Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008759.1 Hibiscus syriacus cultivar Beakdansim tig00111851_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: 899239
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 3 of 4
Found at i:531954 original size:60 final size:60
Alignment explanation
Indices: 531847--531961 Score: 135
Period size: 60 Copynumber: 1.9 Consensus size: 60
531837 ACATGTTCCA
* * *
531847 AAATCGTAACGCGAATAGGTAAATCGCAACGATAATATGTAAATCGCATCGCGAATATGT
1 AAATCGAAACGCGAATAGGTAAATCGCAACGATAATAAGTAAATCGCAACGCGAATATGT
** * *
531907 AAATCGAAACGCGAATTTGTAAATTGCAAC-A-CATAAGTCAAATTCGCAACGCGAA
1 AAATCGAAACGCGAATAGGTAAATCGCAACGATAATAAGT-AAA-TCGCAACGCGAA
531962 CTTCAATTTC
Statistics
Matches: 46, Mismatches: 7, Indels: 4
0.81 0.12 0.07
Matches are distributed among these distances:
58 5 0.11
59 4 0.09
60 37 0.80
ACGTcount: A:0.42, C:0.18, G:0.18, T:0.22
Consensus pattern (60 bp):
AAATCGAAACGCGAATAGGTAAATCGCAACGATAATAAGTAAATCGCAACGCGAATATGT
Found at i:532101 original size:21 final size:20
Alignment explanation
Indices: 532075--532126 Score: 77
Period size: 21 Copynumber: 2.5 Consensus size: 20
532065 ATAATTCGCG
532075 ATTCGCAACGCGATTTTCCAA
1 ATTCGCAACGCGATTTT-CAA
*
532096 ATTCGCAACGCGATTTTCTA
1 ATTCGCAACGCGATTTTCAA
*
532116 ATTCGCGACGC
1 ATTCGCAACGC
532127 TAATTCCTAA
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
20 12 0.41
21 17 0.59
ACGTcount: A:0.25, C:0.29, G:0.17, T:0.29
Consensus pattern (20 bp):
ATTCGCAACGCGATTTTCAA
Found at i:532142 original size:20 final size:20
Alignment explanation
Indices: 531987--532143 Score: 84
Period size: 20 Copynumber: 7.5 Consensus size: 20
531977 GCGATTTTTA
*
531987 AATTCGCGACGCTAATT-AT
1 AATTCGCGACGCTAATTCCT
* * *
532006 GAATACACTACGCTAATT-CT
1 -AATTCGCGACGCTAATTCCT
*
532026 GAATTCACGACGCTAATTCCT
1 -AATTCGCGACGCTAATTCCT
* * *
532047 AATTCGCAACGTTAATTCAT
1 AATTCGCGACGCTAATTCCT
* *
532067 AATTCGCGATTCGCAACGCGATTTTCCA
1 AATTCGCGA--CGCTA----A--TTCCT
* * * *
532095 AATTCGCAACGCGATTTTCT
1 AATTCGCGACGCTAATTCCT
532115 AATTCGCGACGCTAATTCCT
1 AATTCGCGACGCTAATTCCT
532135 AATTCGCGA
1 AATTCGCGA
532144 TTCGCAACGC
Statistics
Matches: 104, Mismatches: 24, Indels: 18
0.71 0.16 0.12
Matches are distributed among these distances:
20 83 0.80
21 2 0.02
22 3 0.03
26 5 0.05
28 11 0.11
ACGTcount: A:0.29, C:0.25, G:0.15, T:0.31
Consensus pattern (20 bp):
AATTCGCGACGCTAATTCCT
Found at i:532230 original size:20 final size:20
Alignment explanation
Indices: 532205--532255 Score: 75
Period size: 20 Copynumber: 2.5 Consensus size: 20
532195 GCGTTGCGAA
532205 TCGCGAATTAGGAATTAACG
1 TCGCGAATTAGGAATTAACG
* *
532225 TCGCGAATCAGGAATTAGCG
1 TCGCGAATTAGGAATTAACG
*
532245 TCGCAAATTAG
1 TCGCGAATTAG
532256 AAAAATACAT
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 27 1.00
ACGTcount: A:0.33, C:0.18, G:0.25, T:0.24
Consensus pattern (20 bp):
TCGCGAATTAGGAATTAACG
Found at i:532280 original size:20 final size:21
Alignment explanation
Indices: 532257--532298 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
532247 GCAAATTAGA
*
532257 AAAAT-ACATTGCGAATTTGG
1 AAAATCACATTACGAATTTGG
*
532277 AAAATCGCATTACGAATTTGG
1 AAAATCACATTACGAATTTGG
532298 A
1 A
532299 GTTCGCGTTG
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
20 5 0.26
21 14 0.74
ACGTcount: A:0.40, C:0.12, G:0.19, T:0.29
Consensus pattern (21 bp):
AAAATCACATTACGAATTTGG
Found at i:532312 original size:20 final size:21
Alignment explanation
Indices: 532263--532316 Score: 65
Period size: 20 Copynumber: 2.6 Consensus size: 21
532253 TAGAAAAATA
532263 CATTGCGAATTTGGAAAATCG
1 CATTGCGAATTTGGAAAATCG
* **
532284 CATTACGAATTTGG-AGTTCG
1 CATTGCGAATTTGGAAAATCG
*
532304 CGTTGCGAATTTG
1 CATTGCGAATTTG
532317 AAATTCCGTG
Statistics
Matches: 28, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
20 15 0.54
21 13 0.46
ACGTcount: A:0.26, C:0.15, G:0.26, T:0.33
Consensus pattern (21 bp):
CATTGCGAATTTGGAAAATCG
Found at i:532335 original size:21 final size:20
Alignment explanation
Indices: 532268--532338 Score: 70
Period size: 21 Copynumber: 3.5 Consensus size: 20
532258 AAATACATTG
* *
532268 CGAATTTGGAAAATCGCATTA
1 CGAATTT-GAAATTCGCGTTA
* * *
532289 CGAATTTGGAGTTCGCGTTG
1 CGAATTTGAAATTCGCGTTA
*
532309 CGAATTTGAAATTCCGTGTTA
1 CGAATTTGAAATT-CGCGTTA
532330 CGAATTTGA
1 CGAATTTGA
532339 CTTCTGTGTT
Statistics
Matches: 40, Mismatches: 9, Indels: 2
0.78 0.18 0.04
Matches are distributed among these distances:
20 19 0.47
21 21 0.52
ACGTcount: A:0.28, C:0.14, G:0.24, T:0.34
Consensus pattern (20 bp):
CGAATTTGAAATTCGCGTTA
Found at i:532630 original size:3 final size:3
Alignment explanation
Indices: 532622--532694 Score: 53
Period size: 3 Copynumber: 24.3 Consensus size: 3
532612 TTTATTAAAA
* *
532622 ATT ATT ATT ATT ATT ATT ATT -TT A-T ATT ATT ATA ATA ATTT ATTT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT A-TT A-TT
* * *
532667 AAT ATT ATT -TAT ATT AAT AAT ATT ATT A
1 ATT ATT ATT AT-T ATT ATT ATT ATT ATT A
532695 AATTTAAAAT
Statistics
Matches: 59, Mismatches: 6, Indels: 10
0.79 0.08 0.13
Matches are distributed among these distances:
2 5 0.08
3 47 0.80
4 7 0.12
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (3 bp):
ATT
Found at i:532649 original size:22 final size:23
Alignment explanation
Indices: 532624--532684 Score: 70
Period size: 22 Copynumber: 2.7 Consensus size: 23
532614 TATTAAAAAT
* * *
532624 TATTATTATTATTA-TTATTTTA
1 TATTATTATAATAATTTATTTAA
532646 TATTATTATAATAATTTATTTAA
1 TATTATTATAATAATTTATTTAA
*
532669 TATTATTTATATTAAT
1 TATTA-TTATAATAAT
532685 AATATTATTA
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
22 12 0.36
23 12 0.36
24 9 0.27
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (23 bp):
TATTATTATAATAATTTATTTAA
Found at i:532707 original size:17 final size:18
Alignment explanation
Indices: 532666--532721 Score: 57
Period size: 18 Copynumber: 3.3 Consensus size: 18
532656 ATAATTTATT
*
532666 TAATATTATTTATATTAA
1 TAATATTATTAATATTAA
532684 TAATATTATTAA-ATTTAA
1 TAATATTATTAATA-TTAA
*
532702 -AATATTA-TATTATTAA
1 TAATATTATTAATATTAA
532718 -AATA
1 TAATA
532722 ATAAATATAT
Statistics
Matches: 34, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
16 10 0.29
17 9 0.26
18 15 0.44
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (18 bp):
TAATATTATTAATATTAA
Found at i:533101 original size:35 final size:35
Alignment explanation
Indices: 533045--533156 Score: 136
Period size: 35 Copynumber: 3.2 Consensus size: 35
533035 AAAACATTCC
* * *
533045 TCAATTTCATTATAAATCCTAAATTTCAAAGTAAT
1 TCAATTTCATTCTAAACCCTAAATTTCAAAATAAT
**
533080 TCAATTTCATTCTAAACCCTAAATCCCAAAATAAT
1 TCAATTTCATTCTAAACCCTAAATTTCAAAATAAT
* * *
533115 TCAATTACATTCTAAACCCCAAA-TTCTAAAATACT
1 TCAATTTCATTCTAAACCCTAAATTTC-AAAATAAT
533150 TCAATTT
1 TCAATTT
533157 AAGGAGAAAT
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:0.42, C:0.21, G:0.01, T:0.36
Consensus pattern (35 bp):
TCAATTTCATTCTAAACCCTAAATTTCAAAATAAT
Found at i:534226 original size:35 final size:34
Alignment explanation
Indices: 534177--534288 Score: 145
Period size: 35 Copynumber: 3.2 Consensus size: 34
534167 AAAAAAGACA
* *
534177 GAAATTGAAGTATTTTAGAATTTGGGTTTTAGAAT
1 GAAATTGAATTATTTTGGAATTTGGG-TTTAGAAT
*
534212 GTAATTGAATTATTTTGGAATTTAGGG-TTAGAAT
1 GAAATTGAATTATTTTGGAATTT-GGGTTTAGAAT
* *
534246 GAAATTGAATTACTTTGGAATTTTTGGTTTAGAAT
1 GAAATTGAATTATTTTGGAA-TTTGGGTTTAGAAT
534281 GAAATTGA
1 GAAATTGA
534289 GAATTGTTTT
Statistics
Matches: 68, Mismatches: 6, Indels: 6
0.85 0.08 0.08
Matches are distributed among these distances:
34 27 0.40
35 38 0.56
36 3 0.04
ACGTcount: A:0.34, C:0.01, G:0.22, T:0.43
Consensus pattern (34 bp):
GAAATTGAATTATTTTGGAATTTGGGTTTAGAAT
Found at i:535339 original size:2 final size:2
Alignment explanation
Indices: 535332--535373 Score: 66
Period size: 2 Copynumber: 21.0 Consensus size: 2
535322 CGGAACGGAC
* *
535332 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AC AT AC 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
535374 GAGTTCAAAA
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.05, G:0.00, T:0.45
Consensus pattern (2 bp):
AT
Found at i:544803 original size:9 final size:9
Alignment explanation
Indices: 544791--544817 Score: 54
Period size: 9 Copynumber: 3.0 Consensus size: 9
544781 AATGTATTCG
544791 TGTTTGATT
1 TGTTTGATT
544800 TGTTTGATT
1 TGTTTGATT
544809 TGTTTGATT
1 TGTTTGATT
544818 GACTTCTTTA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 18 1.00
ACGTcount: A:0.11, C:0.00, G:0.22, T:0.67
Consensus pattern (9 bp):
TGTTTGATT
Found at i:544910 original size:33 final size:32
Alignment explanation
Indices: 544848--544913 Score: 80
Period size: 33 Copynumber: 2.0 Consensus size: 32
544838 TCTATTGATT
*
544848 ATAATTTAAATTAATTTACATGATTGAATTAA
1 ATAATTTAAATTAATTTACATGATCGAATTAA
* *
544880 ATAATTTGAATTGATTTTAC-TGAATCGAATTAA
1 ATAATTTAAATT-AATTTACATG-ATCGAATTAA
544913 A
1 A
544914 ATTAATAGGT
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
32 13 0.45
33 16 0.55
ACGTcount: A:0.44, C:0.05, G:0.09, T:0.42
Consensus pattern (32 bp):
ATAATTTAAATTAATTTACATGATCGAATTAA
Found at i:545264 original size:11 final size:11
Alignment explanation
Indices: 545250--545274 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
545240 TTTAATAGAA
545250 TTATAATTAAT
1 TTATAATTAAT
545261 TTATAATTAAT
1 TTATAATTAAT
545272 TTA
1 TTA
545275 AGTAATTTAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (11 bp):
TTATAATTAAT
Found at i:550132 original size:20 final size:20
Alignment explanation
Indices: 550107--550156 Score: 57
Period size: 20 Copynumber: 2.5 Consensus size: 20
550097 GCGAAATAAA
550107 AATCGCAACGC-GATCTCCAG
1 AATCGCAACGCAGATC-CCAG
** *
550127 AATCGCAAATCAGTTCCCAG
1 AATCGCAACGCAGATCCCAG
550147 AATCGCAACG
1 AATCGCAACG
550157 GGATTATGAA
Statistics
Matches: 24, Mismatches: 5, Indels: 2
0.77 0.16 0.06
Matches are distributed among these distances:
20 21 0.88
21 3 0.12
ACGTcount: A:0.34, C:0.32, G:0.18, T:0.16
Consensus pattern (20 bp):
AATCGCAACGCAGATCCCAG
Found at i:550221 original size:21 final size:21
Alignment explanation
Indices: 550107--550222 Score: 60
Period size: 21 Copynumber: 5.6 Consensus size: 21
550097 GCGAAATAAA
* *
550107 AATCGCAACGCGA-TCTCCAG
1 AATCGCAATGCGATTTTCCAG
* *
550127 AATCGCAAAT-C-AGTTCCCAG
1 AATCGC-AATGCGATTTTCCAG
* * * **
550147 AATCGCAACGGGATTATGAAG
1 AATCGCAATGCGATTTTCCAG
** *
550168 AATCGCAATGCGATAGTACA-
1 AATCGCAATGCGATTTTCCAG
* *
550188 AATTAGCATTGCGATTTTCCAG
1 AA-TCGCAATGCGATTTTCCAG
550210 AATCGCAATGCGA
1 AATCGCAATGCGA
550223 ATATGAAAAT
Statistics
Matches: 67, Mismatches: 23, Indels: 11
0.66 0.23 0.11
Matches are distributed among these distances:
19 3 0.04
20 20 0.30
21 42 0.63
22 2 0.03
ACGTcount: A:0.34, C:0.23, G:0.21, T:0.22
Consensus pattern (21 bp):
AATCGCAATGCGATTTTCCAG
Found at i:550314 original size:20 final size:20
Alignment explanation
Indices: 550270--550463 Score: 185
Period size: 20 Copynumber: 9.6 Consensus size: 20
550260 GATTCTGACT
* *
550270 ATCGCAATGAGTATCCGTAAA
1 ATCGCAACGCGTATCCGT-AA
550291 ATCGCAACGCGTATCCGTAA
1 ATCGCAACGCGTATCCGTAA
* *
550311 ATCGCAACGAC-AATACGTAAA
1 ATCGCAACG-CGTATCCGT-AA
550332 ATCGCAACGCGTATCCGTAA
1 ATCGCAACGCGTATCCGTAA
* * *
550352 ATCGCAACGAGAATACGTAA
1 ATCGCAACGCGTATCCGTAA
*
550372 ATCGCAACGCGTATCTGTAA
1 ATCGCAACGCGTATCCGTAA
* * * *
550392 ATCGCAATGAGAATACGTAA
1 ATCGCAACGCGTATCCGTAA
* *
550412 ATCGCAATGCGTATCCATAA
1 ATCGCAACGCGTATCCGTAA
* *
550432 ATCGCAACGAC-AATACGTAAA
1 ATCGCAACG-CGTATCCGT-AA
550453 ATCGCAACGCG
1 ATCGCAACGCG
550464 ATTTTTAAAG
Statistics
Matches: 141, Mismatches: 26, Indels: 12
0.79 0.15 0.07
Matches are distributed among these distances:
20 96 0.68
21 45 0.32
ACGTcount: A:0.38, C:0.24, G:0.19, T:0.19
Consensus pattern (20 bp):
ATCGCAACGCGTATCCGTAA
Found at i:550385 original size:40 final size:41
Alignment explanation
Indices: 550270--550463 Score: 293
Period size: 40 Copynumber: 4.8 Consensus size: 41
550260 GATTCTGACT
* * *
550270 ATCGCAATGAGTATCCGTAAAATCGCAACGCGTATCCGTAA
1 ATCGCAACGAGAATACGTAAAATCGCAACGCGTATCCGTAA
*
550311 ATCGCAACGACAATACGTAAAATCGCAACGCGTATCCGTAA
1 ATCGCAACGAGAATACGTAAAATCGCAACGCGTATCCGTAA
*
550352 ATCGCAACGAGAATACGT-AAATCGCAACGCGTATCTGTAA
1 ATCGCAACGAGAATACGTAAAATCGCAACGCGTATCCGTAA
* * *
550392 ATCGCAATGAGAATACGT-AAATCGCAATGCGTATCCATAA
1 ATCGCAACGAGAATACGTAAAATCGCAACGCGTATCCGTAA
*
550432 ATCGCAACGACAATACGTAAAATCGCAACGCG
1 ATCGCAACGAGAATACGTAAAATCGCAACGCG
550464 ATTTTTAAAG
Statistics
Matches: 139, Mismatches: 13, Indels: 2
0.90 0.08 0.01
Matches are distributed among these distances:
40 73 0.53
41 66 0.47
ACGTcount: A:0.38, C:0.24, G:0.19, T:0.19
Consensus pattern (41 bp):
ATCGCAACGAGAATACGTAAAATCGCAACGCGTATCCGTAA
Found at i:550485 original size:80 final size:81
Alignment explanation
Indices: 550289--550485 Score: 263
Period size: 80 Copynumber: 2.4 Consensus size: 81
550279 AGTATCCGTA
* * * * *
550289 AAATCGCAACGCGTATCCGTAAATCGCAACGACAATACGTAAAATCGCAACGCGTATCCGTAAAT
1 AAATCGCAACGCGTATCTGTAAAGCGCAATGAGAATACGTAAAATCGCAACGCGTATCCATAAAT
*
550354 CGCAACGAGAATACGT
66 CGCAACGACAATACGT
* *
550370 AAATCGCAACGCGTATCTGTAAATCGCAATGAGAATACGT-AAATCGCAATGCGTATCCATAAAT
1 AAATCGCAACGCGTATCTGTAAAGCGCAATGAGAATACGTAAAATCGCAACGCGTATCCATAAAT
550434 CGCAACGACAATACGT
66 CGCAACGACAATACGT
* * * *
550450 AAAATCGCAACGCG-ATTTTTAAAGCGCCATTAGAAT
1 -AAATCGCAACGCGTATCTGTAAAGCGCAATGAGAAT
550486 CGCTACGCAT
Statistics
Matches: 104, Mismatches: 11, Indels: 3
0.88 0.09 0.03
Matches are distributed among these distances:
80 54 0.52
81 50 0.48
ACGTcount: A:0.39, C:0.23, G:0.18, T:0.20
Consensus pattern (81 bp):
AAATCGCAACGCGTATCTGTAAAGCGCAATGAGAATACGTAAAATCGCAACGCGTATCCATAAAT
CGCAACGACAATACGT
Found at i:551082 original size:21 final size:21
Alignment explanation
Indices: 551021--551099 Score: 85
Period size: 20 Copynumber: 3.9 Consensus size: 21
551011 TTCTAAACTT
551021 AAAATCGCAAC-ATGA-AAATG
1 AAAATCGCAACGA-GAGAAATG
551041 AAAATCGCAAC-ACGA-AAATG
1 AAAATCGCAACGA-GAGAAATG
**
551061 ACTATCGCAACGAGAGAAATG
1 AAAATCGCAACGAGAGAAATG
*
551082 AAAATCGTAACGAGAGAA
1 AAAATCGCAACGAGAGAA
551100 TCGCAACGCG
Statistics
Matches: 51, Mismatches: 6, Indels: 3
0.85 0.10 0.05
Matches are distributed among these distances:
20 30 0.59
21 21 0.41
ACGTcount: A:0.52, C:0.16, G:0.19, T:0.13
Consensus pattern (21 bp):
AAAATCGCAACGAGAGAAATG
Found at i:551117 original size:33 final size:33
Alignment explanation
Indices: 551076--551156 Score: 126
Period size: 33 Copynumber: 2.5 Consensus size: 33
551066 CGCAACGAGA
*
551076 GAAATGAAAATCGTAACGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
*
551109 GAAATGAAAATCGCAACGAGATAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
**
551142 GAAACCAAAATCGCA
1 GAAATGAAAATCGCA
551157 TTGCAATTTT
Statistics
Matches: 44, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
33 44 1.00
ACGTcount: A:0.47, C:0.21, G:0.21, T:0.11
Consensus pattern (33 bp):
GAAATGAAAATCGCAACGAGAGAATCGCAACGC
Found at i:553043 original size:17 final size:17
Alignment explanation
Indices: 553013--553045 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
553003 GTTGCTGCCA
553013 ATTCTGTTAAACTGTGT
1 ATTCTGTTAAACTGTGT
553030 ATTCT-TTAACACTGTG
1 ATTCTGTTAA-ACTGTG
553046 AAGTTAGTAT
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 4 0.27
17 11 0.73
ACGTcount: A:0.24, C:0.15, G:0.15, T:0.45
Consensus pattern (17 bp):
ATTCTGTTAAACTGTGT
Found at i:553056 original size:94 final size:94
Alignment explanation
Indices: 552895--553274 Score: 613
Period size: 94 Copynumber: 4.1 Consensus size: 94
552885 TAGATTGCTT
* * *
552895 AGTAAATTTATTCGGTTGATGCCAATACTGCTAAACTGTTTATTCTTTAACACTGTGAAGTTAGT
1 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAGTTAGT
*
552960 ATTTATCTTTTGTTTTTTCTTTTGGTTG-A
66 ATTTATC-TTTGTTTTGTCTTTTGGTTGAA
*
552989 AGTAAATTTATTCGGTTGCTGCCAATTCTGTTAAACTGTGTATTCTTTAACACTGTGAAGTTAGT
1 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAGTTAGT
*
553054 ATTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 ATTTATCTTTGTTTTGTCTTTTGGTTGAA
* *
553083 AGTAAATTTGTTCGGTTGTTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAGTTAGT
1 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAGTTAGT
*
553148 ATTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 ATTTATCTTTGTTTTGTCTTTTGGTTGAA
* * *
553177 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAATACTCTGAAGTTAGT
1 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAGTTAGT
553242 ATTTGA-CTTTGTTTTGTCTTTTGGTTG-A
66 ATTT-ATCTTTGTTTTGTCTTTTGGTTGAA
553270 AGTAA
1 AGTAA
553275 TGCAATCCAT
Statistics
Matches: 271, Mismatches: 13, Indels: 5
0.94 0.04 0.02
Matches are distributed among these distances:
93 25 0.09
94 246 0.91
ACGTcount: A:0.22, C:0.12, G:0.19, T:0.48
Consensus pattern (94 bp):
AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAGTTAGT
ATTTATCTTTGTTTTGTCTTTTGGTTGAA
Found at i:553378 original size:19 final size:19
Alignment explanation
Indices: 553362--553406 Score: 90
Period size: 19 Copynumber: 2.4 Consensus size: 19
553352 AAAAATGACT
553362 ATCGCAACGCGAAATGAAA
1 ATCGCAACGCGAAATGAAA
553381 ATCGCAACGCGAAATGAAA
1 ATCGCAACGCGAAATGAAA
553400 ATCGCAA
1 ATCGCAA
553407 AGACAAAATC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 26 1.00
ACGTcount: A:0.47, C:0.22, G:0.20, T:0.11
Consensus pattern (19 bp):
ATCGCAACGCGAAATGAAA
Found at i:553456 original size:19 final size:19
Alignment explanation
Indices: 553434--553540 Score: 98
Period size: 19 Copynumber: 5.8 Consensus size: 19
553424 GAAACTATAA
553434 TCGCGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
* *
553453 TCGCATTACGA--TTC---
1 TCGCGTTGCGATTTTCATT
*
553467 TCTCGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
553486 TCGCGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
* **
553505 TCACGTTGCGATAGTCATTTT
1 TCGCGTTGCGATTTTCA--TT
*
553526 TCACGTTGCGATTTT
1 TCGCGTTGCGATTTT
553541 AAGTTCCAGA
Statistics
Matches: 70, Mismatches: 11, Indels: 12
0.75 0.12 0.13
Matches are distributed among these distances:
14 8 0.11
16 3 0.04
17 3 0.04
19 41 0.59
21 15 0.21
ACGTcount: A:0.14, C:0.21, G:0.19, T:0.46
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Found at i:554018 original size:42 final size:42
Alignment explanation
Indices: 553941--554059 Score: 102
Period size: 42 Copynumber: 2.8 Consensus size: 42
553931 GACTCGCCTG
* * * *
553941 TCATCCCTC-AAGA-GTCCACTCCTATCGTTGAAGAGGCCCCTA
1 TCAT-CCTCGAAGAGGTCC-CTCCCACCGTTCAAGAGGCCACTA
*
553983 TCATTCCTCG-AGA-GTACCCTCCCACCGTTCAAGAGGCCACTG
1 TCA-TCCTCGAAGAGGT-CCCTCCCACCGTTCAAGAGGCCACTA
* * *
554025 TCATCGTTGAAGAGGTCCCTCCCACCATTCAAGAG
1 TCATCCTCGAAGAGGTCCCTCCCACCGTTCAAGAG
554060 CCCGATTCAC
Statistics
Matches: 64, Mismatches: 8, Indels: 10
0.78 0.10 0.12
Matches are distributed among these distances:
41 4 0.06
42 55 0.86
43 5 0.08
ACGTcount: A:0.24, C:0.35, G:0.18, T:0.23
Consensus pattern (42 bp):
TCATCCTCGAAGAGGTCCCTCCCACCGTTCAAGAGGCCACTA
Found at i:554058 original size:21 final size:20
Alignment explanation
Indices: 553999--554059 Score: 59
Period size: 21 Copynumber: 3.0 Consensus size: 20
553989 CTCGAGAGTA
553999 CCCTCCCACCGTTCAAGAGG
1 CCCTCCCACCGTTCAAGAGG
** * *
554019 CCACTGTCATCGTTGAAGAGG
1 CC-CTCCCACCGTTCAAGAGG
*
554040 TCCCTCCCACCATTCAAGAG
1 -CCCTCCCACCGTTCAAGAG
554060 CCCGATTCAC
Statistics
Matches: 30, Mismatches: 9, Indels: 3
0.71 0.21 0.07
Matches are distributed among these distances:
20 2 0.07
21 26 0.87
22 2 0.07
ACGTcount: A:0.23, C:0.38, G:0.20, T:0.20
Consensus pattern (20 bp):
CCCTCCCACCGTTCAAGAGG
Found at i:556037 original size:14 final size:14
Alignment explanation
Indices: 556018--556053 Score: 63
Period size: 14 Copynumber: 2.6 Consensus size: 14
556008 ATTGTTTAAT
556018 TGATTTGTAAAAGA
1 TGATTTGTAAAAGA
*
556032 TGATTTGTAAAAGT
1 TGATTTGTAAAAGA
556046 TGATTTGT
1 TGATTTGT
556054 TTAATTGATG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.33, C:0.00, G:0.22, T:0.44
Consensus pattern (14 bp):
TGATTTGTAAAAGA
Found at i:556228 original size:19 final size:19
Alignment explanation
Indices: 556164--556264 Score: 88
Period size: 20 Copynumber: 5.5 Consensus size: 19
556154 ATGACTATCT
*
556164 CATTGCGATAGTT-ATTTCCG
1 CATTGCGAT-TTTCATTT-CG
* *
556184 CGTTGCGATATTCATATTCG
1 CATTGCGATTTTCAT-TTCG
*
556204 CGTTGCGATTTTCATTTCG
1 CATTGCGATTTTCATTTCG
*
556223 CATTGCGA--TTC-TCTCG
1 CATTGCGATTTTCATTTCG
556239 --TTGCGATTTTCATTTCG
1 CATTGCGATTTTCATTTCG
556256 CATTGCGAT
1 CATTGCGAT
556265 AGACATTAAG
Statistics
Matches: 68, Mismatches: 6, Indels: 15
0.76 0.07 0.17
Matches are distributed among these distances:
14 6 0.09
16 7 0.10
17 7 0.10
19 20 0.29
20 26 0.38
21 2 0.03
ACGTcount: A:0.16, C:0.22, G:0.20, T:0.43
Consensus pattern (19 bp):
CATTGCGATTTTCATTTCG
Found at i:558815 original size:24 final size:24
Alignment explanation
Indices: 558781--558834 Score: 81
Period size: 24 Copynumber: 2.2 Consensus size: 24
558771 CTGAAAAATC
*
558781 ATCAAAATCCGAGTATTGACCAAT
1 ATCAAAATCCGAGTATTGACCAAG
* *
558805 ATCAAAGTCCGGGTATTGACCAAG
1 ATCAAAATCCGAGTATTGACCAAG
558829 ATCAAA
1 ATCAAA
558835 TTTCGAATAC
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.41, C:0.20, G:0.17, T:0.22
Consensus pattern (24 bp):
ATCAAAATCCGAGTATTGACCAAG
Found at i:559731 original size:19 final size:20
Alignment explanation
Indices: 559698--559766 Score: 70
Period size: 20 Copynumber: 3.5 Consensus size: 20
559688 GAATCTCGTT
559698 GCGATTTAC-TAAATCGCAAC
1 GCGATTTACGT-AATCGCAAC
**
559718 GCGA-TTACGTAATCGCATT
1 GCGATTTACGTAATCGCAAC
* **
559737 GCGATTTACGTATTCGCATT
1 GCGATTTACGTAATCGCAAC
559757 GCGATTTACG
1 GCGATTTACG
559767 GATACGCGTT
Statistics
Matches: 44, Mismatches: 3, Indels: 4
0.86 0.06 0.08
Matches are distributed among these distances:
19 15 0.34
20 29 0.66
ACGTcount: A:0.26, C:0.22, G:0.20, T:0.32
Consensus pattern (20 bp):
GCGATTTACGTAATCGCAAC
Found at i:559754 original size:39 final size:41
Alignment explanation
Indices: 559696--559786 Score: 100
Period size: 39 Copynumber: 2.3 Consensus size: 41
559686 CAGAATCTCG
559696 TTGCGATTTAC-TAAATCGCAACGCGA-TTACGTAAT-CGCA
1 TTGCGATTTACGTAAATCGCAACGCGATTTACG-AATACGCA
* ** * *
559735 TTGCGATTTACGT-ATTCGCATTGCGATTTACGGATACGCG
1 TTGCGATTTACGTAAATCGCAACGCGATTTACGAATACGCA
559775 TTGCGATTTACG
1 TTGCGATTTACG
559787 GATACGCGTT
Statistics
Matches: 44, Mismatches: 5, Indels: 5
0.81 0.09 0.09
Matches are distributed among these distances:
39 23 0.52
40 21 0.48
ACGTcount: A:0.24, C:0.21, G:0.22, T:0.33
Consensus pattern (41 bp):
TTGCGATTTACGTAAATCGCAACGCGATTTACGAATACGCA
Found at i:559778 original size:20 final size:20
Alignment explanation
Indices: 559735--559863 Score: 152
Period size: 20 Copynumber: 6.3 Consensus size: 20
559725 CGTAATCGCA
* * *
559735 TTGCGATTTACGTATTCGCA
1 TTGCGATTTACGGATACGCG
559755 TTGCGATTTACGGATACGCG
1 TTGCGATTTACGGATACGCG
559775 TTGCGATTTACGGATACGCG
1 TTGCGATTTACGGATACGCG
* *
559795 TTGCGATTTTACGTAT-TGTCG
1 TTGCGA-TTTACGGATACG-CG
**
559816 TTGCGATTTACCAATACGCG
1 TTGCGATTTACGGATACGCG
*
559836 TTGCGATTTTACGGATACTCG
1 TTGCGA-TTTACGGATACGCG
559857 TTGCGAT
1 TTGCGAT
559864 AGTCAGAATC
Statistics
Matches: 94, Mismatches: 11, Indels: 8
0.83 0.10 0.07
Matches are distributed among these distances:
20 60 0.64
21 34 0.36
ACGTcount: A:0.19, C:0.19, G:0.25, T:0.36
Consensus pattern (20 bp):
TTGCGATTTACGGATACGCG
Found at i:559818 original size:41 final size:41
Alignment explanation
Indices: 559735--559885 Score: 166
Period size: 41 Copynumber: 3.7 Consensus size: 41
559725 CGTAATCGCA
* * *
559735 TTGCGATTTACGTATTCGCATTGCGA-TTTACGGATACG-CG
1 TTGCGATTTACGAATACGCGTTGCGATTTTACGGATA-GTCG
* * *
559775 TTGCGATTTACGGATACGCGTTGCGATTTTACGTATTGTCG
1 TTGCGATTTACGAATACGCGTTGCGATTTTACGGATAGTCG
* *
559816 TTGCGATTTACCAATACGCGTTGCGATTTTACGGATACTCG
1 TTGCGATTTACGAATACGCGTTGCGATTTTACGGATAGTCG
*
559857 TTGCGATAGT-CAGAAT-CGCGTTGCGATTT
1 TTGCGAT-TTAC-GAATACGCGTTGCGATTT
559886 ATATGTTCGC
Statistics
Matches: 95, Mismatches: 12, Indels: 7
0.83 0.11 0.06
Matches are distributed among these distances:
40 24 0.25
41 67 0.71
42 4 0.04
ACGTcount: A:0.20, C:0.19, G:0.25, T:0.36
Consensus pattern (41 bp):
TTGCGATTTACGAATACGCGTTGCGATTTTACGGATAGTCG
Found at i:559822 original size:61 final size:62
Alignment explanation
Indices: 559735--559863 Score: 192
Period size: 61 Copynumber: 2.1 Consensus size: 62
559725 CGTAATCGCA
**
559735 TTGCGA-TTTACGTATTCGCATTGCGATTTACGGATACGCGTTGCGA-TTTACGGATACGCG
1 TTGCGATTTTACGTATTCGCATTGCGATTTACCAATACGCGTTGCGATTTTACGGATACGCG
* *
559795 TTGCGATTTTACGTATT-GTCGTTGCGATTTACCAATACGCGTTGCGATTTTACGGATACTCG
1 TTGCGATTTTACGTATTCG-CATTGCGATTTACCAATACGCGTTGCGATTTTACGGATACGCG
559857 TTGCGAT
1 TTGCGAT
559864 AGTCAGAATC
Statistics
Matches: 62, Mismatches: 4, Indels: 4
0.89 0.06 0.06
Matches are distributed among these distances:
60 7 0.11
61 35 0.56
62 20 0.32
ACGTcount: A:0.19, C:0.19, G:0.25, T:0.36
Consensus pattern (62 bp):
TTGCGATTTTACGTATTCGCATTGCGATTTACCAATACGCGTTGCGATTTTACGGATACGCG
Found at i:559895 original size:20 final size:20
Alignment explanation
Indices: 559872--559924 Score: 81
Period size: 20 Copynumber: 2.6 Consensus size: 20
559862 ATAGTCAGAA
*
559872 TCGCGTTGCGATTTAT-ATGT
1 TCGCGTTGCGATTT-TCATAT
559892 TCGCGTTGCGATTTTCATAT
1 TCGCGTTGCGATTTTCATAT
559912 TCGCGTTGCGATT
1 TCGCGTTGCGATT
559925 CTAGAAAATC
Statistics
Matches: 31, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
19 1 0.03
20 30 0.97
ACGTcount: A:0.13, C:0.19, G:0.25, T:0.43
Consensus pattern (20 bp):
TCGCGTTGCGATTTTCATAT
Found at i:559906 original size:61 final size:62
Alignment explanation
Indices: 559755--559886 Score: 171
Period size: 61 Copynumber: 2.2 Consensus size: 62
559745 CGTATTCGCA
** * * * *
559755 TTGCGATTTACGGATACGCGTTGCGA-TTTACGGATACGCGTTGCGATTTTACGTATTGTCG
1 TTGCGATTTACCAATACGCGTTGCGATTTTACGGATACGCGTTGCGATGTCACGAATCGTCG
*
559816 TTGCGATTTACCAATACGCGTTGCGATTTTACGGATACTCGTTGCGATAGTCA-GAATCG-CG
1 TTGCGATTTACCAATACGCGTTGCGATTTTACGGATACGCGTTGCGAT-GTCACGAATCGTCG
559877 TTGCGATTTA
1 TTGCGATTTA
559887 TATGTTCGCG
Statistics
Matches: 62, Mismatches: 7, Indels: 4
0.85 0.10 0.05
Matches are distributed among these distances:
61 36 0.58
62 24 0.39
63 2 0.03
ACGTcount: A:0.20, C:0.19, G:0.26, T:0.35
Consensus pattern (62 bp):
TTGCGATTTACCAATACGCGTTGCGATTTTACGGATACGCGTTGCGATGTCACGAATCGTCG
Found at i:560023 original size:20 final size:19
Alignment explanation
Indices: 559974--560027 Score: 63
Period size: 20 Copynumber: 2.7 Consensus size: 19
559964 ATTCTTCATA
559974 ATCGCGTTGCGATTCTGGG
1 ATCGCGTTGCGATTCTGGG
* **
559993 AACTGATTTGCGATTCTGGAG
1 ATC-GCGTTGCGATTCTGG-G
560014 ATCGCGTTGCGATT
1 ATCGCGTTGCGATT
560028 TTTATTTCGC
Statistics
Matches: 27, Mismatches: 6, Indels: 3
0.75 0.17 0.08
Matches are distributed among these distances:
19 2 0.07
20 22 0.81
21 3 0.11
ACGTcount: A:0.17, C:0.19, G:0.31, T:0.33
Consensus pattern (19 bp):
ATCGCGTTGCGATTCTGGG
Found at i:561888 original size:28 final size:28
Alignment explanation
Indices: 561857--561917 Score: 88
Period size: 28 Copynumber: 2.2 Consensus size: 28
561847 ATGAAAAATT
561857 AAATACTTTA-AGTACCAATTTTGACAAA
1 AAATACTTTATA-TACCAATTTTGACAAA
* *
561885 AAATACTTTATATACCTATTTTGACTAA
1 AAATACTTTATATACCAATTTTGACAAA
561913 AAATA
1 AAATA
561918 TGAATTTAGA
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
28 29 0.97
29 1 0.03
ACGTcount: A:0.46, C:0.13, G:0.05, T:0.36
Consensus pattern (28 bp):
AAATACTTTATATACCAATTTTGACAAA
Found at i:564622 original size:60 final size:60
Alignment explanation
Indices: 564495--564631 Score: 143
Period size: 60 Copynumber: 2.3 Consensus size: 60
564485 ATATCCAGAT
** * ** *
564495 GATCATTTTGTAACTTTTAATAGTCGATGGAGTTAATAAAGCAACACTCTACAGTTGGAT
1 GATCATTTTGTAACTTTTAATAGTCGATGGACATAATAAAGCAACACCCTACAGCCGGAG
* * * * *
564555 GACCATTTTGTAACTTTTAATAGTCGATGGACATAATAATGTAGCACCCTATAGCC-GAGG
1 GATCATTTTGTAACTTTTAATAGTCGATGGACATAATAAAGCAACACCCTACAGCCGGA-G
564615 GATCATTTGTGT-ACTTT
1 GATCATTT-TGTAACTTT
564632 ACTCTTATTT
Statistics
Matches: 63, Mismatches: 12, Indels: 4
0.80 0.15 0.05
Matches are distributed among these distances:
59 2 0.03
60 58 0.92
61 3 0.05
ACGTcount: A:0.31, C:0.15, G:0.19, T:0.35
Consensus pattern (60 bp):
GATCATTTTGTAACTTTTAATAGTCGATGGACATAATAAAGCAACACCCTACAGCCGGAG
Found at i:575148 original size:50 final size:50
Alignment explanation
Indices: 575089--575203 Score: 131
Period size: 50 Copynumber: 2.3 Consensus size: 50
575079 TGTAGTGATT
* * ** *
575089 AACACATACTTGCATAGATGTAAATATTTACATATCTCAACCTAAATATA
1 AACACATACTTACACAGATGTAAATATGCACATATCTCAACCTAAAAATA
* * * * * *
575139 AACATATACTTACACCGGTGTAAGTATGCACATCTCTCAACTTAAAAATA
1 AACACATACTTACACAGATGTAAATATGCACATATCTCAACCTAAAAATA
575189 AACACATACTTACAC
1 AACACATACTTACAC
575204 CGGCGTAAGT
Statistics
Matches: 53, Mismatches: 12, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
50 53 1.00
ACGTcount: A:0.43, C:0.22, G:0.07, T:0.29
Consensus pattern (50 bp):
AACACATACTTACACAGATGTAAATATGCACATATCTCAACCTAAAAATA
Found at i:575204 original size:50 final size:50
Alignment explanation
Indices: 575118--575224 Score: 160
Period size: 50 Copynumber: 2.1 Consensus size: 50
575108 GTAAATATTT
* * * *
575118 ACATATCTCAACCTAAATATAAACATATACTTACACCGGTGTAAGTATGC
1 ACATCTCTCAACCTAAAAATAAACACATACTTACACCGGCGTAAGTATGC
* *
575168 ACATCTCTCAACTTAAAAATAAACACATACTTACACCGGCGTAAGTATGT
1 ACATCTCTCAACCTAAAAATAAACACATACTTACACCGGCGTAAGTATGC
575218 ACATCTC
1 ACATCTC
575225 CCAATATTTT
Statistics
Matches: 51, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
50 51 1.00
ACGTcount: A:0.39, C:0.24, G:0.09, T:0.27
Consensus pattern (50 bp):
ACATCTCTCAACCTAAAAATAAACACATACTTACACCGGCGTAAGTATGC
Found at i:586224 original size:2 final size:2
Alignment explanation
Indices: 586217--586249 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
586207 CAACAAATAG
586217 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 A
586250 ATTTTAAGAT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:586307 original size:61 final size:61
Alignment explanation
Indices: 586239--586354 Score: 232
Period size: 61 Copynumber: 1.9 Consensus size: 61
586229 ATATATATAT
586239 ATATATATATAATTTTAAGATCGTTCGATGAGTGAAATAAATGGCTGAGATTAACAAGTTC
1 ATATATATATAATTTTAAGATCGTTCGATGAGTGAAATAAATGGCTGAGATTAACAAGTTC
586300 ATATATATATAATTTTAAGATCGTTCGATGAGTGAAATAAATGGCTGAGATTAAC
1 ATATATATATAATTTTAAGATCGTTCGATGAGTGAAATAAATGGCTGAGATTAAC
586355 TACTTGTTTT
Statistics
Matches: 55, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
61 55 1.00
ACGTcount: A:0.40, C:0.08, G:0.18, T:0.34
Consensus pattern (61 bp):
ATATATATATAATTTTAAGATCGTTCGATGAGTGAAATAAATGGCTGAGATTAACAAGTTC
Found at i:587901 original size:33 final size:33
Alignment explanation
Indices: 587863--587929 Score: 116
Period size: 33 Copynumber: 2.0 Consensus size: 33
587853 TTTTCTTTCA
* *
587863 ATACAAGTGTGAAACTCTCTTAAAGCCAAGTTG
1 ATACAAGTGTGAAACTCTCTTAAACCCAAATTG
587896 ATACAAGTGTGAAACTCTCTTAAACCCAAATTG
1 ATACAAGTGTGAAACTCTCTTAAACCCAAATTG
587929 A
1 A
587930 GCTGGGTCAG
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
33 32 1.00
ACGTcount: A:0.39, C:0.19, G:0.15, T:0.27
Consensus pattern (33 bp):
ATACAAGTGTGAAACTCTCTTAAACCCAAATTG
Found at i:594713 original size:31 final size:31
Alignment explanation
Indices: 594678--594776 Score: 101
Period size: 31 Copynumber: 3.2 Consensus size: 31
594668 AGATAAATGG
* *
594678 TCCCTAACGTTATCGGT-TCATCCAGTTTAAA
1 TCCCTAACATTATCGATCT-ATCCAGTTTAAA
* * *
594709 TCCCTATCATTATCGATCTGTCTAGTTTAAA
1 TCCCTAACATTATCGATCTATCCAGTTTAAA
* * * *
594740 TCCCTATCATTATTGATCTGTCTAGTTTAAA
1 TCCCTAACATTATCGATCTATCCAGTTTAAA
594771 TCCCTA
1 TCCCTA
594777 TGCCGTTAAC
Statistics
Matches: 61, Mismatches: 6, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
31 60 0.98
32 1 0.02
ACGTcount: A:0.25, C:0.24, G:0.10, T:0.40
Consensus pattern (31 bp):
TCCCTAACATTATCGATCTATCCAGTTTAAA
Found at i:594777 original size:31 final size:31
Alignment explanation
Indices: 594701--594777 Score: 145
Period size: 31 Copynumber: 2.5 Consensus size: 31
594691 CGGTTCATCC
594701 AGTTTAAATCCCTATCATTATCGATCTGTCT
1 AGTTTAAATCCCTATCATTATCGATCTGTCT
*
594732 AGTTTAAATCCCTATCATTATTGATCTGTCT
1 AGTTTAAATCCCTATCATTATCGATCTGTCT
594763 AGTTTAAATCCCTAT
1 AGTTTAAATCCCTAT
594778 GCCGTTAACT
Statistics
Matches: 45, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
31 45 1.00
ACGTcount: A:0.27, C:0.21, G:0.09, T:0.43
Consensus pattern (31 bp):
AGTTTAAATCCCTATCATTATCGATCTGTCT
Found at i:594868 original size:3 final size:3
Alignment explanation
Indices: 594860--594888 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
594850 TCCACGTGTA
594860 TTC TTC TTC TTC TTC TTC TTC TTC TTC TT
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TT
594889 ACTTTCGTAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.00, C:0.31, G:0.00, T:0.69
Consensus pattern (3 bp):
TTC
Found at i:597561 original size:16 final size:16
Alignment explanation
Indices: 597524--597562 Score: 53
Period size: 16 Copynumber: 2.4 Consensus size: 16
597514 AATCTTGTAT
597524 TCGAACTTGAAACGAC
1 TCGAACTTGAAACGAC
*
597540 -CGGAACTTGAAATGAC
1 TC-GAACTTGAAACGAC
597556 TCGAACT
1 TCGAACT
597563 CGATTATCAA
Statistics
Matches: 20, Mismatches: 1, Indels: 4
0.80 0.04 0.16
Matches are distributed among these distances:
15 1 0.05
16 18 0.90
17 1 0.05
ACGTcount: A:0.36, C:0.23, G:0.21, T:0.21
Consensus pattern (16 bp):
TCGAACTTGAAACGAC
Found at i:600751 original size:23 final size:23
Alignment explanation
Indices: 600725--600776 Score: 54
Period size: 22 Copynumber: 2.3 Consensus size: 23
600715 TCGAAAACTT
600725 AAATATAATAATA-CCAAAAATAA
1 AAATATAA-AATATCCAAAAATAA
* * *
600748 AAAT-TAAATTATTCAAAAATTA
1 AAATATAAAATATCCAAAAATAA
600770 AAATATA
1 AAATATA
600777 TATATTTTTA
Statistics
Matches: 24, Mismatches: 3, Indels: 4
0.77 0.10 0.13
Matches are distributed among these distances:
21 3 0.12
22 15 0.62
23 6 0.25
ACGTcount: A:0.65, C:0.06, G:0.00, T:0.29
Consensus pattern (23 bp):
AAATATAAAATATCCAAAAATAA
Found at i:609976 original size:2 final size:2
Alignment explanation
Indices: 609969--610059 Score: 56
Period size: 2 Copynumber: 49.5 Consensus size: 2
609959 GTTATCGCCG
* *
609969 AT AT AT AT AT -T AA AT -T AA AT A- 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
* * * *
610008 AT AT AT AT -T CA- AT TT AA AT -T AA AT TT AT -T A- AT AT -T AT
1 AT AT AT AT AT -AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
610045 AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT A
610060 ATAATTATTT
Statistics
Matches: 67, Mismatches: 12, Indels: 20
0.68 0.12 0.20
Matches are distributed among these distances:
1 9 0.13
2 58 0.87
ACGTcount: A:0.51, C:0.01, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:610209 original size:36 final size:36
Alignment explanation
Indices: 610133--610209 Score: 93
Period size: 36 Copynumber: 2.1 Consensus size: 36
610123 ATTATTAAAC
* * **
610133 CCGTCCCCGTTTAACATAAACGGATTTTTTTCGTCT
1 CCGTTCCCGTTTAACATAAACGGATTTTTTCCGTAA
*
610169 CCGTTCCCGTTTAGCATAAACGG-TTTTTTCCCGTAA
1 CCGTTCCCGTTTAACATAAACGGATTTTTT-CCGTAA
610205 CCGTT
1 CCGTT
610210 TAATTCGATT
Statistics
Matches: 35, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
35 6 0.17
36 29 0.83
ACGTcount: A:0.18, C:0.29, G:0.16, T:0.38
Consensus pattern (36 bp):
CCGTTCCCGTTTAACATAAACGGATTTTTTCCGTAA
Found at i:614499 original size:281 final size:279
Alignment explanation
Indices: 613987--614554 Score: 1012
Period size: 281 Copynumber: 2.0 Consensus size: 279
613977 TCTGCCCTTT
613987 CCTTTT-CCCCATCATTTTCACTCTCTGCTCTTTCTCCAAATTTGTCAAATTCTTTCACCTCCCT
1 CCTTTTCCCCCATCATTTTCACTCTCTGCTCTTTCTCCAAATTTGTCAAATTCTTTCACCTCCCT
614051 AAATATTCCAAAGTTGTAAATTTAATCTACGATCTTTTCACATTTCAAATTAACAAATCATTTTA
66 AAATATTCCAAAGTTGTAAATTTAATCTACGATCTTTTCACATTTCAAATTAACAAATCATTTTA
*
614116 CACACTAAATTAAAATTCTTATATAAACACATGTAATTAATCATTTGTGGAGATAATCATGGACC
131 CACACTAAATTAAAATTCTTATATAAACACATGTAATTAATCATTTCTGGAGATAATCATGGACC
* *
614181 AATTTTTCTGTTAACTTAAATTTGGTTCGAATATTATATTTTTCTATCCGACACTCGATCCAATT
196 AATTTTTCTGTTAACTCAAATTTGGTTCGAATATTATATTTTTCTATACGACACTCGATCCAATT
614246 CAGGTTTAGAAAAATTTAA
261 CAGGTTTAGAAAAATTTAA
614265 CCTTTTCCCCCATCATTTTCACTCTCTGCTCTTTCTCCAAATTTGTCAAATTCTTTCACTACTCC
1 CCTTTTCCCCCATCATTTTCACTCTCTGCTCTTTCTCCAAATTTGTCAAATTCTTTCAC--CTCC
* * *
614330 CTAAATATTCCAAAGTTGTAAATTTAATCTATGATCTTTTCACATTTTAAGTTAACAAATCATTT
64 CTAAATATTCCAAAGTTGTAAATTTAATCTACGATCTTTTCACATTTCAAATTAACAAATCATTT
* *
614395 TACACACTAAATTAAAATTCTTATATAAATACCTGTAATTAATCATTTCTGGAGATAATCATGGA
129 TACACACTAAATTAAAATTCTTATATAAACACATGTAATTAATCATTTCTGGAGATAATCATGGA
* * *
614460 CCGATTTTTCTGTTAACTCAAATTTGGTTCGATTATTATATTTTTCTATATGACACTCGATCCAA
194 CCAATTTTTCTGTTAACTCAAATTTGGTTCGAATATTATATTTTTCTATACGACACTCGATCCAA
614525 TTCAGGTTTAGAAAAATTTAA
259 TTCAGGTTTAGAAAAATTTAA
614546 CCTTTTCCC
1 CCTTTTCCC
614555 GAACTTGATC
Statistics
Matches: 276, Mismatches: 11, Indels: 3
0.95 0.04 0.01
Matches are distributed among these distances:
278 6 0.02
279 52 0.19
281 218 0.79
ACGTcount: A:0.31, C:0.20, G:0.08, T:0.41
Consensus pattern (279 bp):
CCTTTTCCCCCATCATTTTCACTCTCTGCTCTTTCTCCAAATTTGTCAAATTCTTTCACCTCCCT
AAATATTCCAAAGTTGTAAATTTAATCTACGATCTTTTCACATTTCAAATTAACAAATCATTTTA
CACACTAAATTAAAATTCTTATATAAACACATGTAATTAATCATTTCTGGAGATAATCATGGACC
AATTTTTCTGTTAACTCAAATTTGGTTCGAATATTATATTTTTCTATACGACACTCGATCCAATT
CAGGTTTAGAAAAATTTAA
Found at i:615143 original size:37 final size:37
Alignment explanation
Indices: 615101--615177 Score: 154
Period size: 37 Copynumber: 2.1 Consensus size: 37
615091 AATGTAAAGT
615101 AAATATATAATTAAGATTTTTTTATAATTATTAAAAC
1 AAATATATAATTAAGATTTTTTTATAATTATTAAAAC
615138 AAATATATAATTAAGATTTTTTTATAATTATTAAAAC
1 AAATATATAATTAAGATTTTTTTATAATTATTAAAAC
615175 AAA
1 AAA
615178 CATTAGTCAC
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
37 40 1.00
ACGTcount: A:0.51, C:0.03, G:0.03, T:0.44
Consensus pattern (37 bp):
AAATATATAATTAAGATTTTTTTATAATTATTAAAAC
Found at i:616393 original size:39 final size:39
Alignment explanation
Indices: 616350--616466 Score: 99
Period size: 33 Copynumber: 3.2 Consensus size: 39
616340 AATATTATAA
616350 AATTTATAATATTTTTGATTTGGTGTAATTTAAAATATT
1 AATTTATAATATTTTTGATTTGGTGTAATTTAAAATATT
*** * *
616389 AA-TT-T-AT-TTTAACATTCT--T-TAGTTGAAAACT-TT
1 AATTTATAATATTTTTGATT-TGGTGTAATTTAAAA-TATT
*
616422 -TTTTATAATATTTTTGATTTGGTGTAATTTAAAATATT
1 AATTTATAATATTTTTGATTTGGTGTAATTTAAAATATT
616460 AATTTAT
1 AATTTAT
616467 TTTTAACATT
Statistics
Matches: 55, Mismatches: 12, Indels: 22
0.62 0.13 0.25
Matches are distributed among these distances:
33 12 0.22
34 3 0.05
35 9 0.16
36 9 0.16
37 3 0.05
38 12 0.22
39 7 0.13
ACGTcount: A:0.34, C:0.03, G:0.09, T:0.55
Consensus pattern (39 bp):
AATTTATAATATTTTTGATTTGGTGTAATTTAAAATATT
Found at i:616433 original size:71 final size:68
Alignment explanation
Indices: 616352--616504 Score: 263
Period size: 71 Copynumber: 2.2 Consensus size: 68
616342 TATTATAAAA
616352 TTTATAATATTTTTGATTTGGTGTAATTTAAAATATTAATTTA-TTTTAACATTCTTTAGTTGAA
1 TTTATAATATTTTTGATTTGGTGTAATTTAAAATATTAATTTATTTTTAACATTCTTTAGTTG--
616416 AACTTTT
64 -A-TTTT
616423 TTTATAATATTTTTGATTTGGTGTAATTTAAAATATTAATTTATTTTTAACATTCTTTAGTTGAT
1 TTTATAATATTTTTGATTTGGTGTAATTTAAAATATTAATTTATTTTTAACATTCTTTAGTTGAT
616488 TTT
66 TTT
616491 TTTATAATATTTTT
1 TTTATAATATTTTT
616505 TGGTTGATAA
Statistics
Matches: 81, Mismatches: 0, Indels: 5
0.94 0.00 0.06
Matches are distributed among these distances:
68 18 0.22
69 1 0.01
71 43 0.53
72 19 0.23
ACGTcount: A:0.31, C:0.03, G:0.08, T:0.58
Consensus pattern (68 bp):
TTTATAATATTTTTGATTTGGTGTAATTTAAAATATTAATTTATTTTTAACATTCTTTAGTTGAT
TTT
Found at i:616489 original size:25 final size:25
Alignment explanation
Indices: 616461--616512 Score: 61
Period size: 25 Copynumber: 2.1 Consensus size: 25
616451 TAAAATATTA
616461 ATTTATTTT-TAACATTCTTTAGTTG
1 ATTT-TTTTATAACATTCTTTAGTTG
* * *
616486 ATTTTTTTATAATATTTTTTGGTTG
1 ATTTTTTTATAACATTCTTTAGTTG
616511 AT
1 AT
616513 AATAAAAAAT
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
24 4 0.17
25 19 0.83
ACGTcount: A:0.23, C:0.04, G:0.10, T:0.63
Consensus pattern (25 bp):
ATTTTTTTATAACATTCTTTAGTTG
Found at i:616820 original size:2 final size:2
Alignment explanation
Indices: 616815--616850 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
616805 AAAATTATGG
616815 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
616851 TATCTAAAAA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:618270 original size:156 final size:155
Alignment explanation
Indices: 618110--618457 Score: 520
Period size: 156 Copynumber: 2.2 Consensus size: 155
618100 AACAATTTAC
* * *
618110 TCCTATCAATTTTGAAAATCATCAACTAAGGACAATTGATCGTAATGTTAATGTTTTCTTCAATG
1 TCCTATCAATTTTGAAAATCATCAA-TAAGGACAATTGATCATAATGCTAACGTTTTCTTCAATG
*
618175 TTACATAGCTTTGATTGGTAAAAGGACCTTTTAGACCCTTCCAATTTTGAATTTGGCT-AAATTG
65 TTACATAACTTTGATTGGTAAAAGGACCTTTTAGACCCTTCCAATTTTGAATTTGGCTAAAATTG
*
618239 ATCCTTTTGAAAAGAAAACAACTCAAG
130 ATCCTTTTAAAAAGAAAACAACT-AAG
* *
618266 TCCTATCAATTTTGAAAATCATCAATCAAGGACAATTGATCATAGTGCTAACGTTTTCTTCAGTG
1 TCCTATCAATTTTGAAAATCATCAAT-AAGGACAATTGATCATAATGCTAACGTTTTCTTCAATG
*
618331 TTACATAACTTTGATTGGTAAAAGGACCTTTTAGACCCTTCCAGTTTTGAATTTGGCTAAAATTG
65 TTACATAACTTTGATTGGTAAAAGGACCTTTTAGACCCTTCCAATTTTGAATTTGGCTAAAATTG
* *
618396 GTCCTTTTAAAAAGAAAACAACTTAG
130 ATCCTTTTAAAAAGAAAACAACTAAG
* * *
618422 TCCTATCGATTTAT-AAGATCAGCAATTAAGGACAAT
1 TCCTATCAATTT-TGAAAATCATCAA-TAAGGACAAT
618458 CAATAACAAC
Statistics
Matches: 175, Mismatches: 13, Indels: 8
0.89 0.07 0.04
Matches are distributed among these distances:
155 1 0.01
156 145 0.83
157 29 0.17
ACGTcount: A:0.34, C:0.16, G:0.14, T:0.35
Consensus pattern (155 bp):
TCCTATCAATTTTGAAAATCATCAATAAGGACAATTGATCATAATGCTAACGTTTTCTTCAATGT
TACATAACTTTGATTGGTAAAAGGACCTTTTAGACCCTTCCAATTTTGAATTTGGCTAAAATTGA
TCCTTTTAAAAAGAAAACAACTAAG
Found at i:618478 original size:156 final size:155
Alignment explanation
Indices: 618110--618506 Score: 482
Period size: 156 Copynumber: 2.5 Consensus size: 155
618100 AACAATTTAC
* ** * * *
618110 TCCTATCAATTTTGAAAATCATCAA-CTAAGGACAATTGATCGTAATGTTAATGTTTTCTTCAAT
1 TCCTATCAATTTTGAAAATCAGCAATC-AAGGACAATCAATCATAGTGCTAATGTTTTCTTC-AT
*
618174 GTTACATAGCTTTGATTGGTAAAAGGACCTTTTAGACCCTTCCAATTTTGAATTTGGCTAAATTG
64 GTTACATAACTTTGATTGGTAAAAGGACCTTTTAGACCCTTCCAATTTTGAATTTGGCTAAATTG
*
618239 ATCCTTTTGAAAAGAAAACAACTCAAG
129 ATCCTTTTAAAAAGAAAACAACTCAAG
* ** *
618266 TCCTATCAATTTTGAAAATCATCAATCAAGGACAATTGATCATAGTGCTAACGTTTTCTTCAGTG
1 TCCTATCAATTTTGAAAATCAGCAATCAAGGACAATCAATCATAGTGCTAATGTTTTCTTCA-TG
*
618331 TTACATAACTTTGATTGGTAAAAGGACCTTTTAGACCCTTCCAGTTTTGAATTTGGCTAAAATTG
65 TTACATAACTTTGATTGGTAAAAGGACCTTTTAGACCCTTCCAATTTTGAATTTGGCT-AAATTG
* *
618396 GTCCTTTTAAAAAGAAAACAACT-TAG
129 ATCCTTTTAAAAAGAAAACAACTCAAG
* * *
618422 TCCTATCGATTTAT-AAGATCAGCAATTAAGGACAATCAATAACA-ACGT-C-AATGTTTTACTT
1 TCCTATCAATTT-TGAAAATCAGCAATCAAGGACAATCAAT--CATA-GTGCTAATGTTTT-C-T
* *
618483 TTATGTTACATAATTTTGATTGGT
60 TCATGTTACATAACTTTGATTGGT
618507 TTAGTAATAA
Statistics
Matches: 214, Mismatches: 18, Indels: 17
0.86 0.07 0.07
Matches are distributed among these distances:
155 1 0.00
156 154 0.72
157 52 0.24
158 7 0.03
ACGTcount: A:0.34, C:0.16, G:0.14, T:0.36
Consensus pattern (155 bp):
TCCTATCAATTTTGAAAATCAGCAATCAAGGACAATCAATCATAGTGCTAATGTTTTCTTCATGT
TACATAACTTTGATTGGTAAAAGGACCTTTTAGACCCTTCCAATTTTGAATTTGGCTAAATTGAT
CCTTTTAAAAAGAAAACAACTCAAG
Found at i:618647 original size:31 final size:31
Alignment explanation
Indices: 618593--618664 Score: 78
Period size: 31 Copynumber: 2.4 Consensus size: 31
618583 CATAATATTT
*
618593 AAATATTTTA-TTGATTTTAAAAATTCAAA-AA
1 AAATAATTTATTTGATTTTAAAAA-T-AAATAA
* *
618624 AAATTATTTATTTG-TTTTTAAAATAAATAA
1 AAATAATTTATTTGATTTTAAAAATAAATAA
618654 AAATAATTTAT
1 AAATAATTTAT
618665 ATAATTTCCA
Statistics
Matches: 35, Mismatches: 4, Indels: 5
0.80 0.09 0.11
Matches are distributed among these distances:
29 3 0.09
30 13 0.37
31 16 0.46
32 3 0.09
ACGTcount: A:0.50, C:0.01, G:0.03, T:0.46
Consensus pattern (31 bp):
AAATAATTTATTTGATTTTAAAAATAAATAA
Found at i:622804 original size:20 final size:20
Alignment explanation
Indices: 622772--622809 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
622762 GCACCAGAAT
622772 TCAATAGACGAA-GAATACA
1 TCAATAGACGAAGGAATACA
*
622791 TCAACTAGAGGAAGGAATA
1 TCAA-TAGACGAAGGAATA
622810 AAAGAAAAGA
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
19 4 0.25
20 7 0.44
21 5 0.31
ACGTcount: A:0.50, C:0.13, G:0.21, T:0.16
Consensus pattern (20 bp):
TCAATAGACGAAGGAATACA
Found at i:632844 original size:24 final size:25
Alignment explanation
Indices: 632795--632856 Score: 76
Period size: 24 Copynumber: 2.6 Consensus size: 25
632785 TTTTTGGTAA
** *
632795 TTTTATA-TTTAAAATTTTGAATAT
1 TTTTATATTTTAAAATTTAAAAGAT
632819 TTTTATATTTTAAAA-TTAAAAGAT
1 TTTTATATTTTAAAATTTAAAAGAT
632843 TTTTAT-TTTTAAAA
1 TTTTATATTTTAAAA
632857 GAAACCAAAT
Statistics
Matches: 34, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
23 8 0.24
24 19 0.56
25 7 0.21
ACGTcount: A:0.40, C:0.00, G:0.03, T:0.56
Consensus pattern (25 bp):
TTTTATATTTTAAAATTTAAAAGAT
Found at i:639013 original size:2 final size:2
Alignment explanation
Indices: 639006--639031 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
638996 TGTTCAAATG
639006 TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA
639032 AAGAAGATAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:655646 original size:25 final size:25
Alignment explanation
Indices: 655602--655659 Score: 73
Period size: 25 Copynumber: 2.3 Consensus size: 25
655592 ATAATCTGTT
*
655602 TTCACCCCCCTAAAATTTTTATAAG
1 TTCACCCCACTAAAATTTTTATAAG
*
655627 TTCACCCCACTGAAAA-TTTTATATG
1 TTCACCCCACT-AAAATTTTTATAAG
*
655652 TTCGCCCC
1 TTCACCCC
655660 CAACATAAAA
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
25 25 0.86
26 4 0.14
ACGTcount: A:0.28, C:0.31, G:0.07, T:0.34
Consensus pattern (25 bp):
TTCACCCCACTAAAATTTTTATAAG
Found at i:655660 original size:26 final size:25
Alignment explanation
Indices: 655606--655671 Score: 64
Period size: 25 Copynumber: 2.6 Consensus size: 25
655596 TCTGTTTTCA
655606 CCCCC-CTAAAATTTTTATAAGTTC
1 CCCCCACTAAAATTTTTATAAGTTC
* *
655630 ACCCCACTGAAAA-TTTTATATGTTC
1 CCCCCACT-AAAATTTTTATAAGTTC
655655 GCCCCCAACATAAAATT
1 -CCCCC-AC-TAAAATT
655672 ATTTGTTCGT
Statistics
Matches: 33, Mismatches: 3, Indels: 8
0.75 0.07 0.18
Matches are distributed among these distances:
24 4 0.12
25 13 0.39
26 8 0.24
27 6 0.18
28 2 0.06
ACGTcount: A:0.33, C:0.29, G:0.06, T:0.32
Consensus pattern (25 bp):
CCCCCACTAAAATTTTTATAAGTTC
Found at i:661696 original size:15 final size:15
Alignment explanation
Indices: 661676--661708 Score: 66
Period size: 15 Copynumber: 2.2 Consensus size: 15
661666 CGTAGGACCC
661676 CTACATCCCGAAGGA
1 CTACATCCCGAAGGA
661691 CTACATCCCGAAGGA
1 CTACATCCCGAAGGA
661706 CTA
1 CTA
661709 TTATACCCTC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.33, C:0.33, G:0.18, T:0.15
Consensus pattern (15 bp):
CTACATCCCGAAGGA
Found at i:661857 original size:23 final size:26
Alignment explanation
Indices: 661820--661888 Score: 85
Period size: 24 Copynumber: 2.8 Consensus size: 26
661810 TTCTCTTGTG
661820 ATCATGTATCTCATATCAC-T-TCAT
1 ATCATGTATCTCATATCACATGTCAT
661844 ATCATGT-TCTCATATCACATGTCAT
1 ATCATGTATCTCATATCACATGTCAT
* *
661869 ATCA--CATATCATATCACATG
1 ATCATGTATCTCATATCACATG
661889 AACATATATA
Statistics
Matches: 40, Mismatches: 2, Indels: 6
0.83 0.04 0.12
Matches are distributed among these distances:
23 11 0.28
24 21 0.52
25 8 0.20
ACGTcount: A:0.32, C:0.25, G:0.06, T:0.38
Consensus pattern (26 bp):
ATCATGTATCTCATATCACATGTCAT
Found at i:661870 original size:12 final size:12
Alignment explanation
Indices: 661853--661888 Score: 63
Period size: 12 Copynumber: 3.0 Consensus size: 12
661843 TATCATGTTC
661853 TCATATCACATG
1 TCATATCACATG
*
661865 TCATATCACATA
1 TCATATCACATG
661877 TCATATCACATG
1 TCATATCACATG
661889 AACATATATA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
12 22 1.00
ACGTcount: A:0.36, C:0.25, G:0.06, T:0.33
Consensus pattern (12 bp):
TCATATCACATG
Found at i:662374 original size:45 final size:45
Alignment explanation
Indices: 662279--662383 Score: 124
Period size: 45 Copynumber: 2.3 Consensus size: 45
662269 TGCACTCCTT
* *
662279 ATGCATCGATGCACCAATTGCATTCGATGTTTCATTATTAATGGG
1 ATGCATCGATGCACCAATTGCATTCGATGTTTCATTATTAAAGAG
** *
662324 ATGCATCGATGCATGAATTGCATTCGATGTTTTTATT-TTAAA-AG
1 ATGCATCGATGCACCAATTGCATTCGATG-TTTCATTATTAAAGAG
*
662368 AGTGCATCGATACACC
1 A-TGCATCGATGCACC
662384 TTCAAACAAT
Statistics
Matches: 50, Mismatches: 8, Indels: 4
0.81 0.13 0.06
Matches are distributed among these distances:
44 2 0.04
45 42 0.84
46 6 0.12
ACGTcount: A:0.29, C:0.17, G:0.19, T:0.35
Consensus pattern (45 bp):
ATGCATCGATGCACCAATTGCATTCGATGTTTCATTATTAAAGAG
Found at i:668717 original size:23 final size:26
Alignment explanation
Indices: 668680--668748 Score: 85
Period size: 24 Copynumber: 2.8 Consensus size: 26
668670 TTCTCTTGTG
668680 ATCATGTATCTCATATCAC-T-TCAT
1 ATCATGTATCTCATATCACATGTCAT
668704 ATCATGT-TCTCATATCACATGTCAT
1 ATCATGTATCTCATATCACATGTCAT
* *
668729 ATCA--CATATCATATCACATG
1 ATCATGTATCTCATATCACATG
668749 AACATATATA
Statistics
Matches: 40, Mismatches: 2, Indels: 6
0.83 0.04 0.12
Matches are distributed among these distances:
23 11 0.28
24 21 0.52
25 8 0.20
ACGTcount: A:0.32, C:0.25, G:0.06, T:0.38
Consensus pattern (26 bp):
ATCATGTATCTCATATCACATGTCAT
Found at i:668730 original size:12 final size:12
Alignment explanation
Indices: 668713--668748 Score: 63
Period size: 12 Copynumber: 3.0 Consensus size: 12
668703 TATCATGTTC
668713 TCATATCACATG
1 TCATATCACATG
*
668725 TCATATCACATA
1 TCATATCACATG
668737 TCATATCACATG
1 TCATATCACATG
668749 AACATATATA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
12 22 1.00
ACGTcount: A:0.36, C:0.25, G:0.06, T:0.33
Consensus pattern (12 bp):
TCATATCACATG
Found at i:669164 original size:64 final size:64
Alignment explanation
Indices: 669056--669216 Score: 218
Period size: 64 Copynumber: 2.5 Consensus size: 64
669046 TAATGAAGGT
* * * * *
669056 ATGCATCGATGCACTACTGATGCATCGGTGCATAAAAGGTATTCGATGTATT-ATTATTGATGGG
1 ATGCATCGATGCACTACTTATGCATCGATGCACAAAAGGCATTCGATGT-TTCATTATTAATGGG
* **
669120 ATGCATCGATGCACT-CTTTATGCATCGATGCACCAATTGCATTCGATGTTTCATTATTAATGGG
1 ATGCATCGATGCACTAC-TTATGCATCGATGCACAAAAGGCATTCGATGTTTCATTATTAATGGG
669184 ATGCATCGATGCACTACTTATGCATCGATGCAC
1 ATGCATCGATGCACTACTTATGCATCGATGCAC
669217 TACTTATGCA
Statistics
Matches: 86, Mismatches: 8, Indels: 6
0.86 0.08 0.06
Matches are distributed among these distances:
63 3 0.03
64 82 0.95
65 1 0.01
ACGTcount: A:0.27, C:0.19, G:0.21, T:0.33
Consensus pattern (64 bp):
ATGCATCGATGCACTACTTATGCATCGATGCACAAAAGGCATTCGATGTTTCATTATTAATGGG
Found at i:669208 original size:19 final size:19
Alignment explanation
Indices: 669184--669234 Score: 102
Period size: 19 Copynumber: 2.7 Consensus size: 19
669174 TATTAATGGG
669184 ATGCATCGATGCACTACTT
1 ATGCATCGATGCACTACTT
669203 ATGCATCGATGCACTACTT
1 ATGCATCGATGCACTACTT
669222 ATGCATCGATGCA
1 ATGCATCGATGCA
669235 TGAATTGCAT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 32 1.00
ACGTcount: A:0.27, C:0.25, G:0.18, T:0.29
Consensus pattern (19 bp):
ATGCATCGATGCACTACTT
Found at i:670997 original size:31 final size:31
Alignment explanation
Indices: 670959--671017 Score: 100
Period size: 31 Copynumber: 1.9 Consensus size: 31
670949 GTTAACTCGG
670959 AGTGACCACATCTTAATTAAACAAAAAAGAA
1 AGTGACCACATCTTAATTAAACAAAAAAGAA
* *
670990 AGTGACCACATCTTAGTTAAATAAAAAA
1 AGTGACCACATCTTAATTAAACAAAAAA
671018 TAAAATGGTC
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
31 26 1.00
ACGTcount: A:0.53, C:0.15, G:0.10, T:0.22
Consensus pattern (31 bp):
AGTGACCACATCTTAATTAAACAAAAAAGAA
Found at i:674383 original size:21 final size:21
Alignment explanation
Indices: 674358--674415 Score: 80
Period size: 21 Copynumber: 2.7 Consensus size: 21
674348 CCTAATATTG
674358 CAATGTTAAAATTAGGTGCAA
1 CAATGTTAAAATTAGGTGCAA
*
674379 CAATGTCAAAATTAGGTGCAA
1 CAATGTTAAAATTAGGTGCAA
*
674400 TAATGTTTGAAAATTA
1 CAATG-TT-AAAATTA
674416 AATGGATAAA
Statistics
Matches: 32, Mismatches: 3, Indels: 2
0.86 0.08 0.05
Matches are distributed among these distances:
21 24 0.75
22 1 0.03
23 7 0.22
ACGTcount: A:0.43, C:0.09, G:0.17, T:0.31
Consensus pattern (21 bp):
CAATGTTAAAATTAGGTGCAA
Found at i:681270 original size:310 final size:306
Alignment explanation
Indices: 680673--681287 Score: 1137
Period size: 310 Copynumber: 2.0 Consensus size: 306
680663 CAAAGGCAAA
680673 TGATTAAATCTCAGAAGAAGAAGGGAAAAAAGAACAAATGAGACTTGTGTACAACAAAAATATTG
1 TGATTAAATCTCAGAAGAAGAAGGGAAAAAAGAACAAATGAGACTTGTGTACAACAAAAATATTG
680738 CAGACGGAAAAGGGAGAGCAGAAATACAAGATGAAGAGAAACAACTTACCGCAAATCAGAAAAAA
66 CAGACGGAAAAGGGAGAGCAGAAATACAAGATGAAGAGAAACAACTTACCGCAAATCAGAAAAAA
680803 GCCCAGTAAAGTATTAGTTGTGTTGTGCAAGAGAAGAAACAGCTTCATTTAGAGCTGGTAGTGAG
131 GCCCAGTAAAGTATTAGTTGTGTTGTGCAAGAGAAGAAACAGCTTCATTTAGAGCTGGTAGTGAG
680868 GTAAATAACTGAGGAATAAGCCCGTTAAATCCATGATCATCATTTTGTGCCTGACAGAAGGATGA
196 GTAAATAACTGAGGAATAAGCCCGTTAAATCCATGATCATCATTTTGTGCCTGACAGAAGGATGA
680933 TGTTACTTGAAGTTTAGGATAAAGGGAAGATGCAGTCTTAATGAAT
261 TGTTACTTGAAGTTTAGGATAAAGGGAAGATGCAGTCTTAATGAAT
680979 TGATTAAATCTCAGAAAAGAAGAAGGGAAAAAAGAACAAAAATGAGACTTGTGTACAACAAAAAT
1 TGATTAAATCTCAG--AAGAAGAAGGGAAAAAAGAAC--AAATGAGACTTGTGTACAACAAAAAT
681044 ATTGCAGACGGAAAAGGGAGAGCAGAAATACAAGATGAAGAGAAACAACTTACCGCAATATCAG-
62 ATTGCAGACGGAAAAGGGAGAGCAGAAATACAAGATGAAGAGAAACAACTTACCGCAA-ATCAGA
681108 AAAAAGCCCAGTAAAGTAATTAGTTGT-TTGTGCAAGAGAA-AAACAGCTTCATTTAGAGCTGGT
126 AAAAAGCCCAGTAAAGT-ATTAGTTGTGTTGTGCAAGAGAAGAAACAGCTTCATTTAGAGCTGGT
681171 AGTGAGGTAAATAACTGAGGAATAAGCCCGTTAAATCCATGATCATCATTTTGTGCCTGACAGAA
190 AGTGAGGTAAATAACTGAGGAATAAGCCCGTTAAATCCATGATCATCATTTTGTGCCTGACAGAA
*
681236 GGGATGATGTTACTTGAAGTTTATGATAAAGGGAAGATGCAGTCTTAATGAA
255 -GGATGATGTTACTTGAAGTTTAGGATAAAGGGAAGATGCAGTCTTAATGAA
681288 ATTAACCAAA
Statistics
Matches: 301, Mismatches: 1, Indels: 10
0.96 0.00 0.03
Matches are distributed among these distances:
306 14 0.05
308 21 0.07
309 88 0.29
310 164 0.54
311 14 0.05
ACGTcount: A:0.42, C:0.12, G:0.23, T:0.22
Consensus pattern (306 bp):
TGATTAAATCTCAGAAGAAGAAGGGAAAAAAGAACAAATGAGACTTGTGTACAACAAAAATATTG
CAGACGGAAAAGGGAGAGCAGAAATACAAGATGAAGAGAAACAACTTACCGCAAATCAGAAAAAA
GCCCAGTAAAGTATTAGTTGTGTTGTGCAAGAGAAGAAACAGCTTCATTTAGAGCTGGTAGTGAG
GTAAATAACTGAGGAATAAGCCCGTTAAATCCATGATCATCATTTTGTGCCTGACAGAAGGATGA
TGTTACTTGAAGTTTAGGATAAAGGGAAGATGCAGTCTTAATGAAT
Found at i:684436 original size:39 final size:39
Alignment explanation
Indices: 684374--684452 Score: 142
Period size: 39 Copynumber: 2.0 Consensus size: 39
684364 AAATAGGTTA
684374 GGAGAATCCAATTGATCAGCTGATGGCTGTTATCGGTCCT
1 GGAGAATCCAATTGATCAGCTGATGGCTGTTATC-GTCCT
684414 GGAGAATCCAA-TGATCAGCTGATGGCTGTTATCGTCCT
1 GGAGAATCCAATTGATCAGCTGATGGCTGTTATCGTCCT
684452 G
1 G
684453 TTTTGACGTC
Statistics
Matches: 39, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
38 6 0.15
39 22 0.56
40 11 0.28
ACGTcount: A:0.23, C:0.20, G:0.28, T:0.29
Consensus pattern (39 bp):
GGAGAATCCAATTGATCAGCTGATGGCTGTTATCGTCCT
Found at i:689680 original size:25 final size:25
Alignment explanation
Indices: 689635--689685 Score: 59
Period size: 25 Copynumber: 2.0 Consensus size: 25
689625 ATGTAATTTT
* * *
689635 AAAAATTTTATTTAAATTAAAGAAC
1 AAAAATTATATATAAATTAAAAAAC
689660 AAAAATTATATATATAA-TAAAAAAC
1 AAAAATTATATATA-AATTAAAAAAC
689685 A
1 A
689686 CATTTTTTTG
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
25 20 0.91
26 2 0.09
ACGTcount: A:0.63, C:0.04, G:0.02, T:0.31
Consensus pattern (25 bp):
AAAAATTATATATAAATTAAAAAAC
Found at i:689901 original size:21 final size:21
Alignment explanation
Indices: 689877--689916 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
689867 AATAATTTGA
689877 GATTAGGGTAAGAGATTTAGG
1 GATTAGGGTAAGAGATTTAGG
* * *
689898 GATTTGGGTTAGGGATTTA
1 GATTAGGGTAAGAGATTTA
689917 TGTTTAGGGA
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:0.28, C:0.00, G:0.38, T:0.35
Consensus pattern (21 bp):
GATTAGGGTAAGAGATTTAGG
Found at i:689909 original size:13 final size:14
Alignment explanation
Indices: 689893--689933 Score: 57
Period size: 14 Copynumber: 3.0 Consensus size: 14
689883 GGTAAGAGAT
689893 TTAGGGATTT-GGG
1 TTAGGGATTTAGGG
* *
689906 TTAGGGATTTATGT
1 TTAGGGATTTAGGG
689920 TTAGGGATTTAGGG
1 TTAGGGATTTAGGG
689934 GGATTGAGAT
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
13 10 0.43
14 13 0.57
ACGTcount: A:0.20, C:0.00, G:0.39, T:0.41
Consensus pattern (14 bp):
TTAGGGATTTAGGG
Found at i:690543 original size:14 final size:15
Alignment explanation
Indices: 690512--690547 Score: 56
Period size: 14 Copynumber: 2.5 Consensus size: 15
690502 TGGCGGCCAC
690512 TTTAATTTCAAATAA
1 TTTAATTTCAAATAA
*
690527 TTTAATTT-AAATCA
1 TTTAATTTCAAATAA
690541 TTTAATT
1 TTTAATT
690548 AATCAATTAT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
14 12 0.60
15 8 0.40
ACGTcount: A:0.42, C:0.06, G:0.00, T:0.53
Consensus pattern (15 bp):
TTTAATTTCAAATAA
Found at i:692624 original size:26 final size:24
Alignment explanation
Indices: 692581--692632 Score: 70
Period size: 26 Copynumber: 2.1 Consensus size: 24
692571 TCTCTTCTAA
692581 TTTTAAATTTAAATATTAAATGAAT
1 TTTTAAATTTAAATATTAAAT-AAT
692606 TTTTATAATTATAAA-ATTAAATAAT
1 TTTTA-AATT-TAAATATTAAATAAT
692631 TT
1 TT
692633 GACATCTCCC
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
25 10 0.40
26 11 0.44
27 4 0.16
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (24 bp):
TTTTAAATTTAAATATTAAATAAT
Found at i:702277 original size:16 final size:16
Alignment explanation
Indices: 702253--702284 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
702243 TATCGCCGAT
*
702253 CAAATTTCACTATTCA
1 CAAAATTCACTATTCA
702269 CAAAATTCACTATTCA
1 CAAAATTCACTATTCA
702285 TGTGAATAGT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.41, C:0.25, G:0.00, T:0.34
Consensus pattern (16 bp):
CAAAATTCACTATTCA
Found at i:706389 original size:6 final size:6
Alignment explanation
Indices: 706378--706411 Score: 68
Period size: 6 Copynumber: 5.7 Consensus size: 6
706368 GTTTTATTAT
706378 GGAGTG GGAGTG GGAGTG GGAGTG GGAGTG GGAG
1 GGAGTG GGAGTG GGAGTG GGAGTG GGAGTG GGAG
706412 GAAAGTATTA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 28 1.00
ACGTcount: A:0.18, C:0.00, G:0.68, T:0.15
Consensus pattern (6 bp):
GGAGTG
Found at i:708727 original size:12 final size:12
Alignment explanation
Indices: 708710--708738 Score: 58
Period size: 12 Copynumber: 2.4 Consensus size: 12
708700 TTTGAATTTT
708710 TTATAAAAATTA
1 TTATAAAAATTA
708722 TTATAAAAATTA
1 TTATAAAAATTA
708734 TTATA
1 TTATA
708739 CTTATAAAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (12 bp):
TTATAAAAATTA
Found at i:709391 original size:13 final size:13
Alignment explanation
Indices: 709373--709418 Score: 56
Period size: 13 Copynumber: 3.5 Consensus size: 13
709363 TTTTTTATCA
709373 AAAATAAAGAGAT
1 AAAATAAAGAGAT
* * *
709386 AAAATATATGATAA
1 AAAATA-AAGAGAT
709400 AAAATAAAGAGAT
1 AAAATAAAGAGAT
709413 AAAATA
1 AAAATA
709419 TATGATCAAT
Statistics
Matches: 26, Mismatches: 6, Indels: 2
0.76 0.18 0.06
Matches are distributed among these distances:
13 16 0.62
14 10 0.38
ACGTcount: A:0.70, C:0.00, G:0.11, T:0.20
Consensus pattern (13 bp):
AAAATAAAGAGAT
Found at i:709409 original size:27 final size:28
Alignment explanation
Indices: 709372--709434 Score: 110
Period size: 27 Copynumber: 2.2 Consensus size: 28
709362 TTTTTTTATC
709372 AAAAATAAAGAGATAAAATATATGAT-A
1 AAAAATAAAGAGATAAAATATATGATCA
709399 AAAAATAAAGAGATAAAATATATGATCA
1 AAAAATAAAGAGATAAAATATATGATCA
709427 ATAAAATA
1 A-AAAATA
709435 TGCAATCTAA
Statistics
Matches: 34, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
27 26 0.76
28 2 0.06
29 6 0.18
ACGTcount: A:0.67, C:0.02, G:0.10, T:0.22
Consensus pattern (28 bp):
AAAAATAAAGAGATAAAATATATGATCA
Found at i:713431 original size:21 final size:21
Alignment explanation
Indices: 713407--713452 Score: 65
Period size: 21 Copynumber: 2.2 Consensus size: 21
713397 TTTCATTTTT
*
713407 GTTTCAAAACTTAACATTGAA
1 GTTTCAAAACTTAACATTAAA
* *
713428 GTTTGAACACTTAACATTAAA
1 GTTTCAAAACTTAACATTAAA
713449 GTTT
1 GTTT
713453 GAACAAAATA
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.39, C:0.13, G:0.11, T:0.37
Consensus pattern (21 bp):
GTTTCAAAACTTAACATTAAA
Found at i:713453 original size:21 final size:21
Alignment explanation
Indices: 713415--713457 Score: 77
Period size: 21 Copynumber: 2.0 Consensus size: 21
713405 TTGTTTCAAA
*
713415 ACTTAACATTGAAGTTTGAAC
1 ACTTAACATTAAAGTTTGAAC
713436 ACTTAACATTAAAGTTTGAAC
1 ACTTAACATTAAAGTTTGAAC
713457 A
1 A
713458 AAATACTAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.42, C:0.14, G:0.12, T:0.33
Consensus pattern (21 bp):
ACTTAACATTAAAGTTTGAAC
Found at i:714108 original size:29 final size:29
Alignment explanation
Indices: 714035--714106 Score: 83
Period size: 29 Copynumber: 2.5 Consensus size: 29
714025 AAAACCGAAT
* *
714035 TAAACGGGGACAAGGAAAAATCATTTATGC
1 TAAACGGGGAC-GGGAAAAACCATTTATGC
* *
714065 TAAAAGGGGACGGGAAAAACCGTTTATG-
1 TAAACGGGGACGGGAAAAACCATTTATGC
*
714093 TTAACGGGGACGGG
1 TAAACGGGGACGGG
714107 GACGGAGACG
Statistics
Matches: 36, Mismatches: 6, Indels: 2
0.82 0.14 0.05
Matches are distributed among these distances:
28 12 0.33
29 14 0.39
30 10 0.28
ACGTcount: A:0.38, C:0.12, G:0.32, T:0.18
Consensus pattern (29 bp):
TAAACGGGGACGGGAAAAACCATTTATGC
Found at i:716324 original size:3 final size:3
Alignment explanation
Indices: 716318--716353 Score: 72
Period size: 3 Copynumber: 12.0 Consensus size: 3
716308 TCATATCCTC
716318 CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT
1 CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT
716354 GTTTAATATT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 33 1.00
ACGTcount: A:0.00, C:0.33, G:0.00, T:0.67
Consensus pattern (3 bp):
CTT
Found at i:721002 original size:17 final size:16
Alignment explanation
Indices: 720961--720993 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
720951 TGAACGAGAT
*
720961 ACTAAAGTGAAACAAA
1 ACTAAAGTTAAACAAA
720977 ACTAAAGTTAAACAAA
1 ACTAAAGTTAAACAAA
720993 A
1 A
720994 ATTAAAGTTT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.64, C:0.12, G:0.09, T:0.15
Consensus pattern (16 bp):
ACTAAAGTTAAACAAA
Found at i:723288 original size:12 final size:12
Alignment explanation
Indices: 723271--723301 Score: 62
Period size: 12 Copynumber: 2.6 Consensus size: 12
723261 ATAAATTCGA
723271 CTAATTAAGCAT
1 CTAATTAAGCAT
723283 CTAATTAAGCAT
1 CTAATTAAGCAT
723295 CTAATTA
1 CTAATTA
723302 GAAACACCAC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.42, C:0.16, G:0.06, T:0.35
Consensus pattern (12 bp):
CTAATTAAGCAT
Found at i:730361 original size:366 final size:364
Alignment explanation
Indices: 729674--730403 Score: 1410
Period size: 366 Copynumber: 2.0 Consensus size: 364
729664 GCACATATAG
729674 AGATAACCGTACAGTCAGTAGCAGATTCAGAAATATTTTTGAGCGTGGACATTCACGTGTTAACA
1 AGATAACCGTACAGTCAGTAGCAGATTCAGAAATATTTTTGAGCGTGGACATTCACGTGTTAACA
729739 ACTTAAAATTTTTAAATAAACGGGTACAAATAAAATTTAATGTGGATAATGTCCGTAAAATAAGT
66 ACTTAAAATTTTTAAATAAACGGGTACAAATAAAATTTAATGTGGATAATGTCCGTAAAATAAGT
*
729804 ACCTAATCGAAGAAAACTCAAATTTCAAGATGAACACGAAAAATTAAATAAGTAACTAATCGAAG
131 ACCTAATCGAAGAAAACTCAAATTTCAAGATGAACACGAAAAATAAAATAAGTAACTAATCGAAG
729869 AAAGTTTGGATTTTAAATCACCCTCACCAAGTTGTAGCTCCGCCACTGCATAAAATCTTTAATGC
196 AAAGTTTGGATTTTAAATCACCCTCACCAAGTTGTAGCTCCGCCACTGCATAAAATCTTTAATGC
729934 ACCATCCATAACATTTTAAATTTAATTCTATTTCGATCTCAATTCTAACATTCTCAAAAAAAAAA
261 ACCATCCATAACATTTTAAATTTAATTCTATTTCGATCTCAATTCTAACATTCTC--AAAAAAAA
729999 TCTATCCAACACATCTTGAATTCAATTA-TTTTTTAAAACT
324 TCTATCCAACACATCTTGAATTCAATTATTTTTTTAAAACT
730039 AGATAATCCGTACAGTCAGTAGCAGATTCAGAAATATTTTTGAGCGTGGACATTCACGTGTTAAC
1 AGATAA-CCGTACAGTCAGTAGCAGATTCAGAAATATTTTTGAGCGTGGACATTCACGTGTTAAC
730104 AACTTAAAATTTTTAAATAAACGGGTACAAATAAAATTTAATGTGGATAATGTCCGTAAAATAAG
65 AACTTAAAATTTTTAAATAAACGGGTACAAATAAAATTTAATGTGGATAATGTCCGTAAAATAAG
730169 TACCTAATCGAAGAAAACTCAAATTTCAAGATGAACACGAAAAATAAAATAAGTAACTAATCGAA
130 TACCTAATCGAAGAAAACTCAAATTTCAAGATGAACACGAAAAATAAAATAAGTAACTAATCGAA
730234 GAAAG-TTGGATTTTAAATCACCCTCACCAAGTTGTAGCTCCGCCACTGCATAAAATCTTTAATG
195 GAAAGTTTGGATTTTAAATCACCCTCACCAAGTTGTAGCTCCGCCACTGCATAAAATCTTTAATG
730298 CACCATCCATAACATTTTAAATTTAATTCTATTTCGATCTCAATTCTAACATTCTCAAAAAAAAT
260 CACCATCCATAACATTTTAAATTTAATTCTATTTCGATCTCAATTCTAACATTCTCAAAAAAAAT
730363 CTATCCAACACATCTTGAATTCAATTATTTTTTTAAAACT
325 CTATCCAACACATCTTGAATTCAATTATTTTTTTAAAACT
730403 A
1 A
730404 ATTCAATACG
Statistics
Matches: 362, Mismatches: 1, Indels: 5
0.98 0.00 0.01
Matches are distributed among these distances:
363 36 0.10
364 13 0.04
365 121 0.33
366 192 0.53
ACGTcount: A:0.41, C:0.17, G:0.12, T:0.31
Consensus pattern (364 bp):
AGATAACCGTACAGTCAGTAGCAGATTCAGAAATATTTTTGAGCGTGGACATTCACGTGTTAACA
ACTTAAAATTTTTAAATAAACGGGTACAAATAAAATTTAATGTGGATAATGTCCGTAAAATAAGT
ACCTAATCGAAGAAAACTCAAATTTCAAGATGAACACGAAAAATAAAATAAGTAACTAATCGAAG
AAAGTTTGGATTTTAAATCACCCTCACCAAGTTGTAGCTCCGCCACTGCATAAAATCTTTAATGC
ACCATCCATAACATTTTAAATTTAATTCTATTTCGATCTCAATTCTAACATTCTCAAAAAAAATC
TATCCAACACATCTTGAATTCAATTATTTTTTTAAAACT
Found at i:731680 original size:13 final size:13
Alignment explanation
Indices: 731659--731690 Score: 55
Period size: 13 Copynumber: 2.5 Consensus size: 13
731649 GAGTTTGAGC
*
731659 TTAAAATATATAT
1 TTAATATATATAT
731672 TTAATATATATAT
1 TTAATATATATAT
731685 TTAATA
1 TTAATA
731691 ATTTAAATTA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (13 bp):
TTAATATATATAT
Found at i:735472 original size:53 final size:53
Alignment explanation
Indices: 735407--735512 Score: 212
Period size: 53 Copynumber: 2.0 Consensus size: 53
735397 AAGAACGCTT
735407 CGTCGAGCTTTGAAGAGAGTAACCTAGTTGCTAAGGCAATTGAATCATTTTTA
1 CGTCGAGCTTTGAAGAGAGTAACCTAGTTGCTAAGGCAATTGAATCATTTTTA
735460 CGTCGAGCTTTGAAGAGAGTAACCTAGTTGCTAAGGCAATTGAATCATTTTTA
1 CGTCGAGCTTTGAAGAGAGTAACCTAGTTGCTAAGGCAATTGAATCATTTTTA
735513 GTTGTCAAGG
Statistics
Matches: 53, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
53 53 1.00
ACGTcount: A:0.30, C:0.15, G:0.23, T:0.32
Consensus pattern (53 bp):
CGTCGAGCTTTGAAGAGAGTAACCTAGTTGCTAAGGCAATTGAATCATTTTTA
Found at i:736339 original size:35 final size:37
Alignment explanation
Indices: 736286--736359 Score: 98
Period size: 36 Copynumber: 2.1 Consensus size: 37
736276 ATCTAAGGAC
*
736286 TAAAACCAACATTAAAAATAC-TTTAAATTCAAGCAT
1 TAAAACCAACATTAAAAATACTTTTAAATGCAAGCAT
* * *
736322 TAAACCCAACATT-AAAATGCTTTTAAGTGCAAGCAT
1 TAAAACCAACATTAAAAATACTTTTAAATGCAAGCAT
736358 TA
1 TA
736360 CCAACGTATC
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
35 6 0.18
36 27 0.82
ACGTcount: A:0.47, C:0.18, G:0.07, T:0.28
Consensus pattern (37 bp):
TAAAACCAACATTAAAAATACTTTTAAATGCAAGCAT
Found at i:739438 original size:15 final size:15
Alignment explanation
Indices: 739418--739451 Score: 68
Period size: 15 Copynumber: 2.3 Consensus size: 15
739408 TTGATTATTC
739418 ATAAAATATTTTAAT
1 ATAAAATATTTTAAT
739433 ATAAAATATTTTAAT
1 ATAAAATATTTTAAT
739448 ATAA
1 ATAA
739452 TTTTATAAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (15 bp):
ATAAAATATTTTAAT
Found at i:739458 original size:23 final size:24
Alignment explanation
Indices: 739432--739488 Score: 73
Period size: 23 Copynumber: 2.5 Consensus size: 24
739422 AATATTTTAA
*
739432 TATAAAATATTTTAATATAAT-TT
1 TATAAAATATTTAAATATAATCTT
* *
739455 TATAAAATATATAAATGTAATCTT
1 TATAAAATATTTAAATATAATCTT
739479 TA-AAAATATT
1 TATAAAATATT
739489 ATGATTTTTT
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
23 25 0.86
24 4 0.14
ACGTcount: A:0.51, C:0.02, G:0.02, T:0.46
Consensus pattern (24 bp):
TATAAAATATTTAAATATAATCTT
Found at i:741530 original size:42 final size:42
Alignment explanation
Indices: 741483--741629 Score: 105
Period size: 42 Copynumber: 3.3 Consensus size: 42
741473 ACTTAAAACC
741483 CTAAACTATAACCCCATAACCTATAGATTATAAACACGAAAT
1 CTAAACTATAACCCCATAACCTATAGATTATAAACACGAAAT
* * ** ** * *** *
741525 CTAAACTCTAACTCGGAGCATCATTCTATACCTTACCTCTAACTTAAAACC
1 CTAAACTATAAC-C---CCAT-AACCTATAGATTA--T-AAACACGAAA-T
741576 CTAAACTATAACCCCATAACCTATAGATTATAAACACGAAAT
1 CTAAACTATAACCCCATAACCTATAGATTATAAACACGAAAT
*
741618 CTAAACTCTAAC
1 CTAAACTATAAC
741630 TCGGAGTTTA
Statistics
Matches: 73, Mismatches: 23, Indels: 18
0.64 0.20 0.16
Matches are distributed among these distances:
42 22 0.30
43 7 0.10
44 1 0.01
46 12 0.16
47 12 0.16
49 1 0.01
50 7 0.10
51 11 0.15
ACGTcount: A:0.42, C:0.27, G:0.05, T:0.26
Consensus pattern (42 bp):
CTAAACTATAACCCCATAACCTATAGATTATAAACACGAAAT
Found at i:741568 original size:93 final size:93
Alignment explanation
Indices: 741449--741635 Score: 374
Period size: 93 Copynumber: 2.0 Consensus size: 93
741439 TTATTCAATT
741449 GCATCATTCTATACCTTACCTCTAACTTAAAACCCTAAACTATAACCCCATAACCTATAGATTAT
1 GCATCATTCTATACCTTACCTCTAACTTAAAACCCTAAACTATAACCCCATAACCTATAGATTAT
741514 AAACACGAAATCTAAACTCTAACTCGGA
66 AAACACGAAATCTAAACTCTAACTCGGA
741542 GCATCATTCTATACCTTACCTCTAACTTAAAACCCTAAACTATAACCCCATAACCTATAGATTAT
1 GCATCATTCTATACCTTACCTCTAACTTAAAACCCTAAACTATAACCCCATAACCTATAGATTAT
741607 AAACACGAAATCTAAACTCTAACTCGGA
66 AAACACGAAATCTAAACTCTAACTCGGA
741635 G
1 G
741636 TTTATAATTT
Statistics
Matches: 94, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
93 94 1.00
ACGTcount: A:0.40, C:0.28, G:0.06, T:0.27
Consensus pattern (93 bp):
GCATCATTCTATACCTTACCTCTAACTTAAAACCCTAAACTATAACCCCATAACCTATAGATTAT
AAACACGAAATCTAAACTCTAACTCGGA
Found at i:742627 original size:4 final size:4
Alignment explanation
Indices: 742618--742646 Score: 58
Period size: 4 Copynumber: 7.2 Consensus size: 4
742608 CATCTCCTTT
742618 CTCC CTCC CTCC CTCC CTCC CTCC CTCC C
1 CTCC CTCC CTCC CTCC CTCC CTCC CTCC C
742647 CATTTTCTTA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 25 1.00
ACGTcount: A:0.00, C:0.76, G:0.00, T:0.24
Consensus pattern (4 bp):
CTCC
Found at i:747192 original size:18 final size:17
Alignment explanation
Indices: 747169--747215 Score: 58
Period size: 18 Copynumber: 2.7 Consensus size: 17
747159 AATATTTATG
747169 AGGAATTGAAATCTGTGA
1 AGGAATTGAAATCTGT-A
* *
747187 AGGAATTGGAATCTGTC
1 AGGAATTGAAATCTGTA
*
747204 ATGAATTGAAAT
1 AGGAATTGAAAT
747216 TCAATTTCAT
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
17 10 0.40
18 15 0.60
ACGTcount: A:0.38, C:0.06, G:0.26, T:0.30
Consensus pattern (17 bp):
AGGAATTGAAATCTGTA
Found at i:747905 original size:254 final size:248
Alignment explanation
Indices: 747583--748173 Score: 727
Period size: 254 Copynumber: 2.4 Consensus size: 248
747573 TCCGAGACCC
*
747583 GACCCGACCAAAATAAAA-TT---TC-ACCCGACCCGAATATATGAATTAGAAACCCGATCCGA-
1 GACCCGACCAAAATAAAATTTCACTCGACCCGACCCGAATATATGAATTAGAAA-CCGATCCAAC
*
747642 CTCGAAATAATAAAAAAATTATTTTTATTCAATGAAAACAGTGACTTAATTC-AGAAAATATATA
65 CT-GAAATAATAAAAAAATTATTTTTATTCAAT-AAAACAGTGACTTAATTCAAAAAAAT-TATA
* * *
747706 TATATG-GA-TATTATTGTAATTATTCCTAAGTATATAAGGTAAAATTATATAT-TTTTGGATCG
127 TATA-GAGAGTATTATTGTAATTATTCCTAAATATATAAGGTAAAATTATATATATATTCG---G
*
747768 AGTCGGGTTAGGTACTTTTCACCCTAAACTCAAACCCGACCCGAATATCACACTTAAAAAAA-C-
188 A-TCGGG-TA--T--TTTTCACCCTAAACCCAAACCCGACCCGAATATCACACTTAAAAAAATCA
747831 C-
247 CT
* * *
747832 GACTCGACCAAAATAAAGTTTCAC-CTGACCCGACTCGAATATATGAATTAGAAATCCGATCCAA
1 GACCCGACCAAAATAAAATTTCACTC-GACCCGACCCGAATATATGAATTAGAAA-CCGATCCAA
* *
747896 CCTGAAATAATAAAAAAAATTA-TTTTATTTAATAAAACAGTGACTTAATTGAAAAAAATTATAT
64 CCTGAAATAAT-AAAAAAATTATTTTTATTCAATAAAACAGTGACTTAATTCAAAAAAATTATAT
* *
747960 ATAGAGAGTATTATTGTAATTATTCCTAAATATATAATGTAAACTTATATATATATTCGGATCGG
128 ATAGAGAGTATTATTGTAATTATTCCTAAATATATAAGGTAAAATTATATATATATTCGGATCGG
* **
748025 GTATTTTTCACCCTAAACCCGAATTCGACCCGAATATCACACTTAAAAAAATCGACT
193 GTATTTTTCACCCTAAACCCAAACCCGACCCGAATATCACACTTAAAAAAATC-ACT
748082 GACCCGACCAAAATAAAATTTCACTCGACCCGACCCGAATATATGAATTAGAAA-C---CCAACC
1 GACCCGACCAAAATAAAATTTCACTCGACCCGACCCGAATATATGAATTAGAAACCGATCCAACC
*
748143 CGAAATAATAAAAAAA-TATTTTTATTCAATA
66 TGAAATAATAAAAAAATTATTTTTATTCAATA
748174 TATGAATAAG
Statistics
Matches: 302, Mismatches: 22, Indels: 41
0.83 0.06 0.11
Matches are distributed among these distances:
243 2 0.01
244 18 0.06
245 14 0.05
246 43 0.14
247 1 0.00
248 2 0.01
249 17 0.06
250 53 0.18
251 6 0.02
252 4 0.01
253 27 0.09
254 99 0.33
255 16 0.05
ACGTcount: A:0.42, C:0.18, G:0.11, T:0.29
Consensus pattern (248 bp):
GACCCGACCAAAATAAAATTTCACTCGACCCGACCCGAATATATGAATTAGAAACCGATCCAACC
TGAAATAATAAAAAAATTATTTTTATTCAATAAAACAGTGACTTAATTCAAAAAAATTATATATA
GAGAGTATTATTGTAATTATTCCTAAATATATAAGGTAAAATTATATATATATTCGGATCGGGTA
TTTTTCACCCTAAACCCAAACCCGACCCGAATATCACACTTAAAAAAATCACT
Found at i:753102 original size:38 final size:38
Alignment explanation
Indices: 753060--753137 Score: 106
Period size: 38 Copynumber: 2.1 Consensus size: 38
753050 ACTTAATGGT
*
753060 AAATTT-TAA-ACGGGAGTACTACAATAAAACAAAAACTA
1 AAATTTCTAATAC-GGA-TACTAAAATAAAACAAAAACTA
*
753098 AAATTTCTAATACGGATACTAAAATGAAACAAAAACTA
1 AAATTTCTAATACGGATACTAAAATAAAACAAAAACTA
753136 AA
1 AA
753138 CTTTAGATAT
Statistics
Matches: 36, Mismatches: 2, Indels: 4
0.86 0.05 0.10
Matches are distributed among these distances:
38 28 0.78
39 6 0.17
40 2 0.06
ACGTcount: A:0.56, C:0.13, G:0.09, T:0.22
Consensus pattern (38 bp):
AAATTTCTAATACGGATACTAAAATAAAACAAAAACTA
Found at i:764880 original size:7 final size:7
Alignment explanation
Indices: 764868--764893 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
764858 AGTACAAGTA
764868 CATGCAT
1 CATGCAT
764875 CATGCAT
1 CATGCAT
764882 CATGCAT
1 CATGCAT
764889 CATGC
1 CATGC
764894 GTGATATTGA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.27, C:0.31, G:0.15, T:0.27
Consensus pattern (7 bp):
CATGCAT
Found at i:766438 original size:23 final size:23
Alignment explanation
Indices: 766395--766456 Score: 63
Period size: 23 Copynumber: 2.7 Consensus size: 23
766385 AGAGGAAAGT
*
766395 GTGTCACAAAAGTAAATATAAAC
1 GTGTCACAAAAGTAAAGATAAAC
* *
766418 GTGTCACAAATA-TATAGATAAAT
1 GTGTCACAAA-AGTAAAGATAAAC
* *
766441 GTGTCATAAAAATAAA
1 GTGTCACAAAAGTAAA
766457 ATTAAAAAGA
Statistics
Matches: 32, Mismatches: 5, Indels: 4
0.78 0.12 0.10
Matches are distributed among these distances:
22 1 0.03
23 30 0.94
24 1 0.03
ACGTcount: A:0.52, C:0.10, G:0.13, T:0.26
Consensus pattern (23 bp):
GTGTCACAAAAGTAAAGATAAAC
Found at i:766556 original size:19 final size:18
Alignment explanation
Indices: 766530--766580 Score: 57
Period size: 19 Copynumber: 2.7 Consensus size: 18
766520 AAACAAAATA
766530 AAAAAATGATATAACTTAT
1 AAAAAATGATATAA-TTAT
* *
766549 AGAAAATGACAATAATTAT
1 AAAAAATGA-TATAATTAT
766568 AAAAAATAGATAT
1 AAAAAAT-GATAT
766581 TCAAATTTAT
Statistics
Matches: 26, Mismatches: 4, Indels: 4
0.76 0.12 0.12
Matches are distributed among these distances:
19 20 0.77
20 6 0.23
ACGTcount: A:0.61, C:0.04, G:0.08, T:0.27
Consensus pattern (18 bp):
AAAAAATGATATAATTAT
Found at i:771323 original size:21 final size:23
Alignment explanation
Indices: 771271--771312 Score: 61
Period size: 21 Copynumber: 1.9 Consensus size: 23
771261 CATCAGAATG
771271 CTGTAATTTTCTTTCTTTCTTCT
1 CTGTAATTTTCTTTCTTTCTTCT
*
771294 CTGT-TTTTTC-TTCTTTCTT
1 CTGTAATTTTCTTTCTTTCTT
771313 TTGGTAATTT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 9 0.50
22 5 0.28
23 4 0.22
ACGTcount: A:0.05, C:0.21, G:0.05, T:0.69
Consensus pattern (23 bp):
CTGTAATTTTCTTTCTTTCTTCT
Found at i:772097 original size:11 final size:12
Alignment explanation
Indices: 772073--772097 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
772063 AAATTTCAGT
772073 AAAAATTTTAAA
1 AAAAATTTTAAA
772085 AAAAATTTTAAA
1 AAAAATTTTAAA
772097 A
1 A
772098 TTCAATAAAC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (12 bp):
AAAAATTTTAAA
Found at i:774787 original size:44 final size:44
Alignment explanation
Indices: 774724--774811 Score: 176
Period size: 44 Copynumber: 2.0 Consensus size: 44
774714 TGTAATGCAA
774724 ACAAAAACTTTATTTTACCATCCTTTCTCTAGCTTTATTTGTTT
1 ACAAAAACTTTATTTTACCATCCTTTCTCTAGCTTTATTTGTTT
774768 ACAAAAACTTTATTTTACCATCCTTTCTCTAGCTTTATTTGTTT
1 ACAAAAACTTTATTTTACCATCCTTTCTCTAGCTTTATTTGTTT
774812 TTGTTCTGTA
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
44 44 1.00
ACGTcount: A:0.25, C:0.20, G:0.05, T:0.50
Consensus pattern (44 bp):
ACAAAAACTTTATTTTACCATCCTTTCTCTAGCTTTATTTGTTT
Found at i:795578 original size:22 final size:21
Alignment explanation
Indices: 795549--795598 Score: 66
Period size: 21 Copynumber: 2.3 Consensus size: 21
795539 TATATTCTAC
*
795549 CCCTAAATTATAA-CTCATAAA
1 CCCTAAAATATAATCTCAT-AA
795570 CCCTAAAATATAATCTCATAA
1 CCCTAAAATATAATCTCATAA
795591 CCTCTAAA
1 CC-CTAAA
795599 CCCTAACTTA
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
21 16 0.62
22 10 0.38
ACGTcount: A:0.46, C:0.26, G:0.00, T:0.28
Consensus pattern (21 bp):
CCCTAAAATATAATCTCATAA
Found at i:799122 original size:39 final size:39
Alignment explanation
Indices: 799068--799145 Score: 138
Period size: 39 Copynumber: 2.0 Consensus size: 39
799058 ACGTCTTATT
*
799068 TGCGTCTTTAGACGATTTATTCTAATGATCTTTTCAATC
1 TGCGTCTTTAGACGATTTATTCTAATAATCTTTTCAATC
*
799107 TGCGTCTTTATACGATTTATTCTAATAATCTTTTCAATC
1 TGCGTCTTTAGACGATTTATTCTAATAATCTTTTCAATC
799146 CAGTTGTTCC
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
39 37 1.00
ACGTcount: A:0.24, C:0.18, G:0.10, T:0.47
Consensus pattern (39 bp):
TGCGTCTTTAGACGATTTATTCTAATAATCTTTTCAATC
Found at i:800932 original size:108 final size:108
Alignment explanation
Indices: 800766--800986 Score: 433
Period size: 108 Copynumber: 2.0 Consensus size: 108
800756 GTTTATCTAC
*
800766 GAAACATGAAAAGTTCTCTGTGGTTGAATATCAAATATAAAGAAGTATATTTATGATCCCATCTC
1 GAAATATGAAAAGTTCTCTGTGGTTGAATATCAAATATAAAGAAGTATATTTATGATCCCATCTC
800831 TGTGGTTGAATATCAAATATAAAGAAGTATATTTATATTAGAA
66 TGTGGTTGAATATCAAATATAAAGAAGTATATTTATATTAGAA
800874 GAAATATGAAAAGTTCTCTGTGGTTGAATATCAAATATAAAGAAGTATATTTATGATCCCATCTC
1 GAAATATGAAAAGTTCTCTGTGGTTGAATATCAAATATAAAGAAGTATATTTATGATCCCATCTC
800939 TGTGGTTGAATATCAAATATAAAGAAGTATATTTATATTAGAA
66 TGTGGTTGAATATCAAATATAAAGAAGTATATTTATATTAGAA
800982 GAAAT
1 GAAAT
800987 TAAAGAGAAC
Statistics
Matches: 112, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
108 112 1.00
ACGTcount: A:0.41, C:0.09, G:0.16, T:0.34
Consensus pattern (108 bp):
GAAATATGAAAAGTTCTCTGTGGTTGAATATCAAATATAAAGAAGTATATTTATGATCCCATCTC
TGTGGTTGAATATCAAATATAAAGAAGTATATTTATATTAGAA
Found at i:802587 original size:204 final size:205
Alignment explanation
Indices: 802182--802588 Score: 791
Period size: 203 Copynumber: 2.0 Consensus size: 205
802172 ATATCTTAGT
802182 TAACAGGTTAATGTCTAGCTCAGGTTGCCATTAATTTTTTAACGAAAAATGACGAATTTGGAATA
1 TAACAGGTTAATGTCTAGCTCAGGTTGCCATTAATTTTTTAACGAAAAATGACGAATTTGGAATA
802247 TATGAATAGTCAAGTGACTATTTTGTAATTTTTTATAGTCGATAGACTCAACAAAATAACATCGT
66 TATGAATAGTCAAGTGACTATTTTGTAATTTTTTATAGTCGATAGACTCAACAAAATAACATCGT
802312 ATTGTCGATAAACTATTTTGTAACTTTTATAATCAATTGACTCGACAAAGGCCTAAATCAATAGA
131 ATTGTCGATAAACTATTTTGTAACTTTTATAATCAATTGACTCGACAAAGGCCTAAATCAATAGA
802377 TCATTTGTAC
196 TCATTTGTAC
802387 TAACA-GTTAATGTCTA-CTCAGGTTGCCATTAATTTTTTAACGAAAAATGACGAATTTGGAATA
1 TAACAGGTTAATGTCTAGCTCAGGTTGCCATTAATTTTTTAACGAAAAATGACGAATTTGGAATA
802450 TATGAATAGTCAAGTGACTATTTTGTAATTTTTTATAGTCGATAGACTCAACAAAATAACATCGT
66 TATGAATAGTCAAGTGACTATTTTGTAATTTTTTATAGTCGATAGACTCAACAAAATAACATCGT
802515 ATTGTCGATAAACTATTTTGTAACTTTTTATAATCAATTGACTCGACAAAGGCCTAAATCAATAG
131 ATTGTCGATAAACTATTTTGTAAC-TTTTATAATCAATTGACTCGACAAAGGCCTAAATCAATAG
802580 ATCATTTGT
195 ATCATTTGT
802589 GTACTTTACC
Statistics
Matches: 201, Mismatches: 0, Indels: 3
0.99 0.00 0.01
Matches are distributed among these distances:
203 136 0.68
204 60 0.30
205 5 0.02
ACGTcount: A:0.36, C:0.14, G:0.14, T:0.36
Consensus pattern (205 bp):
TAACAGGTTAATGTCTAGCTCAGGTTGCCATTAATTTTTTAACGAAAAATGACGAATTTGGAATA
TATGAATAGTCAAGTGACTATTTTGTAATTTTTTATAGTCGATAGACTCAACAAAATAACATCGT
ATTGTCGATAAACTATTTTGTAACTTTTATAATCAATTGACTCGACAAAGGCCTAAATCAATAGA
TCATTTGTAC
Found at i:808582 original size:20 final size:20
Alignment explanation
Indices: 808546--808583 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
808536 ATCCTATTCC
**
808546 CTGGTAATCTTTTATTCCCA
1 CTGGTAATCTTACATTCCCA
808566 CTGGTAATCTTACATTCC
1 CTGGTAATCTTACATTCC
808584 GTGAACCAAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.21, C:0.26, G:0.11, T:0.42
Consensus pattern (20 bp):
CTGGTAATCTTACATTCCCA
Found at i:808965 original size:22 final size:23
Alignment explanation
Indices: 808935--808978 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 23
808925 TTGATTGATT
808935 TATTAATATTTATAATAATATAA
1 TATTAATATTTATAATAATATAA
* *
808958 TATT-ATATTTTTAATATTATA
1 TATTAATATTTATAATAATATA
808979 TAAAATAATC
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
22 15 0.79
23 4 0.21
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (23 bp):
TATTAATATTTATAATAATATAA
Done.