Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold18
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: 4432388
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Warning! 63034 characters in sequence are not A, C, G, or T
File 21 of 27
Found at i:3389286 original size:13 final size:13
Alignment explanation
Indices: 3389268--3389293 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
3389258 TACACACAAG
3389268 ATGTATCGATACA
1 ATGTATCGATACA
3389281 ATGTATCGATACA
1 ATGTATCGATACA
3389294 TCCCAAAATG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:3389310 original size:33 final size:32
Alignment explanation
Indices: 3389250--3389313 Score: 101
Period size: 33 Copynumber: 2.0 Consensus size: 32
3389240 CTTAACTGTT
*
3389250 TGTATCGATACACACAAGATGTATCGATACAA
1 TGTATCGATACACACAAAATGTATCGATACAA
*
3389282 TGTATCGATACATCCCAAAATGTATCGATACA
1 TGTATCGATACA-CACAAAATGTATCGATACA
3389314 TTGGCTTGTA
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
32 12 0.41
33 17 0.59
ACGTcount: A:0.39, C:0.20, G:0.14, T:0.27
Consensus pattern (32 bp):
TGTATCGATACACACAAAATGTATCGATACAA
Found at i:3398750 original size:20 final size:20
Alignment explanation
Indices: 3398725--3398772 Score: 87
Period size: 20 Copynumber: 2.4 Consensus size: 20
3398715 ACCCTAGAAA
*
3398725 GTATCGATGCATTATGCTTT
1 GTATCGATGCATTAAGCTTT
3398745 GTATCGATGCATTAAGCTTT
1 GTATCGATGCATTAAGCTTT
3398765 GTATCGAT
1 GTATCGAT
3398773 ACATGTTCAT
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 27 1.00
ACGTcount: A:0.23, C:0.15, G:0.21, T:0.42
Consensus pattern (20 bp):
GTATCGATGCATTAAGCTTT
Found at i:3398787 original size:19 final size:20
Alignment explanation
Indices: 3398763--3398813 Score: 59
Period size: 19 Copynumber: 2.6 Consensus size: 20
3398753 GCATTAAGCT
***
3398763 TTGTATCGATACATGTTC-A
1 TTGTATCGATACACACTCAA
*
3398782 TTGTATCGTTACACACTCAA
1 TTGTATCGATACACACTCAA
3398802 TTGTATCGATAC
1 TTGTATCGATAC
3398814 CTAAAACTGC
Statistics
Matches: 26, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
19 14 0.54
20 12 0.46
ACGTcount: A:0.27, C:0.20, G:0.14, T:0.39
Consensus pattern (20 bp):
TTGTATCGATACACACTCAA
Found at i:3400125 original size:7 final size:6
Alignment explanation
Indices: 3400115--3400145 Score: 53
Period size: 6 Copynumber: 5.0 Consensus size: 6
3400105 TCCTTTTTAG
3400115 TTTTTC TTTTTC TTTTTTC TTTTTC TTTTTC
1 TTTTTC TTTTTC -TTTTTC TTTTTC TTTTTC
3400146 AAAACCTTTA
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
6 18 0.75
7 6 0.25
ACGTcount: A:0.00, C:0.16, G:0.00, T:0.84
Consensus pattern (6 bp):
TTTTTC
Found at i:3400131 original size:19 final size:19
Alignment explanation
Indices: 3400107--3400145 Score: 60
Period size: 19 Copynumber: 2.1 Consensus size: 19
3400097 TGTCTCATTC
*
3400107 CTTTTTAGTTTTTCTTTTT
1 CTTTTTACTTTTTCTTTTT
*
3400126 CTTTTTTCTTTTTCTTTTT
1 CTTTTTACTTTTTCTTTTT
3400145 C
1 C
3400146 AAAACCTTTA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.03, C:0.15, G:0.03, T:0.79
Consensus pattern (19 bp):
CTTTTTACTTTTTCTTTTT
Found at i:3400139 original size:13 final size:13
Alignment explanation
Indices: 3400115--3400144 Score: 60
Period size: 13 Copynumber: 2.3 Consensus size: 13
3400105 TCCTTTTTAG
3400115 TTTTTCTTTTTCT
1 TTTTTCTTTTTCT
3400128 TTTTTCTTTTTCT
1 TTTTTCTTTTTCT
3400141 TTTT
1 TTTT
3400145 CAAAACCTTT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.00, C:0.13, G:0.00, T:0.87
Consensus pattern (13 bp):
TTTTTCTTTTTCT
Found at i:3407582 original size:20 final size:20
Alignment explanation
Indices: 3407557--3407633 Score: 84
Period size: 20 Copynumber: 3.9 Consensus size: 20
3407547 GTAAAAAGAT
3407557 AGAATGTATCGATACATTGA
1 AGAATGTATCGATACATTGA
* *
3407577 AGAATGTATCAATACATTTA
1 AGAATGTATCGATACATTGA
*
3407597 TA-CATGTATCGATACATTGA
1 -AGAATGTATCGATACATTGA
* * *
3407617 AAAATATATTGATACAT
1 AGAATGTATCGATACAT
3407634 CTGGGTAACA
Statistics
Matches: 47, Mismatches: 8, Indels: 4
0.80 0.14 0.07
Matches are distributed among these distances:
19 1 0.02
20 45 0.96
21 1 0.02
ACGTcount: A:0.43, C:0.10, G:0.13, T:0.34
Consensus pattern (20 bp):
AGAATGTATCGATACATTGA
Found at i:3407664 original size:91 final size:91
Alignment explanation
Indices: 3407536--3407704 Score: 241
Period size: 91 Copynumber: 1.9 Consensus size: 91
3407526 TCAATGTATC
* * * * * *
3407536 GATACATCTGGGTAAAAAGATAGAATGTATCGATACATTGA-AGAATGTATCAATACATTTATAC
1 GATACATCTGGGTAAAAAGACAGAATATATCGATACATTCATA-AATGTATCAATACATTGAAAA
3407600 ATGTATCGATACATTGAAAAATATATT
65 ATGTATCGATACATTGAAAAATATATT
* * *
3407627 GATACATCTGGGTAACAAGACAGAATATATCGATACATTCATACATGTATCCATACATTGAAAAA
1 GATACATCTGGGTAAAAAGACAGAATATATCGATACATTCATAAATGTATCAATACATTGAAAAA
3407692 TGTATCGATACAT
66 TGTATCGATACAT
3407705 CTGGGTAAAA
Statistics
Matches: 68, Mismatches: 9, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
91 67 0.99
92 1 0.01
ACGTcount: A:0.42, C:0.13, G:0.15, T:0.30
Consensus pattern (91 bp):
GATACATCTGGGTAAAAAGACAGAATATATCGATACATTCATAAATGTATCAATACATTGAAAAA
TGTATCGATACATTGAAAAATATATT
Found at i:3407682 original size:20 final size:20
Alignment explanation
Indices: 3407654--3407704 Score: 66
Period size: 20 Copynumber: 2.5 Consensus size: 20
3407644 AGACAGAATA
* *
3407654 TATCGATACATTCATACATG
1 TATCGATACATTCAAAAATG
* *
3407674 TATCCATACATTGAAAAATG
1 TATCGATACATTCAAAAATG
3407694 TATCGATACAT
1 TATCGATACAT
3407705 CTGGGTAAAA
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 26 1.00
ACGTcount: A:0.39, C:0.18, G:0.10, T:0.33
Consensus pattern (20 bp):
TATCGATACATTCAAAAATG
Found at i:3407699 original size:40 final size:39
Alignment explanation
Indices: 3407654--3407776 Score: 118
Period size: 40 Copynumber: 3.3 Consensus size: 39
3407644 AGACAGAATA
3407654 TATCGATACATTCATACATGTATCCATACATTGAAAAATG
1 TATCGATACATTCATACATGTAT-CATACATTGAAAAATG
** ** *
3407694 TATCGATACA-TC-T--GGGTA--A-A-AAAGACAGAATG
1 TATCGATACATTCATACATGTATCATACATTGA-AAAATG
3407726 TATCGATACATTCATACATGTATCGATACATTGAAAAATG
1 TATCGATACATTCATACATGTATC-ATACATTGAAAAATG
3407766 TATCGATACAT
1 TATCGATACAT
3407777 CTGGGTAAAA
Statistics
Matches: 63, Mismatches: 10, Indels: 20
0.68 0.11 0.22
Matches are distributed among these distances:
31 3 0.05
32 16 0.25
33 3 0.05
34 1 0.02
36 6 0.10
38 1 0.02
39 3 0.05
40 27 0.43
41 3 0.05
ACGTcount: A:0.41, C:0.15, G:0.14, T:0.30
Consensus pattern (39 bp):
TATCGATACATTCATACATGTATCATACATTGAAAAATG
Found at i:3407748 original size:20 final size:20
Alignment explanation
Indices: 3407722--3407776 Score: 83
Period size: 20 Copynumber: 2.8 Consensus size: 20
3407712 AAAAAGACAG
*
3407722 AATGTATCGATACATTCATA
1 AATGTATCGATACATTCAAA
* *
3407742 CATGTATCGATACATTGAAA
1 AATGTATCGATACATTCAAA
3407762 AATGTATCGATACAT
1 AATGTATCGATACAT
3407777 CTGGGTAAAA
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.40, C:0.15, G:0.13, T:0.33
Consensus pattern (20 bp):
AATGTATCGATACATTCAAA
Found at i:3407748 original size:72 final size:72
Alignment explanation
Indices: 3407577--3407787 Score: 352
Period size: 72 Copynumber: 2.9 Consensus size: 72
3407567 GATACATTGA
* * * *
3407577 AGAATGTATCAATACATTTATACATGTATCGATACATTGAAAAATATATTGATACATCTGGGT-A
1 AGAATGTATCGATACATTCATACATGTATCGATACATTGAAAAATGTATCGATACATCTGGGTAA
*
3407641 ACAAGAC
66 AAAAGAC
* *
3407648 AGAATATATCGATACATTCATACATGTATCCATACATTGAAAAATGTATCGATACATCTGGGTAA
1 AGAATGTATCGATACATTCATACATGTATCGATACATTGAAAAATGTATCGATACATCTGGGTAA
3407713 AAAAGAC
66 AAAAGAC
3407720 AGAATGTATCGATACATTCATACATGTATCGATACATTGAAAAATGTATCGATACATCTGGGTAA
1 AGAATGTATCGATACATTCATACATGTATCGATACATTGAAAAATGTATCGATACATCTGGGTAA
3407785 AAA
66 AAA
3407788 CGTGACTTTT
Statistics
Matches: 130, Mismatches: 9, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
71 57 0.44
72 73 0.56
ACGTcount: A:0.42, C:0.14, G:0.15, T:0.29
Consensus pattern (72 bp):
AGAATGTATCGATACATTCATACATGTATCGATACATTGAAAAATGTATCGATACATCTGGGTAA
AAAAGAC
Found at i:3408786 original size:30 final size:28
Alignment explanation
Indices: 3408647--3409104 Score: 386
Period size: 28 Copynumber: 15.9 Consensus size: 28
3408637 ATAAAAAAAA
* *
3408647 GGTGCCACTAACTTGTGTGGGCTTCGAAAAG
1 GGTGCCACTGAC-T-TGTGGGCTTTG-AAAG
* * * *
3408678 AGTTGCCACCGACTTGTGTCGGATTTGAAGG
1 -GGTGCCACTGACTTGTG--GGCTTTGAAAG
* * **
3408709 GGTACCACTGACTTATGGTTTTTGAAAG
1 GGTGCCACTGACTTGTGGGCTTTGAAAG
*
3408737 GGTGCCACTGACTTGTGGGCTTTGGAAG
1 GGTGCCACTGACTTGTGGGCTTTGAAAG
*
3408765 GGTGCCACTGATTTGTGTGGGCTTTGAAAG
1 GGTGCCACTGA-CT-TGTGGGCTTTGAAAG
*
3408795 GGTATGCCACTGACTTGTGGGCTTTGAAGG
1 GG--TGCCACTGACTTGTGGGCTTTGAAAG
*
3408825 GGTACCACTGACTTGTGGGCTTTGAAAG
1 GGTGCCACTGACTTGTGGGCTTTGAAAG
* * *
3408853 GATGCCA-TAACTTGTGGTCTTTTG-AAG
1 GGTGCCACTGACTTGTGGGC-TTTGAAAG
* *
3408880 AGATGCCATTGACTTGTGGGCTTTGAAAAG
1 -GGTGCCACTGACTTGTGGGCTTTG-AAAG
* *
3408910 AGTTGCCACCGACTTGTGTGGGCTTTGAAAG
1 -GGTGCCACTGAC-T-TGTGGGCTTTGAAAG
3408941 GGTGCCA-TCGAC-TGTGGGCTTTGAAAG
1 GGTGCCACT-GACTTGTGGGCTTTGAAAG
**
3408968 GGTGTTACTGACTTGT-GGCTTTGAAAG
1 GGTGCCACTGACTTGTGGGCTTTGAAAG
** * * * *
3408995 AATACCACTAACGTGTGGGCTTTAAAAG
1 GGTGCCACTGACTTGTGGGCTTTGAAAG
* *
3409023 GATGCCACTAACTTGTGGGCTTTGAAAG
1 GGTGCCACTGACTTGTGGGCTTTGAAAG
* * *
3409051 GATGCCACTAACTTGTGGGCTTTGAAAA
1 GGTGCCACTGACTTGTGGGCTTTGAAAG
* * * *
3409079 GATGCCACTAACCTATGGGCTTTGAA
1 GGTGCCACTGACTTGTGGGCTTTGAA
3409105 GAGATGAACG
Statistics
Matches: 357, Mismatches: 52, Indels: 38
0.80 0.12 0.09
Matches are distributed among these distances:
27 56 0.16
28 175 0.49
29 11 0.03
30 71 0.20
31 10 0.03
32 34 0.10
ACGTcount: A:0.22, C:0.17, G:0.31, T:0.30
Consensus pattern (28 bp):
GGTGCCACTGACTTGTGGGCTTTGAAAG
Found at i:3409040 original size:198 final size:203
Alignment explanation
Indices: 3408729--3409104 Score: 505
Period size: 198 Copynumber: 1.9 Consensus size: 203
3408719 ACTTATGGTT
* *
3408729 TTTGAAAGGGTGCCACTGACTTGTGGGCTTTGGAAGGGTGCCACTGATTTGTGTGGGCTTTGAAA
1 TTTGAAAGGGTGCCACTGACTTGTGGGCTTTGAAAGGGTGCCACTGATCTGTGTGGGCTTTGAAA
* * * * * * * *
3408794 GGGTATGCCACTGACTTGTGGGCTTTGAAGGGGTACCACTGACTTGTGGGCTTTGAAAGGATGCC
66 -GGAATACCACTAACGTGTGGGCTTTAAAAGGATACCACTAACTTGTGGGCTTTGAAAGGATGCC
* * * * * *
3408859 A-TAACTTGTGGTCTTTTGAAGAGATGCCATTGACTTGTGGGCTTTGAAAAGAGTTGCCACCGAC
130 ACTAACTTGTGGGC-TTTGAAAAGATGCCACTAACCTATGGGCTTTGAAAAGAGTTGCCACCGAC
3408923 TTGTGTGGGC
194 TTGTGTGGGC
**
3408933 TTTGAAAGGGTGCCA-TCGAC-TGTGGGCTTTGAAAGGGTGTTACTGA-CT-TGT-GGCTTTGAA
1 TTTGAAAGGGTGCCACT-GACTTGTGGGCTTTGAAAGGGTGCCACTGATCTGTGTGGGCTTTGAA
*
3408993 A-GAATACCACTAACGTGTGGGCTTTAAAAGGATGCCACTAACTTGTGGGCTTTGAAAGGATGCC
65 AGGAATACCACTAACGTGTGGGCTTTAAAAGGATACCACTAACTTGTGGGCTTTGAAAGGATGCC
3409057 ACTAACTTGTGGGCTTTGAAAAGATGCCACTAACCTATGGGCTTTGAA
130 ACTAACTTGTGGGCTTTGAAAAGATGCCACTAACCTATGGGCTTTGAA
3409105 GAGATGAACG
Statistics
Matches: 151, Mismatches: 19, Indels: 10
0.84 0.11 0.06
Matches are distributed among these distances:
198 84 0.56
199 11 0.07
200 10 0.07
201 3 0.02
202 1 0.01
203 24 0.16
204 18 0.12
ACGTcount: A:0.23, C:0.16, G:0.31, T:0.30
Consensus pattern (203 bp):
TTTGAAAGGGTGCCACTGACTTGTGGGCTTTGAAAGGGTGCCACTGATCTGTGTGGGCTTTGAAA
GGAATACCACTAACGTGTGGGCTTTAAAAGGATACCACTAACTTGTGGGCTTTGAAAGGATGCCA
CTAACTTGTGGGCTTTGAAAAGATGCCACTAACCTATGGGCTTTGAAAAGAGTTGCCACCGACTT
GTGTGGGC
Found at i:3410269 original size:13 final size:13
Alignment explanation
Indices: 3410251--3410276 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
3410241 CAATTTTTTG
3410251 TGTATCGATACAT
1 TGTATCGATACAT
3410264 TGTATCGATACAT
1 TGTATCGATACAT
3410277 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:3411538 original size:17 final size:15
Alignment explanation
Indices: 3411518--3411595 Score: 61
Period size: 17 Copynumber: 4.8 Consensus size: 15
3411508 TAAACCCCTT
3411518 TTTGTTTGTTTATTTTG
1 TTTGTTT-TTT-TTTTG
3411535 TTTGTTTTTTTTTTGG
1 TTTGTTTTTTTTTT-G
3411551 TTT-TTTTCTGTTTTT-
1 TTTGTTTT-T-TTTTTG
*
3411566 TATTGTTTTTTTATTTTT
1 T-TTG-TTTTTT-TTTTG
3411584 TTTGTTTTTTTT
1 TTTGTTTTTTTT
3411596 GTACGAATGA
Statistics
Matches: 53, Mismatches: 0, Indels: 18
0.75 0.00 0.25
Matches are distributed among these distances:
15 11 0.21
16 17 0.32
17 20 0.38
18 5 0.09
ACGTcount: A:0.04, C:0.01, G:0.12, T:0.83
Consensus pattern (15 bp):
TTTGTTTTTTTTTTG
Found at i:3411554 original size:10 final size:9
Alignment explanation
Indices: 3411516--3411597 Score: 80
Period size: 9 Copynumber: 9.1 Consensus size: 9
3411506 TCTAAACCCC
3411516 TTTTTGTTTG
1 TTTTT-TTTG
*
3411526 TTTATTTTG
1 TTTTTTTTG
*
3411535 -TTTGTTT-
1 TTTTTTTTG
*
3411542 TTTTTTTGG
1 TTTTTTTTG
3411551 TTTTTTTCTG
1 TTTTTTT-TG
3411561 TTTTTTATTG
1 TTTTTT-TTG
*
3411571 -TTTTTTTA
1 TTTTTTTTG
3411579 TTTTTTTTG
1 TTTTTTTTG
3411588 TTTTTTTTG
1 TTTTTTTTG
3411597 T
1 T
3411598 ACGAATGATG
Statistics
Matches: 59, Mismatches: 8, Indels: 11
0.76 0.10 0.14
Matches are distributed among these distances:
8 12 0.20
9 33 0.56
10 13 0.22
11 1 0.02
ACGTcount: A:0.04, C:0.01, G:0.12, T:0.83
Consensus pattern (9 bp):
TTTTTTTTG
Found at i:3417114 original size:19 final size:18
Alignment explanation
Indices: 3417052--3417150 Score: 74
Period size: 19 Copynumber: 5.8 Consensus size: 18
3417042 AATTTCAACG
3417052 ATTTGTATCGATACATAA
1 ATTTGTATCGATACATAA
3417070 AGTGTTGTATCGATAC---A
1 A-T-TTGTATCGATACATAA
*
3417087 A--TCTATCGATACATAA
1 ATTTGTATCGATACATAA
3417103 ATGTTGTATCGATAC---A
1 AT-TTGTATCGATACATAA
3417119 A--TGTATCGATACATAA
1 ATTTGTATCGATACATAA
*
3417135 GTTTTGTATCGATACA
1 -ATTTGTATCGATACA
3417151 ATGTAAGCTA
Statistics
Matches: 64, Mismatches: 3, Indels: 27
0.68 0.03 0.29
Matches are distributed among these distances:
13 21 0.33
16 5 0.08
17 2 0.03
18 1 0.02
19 23 0.36
20 12 0.19
ACGTcount: A:0.35, C:0.13, G:0.15, T:0.36
Consensus pattern (18 bp):
ATTTGTATCGATACATAA
Found at i:3417125 original size:13 final size:13
Alignment explanation
Indices: 3417107--3417131 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
3417097 ACATAAATGT
3417107 TGTATCGATACAA
1 TGTATCGATACAA
3417120 TGTATCGATACA
1 TGTATCGATACA
3417132 TAAGTTTTGT
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:3417153 original size:32 final size:32
Alignment explanation
Indices: 3417055--3417155 Score: 166
Period size: 32 Copynumber: 3.1 Consensus size: 32
3417045 TTCAACGATT
3417055 TGTATCGATACATAAAGTGTTGTATCGATACAA
1 TGTATCGATACAT-AAGTGTTGTATCGATACAA
* *
3417088 TCTATCGATACATAAATGTTGTATCGATACAA
1 TGTATCGATACATAAGTGTTGTATCGATACAA
*
3417120 TGTATCGATACATAAGTTTTGTATCGATACAA
1 TGTATCGATACATAAGTGTTGTATCGATACAA
3417152 TGTA
1 TGTA
3417156 AGCTACTGCC
Statistics
Matches: 63, Mismatches: 5, Indels: 1
0.91 0.07 0.01
Matches are distributed among these distances:
32 51 0.81
33 12 0.19
ACGTcount: A:0.36, C:0.13, G:0.16, T:0.36
Consensus pattern (32 bp):
TGTATCGATACATAAGTGTTGTATCGATACAA
Found at i:3417211 original size:13 final size:13
Alignment explanation
Indices: 3417193--3417217 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
3417183 ATTACTCAAA
3417193 TGTATCGATACAT
1 TGTATCGATACAT
3417206 TGTATCGATACA
1 TGTATCGATACA
3417218 CTGATCTTTG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:3417270 original size:52 final size:52
Alignment explanation
Indices: 3417226--3417354 Score: 249
Period size: 52 Copynumber: 2.5 Consensus size: 52
3417216 CACTGATCTT
3417226 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATAAAA
1 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATAAAA
3417278 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATAAAA
1 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATAAAA
*
3417330 TGTATCGATACATGCACGCAAATTT
1 TGTATCGATACATGCAGGCAAATTT
3417355 TCATATTTCG
Statistics
Matches: 76, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
52 76 1.00
ACGTcount: A:0.36, C:0.19, G:0.17, T:0.28
Consensus pattern (52 bp):
TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATAAAA
Found at i:3421451 original size:13 final size:13
Alignment explanation
Indices: 3421433--3421458 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
3421423 TACAGCAAGT
3421433 ATGTATCGATACA
1 ATGTATCGATACA
3421446 ATGTATCGATACA
1 ATGTATCGATACA
3421459 CAAAAAATTG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:3423706 original size:21 final size:21
Alignment explanation
Indices: 3423673--3423717 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 21
3423663 TTGCAAGTTG
*
3423673 AAATAAAGAAGTTGGCTAATGA
1 AAATAAAGAAGTTAGCTAA-GA
*
3423695 AAATAATG-AGTTAGCTAAGA
1 AAATAAAGAAGTTAGCTAAGA
3423715 AAA
1 AAA
3423718 ATGAAAACTT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 5 0.24
21 9 0.43
22 7 0.33
ACGTcount: A:0.53, C:0.04, G:0.20, T:0.22
Consensus pattern (21 bp):
AAATAAAGAAGTTAGCTAAGA
Found at i:3425540 original size:15 final size:15
Alignment explanation
Indices: 3425520--3425550 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
3425510 TAAAAATGTC
*
3425520 CAAAATGAGGAAGCT
1 CAAAATGAAGAAGCT
3425535 CAAAATGAAGAAGCT
1 CAAAATGAAGAAGCT
3425550 C
1 C
3425551 CAAACGAAAT
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:0.48, C:0.16, G:0.23, T:0.13
Consensus pattern (15 bp):
CAAAATGAAGAAGCT
Found at i:3427641 original size:13 final size:13
Alignment explanation
Indices: 3427623--3427648 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
3427613 ACATTTTTCT
3427623 TTGTATCGATACA
1 TTGTATCGATACA
3427636 TTGTATCGATACA
1 TTGTATCGATACA
3427649 AGGTGATTAT
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):
TTGTATCGATACA
Found at i:3430215 original size:13 final size:13
Alignment explanation
Indices: 3430197--3430222 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
3430187 TACAGCAAGT
3430197 ATGTATCGATACA
1 ATGTATCGATACA
3430210 ATGTATCGATACA
1 ATGTATCGATACA
3430223 CAAAAAATTG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:3434798 original size:52 final size:52
Alignment explanation
Indices: 3434733--3434861 Score: 240
Period size: 52 Copynumber: 2.5 Consensus size: 52
3434723 CCGAATATGA
*
3434733 AAATTTGCATGCATGTATCGATACATTTAATAGTGTATCGATACATCTGGGC
1 AAATTTGCCTGCATGTATCGATACATTTAATAGTGTATCGATACATCTGGGC
*
3434785 AAATTTGCCTGCATGTATCGATACATTTTATAGTGTATCGATACATCTGGGC
1 AAATTTGCCTGCATGTATCGATACATTTAATAGTGTATCGATACATCTGGGC
3434837 AAATTTGCCTGCATGTATCGATACA
1 AAATTTGCCTGCATGTATCGATACA
3434862 AAGATCAGTG
Statistics
Matches: 75, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
52 75 1.00
ACGTcount: A:0.29, C:0.17, G:0.19, T:0.35
Consensus pattern (52 bp):
AAATTTGCCTGCATGTATCGATACATTTAATAGTGTATCGATACATCTGGGC
Found at i:3434872 original size:52 final size:51
Alignment explanation
Indices: 3434733--3434881 Score: 228
Period size: 52 Copynumber: 2.9 Consensus size: 51
3434723 CCGAATATGA
*
3434733 AAATTTGCATGCATGTATCGATACATTTAATAGTGTATCGATACATCTGGGC
1 AAATTTGCCTGCATGTATCGATACA-TTAATAGTGTATCGATACATCTGGGC
*
3434785 AAATTTGCCTGCATGTATCGATACATTTTATAGTGTATCGATACATCTGGGC
1 AAATTTGCCTGCATGTATCGATACA-TTAATAGTGTATCGATACATCTGGGC
*
3434837 AAATTTGCCTGCATGTATCGATACA-AAGATCAGTGTATCGATACA
1 AAATTTGCCTGCATGTATCGATACATTA-AT-AGTGTATCGATACA
3434882 ATGTATCGAT
Statistics
Matches: 91, Mismatches: 4, Indels: 4
0.92 0.04 0.04
Matches are distributed among these distances:
51 2 0.02
52 89 0.98
ACGTcount: A:0.31, C:0.17, G:0.19, T:0.34
Consensus pattern (51 bp):
AAATTTGCCTGCATGTATCGATACATTAATAGTGTATCGATACATCTGGGC
Found at i:3434888 original size:13 final size:13
Alignment explanation
Indices: 3434870--3434894 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
3434860 CAAAGATCAG
3434870 TGTATCGATACAA
1 TGTATCGATACAA
3434883 TGTATCGATACA
1 TGTATCGATACA
3434895 TTTGGGTAGT
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:3434961 original size:19 final size:18
Alignment explanation
Indices: 3434937--3434999 Score: 73
Period size: 19 Copynumber: 3.7 Consensus size: 18
3434927 TAGCTTACAT
3434937 TGTATCGATACAAAACTTA
1 TGTATCGATAC-AAACTTA
3434956 TGTATCGATAC--A--T-
1 TGTATCGATACAAACTTA
3434969 TGTATCGATACAACACTTA
1 TGTATCGATACAA-ACTTA
3434988 TGTATCGATACA
1 TGTATCGATACA
3435000 TTGTATCGAT
Statistics
Matches: 38, Mismatches: 0, Indels: 12
0.76 0.00 0.24
Matches are distributed among these distances:
13 11 0.29
14 1 0.03
16 2 0.05
18 1 0.03
19 23 0.61
ACGTcount: A:0.37, C:0.17, G:0.13, T:0.33
Consensus pattern (18 bp):
TGTATCGATACAAACTTA
Found at i:3434973 original size:32 final size:32
Alignment explanation
Indices: 3434932--3435014 Score: 157
Period size: 32 Copynumber: 2.6 Consensus size: 32
3434922 GGCAGTAGCT
3434932 TACATTGTATCGATACAAAACTTATGTATCGA
1 TACATTGTATCGATACAAAACTTATGTATCGA
*
3434964 TACATTGTATCGATACAACACTTATGTATCGA
1 TACATTGTATCGATACAAAACTTATGTATCGA
3434996 TACATTGTATCGATACAAA
1 TACATTGTATCGATACAAA
3435015 TCGTTGAAAT
Statistics
Matches: 49, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
32 49 1.00
ACGTcount: A:0.37, C:0.17, G:0.12, T:0.34
Consensus pattern (32 bp):
TACATTGTATCGATACAAAACTTATGTATCGA
Found at i:3434974 original size:13 final size:13
Alignment explanation
Indices: 3434956--3435012 Score: 60
Period size: 13 Copynumber: 3.9 Consensus size: 13
3434946 ACAAAACTTA
3434956 TGTATCGATACAT
1 TGTATCGATACAT
3434969 TGTATCGATACAACACTT
1 TGTATCGAT---ACA--T
3434987 ATGTATCGATACAT
1 -TGTATCGATACAT
3435001 TGTATCGATACA
1 TGTATCGATACA
3435013 AATCGTTGAA
Statistics
Matches: 38, Mismatches: 0, Indels: 12
0.76 0.00 0.24
Matches are distributed among these distances:
13 21 0.55
14 1 0.03
16 6 0.16
18 1 0.03
19 9 0.24
ACGTcount: A:0.33, C:0.18, G:0.14, T:0.35
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:3435925 original size:67 final size:68
Alignment explanation
Indices: 3435803--3435929 Score: 184
Period size: 67 Copynumber: 1.9 Consensus size: 68
3435793 ATTGGGTTTT
* * *
3435803 AAAGATGATGAAGGTGCCAATATGCTGATTCAAGGCCAGCAATATTGGACTTAAAGATGAAGATG
1 AAAGATGATAAAGATGCCAATATGCTGATTCAAGGCCAACAATATTGGACTTAAAGATGAAGATG
3435868 AGA
66 AGA
* * * *
3435871 AAAG-TGATAAAGATGCCAATATGTTGATTCACGGCCAACGATATTGGGCTTAAAGATGA
1 AAAGATGATAAAGATGCCAATATGCTGATTCAAGGCCAACAATATTGGACTTAAAGATGA
3435930 GAAAAAGGAT
Statistics
Matches: 52, Mismatches: 7, Indels: 1
0.87 0.12 0.02
Matches are distributed among these distances:
67 48 0.92
68 4 0.08
ACGTcount: A:0.39, C:0.13, G:0.25, T:0.24
Consensus pattern (68 bp):
AAAGATGATAAAGATGCCAATATGCTGATTCAAGGCCAACAATATTGGACTTAAAGATGAAGATG
AGA
Found at i:3435979 original size:55 final size:52
Alignment explanation
Indices: 3435879--3436809 Score: 535
Period size: 43 Copynumber: 19.9 Consensus size: 52
3435869 GAAAAGTGAT
* * * * * * **
3435879 AAAGATGCCAATATGTTGATTCACGGCCAACGATATTGGGCTTAAAGATGAGAA
1 AAAGGTGCCAATATGCTGATTCAAGGCCAGCTACATTGAACTTAAAGATG-G-A
* *
3435933 AAAGGATGTCAATGTGCTGATTCAAGGCCAGCTACATTGAACTTAAAGATGGA
1 AAAGG-TGCCAATATGCTGATTCAAGGCCAGCTACATTGAACTTAAAGATGGA
* *
3435986 AAAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGAC-T-----T---
1 AAAGGTGCCAATATGCTGATTCAAGGCCAGCTACATTGAACTTAAAGATGGA
*
3436029 AAAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGAACTTAAAGA---A
1 AAAGGTGCCAATATGCTGATTCAAGGCCAGCTACATTGAACTTAAAGATGGA
* * *
3436078 GAAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGAC-T-----T---
1 AAAGGTGCCAATATGCTGATTCAAGGCCAGCTACATTGAACTTAAAGATGGA
* *
3436121 AAAGGTGCCAATGTGCTAATTCAAGGCCAGCTACATTGAACTTAAAGA---A
1 AAAGGTGCCAATATGCTGATTCAAGGCCAGCTACATTGAACTTAAAGATGGA
* * * *
3436170 GAAGGTGCCAATATGCTGATTCAAGGCCAGCGATATTGGAC-T-----T---
1 AAAGGTGCCAATATGCTGATTCAAGGCCAGCTACATTGAACTTAAAGATGGA
* *
3436213 AAAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGGA
1 AAAGGTGCCAATATGCTGATTCAAGGCCAGCTACATTGAACTTAAAGATGGA
* * *
3436265 AAAGGTGCCAATATGCTGATTCAAGGCCAGCGATATTGGAC-T-----T-G-
1 AAAGGTGCCAATATGCTGATTCAAGGCCAGCTACATTGAACTTAAAGATGGA
* * *
3436309 -AAGGTGTCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGA---A
1 AAAGGTGCCAATATGCTGATTCAAGGCCAGCTACATTGAACTTAAAGATGGA
* * * *
3436357 AAAGATGCCAATATGCTGATTCAAGGCCAGCGATATTGGAC-T-----T---
1 AAAGGTGCCAATATGCTGATTCAAGGCCAGCTACATTGAACTTAAAGATGGA
* *
3436400 AAAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTTAAAGAT-G-
1 AAAGGTGCCAATATGCTGATTCAAGGCCAGCTACATTGAACTTAAAGATGGA
* * *
3436450 -AAGGTGCCAATATGCTGATTCAAGGCCAGCGATATTGGAC-T-----T---
1 AAAGGTGCCAATATGCTGATTCAAGGCCAGCTACATTGAACTTAAAGATGGA
* *
3436492 AAAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGA---A
1 AAAGGTGCCAATATGCTGATTCAAGGCCAGCTACATTGAACTTAAAGATGGA
** * * ** *
3436541 AAAAATGCCAATATGCTGATTCAAGGACAGCGATGTTGGAC-T-----T-G-
1 AAAGGTGCCAATATGCTGATTCAAGGCCAGCTACATTGAACTTAAAGATGGA
* *
3436585 -AAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGA---A
1 AAAGGTGCCAATATGCTGATTCAAGGCCAGCTACATTGAACTTAAAGATGGA
* * * *
3436633 AAAGATG-CAATATGCTGATTCAAGGCCAGCGATATTGGAC-T-----T---
1 AAAGGTGCCAATATGCTGATTCAAGGCCAGCTACATTGAACTTAAAGATGGA
* *
3436675 AAAGGTGCCAATGTGC--A-TCAAGGCCAGCTACATTGGACTTAAAGA---A
1 AAAGGTGCCAATATGCTGATTCAAGGCCAGCTACATTGAACTTAAAGATGGA
* * * *
3436721 AAAGATGCCAATATGCTGATTCAAGGCCAGCGATATTGGAC------AT---
1 AAAGGTGCCAATATGCTGATTCAAGGCCAGCTACATTGAACTTAAAGATGGA
* *
3436764 AAAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAA
1 AAAGGTGCCAATATGCTGATTCAAGGCCAGCTACATTGAACTTAAA
3436810 AGTGCCAATA
Statistics
Matches: 715, Mismatches: 84, Indels: 162
0.74 0.09 0.17
Matches are distributed among these distances:
40 19 0.03
41 2 0.00
42 6 0.01
43 302 0.42
44 7 0.01
45 1 0.00
46 16 0.02
47 1 0.00
48 36 0.05
49 206 0.29
51 2 0.00
52 70 0.10
53 6 0.01
54 5 0.01
55 36 0.05
ACGTcount: A:0.33, C:0.18, G:0.24, T:0.24
Consensus pattern (52 bp):
AAAGGTGCCAATATGCTGATTCAAGGCCAGCTACATTGAACTTAAAGATGGA
Found at i:3436047 original size:43 final size:43
Alignment explanation
Indices: 3435986--3436825 Score: 887
Period size: 43 Copynumber: 18.4 Consensus size: 43
3435976 TAAAGATGGA
3435986 AAAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTT
1 AAAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTT
* * *
3436029 AAAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGAACTT
1 AAAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTT
3436072 AAAGAAGAAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTT
1 -----A-AAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTT
* * * *
3436121 AAAGGTGCCAATGTGCTAATTCAAGGCCAGCTACATTGAACTT
1 AAAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTT
*
3436164 AAAGAAGAAGGTGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTT
1 -----A-AAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTT
* *
3436213 AAAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGAT
1 AAAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGAC-T-----T
*
3436262 GGAAAAGGTGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTT
1 ---AAAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTT
* * * *
3436308 GAAGGTGTCAATGTGCTGATTCAAGGCCAGCTACATTGGACTT
1 AAAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTT
*
3436351 AAAGAAAAAGATGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTT
1 AAAG-----G-TGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTT
3436400 AAAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTT
1 AAAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTT
*
3436443 AAAGATGAAGGTGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTT
1 ----A--AAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTT
* *
3436492 AAAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTT
1 AAAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTT
* * * *
3436535 AAAGAAAAAAATGCCAATATGCTGATTCAAGGACAGCGATGTTGGACTT
1 AAAG------GTGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTT
* * *
3436584 GAAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTT
1 AAAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTT
*
3436627 AAAGAAAAAGATG-CAATATGCTGATTCAAGGCCAGCGATATTGGACTT
1 AAAG-----G-TGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTT
* *
3436675 AAAGGTGCCAATGTGC--A-TCAAGGCCAGCTACATTGGACTT
1 AAAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTT
* *
3436715 AAAGAAAAAGATGCCAATATGCTGATTCAAGGCCAGCGATATTGGACAT
1 AAAG-----G-TGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTT
* *
3436764 AAAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTT
1 AAAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTT
*
3436807 AAAAGTGCCAATATGCTGA
1 AAAGGTGCCAATATGCTGA
3436826 ATTCGTCTTC
Statistics
Matches: 676, Mismatches: 66, Indels: 110
0.79 0.08 0.13
Matches are distributed among these distances:
40 25 0.04
41 1 0.00
42 2 0.00
43 331 0.49
44 5 0.01
45 2 0.00
46 11 0.02
47 1 0.00
48 41 0.06
49 218 0.32
51 1 0.00
52 38 0.06
ACGTcount: A:0.33, C:0.18, G:0.25, T:0.24
Consensus pattern (43 bp):
AAAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTT
Found at i:3436118 original size:92 final size:92
Alignment explanation
Indices: 3435933--3436809 Score: 1447
Period size: 92 Copynumber: 9.5 Consensus size: 92
3435923 AAGATGAGAA
* *
3435933 AAAGGATGTCAATGTGCTGATTCAAGGCCAGCTACATTGAACTTAAAGATGGAAAAGGTGCCAAT
1 AAAGG-TGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGA---AAAAGGTGCCAAT
*
3435998 ATGCTGATTCAAGGCCAGCTATATTGGACTT
62 ATGCTGATTCAAGGCCAGCGATATTGGACTT
* *
3436029 AAAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGAACTTAAAGAAGAAGGTGCCAATATGC
1 AAAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGAAAAAGGTGCCAATATGC
*
3436094 TGATTCAAGGCCAGCTATATTGGACTT
66 TGATTCAAGGCCAGCGATATTGGACTT
* * *
3436121 AAAGGTGCCAATGTGCTAATTCAAGGCCAGCTACATTGAACTTAAAGAAGAAGGTGCCAATATGC
1 AAAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGAAAAAGGTGCCAATATGC
3436186 TGATTCAAGGCCAGCGATATTGGACTT
66 TGATTCAAGGCCAGCGATATTGGACTT
3436213 AAAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGGAAAAGGTGCCAATA
1 AAAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGA---AAAAGGTGCCAATA
3436278 TGCTGATTCAAGGCCAGCGATATTGGACTT
63 TGCTGATTCAAGGCCAGCGATATTGGACTT
* * *
3436308 GAAGGTGTCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGAAAAAGATGCCAATATGC
1 AAAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGAAAAAGGTGCCAATATGC
3436373 TGATTCAAGGCCAGCGATATTGGACTT
66 TGATTCAAGGCCAGCGATATTGGACTT
* * **
3436400 AAAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTTAAAGATGAAGGTGCCAATATGC
1 AAAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGAAAAAGGTGCCAATATGC
3436465 TGATTCAAGGCCAGCGATATTGGACTT
66 TGATTCAAGGCCAGCGATATTGGACTT
**
3436492 AAAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGAAAAAAATGCCAATATGC
1 AAAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGAAAAAGGTGCCAATATGC
* *
3436557 TGATTCAAGGACAGCGATGTTGGACTT
66 TGATTCAAGGCCAGCGATATTGGACTT
* *
3436584 GAAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGAAAAAGATG-CAATATGC
1 AAAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGAAAAAGGTGCCAATATGC
3436648 TGATTCAAGGCCAGCGATATTGGACTT
66 TGATTCAAGGCCAGCGATATTGGACTT
*
3436675 AAAGGTGCCAATGTGC--A-TCAAGGCCAGCTACATTGGACTTAAAGAAAAAGATGCCAATATGC
1 AAAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGAAAAAGGTGCCAATATGC
*
3436737 TGATTCAAGGCCAGCGATATTGGACAT
66 TGATTCAAGGCCAGCGATATTGGACTT
3436764 AAAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAA
1 AAAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAA
3436810 AGTGCCAATA
Statistics
Matches: 743, Mismatches: 31, Indels: 18
0.94 0.04 0.02
Matches are distributed among these distances:
88 36 0.05
89 51 0.07
91 49 0.07
92 471 0.63
95 131 0.18
96 5 0.01
ACGTcount: A:0.33, C:0.18, G:0.25, T:0.24
Consensus pattern (92 bp):
AAAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGAAAAAGGTGCCAATATGC
TGATTCAAGGCCAGCGATATTGGACTT
Found at i:3436267 original size:279 final size:278
Alignment explanation
Indices: 3435933--3436809 Score: 1505
Period size: 279 Copynumber: 3.2 Consensus size: 278
3435923 AAGATGAGAA
* *
3435933 AAAGGATGTCAATGTGCTGATTCAAGGCCAGCTACATTGAACTTAAAGATGGAAAAGGTGCCAAT
1 AAAGG-TGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGGAAAAGGTGCCAAT
* *
3435998 ATGCTGATTCAAGGCCAGCTATATTGGACTTAAAGGTGCCAATGTGCTGATTCAAGGCCAGCTAC
65 ATGCTGATTCAAGGCCAGCGATATTGGACTTGAAGGTGCCAATGTGCTGATTCAAGGCCAGCTAC
* * * *
3436063 ATTGAACTTAAAGAAGAAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTTAAAGGTG
130 ATTGGACTTAAAGAAAAAGATGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGGTG
*
3436128 CCAATGTGCTAATTCAAGGCCAGCTACATTGAACTTAAAGAAGAAGGTGCCAATATGCTGATTCA
195 CCAATGTGCT-ATTCAAGGCCAGCTACATTGGACTTAAAGAAGAAGGTGCCAATATGCTGATTCA
3436193 AGGCCAGCGATATTGGACTT
259 AGGCCAGCGATATTGGACTT
3436213 AAAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGGAAAAGGTGCCAATA
1 AAAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGGAAAAGGTGCCAATA
*
3436278 TGCTGATTCAAGGCCAGCGATATTGGACTTGAAGGTGTCAATGTGCTGATTCAAGGCCAGCTACA
66 TGCTGATTCAAGGCCAGCGATATTGGACTTGAAGGTGCCAATGTGCTGATTCAAGGCCAGCTACA
3436343 TTGGACTTAAAGAAAAAGATGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGGTGC
131 TTGGACTTAAAGAAAAAGATGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGGTGC
* * *
3436408 CAATATGCTGATTCAAGGCCAGCTATATTGGACTTAAAGATGAAGGTGCCAATATGCTGATTCAA
196 CAATGTGCT-ATTCAAGGCCAGCTACATTGGACTTAAAGAAGAAGGTGCCAATATGCTGATTCAA
3436473 GGCCAGCGATATTGGACTT
260 GGCCAGCGATATTGGACTT
**
3436492 AAAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGA---AAAAAATGCCAATA
1 AAAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGGAAAAGGTGCCAATA
* *
3436554 TGCTGATTCAAGGACAGCGATGTTGGACTTGAAGGTGCCAATGTGCTGATTCAAGGCCAGCTACA
66 TGCTGATTCAAGGCCAGCGATATTGGACTTGAAGGTGCCAATGTGCTGATTCAAGGCCAGCTACA
3436619 TTGGACTTAAAGAAAAAGATG-CAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGGTGC
131 TTGGACTTAAAGAAAAAGATGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGGTGC
* *
3436683 CAATGTGC-A-TCAAGGCCAGCTACATTGGACTTAAAGAAAAAGATGCCAATATGCTGATTCAAG
196 CAATGTGCTATTCAAGGCCAGCTACATTGGACTTAAAGAAGAAGGTGCCAATATGCTGATTCAAG
*
3436746 GCCAGCGATATTGGACAT
261 GCCAGCGATATTGGACTT
3436764 AAAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAA
1 AAAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAA
3436810 AGTGCCAATA
Statistics
Matches: 572, Mismatches: 25, Indels: 8
0.95 0.04 0.01
Matches are distributed among these distances:
272 113 0.20
273 1 0.00
275 50 0.09
276 95 0.17
279 308 0.54
280 5 0.01
ACGTcount: A:0.33, C:0.18, G:0.25, T:0.24
Consensus pattern (278 bp):
AAAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGGAAAAGGTGCCAATA
TGCTGATTCAAGGCCAGCGATATTGGACTTGAAGGTGCCAATGTGCTGATTCAAGGCCAGCTACA
TTGGACTTAAAGAAAAAGATGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGGTGC
CAATGTGCTATTCAAGGCCAGCTACATTGGACTTAAAGAAGAAGGTGCCAATATGCTGATTCAAG
GCCAGCGATATTGGACTT
Found at i:3446346 original size:19 final size:19
Alignment explanation
Indices: 3446322--3446389 Score: 76
Period size: 19 Copynumber: 3.9 Consensus size: 19
3446312 AATTCAACAA
3446322 TTTGTATCGATACATAAGT
1 TTTGTATCGATACATAAGT
3446341 TTTGTATCGATAC--AA--
1 TTTGTATCGATACATAAGT
3446356 --TGTATCGATACATAAGT
1 TTTGTATCGATACATAAGT
**
3446373 AATGTATCGATACATAA
1 TTTGTATCGATACATAA
3446390 TTAGCTACTG
Statistics
Matches: 43, Mismatches: 0, Indels: 12
0.78 0.00 0.22
Matches are distributed among these distances:
13 11 0.26
15 2 0.05
17 2 0.05
19 28 0.65
ACGTcount: A:0.37, C:0.12, G:0.15, T:0.37
Consensus pattern (19 bp):
TTTGTATCGATACATAAGT
Found at i:3446361 original size:13 final size:13
Alignment explanation
Indices: 3446343--3446367 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
3446333 ACATAAGTTT
3446343 TGTATCGATACAA
1 TGTATCGATACAA
3446356 TGTATCGATACA
1 TGTATCGATACA
3446368 TAAGTAATGT
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:3446365 original size:32 final size:32
Alignment explanation
Indices: 3446324--3446386 Score: 108
Period size: 32 Copynumber: 2.0 Consensus size: 32
3446314 TTCAACAATT
**
3446324 TGTATCGATACATAAGTTTTGTATCGATACAA
1 TGTATCGATACATAAGTAATGTATCGATACAA
3446356 TGTATCGATACATAAGTAATGTATCGATACA
1 TGTATCGATACATAAGTAATGTATCGATACA
3446387 TAATTAGCTA
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
32 29 1.00
ACGTcount: A:0.37, C:0.13, G:0.16, T:0.35
Consensus pattern (32 bp):
TGTATCGATACATAAGTAATGTATCGATACAA
Found at i:3446447 original size:13 final size:13
Alignment explanation
Indices: 3446429--3446454 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
3446419 CATTTTTCTG
3446429 TGTATCGATACAT
1 TGTATCGATACAT
3446442 TGTATCGATACAT
1 TGTATCGATACAT
3446455 GGATCTTTGT
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:3446451 original size:33 final size:33
Alignment explanation
Indices: 3446409--3446475 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
3446399 GCCAAGGAAA
***
3446409 TGTATCGATACATTTTTCTGTGTATCGATACAT
1 TGTATCGATACATGGATCTGTGTATCGATACAT
*
3446442 TGTATCGATACATGGATCTTTGTATCGATACAT
1 TGTATCGATACATGGATCTGTGTATCGATACAT
3446475 T
1 T
3446476 TGGAAATTTT
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.25, C:0.15, G:0.16, T:0.43
Consensus pattern (33 bp):
TGTATCGATACATGGATCTGTGTATCGATACAT
Found at i:3447005 original size:14 final size:14
Alignment explanation
Indices: 3446986--3447017 Score: 57
Period size: 13 Copynumber: 2.4 Consensus size: 14
3446976 ATCCCTTAGC
3446986 AAAAAAAAAC-CAA
1 AAAAAAAAACACAA
3446999 AAAAAAAAACACAA
1 AAAAAAAAACACAA
3447013 AAAAA
1 AAAAA
3447018 CACTATTCCA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
13 10 0.56
14 8 0.44
ACGTcount: A:0.88, C:0.12, G:0.00, T:0.00
Consensus pattern (14 bp):
AAAAAAAAACACAA
Found at i:3448903 original size:51 final size:52
Alignment explanation
Indices: 3448822--3448920 Score: 146
Period size: 51 Copynumber: 1.9 Consensus size: 52
3448812 AATTCTCTGC
* * * * *
3448822 AATCGGGGATATTCCATCTCCGATTTTATTTTC-AAAACACTAATTTTCTAT
1 AATCAGGGATACTCCAGCTCCGATTTTATTTCCAAAAACACCAATTTTCTAT
3448873 AATCAGGGATACTCCAGCTCCGATTTTATTTCCAAAAACACCAATTTT
1 AATCAGGGATACTCCAGCTCCGATTTTATTTCCAAAAACACCAATTTT
3448921 TTTCACAATC
Statistics
Matches: 42, Mismatches: 5, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
51 29 0.69
52 13 0.31
ACGTcount: A:0.31, C:0.22, G:0.10, T:0.36
Consensus pattern (52 bp):
AATCAGGGATACTCCAGCTCCGATTTTATTTCCAAAAACACCAATTTTCTAT
Found at i:3452395 original size:12 final size:11
Alignment explanation
Indices: 3452373--3452448 Score: 52
Period size: 12 Copynumber: 6.9 Consensus size: 11
3452363 AAAGAAAGAA
*
3452373 GAGAGAGGAGG
1 GAGATAGGAGG
3452384 GATGATAGGAGG
1 GA-GATAGGAGG
*
3452396 AGAGACAGGA--
1 -GAGATAGGAGG
*
3452406 GAGATAGTA--
1 GAGATAGGAGG
3452415 GAGATAGGAGG
1 GAGATAGGAGG
3452426 GATGATAGGAGG
1 GA-GATAGGAGG
*
3452438 AGAGACAGGAG
1 -GAGATAGGAG
3452449 AGATAATAGA
Statistics
Matches: 53, Mismatches: 6, Indels: 11
0.76 0.09 0.16
Matches are distributed among these distances:
9 15 0.28
11 4 0.08
12 30 0.57
13 4 0.08
ACGTcount: A:0.39, C:0.03, G:0.49, T:0.09
Consensus pattern (11 bp):
GAGATAGGAGG
Found at i:3452405 original size:24 final size:24
Alignment explanation
Indices: 3452372--3452457 Score: 85
Period size: 24 Copynumber: 3.8 Consensus size: 24
3452362 AAAAGAAAGA
*
3452372 AGAGAGAGGAGGGATGATAGGAGG
1 AGAGACAGGAGGGATGATAGGAGG
*
3452396 AGAGACAGGA--GA-GAT---AGT
1 AGAGACAGGAGGGATGATAGGAGG
*
3452414 AGAGATAGGAGGGATGATAGGAGG
1 AGAGACAGGAGGGATGATAGGAGG
* *
3452438 AGAGACAGGAGAGATAATAG
1 AGAGACAGGAGGGATGATAG
3452458 AGAGCGGAGG
Statistics
Matches: 49, Mismatches: 7, Indels: 12
0.72 0.10 0.18
Matches are distributed among these distances:
18 11 0.22
20 2 0.04
21 6 0.12
22 2 0.04
24 28 0.57
ACGTcount: A:0.42, C:0.02, G:0.45, T:0.10
Consensus pattern (24 bp):
AGAGACAGGAGGGATGATAGGAGG
Found at i:3452431 original size:42 final size:42
Alignment explanation
Indices: 3452372--3452481 Score: 184
Period size: 42 Copynumber: 2.6 Consensus size: 42
3452362 AAAAGAAAGA
*
3452372 AGAGAGAGGAGGGATGATAGGAGGAGAGACAGGAGAGATAGT
1 AGAGAGAGGAGGGATGATAGGAGGAGAGACAGGAGAGATAAT
*
3452414 AGAGATAGGAGGGATGATAGGAGGAGAGACAGGAGAGATAAT
1 AGAGAGAGGAGGGATGATAGGAGGAGAGACAGGAGAGATAAT
* *
3452456 AGAGAGCGGAGGGATGACAGGAGGAG
1 AGAGAGAGGAGGGATGATAGGAGGAG
3452482 GAGAGAAGAA
Statistics
Matches: 63, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
42 63 1.00
ACGTcount: A:0.40, C:0.04, G:0.47, T:0.09
Consensus pattern (42 bp):
AGAGAGAGGAGGGATGATAGGAGGAGAGACAGGAGAGATAAT
Found at i:3458451 original size:20 final size:20
Alignment explanation
Indices: 3458428--3458500 Score: 101
Period size: 20 Copynumber: 3.6 Consensus size: 20
3458418 ACAATTCAAA
3458428 GTATCGATACATGTTGCAAT
1 GTATCGATACATGTTGCAAT
****
3458448 GTATCGATACATGAAAAAGAT
1 GTATCGATACATGTTGCA-AT
3458469 GTATCGATACATGTTGCAAT
1 GTATCGATACATGTTGCAAT
3458489 GTATCGATACAT
1 GTATCGATACAT
3458501 AAAAAAAGAT
Statistics
Matches: 44, Mismatches: 8, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
20 28 0.64
21 16 0.36
ACGTcount: A:0.36, C:0.14, G:0.19, T:0.32
Consensus pattern (20 bp):
GTATCGATACATGTTGCAAT
Found at i:3458479 original size:41 final size:42
Alignment explanation
Indices: 3458428--3458522 Score: 174
Period size: 41 Copynumber: 2.3 Consensus size: 42
3458418 ACAATTCAAA
*
3458428 GTATCGATACATGTTGCAATGTATCGATACAT-GAAAAAGAT
1 GTATCGATACATGTTGCAATGTATCGATACATAAAAAAAGAT
3458469 GTATCGATACATGTTGCAATGTATCGATACATAAAAAAAGAT
1 GTATCGATACATGTTGCAATGTATCGATACATAAAAAAAGAT
3458511 GTATCGATACAT
1 GTATCGATACAT
3458523 TTCTTGGCAG
Statistics
Matches: 52, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
41 32 0.62
42 20 0.38
ACGTcount: A:0.40, C:0.13, G:0.18, T:0.29
Consensus pattern (42 bp):
GTATCGATACATGTTGCAATGTATCGATACATAAAAAAAGAT
Found at i:3458579 original size:13 final size:13
Alignment explanation
Indices: 3458561--3458586 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
3458551 TACAGCAAGT
3458561 ATGTATCGATACA
1 ATGTATCGATACA
3458574 ATGTATCGATACA
1 ATGTATCGATACA
3458587 CAAAAAATTG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:3463469 original size:55 final size:56
Alignment explanation
Indices: 3463211--3464758 Score: 2030
Period size: 55 Copynumber: 27.8 Consensus size: 56
3463201 TTTTCCTTTT
* *
3463211 AAAGCCCACACAAGTTGGTGGCACCTTTC--GTCCTCAAAAAGCAGGACGCCT-TTT
1 AAAGCCCACACAAGTTGGTGGCA-CTTTCTAGTCCTCAAAGAGCAGGACGCCTCTTC
* * * * *
3463265 AAAGCCCATACAAGTTGGTGGCACTTCCCAGTCCTCAAAGAGCAAGACGCCTTCGCCTCTT
1 AAAGCCCACACAAGTTGGTGGCACTTTCTAGTCCTCAAAGAGCAGGACGCC-T---CT-TC
* * * *
3463326 AAAGCCCACAAAAGTTGGTGGCACTTCCCAGTCCTCAAAGAGCAGGACGCCTTCTCCTTTT
1 AAAGCCCACACAAGTTGGTGGCACTTTCTAGTCCTCAAAGAGCAGGACG-C--CT-C-TTC
*
3463387 AAAGCCCACACAAGTTGGTGGCACTTCCTAGTCCTCAAAGAGCAGGACGCCTCTT-
1 AAAGCCCACACAAGTTGGTGGCACTTTCTAGTCCTCAAAGAGCAGGACGCCTCTTC
* * * *
3463442 AAAGCCCACACAAGTTGGTGGCACTTCCCAGTCCTCAAAGAGCAAGACGCCTTCTCCTTTT
1 AAAGCCCACACAAGTTGGTGGCACTTTCTAGTCCTCAAAGAGCAGGACG-C--CT-C-TTC
* * **
3463503 AAAGCCCACACAAGTTGGTGGTACTTCCTAGTCCTCAAAGAGCAGGACATCT-TTC
1 AAAGCCCACACAAGTTGGTGGCACTTTCTAGTCCTCAAAGAGCAGGACGCCTCTTC
* * *
3463558 AAAGCCCACACAAGTTGGTGGCATTTTCCAGTCCTCAAAGAGCAGGACACCTCTT-
1 AAAGCCCACACAAGTTGGTGGCACTTTCTAGTCCTCAAAGAGCAGGACGCCTCTTC
* * *
3463613 AAAGCCCACACAAGTTGGTGGCAC-CTCTCAGTCCCCAAAGAGCAGGACACCT-TTC
1 AAAGCCCACACAAGTTGGTGGCACTTTCT-AGTCCTCAAAGAGCAGGACGCCTCTTC
* * * * *
3463668 AAAGCCCACACAAGTTGGTGGCATTTTCCAGTCCTCAAAGAGCAAGACACCTCTTA
1 AAAGCCCACACAAGTTGGTGGCACTTTCTAGTCCTCAAAGAGCAGGACGCCTCTTC
* *
3463724 AAAGCCCACACAAGTTGGTGGTACCTTTC-AGTCCCCAAAGAGCAGGACGCCT-TTC
1 AAAGCCCACACAAGTTGGTGGCA-CTTTCTAGTCCTCAAAGAGCAGGACGCCTCTTC
* *
3463779 AAAGCCCACACGAGTTGGTGGCACTTTCTAGTCCTCAAAGAGCAGGACACCTCTT-
1 AAAGCCCACACAAGTTGGTGGCACTTTCTAGTCCTCAAAGAGCAGGACGCCTCTTC
*
3463834 AAAGCCCACACAAGTTGGTGGCACCTTTC-AGTCCTCAAAGAGCAGGATGCCT-TTC
1 AAAGCCCACACAAGTTGGTGGCA-CTTTCTAGTCCTCAAAGAGCAGGACGCCTCTTC
* *
3463889 AAAGCCCACACGAGTTGGTGGCACTTTTTAGTCCTCAAAGAGCAGGACGCCT-TTC
1 AAAGCCCACACAAGTTGGTGGCACTTTCTAGTCCTCAAAGAGCAGGACGCCTCTTC
* * *
3463944 AAAGCCCACACGAGTTGGTGGCACTTTTTAGTCCTCAAAGAGCAGGACACCTCTT-
1 AAAGCCCACACAAGTTGGTGGCACTTTCTAGTCCTCAAAGAGCAGGACGCCTCTTC
* *
3463999 AAAGCCCACACAAGTTGGTGGCACCTTTC-ATTCCTCAAAGAGCAGGACG-CTTTTC
1 AAAGCCCACACAAGTTGGTGGCA-CTTTCTAGTCCTCAAAGAGCAGGACGCCTCTTC
* * *
3464054 AAAGCCCACACGAGTTGGTGGCACTTTCCAGTCCTCAAAGAGCAGGACACCTCTT-
1 AAAGCCCACACAAGTTGGTGGCACTTTCTAGTCCTCAAAGAGCAGGACGCCTCTTC
3464109 AAAGCCCACACAAGTTGGTGGCACCTTTC-AGTCCTCAAAGAGCAGGACGCCT-TTC
1 AAAGCCCACACAAGTTGGTGGCA-CTTTCTAGTCCTCAAAGAGCAGGACGCCTCTTC
* *
3464164 AAAGCCCACACGAGTTGGTGGCACTTTTTAGTCCTCAAAGAGCAGGACGCCT-TTC
1 AAAGCCCACACAAGTTGGTGGCACTTTCTAGTCCTCAAAGAGCAGGACGCCTCTTC
* * *
3464219 AAAGCCCACACGAGTTGGTGGCACTTTTTAGTCCTCAAAGAGCAGGACACCTCTT-
1 AAAGCCCACACAAGTTGGTGGCACTTTCTAGTCCTCAAAGAGCAGGACGCCTCTTC
3464274 AAAGCCCACACAAGTTGGTGGCACCTTTC-AGTCCTCAAAGAGCAGGACGCCT-TTC
1 AAAGCCCACACAAGTTGGTGGCA-CTTTCTAGTCCTCAAAGAGCAGGACGCCTCTTC
* * *
3464329 AAAGCCCACACGAGTTGGTGGCACTTTCCAGTCCTCAAAGAGCAGGACACCTCTT-
1 AAAGCCCACACAAGTTGGTGGCACTTTCTAGTCCTCAAAGAGCAGGACGCCTCTTC
3464384 AAAGCCCACACAAGTTGGTGGCACCTTTC-AGTCCTCAAAGAGCAGGACGCCT-TTC
1 AAAGCCCACACAAGTTGGTGGCA-CTTTCTAGTCCTCAAAGAGCAGGACGCCTCTTC
* * *
3464439 AAAACCCACACGAGTTGGTGGCACTTTTTAGTCCTCAAAGAGCAGGACGCCT-TTC
1 AAAGCCCACACAAGTTGGTGGCACTTTCTAGTCCTCAAAGAGCAGGACGCCTCTTC
* * * *
3464494 AAAACCCACACGAGTTGGTGGCACTTTTTAGTCCTCAAAGAGCAGGACACCTCTT-
1 AAAGCCCACACAAGTTGGTGGCACTTTCTAGTCCTCAAAGAGCAGGACGCCTCTTC
3464549 AAAGCCCACACAAGTTGGTGGCACCTTTC-AGTCCTCAAAGAGCAGGACGCCT-TTC
1 AAAGCCCACACAAGTTGGTGGCA-CTTTCTAGTCCTCAAAGAGCAGGACGCCTCTTC
* * *
3464604 AAAGCCCACACGAGTTGGTGGCACTTTTTAGTCCTCAAAGAGCAGGACACCTCTT-
1 AAAGCCCACACAAGTTGGTGGCACTTTCTAGTCCTCAAAGAGCAGGACGCCTCTTC
*
3464659 GAAGCCCACACAAGTTGGTGGCACCTTTC-AGTCCTCAAAGAGCAGGACGCCT-TTC
1 AAAGCCCACACAAGTTGGTGGCA-CTTTCTAGTCCTCAAAGAGCAGGACGCCTCTTC
* *
3464714 AAAGCCCACACGAGTTGGTGGCACTTTTTAGTCCTCAAAGAGCAG
1 AAAGCCCACACAAGTTGGTGGCACTTTCTAGTCCTCAAAGAGCAG
3464759 AATACACTTT
Statistics
Matches: 1353, Mismatches: 88, Indels: 105
0.88 0.06 0.07
Matches are distributed among these distances:
53 4 0.00
54 77 0.06
55 1009 0.75
56 99 0.07
57 5 0.00
58 6 0.00
59 1 0.00
60 4 0.00
61 144 0.11
62 2 0.00
63 1 0.00
64 1 0.00
ACGTcount: A:0.27, C:0.30, G:0.21, T:0.22
Consensus pattern (56 bp):
AAAGCCCACACAAGTTGGTGGCACTTTCTAGTCCTCAAAGAGCAGGACGCCTCTTC
Found at i:3465535 original size:21 final size:21
Alignment explanation
Indices: 3465509--3465585 Score: 111
Period size: 21 Copynumber: 3.7 Consensus size: 21
3465499 AAATTATCCA
3465509 AATGTATCGATACATTTGTAG
1 AATGTATCGATACATTTGTAG
*
3465530 AATGTATCGATACATTTGTGG
1 AATGTATCGATACATTTGTAG
* *
3465551 AATGTATCGATACA-TTCTACA
1 AATGTATCGATACATTTGTA-G
3465572 AATGTATCGATACA
1 AATGTATCGATACA
3465586 GGGTCCCAAC
Statistics
Matches: 51, Mismatches: 4, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
20 3 0.06
21 48 0.94
ACGTcount: A:0.35, C:0.13, G:0.17, T:0.35
Consensus pattern (21 bp):
AATGTATCGATACATTTGTAG
Found at i:3465664 original size:32 final size:32
Alignment explanation
Indices: 3465623--3465723 Score: 121
Period size: 38 Copynumber: 3.0 Consensus size: 32
3465613 TTCAACAATT
** *
3465623 TGTATCGATACATAAGTTTTGTATTGATACAA
1 TGTATCGATACATAAGTAATGTATCGATACAA
3465655 TGTATCGATACATAAGTAATGTATCGATACATAAGTAA
1 TGTATCGATACATAAGTAATGTATCGATAC------AA
3465693 TGTATCGATACATAAGTAATGTATCGATACA
1 TGTATCGATACATAAGTAATGTATCGATACA
3465724 TAAGTAATGT
Statistics
Matches: 60, Mismatches: 3, Indels: 12
0.80 0.04 0.16
Matches are distributed among these distances:
32 28 0.47
38 32 0.53
ACGTcount: A:0.39, C:0.11, G:0.16, T:0.35
Consensus pattern (32 bp):
TGTATCGATACATAAGTAATGTATCGATACAA
Found at i:3465677 original size:19 final size:19
Alignment explanation
Indices: 3465653--3465745 Score: 186
Period size: 19 Copynumber: 4.9 Consensus size: 19
3465643 GTATTGATAC
3465653 AATGTATCGATACATAAGT
1 AATGTATCGATACATAAGT
3465672 AATGTATCGATACATAAGT
1 AATGTATCGATACATAAGT
3465691 AATGTATCGATACATAAGT
1 AATGTATCGATACATAAGT
3465710 AATGTATCGATACATAAGT
1 AATGTATCGATACATAAGT
3465729 AATGTATCGATACATAA
1 AATGTATCGATACATAA
3465746 TTAGCTACTG
Statistics
Matches: 74, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 74 1.00
ACGTcount: A:0.43, C:0.11, G:0.15, T:0.31
Consensus pattern (19 bp):
AATGTATCGATACATAAGT
Found at i:3466358 original size:11 final size:13
Alignment explanation
Indices: 3466342--3466373 Score: 50
Period size: 11 Copynumber: 2.6 Consensus size: 13
3466332 AATCCCTTAG
3466342 CAAAAAAAA-AC-
1 CAAAAAAAACACA
3466353 CAAAAAAAACACA
1 CAAAAAAAACACA
3466366 CAAAAAAA
1 CAAAAAAA
3466374 CACTATTCCA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
11 9 0.47
12 2 0.11
13 8 0.42
ACGTcount: A:0.81, C:0.19, G:0.00, T:0.00
Consensus pattern (13 bp):
CAAAAAAAACACA
Found at i:3466374 original size:12 final size:11
Alignment explanation
Indices: 3466344--3466376 Score: 50
Period size: 12 Copynumber: 3.0 Consensus size: 11
3466334 TCCCTTAGCA
3466344 AAAAAAAAC-C
1 AAAAAAAACAC
3466354 AAAAAAAACAC
1 AAAAAAAACAC
3466365 ACAAAAAAACAC
1 A-AAAAAAACAC
3466377 TATTCCATTG
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
10 9 0.43
11 2 0.10
12 10 0.48
ACGTcount: A:0.79, C:0.21, G:0.00, T:0.00
Consensus pattern (11 bp):
AAAAAAAACAC
Found at i:3467971 original size:51 final size:52
Alignment explanation
Indices: 3467895--3467993 Score: 155
Period size: 51 Copynumber: 1.9 Consensus size: 52
3467885 AATTCTCCGC
* * * *
3467895 AATCGGGGATATTCCATCTCCGATTTTATTTTC-AAAACACTAATTTTCTAT
1 AATCGGGGATACTCCAGCTCCGATTTTATTTCCAAAAACACCAATTTTCTAT
3467946 AATCGGGGATACTCCAGCTCCGATTTTATTTCCAAAAACACCAATTTT
1 AATCGGGGATACTCCAGCTCCGATTTTATTTCCAAAAACACCAATTTT
3467994 TTTCACAATC
Statistics
Matches: 43, Mismatches: 4, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
51 30 0.70
52 13 0.30
ACGTcount: A:0.30, C:0.22, G:0.11, T:0.36
Consensus pattern (52 bp):
AATCGGGGATACTCCAGCTCCGATTTTATTTCCAAAAACACCAATTTTCTAT
Found at i:3468038 original size:28 final size:27
Alignment explanation
Indices: 3468006--3468077 Score: 92
Period size: 28 Copynumber: 2.6 Consensus size: 27
3467996 TCACAATCGA
*
3468006 GGATACTCCAACCTCGTTATCTCACCG-G
1 GGATACTCCAACCCCGTTA-CT-ACCGAG
*
3468034 GGATACTCCAACCCCGTTACTTCCGAG
1 GGATACTCCAACCCCGTTACTACCGAG
3468061 GGAATACTCCAACCCCG
1 GG-ATACTCCAACCCCG
3468078 GCTTTATTCC
Statistics
Matches: 40, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
26 3 0.08
27 5 0.12
28 32 0.80
ACGTcount: A:0.24, C:0.38, G:0.18, T:0.21
Consensus pattern (27 bp):
GGATACTCCAACCCCGTTACTACCGAG
Found at i:3469527 original size:50 final size:50
Alignment explanation
Indices: 3469449--3469580 Score: 192
Period size: 50 Copynumber: 2.6 Consensus size: 50
3469439 TAACTAGATG
*
3469449 TATCGATACATTATTCAATGTATCGATACATCTGGGTAAAAAGACAGAATA
1 TATCGATACATTA-TAAATGTATCGATACATCTGGGTAAAAAGACAGAATA
* * *
3469500 TATCGATACATTAAAAATGTATCGATACATCTGGGTAAAAAGATAGAATG
1 TATCGATACATTATAAATGTATCGATACATCTGGGTAAAAAGACAGAATA
* *
3469550 TATCGATACATTCATACATGTATCAATACAT
1 TATCGATACATT-ATAAATGTATCGATACAT
3469581 TGAAAAATGT
Statistics
Matches: 73, Mismatches: 7, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
50 45 0.62
51 28 0.38
ACGTcount: A:0.42, C:0.14, G:0.14, T:0.30
Consensus pattern (50 bp):
TATCGATACATTATAAATGTATCGATACATCTGGGTAAAAAGACAGAATA
Found at i:3469572 original size:20 final size:20
Alignment explanation
Indices: 3469546--3469600 Score: 74
Period size: 20 Copynumber: 2.8 Consensus size: 20
3469536 AAAAAGATAG
* *
3469546 AATGTATCGATACATTCATA
1 AATGTATCAATACATTCAAA
* *
3469566 CATGTATCAATACATTGAAA
1 AATGTATCAATACATTCAAA
3469586 AATGTATCAATACAT
1 AATGTATCAATACAT
3469601 CTAGGTAAAA
Statistics
Matches: 30, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 30 1.00
ACGTcount: A:0.44, C:0.15, G:0.09, T:0.33
Consensus pattern (20 bp):
AATGTATCAATACATTCAAA
Found at i:3469591 original size:40 final size:38
Alignment explanation
Indices: 3469546--3469672 Score: 115
Period size: 40 Copynumber: 3.4 Consensus size: 38
3469536 AAAAAGATAG
*
3469546 AATGTATCGATACATTCATACATGTATCAATACATTGAAA
1 AATGTATCAATACATTCATA-ATGTATCAATACA-TGAAA
* *
3469586 AATGTATCAATACA-TC-T-AGGTA--AA-A-AAGATAA
1 AATGTATCAATACATTCATAATGTATCAATACATGA-AA
*
3469618 AATGTATCAATACATTCATATATGTATCGATACAATGAAA
1 AATGTATCAATACATTCATA-ATGTATCAATAC-ATGAAA
*
3469658 AATGTATCGATACAT
1 AATGTATCAATACAT
3469673 CTGGGTAAAA
Statistics
Matches: 70, Mismatches: 7, Indels: 20
0.72 0.07 0.21
Matches are distributed among these distances:
31 2 0.03
32 17 0.24
33 3 0.04
34 3 0.04
36 8 0.11
38 2 0.03
39 3 0.04
40 29 0.41
41 3 0.04
ACGTcount: A:0.46, C:0.13, G:0.11, T:0.31
Consensus pattern (38 bp):
AATGTATCAATACATTCATAATGTATCAATACATGAAA
Found at i:3469636 original size:72 final size:72
Alignment explanation
Indices: 3469500--3469683 Score: 291
Period size: 72 Copynumber: 2.6 Consensus size: 72
3469490 AGACAGAATA
* *
3469500 TATCGATACATT-AAAAATGTATCGATACATCTGGGT-AAAAAGATAGAATGTATCGATACATTC
1 TATCGATACATTGAAAAATGTATCGATACATCTGGGTAAAAAAGATAAAATGTATCAATACATTC
3469563 ATACATG
66 ATACATG
* * *
3469570 TATCAATACATTGAAAAATGTATCAATACATCTAGGTAAAAAAGATAAAATGTATCAATACATTC
1 TATCGATACATTGAAAAATGTATCGATACATCTGGGTAAAAAAGATAAAATGTATCAATACATTC
*
3469635 ATATATG
66 ATACATG
*
3469642 TATCGATACAATGAAAAATGTATCGATACATCTGGGTAAAAA
1 TATCGATACATTGAAAAATGTATCGATACATCTGGGTAAAAA
3469684 CGTGACTTTT
Statistics
Matches: 102, Mismatches: 10, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
70 11 0.11
71 22 0.22
72 69 0.68
ACGTcount: A:0.45, C:0.12, G:0.14, T:0.29
Consensus pattern (72 bp):
TATCGATACATTGAAAAATGTATCGATACATCTGGGTAAAAAAGATAAAATGTATCAATACATTC
ATACATG
Found at i:3469662 original size:20 final size:20
Alignment explanation
Indices: 3469616--3469671 Score: 67
Period size: 20 Copynumber: 2.8 Consensus size: 20
3469606 TAAAAAAGAT
* *
3469616 AAAATGTATCAATACATTCA
1 AAAATGTATCGATACAATCA
* * *
3469636 TATATGTATCGATACAATGA
1 AAAATGTATCGATACAATCA
3469656 AAAATGTATCGATACA
1 AAAATGTATCGATACA
3469672 TCTGGGTAAA
Statistics
Matches: 29, Mismatches: 7, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
20 29 1.00
ACGTcount: A:0.46, C:0.12, G:0.11, T:0.30
Consensus pattern (20 bp):
AAAATGTATCGATACAATCA
Found at i:3471063 original size:374 final size:374
Alignment explanation
Indices: 3470374--3471116 Score: 1369
Period size: 374 Copynumber: 2.0 Consensus size: 374
3470364 CATTCCCTTA
* *
3470374 TGCATGGAAGAAAGTTATATTTCCATCCCCTTCCTTAAATCATGTGATATGTGCCCATTGTGCCC
1 TGCATGGAAGAAAGTTATATTTCCAGCCCCTTCCTTAAATCATGTGAAATGTGCCCATTGTGCCC
* *
3470439 AAAAACCTTTTTCCTTTTCAAATTAATTATTCAAGTCGTCCTTAATTTGTCTTTCTTGGAGCTTA
66 AAAAACCTTTTTCCTTTTCAAATTAATTAATCAAGTCATCCTTAATTTGTCTTTCTTGGAGCTTA
*
3470504 GTACCGCATTCTTGTCCACCCATTGCACCTTATGCAACTCTTTCACCAAACTATCAATCTGCTCT
131 GTACCGCATTCTTGTCCACCCATTGCACCTCATGCAACTCTTTCACCAAACTATCAATCTGCTCT
*
3470569 CTCATTACTCTTAAGTTTGTATTTATACCATAGATAGGGCTATCTATTTATCGATTTTAGTTTGT
196 CTCATTACTCTTAAGTTTGTATTTATACCATAGATAGGGCTATCTATTTACCGATTTTAGTTTGT
*
3470634 TTGCAATAATTCCATTGTTATCATGTACACAAATTCTATGGACTTCTCCTTCACACTTAGTGTCT
261 TTGCAATAATTCCATTGTTATCATGTACACAAATTCTATGGACTTCTCCTTCACACCTAGTGTCT
*
3470699 TTGGCCAACGCTACTTTAAAGTAACTTCGTTTTTCCCTTCTTTCCCCTG
326 TTGGCCAACGCTACTTTAAAGTAACTTCATTTTTCCCTTCTTTCCCCTG
* *
3470748 TGCATGGAAGAAAGTTATATTTCTAGCCCTTTCCTTAAATCATGTGAAATGTGCCCATTGTGCCC
1 TGCATGGAAGAAAGTTATATTTCCAGCCCCTTCCTTAAATCATGTGAAATGTGCCCATTGTGCCC
*
3470813 AAAAACCTTTTTCCTTTTCAAATTAATTAATCAAGTCATCCTTAATTTGTTTTTCTTGGAGCTTA
66 AAAAACCTTTTTCCTTTTCAAATTAATTAATCAAGTCATCCTTAATTTGTCTTTCTTGGAGCTTA
*
3470878 GTGCCGCATTCTTGTCCACCCATTGCACCTCATGCAACTCTTTCACCAAACTATCAATCTGCTCT
131 GTACCGCATTCTTGTCCACCCATTGCACCTCATGCAACTCTTTCACCAAACTATCAATCTGCTCT
3470943 CTCATTACTCTTAAGTTTGTATTTATACCATAGATAGGGCTATCTATTTACCGATTTTAGTTTGT
196 CTCATTACTCTTAAGTTTGTATTTATACCATAGATAGGGCTATCTATTTACCGATTTTAGTTTGT
*
3471008 TTGCAATAATTCCATTGTTATCATGTACAGAAATTCTATGGACTTCTCCTTCACACCTAGTGTCT
261 TTGCAATAATTCCATTGTTATCATGTACACAAATTCTATGGACTTCTCCTTCACACCTAGTGTCT
3471073 TTGGCCAACGCTACTTTAAAGTAACTTCATTTTTCCCTTCTTTC
326 TTGGCCAACGCTACTTTAAAGTAACTTCATTTTTCCCTTCTTTC
3471117 TTACCTTGAC
Statistics
Matches: 356, Mismatches: 13, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
374 356 1.00
ACGTcount: A:0.24, C:0.24, G:0.12, T:0.40
Consensus pattern (374 bp):
TGCATGGAAGAAAGTTATATTTCCAGCCCCTTCCTTAAATCATGTGAAATGTGCCCATTGTGCCC
AAAAACCTTTTTCCTTTTCAAATTAATTAATCAAGTCATCCTTAATTTGTCTTTCTTGGAGCTTA
GTACCGCATTCTTGTCCACCCATTGCACCTCATGCAACTCTTTCACCAAACTATCAATCTGCTCT
CTCATTACTCTTAAGTTTGTATTTATACCATAGATAGGGCTATCTATTTACCGATTTTAGTTTGT
TTGCAATAATTCCATTGTTATCATGTACACAAATTCTATGGACTTCTCCTTCACACCTAGTGTCT
TTGGCCAACGCTACTTTAAAGTAACTTCATTTTTCCCTTCTTTCCCCTG
Found at i:3474121 original size:31 final size:29
Alignment explanation
Indices: 3474085--3474175 Score: 85
Period size: 30 Copynumber: 3.0 Consensus size: 29
3474075 TATATATGTT
*
3474085 TATATACAAATGTAAAATTTTAAATTATAAA
1 TATATA-AAATATAAAATTTTAAA-TATAAA
* *
3474116 TATATAACATCTAAAATTCTTAAATATCAAA
1 TATATAAAATATAAAATT-TTAAATAT-AAA
*
3474147 TAAAT-AAATATAAAATATTTAAAATATAA
1 TATATAAAATATAAAAT-TTT-AAATATAA
3474176 TAAATTATTA
Statistics
Matches: 51, Mismatches: 5, Indels: 9
0.78 0.08 0.14
Matches are distributed among these distances:
30 26 0.51
31 25 0.49
ACGTcount: A:0.57, C:0.05, G:0.01, T:0.36
Consensus pattern (29 bp):
TATATAAAATATAAAATTTTAAATATAAA
Found at i:3474169 original size:15 final size:15
Alignment explanation
Indices: 3474092--3474175 Score: 57
Period size: 15 Copynumber: 5.5 Consensus size: 15
3474082 GTTTATATAC
*
3474092 AAATGTAAAAT-TTT
1 AAATATAAAATATTT
*
3474106 AAAT-TATAAATATAT
1 AAATATA-AAATATTT
*
3474121 AACATCTAAAAT-TCTT
1 AA-ATATAAAATAT-TT
* **
3474137 AAATATCAAATAAAT
1 AAATATAAAATATTT
3474152 AAATATAAAATATTT
1 AAATATAAAATATTT
3474167 AAAATATAA
1 -AAATATAA
3474176 TAAATTATTA
Statistics
Matches: 54, Mismatches: 9, Indels: 12
0.72 0.12 0.16
Matches are distributed among these distances:
13 2 0.04
14 8 0.15
15 25 0.46
16 17 0.31
17 2 0.04
ACGTcount: A:0.58, C:0.05, G:0.01, T:0.36
Consensus pattern (15 bp):
AAATATAAAATATTT
Found at i:3477401 original size:12 final size:12
Alignment explanation
Indices: 3477380--3477412 Score: 57
Period size: 12 Copynumber: 2.8 Consensus size: 12
3477370 CATGCATGAA
*
3477380 ATGAAGGTATGC
1 ATGAAAGTATGC
3477392 ATGAAAGTATGC
1 ATGAAAGTATGC
3477404 ATGAAAGTA
1 ATGAAAGTA
3477413 AAAGCATGCA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.42, C:0.06, G:0.27, T:0.24
Consensus pattern (12 bp):
ATGAAAGTATGC
Found at i:3477552 original size:104 final size:103
Alignment explanation
Indices: 3477437--3477657 Score: 381
Period size: 104 Copynumber: 2.1 Consensus size: 103
3477427 CACGTACGGA
3477437 ATGCAATGTAATGCATTGCATTTCTTTATTTTTTTGCCAAGTTTGTTTATTCAATTTCATGCATG
1 ATGCAATGTAATGCATTGCATTTCTTTATTTTTTTGCCAAGTTTGTTTATTCAATTTCATGCATG
* *
3477502 AATGCATGAATTGCCACCTAATCGGTTTAGGTGGCATTG-
66 AATGCATGAATTGCCACCTAATCGATTTACGTGGCA--GC
3477541 ATGCAATGTAATGCATTGCATTTCTTTATTTTTTTGCCAAGTTTGTTTATTCAATTTCATGCATG
1 ATGCAATGTAATGCATTGCATTTCTTTATTTTTTTGCCAAGTTTGTTTATTCAATTTCATGCATG
*
3477606 AATGCATGAATTGCCACCTAATTGATTTACGTGGCAGC
66 AATGCATGAATTGCCACCTAATCGATTTACGTGGCAGC
*
3477644 ATGCAATGCAATGC
1 ATGCAATGTAATGC
3477658 CACCTAAATC
Statistics
Matches: 112, Mismatches: 4, Indels: 3
0.94 0.03 0.03
Matches are distributed among these distances:
102 1 0.01
103 13 0.12
104 98 0.88
ACGTcount: A:0.25, C:0.16, G:0.18, T:0.41
Consensus pattern (103 bp):
ATGCAATGTAATGCATTGCATTTCTTTATTTTTTTGCCAAGTTTGTTTATTCAATTTCATGCATG
AATGCATGAATTGCCACCTAATCGATTTACGTGGCAGC
Found at i:3477745 original size:17 final size:17
Alignment explanation
Indices: 3477706--3477805 Score: 82
Period size: 16 Copynumber: 5.9 Consensus size: 17
3477696 GATCTTTTTT
*
3477706 ATTTTTTATTATTTTTTA
1 ATTTTTTA-TATTTATTA
* *
3477724 TTTTTTTATGTTTATTA
1 ATTTTTTATATTTATTA
*
3477741 ATTTTTTA-ATTAATTA
1 ATTTTTTATATTTATTA
*
3477757 ATTTTTTA-ATTAATTA
1 ATTTTTTATATTTATTA
* *
3477773 ATTATTGT-T-CTTATTA
1 ATT-TTTTATATTTATTA
3477789 TATTTTTTATATTTATT
1 -ATTTTTTATATTTATT
3477806 TGTTTTTTCT
Statistics
Matches: 66, Mismatches: 11, Indels: 10
0.76 0.13 0.11
Matches are distributed among these distances:
16 33 0.50
17 21 0.32
18 12 0.18
ACGTcount: A:0.27, C:0.01, G:0.02, T:0.70
Consensus pattern (17 bp):
ATTTTTTATATTTATTA
Found at i:3477749 original size:8 final size:8
Alignment explanation
Indices: 3477700--3477767 Score: 59
Period size: 8 Copynumber: 8.2 Consensus size: 8
3477690 TAATTCGATC
3477700 TTTTTT-A
1 TTTTTTAA
3477707 TTTTTTATTA
1 TTTTTTA--A
3477717 TTTTTT-A
1 TTTTTTAA
*
3477724 TTTTTTTA
1 TTTTTTAA
3477732 TGTTTATTAA
1 T-TTT-TTAA
3477742 TTTTTTAA
1 TTTTTTAA
**
3477750 TTAATTAA
1 TTTTTTAA
3477758 TTTTTTAA
1 TTTTTTAA
3477766 TT
1 TT
3477768 AATTAATTAT
Statistics
Matches: 50, Mismatches: 5, Indels: 11
0.76 0.08 0.17
Matches are distributed among these distances:
7 13 0.26
8 20 0.40
9 6 0.12
10 11 0.22
ACGTcount: A:0.24, C:0.00, G:0.01, T:0.75
Consensus pattern (8 bp):
TTTTTTAA
Found at i:3478377 original size:42 final size:43
Alignment explanation
Indices: 3478331--3478993 Score: 152
Period size: 42 Copynumber: 15.8 Consensus size: 43
3478321 GGTAGACAAA
* *
3478331 AGGTGGA-AAAGTCTTTGGGGTCAAAGCCGACAAGCAAACTTG
1 AGGTGGAGAAAGTCTCTAGGGTCAAAGCCGACAAGCAAACTTG
* * *
3478373 AGGT-GAGACAGTCTCCAGGGTCAAAGCCGACAGGCAAAC-TG
1 AGGTGGAGAAAGTCTCTAGGGTCAAAGCCGACAAGCAAACTTG
* *
3478414 AAGG-GTAAGAAAGTCTCTAGGGTCAAAGCCGACAAGCAGACTTG
1 -AGGTG-GAGAAAGTCTCTAGGGTCAAAGCCGACAAGCAAACTTG
* ** * * * * *
3478458 AGAT-GAGGCAGTGT-TCAGGGTCAAAGCCAATAGGCAGA-TTG
1 AGGTGGAGAAAGTCTCT-AGGGTCAAAGCCGACAAGCAAACTTG
* * * ** * * * *
3478499 AAAGT-AAGAAAGTCTCCAAAGTCAAAGCTG--AGGCAGACTTT
1 -AGGTGGAGAAAGTCTCTAGGGTCAAAGCCGACAAGCAAACTTG
* ** * * * * **
3478540 AGAT-GAGGCAGTCTCTAGGGTCAAAGTCGACAGGTAGACTAA
1 AGGTGGAGAAAGTCTCTAGGGTCAAAGCCGACAAGCAAACTTG
* * * * * * * *
3478582 AAGTAG-GAAAGTCTCCAAGGTCAAAGCCGATAGGCAGACTTT
1 AGGTGGAGAAAGTCTCTAGGGTCAAAGCCGACAAGCAAACTTG
* * * *
3478624 AGAT-GAGGCAA-TCTCTAAGGTCAAAGTCGACAAGCAAAC-TG
1 AGGTGGA-GAAAGTCTCTAGGGTCAAAGCCGACAAGCAAACTTG
* ** * * * * * *
3478665 AAAG-CAAAAAAGTCTCCAGGGTTAAAGCCGATAGGCAAACTTT
1 -AGGTGGAGAAAGTCTCTAGGGTCAAAGCCGACAAGCAAACTTG
* * ** * * *
3478708 AGAT-AAGGCAGTCTCCAGGGTCAAAGCCAACAGGCAAACTTG
1 AGGTGGAGAAAGTCTCTAGGGTCAAAGCCGACAAGCAAACTTG
** * ** * * * * *
3478750 AAAT-AAGGCAGTCTCCAGGGTCAAAGCCGATAGGTAGAC-TG
1 AGGTGGAGAAAGTCTCTAGGGTCAAAGCCGACAAGCAAACTTG
* * * * * *
3478791 AAGGTAG-GAAAGTCTCCAAGGTCAAAGTCGACAAGCAGACTCG
1 -AGGTGGAGAAAGTCTCTAGGGTCAAAGCCGACAAGCAAACTTG
* ** * * * * **
3478834 AGAT-GAGGTAGTCTATAGGGTCAAAGCCGAAAAGTAGACTAAA
1 AGGTGGAGAAAGTCTCTAGGGTCAAAGCCGACAAGCAAACT-TG
* * * * *
3478877 AGGT-AAGAAAGTCTCTAGGATCAAAGCCGATAGGCAGACTTG
1 AGGTGGAGAAAGTCTCTAGGGTCAAAGCCGACAAGCAAACTTG
** ** * * * *
3478919 AACT-GAGGCAGTCTCTAGGGTCAAAGCTGACAGGTAGAC-TG
1 AGGTGGAGAAAGTCTCTAGGGTCAAAGCCGACAAGCAAACTTG
* *
3478960 AAGG-GTAAGAAAGTCTATAGGGTCAAAGCCGACA
1 -AGGTG-GAGAAAGTCTCTAGGGTCAAAGCCGACA
3478994 GGCAGACTAA
Statistics
Matches: 455, Mismatches: 138, Indels: 55
0.70 0.21 0.08
Matches are distributed among these distances:
40 26 0.06
41 19 0.04
42 316 0.69
43 92 0.20
44 2 0.00
ACGTcount: A:0.36, C:0.18, G:0.28, T:0.17
Consensus pattern (43 bp):
AGGTGGAGAAAGTCTCTAGGGTCAAAGCCGACAAGCAAACTTG
Found at i:3478647 original size:84 final size:84
Alignment explanation
Indices: 3478348--3478789 Score: 476
Period size: 84 Copynumber: 5.3 Consensus size: 84
3478338 AAAGTCTTTG
* * * * * *
3478348 GGGTCAAAGCCGACAAGCAAACTTGAGGTGAGACAGTCTCCAGGGTCAAAGCCGACAGGCAAACT
1 GGGTCAAAGCCGATAGGCAGACTTTAGATGAGGCAGTCTCCAGGGTCAAAGCCGACAGGCAAACT
* *
3478413 GAAGGGTAAGAAAGTCTCTA
66 GAA-AGTAAGAAAGTCTCCA
* * * * * * * * *
3478433 GGGTCAAAGCCGACAAGCAGACTTGAGATGAGGCAGTGTTCAGGGTCAAAGCCAATAGGCAGATT
1 GGGTCAAAGCCGATAGGCAGACTTTAGATGAGGCAGTCTCCAGGGTCAAAGCCGACAGGCAAACT
3478498 GAAAGTAAGAAAGTCTCCA
66 GAAAGTAAGAAAGTCTCCA
** * * * * *
3478517 AAGTCAAAGCTG--AGGCAGACTTTAGATGAGGCAGTCTCTAGGGTCAAAGTCGACAGGTAGACT
1 GGGTCAAAGCCGATAGGCAGACTTTAGATGAGGCAGTCTCCAGGGTCAAAGCCGACAGGCAAACT
* *
3478580 AAAAGTAGGAAAGTCTCCA
66 GAAAGTAAGAAAGTCTCCA
* * * * * *
3478599 AGGTCAAAGCCGATAGGCAGACTTTAGATGAGGCAATCTCTAAGGTCAAAGTCGACAAGCAAACT
1 GGGTCAAAGCCGATAGGCAGACTTTAGATGAGGCAGTCTCCAGGGTCAAAGCCGACAGGCAAACT
* *
3478664 GAAAGCAAAAAAGTCTCCA
66 GAAAGTAAGAAAGTCTCCA
* * * *
3478683 GGGTTAAAGCCGATAGGCAAACTTTAGATAAGGCAGTCTCCAGGGTCAAAGCCAACAGGCAAACT
1 GGGTCAAAGCCGATAGGCAGACTTTAGATGAGGCAGTCTCCAGGGTCAAAGCCGACAGGCAAAC-
**
3478748 TGAAA-TAAGGCAGTCTCCA
65 TGAAAGTAAGAAAGTCTCCA
*
3478767 GGGTCAAAGCCGATAGGTAGACT
1 GGGTCAAAGCCGATAGGCAGACT
3478790 GAAGGTAGGA
Statistics
Matches: 300, Mismatches: 54, Indels: 7
0.83 0.15 0.02
Matches are distributed among these distances:
82 68 0.23
84 168 0.56
85 64 0.21
ACGTcount: A:0.36, C:0.19, G:0.27, T:0.17
Consensus pattern (84 bp):
GGGTCAAAGCCGATAGGCAGACTTTAGATGAGGCAGTCTCCAGGGTCAAAGCCGACAGGCAAACT
GAAAGTAAGAAAGTCTCCA
Found at i:3478803 original size:126 final size:125
Alignment explanation
Indices: 3478348--3478861 Score: 388
Period size: 126 Copynumber: 4.1 Consensus size: 125
3478338 AAAGTCTTTG
* * ** * *
3478348 GGGTCAAAGCCGACAAGCAAACTTGAGGTGAGACAGTCTCCAGGGTCAAAGCCGACAGGCAAACT
1 GGGTCAAAGCCAACAGGCAAACTTGAAATAAGACAGTCTCCAAGGTCAAAGCCGACAGGCAAACT
* * * * *
3478413 GAAGGGTAAGAAAGTCTCTAGGGTCAAAGCCGACAAGCAGACTTGAGATGAGGCAGTGTTCA
66 GAA-GGTAAGAAAGTCTCCAGGGTCAAAGCCGACAGGCAGACTTAAGAT-AGGCAGTCTCCA
* * * * * *
3478475 GGGTCAAAGCCAATAGGCAGA-TTGAAAGTAAGAAAGTCTCCAAAGTCAAAGCTG--AGGCAGAC
1 GGGTCAAAGCCAACAGGCAAACTTGAAA-TAAGACAGTCTCCAAGGTCAAAGCCGACAGGCAAAC
** * * ** * * * * *
3478537 TTTAGATGAGGCAGTCTCTAGGGTCAAAGTCGACAGGTAGAC-TAAAAGTAGGAAAGTCTCCA
65 TGAAGGTAAGAAAGTCTCCAGGGTCAAAGCCGACAGGCAGACTTAAGA-TAGG-CAGTCTCCA
* * * * * * * * * * * *
3478599 AGGTCAAAGCCGATAGGCAGACTTTAGATGAGGCAATCTCTAAGGTCAAAGTCGACAAGCAAACT
1 GGGTCAAAGCCAACAGGCAAACTTGAAATAAGACAGTCTCCAAGGTCAAAGCCGACAGGCAAACT
* * * * * * *
3478664 GAAAGCAAAAAAGTCTCCAGGGTTAAAGCCGATAGGCAAACTTTAGATAAGGCAGTCTCCA
66 GAAGGTAAGAAAGTCTCCAGGGTCAAAGCCGACAGGCAGACTTAAGAT-AGGCAGTCTCCA
* * * * *
3478725 GGGTCAAAGCCAACAGGCAAACTTGAAATAAGGCAGTCTCCAGGGTCAAAGCCGATAGGTAGACT
1 GGGTCAAAGCCAACAGGCAAACTTGAAATAAGACAGTCTCCAAGGTCAAAGCCGACAGGCAAACT
* * * * ** * **
3478790 GAAGGTAGGAAAGTCTCCAAGGTCAAAGTCGACAAGCAGACTCGAGATGAGGTAGTCTATA
66 GAAGGTAAGAAAGTCTCCAGGGTCAAAGCCGACAGGCAGACTTAAGAT-AGGCAGTCTCCA
3478851 GGGTCAAAGCC
1 GGGTCAAAGCC
3478862 GAAAAGTAGA
Statistics
Matches: 290, Mismatches: 89, Indels: 17
0.73 0.22 0.04
Matches are distributed among these distances:
123 6 0.02
124 75 0.26
125 13 0.04
126 152 0.52
127 44 0.15
ACGTcount: A:0.36, C:0.19, G:0.28, T:0.17
Consensus pattern (125 bp):
GGGTCAAAGCCAACAGGCAAACTTGAAATAAGACAGTCTCCAAGGTCAAAGCCGACAGGCAAACT
GAAGGTAAGAAAGTCTCCAGGGTCAAAGCCGACAGGCAGACTTAAGATAGGCAGTCTCCA
Found at i:3478805 original size:84 final size:84
Alignment explanation
Indices: 3478348--3479001 Score: 396
Period size: 84 Copynumber: 7.8 Consensus size: 84
3478338 AAAGTCTTTG
* * * * *
3478348 GGGTCAAAGCCGACAAGCAAACTTG-AGGTGA-GACAGTCTCCAGGGTCAAAGCCGACAGGCAAA
1 GGGTCAAAGCCGATAGGCAGAC-TGAAGATGAGGA-AGTCTCCAGGGTCAAAGCCGACAGGCAGA
* * *
3478411 C-TGAAGGGTAAGAAAGTCTCTA
64 CTTGAA--ATAAGGAAGTCTCCA
* * * * * * *
3478433 GGGTCAAAGCCGACAAGCAGACTTG-AGATGAGGCAGTGTTCAGGGTCAAAGCCAATAGGCAGA-
1 GGGTCAAAGCCGATAGGCAGAC-TGAAGATGAGGAAGTCTCCAGGGTCAAAGCCGACAGGCAGAC
*
3478496 TTGAAAGTAAGAAAGTCTCCA
65 TTGAAA-TAAGGAAGTCTCCA
** * ** * * * *
3478517 AAGTCAAAGCTG--AGGCAGACTTTAGATGAGGCAGTCTCTAGGGTCAAAGTCGACAGGTAGAC-
1 GGGTCAAAGCCGATAGGCAGACTGAAGATGAGGAAGTCTCCAGGGTCAAAGCCGACAGGCAGACT
*
3478579 TAAAAGT-AGGAAAGTCTCCA
66 TGAAA-TAAGG-AAGTCTCCA
* ** * * * * *
3478599 AGGTCAAAGCCGATAGGCAGACTTTAGATGAGGCAA-TCTCTAAGGTCAAAGTCGACAAGCAAAC
1 GGGTCAAAGCCGATAGGCAGACTGAAGATGAGG-AAGTCTCCAGGGTCAAAGCCGACAGGCAGAC
* **
3478663 -TGAAAGCAAAAAAGTCTCCA
65 TTGAAA-TAAGGAAGTCTCCA
* * ** * * * *
3478683 GGGTTAAAGCCGATAGGCAAACTTTAGATAAGGCAGTCTCCAGGGTCAAAGCCAACAGGCAAACT
1 GGGTCAAAGCCGATAGGCAGACTGAAGATGAGGAAGTCTCCAGGGTCAAAGCCGACAGGCAGACT
*
3478748 TGAAATAAGGCAGTCTCCA
66 TGAAATAAGGAAGTCTCCA
* * * * *
3478767 GGGTCAAAGCCGATAGGTAGACTGAAGGT-AGGAAAGTCTCCAAGGTCAAAGTCGACAAGCAGAC
1 GGGTCAAAGCCGATAGGCAGACTGAAGATGAGG-AAGTCTCCAGGGTCAAAGCCGACAGGCAGAC
* * * * **
3478831 TCGAGATGAGGTAGTCTATA
65 TTGAAATAAGGAAGTCTCCA
* * * * * * * * * *
3478851 GGGTCAAAGCCGAAAAGTAGACTAAAAGGTAAGAAAGTCTCTAGGATCAAAGCCGATAGGCAGAC
1 GGGTCAAAGCCGATAGGCAGACT-GAAGATGAGGAAGTCTCCAGGGTCAAAGCCGACAGGCAGAC
* * * *
3478916 TTGAACTGAGGCAGTCTCTA
65 TTGAAATAAGGAAGTCTCCA
* * * * * * **
3478936 GGGTCAAAGCTGACAGGTAGACTGAAGGGTAAGAAAGTCTATAGGGTCAAAGCCGACAGGCAGAC
1 GGGTCAAAGCCGATAGGCAGACTGAA-GATGAGGAAGTCTCCAGGGTCAAAGCCGACAGGCAGAC
3479001 T
65 T
3479002 AAAAGTAGGA
Statistics
Matches: 464, Mismatches: 89, Indels: 32
0.79 0.15 0.05
Matches are distributed among these distances:
81 3 0.01
82 63 0.14
83 4 0.01
84 226 0.49
85 165 0.36
86 3 0.01
ACGTcount: A:0.36, C:0.19, G:0.28, T:0.17
Consensus pattern (84 bp):
GGGTCAAAGCCGATAGGCAGACTGAAGATGAGGAAGTCTCCAGGGTCAAAGCCGACAGGCAGACT
TGAAATAAGGAAGTCTCCA
Found at i:3478914 original size:85 final size:83
Alignment explanation
Indices: 3478717--3479001 Score: 293
Period size: 85 Copynumber: 3.4 Consensus size: 83
3478707 TAGATAAGGC
* * * * * * ** *
3478717 AGTCTCCAGGGTCAAAGCCAACAGGCAAACTTGAAATAAGGCAGTCTCCAGGGTCAAAGCCGATA
1 AGTCTCTA-GGTCAAAGCCGACAGGCAGACTCGAACTGAGGCAGTCTATAGGGTCAAAGCCGAAA
* *
3478782 GGTAGACTGAAGGTAGGAA
65 GGTAGACTAAAGGTAAGAA
* * * *
3478801 AGTCTCCAAGGTCAAAGTCGACAAGCAGACTCGAGA-TGAGGTAGTCTATAGGGTCAAAGCCGAA
1 AGTCT-CTAGGTCAAAGCCGACAGGCAGACTCGA-ACTGAGGCAGTCTATAGGGTCAAAGCCGAA
*
3478865 AAGTAGACTAAAAGGTAAGAA
64 AGGTAGACT-AAAGGTAAGAA
* * * * *
3478886 AGTCTCTAGGATCAAAGCCGATAGGCAGACTTGAACTGAGGCAGTCTCTAGGGTCAAAGCTGACA
1 AGTCTCTAGG-TCAAAGCCGACAGGCAGACTCGAACTGAGGCAGTCTATAGGGTCAAAGCCGAAA
*
3478951 GGTAGACTGAAGGGTAAGAA
65 GGTAGACT-AAAGGTAAGAA
*
3478971 AGTCTATAGGGTCAAAGCCGACAGGCAGACT
1 AGTCTCTA-GGTCAAAGCCGACAGGCAGACT
3479002 AAAAGTAGGA
Statistics
Matches: 167, Mismatches: 28, Indels: 11
0.81 0.14 0.05
Matches are distributed among these distances:
84 61 0.37
85 104 0.62
86 2 0.01
ACGTcount: A:0.36, C:0.19, G:0.29, T:0.17
Consensus pattern (83 bp):
AGTCTCTAGGTCAAAGCCGACAGGCAGACTCGAACTGAGGCAGTCTATAGGGTCAAAGCCGAAAG
GTAGACTAAAGGTAAGAA
Found at i:3490702 original size:33 final size:33
Alignment explanation
Indices: 3490665--3490731 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
3490655 TTCAATGATT
3490665 TGTATCGATACATAAAATGTTGTATCGATACAA
1 TGTATCGATACATAAAATGTTGTATCGATACAA
*** *
3490698 TGTATCGATACATATTTTTTTGTATCGATACAA
1 TGTATCGATACATAAAATGTTGTATCGATACAA
3490731 T
1 T
3490732 TTAAGCTACT
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.34, C:0.12, G:0.13, T:0.40
Consensus pattern (33 bp):
TGTATCGATACATAAAATGTTGTATCGATACAA
Found at i:3490703 original size:13 final size:13
Alignment explanation
Indices: 3490685--3490709 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
3490675 CATAAAATGT
3490685 TGTATCGATACAA
1 TGTATCGATACAA
3490698 TGTATCGATACA
1 TGTATCGATACA
3490710 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:3490791 original size:13 final size:13
Alignment explanation
Indices: 3490773--3490797 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
3490763 ATTACTCAAA
3490773 TGTATCGATACAT
1 TGTATCGATACAT
3490786 TGTATCGATACA
1 TGTATCGATACA
3490798 CCGATCTTTG
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:3490934 original size:52 final size:52
Alignment explanation
Indices: 3490806--3490926 Score: 215
Period size: 52 Copynumber: 2.3 Consensus size: 52
3490796 CACCGATCTT
* *
3490806 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACATTATAAAA
1 TGTATCGATACATGCAAGCAAATTTGCCCAGATGTATCGATACACTATAAAA
*
3490858 TGTATCGATACATGCAAGCAAATTTGCCCAGATGTATCGATACACTATTAAA
1 TGTATCGATACATGCAAGCAAATTTGCCCAGATGTATCGATACACTATAAAA
3490910 TGTATCGATACATGCAA
1 TGTATCGATACATGCAA
3490927 ATAAATTTTC
Statistics
Matches: 66, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
52 66 1.00
ACGTcount: A:0.36, C:0.18, G:0.17, T:0.29
Consensus pattern (52 bp):
TGTATCGATACATGCAAGCAAATTTGCCCAGATGTATCGATACACTATAAAA
Found at i:3497541 original size:8 final size:8
Alignment explanation
Indices: 3497523--3497560 Score: 51
Period size: 9 Copynumber: 4.6 Consensus size: 8
3497513 TAATTCGATC
3497523 TTTTTTA-
1 TTTTTTAT
3497530 TTTTTTATT
1 TTTTTTA-T
3497539 TTTTTTAT
1 TTTTTTAT
3497547 TTTTTTAT
1 TTTTTTAT
3497555 TCTTTT
1 T-TTTT
3497561 GCGTTTATTA
Statistics
Matches: 28, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
7 7 0.25
8 10 0.36
9 11 0.39
ACGTcount: A:0.11, C:0.03, G:0.00, T:0.87
Consensus pattern (8 bp):
TTTTTTAT
Found at i:3497550 original size:17 final size:17
Alignment explanation
Indices: 3497521--3497560 Score: 64
Period size: 17 Copynumber: 2.4 Consensus size: 17
3497511 ATTAATTCGA
3497521 TCTTTTTTATTTTTTAT
1 TCTTTTTTATTTTTTAT
3497538 T-TTTTTTATTTTTTTAT
1 TCTTTTTTA-TTTTTTAT
3497555 TCTTTT
1 TCTTTT
3497561 GCGTTTATTA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
16 7 0.33
17 10 0.48
18 4 0.19
ACGTcount: A:0.10, C:0.05, G:0.00, T:0.85
Consensus pattern (17 bp):
TCTTTTTTATTTTTTAT
Found at i:3497560 original size:9 final size:8
Alignment explanation
Indices: 3497523--3497560 Score: 51
Period size: 8 Copynumber: 4.8 Consensus size: 8
3497513 TAATTCGATC
3497523 TTTTTTA-
1 TTTTTTAT
3497530 TTTTTTATT
1 TTTTTTA-T
3497539 TTTTTTAT
1 TTTTTTAT
3497547 TTTTTTAT
1 TTTTTTAT
*
3497555 TCTTTT
1 TTTTTT
3497561 GCGTTTATTA
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
7 7 0.25
8 14 0.50
9 7 0.25
ACGTcount: A:0.11, C:0.03, G:0.00, T:0.87
Consensus pattern (8 bp):
TTTTTTAT
Found at i:3500063 original size:21 final size:21
Alignment explanation
Indices: 3500039--3500081 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 21
3500029 TTTCATGGTC
*
3500039 TTCCATGAAGCAACCAACTGT
1 TTCCAAGAAGCAACCAACTGT
*
3500060 TTCCAAGAAGCAACCAATTGT
1 TTCCAAGAAGCAACCAACTGT
3500081 T
1 T
3500082 ACGTTGTCAA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.35, C:0.26, G:0.14, T:0.26
Consensus pattern (21 bp):
TTCCAAGAAGCAACCAACTGT
Found at i:3500582 original size:20 final size:20
Alignment explanation
Indices: 3500557--3500615 Score: 91
Period size: 20 Copynumber: 3.0 Consensus size: 20
3500547 CAACAGCTTT
3500557 CTTCATTTTTGTCTTTGGTC
1 CTTCATTTTTGTCTTTGGTC
* *
3500577 CTTCATTGTTGTCTTTGGTT
1 CTTCATTTTTGTCTTTGGTC
*
3500597 CTTCATTTTTATCTTTGGT
1 CTTCATTTTTGTCTTTGGT
3500616 AATTTTAATC
Statistics
Matches: 35, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 35 1.00
ACGTcount: A:0.07, C:0.17, G:0.15, T:0.61
Consensus pattern (20 bp):
CTTCATTTTTGTCTTTGGTC
Found at i:3501380 original size:184 final size:184
Alignment explanation
Indices: 3501071--3501442 Score: 692
Period size: 184 Copynumber: 2.0 Consensus size: 184
3501061 AGCCGGTAGT
* *
3501071 TATGGGTATTTGCATTTGTTTATTATTACTTCTACGACTTTGGCAAGGTTGATTTTAGATTGTAC
1 TATGGGTATTTGCATTTGTTTAATATTACTTCTAAGACTTTGGCAAGGTTGATTTTAGATTGTAC
*
3501136 CAAGTTCTATATCCTAAGAGGCAAACCTGGCCGTTTTTAACGGCATGTCTTAAGTTATTGCGACT
66 CAAGTTCTATATCCTAAGAGGCAAACCTGGCCGTTTTTAACGGCATGTCTTAAGTTATTGCCA-T
3501201 -GATTTTATTTAACCAACAAACATCCTTAGATCTATCTATCACCAACATGCATCA
130 GGATTTTATTTAACCAACAAACATCCTTAGATCTATCTATCACCAACATGCATCA
3501255 TATGGGTATTTGCATTTGTTTAATATTACTTCTAAGACTTTGGCAAGGTTGATTTTAGATTGTAC
1 TATGGGTATTTGCATTTGTTTAATATTACTTCTAAGACTTTGGCAAGGTTGATTTTAGATTGTAC
*
3501320 CAAGTTCTATATCCTACGAGGCAAACCTGGCCGTTTTTAACGGCATGTCTTAAGTTATTGCCATG
66 CAAGTTCTATATCCTAAGAGGCAAACCTGGCCGTTTTTAACGGCATGTCTTAAGTTATTGCCATG
3501385 GATTTTATTTAACCAACAAACATCCTTAGATCTATCTATCACCAACATGCATCA
131 GATTTTATTTAACCAACAAACATCCTTAGATCTATCTATCACCAACATGCATCA
3501439 TATG
1 TATG
3501443 TGATATATTA
Statistics
Matches: 183, Mismatches: 4, Indels: 2
0.97 0.02 0.01
Matches are distributed among these distances:
183 1 0.01
184 182 0.99
ACGTcount: A:0.28, C:0.19, G:0.16, T:0.37
Consensus pattern (184 bp):
TATGGGTATTTGCATTTGTTTAATATTACTTCTAAGACTTTGGCAAGGTTGATTTTAGATTGTAC
CAAGTTCTATATCCTAAGAGGCAAACCTGGCCGTTTTTAACGGCATGTCTTAAGTTATTGCCATG
GATTTTATTTAACCAACAAACATCCTTAGATCTATCTATCACCAACATGCATCA
Found at i:3502468 original size:27 final size:28
Alignment explanation
Indices: 3502390--3502468 Score: 74
Period size: 27 Copynumber: 2.8 Consensus size: 28
3502380 TAATAAAAGA
3502390 ATAAAATAAATAATTATTATTTAATTATTTT
1 ATAAAAT-AATAA--ATTATTTAATTATTTT
** *
3502421 ATGTAAT-ATATAATTA-ATAATTATTTT
1 ATAAAATAATA-AATTATTTAATTATTTT
3502448 A-AAAATAATAAATTATTTAAT
1 ATAAAATAATAAATTATTTAAT
3502469 ATAATTTGAA
Statistics
Matches: 39, Mismatches: 6, Indels: 10
0.71 0.11 0.18
Matches are distributed among these distances:
26 8 0.21
27 18 0.46
28 4 0.10
29 3 0.08
30 1 0.03
31 5 0.13
ACGTcount: A:0.51, C:0.00, G:0.01, T:0.48
Consensus pattern (28 bp):
ATAAAATAATAAATTATTTAATTATTTT
Found at i:3502786 original size:29 final size:27
Alignment explanation
Indices: 3502737--3502803 Score: 73
Period size: 28 Copynumber: 2.4 Consensus size: 27
3502727 TCTAAAAATT
3502737 AAATTATAAAATAAATAATATATTTATA
1 AAATTATAAAATAAATAATAT-TTTATA
* * * *
3502765 AAATTATATTAATAATTTATATTTTTTA
1 AAATTATA-AAATAAATAATATTTTATA
3502793 AAA-TATAAAAT
1 AAATTATAAAAT
3502804 TATATTCATT
Statistics
Matches: 33, Mismatches: 5, Indels: 4
0.79 0.12 0.10
Matches are distributed among these distances:
26 3 0.09
27 4 0.12
28 16 0.48
29 10 0.30
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (27 bp):
AAATTATAAAATAAATAATATTTTATA
Found at i:3503103 original size:76 final size:74
Alignment explanation
Indices: 3502984--3503136 Score: 279
Period size: 76 Copynumber: 2.0 Consensus size: 74
3502974 GAATAATAAT
3502984 AATTTTTTTAATTTTTTAAATAAGTTTTTAAAAAAATATTTCTCAAAATATATTTTTTTATGAAT
1 AATTTTTTTAATTTTTTAAATAAGTTTTTAAAAAAATATTTCTCAAAATATATTTTTTTATGAAT
3503049 ATATTAAAA
66 ATATTAAAA
*
3503058 AATTATTTTTAATTTTTTAAATAAATTTTTTAAAAAAATATTTCTCAAAATATATTTTTTTATGA
1 AATT-TTTTTAATTTTTTAAAT-AAGTTTTTAAAAAAATATTTCTCAAAATATATTTTTTTATGA
3503123 ATATATTAAAA
64 ATATATTAAAA
3503134 AAT
1 AAT
3503137 CATCACCTAA
Statistics
Matches: 76, Mismatches: 1, Indels: 2
0.96 0.01 0.03
Matches are distributed among these distances:
74 4 0.05
75 17 0.22
76 55 0.72
ACGTcount: A:0.44, C:0.03, G:0.02, T:0.51
Consensus pattern (74 bp):
AATTTTTTTAATTTTTTAAATAAGTTTTTAAAAAAATATTTCTCAAAATATATTTTTTTATGAAT
ATATTAAAA
Found at i:3503727 original size:24 final size:23
Alignment explanation
Indices: 3503689--3503745 Score: 68
Period size: 21 Copynumber: 2.6 Consensus size: 23
3503679 TTAAAGTATG
3503689 ATTTATTTTTATTTATAAAATTA
1 ATTTATTTTTATTTATAAAATTA
*
3503712 ATTTA-TTTTATTT-T--TATTAA
1 ATTTATTTTTATTTATAAAATT-A
3503732 ATTTATTTTTATTT
1 ATTTATTTTTATTT
3503746 GATTATGTGG
Statistics
Matches: 31, Mismatches: 1, Indels: 6
0.82 0.03 0.16
Matches are distributed among these distances:
19 3 0.10
20 6 0.19
21 9 0.29
22 8 0.26
23 5 0.16
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (23 bp):
ATTTATTTTTATTTATAAAATTA
Found at i:3503750 original size:20 final size:20
Alignment explanation
Indices: 3503711--3503750 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
3503701 TTATAAAATT
*
3503711 AATTTATTTTATTTTTATTA
1 AATTTATTTTATTTTGATTA
3503731 AATTTATTTT-TATTTGATTA
1 AATTTATTTTAT-TTTGATTA
3503751 TGTGGATTTA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
19 1 0.06
20 17 0.94
ACGTcount: A:0.30, C:0.00, G:0.03, T:0.68
Consensus pattern (20 bp):
AATTTATTTTATTTTGATTA
Found at i:3507930 original size:28 final size:27
Alignment explanation
Indices: 3507899--3507995 Score: 81
Period size: 28 Copynumber: 3.4 Consensus size: 27
3507889 TCATTAATAT
3507899 TTTAATTAATTAATGTAATTTTTTTAAA
1 TTTAATTAATTAAT-TAATTTTTTTAAA
* *
3507927 TTTAATTACTT-ATTATTTTTTATTAAAAA
1 TTTAATTAATTAATTAATTTTT-TT--AAA
* *
3507956 TAATAATTAA-TATATTATTATTTTTTAAA
1 T-TTAATTAATTA-ATTAAT-TTTTTTAAA
3507985 TTTAATTAATT
1 TTTAATTAATT
3507996 TATAAAAATA
Statistics
Matches: 56, Mismatches: 5, Indels: 15
0.74 0.07 0.20
Matches are distributed among these distances:
26 7 0.12
27 4 0.07
28 17 0.30
29 10 0.18
30 6 0.11
31 8 0.14
32 4 0.07
ACGTcount: A:0.40, C:0.01, G:0.01, T:0.58
Consensus pattern (27 bp):
TTTAATTAATTAATTAATTTTTTTAAA
Found at i:3507967 original size:135 final size:134
Alignment explanation
Indices: 3507714--3507962 Score: 346
Period size: 135 Copynumber: 1.9 Consensus size: 134
3507704 AAAAAACCTT
* *
3507714 TTTTTTCAATTTAAAATTTTTTATTTTTTAAAAAATATTATAATTAATATTTTAATTGTTAATGT
1 TTTTTTCAATTTAAAATTTTTTATTTTTTAAAAAATATAATAATTAATATTTTAATTATTAATGT
* *
3507779 AAATTATTTTAAAATTAATTAAATATTATTTTTTATTTTATTAAATTTATAATAAAAAACCTTTT
66 AAATTATTTTAAAATTAATTAAATATTATTTTTTA-TTTATAAAATTAATAATAAAAAACCTTTT
3507844 TTTAC
130 TTTAC
* *
3507849 TTTTTT-AATTTATAATTTTTTATTTTTTTAAAAAATATAATCATTAATATTTTAATTAATTAAT
1 TTTTTTCAATTTAAAATTTTTTA-TTTTTTAAAAAATATAATAATTAATATTTTAATT-ATTAAT
* * **
3507913 GT-AATTTTTTTAAATTTAATTACTTATTATTTTTTA-TTA-AAAA-TAATAAT
64 GTAAATTATTTTAAAATTAATTAAATATTATTTTTTATTTATAAAATTAATAAT
3507963 TAATATATTA
Statistics
Matches: 102, Mismatches: 10, Indels: 8
0.85 0.08 0.07
Matches are distributed among these distances:
131 6 0.06
132 3 0.03
133 3 0.03
134 15 0.15
135 68 0.67
136 7 0.07
ACGTcount: A:0.40, C:0.02, G:0.01, T:0.57
Consensus pattern (134 bp):
TTTTTTCAATTTAAAATTTTTTATTTTTTAAAAAATATAATAATTAATATTTTAATTATTAATGT
AAATTATTTTAAAATTAATTAAATATTATTTTTTATTTATAAAATTAATAATAAAAAACCTTTTT
TTAC
Found at i:3508330 original size:19 final size:18
Alignment explanation
Indices: 3508278--3508335 Score: 50
Period size: 18 Copynumber: 3.3 Consensus size: 18
3508268 TTATTTTTAA
*
3508278 ATTTAAG-TATAAAT-TTA
1 ATTTAAGTTA-AAATATTT
* *
3508295 ATTTAATTTAATATATTT
1 ATTTAAGTTAAAATATTT
3508313 ATTTAAGTTAAAAT-TATT
1 ATTTAAGTTAAAATAT-TT
3508331 ATTTA
1 ATTTA
3508336 TTTTATTAAA
Statistics
Matches: 33, Mismatches: 5, Indels: 5
0.77 0.12 0.12
Matches are distributed among these distances:
17 10 0.30
18 23 0.70
ACGTcount: A:0.43, C:0.00, G:0.03, T:0.53
Consensus pattern (18 bp):
ATTTAAGTTAAAATATTT
Found at i:3508346 original size:21 final size:23
Alignment explanation
Indices: 3508308--3508362 Score: 71
Period size: 22 Copynumber: 2.5 Consensus size: 23
3508298 TAATTTAATA
3508308 TATTTATTTAAGTT-AAAATTAT
1 TATTTATTTAAGTTAAAAATTAT
*
3508330 TATTTATTTTA-TTAAAAATTAT
1 TATTTATTTAAGTTAAAAATTAT
3508352 T-TTTATATTAA
1 TATTTAT-TTAA
3508363 TATTTATTTA
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
21 7 0.24
22 22 0.76
ACGTcount: A:0.40, C:0.00, G:0.02, T:0.58
Consensus pattern (23 bp):
TATTTATTTAAGTTAAAAATTAT
Found at i:3508381 original size:18 final size:19
Alignment explanation
Indices: 3508328--3508378 Score: 68
Period size: 18 Copynumber: 2.7 Consensus size: 19
3508318 AGTTAAAATT
* *
3508328 ATTATTTATTTTATTAAAA
1 ATTATTTATTATATTAATA
3508347 ATTATTT-TTATATTAATA
1 ATTATTTATTATATTAATA
*
3508365 TTTATTTATTATAT
1 ATTATTTATTATAT
3508379 AATTAAATTT
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
18 15 0.54
19 13 0.46
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (19 bp):
ATTATTTATTATATTAATA
Found at i:3509774 original size:21 final size:22
Alignment explanation
Indices: 3509736--3509776 Score: 66
Period size: 21 Copynumber: 1.9 Consensus size: 22
3509726 TTCTATTTTC
*
3509736 TCTCTTTTCCCTCTCCTTTCGT
1 TCTCTTTTCCCTCCCCTTTCGT
3509758 TCTCTTTT-CCTCCCCTTTC
1 TCTCTTTTCCCTCCCCTTTC
3509777 TTCACTTCCT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 10 0.56
22 8 0.44
ACGTcount: A:0.00, C:0.44, G:0.02, T:0.54
Consensus pattern (22 bp):
TCTCTTTTCCCTCCCCTTTCGT
Found at i:3509890 original size:2 final size:2
Alignment explanation
Indices: 3509879--3509919 Score: 75
Period size: 2 Copynumber: 21.0 Consensus size: 2
3509869 CCTCTTCTTC
3509879 AT AT -T AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
3509920 GTTGCTCAAG
Statistics
Matches: 38, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.03
2 37 0.97
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
AT
Found at i:3510575 original size:27 final size:27
Alignment explanation
Indices: 3510529--3510590 Score: 67
Period size: 27 Copynumber: 2.3 Consensus size: 27
3510519 ATAATTAAAT
3510529 AACATAAACACAATATAAAA-AAATTAA
1 AACATAAACACAATATAAAATAAA-TAA
*
3510556 AACATAATACA-ACATA-AAAATAAATAT
1 AACATAA-ACACA-ATATAAAATAAATAA
3510583 AACATAAA
1 AACATAAA
3510591 TATATAAATG
Statistics
Matches: 31, Mismatches: 1, Indels: 7
0.79 0.03 0.18
Matches are distributed among these distances:
26 1 0.03
27 21 0.68
28 9 0.29
ACGTcount: A:0.69, C:0.11, G:0.00, T:0.19
Consensus pattern (27 bp):
AACATAAACACAATATAAAATAAATAA
Found at i:3510688 original size:12 final size:12
Alignment explanation
Indices: 3510668--3510716 Score: 55
Period size: 12 Copynumber: 4.0 Consensus size: 12
3510658 TGAATTTAAT
*
3510668 ATAACATAAAAA
1 ATAATATAAAAA
*
3510680 ATAATAT-AAAT
1 ATAATATAAAAA
3510691 ATGATATATAAAAA
1 AT-A-ATATAAAAA
3510705 ATAATATAAAAA
1 ATAATATAAAAA
3510717 TCTCGTAAAA
Statistics
Matches: 31, Mismatches: 3, Indels: 6
0.77 0.08 0.15
Matches are distributed among these distances:
11 5 0.16
12 16 0.52
13 5 0.16
14 5 0.16
ACGTcount: A:0.69, C:0.02, G:0.02, T:0.27
Consensus pattern (12 bp):
ATAATATAAAAA
Found at i:3513276 original size:17 final size:16
Alignment explanation
Indices: 3513254--3513286 Score: 57
Period size: 17 Copynumber: 2.0 Consensus size: 16
3513244 TAATTTATTT
3513254 AATTAATAATTCTTTAA
1 AATTAATAATT-TTTAA
3513271 AATTAATAATTTTTAA
1 AATTAATAATTTTTAA
3513287 TTCCAATATT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 5 0.31
17 11 0.69
ACGTcount: A:0.48, C:0.03, G:0.00, T:0.48
Consensus pattern (16 bp):
AATTAATAATTTTTAA
Found at i:3515310 original size:22 final size:21
Alignment explanation
Indices: 3515272--3515333 Score: 56
Period size: 22 Copynumber: 2.9 Consensus size: 21
3515262 TATGTTAAAA
*
3515272 ATATTATT-TTTATTATATGTAC
1 ATATAATTATTTA-TATAT-TAC
3515294 ATATAATTATTTATATA-TAC
1 ATATAATTATTTATATATTAC
*
3515314 ATATTATTTATATTATATAT
1 ATA-TAATTAT-TTATATAT
3515334 ATATTATTTT
Statistics
Matches: 34, Mismatches: 2, Indels: 7
0.79 0.05 0.16
Matches are distributed among these distances:
20 6 0.18
21 6 0.18
22 18 0.53
23 4 0.12
ACGTcount: A:0.39, C:0.03, G:0.02, T:0.56
Consensus pattern (21 bp):
ATATAATTATTTATATATTAC
Found at i:3515334 original size:22 final size:22
Alignment explanation
Indices: 3515272--3515342 Score: 87
Period size: 20 Copynumber: 3.4 Consensus size: 22
3515262 TATGTTAAAA
* *
3515272 ATATTATTTTTATTATATGTAC
1 ATATTATTTATATTATATATAC
*
3515294 ATA-TAATTAT-TTATATATAC
1 ATATTATTTATATTATATATAC
3515314 ATATTATTTATATTATATAT--
1 ATATTATTTATATTATATATAC
3515334 ATATTATTT
1 ATATTATTT
3515343 TTGGTGGATG
Statistics
Matches: 43, Mismatches: 4, Indels: 6
0.81 0.08 0.11
Matches are distributed among these distances:
20 21 0.49
21 11 0.26
22 11 0.26
ACGTcount: A:0.38, C:0.03, G:0.01, T:0.58
Consensus pattern (22 bp):
ATATTATTTATATTATATATAC
Found at i:3518502 original size:22 final size:22
Alignment explanation
Indices: 3518474--3518550 Score: 145
Period size: 22 Copynumber: 3.5 Consensus size: 22
3518464 ATCTCATTTT
3518474 TCACTGTTCATGTATCGATACA
1 TCACTGTTCATGTATCGATACA
3518496 TCACTGTTCATGTATCGATACA
1 TCACTGTTCATGTATCGATACA
*
3518518 TCACTGTTTATGTATCGATACA
1 TCACTGTTCATGTATCGATACA
3518540 TCACTGTTCAT
1 TCACTGTTCAT
3518551 CATTATACAT
Statistics
Matches: 53, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 53 1.00
ACGTcount: A:0.26, C:0.22, G:0.13, T:0.39
Consensus pattern (22 bp):
TCACTGTTCATGTATCGATACA
Found at i:3518644 original size:22 final size:22
Alignment explanation
Indices: 3518589--3518645 Score: 69
Period size: 22 Copynumber: 2.6 Consensus size: 22
3518579 TTTCACTGTT
** *
3518589 CATCATTGTTCATGTATTGATA
1 CATCATTGTTCATGTATCAACA
* *
3518611 CATCACTATTCATGTATCAACA
1 CATCATTGTTCATGTATCAACA
3518633 CATCATTGTTCAT
1 CATCATTGTTCAT
3518646 CATATACATT
Statistics
Matches: 28, Mismatches: 7, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
22 28 1.00
ACGTcount: A:0.30, C:0.21, G:0.09, T:0.40
Consensus pattern (22 bp):
CATCATTGTTCATGTATCAACA
Found at i:3519132 original size:35 final size:36
Alignment explanation
Indices: 3519065--3519132 Score: 102
Period size: 36 Copynumber: 1.9 Consensus size: 36
3519055 AGTGATAGTG
* **
3519065 AGGTTGTATCTTAGCCTTTGAAAAAGATAGGGAAAA
1 AGGTTCTATCTTAGCCCATGAAAAAGATAGGGAAAA
3519101 AGGTTCTATCTTAGCCCATG-AAAAGATAGGGA
1 AGGTTCTATCTTAGCCCATGAAAAAGATAGGGA
3519133 GGTTTCTATG
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
35 12 0.41
36 17 0.59
ACGTcount: A:0.37, C:0.12, G:0.25, T:0.26
Consensus pattern (36 bp):
AGGTTCTATCTTAGCCCATGAAAAAGATAGGGAAAA
Found at i:3520766 original size:21 final size:21
Alignment explanation
Indices: 3520742--3520799 Score: 66
Period size: 21 Copynumber: 2.8 Consensus size: 21
3520732 GAACTAAAGG
*
3520742 AGAAAATGAATGAGTTGGAAA
1 AGAAAATGAATGAGTTGCAAA
*
3520763 AGAAAA-GAAATAAGTTGCAAA
1 AGAAAATG-AATGAGTTGCAAA
3520784 ATGAAAATG-ATGAGTT
1 A-GAAAATGAATGAGTT
3520800 AACTAATAAA
Statistics
Matches: 31, Mismatches: 3, Indels: 6
0.77 0.08 0.15
Matches are distributed among these distances:
20 1 0.03
21 24 0.77
22 5 0.16
23 1 0.03
ACGTcount: A:0.53, C:0.02, G:0.24, T:0.21
Consensus pattern (21 bp):
AGAAAATGAATGAGTTGCAAA
Found at i:3524323 original size:32 final size:30
Alignment explanation
Indices: 3524287--3524345 Score: 75
Period size: 32 Copynumber: 1.9 Consensus size: 30
3524277 GAAATCAAAT
3524287 ACAAAGAGCT-TAGAAAAATAATAACAATATGA
1 ACAAA-AGCTCTAGAAAAAT-ATAA-AATATGA
*
3524319 ACAAAAGCTCTTGAAAAATATAAAATA
1 ACAAAAGCTCTAGAAAAATATAAAATA
3524346 CTTTGATCTA
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
30 4 0.16
31 8 0.32
32 13 0.52
ACGTcount: A:0.59, C:0.10, G:0.10, T:0.20
Consensus pattern (30 bp):
ACAAAAGCTCTAGAAAAATATAAAATATGA
Found at i:3531152 original size:21 final size:21
Alignment explanation
Indices: 3531123--3531167 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 21
3531113 AAGTTTTTAT
*
3531123 TTTTCTTAGCTAAC-TCATTA
1 TTTTCTTAGCCAACTTCATTA
*
3531143 TTTTCATTAGCCAACTTCTTTA
1 TTTTC-TTAGCCAACTTCATTA
3531165 TTT
1 TTT
3531168 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:3533395 original size:13 final size:13
Alignment explanation
Indices: 3533377--3533402 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
3533367 CAATTTTTTG
3533377 TGTATCGATACAT
1 TGTATCGATACAT
3533390 TGTATCGATACAT
1 TGTATCGATACAT
3533403 ACTTTGTGTA
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:3533414 original size:32 final size:33
Alignment explanation
Indices: 3533357--3533420 Score: 103
Period size: 32 Copynumber: 2.0 Consensus size: 33
3533347 TATAAGCCAA
**
3533357 TGTATCGATACAATTTTTTGTGTATCGATACAT
1 TGTATCGATACAATACTTTGTGTATCGATACAT
3533390 TGTATCGATAC-ATACTTTGTGTATCGATACA
1 TGTATCGATACAATACTTTGTGTATCGATACA
3533421 AGTTTGGCTA
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
32 18 0.62
33 11 0.38
ACGTcount: A:0.28, C:0.14, G:0.16, T:0.42
Consensus pattern (33 bp):
TGTATCGATACAATACTTTGTGTATCGATACAT
Found at i:3534036 original size:22 final size:22
Alignment explanation
Indices: 3534006--3534062 Score: 96
Period size: 22 Copynumber: 2.6 Consensus size: 22
3533996 TTTCACTGTT
3534006 CATCACTGTTCATGTATCAATA
1 CATCACTGTTCATGTATCAATA
*
3534028 CGTCACTGTTCATGTATCAATA
1 CATCACTGTTCATGTATCAATA
*
3534050 CATCACTATTCAT
1 CATCACTGTTCAT
3534063 CACTATACAT
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 32 1.00
ACGTcount: A:0.30, C:0.25, G:0.09, T:0.37
Consensus pattern (22 bp):
CATCACTGTTCATGTATCAATA
Found at i:3539285 original size:36 final size:35
Alignment explanation
Indices: 3539203--3539435 Score: 204
Period size: 36 Copynumber: 6.9 Consensus size: 35
3539193 CTTACAACAT
* *
3539203 TATC-TTTCAAA-GCTACGATAGAAAC-CT-CC-C
1 TATCTTTTCAAAGGCTAAGATAGAACCTCTCCCTC
**
3539233 TATCTTTTCATGGGCTAAGATAGAACCTCTCCCTC
1 TATCTTTTCAAAGGCTAAGATAGAACCTCTCCCTC
* * *
3539268 TATCTTTTTCAAAGGCTAACATAAAAAC-CT-CC-C
1 TATC-TTTTCAAAGGCTAAGATAGAACCTCTCCCTC
* *
3539301 TATCTTTTCACAA-GCTAAGATAGAACCTTTCTCTC
1 TATCTTTTCA-AAGGCTAAGATAGAACCTCTCCCTC
* **
3539336 TATCTTTTGCAAAGGCTAAGATACAA-AACT-CCT-
1 TATCTTTT-CAAAGGCTAAGATAGAACCTCTCCCTC
* *
3539369 TATCTTTTCACAGGCTAAGATAAAACCTCTCTCCT-
1 TATCTTTTCAAAGGCTAAGATAGAACCTCTC-CCTC
3539404 TATCTTTTTCAAAGGCTAAGATAGAACCTCTC
1 TATC-TTTTCAAAGGCTAAGATAGAACCTCTC
3539436 AATCAATTGA
Statistics
Matches: 162, Mismatches: 25, Indels: 26
0.76 0.12 0.12
Matches are distributed among these distances:
30 4 0.02
31 5 0.03
32 44 0.27
33 20 0.12
34 7 0.04
35 26 0.16
36 56 0.35
ACGTcount: A:0.31, C:0.26, G:0.10, T:0.33
Consensus pattern (35 bp):
TATCTTTTCAAAGGCTAAGATAGAACCTCTCCCTC
Found at i:3539423 original size:68 final size:68
Alignment explanation
Indices: 3539207--3539426 Score: 295
Period size: 68 Copynumber: 3.2 Consensus size: 68
3539197 CAACATTATC
* * **
3539207 TTTCAAA-GCTACGATAGAAACCTCCCTATCTTTTCATGGGCTAAGATAGAACCTCTC-CCTCTA
1 TTTCAAAGGCTAAGATA-AAAACTCCCTATCTTTTCACAGGCTAAGATAGAACCTCTCTCCTCTA
3539270 TCTT
65 TCTT
* * *
3539274 TTTCAAAGGCTAACATAAAAACCTCCCTATCTTTTCACAAGCTAAGATAGAACCTTTCT-CTCTA
1 TTTCAAAGGCTAAGATAAAAA-CTCCCTATCTTTTCACAGGCTAAGATAGAACCTCTCTCCTCTA
3539338 TCTT
65 TCTT
* * *
3539342 TTGCAAAGGCTAAGATACAAAACTCCTTATCTTTTCACAGGCTAAGATAAAACCTCTCTCCT-TA
1 TTTCAAAGGCTAAGATA-AAAACTCCCTATCTTTTCACAGGCTAAGATAGAACCTCTCTCCTCTA
3539406 TCTT
65 TCTT
3539410 TTTCAAAGGCTAAGATA
1 TTTCAAAGGCTAAGATA
3539427 GAACCTCTCA
Statistics
Matches: 134, Mismatches: 14, Indels: 9
0.85 0.09 0.06
Matches are distributed among these distances:
67 10 0.07
68 118 0.88
69 6 0.04
ACGTcount: A:0.31, C:0.25, G:0.10, T:0.33
Consensus pattern (68 bp):
TTTCAAAGGCTAAGATAAAAACTCCCTATCTTTTCACAGGCTAAGATAGAACCTCTCTCCTCTAT
CTT
Found at i:3539988 original size:13 final size:13
Alignment explanation
Indices: 3539970--3539994 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
3539960 TACTAAGAAC
3539970 ATGTATCGATACA
1 ATGTATCGATACA
3539983 ATGTATCGATAC
1 ATGTATCGATAC
3539995 TAAGCAATAT
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:3539993 original size:32 final size:33
Alignment explanation
Indices: 3539952--3540015 Score: 112
Period size: 32 Copynumber: 2.0 Consensus size: 33
3539942 CAATTCACTG
3539952 TGTATCGATACTAAG-AACATGTATCGATACAA
1 TGTATCGATACTAAGCAACATGTATCGATACAA
*
3539984 TGTATCGATACTAAGCAATATGTATCGATACA
1 TGTATCGATACTAAGCAACATGTATCGATACA
3540016 TCTGGGTGTG
Statistics
Matches: 30, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
32 15 0.50
33 15 0.50
ACGTcount: A:0.39, C:0.16, G:0.16, T:0.30
Consensus pattern (33 bp):
TGTATCGATACTAAGCAACATGTATCGATACAA
Found at i:3540136 original size:20 final size:21
Alignment explanation
Indices: 3540111--3540154 Score: 72
Period size: 22 Copynumber: 2.1 Consensus size: 21
3540101 GATACTTCAG
3540111 ATTATTTTTA-CTTGAAAAAC
1 ATTATTTTTAGCTTGAAAAAC
3540131 ATTATTTTTATGCTTGAAAAAC
1 ATTATTTTTA-GCTTGAAAAAC
3540153 AT
1 AT
3540155 CTATACTTAA
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
20 10 0.45
22 12 0.55
ACGTcount: A:0.39, C:0.09, G:0.07, T:0.45
Consensus pattern (21 bp):
ATTATTTTTAGCTTGAAAAAC
Found at i:3540929 original size:21 final size:21
Alignment explanation
Indices: 3540907--3540945 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
3540897 GCAAGCTCTC
3540907 CCCCT-TAATACAAATTTTCT
1 CCCCTATAATACAAATTTTCT
*
3540927 CCCCTATAATACGAATTTT
1 CCCCTATAATACAAATTTT
3540946 ATGCAAACTC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 5 0.29
21 12 0.71
ACGTcount: A:0.31, C:0.28, G:0.03, T:0.38
Consensus pattern (21 bp):
CCCCTATAATACAAATTTTCT
Found at i:3573015 original size:13 final size:13
Alignment explanation
Indices: 3572997--3573021 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
3572987 CTAAGATCAG
3572997 TGTATCGATACAA
1 TGTATCGATACAA
3573010 TGTATCGATACA
1 TGTATCGATACA
3573022 TTTTAGTAAT
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
Done.