.28
16 10 0.34
17 11 0.38
ACGTcount: A:0.62, C:0.00, G:0.20, T:0.18
Consensus pattern (16 bp):
AAGAAAATTGAAAGAT
Found at i:1389884 original size:18 final size:19
Alignment explanation
Indices: 1389847--1389886 Score: 55
Period size: 18 Copynumber: 2.2 Consensus size: 19
1389837 ATATTAATTT
*
1389847 AATTAAAAAATTATATAAA
1 AATTAAAAAATTAAATAAA
*
1389866 AATTAAATAA-TAAATAAA
1 AATTAAAAAATTAAATAAA
1389884 AAT
1 AAT
1389887 ATATATGTAT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
18 10 0.53
19 9 0.47
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (19 bp):
AATTAAAAAATTAAATAAA
Found at i:1390882 original size:2 final size:2
Alignment explanation
Indices: 1390864--1390897 Score: 50
Period size: 2 Copynumber: 17.0 Consensus size: 2
1390854 CAAATTCACG
* *
1390864 TA TA CA TA TA TA CA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1390898 AAATGCTATT
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.06, G:0.00, T:0.44
Consensus pattern (2 bp):
TA
Found at i:1390980 original size:27 final size:28
Alignment explanation
Indices: 1390950--1391004 Score: 69
Period size: 27 Copynumber: 2.0 Consensus size: 28
1390940 TATATTCATA
*
1390950 TTTAAAATAT-TATATATTTATA-TAAAT
1 TTTAAAATATAAATA-ATTTATATTAAAT
*
1390977 TTTAATATATAAATAATTTATATTAAAT
1 TTTAAAATATAAATAATTTATATTAAAT
1391005 AAATTTTAAT
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
27 16 0.67
28 8 0.33
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (28 bp):
TTTAAAATATAAATAATTTATATTAAAT
Found at i:1390987 original size:14 final size:14
Alignment explanation
Indices: 1390968--1391018 Score: 57
Period size: 14 Copynumber: 3.4 Consensus size: 14
1390958 ATTATATATT
1390968 TATATAAATTTTAA
1 TATATAAATTTTAA
1390982 TATATAAATAATTTATA
1 TATATAAAT--TTTA-A
*
1390999 TTAAATAAATTTTAA
1 -TATATAAATTTTAA
1391014 TATAT
1 TATAT
1391019 TTATTTATAT
Statistics
Matches: 31, Mismatches: 2, Indels: 8
0.76 0.05 0.20
Matches are distributed among these distances:
14 13 0.42
15 1 0.03
16 8 0.26
17 1 0.03
18 8 0.26
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (14 bp):
TATATAAATTTTAA
Found at i:1390992 original size:18 final size:18
Alignment explanation
Indices: 1390971--1391018 Score: 68
Period size: 15 Copynumber: 2.9 Consensus size: 18
1390961 ATATATTTAT
1390971 ATAAATTTTAATATATAA
1 ATAAATTTTAATATATAA
1390989 AT-AA-TTT-ATAT-TAA
1 ATAAATTTTAATATATAA
1391003 ATAAATTTTAATATAT
1 ATAAATTTTAATATAT
1391019 TTATTTATAT
Statistics
Matches: 26, Mismatches: 0, Indels: 8
0.76 0.00 0.24
Matches are distributed among these distances:
14 5 0.19
15 6 0.23
16 6 0.23
17 6 0.23
18 3 0.12
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (18 bp):
ATAAATTTTAATATATAA
Found at i:1391012 original size:32 final size:33
Alignment explanation
Indices: 1390954--1391018 Score: 98
Period size: 32 Copynumber: 2.0 Consensus size: 33
1390944 TTCATATTTA
*
1390954 AAATATTATATATTTATATAAATTTTAATATAT
1 AAATATTATATATTTAAATAAATTTTAATATAT
1390987 AAATAATT-TATA-TTAAATAAATTTTAATATAT
1 AAAT-ATTATATATTTAAATAAATTTTAATATAT
1391019 TTATTTATAT
Statistics
Matches: 30, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
32 19 0.63
33 8 0.27
34 3 0.10
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (33 bp):
AAATATTATATATTTAAATAAATTTTAATATAT
Found at i:1391032 original size:11 final size:11
Alignment explanation
Indices: 1391013--1391075 Score: 58
Period size: 11 Copynumber: 5.6 Consensus size: 11
1391003 ATAAATTTTA
1391013 ATATATTTATTT
1 ATAT-TTTATTT
1391025 ATATTTTATTT
1 ATATTTTATTT
*
1391036 ATATAATTTTTTT
1 ATAT--TTTATTT
*
1391049 ATATTATA-TT
1 ATATTTTATTT
*
1391059 ATATTTTAATT
1 ATATTTTATTT
1391070 AT-TTTT
1 ATATTTT
1391076 TGATATTATG
Statistics
Matches: 44, Mismatches: 4, Indels: 8
0.79 0.07 0.14
Matches are distributed among these distances:
10 13 0.30
11 17 0.39
12 4 0.09
13 10 0.23
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (11 bp):
ATATTTTATTT
Found at i:1391036 original size:24 final size:24
Alignment explanation
Indices: 1391013--1391062 Score: 68
Period size: 24 Copynumber: 2.2 Consensus size: 24
1391003 ATAAATTTTA
*
1391013 ATAT-ATTTATTTATATTTTATTT
1 ATATAATTTATTTATATTATATTT
*
1391036 ATATAATTTTTTTATATTATA-TT
1 ATATAATTTATTTATATTATATTT
1391059 ATAT
1 ATAT
1391063 TTTAATTATT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
23 10 0.42
24 14 0.58
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (24 bp):
ATATAATTTATTTATATTATATTT
Found at i:1391055 original size:29 final size:29
Alignment explanation
Indices: 1391018--1391084 Score: 84
Period size: 29 Copynumber: 2.3 Consensus size: 29
1391008 TTTTAATATA
*
1391018 TTTAT-TTATATTTTA-TTTATATAATTTT
1 TTTATATTATATTATATTTTA-ATAATTTT
*
1391046 TTTATATTATATTATATTTTAATTATTTT
1 TTTATATTATATTATATTTTAATAATTTT
*
1391075 TTGATATTAT
1 TTTATATTAT
1391085 GCTTAAAATT
Statistics
Matches: 34, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
28 5 0.15
29 25 0.74
30 4 0.12
ACGTcount: A:0.30, C:0.00, G:0.01, T:0.69
Consensus pattern (29 bp):
TTTATATTATATTATATTTTAATAATTTT
Found at i:1392480 original size:28 final size:28
Alignment explanation
Indices: 1392448--1392503 Score: 112
Period size: 28 Copynumber: 2.0 Consensus size: 28
1392438 GCAAGTATCA
1392448 ACTTGATGCCTCTTTCCATTTACAAAAG
1 ACTTGATGCCTCTTTCCATTTACAAAAG
1392476 ACTTGATGCCTCTTTCCATTTACAAAAG
1 ACTTGATGCCTCTTTCCATTTACAAAAG
1392504 GCATTGTTAA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 28 1.00
ACGTcount: A:0.29, C:0.25, G:0.11, T:0.36
Consensus pattern (28 bp):
ACTTGATGCCTCTTTCCATTTACAAAAG
Found at i:1394322 original size:19 final size:19
Alignment explanation
Indices: 1394277--1394332 Score: 76
Period size: 19 Copynumber: 2.9 Consensus size: 19
1394267 CTGCCAGTTT
**
1394277 CATGTATCGATACAATTGTC
1 CATGTATCGATACAA-TGAA
1394297 CATGTATCGATACAATGAA
1 CATGTATCGATACAATGAA
*
1394316 TATGTATCGATACAATG
1 CATGTATCGATACAATG
1394333 TATCGATTCA
Statistics
Matches: 33, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
19 18 0.55
20 15 0.45
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (19 bp):
CATGTATCGATACAATGAA
Found at i:1394961 original size:22 final size:22
Alignment explanation
Indices: 1394936--1394977 Score: 75
Period size: 22 Copynumber: 1.9 Consensus size: 22
1394926 AGATAAACAT
1394936 ATTTCTCCCCCTTTATCAAAGC
1 ATTTCTCCCCCTTTATCAAAGC
*
1394958 ATTTCTCCCCCTTTGTCAAA
1 ATTTCTCCCCCTTTATCAAA
1394978 TCAAAAAAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.21, C:0.36, G:0.05, T:0.38
Consensus pattern (22 bp):
ATTTCTCCCCCTTTATCAAAGC
Done.