Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold227
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: 617646
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
File 4 of 5
Found at i:483542 original size:32 final size:32
Alignment explanation
Indices: 483501--483571 Score: 124
Period size: 32 Copynumber: 2.2 Consensus size: 32
483491 AGCTTCGTAG
*
483501 CGATACATTGTATCGATACAATACTTATGTAT
1 CGATACATTGTATCGATACAACACTTATGTAT
*
483533 CGATACATTGTATCGATACACCACTTATGTAT
1 CGATACATTGTATCGATACAACACTTATGTAT
483565 CGATACA
1 CGATACA
483572 ACACTTATGT
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
32 37 1.00
ACGTcount: A:0.34, C:0.20, G:0.13, T:0.34
Consensus pattern (32 bp):
CGATACATTGTATCGATACAACACTTATGTAT
Found at i:484362 original size:27 final size:30
Alignment explanation
Indices: 484303--484362 Score: 72
Period size: 27 Copynumber: 2.1 Consensus size: 30
484293 TCTAATCAAC
* *
484303 TTTATTATTGATTTTTTATTTTGTTTTCAT
1 TTTATTATTGATTATTTATTTTGTTTGCAT
*
484333 TTTATT-TTGA-TATTT-TTTTGTTTGCCT
1 TTTATTATTGATTATTTATTTTGTTTGCAT
484360 TTT
1 TTT
484363 TTGTTATTTC
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
27 13 0.48
28 4 0.15
29 4 0.15
30 6 0.22
ACGTcount: A:0.13, C:0.05, G:0.08, T:0.73
Consensus pattern (30 bp):
TTTATTATTGATTATTTATTTTGTTTGCAT
Found at i:484415 original size:25 final size:26
Alignment explanation
Indices: 484387--484443 Score: 64
Period size: 25 Copynumber: 2.2 Consensus size: 26
484377 TTTTTCTTTA
*
484387 TTTTTCCTTTCT-ATTTATTT-TTCAT
1 TTTTTCCTTT-TAACTTATTTGTTCAT
* *
484412 TTTTTTCTTTTAACTTATTTGTTCCT
1 TTTTTCCTTTTAACTTATTTGTTCAT
484438 TTTTTC
1 TTTTTC
484444 TTCTTAATCT
Statistics
Matches: 26, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
24 1 0.04
25 16 0.62
26 9 0.35
ACGTcount: A:0.11, C:0.16, G:0.02, T:0.72
Consensus pattern (26 bp):
TTTTTCCTTTTAACTTATTTGTTCAT
Found at i:484440 original size:26 final size:25
Alignment explanation
Indices: 484401--484450 Score: 66
Period size: 25 Copynumber: 2.0 Consensus size: 25
484391 TCCTTTCTAT
484401 TTATTTTTCATTTTTTTCTT-TTAAC
1 TTATTTTTCA-TTTTTTCTTCTTAAC
*
484426 TTATTTGTTCCTTTTTTCTTCTTAA
1 TTATTT-TTCATTTTTTCTTCTTAA
484451 TCTCTTTTTT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
25 15 0.68
26 7 0.32
ACGTcount: A:0.14, C:0.14, G:0.02, T:0.70
Consensus pattern (25 bp):
TTATTTTTCATTTTTTCTTCTTAAC
Found at i:490270 original size:22 final size:22
Alignment explanation
Indices: 490233--490274 Score: 68
Period size: 22 Copynumber: 1.9 Consensus size: 22
490223 ATAGACAACA
490233 TATTTTAAGAAGAAAATTAAGT
1 TATTTTAAGAAGAAAATTAAGT
490255 TATTATTAAGAA-AAAATTAA
1 TATT-TTAAGAAGAAAATTAA
490275 ATATAATACC
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
22 12 0.63
23 7 0.37
ACGTcount: A:0.55, C:0.00, G:0.10, T:0.36
Consensus pattern (22 bp):
TATTTTAAGAAGAAAATTAAGT
Found at i:493191 original size:26 final size:26
Alignment explanation
Indices: 493157--493214 Score: 116
Period size: 26 Copynumber: 2.2 Consensus size: 26
493147 TGTTTATAAT
493157 GTTTGATTTGTGAGCTCGTAGTTTAA
1 GTTTGATTTGTGAGCTCGTAGTTTAA
493183 GTTTGATTTGTGAGCTCGTAGTTTAA
1 GTTTGATTTGTGAGCTCGTAGTTTAA
493209 GTTTGA
1 GTTTGA
493215 ATGCTTATAA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 32 1.00
ACGTcount: A:0.19, C:0.07, G:0.28, T:0.47
Consensus pattern (26 bp):
GTTTGATTTGTGAGCTCGTAGTTTAA
Found at i:493872 original size:127 final size:130
Alignment explanation
Indices: 493726--493976 Score: 400
Period size: 128 Copynumber: 1.9 Consensus size: 130
493716 TAAATTCCTC
* * *
493726 TAAATAATACAATTCAAAATTGTGTAAATTAAAATATTAAAAATCT-AAAAATTTCAAAATCCAA
1 TAAATAATACAATTCAAAATTGTATAAATCAAAATATTAAAAATCTAAAAAACTTCAAAATCCAA
*
493790 ATACAAGTTTTCAAATGTAACTTAAATATTG-AAACTTTTC-TTTTTTAATATCTATATTTATTT
66 ATACAAGTTTTCAAACGTAACTTAAATATTGAAAACTTTTCTTTTTTTAATATCTATATTTATTT
* * *
493853 TAAATAATACAATTTAAAATTTTATAAATCAAAATGTTAAAAATCTAAAAAACTTCAAAATCCAA
1 TAAATAATACAATTCAAAATTGTATAAATCAAAATATTAAAAATCTAAAAAACTTCAAAATCCAA
*
493918 ATACAGGTTTTCAAACGTAACTTAAATATTGAAAACTTTTCTTTTTTTTAATATCTATA
66 ATACAAGTTTTCAAACGTAACTTAAATATTGAAAACTTTTC-TTTTTTTAATATCTATA
493977 CTAATTTTTT
Statistics
Matches: 112, Mismatches: 8, Indels: 4
0.90 0.06 0.03
Matches are distributed among these distances:
127 41 0.37
128 46 0.41
129 9 0.08
131 16 0.14
ACGTcount: A:0.46, C:0.10, G:0.04, T:0.39
Consensus pattern (130 bp):
TAAATAATACAATTCAAAATTGTATAAATCAAAATATTAAAAATCTAAAAAACTTCAAAATCCAA
ATACAAGTTTTCAAACGTAACTTAAATATTGAAAACTTTTCTTTTTTTAATATCTATATTTATTT
Found at i:493992 original size:7 final size:7
Alignment explanation
Indices: 493980--494031 Score: 59
Period size: 7 Copynumber: 7.0 Consensus size: 7
493970 ATCTATACTA
493980 ATTTTTT
1 ATTTTTT
493987 ATTTTTT
1 ATTTTTT
493994 CATTATTTTT
1 -A-T-TTTTT
494004 ATTTTTT
1 ATTTTTT
494011 ATTTTTT
1 ATTTTTT
* *
494018 AATTTCT
1 ATTTTTT
494025 ATTTTTT
1 ATTTTTT
494032 TGCTTTTTTA
Statistics
Matches: 38, Mismatches: 4, Indels: 6
0.79 0.08 0.12
Matches are distributed among these distances:
7 29 0.76
8 2 0.05
9 2 0.05
10 5 0.13
ACGTcount: A:0.17, C:0.04, G:0.00, T:0.79
Consensus pattern (7 bp):
ATTTTTT
Found at i:494007 original size:24 final size:24
Alignment explanation
Indices: 493980--494075 Score: 81
Period size: 24 Copynumber: 4.0 Consensus size: 24
493970 ATCTATACTA
493980 ATTTTTTATTTTTTCATTATTTTT
1 ATTTTTTATTTTTTCATTATTTTT
*
494004 ATTTTTTATTTTTT-A--ATTTCT
1 ATTTTTTATTTTTTCATTATTTTT
* * *
494025 ATTTTTTTGCTTTTTTAATTTTTTTT
1 A-TTTTTT-ATTTTTTCATTATTTTT
* * *
494051 CTCTTTTATATTTTCATTATGTTTT
1 ATTTTTTATTTTTTCATTAT-TTTT
494076 TTCATTTTAA
Statistics
Matches: 56, Mismatches: 10, Indels: 11
0.73 0.13 0.14
Matches are distributed among these distances:
21 6 0.11
22 6 0.11
23 7 0.12
24 24 0.43
25 9 0.16
26 4 0.07
ACGTcount: A:0.16, C:0.06, G:0.02, T:0.76
Consensus pattern (24 bp):
ATTTTTTATTTTTTCATTATTTTT
Found at i:494018 original size:31 final size:31
Alignment explanation
Indices: 493978--494048 Score: 83
Period size: 31 Copynumber: 2.3 Consensus size: 31
493968 ATATCTATAC
* *
493978 TAATTTTTTATTTTTTCATTATTTTT-ATTTTT
1 TAATTTTTTAATTTCT-ATT-TTTTTGATTTTT
*
494010 T-ATTTTTTAATTTCTATTTTTTTGCTTTTT
1 TAATTTTTTAATTTCTATTTTTTTGATTTTT
494040 TAATTTTTT
1 TAATTTTTT
494049 TTCTCTTTTA
Statistics
Matches: 34, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
29 5 0.15
30 9 0.26
31 19 0.56
32 1 0.03
ACGTcount: A:0.17, C:0.04, G:0.01, T:0.77
Consensus pattern (31 bp):
TAATTTTTTAATTTCTATTTTTTTGATTTTT
Found at i:494049 original size:18 final size:18
Alignment explanation
Indices: 494024--494064 Score: 57
Period size: 17 Copynumber: 2.3 Consensus size: 18
494014 TTTTAATTTC
* *
494024 TATTTTTTTGCTTTTTTA
1 TATTTTTTTTCTCTTTTA
494042 -ATTTTTTTTCTCTTTTA
1 TATTTTTTTTCTCTTTTA
494059 TATTTT
1 TATTTT
494065 CATTATGTTT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
17 15 0.75
18 5 0.25
ACGTcount: A:0.12, C:0.07, G:0.02, T:0.78
Consensus pattern (18 bp):
TATTTTTTTTCTCTTTTA
Found at i:494244 original size:18 final size:17
Alignment explanation
Indices: 494214--494281 Score: 59
Period size: 18 Copynumber: 3.9 Consensus size: 17
494204 TTTTCTTTGC
*
494214 TTTATTGTT-TTTTTCA
1 TTTATTTTTATTTTTCA
494230 TTTGATTTTTATTTTTCA
1 TTT-ATTTTTATTTTTCA
*
494248 TGTATTTTTTATTTTT-A
1 TTTA-TTTTTATTTTTCA
*
494265 TTTTTCTTTTTATTTTT
1 --TTTATTTTTATTTTT
494282 TTTTGTTGCT
Statistics
Matches: 43, Mismatches: 4, Indels: 8
0.78 0.07 0.15
Matches are distributed among these distances:
16 3 0.07
17 7 0.16
18 31 0.72
19 2 0.05
ACGTcount: A:0.13, C:0.04, G:0.04, T:0.78
Consensus pattern (17 bp):
TTTATTTTTATTTTTCA
Found at i:494262 original size:5 final size:6
Alignment explanation
Indices: 494234--494285 Score: 54
Period size: 6 Copynumber: 8.8 Consensus size: 6
494224 TTTTCATTTG
* * *
494234 ATTTTT ATTTTT CATGTAT -TTTTT ATTTTT ATTTTT CTTTTT ATTTTT
1 ATTTTT ATTTTT -ATTTTT ATTTTT ATTTTT ATTTTT ATTTTT ATTTTT
494282 -TTTT
1 ATTTT
494286 GTTGCTTATC
Statistics
Matches: 38, Mismatches: 6, Indels: 5
0.78 0.12 0.10
Matches are distributed among these distances:
5 7 0.18
6 27 0.71
7 4 0.11
ACGTcount: A:0.13, C:0.04, G:0.02, T:0.81
Consensus pattern (6 bp):
ATTTTT
Found at i:494431 original size:21 final size:21
Alignment explanation
Indices: 494405--494476 Score: 56
Period size: 21 Copynumber: 3.2 Consensus size: 21
494395 TATTTTTACT
494405 TTTTTTATTTCTTTTCTTTTA
1 TTTTTTATTTCTTTTCTTTTA
* *
494426 TTTTTTGTTTTTTTAAAGATCTTTTA
1 TTTTTTATTTCTTT-----TCTTTTA
*
494452 TTTTTTATTATC-TTTATTTTA
1 TTTTTTATT-TCTTTTCTTTTA
494473 TTTT
1 TTTT
494477 ACTTTGCTAT
Statistics
Matches: 40, Mismatches: 5, Indels: 12
0.70 0.09 0.21
Matches are distributed among these distances:
21 22 0.55
26 17 0.43
27 1 0.03
ACGTcount: A:0.15, C:0.06, G:0.03, T:0.76
Consensus pattern (21 bp):
TTTTTTATTTCTTTTCTTTTA
Found at i:494715 original size:16 final size:15
Alignment explanation
Indices: 494692--494746 Score: 65
Period size: 16 Copynumber: 3.5 Consensus size: 15
494682 GTATTTTCAC
494692 TATTTTTTATTTTGT
1 TATTTTTTATTTTGT
*
494707 TATTATTTTGTTTTGTT
1 TATT-TTTTATTTTG-T
* *
494724 TTTTTTTTATTTTGA
1 TATTTTTTATTTTGT
494739 TATTTTTT
1 TATTTTTT
494747 CCTTTTATTT
Statistics
Matches: 33, Mismatches: 5, Indels: 4
0.79 0.12 0.10
Matches are distributed among these distances:
15 11 0.33
16 18 0.55
17 4 0.12
ACGTcount: A:0.13, C:0.00, G:0.07, T:0.80
Consensus pattern (15 bp):
TATTTTTTATTTTGT
Found at i:494725 original size:21 final size:21
Alignment explanation
Indices: 494696--494737 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
494686 TTTCACTATT
494696 TTTTATTTTGTTATTATTTTG
1 TTTTATTTTGTTATTATTTTG
* * *
494717 TTTTGTTTTTTTTTTATTTTG
1 TTTTATTTTGTTATTATTTTG
494738 ATATTTTTTC
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.10, C:0.00, G:0.10, T:0.81
Consensus pattern (21 bp):
TTTTATTTTGTTATTATTTTG
Found at i:494746 original size:21 final size:21
Alignment explanation
Indices: 494709--494756 Score: 53
Period size: 21 Copynumber: 2.3 Consensus size: 21
494699 TATTTTGTTA
* **
494709 TTATTTTGTTTTGTTTTTTTT
1 TTATTTTGTATTGTTTTCCTT
494730 TTATTTTGATATT-TTTTCCTT
1 TTATTTTG-TATTGTTTTCCTT
494751 TTATTT
1 TTATTT
494757 GCCTTTTTTA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
21 20 0.87
22 3 0.13
ACGTcount: A:0.10, C:0.04, G:0.06, T:0.79
Consensus pattern (21 bp):
TTATTTTGTATTGTTTTCCTT
Found at i:494953 original size:14 final size:14
Alignment explanation
Indices: 494933--494972 Score: 55
Period size: 14 Copynumber: 2.9 Consensus size: 14
494923 TTTGCTATTC
*
494933 TTATTTTTT-TCTA
1 TTATTTTTTCTTTA
494946 TTATTTTTTCTTTA
1 TTATTTTTTCTTTA
*
494960 TTATCTTTTCTTT
1 TTATTTTTTCTTT
494973 TCGCTTTTTT
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
13 9 0.38
14 15 0.62
ACGTcount: A:0.12, C:0.10, G:0.00, T:0.78
Consensus pattern (14 bp):
TTATTTTTTCTTTA
Found at i:501000 original size:7 final size:6
Alignment explanation
Indices: 500972--501030 Score: 52
Period size: 6 Copynumber: 10.0 Consensus size: 6
500962 CTTGCCATAA
* *
500972 GTTGCT -TTGTCT TTTGCT GTTGCT AGTTGCT GTTG-- GTTGCT GTTGCC
1 GTTGCT GTTG-CT GTTGCT GTTGCT -GTTGCT GTTGCT GTTGCT GTTGCT
*
501019 GTTGCC GTTGCT
1 GTTGCT GTTGCT
501031 TCTTATTGCT
Statistics
Matches: 45, Mismatches: 3, Indels: 10
0.78 0.05 0.17
Matches are distributed among these distances:
4 4 0.09
5 3 0.07
6 29 0.64
7 9 0.20
ACGTcount: A:0.02, C:0.19, G:0.31, T:0.49
Consensus pattern (6 bp):
GTTGCT
Found at i:501022 original size:16 final size:17
Alignment explanation
Indices: 500990--501022 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
500980 GTCTTTTGCT
*
500990 GTTGCTAGTTGCTGTTG
1 GTTGCTAGTTGCCGTTG
501007 GTTGCT-GTTGCCGTTG
1 GTTGCTAGTTGCCGTTG
501023 CCGTTGCTTC
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 9 0.60
17 6 0.40
ACGTcount: A:0.03, C:0.15, G:0.36, T:0.45
Consensus pattern (17 bp):
GTTGCTAGTTGCCGTTG
Found at i:501260 original size:22 final size:22
Alignment explanation
Indices: 501215--501260 Score: 56
Period size: 22 Copynumber: 2.1 Consensus size: 22
501205 TGCTGCTTAC
* *
501215 TGGAGTTTCAGTTACTGCTTGT
1 TGGAGTTTCAGTTACTGATGGT
* *
501237 TGGAGTTTCGGTTGCTGATGGT
1 TGGAGTTTCAGTTACTGATGGT
501259 TG
1 TG
501261 TTGGTGTTGA
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.11, C:0.11, G:0.35, T:0.43
Consensus pattern (22 bp):
TGGAGTTTCAGTTACTGATGGT
Found at i:501795 original size:54 final size:56
Alignment explanation
Indices: 501732--501862 Score: 187
Period size: 57 Copynumber: 2.4 Consensus size: 56
501722 TTTCAGCAAT
* * *
501732 TGAATTGCTTTTAT-TTTCA-TTC-CCTGTTGCTGTTTCATTCTTATTATTAGCAGC
1 TGAATTGCTTTT-TCTTTAATTTCTCCTGTTACCGTTTCATTCTTATTATTAGCAGC
*
501786 TGAATTGCTTTTTCTTTAATTTCTTCTTGTTACCGTTTCATTCTTATTATTAGCAGC
1 TGAATTGCTTTTTCTTTAATTTC-TCCTGTTACCGTTTCATTCTTATTATTAGCAGC
501843 TGAATTGCTTTTTCTTTAAT
1 TGAATTGCTTTTTCTTTAAT
501863 GTTGCTGCAA
Statistics
Matches: 69, Mismatches: 4, Indels: 5
0.88 0.05 0.06
Matches are distributed among these distances:
53 1 0.01
54 16 0.23
55 3 0.04
57 49 0.71
ACGTcount: A:0.18, C:0.17, G:0.11, T:0.54
Consensus pattern (56 bp):
TGAATTGCTTTTTCTTTAATTTCTCCTGTTACCGTTTCATTCTTATTATTAGCAGC
Found at i:503600 original size:51 final size:52
Alignment explanation
Indices: 503484--503675 Score: 133
Period size: 51 Copynumber: 3.8 Consensus size: 52
503474 ACTAAAGGGC
* * * *
503484 TTGACCTCCTTATACAGGTGCTAGCTAGTGTGGACTTTGATTCTATAAGGCT
1 TTGACCTCCTTATACAAGTGCTAACTAGTATGGACTTTGATTCAATAAGGCT
* * * *
503536 TCG-CTTCCCTATACAAGTGC-AACTAGTATGGACTTTAGGTTCAATAAGG-T
1 TTGACCTCCTTATACAAGTGCTAACTAGTATGGACTTT-GATTCAATAAGGCT
* ** ** * ** * * *
503586 TTGACCTCTTTATACGGGTGCTGGCTAGTGTAAACTTGGATTCTATAGGGC-
1 TTGACCTCCTTATACAAGTGCTAACTAGTATGGACTTTGATTCAATAAGGCT
** *
503637 TTGACCT-CTCTATACAAGTGCTAGTTATTATGGACTTTG
1 TTGACCTCCT-TATACAAGTGCTAACTAGTATGGACTTTG
503676 TCTGGTTGAG
Statistics
Matches: 102, Mismatches: 33, Indels: 11
0.70 0.23 0.08
Matches are distributed among these distances:
50 18 0.18
51 72 0.71
52 12 0.12
ACGTcount: A:0.23, C:0.19, G:0.22, T:0.36
Consensus pattern (52 bp):
TTGACCTCCTTATACAAGTGCTAACTAGTATGGACTTTGATTCAATAAGGCT
Found at i:511170 original size:50 final size:50
Alignment explanation
Indices: 511114--511227 Score: 192
Period size: 50 Copynumber: 2.3 Consensus size: 50
511104 AATTAACTAG
511114 ATGTATCAATACATTGAAAAATGTATCGATACATCTAGGTAAAAAACAGA
1 ATGTATCAATACATTGAAAAATGTATCGATACATCTAGGTAAAAAACAGA
* * * *
511164 ATGTATCGATACATTGAAAAATGTATCGATACATTTGGGTAAAAAATAGA
1 ATGTATCAATACATTGAAAAATGTATCGATACATCTAGGTAAAAAACAGA
511214 ATGTATCAATACAT
1 ATGTATCAATACAT
511228 GTACTATTTA
Statistics
Matches: 59, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
50 59 1.00
ACGTcount: A:0.46, C:0.11, G:0.15, T:0.29
Consensus pattern (50 bp):
ATGTATCAATACATTGAAAAATGTATCGATACATCTAGGTAAAAAACAGA
Found at i:512192 original size:142 final size:142
Alignment explanation
Indices: 511952--512211 Score: 301
Period size: 142 Copynumber: 1.8 Consensus size: 142
511942 ACGAATACCT
* * *
511952 GTGAGTGCAAATGGACATGAATAGGAATGTACAAGTGCAAAAACAAGTGAATGAGAATGCACGTG
1 GTGAGTGCAAATGGACATGAATAAGAATGCACAAGTGCAAAAACAAGTGAATGAGAATACACGTG
* * * *
512017 AGTGCAAATGCTCGTGATTAAGAATGCATATGAATAAGAATGAA-ATAAGTGTAATTGTAAGTGA
66 AGTACAAATGCTCATAATTAAGAATGCACATGAATAAGAATGAACATAAGTGTAATTGTAAGTGA
512081 GTACAGATGCCC
131 GTACAGATGCCC
* * * *
512093 GTGAGTGCAAATGGACAT-AATAAGAATGCACATAAGTGCAAATA-TAGATGAATGTGATTACAC
1 GTGAGTGCAAATGGACATGAATAAGAATGCAC--AAGTGCAAAAACAAG-TGAATGAGAATACAC
** * * * ** *
512156 GTGAGTATGAATGCTCATAATTATGAGTGGACATGAATGGGAATGAACATGAGTGT
63 GTGAGTACAAATGCTCATAATTAAGAATGCACATGAATAAGAATGAACATAAGTGT
512212 GAAGGCACAT
Statistics
Matches: 96, Mismatches: 19, Indels: 6
0.79 0.16 0.05
Matches are distributed among these distances:
140 11 0.11
141 20 0.21
142 58 0.60
143 7 0.07
ACGTcount: A:0.40, C:0.10, G:0.26, T:0.24
Consensus pattern (142 bp):
GTGAGTGCAAATGGACATGAATAAGAATGCACAAGTGCAAAAACAAGTGAATGAGAATACACGTG
AGTACAAATGCTCATAATTAAGAATGCACATGAATAAGAATGAACATAAGTGTAATTGTAAGTGA
GTACAGATGCCC
Found at i:512207 original size:16 final size:16
Alignment explanation
Indices: 512186--512274 Score: 72
Period size: 16 Copynumber: 5.6 Consensus size: 16
512176 TTATGAGTGG
* *
512186 ACATGAATGGGAATGA
1 ACATGAATGAGAATGC
* * *
512202 ACATGAGTGTGAAGGC
1 ACATGAATGAGAATGC
*
512218 ACATAAATGAGAATGC
1 ACATGAATGAGAATGC
512234 ACATGAATGCA-AATGC
1 ACATGAATG-AGAATGC
** *
512250 TTATGAATGAGAATGA
1 ACATGAATGAGAATGC
*
512266 ATATGAATG
1 ACATGAATG
512275 CCGATACTTG
Statistics
Matches: 58, Mismatches: 13, Indels: 4
0.77 0.17 0.05
Matches are distributed among these distances:
15 1 0.02
16 56 0.97
17 1 0.02
ACGTcount: A:0.43, C:0.09, G:0.26, T:0.22
Consensus pattern (16 bp):
ACATGAATGAGAATGC
Found at i:512334 original size:10 final size:10
Alignment explanation
Indices: 512321--512350 Score: 51
Period size: 10 Copynumber: 3.0 Consensus size: 10
512311 GGTTCGTGAG
512321 CATGAATGCA
1 CATGAATGCA
512331 CATGAATGCA
1 CATGAATGCA
*
512341 GATGAATGCA
1 CATGAATGCA
512351 TGTGAATATG
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
10 19 1.00
ACGTcount: A:0.40, C:0.17, G:0.23, T:0.20
Consensus pattern (10 bp):
CATGAATGCA
Found at i:513607 original size:22 final size:23
Alignment explanation
Indices: 513582--513630 Score: 66
Period size: 22 Copynumber: 2.2 Consensus size: 23
513572 TCAATTTTGC
513582 TTTTGCTTTGT-TATTTTTT-TTT
1 TTTTGCTTT-TCTATTTTTTATTT
*
513604 TTTTGCTTTTCTTTTTTTTATTT
1 TTTTGCTTTTCTATTTTTTATTT
513627 TTTT
1 TTTT
513631 ATTTTGAGCT
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
21 1 0.04
22 16 0.67
23 7 0.29
ACGTcount: A:0.04, C:0.06, G:0.06, T:0.84
Consensus pattern (23 bp):
TTTTGCTTTTCTATTTTTTATTT
Found at i:513607 original size:28 final size:28
Alignment explanation
Indices: 513575--513636 Score: 83
Period size: 28 Copynumber: 2.2 Consensus size: 28
513565 ATTTTTCTCA
513575 ATTTTGCTTTTGCTTTGTTATT-TTTTTTT
1 ATTTTGCTTTT-CTTT-TTATTATTTTTTT
*
513604 -TTTTGCTTTTCTTTTTTTTATTTTTTT
1 ATTTTGCTTTTCTTTTTATTATTTTTTT
513631 ATTTTG
1 ATTTTG
513637 AGCTTTTGTT
Statistics
Matches: 30, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
26 4 0.13
27 11 0.37
28 15 0.50
ACGTcount: A:0.06, C:0.06, G:0.08, T:0.79
Consensus pattern (28 bp):
ATTTTGCTTTTCTTTTTATTATTTTTTT
Found at i:513624 original size:29 final size:30
Alignment explanation
Indices: 513576--513650 Score: 84
Period size: 30 Copynumber: 2.6 Consensus size: 30
513566 TTTTTCTCAA
513576 TTTTGCTTTTGC--TTTGTTATTTTTTT-TT
1 TTTTGCTTTT-CTTTTTGTTATTTTTTTATT
*
513604 TTTTGCTTTTCTTTTTTTTATTTTTTTATT
1 TTTTGCTTTTCTTTTTGTTATTTTTTTATT
** *
513634 TTGAGCTTTTGTTTTTG
1 TTTTGCTTTTCTTTTTG
513651 ACTTTTCCAT
Statistics
Matches: 39, Mismatches: 5, Indels: 4
0.81 0.10 0.08
Matches are distributed among these distances:
27 1 0.03
28 10 0.26
29 13 0.33
30 15 0.38
ACGTcount: A:0.05, C:0.07, G:0.11, T:0.77
Consensus pattern (30 bp):
TTTTGCTTTTCTTTTTGTTATTTTTTTATT
Found at i:513635 original size:22 final size:21
Alignment explanation
Indices: 513595--513635 Score: 55
Period size: 22 Copynumber: 1.9 Consensus size: 21
513585 TGCTTTGTTA
*
513595 TTTTTTTTTTTTTGCTTTTCT
1 TTTTTTTTTTTTTGATTTTCT
*
513616 TTTTTTTATTTTTTTATTTT
1 TTTTTTT-TTTTTTGATTTT
513636 GAGCTTTTGT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 7 0.41
22 10 0.59
ACGTcount: A:0.05, C:0.05, G:0.02, T:0.88
Consensus pattern (21 bp):
TTTTTTTTTTTTTGATTTTCT
Found at i:513648 original size:28 final size:27
Alignment explanation
Indices: 513580--513649 Score: 68
Period size: 29 Copynumber: 2.4 Consensus size: 27
513570 TCTCAATTTT
* **
513580 GCTTTTGCTTTGTTATTTTTTTTTTTTT
1 GCTTTTG-TTTTTTATTTTTTTTTTTGA
*
513608 GCTTTTCTTTTTTTTATTTTTTTATTTTGA
1 GC-TTT-TGTTTTTTATTTTTTT-TTTTGA
513638 GCTTTTGTTTTT
1 GCTTTTGTTTTT
513650 GACTTTTCCA
Statistics
Matches: 34, Mismatches: 5, Indels: 6
0.76 0.11 0.13
Matches are distributed among these distances:
28 8 0.24
29 19 0.56
30 7 0.21
ACGTcount: A:0.06, C:0.07, G:0.10, T:0.77
Consensus pattern (27 bp):
GCTTTTGTTTTTTATTTTTTTTTTTGA
Found at i:519753 original size:77 final size:78
Alignment explanation
Indices: 519654--519856 Score: 241
Period size: 77 Copynumber: 2.6 Consensus size: 78
519644 GATAACAACA
* * * * *
519654 GGGTTGGAGTGTTCCCTT-GAAAATAACGGGGCTGGAGTATCCCCGGTTGTGAGAAATCGATGA-
1 GGGTTGGAGT-ATCCCTTCGAAAATAACGGGGTTGGAGTATCCCCGATTATGAGAAATCAAT-AT
519717 TTAAAAAAAAAATC-
64 TTAAAAAAAAAATCG
*
519731 GGGTTGGAGTATCCCTTCGAAAATAACGGGGTTGGAGTATCCCCAATTATGAGAAATCAATATTT
1 GGGTTGGAGTATCCCTTCGAAAATAACGGGGTTGGAGTATCCCCGATTATGAGAAATCAATA-TT
*** * *
519796 TGGGAATAAAGTCG
65 TAAAAAAAAAATCG
* *
519810 GGGTTGGAGTATCCCCTCGAAAGTAACGGGGTTGGAGTATCCCCGAT
1 GGGTTGGAGTATCCCTTCGAAAATAACGGGGTTGGAGTATCCCCGAT
519857 GAAATAATGA
Statistics
Matches: 108, Mismatches: 14, Indels: 6
0.84 0.11 0.05
Matches are distributed among these distances:
76 7 0.06
77 48 0.44
78 9 0.08
79 44 0.41
ACGTcount: A:0.30, C:0.16, G:0.29, T:0.26
Consensus pattern (78 bp):
GGGTTGGAGTATCCCTTCGAAAATAACGGGGTTGGAGTATCCCCGATTATGAGAAATCAATATTT
AAAAAAAAAATCG
Found at i:519841 original size:28 final size:27
Alignment explanation
Indices: 519808--519879 Score: 92
Period size: 28 Copynumber: 2.6 Consensus size: 27
519798 GGAATAAAGT
519808 CGGGGTTGGAGTATCCCC-TCGAAAGTAA
1 CGGGGTTGGAGTATCCCCAT-GAAA-TAA
519836 CGGGGTTGGAGTATCCCCGATGAAATAA
1 CGGGGTTGGAGTATCCCC-ATGAAATAA
* *
519864 TGAGGTTGGAGTATCC
1 CGGGGTTGGAGTATCC
519880 TCGATTGTGA
Statistics
Matches: 40, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
28 35 0.88
29 4 0.10
30 1 0.03
ACGTcount: A:0.25, C:0.18, G:0.33, T:0.24
Consensus pattern (27 bp):
CGGGGTTGGAGTATCCCCATGAAATAA
Found at i:519937 original size:52 final size:51
Alignment explanation
Indices: 519867--520037 Score: 191
Period size: 52 Copynumber: 3.3 Consensus size: 51
519857 GAAATAATGA
* * *
519867 GGTTGGAGTATCCTCGATTGTGAAAAATTGGTATTTTTGGAAATAAAATC-G
1 GGTTGGAGTATCCCCGATTGTGAAAAATTGGT-GTTTTGGAAATAAAACCAG
** * * * *
519918 GAGTTGGAGTATCCCCGATTAAAGGAAAATTGGCGTTTTGAAAAAAAAACCAG
1 G-GTTGGAGTATCCCCGATT-GTGAAAAATTGGTGTTTTGGAAATAAAACCAG
* * *
519971 GGTTGGAGTATCCCCGATTGTGGAAAAATTAGTGTTTTAGCAATAAAACCAG
1 GGTTGGAGTATCCCCGATTGT-GAAAAATTGGTGTTTTGGAAATAAAACCAG
520023 GGTTGGAGTATCCCC
1 GGTTGGAGTATCCCC
520038 TCAGAAATAA
Statistics
Matches: 98, Mismatches: 18, Indels: 7
0.80 0.15 0.06
Matches are distributed among these distances:
51 1 0.01
52 86 0.88
53 11 0.11
ACGTcount: A:0.33, C:0.13, G:0.26, T:0.29
Consensus pattern (51 bp):
GGTTGGAGTATCCCCGATTGTGAAAAATTGGTGTTTTGGAAATAAAACCAG
Found at i:520060 original size:212 final size:212
Alignment explanation
Indices: 519810--520206 Score: 577
Period size: 212 Copynumber: 1.9 Consensus size: 212
519800 AATAAAGTCG
*
519810 GGGTTGGAGTATCCCCTCGAAAGTAACGGGGTTGGAGTATCCCCGATGAAATAATGAGGTTGGAG
1 GGGTTGGAGTATCCCCTCGAAAGTAACGGGGTTGGAGTATCCCCGATG-AATAACGAGGTTGGAG
* * *
519875 TATCCTCGATTGTGAA-AAATTGGT-ATTTTTGGAAATAAAATCGGAGTTGGAGTATCCCCGATT
65 TATCCCCGATTGTGAAGAAATGGGTGATTTTTGGAAATAAAATCGGAGTTAGAGTATCCCCGATT
* * *
519938 AAAGGAAAATTGGCGTTTTGAAAAAAAAACCAGG-GTTGGAGTATCCCCGATTGTGGAAAAATTA
130 AAA-GAAAATTAGCGTTTTGAAAAAAAAACC-GGAGTTGGAATATCCCCAATTGTGGAAAAATTA
520002 GTGTTTTAGCAATAAAACCA
193 GTGTTTTAGCAATAAAACCA
* * *
520022 GGGTTGGAGTATCCCCTCAGAAA-TAATGGGGTTGGAGTATCCCCGATGATTAACGGGGTTGGAG
1 GGGTTGGAGTATCCCCTC-GAAAGTAACGGGGTTGGAGTATCCCCGATGAATAACGAGGTTGGAG
* **
520086 TATCCCCGATTGTGAAGAAATGGGTGTTTTTTGGAAATAAAATCGGAGTTAGAGTATCCTTGATT
65 TATCCCCGATTGTGAAGAAATGGGTGATTTTTGGAAATAAAATCGGAGTTAGAGTATCCCCGATT
* * * *
520151 ATAGAAAATTAGTGTTTTGAAAATAAAATCGGAGTTGGAATATCCCCAATTGTGGA
130 AAAGAAAATTAGCGTTTTGAAAAAAAAACCGGAGTTGGAATATCCCCAATTGTGGA
520207 GAATTGAGAA
Statistics
Matches: 164, Mismatches: 17, Indels: 8
0.87 0.09 0.04
Matches are distributed among these distances:
211 30 0.18
212 93 0.57
213 41 0.25
ACGTcount: A:0.32, C:0.13, G:0.27, T:0.29
Consensus pattern (212 bp):
GGGTTGGAGTATCCCCTCGAAAGTAACGGGGTTGGAGTATCCCCGATGAATAACGAGGTTGGAGT
ATCCCCGATTGTGAAGAAATGGGTGATTTTTGGAAATAAAATCGGAGTTAGAGTATCCCCGATTA
AAGAAAATTAGCGTTTTGAAAAAAAAACCGGAGTTGGAATATCCCCAATTGTGGAAAAATTAGTG
TTTTAGCAATAAAACCA
Found at i:520087 original size:27 final size:28
Alignment explanation
Indices: 520022--520095 Score: 98
Period size: 27 Copynumber: 2.7 Consensus size: 28
520012 AATAAAACCA
* *
520022 GGGTTGGAGTATCCCCTCA-GAAATAATG
1 GGGTTGGAGTATCCCC-GATGAAATAACG
*
520050 GGGTTGGAGTATCCCCGATG-ATTAACG
1 GGGTTGGAGTATCCCCGATGAAATAACG
520077 GGGTTGGAGTATCCCCGAT
1 GGGTTGGAGTATCCCCGAT
520096 TGTGAAGAAA
Statistics
Matches: 42, Mismatches: 3, Indels: 3
0.88 0.06 0.06
Matches are distributed among these distances:
27 25 0.60
28 17 0.40
ACGTcount: A:0.23, C:0.19, G:0.32, T:0.26
Consensus pattern (28 bp):
GGGTTGGAGTATCCCCGATGAAATAACG
Found at i:522586 original size:13 final size:13
Alignment explanation
Indices: 522568--522593 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
522558 ACAAAGATCC
522568 ATGTATCGATACA
1 ATGTATCGATACA
522581 ATGTATCGATACA
1 ATGTATCGATACA
522594 CAGAAAAATG
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:522589 original size:33 final size:33
Alignment explanation
Indices: 522547--522613 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
522537 AAAATTTCCA
***
522547 AATGTATCGATACAAAGATCCATGTATCGATAC
1 AATGTATCGATACAAAGAAAAATGTATCGATAC
*
522580 AATGTATCGATACACAGAAAAATGTATCGATAC
1 AATGTATCGATACAAAGAAAAATGTATCGATAC
522613 A
1 A
522614 TTTCCTTGGC
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:0.43, C:0.16, G:0.15, T:0.25
Consensus pattern (33 bp):
AATGTATCGATACAAAGAAAAATGTATCGATAC
Found at i:522657 original size:19 final size:18
Alignment explanation
Indices: 522633--522700 Score: 83
Period size: 19 Copynumber: 3.9 Consensus size: 18
522623 CAGTAGCTAA
522633 TTATGTATCGATACAATAC
1 TTATGTATCGATACAA-AC
522652 TTATGTATCGATAC--A-
1 TTATGTATCGATACAAAC
522667 -T-TGTATCGATACAAAAC
1 TTATGTATCGATAC-AAAC
522684 TTATGTATCGATACAAA
1 TTATGTATCGATACAAA
522701 TTGTTGAATT
Statistics
Matches: 43, Mismatches: 0, Indels: 13
0.77 0.00 0.23
Matches are distributed among these distances:
13 11 0.26
14 1 0.02
16 2 0.05
18 4 0.09
19 25 0.58
ACGTcount: A:0.38, C:0.15, G:0.12, T:0.35
Consensus pattern (18 bp):
TTATGTATCGATACAAAC
Found at i:522673 original size:13 final size:13
Alignment explanation
Indices: 522655--522679 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
522645 ACAATACTTA
522655 TGTATCGATACAT
1 TGTATCGATACAT
522668 TGTATCGATACA
1 TGTATCGATACA
522680 AAACTTATGT
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:522677 original size:32 final size:32
Alignment explanation
Indices: 522636--522698 Score: 117
Period size: 32 Copynumber: 2.0 Consensus size: 32
522626 TAGCTAATTA
*
522636 TGTATCGATACAATACTTATGTATCGATACAT
1 TGTATCGATACAAAACTTATGTATCGATACAT
522668 TGTATCGATACAAAACTTATGTATCGATACA
1 TGTATCGATACAAAACTTATGTATCGATACA
522699 AATTGTTGAA
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 30 1.00
ACGTcount: A:0.37, C:0.16, G:0.13, T:0.35
Consensus pattern (32 bp):
TGTATCGATACAAAACTTATGTATCGATACAT
Found at i:523693 original size:26 final size:26
Alignment explanation
Indices: 523664--523751 Score: 72
Period size: 26 Copynumber: 3.3 Consensus size: 26
523654 GTGGGCTTTA
523664 AAAGGTGTCCTGCTCTTTGGGGACTG
1 AAAGGTGTCCTGCTCTTTGGGGACTG
** *
523690 AAAGGTG-CCACCAACTTGTGTGGG-CTTTG
1 AAAGGTGTCCTGC-TCTT-TG-GGGAC--TG
* *
523719 AAAGGGGTCCTGCTCTTTGGGGAATG
1 AAAGGTGTCCTGCTCTTTGGGGACTG
523745 AAAGGTG
1 AAAGGTG
523752 CCACCAACTT
Statistics
Matches: 46, Mismatches: 9, Indels: 14
0.67 0.13 0.20
Matches are distributed among these distances:
25 3 0.07
26 18 0.39
27 6 0.13
28 5 0.11
29 11 0.24
30 3 0.07
ACGTcount: A:0.20, C:0.17, G:0.35, T:0.27
Consensus pattern (26 bp):
AAAGGTGTCCTGCTCTTTGGGGACTG
Found at i:523866 original size:59 final size:58
Alignment explanation
Indices: 523506--524272 Score: 863
Period size: 55 Copynumber: 13.4 Consensus size: 58
523496 ATAAAGTGTA
* * * * *
523506 TCCTGCTCATTGAGGAGTAAAAAGTGCCACCAACTCGTGTGGGCTTT----GAAAGGCG
1 TCCTGCTCTTTGAGGACT-GAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGAAAGGCG
*
523561 TCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTT---A-AAAGGTG
1 TCCTGCTCTTTGAGGACTG-AAGGTGCCACCAACTTGTGTGGGCTTTAAAAGAAAGGCG
* ** *
523616 TCCTGCTCTTTAAGGACTGGAAAATGCCACCAACTTGTGTGGGCTTT---A-AAAGGTG
1 TCCTGCTCTTTGAGGACT-GAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGAAAGGCG
* *
523671 TCCTGCTCTTTGGGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTT----GAAAGGGG
1 TCCTGCTCTTTGAGGACTG-AAGGTGCCACCAACTTGTGTGGGCTTTAAAAGAAAGGCG
* * * * *
523726 TCCTGCTCTTTGGGGAATGAAAGGTGCCACCAACTTATGTGGGCTTTGAAAAGAAAAAGCA
1 TCCTGCTCTTTGAGGACTG-AAGGTGCCACCAACTTGTGTGGGCTTT-AAAAG-AAAGGCG
* *
523787 TCCTGCTCTTTGAGGACTGAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGAAAATGTG
1 TCCTGCTCTTTGAGGACTGAAGGTGCCACCAACTTGTGTGGGCTTTAAAAG-AAAGGCG
* *
523846 TCCCGCTCTTTGAGGACTGAAGGTGCCACCAACTTGTGTGGGCTTT--AAG--AGGTG
1 TCCTGCTCTTTGAGGACTGAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGAAAGGCG
* ** *
523900 TCCTGCTCTCTGAGGACTGGAAAATGCCACCAACTTGTGTGGGCTTT----GAAAGGTG
1 TCCTGCTCTTTGAGGACT-GAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGAAAGGCG
** *
523955 TCCTGCTCTTTGAGGACTGGAAAATGCCACCAACTTGTGTGGGCTTT----GAAAGGTG
1 TCCTGCTCTTTGAGGACT-GAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGAAAGGCG
* *
524010 TCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTGAAAAGAAAAAGCA
1 TCCTGCTCTTTGAGGACTG-AAGGTGCCACCAACTTGTGTGGGCTTT-AAAAG-AAAGGCG
* * *
524071 TCCTGCTCTTTGAGGACTGAAGGTACCACCAACTCGGGTGGGCTTTAAAAGAAAAGGCG
1 TCCTGCTCTTTGAGGACTGAAGGTGCCACCAACTTGTGTGGGCTTTAAAAG-AAAGGCG
*
524130 TCCCGCTCTTTGAGGACTGAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGAAAAGGCG
1 TCCTGCTCTTTGAGGACTGAAGGTGCCACCAACTTGTGTGGGCTTTAAAAG-AAAGGCG
524189 T-CTCGCTCTTTGAGGACTGAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGAAAAGGCG
1 TCCT-GCTCTTTGAGGACTGAAGGTGCCACCAACTTGTGTGGGCTTTAAAAG-AAAGGCG
*
524248 TCCCGCTCTTTGAGGACTGAAGGTG
1 TCCTGCTCTTTGAGGACTGAAGGTG
524273 GAAGGAGAAG
Statistics
Matches: 641, Mismatches: 48, Indels: 42
0.88 0.07 0.06
Matches are distributed among these distances:
53 1 0.00
54 22 0.03
55 317 0.49
56 1 0.00
57 3 0.00
58 1 0.00
59 199 0.31
60 53 0.08
61 44 0.07
ACGTcount: A:0.24, C:0.21, G:0.29, T:0.26
Consensus pattern (58 bp):
TCCTGCTCTTTGAGGACTGAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGAAAGGCG
Found at i:524091 original size:284 final size:285
Alignment explanation
Indices: 523505--524266 Score: 1119
Period size: 284 Copynumber: 2.7 Consensus size: 285
523495 AATAAAGTGT
* * * * *
523505 ATCCTGCTCATTGAGGAGTAAAAAGTGCCACCAACTCGTGTGGGCTTT----G-AAAGGCGTCCT
1 ATCCTGCTCTTTGAGGACT-GAAGGTGCCACCAACTCGTGTGGGCTTTAAAAGAAAAGGCGTCCC
* *
523565 GCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGGTGTCCTGCTCTTTAAG
65 GCTCTTTGAGGACTG-AAGGTGCCACCAACTTGTGTGGGCTTTAAGAGGTGTCCTGCTCTTTGAG
* *
523630 GACTGGAAAATGCCACCAACTTGTGTGGGCTTTAAAAGGTGTCCTGCTCTTTGGGGACT-GAAAG
129 GACTGGAAAATGCCACCAACTTGTGTGGGCTTTGAAAGGTGTCCTGCTCTTTGAGGACTGGAAAG
* *
523694 GTGCCACCAACTTGTGTGGGCTTTGAAAGGGGTCCTGCTCTTTGGGGAATGAAAGGTGCCACCAA
194 ATGCCACCAACTTGTGTGGGCTTTGAAAGGGGTCCTGCTCTTTGAGGAATGAAAGGTGCCACCAA
523759 CTTATGTGGGCTTTGAAAAGAAAAAGC
259 CTTATGTGGGCTTTGAAAAGAAAAAGC
* * *
523786 ATCCTGCTCTTTGAGGACTGAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGAAAATGTGTCCCG
1 ATCCTGCTCTTTGAGGACTGAAGGTGCCACCAACTCGTGTGGGCTTTAAAAGAAAAGGCGTCCCG
*
523851 CTCTTTGAGGACTGAAGGTGCCACCAACTTGTGTGGGCTTTAAGAGGTGTCCTGCTCTCTGAGGA
66 CTCTTTGAGGACTGAAGGTGCCACCAACTTGTGTGGGCTTTAAGAGGTGTCCTGCTCTTTGAGGA
523916 CTGGAAAATGCCACCAACTTGTGTGGGCTTTGAAAGGTGTCCTGCTCTTTGAGGACTGGAAA-AT
131 CTGGAAAATGCCACCAACTTGTGTGGGCTTTGAAAGGTGTCCTGCTCTTTGAGGACTGGAAAGAT
* *
523980 GCCACCAACTTGTGTGGGCTTTGAAAGGTGTCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACT
196 GCCACCAACTTGTGTGGGCTTTGAAAGGGGTCCTGCTCTTTGAGGAATGAAAGGTGCCACCAACT
*
524045 TGTGTGGGCTTTGAAAAGAAAAAGC
261 TATGTGGGCTTTGAAAAGAAAAAGC
* *
524070 ATCCTGCTCTTTGAGGACTGAAGGTACCACCAACTCGGGTGGGCTTTAAAAGAAAAGGCGTCCCG
1 ATCCTGCTCTTTGAGGACTGAAGGTGCCACCAACTCGTGTGGGCTTTAAAAGAAAAGGCGTCCCG
*
524135 CTCTTTGAGGACTGAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGAAAAGGCGT-CTCGCTCTT
66 CTCTTTGAGGACTGAAGGTGCCACCAACTTGTGTGGGCTTT--AAG---AGGTGTCCT-GCTCTT
** * *
524199 TGAGGACT-GAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGAAAAGGCGTCCCGCTCTTTGAGG
125 TGAGGACTGGAAAATGCCACCAACTTGTGTGGGCTTT----G-AAAGGTGTCCTGCTCTTTGAGG
524263 ACTG
185 ACTG
524267 AAGGTGGAAG
Statistics
Matches: 435, Mismatches: 29, Indels: 22
0.90 0.06 0.05
Matches are distributed among these distances:
280 25 0.06
281 17 0.04
284 292 0.67
285 27 0.06
286 3 0.01
288 28 0.06
289 18 0.04
292 1 0.00
293 24 0.06
ACGTcount: A:0.24, C:0.21, G:0.29, T:0.26
Consensus pattern (285 bp):
ATCCTGCTCTTTGAGGACTGAAGGTGCCACCAACTCGTGTGGGCTTTAAAAGAAAAGGCGTCCCG
CTCTTTGAGGACTGAAGGTGCCACCAACTTGTGTGGGCTTTAAGAGGTGTCCTGCTCTTTGAGGA
CTGGAAAATGCCACCAACTTGTGTGGGCTTTGAAAGGTGTCCTGCTCTTTGAGGACTGGAAAGAT
GCCACCAACTTGTGTGGGCTTTGAAAGGGGTCCTGCTCTTTGAGGAATGAAAGGTGCCACCAACT
TATGTGGGCTTTGAAAAGAAAAAGC
Found at i:525297 original size:9 final size:8
Alignment explanation
Indices: 525237--525297 Score: 65
Period size: 8 Copynumber: 7.6 Consensus size: 8
525227 CAGATTTTTC
525237 TTTTTT-T
1 TTTTTTGT
525244 TTTTTTGT
1 TTTTTTGT
525252 TTGTTTTGT
1 TT-TTTTGT
525261 TTGTTTTGT
1 TT-TTTTGT
525270 TTTTTT-T
1 TTTTTTGT
525277 TGTTTTT-T
1 T-TTTTTGT
525285 TTTTTTGT
1 TTTTTTGT
*
525293 GTTTT
1 TTTTT
525298 CTTTTTGAAA
Statistics
Matches: 49, Mismatches: 1, Indels: 7
0.86 0.02 0.12
Matches are distributed among these distances:
7 13 0.27
8 19 0.39
9 17 0.35
ACGTcount: A:0.00, C:0.00, G:0.13, T:0.87
Consensus pattern (8 bp):
TTTTTTGT
Found at i:525297 original size:13 final size:13
Alignment explanation
Indices: 525238--525304 Score: 62
Period size: 13 Copynumber: 4.8 Consensus size: 13
525228 AGATTTTTCT
*
525238 TTTTTTTTTTTTG
1 TTTTTTTTTTGTG
*
525251 TTTGTTTTGTTTGTTT
1 TTT-TTTT-TTTG-TG
*
525267 TGTTTTTTTTTGTT
1 T-TTTTTTTTTGTG
525281 TTTTTTTTTTGTG
1 TTTTTTTTTTGTG
*
525294 TTTTCTTTTTG
1 TTTTTTTTTTG
525305 AAAAAGAATG
Statistics
Matches: 46, Mismatches: 4, Indels: 8
0.79 0.07 0.14
Matches are distributed among these distances:
13 24 0.52
14 7 0.15
15 7 0.15
16 6 0.13
17 2 0.04
ACGTcount: A:0.00, C:0.01, G:0.13, T:0.85
Consensus pattern (13 bp):
TTTTTTTTTTGTG
Found at i:525303 original size:1 final size:1
Alignment explanation
Indices: 525231--525290 Score: 57
Period size: 1 Copynumber: 60.0 Consensus size: 1
525221 CTTAAGCAGA
* * * * * * *
525231 TTTTTCTTTTTTTTTTTTTGTTTGTTTTGTTTGTTTTGTTTTTTTTTGTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
525291 GTGTTTTCTT
Statistics
Matches: 45, Mismatches: 14, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
1 45 1.00
ACGTcount: A:0.00, C:0.02, G:0.10, T:0.88
Consensus pattern (1 bp):
T
Found at i:537650 original size:28 final size:28
Alignment explanation
Indices: 537594--537670 Score: 91
Period size: 28 Copynumber: 2.8 Consensus size: 28
537584 GGAATAAAGC
*** *
537594 CGAGGTTGGAGTATCCCCTCGGAAGTAA
1 CGAGGTTGGAGTATCCCCGATGAAATAA
*
537622 CGGGGTTGGAGTATCCCCGATGAAATAA
1 CGAGGTTGGAGTATCCCCGATGAAATAA
* *
537650 CGAGATTGGAGTATCCTCGAT
1 CGAGGTTGGAGTATCCCCGAT
537671 TGTGAGAAAT
Statistics
Matches: 41, Mismatches: 8, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
28 41 1.00
ACGTcount: A:0.26, C:0.19, G:0.31, T:0.23
Consensus pattern (28 bp):
CGAGGTTGGAGTATCCCCGATGAAATAA
Found at i:537717 original size:52 final size:49
Alignment explanation
Indices: 537655--537823 Score: 169
Period size: 52 Copynumber: 3.3 Consensus size: 49
537645 AATAACGAGA
* *
537655 TTGGAGTATCCTCGATTGTGAGAAATTGGTATTTTTGGAAATAAAATCGGAG
1 TTGGAGTATCCCCGATTGTGA-AAATTGGT-GTTTTGGAAATAAAATCGG-G
* * *
537707 TTGGAGTATCCCCGATTAAAG-GAAAATTGGCGTTTTGAAAATAAAACCAGGG
1 TTGGAGTATCCCCGATT---GTGAAAATTGGTGTTTTGGAAATAAAATC-GGG
* * *
537759 TTGGAGTATCCCCGATTGTGGAAAAATTAGTGTTTTAGCAATAAAATCGGGG
1 TTGGAGTATCCCCGATTGT-G-AAAATTGGTGTTTTGGAAATAAAATC-GGG
537811 TTGGAGTATCCCC
1 TTGGAGTATCCCC
537824 TCAGAAATAA
Statistics
Matches: 98, Mismatches: 12, Indels: 14
0.79 0.10 0.11
Matches are distributed among these distances:
49 1 0.01
51 1 0.01
52 84 0.86
53 9 0.09
54 2 0.02
55 1 0.01
ACGTcount: A:0.31, C:0.12, G:0.26, T:0.30
Consensus pattern (49 bp):
TTGGAGTATCCCCGATTGTGAAAATTGGTGTTTTGGAAATAAAATCGGG
Found at i:537873 original size:27 final size:28
Alignment explanation
Indices: 537806--537881 Score: 102
Period size: 27 Copynumber: 2.8 Consensus size: 28
537796 GCAATAAAAT
*
537806 CGGGGTTGGAGTATCCCCTCA-GAAATAA
1 CGGGGTTGGAGTATCCCC-GATGAAATAA
* *
537834 TGGGGTTGGAGTATCCCCGATG-ATTAA
1 CGGGGTTGGAGTATCCCCGATGAAATAA
537861 CGGGGTTGGAGTATCCCCGAT
1 CGGGGTTGGAGTATCCCCGAT
537882 TGTAAAGAAA
Statistics
Matches: 43, Mismatches: 4, Indels: 3
0.86 0.08 0.06
Matches are distributed among these distances:
27 25 0.58
28 18 0.42
ACGTcount: A:0.22, C:0.20, G:0.33, T:0.25
Consensus pattern (28 bp):
CGGGGTTGGAGTATCCCCGATGAAATAA
Found at i:537946 original size:212 final size:212
Alignment explanation
Indices: 537597--537992 Score: 582
Period size: 212 Copynumber: 1.9 Consensus size: 212
537587 ATAAAGCCGA
* *
537597 GGTTGGAGTATCCCCTCGGAAGTAACGGGGTTGGAGTATCCCCGATGAAATAACGAGATTGGAGT
1 GGTTGGAGTATCCCCTCAGAAATAACGGGGTTGGAGTATCCCCGATGAAATAACGAGATTGGAGT
* * * *
537662 ATCCTCGATTGTGAGAAATTGGTATTTTTGGAAATAAAATCGGAGTTGGAGTATCCCCGATTAAA
66 ATCCCCGATTGTAAGAAATGGGTATTTTTGGAAATAAAATCGGAGTTAGAGTATCCCCGATTAAA
* * *
537727 GGAAAATTGGCGTTTTGAAAATAAAACCAGG-GTTGGAGTATCCCCGATTGTGGAAAAATTAGTG
131 GGAAAATTAGCGTTTTGAAAATAAAACC-GGAGTTGGAATATCCCCAATTGTGGAAAAATTAGTG
537791 TTTTAGCAATAAAATCGG
195 TTTTAGCAATAAAATCGG
* * * *
537809 GGTTGGAGTATCCCCTCAGAAATAATGGGGTTGGAGTATCCCCGATG-ATTAACGGGGTTGGAGT
1 GGTTGGAGTATCCCCTCAGAAATAACGGGGTTGGAGTATCCCCGATGAAATAACGAGATTGGAGT
* *
537873 ATCCCCGATTGTAAAGAAATGGGTGTTTTTTGGAAATAAAATCGGAGTTAGAGTATCCCTGATTA
66 ATCCCCGATTGT-AAGAAATGGGT-ATTTTTGGAAATAAAATCGGAGTTAGAGTATCCCCGATTA
* * *
537938 TA-GAAAATTAGTGTTTTGAAAATAAAATCGGAGTTGGAATATCCCCAATTGTGGA
129 AAGGAAAATTAGCGTTTTGAAAATAAAACCGGAGTTGGAATATCCCCAATTGTGGA
537993 GAATTGAGAA
Statistics
Matches: 163, Mismatches: 18, Indels: 6
0.87 0.10 0.03
Matches are distributed among these distances:
211 27 0.17
212 98 0.60
213 38 0.23
ACGTcount: A:0.31, C:0.13, G:0.27, T:0.29
Consensus pattern (212 bp):
GGTTGGAGTATCCCCTCAGAAATAACGGGGTTGGAGTATCCCCGATGAAATAACGAGATTGGAGT
ATCCCCGATTGTAAGAAATGGGTATTTTTGGAAATAAAATCGGAGTTAGAGTATCCCCGATTAAA
GGAAAATTAGCGTTTTGAAAATAAAACCGGAGTTGGAATATCCCCAATTGTGGAAAAATTAGTGT
TTTAGCAATAAAATCGG
Found at i:540375 original size:13 final size:13
Alignment explanation
Indices: 540357--540382 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
540347 ACAAAGATCC
540357 ATGTATCGATACA
1 ATGTATCGATACA
540370 ATGTATCGATACA
1 ATGTATCGATACA
540383 CAGAAAAATG
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:540378 original size:33 final size:33
Alignment explanation
Indices: 540336--540402 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
540326 AAAATTTCCA
***
540336 AATGTATCGATACAAAGATCCATGTATCGATAC
1 AATGTATCGATACAAAGAAAAATGTATCGATAC
*
540369 AATGTATCGATACACAGAAAAATGTATCGATAC
1 AATGTATCGATACAAAGAAAAATGTATCGATAC
540402 A
1 A
540403 TTTCCTTGGC
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:0.43, C:0.16, G:0.15, T:0.25
Consensus pattern (33 bp):
AATGTATCGATACAAAGAAAAATGTATCGATAC
Found at i:540446 original size:19 final size:18
Alignment explanation
Indices: 540422--540489 Score: 83
Period size: 19 Copynumber: 3.9 Consensus size: 18
540412 CAGTAGCTAA
540422 TTATGTATCGATACAATAC
1 TTATGTATCGATACAA-AC
540441 TTATGTATCGATAC--A-
1 TTATGTATCGATACAAAC
540456 -T-TGTATCGATACAAAAC
1 TTATGTATCGATAC-AAAC
540473 TTATGTATCGATACAAA
1 TTATGTATCGATACAAA
540490 TTGTTGAATT
Statistics
Matches: 43, Mismatches: 0, Indels: 13
0.77 0.00 0.23
Matches are distributed among these distances:
13 11 0.26
14 1 0.02
16 2 0.05
18 4 0.09
19 25 0.58
ACGTcount: A:0.38, C:0.15, G:0.12, T:0.35
Consensus pattern (18 bp):
TTATGTATCGATACAAAC
Found at i:540462 original size:13 final size:13
Alignment explanation
Indices: 540444--540468 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
540434 ACAATACTTA
540444 TGTATCGATACAT
1 TGTATCGATACAT
540457 TGTATCGATACA
1 TGTATCGATACA
540469 AAACTTATGT
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:540466 original size:32 final size:32
Alignment explanation
Indices: 540425--540487 Score: 117
Period size: 32 Copynumber: 2.0 Consensus size: 32
540415 TAGCTAATTA
*
540425 TGTATCGATACAATACTTATGTATCGATACAT
1 TGTATCGATACAAAACTTATGTATCGATACAT
540457 TGTATCGATACAAAACTTATGTATCGATACA
1 TGTATCGATACAAAACTTATGTATCGATACA
540488 AATTGTTGAA
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 30 1.00
ACGTcount: A:0.37, C:0.16, G:0.13, T:0.35
Consensus pattern (32 bp):
TGTATCGATACAAAACTTATGTATCGATACAT
Found at i:549459 original size:5 final size:5
Alignment explanation
Indices: 549440--549496 Score: 68
Period size: 5 Copynumber: 12.2 Consensus size: 5
549430 GAGTTCCCTT
* *
549440 AAAA- AAAAC AAAA- AACA- AAAAG AAAAC AAAAC AAAAC AAAAC AAAAC
1 AAAAC AAAAC AAAAC AAAAC AAAAC AAAAC AAAAC AAAAC AAAAC AAAAC
549487 AAAA- AAAAC A
1 AAAAC AAAAC A
549497 CAAAAAAAGG
Statistics
Matches: 47, Mismatches: 3, Indels: 5
0.85 0.05 0.09
Matches are distributed among these distances:
4 14 0.30
5 33 0.70
ACGTcount: A:0.84, C:0.14, G:0.02, T:0.00
Consensus pattern (5 bp):
AAAAC
Found at i:549470 original size:10 final size:9
Alignment explanation
Indices: 549440--549504 Score: 78
Period size: 10 Copynumber: 6.9 Consensus size: 9
549430 GAGTTCCCTT
549440 AAAAAAAAC
1 AAAAAAAAC
549449 AAAAAACAA-
1 AAAAAA-AAC
*
549458 AAAGAAAAC
1 AAAAAAAAC
549467 AAAACAAAAC
1 AAAA-AAAAC
549477 AAAACAAAAC
1 AAAA-AAAAC
549487 AAAAAAAAC
1 AAAAAAAAC
549496 ACAAAAAAA
1 A-AAAAAAA
549505 GGTGCAAAGG
Statistics
Matches: 50, Mismatches: 2, Indels: 7
0.85 0.03 0.12
Matches are distributed among these distances:
8 2 0.04
9 20 0.40
10 28 0.56
ACGTcount: A:0.85, C:0.14, G:0.02, T:0.00
Consensus pattern (9 bp):
AAAAAAAAC
Found at i:549770 original size:8 final size:8
Alignment explanation
Indices: 549742--549813 Score: 54
Period size: 8 Copynumber: 8.6 Consensus size: 8
549732 GTTCTTTTCC
549742 AAAAAAAG
1 AAAAAAAG
*
549750 AAACAAAAC
1 AAA-AAAAG
549759 AAAAAAAG
1 AAAAAAAG
*
549767 AAAAAAAA
1 AAAAAAAG
*
549775 AAGAAGAAAC
1 AA-AA-AAAG
* *
549785 AAACAAAC
1 AAAAAAAG
549793 AAAAAAAG
1 AAAAAAAG
* *
549801 AAGAAAGG
1 AAAAAAAG
549809 AAAAA
1 AAAAA
549814 CCCCTTTTTC
Statistics
Matches: 51, Mismatches: 10, Indels: 6
0.76 0.15 0.09
Matches are distributed among these distances:
8 36 0.71
9 10 0.20
10 5 0.10
ACGTcount: A:0.82, C:0.07, G:0.11, T:0.00
Consensus pattern (8 bp):
AAAAAAAG
Found at i:549771 original size:14 final size:14
Alignment explanation
Indices: 549742--549783 Score: 52
Period size: 14 Copynumber: 3.0 Consensus size: 14
549732 GTTCTTTTCC
549742 AAAAAAAGAA-ACAA
1 AAAAAAAGAAGA-AA
549756 AACAAAAA-AAGAAA
1 AA-AAAAAGAAGAAA
549770 AAAAAAAGAAGAAA
1 AAAAAAAGAAGAAA
549784 CAAACAAACA
Statistics
Matches: 25, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
13 5 0.20
14 14 0.56
15 6 0.24
ACGTcount: A:0.86, C:0.05, G:0.10, T:0.00
Consensus pattern (14 bp):
AAAAAAAGAAGAAA
Found at i:549784 original size:26 final size:26
Alignment explanation
Indices: 549755--549805 Score: 75
Period size: 26 Copynumber: 2.0 Consensus size: 26
549745 AAAAGAAACA
*
549755 AAACAAAAAAAGAAAAAAAAAAGAAG
1 AAACAAAAAAACAAAAAAAAAAGAAG
* *
549781 AAACAAACAAACAAAAAAAGAAGAA
1 AAACAAAAAAACAAAAAAAAAAGAA
549806 AGGAAAAACC
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
26 22 1.00
ACGTcount: A:0.82, C:0.08, G:0.10, T:0.00
Consensus pattern (26 bp):
AAACAAAAAAACAAAAAAAAAAGAAG
Found at i:549785 original size:31 final size:32
Alignment explanation
Indices: 549742--549802 Score: 90
Period size: 34 Copynumber: 1.9 Consensus size: 32
549732 GTTCTTTTCC
549742 AAAAAAAGAAAC-A-AAACAAAAAAAGAAAAA
1 AAAAAAAGAAACAACAAACAAAAAAAGAAAAA
549772 AAAAAGAAGAAACAAACAAACAAAAAAAGAA
1 AAAAA-AAGAAAC-AACAAACAAAAAAAGAA
549803 GAAAGGAAAA
Statistics
Matches: 27, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
30 5 0.19
31 7 0.26
33 1 0.04
34 14 0.52
ACGTcount: A:0.84, C:0.08, G:0.08, T:0.00
Consensus pattern (32 bp):
AAAAAAAGAAACAACAAACAAAAAAAGAAAAA
Found at i:550878 original size:23 final size:23
Alignment explanation
Indices: 550848--550893 Score: 83
Period size: 23 Copynumber: 2.0 Consensus size: 23
550838 GCATCTTGTC
550848 TCAAAGTCCACGACTCAGTGGCA
1 TCAAAGTCCACGACTCAGTGGCA
*
550871 TCAAAGTCCACGACTCCGTGGCA
1 TCAAAGTCCACGACTCAGTGGCA
550894 CCTTTTTCTT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.28, C:0.33, G:0.22, T:0.17
Consensus pattern (23 bp):
TCAAAGTCCACGACTCAGTGGCA
Found at i:550971 original size:35 final size:35
Alignment explanation
Indices: 550871--551305 Score: 380
Period size: 31 Copynumber: 13.0 Consensus size: 35
550861 CTCAGTGGCA
* * *
550871 TCAAAGTCCACGACTCCGTGGCACCTTTTT-CTTT
1 TCAAAGCCCACAACTCCGTGGCATCTTTTTCCTTT
* * *
550905 TCAAAGTCCACGACTCCGTGGCA-C--CTT-CTTT
1 TCAAAGCCCACAACTCCGTGGCATCTTTTTCCTTT
* *
550936 TCAAAGCCCACAACTCTGTGACATCTTTTTCCTTT
1 TCAAAGCCCACAACTCCGTGGCATCTTTTTCCTTT
* *
550971 TTAAAGCCCACAACTCCATGGCACTCTTTTT-C-TT
1 TCAAAGCCCACAACTCCGTGGCA-TCTTTTTCCTTT
* * *
551005 TCTAAGTCCACAACTCCGTGGCA-C--CTT-CTTT
1 TCAAAGCCCACAACTCCGTGGCATCTTTTTCCTTT
*
551036 TCAAAGCCCACAACTCTGTGGCATCTTTTTCCTTT
1 TCAAAGCCCACAACTCCGTGGCATCTTTTTCCTTT
* *
551071 TTAAAGCCCACAACTCCGCGGCACTCTTTTT-C-TT
1 TCAAAGCCCACAACTCCGTGGCA-TCTTTTTCCTTT
* * *
551105 TCTAAGTCCACAACTCCGTGGCA-C--CTT-CTTT
1 TCAAAGCCCACAACTCCGTGGCATCTTTTTCCTTT
551136 TCAAAGCCCACAACTCCGTGGCACTCTTTTTCCCTTT
1 TCAAAGCCCACAACTCCGTGGCA-TCTTTTT-CCTTT
* * * *
551173 T-AAAGTCCACAACTCTGTGGCACCTTGTTCCTTT
1 TCAAAGCCCACAACTCCGTGGCATCTTTTTCCTTT
* * * *
551207 T--ATGTCCACGACTCCGTGGCA-C--CTT-CTTT
1 TCAAAGCCCACAACTCCGTGGCATCTTTTTCCTTT
*
551236 TCAAAGCCCACAACTCTGTGGCATCTTTTTCCCTTT
1 TCAAAGCCCACAACTCCGTGGCATCTTTTT-CCTTT
*
551272 T-AAAGCCCACAACTTCGTGGCACTCTTTTTCCTT
1 TCAAAGCCCACAACTCCGTGGCA-TCTTTTTCCTT
551306 CTAAGTTCAC
Statistics
Matches: 330, Mismatches: 45, Indels: 51
0.77 0.11 0.12
Matches are distributed among these distances:
29 5 0.02
30 8 0.02
31 86 0.26
32 6 0.02
33 19 0.06
34 77 0.23
35 79 0.24
36 45 0.14
37 5 0.02
ACGTcount: A:0.20, C:0.34, G:0.12, T:0.34
Consensus pattern (35 bp):
TCAAAGCCCACAACTCCGTGGCATCTTTTTCCTTT
Found at i:551002 original size:65 final size:65
Alignment explanation
Indices: 550871--551380 Score: 362
Period size: 65 Copynumber: 7.7 Consensus size: 65
550861 CTCAGTGGCA
* * * * *
550871 TCAAAGTCCACGACTCCGTGGCACCTTTTTCTTTTCAAAGTCCACGACTCCGTGGCACCTTCTTT
1 TCAAAGCCCACAACTCCGTGGCATCTTTTTCTTTTTAAAGTCCACAACTCCGTGGCACCTTCTTT
* * * * *
550936 TCAAAGCCCACAACTCTGTGACATCTTTTTCCTTTTTAAAGCCCACAACTCCATGGCACTCTTTT
1 TCAAAGCCCACAACTCCGTGGCATCTTTTT-CTTTTTAAAGTCCACAACTCCGTGGCAC-C-TTC
551001 TCTT
63 T-TT
* * * * * * *
551005 TCTAAGTCCACAACTCCGTGGCA-C--CTTCTTTTCAAAGCCCACAACTCTGTGGCATCTTTTTC
1 TCAAAGCCCACAACTCCGTGGCATCTTTTTCTTTTTAAAGTCCACAACTCCGTGGCA-C--CTT-
551067 CTTT
62 CTTT
* * *
551071 TTAAAGCCCACAACTCCGCGGCACTCTTTTTCTTTCT-AAGTCCACAACTCCGTGGCACCTTCTT
1 TCAAAGCCCACAACTCCGTGGCA-TCTTTTTCTTTTTAAAGTCCACAACTCCGTGGCACCTTCTT
551135 T
65 T
* * *
551136 TCAAAGCCCACAACTCCGTGGCACTCTTTTTCCCTTTTAAAGTCCACAACTCTGTGGCACCTTGT
1 TCAAAGCCCACAACTCCGTGGCA-TCTTTTT-CTTTTTAAAGTCCACAACTCCGTGGCACCTTCT
551201 TCCT
64 T--T
** * * * * * * * *
551205 TTTATGTCCACGACTCCGTGGCA-C--CTTCTTTTCAAAGCCCACAACTCTGTGGCATCTTTTTC
1 TCAAAGCCCACAACTCCGTGGCATCTTTTTCTTTTTAAAGTCCACAACTCCGTGGCA-C--CTT-
551267 CCTTT
62 -CTTT
* * * * * *
551272 T-AAAGCCCACAACTTCGTGGCACTCTTTTTCCTTCT-AAGTTCACAACTCTGTGGCACC--CGT
1 TCAAAGCCCACAACTCCGTGGCA-TCTTTTTCTTTTTAAAGTCCACAACTCCGTGGCACCTTCTT
551333 T
65 T
* *
551334 T--AAGCCCACAACTCCGTGGCATTCTTTTTGTTTCTCTAAAGCCCACA
1 TCAAAGCCCACAACTCCGTGGCA-TCTTTTTCTTT-T-TAAAGTCCACA
551381 CAAGTCGATG
Statistics
Matches: 351, Mismatches: 67, Indels: 55
0.74 0.14 0.12
Matches are distributed among these distances:
61 28 0.08
62 4 0.01
63 1 0.00
64 31 0.09
65 85 0.24
66 72 0.21
67 33 0.09
68 8 0.02
69 78 0.22
70 11 0.03
ACGTcount: A:0.20, C:0.33, G:0.13, T:0.34
Consensus pattern (65 bp):
TCAAAGCCCACAACTCCGTGGCATCTTTTTCTTTTTAAAGTCCACAACTCCGTGGCACCTTCTTT
Found at i:551061 original size:100 final size:100
Alignment explanation
Indices: 550873--551380 Score: 708
Period size: 100 Copynumber: 5.1 Consensus size: 100
550863 CAGTGGCATC
* * * *
550873 AAAGTCCACGACTCCGTGGCAC-CTTTTTCTTTTCAAAGTCCACGACTCCGTGGCACCTTCTTTT
1 AAAGCCCACAACTCCGTGGCACTCTTTTTC-TTTCTAAGTCCACAACTCCGTGGCACCTTCTTTT
*
550937 CAAAGCCCACAACTCTGTGACATCTTTTTCCTTTTT
65 CAAAGCCCACAACTCTGTGGCATCTTTTTCCTTTTT
*
550973 AAAGCCCACAACTCCATGGCACTCTTTTTCTTTCTAAGTCCACAACTCCGTGGCACCTTCTTTTC
1 AAAGCCCACAACTCCGTGGCACTCTTTTTCTTTCTAAGTCCACAACTCCGTGGCACCTTCTTTTC
551038 AAAGCCCACAACTCTGTGGCATCTTTTTCCTTTTT
66 AAAGCCCACAACTCTGTGGCATCTTTTTCCTTTTT
*
551073 AAAGCCCACAACTCCGCGGCACTCTTTTTCTTTCTAAGTCCACAACTCCGTGGCACCTTCTTTTC
1 AAAGCCCACAACTCCGTGGCACTCTTTTTCTTTCTAAGTCCACAACTCCGTGGCACCTTCTTTTC
* *
551138 AAAGCCCACAACTCCGTGGCACTCTTTTTCCCTTTT
66 AAAGCCCACAACTCTGTGGCA-TCTTTTTCCTTTTT
* * * * *
551174 AAAGTCCACAACTCTGTGGCAC-CTTGTTCCTTT-TATGTCCACGACTCCGTGGCACCTTCTTTT
1 AAAGCCCACAACTCCGTGGCACTCTT-TTTCTTTCTAAGTCCACAACTCCGTGGCACCTTCTTTT
*
551237 CAAAGCCCACAACTCTGTGGCATCTTTTTCCCTTTT
65 CAAAGCCCACAACTCTGTGGCATCTTTTTCCTTTTT
* * * * *
551273 AAAGCCCACAACTTCGTGGCACTCTTTTTCCTTCTAAGTTCACAACTCTGTGGCACC--CGTTT-
1 AAAGCCCACAACTCCGTGGCACTCTTTTTCTTTCTAAGTCCACAACTCCGTGGCACCTTCTTTTC
* *
551335 -AAGCCCACAACTCCGTGGCATTCTTTTT-GTTTCTCT
66 AAAGCCCACAACTCTGTGGCA-TCTTTTTCCTTT-T-T
551371 AAAGCCCACA
1 AAAGCCCACA
551381 CAAGTCGATG
Statistics
Matches: 370, Mismatches: 30, Indels: 18
0.89 0.07 0.04
Matches are distributed among these distances:
96 21 0.06
97 8 0.02
98 15 0.04
99 38 0.10
100 243 0.66
101 45 0.12
ACGTcount: A:0.20, C:0.33, G:0.13, T:0.34
Consensus pattern (100 bp):
AAAGCCCACAACTCCGTGGCACTCTTTTTCTTTCTAAGTCCACAACTCCGTGGCACCTTCTTTTC
AAAGCCCACAACTCTGTGGCATCTTTTTCCTTTTT
Found at i:551393 original size:135 final size:132
Alignment explanation
Indices: 550871--551361 Score: 351
Period size: 134 Copynumber: 3.7 Consensus size: 132
550861 CTCAGTGGCA
* * ** * * * *
550871 TCAAAGTCCACGACTCCGTGGCAC-CTTTTTCTTTTC-AAAGTCCACGACTCCGTGGCACCTTCT
1 TCAAAGCCCACAACTCCGTGGCACTCTTTTTCCCTTCTAAAGTCCACAACTCTGTGGCACCTCCG
* * * * **
550934 TTTCAAAGCCCACAACTCTGTGACATCTTTTTCCTTTTTAAAGCCCACAACTCCATGGCACTCTT
66 TTT--AAGCCCACAACTCCGTGGCA-C--CTT-CTTTTCAAAGCCCACAACTCTGTGGCA-TCTT
550999 TTT--C-TT
124 TTTCCCTTT
* * * * *
551005 TCTAAGTCCACAACTCCGTGGCAC-CTTCTT---TTC-AAAGCCCACAACTCTGTGGCATCTTTT
1 TCAAAGCCCACAACTCCGTGGCACTCTTTTTCCCTTCTAAAGTCCACAACTCTGTGGCA-C---C
* * * * * *
551065 TCCTTTTTAAAGCCCACAACTCCGCGGCACTCTTTTTCTTTCTAAGTCCACAACTCCGTGGCA-C
62 TCC-GTTT-AAGCCCACAACTCCGTGGCAC-C-TTCT-TTTCAAAGCCCACAACTCTGTGGCATC
*
551129 --CTT--CTTT
122 TTTTTCCCTTT
*
551136 TCAAAGCCCACAACTCCGTGGCACTCTTTTTCCCTTTTAAAGTCCACAACTCTGTGGCACCTTGT
1 TCAAAGCCCACAACTCCGTGGCACTCTTTTTCCCTTCTAAAGTCCACAACTCTGTGGCACC----
* * * *
551201 TCCTTTTATGTCCACGACTCCGTGGCACCTTCTTTTCAAAGCCCACAACTCTGTGGCATCTTTTT
62 TCCGTTTAAGCCCACAACTCCGTGGCACCTTCTTTTCAAAGCCCACAACTCTGTGGCATCTTTTT
551266 CCCTTT
127 CCCTTT
* *
551272 T-AAAGCCCACAACTTCGTGGCACTCTTTTT-CCTTCT-AAGTTCACAACTCTGTGGCA-C-CCG
1 TCAAAGCCCACAACTCCGTGGCACTCTTTTTCCCTTCTAAAGTCCACAACTCTGTGGCACCTCCG
551332 TTTAAGCCCACAACTCCGTGGCA--TTCTTTT
66 TTTAAGCCCACAACTCCGTGGCACCTTCTTTT
551362 TGTTTCTCTA
Statistics
Matches: 295, Mismatches: 40, Indels: 53
0.76 0.10 0.14
Matches are distributed among these distances:
125 7 0.02
127 22 0.07
130 3 0.01
131 67 0.23
132 12 0.04
133 22 0.07
134 75 0.25
135 55 0.19
136 32 0.11
ACGTcount: A:0.20, C:0.33, G:0.13, T:0.34
Consensus pattern (132 bp):
TCAAAGCCCACAACTCCGTGGCACTCTTTTTCCCTTCTAAAGTCCACAACTCTGTGGCACCTCCG
TTTAAGCCCACAACTCCGTGGCACCTTCTTTTCAAAGCCCACAACTCTGTGGCATCTTTTTCCCT
TT
Found at i:551414 original size:33 final size:32
Alignment explanation
Indices: 551365--551469 Score: 142
Period size: 33 Copynumber: 3.2 Consensus size: 32
551355 TTCTTTTTGT
551365 TTCTCTAAAGCCCACACAAGTCGATGGCAACC
1 TTCTCTAAAGCCCACACAAGTCGATGGCAACC
* * *
551397 TTCTTCTATAGCCCACACAAGTTGGTGGCAACC
1 TTC-TCTAAAGCCCACACAAGTCGATGGCAACC
551430 ATTCTCTAAAGCCCACACAAGTC-AGTGGCAACC
1 -TTCTCTAAAGCCCACACAAGTCGA-TGGCAACC
551463 TT-TCTAA
1 TTCTCTAA
551470 GTCCAATGTA
Statistics
Matches: 64, Mismatches: 6, Indels: 7
0.83 0.08 0.09
Matches are distributed among these distances:
31 5 0.08
32 5 0.08
33 51 0.80
34 3 0.05
ACGTcount: A:0.30, C:0.31, G:0.15, T:0.24
Consensus pattern (32 bp):
TTCTCTAAAGCCCACACAAGTCGATGGCAACC
Found at i:551509 original size:21 final size:21
Alignment explanation
Indices: 551485--551552 Score: 59
Period size: 21 Copynumber: 3.2 Consensus size: 21
551475 ATGTAGCTGG
551485 CCTTGAATCAGCATATTGGCA
1 CCTTGAATCAGCATATTGGCA
* ** *
551506 CCTTTAAGTCCAATATCACTGG--
1 CCTTGAA-T-CAGCAT-ATTGGCA
551528 CCTTGAATCAGCATATTGGCA
1 CCTTGAATCAGCATATTGGCA
551549 CCTT
1 CCTT
551553 CATCTTTAAG
Statistics
Matches: 34, Mismatches: 8, Indels: 10
0.65 0.15 0.19
Matches are distributed among these distances:
19 4 0.12
20 4 0.12
21 11 0.32
22 7 0.21
23 4 0.12
24 4 0.12
ACGTcount: A:0.26, C:0.26, G:0.16, T:0.31
Consensus pattern (21 bp):
CCTTGAATCAGCATATTGGCA
Found at i:551624 original size:92 final size:92
Alignment explanation
Indices: 551467--552346 Score: 1463
Period size: 92 Copynumber: 9.5 Consensus size: 92
551457 GCAACCTTTC
* *
551467 TAAGTCCAATGTAGCTGGCCTTGAATCAGCATATTGGCACCTTTAAGTCCAATATCACTGGCCTT
1 TAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCACCTTTAAGTCCAATATCGCTGGCCTT
551532 GAATCAGCATATTGGCACCTTCATCTT
66 GAATCAGCATATTGGCACCTTCATCTT
* * *
551559 TAAGTCCAATGTAGCTGGCCTAGAATCAGCACATTGGCACCTTTAAGTCTAATATCGCTAGCCTT
1 TAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCACCTTTAAGTCCAATATCGCTGGCCTT
551624 GAATCAGCATATTGGCACCTTCATCTT
66 GAATCAGCATATTGGCACCTTCATCTT
551651 TAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCACCTTTAAGTCCAATATCGCTGGCCTT
1 TAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCACCTTTAAGTCCAATATCGCTGGCCTT
*
551716 GAATTAGCATATTGGCACCTTCATCTT
66 GAATCAGCATATTGGCACCTTCATCTT
551743 TAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCACCTTTAAGTCCAATATCGCTGGCCTT
1 TAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCACCTTTAAGTCCAATATCGCTGGCCTT
*
551808 GAATTAGCATATTGGCACCTTCATCTT
66 GAATCAGCATATTGGCACCTTCATCTT
*
551835 TAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCATCTTTAAGTCCAATATCGCTGGCCTT
1 TAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCACCTTTAAGTCCAATATCGCTGGCCTT
551900 GAATCAGCATATTGGCACCTTCATCTT
66 GAATCAGCATATTGGCACCTTCATCTT
* * *
551927 TAAGTCCAACGTAGCTGGCCTTGAATTAGCACATTGGCACCTTTAAGTCCAATATAGCTGGCCTT
1 TAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCACCTTTAAGTCCAATATCGCTGGCCTT
*
551992 GAATCAGCATATTGGCACCTTCTTCTT
66 GAATCAGCATATTGGCACCTTCATCTT
* *
552019 TAAGTCTAATGTAGCTGGCCTTAAATCAGCACATTGGCACCTTTAAGTCCAATATCGCTGGCCTT
1 TAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCACCTTTAAGTCCAATATCGCTGGCCTT
552084 GAATCAGCATATTGGCACCTTCATCTT
66 GAATCAGCATATTGGCACCTTCATCTT
**
552111 TAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCACCTCCAAGTCCAATATCGCTGGCCTT
1 TAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCACCTTTAAGTCCAATATCGCTGGCCTT
*
552176 GAATCAGCATATTGGCACCTTTATCTT
66 GAATCAGCATATTGGCACCTTCATCTT
* * *
552203 TAAGTCCAATGTCGCTGGCCTTGAATCAGCACATTAGCACCTTCATCTTTAAGTCCAATATCACT
1 TAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCA----C--CTTTAAGTCCAATATCGCT
* *
552268 GGCCTTGAATCAGCATATTGGCGTCTTTGTCATCTT
60 GGCCTTGAATCAGCATATTGGC-AC-CT-TCATCTT
* *
552304 TAAGTCCAATGTCGCTAGCCTTGAATCAGCACATTGGCACCTT
1 TAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCACCTT
552347 CATCTTTAAC
Statistics
Matches: 742, Mismatches: 37, Indels: 15
0.93 0.05 0.02
Matches are distributed among these distances:
92 654 0.88
95 3 0.00
96 1 0.00
97 1 0.00
98 38 0.05
99 1 0.00
100 1 0.00
101 43 0.06
ACGTcount: A:0.25, C:0.25, G:0.18, T:0.31
Consensus pattern (92 bp):
TAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCACCTTTAAGTCCAATATCGCTGGCCTT
GAATCAGCATATTGGCACCTTCATCTT
Found at i:553236 original size:32 final size:32
Alignment explanation
Indices: 553181--553278 Score: 169
Period size: 32 Copynumber: 3.0 Consensus size: 32
553171 TTCAACGATT
*
553181 TGTATCGATACATAAAGTGTTGTATCGATATAA
1 TGTATCGATACAT-AAGTGTTGTATCGATACAA
553214 TGTATCGATACATAAGTGTTGTATCGATACAA
1 TGTATCGATACATAAGTGTTGTATCGATACAA
*
553246 TGTATCGATACATAAGTTTTGTATCGATACAA
1 TGTATCGATACATAAGTGTTGTATCGATACAA
553278 T
1 T
553279 ATAAGCTACT
Statistics
Matches: 63, Mismatches: 2, Indels: 1
0.95 0.03 0.02
Matches are distributed among these distances:
32 50 0.79
33 13 0.21
ACGTcount: A:0.35, C:0.11, G:0.17, T:0.37
Consensus pattern (32 bp):
TGTATCGATACATAAGTGTTGTATCGATACAA
Found at i:553238 original size:19 final size:18
Alignment explanation
Indices: 553179--553276 Score: 90
Period size: 19 Copynumber: 5.8 Consensus size: 18
553169 ATTTCAACGA
553179 TTTGTATCGATACATAAAG
1 TTTGTATCGATACAT-AAG
553198 TGTTGTATCGAT--ATAA-
1 T-TTGTATCGATACATAAG
553214 --TGTATCGATACATAAG
1 TTTGTATCGATACATAAG
553230 TGTTGTATCGATAC--AA-
1 T-TTGTATCGATACATAAG
553246 --TGTATCGATACATAAG
1 TTTGTATCGATACATAAG
553262 TTTTGTATCGATACA
1 -TTTGTATCGATACA
553277 ATATAAGCTA
Statistics
Matches: 66, Mismatches: 0, Indels: 26
0.72 0.00 0.28
Matches are distributed among these distances:
13 20 0.30
15 6 0.09
17 4 0.06
18 2 0.03
19 24 0.36
20 10 0.15
ACGTcount: A:0.34, C:0.11, G:0.17, T:0.38
Consensus pattern (18 bp):
TTTGTATCGATACATAAG
Found at i:553256 original size:13 final size:13
Alignment explanation
Indices: 553201--553257 Score: 51
Period size: 13 Copynumber: 3.9 Consensus size: 13
553191 CATAAAGTGT
*
553201 TGTATCGATATAA
1 TGTATCGATACAA
553214 TGTATCGATACATAA
1 TGTATCGATAC--AA
553229 GTGTTGTATCGATACAA
1 ----TGTATCGATACAA
553246 TGTATCGATACA
1 TGTATCGATACA
553258 TAAGTTTTGT
Statistics
Matches: 37, Mismatches: 1, Indels: 12
0.74 0.02 0.24
Matches are distributed among these distances:
13 22 0.59
15 2 0.05
17 2 0.05
19 11 0.30
ACGTcount: A:0.35, C:0.12, G:0.18, T:0.35
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:553337 original size:13 final size:13
Alignment explanation
Indices: 553319--553377 Score: 58
Period size: 13 Copynumber: 5.0 Consensus size: 13
553309 ATTACTCAAA
553319 TGTATCGATACAT
1 TGTATCGATACAT
* *
553332 TGTATCAATACAC
1 TGTATCGATACAT
553345 TG-ATC--T---T
1 TGTATCGATACAT
553352 TGTATCGATACAT
1 TGTATCGATACAT
553365 TGTATCGATACAT
1 TGTATCGATACAT
553378 GCAGGCAAAT
Statistics
Matches: 37, Mismatches: 3, Indels: 12
0.71 0.06 0.23
Matches are distributed among these distances:
7 2 0.05
8 3 0.08
10 2 0.05
12 3 0.08
13 27 0.73
ACGTcount: A:0.31, C:0.17, G:0.14, T:0.39
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:553443 original size:52 final size:52
Alignment explanation
Indices: 553365--553493 Score: 240
Period size: 52 Copynumber: 2.5 Consensus size: 52
553355 ATCGATACAT
553365 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATAAAA
1 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATAAAA
* *
553417 TGTATCGATACATGCAGGTAAATTTGCCCAGATGTATCGATACACTATGAAA
1 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATAAAA
553469 TGTATCGATACATGCAGGCAAATTT
1 TGTATCGATACATGCAGGCAAATTT
553494 TCATATTTCG
Statistics
Matches: 74, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
52 74 1.00
ACGTcount: A:0.35, C:0.18, G:0.19, T:0.29
Consensus pattern (52 bp):
TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATAAAA
Found at i:556591 original size:18 final size:17
Alignment explanation
Indices: 556557--556594 Score: 51
Period size: 17 Copynumber: 2.2 Consensus size: 17
556547 CGACACACAC
556557 AAAAAAAATCAAACAAG
1 AAAAAAAATCAAACAAG
556574 AAAAAAAA-CAACATCAAG
1 AAAAAAAATCAA-A-CAAG
556592 AAA
1 AAA
556595 TATTTTATGA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
16 3 0.16
17 9 0.47
18 7 0.37
ACGTcount: A:0.76, C:0.13, G:0.05, T:0.05
Consensus pattern (17 bp):
AAAAAAAATCAAACAAG
Found at i:559656 original size:13 final size:13
Alignment explanation
Indices: 559638--559663 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
559628 TACACCAAGT
559638 ATGTATCGATACA
1 ATGTATCGATACA
559651 ATGTATCGATACA
1 ATGTATCGATACA
559664 CAAAAAAATT
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:561910 original size:21 final size:21
Alignment explanation
Indices: 561877--561926 Score: 57
Period size: 21 Copynumber: 2.3 Consensus size: 21
561867 TTGCAAGTTG
*
561877 AAATAAAGAAGTTGGCTAATGA
1 AAATAAAGAAGTTAGCTAA-GA
*
561899 AAATAATG-AGTTAGCTAAGAA
1 AAATAAAGAAGTTAGCTAAG-A
561920 AAATAAA
1 AAATAAA
561927 AACTTGCATA
Statistics
Matches: 24, Mismatches: 3, Indels: 3
0.80 0.10 0.10
Matches are distributed among these distances:
20 1 0.04
21 16 0.67
22 7 0.29
ACGTcount: A:0.56, C:0.04, G:0.18, T:0.22
Consensus pattern (21 bp):
AAATAAAGAAGTTAGCTAAGA
Found at i:563744 original size:15 final size:15
Alignment explanation
Indices: 563724--563754 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
563714 TAAAAATGTC
*
563724 CAAAATGAGGAAGCT
1 CAAAATGAAGAAGCT
563739 CAAAATGAAGAAGCT
1 CAAAATGAAGAAGCT
563754 C
1 C
563755 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:565838 original size:20 final size:20
Alignment explanation
Indices: 565767--565844 Score: 75
Period size: 20 Copynumber: 3.6 Consensus size: 20
565757 AGTGTCCAAA
*
565767 ATGTATCGATACATGTTTCT
1 ATGTATCGATACATTTTTCT
* *
565787 GTGTATCGATACATTTGGAAATTCA
1 ATGTATCGATACATTT-----TTCT
565812 ATGTATCGATACATTTTTCT
1 ATGTATCGATACATTTTTCT
*
565832 TTGTATCGATACA
1 ATGTATCGATACA
565845 GGGTGATTAT
Statistics
Matches: 47, Mismatches: 6, Indels: 10
0.75 0.10 0.16
Matches are distributed among these distances:
20 29 0.62
25 18 0.38
ACGTcount: A:0.28, C:0.14, G:0.15, T:0.42
Consensus pattern (20 bp):
ATGTATCGATACATTTTTCT
Found at i:566008 original size:20 final size:20
Alignment explanation
Indices: 565965--566010 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 20
565955 AAATCTTTTG
565965 CAAAATACTTGTTTTTCACTT
1 CAAAATACTTGTTTTTCAC-T
*
565986 CAAATTACTTCGTTTTTCA-T
1 CAAAATACTT-GTTTTTCACT
566006 CAAAA
1 CAAAA
566011 CCAGCATCAA
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
20 5 0.23
21 9 0.41
22 8 0.36
ACGTcount: A:0.33, C:0.20, G:0.04, T:0.43
Consensus pattern (20 bp):
CAAAATACTTGTTTTTCACT
Found at i:568822 original size:15 final size:14
Alignment explanation
Indices: 568802--568865 Score: 73
Period size: 13 Copynumber: 4.6 Consensus size: 14
568792 ACCTTCTCTT
568802 CAAAAAAAAAAAGAG
1 CAAAAAAAAAAA-AG
568817 C--AAAAAAAAAAG
1 CAAAAAAAAAAAAG
568829 CAAAAAAAAAAAA-
1 CAAAAAAAAAAAAG
568842 CAAAAAAAACAAAA-
1 CAAAAAAAA-AAAAG
568856 CAAAGAAAAA
1 CAAA-AAAAA
568866 GAGAGAAAAG
Statistics
Matches: 45, Mismatches: 0, Indels: 8
0.85 0.00 0.15
Matches are distributed among these distances:
12 3 0.07
13 18 0.40
14 18 0.40
15 6 0.13
ACGTcount: A:0.84, C:0.09, G:0.06, T:0.00
Consensus pattern (14 bp):
CAAAAAAAAAAAAG
Found at i:569930 original size:55 final size:55
Alignment explanation
Indices: 569846--570530 Score: 932
Period size: 55 Copynumber: 12.3 Consensus size: 55
569836 TCCGCTTTTT
*
569846 AGTCCTCAAAGAGCAGGACACGTCTTAAAGCCCACACAAGTTGGTGGCACCTTTC
1 AGTCCTCAAAGAGCAGGACACCTCTTAAAGCCCACACAAGTTGGTGGCACCTTTC
*
569901 AGTCCTCAAAGAGCAGGACACCTCTTAAAGCCCACACAAGTTGGTGGCA-TTTTCC
1 AGTCCTCAAAGAGCAGGACACCTCTTAAAGCCCACACAAGTTGGTGGCACCTTT-C
*
569956 AGTCCTCAAAGAGCAGGACACCT-TTCAAAGCCCACACAAGTTGGTGGCA-TTTTCC
1 AGTCCTCAAAGAGCAGGACACCTCTT-AAAGCCCACACAAGTTGGTGGCACCTTT-C
* *
570011 AGTCCTCAAAGAGCAGGACACCTCTTAAAGCCCACACAAGTTGGTGGCGCCTTCC
1 AGTCCTCAAAGAGCAGGACACCTCTTAAAGCCCACACAAGTTGGTGGCACCTTTC
*
570066 AGTCCTCAAAGAGCAGGACACCTCTCAAAGCCCACACAAGTTGGTGGCACCTTTCC
1 AGTCCTCAAAGAGCAGGACACCTCTTAAAGCCCACACAAGTTGGTGGCACCTTT-C
** *
570122 AGTCCTCAAAGAGCAGGACACCTCTTAAAGCCCACACAAGTTGGTGGCGTCTTCC
1 AGTCCTCAAAGAGCAGGACACCTCTTAAAGCCCACACAAGTTGGTGGCACCTTTC
*
570177 AGTCCTCAAAGAGCAGGACACCTCTCAAAGCCCACACAAGTTGGTGGCACCTTTC
1 AGTCCTCAAAGAGCAGGACACCTCTTAAAGCCCACACAAGTTGGTGGCACCTTTC
* * *
570232 AGTCCCCGAAGAGCAGGACACCT-TTCAAAGCCCACACAAGTTGGTGGCA-TTTTCC
1 AGTCCTCAAAGAGCAGGACACCTCTT-AAAGCCCACACAAGTTGGTGGCACCTTT-C
* * * **
570287 AGTCTTCAAAGAGCAGGACACCTTTTAAAGCCCACACAGGTTGGTGGCATTTTTC
1 AGTCCTCAAAGAGCAGGACACCTCTTAAAGCCCACACAAGTTGGTGGCACCTTTC
*** * *
570342 AGTCCTCAAAGAGCAGGATGCTTTTTATTTTCAAAGCCTACACAAGTTGGTGGCACCTTTC
1 AGTCCTCAAAGAGCAGGA--C---ACCTCTT-AAAGCCCACACAAGTTGGTGGCACCTTTC
*
570403 AGTCCCCAAAGAGCAGGACACCTCTTAAAGCCCACACAAGTTGGTGGCACCTTTC
1 AGTCCTCAAAGAGCAGGACACCTCTTAAAGCCCACACAAGTTGGTGGCACCTTTC
* * * *
570458 AGTCCTCAAAGAGCAGGACGCCT-TTCAAAGCCCACACGAGTTGGTGGCACTTTTT
1 AGTCCTCAAAGAGCAGGACACCTCTT-AAAGCCCACACAAGTTGGTGGCACCTTTC
* * *
570513 ACTCCTCAATGAGAAGGA
1 AGTCCTCAAAGAGCAGGA
570531 TACACTTTAT
Statistics
Matches: 568, Mismatches: 46, Indels: 32
0.88 0.07 0.05
Matches are distributed among these distances:
54 11 0.02
55 445 0.78
56 64 0.11
57 1 0.00
59 1 0.00
60 4 0.01
61 42 0.07
ACGTcount: A:0.28, C:0.29, G:0.21, T:0.21
Consensus pattern (55 bp):
AGTCCTCAAAGAGCAGGACACCTCTTAAAGCCCACACAAGTTGGTGGCACCTTTC
Found at i:570347 original size:276 final size:277
Alignment explanation
Indices: 569846--570507 Score: 1035
Period size: 276 Copynumber: 2.4 Consensus size: 277
569836 TCCGCTTTTT
*
569846 AGTCCTCAAAGAGCAGGACACGTCTTAAAGCCCACACAAGTTGGTGGCACCTTTCAGTCCTCAAA
1 AGTCCTCAAAGAGCAGGACACCTCTTAAAGCCCACACAAGTTGGTGGCACCTTTCAGTCCTCAAA
* * *
569911 GAGCAGGACACCTCTTAAAGCCCACACAAGTTGGTGGCA-TTTTCCAGTCCTCAAAGAGCAGGAC
66 GAGCAGGACACCTCTCAAAGCCCACACAAGTTGGTGGCACCTTTCCAGTCCCCAAAGAGCAGGAC
569975 ACCTTTCAAAGCCCACACAAGTTGGTGGCATTTTCCAGTCCTCAAAGAGCAGGACACCTCTTAAA
131 ACCTTTCAAAGCCCACACAAGTTGGTGGCATTTTCCAGTCCTCAAAGAGCAGGACACCTCTTAAA
*
570040 GCCCACACAAGTTGGTGGCGCCTTCCAGTCCTCAAAGAGCAGGA-C-ACCTCTCAAAGCCCACAC
196 GCCCACACAAGTTGGTGGCACCTTCCAGTCCTCAAAGAGCAGGAGCTA-CTCTCAAAGCCCACAC
570103 AAGTTGGTGGCACCTTTCC
260 AAGTTGGTGGCACCTTT-C
** *
570122 AGTCCTCAAAGAGCAGGACACCTCTTAAAGCCCACACAAGTTGGTGGCGTCTTCCAGTCCTCAAA
1 AGTCCTCAAAGAGCAGGACACCTCTTAAAGCCCACACAAGTTGGTGGCACCTTTCAGTCCTCAAA
*
570187 GAGCAGGACACCTCTCAAAGCCCACACAAGTTGGTGGCACCTTT-CAGTCCCCGAAGAGCAGGAC
66 GAGCAGGACACCTCTCAAAGCCCACACAAGTTGGTGGCACCTTTCCAGTCCCCAAAGAGCAGGAC
* *
570251 ACCTTTCAAAGCCCACACAAGTTGGTGGCATTTTCCAGTCTTCAAAGAGCAGGACACCTTTTAAA
131 ACCTTTCAAAGCCCACACAAGTTGGTGGCATTTTCCAGTCCTCAAAGAGCAGGACACCTCTTAAA
* ** * * * *
570316 GCCCACACAGGTTGGTGGCATTTTTCAGTCCTCAAAGAGCAGGATGCTTTTTATTTTCAAAGCCT
196 GCCCACACAAGTTGGTGGCACCTTCCAGTCCTCAAAGAGCAGGA-GC----TACTCTCAAAGCCC
570381 ACACAAGTTGGTGGCACCTTTC
256 ACACAAGTTGGTGGCACCTTTC
*
570403 AGTCCCCAAAGAGCAGGACACCTCTTAAAGCCCACACAAGTTGGTGGCACCTTTCAGTCCTCAAA
1 AGTCCTCAAAGAGCAGGACACCTCTTAAAGCCCACACAAGTTGGTGGCACCTTTCAGTCCTCAAA
* * *
570468 GAGCAGGACGCCTTTCAAAGCCCACACGAGTTGGTGGCAC
66 GAGCAGGACACCTCTCAAAGCCCACACAAGTTGGTGGCAC
570508 TTTTTACTCC
Statistics
Matches: 353, Mismatches: 25, Indels: 11
0.91 0.06 0.03
Matches are distributed among these distances:
276 219 0.62
277 3 0.01
278 1 0.00
281 99 0.28
282 30 0.08
283 1 0.00
ACGTcount: A:0.28, C:0.30, G:0.21, T:0.21
Consensus pattern (277 bp):
AGTCCTCAAAGAGCAGGACACCTCTTAAAGCCCACACAAGTTGGTGGCACCTTTCAGTCCTCAAA
GAGCAGGACACCTCTCAAAGCCCACACAAGTTGGTGGCACCTTTCCAGTCCCCAAAGAGCAGGAC
ACCTTTCAAAGCCCACACAAGTTGGTGGCATTTTCCAGTCCTCAAAGAGCAGGACACCTCTTAAA
GCCCACACAAGTTGGTGGCACCTTCCAGTCCTCAAAGAGCAGGAGCTACTCTCAAAGCCCACACA
AGTTGGTGGCACCTTTC
Found at i:570425 original size:26 final size:26
Alignment explanation
Indices: 570395--570484 Score: 67
Period size: 26 Copynumber: 3.3 Consensus size: 26
570385 AAGTTGGTGG
570395 CACCTTTCAGTCCCCAAAGAGCAGGA
1 CACCTTTCAGTCCCCAAAGAGCAGGA
* * **
570421 CACCTCTTAAAG-CCCACACAAGTTGGTGG-
1 CACCT-TT-CAGTCCC-CA-AAG-AGCAGGA
*
570450 CACCTTTCAGTCCTCAAAGAGCAGGA
1 CACCTTTCAGTCCCCAAAGAGCAGGA
*
570476 CGCCTTTCA
1 CACCTTTCA
570485 AAGCCCACAC
Statistics
Matches: 47, Mismatches: 10, Indels: 14
0.66 0.14 0.20
Matches are distributed among these distances:
25 3 0.06
26 16 0.34
27 9 0.19
28 8 0.17
29 8 0.17
30 3 0.06
ACGTcount: A:0.28, C:0.33, G:0.19, T:0.20
Consensus pattern (26 bp):
CACCTTTCAGTCCCCAAAGAGCAGGA
Found at i:571357 original size:19 final size:19
Alignment explanation
Indices: 571333--571400 Score: 85
Period size: 19 Copynumber: 3.9 Consensus size: 19
571323 AATTCAATGA
571333 TTTGTATCGATACATAAGT
1 TTTGTATCGATACATAAGT
571352 TTTGTATCGATAC--AA--
1 TTTGTATCGATACATAAGT
571367 --TGTATCGATACATAAGT
1 TTTGTATCGATACATAAGT
*
571384 ATTGTATCGATACATAA
1 TTTGTATCGATACATAA
571401 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:0.35, C:0.12, G:0.15, T:0.38
Consensus pattern (19 bp):
TTTGTATCGATACATAAGT
Found at i:571371 original size:32 final size:32
Alignment explanation
Indices: 571335--571397 Score: 117
Period size: 32 Copynumber: 2.0 Consensus size: 32
571325 TTCAATGATT
*
571335 TGTATCGATACATAAGTTTTGTATCGATACAA
1 TGTATCGATACATAAGTATTGTATCGATACAA
571367 TGTATCGATACATAAGTATTGTATCGATACA
1 TGTATCGATACATAAGTATTGTATCGATACA
571398 TAATTAGCTA
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 30 1.00
ACGTcount: A:0.35, C:0.13, G:0.16, T:0.37
Consensus pattern (32 bp):
TGTATCGATACATAAGTATTGTATCGATACAA
Found at i:571372 original size:13 final size:13
Alignment explanation
Indices: 571354--571378 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
571344 ACATAAGTTT
571354 TGTATCGATACAA
1 TGTATCGATACAA
571367 TGTATCGATACA
1 TGTATCGATACA
571379 TAAGTATTGT
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:571458 original size:13 final size:13
Alignment explanation
Indices: 571440--571465 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
571430 CATTTTTCTG
571440 TGTATCGATACAT
1 TGTATCGATACAT
571453 TGTATCGATACAT
1 TGTATCGATACAT
571466 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:571462 original size:33 final size:33
Alignment explanation
Indices: 571420--571486 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
571410 GCCAAGGAAA
***
571420 TGTATCGATACATTTTTCTGTGTATCGATACAT
1 TGTATCGATACATGGATCTGTGTATCGATACAT
*
571453 TGTATCGATACATGGATCTTTGTATCGATACAT
1 TGTATCGATACATGGATCTGTGTATCGATACAT
571486 T
1 T
571487 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:574001 original size:28 final size:27
Alignment explanation
Indices: 573934--574006 Score: 94
Period size: 27 Copynumber: 2.7 Consensus size: 27
573924 CTTCACAATC
* *
573934 GGGGACACTCCAACCCCGTTAATCATC
1 GGGGATACTCCAACCCCGTTAATCATA
*
573961 GGGGATACTCCAACCCCGTTATTTC-TGA
1 GGGGATACTCCAACCCCGTTA-ATCAT-A
573989 GGGGATACTCCAACCCCG
1 GGGGATACTCCAACCCCG
574007 ACTTTATTTT
Statistics
Matches: 41, Mismatches: 3, Indels: 3
0.87 0.06 0.06
Matches are distributed among these distances:
27 21 0.51
28 20 0.49
ACGTcount: A:0.23, C:0.34, G:0.22, T:0.21
Consensus pattern (27 bp):
GGGGATACTCCAACCCCGTTAATCATA
Found at i:574051 original size:51 final size:51
Alignment explanation
Indices: 573989--574159 Score: 198
Period size: 51 Copynumber: 3.3 Consensus size: 51
573979 TTATTTCTGA
* * *
573989 GGGGATACTCCAACCCCGACTTTATTTTCAAAATATCGATTTTTCATAATC
1 GGGGATACTCCAACCCCGATTTTATTTTCAAAATACCAATTTTTCATAATC
* * * * *
574040 GGGGATACTCCAACCCCGGTTTTATTTTCACAACACCAATTTCTCCTTTAATC
1 GGGGATACTCCAACCCCGATTTTATTTTCAAAATACCAATTT-TTC-ATAATC
** * *
574093 GGGGATACTCCAATTCCGATTTTATTTCCAAAAATACCAATTTTTCACAATC
1 GGGGATACTCCAACCCCGATTTTATTTTC-AAAATACCAATTTTTCATAATC
*
574145 GAGGATACTCCAACC
1 GGGGATACTCCAACC
574160 TCGTTATTTC
Statistics
Matches: 97, Mismatches: 20, Indels: 5
0.80 0.16 0.04
Matches are distributed among these distances:
51 36 0.37
52 18 0.19
53 32 0.33
54 11 0.11
ACGTcount: A:0.29, C:0.26, G:0.12, T:0.33
Consensus pattern (51 bp):
GGGGATACTCCAACCCCGATTTTATTTTCAAAATACCAATTTTTCATAATC
Found at i:574178 original size:28 final size:28
Alignment explanation
Indices: 574142--574223 Score: 96
Period size: 28 Copynumber: 2.9 Consensus size: 28
574132 ATTTTTCACA
*
574142 ATCGAGGATACTCCAACCTCGTTATTTC
1 ATCGGGGATACTCCAACCTCGTTATTTC
* *
574170 ATCGGGGATACTCCAACCCCGTTACTTC
1 ATCGGGGATACTCCAACCTCGTTATTTC
*
574198 --CGAGGGAACACTCCAACCTCGTTATT
1 ATCG-GGG-ATACTCCAACCTCGTTATT
574224 ATCTCCAAAA
Statistics
Matches: 46, Mismatches: 6, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
26 2 0.04
27 3 0.07
28 41 0.89
ACGTcount: A:0.24, C:0.32, G:0.17, T:0.27
Consensus pattern (28 bp):
ATCGGGGATACTCCAACCTCGTTATTTC
Found at i:578556 original size:21 final size:22
Alignment explanation
Indices: 578531--578578 Score: 64
Period size: 21 Copynumber: 2.3 Consensus size: 22
578521 TTATCTTTTT
*
578531 ATCTAAC-AAATGCATTATTTC
1 ATCTAACTAAAAGCATTATTTC
*
578552 GTCT-ACTAAAAGCATTATTTC
1 ATCTAACTAAAAGCATTATTTC
578573 ATCTAA
1 ATCTAA
578579 ATTGTGATTA
Statistics
Matches: 22, Mismatches: 3, Indels: 3
0.79 0.11 0.11
Matches are distributed among these distances:
20 2 0.09
21 19 0.86
22 1 0.05
ACGTcount: A:0.38, C:0.19, G:0.06, T:0.38
Consensus pattern (22 bp):
ATCTAACTAAAAGCATTATTTC
Found at i:579397 original size:16 final size:16
Alignment explanation
Indices: 579376--579406 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
579366 CACAAAATAA
579376 TTATTTTATTATAGTT
1 TTATTTTATTATAGTT
*
579392 TTATTTTATTTTAGT
1 TTATTTTATTATAGT
579407 AAATCAAATT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.23, C:0.00, G:0.06, T:0.71
Consensus pattern (16 bp):
TTATTTTATTATAGTT
Found at i:580210 original size:107 final size:105
Alignment explanation
Indices: 580085--580418 Score: 284
Period size: 120 Copynumber: 3.0 Consensus size: 105
580075 TTTTTTATAA
*
580085 ATTAATTAAATTTTAAAAATTTAATAAATAATAATATATTAATTATTATTTTTAATA-AAAAATA
1 ATTAATT-ATTTTTAAAAA--TAATAAATAATAATATATTAATTATTATTTTTAATATAAAAATA
* * *
580149 ATATTTAATTAACTTTAAAAAAATTATATTAATAAATTAAAAT
63 ATATTTAATTAAATTTAAAAAAATTACATTAACAAATTAAAAT
* * *
580192 ATTAATTATTTTTAAAAAATAAAAAAATTAAATTAAAAAAGGTTTATTATTATTATTTTTTAATA
1 ATTAATTATTTTT-AAAAAT-AATAAA-T-AA-TAATATA---TTA--ATTATTA-TTTTTAAT-
* *
580257 AAATTAAAAATAATATTTAATTAAGTTTAAAAAAATTACATTAGCAAATTAAAAT
54 --A-TAAAAATAATATTTAATTAAATTTAAAAAAATTACATTAACAAATTAAAAT
* *
580312 ATTAATTATATATTTTTATAAA-AATAAA-AAAAAT-TATT-ATTATT-TTTTAATAATATAAAA
1 ATT-A--AT-TATTTTTAAAAATAATAAATAATAATATATTAATTATTATTTT--TAATATAAAA
*
580372 AAAGATATTTAATTAAATTTAAAAAAATTTACATTAACAAATTAAAA
60 ATA-ATATTTAATTAAATTTAAAAAAA-TTACATTAACAAATTAAAA
580419 AAATAACATT
Statistics
Matches: 187, Mismatches: 16, Indels: 47
0.75 0.06 0.19
Matches are distributed among these distances:
105 1 0.01
106 17 0.09
107 36 0.19
108 24 0.13
109 5 0.03
110 10 0.05
112 3 0.02
113 2 0.01
114 7 0.04
115 8 0.04
116 1 0.01
117 2 0.01
118 3 0.02
120 49 0.26
121 6 0.03
123 6 0.03
124 7 0.04
ACGTcount: A:0.55, C:0.01, G:0.01, T:0.42
Consensus pattern (105 bp):
ATTAATTATTTTTAAAAATAATAAATAATAATATATTAATTATTATTTTTAATATAAAAATAATA
TTTAATTAAATTTAAAAAAATTACATTAACAAATTAAAAT
Found at i:580316 original size:53 final size:52
Alignment explanation
Indices: 580259--580418 Score: 126
Period size: 53 Copynumber: 3.0 Consensus size: 52
580249 TTTTAATAAA
*
580259 ATTAAAAATAATATTTAATTAAGTTTAAAAAAATTACATTAGCAAATTAAAAT
1 ATTAAAAATAATATTTAATTAAATTTAAAAAAATTACATTA-CAAATTAAAAT
** * * * * * ****
580312 ATTAATTAT-ATATTTTTATAAAAATAAAAAAAATTATTATTATTTTTTAATAAT
1 ATTAAAAATAATA-TTTAATTAAATTTAAAAAAATTA-CATTACAAATTAA-AAT
*
580366 A-TAAAAAAAGATATTTAATTAAATTTAAAAAAATTTACATTAACAAATTAAAA
1 ATTAAAAATA-ATATTTAATTAAATTTAAAAAAA-TTACATT-ACAAATTAAAA
580419 AAATAACATT
Statistics
Matches: 76, Mismatches: 24, Indels: 13
0.67 0.21 0.12
Matches are distributed among these distances:
52 3 0.04
53 33 0.43
54 29 0.38
55 11 0.14
ACGTcount: A:0.56, C:0.03, G:0.02, T:0.39
Consensus pattern (52 bp):
ATTAAAAATAATATTTAATTAAATTTAAAAAAATTACATTACAAATTAAAAT
Found at i:580359 original size:31 final size:32
Alignment explanation
Indices: 580307--580374 Score: 79
Period size: 31 Copynumber: 2.2 Consensus size: 32
580297 TTAGCAAATT
*
580307 AAAATATTAATTATATATTTTT-ATAAAAATAA
1 AAAAAATTAATTATATATTTTTAAT-AAAATAA
*
580339 AAAAAATT-ATTAT-TATTTTTTAATAATATAA
1 AAAAAATTAATTATATA-TTTTTAATAAAATAA
580370 AAAAA
1 AAAAA
580375 GATATTTAAT
Statistics
Matches: 32, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
30 2 0.06
31 21 0.66
32 9 0.28
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (32 bp):
AAAAAATTAATTATATATTTTTAATAAAATAA
Found at i:580416 original size:23 final size:24
Alignment explanation
Indices: 580390--580448 Score: 77
Period size: 23 Copynumber: 2.5 Consensus size: 24
580380 TTAATTAAAT
*
580390 TTAAAAAAATTTACA-TTAACAAA
1 TTAAAAAAATTAACATTTAACAAA
**
580413 TTAAAAAAA-TAACATTTAAGGAA
1 TTAAAAAAATTAACATTTAACAAA
580436 TTAAAAAAATTAA
1 TTAAAAAAATTAA
580449 TATTATTCAA
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
22 4 0.13
23 24 0.77
24 3 0.10
ACGTcount: A:0.63, C:0.05, G:0.03, T:0.29
Consensus pattern (24 bp):
TTAAAAAAATTAACATTTAACAAA
Found at i:580441 original size:107 final size:107
Alignment explanation
Indices: 580237--580442 Score: 258
Period size: 107 Copynumber: 1.9 Consensus size: 107
580227 AAAAAGGTTT
* * *
580237 ATTATTATTATTTTTTAATAAAATTAAAAATAATATTTAATTAAGTTTAAAAAAATTACATTAGC
1 ATTATTATTATTTTTTAATAAAATTAAAAAAAATATTTAATTAAATTTAAAAAAATTACATTAAC
* * ****
580302 AAATTAAAATATTAATTATATATTTTTATAAAAATAAAAAAA
66 AAATTAAAAAATAAATTATATAGGAATATAAAAATAAAAAAA
*
580344 ATTATTATTATTTTTTAATAATA-TAAAAAAAGATATTTAATTAAATTTAAAAAAATTTACATTA
1 ATTATTATTATTTTTTAATAAAATTAAAAAAA-ATATTTAATTAAATTTAAAAAAA-TTACATTA
580408 ACAAATTAAAAAAATAACATT-TA-AGGAAT-TAAAAA
64 ACAAATT-AAAAAATAA-ATTATATAGGAATATAAAAA
580443 AATTAATATT
Statistics
Matches: 85, Mismatches: 10, Indels: 8
0.83 0.10 0.08
Matches are distributed among these distances:
106 7 0.08
107 50 0.59
108 16 0.19
109 9 0.11
110 3 0.04
ACGTcount: A:0.55, C:0.02, G:0.02, T:0.40
Consensus pattern (107 bp):
ATTATTATTATTTTTTAATAAAATTAAAAAAAATATTTAATTAAATTTAAAAAAATTACATTAAC
AAATTAAAAAATAAATTATATAGGAATATAAAAATAAAAAAA
Found at i:580902 original size:121 final size:124
Alignment explanation
Indices: 580704--581060 Score: 434
Period size: 121 Copynumber: 2.9 Consensus size: 124
580694 AAAAAATATT
* * *
580704 ATTATAATAAAAAA-AATTTTAATTTAAAA-TTTTTA-TTTTA-AGAAACATAATAATTAATATT
1 ATTATAATAAAAAACATTTTTATTTTAAAATTTTTTATTTTTATAAAAACATAATAATTAATATT
580765 TTAATTTGTTAATGTAAATTTTTAAACTTAATTAAATATT-TTTTTATTTTATT-AAAA
66 TTAATTTGTTAATGTAAATTTTTAAACTTAATTAAATATTATTTTTATTTTATTAAAAA
580822 ATTATAATAAAAAACATTTTTATTTTAAAATTTTTTATTTTTATAAAAACATAATAATTAA-ATT
1 ATTATAATAAAAAACATTTTTATTTTAAAATTTTTTATTTTTATAAAAACATAATAATTAATATT
* *
580886 TTAATTTGTTATTGT-AATTTTATAAACTTAAGTAAATATTATTTTTAATTTTATTAAAAA
66 TTAATTTGTTAATGTAAATTTT-TAAACTTAATTAAATATTATTTTT-ATTTTATTAAAAA
* * * *
580946 ATAATAATAATAAACCCTTTTTATTTTATTTAAATTTTTT-TATTT-T-AAAA-A-AATAATTAA
1 ATTATAATAA-AAAACATTTTTATTTTA---AAATTTTTTATTTTTATAAAAACATAATAATTAA
* * * *
581006 TATTTTAATTTATTAATATAATTTTTTTAAAAGTTAATTAAATATTATTTTTATT
62 TATTTTAATTTGTTAATGTAA-ATTTTT-AAACTTAATTAAATATTATTTTTATT
581061 AAAAATAATA
Statistics
Matches: 208, Mismatches: 15, Indels: 25
0.84 0.06 0.10
Matches are distributed among these distances:
118 14 0.07
119 13 0.06
120 12 0.06
121 39 0.19
122 21 0.10
123 17 0.08
124 29 0.14
125 24 0.12
126 26 0.12
127 4 0.02
128 9 0.04
ACGTcount: A:0.44, C:0.02, G:0.02, T:0.52
Consensus pattern (124 bp):
ATTATAATAAAAAACATTTTTATTTTAAAATTTTTTATTTTTATAAAAACATAATAATTAATATT
TTAATTTGTTAATGTAAATTTTTAAACTTAATTAAATATTATTTTTATTTTATTAAAAA
Found at i:581072 original size:29 final size:26
Alignment explanation
Indices: 581012--581066 Score: 67
Period size: 26 Copynumber: 2.1 Consensus size: 26
581002 TTAATATTTT
*
581012 AATTTATT-AATATAATTTTTTTAAA
1 AATTAATTAAATATAATTTTTTTAAA
* *
581037 AGTTAATTAAATATTATTTTTATTAAA
1 AATTAATTAAATATAATTTTT-TTAAA
581064 AAT
1 AAT
581067 AATAATTATT
Statistics
Matches: 24, Mismatches: 4, Indels: 2
0.80 0.13 0.07
Matches are distributed among these distances:
25 6 0.25
26 11 0.46
27 7 0.29
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.53
Consensus pattern (26 bp):
AATTAATTAAATATAATTTTTTTAAA
Found at i:581076 original size:25 final size:26
Alignment explanation
Indices: 581020--581077 Score: 66
Period size: 26 Copynumber: 2.3 Consensus size: 26
581010 TTAATTTATT
* *
581020 AATATAATTTTTTTAAAAGTTAATTA
1 AATATTATTTTTTTAAAAGATAATTA
581046 AATATTATTTTTATTAAAA-ATAA-TA
1 AATATTATTTTT-TTAAAAGATAATTA
*
581071 ATTATTA
1 AATATTA
581078 CATTATTATT
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
25 8 0.29
26 14 0.50
27 6 0.21
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (26 bp):
AATATTATTTTTTTAAAAGATAATTA
Found at i:581516 original size:18 final size:18
Alignment explanation
Indices: 581492--581538 Score: 76
Period size: 18 Copynumber: 2.6 Consensus size: 18
581482 AAATGCATAT
581492 ATTCTTACTGAGAATCAG
1 ATTCTTACTGAGAATCAG
*
581510 GTTCTTACTGAGAATCAG
1 ATTCTTACTGAGAATCAG
*
581528 ATTCTTTCTGA
1 ATTCTTACTGA
581539 TATTGTGCAT
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 26 1.00
ACGTcount: A:0.28, C:0.17, G:0.17, T:0.38
Consensus pattern (18 bp):
ATTCTTACTGAGAATCAG
Found at i:581614 original size:11 final size:11
Alignment explanation
Indices: 581598--581634 Score: 56
Period size: 11 Copynumber: 3.4 Consensus size: 11
581588 TTATTACTTT
581598 TTATTTATAAA
1 TTATTTATAAA
* *
581609 TTATTTTTAAT
1 TTATTTATAAA
581620 TTATTTATAAA
1 TTATTTATAAA
581631 TTAT
1 TTAT
581635 ACAAATTTAT
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
11 22 1.00
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (11 bp):
TTATTTATAAA
Found at i:583249 original size:13 final size:13
Alignment explanation
Indices: 583231--583256 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
583221 CAATTTTTTG
583231 TGTATCGATACAT
1 TGTATCGATACAT
583244 TGTATCGATACAT
1 TGTATCGATACAT
583257 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:583321 original size:21 final size:21
Alignment explanation
Indices: 583295--583370 Score: 91
Period size: 21 Copynumber: 3.7 Consensus size: 21
583285 CTGCCAAGAA
*
583295 ATGTATCGATACATCTTTTTT
1 ATGTATCGATACATCTTTTTC
* ****
583316 ATGTATTGATACAT-TGCAAC
1 ATGTATCGATACATCTTTTTC
583336 ATGTATCGATACATCTTTTTC
1 ATGTATCGATACATCTTTTTC
583357 ATGTATCGATACAT
1 ATGTATCGATACAT
583371 TGCAACATGT
Statistics
Matches: 43, Mismatches: 11, Indels: 2
0.77 0.20 0.04
Matches are distributed among these distances:
20 14 0.33
21 29 0.67
ACGTcount: A:0.29, C:0.16, G:0.12, T:0.43
Consensus pattern (21 bp):
ATGTATCGATACATCTTTTTC
Found at i:583341 original size:20 final size:20
Alignment explanation
Indices: 583316--583388 Score: 92
Period size: 20 Copynumber: 3.6 Consensus size: 20
583306 CATCTTTTTT
*
583316 ATGTATTGATACATTGCAAC
1 ATGTATCGATACATTGCAAC
****
583336 ATGTATCGATACATCTTTTTC
1 ATGTATCGATACAT-TGCAAC
583357 ATGTATCGATACATTGCAAC
1 ATGTATCGATACATTGCAAC
583377 ATGTATCGATAC
1 ATGTATCGATAC
583389 TTTGAATTGT
Statistics
Matches: 43, Mismatches: 9, Indels: 2
0.80 0.17 0.04
Matches are distributed among these distances:
20 27 0.63
21 16 0.37
ACGTcount: A:0.32, C:0.18, G:0.14, T:0.37
Consensus pattern (20 bp):
ATGTATCGATACATTGCAAC
Found at i:583352 original size:41 final size:41
Alignment explanation
Indices: 583295--583388 Score: 170
Period size: 41 Copynumber: 2.3 Consensus size: 41
583285 CTGCCAAGAA
* *
583295 ATGTATCGATACATCTTTTTTATGTATTGATACATTGCAAC
1 ATGTATCGATACATCTTTTTCATGTATCGATACATTGCAAC
583336 ATGTATCGATACATCTTTTTCATGTATCGATACATTGCAAC
1 ATGTATCGATACATCTTTTTCATGTATCGATACATTGCAAC
583377 ATGTATCGATAC
1 ATGTATCGATAC
583389 TTTGAATTGT
Statistics
Matches: 51, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
41 51 1.00
ACGTcount: A:0.30, C:0.17, G:0.13, T:0.40
Consensus pattern (41 bp):
ATGTATCGATACATCTTTTTCATGTATCGATACATTGCAAC
Found at i:585835 original size:13 final size:13
Alignment explanation
Indices: 585817--585854 Score: 67
Period size: 13 Copynumber: 2.9 Consensus size: 13
585807 ATAAACACCC
585817 TGTATCGATACAG
1 TGTATCGATACAG
*
585830 TGTATCGATACAT
1 TGTATCGATACAG
585843 TGTATCGATACA
1 TGTATCGATACA
585855 AATAAAAATG
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
13 24 1.00
ACGTcount: A:0.32, C:0.16, G:0.18, T:0.34
Consensus pattern (13 bp):
TGTATCGATACAG
Found at i:587954 original size:15 final size:15
Alignment explanation
Indices: 587934--587964 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
587924 ATTTCGTTTG
*
587934 GAGCTTCTTCATTTT
1 GAGCTTCCTCATTTT
587949 GAGCTTCCTCATTTT
1 GAGCTTCCTCATTTT
587964 G
1 G
587965 GACATTTTTA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.13, C:0.23, G:0.16, T:0.48
Consensus pattern (15 bp):
GAGCTTCCTCATTTT
Found at i:589796 original size:21 final size:21
Alignment explanation
Indices: 589767--589811 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 21
589757 AAGTTTTCAT
*
589767 TTTTCTTAGCTAAC-TCATTA
1 TTTTCTTAGCCAACTTCATTA
*
589787 TTTTCATTAGCCAACTTCTTTA
1 TTTTC-TTAGCCAACTTCATTA
589809 TTT
1 TTT
589812 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:591968 original size:13 final size:13
Alignment explanation
Indices: 591950--591975 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
591940 CAATTTTTTG
591950 TGTATCGATACAT
1 TGTATCGATACAT
591963 TGTATCGATACAT
1 TGTATCGATACAT
591976 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:592040 original size:21 final size:21
Alignment explanation
Indices: 592014--592089 Score: 100
Period size: 21 Copynumber: 3.7 Consensus size: 21
592004 CTGCCAAGAA
*
592014 ATGTATCGATACATCTTTTTT
1 ATGTATCGATACATCTTTTTC
****
592035 ATGTATCGATACAT-TGCAAC
1 ATGTATCGATACATCTTTTTC
592055 ATGTATCGATACATCTTTTTC
1 ATGTATCGATACATCTTTTTC
592076 ATGTATCGATACAT
1 ATGTATCGATACAT
592090 TGCAACATGT
Statistics
Matches: 45, Mismatches: 9, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
20 15 0.33
21 30 0.67
ACGTcount: A:0.29, C:0.17, G:0.12, T:0.42
Consensus pattern (21 bp):
ATGTATCGATACATCTTTTTC
Found at i:592060 original size:20 final size:20
Alignment explanation
Indices: 592035--592107 Score: 101
Period size: 20 Copynumber: 3.6 Consensus size: 20
592025 CATCTTTTTT
592035 ATGTATCGATACATTGCAAC
1 ATGTATCGATACATTGCAAC
****
592055 ATGTATCGATACATCTTTTTC
1 ATGTATCGATACAT-TGCAAC
592076 ATGTATCGATACATTGCAAC
1 ATGTATCGATACATTGCAAC
592096 ATGTATCGATAC
1 ATGTATCGATAC
592108 TTTGAATTGT
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:0.32, C:0.19, G:0.14, T:0.36
Consensus pattern (20 bp):
ATGTATCGATACATTGCAAC
Found at i:592071 original size:41 final size:41
Alignment explanation
Indices: 592014--592107 Score: 179
Period size: 41 Copynumber: 2.3 Consensus size: 41
592004 CTGCCAAGAA
*
592014 ATGTATCGATACATCTTTTTTATGTATCGATACATTGCAAC
1 ATGTATCGATACATCTTTTTCATGTATCGATACATTGCAAC
592055 ATGTATCGATACATCTTTTTCATGTATCGATACATTGCAAC
1 ATGTATCGATACATCTTTTTCATGTATCGATACATTGCAAC
592096 ATGTATCGATAC
1 ATGTATCGATAC
592108 TTTGAATTGT
Statistics
Matches: 52, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
41 52 1.00
ACGTcount: A:0.30, C:0.18, G:0.13, T:0.39
Consensus pattern (41 bp):
ATGTATCGATACATCTTTTTCATGTATCGATACATTGCAAC
Found at i:594302 original size:281 final size:284
Alignment explanation
Indices: 593762--594327 Score: 904
Period size: 281 Copynumber: 2.0 Consensus size: 284
593752 CATAAATATG
* * * *
593762 AGGCCCGTTATATTTTTTTAATCTCCCATACTTGTTTTTTTTTCAATAATGTTGCTCTTACACTT
1 AGGCCCATTATATTTTTCTAATCTCCCATACTTG-TTTTTTTTCAACAATGTTGCTCTTACACTC
* * *
593827 CAATTGCACCCTTACCCATACATTAGACATTTACTATGGTATTGCTTCATGTTAGATTCTATTAC
65 CAATTGCACCCTTACCCATACATTAGACACTTACCATGGTATTGCTTCAGGTTAGATTCTATTAC
* *
593892 TTTGTAATCTACAGAGTTTTTGATGTTATAGTACTTTATAGCTGAAACCATGGCCTCTTTCATTG
130 TCTATAATCTACAGAGTTTTTGATGTTATAGTACTTTATAGCTGAAACCATGGCCTCTTTCATTG
** *
593957 CAAATTGTATCCCAACACAGAGATCACCGCTAGATGGATTCCAGCTTGTTAGTACACCTAATGTT
195 CAAATTACATCCCAACACAGAGATCACCGCTAGATGGATTCCAGCTTGTTAGCACACCTAATGTT
*
594022 TGAACATATTCTGAAAATTCTGGCA
260 TGAACATATTCTAAAAATTCTGGCA
*
594047 AGGCCCATTATA-TTTTCTAATCTCCCATACTTG-TTTTTTTCAACAATGTTGGTCTTACACTCC
1 AGGCCCATTATATTTTTCTAATCTCCCATACTTGTTTTTTTTCAACAATGTTGCTCTTACACTCC
**
594110 AATTGCACCCTTACCCATACATTAGACACTTACCATGGTA-TGCTTTGGGTTAGATTCTATTACT
66 AATTGCACCCTTACCCATACATTAGACACTTACCATGGTATTGCTTCAGGTTAGATTCTATTACT
* * *
594174 CTATAATCTACAGAGTTTTTGATGTTATAGTGCTTTATAGCTGAAACCATGGCCTTTTTCGTTGC
131 CTATAATCTACAGAGTTTTTGATGTTATAGTACTTTATAGCTGAAACCATGGCCTCTTTCATTGC
* * *
594239 AAATTACATTCCAATACAGAGATCACCGCTAGATGGATTCTAGCTTGTTAGCACACCTAATGTTT
196 AAATTACATCCCAACACAGAGATCACCGCTAGATGGATTCCAGCTTGTTAGCACACCTAATGTTT
594304 GAACATATTCTAAAAATTCTGGCA
261 GAACATATTCTAAAAATTCTGGCA
594328 TATGCATTTC
Statistics
Matches: 259, Mismatches: 22, Indels: 4
0.91 0.08 0.01
Matches are distributed among these distances:
281 163 0.63
282 65 0.25
284 20 0.08
285 11 0.04
ACGTcount: A:0.27, C:0.21, G:0.14, T:0.38
Consensus pattern (284 bp):
AGGCCCATTATATTTTTCTAATCTCCCATACTTGTTTTTTTTCAACAATGTTGCTCTTACACTCC
AATTGCACCCTTACCCATACATTAGACACTTACCATGGTATTGCTTCAGGTTAGATTCTATTACT
CTATAATCTACAGAGTTTTTGATGTTATAGTACTTTATAGCTGAAACCATGGCCTCTTTCATTGC
AAATTACATCCCAACACAGAGATCACCGCTAGATGGATTCCAGCTTGTTAGCACACCTAATGTTT
GAACATATTCTAAAAATTCTGGCA
Found at i:594724 original size:29 final size:29
Alignment explanation
Indices: 594688--594767 Score: 83
Period size: 31 Copynumber: 2.7 Consensus size: 29
594678 TTTTTTATAA
*
594688 ATTAATTAAATTTTAAAAAATAATAATGT
1 ATTAATTAAATTTTAAAAAATAATAATAT
*
594717 ATTAATTATTATTTTTAATAAAA-AATAATAT
1 ATTAATTA--AATTTTAA-AAAATAATAATAT
* *
594748 -TTAATTAACTTTAAAAAAAT
1 ATTAATTAAATTTTAAAAAAT
594768 TTATATTAAC
Statistics
Matches: 43, Mismatches: 4, Indels: 9
0.77 0.07 0.16
Matches are distributed among these distances:
27 4 0.09
28 6 0.14
29 8 0.19
30 7 0.16
31 14 0.33
32 4 0.09
ACGTcount: A:0.54, C:0.01, G:0.01, T:0.44
Consensus pattern (29 bp):
ATTAATTAAATTTTAAAAAATAATAATAT
Found at i:595098 original size:124 final size:123
Alignment explanation
Indices: 594733--595100 Score: 444
Period size: 124 Copynumber: 3.0 Consensus size: 123
594723 TATTATTTTT
* * *
594733 AATAAAAAATAATATTTAATTAACTTTAAAAAAATTTATATTAACAAATCAAAATATT-A--ATT
1 AATAAAAAATAATATTTAATTAAGTTT--AAAAATTTAAATTAACAAATTAAAATATTAATTATT
* * * ***
594795 AT-TTTTTAAAAATAAAAAAATTAAATAAAAATAAAAAGGGATTATTAT-TATTTTTTAATAA
64 ATGTTTTTTAAAATAAAAAATTTAAAT-TAAA-AAAAATTTATTATTATATA-TTTTTAATAA
* *
594856 AATTAAAAAATAATATTTAATTAAGTTTAAAAAATTAAATTAACAAATTAAAAT-TTAATTGTTA
1 AA-TAAAAAATAATATTTAATTAAGTTTAAAAATTTAAATTAACAAATTAAAATATTAATTATTA
* ** *
594920 TGTTTTTATAAAAATAAAAAATTTTAAAATAAAAAATGTTTTTTATTATA-ATTTTTAATAA
65 TGTTTTT-T-AAAATAAAAAA-TTTAAATTAAAAAAAATTTATTATTATATATTTTTAATAA
*
594981 AATAAAAAATAATATTTAATTAAGTTTAAAAATTTACATTAACAAATTAAAATATTAATTATTAT
1 AATAAAAAATAATATTTAATTAAGTTTAAAAATTTAAATTAACAAATTAAAATATTAATTATTAT
*
595046 GTTTTTTAAAATAAAAAATTTAAATTAAAAAAAATTTATTATAATAATATTTTTA
66 GTTTTTTAAAATAAAAAATTTAAATTAAAAAAAATTTATTATTAT-ATATTTTTA
595101 TTTTTTAAAT
Statistics
Matches: 210, Mismatches: 23, Indels: 23
0.82 0.09 0.09
Matches are distributed among these distances:
121 2 0.01
122 46 0.22
123 14 0.07
124 85 0.40
125 33 0.16
126 11 0.05
127 14 0.07
128 5 0.02
ACGTcount: A:0.55, C:0.02, G:0.02, T:0.41
Consensus pattern (123 bp):
AATAAAAAATAATATTTAATTAAGTTTAAAAATTTAAATTAACAAATTAAAATATTAATTATTAT
GTTTTTTAAAATAAAAAATTTAAATTAAAAAAAATTTATTATTATATATTTTTAATAA
Done.