Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01001448.1 Hibiscus syriacus cultivar Beakdansim tig00002799_pilon, whole genome shotgun sequence
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: 1849635
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 4 of 9
Found at i:874379 original size:32 final size:31
Alignment explanation
Indices: 874343--874419 Score: 91
Period size: 31 Copynumber: 2.5 Consensus size: 31
874333 CGGGGCCGTG
*
874343 GGGCCTACCTAAGAACACATCTTAGGGCCGCA
1 GGGCCTACCTAAGAA-ACATCTCAGGGCCGCA
** **
874375 GGGCCTACCCGAGAATGATCTCAGGGCCGCA
1 GGGCCTACCTAAGAAACATCTCAGGGCCGCA
*
874406 GAGCCTACCTAAGA
1 GGGCCTACCTAAGA
874420 GTCACATTAG
Statistics
Matches: 37, Mismatches: 8, Indels: 1
0.80 0.17 0.02
Matches are distributed among these distances:
31 24 0.65
32 13 0.35
ACGTcount: A:0.27, C:0.31, G:0.27, T:0.14
Consensus pattern (31 bp):
GGGCCTACCTAAGAAACATCTCAGGGCCGCA
Found at i:874402 original size:63 final size:63
Alignment explanation
Indices: 874296--874419 Score: 153
Period size: 63 Copynumber: 2.0 Consensus size: 63
874286 CCCTAAGGGA
* * ** *
874296 ACATCTTAGGGCCTGAGAGCCTACCCAAGATAGATTTCGGGGCCGTGGGGCCTACCTAAGAAC
1 ACATCTTAGGGCCTGAGAGCCTACCCAAGATAGATCTCAGGGCCGCAGAGCCTACCTAAGAAC
* *
874359 ACATCTTAGGGCC-GCAGGGCCTACCCGAGA-ATGATCTCAGGGCCGCAGAGCCTACCTAAGA
1 ACATCTTAGGGCCTG-AGAGCCTACCCAAGATA-GATCTCAGGGCCGCAGAGCCTACCTAAGA
874420 GTCACATTAG
Statistics
Matches: 52, Mismatches: 7, Indels: 4
0.83 0.11 0.06
Matches are distributed among these distances:
62 2 0.04
63 50 0.96
ACGTcount: A:0.26, C:0.29, G:0.28, T:0.17
Consensus pattern (63 bp):
ACATCTTAGGGCCTGAGAGCCTACCCAAGATAGATCTCAGGGCCGCAGAGCCTACCTAAGAAC
Found at i:875311 original size:13 final size:13
Alignment explanation
Indices: 875293--875318 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
875283 AAGAAAGTCA
875293 ACGGTCAACGGTC
1 ACGGTCAACGGTC
875306 ACGGTCAACGGTC
1 ACGGTCAACGGTC
875319 GGGTCGGGTC
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:0.23, C:0.31, G:0.31, T:0.15
Consensus pattern (13 bp):
ACGGTCAACGGTC
Found at i:875330 original size:17 final size:17
Alignment explanation
Indices: 875308--875365 Score: 107
Period size: 17 Copynumber: 3.4 Consensus size: 17
875298 CAACGGTCAC
875308 GGTCAACGGTCGGGTCG
1 GGTCAACGGTCGGGTCG
875325 GGTCAACGGTCGGGTCG
1 GGTCAACGGTCGGGTCG
*
875342 GGTCAACAGTCGGGTCG
1 GGTCAACGGTCGGGTCG
875359 GGTCAAC
1 GGTCAAC
875366 CCGGTTCAGA
Statistics
Matches: 40, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
17 40 1.00
ACGTcount: A:0.16, C:0.24, G:0.43, T:0.17
Consensus pattern (17 bp):
GGTCAACGGTCGGGTCG
Found at i:875335 original size:7 final size:7
Alignment explanation
Indices: 875289--875318 Score: 53
Period size: 7 Copynumber: 4.4 Consensus size: 7
875279 GTCAAAGAAA
875289 GTCAACG
1 GTCAACG
875296 GTCAACG
1 GTCAACG
875303 GTC-ACG
1 GTCAACG
875309 GTCAACG
1 GTCAACG
875316 GTC
1 GTC
875319 GGGTCGGGTC
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
6 6 0.27
7 16 0.73
ACGTcount: A:0.23, C:0.30, G:0.30, T:0.17
Consensus pattern (7 bp):
GTCAACG
Found at i:875383 original size:19 final size:19
Alignment explanation
Indices: 875359--875448 Score: 119
Period size: 19 Copynumber: 4.7 Consensus size: 19
875349 AGTCGGGTCG
*
875359 GGTCAACCCGGTTCAGACC
1 GGTCAAACCGGTTCAGACC
875378 GGTCAAACCGGTTCAGACC
1 GGTCAAACCGGTTCAGACC
*
875397 GGTCAAACTGGTTC-GAACC
1 GGTCAAACCGGTTCAG-ACC
* *
875416 GGTCAAACCGGTTCAAAACT
1 GGTCAAACCGGTTC-AGACC
875436 GGTCAAACCGGTT
1 GGTCAAACCGGTT
875449 TTCCAGCAGC
Statistics
Matches: 63, Mismatches: 5, Indels: 5
0.86 0.07 0.07
Matches are distributed among these distances:
18 1 0.02
19 47 0.75
20 15 0.24
ACGTcount: A:0.27, C:0.29, G:0.26, T:0.19
Consensus pattern (19 bp):
GGTCAAACCGGTTCAGACC
Found at i:875389 original size:9 final size:9
Alignment explanation
Indices: 875359--875447 Score: 79
Period size: 9 Copynumber: 9.3 Consensus size: 9
875349 AGTCGGGTCG
*
875359 GGTCAACCC
1 GGTCAAACC
*
875368 GGTTCAGACC
1 GG-TCAAACC
875378 GGTCAAACC
1 GGTCAAACC
*
875387 GGTTCAGACC
1 GG-TCAAACC
*
875397 GGTCAAACT
1 GGTCAAACC
*
875406 GGTTCGAACC
1 GG-TCAAACC
875416 GGTCAAACC
1 GGTCAAACC
*
875425 GGTTCAAAACT
1 GG-TC-AAACC
875436 GGTCAAACC
1 GGTCAAACC
875445 GGT
1 GGT
875448 TTTCCAGCAG
Statistics
Matches: 64, Mismatches: 11, Indels: 10
0.75 0.13 0.12
Matches are distributed among these distances:
9 32 0.50
10 26 0.41
11 6 0.09
ACGTcount: A:0.27, C:0.29, G:0.26, T:0.18
Consensus pattern (9 bp):
GGTCAAACC
Found at i:875415 original size:29 final size:30
Alignment explanation
Indices: 875394--875448 Score: 71
Period size: 29 Copynumber: 1.9 Consensus size: 30
875384 ACCGGTTCAG
*
875394 ACCGG-TC-AAACTGGTTCGAACCGG-TCAA
1 ACCGGTTCAAAACTGG-TCAAACCGGTTCAA
875422 ACCGGTTCAAAACTGGTCAAACCGGTT
1 ACCGGTTCAAAACTGGTCAAACCGGTT
875449 TTCCAGCAGC
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
28 5 0.22
29 10 0.43
30 8 0.35
ACGTcount: A:0.29, C:0.27, G:0.24, T:0.20
Consensus pattern (30 bp):
ACCGGTTCAAAACTGGTCAAACCGGTTCAA
Found at i:881727 original size:32 final size:31
Alignment explanation
Indices: 881691--881767 Score: 91
Period size: 31 Copynumber: 2.5 Consensus size: 31
881681 CGGGGCCGTG
*
881691 GGGCCTACCTAAGAACACATCTTAGGGCCGCA
1 GGGCCTACCTAAGAA-ACATCTCAGGGCCGCA
** **
881723 GGGCCTACCCGAGAATGATCTCAGGGCCGCA
1 GGGCCTACCTAAGAAACATCTCAGGGCCGCA
*
881754 GAGCCTACCTAAGA
1 GGGCCTACCTAAGA
881768 GTCACATTAG
Statistics
Matches: 37, Mismatches: 8, Indels: 1
0.80 0.17 0.02
Matches are distributed among these distances:
31 24 0.65
32 13 0.35
ACGTcount: A:0.27, C:0.31, G:0.27, T:0.14
Consensus pattern (31 bp):
GGGCCTACCTAAGAAACATCTCAGGGCCGCA
Found at i:881750 original size:63 final size:63
Alignment explanation
Indices: 881644--881767 Score: 153
Period size: 63 Copynumber: 2.0 Consensus size: 63
881634 CCCTAAGGGA
* * ** *
881644 ACATCTTAGGGCCTGAGAGCCTACCCAAGATAGATTTCGGGGCCGTGGGGCCTACCTAAGAAC
1 ACATCTTAGGGCCTGAGAGCCTACCCAAGATAGATCTCAGGGCCGCAGAGCCTACCTAAGAAC
* *
881707 ACATCTTAGGGCC-GCAGGGCCTACCCGAGA-ATGATCTCAGGGCCGCAGAGCCTACCTAAGA
1 ACATCTTAGGGCCTG-AGAGCCTACCCAAGATA-GATCTCAGGGCCGCAGAGCCTACCTAAGA
881768 GTCACATTAG
Statistics
Matches: 52, Mismatches: 7, Indels: 4
0.83 0.11 0.06
Matches are distributed among these distances:
62 2 0.04
63 50 0.96
ACGTcount: A:0.26, C:0.29, G:0.28, T:0.17
Consensus pattern (63 bp):
ACATCTTAGGGCCTGAGAGCCTACCCAAGATAGATCTCAGGGCCGCAGAGCCTACCTAAGAAC
Found at i:882659 original size:13 final size:13
Alignment explanation
Indices: 882641--882666 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
882631 AAGAAAGTCA
882641 ACGGTCAACGGTC
1 ACGGTCAACGGTC
882654 ACGGTCAACGGTC
1 ACGGTCAACGGTC
882667 GGGTCGGGTC
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:0.23, C:0.31, G:0.31, T:0.15
Consensus pattern (13 bp):
ACGGTCAACGGTC
Found at i:882678 original size:17 final size:17
Alignment explanation
Indices: 882656--882713 Score: 107
Period size: 17 Copynumber: 3.4 Consensus size: 17
882646 CAACGGTCAC
882656 GGTCAACGGTCGGGTCG
1 GGTCAACGGTCGGGTCG
882673 GGTCAACGGTCGGGTCG
1 GGTCAACGGTCGGGTCG
*
882690 GGTCAACAGTCGGGTCG
1 GGTCAACGGTCGGGTCG
882707 GGTCAAC
1 GGTCAAC
882714 CCGGTTCAGA
Statistics
Matches: 40, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
17 40 1.00
ACGTcount: A:0.16, C:0.24, G:0.43, T:0.17
Consensus pattern (17 bp):
GGTCAACGGTCGGGTCG
Found at i:882683 original size:7 final size:7
Alignment explanation
Indices: 882637--882666 Score: 53
Period size: 7 Copynumber: 4.4 Consensus size: 7
882627 GTCAAAGAAA
882637 GTCAACG
1 GTCAACG
882644 GTCAACG
1 GTCAACG
882651 GTC-ACG
1 GTCAACG
882657 GTCAACG
1 GTCAACG
882664 GTC
1 GTC
882667 GGGTCGGGTC
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
6 6 0.27
7 16 0.73
ACGTcount: A:0.23, C:0.30, G:0.30, T:0.17
Consensus pattern (7 bp):
GTCAACG
Found at i:882731 original size:19 final size:19
Alignment explanation
Indices: 882707--882778 Score: 119
Period size: 19 Copynumber: 3.8 Consensus size: 19
882697 AGTCGGGTCG
*
882707 GGTCAACCCGGTTCAGACC
1 GGTCAAACCGGTTCAGACC
882726 GGTCAAACCGGTTCAGACC
1 GGTCAAACCGGTTCAGACC
882745 GGTCAAACCGGTTC-GAACC
1 GGTCAAACCGGTTCAG-ACC
882764 GGTCAAACCGGTTCA
1 GGTCAAACCGGTTCA
882779 AAACTGGTTA
Statistics
Matches: 50, Mismatches: 1, Indels: 3
0.93 0.02 0.06
Matches are distributed among these distances:
18 1 0.02
19 49 0.98
ACGTcount: A:0.25, C:0.32, G:0.26, T:0.17
Consensus pattern (19 bp):
GGTCAAACCGGTTCAGACC
Found at i:882737 original size:9 final size:9
Alignment explanation
Indices: 882707--882795 Score: 79
Period size: 9 Copynumber: 9.3 Consensus size: 9
882697 AGTCGGGTCG
*
882707 GGTCAACCC
1 GGTCAAACC
*
882716 GGTTCAGACC
1 GG-TCAAACC
882726 GGTCAAACC
1 GGTCAAACC
*
882735 GGTTCAGACC
1 GG-TCAAACC
882745 GGTCAAACC
1 GGTCAAACC
*
882754 GGTTCGAACC
1 GG-TCAAACC
882764 GGTCAAACC
1 GGTCAAACC
*
882773 GGTTCAAAACT
1 GG-TC-AAACC
*
882784 GGTTAAACC
1 GGTCAAACC
882793 GGT
1 GGT
882796 TTTCCAGCAG
Statistics
Matches: 65, Mismatches: 10, Indels: 10
0.76 0.12 0.12
Matches are distributed among these distances:
9 33 0.51
10 26 0.40
11 6 0.09
ACGTcount: A:0.27, C:0.29, G:0.26, T:0.18
Consensus pattern (9 bp):
GGTCAAACC
Found at i:890699 original size:19 final size:20
Alignment explanation
Indices: 890672--890710 Score: 53
Period size: 19 Copynumber: 2.0 Consensus size: 20
890662 CAACTCGAAG
*
890672 TCAATTCGAG-TCGAATTTT
1 TCAAGTCGAGATCGAATTTT
*
890691 TCAAGTCGAGATCGAGTTTT
1 TCAAGTCGAGATCGAATTTT
890711 GCTCACCCCT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
19 9 0.53
20 8 0.47
ACGTcount: A:0.26, C:0.15, G:0.21, T:0.38
Consensus pattern (20 bp):
TCAAGTCGAGATCGAATTTT
Found at i:896370 original size:15 final size:15
Alignment explanation
Indices: 896350--896390 Score: 82
Period size: 15 Copynumber: 2.7 Consensus size: 15
896340 TGTTTCTTTT
896350 TCATTATCTAAGCCA
1 TCATTATCTAAGCCA
896365 TCATTATCTAAGCCA
1 TCATTATCTAAGCCA
896380 TCATTATCTAA
1 TCATTATCTAA
896391 TCCAAATGCG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 26 1.00
ACGTcount: A:0.34, C:0.24, G:0.05, T:0.37
Consensus pattern (15 bp):
TCATTATCTAAGCCA
Found at i:896784 original size:12 final size:12
Alignment explanation
Indices: 896767--896803 Score: 56
Period size: 12 Copynumber: 3.1 Consensus size: 12
896757 TTGTTAAATA
896767 GGAGGTGGGTTT
1 GGAGGTGGGTTT
896779 GGAGGTGGGTTT
1 GGAGGTGGGTTT
* *
896791 GGTGGTCGGTTT
1 GGAGGTGGGTTT
896803 G
1 G
896804 AACGACTAGA
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
12 23 1.00
ACGTcount: A:0.05, C:0.03, G:0.57, T:0.35
Consensus pattern (12 bp):
GGAGGTGGGTTT
Found at i:897518 original size:23 final size:23
Alignment explanation
Indices: 897490--897548 Score: 100
Period size: 23 Copynumber: 2.6 Consensus size: 23
897480 ACCCTCATGG
897490 GGGTATCGGTACCCATTCAAAGA
1 GGGTATCGGTACCCATTCAAAGA
*
897513 GGGTATCGGTACCCATTCAAAGG
1 GGGTATCGGTACCCATTCAAAGA
*
897536 GGGTATCGATACC
1 GGGTATCGGTACC
897549 TAGCATACAT
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
23 34 1.00
ACGTcount: A:0.27, C:0.22, G:0.29, T:0.22
Consensus pattern (23 bp):
GGGTATCGGTACCCATTCAAAGA
Found at i:901242 original size:20 final size:21
Alignment explanation
Indices: 901204--901242 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 21
901194 AAGTTTTCAT
* *
901204 ATCATCAATTTTCTTTTGATG
1 ATCATCAATTTACTCTTGATG
901225 ATCATC-ATTTACTCTTGA
1 ATCATCAATTTACTCTTGA
901243 AAATTAGTTA
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 10 0.62
21 6 0.38
ACGTcount: A:0.26, C:0.18, G:0.08, T:0.49
Consensus pattern (21 bp):
ATCATCAATTTACTCTTGATG
Found at i:907589 original size:101 final size:101
Alignment explanation
Indices: 907386--907591 Score: 360
Period size: 101 Copynumber: 2.0 Consensus size: 101
907376 CTCTCTGACA
*
907386 ACTACAACTATCACAAGTATTCATATTTTAGTGATCATTTATGTAATTTACCTTATAATATGTAT
1 ACTACAACTATCACAAGTATTCATATTATAGTGATCATTTATGTAATTTACCTTATAATATGTAT
**
907451 TTTTTTAATTAATTATTAATATCTAATTTTTTTTCG
66 TTTTTTAATTAATTATTAATATCTAATTTTTGATCG
907487 ACTACAACTATCACAAGTATTCATATTATAGTGATCATTTATGTAATTTACCTTATAATATGTA-
1 ACTACAACTATCACAAGTATTCATATTATAGTGATCATTTATGTAATTTACCTTATAATATGTAT
*
907551 TTTTTTAATTAATTATTAGTATCTAATTTATTGATCG
66 TTTTTTAATTAATTATTAATATCTAATTT-TTGATCG
907588 ACTA
1 ACTA
907592 ATCCAAATTG
Statistics
Matches: 100, Mismatches: 4, Indels: 2
0.94 0.04 0.02
Matches are distributed among these distances:
100 28 0.28
101 72 0.72
ACGTcount: A:0.34, C:0.11, G:0.07, T:0.48
Consensus pattern (101 bp):
ACTACAACTATCACAAGTATTCATATTATAGTGATCATTTATGTAATTTACCTTATAATATGTAT
TTTTTTAATTAATTATTAATATCTAATTTTTGATCG
Found at i:908529 original size:38 final size:38
Alignment explanation
Indices: 908485--908610 Score: 130
Period size: 38 Copynumber: 3.3 Consensus size: 38
908475 ATTTCTAATT
*
908485 TATATATTTTTAATAAAATTTATATATAAATAATTTAA
1 TATATATTTTTAATAAAATTTATATATAAATAAATTAA
* * * * *
908523 TATATATTTTT-ATTACATTTA-ATTTTTAATAAATTATT
1 TATATATTTTTAATAAAATTTATA-TATAAATAAATTA-A
* * * *
908561 TATATATTTTTAATAAATTTTTTACATAAATAACTTAA
1 TATATATTTTTAATAAAATTTATATATAAATAAATTAA
908599 TATATATTTTTA
1 TATATATTTTTA
908611 TTATATTTAT
Statistics
Matches: 69, Mismatches: 15, Indels: 8
0.75 0.16 0.09
Matches are distributed among these distances:
36 1 0.01
37 18 0.26
38 34 0.49
39 15 0.22
40 1 0.01
ACGTcount: A:0.43, C:0.02, G:0.00, T:0.55
Consensus pattern (38 bp):
TATATATTTTTAATAAAATTTATATATAAATAAATTAA
Found at i:908557 original size:11 final size:11
Alignment explanation
Indices: 908543--908582 Score: 55
Period size: 11 Copynumber: 3.6 Consensus size: 11
908533 TATTACATTT
908543 AATTTTTAATA
1 AATTTTTAATA
908554 AATTATTT-ATA
1 AATT-TTTAATA
*
908565 TATTTTTAATA
1 AATTTTTAATA
908576 AATTTTT
1 AATTTTT
908583 TACATAAATA
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
10 3 0.12
11 19 0.76
12 3 0.12
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (11 bp):
AATTTTTAATA
Found at i:908565 original size:76 final size:75
Alignment explanation
Indices: 908482--908625 Score: 234
Period size: 76 Copynumber: 1.9 Consensus size: 75
908472 GTTATTTCTA
* *
908482 ATTTATATATTTTTAATAAAATTTATATATAAATAATTTAATATATATTTTTATTACATTTAATT
1 ATTTATATATTTTTAATAAAATTTATACATAAATAACTTAATATATATTTTTATTACATTT-ATT
908547 TTTAATAAATT
65 TTTAATAAATT
* * *
908558 ATTTATATATTTTTAATAAATTTTTTACATAAATAACTTAATATATATTTTTATTATATTTATTT
1 ATTTATATATTTTTAATAAAATTTATACATAAATAACTTAATATATATTTTTATTACATTTATTT
908623 TTA
66 TTA
908626 TTTCTTGAAA
Statistics
Matches: 63, Mismatches: 5, Indels: 1
0.91 0.07 0.01
Matches are distributed among these distances:
75 7 0.11
76 56 0.89
ACGTcount: A:0.41, C:0.02, G:0.00, T:0.57
Consensus pattern (75 bp):
ATTTATATATTTTTAATAAAATTTATACATAAATAACTTAATATATATTTTTATTACATTTATTT
TTAATAAATT
Found at i:908569 original size:27 final size:27
Alignment explanation
Indices: 908490--908569 Score: 69
Period size: 27 Copynumber: 3.0 Consensus size: 27
908480 TAATTTATAT
*
908490 ATTTTTAATAAA--ATTTATATA-TAA
1 ATTTTTAATAAATTATTTATATATTTA
* *
908514 ATAATTTAATATATATT-TTTATTACATTTA
1 AT-TTTTAATA-A-ATTATTTA-TATATTTA
908544 ATTTTTAATAAATTATTTATATATTT
1 ATTTTTAATAAATTATTTATATATTT
908570 TTAATAAATT
Statistics
Matches: 43, Mismatches: 5, Indels: 13
0.70 0.08 0.21
Matches are distributed among these distances:
24 2 0.05
25 7 0.16
26 1 0.02
27 10 0.23
28 9 0.21
29 10 0.23
30 4 0.09
ACGTcount: A:0.42, C:0.01, G:0.00, T:0.56
Consensus pattern (27 bp):
ATTTTTAATAAATTATTTATATATTTA
Found at i:908589 original size:13 final size:12
Alignment explanation
Indices: 908545--908591 Score: 53
Period size: 12 Copynumber: 4.0 Consensus size: 12
908535 TTACATTTAA
908545 TTTTTAATAAAT
1 TTTTTAATAAAT
* *
908557 TATTT-ATATA-
1 TTTTTAATAAAT
908567 TTTTTAATAAAT
1 TTTTTAATAAAT
908579 TTTTTACATAAAT
1 TTTTTA-ATAAAT
908592 AACTTAATAT
Statistics
Matches: 28, Mismatches: 4, Indels: 5
0.76 0.11 0.14
Matches are distributed among these distances:
10 4 0.14
11 8 0.29
12 10 0.36
13 6 0.21
ACGTcount: A:0.40, C:0.02, G:0.00, T:0.57
Consensus pattern (12 bp):
TTTTTAATAAAT
Found at i:908621 original size:15 final size:15
Alignment explanation
Indices: 908598--908627 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
908588 AAATAACTTA
908598 ATATATATTTTTATT
1 ATATATATTTTTATT
*
908613 ATATTTATTTTTATT
1 ATATATATTTTTATT
908628 TCTTGAAATT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (15 bp):
ATATATATTTTTATT
Found at i:909895 original size:28 final size:28
Alignment explanation
Indices: 909854--909937 Score: 150
Period size: 28 Copynumber: 3.0 Consensus size: 28
909844 ATATATTTTC
909854 ATCTCCTAAAATTTTATAAATTTAAATTT
1 ATCT-CTAAAATTTTATAAATTTAAATTT
909883 ATCTCTAAAATTTTATAAATTTAAATTT
1 ATCTCTAAAATTTTATAAATTTAAATTT
*
909911 ATCTCTAAAATTTTATAAAATTAAATT
1 ATCTCTAAAATTTTATAAATTTAAATT
909938 CATTCCCCTA
Statistics
Matches: 54, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
28 50 0.93
29 4 0.07
ACGTcount: A:0.44, C:0.08, G:0.00, T:0.48
Consensus pattern (28 bp):
ATCTCTAAAATTTTATAAATTTAAATTT
Found at i:909951 original size:56 final size:54
Alignment explanation
Indices: 909854--909958 Score: 124
Period size: 56 Copynumber: 1.9 Consensus size: 54
909844 ATATATTTTC
* * *
909854 ATCTCCTAAAATTTTATAAATTTAAATTTATCTCTAAAATTTTATAAATTTAAATTT
1 ATCTCCTAAAATTTTATAAAATTAAATTCATCCCT-AAA-TTTA-AAATTTAAATTT
909911 ATCT-CTAAAATTTTATAAAATTAAATTCATTCCCCT-AATTTAAAATTT
1 ATCTCCTAAAATTTTATAAAATTAAATTCA-T-CCCTAAATTTAAAATTT
909959 TGCGTCCATT
Statistics
Matches: 43, Mismatches: 3, Indels: 7
0.81 0.06 0.13
Matches are distributed among these distances:
54 6 0.14
55 4 0.09
56 25 0.58
57 5 0.12
58 3 0.07
ACGTcount: A:0.42, C:0.11, G:0.00, T:0.47
Consensus pattern (54 bp):
ATCTCCTAAAATTTTATAAAATTAAATTCATCCCTAAATTTAAAATTTAAATTT
Found at i:923853 original size:14 final size:14
Alignment explanation
Indices: 923834--923860 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
923824 TACATTTTCA
923834 TTCTTCATTCTTTG
1 TTCTTCATTCTTTG
923848 TTCTTCATTCTTT
1 TTCTTCATTCTTT
923861 ACATTCATTT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.07, C:0.22, G:0.04, T:0.67
Consensus pattern (14 bp):
TTCTTCATTCTTTG
Found at i:928351 original size:105 final size:105
Alignment explanation
Indices: 928169--928438 Score: 443
Period size: 105 Copynumber: 2.6 Consensus size: 105
928159 CAACAACTAT
* *
928169 AATTCACTCAAGAATGAGGTGAATCAACATTTCCAGAAGAGTTCATAATGAGAAGAACTCGTCCT
1 AATTCACCCCAGAATGAGGTGAATCAACATTTCCAGAAGAGTTCATAATGAGAAGAACTCGTCCT
*
928234 AAAGGAGAAGGTTCGTAATGAGAAGAGCCTATTCCTTTCA
66 AAAGAAGAAGGTTCGTAATGAGAAGAGCCTATTCCTTTCA
* *
928274 AATTCACCCTAGAAATGAGGTGAATCGACATTTCCAGAAGAGTTCA-AATGAGAAGAACTCGTCC
1 AATTCACCCCAG-AATGAGGTGAATCAACATTTCCAGAAGAGTTCATAATGAGAAGAACTCGTCC
* * * *
928338 TAAATAAGAAGGTTCGTAATGAGAAGATCTTGTTCCTTTCA
65 TAAAGAAGAAGGTTCGTAATGAGAAGAGCCTATTCCTTTCA
928379 AATTCACCCCAGAATGAGGTGAATCAACATTTCCAGAAGAGTTCATAATGAGAAGAACTC
1 AATTCACCCCAGAATGAGGTGAATCAACATTTCCAGAAGAGTTCATAATGAGAAGAACTC
928439 ATCCGAAAAA
Statistics
Matches: 153, Mismatches: 10, Indels: 4
0.92 0.06 0.02
Matches are distributed among these distances:
104 32 0.21
105 89 0.58
106 32 0.21
ACGTcount: A:0.37, C:0.18, G:0.20, T:0.25
Consensus pattern (105 bp):
AATTCACCCCAGAATGAGGTGAATCAACATTTCCAGAAGAGTTCATAATGAGAAGAACTCGTCCT
AAAGAAGAAGGTTCGTAATGAGAAGAGCCTATTCCTTTCA
Found at i:928484 original size:105 final size:101
Alignment explanation
Indices: 928169--928484 Score: 356
Period size: 105 Copynumber: 3.0 Consensus size: 101
928159 CAACAACTAT
*
928169 AATTCACTCAAGAATGAGGTGAATCAACATTTCCAGAAGAGTTCATAATGAGAAGAACTCGTCC-
1 AATTCACCCAAGAATGAGGTGAATCAACATTTCCAGAAGAGTTCATAATGAGAAGAACTCGTCCA
*
928233 TAAAGGAGAAGGTTCGTAATGAGAAGAGCCTATTCCT-TTCA
66 AAAAGGAGAAGGTTCGTAATGAGAAGA----ATT--TGTTCA
* *
928274 AATTCACCCTAGAAATGAGGTGAATCGACATTTCCAGAAGAGTTCA-AATGAGAAGAACTCGTCC
1 AATTCACCCAAG-AATGAGGTGAATCAACATTTCCAGAAGAGTTCATAATGAGAAGAACTCGTCC
*
928338 TAAATA--AGAAGGTTCGTAATGAGAAG-ATCTTGTTCCTTTCA
65 -AAAAAGGAGAAGGTTCGTAATGAGAAGAAT-TTG-----TTCA
* *
928379 AATTCACCCCAGAATGAGGTGAATCAACATTTCCAGAAGAGTTCATAATGAGAAGAACTCATCCG
1 AATTCACCCAAGAATGAGGTGAATCAACATTTCCAGAAGAGTTCATAATGAGAAGAACTCGTCC-
*
928444 AAAAAAGGAGAAGAAGTTCATAATGAGAAGAATTTGTTCA
65 -AAAAAGGAGAAG--GTTCGTAATGAGAAGAATTTGTTCA
928484 A
1 A
928485 CCTTAGCTCG
Statistics
Matches: 183, Mismatches: 11, Indels: 34
0.80 0.05 0.15
Matches are distributed among these distances:
99 1 0.01
100 2 0.01
101 1 0.01
104 32 0.17
105 85 0.46
106 36 0.20
107 2 0.01
108 5 0.03
110 17 0.09
111 2 0.01
ACGTcount: A:0.39, C:0.16, G:0.20, T:0.24
Consensus pattern (101 bp):
AATTCACCCAAGAATGAGGTGAATCAACATTTCCAGAAGAGTTCATAATGAGAAGAACTCGTCCA
AAAAGGAGAAGGTTCGTAATGAGAAGAATTTGTTCA
Found at i:941683 original size:41 final size:44
Alignment explanation
Indices: 941597--941686 Score: 114
Period size: 41 Copynumber: 2.1 Consensus size: 44
941587 ACGTTTATCT
* * * *
941597 AAAAAAATTATGAGCCTTAATTATAAAGGTAGAAAGTGAGATTG
1 AAAAAAATTATGAACCTCAATTATAAAGATAAAAAGTGAGATTG
*
941641 AAAAAAA-TA-GAACCTCAATTAT-AAGATAAAAAGTGATATTG
1 AAAAAAATTATGAACCTCAATTATAAAGATAAAAAGTGAGATTG
941682 AAAAA
1 AAAAA
941687 TTAGGGTCAT
Statistics
Matches: 41, Mismatches: 5, Indels: 3
0.84 0.10 0.06
Matches are distributed among these distances:
41 21 0.51
42 11 0.27
43 2 0.05
44 7 0.17
ACGTcount: A:0.54, C:0.06, G:0.16, T:0.24
Consensus pattern (44 bp):
AAAAAAATTATGAACCTCAATTATAAAGATAAAAAGTGAGATTG
Found at i:941756 original size:22 final size:21
Alignment explanation
Indices: 941731--941798 Score: 57
Period size: 22 Copynumber: 3.1 Consensus size: 21
941721 ATTATAAAGA
941731 TAAAAAATAAAACTAAAAAAAT
1 TAAAAAATAAAA-TAAAAAAAT
* * * *
941753 TAAAAGATTCAATTATAAAAA-
1 TAAAA-AATAAAATAAAAAAAT
*
941774 TAAAAAATATATATAAAAAAAT
1 TAAAAAATA-AAATAAAAAAAT
941796 TAA
1 TAA
941799 GAGCCCTAAA
Statistics
Matches: 34, Mismatches: 9, Indels: 6
0.69 0.18 0.12
Matches are distributed among these distances:
20 2 0.06
21 13 0.38
22 15 0.44
23 4 0.12
ACGTcount: A:0.71, C:0.03, G:0.01, T:0.25
Consensus pattern (21 bp):
TAAAAAATAAAATAAAAAAAT
Found at i:969361 original size:36 final size:36
Alignment explanation
Indices: 969299--969466 Score: 203
Period size: 36 Copynumber: 4.6 Consensus size: 36
969289 TAAAGGTTGG
* *
969299 TGTTTCAAGGGAAAGTGTCTCAAGGGAGACAAAATT
1 TGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATT
* * * *
969335 TGTTTCAAGTGAAACTATCTCGAGGGAGACGAAATTT
1 TGTTTCAAGAGAAACTGTCTCAAGGGAGAC-AAAATT
**
969372 TGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAGCT
1 TGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATT
* * * *
969408 TATTTCAAGGGAAATTGTCTCAAGGGAGACAGAATT
1 TGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATT
969444 TGTTTCAAGAGAAAC-GATCTCAA
1 TGTTTCAAGAGAAACTG-TCTCAA
969467 AGATTTATGT
Statistics
Matches: 111, Mismatches: 19, Indels: 4
0.83 0.14 0.03
Matches are distributed among these distances:
35 1 0.01
36 78 0.70
37 32 0.29
ACGTcount: A:0.36, C:0.14, G:0.24, T:0.26
Consensus pattern (36 bp):
TGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATT
Found at i:969434 original size:73 final size:72
Alignment explanation
Indices: 969299--969466 Score: 214
Period size: 73 Copynumber: 2.3 Consensus size: 72
969289 TAAAGGTTGG
* * * * * *
969299 TGTTTCAAGGGAAAGTGTCTCAAGGGAGACAAAATTTGTTTCAAGTGAAACTATCTCGAGGGAGA
1 TGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAACTTATTTCAAGGGAAACTATCTCAAGGGAGA
969364 C-GAAATTT
66 CAG-AA-TT
* * *
969372 TGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAGCTTATTTCAAGGGAAATTGTCTCAAGGGAGA
1 TGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAACTTATTTCAAGGGAAACTATCTCAAGGGAGA
969437 CAGAATT
66 CAGAATT
969444 TGTTTCAAGAGAAAC-GATCTCAA
1 TGTTTCAAGAGAAACTG-TCTCAA
969467 AGATTTATGT
Statistics
Matches: 84, Mismatches: 9, Indels: 5
0.86 0.09 0.05
Matches are distributed among these distances:
71 1 0.01
72 23 0.27
73 59 0.70
74 1 0.01
ACGTcount: A:0.36, C:0.14, G:0.24, T:0.26
Consensus pattern (72 bp):
TGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAACTTATTTCAAGGGAAACTATCTCAAGGGAGA
CAGAATT
Found at i:971021 original size:32 final size:32
Alignment explanation
Indices: 970975--971199 Score: 364
Period size: 32 Copynumber: 7.1 Consensus size: 32
970965 GAGTCGATGG
*
970975 TTACCTATGTTCTTCGCGACATATGGACATGA
1 TTACCTATGTTCTTCGGGACATATGGACATGA
*
971007 TTACTTATGTTCTTCGGGACATATGGACATGA
1 TTACCTATGTTCTTCGGGACATATGGACATGA
*
971039 TTACCTATGTTCTTCGGGACATATGGACAGGA
1 TTACCTATGTTCTTCGGGACATATGGACATGA
*
971071 TTACCTATGTTCTTTGGGACATATGGACATGA
1 TTACCTATGTTCTTCGGGACATATGGACATGA
* *
971103 TTACCTATATTCTTCGGGACATATGGACAAGA
1 TTACCTATGTTCTTCGGGACATATGGACATGA
*
971135 TTACCTATGTTCTTCGGGACATATGAACAT-A
1 TTACCTATGTTCTTCGGGACATATGGACATGA
*
971166 TTACCTATGTTCTTCGGAACATATGGACA-GA
1 TTACCTATGTTCTTCGGGACATATGGACATGA
971197 TTA
1 TTA
971200 TTATACGAGC
Statistics
Matches: 178, Mismatches: 14, Indels: 3
0.91 0.07 0.02
Matches are distributed among these distances:
31 32 0.18
32 146 0.82
ACGTcount: A:0.27, C:0.18, G:0.20, T:0.35
Consensus pattern (32 bp):
TTACCTATGTTCTTCGGGACATATGGACATGA
Found at i:972065 original size:18 final size:18
Alignment explanation
Indices: 972042--972078 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
972032 TTTGAATCAG
*
972042 TACTGTTCACGGTATTAT
1 TACTGTTCACAGTATTAT
*
972060 TACTGTTTACAGTATTAT
1 TACTGTTCACAGTATTAT
972078 T
1 T
972079 CATACAATAT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.24, C:0.14, G:0.14, T:0.49
Consensus pattern (18 bp):
TACTGTTCACAGTATTAT
Found at i:972611 original size:20 final size:20
Alignment explanation
Indices: 972583--972633 Score: 84
Period size: 20 Copynumber: 2.5 Consensus size: 20
972573 TCATCTTGCT
*
972583 CGAAAGACTTATAGATGACC
1 CGAATGACTTATAGATGACC
*
972603 CGAATGACTTATAGATGGCC
1 CGAATGACTTATAGATGACC
972623 CGAATGACTTA
1 CGAATGACTTA
972634 CGTCATACTC
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 29 1.00
ACGTcount: A:0.35, C:0.20, G:0.22, T:0.24
Consensus pattern (20 bp):
CGAATGACTTATAGATGACC
Found at i:972859 original size:102 final size:102
Alignment explanation
Indices: 972672--972914 Score: 389
Period size: 102 Copynumber: 2.4 Consensus size: 102
972662 CCGAAGGACT
* * * *
972672 TAATTATCAAGAAACTCTTGAAAATCAAGCTTAGTTTCTTAGTTGTCATCAAGGAACCCCTAAAT
1 TAATCATCAAGAAACCCCTGAAAATCAAGCTTAGTTTCTTAGTTGTCATCAAGGAACCCCTAAAA
*
972737 ATTAGGCTTAGCTTTCTTTTTTAAAAACTCTTTAGAGA
66 ATTAGGCTTAGCTTTATTTTTTAAAAACT-TTTAGAGA
*
972775 TAATCATCAAGAAACCCCTGAAAATC-AGCTTATTTTCTTAGTTGTCATCAAGGAACCCCTAAAA
1 TAATCATCAAGAAACCCCTGAAAATCAAGCTTAGTTTCTTAGTTGTCATCAAGGAACCCCTAAAA
*
972839 ATTAGGCTTAGCTTTATTTTTTTAAAACTTTTAGAGA
66 ATTAGGCTTAGCTTTATTTTTTAAAAACTTTTAGAGA
**
972876 TAATCATCAAGAAACCCCTGAAAATCGGGCTTAGTTTCT
1 TAATCATCAAGAAACCCCTGAAAATCAAGCTTAGTTTCT
972915 AAACCTCATT
Statistics
Matches: 130, Mismatches: 9, Indels: 3
0.92 0.06 0.02
Matches are distributed among these distances:
101 34 0.26
102 73 0.56
103 23 0.18
ACGTcount: A:0.34, C:0.18, G:0.13, T:0.35
Consensus pattern (102 bp):
TAATCATCAAGAAACCCCTGAAAATCAAGCTTAGTTTCTTAGTTGTCATCAAGGAACCCCTAAAA
ATTAGGCTTAGCTTTATTTTTTAAAAACTTTTAGAGA
Found at i:973031 original size:22 final size:22
Alignment explanation
Indices: 972972--973034 Score: 60
Period size: 22 Copynumber: 3.0 Consensus size: 22
972962 AATGACTTAT
*
972972 CATCTTGCTCGAAAGACTTA-A
1 CATCATGCTCGAAAGACTTACA
* * *
972993 -A-GATGGCCCGAAGGACTTACA
1 CATCAT-GCTCGAAAGACTTACA
973014 CATCATGCTCGAAAGACTTAC
1 CATCATGCTCGAAAGACTTAC
973035 TGATGGCCTG
Statistics
Matches: 31, Mismatches: 7, Indels: 7
0.69 0.16 0.16
Matches are distributed among these distances:
19 1 0.03
20 13 0.42
21 1 0.03
22 14 0.45
23 2 0.06
ACGTcount: A:0.33, C:0.25, G:0.19, T:0.22
Consensus pattern (22 bp):
CATCATGCTCGAAAGACTTACA
Found at i:973040 original size:42 final size:42
Alignment explanation
Indices: 972947--973060 Score: 158
Period size: 42 Copynumber: 2.7 Consensus size: 42
972937 TCCCGAATGT
* * *
972947 CTTATAGATGGCCCGAATGACTTA-TCATCTTGCTCGAAAGA
1 CTTAAAGATGGCCCGAAGGACTTACTCATCATGCTCGAAAGA
*
972988 CTTAAAGATGGCCCGAAGGACTTACACATCATGCTCGAAAGA
1 CTTAAAGATGGCCCGAAGGACTTACTCATCATGCTCGAAAGA
** *
973030 CTTACTGATGGCCTGAAGGACTTACTCATCA
1 CTTAAAGATGGCCCGAAGGACTTACTCATCA
973061 AGAAACCCTT
Statistics
Matches: 64, Mismatches: 8, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
41 22 0.34
42 42 0.66
ACGTcount: A:0.31, C:0.24, G:0.20, T:0.25
Consensus pattern (42 bp):
CTTAAAGATGGCCCGAAGGACTTACTCATCATGCTCGAAAGA
Found at i:973179 original size:21 final size:21
Alignment explanation
Indices: 973154--973215 Score: 55
Period size: 21 Copynumber: 3.2 Consensus size: 21
973144 GGAAACTATC
973154 TCAAGAGAGACAAAACTTGTT
1 TCAAGAGAGACAAAACTTGTT
* *
973175 TCAAG-G-G---AAAC-TATC
1 TCAAGAGAGACAAAACTTGTT
*
973190 TCAAGAGAGACAAAACTCGTT
1 TCAAGAGAGACAAAACTTGTT
973211 TCAAG
1 TCAAG
973216 GGAAACAATC
Statistics
Matches: 30, Mismatches: 5, Indels: 12
0.64 0.11 0.26
Matches are distributed among these distances:
15 7 0.23
16 5 0.17
17 1 0.03
19 1 0.03
20 5 0.17
21 11 0.37
ACGTcount: A:0.42, C:0.18, G:0.19, T:0.21
Consensus pattern (21 bp):
TCAAGAGAGACAAAACTTGTT
Found at i:973182 original size:36 final size:36
Alignment explanation
Indices: 973100--973387 Score: 301
Period size: 36 Copynumber: 8.2 Consensus size: 36
973090 TTAAAATCTT
* *
973100 TTGTTTCGAGGGAAACTATCTCAAGGGAGAC--AAC
1 TTGTTTCAAGGGAAACTATCTCAAGAGAGACAAAAC
*
973134 ATGTTTCAAGGGAAACTATCTCAAGAGAGACAAAAC
1 TTGTTTCAAGGGAAACTATCTCAAGAGAGACAAAAC
973170 TTGTTTCAAGGGAAACTATCTCAAGAGAGACAAAAC
1 TTGTTTCAAGGGAAACTATCTCAAGAGAGACAAAAC
* *
973206 TCGTTTCAAGGGAAACAATCTCAAGAGAGACAAAA-
1 TTGTTTCAAGGGAAACTATCTCAAGAGAGACAAAAC
* ***
973241 TTCGTTTCAAGGGAAA-TATTTTC-A-A-AG--TTTA-
1 TT-GTTTCAAGGGAAACTA-TCTCAAGAGAGACAAAAC
* * * * *
973272 -TGTTTCAAGAGAAACTTTCTCAAGGGAGGCAAAAT
1 TTGTTTCAAGGGAAACTATCTCAAGAGAGACAAAAC
* *
973307 TTGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAAT
1 TTGTTTCAAGGGAAACTATCTCAAGAGAGACAAAAC
* * * *
973343 TTGTTTCAAGGGAAACTGTCTTAAGAGAGATAAAAT
1 TTGTTTCAAGGGAAACTATCTCAAGAGAGACAAAAC
973379 TTGTTTCAA
1 TTGTTTCAA
973388 AGAAAACGTT
Statistics
Matches: 217, Mismatches: 25, Indels: 22
0.82 0.09 0.08
Matches are distributed among these distances:
29 15 0.07
30 3 0.01
31 1 0.00
32 2 0.01
33 2 0.01
34 30 0.14
35 3 0.01
36 161 0.74
ACGTcount: A:0.39, C:0.14, G:0.21, T:0.26
Consensus pattern (36 bp):
TTGTTTCAAGGGAAACTATCTCAAGAGAGACAAAAC
Found at i:973313 original size:65 final size:65
Alignment explanation
Indices: 973208--973580 Score: 322
Period size: 65 Copynumber: 5.6 Consensus size: 65
973198 GACAAAACTC
* ** *
973208 GTTTCAAGGGAAACAATCTCAAGAGAGACAAAA-TTCGTTTCAAGGGAAATATTTTCAAAG-TTT
1 GTTTCAAGAGAAACTGTCTCAAGAGAGACAAAACTT-GTTTCAAGGGAAACATTTTCAAAGATTT
973271 AT
65 -T
* * * * *
973273 GTTTCAAGAGAAACTTTCTCAAGGGAGGCAAAATTTGTTTCAAGGGAAAC-TGTCTCAAGAGAGA
1 GTTTCAAGAGAAACTGTCTCAAGAGAGACAAAACTTGTTTCAAGGGAAACAT-TTTC-A-A-AG-
*
973337 CAAAATTT
61 ---ATTTT
* * * * * * * *
973345 GTTTCAAGGGAAACTGTCTTAAGAGAGATAAAATTTGTTTCAAAGAAAACGTTCTCAAAG-TTTA
1 GTTTCAAGAGAAACTGTCTCAAGAGAGACAAAACTTGTTTCAAGGGAAACATTTTCAAAGATTT-
973409 T
65 T
* * * ** *
973410 GTTTCAAAAGAAACTGTCTCAAAAGAGACAAAACCTGTTTCAAGATAAACATATTCAAAGATTTT
1 GTTTCAAGAGAAACTGTCTCAAGAGAGACAAAACTTGTTTCAAGGGAAACATTTTCAAAGATTTT
* * * *** *
973475 GTTTCAAGGGAAACAGTCTCAAGAGAGACAAAACTTGTTTAAAGGGAAACGGATTCAAAGATTGG
1 GTTTCAAGAGAAACTGTCTCAAGAGAGACAAAACTTGTTTCAAGGGAAACATTTTCAAAGATT-T
973540 T
65 T
*
973541 GTTTCAAGAGAAACTGTCTCAAGGGAGACAAAACTTGTTT
1 GTTTCAAGAGAAACTGTCTCAAGAGAGACAAAACTTGTTT
973581 GAGTAAAAAT
Statistics
Matches: 250, Mismatches: 44, Indels: 27
0.78 0.14 0.08
Matches are distributed among these distances:
64 3 0.01
65 146 0.58
66 44 0.18
67 1 0.00
68 2 0.01
69 2 0.01
70 1 0.00
71 1 0.00
72 47 0.19
73 3 0.01
ACGTcount: A:0.39, C:0.13, G:0.20, T:0.28
Consensus pattern (65 bp):
GTTTCAAGAGAAACTGTCTCAAGAGAGACAAAACTTGTTTCAAGGGAAACATTTTCAAAGATTTT
Found at i:973313 original size:101 final size:101
Alignment explanation
Indices: 973171--973357 Score: 293
Period size: 101 Copynumber: 1.9 Consensus size: 101
973161 AGACAAAACT
*
973171 TGTTTCAAGGGAAACTATCTCAAGAGAGACAAAACTCGTTTCAAGGGAAACAATCTCAAGAGAGA
1 TGTTTCAAGAGAAACTATCTCAAGAGAGACAAAACTCGTTTCAAGGGAAACAATCTCAAGAGAGA
973236 CAAAATTCGTTTCAAGGGAAATATTTTCAAAGTTTA
66 CAAAATTCGTTTCAAGGGAAATATTTTCAAAGTTTA
* * * * * **
973272 TGTTTCAAGAGAAACTTTCTCAAGGGAGGCAAAATTTGTTTCAAGGGAAACTGTCTCAAGAGAGA
1 TGTTTCAAGAGAAACTATCTCAAGAGAGACAAAACTCGTTTCAAGGGAAACAATCTCAAGAGAGA
*
973337 CAAAATTTGTTTCAAGGGAAA
66 CAAAATTCGTTTCAAGGGAAA
973358 CTGTCTTAAG
Statistics
Matches: 77, Mismatches: 9, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
101 77 1.00
ACGTcount: A:0.39, C:0.14, G:0.21, T:0.26
Consensus pattern (101 bp):
TGTTTCAAGAGAAACTATCTCAAGAGAGACAAAACTCGTTTCAAGGGAAACAATCTCAAGAGAGA
CAAAATTCGTTTCAAGGGAAATATTTTCAAAGTTTA
Found at i:973385 original size:137 final size:137
Alignment explanation
Indices: 973134--973611 Score: 524
Period size: 137 Copynumber: 3.5 Consensus size: 137
973124 GGGAGACAAC
* * *
973134 ATGTTTCAAGGGAAACTATCTCAAGAGAGACAAAACTTGTTTCAAGGGAAACTATCTCAAGAGAG
1 ATGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAACTTGTTTCAAGAGAAACTATCTCAAGAGAG
* * * * **
973199 ACAAAACTCGTTTCAAGGGAAACAATCTCAAGAGAGACAAAATTCGTTTCAAGGGAAATATTTTC
66 ACAAAATTTGTTTCAAGGGAAACAGTCTCAAGAGAGACAAAATTTGTTTCAAGGGAAACGTTTTC
973264 AAAGTTT
131 AAAGTTT
* * * * * *
973271 ATGTTTCAAGAGAAACTTTCTCAAGGGAGGCAAAATTTGTTTCAAGGGAAACTGTCTCAAGAGAG
1 ATGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAACTTGTTTCAAGAGAAACTATCTCAAGAGAG
* * * * * *
973336 ACAAAATTTGTTTCAAGGGAAACTGTCTTAAGAGAGATAAAATTTGTTTCAAAGAAAACGTTCTC
66 ACAAAATTTGTTTCAAGGGAAACAGTCTCAAGAGAGACAAAATTTGTTTCAAGGGAAACGTTTTC
973401 AAAGTTT
131 AAAGTTT
* * * *
973408 ATGTTTCAAAAGAAACTGTCTCAAAAGAGACAAAACCTGTTTCAAGATAAACATAT-TC-A-A-A
1 ATGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAACTTGTTTCAAGAGAAAC-TATCTCAAGAGA
* * * **
973469 G----ATTTTGTTTCAAGGGAAACAGTCTCAAGAGAGACAAAACTTGTTTAAAGGGAAACGGATT
65 GACAAAATTTGTTTCAAGGGAAACAGTCTCAAGAGAGACAAAATTTGTTTCAAGGGAAACGTTTT
*
973530 CAAAGATTG
130 CAAAG-TTT
* * * * * * *
973539 GTGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAACTTGTTT-GAGTAAAAATTGTCTCAAGTGA
1 ATGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAACTTGTTTCAAG-AGAAACTATCTCAAGAGA
973603 GACAAAATT
65 GACAAAATT
973612 CATTCTTTAG
Statistics
Matches: 279, Mismatches: 51, Indels: 21
0.79 0.15 0.06
Matches are distributed among these distances:
130 58 0.21
131 45 0.16
132 1 0.00
134 4 0.01
135 1 0.00
136 1 0.00
137 164 0.59
138 5 0.02
ACGTcount: A:0.40, C:0.14, G:0.20, T:0.27
Consensus pattern (137 bp):
ATGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAACTTGTTTCAAGAGAAACTATCTCAAGAGAG
ACAAAATTTGTTTCAAGGGAAACAGTCTCAAGAGAGACAAAATTTGTTTCAAGGGAAACGTTTTC
AAAGTTT
Found at i:973514 original size:101 final size:100
Alignment explanation
Indices: 973170--973524 Score: 289
Period size: 101 Copynumber: 3.5 Consensus size: 100
973160 GAGACAAAAC
* **
973170 TTGTTTCAAGGGAAACTA-TCTCAAGAGAGACAAAACTCGTTTCAAGGGAAACAATCTCAAGAGA
1 TTGTTTCAAGGGAAAC-AGTCTCAAGAGAGACAAAACTTGTTTCAAGGGAAACTGTCTCAAGAGA
* *
973234 GACAAAATTCGTTTCAAGGGAAATATTTTCAAAG-TT
65 GACAAAATT-GTTTCAAGGGAAACATATTCAAAGATT
* ** * * *
973270 TATGTTTCAAGAGAAACTTTCTCAAGGGAGGCAAAATTTGTTTCAAGGGAAACTGTCTCAAGAGA
1 T-TGTTTCAAGGGAAACAGTCTCAAGAGAGACAAAACTTGTTTCAAGGGAAACTGTCTCAAGAGA
* * *
973335 GACAAAATTTGTTTCAAGGGAAACTGTCTTAAGAGAGATAAAAT
65 GACAAAA-TTGTTTCAAGGGAAAC-ATATTCA-A-AGAT----T
* * *** ** *
973379 TTGTTTCAAAGAAAAC-GTTCTC-A-A-AG--TTTA--TGTTTCAAAAGAAACTGTCTCAAAAGA
1 TTGTTTCAAGGGAAACAG-TCTCAAGAGAGACAAAACTTGTTTCAAGGGAAACTGTCTCAAGAGA
* **
973436 GACAAAACCTGTTTCAAGATAAACATATTCAAAGATT
65 GACAAAA-TTGTTTCAAGGGAAACATATTCAAAGATT
*
973473 TTGTTTCAAGGGAAACAGTCTCAAGAGAGACAAAACTTGTTTAAAGGGAAAC
1 TTGTTTCAAGGGAAACAGTCTCAAGAGAGACAAAACTTGTTTCAAGGGAAAC
973525 GGATTCAAAG
Statistics
Matches: 197, Mismatches: 38, Indels: 39
0.72 0.14 0.14
Matches are distributed among these distances:
94 19 0.10
95 2 0.01
96 1 0.01
97 2 0.01
98 4 0.02
99 2 0.01
100 5 0.03
101 130 0.66
102 6 0.03
103 2 0.01
104 2 0.01
105 3 0.02
107 1 0.01
108 16 0.08
109 2 0.01
ACGTcount: A:0.40, C:0.14, G:0.19, T:0.27
Consensus pattern (100 bp):
TTGTTTCAAGGGAAACAGTCTCAAGAGAGACAAAACTTGTTTCAAGGGAAACTGTCTCAAGAGAG
ACAAAATTGTTTCAAGGGAAACATATTCAAAGATT
Found at i:973737 original size:36 final size:35
Alignment explanation
Indices: 973689--973776 Score: 99
Period size: 36 Copynumber: 2.5 Consensus size: 35
973679 CATTTTAAAG
* ***
973689 GAAAAATGTCTCAAGCGA-GACAAAATTTGTTTAGA
1 GAAAATTGTCTCAAGCGACGACAAAA-AAATTTAGA
973724 GAGAAATTGTCTCAAGC-ACGACAAAAAAATTTAGA
1 GA-AAATTGTCTCAAGCGACGACAAAAAAATTTAGA
*
973759 GAAAATTGCCTCAAGCGA
1 GAAAATTGTCTCAAGCGA
973777 AACTTGTTTT
Statistics
Matches: 45, Mismatches: 5, Indels: 6
0.80 0.09 0.11
Matches are distributed among these distances:
34 13 0.29
35 12 0.27
36 20 0.44
ACGTcount: A:0.44, C:0.15, G:0.19, T:0.22
Consensus pattern (35 bp):
GAAAATTGTCTCAAGCGACGACAAAAAAATTTAGA
Found at i:976957 original size:21 final size:21
Alignment explanation
Indices: 976932--976972 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
976922 CCATAACAGG
* *
976932 GGGTATCGGTACCCCTTCATA
1 GGGTATCGATACACCTTCATA
976953 GGGTATCGATACACCTTCAT
1 GGGTATCGATACACCTTCAT
976973 TAAATTCAAA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.22, C:0.27, G:0.22, T:0.29
Consensus pattern (21 bp):
GGGTATCGATACACCTTCATA
Found at i:977036 original size:20 final size:20
Alignment explanation
Indices: 977011--977049 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 20
977001 TCGTTGCAGC
977011 CAGGGTGTAT-GGATACACTT
1 CAGGGTGTATCGG-TACACTT
977031 CAGGGTGTATCGGTACACT
1 CAGGGTGTATCGGTACACT
977050 CATAGGTGTA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 16 0.89
21 2 0.11
ACGTcount: A:0.23, C:0.18, G:0.31, T:0.28
Consensus pattern (20 bp):
CAGGGTGTATCGGTACACTT
Found at i:977057 original size:20 final size:21
Alignment explanation
Indices: 977034--977074 Score: 66
Period size: 20 Copynumber: 2.0 Consensus size: 21
977024 TACACTTCAG
977034 GGTGTATCGGT-ACACTCATA
1 GGTGTATCGGTAACACTCATA
*
977054 GGTGTATCTGTAACACTCATA
1 GGTGTATCGGTAACACTCATA
977075 ACCCATATAA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 10 0.53
21 9 0.47
ACGTcount: A:0.27, C:0.20, G:0.22, T:0.32
Consensus pattern (21 bp):
GGTGTATCGGTAACACTCATA
Found at i:979455 original size:22 final size:22
Alignment explanation
Indices: 979427--979469 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 22
979417 AAAGTTTTTT
* *
979427 ATGAATAGTACTGTGAACAGTA
1 ATGAATAGTACCGTAAACAGTA
979449 ATGAATAGTACCGTAAACAGT
1 ATGAATAGTACCGTAAACAGT
979470 GGACAGTGTA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.42, C:0.12, G:0.21, T:0.26
Consensus pattern (22 bp):
ATGAATAGTACCGTAAACAGTA
Found at i:980236 original size:58 final size:57
Alignment explanation
Indices: 980143--980261 Score: 148
Period size: 58 Copynumber: 2.1 Consensus size: 57
980133 CTAACCCGAG
* * * ** *
980143 TATGACACATAAGGTCGTGTCCACCATCTATACTAGGTATCCTTAAGTACAATCCCAA
1 TATGAAACAGAAGGTCGTGCCCACCATAAACACTAGGTATCCTTAAGT-CAATCCCAA
* **
980201 TATGAAACAGAAGGTCGTGCCCACCATAAACACTAGGTATCCTTTAGTGTATCCCAA
1 TATGAAACAGAAGGTCGTGCCCACCATAAACACTAGGTATCCTTAAGTCAATCCCAA
980258 TATG
1 TATG
980262 CAGCCTACTG
Statistics
Matches: 52, Mismatches: 9, Indels: 1
0.84 0.15 0.02
Matches are distributed among these distances:
57 11 0.21
58 41 0.79
ACGTcount: A:0.33, C:0.24, G:0.16, T:0.27
Consensus pattern (57 bp):
TATGAAACAGAAGGTCGTGCCCACCATAAACACTAGGTATCCTTAAGTCAATCCCAA
Found at i:981010 original size:50 final size:50
Alignment explanation
Indices: 980946--981040 Score: 181
Period size: 50 Copynumber: 1.9 Consensus size: 50
980936 TTTGTGATTT
980946 AAAACTACGTTTTCATAATTTTGCTCAATTTTGATTCGATTCAATTTTGA
1 AAAACTACGTTTTCATAATTTTGCTCAATTTTGATTCGATTCAATTTTGA
*
980996 AAAAGTACGTTTTCATAATTTTGCTCAATTTTGATTCGATTCAAT
1 AAAACTACGTTTTCATAATTTTGCTCAATTTTGATTCGATTCAAT
981041 CATGAATCAA
Statistics
Matches: 44, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
50 44 1.00
ACGTcount: A:0.31, C:0.14, G:0.11, T:0.45
Consensus pattern (50 bp):
AAAACTACGTTTTCATAATTTTGCTCAATTTTGATTCGATTCAATTTTGA
Found at i:982437 original size:18 final size:18
Alignment explanation
Indices: 982390--982446 Score: 62
Period size: 18 Copynumber: 2.9 Consensus size: 18
982380 ATGTTTAATG
982390 AAAAAGATACAAATTGTTA
1 AAAAAGATAC-AATTGTTA
982409 ACAAAACGATATCAATTGTT-
1 A-AAAA-GATA-CAATTGTTA
982429 AAAAAGATACCAATTGTT
1 AAAAAGATA-CAATTGTT
982447 GGAAAATATA
Statistics
Matches: 34, Mismatches: 1, Indels: 7
0.81 0.02 0.17
Matches are distributed among these distances:
18 12 0.35
19 5 0.15
20 5 0.15
21 11 0.32
22 1 0.03
ACGTcount: A:0.51, C:0.11, G:0.11, T:0.28
Consensus pattern (18 bp):
AAAAAGATACAATTGTTA
Found at i:985562 original size:20 final size:19
Alignment explanation
Indices: 985526--985600 Score: 77
Period size: 20 Copynumber: 4.0 Consensus size: 19
985516 TCGTTGCAGC
985526 CAGGGTGTAT-GGATACACT
1 CAGGGTGTATCGG-TACACT
*
985545 ACAGGGTGTATCAGTACAC-
1 -CAGGGTGTATCGGTACACT
985564 CA--GTGTATCGGTACACT
1 CAGGGTGTATCGGTACACT
*
985581 CATAGGTGTATCGGTACACT
1 CA-GGGTGTATCGGTACACT
985601 AATTGCATTT
Statistics
Matches: 48, Mismatches: 2, Indels: 10
0.80 0.03 0.17
Matches are distributed among these distances:
16 13 0.27
17 2 0.04
18 2 0.04
20 30 0.62
21 1 0.02
ACGTcount: A:0.27, C:0.20, G:0.27, T:0.27
Consensus pattern (19 bp):
CAGGGTGTATCGGTACACT
Found at i:985579 original size:36 final size:36
Alignment explanation
Indices: 985530--985599 Score: 90
Period size: 36 Copynumber: 1.9 Consensus size: 36
985520 TGCAGCCAGG
*
985530 GTGTATGGATACACTACA-GGGTGTATCAGTACACCA
1 GTGTATGGATACACT-CATAGGTGTATCAGTACACCA
*
985566 GTGTATCGG-TACACTCATAGGTGTATCGGTACAC
1 GTGTAT-GGATACACTCATAGGTGTATCAGTACAC
985600 TAATTGCATT
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
35 2 0.07
36 26 0.87
37 2 0.07
ACGTcount: A:0.27, C:0.20, G:0.26, T:0.27
Consensus pattern (36 bp):
GTGTATGGATACACTCATAGGTGTATCAGTACACCA
Found at i:989297 original size:3 final size:3
Alignment explanation
Indices: 989289--989330 Score: 84
Period size: 3 Copynumber: 14.0 Consensus size: 3
989279 GTAACATGTA
989289 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
989331 TAGTATTTTT
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 39 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:990303 original size:2 final size:2
Alignment explanation
Indices: 990298--990348 Score: 102
Period size: 2 Copynumber: 25.5 Consensus size: 2
990288 ATATCAACTC
990298 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
990340 AT AT AT AT A
1 AT AT AT AT A
990349 ATGGGAATAT
Statistics
Matches: 49, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 49 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:992945 original size:21 final size:21
Alignment explanation
Indices: 992911--992950 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
992901 ATCATGAGAG
* *
992911 CAGACTAGATGAGTTGGGGTT
1 CAGACTAGACGAGTAGGGGTT
*
992932 CAGACTAGGCGAGTAGGGG
1 CAGACTAGACGAGTAGGGG
992951 AGTAGGACTA
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.25, C:0.12, G:0.42, T:0.20
Consensus pattern (21 bp):
CAGACTAGACGAGTAGGGGTT
Found at i:993148 original size:16 final size:16
Alignment explanation
Indices: 993127--993163 Score: 74
Period size: 16 Copynumber: 2.3 Consensus size: 16
993117 ATTTAAAGGA
993127 GAGCAATTCATAGAGG
1 GAGCAATTCATAGAGG
993143 GAGCAATTCATAGAGG
1 GAGCAATTCATAGAGG
993159 GAGCA
1 GAGCA
993164 TTTGCTTATG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 21 1.00
ACGTcount: A:0.38, C:0.14, G:0.32, T:0.16
Consensus pattern (16 bp):
GAGCAATTCATAGAGG
Found at i:996852 original size:21 final size:20
Alignment explanation
Indices: 996806--996870 Score: 76
Period size: 21 Copynumber: 3.1 Consensus size: 20
996796 AATATTGCTT
* *
996806 CACCACTCTGCTCTTCCATTC
1 CACCACTTTGCTC-TCCATCC
*
996827 AACCACTTTGCTCTCGCATCC
1 CACCACTTTGCTCTC-CATCC
*
996848 CACCACTTTGCTCTCCCTCC
1 CACCACTTTGCTCTCCATCC
996868 CAC
1 CAC
996871 TACTATGTTA
Statistics
Matches: 38, Mismatches: 5, Indels: 3
0.83 0.11 0.07
Matches are distributed among these distances:
20 9 0.24
21 29 0.76
ACGTcount: A:0.15, C:0.49, G:0.06, T:0.29
Consensus pattern (20 bp):
CACCACTTTGCTCTCCATCC
Found at i:997677 original size:2 final size:2
Alignment explanation
Indices: 997616--997660 Score: 90
Period size: 2 Copynumber: 22.5 Consensus size: 2
997606 AAAATAATTA
997616 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
997658 AT A
1 AT A
997661 ATTTTGCCTT
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 43 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:999829 original size:29 final size:29
Alignment explanation
Indices: 999783--999840 Score: 71
Period size: 29 Copynumber: 2.0 Consensus size: 29
999773 CATGTATTTT
* * *
999783 AATACTAACGGTTGTAAGATATTTAAACG
1 AATACCAACGATTATAAGATATTTAAACG
* *
999812 AATACCAACGATTATAAGGTATTTTAACG
1 AATACCAACGATTATAAGATATTTAAACG
999841 TTTATCTTTA
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
29 24 1.00
ACGTcount: A:0.41, C:0.12, G:0.16, T:0.31
Consensus pattern (29 bp):
AATACCAACGATTATAAGATATTTAAACG
Found at i:1005161 original size:2 final size:2
Alignment explanation
Indices: 1005154--1005192 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
1005144 ATGTTTTACA
1005154 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1005193 AAGATAAGAT
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:1011565 original size:29 final size:31
Alignment explanation
Indices: 1011532--1011595 Score: 98
Period size: 30 Copynumber: 2.2 Consensus size: 31
1011522 ATTTGCATTC
*
1011532 TGCATTA-CATTT-ATTTAAGCATTTTCACA
1 TGCATTACCATTTAATTCAAGCATTTTCACA
1011561 TGCA-TACCATTTAATTCAAGCATTTTCACA
1 TGCATTACCATTTAATTCAAGCATTTTCACA
1011591 TGCAT
1 TGCAT
1011596 CATTCATGAA
Statistics
Matches: 31, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
28 2 0.06
29 9 0.29
30 20 0.65
ACGTcount: A:0.31, C:0.20, G:0.08, T:0.41
Consensus pattern (31 bp):
TGCATTACCATTTAATTCAAGCATTTTCACA
Found at i:1012997 original size:4 final size:4
Alignment explanation
Indices: 1012983--1013039 Score: 53
Period size: 4 Copynumber: 13.8 Consensus size: 4
1012973 AGATTAAATT
* * *
1012983 AAAG CAAAG AAAG AAAG AAAAG AAAC AAAG AAAC AAAG AAAA AAACG -AAG
1 AAAG -AAAG AAAG AAAG -AAAG AAAG AAAG AAAG AAAG AAAG AAA-G AAAG
1013033 AAAG AAA
1 AAAG AAA
1013040 ATGGATCAAT
Statistics
Matches: 43, Mismatches: 6, Indels: 7
0.77 0.11 0.12
Matches are distributed among these distances:
3 1 0.02
4 34 0.79
5 8 0.19
ACGTcount: A:0.75, C:0.07, G:0.18, T:0.00
Consensus pattern (4 bp):
AAAG
Found at i:1013004 original size:13 final size:13
Alignment explanation
Indices: 1012983--1013040 Score: 59
Period size: 13 Copynumber: 4.6 Consensus size: 13
1012973 AGATTAAATT
*
1012983 AAAGCAAAGAAAG
1 AAAGAAAAGAAAG
*
1012996 AAAGAAAAGAAAC
1 AAAGAAAAGAAAG
*
1013009 AAAG-AAACAAAG
1 AAAGAAAAGAAAG
1013021 AAA-AAAACG-AAG
1 AAAGAAAA-GAAAG
1013033 AAAGAAAA
1 AAAGAAAA
1013041 TGGATCAATT
Statistics
Matches: 37, Mismatches: 5, Indels: 6
0.77 0.10 0.12
Matches are distributed among these distances:
12 18 0.49
13 19 0.51
ACGTcount: A:0.76, C:0.07, G:0.17, T:0.00
Consensus pattern (13 bp):
AAAGAAAAGAAAG
Found at i:1013011 original size:21 final size:20
Alignment explanation
Indices: 1012987--1013039 Score: 79
Period size: 21 Copynumber: 2.6 Consensus size: 20
1012977 TAAATTAAAG
1012987 CAAAGAAAGAAAGAAAAGAAA
1 CAAAGAAAGAAAGAAAA-AAA
*
1013008 CAAAGAAACAAAGAAAAAAA
1 CAAAGAAAGAAAGAAAAAAA
*
1013028 CGAAGAAAGAAA
1 CAAAGAAAGAAA
1013040 ATGGATCAAT
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
20 13 0.45
21 16 0.55
ACGTcount: A:0.75, C:0.08, G:0.17, T:0.00
Consensus pattern (20 bp):
CAAAGAAAGAAAGAAAAAAA
Found at i:1015225 original size:18 final size:21
Alignment explanation
Indices: 1015185--1015231 Score: 73
Period size: 18 Copynumber: 2.4 Consensus size: 21
1015175 ATGAAAAATG
1015185 TACCAATTGTTTACAAAAGGA
1 TACCAATTGTTTACAAAAGGA
1015206 TACCAATTG-TTA-AAAA-GA
1 TACCAATTGTTTACAAAAGGA
1015224 TACCAATT
1 TACCAATT
1015232 ATTGAAAAAT
Statistics
Matches: 26, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
18 10 0.38
19 4 0.15
20 3 0.12
21 9 0.35
ACGTcount: A:0.45, C:0.15, G:0.11, T:0.30
Consensus pattern (21 bp):
TACCAATTGTTTACAAAAGGA
Found at i:1015239 original size:18 final size:19
Alignment explanation
Indices: 1015185--1015240 Score: 60
Period size: 18 Copynumber: 2.8 Consensus size: 19
1015175 ATGAAAAATG
*
1015185 TACCAATTGTTTACAAAAGGA
1 TACCAATT-ATTA-AAAAGGA
*
1015206 TACCAATTGTTAAAAA-GA
1 TACCAATTATTAAAAAGGA
1015224 TACCAATTATTGAAAAA
1 TACCAATTATT-AAAAA
1015241 TATATGAAAA
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
18 12 0.38
19 9 0.28
20 3 0.09
21 8 0.25
ACGTcount: A:0.48, C:0.12, G:0.11, T:0.29
Consensus pattern (19 bp):
TACCAATTATTAAAAAGGA
Found at i:1021107 original size:19 final size:18
Alignment explanation
Indices: 1021076--1021114 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 18
1021066 AAATCAAAAC
*
1021076 AATTTTTTTAAATTTCGA
1 AATTTTTTAAAATTTCGA
*
1021094 AATTTTTTCAAAATTTTGA
1 AATTTTTT-AAAATTTCGA
1021113 AA
1 AA
1021115 AATTCTTGTG
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
18 8 0.44
19 10 0.56
ACGTcount: A:0.38, C:0.05, G:0.05, T:0.51
Consensus pattern (18 bp):
AATTTTTTAAAATTTCGA
Found at i:1021555 original size:20 final size:21
Alignment explanation
Indices: 1021506--1021562 Score: 62
Period size: 20 Copynumber: 2.6 Consensus size: 21
1021496 CCTGTGGGGC
*
1021506 GGAATCGGTTCCTCTTCAAATGG
1 GGAATC-GTTCC-CTTCAAAGGG
1021529 GGAATCGTTCCCTTC-AAGGG
1 GGAATCGTTCCCTTCAAAGGG
*
1021549 GGTATCGATTCCCT
1 GGAATCG-TTCCCT
1021563 CTGCACTAAA
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
20 10 0.32
21 10 0.32
22 5 0.16
23 6 0.19
ACGTcount: A:0.19, C:0.25, G:0.26, T:0.30
Consensus pattern (21 bp):
GGAATCGTTCCCTTCAAAGGG
Found at i:1022226 original size:86 final size:87
Alignment explanation
Indices: 1022081--1022255 Score: 334
Period size: 86 Copynumber: 2.0 Consensus size: 87
1022071 AATAAAAAAG
1022081 TTGTTGTTTCATCCATAAAACTTGTGCACAACAACTACCAACTAAAATGTATTATGCTTCAGTGG
1 TTGTTGTTTCATCCATAAAACTTGTGCACAACAACTACCAACTAAAATGTATTATGCTTCAGTGG
1022146 TAGATAATGCAACAC-AATTTT
66 TAGATAATGCAACACAAATTTT
*
1022167 TTGTTGTTTCATCCATAAAACTTGTGCACAACAACTACCAGCTAAAATGTATTATGCTTCAGTGG
1 TTGTTGTTTCATCCATAAAACTTGTGCACAACAACTACCAACTAAAATGTATTATGCTTCAGTGG
1022232 TAGATAATGCAACACAAATTTT
66 TAGATAATGCAACACAAATTTT
1022254 TT
1 TT
1022256 TCTTTGAAAA
Statistics
Matches: 87, Mismatches: 1, Indels: 1
0.98 0.01 0.01
Matches are distributed among these distances:
86 79 0.91
87 8 0.09
ACGTcount: A:0.34, C:0.18, G:0.13, T:0.34
Consensus pattern (87 bp):
TTGTTGTTTCATCCATAAAACTTGTGCACAACAACTACCAACTAAAATGTATTATGCTTCAGTGG
TAGATAATGCAACACAAATTTT
Found at i:1027281 original size:36 final size:36
Alignment explanation
Indices: 1027207--1027330 Score: 153
Period size: 36 Copynumber: 3.4 Consensus size: 36
1027197 ACAAAGTGTC
* *
1027207 GTCTCGCTAGAGACAAATTTTC-TTAAAAACAAATTTT
1 GTCTCGCTTGAGAC-AATTTTCTTTAAAAATAAA-TTT
1027244 GTCTCGCTTGAGACAATTTTCTTTAAAAATAAATTT
1 GTCTCGCTTGAGACAATTTTCTTTAAAAATAAATTT
* **
1027280 GTCTCGCTTGAGACAA-TTTCTCTCGAAATAAATTT
1 GTCTCGCTTGAGACAATTTTCTTTAAAAATAAATTT
*
1027315 CGTCTAGCTTGAGACA
1 -GTCTCGCTTGAGACA
1027331 TCTTTCCCCT
Statistics
Matches: 79, Mismatches: 6, Indels: 5
0.88 0.07 0.06
Matches are distributed among these distances:
35 16 0.20
36 40 0.51
37 23 0.29
ACGTcount: A:0.32, C:0.18, G:0.14, T:0.36
Consensus pattern (36 bp):
GTCTCGCTTGAGACAATTTTCTTTAAAAATAAATTT
Found at i:1027547 original size:64 final size:66
Alignment explanation
Indices: 1027474--1027628 Score: 181
Period size: 66 Copynumber: 2.4 Consensus size: 66
1027464 TTTTTACTCA
* * * * * *
1027474 AAACAAATTTCATCTCGCTTGAGATAAT-T-CCCTCGGAACACAAATTTCAAAGTTGTTTTATTT
1 AAACAAATTTCATCTCACTTGAGATAATGTCCCCTAGAAACACAAATTTCAAAATTGTTTCACTT
1027537 G
66 G
* * * * *
1027538 AAACAAATTTCATCTCACTTGAGACAGTGTCCCCTAGAAATAGAAATTTTAAAATTGTTTCACTT
1 AAACAAATTTCATCTCACTTGAGATAATGTCCCCTAGAAACACAAATTTCAAAATTGTTTCACTT
1027603 G
66 G
1027604 AAACAAAGTTT-ATCTCACTTGAGAT
1 AAACAAA-TTTCATCTCACTTGAGAT
1027629 TGTTCTCAAA
Statistics
Matches: 76, Mismatches: 12, Indels: 4
0.83 0.13 0.04
Matches are distributed among these distances:
64 25 0.33
65 1 0.01
66 47 0.62
67 3 0.04
ACGTcount: A:0.35, C:0.18, G:0.12, T:0.34
Consensus pattern (66 bp):
AAACAAATTTCATCTCACTTGAGATAATGTCCCCTAGAAACACAAATTTCAAAATTGTTTCACTT
G
Found at i:1028239 original size:19 final size:18
Alignment explanation
Indices: 1028215--1028261 Score: 58
Period size: 19 Copynumber: 2.5 Consensus size: 18
1028205 TATATATATA
1028215 TATTATTTTATATCAGTTT
1 TATTATTTTATAT-AGTTT
*
1028234 TATTATTTATATATATTTT
1 TATTATTT-TATATAGTTT
*
1028253 TACTATTTT
1 TATTATTTT
1028262 TTATTTTTAT
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
18 1 0.04
19 19 0.76
20 5 0.20
ACGTcount: A:0.28, C:0.04, G:0.02, T:0.66
Consensus pattern (18 bp):
TATTATTTTATATAGTTT
Found at i:1028262 original size:62 final size:63
Alignment explanation
Indices: 1028168--1028289 Score: 160
Period size: 62 Copynumber: 2.0 Consensus size: 63
1028158 ATGCATTTTC
* * *
1028168 TTTTTTACTTTAGTATATATTTTTA-TTTTTTTTAGATTATATATATATATTATTTTATATCAG
1 TTTTTTACTTTAGTATATATTTTTACTATTTTTTA-ATTATATATATATACTATATTATATCAG
* *
1028231 TTTTATTA-TTTA-TATATATTTTTACTATTTTTTATTTTTATATATATACTATATTATAT
1 TTTT-TTACTTTAGTATATATTTTTACTATTTTTTAATTATATATATATACTATATTATAT
1028290 ATATATATTA
Statistics
Matches: 52, Mismatches: 5, Indels: 5
0.84 0.08 0.08
Matches are distributed among these distances:
62 33 0.63
63 16 0.31
64 3 0.06
ACGTcount: A:0.30, C:0.03, G:0.02, T:0.65
Consensus pattern (63 bp):
TTTTTTACTTTAGTATATATTTTTACTATTTTTTAATTATATATATATACTATATTATATCAG
Found at i:1028277 original size:32 final size:31
Alignment explanation
Indices: 1028181--1028278 Score: 92
Period size: 32 Copynumber: 3.1 Consensus size: 31
1028171 TTTACTTTAG
* *
1028181 TATATATTTTTATTTTTTTTA-GATTATATA
1 TATATATTTTTATATTTTTTATTATTATATA
*** *
1028211 TATATATTATTTTATATCAGTT-TTATTATTTA
1 TATATA-T-TTTTATATTTTTTATTATTATATA
*
1028243 TATATATTTTTACTATTTTTTATTTTTATATA
1 TATATATTTTTA-TATTTTTTATTATTATATA
1028275 TATA
1 TATA
1028279 CTATATTATA
Statistics
Matches: 52, Mismatches: 11, Indels: 8
0.73 0.15 0.11
Matches are distributed among these distances:
30 11 0.21
31 7 0.13
32 34 0.65
ACGTcount: A:0.31, C:0.02, G:0.02, T:0.65
Consensus pattern (31 bp):
TATATATTTTTATATTTTTTATTATTATATA
Found at i:1028285 original size:26 final size:29
Alignment explanation
Indices: 1028231--1028285 Score: 71
Period size: 28 Copynumber: 2.0 Consensus size: 29
1028221 TTTATATCAG
**
1028231 TTTTATTATTTATATATATTTTTACTATT
1 TTTTATTATTTATATATATTACTACTATT
1028260 TTTTATT-TTTATATATA-TACTA-TATT
1 TTTTATTATTTATATATATTACTACTATT
1028286 ATATATATAT
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
26 4 0.17
27 3 0.12
28 10 0.42
29 7 0.29
ACGTcount: A:0.29, C:0.04, G:0.00, T:0.67
Consensus pattern (29 bp):
TTTTATTATTTATATATATTACTACTATT
Found at i:1028301 original size:16 final size:16
Alignment explanation
Indices: 1028203--1028301 Score: 80
Period size: 16 Copynumber: 6.2 Consensus size: 16
1028193 TTTTTTTTAG
1028203 ATTATATATATATATT
1 ATTATATATATATATT
*
1028219 ATT-T-TATATCAGTTTT
1 ATTATATATAT-A-TATT
*
1028235 ATTATTTATATATATT
1 ATTATATATATATATT
* * *
1028251 TTTACTAT-TTTTTATT
1 ATTA-TATATATATATT
*
1028267 TTTATATATATACTA-T
1 ATTATATATATA-TATT
1028283 ATTATATATATATATT
1 ATTATATATATATATT
1028299 ATT
1 ATT
1028302 TTTACTTTTT
Statistics
Matches: 66, Mismatches: 9, Indels: 16
0.73 0.10 0.18
Matches are distributed among these distances:
14 5 0.08
15 7 0.11
16 43 0.65
17 6 0.09
18 5 0.08
ACGTcount: A:0.34, C:0.03, G:0.01, T:0.62
Consensus pattern (16 bp):
ATTATATATATATATT
Found at i:1028344 original size:49 final size:49
Alignment explanation
Indices: 1028236--1028428 Score: 137
Period size: 50 Copynumber: 3.8 Consensus size: 49
1028226 ATCAGTTTTA
* *
1028236 TTATTTATATA-TATTTTTACTATTTTTTATT--TTTATATATATACTATATT
1 TTATTTATATATTATTTTTACT-TTTTTTCTTAATTT-TAT-TATA-TTTATT
* * *
1028286 ATATATATATATTATTTTTACTTTTTTAT-TATAATTTTATT-TATTTGTT
1 TTATTTATATATTATTTTTACTTTTTT-TCT-TAATTTTATTATATTTATT
* * *
1028335 TTATTTATATATT-TTTTCTTCTTCTTTTTCTTTATTTTTTTATATTTATT
1 TTATTTATATATTATTTT-TACTT-TTTTTCTTAATTTTATTATATTTATT
* * *
1028385 TTACTTAATATTTTATCTTTACTTTCTTTATCTTAACTTTTATT
1 TTA-TTTATATATTATTTTTACTTT-TTT-TCTTAA-TTTTATT
1028429 TAATTTGTTT
Statistics
Matches: 113, Mismatches: 16, Indels: 25
0.73 0.10 0.16
Matches are distributed among these distances:
48 4 0.04
49 28 0.25
50 33 0.29
51 28 0.25
52 11 0.10
53 9 0.08
ACGTcount: A:0.24, C:0.07, G:0.01, T:0.68
Consensus pattern (49 bp):
TTATTTATATATTATTTTTACTTTTTTTCTTAATTTTATTATATTTATT
Found at i:1028375 original size:13 final size:13
Alignment explanation
Indices: 1028320--1028386 Score: 55
Period size: 13 Copynumber: 5.0 Consensus size: 13
1028310 TTTATTATAA
*
1028320 TTTTATTTATTTG
1 TTTTATTTATTTT
1028333 TTTTATTTATATATT
1 TTTTATTTAT-T-TT
* * *
1028348 TTTT-CTTCTTCT
1 TTTTATTTATTTT
*
1028360 TTTTCTTTATTTT
1 TTTTATTTATTTT
1028373 TTTATATTTATTTT
1 TTT-TATTTATTTT
1028387 ACTTAATATT
Statistics
Matches: 42, Mismatches: 8, Indels: 7
0.74 0.14 0.12
Matches are distributed among these distances:
12 5 0.12
13 19 0.45
14 13 0.31
15 5 0.12
ACGTcount: A:0.15, C:0.06, G:0.01, T:0.78
Consensus pattern (13 bp):
TTTTATTTATTTT
Found at i:1028386 original size:23 final size:23
Alignment explanation
Indices: 1028360--1028415 Score: 60
Period size: 23 Copynumber: 2.4 Consensus size: 23
1028350 TTCTTCTTCT
*
1028360 TTTTCTTTATTTTTTTATATTTA
1 TTTTCTTTATTATTTTATATTTA
* *
1028383 TTTTAC-TTAATATTTTATCTTTA
1 TTTT-CTTTATTATTTTATATTTA
*
1028406 CTTTCTTTAT
1 TTTTCTTTAT
1028416 CTTAACTTTT
Statistics
Matches: 26, Mismatches: 5, Indels: 4
0.74 0.14 0.11
Matches are distributed among these distances:
22 1 0.04
23 24 0.92
24 1 0.04
ACGTcount: A:0.20, C:0.09, G:0.00, T:0.71
Consensus pattern (23 bp):
TTTTCTTTATTATTTTATATTTA
Found at i:1031537 original size:15 final size:14
Alignment explanation
Indices: 1031511--1031559 Score: 64
Period size: 15 Copynumber: 3.4 Consensus size: 14
1031501 AATCAGAACA
1031511 AAAAAGAAAAAAGAG
1 AAAAA-AAAAAAGAG
1031526 AAAAAAAGAAAAGAG
1 AAAAAAA-AAAAGAG
*
1031541 -AAAATAAAAAGAG
1 AAAAAAAAAAAGAG
1031554 AAAAAA
1 AAAAAA
1031560 CAAAGGAAAA
Statistics
Matches: 30, Mismatches: 2, Indels: 5
0.81 0.05 0.14
Matches are distributed among these distances:
13 7 0.23
14 11 0.37
15 12 0.40
ACGTcount: A:0.82, C:0.00, G:0.16, T:0.02
Consensus pattern (14 bp):
AAAAAAAAAAAGAG
Found at i:1031568 original size:12 final size:13
Alignment explanation
Indices: 1031518--1031570 Score: 56
Period size: 13 Copynumber: 4.0 Consensus size: 13
1031508 ACAAAAAAGA
*
1031518 AAAAAGAGAAAAAA
1 AAAAAGAG-AAAAT
1031532 AGAAAAGAGAAAAT
1 A-AAAAGAGAAAAT
1031546 AAAAAGAGAAAA-
1 AAAAAGAGAAAAT
1031558 AACAAAG-GAAAAT
1 AA-AAAGAGAAAAT
1031571 TGAAGAAAAA
Statistics
Matches: 35, Mismatches: 1, Indels: 7
0.81 0.02 0.16
Matches are distributed among these distances:
12 7 0.20
13 15 0.43
14 6 0.17
15 7 0.20
ACGTcount: A:0.77, C:0.02, G:0.17, T:0.04
Consensus pattern (13 bp):
AAAAAGAGAAAAT
Found at i:1032657 original size:32 final size:31
Alignment explanation
Indices: 1032621--1032708 Score: 104
Period size: 32 Copynumber: 2.7 Consensus size: 31
1032611 GGAACAATGA
*
1032621 GGGCATCTTTGAAGATTCAACATCAAATGTTG
1 GGGCATCTTTG-AGATTCAACATCAAATATTG
* **
1032653 GGGCATTTTTTGAGATTCAACATTGAATATTG
1 GGGCA-TCTTTGAGATTCAACATCAAATATTG
*
1032685 GGGCATCTTTGGGAATTCAACATC
1 GGGCATCTTTGAG-ATTCAACATC
1032709 CTGATGCAAA
Statistics
Matches: 47, Mismatches: 7, Indels: 4
0.81 0.12 0.07
Matches are distributed among these distances:
31 6 0.13
32 36 0.77
33 5 0.11
ACGTcount: A:0.28, C:0.15, G:0.23, T:0.34
Consensus pattern (31 bp):
GGGCATCTTTGAGATTCAACATCAAATATTG
Found at i:1033403 original size:106 final size:106
Alignment explanation
Indices: 1033282--1033602 Score: 448
Period size: 106 Copynumber: 3.0 Consensus size: 106
1033272 ATATCGTGCC
* * * *
1033282 ACTCGAGACAACACAAGTTCAACTCCAAAACGAAGGGACGACTGATTGTCAACAAACAATTTCCC
1 ACTCGAGACAACACAAGTTCAACTTCACAACGAAGGGACGGCTGGTTGTCAACAAACAATTTCCC
1033347 AATTTCAGAGCCAATTTCAACTTCAC-ATCGAAGGATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAAT-GAAGGATATTGG
1033388 ACTCGAGACAACACAAGTTCAACTTCACAACGAAGGGACGGCTGGTTGTCAACAAACAATTTCCC
1 ACTCGAGACAACACAAGTTCAACTTCACAACGAAGGGACGGCTGGTTGTCAACAAACAATTTCCC
** *
1033453 AATTTTGGAGCCAATTTCAACTTCACAATGAATGATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAATGAAGGATATTGG
* * * * **
1033494 ACTCGAGACAGCACAAGCTCAACTTCACAGCGAAGGGACGGCTGGCTGTCAACAAACAATTTCTT
1 ACTCGAGACAACACAAGTTCAACTTCACAACGAAGGGACGGCTGGTTGTCAACAAACAATTTCCC
* * * **
1033559 AGTTCCAGAGCCAATTTTAACTTCACGGT-AGAGGATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAATGA-AGGATATTGG
1033600 ACT
1 ACT
1033603 TGGAACAATA
Statistics
Matches: 192, Mismatches: 21, Indels: 4
0.88 0.10 0.02
Matches are distributed among these distances:
105 1 0.01
106 189 0.98
107 2 0.01
ACGTcount: A:0.35, C:0.24, G:0.19, T:0.23
Consensus pattern (106 bp):
ACTCGAGACAACACAAGTTCAACTTCACAACGAAGGGACGGCTGGTTGTCAACAAACAATTTCCC
AATTTCAGAGCCAATTTCAACTTCACAATGAAGGATATTGG
Found at i:1034053 original size:37 final size:37
Alignment explanation
Indices: 1034012--1034159 Score: 104
Period size: 37 Copynumber: 4.2 Consensus size: 37
1034002 GGTAGTGTCC
1034012 CTTGAAACAAAATTTTGTCTCCCTTGAGACAGTTTCT
1 CTTGAAACAAAATTTTGTCTCCCTTGAGACAGTTTCT
* *
1034049 CTTGAAACATAAA---------CATTGAAAACA-TTTC-
1 CTTGAAACA-AAATTTTGTCTCCCTTG-AGACAGTTTCT
** * * * *
1034077 CTTTGAAA-TTAATTTTATCTCTCTTGAGATAGTTTCC
1 C-TTGAAACAAAATTTTGTCTCCCTTGAGACAGTTTCT
*
1034114 CTTGAAACAAAATTTTGTCTCCCTTGAGATAGTTTCT
1 CTTGAAACAAAATTTTGTCTCCCTTGAGACAGTTTCT
1034151 CTTGAAACA
1 CTTGAAACA
1034160 TAAACCTTGA
Statistics
Matches: 83, Mismatches: 13, Indels: 30
0.66 0.10 0.24
Matches are distributed among these distances:
27 2 0.02
28 1 0.01
29 14 0.17
30 4 0.05
35 3 0.04
36 13 0.16
37 43 0.52
38 3 0.04
ACGTcount: A:0.31, C:0.19, G:0.11, T:0.39
Consensus pattern (37 bp):
CTTGAAACAAAATTTTGTCTCCCTTGAGACAGTTTCT
Found at i:1034058 original size:87 final size:87
Alignment explanation
Indices: 1033861--1034038 Score: 277
Period size: 87 Copynumber: 2.1 Consensus size: 87
1033851 GACAGTTTCT
* *
1033861 CTTGAAACAT-AACATTGAAAACATTTCCCTTGAAATGAATTTTATCTCGATTGAGATAGTTTCA
1 CTTGAAACATAAACATTGAAAACATTTCCCTTGAAATAAATTTTATCTCGATTGAGATAGTGTCA
*
1033925 CTTGAAACGAAATTTTGTCTCC
66 CTTGAAACAAAATTTTGTCTCC
** * * *
1033947 CTTGAAACATAAACATTGAAAACATTTCCCTTGAAATAAATTTTATCTCTCTTGGGGTAGTGTCC
1 CTTGAAACATAAACATTGAAAACATTTCCCTTGAAATAAATTTTATCTCGATTGAGATAGTGTCA
1034012 CTTGAAACAAAATTTTGTCTCC
66 CTTGAAACAAAATTTTGTCTCC
1034034 CTTGA
1 CTTGA
1034039 GACAGTTTCT
Statistics
Matches: 83, Mismatches: 8, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
86 10 0.12
87 73 0.88
ACGTcount: A:0.33, C:0.19, G:0.13, T:0.36
Consensus pattern (87 bp):
CTTGAAACATAAACATTGAAAACATTTCCCTTGAAATAAATTTTATCTCGATTGAGATAGTGTCA
CTTGAAACAAAATTTTGTCTCC
Found at i:1034058 original size:102 final size:102
Alignment explanation
Indices: 1033947--1034186 Score: 399
Period size: 102 Copynumber: 2.4 Consensus size: 102
1033937 TTTTGTCTCC
* *
1033947 CTTGAAACATAAACATTGAAAACATTTCCCTTGAAATAAATTTTATCTCTCTTGGGGTAGTGTCC
1 CTTGAAACATAAACATTGAAAACATTTCCCTTGAAATAAATTTTATCTCTCTTGAGATAGTGTCC
1034012 CTTGAAACAAAATTTTGTCTCCCTTGAGACAGTTTCT
66 CTTGAAACAAAATTTTGTCTCCCTTGAGACAGTTTCT
* * *
1034049 CTTGAAACATAAACATTGAAAACATTTCCTTTGAAATTAATTTTATCTCTCTTGAGATAGTTTCC
1 CTTGAAACATAAACATTGAAAACATTTCCCTTGAAATAAATTTTATCTCTCTTGAGATAGTGTCC
*
1034114 CTTGAAACAAAATTTTGTCTCCCTTGAGATAGTTTCT
66 CTTGAAACAAAATTTTGTCTCCCTTGAGACAGTTTCT
* **
1034151 CTTGAAACATAAACCTTGAAAATGTTTCCCTTGAAA
1 CTTGAAACATAAACATTGAAAACATTTCCCTTGAAA
1034187 CACAAAATAG
Statistics
Matches: 128, Mismatches: 10, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
102 128 1.00
ACGTcount: A:0.32, C:0.19, G:0.12, T:0.37
Consensus pattern (102 bp):
CTTGAAACATAAACATTGAAAACATTTCCCTTGAAATAAATTTTATCTCTCTTGAGATAGTGTCC
CTTGAAACAAAATTTTGTCTCCCTTGAGACAGTTTCT
Found at i:1034120 original size:36 final size:37
Alignment explanation
Indices: 1034087--1034159 Score: 119
Period size: 37 Copynumber: 2.0 Consensus size: 37
1034077 CTTTGAAATT
*
1034087 AATTTTATCTCTCTTGAGATAGTTTCCCTTGAAACAA
1 AATTTTATCTCCCTTGAGATAGTTTCCCTTGAAACAA
* *
1034124 AATTTTGTCTCCCTTGAGATAGTTTCTCTTGAAACA
1 AATTTTATCTCCCTTGAGATAGTTTCCCTTGAAACA
1034160 TAAACCTTGA
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
37 33 1.00
ACGTcount: A:0.27, C:0.19, G:0.12, T:0.41
Consensus pattern (37 bp):
AATTTTATCTCCCTTGAGATAGTTTCCCTTGAAACAA
Found at i:1034274 original size:37 final size:37
Alignment explanation
Indices: 1034224--1034326 Score: 165
Period size: 36 Copynumber: 2.8 Consensus size: 37
1034214 AAAACGAGTT
1034224 TTGAGACAATTTCCCTTGAAACAAAATCTTATCTCTC
1 TTGAGACAATTTCCCTTGAAACAAAATCTTATCTCTC
* *
1034261 TTGAGACAATTTCCCTTGAAAC-AAATTTTGTCTCTC
1 TTGAGACAATTTCCCTTGAAACAAAATCTTATCTCTC
1034297 TTGAGA-AAGTTTCCCTTGAAACAAAATCTT
1 TTGAGACAA-TTTCCCTTGAAACAAAATCTT
1034327 TTGAATATCT
Statistics
Matches: 61, Mismatches: 3, Indels: 4
0.90 0.04 0.06
Matches are distributed among these distances:
35 2 0.03
36 31 0.51
37 28 0.46
ACGTcount: A:0.32, C:0.21, G:0.11, T:0.36
Consensus pattern (37 bp):
TTGAGACAATTTCCCTTGAAACAAAATCTTATCTCTC
Found at i:1034440 original size:36 final size:36
Alignment explanation
Indices: 1034342--1034460 Score: 143
Period size: 36 Copynumber: 3.3 Consensus size: 36
1034332 TATCTTTTCC
* *
1034342 TTGAAACAAATTTCGTCTCCGTTGAGACAGTTTCTT
1 TTGAAACAAATTTTGTCTCCTTTGAGACAGTTTCTT
* *
1034378 TT-AGAACTAAGTTTTGTCTCATTTGAGACAGTTTCTT
1 TTGA-AAC-AAATTTTGTCTCCTTTGAGACAGTTTCTT
* *
1034415 TTGAAACAAATTTTGTC-CCTCTTGAGATAGTTTCTC
1 TTGAAACAAATTTTGTCTCCT-TTGAGACAGTTTCTT
1034451 TTGAAACAAA
1 TTGAAACAAA
1034461 AAAAACCCTC
Statistics
Matches: 71, Mismatches: 8, Indels: 8
0.82 0.09 0.09
Matches are distributed among these distances:
35 3 0.04
36 37 0.52
37 30 0.42
38 1 0.01
ACGTcount: A:0.28, C:0.17, G:0.15, T:0.40
Consensus pattern (36 bp):
TTGAAACAAATTTTGTCTCCTTTGAGACAGTTTCTT
Found at i:1035641 original size:39 final size:40
Alignment explanation
Indices: 1035598--1035674 Score: 104
Period size: 41 Copynumber: 1.9 Consensus size: 40
1035588 TTGTTTTGTT
1035598 ATTTTCTTTTTTTA-TGTA-ATATATTTTTATATTTTATGC
1 ATTTTC-TTTTTTACTGTAGATATATTTTTATATTTTATGC
* *
1035637 ATTTTCTTTTTTACTTTAGTATATATTTTTATTTTTTA
1 ATTTTCTTTTTTACTGTAG-ATATATTTTTATATTTTA
1035675 GATTATATAT
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
38 7 0.21
39 9 0.27
41 17 0.52
ACGTcount: A:0.22, C:0.05, G:0.04, T:0.69
Consensus pattern (40 bp):
ATTTTCTTTTTTACTGTAGATATATTTTTATATTTTATGC
Found at i:1035672 original size:25 final size:25
Alignment explanation
Indices: 1035637--1035700 Score: 67
Period size: 25 Copynumber: 2.5 Consensus size: 25
1035627 TATTTTATGC
* *
1035637 ATTTTCTTTTTTACTTTAGTATATAT
1 ATTTTATTTTTTACATTA-TATATAT
*
1035663 -TTTTATTTTTTAGATTATATATAT
1 ATTTTATTTTTTACATTATATATAT
*
1035687 ATATTAGTTTTTTA
1 ATTTTA-TTTTTTA
1035701 TTATCAGTTT
Statistics
Matches: 32, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
24 7 0.22
25 18 0.56
26 7 0.22
ACGTcount: A:0.27, C:0.03, G:0.05, T:0.66
Consensus pattern (25 bp):
ATTTTATTTTTTACATTATATATAT
Found at i:1035726 original size:2 final size:2
Alignment explanation
Indices: 1035719--1035776 Score: 55
Period size: 2 Copynumber: 28.5 Consensus size: 2
1035709 TTTATTAATT
* * * *
1035719 TA TA TA TA TA TA TA TA CTA TT TA CTA T- TT TT TA TT TA TA TA TA
1 TA TA TA TA TA TA TA TA -TA TA TA -TA TA TA TA TA TA TA TA TA TA
1035762 TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA T
1035777 TATTTTTACT
Statistics
Matches: 48, Mismatches: 5, Indels: 6
0.81 0.08 0.10
Matches are distributed among these distances:
1 1 0.02
2 43 0.90
3 4 0.08
ACGTcount: A:0.40, C:0.03, G:0.00, T:0.57
Consensus pattern (2 bp):
TA
Found at i:1035815 original size:13 final size:12
Alignment explanation
Indices: 1035781--1035854 Score: 62
Period size: 12 Copynumber: 6.1 Consensus size: 12
1035771 ATATATTATT
*
1035781 TTTACTTTTTTA
1 TTTATTTTTTTA
*
1035793 -TTATTATTTTA
1 TTTATTTTTTTA
1035804 TTTATTTGTTTTA
1 TTTATTT-TTTTA
*
1035817 TTTATATATTTT-
1 TTTAT-TTTTTTA
* *
1035829 TTTCTTCTTTTTC
1 TTTATT-TTTTTA
1035842 TTTATTTTTTTA
1 TTTATTTTTTTA
1035854 T
1 T
1035855 ATTTATTTAC
Statistics
Matches: 49, Mismatches: 8, Indels: 10
0.73 0.12 0.15
Matches are distributed among these distances:
11 10 0.20
12 19 0.39
13 19 0.39
14 1 0.02
ACGTcount: A:0.16, C:0.05, G:0.01, T:0.77
Consensus pattern (12 bp):
TTTATTTTTTTA
Found at i:1035826 original size:17 final size:16
Alignment explanation
Indices: 1035745--1035831 Score: 61
Period size: 16 Copynumber: 5.4 Consensus size: 16
1035735 CTATTTACTA
1035745 TTTTTTATTTATATAT
1 TTTTTTATTTATATAT
* * * *
1035761 ATATATATATATATAT
1 TTTTTTATTTATATAT
*
1035777 TATTTTTACTTT-TTTAT
1 T-TTTTTA-TTTATATAT
* * *
1035794 TATTAT-TTTATTTAT
1 TTTTTTATTTATATAT
1035809 TTGTTTTATTTATATAT
1 TT-TTTTATTTATATAT
1035826 TTTTTT
1 TTTTTT
1035832 CTTCTTTTTC
Statistics
Matches: 52, Mismatches: 14, Indels: 10
0.68 0.18 0.13
Matches are distributed among these distances:
14 3 0.06
15 6 0.12
16 22 0.42
17 19 0.37
18 2 0.04
ACGTcount: A:0.26, C:0.01, G:0.01, T:0.71
Consensus pattern (16 bp):
TTTTTTATTTATATAT
Found at i:1035830 original size:47 final size:47
Alignment explanation
Indices: 1035770--1035915 Score: 120
Period size: 47 Copynumber: 2.9 Consensus size: 47
1035760 TATATATATA
*
1035770 TATATATTATTTTTACTTTTTTAT-TATTATTTTATTTATTTGTTTTATT
1 TATATA-T-TTTTTACTTTTTTATCT-TTATTTTATTTATTTGTTTTACT
*
1035819 TATATATTTTTTTCTTCTTTT-TCTTTATTTT-TTTATATT-TATTTACT
1 TATATATTTTTTACTT-TTTTATCTTTATTTTATTTAT-TTGT-TTTACT
* *
1035866 TACTATTTTATCTTTACTTTCTTTATCTTATCTTTTATTTAATTTGTTTT
1 TA-TATATT-T-TTTACTTT-TTTATCTT-TATTTTATTT-ATTTGTTTT
1035916 TTTCCTTCAT
Statistics
Matches: 79, Mismatches: 5, Indels: 22
0.75 0.05 0.21
Matches are distributed among these distances:
46 6 0.08
47 25 0.32
48 11 0.14
49 8 0.10
50 9 0.11
51 4 0.05
52 5 0.06
53 8 0.10
54 3 0.04
ACGTcount: A:0.19, C:0.08, G:0.01, T:0.72
Consensus pattern (47 bp):
TATATATTTTTTACTTTTTTATCTTTATTTTATTTATTTGTTTTACT
Found at i:1035839 original size:24 final size:23
Alignment explanation
Indices: 1035770--1035853 Score: 75
Period size: 23 Copynumber: 3.6 Consensus size: 23
1035760 TATATATATA
1035770 TATATATTATTTTTACTTTTTTAT
1 TATATATT-TTTTTACTTTTTTAT
*
1035794 TAT-TATTTTATTTATTTGTTTTATT
1 TATATATTTT-TTTACTT-TTTTA-T
*
1035819 TATATATTTTTTT-CTTCTTT-T
1 TATATATTTTTTTACTTTTTTAT
* *
1035840 TCTTTATTTTTTTA
1 TATATATTTTTTTA
1035854 TATTTATTTA
Statistics
Matches: 50, Mismatches: 5, Indels: 12
0.75 0.07 0.18
Matches are distributed among these distances:
21 12 0.24
22 2 0.04
23 13 0.26
24 10 0.20
25 7 0.14
26 6 0.12
ACGTcount: A:0.19, C:0.05, G:0.01, T:0.75
Consensus pattern (23 bp):
TATATATTTTTTTACTTTTTTAT
Found at i:1036393 original size:37 final size:37
Alignment explanation
Indices: 1036341--1036419 Score: 124
Period size: 37 Copynumber: 2.2 Consensus size: 37
1036331 TTTTTTTTTC
* *
1036341 GAAAC-AAGTTTTGTCTCGCTTGAGACAGTTTCTCTT
1 GAAACAAAGTTATGTCTCGCTTGAGACAGTTTCCCTT
*
1036377 GAAACAAAGTTATGTCTCTCTTGAGACAGTTTCCCTT
1 GAAACAAAGTTATGTCTCGCTTGAGACAGTTTCCCTT
1036414 GAAACA
1 GAAACA
1036420 TTAACTTTGA
Statistics
Matches: 39, Mismatches: 3, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
36 5 0.13
37 34 0.87
ACGTcount: A:0.28, C:0.20, G:0.18, T:0.34
Consensus pattern (37 bp):
GAAACAAAGTTATGTCTCGCTTGAGACAGTTTCCCTT
Found at i:1036468 original size:65 final size:65
Alignment explanation
Indices: 1036368--1036549 Score: 249
Period size: 65 Copynumber: 2.8 Consensus size: 65
1036358 GCTTGAGACA
* *
1036368 GTTTCTCTTGAAACAAAGTTATGTCTCTCTTGAGACAGTTTCCCTTGAAACATTAA-CTTTGAGA
1 GTTTCTCTTGAAACAAA-TTTTGTCTCTCTTGAGACAGTTTCTCTTGAAACA-TAACCTTTGAGA
1036432 TT
64 TT
* * *
1036434 GTTTTTCTTGAAATAAATTTTGTCTCTTTTGAGACAGTTTCTCTTGAAACATAACCTTTGAGATT
1 GTTTCTCTTGAAACAAATTTTGTCTCTCTTGAGACAGTTTCTCTTGAAACATAACCTTTGAGATT
* * * **
1036499 GTTTCCCTTGAAACAAGTTTTGTCTCTCTTAAGGTAGTTTCTCTTGAAACA
1 GTTTCTCTTGAAACAAATTTTGTCTCTCTTGAGACAGTTTCTCTTGAAACA
1036550 AATTATCCCT
Statistics
Matches: 102, Mismatches: 13, Indels: 3
0.86 0.11 0.03
Matches are distributed among these distances:
64 3 0.03
65 84 0.82
66 15 0.15
ACGTcount: A:0.26, C:0.17, G:0.15, T:0.42
Consensus pattern (65 bp):
GTTTCTCTTGAAACAAATTTTGTCTCTCTTGAGACAGTTTCTCTTGAAACATAACCTTTGAGATT
Found at i:1036810 original size:137 final size:136
Alignment explanation
Indices: 1036551--1036943 Score: 565
Period size: 137 Copynumber: 2.9 Consensus size: 136
1036541 CTTGAAACAA
* *
1036551 ATTATCCCTAAATATGGCCAGTCATCCTCATCACGTAGGAATCGTGTCATCCA-CGACCAGATCT
1 ATTATCCCTAAAGATGGCCAGTCATCCTCATCACGTAGGAACCGTGTCATCCACCGA-CAGATCT
** *
1036615 CCTCATCACGTAGGAGTTGCGTCACCCTTAGATAGA-CAGACTTCCTCATCACGTAGGAACCGTG
65 CCTCATCACGTAGGAGCCGCGTCACCCTTAGATA-ACCAGACTTCCTCATCACGTAGGAACCATG
1036679 TTATCTCC
129 TTATCTCC
*
1036687 ATTATCCCTAAAGATGGCCAGTCATCCTCATCACGTAGGAACCATGTCATCCACCGATCAGATCT
1 ATTATCCCTAAAGATGGCCAGTCATCCTCATCACGTAGGAACCGTGTCATCCACCGA-CAGATCT
* * * * *
1036752 CTTCATCACGTAGGAGCCGCATCACTCTTAGATAACCATACTTCCTCATCACGTAGGAACTATGT
65 CCTCATCACGTAGGAGCCGCGTCACCCTTAGATAACCAGACTTCCTCATCACGTAGGAACCATGT
**
1036817 TATCTGT
130 TATCTCC
* * *
1036824 ATTATCCCTAAAGATTGCCAGCCTTCCTCATCACGTAGGAACCGTGTCATCCACCGACTAGATCT
1 ATTATCCCTAAAGATGGCCAGTCATCCTCATCACGTAGGAACCGTGTCATCCACCGAC-AGATCT
* * *
1036889 CCTCATCACGTAGAAGCCGCGTCACCCTTAGATAACAAGATTTCCTCATCACGTA
65 CCTCATCACGTAGGAGCCGCGTCACCCTTAGATAACCAGACTTCCTCATCACGTA
1036944 AGAATATTGT
Statistics
Matches: 229, Mismatches: 25, Indels: 5
0.88 0.10 0.02
Matches are distributed among these distances:
136 52 0.23
137 177 0.77
ACGTcount: A:0.27, C:0.31, G:0.16, T:0.26
Consensus pattern (136 bp):
ATTATCCCTAAAGATGGCCAGTCATCCTCATCACGTAGGAACCGTGTCATCCACCGACAGATCTC
CTCATCACGTAGGAGCCGCGTCACCCTTAGATAACCAGACTTCCTCATCACGTAGGAACCATGTT
ATCTCC
Found at i:1037008 original size:137 final size:133
Alignment explanation
Indices: 1036551--1037008 Score: 396
Period size: 137 Copynumber: 3.3 Consensus size: 133
1036541 CTTGAAACAA
* * * *
1036551 ATTATCCCTAAATATGGCCAGTCATCCTCATCACGTAGGA-ATC-GTGTCATCCA-CGACCAGAT
1 ATTATCCCTAAAGAT-GCCAGACATCCTCAT--CGT-GGAGAACAGTGTCATCCACCGACTAGAT
** **
1036613 CTCCTCATCACGTAGGAGTTGCGTCACCCTTAGATAGACAGACTTCCTCATCACGTAGGAACCGT
62 CTCCTCATCACGTAGGAGCCGCGTCACCCTTAGATA-ACAGACTTCCTCATCACGTAGGAA-TAT
1036678 GTTATCTCC
125 GTTATCTCC
* *
1036687 ATTATCCCTAAAGATGGCCAGTCATCCTCATCACGTAGGA-ACCA-TGTCATCCACCGA-TCAGA
1 ATTATCCCTAAAGAT-GCCAGACATCCTCAT--CGT-GGAGAACAGTGTCATCCACCGACT-AGA
* * * *
1036749 TCTCTTCATCACGTAGGAGCCGCATCACTCTTAGATAACCATACTTCCTCATCACGTAGGAACTA
61 TCTCCTCATCACGTAGGAGCCGCGTCACCCTTAGATAA-CAGACTTCCTCATCACGTAGGAA-TA
**
1036814 TGTTATCTGT
124 TGTTATCTCC
* * * *
1036824 ATTATCCCTAAAGATTGCCAGCCTTCCTCATCACGTAG-GAACCGTGTCATCCACCGACTAGATC
1 ATTATCCCTAAAGA-TGCCAGACATCCTCAT--CGTGGAGAACAGTGTCATCCACCGACTAGATC
* * *
1036888 TCCTCATCACGTAGAAGCCGCGTCACCCTTAGATAACAAGATTTCCTCATCACGTAAGAATATTG
63 TCCTCATCACGTAGGAGCCGCGTCACCCTTAGATAAC-AGACTTCCTCATCACGTAGGAATA-TG
*
1036953 TTGTCTCC
126 TTATCTCC
* * *
1036961 AAATT-TACCTAAA-ATGACCAGA-ACTCTTCATCGTGGATGAGCAGTGTC
1 --ATTATCCCTAAAGATG-CCAGACA-TCCTCATCGTGGA-GAACAGTGTC
1037009 GTCTCTTTTA
Statistics
Matches: 271, Mismatches: 35, Indels: 31
0.80 0.10 0.09
Matches are distributed among these distances:
135 4 0.01
136 59 0.22
137 196 0.72
138 9 0.03
139 3 0.01
ACGTcount: A:0.28, C:0.29, G:0.16, T:0.27
Consensus pattern (133 bp):
ATTATCCCTAAAGATGCCAGACATCCTCATCGTGGAGAACAGTGTCATCCACCGACTAGATCTCC
TCATCACGTAGGAGCCGCGTCACCCTTAGATAACAGACTTCCTCATCACGTAGGAATATGTTATC
TCC
Found at i:1040499 original size:35 final size:35
Alignment explanation
Indices: 1040453--1040562 Score: 148
Period size: 35 Copynumber: 3.1 Consensus size: 35
1040443 AATAGTCCTT
*
1040453 AATTTTATTCTAAACCCCAAATTCCAAAGTAATTC
1 AATTTTATTCTAAACCCCAAATTCCAAAATAATTC
* *
1040488 AATTTTATTCTAAACCCTAGATTCCAAAATAATTC
1 AATTTTATTCTAAACCCCAAATTCCAAAATAATTC
** ** *
1040523 AATTAAATTCTAAACCCCAAATTATAAAATACTTC
1 AATTTTATTCTAAACCCCAAATTCCAAAATAATTC
1040558 AATTT
1 AATTT
1040563 AAGGTTTAGA
Statistics
Matches: 64, Mismatches: 11, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
35 64 1.00
ACGTcount: A:0.43, C:0.20, G:0.02, T:0.35
Consensus pattern (35 bp):
AATTTTATTCTAAACCCCAAATTCCAAAATAATTC
Found at i:1042649 original size:35 final size:34
Alignment explanation
Indices: 1042609--1042720 Score: 134
Period size: 35 Copynumber: 3.2 Consensus size: 34
1042599 TCTAAACCTT
* *
1042609 AAATTGAAGTATTTTACAATTTGGGGTTTAGAATT
1 AAATTGAA-TATTTTAGAATTTGGGGTTTAGAATG
* * *
1042644 TAATTGAATTATTTTAGAATTTAGGGTTTAGAGTG
1 AAATTGAA-TATTTTAGAATTTGGGGTTTAGAATG
* *
1042679 AAATTGAATAACTTTGGAATTTGGGGTTTAGAATG
1 AAATTGAAT-ATTTTAGAATTTGGGGTTTAGAATG
1042714 AAATTGA
1 AAATTGA
1042721 GGATTGTTTT
Statistics
Matches: 65, Mismatches: 11, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
34 1 0.02
35 64 0.98
ACGTcount: A:0.35, C:0.02, G:0.22, T:0.41
Consensus pattern (34 bp):
AAATTGAATATTTTAGAATTTGGGGTTTAGAATG
Found at i:1046718 original size:17 final size:17
Alignment explanation
Indices: 1046696--1046747 Score: 61
Period size: 17 Copynumber: 3.1 Consensus size: 17
1046686 TTATGAGGTG
1046696 AAAATATTATTATTTTA
1 AAAATATTATTATTTTA
* *
1046713 AAAATATAATTATTTAA
1 AAAATATTATTATTTTA
*
1046730 AATAATATT-TAATTTTA
1 AA-AATATTATTATTTTA
1046747 A
1 A
1046748 GTTATTAAAA
Statistics
Matches: 29, Mismatches: 5, Indels: 2
0.81 0.14 0.06
Matches are distributed among these distances:
17 24 0.83
18 5 0.17
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (17 bp):
AAAATATTATTATTTTA
Found at i:1047471 original size:15 final size:15
Alignment explanation
Indices: 1047451--1047481 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
1047441 AAAGTTCAGG
1047451 TGTTAAAATAAAATT
1 TGTTAAAATAAAATT
1047466 TGTTAAAATAAAATT
1 TGTTAAAATAAAATT
1047481 T
1 T
1047482 TACCTTTCAT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.52, C:0.00, G:0.06, T:0.42
Consensus pattern (15 bp):
TGTTAAAATAAAATT
Found at i:1047565 original size:37 final size:36
Alignment explanation
Indices: 1047499--1047575 Score: 95
Period size: 37 Copynumber: 2.1 Consensus size: 36
1047489 CATTAAACCC
*
1047499 TTTTATATATTTAATTTTGTAAAATATATATATAA-A
1 TTTTATATATTTAATTTTGTAAAAAATATATA-AATA
*
1047535 TTTTATGA-ATTTAAATTTTTTAAAAAATATATAAATA
1 TTTTAT-ATATTT-AATTTTGTAAAAAATATATAAATA
1047572 TTTT
1 TTTT
1047576 TCAACTTGTT
Statistics
Matches: 36, Mismatches: 2, Indels: 5
0.84 0.05 0.12
Matches are distributed among these distances:
36 12 0.33
37 24 0.67
ACGTcount: A:0.44, C:0.00, G:0.03, T:0.53
Consensus pattern (36 bp):
TTTTATATATTTAATTTTGTAAAAAATATATAAATA
Found at i:1047755 original size:19 final size:18
Alignment explanation
Indices: 1047722--1047761 Score: 62
Period size: 19 Copynumber: 2.2 Consensus size: 18
1047712 CAGTAATCAT
*
1047722 ATTTCCTGGTAATCTTAC
1 ATTTCCTGATAATCTTAC
1047740 ATTTCACTGATAATCTTAC
1 ATTTC-CTGATAATCTTAC
1047759 ATT
1 ATT
1047762 CTGTAAACCA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
18 5 0.25
19 15 0.75
ACGTcount: A:0.28, C:0.20, G:0.07, T:0.45
Consensus pattern (18 bp):
ATTTCCTGATAATCTTAC
Found at i:1054694 original size:57 final size:56
Alignment explanation
Indices: 1054603--1054770 Score: 228
Period size: 57 Copynumber: 2.9 Consensus size: 56
1054593 TCAACCCACA
* *
1054603 CAAGAAATATGCCCAACTACCCCCATGAAATCAACCATCCATTTCACAAACAACAACC
1 CAAGAAATGTGCCCAACGA-CCCCATGAAATCAACCATCC-TTTCACAAACAACAACC
* * * * *
1054661 CAGGAAATGTGCCCACCGACCCTATGAAATCAACCATCCCTTTCACAGACAACATCC
1 CAAGAAATGTGCCCAACGACCCCATGAAATCAACCAT-CCTTTCACAAACAACAACC
* *
1054718 CAAGAAATGTGCCCAACTACCCCATGAAATCAACCATCCTTTCGCAAACAACA
1 CAAGAAATGTGCCCAACGACCCCATGAAATCAACCATCCTTTCACAAACAACA
1054771 TCCCCTTGTT
Statistics
Matches: 96, Mismatches: 13, Indels: 4
0.85 0.12 0.04
Matches are distributed among these distances:
56 14 0.15
57 65 0.68
58 17 0.18
ACGTcount: A:0.39, C:0.36, G:0.09, T:0.17
Consensus pattern (56 bp):
CAAGAAATGTGCCCAACGACCCCATGAAATCAACCATCCTTTCACAAACAACAACC
Found at i:1056216 original size:7 final size:7
Alignment explanation
Indices: 1056204--1056236 Score: 66
Period size: 7 Copynumber: 4.7 Consensus size: 7
1056194 TTTAAAAAAT
1056204 ATTATTA
1 ATTATTA
1056211 ATTATTA
1 ATTATTA
1056218 ATTATTA
1 ATTATTA
1056225 ATTATTA
1 ATTATTA
1056232 ATTAT
1 ATTAT
1056237 AACCTAAACT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 26 1.00
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (7 bp):
ATTATTA
Found at i:1056299 original size:22 final size:21
Alignment explanation
Indices: 1056274--1056317 Score: 70
Period size: 21 Copynumber: 2.0 Consensus size: 21
1056264 CCTACTCACT
1056274 ATCCACCACTAAAACCCACTCA
1 ATCCACCACT-AAACCCACTCA
*
1056296 ATCCACCACTAAATCCACTCA
1 ATCCACCACTAAACCCACTCA
1056317 A
1 A
1056318 AATACCTACT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
21 11 0.52
22 10 0.48
ACGTcount: A:0.41, C:0.43, G:0.00, T:0.16
Consensus pattern (21 bp):
ATCCACCACTAAACCCACTCA
Found at i:1057000 original size:29 final size:29
Alignment explanation
Indices: 1056956--1057048 Score: 84
Period size: 29 Copynumber: 3.2 Consensus size: 29
1056946 TTATAATTAT
*
1056956 TATTTTAGTCCCTTAAATGTTTTTTTTGC
1 TATTTTAGTCCTTTAAATGTTTTTTTTGC
* **
1056985 TATTTTAGTCATTT-AA-GTTTTTGATTTTA
1 TATTTTAGTCCTTTAAATGTTTTT--TTTGC
*
1057014 TATTTTAGTCCTTTAAAT-TCCTGTTTTTGC
1 TATTTTAGTCCTTTAAATGT--TTTTTTTGC
1057044 TATTT
1 TATTT
1057049 AATCTCTTAA
Statistics
Matches: 50, Mismatches: 8, Indels: 11
0.72 0.12 0.16
Matches are distributed among these distances:
27 6 0.12
28 2 0.04
29 28 0.56
30 11 0.22
32 3 0.06
ACGTcount: A:0.19, C:0.11, G:0.10, T:0.60
Consensus pattern (29 bp):
TATTTTAGTCCTTTAAATGTTTTTTTTGC
Found at i:1057076 original size:58 final size:58
Alignment explanation
Indices: 1056951--1057087 Score: 140
Period size: 58 Copynumber: 2.4 Consensus size: 58
1056941 TTTTTTTATA
* * * *
1056951 ATTAT-TATTTTAGTCCCTTAAATGTTTTTTTTGCTATTTTAGTCATTTAAGTTTTTG
1 ATTATATATTTTAGTCCTTTAAATGTTGTTTTTGCTATTTTAATCATTTAAGTTTTCG
*
1057008 ATTTTATATTTTAGTCCTTTAAAT-TCCTGTTTTTGCTA-TTTAATC-TCTTAAGTTTTCG
1 ATTATATATTTTAGTCCTTTAAATGT--TGTTTTTGCTATTTTAATCAT-TTAAGTTTTCG
* *
1057066 -TTATACTATTTTGGTCTTTTAA
1 ATTATA-TATTTTAGTCCTTTAA
1057088 GTTTATAAAT
Statistics
Matches: 67, Mismatches: 8, Indels: 9
0.80 0.10 0.11
Matches are distributed among these distances:
57 10 0.15
58 47 0.70
59 10 0.15
ACGTcount: A:0.21, C:0.11, G:0.09, T:0.58
Consensus pattern (58 bp):
ATTATATATTTTAGTCCTTTAAATGTTGTTTTTGCTATTTTAATCATTTAAGTTTTCG
Found at i:1059279 original size:26 final size:26
Alignment explanation
Indices: 1059243--1059294 Score: 104
Period size: 26 Copynumber: 2.0 Consensus size: 26
1059233 AGTACAGTGG
1059243 AAGCATGATCAGCTACTTGTAGGATT
1 AAGCATGATCAGCTACTTGTAGGATT
1059269 AAGCATGATCAGCTACTTGTAGGATT
1 AAGCATGATCAGCTACTTGTAGGATT
1059295 GAGCCTGTCA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.31, C:0.15, G:0.23, T:0.31
Consensus pattern (26 bp):
AAGCATGATCAGCTACTTGTAGGATT
Found at i:1061461 original size:32 final size:32
Alignment explanation
Indices: 1061417--1061572 Score: 215
Period size: 32 Copynumber: 4.8 Consensus size: 32
1061407 ATGAGGAACA
1061417 TTGGGGACATCTTTGAAGATTCAACATCAAATG
1 TTGGGG-CATCTTTGAAGATTCAACATCAAATG
1061450 TTGGGGCATCTTTGAAGATTCAACATCAAATG
1 TTGGGGCATCTTTGAAGATTCAACATCAAATG
* * *
1061482 TTGGGCCATCTTTAAAGATTCAACGTCAAATG
1 TTGGGGCATCTTTGAAGATTCAACATCAAATG
* * *
1061514 TTGAGGCATCTTT-AGAGATTCAACATCGAATA
1 TTGGGGCATCTTTGA-AGATTCAACATCAAATG
**
1061546 TTGGGGCATCTTTGGGGATTCAACATC
1 TTGGGGCATCTTTGAAGATTCAACATC
1061573 CTGATGCGAA
Statistics
Matches: 110, Mismatches: 11, Indels: 5
0.87 0.09 0.04
Matches are distributed among these distances:
31 1 0.01
32 103 0.94
33 6 0.05
ACGTcount: A:0.30, C:0.17, G:0.22, T:0.31
Consensus pattern (32 bp):
TTGGGGCATCTTTGAAGATTCAACATCAAATG
Found at i:1062045 original size:61 final size:61
Alignment explanation
Indices: 1061949--1062361 Score: 609
Period size: 61 Copynumber: 6.8 Consensus size: 61
1061939 TTAAAGTTTT
*
1061949 CAAGATTGGATTTCAACTTCACAACGAAGGATATCCAACTCAAAGCCAATTTAGTGAAGCA
1 CAAGATTGGATTTCAACTTCACAACGAAGGATATCCAACTCAAAGCCAATTTGGTGAAGCA
* *
1062010 GAAGATTGGATTTCAACTTCACAACGAAGGATATCCAACTCAAAGCCGATTTGGTGAAGCA
1 CAAGATTGGATTTCAACTTCACAACGAAGGATATCCAACTCAAAGCCAATTTGGTGAAGCA
* * * *
1062071 CAAGATTGGATTTCAACTTGACAACGAAGGATATCTAACTCAAAACCAATTTGGTGAAACTTACA
1 CAAGATTGGATTTCAACTTCACAACGAAGGATATCCAACTCAAAGCCAATTTGGTG-AA---GCA
* *
1062136 CAAGCTTGGATTTCAACTTCACAACGAAGGATATCCAACTCAAAGCCGATTTGGTGAAGCA
1 CAAGATTGGATTTCAACTTCACAACGAAGGATATCCAACTCAAAGCCAATTTGGTGAAGCA
*
1062197 -ATA-CTTGGATTTCAACTTCACAACGAAGGATATCCAACTCAAAGCCAATTTGGTGAA--A
1 CA-AGATTGGATTTCAACTTCACAACGAAGGATATCCAACTCAAAGCCAATTTGGTGAAGCA
* *
1062255 CAATATTGGATTTCAACTTCACAACGAAGGATATCCAACTCAAAGCCGATTTGGTGAAGCA
1 CAAGATTGGATTTCAACTTCACAACGAAGGATATCCAACTCAAAGCCAATTTGGTGAAGCA
* * * *
1062316 CAAGATTGGATTTCCACTTCACAATGAAGGACATCCAATTCAAAGC
1 CAAGATTGGATTTCAACTTCACAACGAAGGATATCCAACTCAAAGC
1062362 TTAACTTCAC
Statistics
Matches: 320, Mismatches: 23, Indels: 18
0.89 0.06 0.05
Matches are distributed among these distances:
58 2 0.01
59 53 0.17
60 54 0.17
61 154 0.48
62 2 0.01
64 2 0.01
65 53 0.17
ACGTcount: A:0.37, C:0.21, G:0.17, T:0.24
Consensus pattern (61 bp):
CAAGATTGGATTTCAACTTCACAACGAAGGATATCCAACTCAAAGCCAATTTGGTGAAGCA
Done.