Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr03 ID=Chr03-JGI_221_v2.0
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: 45765648
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 655849 characters in sequence are not A, C, G, or T
File 10 of 150
Found at i:2871721 original size:14 final size:15
Alignment explanation
Indices: 2871697--2871730 Score: 52
Period size: 14 Copynumber: 2.3 Consensus size: 15
2871687 TTAACATTCT
2871697 ATAATTAATTTAATA
1 ATAATTAATTTAATA
*
2871712 TTAATT-ATTTAATA
1 ATAATTAATTTAATA
2871726 ATAAT
1 ATAAT
2871731 ATGAATAAAG
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
14 12 0.71
15 5 0.29
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (15 bp):
ATAATTAATTTAATA
Found at i:2873193 original size:3 final size:3
Alignment explanation
Indices: 2873139--2873239 Score: 123
Period size: 3 Copynumber: 33.3 Consensus size: 3
2873129 AATAAATACG
* * * * * *
2873139 ATA ATA ATCT ATA ATA CTA AGA ATA ATA GTA ATA TATA AT- ATA GTG
1 ATA ATA AT-A ATA ATA ATA ATA ATA ATA ATA ATA -ATA ATA ATA ATA
2873185 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
2873233 ATA ATA A
1 ATA ATA A
2873240 AGTTCACAAA
Statistics
Matches: 83, Mismatches: 12, Indels: 6
0.82 0.12 0.06
Matches are distributed among these distances:
2 2 0.02
3 76 0.92
4 5 0.06
ACGTcount: A:0.60, C:0.02, G:0.04, T:0.34
Consensus pattern (3 bp):
ATA
Found at i:2873328 original size:23 final size:23
Alignment explanation
Indices: 2873296--2873346 Score: 68
Period size: 23 Copynumber: 2.2 Consensus size: 23
2873286 GTTAAAACAT
*
2873296 AAAAATCATGATAA-AAAATGAAA
1 AAAAAACATGA-AACAAAATGAAA
*
2873319 AAAAAACATGAAACAAAATTAAA
1 AAAAAACATGAAACAAAATGAAA
2873342 AAAAA
1 AAAAA
2873347 TAGAGACAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
22 2 0.08
23 23 0.92
ACGTcount: A:0.75, C:0.06, G:0.06, T:0.14
Consensus pattern (23 bp):
AAAAAACATGAAACAAAATGAAA
Found at i:2877466 original size:18 final size:18
Alignment explanation
Indices: 2877443--2877490 Score: 96
Period size: 18 Copynumber: 2.7 Consensus size: 18
2877433 AAAATATGAG
2877443 AAATGATGTTCACATTTC
1 AAATGATGTTCACATTTC
2877461 AAATGATGTTCACATTTC
1 AAATGATGTTCACATTTC
2877479 AAATGATGTTCA
1 AAATGATGTTCA
2877491 AATTGATGGA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 30 1.00
ACGTcount: A:0.35, C:0.15, G:0.12, T:0.38
Consensus pattern (18 bp):
AAATGATGTTCACATTTC
Found at i:2878054 original size:72 final size:72
Alignment explanation
Indices: 2877937--2878100 Score: 208
Period size: 72 Copynumber: 2.3 Consensus size: 72
2877927 CGAAATATGT
* * * * *
2877937 TTTTATCAATAGTTATTTATGTTTGATTTTTGGTTATTGAATTTATGTTCTACTT-ATTTATGT-
1 TTTTATCAATAGTTGTTTATGTTTGATCTTTAGATAGTGAATTTATGTTCTACTTAATTT-T-TA
*
2878000 GT-AATCTAG
64 CTAAAT-TAG
* *
2878009 TTTTATTAATAGTTGTTTATGTTTGGTCTTTAGATAGTGAATTTATGTTCTACTTAATTTTTACT
1 TTTTATCAATAGTTGTTTATGTTTGATCTTTAGATAGTGAATTTATGTTCTACTTAATTTTTACT
2878074 AAATTAG
66 AAATTAG
2878081 TTTTATCAATAGTTGTTTAT
1 TTTTATCAATAGTTGTTTAT
2878101 ATGTGATTTT
Statistics
Matches: 80, Mismatches: 9, Indels: 6
0.84 0.09 0.06
Matches are distributed among these distances:
71 1 0.01
72 72 0.90
73 7 0.09
ACGTcount: A:0.25, C:0.05, G:0.13, T:0.56
Consensus pattern (72 bp):
TTTTATCAATAGTTGTTTATGTTTGATCTTTAGATAGTGAATTTATGTTCTACTTAATTTTTACT
AAATTAG
Found at i:2879498 original size:3 final size:3
Alignment explanation
Indices: 2879490--2879531 Score: 50
Period size: 3 Copynumber: 14.0 Consensus size: 3
2879480 GATGAGAAAG
* *
2879490 TGA TGA TGA TGA TGA TGA TGA CGA CGA TGA T-A GTGA TGA TGA
1 TGA TGA TGA TGA TGA TGA TGA TGA TGA TGA TGA -TGA TGA TGA
2879532 CGGTGAATCA
Statistics
Matches: 35, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
2 1 0.03
3 33 0.94
4 1 0.03
ACGTcount: A:0.33, C:0.05, G:0.33, T:0.29
Consensus pattern (3 bp):
TGA
Found at i:2884833 original size:12 final size:12
Alignment explanation
Indices: 2884816--2884845 Score: 53
Period size: 12 Copynumber: 2.6 Consensus size: 12
2884806 TATGTGTGTC
2884816 TGTATATATATA
1 TGTATATATATA
2884828 TGTATATATATA
1 TGTATATATATA
2884840 T-TATAT
1 TGTATAT
2884846 GAAGGAAAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
11 5 0.28
12 13 0.72
ACGTcount: A:0.40, C:0.00, G:0.07, T:0.53
Consensus pattern (12 bp):
TGTATATATATA
Found at i:2893138 original size:51 final size:51
Alignment explanation
Indices: 2893062--2893243 Score: 328
Period size: 51 Copynumber: 3.6 Consensus size: 51
2893052 CGGATCACAT
*
2893062 TTATCACTTGTCACTTGTCCCTGATCAGATAAGTGTAGCTAAAGCTACCAC
1 TTATCACTTGTCACTTGTCACTGATCAGATAAGTGTAGCTAAAGCTACCAC
*
2893113 TTATCACTTGTTACTTGTCACTGATCAGATAAGTGTAGCTAAAGCTACCAC
1 TTATCACTTGTCACTTGTCACTGATCAGATAAGTGTAGCTAAAGCTACCAC
* *
2893164 TTATCACTTGTCACCTGTCACTGATCAGATAAGTGTAGCTAAAGCTACTAC
1 TTATCACTTGTCACTTGTCACTGATCAGATAAGTGTAGCTAAAGCTACCAC
2893215 TTATCACTTGTCACTTGTCACTGATCAGA
1 TTATCACTTGTCACTTGTCACTGATCAGA
2893244 AGTACCCAAA
Statistics
Matches: 125, Mismatches: 6, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
51 125 1.00
ACGTcount: A:0.28, C:0.24, G:0.15, T:0.33
Consensus pattern (51 bp):
TTATCACTTGTCACTTGTCACTGATCAGATAAGTGTAGCTAAAGCTACCAC
Found at i:2903766 original size:102 final size:102
Alignment explanation
Indices: 2903590--2903820 Score: 390
Period size: 102 Copynumber: 2.3 Consensus size: 102
2903580 ATTGAATATA
* * *
2903590 AAGGGGGTTGCTAAGTGCTGATTCCCCCAAGGGGTTGCTAAGTGTTGATTCCTCGATTCATTGGC
1 AAGGGGGTTGCTAAGTGCTAATTCCCCCAAGGGGTTGCTAAGTGTTGATTCCCCGAATCATTGGC
* * *
2903655 GGTTGCTAAGTGTTGATTCCACCGTATTTTAAATGTG
66 GGTTGCTAAGTGCTGATCCCACCGTATCTTAAATGTG
*
2903692 AAGGGGGTTGCTAAGTGCTAATTCCCCCAAGGGGTTGCTAAGTGTTGATTCCCCGAATCATTGGT
1 AAGGGGGTTGCTAAGTGCTAATTCCCCCAAGGGGTTGCTAAGTGTTGATTCCCCGAATCATTGGC
2903757 GGTTGCTAAGTGCTGATCCCACCGTATCTTAAATGTG
66 GGTTGCTAAGTGCTGATCCCACCGTATCTTAAATGTG
*
2903794 AAAGGGGTTGCTAAGTGCTAATTCCCC
1 AAGGGGGTTGCTAAGTGCTAATTCCCC
2903821 GATTCATTGG
Statistics
Matches: 121, Mismatches: 8, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
102 121 1.00
ACGTcount: A:0.21, C:0.19, G:0.28, T:0.32
Consensus pattern (102 bp):
AAGGGGGTTGCTAAGTGCTAATTCCCCCAAGGGGTTGCTAAGTGTTGATTCCCCGAATCATTGGC
GGTTGCTAAGTGCTGATCCCACCGTATCTTAAATGTG
Found at i:2903846 original size:75 final size:76
Alignment explanation
Indices: 2903720--2903932 Score: 286
Period size: 75 Copynumber: 2.8 Consensus size: 76
2903710 TAATTCCCCC
*
2903720 AAGGGGTTGCTAAGTGTTGATTCCCCGAATCATTGGTGGTTGCTAAGTGCTGATCCCACCGTA-T
1 AAGGGGTTGCTAAGTGCTGATTCCCCGAATCATTGGTGGTTGCTAAGTGCTGAT-CCACCGTATT
2903784 CTTAAATGTG-A
65 CTTAAATGTGAA
* * ** *
2903795 AAGGGGTTGCTAAGTGCTAATTCCCCGATTCATTGGCAGTTGCTAAATGCTGATTCCACCGTATT
1 AAGGGGTTGCTAAGTGCTGATTCCCCGAATCATTGGTGGTTGCTAAGTGCTGA-TCCACCGTATT
* *
2903860 TTTGAATGTGAA
65 CTTAAATGTGAA
* * *
2903872 AAGAGGTTGCTAAATGCTGATTCCCTGAATCATTGGTGGTTGCTAAGTGCTGAATCCACCG
1 AAGGGGTTGCTAAGTGCTGATTCCCCGAATCATTGGTGGTTGCTAAGTGCTG-ATCCACCG
2903933 ATAACGGATA
Statistics
Matches: 118, Mismatches: 16, Indels: 6
0.84 0.11 0.04
Matches are distributed among these distances:
75 55 0.47
76 10 0.08
77 52 0.44
78 1 0.01
ACGTcount: A:0.24, C:0.19, G:0.25, T:0.32
Consensus pattern (76 bp):
AAGGGGTTGCTAAGTGCTGATTCCCCGAATCATTGGTGGTTGCTAAGTGCTGATCCACCGTATTC
TTAAATGTGAA
Found at i:2906097 original size:7 final size:7
Alignment explanation
Indices: 2906085--2906119 Score: 52
Period size: 7 Copynumber: 4.9 Consensus size: 7
2906075 TTCCATTTTA
2906085 TTTTTCT
1 TTTTTCT
2906092 TTTTTCT
1 TTTTTCT
2906099 TTTTTCT
1 TTTTTCT
*
2906106 TTTGTTGT
1 TTT-TTCT
2906114 TTTTTC
1 TTTTTC
2906120 AGATGTTTAT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
7 19 0.76
8 6 0.24
ACGTcount: A:0.00, C:0.11, G:0.06, T:0.83
Consensus pattern (7 bp):
TTTTTCT
Found at i:2909783 original size:21 final size:22
Alignment explanation
Indices: 2909758--2909799 Score: 61
Period size: 21 Copynumber: 2.0 Consensus size: 22
2909748 TTAATTTTTT
2909758 AAATATGTA-AATATT-AATATA
1 AAATAT-TATAATATTCAATATA
2909779 AAATATTATAATATTCAATAT
1 AAATATTATAATATTCAATAT
2909800 TATTAAACAT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
20 2 0.11
21 12 0.63
22 5 0.26
ACGTcount: A:0.55, C:0.02, G:0.02, T:0.40
Consensus pattern (22 bp):
AAATATTATAATATTCAATATA
Found at i:2913474 original size:13 final size:13
Alignment explanation
Indices: 2913431--2913467 Score: 65
Period size: 13 Copynumber: 2.8 Consensus size: 13
2913421 GTGTTGTGAA
*
2913431 AAAGTGCTTTTAC
1 AAAGTGTTTTTAC
2913444 AAAGTGTTTTTAC
1 AAAGTGTTTTTAC
2913457 AAAGTGTTTTT
1 AAAGTGTTTTT
2913468 GAAAAGTTTG
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
13 23 1.00
ACGTcount: A:0.30, C:0.08, G:0.16, T:0.46
Consensus pattern (13 bp):
AAAGTGTTTTTAC
Found at i:2919479 original size:3 final size:3
Alignment explanation
Indices: 2919473--2919509 Score: 65
Period size: 3 Copynumber: 12.0 Consensus size: 3
2919463 AGATTGGTTC
2919473 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATAA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA AT-A ATA ATA
2919510 TTTTCCATGC
Statistics
Matches: 33, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
3 30 0.91
4 3 0.09
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
ATA
Found at i:2920229 original size:18 final size:19
Alignment explanation
Indices: 2920206--2920244 Score: 53
Period size: 18 Copynumber: 2.1 Consensus size: 19
2920196 AAACGGATGG
2920206 TTTAATCTATTAT-GAATT
1 TTTAATCTATTATGGAATT
* *
2920224 TTTAATTTTTTATGGAATT
1 TTTAATCTATTATGGAATT
2920243 TT
1 TT
2920245 AATTTTAATT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
18 11 0.61
19 7 0.39
ACGTcount: A:0.28, C:0.03, G:0.08, T:0.62
Consensus pattern (19 bp):
TTTAATCTATTATGGAATT
Found at i:2920243 original size:19 final size:17
Alignment explanation
Indices: 2920215--2920250 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 17
2920205 GTTTAATCTA
2920215 TTATGAATTTTTAATTTT
1 TTATGAA-TTTTAATTTT
2920233 TTATGGAATTTTAATTTT
1 TTAT-GAATTTTAATTTT
2920251 AATTTTAGTT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 14 0.82
19 3 0.18
ACGTcount: A:0.28, C:0.00, G:0.08, T:0.64
Consensus pattern (17 bp):
TTATGAATTTTAATTTT
Found at i:2924242 original size:7 final size:7
Alignment explanation
Indices: 2924224--2924263 Score: 71
Period size: 7 Copynumber: 5.6 Consensus size: 7
2924214 AGCTCTTGCC
2924224 ACCCTAAA
1 ACCCT-AA
2924232 ACCCTAA
1 ACCCTAA
2924239 ACCCTAA
1 ACCCTAA
2924246 ACCCTAA
1 ACCCTAA
2924253 ACCCTAA
1 ACCCTAA
2924260 ACCC
1 ACCC
2924264 GCCGACTCGC
Statistics
Matches: 32, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
7 27 0.84
8 5 0.16
ACGTcount: A:0.42, C:0.45, G:0.00, T:0.12
Consensus pattern (7 bp):
ACCCTAA
Found at i:2925241 original size:63 final size:63
Alignment explanation
Indices: 2925174--2925345 Score: 220
Period size: 63 Copynumber: 2.7 Consensus size: 63
2925164 ACACACGTCC
* * * * **
2925174 GTGTCTCTAGCTCATATGTCTCTAATTCCAAAATAGTGAGTTACACGATCTGGACACATGC-T
1 GTGTCTCTAGCTCGTATGCCTCTAATTCTAAAACAGTGAGTTACACGATCTGGACACACACAT
* * * *
2925236 AGTGTCCCTAGCCCGTATGCCTCTAATTCTAAAACAGCGAGTTATACGATCTGGACACACACAT
1 -GTGTCTCTAGCTCGTATGCCTCTAATTCTAAAACAGTGAGTTACACGATCTGGACACACACAT
* *
2925300 GTGTCTCTAGCTTGTGTGCCTCTAATTCTAAAACAGTGAGTTACAC
1 GTGTCTCTAGCTCGTATGCCTCTAATTCTAAAACAGTGAGTTACAC
2925346 AACCTACTAT
Statistics
Matches: 92, Mismatches: 16, Indels: 2
0.84 0.15 0.02
Matches are distributed among these distances:
63 91 0.99
64 1 0.01
ACGTcount: A:0.27, C:0.24, G:0.18, T:0.30
Consensus pattern (63 bp):
GTGTCTCTAGCTCGTATGCCTCTAATTCTAAAACAGTGAGTTACACGATCTGGACACACACAT
Found at i:2925961 original size:15 final size:13
Alignment explanation
Indices: 2925918--2925955 Score: 60
Period size: 12 Copynumber: 2.9 Consensus size: 13
2925908 ATGAAGTAAC
2925918 AAAGAAAAGAAGAA
1 AAAG-AAAGAAGAA
2925932 AAAGAAA-AAGAA
1 AAAGAAAGAAGAA
2925944 AAAGAAAGAAGA
1 AAAGAAAGAAGA
2925956 GGAAAAAAAC
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
12 12 0.52
13 7 0.30
14 4 0.17
ACGTcount: A:0.79, C:0.00, G:0.21, T:0.00
Consensus pattern (13 bp):
AAAGAAAGAAGAA
Found at i:2927197 original size:28 final size:28
Alignment explanation
Indices: 2927157--2927214 Score: 116
Period size: 28 Copynumber: 2.1 Consensus size: 28
2927147 AGACAAGCAA
2927157 GAATTCTATGAAGACTTTCAATGTGATC
1 GAATTCTATGAAGACTTTCAATGTGATC
2927185 GAATTCTATGAAGACTTTCAATGTGATC
1 GAATTCTATGAAGACTTTCAATGTGATC
2927213 GA
1 GA
2927215 GTTTTCTTAT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 30 1.00
ACGTcount: A:0.33, C:0.14, G:0.19, T:0.34
Consensus pattern (28 bp):
GAATTCTATGAAGACTTTCAATGTGATC
Found at i:2930010 original size:31 final size:30
Alignment explanation
Indices: 2929971--2930033 Score: 108
Period size: 31 Copynumber: 2.1 Consensus size: 30
2929961 TTGCATCATC
2929971 AAAATTTTATAATTTTCAAATTCAAAGACA
1 AAAATTTTATAATTTTCAAATTCAAAGACA
*
2930001 AAAACTTTTATAATTTTCAAATTCAAATACA
1 AAAA-TTTTATAATTTTCAAATTCAAAGACA
2930032 AA
1 AA
2930034 TGATCTATTT
Statistics
Matches: 31, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
30 4 0.13
31 27 0.87
ACGTcount: A:0.51, C:0.11, G:0.02, T:0.37
Consensus pattern (30 bp):
AAAATTTTATAATTTTCAAATTCAAAGACA
Found at i:2933506 original size:122 final size:122
Alignment explanation
Indices: 2933315--2933695 Score: 496
Period size: 122 Copynumber: 3.1 Consensus size: 122
2933305 ACACAAATAC
* * ** *
2933315 ATATTTTCAGCTCAGACGAGCAATTGATATATCGAAGATACTTGTGACATAGGTTTAGCCTTAAT
1 ATATTTTCAGCTCGGACGAGCAATTGATATATCGAAGATACTTGTGACACAGGTTTAGCCTGGAC
2933380 TGGTAACCTGATGCCAATTTAAAGGTTTAGCTTGGACG-GATAACTTGACATGTATAT
66 TGGTAACCTGATGCCAATTTAAAGGTTTAGCTTGGACGAG-TAACTTGACATGTATAT
* * * * *
2933437 ATATTTTCAGCTTGGACGAGCAATTGATATATCAAATATACTTATGACACATGTTTAGCCTGGAC
1 ATATTTTCAGCTCGGACGAGCAATTGATATATCGAAGATACTTGTGACACAGGTTTAGCCTGGAC
* * **
2933502 TGGTAACTTGATGTCAATTTAAAGGTTTAGCCCGGACGAGTAACTTGACATTTGTATAT
66 TGGTAACCTGATGCCAATTTAAAGGTTTAGCTTGGACGAGTAACTTGACA--TGTATAT
* * *
2933561 ATATTTTTAGCTCGGACGAGTAATTGATGTATCGAAGATACTTGTGACACAGGTTTAGCC-GAGA
1 ATATTTTCAGCTCGGACGAGCAATTGATATATCGAAGATACTTGTGACACAGGTTTAGCCTG-GA
* * * * * *
2933625 CTGGTAACCTAATGCCAACTTAAATGTTTAGCTTGAACGAGTAACCTGACATGTGTAT
65 CTGGTAACCTGATGCCAATTTAAAGGTTTAGCTTGGACGAGTAACTTGACATGTATAT
*
2933683 ATATATTCAGCTC
1 ATATTTTCAGCTC
2933696 AGATAATTGG
Statistics
Matches: 221, Mismatches: 34, Indels: 8
0.84 0.13 0.03
Matches are distributed among these distances:
122 116 0.52
123 2 0.01
124 103 0.47
ACGTcount: A:0.31, C:0.16, G:0.20, T:0.33
Consensus pattern (122 bp):
ATATTTTCAGCTCGGACGAGCAATTGATATATCGAAGATACTTGTGACACAGGTTTAGCCTGGAC
TGGTAACCTGATGCCAATTTAAAGGTTTAGCTTGGACGAGTAACTTGACATGTATAT
Found at i:2933627 original size:124 final size:124
Alignment explanation
Indices: 2933315--2933689 Score: 499
Period size: 124 Copynumber: 3.0 Consensus size: 124
2933305 ACACAAATAC
* * *
2933315 ATATTTTCAGCTCAGACGAGCAATTGATATATCGAAGATACTTGTGACATAGGTTTAGCCTTA-A
1 ATATTTTCAGCTCGGACGAGCAATTGATATATCGAAGATACTTGTGACACAGGTTTAGCCTGAGA
*
2933379 TTGGTAACCTGATGCCAATTTAAAGGTTTAGCTTGGACG-GATAACTTGACA-TGTATAT
66 CTGGTAACCTGATGCCAATTTAAAGGTTTAGCTTGGACGAG-TAACTTGACATTGTATAT
* * * * *
2933437 ATATTTTCAGCTTGGACGAGCAATTGATATATCAAATATACTTATGACACATGTTTAGCCTG-GA
1 ATATTTTCAGCTCGGACGAGCAATTGATATATCGAAGATACTTGTGACACAGGTTTAGCCTGAGA
* * **
2933501 CTGGTAACTTGATGTCAATTTAAAGGTTTAGCCCGGACGAGTAACTTGACATTTGTATAT
66 CTGGTAACCTGATGCCAATTTAAAGGTTTAGCTTGGACGAGTAACTTGACA-TTGTATAT
* * *
2933561 ATATTTTTAGCTCGGACGAGTAATTGATGTATCGAAGATACTTGTGACACAGGTTTAGCC-GAGA
1 ATATTTTCAGCTCGGACGAGCAATTGATATATCGAAGATACTTGTGACACAGGTTTAGCCTGAGA
* * * * *
2933625 CTGGTAACCTAATGCCAACTTAAATGTTTAGCTTGAACGAGTAACCTGACATGTGTATAT
66 CTGGTAACCTGATGCCAATTTAAAGGTTTAGCTTGGACGAGTAACTTGACAT-TGTATAT
2933685 ATATT
1 ATATT
2933690 CAGCTCAGAT
Statistics
Matches: 217, Mismatches: 30, Indels: 10
0.84 0.12 0.04
Matches are distributed among these distances:
122 99 0.46
123 3 0.01
124 115 0.53
ACGTcount: A:0.31, C:0.15, G:0.20, T:0.34
Consensus pattern (124 bp):
ATATTTTCAGCTCGGACGAGCAATTGATATATCGAAGATACTTGTGACACAGGTTTAGCCTGAGA
CTGGTAACCTGATGCCAATTTAAAGGTTTAGCTTGGACGAGTAACTTGACATTGTATAT
Found at i:2944061 original size:19 final size:19
Alignment explanation
Indices: 2944025--2944079 Score: 60
Period size: 19 Copynumber: 2.9 Consensus size: 19
2944015 TTGCCCTTCC
2944025 CTTTTATT-TATTTATTTAT
1 CTTTTATTAT-TTTATTTAT
*
2944044 CTTTTATTATTTTGTTTAT
1 CTTTTATTATTTTATTTAT
*
2944063 -TTGTTTTTATTTTATTT
1 CTT-TTATTATTTTATTT
2944080 TATTTTGGTA
Statistics
Matches: 31, Mismatches: 3, Indels: 4
0.82 0.08 0.11
Matches are distributed among these distances:
18 2 0.06
19 28 0.90
20 1 0.03
ACGTcount: A:0.16, C:0.04, G:0.04, T:0.76
Consensus pattern (19 bp):
CTTTTATTATTTTATTTAT
Found at i:2944064 original size:27 final size:27
Alignment explanation
Indices: 2944026--2944078 Score: 70
Period size: 27 Copynumber: 2.0 Consensus size: 27
2944016 TGCCCTTCCC
*
2944026 TTTTATTTATTTATTTATCTTTTATTA
1 TTTTATTTATTTATTTATATTTTATTA
* * *
2944053 TTTTGTTTATTTGTTTTTATTTTATT
1 TTTTATTTATTTATTTATATTTTATT
2944079 TTATTTTGGT
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
27 22 1.00
ACGTcount: A:0.17, C:0.02, G:0.04, T:0.77
Consensus pattern (27 bp):
TTTTATTTATTTATTTATATTTTATTA
Found at i:2945745 original size:18 final size:20
Alignment explanation
Indices: 2945724--2945766 Score: 54
Period size: 18 Copynumber: 2.2 Consensus size: 20
2945714 ATTTTATTTA
2945724 ATTTTATGTT-TTTT-TTCT
1 ATTTTATGTTGTTTTGTTCT
* *
2945742 ATTTTTTGTTGTTTTGTTTT
1 ATTTTATGTTGTTTTGTTCT
2945762 ATTTT
1 ATTTT
2945767 TATTTTCTTG
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
18 9 0.43
19 4 0.19
20 8 0.38
ACGTcount: A:0.09, C:0.02, G:0.09, T:0.79
Consensus pattern (20 bp):
ATTTTATGTTGTTTTGTTCT
Found at i:2945748 original size:20 final size:20
Alignment explanation
Indices: 2945715--2945767 Score: 52
Period size: 21 Copynumber: 2.5 Consensus size: 20
2945705 TTATTTTTAA
* *
2945715 TTTTATTTAATTTTATGTTTTT
1 TTTTATTT--TTTGATGTTTTG
*
2945737 TTTCTATTTTTTGTTGTTTTG
1 TTT-TATTTTTTGATGTTTTG
2945758 TTTTATTTTT
1 TTTTATTTTT
2945768 ATTTTCTTGT
Statistics
Matches: 27, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
20 7 0.26
21 12 0.44
22 3 0.11
23 5 0.19
ACGTcount: A:0.11, C:0.02, G:0.08, T:0.79
Consensus pattern (20 bp):
TTTTATTTTTTGATGTTTTG
Found at i:2951345 original size:31 final size:31
Alignment explanation
Indices: 2951310--2951370 Score: 88
Period size: 31 Copynumber: 2.0 Consensus size: 31
2951300 GTTACAAAAT
* *
2951310 AGTTATTGAATTATTC-GAAAATTTTCATTTA
1 AGTTATTGAACTATTCAAAAAATTTT-ATTTA
2951341 AGTTATTGAACTATTCAAAAAATTTTATTT
1 AGTTATTGAACTATTCAAAAAATTTTATTT
2951371 GTCACTGGGC
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
31 19 0.70
32 8 0.30
ACGTcount: A:0.38, C:0.07, G:0.08, T:0.48
Consensus pattern (31 bp):
AGTTATTGAACTATTCAAAAAATTTTATTTA
Found at i:2953166 original size:20 final size:21
Alignment explanation
Indices: 2953138--2953176 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 21
2953128 ATAAATATTC
2953138 TAAAAATTCTAAAA-AATATA
1 TAAAAATTCTAAAACAATATA
*
2953158 TAAAGATTCTAAAACAATA
1 TAAAAATTCTAAAACAATA
2953177 ATTTTGAAGA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 13 0.76
21 4 0.24
ACGTcount: A:0.62, C:0.08, G:0.03, T:0.28
Consensus pattern (21 bp):
TAAAAATTCTAAAACAATATA
Found at i:2958828 original size:17 final size:16
Alignment explanation
Indices: 2958793--2958835 Score: 50
Period size: 17 Copynumber: 2.6 Consensus size: 16
2958783 GAAATCAGAT
*
2958793 TAATTTAAATTCGAAA
1 TAATTTAAATTCAAAA
*
2958809 TAATTTATATTTCAAAA
1 TAATTTA-AATTCAAAA
*
2958826 TAATTCAAAT
1 TAATTTAAAT
2958836 AAATAATTAG
Statistics
Matches: 22, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
16 9 0.41
17 13 0.59
ACGTcount: A:0.49, C:0.07, G:0.02, T:0.42
Consensus pattern (16 bp):
TAATTTAAATTCAAAA
Found at i:2961971 original size:12 final size:12
Alignment explanation
Indices: 2961954--2961991 Score: 51
Period size: 12 Copynumber: 3.2 Consensus size: 12
2961944 TATAGAAAAT
2961954 ATGATAATAATA
1 ATGATAATAATA
*
2961966 ATGATAGTAAATA
1 ATGATAAT-AATA
2961979 ATG-TAATAATA
1 ATGATAATAATA
2961990 AT
1 AT
2961992 AGTAATGGAA
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
11 6 0.26
12 10 0.43
13 7 0.30
ACGTcount: A:0.55, C:0.00, G:0.11, T:0.34
Consensus pattern (12 bp):
ATGATAATAATA
Found at i:2961977 original size:24 final size:24
Alignment explanation
Indices: 2961920--2961991 Score: 69
Period size: 25 Copynumber: 3.0 Consensus size: 24
2961910 TAGATATGAT
*
2961920 ATAGAAAAT-ATGTGAAT-GTATATG
1 ATAGAAAATAATGT-AATAATA-ATG
2961944 TATAGAAAAT-ATGATAATAATAATG
1 -ATAGAAAATAATG-TAATAATAATG
*
2961969 ATAGTAAATAATGTAATAATAAT
1 ATAGAAAATAATGTAATAATAAT
2961992 AGTAATGGAA
Statistics
Matches: 42, Mismatches: 2, Indels: 7
0.82 0.04 0.14
Matches are distributed among these distances:
24 18 0.43
25 21 0.50
26 3 0.07
ACGTcount: A:0.53, C:0.00, G:0.14, T:0.33
Consensus pattern (24 bp):
ATAGAAAATAATGTAATAATAATG
Found at i:2966174 original size:80 final size:80
Alignment explanation
Indices: 2966041--2966200 Score: 293
Period size: 80 Copynumber: 2.0 Consensus size: 80
2966031 TTCATAGTTA
* *
2966041 GTAAGAAGGGGATTGAGGTAGACCCGGACAAAGTGAAAGCAATCCGAGACCTACCTCCTCCACGC
1 GTAAGAAGAGGATTGAGGTAGACCCCGACAAAGTGAAAGCAATCCGAGACCTACCTCCTCCACGC
2966106 ACTCAGAAAGAAGTC
66 ACTCAGAAAGAAGTC
*
2966121 GTAAGAAGAGGATTGAGGTGGACCCCGACAAAGTGAAAGCAATCCGAGACCTACCTCCTCCACGC
1 GTAAGAAGAGGATTGAGGTAGACCCCGACAAAGTGAAAGCAATCCGAGACCTACCTCCTCCACGC
2966186 ACTCAGAAAGAAGTC
66 ACTCAGAAAGAAGTC
2966201 CACAGTTTCC
Statistics
Matches: 77, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
80 77 1.00
ACGTcount: A:0.35, C:0.26, G:0.26, T:0.14
Consensus pattern (80 bp):
GTAAGAAGAGGATTGAGGTAGACCCCGACAAAGTGAAAGCAATCCGAGACCTACCTCCTCCACGC
ACTCAGAAAGAAGTC
Found at i:2969990 original size:44 final size:44
Alignment explanation
Indices: 2969942--2970140 Score: 147
Period size: 44 Copynumber: 4.6 Consensus size: 44
2969932 AAGATAGCAG
* *
2969942 ATCTTATCTCTCTAAGCAGTAGAGGAGCAAATCGAAGACGACAA
1 ATCTTATCTCTCTAAGCAGTAGTGGAGCAGATCGAAGACGACAA
* * * ** * *
2969986 ATCTTATATTTCCAAG-A-TAGTGGGAAGCAGATTTAAG-CCACCCA
1 ATCTTATCTCTCTAAGCAGTAGT-GG-AGCAGATCGAAGACGA-CAA
** * * * * ** *
2970030 GCCTTATCTCCCTAAGCAGTAGTGGAGTAGGTTGAAGATAACAG
1 ATCTTATCTCTCTAAGCAGTAGTGGAGCAGATCGAAGACGACAA
*
2970074 ATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCGAAGACGACAA
1 ATCTTATCTCTCTAAGCAGTAGTGGAGCAGATCGAAGACGACAA
* *
2970118 ATCTTATTTTTCTAAG-A-TAGTGG
1 ATCTTATCTCTCTAAGCAGTAGTGG
2970141 GAAACAGATT
Statistics
Matches: 116, Mismatches: 33, Indels: 14
0.71 0.20 0.09
Matches are distributed among these distances:
42 9 0.08
43 6 0.05
44 93 0.80
45 4 0.03
46 4 0.03
ACGTcount: A:0.33, C:0.19, G:0.22, T:0.26
Consensus pattern (44 bp):
ATCTTATCTCTCTAAGCAGTAGTGGAGCAGATCGAAGACGACAA
Found at i:2970040 original size:132 final size:132
Alignment explanation
Indices: 2969800--2970200 Score: 604
Period size: 132 Copynumber: 3.0 Consensus size: 132
2969790 CAGATCAGTA
* * * * *
2969800 AAGATAGCAGATCTTACCTCTCTAAGCAATAGTGGAGCAGATCAAAGACGGCAAATCTTATCTTT
1 AAGATAGCAGATCTTATCTCTCTAAGCAGTAGTGGAGCAGATCGAAGACGACAAATCTTATATTT
* *
2969865 TCAAGGTAGTGGGAAACAGATTTAAGCCACCCAGCCTTGTCTCCCTGAGCAGCAGTGGAGTAGGT
66 CCAAGATAGTGGGAAACAGATTTAAGCCACCCAGCCTTGTCTCCCTGAGCAGCAGTGGAGTAGGT
2969930 TG
131 TG
* *
2969932 AAGATAGCAGATCTTATCTCTCTAAGCAGTAGAGGAGCAAATCGAAGACGACAAATCTTATATTT
1 AAGATAGCAGATCTTATCTCTCTAAGCAGTAGTGGAGCAGATCGAAGACGACAAATCTTATATTT
* * * *
2969997 CCAAGATAGTGGGAAGCAGATTTAAGCCACCCAGCCTTATCTCCCTAAGCAGTAGTGGAGTAGGT
66 CCAAGATAGTGGGAAACAGATTTAAGCCACCCAGCCTTGTCTCCCTGAGCAGCAGTGGAGTAGGT
2970062 TG
131 TG
* * *
2970064 AAGATAACAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCGAAGACGACAAATCTTATTTTT
1 AAGATAGCAGATCTTATCTCTCTAAGCAGTAGTGGAGCAGATCGAAGACGACAAATCTTATATTT
* * * * *
2970129 CTAAGATAGTGGGAAACAGATTTAAGCCACCAAGCCTTGTCTCCCTGAACAGCAGCGAAGTAGGT
66 CCAAGATAGTGGGAAACAGATTTAAGCCACCCAGCCTTGTCTCCCTGAGCAGCAGTGGAGTAGGT
*
2970194 TA
131 TG
2970196 AAGAT
1 AAGAT
2970201 CACAAATCCT
Statistics
Matches: 241, Mismatches: 28, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
132 241 1.00
ACGTcount: A:0.33, C:0.20, G:0.23, T:0.24
Consensus pattern (132 bp):
AAGATAGCAGATCTTATCTCTCTAAGCAGTAGTGGAGCAGATCGAAGACGACAAATCTTATATTT
CCAAGATAGTGGGAAACAGATTTAAGCCACCCAGCCTTGTCTCCCTGAGCAGCAGTGGAGTAGGT
TG
Found at i:2971646 original size:20 final size:21
Alignment explanation
Indices: 2971621--2971667 Score: 78
Period size: 20 Copynumber: 2.3 Consensus size: 21
2971611 TTATTGTTAC
*
2971621 TTTTATTTTTATAC-TTATTT
1 TTTTATTTTTATACTTTATGT
2971641 TTTTATTTTTATACTTTATGT
1 TTTTATTTTTATACTTTATGT
2971662 TTTTAT
1 TTTTAT
2971668 ATACATGCAT
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
20 14 0.56
21 11 0.44
ACGTcount: A:0.19, C:0.04, G:0.02, T:0.74
Consensus pattern (21 bp):
TTTTATTTTTATACTTTATGT
Found at i:2973728 original size:2 final size:2
Alignment explanation
Indices: 2973721--2973750 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
2973711 TTAGTCATTA
2973721 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
2973751 GGTTTACTTT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2975234 original size:31 final size:31
Alignment explanation
Indices: 2975196--2975256 Score: 95
Period size: 31 Copynumber: 2.0 Consensus size: 31
2975186 GTATCAAAAC
*
2975196 AAACATTAAAACCAAACTCAAATACCAAATT
1 AAACATTAAAACCAAACACAAATACCAAATT
* *
2975227 AAACATTAAAATCAAACACAAGTACCAAAT
1 AAACATTAAAACCAAACACAAATACCAAAT
2975257 GGTATATTAA
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
31 27 1.00
ACGTcount: A:0.59, C:0.21, G:0.02, T:0.18
Consensus pattern (31 bp):
AAACATTAAAACCAAACACAAATACCAAATT
Found at i:2976869 original size:19 final size:18
Alignment explanation
Indices: 2976846--2976892 Score: 60
Period size: 19 Copynumber: 2.6 Consensus size: 18
2976836 TAAGTTGTAC
2976846 TTTTAATTTTTTATATAA
1 TTTTAATTTTTTATATAA
**
2976864 TATTTAATAATTTATATAA
1 T-TTTAATTTTTTATATAA
2976883 TTTT-ATTTTT
1 TTTTAATTTTT
2976893 CTAATTTTCT
Statistics
Matches: 24, Mismatches: 4, Indels: 3
0.77 0.13 0.10
Matches are distributed among these distances:
17 4 0.17
18 4 0.17
19 16 0.67
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (18 bp):
TTTTAATTTTTTATATAA
Found at i:2976905 original size:22 final size:22
Alignment explanation
Indices: 2976871--2976912 Score: 59
Period size: 22 Copynumber: 1.9 Consensus size: 22
2976861 TAATATTTAA
2976871 TAATTTATATAATTTTATTTTTC
1 TAATTTATATAATTTT-TTTTTC
*
2976894 TAATTT-TCTAATTTTTTTT
1 TAATTTATATAATTTTTTTT
2976913 GTAATATTTT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 4 0.22
22 8 0.44
23 6 0.33
ACGTcount: A:0.26, C:0.05, G:0.00, T:0.69
Consensus pattern (22 bp):
TAATTTATATAATTTTTTTTTC
Found at i:2977541 original size:29 final size:30
Alignment explanation
Indices: 2977480--2977543 Score: 78
Period size: 29 Copynumber: 2.2 Consensus size: 30
2977470 AAATATATTT
**
2977480 TTAAGGGCTTAATTGATTGGCAACTTTGGA
1 TTAAGGGCTTAATTGATTGGCAACTTTCAA
*
2977510 TTAAGGG-TTAAATTGATT-GCAATTTTCAA
1 TTAAGGGCTT-AATTGATTGGCAACTTTCAA
2977539 TTAAG
1 TTAAG
2977544 AATTTAATTT
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
29 15 0.50
30 15 0.50
ACGTcount: A:0.31, C:0.08, G:0.22, T:0.39
Consensus pattern (30 bp):
TTAAGGGCTTAATTGATTGGCAACTTTCAA
Found at i:2977552 original size:29 final size:30
Alignment explanation
Indices: 2977488--2977552 Score: 69
Period size: 29 Copynumber: 2.2 Consensus size: 30
2977478 TTTTAAGGGC
** **
2977488 TTAATTGATTGGCAACTTTGGATTAAGGGT
1 TTAATTGATTGGCAACTTTCAATTAAGAAT
* *
2977518 TAAATTGATT-GCAATTTTCAATTAAGAAT
1 TTAATTGATTGGCAACTTTCAATTAAGAAT
2977547 TTAATT
1 TTAATT
2977553 TATTTTTTAA
Statistics
Matches: 28, Mismatches: 7, Indels: 1
0.78 0.19 0.03
Matches are distributed among these distances:
29 19 0.68
30 9 0.32
ACGTcount: A:0.34, C:0.06, G:0.17, T:0.43
Consensus pattern (30 bp):
TTAATTGATTGGCAACTTTCAATTAAGAAT
Found at i:2987224 original size:183 final size:183
Alignment explanation
Indices: 2986999--2987350 Score: 492
Period size: 183 Copynumber: 1.9 Consensus size: 183
2986989 GTGGCTTTAA
* * * * *
2986999 TCTACTCCACTGTAACTTCAGGGAGATAAGACTTGCTATGGTAGATTTAATCCGACCTACTGTAA
1 TCTACTCCACTGCAACTTCAGAGAGATAAAACTTGATATGGTAGATTTAATCCGACCTACTGCAA
* * * *
2987064 CCTCAAAGGTA-GATGATTCACCGTTTTAATCCGCTCCACTATAACTTCA-AGGAGATAGGATTA
66 CCTCAAAGGCATG-TGATTCACCGTTTTAATCCGCTCCACTACAAATTCAGA-GAGATAGGATCA
* * * *
2987127 GTAGCTTCAATCTGCTCCGCTTCAATTTCAGGGAGATAAGACTTGCTATATTCAG
129 GTAGCTTCAATCTGCTCCACTGCAACTTCAGGAAGATAAGACTTGCTATATTCAG
* *
2987182 TCTACTCCACTGCAACTTCAGAGCGATAAAACTTGATATGGTAGATTTAATCTGACCTACTGCAA
1 TCTACTCCACTGCAACTTCAGAGAGATAAAACTTGATATGGTAGATTTAATCCGACCTACTGCAA
* * * *
2987247 CCTCAGAGGCATGTGATTCATCGTTTTAATCCGCTCCACTGCAAATTCAGAGAGATAGGATCGGT
66 CCTCAAAGGCATGTGATTCACCGTTTTAATCCGCTCCACTACAAATTCAGAGAGATAGGATCAGT
*
2987312 GGCTTCAATCTGCTCCACTGCAACTTCAGGAAGATAAGA
131 AGCTTCAATCTGCTCCACTGCAACTTCAGGAAGATAAGA
2987351 TCTACCATAA
Statistics
Matches: 147, Mismatches: 20, Indels: 4
0.86 0.12 0.02
Matches are distributed among these distances:
183 145 0.99
184 2 0.01
ACGTcount: A:0.29, C:0.23, G:0.19, T:0.29
Consensus pattern (183 bp):
TCTACTCCACTGCAACTTCAGAGAGATAAAACTTGATATGGTAGATTTAATCCGACCTACTGCAA
CCTCAAAGGCATGTGATTCACCGTTTTAATCCGCTCCACTACAAATTCAGAGAGATAGGATCAGT
AGCTTCAATCTGCTCCACTGCAACTTCAGGAAGATAAGACTTGCTATATTCAG
Found at i:2987663 original size:89 final size:88
Alignment explanation
Indices: 2987362--2987666 Score: 269
Period size: 89 Copynumber: 3.4 Consensus size: 88
2987352 CTACCATAAT
* * * * * * * *
2987362 TTGTAGCTTTAATCTGTTCCACTGCAA-TGCCAAGGAAATAAGATTCGCTGTCTTTAGTCTGCTC
1 TTGTATCTTCAATCTGCTCCACTGCAACT-TCAGGGAAATAAGATTCGCTATCTTCAGTTTGCT-
2987426 CACTGCAACTTCAGAGAGATAAGAC
64 CACTGCAACTTCAGAGAGATAAGAC
* * * * * * * * ** *
2987451 TTGTAACTTCAACCTACTCCATTGCAACTTCAAGGAGATAAGGTTTGCTATGATCTG-TT-CT-A
1 TTGTATCTTCAATCTGCTCCACTGCAACTTCAGGGAAATAAGATTCGCTATCTTCAGTTTGCTCA
2987513 CTGCAACTTCAGAGAGATAAGATC
66 CTGCAACTTCAGAGAGATAAGA-C
* * *
2987537 TTTTCTTTATAGCTTTAATCTGTTCCACTGCAACTTCAGGGAAATAAGATTCGCTATCTTCAGTT
1 ---T-TGTAT--CTTCAATCTGCTCCACTGCAACTTCAGGGAAATAAGATTCGCTATCTTCAGTT
2987602 TGCTCGACTGCAACTTCATG-GAGATAAGAC
60 TGCTC-ACTGCAACTTCA-GAGAGATAAGAC
*
2987632 TTGTATCTTCAATCTGCCCCACTGCAACTTCAGGG
1 TTGTATCTTCAATCTGCTCCACTGCAACTTCAGGG
2987667 GGGTAAGATT
Statistics
Matches: 169, Mismatches: 34, Indels: 26
0.74 0.15 0.11
Matches are distributed among these distances:
85 23 0.14
86 1 0.01
87 2 0.01
88 1 0.01
89 67 0.40
90 4 0.02
91 4 0.02
92 40 0.24
93 2 0.01
94 2 0.01
95 1 0.01
96 21 0.12
97 1 0.01
ACGTcount: A:0.27, C:0.23, G:0.18, T:0.32
Consensus pattern (88 bp):
TTGTATCTTCAATCTGCTCCACTGCAACTTCAGGGAAATAAGATTCGCTATCTTCAGTTTGCTCA
CTGCAACTTCAGAGAGATAAGAC
Found at i:2987674 original size:44 final size:45
Alignment explanation
Indices: 2987399--2987676 Score: 149
Period size: 44 Copynumber: 6.2 Consensus size: 45
2987389 TGCCAAGGAA
* * * * *
2987399 ATAAGATTCGCTGTCTTTAGTCTGCTCCACTGCAACTTCAGAGAG
1 ATAAGATTCGCTATCTTCAATCTGCCCCACTGCAACTTCAGGGAG
* * * * * *
2987444 ATAAGACTT-G-TAACTTCAACCTACTCCATTGCAACTTCAAGGAG
1 ATAAGA-TTCGCTATCTTCAATCTGCCCCACTGCAACTTCAGGGAG
* * * ** * *
2987488 ATAAGGTTTGCTA---T-GATCTGTTCTACTGCAACTTCAGAGAG
1 ATAAGATTCGCTATCTTCAATCTGCCCCACTGCAACTTCAGGGAG
** * ** *
2987529 ATAAGATCTTTTCTTTATAGCTTTAATCTGTTCCACTGCAACTTCAGGGAA
1 ATAAGA----TTCGCTAT--CTTCAATCTGCCCCACTGCAACTTCAGGGAG
* * * * *
2987580 ATAAGATTCGCTATCTTCAGTTTGCTCGACTGCAACTTCATGGAG
1 ATAAGATTCGCTATCTTCAATCTGCCCCACTGCAACTTCAGGGAG
*
2987625 ATAAGACTT-G-TATCTTCAATCTGCCCCACTGCAACTTCAGGGGG
1 ATAAGA-TTCGCTATCTTCAATCTGCCCCACTGCAACTTCAGGGAG
*
2987669 GTAAGATT
1 ATAAGATT
2987677 AGTGGCTTTA
Statistics
Matches: 177, Mismatches: 42, Indels: 30
0.71 0.17 0.12
Matches are distributed among these distances:
41 24 0.14
42 1 0.01
43 4 0.02
44 64 0.36
45 44 0.25
46 4 0.02
47 6 0.03
50 1 0.01
51 29 0.16
ACGTcount: A:0.27, C:0.22, G:0.18, T:0.32
Consensus pattern (45 bp):
ATAAGATTCGCTATCTTCAATCTGCCCCACTGCAACTTCAGGGAG
Found at i:2988654 original size:14 final size:13
Alignment explanation
Indices: 2988607--2988654 Score: 51
Period size: 15 Copynumber: 3.3 Consensus size: 13
2988597 TGGCCTCTCC
2988607 TTTTTCTTTTTTTCT
1 TTTTTC-TTTTTT-T
2988622 TTTTTCTTTTTTT
1 TTTTTCTTTTTTT
2988635 TGTTTTCGTTTCTTTT
1 T-TTTTC-TTT-TTTT
2988651 TTTT
1 TTTT
2988655 AAAATGAAGT
Statistics
Matches: 30, Mismatches: 0, Indels: 6
0.83 0.00 0.17
Matches are distributed among these distances:
13 2 0.07
14 11 0.37
15 12 0.40
16 5 0.17
ACGTcount: A:0.00, C:0.10, G:0.04, T:0.85
Consensus pattern (13 bp):
TTTTTCTTTTTTT
Found at i:3001631 original size:20 final size:19
Alignment explanation
Indices: 3001591--3001631 Score: 55
Period size: 19 Copynumber: 2.1 Consensus size: 19
3001581 TTAATGATAA
* *
3001591 AATATTTAAAGAATAATAT
1 AATATTAAAAGAATAAAAT
3001610 AATATTAAAAGAAATAAAAT
1 AATATTAAAAG-AATAAAAT
3001630 AA
1 AA
3001632 AATAATTAAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
19 10 0.53
20 9 0.47
ACGTcount: A:0.66, C:0.00, G:0.05, T:0.29
Consensus pattern (19 bp):
AATATTAAAAGAATAAAAT
Found at i:3007182 original size:64 final size:64
Alignment explanation
Indices: 3007113--3007240 Score: 213
Period size: 64 Copynumber: 2.0 Consensus size: 64
3007103 AAAATGATTA
* * *
3007113 AATTAAAATACAGAGATTAAATCCACAGTTTTTA-TAAAGTTAAAATTTAACCTTAATTTATTTG
1 AATTAAAATACAAAAATTAAATCCACAATTTTTATTAAA-TTAAAATTTAACCTTAATTTATTTG
3007177 AATTAAAATACAAAAATTAAATCCACAATTTTTATTAAATTAAAATTTAACCTTAATTTATTTG
1 AATTAAAATACAAAAATTAAATCCACAATTTTTATTAAATTAAAATTTAACCTTAATTTATTTG
3007241 CCTATCTTTT
Statistics
Matches: 60, Mismatches: 3, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
64 56 0.93
65 4 0.07
ACGTcount: A:0.46, C:0.09, G:0.05, T:0.40
Consensus pattern (64 bp):
AATTAAAATACAAAAATTAAATCCACAATTTTTATTAAATTAAAATTTAACCTTAATTTATTTG
Found at i:3009734 original size:32 final size:32
Alignment explanation
Indices: 3009696--3009761 Score: 132
Period size: 32 Copynumber: 2.1 Consensus size: 32
3009686 TACCTTGTTG
3009696 TTTTATGTAATCTATGCAAGTTGTTGGTTATC
1 TTTTATGTAATCTATGCAAGTTGTTGGTTATC
3009728 TTTTATGTAATCTATGCAAGTTGTTGGTTATC
1 TTTTATGTAATCTATGCAAGTTGTTGGTTATC
3009760 TT
1 TT
3009762 AGGATTGAGG
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 34 1.00
ACGTcount: A:0.21, C:0.09, G:0.18, T:0.52
Consensus pattern (32 bp):
TTTTATGTAATCTATGCAAGTTGTTGGTTATC
Found at i:3012744 original size:30 final size:30
Alignment explanation
Indices: 3012710--3012766 Score: 78
Period size: 30 Copynumber: 1.9 Consensus size: 30
3012700 TGAACTTAAA
*
3012710 AATTATTTTCATATTGAGGCCTGAATTAGC
1 AATTATTCTCATATTGAGGCCTGAATTAGC
* * *
3012740 AATTATTCTCGTATTGGGGCTTGAATT
1 AATTATTCTCATATTGAGGCCTGAATT
3012767 TTTTTGTCCA
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
30 23 1.00
ACGTcount: A:0.26, C:0.12, G:0.19, T:0.42
Consensus pattern (30 bp):
AATTATTCTCATATTGAGGCCTGAATTAGC
Found at i:3016367 original size:6 final size:6
Alignment explanation
Indices: 3016356--3016384 Score: 58
Period size: 6 Copynumber: 4.8 Consensus size: 6
3016346 ACTCAACTGG
3016356 TGGAGA TGGAGA TGGAGA TGGAGA TGGAG
1 TGGAGA TGGAGA TGGAGA TGGAGA TGGAG
3016385 CTCCATTATT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.31, C:0.00, G:0.52, T:0.17
Consensus pattern (6 bp):
TGGAGA
Found at i:3022485 original size:23 final size:23
Alignment explanation
Indices: 3022435--3022613 Score: 240
Period size: 23 Copynumber: 8.0 Consensus size: 23
3022425 CCTGATCAGT
3022435 ATACGACACAT-AAGTGCCTG--
1 ATACGACACATAAAGTGCCTGAA
* * *
3022455 ATACGACACATGAGGTGCCTAAA
1 ATACGACACATAAAGTGCCTGAA
* *
3022478 ATACGACACATGAGGTGCCTGAA
1 ATACGACACATAAAGTGCCTGAA
*
3022501 ATACGACACATAAAGTGCCTGAT
1 ATACGACACATAAAGTGCCTGAA
* * *
3022524 ATACAACACATAAAATACCTGAA
1 ATACGACACATAAAGTGCCTGAA
*
3022547 ATATGACACATAAAGTGCCTGAA
1 ATACGACACATAAAGTGCCTGAA
3022570 ATA-GACACATAAAGTGCCTGAA
1 ATACGACACATAAAGTGCCTGAA
3022592 ATACGACACATAAAGTGCCTGA
1 ATACGACACATAAAGTGCCTGA
3022614 TCGGCATAGC
Statistics
Matches: 141, Mismatches: 14, Indels: 5
0.88 0.09 0.03
Matches are distributed among these distances:
20 11 0.08
21 7 0.05
22 22 0.16
23 101 0.72
ACGTcount: A:0.42, C:0.21, G:0.18, T:0.19
Consensus pattern (23 bp):
ATACGACACATAAAGTGCCTGAA
Found at i:3025541 original size:31 final size:30
Alignment explanation
Indices: 3025506--3025608 Score: 102
Period size: 31 Copynumber: 3.4 Consensus size: 30
3025496 TGTTTTAATG
3025506 AATTTAATATTTATCTAGATATTATTTTATT
1 AATTTAATATTTATCTAGATA-TATTTTATT
* * *
3025537 AATTTAATATTAATAT-GATATA-TTAACTTT
1 AATTTAATATTTATCTAGATATATTTTA--TT
* *
3025567 AATTTAATATTTATCTAGATAATGTTTTAGT
1 AATTTAATATTTATCTAGAT-ATATTTTATT
*
3025598 AATTTGATATT
1 AATTTAATATT
3025609 AATGTGATTA
Statistics
Matches: 58, Mismatches: 9, Indels: 10
0.75 0.12 0.13
Matches are distributed among these distances:
28 3 0.05
29 2 0.03
30 20 0.34
31 28 0.48
32 2 0.03
33 3 0.05
ACGTcount: A:0.38, C:0.03, G:0.06, T:0.53
Consensus pattern (30 bp):
AATTTAATATTTATCTAGATATATTTTATT
Found at i:3030692 original size:10 final size:10
Alignment explanation
Indices: 3030665--3030707 Score: 50
Period size: 10 Copynumber: 4.3 Consensus size: 10
3030655 CTCTGTCAAT
*
3030665 AAAAAATACA
1 AAAAAATTCA
3030675 AAAAAATTCA
1 AAAAAATTCA
**
3030685 AAAAAATTTT
1 AAAAAATTCA
*
3030695 CAAAAATTCA
1 AAAAAATTCA
3030705 AAA
1 AAA
3030708 TATTTATAAA
Statistics
Matches: 26, Mismatches: 7, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
10 26 1.00
ACGTcount: A:0.70, C:0.09, G:0.00, T:0.21
Consensus pattern (10 bp):
AAAAAATTCA
Found at i:3030712 original size:19 final size:20
Alignment explanation
Indices: 3030676--3030728 Score: 65
Period size: 19 Copynumber: 2.7 Consensus size: 20
3030666 AAAAATACAA
*
3030676 AAAAATTCAAAAAAATTT-T
1 AAAAATTCAAAAATATTTAT
3030695 CAAAAATTC-AAAATATTTAT
1 -AAAAATTCAAAAATATTTAT
*
3030715 AAAAATTCTAAAAT
1 AAAAATTCAAAAAT
3030729 TTATATTTTT
Statistics
Matches: 30, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
19 16 0.53
20 14 0.47
ACGTcount: A:0.60, C:0.08, G:0.00, T:0.32
Consensus pattern (20 bp):
AAAAATTCAAAAATATTTAT
Found at i:3031976 original size:14 final size:14
Alignment explanation
Indices: 3031927--3031989 Score: 51
Period size: 14 Copynumber: 4.6 Consensus size: 14
3031917 ACTTCATTTA
*
3031927 ATTATTATTACTAAT
1 ATTATTATTA-TATT
* *
3031942 ATGAGTATTA-A-T
1 ATTATTATTATATT
* *
3031954 ATTAATATTATGTT
1 ATTATTATTATATT
3031968 ATTATTATTATATT
1 ATTATTATTATATT
3031982 A-TATTATT
1 ATTATTATT
3031990 TTACTCATTA
Statistics
Matches: 39, Mismatches: 7, Indels: 6
0.75 0.13 0.12
Matches are distributed among these distances:
12 9 0.23
13 8 0.21
14 14 0.36
15 8 0.21
ACGTcount: A:0.38, C:0.02, G:0.05, T:0.56
Consensus pattern (14 bp):
ATTATTATTATATT
Found at i:3043115 original size:14 final size:15
Alignment explanation
Indices: 3043087--3043136 Score: 68
Period size: 15 Copynumber: 3.4 Consensus size: 15
3043077 ATTCATCTAT
3043087 TTATTTTATTTATTA
1 TTATTTTATTTATTA
3043102 TTATTTTA-TTATTA
1 TTATTTTATTTATTA
*
3043116 TTA-TCTATTTATTTA
1 TTATTTTATTTA-TTA
3043131 TTATTT
1 TTATTT
3043137 ACTTATTACT
Statistics
Matches: 30, Mismatches: 2, Indels: 5
0.81 0.05 0.14
Matches are distributed among these distances:
13 3 0.10
14 12 0.40
15 14 0.47
16 1 0.03
ACGTcount: A:0.26, C:0.02, G:0.00, T:0.72
Consensus pattern (15 bp):
TTATTTTATTTATTA
Found at i:3043124 original size:21 final size:21
Alignment explanation
Indices: 3043084--3043144 Score: 65
Period size: 21 Copynumber: 2.9 Consensus size: 21
3043074 TTCATTCATC
3043084 TATTTATT-TTATTTATTA-T
1 TATTTATTATTATTTATTATT
3043103 TATTTTATTATTA-TTATCTATT
1 TA-TTTATTATTATTTAT-TATT
*
3043125 TATTTATTATTTACTTATTA
1 TATTTATTA-TTATTTATTA
3043145 CTCTTTTTCT
Statistics
Matches: 36, Mismatches: 0, Indels: 9
0.80 0.00 0.20
Matches are distributed among these distances:
19 2 0.06
20 10 0.28
21 12 0.33
22 8 0.22
23 4 0.11
ACGTcount: A:0.28, C:0.03, G:0.00, T:0.69
Consensus pattern (21 bp):
TATTTATTATTATTTATTATT
Found at i:3043127 original size:11 final size:10
Alignment explanation
Indices: 3043084--3043144 Score: 67
Period size: 11 Copynumber: 6.2 Consensus size: 10
3043074 TTCATTCATC
3043084 TATTTATT-T
1 TATTTATTAT
3043093 TATTTATTAT
1 TATTTATTAT
3043103 TA-TT-TTAT
1 TATTTATTAT
3043111 TA-TTATTAT
1 TATTTATTAT
3043120 CTATTTATTTAT
1 -TATTTA-TTAT
3043132 TATTTACTTAT
1 TATTTA-TTAT
3043143 TA
1 TA
3043145 CTCTTTTTCT
Statistics
Matches: 46, Mismatches: 1, Indels: 8
0.84 0.02 0.15
Matches are distributed among these distances:
8 8 0.17
9 14 0.30
10 5 0.11
11 15 0.33
12 4 0.09
ACGTcount: A:0.28, C:0.03, G:0.00, T:0.69
Consensus pattern (10 bp):
TATTTATTAT
Found at i:3043403 original size:14 final size:14
Alignment explanation
Indices: 3043354--3043416 Score: 51
Period size: 14 Copynumber: 4.6 Consensus size: 14
3043344 ACTTCATTTA
*
3043354 ATTATTATTACTAAT
1 ATTATTATTA-TATT
* *
3043369 ATGAGTATTA-A-T
1 ATTATTATTATATT
* *
3043381 ATTAATATTATGTT
1 ATTATTATTATATT
3043395 ATTATTATTATATT
1 ATTATTATTATATT
3043409 A-TATTATT
1 ATTATTATT
3043417 TTACTCATTA
Statistics
Matches: 39, Mismatches: 7, Indels: 6
0.75 0.13 0.12
Matches are distributed among these distances:
12 9 0.23
13 8 0.21
14 14 0.36
15 8 0.21
ACGTcount: A:0.38, C:0.02, G:0.05, T:0.56
Consensus pattern (14 bp):
ATTATTATTATATT
Found at i:3047010 original size:19 final size:20
Alignment explanation
Indices: 3046976--3047023 Score: 57
Period size: 19 Copynumber: 2.5 Consensus size: 20
3046966 TTTTTTTTTA
3046976 CATT-CATTTCATTCATCA-G
1 CATTACATTTCATTCAT-ATG
3046995 CATTACATTTCA-TCATATG
1 CATTACATTTCATTCATATG
*
3047014 CATTAAATTT
1 CATTACATTT
3047024 TACAAAAAAA
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
18 1 0.04
19 18 0.69
20 7 0.27
ACGTcount: A:0.31, C:0.21, G:0.04, T:0.44
Consensus pattern (20 bp):
CATTACATTTCATTCATATG
Found at i:3051385 original size:18 final size:19
Alignment explanation
Indices: 3051334--3051388 Score: 69
Period size: 19 Copynumber: 2.9 Consensus size: 19
3051324 ATTACAAAAT
3051334 AATTCAAAATAGTTT-TCAAA
1 AATTCAAAATA-TTTAT-AAA
3051354 AATTCAAAATATTTATAAA
1 AATTCAAAATATTTATAAA
*
3051373 AATTCTAAA-ATTTATA
1 AATTCAAAATATTTATA
3051389 TTTTTAAAAC
Statistics
Matches: 33, Mismatches: 1, Indels: 4
0.87 0.03 0.11
Matches are distributed among these distances:
18 7 0.21
19 14 0.42
20 12 0.36
ACGTcount: A:0.53, C:0.07, G:0.02, T:0.38
Consensus pattern (19 bp):
AATTCAAAATATTTATAAA
Found at i:3063492 original size:17 final size:18
Alignment explanation
Indices: 3063440--3063493 Score: 58
Period size: 20 Copynumber: 2.9 Consensus size: 18
3063430 ATTACAAAAT
3063440 AATTCAAAATAGTTT-TCAAA
1 AATTCAAAATA-TTTAT--AA
3063460 AATTCAAAATATTTATAA
1 AATTCAAAATATTTATAA
*
3063478 AATTCTAAA-ATTTATA
1 AATTCAAAATATTTATA
3063494 TTTTTAAAAC
Statistics
Matches: 32, Mismatches: 1, Indels: 5
0.84 0.03 0.13
Matches are distributed among these distances:
17 7 0.22
18 10 0.31
19 3 0.09
20 12 0.38
ACGTcount: A:0.52, C:0.07, G:0.02, T:0.39
Consensus pattern (18 bp):
AATTCAAAATATTTATAA
Found at i:3066584 original size:14 final size:14
Alignment explanation
Indices: 3066535--3066597 Score: 51
Period size: 14 Copynumber: 4.6 Consensus size: 14
3066525 ACTTCATTTA
*
3066535 ATTATTATTACTAAT
1 ATTATTATTA-TATT
* *
3066550 ATGAGTATTA-A-T
1 ATTATTATTATATT
* *
3066562 ATTAATATTATGTT
1 ATTATTATTATATT
3066576 ATTATTATTATATT
1 ATTATTATTATATT
3066590 A-TATTATT
1 ATTATTATT
3066598 TTACTCATTA
Statistics
Matches: 39, Mismatches: 7, Indels: 6
0.75 0.13 0.12
Matches are distributed among these distances:
12 9 0.23
13 8 0.21
14 14 0.36
15 8 0.21
ACGTcount: A:0.38, C:0.02, G:0.05, T:0.56
Consensus pattern (14 bp):
ATTATTATTATATT
Found at i:3076989 original size:43 final size:43
Alignment explanation
Indices: 3076950--3077070 Score: 147
Period size: 43 Copynumber: 2.8 Consensus size: 43
3076940 AATGCCATGT
**
3076950 CCCAGACATGGTCTTACATGGAAATCTTGTAA-CGATGCCAATAG
1 CCCAGACATGGTCTTACAT-GAAATC-TCAAATCGATGCCAATAG
*
3076994 CCCAG-CTATGGTCTTACACGAAATCTCAAATCGATGCCAATAG
1 CCCAGAC-ATGGTCTTACATGAAATCTCAAATCGATGCCAATAG
* * *
3077037 CCCAAACATGGTCTTACATGAAATCACACATCGA
1 CCCAGACATGGTCTTACATGAAATCTCAAATCGA
3077071 AAGTCCTAAT
Statistics
Matches: 67, Mismatches: 7, Indels: 7
0.83 0.09 0.09
Matches are distributed among these distances:
42 3 0.04
43 47 0.70
44 17 0.25
ACGTcount: A:0.34, C:0.26, G:0.17, T:0.23
Consensus pattern (43 bp):
CCCAGACATGGTCTTACATGAAATCTCAAATCGATGCCAATAG
Found at i:3077221 original size:31 final size:30
Alignment explanation
Indices: 3077179--3077322 Score: 168
Period size: 31 Copynumber: 4.8 Consensus size: 30
3077169 ATCCTATGGT
* *
3077179 CAAATC-AATTCAGTAATATATATCCATATA
1 CAAATCAAATTCAGCAATGTATAT-CATATA
*
3077209 CGAATCAAATTCAGCAATGTATAATCATATA
1 CAAATCAAATTCAGCAATGTAT-ATCATATA
*
3077240 CAAATCAAATTC-GACAATGTATATCTATAAA
1 CAAATCAAATTCAG-CAATGTATATC-ATATA
* * *
3077271 CAATTCAAATTCGGTAATGTATAT-ATATA
1 CAAATCAAATTCAGCAATGTATATCATATA
3077300 CAAATCAAATTCAGCAATGTATA
1 CAAATCAAATTCAGCAATGTATA
3077323 AAACATATAC
Statistics
Matches: 98, Mismatches: 11, Indels: 11
0.82 0.09 0.09
Matches are distributed among these distances:
29 24 0.24
30 9 0.09
31 62 0.63
32 3 0.03
ACGTcount: A:0.46, C:0.15, G:0.08, T:0.31
Consensus pattern (30 bp):
CAAATCAAATTCAGCAATGTATATCATATA
Found at i:3079567 original size:44 final size:44
Alignment explanation
Indices: 3079501--3079862 Score: 235
Period size: 44 Copynumber: 7.9 Consensus size: 44
3079491 CATCGCAGCA
* * * * **
3079501 AATCTTATCTTCTTGAATTTGCAGTGGAGCAAATTAGAGCTAAA
1 AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAGAGCTACG
* * *
3079545 AATCTTATCTCCCTAAAGTTGCAGTGGAGTAGATT-GAAGCTATG
1 AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAG-AGCTACG
* * *
3079589 AGTCTTATCTCCCTGAAGTTGCAGTAGAGTAGATT-GAAGCTACG
1 AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAG-AGCTACG
* * *** * *
3079633 AGTCTTATCTCCCTAAAGTTGCAGCCAAGCAGATTAAAGATAGCG
1 AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAGAGCTA-CG
* * * *
3079678 AATCTTATTTCCCTGAAGTTGCAGTGGAACAAATTAAAGCTACATG
1 AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAGAGCTAC--G
* * *
3079724 TTACAGATCTTATCTCCCTGAAGTTACAGTGGAACAGATTAAAGCTACGAG
1 ----A-ATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAGAGCTAC--G
* * * *
3079775 TTACAAATCTTATCACCTTGAAATTGCAGTGGAGTAGATT-GAAGCTACG
1 -----AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAG-AGCTACG
* * * *
3079824 AGTCTTATTTCCCTAAAGTTGTAGTGGAGCAGATTAGAG
1 AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAGAG
3079863 TGACAAACCC
Statistics
Matches: 254, Mismatches: 51, Indels: 26
0.77 0.15 0.08
Matches are distributed among these distances:
43 1 0.00
44 138 0.54
45 36 0.14
46 1 0.00
49 1 0.00
50 1 0.00
51 74 0.29
52 2 0.01
ACGTcount: A:0.32, C:0.17, G:0.21, T:0.30
Consensus pattern (44 bp):
AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAGAGCTACG
Found at i:3079755 original size:51 final size:51
Alignment explanation
Indices: 3079678--3079826 Score: 183
Period size: 51 Copynumber: 2.9 Consensus size: 51
3079668 AAAGATAGCG
*
3079678 AATCTTATTTCCCTGAAGTTGCAGTGGAACAAATTAAAGCTAC-ATGTTACA
1 AATCTTATCTCCCTGAAGTTGCAGTGGAACAAATTAAAGCTACGA-GTTACA
* * *
3079729 GATCTTATCTCCCTGAAGTTACAGTGGAACAGATTAAAGCTACGAGTTACA
1 AATCTTATCTCCCTGAAGTTGCAGTGGAACAAATTAAAGCTACGAGTTACA
* * * ** * *
3079780 AATCTTATCACCTTGAAATTGCAGTGGAGTAGATTGAAGCTACGAGT
1 AATCTTATCTCCCTGAAGTTGCAGTGGAACAAATTAAAGCTACGAGT
3079827 CTTATTTCCC
Statistics
Matches: 85, Mismatches: 12, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
51 84 0.99
52 1 0.01
ACGTcount: A:0.34, C:0.17, G:0.19, T:0.30
Consensus pattern (51 bp):
AATCTTATCTCCCTGAAGTTGCAGTGGAACAAATTAAAGCTACGAGTTACA
Found at i:3081478 original size:3 final size:3
Alignment explanation
Indices: 3081465--3081506 Score: 54
Period size: 3 Copynumber: 14.7 Consensus size: 3
3081455 ATTCGTCTAT
3081465 TTA TT- TTA TTA TTA TT- TTA TTA TTA TT- TTA TTA TTA TCTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T-TA TT
3081507 TATTTATTTA
Statistics
Matches: 35, Mismatches: 0, Indels: 8
0.81 0.00 0.19
Matches are distributed among these distances:
2 6 0.17
3 26 0.74
4 3 0.09
ACGTcount: A:0.26, C:0.02, G:0.00, T:0.71
Consensus pattern (3 bp):
TTA
Found at i:3081481 original size:11 final size:11
Alignment explanation
Indices: 3081465--3081501 Score: 74
Period size: 11 Copynumber: 3.4 Consensus size: 11
3081455 ATTCGTCTAT
3081465 TTATTTTATTA
1 TTATTTTATTA
3081476 TTATTTTATTA
1 TTATTTTATTA
3081487 TTATTTTATTA
1 TTATTTTATTA
3081498 TTAT
1 TTAT
3081502 CTATTTATTT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 26 1.00
ACGTcount: A:0.27, C:0.00, G:0.00, T:0.73
Consensus pattern (11 bp):
TTATTTTATTA
Found at i:3081509 original size:22 final size:22
Alignment explanation
Indices: 3081465--3081523 Score: 68
Period size: 22 Copynumber: 2.6 Consensus size: 22
3081455 ATTCGTCTAT
*
3081465 TTATTTTATTATTATTTTATTA
1 TTATTTTATTATTATTATATTA
3081487 TTATTTTATTATTATCTAT-TTA
1 TTATTTTATTATTAT-TATATTA
3081509 TT-TATTTACTTATTA
1 TTAT-TTTA-TTATTA
3081524 CTCATTTTCT
Statistics
Matches: 33, Mismatches: 1, Indels: 5
0.85 0.03 0.13
Matches are distributed among these distances:
21 1 0.03
22 24 0.73
23 8 0.24
ACGTcount: A:0.27, C:0.03, G:0.00, T:0.69
Consensus pattern (22 bp):
TTATTTTATTATTATTATATTA
Found at i:3081744 original size:3 final size:3
Alignment explanation
Indices: 3081736--3081822 Score: 56
Period size: 3 Copynumber: 30.0 Consensus size: 3
3081726 ACTTCATTTA
* * * * * * *
3081736 ATT ATT ATT ACT AAT ATG ATT ATT AAT ATT AAT ATT ATA ATT ATA ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
* *
3081784 A-T GTT ATT ATT ATT A-T ATT CTT -TT ATT -TT ACTT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT A-TT ATT ATT
3081823 TATCATTCTA
Statistics
Matches: 63, Mismatches: 16, Indels: 10
0.71 0.18 0.11
Matches are distributed among these distances:
2 7 0.11
3 53 0.84
4 3 0.05
ACGTcount: A:0.36, C:0.03, G:0.02, T:0.59
Consensus pattern (3 bp):
ATT
Found at i:3084486 original size:29 final size:30
Alignment explanation
Indices: 3084443--3084501 Score: 93
Period size: 29 Copynumber: 2.0 Consensus size: 30
3084433 GAATTGGATC
*
3084443 AAATCAAAATTTCATGTATAAAATTGCACA
1 AAATCAAAAGTTCATGTATAAAATTGCACA
*
3084473 AAATC-AAAGTTCATGTATACAATTGCACA
1 AAATCAAAAGTTCATGTATAAAATTGCACA
3084502 TTAAACCATA
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
29 22 0.81
30 5 0.19
ACGTcount: A:0.47, C:0.15, G:0.08, T:0.29
Consensus pattern (30 bp):
AAATCAAAAGTTCATGTATAAAATTGCACA
Found at i:3084521 original size:31 final size:29
Alignment explanation
Indices: 3084453--3084522 Score: 86
Period size: 29 Copynumber: 2.3 Consensus size: 29
3084443 AAATCAAAAT
*
3084453 TTCATGTATAAAATTGCACAAAATCAAAG
1 TTCATGTATAAAATTGCACAAAACCAAAG
* *
3084482 TTCATGTATACAATTGCACATTAAACCATAG
1 TTCATGTATAAAATTGCACA--AAACCAAAG
*
3084513 TTCTTGTATA
1 TTCATGTATA
3084523 GTTTTGGGAT
Statistics
Matches: 35, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
29 19 0.54
31 16 0.46
ACGTcount: A:0.40, C:0.16, G:0.10, T:0.34
Consensus pattern (29 bp):
TTCATGTATAAAATTGCACAAAACCAAAG
Found at i:3085243 original size:13 final size:13
Alignment explanation
Indices: 3085225--3085249 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
3085215 TGATTTATAT
3085225 GTGTGAAAATTTC
1 GTGTGAAAATTTC
3085238 GTGTGAAAATTT
1 GTGTGAAAATTT
3085250 TATCGTTTGT
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:0.04, G:0.24, T:0.40
Consensus pattern (13 bp):
GTGTGAAAATTTC
Found at i:3087431 original size:6 final size:6
Alignment explanation
Indices: 3087377--3087412 Score: 72
Period size: 6 Copynumber: 6.0 Consensus size: 6
3087367 GCTTTAGCCC
3087377 ATTTTT ATTTTT ATTTTT ATTTTT ATTTTT ATTTTT
1 ATTTTT ATTTTT ATTTTT ATTTTT ATTTTT ATTTTT
3087413 TCTTATTATT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 30 1.00
ACGTcount: A:0.17, C:0.00, G:0.00, T:0.83
Consensus pattern (6 bp):
ATTTTT
Found at i:3087441 original size:28 final size:28
Alignment explanation
Indices: 3087387--3087442 Score: 69
Period size: 28 Copynumber: 2.0 Consensus size: 28
3087377 ATTTTTATTT
* * *
3087387 TTATTTTTATTTTTATTTTTATTTTTTC
1 TTATTATTATTATTATTTTTATGTTTTC
3087415 TTATTATTATTATTATTTGTT-TGTTTTC
1 TTATTATTATTATTATTT-TTATGTTTTC
3087443 ATAATAATTT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
28 22 0.92
29 2 0.08
ACGTcount: A:0.16, C:0.04, G:0.04, T:0.77
Consensus pattern (28 bp):
TTATTATTATTATTATTTTTATGTTTTC
Found at i:3089138 original size:17 final size:17
Alignment explanation
Indices: 3089116--3089394 Score: 139
Period size: 17 Copynumber: 15.5 Consensus size: 17
3089106 CTTTTCGCAT
*
3089116 TTTCAAAAGTTTTCGTG
1 TTTCAAAAATTTTCGTG
**
3089133 TTTCAAAAAATTTTCGCA
1 TTTC-AAAAATTTTCGTG
** * *
3089151 TTAAAAAAAATTCTCGTA
1 TT-TCAAAAATTTTCGTG
*
3089169 TTTCAAAAATTGTCGTG
1 TTTCAAAAATTTTCGTG
*
3089186 TTTTAAAAAATTTTCGTG
1 -TTTCAAAAATTTTCGTG
* *
3089204 TTTTCAATAATTCTCGTG
1 -TTTCAAAAATTTTCGTG
* *
3089222 TTTCACAAATTTCCGTG
1 TTTCAAAAATTTTCGTG
* *
3089239 TTTCAAAATTTTTTTTGTG
1 TTTCAAAA--ATTTTCGTG
* *
3089258 TTTTTAAAAAAAATTCTCGTG
1 --TTT--CAAAAATTTTCGTG
* *
3089279 TTT-AAAAAATTTCATGTTTTT
1 TTTCAAAAATTTTC--G---TG
*
3089300 TTTTAAAAATTTTCGTG
1 TTTCAAAAATTTTCGTG
3089317 TTTTC-AAAATTTTCGTG
1 -TTTCAAAAATTTTCGTG
* *
3089334 TTTTAAAAAATTTCGTG
1 TTTCAAAAATTTTCGTG
* * * *
3089351 TTACCAAAATTCTCATG
1 TTTCAAAAATTTTCGTG
* *
3089368 TATCAAAAATTTCCGTG
1 TTTCAAAAATTTTCGTG
3089385 TTTTCAAAAA
1 -TTTCAAAAA
3089395 AAGTTATTGT
Statistics
Matches: 195, Mismatches: 49, Indels: 35
0.70 0.18 0.13
Matches are distributed among these distances:
16 11 0.06
17 81 0.42
18 67 0.34
19 9 0.05
20 1 0.01
21 13 0.07
22 9 0.05
23 4 0.02
ACGTcount: A:0.32, C:0.12, G:0.10, T:0.46
Consensus pattern (17 bp):
TTTCAAAAATTTTCGTG
Found at i:3089147 original size:36 final size:35
Alignment explanation
Indices: 3089107--3089361 Score: 115
Period size: 35 Copynumber: 7.1 Consensus size: 35
3089097 AAATTTTGAC
* *
3089107 TTTTCGCATTTTCAAAAGTTTTCGTGTTTCAAAAAA
1 TTTTCGCATTTTAAAAAATTTTCGTGTTTC-AAAAA
** * *
3089143 TTTTCGCATTAAAAAAAATTCTCGTATTTCAAAAA
1 TTTTCGCATTTTAAAAAATTTTCGTGTTTCAAAAA
* ** *
3089178 TTGTCGTGTTTTAAAAAATTTTCGTGTTTTCAATAA
1 TTTTCGCATTTTAAAAAATTTTCGTG-TTTCAAAAA
* * * * *
3089214 TTCTCG--TGTTTCACAAATTTCCGTGTTTCAAAATTT
1 TTTTCGCAT-TTTAAAAAATTTTCGTGTTTCAAAA--A
* ** *
3089250 TTTTTGTGTTTTTAAAAAAAATTCTCGTGTTT-AAAAA
1 TTTTCG-CATTTT--AAAAAATTTTCGTGTTTCAAAAA
* ** *
3089287 ATTTCATGTTTTTTTTTAAAAATTTTCGTGTTTTC-AAAA
1 TTTTC--G--CATTTTAAAAAATTTTCGTG-TTTCAAAAA
** * *
3089326 TTTTCGTGTTTTAAAAAA-TTTCGTGTTACCAAAA
1 TTTTCGCATTTTAAAAAATTTTCGTGTTTCAAAAA
3089360 TT
1 TT
3089362 CTCATGTATC
Statistics
Matches: 168, Mismatches: 36, Indels: 32
0.71 0.15 0.14
Matches are distributed among these distances:
33 3 0.02
34 21 0.12
35 48 0.29
36 41 0.24
37 4 0.02
38 15 0.09
39 17 0.10
40 19 0.11
ACGTcount: A:0.31, C:0.11, G:0.10, T:0.47
Consensus pattern (35 bp):
TTTTCGCATTTTAAAAAATTTTCGTGTTTCAAAAA
Found at i:3089174 original size:53 final size:52
Alignment explanation
Indices: 3089116--3089246 Score: 145
Period size: 53 Copynumber: 2.5 Consensus size: 52
3089106 CTTTTCGCAT
3089116 TTTCAAAAGTTTTCGTGTTTCAAAAAATTTTCGCATTAAAAAAAATTCTCGTA
1 TTTCAAAA-TTTTCGTGTTTCAAAAAATTTTCGCATTAAAAAAAATTCTCGTA
* * ** *** * *
3089169 TTTCAAAAATTGTCGTGTTTTAAAAAATTTTCGTGTTTTCAATAATTCTCGTG
1 TTTC-AAAATTTTCGTGTTTCAAAAAATTTTCGCATTAAAAAAAATTCTCGTA
*
3089222 TTTCACAAATTTCCGTGTTTCAAAA
1 TTTCA-AAATTTTCGTGTTTCAAAA
3089247 TTTTTTTTGT
Statistics
Matches: 64, Mismatches: 12, Indels: 4
0.80 0.15 0.05
Matches are distributed among these distances:
52 1 0.02
53 59 0.92
54 4 0.06
ACGTcount: A:0.33, C:0.14, G:0.11, T:0.43
Consensus pattern (52 bp):
TTTCAAAATTTTCGTGTTTCAAAAAATTTTCGCATTAAAAAAAATTCTCGTA
Found at i:3089202 original size:18 final size:18
Alignment explanation
Indices: 3089115--3089352 Score: 137
Period size: 18 Copynumber: 13.1 Consensus size: 18
3089105 ACTTTTCGCA
* *
3089115 TTTTCAAAAGTTTTCGTG
1 TTTTAAAAAATTTTCGTG
* **
3089133 TTTCAAAAAATTTTCGCA
1 TTTTAAAAAATTTTCGTG
** *
3089151 TTAAAAAAAATTCTCGT-
1 TTTTAAAAAATTTTCGTG
* * *
3089168 ATTTCAAAAATTGTCGTG
1 TTTTAAAAAATTTTCGTG
3089186 TTTTAAAAAATTTTCGTG
1 TTTTAAAAAATTTTCGTG
* * *
3089204 TTTTCAATAATTCTCGTG
1 TTTTAAAAAATTTTCGTG
* * *
3089222 -TTTCACAAATTTCCGTG
1 TTTTAAAAAATTTTCGTG
* ** *
3089239 TTTCAAAATTTTTTTTGTG
1 TTTTAAAA-AATTTTCGTG
*
3089258 TTTTTAAAAAAAATTCTCGTG
1 -TTTT--AAAAAATTTTCGTG
*
3089279 -TTTAAAAAA-TTTCATGTTTT
1 TTTTAAAAAATTTTC--G--TG
*
3089299 TTTTTAAAAATTTTCGTG
1 TTTTAAAAAATTTTCGTG
*
3089317 TTTT-CAAAATTTTCGTG
1 TTTTAAAAAATTTTCGTG
3089334 TTTTAAAAAA-TTTCGTG
1 TTTTAAAAAATTTTCGTG
3089351 TT
1 TT
3089353 ACCAAAATTC
Statistics
Matches: 165, Mismatches: 42, Indels: 27
0.71 0.18 0.12
Matches are distributed among these distances:
16 3 0.02
17 56 0.34
18 70 0.42
19 9 0.05
20 5 0.03
21 14 0.08
22 8 0.05
ACGTcount: A:0.31, C:0.11, G:0.11, T:0.48
Consensus pattern (18 bp):
TTTTAAAAAATTTTCGTG
Found at i:3089279 original size:40 final size:39
Alignment explanation
Indices: 3089235--3089337 Score: 93
Period size: 39 Copynumber: 2.6 Consensus size: 39
3089225 CACAAATTTC
**
3089235 CGTGTTTCAAAATTTTTTTTGTGTTTTTAAAAAAAATTCT
1 CGTGTTTCAAAATTTTTCATGT-TTTTTAAAAAAAATTCT
** *** *
3089275 CGTGTTT-AAAAAATTTCATGTTTTTTTTTAAAAATTTT
1 CGTGTTTCAAAATTTTTCATGTTTTTTAAAAAAAATTCT
*
3089313 CGTGTTTTCAAAA-TTTTCGTGTTTT
1 CGTG-TTTCAAAATTTTTCATGTTTT
3089338 AAAAAATTTC
Statistics
Matches: 51, Mismatches: 10, Indels: 5
0.77 0.15 0.08
Matches are distributed among these distances:
38 17 0.33
39 23 0.45
40 11 0.22
ACGTcount: A:0.27, C:0.08, G:0.11, T:0.54
Consensus pattern (39 bp):
CGTGTTTCAAAATTTTTCATGTTTTTTAAAAAAAATTCT
Found at i:3089307 original size:22 final size:22
Alignment explanation
Indices: 3089279--3089320 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
3089269 AATTCTCGTG
3089279 TTTAAAAAATTTCATGTTTTTT
1 TTTAAAAAATTTCATGTTTTTT
* *
3089301 TTTAAAAATTTTCGTGTTTT
1 TTTAAAAAATTTCATGTTTT
3089321 CAAAATTTTC
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.29, C:0.05, G:0.07, T:0.60
Consensus pattern (22 bp):
TTTAAAAAATTTCATGTTTTTT
Found at i:3089393 original size:18 final size:18
Alignment explanation
Indices: 3089169--3089394 Score: 103
Period size: 18 Copynumber: 12.5 Consensus size: 18
3089159 AATTCTCGTA
3089169 TTTCAAAAATTGT-CGTGT
1 TTTCAAAAATT-TCCGTGT
* *
3089187 TTTAAAAAATTTTCGTGT
1 TTTCAAAAATTTCCGTGT
*
3089205 TTTCAATAA-TTCTCGTG-
1 TTTCAAAAATTTC-CGTGT
*
3089222 TTTCACAAATTTCCGTG-
1 TTTCAAAAATTTCCGTGT
* **
3089239 TTTCAAAATTTTTTTTGTGTT
1 TTTCAAAA--ATTTCCGTG-T
* *
3089260 TTTAAAAAAAATTCTCGTG-
1 TTT-CAAAAATTTC-CGTGT
* * *
3089279 TTTAAAAAATTTCATGTTTTT
1 TTTCAAAAATTTC-CG--TGT
* *
3089300 TTTTAAAAATTTTCGTGT
1 TTTCAAAAATTTCCGTGT
*
3089318 TTTC-AAAATTTTCGTGT
1 TTTCAAAAATTTCCGTGT
*
3089335 TTTAAAAAATTT-CGTG-
1 TTTCAAAAATTTCCGTGT
* * *
3089351 TTACCAAAA-TTCTCATG-
1 TTTCAAAAATTTC-CGTGT
*
3089368 TATCAAAAATTTCCGTGT
1 TTTCAAAAATTTCCGTGT
3089386 TTTCAAAAA
1 TTTCAAAAA
3089395 AAGTTATTGT
Statistics
Matches: 157, Mismatches: 34, Indels: 34
0.70 0.15 0.15
Matches are distributed among these distances:
15 2 0.01
16 6 0.04
17 53 0.34
18 62 0.39
19 9 0.06
20 4 0.03
21 17 0.11
22 4 0.03
ACGTcount: A:0.31, C:0.12, G:0.10, T:0.47
Consensus pattern (18 bp):
TTTCAAAAATTTCCGTGT
Found at i:3091628 original size:68 final size:68
Alignment explanation
Indices: 3091513--3091669 Score: 226
Period size: 68 Copynumber: 2.3 Consensus size: 68
3091503 GAGATGATAG
* * *
3091513 ACGACGTCGAGACGAGCAAGGTGTAGCGCGTCAAGATGACGCAACATCCTTGGCAACCAAGCAAG
1 ACGACGTCGAGACGAGCAAGGTGTAGCACGTCAAGATGACACAACATCCTTAGCAACCAAGCAAG
3091578 GCT
66 GCT
* * **
3091581 ACGATGTCGAGACGAGCAAGGTGTAGCACGTCGAGATGACATGACATCCTTAGCAACCAAGCAAG
1 ACGACGTCGAGACGAGCAAGGTGTAGCACGTCAAGATGACACAACATCCTTAGCAACCAAGCAAG
3091646 GCT
66 GCT
* *
3091649 ACGACATCGTGACGAG-AAGGT
1 ACGACGTCGAGACGAGCAAGGT
3091670 ATGCCACATC
Statistics
Matches: 79, Mismatches: 10, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
67 5 0.06
68 74 0.94
ACGTcount: A:0.32, C:0.24, G:0.29, T:0.15
Consensus pattern (68 bp):
ACGACGTCGAGACGAGCAAGGTGTAGCACGTCAAGATGACACAACATCCTTAGCAACCAAGCAAG
GCT
Found at i:3094380 original size:20 final size:19
Alignment explanation
Indices: 3094347--3094385 Score: 51
Period size: 20 Copynumber: 2.0 Consensus size: 19
3094337 TTCAATAATT
3094347 TTAATTAAAAATAATAAAAA
1 TTAATTAAAAATAA-AAAAA
**
3094367 TTAATTAATTATAAAAAAA
1 TTAATTAAAAATAAAAAAA
3094386 CATTTTAATT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
19 5 0.29
20 12 0.71
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (19 bp):
TTAATTAAAAATAAAAAAA
Found at i:3096310 original size:40 final size:41
Alignment explanation
Indices: 3096234--3096310 Score: 120
Period size: 41 Copynumber: 1.9 Consensus size: 41
3096224 GGGCATGCGG
* *
3096234 GGATTTAGCGGCGTTTTTTATTAAGCGCCGCTAAAGATCAA
1 GGATTTAGCGGCGTTTTTCATAAAGCGCCGCTAAAGATCAA
*
3096275 GGATTTAGCGGCGTTTTTCATAAATCGCCGC-AAAGA
1 GGATTTAGCGGCGTTTTTCATAAAGCGCCGCTAAAGA
3096311 AACCTAAGAC
Statistics
Matches: 33, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
40 5 0.15
41 28 0.85
ACGTcount: A:0.27, C:0.18, G:0.25, T:0.30
Consensus pattern (41 bp):
GGATTTAGCGGCGTTTTTCATAAAGCGCCGCTAAAGATCAA
Found at i:3096365 original size:114 final size:114
Alignment explanation
Indices: 3096239--3096480 Score: 267
Period size: 114 Copynumber: 2.1 Consensus size: 114
3096229 TGCGGGGATT
* * * * *
3096239 TAGCGGCGTTTTTTA-TTAAGCGCCGCTAAAGATCAAGGA-TTTAGCGGCGTTTTTCAT-AAATC
1 TAGCGGCGTTTTTGAGGT-AGCGCCGCTAAAGATC-AGGACTTTAGCGGCATTTGT-ATGAAAGC
* * *
3096301 GCCGCAAAGAAACCTAAGACC-AACGACACCGTTTTCTGAGCATTCGGTAACC
63 GCCGCAAAGAAACATAAG-CCGAACGACACCGTTCTCTGAGCATTCGGGAACC
* * * *
3096353 TAGCGGCGTTTTTGAGGTAGCGCCGCTAATGTTCAGTACTTTAGCGGCATTTGTATGGAAGCGCC
1 TAGCGGCGTTTTTGAGGTAGCGCCGCTAAAGATCAGGACTTTAGCGGCATTTGTATGAAAGCGCC
* * * **
3096418 GCAAATAAACATAAGCCGAACGACACCGTTCTCTGAGTATTCGGGGATT
66 GCAAAGAAACATAAGCCGAACGACACCGTTCTCTGAGCATTCGGGAACC
3096467 TAGCGGCGTTTTTG
1 TAGCGGCGTTTTTG
3096481 GTAAGCGCCG
Statistics
Matches: 107, Mismatches: 17, Indels: 8
0.81 0.13 0.06
Matches are distributed among these distances:
113 7 0.07
114 99 0.93
115 1 0.01
ACGTcount: A:0.26, C:0.22, G:0.25, T:0.28
Consensus pattern (114 bp):
TAGCGGCGTTTTTGAGGTAGCGCCGCTAAAGATCAGGACTTTAGCGGCATTTGTATGAAAGCGCC
GCAAAGAAACATAAGCCGAACGACACCGTTCTCTGAGCATTCGGGAACC
Found at i:3098173 original size:146 final size:146
Alignment explanation
Indices: 3097995--3098329 Score: 372
Period size: 146 Copynumber: 2.3 Consensus size: 146
3097985 AACGACTTCG
* * * * *
3097995 TTTGATCTTATATTTAGTGGCGCTTTACTTAAAACGCCGCCACATTGTTCTAACATTTATAGAAA
1 TTTGAT-TTATAGTTAGTGGCGCTTTAATTAAAACGCCGCAAAAATGTTCTAACATTTATAGAAA
** * * * * * *
3098060 CGCTGTCGTTTT-TTAAATGTTATTAGTGGCGATTT-TT-TAAAACGCCACGGGTTTGAGGTAAG
65 CGAGGCCGTTTTGTT--ATATTATTAGTGGCG-TTTATTCAAAAACGCCACAGGTGTGAGCTAAG
*
3098122 TGTTGATGAAGCGACTGCAT
127 TGTTGATGAAACGACTGCAT
* * *
3098142 TTTGATTTATAGTTAGTGGCGCTTTAATTAAAACGCCGCAAAAATGTTTTAACATTTATCGATAC
1 TTTGATTTATAGTTAGTGGCGCTTTAATTAAAACGCCGCAAAAATGTTCTAACATTTATAGAAAC
* * **
3098207 GAGGCCGTTTTGTTGTATTATTAGTGGCGTTTATTCAAAAACGCCACAGGTGTGCGCTATTTGTT
66 GAGGCCGTTTTGTTATATTATTAGTGGCGTTTATTCAAAAACGCCACAGGTGTGAGCTAAGTGTT
*
3098272 GATGAAACGACTGCGT
131 GATGAAACGACTGCAT
* * *
3098288 TTCGACTTATAGTTAGTGGCGC-TTATTTATAAACGCCGCAAA
1 TTTGATTTATAGTTAGTGGCGCTTTAATTA-AAACGCCGCAAA
3098330 TGGTTAATTT
Statistics
Matches: 159, Mismatches: 25, Indels: 9
0.82 0.13 0.05
Matches are distributed among these distances:
144 3 0.02
145 21 0.13
146 127 0.80
147 8 0.05
ACGTcount: A:0.27, C:0.16, G:0.21, T:0.36
Consensus pattern (146 bp):
TTTGATTTATAGTTAGTGGCGCTTTAATTAAAACGCCGCAAAAATGTTCTAACATTTATAGAAAC
GAGGCCGTTTTGTTATATTATTAGTGGCGTTTATTCAAAAACGCCACAGGTGTGAGCTAAGTGTT
GATGAAACGACTGCAT
Found at i:3100902 original size:63 final size:63
Alignment explanation
Indices: 3100828--3101005 Score: 347
Period size: 63 Copynumber: 2.8 Consensus size: 63
3100818 ATTAAATTTA
3100828 TTACTTAAATACATTACTTACTAAAATTTAAGTAAGTTTACTTATATGTAAAATTTAAGTATG
1 TTACTTAAATACATTACTTACTAAAATTTAAGTAAGTTTACTTATATGTAAAATTTAAGTATG
3100891 TTACTTAAATACATTACTTACTAAAATTTAAGTAAGTTTACTTATATGTAAAATTTAAGTATG
1 TTACTTAAATACATTACTTACTAAAATTTAAGTAAGTTTACTTATATGTAAAATTTAAGTATG
*
3100954 TTACTTAAATACATTACTTACTAAAATTTAAGTAAGTTTACATATATGTAAA
1 TTACTTAAATACATTACTTACTAAAATTTAAGTAAGTTTACTTATATGTAAA
3101006 CTTACATAAT
Statistics
Matches: 114, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
63 114 1.00
ACGTcount: A:0.42, C:0.08, G:0.07, T:0.42
Consensus pattern (63 bp):
TTACTTAAATACATTACTTACTAAAATTTAAGTAAGTTTACTTATATGTAAAATTTAAGTATG
Found at i:3100918 original size:36 final size:36
Alignment explanation
Indices: 3100876--3100987 Score: 127
Period size: 36 Copynumber: 3.4 Consensus size: 36
3100866 TACTTATATG
3100876 TAAAATTTAAGTATGTTACTTAAATACATTACTTAC
1 TAAAATTTAAGTATGTTACTTAAATACATTACTTAC
* *
3100912 TAAAATTTAAGTA----AGTT---TAC-TTA--TATG
1 TAAAATTTAAGTATGTTACTTAAATACATTACTTA-C
3100939 TAAAATTTAAGTATGTTACTTAAATACATTACTTAC
1 TAAAATTTAAGTATGTTACTTAAATACATTACTTAC
3100975 TAAAATTTAAGTA
1 TAAAATTTAAGTA
3100988 AGTTTACATA
Statistics
Matches: 61, Mismatches: 4, Indels: 22
0.70 0.05 0.25
Matches are distributed among these distances:
26 2 0.03
27 13 0.21
28 3 0.05
29 3 0.05
31 3 0.05
32 3 0.05
34 3 0.05
35 3 0.05
36 26 0.43
37 2 0.03
ACGTcount: A:0.43, C:0.08, G:0.07, T:0.42
Consensus pattern (36 bp):
TAAAATTTAAGTATGTTACTTAAATACATTACTTAC
Found at i:3101030 original size:23 final size:23
Alignment explanation
Indices: 3101004--3101047 Score: 79
Period size: 23 Copynumber: 1.9 Consensus size: 23
3100994 CATATATGTA
*
3101004 AACTTACATAATACATTACTTTT
1 AACTTACATAATACATAACTTTT
3101027 AACTTACATAATACATAACTT
1 AACTTACATAATACATAACTT
3101048 ATAAAAAAAT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.43, C:0.18, G:0.00, T:0.39
Consensus pattern (23 bp):
AACTTACATAATACATAACTTTT
Found at i:3101126 original size:39 final size:38
Alignment explanation
Indices: 3101027--3101118 Score: 132
Period size: 37 Copynumber: 2.4 Consensus size: 38
3101017 CATTACTTTT
3101027 AACTTACATAATACATAACTTATAAAAAAATTTTAAATA
1 AACTTACATAATACATAACTTAT-AAAAAATTTTAAATA
*** *
3101066 AACTTACATAATACATAACTTAT-AATTTTTTTATATA
1 AACTTACATAATACATAACTTATAAAAAATTTTAAATA
3101103 AACTTACATAATACAT
1 AACTTACATAATACAT
3101119 TTAACTTACA
Statistics
Matches: 49, Mismatches: 4, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
37 26 0.53
39 23 0.47
ACGTcount: A:0.50, C:0.12, G:0.00, T:0.38
Consensus pattern (38 bp):
AACTTACATAATACATAACTTATAAAAAATTTTAAATA
Found at i:3101134 original size:9 final size:9
Alignment explanation
Indices: 3101103--3101590 Score: 395
Period size: 9 Copynumber: 54.0 Consensus size: 9
3101093 TTTTTATATA
3101103 AACTTACAT
1 AACTTACAT
3101112 AA--TACATTT
1 AACTTACA--T
3101121 AACTTACAT
1 AACTTACAT
3101130 AACTTACAT
1 AACTTACAT
*
3101139 AACTTACAC
1 AACTTACAT
3101148 AACTTACAT
1 AACTTACAT
3101157 AACCTT-CAT
1 AA-CTTACAT
3101166 AA--TACATTT
1 AACTTACA--T
3101175 AACTTACAT
1 AACTTACAT
3101184 AACTTACAT
1 AACTTACAT
3101193 AACTTACAT
1 AACTTACAT
* *
3101202 AA--TGCAA
1 AACTTACAT
3101209 AACTTACAT
1 AACTTACAT
3101218 AACAACTTACAT
1 ---AACTTACAT
*
3101230 AACATACAT
1 AACTTACAT
* **
3101239 TACTTTGAT
1 AACTTACAT
3101248 AACTTACAT
1 AACTTACAT
3101257 AACTTACAT
1 AACTTACAT
* *
3101266 AA--TGCAA
1 AACTTACAT
3101273 AACTTACAT
1 AACTTACAT
*
3101282 AAC-AAC-T
1 AACTTACAT
*
3101289 TACTTACAT
1 AACTTACAT
*
3101298 AACATACAT
1 AACTTACAT
* *
3101307 TACTTAAAT
1 AACTTACAT
* *
3101316 TATTTACAT
1 AACTTACAT
3101325 AA--TACAT
1 AACTTACAT
3101332 AACTTAGTACAT
1 AAC-T--TACAT
*
3101344 AATTTACAT
1 AACTTACAT
3101353 AA--TACAT
1 AACTTACAT
3101360 AACTTAGTACAT
1 AAC-T--TACAT
3101372 AACTTACAT
1 AACTTACAT
* *
3101381 AATTTTTTC-T
1 AA--CTTACAT
3101391 AAATTGCTTACAT
1 -AA---CTTACAT
* *
3101404 AAATTATAT
1 AACTTACAT
3101413 AACTTACAT
1 AACTTACAT
3101422 AACTTACATT
1 AACTTACA-T
*
3101432 AA-TTAAAT
1 AACTTACAT
3101440 AACTTACAT
1 AACTTACAT
3101449 AACTTACAT
1 AACTTACAT
3101458 AACTTACAT
1 AACTTACAT
3101467 AACTTACAT
1 AACTTACAT
3101476 AACTTACAT
1 AACTTACAT
3101485 AACTTACAT
1 AACTTACAT
*
3101494 ATCTTACAT
1 AACTTACAT
3101503 AACTTACAT
1 AACTTACAT
* *
3101512 AAATTAAAT
1 AACTTACAT
3101521 AACTTACAT
1 AACTTACAT
3101530 AACTTACAT
1 AACTTACAT
*
3101539 AAATTACAT
1 AACTTACAT
3101548 AACTTACAT
1 AACTTACAT
3101557 AACTTACAT
1 AACTTACAT
3101566 AA--TACAT
1 AACTTACAT
*
3101573 AACCTT-CCT
1 AA-CTTACAT
3101582 AACTTACAT
1 AACTTACAT
3101591 TATTGTTTAA
Statistics
Matches: 388, Mismatches: 51, Indels: 80
0.75 0.10 0.15
Matches are distributed among these distances:
6 1 0.00
7 40 0.10
8 10 0.03
9 283 0.73
10 8 0.02
11 15 0.04
12 30 0.08
13 1 0.00
ACGTcount: A:0.45, C:0.19, G:0.01, T:0.35
Consensus pattern (9 bp):
AACTTACAT
Found at i:3101226 original size:12 final size:12
Alignment explanation
Indices: 3101209--3101291 Score: 55
Period size: 12 Copynumber: 6.6 Consensus size: 12
3101199 CATAATGCAA
3101209 AACTTACATAAC
1 AACTTACATAAC
3101221 AACTTACATAAC
1 AACTTACATAAC
* * *
3101233 ATACATTACTTTGAT
1 A-AC-TTAC-ATAAC
3101248 AACTTACAT---
1 AACTTACATAAC
3101257 AACTTACATAATGC
1 AACTTACATAA--C
3101271 AAAACTTACATAAC
1 --AACTTACATAAC
3101285 AACTTAC
1 AACTTAC
3101292 TTACATAACA
Statistics
Matches: 57, Mismatches: 4, Indels: 20
0.70 0.05 0.25
Matches are distributed among these distances:
9 9 0.16
12 21 0.37
13 6 0.11
14 7 0.12
15 3 0.05
16 11 0.19
ACGTcount: A:0.46, C:0.22, G:0.02, T:0.30
Consensus pattern (12 bp):
AACTTACATAAC
Found at i:3101261 original size:64 final size:64
Alignment explanation
Indices: 3101120--3101333 Score: 244
Period size: 64 Copynumber: 3.3 Consensus size: 64
3101110 ATAATACATT
* *
3101120 TAACTTACATAACTTACATAACTTACACAACTTACATAAC--CTT-CAT-A-ATACATTTAACTT
1 TAACTTACATAACTTACATAA--TGCAAAACTTACATAACAACTTACATAACATACA-TT-ACTT
3101180 ACA
62 ACA
**
3101183 TAACTTACATAACTTACATAATGCAAAACTTACATAACAACTTACATAACATACATTACTTTGA
1 TAACTTACATAACTTACATAATGCAAAACTTACATAACAACTTACATAACATACATTACTTACA
3101247 TAACTTACATAACTTACATAATGCAAAACTTACATAACAACTTACTTACATAACATACATTACTT
1 TAACTTACATAACTTACATAATGCAAAACTTACATAAC-A---ACTTACATAACATACATTACTT
*
3101312 AAA
62 ACA
* *
3101315 TTATTTACATAA--TACATAA
1 TAACTTACATAACTTACATAA
3101334 CTTAGTACAT
Statistics
Matches: 134, Mismatches: 8, Indels: 15
0.85 0.05 0.10
Matches are distributed among these distances:
61 15 0.11
63 24 0.18
64 46 0.34
65 4 0.03
66 12 0.09
68 33 0.25
ACGTcount: A:0.45, C:0.21, G:0.01, T:0.33
Consensus pattern (64 bp):
TAACTTACATAACTTACATAATGCAAAACTTACATAACAACTTACATAACATACATTACTTACA
Found at i:3101355 original size:28 final size:28
Alignment explanation
Indices: 3101317--3101383 Score: 125
Period size: 28 Copynumber: 2.4 Consensus size: 28
3101307 TACTTAAATT
3101317 ATTTACATAATACATAACTTAGTACATA
1 ATTTACATAATACATAACTTAGTACATA
3101345 ATTTACATAATACATAACTTAGTACATA
1 ATTTACATAATACATAACTTAGTACATA
*
3101373 ACTTACATAAT
1 ATTTACATAAT
3101384 TTTTTCTAAA
Statistics
Matches: 38, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
28 38 1.00
ACGTcount: A:0.46, C:0.15, G:0.03, T:0.36
Consensus pattern (28 bp):
ATTTACATAATACATAACTTAGTACATA
Found at i:3101607 original size:33 final size:33
Alignment explanation
Indices: 3101565--3101658 Score: 127
Period size: 32 Copynumber: 2.8 Consensus size: 33
3101555 ATAACTTACA
*
3101565 TAATACATAACCTTCCTAACTTACATTATTGTT
1 TAATACATAACCTTACTAACTTACATTATTGTT
*
3101598 TAATACATAA-CTTAGTAACTTACATTATTGTT
1 TAATACATAACCTTACTAACTTACATTATTGTT
*
3101630 TAATACATAACTTAGTACATAACTTACAT
1 TAATACATAACCT--TAC-TAACTTACAT
3101659 AACTCATTTA
Statistics
Matches: 53, Mismatches: 4, Indels: 5
0.85 0.06 0.08
Matches are distributed among these distances:
32 30 0.57
33 11 0.21
35 2 0.04
36 10 0.19
ACGTcount: A:0.38, C:0.17, G:0.04, T:0.40
Consensus pattern (33 bp):
TAATACATAACCTTACTAACTTACATTATTGTT
Found at i:3101622 original size:32 final size:32
Alignment explanation
Indices: 3101565--3101646 Score: 137
Period size: 32 Copynumber: 2.5 Consensus size: 32
3101555 ATAACTTACA
**
3101565 TAATACATAACCTTCCTAACTTACATTATTGTT
1 TAATACATAA-CTTAGTAACTTACATTATTGTT
3101598 TAATACATAACTTAGTAACTTACATTATTGTT
1 TAATACATAACTTAGTAACTTACATTATTGTT
3101630 TAATACATAACTTAGTA
1 TAATACATAACTTAGTA
3101647 CATAACTTAC
Statistics
Matches: 47, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
32 37 0.79
33 10 0.21
ACGTcount: A:0.38, C:0.16, G:0.05, T:0.41
Consensus pattern (32 bp):
TAATACATAACTTAGTAACTTACATTATTGTT
Found at i:3107269 original size:21 final size:21
Alignment explanation
Indices: 3107235--3107299 Score: 76
Period size: 21 Copynumber: 3.1 Consensus size: 21
3107225 AAATTAAATT
* *
3107235 AGAGGCCGCAGCGAGGGAAGC
1 AGAGGCCACAGCGAGAGAAGC
* * *
3107256 AGATGCTACAGCGAGAGAAGT
1 AGAGGCCACAGCGAGAGAAGC
*
3107277 AGAGGCCGCAGCGAGAGAAGC
1 AGAGGCCACAGCGAGAGAAGC
3107298 AG
1 AG
3107300 CGATAGAAGC
Statistics
Matches: 35, Mismatches: 9, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
21 35 1.00
ACGTcount: A:0.34, C:0.20, G:0.42, T:0.05
Consensus pattern (21 bp):
AGAGGCCACAGCGAGAGAAGC
Found at i:3107826 original size:42 final size:42
Alignment explanation
Indices: 3107747--3107847 Score: 107
Period size: 42 Copynumber: 2.4 Consensus size: 42
3107737 TTTGTGAAAT
*
3107747 AAGCGCCGCTAAAGAACACTACTATTAACGGCATTTTTGAAC-
1 AAGCGCCGCTAAAGAACACGACTATTAACGGCATTTTT-AACA
* * ** **
3107789 AAGCGCCGCTAAAGTACACGATCT-TTAGCGGTGTTTTTTTCA
1 AAGCGCCGCTAAAGAACACGA-CTATTAACGGCATTTTTAACA
3107831 AAGCGCCGCTAAAGAAC
1 AAGCGCCGCTAAAGAAC
3107848 GTTTTTTCCT
Statistics
Matches: 49, Mismatches: 8, Indels: 4
0.80 0.13 0.07
Matches are distributed among these distances:
41 1 0.02
42 46 0.94
43 2 0.04
ACGTcount: A:0.32, C:0.24, G:0.20, T:0.25
Consensus pattern (42 bp):
AAGCGCCGCTAAAGAACACGACTATTAACGGCATTTTTAACA
Found at i:3107861 original size:27 final size:27
Alignment explanation
Indices: 3107821--3107874 Score: 81
Period size: 27 Copynumber: 2.0 Consensus size: 27
3107811 CTTTAGCGGT
* *
3107821 GTTTTTTTCAAAGCGCCGCTAAAGAAC
1 GTTTTTTCCAAAGCACCGCTAAAGAAC
*
3107848 GTTTTTTCCTAAGCACCGCTAAAGAAC
1 GTTTTTTCCAAAGCACCGCTAAAGAAC
3107875 ATGATCTTTA
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
27 24 1.00
ACGTcount: A:0.30, C:0.24, G:0.17, T:0.30
Consensus pattern (27 bp):
GTTTTTTCCAAAGCACCGCTAAAGAAC
Found at i:3107962 original size:43 final size:42
Alignment explanation
Indices: 3107847--3108000 Score: 209
Period size: 42 Copynumber: 3.6 Consensus size: 42
3107837 CGCTAAAGAA
*
3107847 CGTTTTTTCCTAAGCACCGCTAAAGAACATGATCTTTAGCGG
1 CGTTTTTTCCTAAGCGCCGCTAAAGAACATGATCTTTAGCGG
* *
3107889 CGTTTTTTCATAAGCGCCGCTAAATAACATGATCTTTAGCGG
1 CGTTTTTTCCTAAGCGCCGCTAAAGAACATGATCTTTAGCGG
* **
3107931 CGTTTATTTCCTTAGCGCCGCTAAAGAACATGATCTTTAGTAG
1 CGTTT-TTTCCTAAGCGCCGCTAAAGAACATGATCTTTAGCGG
* *
3107974 CGTTTTTTTCTGTAAGCGCCGCAAAAG
1 CG-TTTTTTC-CTAAGCGCCGCTAAAG
3108001 TTAGCGACAT
Statistics
Matches: 98, Mismatches: 11, Indels: 4
0.87 0.10 0.04
Matches are distributed among these distances:
42 44 0.45
43 38 0.39
44 16 0.16
ACGTcount: A:0.25, C:0.22, G:0.19, T:0.33
Consensus pattern (42 bp):
CGTTTTTTCCTAAGCGCCGCTAAAGAACATGATCTTTAGCGG
Found at i:3115146 original size:17 final size:18
Alignment explanation
Indices: 3115132--3115173 Score: 57
Period size: 18 Copynumber: 2.3 Consensus size: 18
3115122 TAATATAACT
3115132 TATTTAATAAAATAAATA
1 TATTTAATAAAATAAATA
* *
3115150 TTTTTAATAAAGTAAATTA
1 TATTTAATAAAATAAA-TA
3115169 TATTT
1 TATTT
3115174 TCAATTTGGT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
18 14 0.70
19 6 0.30
ACGTcount: A:0.50, C:0.00, G:0.02, T:0.48
Consensus pattern (18 bp):
TATTTAATAAAATAAATA
Found at i:3117029 original size:3 final size:3
Alignment explanation
Indices: 3117021--3117100 Score: 160
Period size: 3 Copynumber: 26.7 Consensus size: 3
3117011 CTAATTAGTT
3117021 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
3117069 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
3117101 GTCATTTACC
Statistics
Matches: 77, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 77 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:3122131 original size:99 final size:102
Alignment explanation
Indices: 3121947--3122245 Score: 379
Period size: 100 Copynumber: 2.9 Consensus size: 102
3121937 TTATTCTCAT
* * *
3121947 TTTGTATCTTAGCAAATTTTGCTATCTTGATTTATTCATTTCGAGCTTTTTTCTCAATAAAATTC
1 TTTGTATCTTAGCAAAATTTGCTATCTTGA-TTATTCATTTCGAGCCTTATTCTCAATAAAATTC
*
3122012 CATATTGTCCATTGTGATAATCTTTTTATCTTATTCAA
65 CATATTGTCCATTTTGATAATCTTTTTATCTTATTCAA
* *
3122050 TTTGTATCTTAGCAAAATTTGCTATCTTGA-T-TT-ATTTCGAGCCTTGTTCTCAATAAAATTCT
1 TTTGTATCTTAGCAAAATTTGCTATCTTGATTATTCATTTCGAGCCTTATTCTCAATAAAATTCC
* * * * *
3122112 ATCTTATCCATTTTCATAATACTTTTCATCTTATTCAG
66 ATATTGTCCATTTTGATAAT-CTTTTTATCTTATTCAA
** *
3122150 TTCATATCTTAGCAAAATTTGCTATCTTGATTAATTTATTCATTTTGAGCCTTATTCTCAATAAA
1 TTTGTATCTTAGCAAAATTTGCTATCTTG----A-TTATTCATTTCGAGCCTTATTCTCAATAAA
*
3122215 ATTCCATTTTGTCCATTTTGATAATCTTTTT
61 ATTCCATATTGTCCATTTTGATAATCTTTTT
3122246 CAAGCATTTT
Statistics
Matches: 168, Mismatches: 19, Indels: 14
0.84 0.09 0.07
Matches are distributed among these distances:
99 42 0.25
100 44 0.26
101 1 0.01
103 29 0.17
104 1 0.01
106 1 0.01
107 7 0.04
108 43 0.26
ACGTcount: A:0.26, C:0.16, G:0.08, T:0.49
Consensus pattern (102 bp):
TTTGTATCTTAGCAAAATTTGCTATCTTGATTATTCATTTCGAGCCTTATTCTCAATAAAATTCC
ATATTGTCCATTTTGATAATCTTTTTATCTTATTCAA
Found at i:3122783 original size:26 final size:26
Alignment explanation
Indices: 3122747--3122799 Score: 106
Period size: 26 Copynumber: 2.0 Consensus size: 26
3122737 ATTACAGTGG
3122747 GGGCAATCCGGCTAAGTAAGAGATAA
1 GGGCAATCCGGCTAAGTAAGAGATAA
3122773 GGGCAATCCGGCTAAGTAAGAGATAA
1 GGGCAATCCGGCTAAGTAAGAGATAA
3122799 G
1 G
3122800 TGTTACCAGC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 27 1.00
ACGTcount: A:0.38, C:0.15, G:0.32, T:0.15
Consensus pattern (26 bp):
GGGCAATCCGGCTAAGTAAGAGATAA
Found at i:3123212 original size:46 final size:46
Alignment explanation
Indices: 3123143--3123877 Score: 1034
Period size: 46 Copynumber: 16.0 Consensus size: 46
3123133 GACTAAAAGC
* * *
3123143 AGCAAATCTTGTCTTCCTATATTTGGCAGTGGAGTGGATCGAAGAT
1 AGCAGATCTTGTCTTCCTGTATTTGGCAGCGGAGTGGATCGAAGAT
* * *
3123189 AGCAGATCTTGTCTTCCTGTATTTAGCAGTGGAGTGGATCGAATAT
1 AGCAGATCTTGTCTTCCTGTATTTGGCAGCGGAGTGGATCGAAGAT
*
3123235 AGCAGATCTTGTCTTCCTGTATTTGGCAGCGGAAG-AGATCGAAGAT
1 AGCAGATCTTGTCTTCCTGTATTTGGCAGCGG-AGTGGATCGAAGAT
3123281 AGCAGATCTTGTCTTCCTGTATTTGGCAGCGGAGTGGATCGAAGAT
1 AGCAGATCTTGTCTTCCTGTATTTGGCAGCGGAGTGGATCGAAGAT
* *
3123327 AGCAGATCTTGTTTTCCTGTATTTGGCAGCAGAGTGGATCGAAGAT
1 AGCAGATCTTGTCTTCCTGTATTTGGCAGCGGAGTGGATCGAAGAT
* *
3123373 AGCAGATCTTGTCTTTCTGTATTTGGTAGCGGAG-GAGATCGAAGAT
1 AGCAGATCTTGTCTTCCTGTATTTGGCAGCGGAGTG-GATCGAAGAT
3123419 AGCAGATCTTGTCTTCCTGTATTTGGCAGCGGAGTGGATCGAAGAT
1 AGCAGATCTTGTCTTCCTGTATTTGGCAGCGGAGTGGATCGAAGAT
* *
3123465 AGCAGATCTTATCTTCTTGTATTTGGCAGCGGAG-GAGATCGAAGAT
1 AGCAGATCTTGTCTTCCTGTATTTGGCAGCGGAGTG-GATCGAAGAT
* * *
3123511 AGTAAATCTTGTCTTCCTGTATTTGGCAGCGAAG-GAGATCGAAGAT
1 AGCAGATCTTGTCTTCCTGTATTTGGCAGCGGAGTG-GATCGAAGAT
* * * *
3123557 AGCAGATCTTGTTTTCCTATATTTGGCAGCGAAAG-AGATCGAAGAT
1 AGCAGATCTTGTCTTCCTGTATTTGGCAGCG-GAGTGGATCGAAGAT
* * * *
3123603 AACAGATTTTATCTTCTTGTATTTGGCAGCGGAGTGGATCGAAGAT
1 AGCAGATCTTGTCTTCCTGTATTTGGCAGCGGAGTGGATCGAAGAT
* *
3123649 AGCAGATCTTATCTTCCTGTATTTGGCAGTGGAGTGGATCGAAGAT
1 AGCAGATCTTGTCTTCCTGTATTTGGCAGCGGAGTGGATCGAAGAT
3123695 AGCAGATCTTGTCTTCCTGTATTTGGCAGCGGAGTGGATCGAAGAT
1 AGCAGATCTTGTCTTCCTGTATTTGGCAGCGGAGTGGATCGAAGAT
* * *
3123741 AGCAGATTTTGTCTTCCTATATTTAGCAGCGGAGTGGATCGAAGAT
1 AGCAGATCTTGTCTTCCTGTATTTGGCAGCGGAGTGGATCGAAGAT
* *
3123787 AGCAGATCTTGT-TTTCTGTATTTGGCAGCGGAG-GAGATTGAAGAT
1 AGCAGATCTTGTCTTCCTGTATTTGGCAGCGGAGTG-GATCGAAGAT
** * **
3123832 AGCAGATTCTTGTCTTCCTGTATCCGGCAGCGAAGCAGATCGAAGA
1 AGCAGA-TCTTGTCTTCCTGTATTTGGCAGCGGAGTGGATCGAAGA
3123878 CACAAGCCTG
Statistics
Matches: 621, Mismatches: 57, Indels: 21
0.89 0.08 0.03
Matches are distributed among these distances:
44 1 0.00
45 39 0.06
46 550 0.89
47 31 0.05
ACGTcount: A:0.25, C:0.16, G:0.28, T:0.31
Consensus pattern (46 bp):
AGCAGATCTTGTCTTCCTGTATTTGGCAGCGGAGTGGATCGAAGAT
Found at i:3124091 original size:44 final size:43
Alignment explanation
Indices: 3123973--3124105 Score: 128
Period size: 44 Copynumber: 3.0 Consensus size: 43
3123963 TCAAATTTTG
* * * **
3123973 TCTCTCTGAAGTTGCAGTAGAGCAGGTTAAAATAGCAAAACTTA
1 TCTCCCTGAAGTTGCAGT-GAGCAGATTGAAATAGCAAGTCTTA
* *
3124017 TC-CCCATGAAGTTGTAATGAGGCA-AGTTGAAGATA-CAAGTCTTA
1 TCTCCC-TGAAGTTGCAGTGA-GCAGA-TTGAA-ATAGCAAGTCTTA
3124061 TCTCCCTGAAGTTGCAGTGGAGCAGATTGAAATAGCAAGTCTTA
1 TCTCCCTGAAGTTGCAGT-GAGCAGATTGAAATAGCAAGTCTTA
3124105 T
1 T
3124106 GGAAGCTATA
Statistics
Matches: 72, Mismatches: 9, Indels: 16
0.74 0.09 0.16
Matches are distributed among these distances:
43 7 0.10
44 56 0.78
45 9 0.12
ACGTcount: A:0.33, C:0.17, G:0.23, T:0.28
Consensus pattern (43 bp):
TCTCCCTGAAGTTGCAGTGAGCAGATTGAAATAGCAAGTCTTA
Found at i:3124170 original size:44 final size:44
Alignment explanation
Indices: 3124136--3124284 Score: 129
Period size: 44 Copynumber: 3.4 Consensus size: 44
3124126 CTTACATCTT
*
3124136 TGAAGTTGCAGTAGAGTAGGTTGAAATAACAAACCATGTCTCTC
1 TGAAGTTGCAGTAGAGCAGGTTGAAATAACAAACCATGTCTCTC
* * * * * * *
3124180 TGAAGTTGCAGTAGAGCAGGTTGAAGTCACTAACCTTATCCCCC
1 TGAAGTTGCAGTAGAGCAGGTTGAAATAACAAACCATGTCTCTC
* * ** * * * *
3124224 TGAAGTTGCAGTGGGGCAAATTGAAGCT-ACAAACCTTATCTCCC
1 TGAAGTTGCAGTAGAGCAGGTTGAA-ATAACAAACCATGTCTCTC
*
3124268 CGAAGTTGCAGTAGAGC
1 TGAAGTTGCAGTAGAGC
3124285 CGATCACATC
Statistics
Matches: 86, Mismatches: 18, Indels: 2
0.81 0.17 0.02
Matches are distributed among these distances:
44 85 0.99
45 1 0.01
ACGTcount: A:0.30, C:0.21, G:0.24, T:0.25
Consensus pattern (44 bp):
TGAAGTTGCAGTAGAGCAGGTTGAAATAACAAACCATGTCTCTC
Found at i:3124356 original size:41 final size:42
Alignment explanation
Indices: 3124258--3124368 Score: 154
Period size: 42 Copynumber: 2.7 Consensus size: 42
3124248 AGCTACAAAC
* * *
3124258 CTTATCTCCCCGAAGTTGCAGTAGAGCCGATCACATCCAGTT
1 CTTATCTCTCTGAAGTTGCAGTAGAGCAGATCACATCCAGTT
*
3124300 CTTATCTCTCTGAAGTTGCAGTAGAGCAGATCGCATCCAG-T
1 CTTATCTCTCTGAAGTTGCAGTAGAGCAGATCACATCCAGTT
*
3124341 CTTATC-CTCCTGAAGTTGCAGTGGAGCA
1 CTTATCTCT-CTGAAGTTGCAGTAGAGCA
3124369 TACGAAAGCT
Statistics
Matches: 63, Mismatches: 5, Indels: 3
0.89 0.07 0.04
Matches are distributed among these distances:
40 2 0.03
41 25 0.40
42 36 0.57
ACGTcount: A:0.23, C:0.27, G:0.22, T:0.28
Consensus pattern (42 bp):
CTTATCTCTCTGAAGTTGCAGTAGAGCAGATCACATCCAGTT
Found at i:3124378 original size:127 final size:130
Alignment explanation
Indices: 3124174--3124411 Score: 315
Period size: 127 Copynumber: 1.9 Consensus size: 130
3124164 ACAAACCATG
* * *
3124174 TCTCTCTGAAGTTGCAGTAGAGCAGGTTGAAGTCACTAACCTTATCCCCCTGAAGTTGCAGTGGG
1 TCTCTCTGAAGTTGCAGTAGAGCAGATCGAAGTCACTAACCTTATCCCCCTGAAGTTGCAGTGGA
*
3124239 GCAAATTGAAGCTAC-AAACCTTATCTCCCCGAAGTTGCAGTAGAGCCGATCACATCCAGTTCTT
66 GCAAATCGAAGCTACTAAACC-TATCTCCCCGAAGTTGCAGTAGAGCCGATCACATCCAGTTCTT
3124303 A
130 A
* ** *
3124304 TCTCTCTGAAGTTGCAGTAGAGCAGATCGCA-TC-C-AGTCTTATCCTCCTGAAGTTGCAGTGGA
1 TCTCTCTGAAGTTGCAGTAGAGCAGATCGAAGTCACTAACCTTATCCCCCTGAAGTTGCAGTGGA
* * * *
3124366 GCATA-CGAAAGCTACTAATCCTATCTCCCTGAAGTTGCAGTGGAGC
66 GCAAATCG-AAGCTACTAAACCTATCTCCCCGAAGTTGCAGTAGAGC
3124412 GGATTAAGAC
Statistics
Matches: 94, Mismatches: 12, Indels: 7
0.83 0.11 0.06
Matches are distributed among these distances:
126 1 0.01
127 58 0.62
128 5 0.05
129 2 0.02
130 28 0.30
ACGTcount: A:0.26, C:0.25, G:0.22, T:0.26
Consensus pattern (130 bp):
TCTCTCTGAAGTTGCAGTAGAGCAGATCGAAGTCACTAACCTTATCCCCCTGAAGTTGCAGTGGA
GCAAATCGAAGCTACTAAACCTATCTCCCCGAAGTTGCAGTAGAGCCGATCACATCCAGTTCTTA
Found at i:3125294 original size:6 final size:6
Alignment explanation
Indices: 3125283--3125334 Score: 104
Period size: 6 Copynumber: 8.7 Consensus size: 6
3125273 CGCATTTCTT
3125283 TTTTTA TTTTTA TTTTTA TTTTTA TTTTTA TTTTTA TTTTTA TTTTTA
1 TTTTTA TTTTTA TTTTTA TTTTTA TTTTTA TTTTTA TTTTTA TTTTTA
3125331 TTTT
1 TTTT
3125335 GTATATTATA
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 46 1.00
ACGTcount: A:0.15, C:0.00, G:0.00, T:0.85
Consensus pattern (6 bp):
TTTTTA
Found at i:3126048 original size:3 final size:3
Alignment explanation
Indices: 3126042--3126124 Score: 166
Period size: 3 Copynumber: 27.7 Consensus size: 3
3126032 ACTAATTAGT
3126042 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
3126090 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
3126125 GTCATTTACC
Statistics
Matches: 80, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 80 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:3126188 original size:14 final size:14
Alignment explanation
Indices: 3126165--3126199 Score: 52
Period size: 14 Copynumber: 2.5 Consensus size: 14
3126155 TTGTTATATA
*
3126165 TATATGTACATACT
1 TATATATACATACT
3126179 TATATATACATACT
1 TATATATACATACT
*
3126193 TACATAT
1 TATATAT
3126200 GTACTTTTAT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.40, C:0.14, G:0.03, T:0.43
Consensus pattern (14 bp):
TATATATACATACT
Found at i:3127495 original size:16 final size:16
Alignment explanation
Indices: 3127474--3127507 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 16
3127464 TTATAATCAT
3127474 AATTAATATATT-AATA
1 AATTAAT-TATTGAATA
3127490 AATTAATTATTGAATA
1 AATTAATTATTGAATA
3127506 AA
1 AA
3127508 ATATAATGAT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 4 0.24
16 13 0.76
ACGTcount: A:0.56, C:0.00, G:0.03, T:0.41
Consensus pattern (16 bp):
AATTAATTATTGAATA
Found at i:3133448 original size:24 final size:25
Alignment explanation
Indices: 3133405--3133451 Score: 78
Period size: 24 Copynumber: 1.9 Consensus size: 25
3133395 GCGTGTGAAA
3133405 ATTAAGTTATAAATTTTATTATTGT
1 ATTAAGTTATAAATTTTATTATTGT
*
3133430 ATTAATTTAT-AATTTTATTATT
1 ATTAAGTTATAAATTTTATTATT
3133452 CTAGTAGGGT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
24 12 0.57
25 9 0.43
ACGTcount: A:0.36, C:0.00, G:0.04, T:0.60
Consensus pattern (25 bp):
ATTAAGTTATAAATTTTATTATTGT
Found at i:3134657 original size:18 final size:17
Alignment explanation
Indices: 3134634--3134667 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
3134624 TTTTTTTTCG
3134634 TTAAAAAATAACATTAAA
1 TTAAAAAATAA-ATTAAA
*
3134652 TTAAAAAGTAAATTAA
1 TTAAAAAATAAATTAA
3134668 TTATTTTTAT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 5 0.33
18 10 0.67
ACGTcount: A:0.65, C:0.03, G:0.03, T:0.29
Consensus pattern (17 bp):
TTAAAAAATAAATTAAA
Found at i:3139106 original size:49 final size:47
Alignment explanation
Indices: 3138947--3139106 Score: 149
Period size: 49 Copynumber: 3.3 Consensus size: 47
3138937 TTATGTGTTC
* * * *
3138947 TGCATTTAATTAAGTCATGCATTAAAGCATCTCATATGTTCATAAAGTT
1 TGCATTTAATTATGTCATGCATT-AAGTAACTCATATGTTCATTAA-TT
** * * * *
3138996 TGTGTTTTAATTATGTCATGTATTAAGTAACTCCTATGTTAATTAAGT
1 TG-CATTTAATTATGTCATGCATTAAGTAACTCATATGTTCATTAATT
* *
3139044 TGCATCTTAAATTATGTCATGCATTATGTAACTCATTTGTTCATTTAATT
1 TGCAT-TT-AATTATGTCATGCATTAAGTAACTCATATGTTCA-TTAATT
3139094 TGCATTTCAATTA
1 TGCATTT-AATTA
3139107 AACCATGCAT
Statistics
Matches: 88, Mismatches: 19, Indels: 8
0.77 0.17 0.07
Matches are distributed among these distances:
47 1 0.01
48 5 0.06
49 55 0.62
50 27 0.31
ACGTcount: A:0.31, C:0.12, G:0.12, T:0.45
Consensus pattern (47 bp):
TGCATTTAATTATGTCATGCATTAAGTAACTCATATGTTCATTAATT
Found at i:3141405 original size:2 final size:2
Alignment explanation
Indices: 3141398--3141423 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
3141388 ATAAATAAAT
3141398 TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA
3141424 AAGTGGTAAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Done.