Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018397261.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_50.0, 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: 9139585
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 37885 characters in sequence are not A, C, G, or T
File 7 of 19
Found at i:2312622 original size:18 final size:18
Alignment explanation
Indices: 2312601--2312650 Score: 82
Period size: 18 Copynumber: 2.8 Consensus size: 18
2312591 ACCTCAACAA
*
2312601 TAGGAATAACCTTAGTTT
1 TAGGAATAACCTTAGTAT
2312619 TAGGAATAACCTTAGTAT
1 TAGGAATAACCTTAGTAT
*
2312637 TAGGAATACCCTTA
1 TAGGAATAACCTTA
2312651 TCTTGAGTAG
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 30 1.00
ACGTcount: A:0.36, C:0.14, G:0.16, T:0.34
Consensus pattern (18 bp):
TAGGAATAACCTTAGTAT
Found at i:2315851 original size:31 final size:31
Alignment explanation
Indices: 2315786--2315851 Score: 78
Period size: 31 Copynumber: 2.1 Consensus size: 31
2315776 TTTTCTAAAA
* *
2315786 AAAAATACAAGTAACAAATTACTAGGAGACG
1 AAAAATACAAGTAACAAATTACAAGGAGAAG
* * * *
2315817 AAAAATTCAAGTAAGAAATTTCAATGAGAAG
1 AAAAATACAAGTAACAAATTACAAGGAGAAG
2315848 AAAA
1 AAAA
2315852 GAAAACTTGC
Statistics
Matches: 29, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
31 29 1.00
ACGTcount: A:0.58, C:0.09, G:0.15, T:0.18
Consensus pattern (31 bp):
AAAAATACAAGTAACAAATTACAAGGAGAAG
Found at i:2317784 original size:50 final size:50
Alignment explanation
Indices: 2317730--2317852 Score: 219
Period size: 50 Copynumber: 2.5 Consensus size: 50
2317720 NNNNNNNNNN
2317730 ATTATAAATAAAAATAATAATAAAAGAAAAATAATTTTAAATTTAAAAAT
1 ATTATAAATAAAAATAATAATAAAAGAAAAATAATTTTAAATTTAAAAAT
*
2317780 ATTATAAATAAAAATAATAATAAAAGAAAATTAATTTTAAATTTAAAAAT
1 ATTATAAATAAAAATAATAATAAAAGAAAAATAATTTTAAATTTAAAAAT
* *
2317830 ATTATAAATAATAGTAATAATAA
1 ATTATAAATAAAAATAATAATAA
2317853 TAAATTAGAG
Statistics
Matches: 70, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
50 70 1.00
ACGTcount: A:0.64, C:0.00, G:0.02, T:0.33
Consensus pattern (50 bp):
ATTATAAATAAAAATAATAATAAAAGAAAAATAATTTTAAATTTAAAAAT
Found at i:2317837 original size:17 final size:18
Alignment explanation
Indices: 2317730--2317838 Score: 81
Period size: 17 Copynumber: 6.5 Consensus size: 18
2317720 NNNNNNNNNN
2317730 ATTATAAA--TAAAAATA
1 ATTATAAATTTAAAAATA
* **
2317746 ATAATAAA-AGAAAAATA
1 ATTATAAATTTAAAAATA
*
2317763 ATTTTAAATTTAAAAAT-
1 ATTATAAATTTAAAAATA
2317780 ATTATAAA--TAAAAATA
1 ATTATAAATTTAAAAATA
* ** *
2317796 ATAATAAA-AGAAAATTA
1 ATTATAAATTTAAAAATA
*
2317813 ATTTTAAATTTAAAAAT-
1 ATTATAAATTTAAAAATA
2317830 ATTATAAAT
1 ATTATAAAT
2317839 AATAGTAATA
Statistics
Matches: 72, Mismatches: 16, Indels: 9
0.74 0.16 0.09
Matches are distributed among these distances:
15 7 0.10
16 14 0.19
17 40 0.56
18 11 0.15
ACGTcount: A:0.64, C:0.00, G:0.02, T:0.34
Consensus pattern (18 bp):
ATTATAAATTTAAAAATA
Found at i:2337411 original size:39 final size:39
Alignment explanation
Indices: 2337346--2337424 Score: 122
Period size: 39 Copynumber: 2.0 Consensus size: 39
2337336 CACCAATTTC
* *
2337346 CCTTCAATTACATCTCCACTTATCTTAGGGATCCTAATT
1 CCTTCAATTACATCTCCACTCATCTTAGGAATCCTAATT
* *
2337385 CCTTCAATTACATCTGCACTCCTCTTAGGAATCCTAATT
1 CCTTCAATTACATCTCCACTCATCTTAGGAATCCTAATT
2337424 C
1 C
2337425 TGTATTGTTG
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
39 36 1.00
ACGTcount: A:0.25, C:0.30, G:0.08, T:0.37
Consensus pattern (39 bp):
CCTTCAATTACATCTCCACTCATCTTAGGAATCCTAATT
Found at i:2341536 original size:26 final size:28
Alignment explanation
Indices: 2341489--2341541 Score: 74
Period size: 26 Copynumber: 2.0 Consensus size: 28
2341479 GATTGGTGAA
2341489 ATAAAATAAAAAAATAATATAATTATTT
1 ATAAAATAAAAAAATAATATAATTATTT
* *
2341517 ATAAAA-AATAAATTAA-ATAATTATT
1 ATAAAATAAAAAAATAATATAATTATT
2341542 ATGTAATTTA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
26 9 0.39
27 8 0.35
28 6 0.26
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (28 bp):
ATAAAATAAAAAAATAATATAATTATTT
Found at i:2341540 original size:22 final size:22
Alignment explanation
Indices: 2341497--2341540 Score: 54
Period size: 22 Copynumber: 2.0 Consensus size: 22
2341487 AAATAAAATA
* *
2341497 AAAAAATAATATAATTATTTAT
1 AAAAAATAATATAAATAATTAT
2341519 AAAAAATAA-ATTAAATAATTAT
1 AAAAAATAATA-TAAATAATTAT
2341541 TATGTAATTT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
21 1 0.05
22 18 0.95
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (22 bp):
AAAAAATAATATAAATAATTAT
Found at i:2341736 original size:22 final size:22
Alignment explanation
Indices: 2341692--2341736 Score: 54
Period size: 22 Copynumber: 2.0 Consensus size: 22
2341682 TTTTTGAAAT
* *
2341692 TTATTAGTTTAATAATATGTTA
1 TTATTAATTTAATAATATATTA
* *
2341714 TTATTAATTTAATATTTTATTA
1 TTATTAATTTAATAATATATTA
2341736 T
1 T
2341737 CAACATATTA
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.36, C:0.00, G:0.04, T:0.60
Consensus pattern (22 bp):
TTATTAATTTAATAATATATTA
Found at i:2344135 original size:17 final size:17
Alignment explanation
Indices: 2344113--2344148 Score: 72
Period size: 17 Copynumber: 2.1 Consensus size: 17
2344103 TATGCATAAA
2344113 TTGGATAATGTTTCTGG
1 TTGGATAATGTTTCTGG
2344130 TTGGATAATGTTTCTGG
1 TTGGATAATGTTTCTGG
2344147 TT
1 TT
2344149 TCTTTGTTGA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.17, C:0.06, G:0.28, T:0.50
Consensus pattern (17 bp):
TTGGATAATGTTTCTGG
Found at i:2348800 original size:18 final size:18
Alignment explanation
Indices: 2348777--2348825 Score: 53
Period size: 18 Copynumber: 2.7 Consensus size: 18
2348767 GAAAGTATTC
*
2348777 ATCCACTTTTGGTTGGTG
1 ATCCACTTATGGTTGGTG
* *
2348795 ATCCACTTATGATTGGTT
1 ATCCACTTATGGTTGGTG
* *
2348813 ATCTACTTCTGGT
1 ATCCACTTATGGT
2348826 GAATTATCCA
Statistics
Matches: 25, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
18 25 1.00
ACGTcount: A:0.16, C:0.18, G:0.20, T:0.45
Consensus pattern (18 bp):
ATCCACTTATGGTTGGTG
Found at i:2349408 original size:21 final size:21
Alignment explanation
Indices: 2349378--2349427 Score: 73
Period size: 21 Copynumber: 2.4 Consensus size: 21
2349368 AAGAAAGATA
* * *
2349378 AGAAATAAAGTATTTAGAGGG
1 AGAAAAAAAGTATTTAAAAGG
2349399 AGAAAAAAAGTATTTAAAAGG
1 AGAAAAAAAGTATTTAAAAGG
2349420 AGAAAAAA
1 AGAAAAAA
2349428 GATCTTATTC
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:0.60, C:0.00, G:0.22, T:0.18
Consensus pattern (21 bp):
AGAAAAAAAGTATTTAAAAGG
Found at i:2349613 original size:10 final size:10
Alignment explanation
Indices: 2349583--2349615 Score: 50
Period size: 10 Copynumber: 3.4 Consensus size: 10
2349573 CATTCAAATG
2349583 TAAATATAAA
1 TAAATATAAA
2349593 T-AATATAAA
1 TAAATATAAA
*
2349602 TAAATATTAA
1 TAAATATAAA
2349612 TAAA
1 TAAA
2349616 AATATTCATA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
9 9 0.43
10 12 0.57
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (10 bp):
TAAATATAAA
Found at i:2350645 original size:2 final size:2
Alignment explanation
Indices: 2350640--2350668 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
2350630 ATAAACGGTT
2350640 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
2350669 TTGCAGGGCA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:2369788 original size:2 final size:2
Alignment explanation
Indices: 2369781--2369823 Score: 86
Period size: 2 Copynumber: 21.5 Consensus size: 2
2369771 TAATAGTTTC
2369781 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
2369823 A
1 A
2369824 AAAGCATAGA
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:2370206 original size:3 final size:3
Alignment explanation
Indices: 2370198--2370225 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
2370188 AATTTTAATG
2370198 ATT ATT ATT ATT ATT ATT ATT ATT ATT A
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT A
2370226 CATTTCGACA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (3 bp):
ATT
Found at i:2370348 original size:3 final size:3
Alignment explanation
Indices: 2370340--2370381 Score: 75
Period size: 3 Copynumber: 14.0 Consensus size: 3
2370330 CCTAAAAATG
*
2370340 TAA TAA TAA TAA TAA TAA TAA CAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
2370382 AATTATTATT
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
3 37 1.00
ACGTcount: A:0.67, C:0.02, G:0.00, T:0.31
Consensus pattern (3 bp):
TAA
Found at i:2382979 original size:228 final size:223
Alignment explanation
Indices: 2382609--2383060 Score: 653
Period size: 228 Copynumber: 2.0 Consensus size: 223
2382599 TTTGTGAGAG
* * * *
2382609 AAAAAAATTATACATATTTTGACAGTTAGAGATAAACCTCCATATTTTCAACTAAATTTACCTAA
1 AAAAAAATAATACATATTTTGAAAGTTAGAGATAAACCTACATATTTTCAACTAAATTGACCTAA
2382674 AAATTGACACTTAGAAAAGGAACCAATTTTATTTTTCATGGAAAAACAAAATATTTTAAGTATCA
66 AAATTGACACTTAGAAAAGGAACCAATTTTATTTTTCATGGAAAAACAAAATATTTTAAGTATCA
* * *
2382739 TTTTTAGCAAAAATTGTTATATATACATGACTAGTT-TTTCATCAATAAAACAAAAA-ATT-TAC
131 TTTTTAGCAAAAACTGTTATATATACATAAC-AATTGTTTCATCAATAAAACAAAAAGATTATAC
**
2382801 TTTTCATGGAAAAGCGCAATATTTTAAGTATT
195 --TTCATGGAAAA-CAAAATATTTTAAGTATT
* * *
2382833 AAAAAAA-AATACATATTTTTAAATTTAGTGATAAACCTACATA-TTTCAACTAAATTGACCTAA
1 AAAAAAATAATACATATTTTGAAAGTTAGAGATAAACCTACATATTTTCAACTAAATTGACCTAA
2382896 AAATTGTTGACACTTAGAAAAGGAACCAATTTTATTTTTCATGATTGAAAAACAAAATATTTTAA
66 AAA---TTGACACTTAGAAAAGGAACCAATTTTATTTTTCATG---GAAAAACAAAATATTTTAA
* *
2382961 GTATTATTTTTAGCAAAAACTGTTATATATACATAACAATTGTTTCATCAATAAAACAAAAAGGT
125 GTATCATTTTTAGCAAAAACTGTTATATATACATAACAATTGTTTCATCAATAAAACAAAAAGAT
2383026 TATACTTCATGGAAAACAAAATATTTTAAGTATT
190 TATACTTCATGGAAAACAAAATATTTTAAGTATT
2383060 A
1 A
2383061 TCTTTATTTT
Statistics
Matches: 205, Mismatches: 14, Indels: 15
0.88 0.06 0.06
Matches are distributed among these distances:
222 22 0.11
223 30 0.15
224 7 0.03
225 37 0.18
227 20 0.10
228 84 0.41
229 2 0.01
230 3 0.01
ACGTcount: A:0.45, C:0.11, G:0.09, T:0.35
Consensus pattern (223 bp):
AAAAAAATAATACATATTTTGAAAGTTAGAGATAAACCTACATATTTTCAACTAAATTGACCTAA
AAATTGACACTTAGAAAAGGAACCAATTTTATTTTTCATGGAAAAACAAAATATTTTAAGTATCA
TTTTTAGCAAAAACTGTTATATATACATAACAATTGTTTCATCAATAAAACAAAAAGATTATACT
TCATGGAAAACAAAATATTTTAAGTATT
Found at i:2383119 original size:100 final size:94
Alignment explanation
Indices: 2382944--2383122 Score: 236
Period size: 100 Copynumber: 1.8 Consensus size: 94
2382934 TCATGATTGA
*
2382944 AAAACAAAATATTTTAAGTATTATTTTTAGCAAAAACTGTTATATATACATAACAATTGTTTCAT
1 AAAACAAAATATTTTAAGTATTATTTTTAGAAAAAACTGTTATATATACATAACAATTGTTTCAT
2383009 CAATAAAACAAAAAGGTTATACTTCATGG
66 CAATAAAACAAAAAGGTTATACTTCATGG
* *
2383038 AAAACAAAATATTTTAAGTATTATCTTTATTTTA-AAAAATATTGTTATATATATC-TAACTATT
1 AAAACAAAATATTTTAAGTATTA----T-TTTTAGAAAAA-ACTGTTATATATA-CATAAC-AAT
*
2383101 TTTTTCATCAATAAAACAAAAA
58 TGTTTCATCAATAAAACAAAAA
2383123 AAATTATCCG
Statistics
Matches: 73, Mismatches: 4, Indels: 10
0.84 0.05 0.11
Matches are distributed among these distances:
94 23 0.32
98 5 0.07
99 21 0.29
100 24 0.33
ACGTcount: A:0.46, C:0.09, G:0.06, T:0.39
Consensus pattern (94 bp):
AAAACAAAATATTTTAAGTATTATTTTTAGAAAAAACTGTTATATATACATAACAATTGTTTCAT
CAATAAAACAAAAAGGTTATACTTCATGG
Found at i:2393466 original size:28 final size:27
Alignment explanation
Indices: 2393414--2393466 Score: 70
Period size: 27 Copynumber: 1.9 Consensus size: 27
2393404 TCTAAAAATA
*
2393414 TACAAAAAAAAACTATACATGAATAGG
1 TACAAAAAAAAACTATACATAAATAGG
* *
2393441 TACAAAAAAAAAGTTATACGTAAATA
1 TACAAAAAAAAA-CTATACATAAATA
2393467 AGCACAAGAG
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
27 12 0.55
28 10 0.45
ACGTcount: A:0.60, C:0.09, G:0.09, T:0.21
Consensus pattern (27 bp):
TACAAAAAAAAACTATACATAAATAGG
Found at i:2393473 original size:28 final size:27
Alignment explanation
Indices: 2393415--2393473 Score: 64
Period size: 28 Copynumber: 2.1 Consensus size: 27
2393405 CTAAAAATAT
* * *
2393415 ACAAAAAAAAACTATACATGAATAGGT
1 ACAAAAAAAAACTATACATAAATAAGC
* *
2393442 ACAAAAAAAAAGTTATACGTAAATAAGC
1 ACAAAAAAAAA-CTATACATAAATAAGC
2393470 ACAA
1 ACAA
2393474 GAGAAGAAAA
Statistics
Matches: 26, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
27 11 0.42
28 15 0.58
ACGTcount: A:0.61, C:0.12, G:0.10, T:0.17
Consensus pattern (27 bp):
ACAAAAAAAAACTATACATAAATAAGC
Found at i:2393694 original size:18 final size:17
Alignment explanation
Indices: 2393667--2393701 Score: 61
Period size: 18 Copynumber: 2.0 Consensus size: 17
2393657 TTTTACTGTC
2393667 ATTCATATGAAGTGGTT
1 ATTCATATGAAGTGGTT
2393684 ATTCTATATGAAGTGGTT
1 ATTC-ATATGAAGTGGTT
2393702 GTTTTACTTG
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 4 0.24
18 13 0.76
ACGTcount: A:0.29, C:0.06, G:0.23, T:0.43
Consensus pattern (17 bp):
ATTCATATGAAGTGGTT
Found at i:2397342 original size:2 final size:2
Alignment explanation
Indices: 2397335--2397360 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
2397325 TTAAATTTTG
2397335 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
2397361 CAGAATTTAA
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):
AT
Found at i:2408150 original size:42 final size:42
Alignment explanation
Indices: 2408102--2408185 Score: 168
Period size: 42 Copynumber: 2.0 Consensus size: 42
2408092 CTTGATTATG
2408102 AACACCTCCACCAACAGAATCTTCTCTTTTGTGATTAATATT
1 AACACCTCCACCAACAGAATCTTCTCTTTTGTGATTAATATT
2408144 AACACCTCCACCAACAGAATCTTCTCTTTTGTGATTAATATT
1 AACACCTCCACCAACAGAATCTTCTCTTTTGTGATTAATATT
2408186 CATATCTCTT
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
42 42 1.00
ACGTcount: A:0.31, C:0.26, G:0.07, T:0.36
Consensus pattern (42 bp):
AACACCTCCACCAACAGAATCTTCTCTTTTGTGATTAATATT
Found at i:2408539 original size:30 final size:30
Alignment explanation
Indices: 2408503--2408631 Score: 188
Period size: 30 Copynumber: 4.3 Consensus size: 30
2408493 CGCCGAAAAT
* * *
2408503 TAGGAGACCTGCTCTTGCTCCTATGATTTC
1 TAGGAGACCTGCTCCTGCTTCTACGATTTC
*
2408533 TAGGAGACCTGCTCCTGCTTCTGCGATTTC
1 TAGGAGACCTGCTCCTGCTTCTACGATTTC
*
2408563 TGGGAGACCTGCTCCTGCTTCTACGATTTC
1 TAGGAGACCTGCTCCTGCTTCTACGATTTC
2408593 TCA-GAGACCTGCTCCTGCTTCTACGATTTC
1 T-AGGAGACCTGCTCCTGCTTCTACGATTTC
*
2408623 TTGGAGACC
1 TAGGAGACC
2408632 AGCTAAAACA
Statistics
Matches: 89, Mismatches: 8, Indels: 4
0.88 0.08 0.04
Matches are distributed among these distances:
30 89 1.00
ACGTcount: A:0.16, C:0.29, G:0.22, T:0.33
Consensus pattern (30 bp):
TAGGAGACCTGCTCCTGCTTCTACGATTTC
Found at i:2410342 original size:32 final size:31
Alignment explanation
Indices: 2410288--2410378 Score: 101
Period size: 32 Copynumber: 2.8 Consensus size: 31
2410278 TACATGATGT
* *
2410288 TAAAAGATTCTAAACCAATAGGAAGCAAAAGC
1 TAAAAGATTCTGAA-CATTAGGAAGCAAAAGC
* *
2410320 TAAAAGGATTCTGAACATTAGGAAGCAGAAGT
1 TAAAA-GATTCTGAACATTAGGAAGCAAAAGC
* *
2410352 TAAAATAATTCTGACCATTAGGAAGCA
1 TAAAA-GATTCTGAACATTAGGAAGCA
2410379 TAACTATAAC
Statistics
Matches: 51, Mismatches: 7, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
32 43 0.84
33 8 0.16
ACGTcount: A:0.47, C:0.13, G:0.19, T:0.21
Consensus pattern (31 bp):
TAAAAGATTCTGAACATTAGGAAGCAAAAGC
Found at i:2413193 original size:19 final size:19
Alignment explanation
Indices: 2413169--2413216 Score: 78
Period size: 19 Copynumber: 2.5 Consensus size: 19
2413159 TCCCTCTCTC
*
2413169 TACAAATCACTCTCTCCAA
1 TACAAATCACCCTCTCCAA
2413188 TACAAATCACCCTCTCCAA
1 TACAAATCACCCTCTCCAA
*
2413207 AACAAATCAC
1 TACAAATCAC
2413217 GATCTCCCTC
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
19 27 1.00
ACGTcount: A:0.42, C:0.38, G:0.00, T:0.21
Consensus pattern (19 bp):
TACAAATCACCCTCTCCAA
Found at i:2417121 original size:14 final size:13
Alignment explanation
Indices: 2417091--2417133 Score: 52
Period size: 14 Copynumber: 3.2 Consensus size: 13
2417081 TTTAAATATT
2417091 AAAT-AAAATAAA
1 AAATAAAAATAAA
2417103 TAAATAAAAATTAAA
1 -AAATAAAAA-TAAA
2417118 AAATACAAAATAAA
1 AAATA-AAAATAAA
2417132 AA
1 AA
2417134 TCCTACAGGA
Statistics
Matches: 27, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
13 4 0.15
14 15 0.56
15 8 0.30
ACGTcount: A:0.79, C:0.02, G:0.00, T:0.19
Consensus pattern (13 bp):
AAATAAAAATAAA
Found at i:2427466 original size:21 final size:21
Alignment explanation
Indices: 2427426--2427467 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
2427416 TCATGCAAAG
*
2427426 AAATAAAATGAAATATGAAAT
1 AAATAAAATGAAATACGAAAT
2427447 AAATAAAAT-AAATAACGAAAT
1 AAATAAAATGAAAT-ACGAAAT
2427468 GGCTACATCC
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
20 4 0.21
21 15 0.79
ACGTcount: A:0.69, C:0.02, G:0.07, T:0.21
Consensus pattern (21 bp):
AAATAAAATGAAATACGAAAT
Found at i:2429338 original size:5 final size:5
Alignment explanation
Indices: 2429328--2429352 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
2429318 AAGTGAACAA
2429328 AAAAT AAAAT AAAAT AAAAT AAAAT
1 AAAAT AAAAT AAAAT AAAAT AAAAT
2429353 TTGGCATCAC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 20 1.00
ACGTcount: A:0.80, C:0.00, G:0.00, T:0.20
Consensus pattern (5 bp):
AAAAT
Found at i:2431461 original size:65 final size:65
Alignment explanation
Indices: 2431357--2431488 Score: 255
Period size: 65 Copynumber: 2.0 Consensus size: 65
2431347 TATTTTCCGG
2431357 GAGTGATGCTGACGATCCACCATTGGCATTGACACATATTCATGGACAGAATTATAAGAAATAAT
1 GAGTGATGCTGACGATCCACCATTGGCATTGACACATATTCATGGACAGAATTATAAGAAATAAT
*
2431422 GAGTGATGCTGACGATCCACCATTGGCATTGAGACATATTCATGGACAGAATTATAAGAAATAAT
1 GAGTGATGCTGACGATCCACCATTGGCATTGACACATATTCATGGACAGAATTATAAGAAATAAT
2431487 GA
1 GA
2431489 ACTAACCCCA
Statistics
Matches: 66, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
65 66 1.00
ACGTcount: A:0.37, C:0.16, G:0.21, T:0.26
Consensus pattern (65 bp):
GAGTGATGCTGACGATCCACCATTGGCATTGACACATATTCATGGACAGAATTATAAGAAATAAT
Found at i:2446795 original size:13 final size:14
Alignment explanation
Indices: 2446769--2446798 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
2446759 TAATATAAAA
2446769 AAAATAAGTTTTTT
1 AAAATAAGTTTTTT
*
2446783 AAAATAATTTTTTT
1 AAAATAAGTTTTTT
2446797 AA
1 AA
2446799 GAAAAATAGT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (14 bp):
AAAATAAGTTTTTT
Found at i:2473446 original size:14 final size:15
Alignment explanation
Indices: 2473411--2473464 Score: 56
Period size: 16 Copynumber: 3.4 Consensus size: 15
2473401 CTTGAAGTTA
2473411 TTATTTATAGAACTTTT
1 TTATTTATA-AA-TTTT
*
2473428 CTTATTTAT-GATTTT
1 -TTATTTATAAATTTT
2473443 TTATTTATAAATTCTT
1 TTATTTATAAATT-TT
2473459 TTATTT
1 TTATTT
2473465 CACTTTTATT
Statistics
Matches: 32, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
14 8 0.25
15 7 0.22
16 9 0.28
18 8 0.25
ACGTcount: A:0.26, C:0.06, G:0.04, T:0.65
Consensus pattern (15 bp):
TTATTTATAAATTTT
Found at i:2478329 original size:17 final size:18
Alignment explanation
Indices: 2478304--2478348 Score: 56
Period size: 18 Copynumber: 2.6 Consensus size: 18
2478294 TTGTGGTAGC
*
2478304 TTGTGTGCTTGGCT-GTA
1 TTGTTTGCTTGGCTGGTA
* *
2478321 TTGTTTGCTCGGTTGGTA
1 TTGTTTGCTTGGCTGGTA
2478339 TTGTTTGCTT
1 TTGTTTGCTT
2478349 TGTTATTACT
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
17 11 0.48
18 12 0.52
ACGTcount: A:0.04, C:0.11, G:0.31, T:0.53
Consensus pattern (18 bp):
TTGTTTGCTTGGCTGGTA
Found at i:2483964 original size:17 final size:17
Alignment explanation
Indices: 2483942--2483994 Score: 51
Period size: 17 Copynumber: 3.4 Consensus size: 17
2483932 AAGCAAAGAT
2483942 ATCAAGCGAAGTTCATG
1 ATCAAGCGAAGTTCATG
*
2483959 ATCAAGGGAAG---AT-
1 ATCAAGCGAAGTTCATG
* *
2483972 ATCAAGTGAAGTTCGTG
1 ATCAAGCGAAGTTCATG
2483989 ATCAAG
1 ATCAAG
2483995 ACCAAGTTCG
Statistics
Matches: 29, Mismatches: 3, Indels: 8
0.73 0.08 0.20
Matches are distributed among these distances:
13 10 0.34
14 2 0.07
16 1 0.03
17 16 0.55
ACGTcount: A:0.38, C:0.13, G:0.26, T:0.23
Consensus pattern (17 bp):
ATCAAGCGAAGTTCATG
Found at i:2483971 original size:30 final size:30
Alignment explanation
Indices: 2483937--2483994 Score: 98
Period size: 30 Copynumber: 1.9 Consensus size: 30
2483927 TTCTGAAGCA
2483937 AAGATATCAAGCGAAGTTCATGATCAAGGG
1 AAGATATCAAGCGAAGTTCATGATCAAGGG
* *
2483967 AAGATATCAAGTGAAGTTCGTGATCAAG
1 AAGATATCAAGCGAAGTTCATGATCAAG
2483995 ACCAAGTTCG
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 26 1.00
ACGTcount: A:0.40, C:0.12, G:0.26, T:0.22
Consensus pattern (30 bp):
AAGATATCAAGCGAAGTTCATGATCAAGGG
Found at i:2484893 original size:23 final size:21
Alignment explanation
Indices: 2484866--2484926 Score: 68
Period size: 23 Copynumber: 2.8 Consensus size: 21
2484856 CTATTTCTTC
*
2484866 TTTTTCTTTCTGTTTTGTTTT
1 TTTTTCTTTCTGTTTTCTTTT
*
2484887 TCATTTTCTTTCTGTCATTCTTTT
1 T--TTTTCTTTCTGT-TTTCTTTT
*
2484911 TTTTTCTTTTTGTTTT
1 TTTTTCTTTCTGTTTT
2484927 TTTGGGTCTC
Statistics
Matches: 33, Mismatches: 4, Indels: 6
0.77 0.09 0.14
Matches are distributed among these distances:
21 3 0.09
22 11 0.33
23 12 0.36
24 7 0.21
ACGTcount: A:0.03, C:0.13, G:0.07, T:0.77
Consensus pattern (21 bp):
TTTTTCTTTCTGTTTTCTTTT
Found at i:2484917 original size:10 final size:11
Alignment explanation
Indices: 2484867--2484926 Score: 50
Period size: 12 Copynumber: 5.4 Consensus size: 11
2484857 TATTTCTTCT
*
2484867 TTTTCTTTCTG
1 TTTTCTTTTTG
* *
2484878 TTTTGTTTTTCA
1 TTTTCTTTTT-G
*
2484890 TTTTCTTTCTG
1 TTTTCTTTTTG
*
2484901 TCATTCTTTTT-
1 T-TTTCTTTTTG
2484912 TTTTCTTTTTG
1 TTTTCTTTTTG
2484923 TTTT
1 TTTT
2484927 TTTGGGTCTC
Statistics
Matches: 37, Mismatches: 9, Indels: 6
0.71 0.17 0.12
Matches are distributed among these distances:
10 8 0.22
11 14 0.38
12 15 0.41
ACGTcount: A:0.03, C:0.13, G:0.07, T:0.77
Consensus pattern (11 bp):
TTTTCTTTTTG
Found at i:2485970 original size:18 final size:18
Alignment explanation
Indices: 2485943--2485982 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
2485933 AATTATTAAT
* *
2485943 TTATGAGTTATTTATGAA
1 TTATGAGTTACTTATAAA
*
2485961 TTATGTGTTACTTATAAA
1 TTATGAGTTACTTATAAA
2485979 TTAT
1 TTAT
2485983 TTGTGAAACT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.33, C:0.03, G:0.12, T:0.53
Consensus pattern (18 bp):
TTATGAGTTACTTATAAA
Found at i:2487574 original size:41 final size:42
Alignment explanation
Indices: 2487497--2487575 Score: 117
Period size: 41 Copynumber: 1.9 Consensus size: 42
2487487 ATAGTACAAT
* *
2487497 TGTTCATAAAAAATTATATTTTATAAACTTTTATAATATAAC
1 TGTTCATAAAAAATTATATTTAATAAACTTTCATAATATAAC
2487539 TGTTCAT-AAAAATTATATTTAAT-AACATTTCATAATA
1 TGTTCATAAAAAATTATATTTAATAAAC-TTTCATAATA
2487576 CAACAATTAA
Statistics
Matches: 34, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
40 3 0.09
41 24 0.71
42 7 0.21
ACGTcount: A:0.46, C:0.08, G:0.03, T:0.44
Consensus pattern (42 bp):
TGTTCATAAAAAATTATATTTAATAAACTTTCATAATATAAC
Found at i:2498373 original size:16 final size:17
Alignment explanation
Indices: 2498352--2498390 Score: 55
Period size: 17 Copynumber: 2.4 Consensus size: 17
2498342 TTCTCCACAC
2498352 CTTTTTC-CC-TCTCTTT
1 CTTTTTCTCCTTCT-TTT
2498368 CTTTTTCTCCTTCTTTT
1 CTTTTTCTCCTTCTTTT
2498385 CTTTTT
1 CTTTTT
2498391 TATCTTTTCA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
16 7 0.33
17 11 0.52
18 3 0.14
ACGTcount: A:0.00, C:0.31, G:0.00, T:0.69
Consensus pattern (17 bp):
CTTTTTCTCCTTCTTTT
Found at i:2503421 original size:26 final size:26
Alignment explanation
Indices: 2503369--2503422 Score: 74
Period size: 26 Copynumber: 2.1 Consensus size: 26
2503359 GAATCAAAAA
* *
2503369 ATAATTTTACCACTAGAAGTAGGTGG
1 ATAATTTTACCACCAGAAATAGGTGG
2503395 ATAATTTTACCACCAGAAAT-GGATGG
1 ATAATTTTACCACCAGAAATAGG-TGG
2503421 AT
1 AT
2503423 GCCGTAACCC
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
25 2 0.08
26 23 0.92
ACGTcount: A:0.37, C:0.13, G:0.20, T:0.30
Consensus pattern (26 bp):
ATAATTTTACCACCAGAAATAGGTGG
Found at i:2504306 original size:75 final size:75
Alignment explanation
Indices: 2504152--2504295 Score: 243
Period size: 75 Copynumber: 1.9 Consensus size: 75
2504142 CTATCTTGAG
* * * *
2504152 GAATAAAGTAATAAAGGATGTATTATTTTCTATTAAGTCTCAAAGAAGTTTATTAAGTTTTAAAG
1 GAATAAAGCAATAAAGGATGGATTATTTTCTATTAAGTCTCAAAAAAGTTTATTAAGTTTTAAAA
2504217 ATATATATAT
66 ATATATATAT
*
2504227 GAATAAAGCAATAGAGGATGGATTATTTTCTATTAAGTCTCAAAAAAGTTTATTAAGTTTTAAAA
1 GAATAAAGCAATAAAGGATGGATTATTTTCTATTAAGTCTCAAAAAAGTTTATTAAGTTTTAAAA
2504292 ATAT
66 ATAT
2504296 TTTTCTGAAT
Statistics
Matches: 64, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
75 64 1.00
ACGTcount: A:0.43, C:0.05, G:0.14, T:0.38
Consensus pattern (75 bp):
GAATAAAGCAATAAAGGATGGATTATTTTCTATTAAGTCTCAAAAAAGTTTATTAAGTTTTAAAA
ATATATATAT
Found at i:2504637 original size:10 final size:10
Alignment explanation
Indices: 2504622--2504687 Score: 53
Period size: 10 Copynumber: 5.9 Consensus size: 10
2504612 TTTATTCATA
2504622 TATTTATTTT
1 TATTTATTTT
2504632 TATTTATTATT
1 TATTTATT-TT
2504643 ATATCTTATATATT
1 -TAT-TTAT-T-TT
2504657 TATTAATATTTT
1 TATT--TATTTT
2504669 ATATTTA-TTT
1 -TATTTATTTT
2504679 TATTTATTT
1 TATTTATTT
2504688 ATTAATATCA
Statistics
Matches: 48, Mismatches: 0, Indels: 16
0.75 0.00 0.25
Matches are distributed among these distances:
9 6 0.12
10 13 0.27
11 4 0.08
12 6 0.12
13 12 0.25
14 7 0.15
ACGTcount: A:0.29, C:0.02, G:0.00, T:0.70
Consensus pattern (10 bp):
TATTTATTTT
Found at i:2504658 original size:21 final size:19
Alignment explanation
Indices: 2504606--2504681 Score: 74
Period size: 18 Copynumber: 4.2 Consensus size: 19
2504596 ATCTCTTTAA
*
2504606 TATATTTT-TATTCATATAT
1 TATATTTTATATTTAT-TAT
2504625 T-TATTTT-TATTTATTAT
1 TATATTTTATATTTATTAT
2504642 TATATCTTATATATTTATTA-
1 TATAT-TT-TATATTTATTAT
2504662 -ATATTTTATATTTATT-T
1 TATATTTTATATTTATTAT
2504679 TAT
1 TAT
2504682 TTATTTATTA
Statistics
Matches: 50, Mismatches: 1, Indels: 13
0.78 0.02 0.20
Matches are distributed among these distances:
17 14 0.28
18 19 0.38
19 7 0.14
20 1 0.02
21 9 0.18
ACGTcount: A:0.30, C:0.03, G:0.00, T:0.67
Consensus pattern (19 bp):
TATATTTTATATTTATTAT
Found at i:2504666 original size:55 final size:52
Alignment explanation
Indices: 2504605--2504768 Score: 175
Period size: 52 Copynumber: 3.2 Consensus size: 52
2504595 CATCTCTTTA
2504605 ATATATTTTTATTCATATATTTATTTTTATTTATTATTAT-ATCTTATATATTT
1 ATATATTTTTATTCATATATTTATTTTTATTTATTATTATAATCTT-TATA-TT
* *
2504658 ATTAATATTTTATATT--TAT-TTTA--TTTATTTATTAATATCATCTTTA-A--
1 A-T-ATATTTT-TATTCATATATTTATTTTTATTTATTATTATAATCTTTATATT
2504705 ATATATTTTTAATGTCATATATTTTATTTTTATTTATTATTATAATCTTTATATT
1 ATATATTTTT-AT-TCATATA-TTTATTTTTATTTATTATTATAATCTTTATATT
2504760 ATATATTTT
1 ATATATTTT
2504769 ATTTAATTTG
Statistics
Matches: 93, Mismatches: 3, Indels: 28
0.75 0.02 0.23
Matches are distributed among these distances:
44 1 0.01
45 9 0.10
46 2 0.02
47 1 0.01
48 3 0.03
50 5 0.05
51 16 0.17
52 26 0.28
53 6 0.06
54 4 0.04
55 16 0.17
56 4 0.04
ACGTcount: A:0.32, C:0.04, G:0.01, T:0.64
Consensus pattern (52 bp):
ATATATTTTTATTCATATATTTATTTTTATTTATTATTATAATCTTTATATT
Found at i:2504689 original size:30 final size:32
Alignment explanation
Indices: 2504619--2504695 Score: 97
Period size: 30 Copynumber: 2.5 Consensus size: 32
2504609 ATTTTTATTC
**
2504619 ATATATTTATTTTTA-TTTATTATTATATCTT
1 ATATATTTATTAATATTTTATTATTATATCTT
*
2504650 ATATATTTATTAATATTTTA-TATT-TATTTT
1 ATATATTTATTAATATTTTATTATTATATCTT
*
2504680 ATTTATTTATTAATAT
1 ATATATTTATTAATAT
2504696 CATCTTTAAA
Statistics
Matches: 41, Mismatches: 4, Indels: 3
0.85 0.08 0.06
Matches are distributed among these distances:
30 20 0.49
31 17 0.41
32 4 0.10
ACGTcount: A:0.32, C:0.01, G:0.00, T:0.66
Consensus pattern (32 bp):
ATATATTTATTAATATTTTATTATTATATCTT
Found at i:2504690 original size:17 final size:17
Alignment explanation
Indices: 2504614--2504690 Score: 65
Period size: 17 Copynumber: 4.7 Consensus size: 17
2504604 AATATATTTT
*
2504614 TATTCATATATTTA-T-
1 TATTTATATATTTATTA
*
2504629 T-TTTATTTA-TTATTA
1 TATTTATATATTTATTA
2504644 TATCTTATATATTTATTAA
1 TAT-TTATATATTTATT-A
*
2504663 TATTT-TATATTTATTT
1 TATTTATATATTTATTA
*
2504679 TATTTATTTATT
1 TATTTATATATT
2504691 AATATCATCT
Statistics
Matches: 50, Mismatches: 5, Indels: 12
0.75 0.07 0.18
Matches are distributed among these distances:
13 3 0.06
14 7 0.14
15 2 0.04
16 6 0.12
17 21 0.42
18 7 0.14
19 4 0.08
ACGTcount: A:0.30, C:0.03, G:0.00, T:0.68
Consensus pattern (17 bp):
TATTTATATATTTATTA
Found at i:2504783 original size:103 final size:101
Alignment explanation
Indices: 2504555--2504770 Score: 284
Period size: 103 Copynumber: 2.1 Consensus size: 101
2504545 AAATACAAGT
* *
2504555 TTAATATATTTATATTT-TTCATTATTAATTT-TATATATATCATCTCTTTAATATATTTTTATT
1 TTAATAT-TTTATATTTATT--TTATTTATTTAT-TA-ATATCATCTCTTAAATATATTTTTATT
2504618 CATATATTTATTTTTATTTATTATTATATCTTATATATTTA
61 CATATATTTATTTTTATTTATTATTATATCTTATATATTTA
2504659 TTAATATTTTATATTTATTTTATTTATTTATTAATATCATCT-TTAAATATATTTTTAATGTCAT
1 TTAATATTTTATATTTATTTTATTTATTTATTAATATCATCTCTTAAATATATTTTT-AT-TCAT
2504723 ATATTTTATTTTTATTTATTATTATAATCTT-TATA-TTA
64 ATA-TTTATTTTTATTTATTATTAT-ATCTTATATATTTA
2504761 -T-ATATTTTAT
1 TTAATATTTTAT
2504771 TTAATTTGTT
Statistics
Matches: 104, Mismatches: 2, Indels: 16
0.85 0.02 0.13
Matches are distributed among these distances:
100 22 0.21
101 12 0.12
102 21 0.20
103 35 0.34
104 14 0.13
ACGTcount: A:0.32, C:0.05, G:0.00, T:0.63
Consensus pattern (101 bp):
TTAATATTTTATATTTATTTTATTTATTTATTAATATCATCTCTTAAATATATTTTTATTCATAT
ATTTATTTTTATTTATTATTATATCTTATATATTTA
Found at i:2504804 original size:100 final size:100
Alignment explanation
Indices: 2504599--2504797 Score: 250
Period size: 100 Copynumber: 2.0 Consensus size: 100
2504589 ATATATCATC
2504599 TCTTT-AATATATTTTTATTCATATATTTATTTTTATTTATTATTATATCTTATATATTTATTAA
1 TCTTTAAATATATTTTTATTCATATATTTATTTTTATTTATTATTATATCTTATATATTTATTAA
* ** *
2504663 TATTTTATATTTATTTTATTTATTTATTAATATCA
66 TATTTTATATTAATTTTATTTACCTATTAATATAA
2504698 TCTTTAAATATATTTTTAATGTCATATATTTTATTTTTATTTATTATTATAATCTT-TATA-TTA
1 TCTTTAAATATATTTTT-AT-TCATATA-TTTATTTTTATTTATTATTAT-ATCTTATATATTTA
*
2504761 -T-ATATTTTAT-TTAATTTGT-TTTACCTATATCATATAA
62 TTAATATTTTATATTAATTT-TATTTACCTAT-TAATATAA
2504798 ATTTTAATTT
Statistics
Matches: 88, Mismatches: 5, Indels: 13
0.83 0.05 0.12
Matches are distributed among these distances:
99 18 0.20
100 27 0.31
101 3 0.03
102 10 0.11
103 25 0.28
104 5 0.06
ACGTcount: A:0.32, C:0.05, G:0.01, T:0.62
Consensus pattern (100 bp):
TCTTTAAATATATTTTTATTCATATATTTATTTTTATTTATTATTATATCTTATATATTTATTAA
TATTTTATATTAATTTTATTTACCTATTAATATAA
Found at i:2506332 original size:75 final size:75
Alignment explanation
Indices: 2506196--2506346 Score: 212
Period size: 75 Copynumber: 2.0 Consensus size: 75
2506186 ATGCCCTATT
* * *
2506196 AGCATTAATGTCCCTGTAAAACAAGGCACGTCAGAAGCATGGAGACTAAACGATTCCAAATATAA
1 AGCATTAATGTCCCTATAAAACAAGGCACGTCAAAAGCATGGAGACCAAACGATTCCAAATATAA
2506261 AATCATCAAA
66 AATCATCAAA
* ** * * *
2506271 AGCATTAATGTCCTTATAGGACAAGGCACGTCAAAAGCATGGAGACCAAATGGTTCTAAATATAA
1 AGCATTAATGTCCCTATAAAACAAGGCACGTCAAAAGCATGGAGACCAAACGATTCCAAATATAA
*
2506336 AATCCTCAAA
66 AATCATCAAA
2506346 A
1 A
2506347 AAAAATCGAA
Statistics
Matches: 66, Mismatches: 10, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
75 66 1.00
ACGTcount: A:0.43, C:0.19, G:0.17, T:0.21
Consensus pattern (75 bp):
AGCATTAATGTCCCTATAAAACAAGGCACGTCAAAAGCATGGAGACCAAACGATTCCAAATATAA
AATCATCAAA
Found at i:2507021 original size:24 final size:25
Alignment explanation
Indices: 2506975--2507021 Score: 62
Period size: 24 Copynumber: 1.9 Consensus size: 25
2506965 TAAAAAACCT
*
2506975 TAAAAGATTTAAATTGCCTAAAATA
1 TAAAAGATTTAAATTGCCAAAAATA
2507000 TAAAA-ATTTAAATT-CTCAAAAA
1 TAAAAGATTTAAATTGC-CAAAAA
2507022 ATTTACTTGA
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
23 1 0.05
24 14 0.70
25 5 0.25
ACGTcount: A:0.55, C:0.09, G:0.04, T:0.32
Consensus pattern (25 bp):
TAAAAGATTTAAATTGCCAAAAATA
Found at i:2508818 original size:9 final size:10
Alignment explanation
Indices: 2508789--2508816 Score: 56
Period size: 10 Copynumber: 2.8 Consensus size: 10
2508779 TATTTAATCT
2508789 AAAATATTTA
1 AAAATATTTA
2508799 AAAATATTTA
1 AAAATATTTA
2508809 AAAATATT
1 AAAATATT
2508817 AATATTTAAC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 18 1.00
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (10 bp):
AAAATATTTA
Found at i:2508860 original size:15 final size:16
Alignment explanation
Indices: 2508840--2508881 Score: 50
Period size: 15 Copynumber: 2.6 Consensus size: 16
2508830 TAAAAAAATA
2508840 ATTTAAAATATT-AAT
1 ATTTAAAATATTCAAT
*
2508855 ATTTAAATTATTCAAT
1 ATTTAAAATATTCAAT
2508871 ACTATTAAAAT
1 A-T-TTAAAAT
2508882 TAAAAATATA
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
15 11 0.50
16 4 0.18
17 1 0.05
18 6 0.27
ACGTcount: A:0.50, C:0.05, G:0.00, T:0.45
Consensus pattern (16 bp):
ATTTAAAATATTCAAT
Found at i:2509448 original size:6 final size:6
Alignment explanation
Indices: 2509432--2509461 Score: 51
Period size: 6 Copynumber: 5.0 Consensus size: 6
2509422 AAAGTGAGGT
*
2509432 ATTTTA TTTTTA ATTTTA ATTTTA ATTTTA
1 ATTTTA ATTTTA ATTTTA ATTTTA ATTTTA
2509462 TAGTGATATA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
6 22 1.00
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (6 bp):
ATTTTA
Found at i:2509860 original size:18 final size:19
Alignment explanation
Indices: 2509839--2509874 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
2509829 AATACATTTT
*
2509839 AAATT-TTAATTAAATAAA
1 AAATTATTAATAAAATAAA
2509857 AAATTATTAATAAAATAA
1 AAATTATTAATAAAATAA
2509875 TATTTCGAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 5 0.31
19 11 0.69
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (19 bp):
AAATTATTAATAAAATAAA
Found at i:2525433 original size:2 final size:2
Alignment explanation
Indices: 2525426--2525457 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
2525416 ATGAAATGGT
2525426 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
2525458 CTCAGTGAAA
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:0.50, T:0.00
Consensus pattern (2 bp):
GA
Found at i:2531374 original size:32 final size:32
Alignment explanation
Indices: 2531315--2531375 Score: 95
Period size: 32 Copynumber: 1.9 Consensus size: 32
2531305 GATATTTTAT
* *
2531315 AATATAATGCGATTATAAGTAATGTGATTGCA
1 AATATAATGCGATTATAAGCAACGTGATTGCA
*
2531347 AATATAATGCGATTATTAGCAACGTGATT
1 AATATAATGCGATTATAAGCAACGTGATT
2531376 ACAAGGAAAA
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
32 26 1.00
ACGTcount: A:0.39, C:0.08, G:0.18, T:0.34
Consensus pattern (32 bp):
AATATAATGCGATTATAAGCAACGTGATTGCA
Found at i:2531420 original size:23 final size:23
Alignment explanation
Indices: 2531394--2531446 Score: 56
Period size: 23 Copynumber: 2.3 Consensus size: 23
2531384 AATAATATTG
* *
2531394 TAATATTTGATATATAAATAAA-A
1 TAATATTTAAAATATAAA-AAAGA
2531417 TAATGA-TTAAAATATAAAAAAGA
1 TAAT-ATTTAAAATATAAAAAAGA
2531440 TAATATT
1 TAATATT
2531447 AAAGTGTTTG
Statistics
Matches: 25, Mismatches: 2, Indels: 6
0.76 0.06 0.18
Matches are distributed among these distances:
22 4 0.16
23 20 0.80
24 1 0.04
ACGTcount: A:0.58, C:0.00, G:0.06, T:0.36
Consensus pattern (23 bp):
TAATATTTAAAATATAAAAAAGA
Found at i:2531631 original size:25 final size:26
Alignment explanation
Indices: 2531594--2531671 Score: 95
Period size: 25 Copynumber: 3.0 Consensus size: 26
2531584 TTTTAATGTC
2531594 ATATATTTTATTTTTATTATAATTTT
1 ATATATTTTATTTTTATTATAATTTT
*
2531620 ATAT-TTTTATTTTTAATATAATTTT
1 ATATATTTTATTTTTATTATAATTTT
* ** *
2531645 TTATATTACATATTTTATTTTAATTTT
1 ATATATTTTAT-TTTTATTATAATTTT
2531672 TTTTCCTTTA
Statistics
Matches: 44, Mismatches: 6, Indels: 3
0.83 0.11 0.06
Matches are distributed among these distances:
25 23 0.52
26 8 0.18
27 13 0.30
ACGTcount: A:0.31, C:0.01, G:0.00, T:0.68
Consensus pattern (26 bp):
ATATATTTTATTTTTATTATAATTTT
Found at i:2535930 original size:21 final size:21
Alignment explanation
Indices: 2535892--2535931 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
2535882 TACAAAATAG
* *
2535892 AAAGTAAATATGTTTATATTT
1 AAAGTAAATATATATATATTT
*
2535913 AAAGTACATATATATATAT
1 AAAGTAAATATATATATAT
2535932 ATATATACAC
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:0.47, C:0.03, G:0.07, T:0.42
Consensus pattern (21 bp):
AAAGTAAATATATATATATTT
Found at i:2536488 original size:338 final size:350
Alignment explanation
Indices: 2535953--2536641 Score: 831
Period size: 338 Copynumber: 2.0 Consensus size: 350
2535943 TAGAGGCACG
* * *
2535953 TATTAAAATTATTTTAATATATATAATAGTAATTATATTTTTTATAAATGAATCTAATATATATA
1 TATTAAAAATATTTTAATATATATAATAGTAATTATATTTCTTATAAATGAATC-AACATATATA
* * *
2536018 TATAACGTATATATAGTAAAGAACATTACAAGTTAATTAATAGTTATAGTGTCATGAATTAATTT
65 CATAACGTATATATAGTAAAGAACATTACAAGTTAATTAATAATAATAGTGTCATGAATTAATTT
** *
2536083 AATTAACTATACGAGTTTATCCTTAATTACATAAAATTAAAAAAAATAAACTAAGTTTTAGAACT
130 AATTAACTATACGAGTTTATCCTTAATTACATAAAATTAAAAAAAATAAACTAAGTTCCAAAACT
* * * *
2536148 ATTCTAATCTCAAAACTTCTCTTT-AG-GT-T-TA-TATAAGTTTATATAAACAA-AGT-TATAT
195 ATTCTAATCCCAAAACTTCTCTTTAAGTATATATATTATAAGATTATACAAACAATAGTATATAT
* * *
2536206 ATATTATAATTAATAATTTTATAAGTTATAA-TTTTGTAATGTTAACACAAAA-TAGAAAGTAAA
260 ATATTATAATTAATAATTTTATAAGTCATAATTTTTGTAATGTTAACA-AAAAGTAAAAAATAAA
* *
2536269 TATGCTTATATTTAAAGTATATATATA
324 TATACTTATATTAAAAGTATATATATA
* *
2536296 TATTAAAAATATTTTAGTATATATATAATAGTAATTATGTTTCTTATAAATTAA-C-ACA-ATAT
1 TATTAAAAATATTTTA--ATATATATAATAGTAATTATATTTCTTATAAATGAATCAACATATAT
* * * **
2536358 ACA-AA-TTATATATATTAAA-AGATATTACAAGTTAATTAATAATAATAGT-TTTTGAATTAAT
64 ACATAACGTATATATAGTAAAGA-ACATTACAAGTTAATTAATAATAATAGTGTCATGAATTAAT
* * * * * * *
2536419 TTAATTAA-TAATATG-GATTTGTTCTTAATTTCATGAAATTAAAAAAAA-ACACTTAGGTTCCA
128 TTAATTAACT-ATACGAG-TTTATCCTTAATTACATAAAATTAAAAAAAATAAAC-TAAGTTCCA
* * *
2536481 AAACTATTCTAATCCCAAAAGTTTTCTTTAAGTATATATATATTATAAGATTATACAAACAATGG
190 AAACTATTCTAATCCCAAAACTTCTCTTTAAG--TATATATATTATAAGATTATACAAACAATAG
2536546 TATATATATATTATAATTAATAATTTTATAAGTCATAATTTTTGTAATGTTAACAAAAAGTAAAA
253 TATATATATATTATAATTAATAATTTTATAAGTCATAATTTTTGTAATGTTAACAAAAAGTAAAA
*
2536611 AATAAATATATTTATATTAAAAGTATATATA
318 AATAAATATACTTATATTAAAAGTATATATA
2536642 ATAATTATTA
Statistics
Matches: 293, Mismatches: 36, Indels: 29
0.82 0.10 0.08
Matches are distributed among these distances:
337 5 0.02
338 81 0.28
339 39 0.13
340 2 0.01
341 6 0.02
342 3 0.01
343 16 0.05
344 3 0.01
345 50 0.17
346 2 0.01
347 39 0.13
348 47 0.16
ACGTcount: A:0.46, C:0.06, G:0.07, T:0.41
Consensus pattern (350 bp):
TATTAAAAATATTTTAATATATATAATAGTAATTATATTTCTTATAAATGAATCAACATATATAC
ATAACGTATATATAGTAAAGAACATTACAAGTTAATTAATAATAATAGTGTCATGAATTAATTTA
ATTAACTATACGAGTTTATCCTTAATTACATAAAATTAAAAAAAATAAACTAAGTTCCAAAACTA
TTCTAATCCCAAAACTTCTCTTTAAGTATATATATTATAAGATTATACAAACAATAGTATATATA
TATTATAATTAATAATTTTATAAGTCATAATTTTTGTAATGTTAACAAAAAGTAAAAAATAAATA
TACTTATATTAAAAGTATATATATA
Found at i:2537934 original size:19 final size:17
Alignment explanation
Indices: 2537902--2537936 Score: 52
Period size: 19 Copynumber: 1.9 Consensus size: 17
2537892 GGAAAGATCC
2537902 AAAAATAAAATTTAATA
1 AAAAATAAAATTTAATA
2537919 AAAATATAAGAATTTAAT
1 AAAA-ATAA-AATTTAAT
2537937 TTATTAAAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 4 0.25
18 4 0.25
19 8 0.50
ACGTcount: A:0.66, C:0.00, G:0.03, T:0.31
Consensus pattern (17 bp):
AAAAATAAAATTTAATA
Found at i:2545649 original size:18 final size:19
Alignment explanation
Indices: 2545626--2545663 Score: 60
Period size: 18 Copynumber: 2.1 Consensus size: 19
2545616 AAGTGAGTTA
*
2545626 TTTTAATTTTA-TGTTATT
1 TTTTAATTTGATTGTTATT
2545644 TTTTAATTTGATTGTTATT
1 TTTTAATTTGATTGTTATT
2545663 T
1 T
2545664 ATNNNNNNNN
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 10 0.56
19 8 0.44
ACGTcount: A:0.21, C:0.00, G:0.08, T:0.71
Consensus pattern (19 bp):
TTTTAATTTGATTGTTATT
Found at i:2549623 original size:16 final size:16
Alignment explanation
Indices: 2549587--2549624 Score: 58
Period size: 16 Copynumber: 2.4 Consensus size: 16
2549577 GCAAGTTTAT
2549587 TTTTTATCATTCCTTG
1 TTTTTATCATTCCTTG
* *
2549603 CTTTTGTCATTCCTTG
1 TTTTTATCATTCCTTG
2549619 TTTTTA
1 TTTTTA
2549625 CACATCAGTG
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.11, C:0.18, G:0.08, T:0.63
Consensus pattern (16 bp):
TTTTTATCATTCCTTG
Found at i:2551302 original size:27 final size:27
Alignment explanation
Indices: 2551272--2551356 Score: 98
Period size: 29 Copynumber: 3.1 Consensus size: 27
2551262 CATTAAAGTA
2551272 TAACAAAATTTTTTTTAATATGGTGTG
1 TAACAAAATTTTTTTTAATATGGTGTG
* *
2551299 TAACAATAATATTTTTTCAATATGGCGTG
1 TAACAA-AAT-TTTTTTTAATATGGTGTG
* * * *
2551328 TAACAACATTTTCTTTAACATAGTGTG
1 TAACAAAATTTTTTTTAATATGGTGTG
2551355 TA
1 TA
2551357 TCATTGTTTT
Statistics
Matches: 48, Mismatches: 8, Indels: 4
0.80 0.13 0.07
Matches are distributed among these distances:
27 21 0.44
28 5 0.10
29 22 0.46
ACGTcount: A:0.34, C:0.09, G:0.13, T:0.44
Consensus pattern (27 bp):
TAACAAAATTTTTTTTAATATGGTGTG
Found at i:2551496 original size:80 final size:80
Alignment explanation
Indices: 2551297--2551508 Score: 222
Period size: 80 Copynumber: 2.6 Consensus size: 80
2551287 TAATATGGTG
* * * * *
2551297 TGTAACAATA-ATA-TTTTTTCAATATGGCGTGTAACAACATTTTCTTTAA-CATAGTGTGTATC
1 TGTAACAAAATATATTTTTTTCAATATGACGTGTAATAAC-TTTT-TTTAACCACACTGTGTATC
2551359 ATTGTTTTGTACATGAAA
64 ATTGTTTTGTACATG-AA
* * * *
2551377 TGAAACAATAATAT-TCTTTTTTCTACATGACGTGCAATAACTTTTTTTAACCACACTGTGTA--
1 TGTAACAA-AATATAT-TTTTTTCAATATGACGTGTAATAACTTTTTTTAACCACACTGTGTATC
2551439 ATATGTTTTTGTACATG-A
64 AT-TG-TTTTGTACATGAA
2551457 TGGTAACAAAATATATTTTTTTCAATATGACGTGTAATAACTTTTTTTAACC
1 T-GTAACAAAATATATTTTTTTCAATATGACGTGTAATAACTTTTTTTAACC
2551509 GTGACGTGTA
Statistics
Matches: 110, Mismatches: 13, Indels: 18
0.78 0.09 0.13
Matches are distributed among these distances:
80 49 0.45
81 15 0.14
82 26 0.24
83 20 0.18
ACGTcount: A:0.33, C:0.13, G:0.12, T:0.43
Consensus pattern (80 bp):
TGTAACAAAATATATTTTTTTCAATATGACGTGTAATAACTTTTTTTAACCACACTGTGTATCAT
TGTTTTGTACATGAA
Found at i:2551501 original size:26 final size:26
Alignment explanation
Indices: 2551472--2551563 Score: 96
Period size: 26 Copynumber: 3.3 Consensus size: 26
2551462 ACAAAATATA
*
2551472 TTTTTTTCAATATGACGTGTAATAAC
1 TTTTTTTCAATATGACGTGTAATAAT
**
2551498 TTTTTTT-AACCGTGACGTGTAATAATAATAT
1 TTTTTTTCAA-TATGACGTG---TAAT-A-AT
2551529 TTTTTTTCAATATGACGTGTAATAAT
1 TTTTTTTCAATATGACGTGTAATAAT
2551555 TTTTTTTCA
1 TTTTTTTCA
2551564 CTACAGCATA
Statistics
Matches: 54, Mismatches: 5, Indels: 14
0.74 0.07 0.19
Matches are distributed among these distances:
25 2 0.04
26 25 0.46
27 1 0.02
28 4 0.07
29 4 0.07
30 1 0.02
31 15 0.28
32 2 0.04
ACGTcount: A:0.29, C:0.10, G:0.11, T:0.50
Consensus pattern (26 bp):
TTTTTTTCAATATGACGTGTAATAAT
Found at i:2551545 original size:31 final size:31
Alignment explanation
Indices: 2551466--2551554 Score: 91
Period size: 31 Copynumber: 3.0 Consensus size: 31
2551456 ATGGTAACAA
2551466 AATATATTTTTTTCAATATGACGTG---TAAT
1 AATAT-TTTTTTTCAATATGACGTGTAATAAT
* **
2551495 -A-ACTTTTTTT-AACCGTGACGTGTAATAAT
1 AATATTTTTTTTCAA-TATGACGTGTAATAAT
2551524 AATATTTTTTTTCAATATGACGTGTAATAAT
1 AATATTTTTTTTCAATATGACGTGTAATAAT
2551555 TTTTTTTCAC
Statistics
Matches: 47, Mismatches: 6, Indels: 12
0.72 0.09 0.18
Matches are distributed among these distances:
25 2 0.04
26 14 0.30
27 1 0.02
28 1 0.02
29 4 0.09
30 1 0.02
31 22 0.47
32 2 0.04
ACGTcount: A:0.34, C:0.09, G:0.11, T:0.46
Consensus pattern (31 bp):
AATATTTTTTTTCAATATGACGTGTAATAAT
Found at i:2551553 original size:137 final size:137
Alignment explanation
Indices: 2551383--2551629 Score: 320
Period size: 137 Copynumber: 1.8 Consensus size: 137
2551373 GAAATGAAAC
* * * *
2551383 AATAATATTCTTTTTTCTACATGACGTGCAATAACTTTTTTTAACCACA-CTGTGTAATATGTTT
1 AATAATATTCTTTTTTCAACATGACGTGCAATAACTTTTTTTAACCACAGC-ATATAACATGTTT
* * *
2551447 TTGTACATGATG-GTAACAAAATATATTTTTTTCAATATGACGTGTAATAACTTTTTTTAACCGT
65 TTGTACATAATGTGTAACAAAA-ATATTTTTTT-AATAAGAAGTGTAATAACTTTTTTTAACCGT
2551511 GACGTGTAAT
128 GACGTGTAAT
* * * * *
2551521 AATAATATT-TTTTTTCAATATGACGTGTAATAATTTTTTTTCACTACAGCATATAACATGTTTT
1 AATAATATTCTTTTTTCAACATGACGTGCAATAACTTTTTTTAACCACAGCATATAACATGTTTT
* *
2551585 TGTACATAATGTGTAATAATAATATTTTTTTAATAAGAAGTGTAA
66 TGTACATAATGTGTAACAAAAATATTTTTTTAATAAGAAGTGTAA
2551630 CATAAATAAA
Statistics
Matches: 93, Mismatches: 14, Indels: 6
0.82 0.12 0.05
Matches are distributed among these distances:
136 12 0.13
137 64 0.69
138 17 0.18
ACGTcount: A:0.34, C:0.11, G:0.11, T:0.45
Consensus pattern (137 bp):
AATAATATTCTTTTTTCAACATGACGTGCAATAACTTTTTTTAACCACAGCATATAACATGTTTT
TGTACATAATGTGTAACAAAAATATTTTTTTAATAAGAAGTGTAATAACTTTTTTTAACCGTGAC
GTGTAAT
Found at i:2554050 original size:41 final size:41
Alignment explanation
Indices: 2554004--2554086 Score: 112
Period size: 41 Copynumber: 2.0 Consensus size: 41
2553994 TATAAATCTA
* * *
2554004 AGCCTATTACAATATAGTATATCTTAATAGTTCAACCTAAT
1 AGCCTATCACAATATAGTATATCTCAATAGTTAAACCTAAT
* * *
2554045 AGCCTATCATAATATATTATATCTCAATAGTTAAATCTAAT
1 AGCCTATCACAATATAGTATATCTCAATAGTTAAACCTAAT
2554086 A
1 A
2554087 AGCCAATATG
Statistics
Matches: 36, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
41 36 1.00
ACGTcount: A:0.41, C:0.16, G:0.06, T:0.37
Consensus pattern (41 bp):
AGCCTATCACAATATAGTATATCTCAATAGTTAAACCTAAT
Found at i:2554125 original size:22 final size:22
Alignment explanation
Indices: 2554100--2554141 Score: 75
Period size: 22 Copynumber: 1.9 Consensus size: 22
2554090 CAATATGTTA
2554100 ATTAGCAATTTAAGAGGCAAAC
1 ATTAGCAATTTAAGAGGCAAAC
*
2554122 ATTAGTAATTTAAGAGGCAA
1 ATTAGCAATTTAAGAGGCAA
2554142 CAGAAAATAA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.45, C:0.10, G:0.19, T:0.26
Consensus pattern (22 bp):
ATTAGCAATTTAAGAGGCAAAC
Found at i:2560959 original size:2 final size:2
Alignment explanation
Indices: 2560952--2560979 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
2560942 TTTCTACTTA
2560952 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
2560980 GATCTCATAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2570444 original size:28 final size:28
Alignment explanation
Indices: 2570413--2570486 Score: 85
Period size: 28 Copynumber: 2.6 Consensus size: 28
2570403 TCATTATTTG
*
2570413 TTCACTTCTAGTGAATTAAAAGTATTCA
1 TTCACTTCTGGTGAATTAAAAGTATTCA
* * * *
2570441 TTCACTTTTGGTGGATTATAAGTATTTA
1 TTCACTTCTGGTGAATTAAAAGTATTCA
* *
2570469 TCCACTTCTGGTGTATTA
1 TTCACTTCTGGTGAATTA
2570487 GTGGGTTAAA
Statistics
Matches: 38, Mismatches: 8, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
28 38 1.00
ACGTcount: A:0.27, C:0.14, G:0.15, T:0.45
Consensus pattern (28 bp):
TTCACTTCTGGTGAATTAAAAGTATTCA
Found at i:2576964 original size:31 final size:31
Alignment explanation
Indices: 2576879--2576967 Score: 124
Period size: 32 Copynumber: 2.8 Consensus size: 31
2576869 TTTAAACTCT
* *
2576879 CTACCTTTCCAATAGTTAAGGTATAATCAACA
1 CTACCTTT-TAATAGTTAAGGTATAATCAAAA
*
2576911 CTACCTTTTAATGGTTTAAGGTATAATCAAAA
1 CTACCTTTTAATAG-TTAAGGTATAATCAAAA
*
2576943 CTACCTTTTAATTGTTAAGGTATAA
1 CTACCTTTTAATAGTTAAGGTATAA
2576968 CCTTTTCAAT
Statistics
Matches: 52, Mismatches: 4, Indels: 3
0.88 0.07 0.05
Matches are distributed among these distances:
31 15 0.29
32 37 0.71
ACGTcount: A:0.36, C:0.16, G:0.11, T:0.37
Consensus pattern (31 bp):
CTACCTTTTAATAGTTAAGGTATAATCAAAA
Found at i:2579850 original size:2 final size:2
Alignment explanation
Indices: 2579839--2579867 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
2579829 TTATTATTAT
2579839 TA TA -A 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 TA TA
2579868 AGTTATTCAT
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):
TA
Found at i:2581114 original size:11 final size:11
Alignment explanation
Indices: 2581098--2581122 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
2581088 CACTCTCTCC
2581098 TTTTTTTTTTG
1 TTTTTTTTTTG
2581109 TTTTTTTTTTG
1 TTTTTTTTTTG
2581120 TTT
1 TTT
2581123 GTGTGTATGT
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:0.00, C:0.00, G:0.08, T:0.92
Consensus pattern (11 bp):
TTTTTTTTTTG
Found at i:2582823 original size:13 final size:13
Alignment explanation
Indices: 2582805--2582836 Score: 64
Period size: 13 Copynumber: 2.5 Consensus size: 13
2582795 TCAAATCTTC
2582805 TGTCTCTACATCT
1 TGTCTCTACATCT
2582818 TGTCTCTACATCT
1 TGTCTCTACATCT
2582831 TGTCTC
1 TGTCTC
2582837 ATTGTCTATC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 19 1.00
ACGTcount: A:0.12, C:0.31, G:0.09, T:0.47
Consensus pattern (13 bp):
TGTCTCTACATCT
Found at i:2584517 original size:22 final size:22
Alignment explanation
Indices: 2584482--2584523 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
2584472 ATATAGATAT
*
2584482 TATATATAGTGATTTTTTTTTA
1 TATATATAGAGATTTTTTTTTA
*
2584504 TATATTTAGAGATTTTTTTT
1 TATATATAGAGATTTTTTTT
2584524 GAAAGAGAAA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.26, C:0.00, G:0.10, T:0.64
Consensus pattern (22 bp):
TATATATAGAGATTTTTTTTTA
Found at i:2585683 original size:23 final size:23
Alignment explanation
Indices: 2585652--2585698 Score: 69
Period size: 23 Copynumber: 2.0 Consensus size: 23
2585642 GGATGCATAC
2585652 ATATATATGCA-TCTTTCATGTAA
1 ATATATATGCAGT-TTTCATGTAA
*
2585675 ATATGTATGCAGTTTTCATGTAA
1 ATATATATGCAGTTTTCATGTAA
2585698 A
1 A
2585699 ATGAATACCT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 21 0.95
24 1 0.05
ACGTcount: A:0.34, C:0.11, G:0.13, T:0.43
Consensus pattern (23 bp):
ATATATATGCAGTTTTCATGTAA
Found at i:2589041 original size:2 final size:2
Alignment explanation
Indices: 2589036--2589063 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
2589026 TATATATATA
2589036 TG TG TG TG TG TG TG TG TG TG TG TG TG TG
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG
2589064 GCATGTCTTT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.00, C:0.00, G:0.50, T:0.50
Consensus pattern (2 bp):
TG
Found at i:2589204 original size:22 final size:21
Alignment explanation
Indices: 2589154--2589204 Score: 50
Period size: 22 Copynumber: 2.3 Consensus size: 21
2589144 AAAAAAGTAA
* *
2589154 ACAAATGTTTTTGAAGAAACT
1 ACAAATATTTTTGAAAAAACT
2589175 A-AGCAATATTTTTGAAAAAAGCT
1 ACA--AATATTTTTGAAAAAA-CT
2589198 ACAAATA
1 ACAAATA
2589205 AAACATGTAT
Statistics
Matches: 24, Mismatches: 2, Indels: 7
0.73 0.06 0.21
Matches are distributed among these distances:
20 1 0.04
21 1 0.04
22 18 0.75
23 3 0.12
24 1 0.04
ACGTcount: A:0.49, C:0.10, G:0.12, T:0.29
Consensus pattern (21 bp):
ACAAATATTTTTGAAAAAACT
Found at i:2597183 original size:26 final size:25
Alignment explanation
Indices: 2597142--2597203 Score: 76
Period size: 26 Copynumber: 2.5 Consensus size: 25
2597132 CTTACTTTTG
*
2597142 TTTTTTTTCTT-CTTTTCTT-ATCTC
1 TTTTTTTTCTTATTTTTCTTCAT-TC
2597166 TTTTTCTTTCTTATTTTTCTTCATTC
1 TTTTT-TTTCTTATTTTTCTTCATTC
2597192 TTTTTTTT-TTAT
1 TTTTTTTTCTTAT
2597204 CGTTCTTTCC
Statistics
Matches: 34, Mismatches: 1, Indels: 6
0.83 0.02 0.15
Matches are distributed among these distances:
24 9 0.26
25 9 0.26
26 14 0.41
27 2 0.06
ACGTcount: A:0.06, C:0.16, G:0.00, T:0.77
Consensus pattern (25 bp):
TTTTTTTTCTTATTTTTCTTCATTC
Found at i:2598266 original size:364 final size:363
Alignment explanation
Indices: 2597583--2598675 Score: 1516
Period size: 364 Copynumber: 3.0 Consensus size: 363
2597573 TCATGTCAGC
* * * *
2597583 ATGTCAGGGTGACATGACAGTGCCATGTTAGCACCTCAAACTTAGAAGGTGATATGGCATTACAT
1 ATGTCAGGGTGACATGACAGTGCCATGTCAGCACCT--AACTTAGAGGGTGACATGGCATTACAC
** * * * *
2597648 ATTGCCTTGACATGCTGACATGGCACTGCCAC-ATCAACAACTCAAACCCACCTTATATGACACA
64 ATCACCTTGACATGCTAACGTGGCACTGCCACGATCAAGAACCCAAACCCACCTTATATGACACA
* * *
2597712 TCAACATTTGGTGCCATGTCTGCACTAACATCAGCACTATAACAGG-CAATTTGGAT-GAAAATA
129 TCAACA-TTGGTGCCATGTCTGCACTGACATCAACACCATAAC-GGTCAATTTGGATGGAAAATA
** *
2597775 TTGATGGGACTAAATTGAAGCAATTTACAAAACCAAATGACTAAAATGTCACAATTTTGAGTAGA
192 TTGATGGGACTAAATTGAAGCAATTTACAAAACCAAGGGACTAAAATGTCACAATTTTGAGTGGA
* ** * * *
2597840 GGTAAAAGGACTAAATTGAAGAAAACACCTAAGTACAAGGACTTCTTAACTACTTTGACCTTTTA
257 GGTAAAGGGACTAAATTGAAGAAAATGCCTAAGTATAAGGACTTCTCAAATACTTTGACCTTTTA
*
2597905 AAAGGCTTTCTATGTAATTTAGAATGCACACAAATTTCACAT
322 AAAGGCTTTCTAGGTAATTTAGAATGCACACAAATTTCACAT
* * *
2597947 ATGTCAGGGTAACATGACAATGCCATGTCAGCAGCCTTACTTAGAGGGTGACATGGCATTACTAC
1 ATGTCAGGGTGACATGACAGTGCCATGTCAGCA-CCTAACTTAGAGGGTGACATGGCATTAC-AC
*
2598012 ATCACCTTGACATGCTAACGTGGCACTGCCACGAT-AAGAACCCAAACCCACCTTATACGACACA
64 ATCACCTTGACATGCTAACGTGGCACTGCCACGATCAAGAACCCAAACCCACCTTATATGACACA
* * * *
2598076 TGAGCATTGGTGCCATGTCTGCACTGACGTTAACACCATAACGGTCAATTTGGATGGAAAATATT
129 TCAACATTGGTGCCATGTCTGCACTGACATCAACACCATAACGGTCAATTTGGATGGAAAATATT
* *
2598141 AATGGGACTAAATTGAAGCAATTTACAAAATCAAGGGACTAAAATGTCACAATTTTGAGTGGAGG
194 GATGGGACTAAATTGAAGCAATTTACAAAACCAAGGGACTAAAATGTCACAATTTTGAGTGGAGG
*
2598206 TAAAGGGACTAAATTGAAGAAAATGCCTAAGTATAAGGACTTCTCAAATACTTCGACCTTTTAAA
259 TAAAGGGACTAAATTGAAGAAAATGCCTAAGTATAAGGACTTCTCAAATACTTTGACCTTTTAAA
* *
2598271 AGGTTTTCTAGGCAATTTA-AACTGCACACAAATTTCACAT
324 AGGCTTTCTAGGTAATTTAGAA-TGCACACAAATTTCACAT
* * * *
2598311 ATATCAAGGTGACATGACAGTGTCATGTCAGCACTCCAACTTAGAGGGTGACATGGCATTACCAC
1 ATGTCAGGGTGACATGACAGTGCCATGTCAGCAC-CTAACTTAGAGGGTGACATGGCATTA-CAC
* * * * * * *
2598376 ATCACCTTGATATGCTAACGTGGCATTGCCACG-TCAAGAAGCCGAACCCACATTACATGGCACA
64 ATCACCTTGACATGCTAACGTGGCACTGCCACGATCAAGAACCCAAACCCACCTTATATGACACA
* * * * *
2598440 TCAACATCTGGTGCCATGTCTGCATTGACATCAACACCGTAATGGTCAATTTAGAGGGAAAATAT
129 TCAACAT-TGGTGCCATGTCTGCACTGACATCAACACCATAACGGTCAATTTGGATGGAAAATAT
* *
2598505 TGATGGGACTAAATTAAAGCTATTTACAAAACCAAGGGACTAAAATGTCACAATTTTGAG-GAGA
193 TGATGGGACTAAATTGAAGCAATTTACAAAACCAAGGGACTAAAATGTCACAATTTTGAGTG-GA
* *
2598569 GGTAAAGGGACTAAATTGAAGAAAATGCCTAAGTATAAGGACTTCTCAAGTACTTTGACCTTGTA
257 GGTAAAGGGACTAAATTGAAGAAAATGCCTAAGTATAAGGACTTCTCAAATACTTTGACCTTTTA
* *
2598634 AAAGGCTTTCTAGGTAATTTAGACTACACACAAATTTCACAT
322 AAAGGCTTTCTAGGTAATTTAGAATGCACACAAATTTCACAT
2598676 TTTCCATGCA
Statistics
Matches: 646, Mismatches: 71, Indels: 23
0.87 0.10 0.03
Matches are distributed among these distances:
362 2 0.00
363 67 0.10
364 364 0.56
365 212 0.33
366 1 0.00
ACGTcount: A:0.36, C:0.20, G:0.19, T:0.26
Consensus pattern (363 bp):
ATGTCAGGGTGACATGACAGTGCCATGTCAGCACCTAACTTAGAGGGTGACATGGCATTACACAT
CACCTTGACATGCTAACGTGGCACTGCCACGATCAAGAACCCAAACCCACCTTATATGACACATC
AACATTGGTGCCATGTCTGCACTGACATCAACACCATAACGGTCAATTTGGATGGAAAATATTGA
TGGGACTAAATTGAAGCAATTTACAAAACCAAGGGACTAAAATGTCACAATTTTGAGTGGAGGTA
AAGGGACTAAATTGAAGAAAATGCCTAAGTATAAGGACTTCTCAAATACTTTGACCTTTTAAAAG
GCTTTCTAGGTAATTTAGAATGCACACAAATTTCACAT
Found at i:2603942 original size:27 final size:27
Alignment explanation
Indices: 2603911--2603966 Score: 85
Period size: 27 Copynumber: 2.1 Consensus size: 27
2603901 TCAAGCACAC
*
2603911 ATGTTAAAAAAAATATTACTACATGTT
1 ATGTTAAAAAAAATATTACTACACGTT
* *
2603938 ATGTTGAAAAAAATATTATTACACGTT
1 ATGTTAAAAAAAATATTACTACACGTT
2603965 AT
1 AT
2603967 ATTTAAGATG
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
27 26 1.00
ACGTcount: A:0.46, C:0.07, G:0.09, T:0.38
Consensus pattern (27 bp):
ATGTTAAAAAAAATATTACTACACGTT
Found at i:2604121 original size:28 final size:27
Alignment explanation
Indices: 2604040--2604122 Score: 78
Period size: 27 Copynumber: 3.0 Consensus size: 27
2604030 CAGGTGATAT
* * *
2604040 TTAAAAAATAATGTTAGTACACTTCATG
1 TTAAAAAA-AATATTATTACACGTCATG
* *
2604068 TTAAAAAAAATATTATTATATGTCATG
1 TTAAAAAAAATATTATTACACGTCATG
*
2604095 TTAAAAAAAA-ATTTGTTACACGCTCATG
1 TTAAAAAAAATA-TTATTACACG-TCATG
2604123 GATGGACCCA
Statistics
Matches: 45, Mismatches: 8, Indels: 4
0.79 0.14 0.07
Matches are distributed among these distances:
26 1 0.02
27 31 0.69
28 13 0.29
ACGTcount: A:0.45, C:0.10, G:0.10, T:0.36
Consensus pattern (27 bp):
TTAAAAAAAATATTATTACACGTCATG
Found at i:2605443 original size:71 final size:71
Alignment explanation
Indices: 2605310--2605444 Score: 162
Period size: 71 Copynumber: 1.9 Consensus size: 71
2605300 ACATATCATG
* * * * * * * * *
2605310 TTTAGGTGTTTAATTCTAAGAGTTTATGTCTTATTGAAGTACAAAGATAGAGACCAAGTTACATA
1 TTTAGATGTTTAATTCGAAGAATTTATGTCTTAATAAAATACAAAAATAAAGACCAAATTACATA
2605375 GCATAT
66 GCATAT
* * *
2605381 TTTAGATGTTTAATTCGAAGAATTTATTTCTTAATAAAATATAAAAATAAAGATCAAATTACAT
1 TTTAGATGTTTAATTCGAAGAATTTATGTCTTAATAAAATACAAAAATAAAGACCAAATTACAT
2605445 GCTATGTTTA
Statistics
Matches: 52, Mismatches: 12, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
71 52 1.00
ACGTcount: A:0.41, C:0.08, G:0.13, T:0.38
Consensus pattern (71 bp):
TTTAGATGTTTAATTCGAAGAATTTATGTCTTAATAAAATACAAAAATAAAGACCAAATTACATA
GCATAT
Found at i:2616114 original size:44 final size:44
Alignment explanation
Indices: 2616050--2616134 Score: 129
Period size: 44 Copynumber: 1.9 Consensus size: 44
2616040 AAAGATTGTG
*
2616050 AAAATACCAACTCAAGTTGAATCCATCTAAGTGTACCTTTGGCA
1 AAAATACCAACTCAAGTTGAATCCATCGAAGTGTACCTTTGGCA
2616094 AAAATACCAA-TACCAA-TTGAATCCATCGAAGTGTACCTTTG
1 AAAATACCAACT--CAAGTTGAATCCATCGAAGTGTACCTTTG
2616135 TCACTACTTC
Statistics
Matches: 38, Mismatches: 1, Indels: 4
0.88 0.02 0.09
Matches are distributed among these distances:
43 1 0.03
44 34 0.89
45 3 0.08
ACGTcount: A:0.38, C:0.22, G:0.13, T:0.27
Consensus pattern (44 bp):
AAAATACCAACTCAAGTTGAATCCATCGAAGTGTACCTTTGGCA
Found at i:2618641 original size:9 final size:8
Alignment explanation
Indices: 2618620--2618650 Score: 53
Period size: 8 Copynumber: 3.8 Consensus size: 8
2618610 GTGTACACAT
2618620 AAAAAACA
1 AAAAAACA
2618628 AAAAAACA
1 AAAAAACA
2618636 AGAAAAACA
1 A-AAAAACA
2618645 AAAAAA
1 AAAAAA
2618651 AAAGGATTCA
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
8 14 0.64
9 8 0.36
ACGTcount: A:0.87, C:0.10, G:0.03, T:0.00
Consensus pattern (8 bp):
AAAAAACA
Found at i:2619419 original size:34 final size:34
Alignment explanation
Indices: 2619335--2619601 Score: 183
Period size: 34 Copynumber: 7.9 Consensus size: 34
2619325 GTTTATTCCT
* *
2619335 TTTTAAGTTACATAGCCTCAGTCAAGAT-GAAAAG
1 TTTTAAGTTACATAGCCTCATTCAAGATAG-GAAG
* * * *
2619369 TTTTAAGTTTA-GTAGCCTTATTCGAGATAGGGAG
1 TTTTAAG-TTACATAGCCTCATTCAAGATAGGAAG
* *
2619403 TTTTAAGTTACATAGCCTCATTCAAGAAAAGAAG
1 TTTTAAGTTACATAGCCTCATTCAAGATAGGAAG
*
2619437 TTTTAAG-TA-ATGAAACCTCATTCAAGATAAGG-AG
1 TTTTAAGTTACAT--AGCCTCATTCAAGAT-AGGAAG
* * * * *
2619471 TTCTAAGTTACGTAGCTTCATTTAAGATGATG-AG
1 TTTTAAGTTACATAGCCTCATTCAAGAT-AGGAAG
* *
2619505 TTTTAAGTCACGA-AACCTCATTCAAGATGAGG-AG
1 TTTTAAGTTAC-ATAGCCTCATTCAAGAT-AGGAAG
* * *
2619539 CTTTAAGTTACATAGCGTCATTCAAGGT-GAGAAG
1 TTTTAAGTTACATAGCCTCATTCAAGATAG-GAAG
* * * *
2619573 TTTTAAGTTATATGGCCCCATTCTAGATA
1 TTTTAAGTTACATAGCCTCATTCAAGATA
2619602 AAGAGCATTT
Statistics
Matches: 179, Mismatches: 41, Indels: 25
0.73 0.17 0.10
Matches are distributed among these distances:
32 3 0.02
33 7 0.04
34 160 0.89
35 8 0.04
36 1 0.01
ACGTcount: A:0.34, C:0.14, G:0.19, T:0.33
Consensus pattern (34 bp):
TTTTAAGTTACATAGCCTCATTCAAGATAGGAAG
Found at i:2619444 original size:68 final size:69
Alignment explanation
Indices: 2619335--2619580 Score: 270
Period size: 68 Copynumber: 3.6 Consensus size: 69
2619325 GTTTATTCCT
* * * * * *
2619335 TTTTAAGTTACATAGCCTCAGTCAAGATGAA-AAGTTTTAAGTTTA-GTAGCCTTATTCGAGATA
1 TTTTAAGTTACATAGCCTCATTCAAGATGAAGAAGTTTTAAG-TAACGAAACCTCATTCAAGATA
2619398 GGGAG
65 GGGAG
* * *
2619403 TTTTAAGTTACATAGCCTCATTCAAGA-AAAGAAGTTTTAAGTAATGAAACCTCATTCAAGATAA
1 TTTTAAGTTACATAGCCTCATTCAAGATGAAGAAGTTTTAAGTAACGAAACCTCATTCAAGATAG
2619467 GGAG
66 GGAG
* * * * * *
2619471 TTCTAAGTTACGTAGCTTCATTTAAGATGATG-AGTTTTAAGTCACGAAACCTCATTCAAGAT-G
1 TTTTAAGTTACATAGCCTCATTCAAGATGAAGAAGTTTTAAGTAACGAAACCTCATTCAAGATAG
2619534 AGGAG
66 -GGAG
* * *
2619539 CTTTAAGTTACATAGCGTCATTCAAGGTG-AGAAGTTTTAAGT
1 TTTTAAGTTACATAGCCTCATTCAAGATGAAGAAGTTTTAAGT
2619581 TATATGGCCC
Statistics
Matches: 149, Mismatches: 24, Indels: 10
0.81 0.13 0.05
Matches are distributed among these distances:
67 5 0.03
68 142 0.95
69 2 0.01
ACGTcount: A:0.35, C:0.13, G:0.20, T:0.33
Consensus pattern (69 bp):
TTTTAAGTTACATAGCCTCATTCAAGATGAAGAAGTTTTAAGTAACGAAACCTCATTCAAGATAG
GGAG
Found at i:2624982 original size:21 final size:21
Alignment explanation
Indices: 2624957--2625001 Score: 65
Period size: 21 Copynumber: 2.1 Consensus size: 21
2624947 TGATGCATAG
2624957 AACAATTATTT-TACAGTTTGT
1 AACAATT-TTTGTACAGTTTGT
*
2624978 AACAATTTTTGTACATTTTGT
1 AACAATTTTTGTACAGTTTGT
2624999 AAC
1 AAC
2625002 GAATGTTATT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
20 3 0.14
21 19 0.86
ACGTcount: A:0.33, C:0.11, G:0.09, T:0.47
Consensus pattern (21 bp):
AACAATTTTTGTACAGTTTGT
Found at i:2626203 original size:29 final size:25
Alignment explanation
Indices: 2626170--2626243 Score: 78
Period size: 29 Copynumber: 2.8 Consensus size: 25
2626160 TTTAAAAAAA
**
2626170 TTTAAATAAAATTTTATTCTTATATTAT
1 TTTAAATAAAATAATATT-TT-T-TTAT
*
2626198 GTTTAATTAAAATAATATTTTTTTAT
1 -TTTAAATAAAATAATATTTTTTTAT
2626224 TTTAAATAAAATAA-ATTTTT
1 TTTAAATAAAATAATATTTTT
2626244 ATAATTAATA
Statistics
Matches: 41, Mismatches: 4, Indels: 5
0.82 0.08 0.10
Matches are distributed among these distances:
24 6 0.15
25 13 0.32
26 4 0.10
27 1 0.02
28 2 0.05
29 15 0.37
ACGTcount: A:0.42, C:0.01, G:0.01, T:0.55
Consensus pattern (25 bp):
TTTAAATAAAATAATATTTTTTTAT
Found at i:2626227 original size:25 final size:25
Alignment explanation
Indices: 2626194--2626243 Score: 75
Period size: 25 Copynumber: 2.0 Consensus size: 25
2626184 TATTCTTATA
*
2626194 TTATGTTTAATTAAAATAATATTTTT
1 TTATGTTTAAATAAAATAA-ATTTTT
2626220 TTAT-TTTAAATAAAATAAATTTTT
1 TTATGTTTAAATAAAATAAATTTTT
2626244 ATAATTAATA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
24 6 0.26
25 13 0.57
26 4 0.17
ACGTcount: A:0.42, C:0.00, G:0.02, T:0.56
Consensus pattern (25 bp):
TTATGTTTAAATAAAATAAATTTTT
Found at i:2626253 original size:22 final size:24
Alignment explanation
Indices: 2626200--2626254 Score: 60
Period size: 25 Copynumber: 2.3 Consensus size: 24
2626190 TATATTATGT
* *
2626200 TTAATTAAAATAATATTTTTTTATT
1 TTAA-TAAAATAATATTTTTATATA
2626225 TTAAATAAAATAA-ATTTTTATA-A
1 TT-AATAAAATAATATTTTTATATA
2626248 TTAATAA
1 TTAATAA
2626255 TTAACTAGTT
Statistics
Matches: 27, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
22 5 0.19
23 2 0.07
24 8 0.30
25 10 0.37
26 2 0.07
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (24 bp):
TTAATAAAATAATATTTTTATATA
Found at i:2630891 original size:25 final size:27
Alignment explanation
Indices: 2630849--2630907 Score: 65
Period size: 25 Copynumber: 2.3 Consensus size: 27
2630839 TGTTATAATT
2630849 AAAA-TAAAATATATAATATAAGA-AT-A
1 AAAATTAAAATATATAATA-AA-ATATAA
2630875 AAAATTAAAATA-A-AATAAAATATAA
1 AAAATTAAAATATATAATAAAATATAA
2630900 AAAATTAA
1 AAAATTAA
2630908 CATTTATATA
Statistics
Matches: 30, Mismatches: 0, Indels: 7
0.81 0.00 0.19
Matches are distributed among these distances:
23 1 0.03
24 4 0.13
25 13 0.43
26 5 0.17
27 7 0.23
ACGTcount: A:0.73, C:0.00, G:0.02, T:0.25
Consensus pattern (27 bp):
AAAATTAAAATATATAATAAAATATAA
Found at i:2630987 original size:33 final size:33
Alignment explanation
Indices: 2630936--2631021 Score: 84
Period size: 33 Copynumber: 2.5 Consensus size: 33
2630926 AAAACAAATT
* *
2630936 AAATTAAAATATATAATATAAAAAA-TATATTAAAG
1 AAATGAAAATA-A-AATATAAAAAATTATAAT-AAG
* * *
2630971 AAATGAAAATAAAATATATAAGATTATAATAAT
1 AAATGAAAATAAAATATAAAAAATTATAATAAG
*
2631004 AAATGAAAATAACATATA
1 AAATGAAAATAAAATATA
2631022 TGACATTAAA
Statistics
Matches: 44, Mismatches: 6, Indels: 4
0.81 0.11 0.07
Matches are distributed among these distances:
33 28 0.64
34 6 0.14
35 10 0.23
ACGTcount: A:0.65, C:0.01, G:0.05, T:0.29
Consensus pattern (33 bp):
AAATGAAAATAAAATATAAAAAATTATAATAAG
Found at i:2631078 original size:21 final size:22
Alignment explanation
Indices: 2631054--2631127 Score: 84
Period size: 21 Copynumber: 3.5 Consensus size: 22
2631044 ATATGATATT
2631054 ATATAAAA-ATTAATAATAAAA
1 ATATAAAATATTAATAATAAAA
*
2631075 ATATAAATATATTAAAAAT-AAA
1 ATATAAA-ATATTAATAATAAAA
*
2631097 ATATAAAATATT-ATAAAAATAA
1 ATATAAAATATTAATAATAA-AA
2631119 ATA-AAAATA
1 ATATAAAATA
2631128 AAATATATGA
Statistics
Matches: 46, Mismatches: 3, Indels: 8
0.81 0.05 0.14
Matches are distributed among these distances:
20 3 0.07
21 19 0.41
22 16 0.35
23 8 0.17
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (22 bp):
ATATAAAATATTAATAATAAAA
Found at i:2631098 original size:16 final size:16
Alignment explanation
Indices: 2631070--2631204 Score: 59
Period size: 16 Copynumber: 8.2 Consensus size: 16
2631060 AAATTAATAA
2631070 TAAAAATATAAATATAT
1 TAAAAATA-AAATATAT
2631087 TAAAAATAAAATATA-
1 TAAAAATAAAATATAT
*
2631102 -AAATATTATAAAA-ATAAA
1 TAAA-A--ATAAAATAT-AT
2631120 TAAAAATAAAATATA-
1 TAAAAATAAAATATAT
* * *
2631135 TGACATTAAAAATATATT
1 TAAAAAT-AAAATATA-T
* *
2631153 TAAGAAATGATAT-TAT
1 TAA-AAATAAAATATAT
*
2631169 ATAAAAAT-TAATA-AT
1 -TAAAAATAAAATATAT
*
2631184 AAAAAATATAAATATAT
1 TAAAAATA-AAATATAT
2631201 TAAA
1 TAAA
2631205 CTTGTATTTT
Statistics
Matches: 89, Mismatches: 13, Indels: 32
0.66 0.10 0.24
Matches are distributed among these distances:
14 9 0.10
15 9 0.10
16 33 0.37
17 27 0.30
18 6 0.07
19 5 0.06
ACGTcount: A:0.65, C:0.01, G:0.02, T:0.32
Consensus pattern (16 bp):
TAAAAATAAAATATAT
Found at i:2631118 original size:113 final size:114
Alignment explanation
Indices: 2630976--2631204 Score: 397
Period size: 113 Copynumber: 2.0 Consensus size: 114
2630966 TAAAGAAATG
* * * *
2630976 AAAATAAAATATATAAGATTATAATAATAAATGAAAATAACATATATGACATTAAAAATATATTT
1 AAAATAAAATATAAAAGATTATAAAAATAAATAAAAATAAAATATATGACATTAAAAATATATTT
*
2631041 AAGATATGATATTATATAAAAATTAATAAT-AAAAATATAAATATATTA
66 AAGAAATGATATTATATAAAAATTAATAATAAAAAATATAAATATATTA
*
2631089 AAAATAAAATATAAAATATTATAAAAATAAATAAAAATAAAATATATGACATTAAAAATATATTT
1 AAAATAAAATATAAAAGATTATAAAAATAAATAAAAATAAAATATATGACATTAAAAATATATTT
2631154 AAGAAATGATATTATATAAAAATTAATAATAAAAAATATAAATATATTA
66 AAGAAATGATATTATATAAAAATTAATAATAAAAAATATAAATATATTA
2631203 AA
1 AA
2631205 CTTGTATTTT
Statistics
Matches: 109, Mismatches: 6, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
113 89 0.82
114 20 0.18
ACGTcount: A:0.63, C:0.01, G:0.03, T:0.32
Consensus pattern (114 bp):
AAAATAAAATATAAAAGATTATAAAAATAAATAAAAATAAAATATATGACATTAAAAATATATTT
AAGAAATGATATTATATAAAAATTAATAATAAAAAATATAAATATATTA
Found at i:2631371 original size:15 final size:15
Alignment explanation
Indices: 2631351--2631394 Score: 70
Period size: 15 Copynumber: 2.9 Consensus size: 15
2631341 TTATTTTTCC
*
2631351 TGCAATTACATTACT
1 TGCAATCACATTACT
*
2631366 TGCAATCGCATTACT
1 TGCAATCACATTACT
2631381 TGCAATCACATTAC
1 TGCAATCACATTAC
2631395 CTATAATCAC
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
15 26 1.00
ACGTcount: A:0.32, C:0.25, G:0.09, T:0.34
Consensus pattern (15 bp):
TGCAATCACATTACT
Found at i:2633487 original size:45 final size:45
Alignment explanation
Indices: 2633423--2633513 Score: 173
Period size: 45 Copynumber: 2.0 Consensus size: 45
2633413 ATAAAACCAG
*
2633423 GAACTAAACTATTTGACTTAGTCAACAGAAAAGCAAGTGCAAAAA
1 GAACTAAACTATTTAACTTAGTCAACAGAAAAGCAAGTGCAAAAA
2633468 GAACTAAACTATTTAACTTAGTCAACAGAAAAGCAAGTGCAAAAA
1 GAACTAAACTATTTAACTTAGTCAACAGAAAAGCAAGTGCAAAAA
2633513 G
1 G
2633514 CAATGTGTAA
Statistics
Matches: 45, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
45 45 1.00
ACGTcount: A:0.49, C:0.15, G:0.15, T:0.20
Consensus pattern (45 bp):
GAACTAAACTATTTAACTTAGTCAACAGAAAAGCAAGTGCAAAAA
Found at i:2635748 original size:18 final size:18
Alignment explanation
Indices: 2635721--2635757 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
2635711 AGGCTTAGTC
2635721 AATTTATTTTATTTATGT
1 AATTTATTTTATTTATGT
* *
2635739 AATTTCTTTTTTTTATGT
1 AATTTATTTTATTTATGT
2635757 A
1 A
2635758 TGAATTAAAT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.24, C:0.03, G:0.05, T:0.68
Consensus pattern (18 bp):
AATTTATTTTATTTATGT
Found at i:2645381 original size:2 final size:2
Alignment explanation
Indices: 2645374--2645407 Score: 59
Period size: 2 Copynumber: 17.0 Consensus size: 2
2645364 GAATGGAAGA
*
2645374 AT AT AT AT AT AC 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
2645408 GTATTCTTGA
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:2646106 original size:23 final size:22
Alignment explanation
Indices: 2646072--2646116 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 22
2646062 TTGACTTTTT
*
2646072 TTTTAATCTTTGATCT-TAATTA
1 TTTTAATATTTGAT-TATAATTA
2646094 TTTTAATTATTTGATTATAATTA
1 TTTTAA-TATTTGATTATAATTA
2646117 AATTCTAACA
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
22 7 0.35
23 13 0.65
ACGTcount: A:0.31, C:0.04, G:0.04, T:0.60
Consensus pattern (22 bp):
TTTTAATATTTGATTATAATTA
Found at i:2649374 original size:2 final size:2
Alignment explanation
Indices: 2649328--2649359 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
2649318 CAAAAAGTTG
2649328 TA TA T- TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
2649360 TTAAAAAGTA
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 28 0.97
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (2 bp):
TA
Found at i:2657056 original size:24 final size:22
Alignment explanation
Indices: 2657017--2657087 Score: 72
Period size: 23 Copynumber: 3.0 Consensus size: 22
2657007 AAATATTTAG
*
2657017 ATAATTTTAGGCAAGTTTTCAAA
1 ATAA-TTTAGGAAAGTTTTCAAA
*
2657040 ATGCAATTTAGGAAAGTTTCTAAAA
1 AT--AATTTAGGAAAGTTT-TCAAA
2657065 ATAATTTA-GATAAGTTTTCAAA
1 ATAATTTAGGA-AAGTTTTCAAA
2657087 A
1 A
2657088 GAGGAACTTG
Statistics
Matches: 41, Mismatches: 3, Indels: 9
0.77 0.06 0.17
Matches are distributed among these distances:
22 7 0.17
23 14 0.34
24 12 0.29
25 8 0.20
ACGTcount: A:0.44, C:0.07, G:0.13, T:0.37
Consensus pattern (22 bp):
ATAATTTAGGAAAGTTTTCAAA
Found at i:2657876 original size:21 final size:21
Alignment explanation
Indices: 2657834--2657876 Score: 61
Period size: 21 Copynumber: 2.0 Consensus size: 21
2657824 AGTTAAAGCG
*
2657834 TGTAATAATTTTTTTTGCAAC
1 TGTAACAATTTTTTTTGCAAC
2657855 TGTAACAATATTTTTTTG-AAC
1 TGTAACAAT-TTTTTTTGCAAC
2657876 T
1 T
2657877 TGACGTGTAA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
21 12 0.60
22 8 0.40
ACGTcount: A:0.30, C:0.09, G:0.09, T:0.51
Consensus pattern (21 bp):
TGTAACAATTTTTTTTGCAAC
Found at i:2658245 original size:15 final size:15
Alignment explanation
Indices: 2658203--2658246 Score: 61
Period size: 15 Copynumber: 2.9 Consensus size: 15
2658193 GTTTGGTACT
2658203 TTACAATGCAATGTGA
1 TTACAA-GCAATGTGA
* *
2658219 TTACAGGTAATGTGA
1 TTACAAGCAATGTGA
2658234 TTACAAGCAATGT
1 TTACAAGCAATGT
2658247 TATTGCAGGG
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
15 19 0.79
16 5 0.21
ACGTcount: A:0.36, C:0.11, G:0.20, T:0.32
Consensus pattern (15 bp):
TTACAAGCAATGTGA
Found at i:2658506 original size:33 final size:32
Alignment explanation
Indices: 2658469--2658553 Score: 109
Period size: 33 Copynumber: 2.6 Consensus size: 32
2658459 TTTGAATGTC
*
2658469 ATATATTTTATTTTCATTTATTATTATAATCTT
1 ATATATTTTATTTTCATTTATTAATATAAT-TT
*
2658502 ATATATTTTATTTTCATTTTTTAATATAATTT
1 ATATATTTTATTTTCATTTATTAATATAATTT
*
2658534 TTATATTATATATTTT-ATTT
1 ATATATT-T-TATTTTCATTT
2658554 TAATTTATTT
Statistics
Matches: 47, Mismatches: 3, Indels: 4
0.87 0.06 0.07
Matches are distributed among these distances:
32 8 0.17
33 33 0.70
34 6 0.13
ACGTcount: A:0.31, C:0.04, G:0.00, T:0.66
Consensus pattern (32 bp):
ATATATTTTATTTTCATTTATTAATATAATTT
Found at i:2658594 original size:24 final size:25
Alignment explanation
Indices: 2658567--2658642 Score: 66
Period size: 25 Copynumber: 3.0 Consensus size: 25
2658557 TTTATTTTAC
2658567 TTATATTATA-TAAATTTTAATTTT
1 TTATATTATATTAAATTTTAATTTT
* **
2658591 TTATATTTTATTTTATTTTAATTTT
1 TTATATTATATTAAATTTTAATTTT
* *
2658616 TGATTCTTATATTATATATTTT-ATTTT
1 TTA-TATTATATTA-A-ATTTTAATTTT
2658643 AATATTTTTA
Statistics
Matches: 40, Mismatches: 8, Indels: 5
0.75 0.15 0.09
Matches are distributed among these distances:
24 9 0.22
25 14 0.35
26 7 0.17
27 5 0.12
28 5 0.12
ACGTcount: A:0.29, C:0.01, G:0.01, T:0.68
Consensus pattern (25 bp):
TTATATTATATTAAATTTTAATTTT
Found at i:2658598 original size:35 final size:32
Alignment explanation
Indices: 2658534--2658600 Score: 82
Period size: 35 Copynumber: 2.0 Consensus size: 32
2658524 AATATAATTT
2658534 TTATATTATATATTTTATTTTAATTTATTTTAC
1 TTATATTATATATTTTATTTT-ATTTATTTTAC
2658567 TTATATTATATAAATTTTAATTTT-TTATATTTTA
1 TTATATTATAT--ATTTT-ATTTTATT-TATTTTA
2658601 TTTTATTTTA
Statistics
Matches: 30, Mismatches: 0, Indels: 6
0.83 0.00 0.17
Matches are distributed among these distances:
33 11 0.37
34 2 0.07
35 12 0.40
36 5 0.17
ACGTcount: A:0.33, C:0.01, G:0.00, T:0.66
Consensus pattern (32 bp):
TTATATTATATATTTTATTTTATTTATTTTAC
Found at i:2658604 original size:5 final size:5
Alignment explanation
Indices: 2658544--2658657 Score: 56
Period size: 5 Copynumber: 22.4 Consensus size: 5
2658534 TTATATTATA
* * * * * *
2658544 TATTT TATTT TAATT TATTT TA-CT TATAT TATATA AATTT TAATTT T-TTA
1 TATTT TATTT TATTT TATTT TATTT TATTT TAT-TT TATTT T-ATTT TATTT
* *
2658594 TATTT TATTT TATTT TAATTTT TGATTCT TATAT TA-TA TATTT TATTT
1 TATTT TATTT TATTT T-A-TTT T-ATT-T TATTT TATTT TATTT TATTT
* *
2658642 TAATA T-TTT TATTT TA
1 TATTT TATTT TATTT TA
2658658 ATTATAACAT
Statistics
Matches: 80, Mismatches: 20, Indels: 18
0.68 0.17 0.15
Matches are distributed among these distances:
4 10 0.12
5 51 0.64
6 12 0.15
7 7 0.09
ACGTcount: A:0.29, C:0.02, G:0.01, T:0.68
Consensus pattern (5 bp):
TATTT
Found at i:2658604 original size:50 final size:52
Alignment explanation
Indices: 2658525--2658660 Score: 149
Period size: 50 Copynumber: 2.6 Consensus size: 52
2658515 TCATTTTTTA
* *
2658525 ATATAATTTTTATATTATATATTTTATTTTAATTT-A-TTTT-A-CTTATATT
1 ATATAA-TTTTATTTTTTATATTTTATTTTAATTTAATTTTTGATCTTATATT
*
2658574 ATATAAATTTTAATTTTTTATATTTTATTTTATTTTAATTTTTGATTCTTATATT
1 ATAT-AATTTT-ATTTTTTATATTTTATTTTAATTTAATTTTTGA-TCTTATATT
*
2658629 ATAT-ATTTTA-TTTTAATATTTTTATTTTAATT
1 ATATAATTTTATTTTTTATA-TTTTATTTTAATT
2658661 ATAACATTAT
Statistics
Matches: 74, Mismatches: 5, Indels: 13
0.80 0.05 0.14
Matches are distributed among these distances:
49 8 0.11
50 23 0.31
51 8 0.11
52 17 0.23
53 6 0.08
55 12 0.16
ACGTcount: A:0.31, C:0.01, G:0.01, T:0.67
Consensus pattern (52 bp):
ATATAATTTTATTTTTTATATTTTATTTTAATTTAATTTTTGATCTTATATT
Found at i:2658625 original size:55 final size:51
Alignment explanation
Indices: 2658530--2658657 Score: 152
Period size: 55 Copynumber: 2.4 Consensus size: 51
2658520 TTTTAATATA
2658530 ATTTTTATATTATATATTTTATTTTAATTTATTTTACTTATATTATATAAATTTT
1 ATTTTTATATT-T-TATTTTATTTTAATTTATTTTACTTATATTATAT--ATTTT
2658585 AATTTTTTATATTTTATTTTATTTTAATTT-TTGATT-CTTATATTATATATTTT
1 -A-TTTTTATATTTTATTTTATTTTAATTTATT--TTACTTATATTATATATTTT
*
2658638 ATTTTAATATTTTTATTTTA
1 ATTTTTATA-TTTTATTTTA
2658658 ATTATAACAT
Statistics
Matches: 67, Mismatches: 1, Indels: 12
0.84 0.01 0.15
Matches are distributed among these distances:
51 7 0.10
52 11 0.16
53 5 0.07
54 2 0.03
55 28 0.42
56 4 0.06
57 10 0.15
ACGTcount: A:0.30, C:0.02, G:0.01, T:0.68
Consensus pattern (51 bp):
ATTTTTATATTTTATTTTATTTTAATTTATTTTACTTATATTATATATTTT
Found at i:2660662 original size:35 final size:35
Alignment explanation
Indices: 2660623--2660695 Score: 101
Period size: 35 Copynumber: 2.1 Consensus size: 35
2660613 CAACCAAAAC
*
2660623 AAGTGAAATGTTACTTCATGCAAAATAACTAGAAT
1 AAGTGAAATGTTACTTCATGCAAAACAACTAGAAT
* * * *
2660658 AAGTGAAGTGTTATTTTATGCAAAACAATTAGAAT
1 AAGTGAAATGTTACTTCATGCAAAACAACTAGAAT
2660693 AAG
1 AAG
2660696 AAGAGCCGTA
Statistics
Matches: 33, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
35 33 1.00
ACGTcount: A:0.45, C:0.08, G:0.16, T:0.30
Consensus pattern (35 bp):
AAGTGAAATGTTACTTCATGCAAAACAACTAGAAT
Found at i:2663927 original size:1 final size:1
Alignment explanation
Indices: 2663917--2663946 Score: 51
Period size: 1 Copynumber: 30.0 Consensus size: 1
2663907 CAACCACCTT
*
2663917 CCCCCTCCCCCCCCCCCCCCCCCCCCCCCC
1 CCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
2663947 GCCTCTTCCC
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
1 27 1.00
ACGTcount: A:0.00, C:0.97, G:0.00, T:0.03
Consensus pattern (1 bp):
C
Found at i:2666647 original size:19 final size:21
Alignment explanation
Indices: 2666625--2666670 Score: 62
Period size: 19 Copynumber: 2.3 Consensus size: 21
2666615 TAATTTTATC
*
2666625 AATTAAAAAT-AAAA-AAACA
1 AATTAAAAATCAAAAGAAAAA
2666644 AATT-AAAATCAAAAGAAAAA
1 AATTAAAAATCAAAAGAAAAA
2666664 AATTAAA
1 AATTAAA
2666671 TTGTTTCTCT
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
18 5 0.22
19 8 0.35
20 8 0.35
21 2 0.09
ACGTcount: A:0.76, C:0.04, G:0.02, T:0.17
Consensus pattern (21 bp):
AATTAAAAATCAAAAGAAAAA
Found at i:2667472 original size:47 final size:47
Alignment explanation
Indices: 2667415--2667508 Score: 170
Period size: 47 Copynumber: 2.0 Consensus size: 47
2667405 ATTTGGGAAG
*
2667415 TTCTAAAAGTTCGGTTGGGAGGGAAAATTTGAATTTTCCAGCAGCCC
1 TTCTAAAAGTTCGATTGGGAGGGAAAATTTGAATTTTCCAGCAGCCC
*
2667462 TTCTAGAAGTTCGATTGGGAGGGAAAATTTGAATTTTCCAGCAGCCC
1 TTCTAAAAGTTCGATTGGGAGGGAAAATTTGAATTTTCCAGCAGCCC
2667509 CCCTTACATG
Statistics
Matches: 45, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
47 45 1.00
ACGTcount: A:0.28, C:0.17, G:0.26, T:0.30
Consensus pattern (47 bp):
TTCTAAAAGTTCGATTGGGAGGGAAAATTTGAATTTTCCAGCAGCCC
Found at i:2667581 original size:35 final size:35
Alignment explanation
Indices: 2667537--2667638 Score: 168
Period size: 35 Copynumber: 2.9 Consensus size: 35
2667527 GGGTTGGCAC
*
2667537 CCTCTTGGGCCTCTTGGCGGGTCTGGACTGTGTCA
1 CCTCTTGGGCCTCCTGGCGGGTCTGGACTGTGTCA
* *
2667572 CCTTTTGGGCCTCCTGACGGGTCTGGACTGTGTCA
1 CCTCTTGGGCCTCCTGGCGGGTCTGGACTGTGTCA
*
2667607 CCTCTTGGGCCTCCTGGTGGGTCTGGACTGTG
1 CCTCTTGGGCCTCCTGGCGGGTCTGGACTGTG
2667639 GCCTGGTGGT
Statistics
Matches: 61, Mismatches: 6, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
35 61 1.00
ACGTcount: A:0.06, C:0.28, G:0.34, T:0.31
Consensus pattern (35 bp):
CCTCTTGGGCCTCCTGGCGGGTCTGGACTGTGTCA
Found at i:2669160 original size:52 final size:51
Alignment explanation
Indices: 2669090--2669192 Score: 179
Period size: 52 Copynumber: 2.0 Consensus size: 51
2669080 TTTGACCAAG
* *
2669090 AAAAATGGTAATTCTTTCTTGCTTCCCTTGAAACAAATGCTCTCATTTGTCA
1 AAAAATGGTAATTCTTTCTTGCTCCCCTTGAAACAAAAGCTCTCA-TTGTCA
2669142 AAAAATGGTAATTCTTTCTTGCTCCCCTTGAAACAAAAGCTCTCATTGTCA
1 AAAAATGGTAATTCTTTCTTGCTCCCCTTGAAACAAAAGCTCTCATTGTCA
2669193 TTGCCATTGC
Statistics
Matches: 49, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
51 6 0.12
52 43 0.88
ACGTcount: A:0.30, C:0.22, G:0.12, T:0.36
Consensus pattern (51 bp):
AAAAATGGTAATTCTTTCTTGCTCCCCTTGAAACAAAAGCTCTCATTGTCA
Done.