Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01015112.1 Corchorus olitorius cultivar O-4 contig15145, 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: 212229
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Found at i:15 original size:2 final size:2
Alignment explanation
Indices: 9--55 Score: 76
Period size: 2 Copynumber: 23.5 Consensus size: 2
1 ACTACTAC
* *
9 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA CA TA TA CA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
51 TA TA T
1 TA TA T
56 GTGACAAAGG
Statistics
Matches: 41, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.49, C:0.04, G:0.00, T:0.47
Consensus pattern (2 bp):
TA
Found at i:7214 original size:15 final size:15
Alignment explanation
Indices: 7193--7230 Score: 51
Period size: 15 Copynumber: 2.5 Consensus size: 15
7183 TTTATATATA
*
7193 GTATAGATTATTAATT
1 GTATAGAGTATT-ATT
7209 -TATAGAGTATTATT
1 GTATAGAGTATTATT
7223 GTATAGAG
1 GTATAGAG
7231 GTTATACTGT
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
14 3 0.15
15 17 0.85
ACGTcount: A:0.37, C:0.00, G:0.18, T:0.45
Consensus pattern (15 bp):
GTATAGAGTATTATT
Found at i:20692 original size:25 final size:25
Alignment explanation
Indices: 20664--20712 Score: 80
Period size: 25 Copynumber: 2.0 Consensus size: 25
20654 ATTTTTGAAT
* *
20664 GAATTTTTTCTTCTTGTCTTATTTG
1 GAATTTCTTCTTCCTGTCTTATTTG
20689 GAATTTCTTCTTCCTGTCTTATTT
1 GAATTTCTTCTTCCTGTCTTATTT
20713 TGTTGGAAGC
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
25 22 1.00
ACGTcount: A:0.12, C:0.16, G:0.10, T:0.61
Consensus pattern (25 bp):
GAATTTCTTCTTCCTGTCTTATTTG
Found at i:26292 original size:23 final size:23
Alignment explanation
Indices: 26266--26321 Score: 67
Period size: 23 Copynumber: 2.4 Consensus size: 23
26256 ATTAGTTTAT
* *
26266 CACTTTGCATATGGGTTTTGTGA
1 CACTTTACATATGGGCTTTGTGA
* *
26289 CACTTTATATATGGGCTTTGTGC
1 CACTTTACATATGGGCTTTGTGA
*
26312 CCCTTTACAT
1 CACTTTACAT
26322 CGGCTTGATT
Statistics
Matches: 27, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
23 27 1.00
ACGTcount: A:0.18, C:0.20, G:0.20, T:0.43
Consensus pattern (23 bp):
CACTTTACATATGGGCTTTGTGA
Found at i:26317 original size:73 final size:73
Alignment explanation
Indices: 26198--26338 Score: 255
Period size: 73 Copynumber: 1.9 Consensus size: 73
26188 GCTTGTAAAC
*
26198 TGCATATGGGTTTTATGACACTTTATATATGGGGTTTGTGCCCCTTTACATCAGCTTGATTAGTT
1 TGCATATGGGTTTTATGACACTTTATATATGGGCTTTGTGCCCCTTTACATCAGCTTGATTAGTT
26263 TATCACTT
66 TATCACTT
* *
26271 TGCATATGGGTTTTGTGACACTTTATATATGGGCTTTGTGCCCCTTTACATCGGCTTGATTAGTT
1 TGCATATGGGTTTTATGACACTTTATATATGGGCTTTGTGCCCCTTTACATCAGCTTGATTAGTT
26336 TAT
66 TAT
26339 TACCTTTATC
Statistics
Matches: 65, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
73 65 1.00
ACGTcount: A:0.19, C:0.16, G:0.21, T:0.44
Consensus pattern (73 bp):
TGCATATGGGTTTTATGACACTTTATATATGGGCTTTGTGCCCCTTTACATCAGCTTGATTAGTT
TATCACTT
Found at i:29596 original size:2 final size:2
Alignment explanation
Indices: 29589--29617 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
29579 TACTATATTG
29589 AT AT AT AT AT AT AT AT AT AT AT AT A- AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
29618 CTTGATAATA
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 25 0.96
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:33741 original size:7 final size:7
Alignment explanation
Indices: 33726--33766 Score: 50
Period size: 7 Copynumber: 6.1 Consensus size: 7
33716 TTTATTTCTG
*
33726 ATATGAT
1 ATATAAT
33733 ATATAAT
1 ATATAAT
33740 ATATAAT
1 ATATAAT
33747 -TAT-AT
1 ATATAAT
33752 ATATAAT
1 ATATAAT
*
33759 TTATAAT
1 ATATAAT
33766 A
1 A
33767 AAAATATTTA
Statistics
Matches: 29, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
5 2 0.07
6 6 0.21
7 21 0.72
ACGTcount: A:0.51, C:0.00, G:0.02, T:0.46
Consensus pattern (7 bp):
ATATAAT
Found at i:35237 original size:31 final size:30
Alignment explanation
Indices: 35196--35394 Score: 171
Period size: 31 Copynumber: 6.6 Consensus size: 30
35186 TTTGGCTAAT
35196 TGCTCAAATAAGGGCCTAACGTTTGCCAAGA
1 TGCTCAAATAAGGGCCTAACGTTTGCCAA-A
* * * *
35227 TGTTCAAATAAGGGCCTGATC-TTT--TAATT
1 TGCTCAAATAAGGGCCT-AACGTTTGCCAA-A
*
35256 TGGC-CAAATAAGGGCCTACCGTTTGCCAAAA
1 T-GCTCAAATAAGGGCCTAACGTTTGCC-AAA
*
35287 TACTCAAATAAGGGCCTAACGTTTGCCAAAA
1 TGCTCAAATAAGGGCCTAACGTTTGCC-AAA
* * *
35318 TGCTCAAATAAGGGCTCGATC-TTT--TAAA
1 TGCTCAAATAAGGGC-CTAACGTTTGCCAAA
35346 TTGAC-CAAATAAGGGCCTAACGTTTGCCAAA
1 -TG-CTCAAATAAGGGCCTAACGTTTGCCAAA
35377 TTGCTCAAATAAGGGCCT
1 -TGCTCAAATAAGGGCCT
35395 GGCATCAAAA
Statistics
Matches: 136, Mismatches: 18, Indels: 28
0.75 0.10 0.15
Matches are distributed among these distances:
28 8 0.06
29 35 0.26
30 4 0.03
31 82 0.60
32 7 0.05
ACGTcount: A:0.33, C:0.21, G:0.20, T:0.27
Consensus pattern (30 bp):
TGCTCAAATAAGGGCCTAACGTTTGCCAAA
Found at i:35354 original size:91 final size:91
Alignment explanation
Indices: 35198--35394 Score: 315
Period size: 91 Copynumber: 2.2 Consensus size: 91
35188 TGGCTAATTG
* * * *
35198 CTCAAATAAGGGCCTAACGTTTGCCAAGATGTTCAAATAAGGGCCTGATCTTTTAATTTGGCCAA
1 CTCAAATAAGGGCCTAACGTTTGCCAAAATGCTCAAATAAGGGCCTGATCTTTTAAATTGACCAA
*
35263 ATAAGGGCCTACCGTTTGCCAAAATA
66 ATAAGGGCCTAACGTTTGCCAAAATA
35289 CTCAAATAAGGGCCTAACGTTTGCCAAAATGCTCAAATAAGGG-CTCGATCTTTTAAATTGACCA
1 CTCAAATAAGGGCCTAACGTTTGCCAAAATGCTCAAATAAGGGCCT-GATCTTTTAAATTGACCA
* *
35353 AATAAGGGCCTAACGTTTGCCAAATTG
65 AATAAGGGCCTAACGTTTGCCAAAATA
35380 CTCAAATAAGGGCCT
1 CTCAAATAAGGGCCT
35395 GGCATCAAAA
Statistics
Matches: 98, Mismatches: 7, Indels: 2
0.92 0.07 0.02
Matches are distributed among these distances:
90 2 0.02
91 96 0.98
ACGTcount: A:0.33, C:0.21, G:0.19, T:0.26
Consensus pattern (91 bp):
CTCAAATAAGGGCCTAACGTTTGCCAAAATGCTCAAATAAGGGCCTGATCTTTTAAATTGACCAA
ATAAGGGCCTAACGTTTGCCAAAATA
Found at i:37245 original size:21 final size:21
Alignment explanation
Indices: 37216--37275 Score: 79
Period size: 21 Copynumber: 2.9 Consensus size: 21
37206 GCTCATTAAA
*
37216 TTCAAAATTAGGGTTCTTGAG
1 TTCATAATTAGGGTTCTTGAG
37237 TTCATAATTAGGGTTCTTGAG
1 TTCATAATTAGGGTTCTTGAG
*
37258 TT--TCAATTATGGTTCTTG
1 TTCAT-AATTAGGGTTCTTG
37276 GTTGATTGGA
Statistics
Matches: 36, Mismatches: 2, Indels: 3
0.88 0.05 0.07
Matches are distributed among these distances:
19 1 0.03
20 13 0.36
21 22 0.61
ACGTcount: A:0.23, C:0.10, G:0.22, T:0.45
Consensus pattern (21 bp):
TTCATAATTAGGGTTCTTGAG
Found at i:40929 original size:8 final size:8
Alignment explanation
Indices: 40907--40949 Score: 68
Period size: 8 Copynumber: 5.1 Consensus size: 8
40897 TTGAAATAAT
40907 TCTTCAAA
1 TCTTCAAA
40915 GTCTTCAAA
1 -TCTTCAAA
40924 TCTTCAAA
1 TCTTCAAA
40932 GTCTTCAAA
1 -TCTTCAAA
40941 TCTTCAAA
1 TCTTCAAA
40949 T
1 T
40950 TATCTTCAAA
Statistics
Matches: 33, Mismatches: 0, Indels: 3
0.92 0.00 0.08
Matches are distributed among these distances:
8 17 0.52
9 16 0.48
ACGTcount: A:0.35, C:0.23, G:0.05, T:0.37
Consensus pattern (8 bp):
TCTTCAAA
Found at i:40929 original size:17 final size:17
Alignment explanation
Indices: 40907--40948 Score: 84
Period size: 17 Copynumber: 2.5 Consensus size: 17
40897 TTGAAATAAT
40907 TCTTCAAAGTCTTCAAA
1 TCTTCAAAGTCTTCAAA
40924 TCTTCAAAGTCTTCAAA
1 TCTTCAAAGTCTTCAAA
40941 TCTTCAAA
1 TCTTCAAA
40949 TTATCTTCAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 25 1.00
ACGTcount: A:0.36, C:0.24, G:0.05, T:0.36
Consensus pattern (17 bp):
TCTTCAAAGTCTTCAAA
Found at i:40956 original size:11 final size:10
Alignment explanation
Indices: 40907--40970 Score: 50
Period size: 11 Copynumber: 6.8 Consensus size: 10
40897 TTGAAATAAT
*
40907 TCTTCAAA-G
1 TCTTCAAATA
40916 TCTTC-AA-A
1 TCTTCAAATA
*
40924 TCTTCAAA-G
1 TCTTCAAATA
40933 TCTTC-AA-A
1 TCTTCAAATA
40941 TCTTCAAATTA
1 TCTTCAAA-TA
40952 TCTTCAAATA
1 TCTTCAAATA
40962 GTCTTCAAA
1 -TCTTCAAA
40971 CACGAACTTC
Statistics
Matches: 47, Mismatches: 3, Indels: 8
0.81 0.05 0.14
Matches are distributed among these distances:
8 14 0.30
9 14 0.30
10 2 0.04
11 17 0.36
ACGTcount: A:0.36, C:0.22, G:0.05, T:0.38
Consensus pattern (10 bp):
TCTTCAAATA
Found at i:41283 original size:41 final size:40
Alignment explanation
Indices: 41221--41547 Score: 219
Period size: 41 Copynumber: 7.8 Consensus size: 40
41211 TACTTTACCC
41221 AATTTGCCCTTCCTCACCGGAAGGTGTTGTTTAGAATCCTT
1 AATTTGCCCTTCCTCACCGGAAGGTGTTGTTTA-AATCCTT
* * * *
41262 AATTTGTCCTTCCTCATCGGAAGGTATTGTTTAAGTCTACTTT
1 AATTTGCCCTTCCTCACCGGAAGGTGTTGTTTAAATC--C-TT
* * *
41305 ACCCAATTTGCCCTTCCTCACCGGCAGGTGTTGTTTAGAAACCCT
1 ----AATTTGCCCTTCCTCACCGGAAGGTGTTGTTTA-AATCCTT
* * *
41350 AGTTTGCCCTTCC-CAACCGGAAGGTGTTGTTTAAGTTTAGCTT
1 AATTTGCCCTTCCTC-ACCGGAAGGTGTTGTTTAA--AT-CCTT
* * *
41393 ACCAGTTTGCCCTTCCCCACCGAAAGGTGTTGTCTAAATTCC-T
1 A--A-TTTGCCCTTCCTCACCGGAAGGTGTTGTTTAAA-TCCTT
* * * *
41436 AGTTTGCCCTTCCTCATCGGAAGGTGTTGTTTACATTCC-C
1 AATTTGCCCTTCCTCACCGGAAGGTGTTGTTTA-AATCCTT
* * * * * *
41476 AGTCTGCCCTCCCCCACCGGAAGGTGTTGTCTAAATTTCTT
1 AATTTGCCCTTCCTCACCGGAAGGTGTTGTTTAAA-TCCTT
* * * *
41517 AGTTTACCCTTCCTCATCGGAAGGTGCTGTT
1 AATTTGCCCTTCCTCACCGGAAGGTGTTGTT
41548 CCTATTCCTG
Statistics
Matches: 222, Mismatches: 44, Indels: 40
0.73 0.14 0.13
Matches are distributed among these distances:
39 1 0.00
40 65 0.29
41 84 0.38
42 1 0.00
43 7 0.03
44 1 0.00
45 2 0.01
46 29 0.13
47 30 0.14
48 2 0.01
ACGTcount: A:0.19, C:0.27, G:0.19, T:0.35
Consensus pattern (40 bp):
AATTTGCCCTTCCTCACCGGAAGGTGTTGTTTAAATCCTT
Found at i:41361 original size:88 final size:88
Alignment explanation
Indices: 41197--41547 Score: 393
Period size: 88 Copynumber: 4.1 Consensus size: 88
41187 AGCTCAATCA
*
41197 GTGTTGTTTAAGTCTACTTTACCCAATTTGCCCTTCCTCACCGGAAGGTGTTGTTTAGAATCCTT
1 GTGTTGTTTAAGTCTACTTTACCCAATTTGCCCTTCCTCACCGGAAGGTGTTGTTTAGAATCCCT
* *
41262 AATTTGTCCTTCCTCATCGGAAG
66 AGTTTGCCCTTCCTCATCGGAAG
* * *
41285 GTATTGTTTAAGTCTACTTTACCCAATTTGCCCTTCCTCACCGGCAGGTGTTGTTTAGAAACCCT
1 GTGTTGTTTAAGTCTACTTTACCCAATTTGCCCTTCCTCACCGGAAGGTGTTGTTTAGAATCCCT
*
41350 AGTTTGCCCTTCC-CAACCGGAAG
66 AGTTTGCCCTTCCTC-ATCGGAAG
* * * * * *
41373 GTGTTGTTTAAGTTTAGC-TTA-CCAGTTTGCCCTTCCCCACCGAAAGGTGTTGTCTA-AATTCC
1 GTGTTGTTTAAGTCTA-CTTTACCCAATTTGCCCTTCCTCACCGGAAGGTGTTGTTTAGAATCCC
41435 TAGTTTGCCCTTCCTCATCGGAAG
65 TAGTTTGCCCTTCCTCATCGGAAG
* * * * * * *
41459 GTGTTGTTT-A--C-A--TT-CCCAGTCTGCCCTCCCCCACCGGAAGGTGTTGTCTA-AATTTCT
1 GTGTTGTTTAAGTCTACTTTACCCAATTTGCCCTTCCTCACCGGAAGGTGTTGTTTAGAA-TCCC
*
41516 TAGTTTACCCTTCCTCATCGGAAG
65 TAGTTTGCCCTTCCTCATCGGAAG
*
41540 GTGCTGTT
1 GTGTTGTT
41548 CCTATTCCTG
Statistics
Matches: 234, Mismatches: 24, Indels: 17
0.85 0.09 0.06
Matches are distributed among these distances:
80 36 0.15
81 33 0.14
82 1 0.00
85 1 0.00
86 34 0.15
87 32 0.14
88 96 0.41
89 1 0.00
ACGTcount: A:0.19, C:0.26, G:0.19, T:0.36
Consensus pattern (88 bp):
GTGTTGTTTAAGTCTACTTTACCCAATTTGCCCTTCCTCACCGGAAGGTGTTGTTTAGAATCCCT
AGTTTGCCCTTCCTCATCGGAAG
Found at i:41460 original size:40 final size:40
Alignment explanation
Indices: 41311--41547 Score: 217
Period size: 40 Copynumber: 5.7 Consensus size: 40
41301 CTTTACCCAA
* **
41311 TTTGCCCTTCCTCACCGGCAGGTGTTGTTTAGAAACCCTAG
1 TTTGCCCTTCCTCACCGGAAGGTGTTGTTTA-AATTCCTAG
41352 TTTGCCCTTCC-CAACCGGAAGGTGTTGTTTAAGTTTAGCTTACC-AG
1 TTTGCCCTTCCTC-ACCGGAAGGTGTTGTTTAA----A--TT-CCTAG
* * *
41398 TTTGCCCTTCCCCACCGAAAGGTGTTGTCTAAATTCCTAG
1 TTTGCCCTTCCTCACCGGAAGGTGTTGTTTAAATTCCTAG
* * *
41438 TTTGCCCTTCCTCATCGGAAGGTGTTGTTTACATTCCCAG
1 TTTGCCCTTCCTCACCGGAAGGTGTTGTTTAAATTCCTAG
* * * * *
41478 TCTGCCCTCCCCCACCGGAAGGTGTTGTCTAAATTTCTTAG
1 TTTGCCCTTCCTCACCGGAAGGTGTTGTTTAAA-TTCCTAG
* * *
41519 TTTACCCTTCCTCATCGGAAGGTGCTGTT
1 TTTGCCCTTCCTCACCGGAAGGTGTTGTT
41548 CCTATTCCTG
Statistics
Matches: 159, Mismatches: 26, Indels: 22
0.77 0.13 0.11
Matches are distributed among these distances:
39 2 0.01
40 67 0.42
41 55 0.35
42 1 0.01
44 1 0.01
46 30 0.19
47 3 0.02
ACGTcount: A:0.17, C:0.28, G:0.20, T:0.34
Consensus pattern (40 bp):
TTTGCCCTTCCTCACCGGAAGGTGTTGTTTAAATTCCTAG
Found at i:46568 original size:12 final size:12
Alignment explanation
Indices: 46551--46582 Score: 64
Period size: 12 Copynumber: 2.7 Consensus size: 12
46541 TACCCTATGT
46551 AAACACGACACG
1 AAACACGACACG
46563 AAACACGACACG
1 AAACACGACACG
46575 AAACACGA
1 AAACACGA
46583 ATTGCCAAGT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.53, C:0.31, G:0.16, T:0.00
Consensus pattern (12 bp):
AAACACGACACG
Found at i:55250 original size:60 final size:59
Alignment explanation
Indices: 55174--55339 Score: 237
Period size: 59 Copynumber: 2.8 Consensus size: 59
55164 ATAACGCCAT
* *
55174 GCCCTTATTTGAGCATTTTCGATAAAGTTAGGCCCTTATTTGGTCAAATTAAAAGATC-G
1 GCCCTTATTTGAGCATTTTCGATAACGTTAGGCCCTTATTTGG-CAAATTAAAAGATCAA
* *
55233 GACCCTTATTTGTGCATTTTCGATAACGTTAGGTCCTTATTTGGCAAATTAAAAGATCAA
1 G-CCCTTATTTGAGCATTTTCGATAACGTTAGGCCCTTATTTGGCAAATTAAAAGATCAA
*
55293 GCCCTTATTTGAGCATTTTGGCA-AACGTTAGGCCCTTATTTGAGCAA
1 GCCCTTATTTGAGCATTTTCG-ATAACGTTAGGCCCTTATTTG-GCAA
55340 TCAGCCAGAA
Statistics
Matches: 96, Mismatches: 7, Indels: 7
0.87 0.06 0.06
Matches are distributed among these distances:
59 51 0.53
60 45 0.47
ACGTcount: A:0.28, C:0.18, G:0.19, T:0.36
Consensus pattern (59 bp):
GCCCTTATTTGAGCATTTTCGATAACGTTAGGCCCTTATTTGGCAAATTAAAAGATCAA
Found at i:58364 original size:13 final size:13
Alignment explanation
Indices: 58348--58372 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
58338 TTCGATGAAA
58348 AAAAAAAAAAAAC
1 AAAAAAAAAAAAC
58361 AAAAAAAAAAAA
1 AAAAAAAAAAAA
58373 ACCGCTGAAA
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:0.96, C:0.04, G:0.00, T:0.00
Consensus pattern (13 bp):
AAAAAAAAAAAAC
Found at i:58366 original size:14 final size:14
Alignment explanation
Indices: 58347--58374 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
58337 TTTCGATGAA
58347 AAAAAAAAAAAAAC
1 AAAAAAAAAAAAAC
58361 AAAAAAAAAAAAAC
1 AAAAAAAAAAAAAC
58375 CGCTGAAACC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.93, C:0.07, G:0.00, T:0.00
Consensus pattern (14 bp):
AAAAAAAAAAAAAC
Found at i:68433 original size:12 final size:12
Alignment explanation
Indices: 68416--68441 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
68406 CAAAATTGAT
68416 AAAATAAACACC
1 AAAATAAACACC
68428 AAAATAAACACC
1 AAAATAAACACC
68440 AA
1 AA
68442 TAATTATGTA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.69, C:0.23, G:0.00, T:0.08
Consensus pattern (12 bp):
AAAATAAACACC
Found at i:69167 original size:20 final size:20
Alignment explanation
Indices: 69117--69169 Score: 63
Period size: 20 Copynumber: 2.5 Consensus size: 20
69107 TTTTGGAGTG
69117 TTCCATTTTTCTTCTTTTTT
1 TTCCATTTTTCTTCTTTTTT
*
69137 TTCACTTTTTTTCTT-TTTTTT
1 TTC-C-ATTTTTCTTCTTTTTT
69158 TTCCAATTTTTC
1 TTCC-ATTTTTC
69170 CAGAGGGACA
Statistics
Matches: 28, Mismatches: 3, Indels: 4
0.80 0.09 0.11
Matches are distributed among these distances:
20 10 0.36
21 10 0.36
22 8 0.29
ACGTcount: A:0.08, C:0.19, G:0.00, T:0.74
Consensus pattern (20 bp):
TTCCATTTTTCTTCTTTTTT
Found at i:69167 original size:21 final size:22
Alignment explanation
Indices: 69122--69169 Score: 64
Period size: 21 Copynumber: 2.3 Consensus size: 22
69112 GAGTGTTCCA
*
69122 TTTTTCTTCTTTTTTTTCACTT
1 TTTTTCTTCTTTTTTTTCACAT
*
69144 TTTTTCTT-TTTTTTTTC-CAA
1 TTTTTCTTCTTTTTTTTCACAT
69164 TTTTTC
1 TTTTTC
69170 CAGAGGGACA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
20 7 0.29
21 9 0.38
22 8 0.33
ACGTcount: A:0.06, C:0.17, G:0.00, T:0.77
Consensus pattern (22 bp):
TTTTTCTTCTTTTTTTTCACAT
Found at i:69167 original size:22 final size:22
Alignment explanation
Indices: 69122--69168 Score: 69
Period size: 22 Copynumber: 2.1 Consensus size: 22
69112 GAGTGTTCCA
*
69122 TTTTTCTTCTTTTTTTTCACTT
1 TTTTTCTTCTTTTTTTTCAATT
69144 TTTTTCTT-TTTTTTTTCCAATT
1 TTTTTCTTCTTTTTTTT-CAATT
69166 TTT
1 TTT
69169 CCAGAGGGAC
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
21 8 0.35
22 15 0.65
ACGTcount: A:0.06, C:0.15, G:0.00, T:0.79
Consensus pattern (22 bp):
TTTTTCTTCTTTTTTTTCAATT
Found at i:71715 original size:13 final size:14
Alignment explanation
Indices: 71697--71733 Score: 53
Period size: 13 Copynumber: 2.9 Consensus size: 14
71687 AGTAAGAGTT
71697 CAAGAGCAAAAA-A
1 CAAGAGCAAAAAGA
71710 CAAGAG-AAAAAGA
1 CAAGAGCAAAAAGA
71723 CAAG-GCAAAAA
1 CAAGAGCAAAAA
71734 CAAACACCTC
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
12 6 0.27
13 16 0.73
ACGTcount: A:0.68, C:0.14, G:0.19, T:0.00
Consensus pattern (14 bp):
CAAGAGCAAAAAGA
Found at i:72392 original size:16 final size:16
Alignment explanation
Indices: 72371--72420 Score: 55
Period size: 16 Copynumber: 2.9 Consensus size: 16
72361 GATTGGAAAA
72371 GTGACCGGCGGTGGTG
1 GTGACCGGCGGTGGTG
*
72387 GTGACCGGCTGTGGTAATG
1 GTGACCGGCGGTGG---TG
*
72406 GTGGCCGGCGGTGGT
1 GTGACCGGCGGTGGT
72421 TGGTATCTAG
Statistics
Matches: 28, Mismatches: 3, Indels: 6
0.76 0.08 0.16
Matches are distributed among these distances:
16 14 0.50
19 14 0.50
ACGTcount: A:0.08, C:0.18, G:0.52, T:0.22
Consensus pattern (16 bp):
GTGACCGGCGGTGGTG
Found at i:72835 original size:18 final size:18
Alignment explanation
Indices: 72792--72834 Score: 79
Period size: 17 Copynumber: 2.4 Consensus size: 18
72782 CACCTTCATT
72792 TTTATTTTGTTTAATTTA
1 TTTATTTTGTTTAATTTA
72810 TTTATTTTGTTT-ATTTA
1 TTTATTTTGTTTAATTTA
72827 TTTATTTT
1 TTTATTTT
72835 TTTTTTTTGC
Statistics
Matches: 25, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
17 13 0.52
18 12 0.48
ACGTcount: A:0.19, C:0.00, G:0.05, T:0.77
Consensus pattern (18 bp):
TTTATTTTGTTTAATTTA
Found at i:72933 original size:7 final size:6
Alignment explanation
Indices: 72917--72973 Score: 51
Period size: 6 Copynumber: 8.8 Consensus size: 6
72907 ATAAAAAATA
* * *
72917 AAAAAG AAAGAG AAAAGGTG AAAAAAG AAAAAGG AAAAAG AAAAAG AAAAAT
1 AAAAAG AAAAAG AAAA--AG AA-AAAG AAAAA-G AAAAAG AAAAAG AAAAAG
72969 AAAAA
1 AAAAA
72974 AATAAATTGG
Statistics
Matches: 42, Mismatches: 5, Indels: 8
0.76 0.09 0.15
Matches are distributed among these distances:
6 28 0.67
7 9 0.21
8 3 0.07
9 2 0.05
ACGTcount: A:0.77, C:0.00, G:0.19, T:0.04
Consensus pattern (6 bp):
AAAAAG
Found at i:72960 original size:5 final size:6
Alignment explanation
Indices: 72938--72973 Score: 54
Period size: 6 Copynumber: 5.8 Consensus size: 6
72928 GAAAAGGTGA
*
72938 AAAAAG AAAAAGG AAAAAG AAAAAG AAAAAT AAAAA
1 AAAAAG AAAAA-G AAAAAG AAAAAG AAAAAG AAAAA
72974 AATAAATTGG
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
6 22 0.79
7 6 0.21
ACGTcount: A:0.83, C:0.00, G:0.14, T:0.03
Consensus pattern (6 bp):
AAAAAG
Found at i:73661 original size:21 final size:22
Alignment explanation
Indices: 73619--73661 Score: 54
Period size: 22 Copynumber: 2.0 Consensus size: 22
73609 AGAAAAACTC
*
73619 AAAAAAATTGAAAAAAGTAAGA
1 AAAAAAATTGAAAAAAGAAAGA
73641 AAAAAAACTT-AAAAAA-AAAGA
1 AAAAAAA-TTGAAAAAAGAAAGA
73662 TGAGAAAAGG
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
21 4 0.21
22 13 0.68
23 2 0.11
ACGTcount: A:0.77, C:0.02, G:0.09, T:0.12
Consensus pattern (22 bp):
AAAAAAATTGAAAAAAGAAAGA
Found at i:77886 original size:23 final size:23
Alignment explanation
Indices: 77856--77901 Score: 83
Period size: 23 Copynumber: 2.0 Consensus size: 23
77846 TTGAGGGCAA
77856 AATGACCAAACTACAATTTTCTC
1 AATGACCAAACTACAATTTTCTC
*
77879 AATGACCAAACTTCAATTTTCTC
1 AATGACCAAACTACAATTTTCTC
77902 GATGTCTAGG
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:0.37, C:0.26, G:0.04, T:0.33
Consensus pattern (23 bp):
AATGACCAAACTACAATTTTCTC
Found at i:78615 original size:32 final size:33
Alignment explanation
Indices: 78574--78637 Score: 87
Period size: 32 Copynumber: 1.9 Consensus size: 33
78564 AGAGAAAATT
*
78574 AGAAGTGAAAGTGAAA-ATGAAG-ATTGAAAAAA
1 AGAAATGAAAG-GAAAGATGAAGAATTGAAAAAA
78606 AGAAATGAAAGGAAAGATGAAGAAATTGAAAA
1 AGAAATGAAAGGAAAGATGAAG-AATTGAAAA
78638 GATATAAGAT
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
31 4 0.14
32 16 0.57
34 8 0.29
ACGTcount: A:0.61, C:0.00, G:0.25, T:0.14
Consensus pattern (33 bp):
AGAAATGAAAGGAAAGATGAAGAATTGAAAAAA
Found at i:80991 original size:230 final size:221
Alignment explanation
Indices: 80556--81585 Score: 1024
Period size: 230 Copynumber: 4.5 Consensus size: 221
80546 TTTCTTAAAC
* *
80556 AAAAGCTTTTC-A-AGTTGGCATCGGTTGGCCTTC-TAAAAAT--G-TTTTAAGAGTTGGTATCG
1 AAAAG-TTTTCAAGAGTTGGTATCGGTTGGCCTTCTTAAAAATGAGTTTTTAAAAGTTGGTATCG
* *
80615 GTTGGCCTTCTCTAAAAATCGAACTTTTC-AAGTTGGCATCGGTTAGCCTTCTAAAAA-GTTTTC
65 GTTGGCC-T-TCTAAAAA--G---TTTTCAAAGTTGGCATCGGTTGGCCTTCTAAAAAGGTTTAC
* * * * * * *
80678 AAAGTTGGTATCAGTTGACCTTCTTTAAAATTA-AGCTTTCAAAAGTTCGCATCAGTTGGCCTTC
123 AGAGTTGGTATCGGTTGACCTTC--TAAAA--ACAGTTTTTAAAAGTTGGTATCGGTTGGCCTTC
* * *
80742 TAAAAAGTTCTCGAAAGTTGGCATCGATTGGCCTTCTTTAA
184 TAAAAAATT-TCCAAAGTTGGCATCGGTTGGCCTTC--TAA
80783 AATCAAGTTTTCAAGAGTTGGTATCGGTTGGCCTTCTTTAAAAATCGAGTTTTTAAAAGTTGGTA
1 AA--AAGTTTTCAAGAGTTGGTATCGGTTGGCCTTC-TTAAAAAT-GAGTTTTTAAAAGTTGGTA
*
80848 TCGGTTGGCCTTCTAAAAAGTTTTCAAAGTTGGCATCGGTTGGGCTTCTAAAAAGGTTTACAGAG
62 TCGGTTGGCCTTCTAAAAAGTTTTCAAAGTTGGCATCGGTTGGCCTTCTAAAAAGGTTTACAGAG
* * * *
80913 TTGTTATCGGTTGGCCTTCT-AAAA-AG-TTTTCAAAGTTGGTATCGGTTGGCCCTCTTTAAAAT
127 TTGGTATCGGTTGACCTTCTAAAAACAGTTTTTAAAAGTTGGTATCGGTTGG-CCT-TCTAAAA-
*
80975 CGAATTTCCAAAAGTTGGTATCGGTTGGCCTTCTTTAA
189 --AATTTCC-AAAGTTGGCATCGGTTGGCCTTC--TAA
* *
81013 AATCGAGTTTTTAAGAGTTGGTATCGGTTGGCCTTCTCTAAAAATCGAGTTTTTAAAAGTTGGTA
1 AA--AAGTTTTCAAGAGTTGGTATCGGTTGGCCTTCT-TAAAAAT-GAGTTTTTAAAAGTTGGTA
* * *
81078 TCAGTTGGCCTTCTAAAAAGTTTTCAAAGTTGGCATCGGTTGGCCTTCTAAAAATGTTTTCAGAG
62 TCGGTTGGCCTTCTAAAAAGTTTTCAAAGTTGGCATCGGTTGGCCTTCTAAAAAGGTTTACAGAG
81143 TTGGTATCGGTTGACCTTCACTAAAAATCGAGTTTTTAAAAGTTGGTATCGGTTGGCCTTCTAAA
127 TTGGTATCGGTTGACCTT--CTAAAAA-C-AGTTTTTAAAAGTTGGTATCGGTTGGCCTTCTAAA
*
81208 AAATTTTCAAAGTTGGCATCGGTTGGCCTTCTAA
188 AAATTTCCAAAGTTGGCATCGGTTGGCCTTCTAA
* * * *
81242 AAATG-TTTCTAGAGTTGGTATCAGTTGGCCTTC-T-AAAA--AG-TTTTCAAAGTTGGTATCGG
1 AAAAGTTTTCAAGAGTTGGTATCGGTTGGCCTTCTTAAAAATGAGTTTTTAAAAGTTGGTATCGG
* * * *
81301 TTGGCCTTCTTTAAAACCGAATTTCCAAAAGTTGGTATCGGTTGGCCTTCTTTAAAATCGAGTTT
66 TTGGCCTTC--TAAAA---AGTTTTC-AAAGTTGGCATCGGTTGGCCTTC--TAAAA---AG-GT
*
81366 TTA-AGAGTTGGTATCGGTTGGCCTTCTCTAAAAATCGAGTTTTTAAAAGTTGGTATCGGTTGGC
119 TTACAGAGTTGGTATCGGTTGACC-T-TCTAAAAA-C-AGTTTTTAAAAGTTGGTATCGGTTGGC
*
81430 CTTCTAAAAAGGTTT-CAAAGTTGGCATCGGTTGGCCTTCTAA
180 CTTCTAAAAA-ATTTCCAAAGTTGGCATCGGTTGGCCTTCTAA
* * * * *
81472 AAATGTTTTC-AGAGTTGGTATCGGTTGGCCTTCTCTAAAATTTGACTTTTTAAAAGTGGGCATC
1 AAAAGTTTTCAAGAGTTGGTATCGGTTGGCCTTCT-TAAAA-ATGAGTTTTTAAAAGTTGGTATC
* *
81536 GGTTGGTCTTCTAAAAGGTTTTCAAAGTTGGCATCGG-TGGTCCTTCTAAA
64 GGTTGGCCTTCTAAAAAGTTTTCAAAGTTGGCATCGGTTGG-CCTTCTAAA
81586 TGTTTTCAAA
Statistics
Matches: 696, Mismatches: 57, Indels: 98
0.82 0.07 0.12
Matches are distributed among these distances:
219 26 0.04
220 2 0.00
221 5 0.01
223 4 0.01
224 6 0.01
225 40 0.06
226 31 0.04
227 14 0.02
228 8 0.01
229 22 0.03
230 337 0.48
231 75 0.11
232 22 0.03
233 7 0.01
234 8 0.01
235 13 0.02
236 30 0.04
237 46 0.07
ACGTcount: A:0.26, C:0.16, G:0.22, T:0.37
Consensus pattern (221 bp):
AAAAGTTTTCAAGAGTTGGTATCGGTTGGCCTTCTTAAAAATGAGTTTTTAAAAGTTGGTATCGG
TTGGCCTTCTAAAAAGTTTTCAAAGTTGGCATCGGTTGGCCTTCTAAAAAGGTTTACAGAGTTGG
TATCGGTTGACCTTCTAAAAACAGTTTTTAAAAGTTGGTATCGGTTGGCCTTCTAAAAAATTTCC
AAAGTTGGCATCGGTTGGCCTTCTAA
Found at i:81161 original size:113 final size:113
Alignment explanation
Indices: 80562--81616 Score: 1122
Period size: 113 Copynumber: 9.3 Consensus size: 113
80552 AAACAAAAGC
* *
80562 TTTTCA-AGTTGGCATCGGTTGGCC-T-TCTAAAAAT---G-TTTTAAGAGTTGGTATCGGTTGG
1 TTTTCAGAGTTGGTATCGGTTGGCCTTCTCTAAAAATCGAGTTTTTAAAAGTTGGTATCGGTTGG
*
80620 CCTTCTCTAAAAATCGAACTTTTC-AAGTTGGCATCGGTTAGCCTTCTAAAAA-G
66 CC-T-TCTAAAAA--G---TTTTCAAAGTTGGCATCGGTTGGCCTTCTAAAAATG
* * * * ** * * * * *
80673 TTTTCAAAGTTGGTATCAGTTGACCTTCT-TTAAAATTAAGCTTTCAAAAGTTCGCATCAGTTGG
1 TTTTCAGAGTTGGTATCGGTTGGCCTTCTCTAAAAATCGAGTTTTTAAAAGTTGGTATCGGTTGG
* * *
80737 CCTTCTAAAAAGTTCTCGAAAGTTGGCATCGATTGGCCTTCTTTAAAATCAAG
66 CCTTCTAAAAAGTTTTC-AAAGTTGGCATCGGTTGGCCTTC--TAAAA--ATG
*
80790 TTTTCAAGAGTTGGTATCGGTTGGCCTTCTTTAAAAATCGAGTTTTTAAAAGTTGGTATCGGTTG
1 TTTTC-AGAGTTGGTATCGGTTGGCCTTCTCTAAAAATCGAGTTTTTAAAAGTTGGTATCGGTTG
* *
80855 GCCTTCTAAAAAGTTTTCAAAGTTGGCATCGGTTGGGCTTCTAAAAAGG
65 GCCTTCTAAAAAGTTTTCAAAGTTGGCATCGGTTGGCCTTCTAAAAATG
* * *
80904 TTTACAGAGTTGTTATCGGTTGGCC-T-TCT-AAAA---AG-TTTTCAAAGTTGGTATCGGTTGG
1 TTTTCAGAGTTGGTATCGGTTGGCCTTCTCTAAAAATCGAGTTTTTAAAAGTTGGTATCGGTTGG
* * * * *
80962 CCCTCTTTAAAATCGAATTTCCAAAAGTTGGTATCGGTTGGCCTTCTTTAAAATCGAG
66 -CCT-TCTAAAA---AGTTTTC-AAAGTTGGCATCGGTTGGCCTTC-TAAAAAT---G
* *
81020 TTTTTAAGAGTTGGTATCGGTTGGCCTTCTCTAAAAATCGAGTTTTTAAAAGTTGGTATCAGTTG
1 -TTTTCAGAGTTGGTATCGGTTGGCCTTCTCTAAAAATCGAGTTTTTAAAAGTTGGTATCGGTTG
81085 GCCTTCTAAAAAGTTTTCAAAGTTGGCATCGGTTGGCCTTCTAAAAATG
65 GCCTTCTAAAAAGTTTTCAAAGTTGGCATCGGTTGGCCTTCTAAAAATG
* *
81134 TTTTCAGAGTTGGTATCGGTTGACCTTCACTAAAAATCGAGTTTTTAAAAGTTGGTATCGGTTGG
1 TTTTCAGAGTTGGTATCGGTTGGCCTTCTCTAAAAATCGAGTTTTTAAAAGTTGGTATCGGTTGG
*
81199 CCTTCTAAAAAATTTTCAAAGTTGGCATCGGTTGGCCTTCTAAAAATG
66 CCTTCTAAAAAGTTTTCAAAGTTGGCATCGGTTGGCCTTCTAAAAATG
* *
81247 -TTTCTAGAGTTGGTATCAGTTGGCC-T-TCT-AAAA---AG-TTTTCAAAGTTGGTATCGGTTG
1 TTTTC-AGAGTTGGTATCGGTTGGCCTTCTCTAAAAATCGAGTTTTTAAAAGTTGGTATCGGTTG
* * * *
81304 GCCTTCTTTAAAACCGAATTTCCAAAAGTTGGTATCGGTTGGCCTTCTTTAAAATCGAG
65 GCCTTC--TAAAA---AGTTTTC-AAAGTTGGCATCGGTTGGCCTTC-TAAAAAT---G
*
81363 TTTTTAAGAGTTGGTATCGGTTGGCCTTCTCTAAAAATCGAGTTTTTAAAAGTTGGTATCGGTTG
1 -TTTTCAGAGTTGGTATCGGTTGGCCTTCTCTAAAAATCGAGTTTTTAAAAGTTGGTATCGGTTG
*
81428 GCCTTCTAAAAAGGTTTCAAAGTTGGCATCGGTTGGCCTTCTAAAAATG
65 GCCTTCTAAAAAGTTTTCAAAGTTGGCATCGGTTGGCCTTCTAAAAATG
* * * * *
81477 TTTTCAGAGTTGGTATCGGTTGGCCTTCTCTAAAATTTGACTTTTTAAAAGTGGGCATCGGTTGG
1 TTTTCAGAGTTGGTATCGGTTGGCCTTCTCTAAAAATCGAGTTTTTAAAAGTTGGTATCGGTTGG
* *
81542 TCTTCTAAAAGGTTTTCAAAGTTGGCATCGG-TGGTCCTTCT--AAATG
66 CCTTCTAAAAAGTTTTCAAAGTTGGCATCGGTTGG-CCTTCTAAAAATG
* * *
81588 TTTTCAAAGTTGGCATCAGTTGGCCTTCT
1 TTTTCAGAGTTGGTATCGGTTGGCCTTCT
81617 TAATGTTGTT
Statistics
Matches: 809, Mismatches: 80, Indels: 110
0.81 0.08 0.11
Matches are distributed among these distances:
106 49 0.06
107 7 0.01
108 11 0.01
110 12 0.01
111 52 0.06
112 87 0.11
113 257 0.32
114 14 0.02
115 8 0.01
116 10 0.01
117 79 0.10
118 91 0.11
119 58 0.07
120 8 0.01
122 11 0.01
123 7 0.01
124 48 0.06
ACGTcount: A:0.25, C:0.16, G:0.22, T:0.37
Consensus pattern (113 bp):
TTTTCAGAGTTGGTATCGGTTGGCCTTCTCTAAAAATCGAGTTTTTAAAAGTTGGTATCGGTTGG
CCTTCTAAAAAGTTTTCAAAGTTGGCATCGGTTGGCCTTCTAAAAATG
Found at i:81201 original size:343 final size:343
Alignment explanation
Indices: 80568--81616 Score: 1514
Period size: 343 Copynumber: 3.1 Consensus size: 343
80558 AAGCTTTTCA
* *
80568 AGTTGGCATCGGTTGGCCTTCTAAAAATGTTTT-AAGAGTTGGTATCGGTTGGCCTTCTCTAAAA
1 AGTTGGTATCGGTTGGCCTTCTAAAAA-GTTTTCAA-AGTTGGTATCGGTTGGCCTTCT-TTAAA
* * * *
80632 ATCGAACTTTTC--AAGTTGGCATCGGTTAGCCTTC--TAAAA---AGTTTTCAA-AGTTGGTAT
63 ATCGAA-TTTCCAAAAGTTGGTATCGGTTGGCCTTCTTTAAAATCGAGTTTTTAAGAGTTGGTAT
* * * ** * * * * *
80689 CAGTTGACCTTCT-TTAAAATTAAGCTTTCAAAAGTTCGCATCAGTTGGCCTTCTAAAAAGTTCT
127 CGGTTGGCCTTCTCTAAAAATCGAGTTTTTAAAAGTTGGTATCAGTTGGCCTTCTAAAAAGTTTT
* *
80753 CGAAAGTTGGCATCGATTGGCCTTCTTTAAAATCAAGTTTTCAAGAGTTGGTATCGGTTGGCCTT
192 C-AAAGTTGGCATCGGTTGGCCTTC--TAAAA--ATGTTTTC-AGAGTTGGTATCGGTTGGCCTT
*
80818 CTTTAAAAATCGAGTTTTTAAAAGTTGGTATCGGTTGGCCTTCTAAAAAGTTTTCAAAGTTGGCA
251 CTCTAAAAATCGAGTTTTTAAAAGTTGGTATCGGTTGGCCTTCTAAAAAGTTTTCAAAGTTGGCA
*
80883 TCGGTTGGGCTTCTAAAAAGGTTTAC-AG
316 TCGGTTGGCCTTCTAAAAAGGTTT-CTAG
* *
80911 AGTTGTTATCGGTTGGCCTTCTAAAAAGTTTTCAAAGTTGGTATCGGTTGGCCCTCTTTAAAATC
1 AGTTGGTATCGGTTGGCCTTCTAAAAAGTTTTCAAAGTTGGTATCGGTTGGCCTTCTTTAAAATC
80976 GAATTTCCAAAAGTTGGTATCGGTTGGCCTTCTTTAAAATCGAGTTTTTAAGAGTTGGTATCGGT
66 GAATTTCCAAAAGTTGGTATCGGTTGGCCTTCTTTAAAATCGAGTTTTTAAGAGTTGGTATCGGT
81041 TGGCCTTCTCTAAAAATCGAGTTTTTAAAAGTTGGTATCAGTTGGCCTTCTAAAAAGTTTTCAAA
131 TGGCCTTCTCTAAAAATCGAGTTTTTAAAAGTTGGTATCAGTTGGCCTTCTAAAAAGTTTTCAAA
* *
81106 GTTGGCATCGGTTGGCCTTCTAAAAATGTTTTCAGAGTTGGTATCGGTTGACCTTCACTAAAAAT
196 GTTGGCATCGGTTGGCCTTCTAAAAATGTTTTCAGAGTTGGTATCGGTTGGCCTTCTCTAAAAAT
*
81171 CGAGTTTTTAAAAGTTGGTATCGGTTGGCCTTCTAAAAAATTTTCAAAGTTGGCATCGGTTGGCC
261 CGAGTTTTTAAAAGTTGGTATCGGTTGGCCTTCTAAAAAGTTTTCAAAGTTGGCATCGGTTGGCC
*
81236 TTCTAAAAATGTTTCTAG
326 TTCTAAAAAGGTTTCTAG
* *
81254 AGTTGGTATCAGTTGGCCTTCTAAAAAGTTTTCAAAGTTGGTATCGGTTGGCCTTCTTTAAAACC
1 AGTTGGTATCGGTTGGCCTTCTAAAAAGTTTTCAAAGTTGGTATCGGTTGGCCTTCTTTAAAATC
81319 GAATTTCCAAAAGTTGGTATCGGTTGGCCTTCTTTAAAATCGAGTTTTTAAGAGTTGGTATCGGT
66 GAATTTCCAAAAGTTGGTATCGGTTGGCCTTCTTTAAAATCGAGTTTTTAAGAGTTGGTATCGGT
* *
81384 TGGCCTTCTCTAAAAATCGAGTTTTTAAAAGTTGGTATCGGTTGGCCTTCTAAAAAGGTTTCAAA
131 TGGCCTTCTCTAAAAATCGAGTTTTTAAAAGTTGGTATCAGTTGGCCTTCTAAAAAGTTTTCAAA
*
81449 GTTGGCATCGGTTGGCCTTCTAAAAATGTTTTCAGAGTTGGTATCGGTTGGCCTTCTCTAAAATT
196 GTTGGCATCGGTTGGCCTTCTAAAAATGTTTTCAGAGTTGGTATCGGTTGGCCTTCTCTAAAAAT
* * * * * *
81514 TGACTTTTTAAAAGTGGGCATCGGTTGGTCTTCTAAAAGGTTTTCAAAGTTGGCATCGG-TGGTC
261 CGAGTTTTTAAAAGTTGGTATCGGTTGGCCTTCTAAAAAGTTTTCAAAGTTGGCATCGGTTGG-C
* * *
81578 CTTCT-AAATGTTTTC-AA
325 CTTCTAAAAAGGTTTCTAG
* *
81595 AGTTGGCATCAGTTGGCCTTCT
1 AGTTGGTATCGGTTGGCCTTCT
81617 TAATGTTGTT
Statistics
Matches: 647, Mismatches: 47, Indels: 26
0.90 0.07 0.04
Matches are distributed among these distances:
340 4 0.01
341 32 0.05
342 57 0.09
343 443 0.68
344 12 0.02
346 5 0.01
347 8 0.01
348 42 0.06
349 44 0.07
ACGTcount: A:0.25, C:0.16, G:0.22, T:0.37
Consensus pattern (343 bp):
AGTTGGTATCGGTTGGCCTTCTAAAAAGTTTTCAAAGTTGGTATCGGTTGGCCTTCTTTAAAATC
GAATTTCCAAAAGTTGGTATCGGTTGGCCTTCTTTAAAATCGAGTTTTTAAGAGTTGGTATCGGT
TGGCCTTCTCTAAAAATCGAGTTTTTAAAAGTTGGTATCAGTTGGCCTTCTAAAAAGTTTTCAAA
GTTGGCATCGGTTGGCCTTCTAAAAATGTTTTCAGAGTTGGTATCGGTTGGCCTTCTCTAAAAAT
CGAGTTTTTAAAAGTTGGTATCGGTTGGCCTTCTAAAAAGTTTTCAAAGTTGGCATCGGTTGGCC
TTCTAAAAAGGTTTCTAG
Found at i:81622 original size:34 final size:33
Alignment explanation
Indices: 81406--81623 Score: 166
Period size: 35 Copynumber: 6.1 Consensus size: 33
81396 AAAATCGAGT
* * *
81406 TTTTAAAAGTTGGTATCGGTTGGCCTTCTAAAAAG
1 TTTTCAAAGTTGGCATC-GTTGGCCTTCT-AAATG
*
81441 GTTTCAAAGTTGGCATCGGTTGGCCTTCTAAAAATG
1 TTTTCAAAGTTGGCATC-GTTGGCCTTCT--AAATG
* *
81477 TTTTCAGAGTTGGTATCGGTTGGCCTTCTCTAAAATTTG
1 TTTTCAAAGTTGGCATC-GTTGGCC-T-TCT-AAA--TG
* * * *
81516 ACTTTTTAAAAGTGGGCATCGGTTGGTCTTCTAAAAGG
1 ---TTTTCAAAGTTGGCATC-GTTGGCCTTCT-AAATG
*
81554 TTTTCAAAGTTGGCATCGGTGGTCCTTCTAAATG
1 TTTTCAAAGTTGGCATCGTTGG-CCTTCTAAATG
*
81588 TTTTCAAAGTTGGCATCAGTTGGCCTTCTTAATG
1 TTTTCAAAGTTGGCATC-GTTGGCCTTCTAAATG
81622 TT
1 TT
81624 GTTTCCTAAA
Statistics
Matches: 153, Mismatches: 20, Indels: 21
0.79 0.10 0.11
Matches are distributed among these distances:
34 37 0.24
35 50 0.33
36 27 0.18
37 5 0.03
38 4 0.03
39 2 0.01
40 7 0.05
41 1 0.01
42 20 0.13
ACGTcount: A:0.23, C:0.15, G:0.23, T:0.39
Consensus pattern (33 bp):
TTTTCAAAGTTGGCATCGTTGGCCTTCTAAATG
Found at i:82866 original size:21 final size:21
Alignment explanation
Indices: 82836--82875 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
82826 AGATCTAGGA
*
82836 ATTTTGAGGTGTAG-TTTGGTG
1 ATTTTAAGGT-TAGATTTGGTG
82857 ATTTTAAGGTTAGATTTGG
1 ATTTTAAGGTTAGATTTGG
82876 GTTTGGGAGT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 3 0.18
21 14 0.82
ACGTcount: A:0.20, C:0.00, G:0.33, T:0.47
Consensus pattern (21 bp):
ATTTTAAGGTTAGATTTGGTG
Found at i:82962 original size:16 final size:17
Alignment explanation
Indices: 82941--82986 Score: 58
Period size: 19 Copynumber: 2.6 Consensus size: 17
82931 GGAAAAGTGA
82941 CCGGCGGTGGTGGTGGC
1 CCGGCGGTGGTGGTGGC
*
82958 CGGCGGCGGTAGTGGTGG-
1 C--CGGCGGTGGTGGTGGC
82976 CCGGCGGTGGT
1 CCGGCGGTGGT
82987 TGGTTTCCGG
Statistics
Matches: 25, Mismatches: 2, Indels: 5
0.78 0.06 0.16
Matches are distributed among these distances:
16 9 0.36
17 1 0.04
18 1 0.04
19 14 0.56
ACGTcount: A:0.02, C:0.22, G:0.59, T:0.17
Consensus pattern (17 bp):
CCGGCGGTGGTGGTGGC
Found at i:82966 original size:19 final size:19
Alignment explanation
Indices: 82942--82982 Score: 73
Period size: 19 Copynumber: 2.2 Consensus size: 19
82932 GAAAAGTGAC
*
82942 CGGCGGTGGTGGTGGCCGG
1 CGGCGGTAGTGGTGGCCGG
82961 CGGCGGTAGTGGTGGCCGG
1 CGGCGGTAGTGGTGGCCGG
82980 CGG
1 CGG
82983 TGGTTGGTTT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.02, C:0.22, G:0.61, T:0.15
Consensus pattern (19 bp):
CGGCGGTAGTGGTGGCCGG
Found at i:84226 original size:24 final size:23
Alignment explanation
Indices: 84189--84247 Score: 66
Period size: 24 Copynumber: 2.6 Consensus size: 23
84179 AGAAAAACTC
*
84189 AAAAGAATTGAAAAAAGTGAAAAA
1 AAAAGAATTAAAAAAAG-GAAAAA
* *
84213 AAAAGCATTAAAAAAAGGATAAA
1 AAAAGAATTAAAAAAAGGAAAAA
*
84236 AAATGAA-TAAAA
1 AAAAGAATTAAAA
84248 GGTTTAAGGT
Statistics
Matches: 30, Mismatches: 5, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
22 5 0.17
23 10 0.33
24 15 0.50
ACGTcount: A:0.71, C:0.02, G:0.14, T:0.14
Consensus pattern (23 bp):
AAAAGAATTAAAAAAAGGAAAAA
Found at i:87022 original size:25 final size:25
Alignment explanation
Indices: 86994--87044 Score: 102
Period size: 25 Copynumber: 2.0 Consensus size: 25
86984 GAATTGTAAT
86994 GAGATTTCACTAGGTTTGTTTGTTG
1 GAGATTTCACTAGGTTTGTTTGTTG
87019 GAGATTTCACTAGGTTTGTTTGTTG
1 GAGATTTCACTAGGTTTGTTTGTTG
87044 G
1 G
87045 GGAAGGGGTT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 26 1.00
ACGTcount: A:0.16, C:0.08, G:0.29, T:0.47
Consensus pattern (25 bp):
GAGATTTCACTAGGTTTGTTTGTTG
Found at i:88963 original size:29 final size:29
Alignment explanation
Indices: 88913--88991 Score: 86
Period size: 29 Copynumber: 2.7 Consensus size: 29
88903 TGAAGCATTT
* **
88913 TTAAAAGGTTTGGCACTGATTTGAGCAAG
1 TTAAAAGGTTTGGTACCAATTTGAGCAAG
**
88942 TTAAAAGGTTTGGTACCAATTTGAGCATT
1 TTAAAAGGTTTGGTACCAATTTGAGCAAG
*
88971 TCGTCAAAGGTTTGGTACCAA
1 T--TAAAAGGTTTGGTACCAA
88992 ATTTAGCTTT
Statistics
Matches: 42, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
29 25 0.60
31 17 0.40
ACGTcount: A:0.30, C:0.13, G:0.24, T:0.33
Consensus pattern (29 bp):
TTAAAAGGTTTGGTACCAATTTGAGCAAG
Found at i:94262 original size:24 final size:24
Alignment explanation
Indices: 94230--94301 Score: 101
Period size: 24 Copynumber: 3.0 Consensus size: 24
94220 AGGAAAATCT
94230 TTCGACCACATGGTGGTCGTGAGA
1 TTCGACCACATGGTGGTCGTGAGA
94254 TTCGACCACATGGTGGTCGTGAG-
1 TTCGACCACATGGTGGTCGTGAGA
* * *
94277 TAACGGCCACATAGTGGTCGTGAGA
1 T-TCGACCACATGGTGGTCGTGAGA
94302 AAAGACCAAT
Statistics
Matches: 43, Mismatches: 3, Indels: 3
0.88 0.06 0.06
Matches are distributed among these distances:
23 1 0.02
24 42 0.98
ACGTcount: A:0.22, C:0.21, G:0.33, T:0.24
Consensus pattern (24 bp):
TTCGACCACATGGTGGTCGTGAGA
Found at i:98555 original size:24 final size:24
Alignment explanation
Indices: 98523--98616 Score: 125
Period size: 24 Copynumber: 3.9 Consensus size: 24
98513 GAAAATCTTC
98523 CGACCACATGGTGGTCGTGAGATT
1 CGACCACATGGTGGTCGTGAGATT
**
98547 CGACCACATGGTGGTCGTGAGAAA
1 CGACCACATGGTGGTCGTGAGATT
* * *
98571 CGGCCACATAGTGGTTGTGAGATT
1 CGACCACATGGTGGTCGTGAGATT
**
98595 CGGGCACATGGTGGTCGTGAGA
1 CGACCACATGGTGGTCGTGAGA
98617 AAAGACCAAT
Statistics
Matches: 60, Mismatches: 10, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 60 1.00
ACGTcount: A:0.22, C:0.19, G:0.36, T:0.22
Consensus pattern (24 bp):
CGACCACATGGTGGTCGTGAGATT
Found at i:98603 original size:48 final size:48
Alignment explanation
Indices: 98526--98618 Score: 150
Period size: 48 Copynumber: 1.9 Consensus size: 48
98516 AATCTTCCGA
*
98526 CCACATGGTGGTCGTGAGATTCGACCACATGGTGGTCGTGAGAAACGG
1 CCACATAGTGGTCGTGAGATTCGACCACATGGTGGTCGTGAGAAACGG
* **
98574 CCACATAGTGGTTGTGAGATTCGGGCACATGGTGGTCGTGAGAAA
1 CCACATAGTGGTCGTGAGATTCGACCACATGGTGGTCGTGAGAAA
98619 AGACCAATGC
Statistics
Matches: 41, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
48 41 1.00
ACGTcount: A:0.24, C:0.18, G:0.35, T:0.23
Consensus pattern (48 bp):
CCACATAGTGGTCGTGAGATTCGACCACATGGTGGTCGTGAGAAACGG
Found at i:100317 original size:16 final size:15
Alignment explanation
Indices: 100279--100320 Score: 57
Period size: 15 Copynumber: 2.7 Consensus size: 15
100269 ACAGAGATTG
*
100279 ACAGAAAGCAACTAA
1 ACAGAAAACAACTAA
*
100294 ACAGAAAACAATTAA
1 ACAGAAAACAACTAA
100309 ACTAGAAAACAA
1 AC-AGAAAACAA
100321 AGCAGAGTAA
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
15 15 0.62
16 9 0.38
ACGTcount: A:0.64, C:0.17, G:0.10, T:0.10
Consensus pattern (15 bp):
ACAGAAAACAACTAA
Found at i:103622 original size:21 final size:21
Alignment explanation
Indices: 103598--103647 Score: 73
Period size: 21 Copynumber: 2.4 Consensus size: 21
103588 CGGCTTGGAA
*
103598 TGGCACGGGCATGACCGGTGG
1 TGGCACGGGCATAACCGGTGG
*
103619 TGGCACGGGCTTAACCGGTGG
1 TGGCACGGGCATAACCGGTGG
*
103640 TGTCACGG
1 TGGCACGG
103648 TGAATGGCCG
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.14, C:0.24, G:0.44, T:0.18
Consensus pattern (21 bp):
TGGCACGGGCATAACCGGTGG
Found at i:106784 original size:33 final size:31
Alignment explanation
Indices: 106736--106839 Score: 111
Period size: 33 Copynumber: 3.2 Consensus size: 31
106726 AAAATAAAAG
*
106736 AAAATATTTTTTTTTTCTAAAAACGCAGGAACA
1 AAAAT-TTTTTTTTTTCTAAAAACGCA-AAACA
*
106769 AGAAATTTTTTTTTTTTTAGAAAACGCAAAACA
1 A-AAATTTTTTTTTTTCTA-AAAACGCAAAACA
* *
106802 ACAATTTTTTTTTTTC-AAAAACACAAAACTA
1 AAAATTTTTTTTTTTCTAAAAACGCAAAAC-A
106833 ATAAATT
1 A-AAATT
106840 AAAAACGCAA
Statistics
Matches: 61, Mismatches: 6, Indels: 9
0.80 0.08 0.12
Matches are distributed among these distances:
30 11 0.18
31 3 0.05
32 17 0.28
33 18 0.30
34 12 0.20
ACGTcount: A:0.44, C:0.12, G:0.06, T:0.38
Consensus pattern (31 bp):
AAAATTTTTTTTTTTCTAAAAACGCAAAACA
Found at i:106785 original size:34 final size:32
Alignment explanation
Indices: 106736--106839 Score: 106
Period size: 34 Copynumber: 3.2 Consensus size: 32
106726 AAAATAAAAG
* *
106736 AAAATATTTTTTTTTTCTAAAAACGCAGGAACA
1 AAAATTTTTTTTTTTTCTAAAAACGCA-AAACA
106769 AGAAATTTTTTTTTTTT-TAGAAAACGCAAAACA
1 A-AAATTTTTTTTTTTTCTA-AAAACGCAAAACA
* *
106802 ACAA-TTTTTTTTTTTC-AAAAACACAAAACTA
1 AAAATTTTTTTTTTTTCTAAAAACGCAAAAC-A
106833 ATAAATT
1 A-AAATT
106840 AAAAACGCAA
Statistics
Matches: 60, Mismatches: 5, Indels: 12
0.78 0.06 0.16
Matches are distributed among these distances:
30 11 0.18
31 14 0.23
32 4 0.07
33 9 0.15
34 22 0.37
ACGTcount: A:0.44, C:0.12, G:0.06, T:0.38
Consensus pattern (32 bp):
AAAATTTTTTTTTTTTCTAAAAACGCAAAACA
Found at i:106810 original size:30 final size:30
Alignment explanation
Indices: 106741--106839 Score: 92
Period size: 30 Copynumber: 3.1 Consensus size: 30
106731 AAAAGAAAAT
*
106741 ATTTTTTTTTTCTAAAAACGCAGGAACAAGAA
1 ATTTTTTTTTT-TAAAAACGCA-AAACAAGAA
*
106773 ATTTTTTTTTTTTTAGAAAACGCAAAACAA-CA
1 A--TTTTTTTTTTTA-AAAACGCAAAACAAGAA
* *
106805 ATTTTTTTTTTTCAAAAACACAAAACTAATAA
1 ATTTTTTTTTTT-AAAAACGCAAAAC-AAGAA
106837 ATT
1 ATT
106840 AAAAACGCAA
Statistics
Matches: 57, Mismatches: 4, Indels: 12
0.78 0.05 0.16
Matches are distributed among these distances:
30 22 0.39
31 3 0.05
32 7 0.12
33 7 0.12
34 18 0.32
ACGTcount: A:0.42, C:0.12, G:0.06, T:0.39
Consensus pattern (30 bp):
ATTTTTTTTTTTAAAAACGCAAAACAAGAA
Found at i:107310 original size:16 final size:15
Alignment explanation
Indices: 107272--107313 Score: 57
Period size: 15 Copynumber: 2.7 Consensus size: 15
107262 ACAGAGATTG
*
107272 ACAGAAAGCAACTAA
1 ACAGAAAACAACTAA
*
107287 ACAGAAAACAATTAA
1 ACAGAAAACAACTAA
107302 ACTAGAAAACAA
1 AC-AGAAAACAA
107314 AGCAAAGGAA
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
15 15 0.62
16 9 0.38
ACGTcount: A:0.64, C:0.17, G:0.10, T:0.10
Consensus pattern (15 bp):
ACAGAAAACAACTAA
Found at i:114725 original size:2 final size:2
Alignment explanation
Indices: 114718--114742 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
114708 CACACTTTAA
114718 AC AC AC AC AC AC AC AC AC AC AC AC A
1 AC AC AC AC AC AC AC AC AC AC AC AC A
114743 TATATATATA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.48, G:0.00, T:0.00
Consensus pattern (2 bp):
AC
Found at i:117944 original size:40 final size:40
Alignment explanation
Indices: 117882--118001 Score: 152
Period size: 41 Copynumber: 3.0 Consensus size: 40
117872 ATCAGAACAG
*
117882 GTATGCAATATTCCTATTAACTACCAACAAGCAAAACCAA
1 GTATGCAATATTCCTATTAACTACCAGCAAGCAAAACCAA
* * * * *
117922 GTATGCAATATTCATATAAACTACGAGCAAAGCAAAAACAC
1 GTATGCAATATTCCTATTAACTACCAGC-AAGCAAAACCAA
* *
117963 GTATACAACATTCCTATTAACTACCAGCAAGC-AAACCAA
1 GTATGCAATATTCCTATTAACTACCAGCAAGCAAAACCAA
118002 TAACATTCTT
Statistics
Matches: 66, Mismatches: 13, Indels: 3
0.80 0.16 0.04
Matches are distributed among these distances:
39 5 0.08
40 28 0.42
41 33 0.50
ACGTcount: A:0.46, C:0.24, G:0.09, T:0.21
Consensus pattern (40 bp):
GTATGCAATATTCCTATTAACTACCAGCAAGCAAAACCAA
Found at i:117985 original size:41 final size:40
Alignment explanation
Indices: 117877--117997 Score: 152
Period size: 40 Copynumber: 3.0 Consensus size: 40
117867 ATTCAATCAG
* *
117877 AACAGGTATGCAATATTCCTATTAACTACCAACAAGCAAA
1 AACAAGTATGCAATATTCCTATTAACTACCAGCAAGCAAA
* * * *
117917 ACCAAGTATGCAATATTCATATAAACTACGAGCAAAGCAAA
1 AACAAGTATGCAATATTCCTATTAACTACCAGC-AAGCAAA
* * *
117958 AACACGTATACAACATTCCTATTAACTACCAGCAAGCAAA
1 AACAAGTATGCAATATTCCTATTAACTACCAGCAAGCAAA
117998 CCAATAACAT
Statistics
Matches: 67, Mismatches: 13, Indels: 2
0.82 0.16 0.02
Matches are distributed among these distances:
40 34 0.51
41 33 0.49
ACGTcount: A:0.46, C:0.23, G:0.10, T:0.21
Consensus pattern (40 bp):
AACAAGTATGCAATATTCCTATTAACTACCAGCAAGCAAA
Found at i:120426 original size:22 final size:22
Alignment explanation
Indices: 120398--120440 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 22
120388 CATTTCCTTT
*
120398 TTTAAAAAAAATAATAAGAAAA
1 TTTAAAAAAAATAAAAAGAAAA
*
120420 TTTAAAAAAAGTAAAAAGAAA
1 TTTAAAAAAAATAAAAAGAAA
120441 GATAAAAGGG
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:0.72, C:0.00, G:0.07, T:0.21
Consensus pattern (22 bp):
TTTAAAAAAAATAAAAAGAAAA
Found at i:120465 original size:9 final size:9
Alignment explanation
Indices: 120451--120475 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
120441 GATAAAAGGG
120451 AAAAAGAGA
1 AAAAAGAGA
120460 AAAAAGAGA
1 AAAAAGAGA
120469 AAAAAGA
1 AAAAAGA
120476 AAGATTCACT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 16 1.00
ACGTcount: A:0.80, C:0.00, G:0.20, T:0.00
Consensus pattern (9 bp):
AAAAAGAGA
Found at i:124870 original size:22 final size:22
Alignment explanation
Indices: 124842--124887 Score: 92
Period size: 22 Copynumber: 2.1 Consensus size: 22
124832 AATTGCTTAT
124842 AGTCGACTTCTCTCTTGAACCA
1 AGTCGACTTCTCTCTTGAACCA
124864 AGTCGACTTCTCTCTTGAACCA
1 AGTCGACTTCTCTCTTGAACCA
124886 AG
1 AG
124888 GTTATCGAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.24, C:0.30, G:0.15, T:0.30
Consensus pattern (22 bp):
AGTCGACTTCTCTCTTGAACCA
Found at i:132080 original size:22 final size:21
Alignment explanation
Indices: 132028--132081 Score: 60
Period size: 19 Copynumber: 2.6 Consensus size: 21
132018 TGCTTCTTGA
132028 AATAATTCTTC-AATGATCTTC
1 AATAA-TCTTCAAATGATCTTC
*
132049 -A-AATCTTCAAATTATCTTC
1 AATAATCTTCAAATGATCTTC
132068 AATAAGTCTTCAAA
1 AATAA-TCTTCAAA
132082 CACGAACTTC
Statistics
Matches: 28, Mismatches: 1, Indels: 7
0.78 0.03 0.19
Matches are distributed among these distances:
18 5 0.18
19 11 0.39
20 2 0.07
21 2 0.07
22 8 0.29
ACGTcount: A:0.39, C:0.19, G:0.04, T:0.39
Consensus pattern (21 bp):
AATAATCTTCAAATGATCTTC
Found at i:133107 original size:26 final size:26
Alignment explanation
Indices: 133078--133127 Score: 66
Period size: 26 Copynumber: 1.9 Consensus size: 26
133068 AATCAGGGAA
*
133078 CAATT-AACAAGGGCAGCGATTCAATT
1 CAATTAAACAAGGCCA-CGATTCAATT
*
133104 CAATTAAACAATGCCACGATTCAA
1 CAATTAAACAAGGCCACGATTCAA
133128 CACATTTGAG
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
26 13 0.62
27 8 0.38
ACGTcount: A:0.42, C:0.22, G:0.14, T:0.22
Consensus pattern (26 bp):
CAATTAAACAAGGCCACGATTCAATT
Found at i:136056 original size:15 final size:15
Alignment explanation
Indices: 136038--136084 Score: 58
Period size: 15 Copynumber: 3.1 Consensus size: 15
136028 CAAGGGCTGA
*
136038 AATTAATTAATCATT
1 AATTAATTAATAATT
136053 AATTAATTAATAATT
1 AATTAATTAATAATT
* *
136068 ATTTTATTAAATAATT
1 AATTAATT-AATAATT
136084 A
1 A
136085 TTATTAAAAA
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
15 20 0.71
16 8 0.29
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (15 bp):
AATTAATTAATAATT
Found at i:136085 original size:11 final size:11
Alignment explanation
Indices: 136039--136091 Score: 54
Period size: 11 Copynumber: 4.8 Consensus size: 11
136029 AAGGGCTGAA
*
136039 ATTAATTAATC
1 ATTAATTAATT
136050 ATTAATTAATT
1 ATTAATTAATT
* *
136061 AATAATTATTTT
1 ATTAATTA-ATT
*
136073 ATTAAATAATT
1 ATTAATTAATT
136084 ATT-ATTAA
1 ATTAATTAA
136092 AAATAGCACA
Statistics
Matches: 34, Mismatches: 7, Indels: 3
0.77 0.16 0.07
Matches are distributed among these distances:
10 4 0.12
11 22 0.65
12 8 0.24
ACGTcount: A:0.47, C:0.02, G:0.00, T:0.51
Consensus pattern (11 bp):
ATTAATTAATT
Found at i:142114 original size:18 final size:19
Alignment explanation
Indices: 142088--142141 Score: 67
Period size: 19 Copynumber: 2.8 Consensus size: 19
142078 GAGCTTTAGG
142088 TTTATTTTGGGCTTTTA-AT-
1 TTTA-TTTGGG-TTTTAGATC
142107 TTTATTTGGGTTTTAGATC
1 TTTATTTGGGTTTTAGATC
142126 TTTATTTGGGTATTTA
1 TTTATTTGGGT-TTTA
142142 TTTGTGAGTT
Statistics
Matches: 32, Mismatches: 0, Indels: 5
0.86 0.00 0.14
Matches are distributed among these distances:
17 5 0.16
18 8 0.25
19 15 0.47
20 4 0.12
ACGTcount: A:0.17, C:0.04, G:0.19, T:0.61
Consensus pattern (19 bp):
TTTATTTGGGTTTTAGATC
Found at i:142224 original size:20 final size:20
Alignment explanation
Indices: 142185--142234 Score: 66
Period size: 20 Copynumber: 2.5 Consensus size: 20
142175 GTTTCAGTCT
*
142185 AAGTTAATTAAGTGGATTAG
1 AAGTTAATTAAGTAGATTAG
142205 AAGTTAATTAAGTTAG-TTAG
1 AAGTTAATTAAG-TAGATTAG
*
142225 AAGGTAATTA
1 AAGTTAATTA
142235 GGACTTGTTT
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
20 25 0.93
21 2 0.07
ACGTcount: A:0.42, C:0.00, G:0.22, T:0.36
Consensus pattern (20 bp):
AAGTTAATTAAGTAGATTAG
Found at i:142601 original size:36 final size:36
Alignment explanation
Indices: 142551--142839 Score: 361
Period size: 36 Copynumber: 8.0 Consensus size: 36
142541 TTCATGCATC
* * *
142551 AAGTAAAAAT-AGTCAAAGACTTAATTTAGTGAAATT
1 AAGT-AAAATCAGTCAAAGACTTAATTCAGGGTAATT
*
142587 AAGTAAAACCAGTCAAAGACTTAATTCAGGGTAATT
1 AAGTAAAATCAGTCAAAGACTTAATTCAGGGTAATT
*
142623 AAGTAAAATCAGT-ATAGGACTTAATTCAGGGTAATT
1 AAGTAAAATCAGTCA-AAGACTTAATTCAGGGTAATT
* * *
142659 GAGTAAAATCAATCAAAGACTTAATTCAAGGTAATT
1 AAGTAAAATCAGTCAAAGACTTAATTCAGGGTAATT
142695 AAGTAAAATCAGTCAAAGACTTAATTCAGGGTAATT
1 AAGTAAAATCAGTCAAAGACTTAATTCAGGGTAATT
* * *
142731 AAGTAAAATAAGT-ATAGGACTTAATTCAAGGTAATT
1 AAGTAAAATCAGTCA-AAGACTTAATTCAGGGTAATT
* * * *
142767 AAGTGAACTCAATCAAAGACTTAATTCAGGGTAGTT
1 AAGTAAAATCAGTCAAAGACTTAATTCAGGGTAATT
**
142803 AAGTAAAATCAGT-AAAGGACTTAATTCAATGTAATT
1 AAGTAAAATCAGTCAAA-GACTTAATTCAGGGTAATT
142839 A
1 A
142840 CAGTCAAGAA
Statistics
Matches: 218, Mismatches: 29, Indels: 12
0.84 0.11 0.05
Matches are distributed among these distances:
35 9 0.04
36 207 0.95
37 2 0.01
ACGTcount: A:0.45, C:0.10, G:0.16, T:0.29
Consensus pattern (36 bp):
AAGTAAAATCAGTCAAAGACTTAATTCAGGGTAATT
Found at i:142681 original size:108 final size:107
Alignment explanation
Indices: 142563--143112 Score: 604
Period size: 108 Copynumber: 5.2 Consensus size: 107
142553 GTAAAAATAG
* * *
142563 TCAAAGACTTAATTTAGTGAAATTAAGTAAAACCAGTCAAAGACTTAATTCAGGGTAATTAAGTA
1 TCAAAGACTTAATTTAG-GTAATTAAGTAAAATCAGTCAAAGACTTAATTCAAGGTAATTAAGTA
* *
142628 AAATCAGTATAGGACTTAATTCAGGGTAATTGAGTAAAATCAA
65 AAATCAGTATAGGACTTAATTCAAGGTAATTAAGTAAAATCAA
* *
142671 TCAAAGACTTAATTCAAGGTAATTAAGTAAAATCAGTCAAAGACTTAATTCAGGGTAATTAAGTA
1 TCAAAGACTTAATT-TAGGTAATTAAGTAAAATCAGTCAAAGACTTAATTCAAGGTAATTAAGTA
* * *
142736 AAATAAGTATAGGACTTAATTCAAGGTAATTAAGTGAACTCAA
65 AAATCAGTATAGGACTTAATTCAAGGTAATTAAGTAAAATCAA
* * *
142779 TCAAAGACTTAATTCAGGGTAGTTAAGTAAAATCAGT-AAAGGACTTAATTCAATGTAA-T---T
1 TCAAAGACTTAATTTA-GGTAATTAAGTAAAATCAGTCAAA-GACTTAATTCAAGGTAATTAAGT
* * * *
142839 ---A-CAGTCA-AGAACTTAATTCAAGATAATTAAATAAAATCAG
64 AAAATCAGT-ATAGGACTTAATTCAAGGTAATTAAGTAAAATCAA
* * * *
142879 TTAAAGACTTAATTCAGGGCAATTAAGTAAAATCAGTCAAAGACTTAATTCATGGTAATTAAGTA
1 TCAAAGACTTAATTTA-GGTAATTAAGTAAAATCAGTCAAAGACTTAATTCAAGGTAATTAAGTA
* * * * *
142944 AAATCAATCAT-GGGCTTAATTCAGGGCAATTAAGTATAATCAA
65 AAATCAGT-ATAGGACTTAATTCAAGGTAATTAAGTAAAATCAA
* * * *
142987 T-AAAGGACTTTATTCTCGGTAATTAAGTAAAATCAGTCAAGGACTTAGTTCAAGGTAATTAAGT
1 TCAAA-GACTTAATT-TAGGTAATTAAGTAAAATCAGTCAAAGACTTAATTCAAGGTAATTAAGT
* * * * *
143051 AAAATTAGAAAAGGACTTAATTCAAGGTAATTAAATAAAATCAG
64 AAAATCAGTATAGGACTTAATTCAAGGTAATTAAGTAAAATCAA
143095 T-AAAGAACTTAATTTAGG
1 TCAAAG-ACTTAATTTAGG
143113 GGTTGTTTGG
Statistics
Matches: 372, Mismatches: 52, Indels: 37
0.81 0.11 0.08
Matches are distributed among these distances:
100 79 0.21
101 6 0.02
104 2 0.01
107 14 0.04
108 269 0.72
109 2 0.01
ACGTcount: A:0.45, C:0.10, G:0.16, T:0.29
Consensus pattern (107 bp):
TCAAAGACTTAATTTAGGTAATTAAGTAAAATCAGTCAAAGACTTAATTCAAGGTAATTAAGTAA
AATCAGTATAGGACTTAATTCAAGGTAATTAAGTAAAATCAA
Found at i:142852 original size:28 final size:28
Alignment explanation
Indices: 142812--142867 Score: 78
Period size: 28 Copynumber: 2.0 Consensus size: 28
142802 TAAGTAAAAT
*
142812 CAGTAAAGGACTTAATTCAATG-TAATTA
1 CAGTAAAGAACTTAATTCAA-GATAATTA
*
142840 CAGTCAAGAACTTAATTCAAGATAATTA
1 CAGTAAAGAACTTAATTCAAGATAATTA
142868 AATAAAATCA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
27 1 0.04
28 24 0.96
ACGTcount: A:0.45, C:0.12, G:0.12, T:0.30
Consensus pattern (28 bp):
CAGTAAAGAACTTAATTCAAGATAATTA
Found at i:142885 original size:100 final size:100
Alignment explanation
Indices: 142749--142939 Score: 278
Period size: 100 Copynumber: 1.9 Consensus size: 100
142739 TAAGTATAGG
* * * * * *
142749 ACTTAATTCAAGGTAATTAAGTGAACTCAATCAAAGACTTAATTCAGGGTAGTTAAGTAAAATCA
1 ACTTAATTCAAGATAATTAAATAAAATCAATCAAAGACTTAATTCAGGGCAATTAAGTAAAATCA
142814 GT-AAAGGACTTAATTCAAT-GTAATTACAGTCAAGA
66 GTCAAA-GACTTAATTC-ATGGTAATTACAGTCAAGA
* *
142849 ACTTAATTCAAGATAATTAAATAAAATCAGTTAAAGACTTAATTCAGGGCAATTAAGTAAAATCA
1 ACTTAATTCAAGATAATTAAATAAAATCAATCAAAGACTTAATTCAGGGCAATTAAGTAAAATCA
142914 GTCAAAGACTTAATTCATGGTAATTA
66 GTCAAAGACTTAATTCATGGTAATTA
142940 AGTAAAATCA
Statistics
Matches: 81, Mismatches: 8, Indels: 4
0.87 0.09 0.04
Matches are distributed among these distances:
99 2 0.02
100 76 0.94
101 3 0.04
ACGTcount: A:0.45, C:0.12, G:0.14, T:0.30
Consensus pattern (100 bp):
ACTTAATTCAAGATAATTAAATAAAATCAATCAAAGACTTAATTCAGGGCAATTAAGTAAAATCA
GTCAAAGACTTAATTCATGGTAATTACAGTCAAGA
Found at i:142889 original size:36 final size:36
Alignment explanation
Indices: 142840--143108 Score: 276
Period size: 36 Copynumber: 7.5 Consensus size: 36
142830 AATGTAATTA
* *
142840 CAGTC-AAGAACTTAATTCAAGATAATTAAATAAAAT
1 CAGTCAAAG-ACTTAATTCAAGGTAATTAAGTAAAAT
* * *
142876 CAGTTAAAGACTTAATTCAGGGCAATTAAGTAAAAT
1 CAGTCAAAGACTTAATTCAAGGTAATTAAGTAAAAT
*
142912 CAGTCAAAGACTTAATTCATGGTAATTAAGTAAAAT
1 CAGTCAAAGACTTAATTCAAGGTAATTAAGTAAAAT
* ** * * * *
142948 CAATCATGGGCTTAATTCAGGGCAATTAAGTATAAT
1 CAGTCAAAGACTTAATTCAAGGTAATTAAGTAAAAT
* * **
142984 CAAT-AAAGGACTTTATTCTCGGTAATTAAGTAAAAT
1 CAGTCAAA-GACTTAATTCAAGGTAATTAAGTAAAAT
* *
143020 CAGTCAAGGACTTAGTTCAAGGTAATTAAGTAAAAT
1 CAGTCAAAGACTTAATTCAAGGTAATTAAGTAAAAT
* * *
143056 TAG-AAAAGGACTTAATTCAAGGTAATTAAATAAAAT
1 CAGTCAAA-GACTTAATTCAAGGTAATTAAGTAAAAT
143092 CAGT-AAAGAACTTAATT
1 CAGTCAAAG-ACTTAATT
143109 TAGGGGTTGT
Statistics
Matches: 192, Mismatches: 35, Indels: 12
0.80 0.15 0.05
Matches are distributed among these distances:
35 4 0.02
36 183 0.95
37 5 0.03
ACGTcount: A:0.45, C:0.11, G:0.15, T:0.29
Consensus pattern (36 bp):
CAGTCAAAGACTTAATTCAAGGTAATTAAGTAAAAT
Found at i:142925 original size:72 final size:73
Alignment explanation
Indices: 142840--143113 Score: 306
Period size: 72 Copynumber: 3.8 Consensus size: 73
142830 AATGTAATTA
* * *
142840 CAGTC-AAGAACTTAATTCAAGATAATTAAATAAAATCAGTTAAAGACTTAATTCAGGGCAATTA
1 CAGTCAAAGGACTTAATTCAAGGTAATTAAATAAAATCAGTCAAAGACTTAATTCAGGGCAATTA
142904 AGTAAAAT
66 AGTAAAAT
* * * ** *
142912 CAGTCAAA-GACTTAATTCATGGTAATTAAGTAAAATCAATCATGGGCTTAATTCAGGGCAATTA
1 CAGTCAAAGGACTTAATTCAAGGTAATTAAATAAAATCAGTCAAAGACTTAATTCAGGGCAATTA
*
142976 AGTATAAT
66 AGTAAAAT
* * ** * * * * *
142984 CAAT-AAAGGACTTTATTCTCGGTAATTAAGTAAAATCAGTCAAGGACTTAGTTCAAGGTAATTA
1 CAGTCAAAGGACTTAATTCAAGGTAATTAAATAAAATCAGTCAAAGACTTAATTCAGGGCAATTA
143048 AGTAAAAT
66 AGTAAAAT
* * *
143056 TAG-AAAAGGACTTAATTCAAGGTAATTAAATAAAATCAGT-AAAGAACTTAATTTAGGG
1 CAGTCAAAGGACTTAATTCAAGGTAATTAAATAAAATCAGTCAAAG-ACTTAATTCAGGG
143114 GTTGTTTGGT
Statistics
Matches: 167, Mismatches: 31, Indels: 8
0.81 0.15 0.04
Matches are distributed among these distances:
71 6 0.04
72 159 0.95
73 2 0.01
ACGTcount: A:0.45, C:0.11, G:0.16, T:0.29
Consensus pattern (73 bp):
CAGTCAAAGGACTTAATTCAAGGTAATTAAATAAAATCAGTCAAAGACTTAATTCAGGGCAATTA
AGTAAAAT
Found at i:144091 original size:22 final size:23
Alignment explanation
Indices: 144066--144112 Score: 60
Period size: 22 Copynumber: 2.1 Consensus size: 23
144056 ACATTCTCAT
*
144066 TATTATAACTCATAGAACA-TCA
1 TATTATAACTCATAAAACATTCA
* *
144088 TATTTTCACTCATAAAACATTCA
1 TATTATAACTCATAAAACATTCA
144111 TA
1 TA
144113 CAGCTACTGA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
22 16 0.76
23 5 0.24
ACGTcount: A:0.43, C:0.19, G:0.02, T:0.36
Consensus pattern (23 bp):
TATTATAACTCATAAAACATTCA
Found at i:148498 original size:2 final size:2
Alignment explanation
Indices: 148491--148525 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
148481 CCACGTGTCT
148491 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
148526 TTTTCTATTT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.00, C:0.49, G:0.00, T:0.51
Consensus pattern (2 bp):
TC
Found at i:150713 original size:21 final size:21
Alignment explanation
Indices: 150687--150727 Score: 73
Period size: 21 Copynumber: 2.0 Consensus size: 21
150677 GGTAAGTAAT
150687 TTAGTTGTTGTTTCCTTAAAC
1 TTAGTTGTTGTTTCCTTAAAC
*
150708 TTAGTTGTTGTTTTCTTAAA
1 TTAGTTGTTGTTTCCTTAAA
150728 GATTCACTTG
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.20, C:0.10, G:0.15, T:0.56
Consensus pattern (21 bp):
TTAGTTGTTGTTTCCTTAAAC
Found at i:151163 original size:12 final size:12
Alignment explanation
Indices: 151146--151171 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
151136 TACATAATTA
151146 TTGGTGTTTATT
1 TTGGTGTTTATT
151158 TTGGTGTTTATT
1 TTGGTGTTTATT
151170 TT
1 TT
151172 ATCAATTTTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.08, C:0.00, G:0.23, T:0.69
Consensus pattern (12 bp):
TTGGTGTTTATT
Found at i:152521 original size:22 final size:22
Alignment explanation
Indices: 152463--152522 Score: 54
Period size: 22 Copynumber: 2.7 Consensus size: 22
152453 CGGGGAACAC
*
152463 TTTAAT-TTCTATTTTAATTTG
1 TTTAATCTTCTCTTTTAATTTG
*
152484 TTCT-ATCTTTTACTTTT-ATTTAG
1 TT-TAATCTTCT-CTTTTAATTT-G
152507 TTTAATCTTCTCTTTT
1 TTTAATCTTCTCTTTT
152523 CTTTGATTTT
Statistics
Matches: 31, Mismatches: 3, Indels: 9
0.72 0.07 0.21
Matches are distributed among these distances:
21 4 0.13
22 14 0.45
23 13 0.42
ACGTcount: A:0.18, C:0.12, G:0.03, T:0.67
Consensus pattern (22 bp):
TTTAATCTTCTCTTTTAATTTG
Found at i:154678 original size:84 final size:83
Alignment explanation
Indices: 154577--154732 Score: 233
Period size: 84 Copynumber: 1.9 Consensus size: 83
154567 TACTTGAGAT
* *
154577 AAAAACATTTTTCAAAAC-AAATTTTATTCCATCTTTTAAATTTCTATTTTTCCCTTTGTTTTGG
1 AAAAACATTTTTCAAAACGAAATTTTATTACATCTTTTAAATTTCTA-TTTTCCCTTTGTTTTAG
*
154641 ATTTTCTTCTTGAGATAAA
65 ATATTCTTCTTGAGATAAA
* * *
154660 AAAAGACATTTTTCAAAACGAATTTTTATTACATCTTTTAATTTTCTATTTTCCCTTTTTTTTAG
1 AAAA-ACATTTTTCAAAACGAAATTTTATTACATCTTTTAAATTTCTATTTTCCCTTTGTTTTAG
154725 ATATTCTT
65 ATATTCTT
154733 TAATTTCTTA
Statistics
Matches: 65, Mismatches: 6, Indels: 3
0.88 0.08 0.04
Matches are distributed among these distances:
83 4 0.06
84 36 0.55
85 25 0.38
ACGTcount: A:0.29, C:0.14, G:0.05, T:0.51
Consensus pattern (83 bp):
AAAAACATTTTTCAAAACGAAATTTTATTACATCTTTTAAATTTCTATTTTCCCTTTGTTTTAGA
TATTCTTCTTGAGATAAA
Found at i:155627 original size:45 final size:47
Alignment explanation
Indices: 155578--155689 Score: 149
Period size: 48 Copynumber: 2.4 Consensus size: 47
155568 CTGAAACCCT
* *
155578 AGCCGCCCT-CTTCACCGCGA-C-AGTCGCCTTGCTCCACCGCATCGG
1 AGCCGCCCTGCTCCACCGC-ATCGAGCCGCCTTGCTCCACCGCATCGG
*
155623 AGCCGCCTTGCTCCACCGCATCGGAGCCGCCTTGCTCCACCGCATCGG
1 AGCCGCCCTGCTCCACCGCATC-GAGCCGCCTTGCTCCACCGCATCGG
*
155671 AGCCGCCTTGCTCCACCGC
1 AGCCGCCCTGCTCCACCGC
155690 TCAAGATAAG
Statistics
Matches: 60, Mismatches: 3, Indels: 5
0.88 0.04 0.07
Matches are distributed among these distances:
45 9 0.15
46 9 0.15
48 42 0.70
ACGTcount: A:0.12, C:0.47, G:0.23, T:0.17
Consensus pattern (47 bp):
AGCCGCCCTGCTCCACCGCATCGAGCCGCCTTGCTCCACCGCATCGG
Found at i:155631 original size:24 final size:24
Alignment explanation
Indices: 155602--155689 Score: 176
Period size: 24 Copynumber: 3.7 Consensus size: 24
155592 CCGCGACAGT
155602 CGCCTTGCTCCACCGCATCGGAGC
1 CGCCTTGCTCCACCGCATCGGAGC
155626 CGCCTTGCTCCACCGCATCGGAGC
1 CGCCTTGCTCCACCGCATCGGAGC
155650 CGCCTTGCTCCACCGCATCGGAGC
1 CGCCTTGCTCCACCGCATCGGAGC
155674 CGCCTTGCTCCACCGC
1 CGCCTTGCTCCACCGC
155690 TCAAGATAAG
Statistics
Matches: 64, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 64 1.00
ACGTcount: A:0.11, C:0.48, G:0.24, T:0.17
Consensus pattern (24 bp):
CGCCTTGCTCCACCGCATCGGAGC
Found at i:158537 original size:33 final size:33
Alignment explanation
Indices: 158436--158573 Score: 129
Period size: 33 Copynumber: 4.2 Consensus size: 33
158426 TTGCAAAGAG
* * * *
158436 TGTTTTAGATGTTGTTAGTGATGATACTAAACC
1 TGTTTTAGGTGTTGTTTGTGATGAAACTAAATC
** * *
158469 TAATTTAAGTGTTGTTTGTGATGACACTAAATC
1 TGTTTTAGGTGTTGTTTGTGATGAAACTAAATC
158502 TGTTTTAGGTGTTGTTTGTGATGAAAC-AAATTC
1 TGTTTTAGGTGTTGTTTGTGATGAAACTAAA-TC
* **
158535 TGTTTT-GGATGCTAATTGTGATGAAAAC-AAATC
1 TGTTTTAGG-TGTTGTTTGTGATG-AAACTAAATC
158568 TGTTTT
1 TGTTTT
158574 GGTTGATCAT
Statistics
Matches: 88, Mismatches: 14, Indels: 6
0.81 0.13 0.06
Matches are distributed among these distances:
32 5 0.06
33 76 0.86
34 7 0.08
ACGTcount: A:0.28, C:0.08, G:0.21, T:0.43
Consensus pattern (33 bp):
TGTTTTAGGTGTTGTTTGTGATGAAACTAAATC
Found at i:166013 original size:2 final size:2
Alignment explanation
Indices: 166008--166039 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
165998 TATGATAATG
166008 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
166040 TACATTACTA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:169129 original size:42 final size:43
Alignment explanation
Indices: 169082--169171 Score: 137
Period size: 45 Copynumber: 2.1 Consensus size: 43
169072 CATTATCTTA
*
169082 ATTCTA-CTCCATCTCTAGGTAATTCATCAAAATAAAACTAAT
1 ATTCTACCTCCATCTCTAGATAATTCATCAAAATAAAACTAAT
*
169124 ATTCTACTCCTCCATCTCTAGATAATTCATCAAAATAAAGCTAAT
1 ATTCTA--CCTCCATCTCTAGATAATTCATCAAAATAAAACTAAT
169169 ATT
1 ATT
169172 AATTGTTAAA
Statistics
Matches: 43, Mismatches: 2, Indels: 3
0.90 0.04 0.06
Matches are distributed among these distances:
42 6 0.14
45 37 0.86
ACGTcount: A:0.39, C:0.22, G:0.04, T:0.34
Consensus pattern (43 bp):
ATTCTACCTCCATCTCTAGATAATTCATCAAAATAAAACTAAT
Found at i:171847 original size:14 final size:14
Alignment explanation
Indices: 171828--171867 Score: 53
Period size: 14 Copynumber: 2.8 Consensus size: 14
171818 TGAGATTTTT
171828 AATAATAATTATTC
1 AATAATAATTATTC
* *
171842 AATAATTATTATTT
1 AATAATAATTATTC
171856 AATTAATAATTA
1 AA-TAATAATTA
171868 ATTAATTTCA
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
14 14 0.64
15 8 0.36
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (14 bp):
AATAATAATTATTC
Found at i:172243 original size:13 final size:13
Alignment explanation
Indices: 172225--172250 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
172215 AAGGTAACAA
172225 CAAAAATCATCAC
1 CAAAAATCATCAC
172238 CAAAAATCATCAC
1 CAAAAATCATCAC
172251 TCATGCCAAG
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:0.54, C:0.31, G:0.00, T:0.15
Consensus pattern (13 bp):
CAAAAATCATCAC
Found at i:173822 original size:22 final size:22
Alignment explanation
Indices: 173773--173823 Score: 59
Period size: 22 Copynumber: 2.3 Consensus size: 22
173763 AAATATCACC
* **
173773 ATAATTATTTTTGGCAACCATA
1 ATAATTATTTTTGCCAAAAATA
173795 ATAATTATTTTTGCCAAGAAATA
1 ATAATTATTTTTGCCAA-AAATA
173818 A-AATTA
1 ATAATTA
173824 GGCAATAATT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
22 21 0.84
23 4 0.16
ACGTcount: A:0.43, C:0.10, G:0.08, T:0.39
Consensus pattern (22 bp):
ATAATTATTTTTGCCAAAAATA
Found at i:182449 original size:6 final size:6
Alignment explanation
Indices: 182438--182466 Score: 58
Period size: 6 Copynumber: 4.8 Consensus size: 6
182428 ATTCCTTGCG
182438 CCATTA CCATTA CCATTA CCATTA CCATT
1 CCATTA CCATTA CCATTA CCATTA CCATT
182467 CCTCACGTGG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.31, C:0.34, G:0.00, T:0.34
Consensus pattern (6 bp):
CCATTA
Found at i:185138 original size:14 final size:14
Alignment explanation
Indices: 185119--185158 Score: 53
Period size: 14 Copynumber: 2.8 Consensus size: 14
185109 TGAGATTTTT
185119 AATAATAATTATTC
1 AATAATAATTATTC
* *
185133 AATAATTATTATTT
1 AATAATAATTATTC
185147 AATTAATAATTA
1 AA-TAATAATTA
185159 ATTAATTTCA
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
14 14 0.64
15 8 0.36
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (14 bp):
AATAATAATTATTC
Found at i:204712 original size:225 final size:225
Alignment explanation
Indices: 204315--204773 Score: 909
Period size: 225 Copynumber: 2.0 Consensus size: 225
204305 CGTCCAATGG
*
204315 GATTAGTAAACCTTATTTATTTGTCGTGAATGAGTTTGGTTTTACTTGTTATGCATGTGTGAATA
1 GATTAATAAACCTTATTTATTTGTCGTGAATGAGTTTGGTTTTACTTGTTATGCATGTGTGAATA
204380 ATTGTTCTTAATGCTTTTTTCTTATCAATTATTAAGCCTGGGAGGGTGTCAACAAAGCGAGTCCG
66 ATTGTTCTTAATGCTTTTTTCTTATCAATTATTAAGCCTGGGAGGGTGTCAACAAAGCGAGTCCG
204445 GTAGGACCTGCCGCCCACGACTTGAGTACCCCTACTAGATGTTTCTGGGAGTCGCCACTAATCTT
131 GTAGGACCTGCCGCCCACGACTTGAGTACCCCTACTAGATGTTTCTGGGAGTCGCCACTAATCTT
204510 TTTTACCTAGGTGTGATTAGCCACCTATCC
196 TTTTACCTAGGTGTGATTAGCCACCTATCC
204540 GATTAATAAACCTTATTTATTTGTCGTGAATGAGTTTGGTTTTACTTGTTATGCATGTGTGAATA
1 GATTAATAAACCTTATTTATTTGTCGTGAATGAGTTTGGTTTTACTTGTTATGCATGTGTGAATA
204605 ATTGTTCTTAATGCTTTTTTCTTATCAATTATTAAGCCTGGGAGGGTGTCAACAAAGCGAGTCCG
66 ATTGTTCTTAATGCTTTTTTCTTATCAATTATTAAGCCTGGGAGGGTGTCAACAAAGCGAGTCCG
204670 GTAGGACCTGCCGCCCACGACTTGAGTACCCCTACTAGATGTTTCTGGGAGTCGCCACTAATCTT
131 GTAGGACCTGCCGCCCACGACTTGAGTACCCCTACTAGATGTTTCTGGGAGTCGCCACTAATCTT
204735 TTTTACCTAGGTGTGATTAGCCACCTATCC
196 TTTTACCTAGGTGTGATTAGCCACCTATCC
204765 GATTAATAA
1 GATTAATAA
204774 GTCTAATATT
Statistics
Matches: 233, Mismatches: 1, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
225 233 1.00
ACGTcount: A:0.24, C:0.19, G:0.21, T:0.36
Consensus pattern (225 bp):
GATTAATAAACCTTATTTATTTGTCGTGAATGAGTTTGGTTTTACTTGTTATGCATGTGTGAATA
ATTGTTCTTAATGCTTTTTTCTTATCAATTATTAAGCCTGGGAGGGTGTCAACAAAGCGAGTCCG
GTAGGACCTGCCGCCCACGACTTGAGTACCCCTACTAGATGTTTCTGGGAGTCGCCACTAATCTT
TTTTACCTAGGTGTGATTAGCCACCTATCC
Found at i:205295 original size:33 final size:33
Alignment explanation
Indices: 205252--205373 Score: 199
Period size: 33 Copynumber: 3.6 Consensus size: 33
205242 AATTAAGTTC
* *
205252 TTTATTGACTTTACTTAATTACCCCGAATTAAG
1 TTTATCGACTTTACTTAATTACCCAGAATTAAG
205285 TTTATCGACTTTACTTAATTACCCAGAATTAAG
1 TTTATCGACTTTACTTAATTACCCAGAATTAAG
205318 TTTATCGACTTTACTTAATTACCCAGAATTAAG
1 TTTATCGACTTTACTTAATTACCCAGAATTAAG
*
205351 TTTATTGACTCTTTACTTAATTA
1 TTTATCGA--CTTTACTTAATTA
205374 TATTACATTG
Statistics
Matches: 84, Mismatches: 3, Indels: 2
0.94 0.03 0.02
Matches are distributed among these distances:
33 71 0.85
35 13 0.15
ACGTcount: A:0.31, C:0.17, G:0.08, T:0.43
Consensus pattern (33 bp):
TTTATCGACTTTACTTAATTACCCAGAATTAAG
Found at i:205591 original size:111 final size:107
Alignment explanation
Indices: 205410--205716 Score: 343
Period size: 109 Copynumber: 2.8 Consensus size: 107
205400 GATTTTACTT
* * ** ** * *
205410 AATTTCCCTG-AATTAAGTCCTTGTTTGCTTTTACTTAATTACCTCGAAATAAGTCTTTGCTTGA
1 AATTTCCTTGAAATTAAGTCTTTACTTGCTTTTACCCAATTACCTTGAAGTAAGTCTTTGCTTG-
* *
205474 TTTTACCCAATTTCCTTGAAATTAAGTGTTTGCTTGTTCTTACCC
65 TTTTACCTAATTTCCTTGAAATTAAGTCTTTGCTTGTTC--ACCC
* * * *
205519 AATTTCCTTGAAATTAAGTGTTTGCTTG-TTATTACCCAATTTCCTTGAGATTAAGTCTTTGCTT
1 AATTTCCTTGAAATTAAGTCTTTACTTGCTT-TTACCCAATTACCTTGA-AGTAAGTCTTTGCTT
*
205583 GTTCTTACCTAATTTCCTTGAAATTAAGTCTTTGCTTGTTCACCT
64 GTT-TTACCTAATTTCCTTGAAATTAAGTCTTTGCTTGTTCACCC
** *
205628 AATTTCCTTGAAATTAAGTCTTTACTTGCTTTTACTTAATTACCTTGAAGTAAGCCTTTGAC-TG
1 AATTTCCTTGAAATTAAGTCTTTACTTGCTTTTACCCAATTACCTTGAAGTAAGTCTTTG-CTTG
*
205692 TTTTTACCTAATTTCCCTG-AATTAA
65 -TTTTACCTAATTTCCTTGAAATTAA
205717 ACCTTTGACT
Statistics
Matches: 171, Mismatches: 20, Indels: 16
0.83 0.10 0.08
Matches are distributed among these distances:
107 6 0.04
108 27 0.16
109 57 0.33
110 31 0.18
111 50 0.29
ACGTcount: A:0.24, C:0.19, G:0.12, T:0.46
Consensus pattern (107 bp):
AATTTCCTTGAAATTAAGTCTTTACTTGCTTTTACCCAATTACCTTGAAGTAAGTCTTTGCTTGT
TTTACCTAATTTCCTTGAAATTAAGTCTTTGCTTGTTCACCC
Found at i:205674 original size:146 final size:145
Alignment explanation
Indices: 205410--205716 Score: 363
Period size: 146 Copynumber: 2.1 Consensus size: 145
205400 GATTTTACTT
* *
205410 AATTTCCCTGAATTAAGTCCTTGTTTGCTTTTACTTAATTACCTCGAAATAAGTCTTTGCTTGAT
1 AATTTCCCTGAATTAAGTCCTTGCTTGCTTTTACCTAATTACCTCGAAATAAGTCTTTGCTTGA-
* * * *
205475 TTTACCCAATTTCCTTGAAATTAAGTGTTTGCTTGTTCTTACCCAATTTCCTTGAAATTAAGTGT
65 TTCACCCAATTTCCTTGAAATTAAGTCTTTACTTGTTCTTACCCAATTACCTTGAAATTAAGTGT
205540 TTGCTTGTTATTACCC
130 TTGCTTGTTATTACCC
* * * *
205556 AATTTCCTTGAGATTAAGTCTTTGCTTG-TTCTTACCTAATTTCCTTGAAATTAAGTCTTTGCTT
1 AATTTCCCTGA-ATTAAGTCCTTGCTTGCTT-TTACCTAATTACCTCGAAA-TAAGTCTTTGCTT
* ** *
205620 G-TTCACCTAATTTCCTTGAAATTAAGTCTTTACTTGCTT-TTACTTAATTACCTTG-AAGTAAG
63 GATTCACCCAATTTCCTTGAAATTAAGTCTTTACTTG-TTCTTACCCAATTACCTTGAAATTAAG
** * *
205682 CCTTTGAC-TGTTTTTACCT
127 TGTTTG-CTTGTTATTACCC
205701 AATTTCCCTGAATTAA
1 AATTTCCCTGAATTAA
205717 ACCTTTGACT
Statistics
Matches: 137, Mismatches: 19, Indels: 12
0.82 0.11 0.07
Matches are distributed among these distances:
144 5 0.04
145 29 0.21
146 57 0.42
147 32 0.23
148 14 0.10
ACGTcount: A:0.24, C:0.19, G:0.12, T:0.46
Consensus pattern (145 bp):
AATTTCCCTGAATTAAGTCCTTGCTTGCTTTTACCTAATTACCTCGAAATAAGTCTTTGCTTGAT
TCACCCAATTTCCTTGAAATTAAGTCTTTACTTGTTCTTACCCAATTACCTTGAAATTAAGTGTT
TGCTTGTTATTACCC
Found at i:205751 original size:40 final size:39
Alignment explanation
Indices: 205653--205944 Score: 157
Period size: 35 Copynumber: 8.0 Consensus size: 39
205643 AAGTCTTTAC
*
205653 TTGCTTTTACTTAA-TTACCTTGAAGTAAGCCTTTGACTG
1 TTGCTTTTACTTAATTTACC-TGAATTAAGCCTTTGACTG
* * *
205692 -T--TTTTACCTAATTTCCCTGAATTAAACCTTTGACTG
1 TTGCTTTTACTTAATTTACCTGAATTAAGCCTTTGACTG
* *
205728 TTTGCTTTTACTTAATTTTCCTGAATTAAGTCTTTGAC--
1 -TTGCTTTTACTTAATTTACCTGAATTAAGCCTTTGACTG
* ** *
205766 -TG-ATTTACTTAATTGCCCTGAATTAAGTCTTTGAC--
1 TTGCTTTTACTTAATTTACCTGAATTAAGCCTTTGACTG
** ** *
205801 -T-AATTTACTTAA-TTATTTTGAATTAAGTCTTTGAC--
1 TTGCTTTTACTTAATTTA-CCTGAATTAAGCCTTTGACTG
* * *
205836 -TG-ATTTACTTAA-TTACCCTAAATTAAGTCTTTG---G
1 TTGCTTTTACTTAATTTA-CCTGAATTAAGCCTTTGACTG
* * *
205870 CTGATTTTACTTAA-TTACCCTGAATTAAGTCTTTGAC--
1 TTGCTTTTACTTAATTTA-CCTGAATTAAGCCTTTGACTG
* *
205907 -TGCTTTTACTTAATTTCCCTGAATTAAGTCTTTGACTG
1 TTGCTTTTACTTAATTTACCTGAATTAAGCCTTTGACTG
205945 ATTTTACTTA
Statistics
Matches: 214, Mismatches: 23, Indels: 33
0.79 0.09 0.12
Matches are distributed among these distances:
34 1 0.00
35 88 0.41
36 88 0.41
37 6 0.03
38 2 0.01
40 29 0.14
ACGTcount: A:0.25, C:0.17, G:0.12, T:0.46
Consensus pattern (39 bp):
TTGCTTTTACTTAATTTACCTGAATTAAGCCTTTGACTG
Found at i:205786 original size:35 final size:35
Alignment explanation
Indices: 205228--205954 Score: 430
Period size: 36 Copynumber: 20.1 Consensus size: 35
205218 TAATGTCCCC
* * *
205228 ACTTAATTGCCTTGAATTAAGTTCTTT-ATTGACTTT
1 ACTTAATTTCCCTGAATTAAG-TCTTTGACTGA-TTT
* *
205264 ACTTAATTACCCCGAATTAAG--TTT-A-TCGACTTT
1 ACTTAATTTCCCTGAATTAAGTCTTTGACT-GA-TTT
* *
205297 ACTTAATTACCCAGAATTAAG--TTT-A-TCGACTTT
1 ACTTAATTTCCCTGAATTAAGTCTTTGACT-GA-TTT
* * * *
205330 ACTTAATTACCCAGAATTAAGTTTATTGACT-CTTT
1 ACTTAATTTCCCTGAATTAAGTCT-TTGACTGATTT
**
205365 ACTTAATTATATTACATTGAATTAAGTCTTTGACTGATTTT
1 ACTT-A--AT-TT-CCCTGAATTAAGTCTTTGACTGA-TTT
* ** *
205406 ACTTAATTTCCCTGAATTAAGTCCTTGTTTGCTTTT
1 ACTTAATTTCCCTGAATTAAGTCTTTGACTG-ATTT
* *
205442 ACTTAA-TTACCTCGAAATAAGTCTTTG-CTTGATTTT
1 ACTTAATTTCCCT-GAATTAAGTCTTTGAC-TGA-TTT
** * * *
205478 ACCCAATTTCCTTGAAATTAAGTGTTTG-CTTGTTCTT
1 ACTTAATTTCCCTG-AATTAAGTCTTTGAC-TGAT-TT
** * * *
205515 ACCCAATTTCCTTGAAATTAAGTGTTTG-CTTGTTATT
1 ACTTAATTTCCCTG-AATTAAGTCTTTGAC-TGAT-TT
** * *
205552 ACCCAATTTCCTTGAGATTAAGTCTTTG-CTTGTTCTT
1 ACTTAATTTCCCTGA-ATTAAGTCTTTGAC-TGAT-TT
* * *
205589 ACCTAATTTCCTTGAAATTAAGTCTTTG-CTTG-TTC
1 ACTTAATTTCCCTG-AATTAAGTCTTTGAC-TGATTT
* * *
205624 ACCTAATTTCCTTGAAATTAAGTCTTT-ACTTGCTTTT
1 ACTTAATTTCCCTG-AATTAAGTCTTTGAC-TG-ATTT
* * * * *
205661 ACTTAATTACCTTGAAGTAAGCCTTTGACTGTTTTT
1 ACTTAATTTCCCTGAATTAAGTCTTTGACTG-ATTT
* ** *
205697 ACCTAATTTCCCTGAATTAAACCTTTGACTGTTTGCTTTT
1 ACTTAATTTCCCTGAATTAAGTCTTTGAC----TG-ATTT
*
205737 ACTTAATTTTCCTGAATTAAGTCTTTGACTGATTT
1 ACTTAATTTCCCTGAATTAAGTCTTTGACTGATTT
* *
205772 ACTTAATTGCCCTGAATTAAGTCTTTGACTAATTT
1 ACTTAATTTCCCTGAATTAAGTCTTTGACTGATTT
**
205807 ACTTAATTAT-TTTGAATTAAGTCTTTGACTGATTT
1 ACTTAATT-TCCCTGAATTAAGTCTTTGACTGATTT
* * *
205842 ACTTAATTACCCTAAATTAAGTCTTTGGCTGATTTT
1 ACTTAATTTCCCTGAATTAAGTCTTTGACTGA-TTT
* *
205878 ACTTAATTACCCTGAATTAAGTCTTTGACTGCTTTT
1 ACTTAATTTCCCTGAATTAAGTCTTTGACTG-ATTT
205914 ACTTAATTTCCCTGAATTAAGTCTTTGACTGATTTT
1 ACTTAATTTCCCTGAATTAAGTCTTTGACTGA-TTT
205950 ACTTA
1 ACTTA
205955 GGGGCTGTTT
Statistics
Matches: 588, Mismatches: 68, Indels: 70
0.81 0.09 0.10
Matches are distributed among these distances:
32 1 0.00
33 63 0.11
35 136 0.23
36 187 0.32
37 138 0.23
38 6 0.01
39 7 0.01
40 43 0.07
41 7 0.01
ACGTcount: A:0.26, C:0.17, G:0.11, T:0.46
Consensus pattern (35 bp):
ACTTAATTTCCCTGAATTAAGTCTTTGACTGATTT
Done.