Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007916.1 Hibiscus syriacus cultivar Beakdansim tig00110319_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: 3725575
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 4 of 16
Found at i:764737 original size:33 final size:33
Alignment explanation
Indices: 764690--764757 Score: 91
Period size: 33 Copynumber: 2.1 Consensus size: 33
764680 TAAGCACATC
* ** *
764690 TATAGGATATATATATGTTCATTGTCAATTAAT
1 TATAAGATATATATACATTCATTATCAATTAAT
*
764723 TATAAGATATATATACATTCATTATTAATTAAT
1 TATAAGATATATATACATTCATTATCAATTAAT
764756 TA
1 TA
764758 AGAGTATTTT
Statistics
Matches: 30, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.41, C:0.06, G:0.07, T:0.46
Consensus pattern (33 bp):
TATAAGATATATATACATTCATTATCAATTAAT
Found at i:766417 original size:19 final size:19
Alignment explanation
Indices: 766382--766419 Score: 51
Period size: 19 Copynumber: 2.0 Consensus size: 19
766372 TGATTAAAAC
766382 GGTACAAAAGTGATAGTTT
1 GGTACAAAAGTGATAGTTT
*
766401 GGTACTAAATGTG-TAGTTT
1 GGTAC-AAAAGTGATAGTTT
766420 CCCCCAAATA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 11 0.65
20 6 0.35
ACGTcount: A:0.32, C:0.05, G:0.26, T:0.37
Consensus pattern (19 bp):
GGTACAAAAGTGATAGTTT
Found at i:769355 original size:167 final size:171
Alignment explanation
Indices: 769079--769419 Score: 645
Period size: 167 Copynumber: 2.0 Consensus size: 171
769069 ATCAATCTAT
769079 TCTTTTCTTTAGTCTCCTAAACCAACTCCAAACCCATAATTTTGTTCTAGCCCAACTCAGTTCAA
1 TCTTTTCTTTAGTCTCCTAAACCAACTCCAAACCCATAATTTTGTTCTAGCCCAACTCAGTTCAA
769144 TACGATGAAGTCTAAAAACTTATTACCATACAATGTTTC-ATATATGATCCCATTTAATTATTCA
66 TACGATGAAGTCTAAAAACTTATTACCATACAATGTTTCAATATATGATCCCATTTAATTATTCA
769208 ACTAAT-ACTATTA-T-TAGTCAAATAACATTAAATGCTTC
131 ACTAATAACTATTATTATAGTCAAATAACATTAAATGCTTC
769246 TCTTTTCTTTAGTCTCCTAAACCAACTCCAAACCCATAATTTTGTTCTAGCCCAACTCAGTTCAA
1 TCTTTTCTTTAGTCTCCTAAACCAACTCCAAACCCATAATTTTGTTCTAGCCCAACTCAGTTCAA
769311 TACGATGAAGTCTAAAAACTTATTACCATACAATGTTTCATATATATGATCCCATTTAATTATTC
66 TACGATGAAGTCTAAAAACTTATTACCATACAATGTTTCA-ATATATGATCCCATTTAATTATTC
769376 AACTAATAACTATTATTATAGTCAAATAACATTAAATGCTTC
130 AACTAATAACTATTATTATAGTCAAATAACATTAAATGCTTC
769418 TC
1 TC
769420 CCAACTACCT
Statistics
Matches: 169, Mismatches: 0, Indels: 5
0.97 0.00 0.03
Matches are distributed among these distances:
167 104 0.62
169 31 0.18
170 7 0.04
171 1 0.01
172 26 0.15
ACGTcount: A:0.35, C:0.22, G:0.06, T:0.37
Consensus pattern (171 bp):
TCTTTTCTTTAGTCTCCTAAACCAACTCCAAACCCATAATTTTGTTCTAGCCCAACTCAGTTCAA
TACGATGAAGTCTAAAAACTTATTACCATACAATGTTTCAATATATGATCCCATTTAATTATTCA
ACTAATAACTATTATTATAGTCAAATAACATTAAATGCTTC
Found at i:770320 original size:31 final size:31
Alignment explanation
Indices: 770285--770349 Score: 112
Period size: 31 Copynumber: 2.1 Consensus size: 31
770275 TTGTAGTTTG
* *
770285 GGACTCAACAAAGTAACACCCTATATTTGGA
1 GGACTCAACAAAATAAAACCCTATATTTGGA
770316 GGACTCAACAAAATAAAACCCTATATTTGGA
1 GGACTCAACAAAATAAAACCCTATATTTGGA
770347 GGA
1 GGA
770350 TCATTTGTGT
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
31 32 1.00
ACGTcount: A:0.42, C:0.20, G:0.17, T:0.22
Consensus pattern (31 bp):
GGACTCAACAAAATAAAACCCTATATTTGGA
Found at i:771485 original size:2 final size:2
Alignment explanation
Indices: 771480--771505 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
771470 TTTATTGTTA
771480 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
771506 GTACCTATCT
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:772561 original size:19 final size:19
Alignment explanation
Indices: 772537--772588 Score: 104
Period size: 19 Copynumber: 2.7 Consensus size: 19
772527 GAATGCAACT
772537 AGTGCATCGATGCATAAGG
1 AGTGCATCGATGCATAAGG
772556 AGTGCATCGATGCATAAGG
1 AGTGCATCGATGCATAAGG
772575 AGTGCATCGATGCA
1 AGTGCATCGATGCA
772589 CATGTTAAGA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 33 1.00
ACGTcount: A:0.31, C:0.17, G:0.31, T:0.21
Consensus pattern (19 bp):
AGTGCATCGATGCATAAGG
Found at i:772597 original size:24 final size:23
Alignment explanation
Indices: 772537--772633 Score: 74
Period size: 19 Copynumber: 4.7 Consensus size: 23
772527 GAATGCAACT
772537 AGTGCATCGATG--CA--TAAGG
1 AGTGCATCGATGCACATGTAAGG
772556 AGTGCATCGATG--CA--TAAGG
1 AGTGCATCGATGCACATGTAAGG
772575 AGTGCATCGATGCACATGTTAA-G
1 AGTGCATCGATGCACATG-TAAGG
*
772598 AGATGCATCGATACAC-TGT--GG
1 AG-TGCATCGATGCACATGTAAGG
*
772619 AATGCATCGATGCAC
1 AGTGCATCGATGCAC
772634 TTCAAGGGGA
Statistics
Matches: 68, Mismatches: 3, Indels: 13
0.81 0.04 0.15
Matches are distributed among these distances:
19 31 0.46
20 12 0.18
21 4 0.06
22 1 0.01
23 5 0.07
24 15 0.22
ACGTcount: A:0.31, C:0.19, G:0.28, T:0.23
Consensus pattern (23 bp):
AGTGCATCGATGCACATGTAAGG
Found at i:772968 original size:16 final size:18
Alignment explanation
Indices: 772927--772969 Score: 54
Period size: 16 Copynumber: 2.5 Consensus size: 18
772917 TGATTATACG
*
772927 TATATGCATGACATGAAT
1 TATATGTATGACATGAAT
*
772945 TGTATGTATG-CATG-AT
1 TATATGTATGACATGAAT
772961 TATATGTAT
1 TATATGTAT
772970 TAACATGCTT
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
16 10 0.45
17 4 0.18
18 8 0.36
ACGTcount: A:0.33, C:0.07, G:0.19, T:0.42
Consensus pattern (18 bp):
TATATGTATGACATGAAT
Found at i:778209 original size:21 final size:22
Alignment explanation
Indices: 778184--778228 Score: 58
Period size: 21 Copynumber: 2.1 Consensus size: 22
778174 AAATAATATA
778184 TTGTATAA-GTTCTGAAT-AGTT
1 TTGTA-AACGTTCTGAATAAGTT
*
778205 TTGTAAACGTTTTGAATAAGTT
1 TTGTAAACGTTCTGAATAAGTT
778227 TT
1 TT
778229 ATATGTTATA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
20 2 0.10
21 13 0.62
22 6 0.29
ACGTcount: A:0.29, C:0.04, G:0.18, T:0.49
Consensus pattern (22 bp):
TTGTAAACGTTCTGAATAAGTT
Found at i:782597 original size:21 final size:21
Alignment explanation
Indices: 782571--782610 Score: 80
Period size: 21 Copynumber: 1.9 Consensus size: 21
782561 TTTGAACAAA
782571 CTAACCAAAAATTTATCCAAC
1 CTAACCAAAAATTTATCCAAC
782592 CTAACCAAAAATTTATCCA
1 CTAACCAAAAATTTATCCA
782611 GCCGAGCCAG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.47, C:0.28, G:0.00, T:0.25
Consensus pattern (21 bp):
CTAACCAAAAATTTATCCAAC
Found at i:783527 original size:55 final size:55
Alignment explanation
Indices: 783459--783565 Score: 162
Period size: 55 Copynumber: 1.9 Consensus size: 55
783449 GTCTTCTTAG
* *
783459 GTGCGTATGGAATTACCAGCATGATCAGAGT-TGAACCTCCATACTCCAGAATTCA
1 GTGCGTAAGGAATTACCAACATGATCAGA-TCTGAACCTCCATACTCCAGAATTCA
* *
783514 GTGCGTAAGGAATTACCAACCTGATCAGATCTGAACCTCTATACTCCAGAAT
1 GTGCGTAAGGAATTACCAACATGATCAGATCTGAACCTCCATACTCCAGAAT
783566 CCTACCCATG
Statistics
Matches: 47, Mismatches: 4, Indels: 2
0.89 0.08 0.04
Matches are distributed among these distances:
54 1 0.02
55 46 0.98
ACGTcount: A:0.32, C:0.24, G:0.19, T:0.25
Consensus pattern (55 bp):
GTGCGTAAGGAATTACCAACATGATCAGATCTGAACCTCCATACTCCAGAATTCA
Found at i:787748 original size:36 final size:36
Alignment explanation
Indices: 787701--787783 Score: 148
Period size: 36 Copynumber: 2.3 Consensus size: 36
787691 TTTGGTCAAA
787701 GTCAATGATTAACAGTCAGATCGGTCAAATTCAACG
1 GTCAATGATTAACAGTCAGATCGGTCAAATTCAACG
* *
787737 GTCAACGATTAACATTCAGATCGGTCAAATTCAACG
1 GTCAATGATTAACAGTCAGATCGGTCAAATTCAACG
787773 GTCAATGATTA
1 GTCAATGATTA
787784 TACCGGTCAA
Statistics
Matches: 44, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
36 44 1.00
ACGTcount: A:0.36, C:0.19, G:0.18, T:0.27
Consensus pattern (36 bp):
GTCAATGATTAACAGTCAGATCGGTCAAATTCAACG
Found at i:792803 original size:2 final size:2
Alignment explanation
Indices: 792798--792840 Score: 86
Period size: 2 Copynumber: 21.5 Consensus size: 2
792788 TATTTTTTTA
792798 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
792840 A
1 A
792841 CTTTAATAAA
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:793105 original size:21 final size:21
Alignment explanation
Indices: 793064--793120 Score: 62
Period size: 21 Copynumber: 2.6 Consensus size: 21
793054 ATTAAAGGAC
*
793064 TTAACTTTTTGATGAAAATGAG
1 TTAAC-TTTTCATGAAAATGAG
*
793086 TTAACATTTTCATG-AAATGAT
1 TTAAC-TTTTCATGAAAATGAG
793107 TTAATCTTTTCATG
1 TTAA-CTTTTCATG
793121 TAGAAAATTG
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
21 18 0.58
22 13 0.42
ACGTcount: A:0.33, C:0.09, G:0.12, T:0.46
Consensus pattern (21 bp):
TTAACTTTTCATGAAAATGAG
Found at i:793161 original size:140 final size:140
Alignment explanation
Indices: 792902--793165 Score: 352
Period size: 140 Copynumber: 1.9 Consensus size: 140
792892 ATGAAAAGGG
* * * * * *
792902 TTTAACATTTTGATTAAAGTACTTAACTTTTTTATGAGAAGGGTTTATCCTTTTCATGAAATGAC
1 TTTAACATTTTGATTAAAGGACTTAACTTTTTGATGAAAAGAGTTTAACATTTTCATGAAATGAC
* ** * *
792967 TTAATCTTTTCATGAAGAGAATTGTTGAATATGTATGACTTAATAGATGTAACTTTAAATTTAGT
66 TTAATCTTTTCATGAAGAAAATTGTTGAATAAATATGAATTAATAGATGCAACTTTAAATTTAGT
793032 AAGAGTGTTT
131 AAGAGTGTTT
*
793042 TTTAACCTTTTGATTAAAGGACTTAACTTTTTGATGAAAATGAG-TTAACATTTTCATGAAATGA
1 TTTAACATTTTGATTAAAGGACTTAACTTTTTGATGAAAA-GAGTTTAACATTTTCATGAAATGA
* * * *
793106 TTTAATCTTTTCATGTAGAAAATTGTTGAATAAAT-TTAATTGAATGGATGCAACTTTAAA
65 CTTAATCTTTTCATGAAGAAAATTGTTGAATAAATATGAATT-AATAGATGCAACTTTAAA
793166 CCAAAAATTA
Statistics
Matches: 106, Mismatches: 16, Indels: 4
0.84 0.13 0.03
Matches are distributed among these distances:
139 4 0.04
140 100 0.94
141 2 0.02
ACGTcount: A:0.35, C:0.08, G:0.15, T:0.42
Consensus pattern (140 bp):
TTTAACATTTTGATTAAAGGACTTAACTTTTTGATGAAAAGAGTTTAACATTTTCATGAAATGAC
TTAATCTTTTCATGAAGAAAATTGTTGAATAAATATGAATTAATAGATGCAACTTTAAATTTAGT
AAGAGTGTTT
Found at i:798257 original size:65 final size:66
Alignment explanation
Indices: 798178--798313 Score: 249
Period size: 65 Copynumber: 2.1 Consensus size: 66
798168 TTTGTGTTGA
798178 TAAAATGTGACGTAAGATTAAAACTTTCAAATATTCC-T-TTTTTTTTTAGAAAAATAAACAAGA
1 TAAAATGTGACGTAAGATTAAAACTTTCAAATATTCCTTCTTTTTTTTTAGAAAAATAAACAAGA
798241 TT
66 -T
798243 TAAAATGTGACGTAAGATTAAAACTTTCAAATATTCCTTCTTTTTTTTTAGAAAAATAAACAAGA
1 TAAAATGTGACGTAAGATTAAAACTTTCAAATATTCCTTCTTTTTTTTTAGAAAAATAAACAAGA
798308 T
66 T
798309 TAAAA
1 TAAAA
798314 GTCAAGATAG
Statistics
Matches: 69, Mismatches: 0, Indels: 3
0.96 0.00 0.04
Matches are distributed among these distances:
65 37 0.54
66 7 0.10
67 25 0.36
ACGTcount: A:0.44, C:0.10, G:0.09, T:0.38
Consensus pattern (66 bp):
TAAAATGTGACGTAAGATTAAAACTTTCAAATATTCCTTCTTTTTTTTTAGAAAAATAAACAAGA
T
Found at i:802669 original size:3 final size:3
Alignment explanation
Indices: 802663--802702 Score: 80
Period size: 3 Copynumber: 13.3 Consensus size: 3
802653 GCATTTTTTT
802663 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
802703 GTGTTGACCT
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 37 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:818218 original size:24 final size:24
Alignment explanation
Indices: 818186--818237 Score: 95
Period size: 24 Copynumber: 2.2 Consensus size: 24
818176 GTTCTTTAAT
*
818186 TGCTGCCCTAACATCAAGGTCATA
1 TGCTGCCCTAAAATCAAGGTCATA
818210 TGCTGCCCTAAAATCAAGGTCATA
1 TGCTGCCCTAAAATCAAGGTCATA
818234 TGCT
1 TGCT
818238 TTCTTTTTTC
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.29, C:0.27, G:0.17, T:0.27
Consensus pattern (24 bp):
TGCTGCCCTAAAATCAAGGTCATA
Found at i:821121 original size:21 final size:21
Alignment explanation
Indices: 821092--821136 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
821082 CGGTAAAAAA
* *
821092 TTACCTAAAACATTATTTTTT
1 TTACCTAAAACATTAATGTTT
* *
821113 TTACTTAAAATATTAATGTTT
1 TTACCTAAAACATTAATGTTT
821134 TTA
1 TTA
821137 AACATTTATG
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.36, C:0.09, G:0.02, T:0.53
Consensus pattern (21 bp):
TTACCTAAAACATTAATGTTT
Found at i:821270 original size:21 final size:21
Alignment explanation
Indices: 821236--821275 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
821226 TAAAACGTTC
*
821236 AATAATAACATTTTTGATATA
1 AATAATAACATTTTAGATATA
**
821257 AATAATAATGTTTTAGATA
1 AATAATAACATTTTAGATA
821276 AATTTTTATT
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):
AATAATAACATTTTAGATATA
Found at i:822274 original size:25 final size:26
Alignment explanation
Indices: 822213--822274 Score: 67
Period size: 25 Copynumber: 2.4 Consensus size: 26
822203 TAAAGTTAAA
822213 GAAATGTTTATTAAATTATTTTAAAAT
1 GAAAT-TTTATTAAATTATTTTAAAAT
**
822240 -ATTTTTTATTAAA-T-TTTTAAAAT
1 GAAATTTTATTAAATTATTTTAAAAT
822263 GAAATTTATATT
1 GAAATTT-TATT
822275 TTTAATATTA
Statistics
Matches: 29, Mismatches: 4, Indels: 6
0.74 0.10 0.15
Matches are distributed among these distances:
23 9 0.31
24 5 0.17
25 13 0.45
26 2 0.07
ACGTcount: A:0.42, C:0.00, G:0.05, T:0.53
Consensus pattern (26 bp):
GAAATTTTATTAAATTATTTTAAAAT
Found at i:823470 original size:45 final size:45
Alignment explanation
Indices: 823418--823517 Score: 182
Period size: 45 Copynumber: 2.2 Consensus size: 45
823408 GGAGGTAATG
*
823418 ACATTCCCGGTAATATACTCCAAAAAATCTACTATTGATAATAAA
1 ACATTCCCGGTAATATACTCCAAAAAATCTACTATTAATAATAAA
823463 ACATTCCCGGTAATATACTCCAAAAAATCTACTATTAATAATAAA
1 ACATTCCCGGTAATATACTCCAAAAAATCTACTATTAATAATAAA
*
823508 ACATTACCGG
1 ACATTCCCGG
823518 AAATGAGATT
Statistics
Matches: 53, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
45 53 1.00
ACGTcount: A:0.44, C:0.21, G:0.07, T:0.28
Consensus pattern (45 bp):
ACATTCCCGGTAATATACTCCAAAAAATCTACTATTAATAATAAA
Found at i:829191 original size:105 final size:104
Alignment explanation
Indices: 828984--829193 Score: 244
Period size: 105 Copynumber: 2.0 Consensus size: 104
828974 GATTGTCCAT
* * * *
828984 AAGGACCACATATAAATTCCTTAAGAACAATATACATATACCAAGGATCAAGTAAGTGTCTCAAA
1 AAGGACCACATAAAAATTCCTTAAGAACAATATACATATACCAAGGACCAAATAAGTGTCGCAAA
*
829049 AGACCTCATACATGCTCCAAATAATACATATACGTCCCG
66 AGACCTCATACATGCTCCAAAGAATACATATACGTCCCG
* * * *
829088 AAGGACCACGTAGAAAATTCCTTAAGAATC-ATATACATATGCTAAGGACCAAATACGTGTCGC-
1 AAGGACCACATA-AAAATTCCTTAAGAA-CAATATACATATACCAAGGACCAAATAAGTGTCGCA
* * * * * *
829151 AAAGAACCTCATAGATGTTCCATAGGATACCTATATGTCCCG
64 AAAG-ACCTCATACATGCTCCAAAGAATACATATACGTCCCG
829193 A
1 A
829194 CCGCGTAGAC
Statistics
Matches: 88, Mismatches: 15, Indels: 5
0.81 0.14 0.05
Matches are distributed among these distances:
104 15 0.17
105 72 0.82
106 1 0.01
ACGTcount: A:0.40, C:0.22, G:0.14, T:0.23
Consensus pattern (104 bp):
AAGGACCACATAAAAATTCCTTAAGAACAATATACATATACCAAGGACCAAATAAGTGTCGCAAA
AGACCTCATACATGCTCCAAAGAATACATATACGTCCCG
Found at i:833335 original size:19 final size:20
Alignment explanation
Indices: 833294--833339 Score: 58
Period size: 20 Copynumber: 2.3 Consensus size: 20
833284 GGATTATGAG
* *
833294 AAATTATTTTTAAAATATAA
1 AAATGATTTTCAAAATATAA
833314 AAATGATTTTCAAAAT-TGAA
1 AAATGATTTTCAAAATAT-AA
833334 AAATGA
1 AAATGA
833340 AAATAAATAT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
19 1 0.04
20 22 0.96
ACGTcount: A:0.54, C:0.02, G:0.07, T:0.37
Consensus pattern (20 bp):
AAATGATTTTCAAAATATAA
Found at i:833999 original size:19 final size:19
Alignment explanation
Indices: 833975--834013 Score: 69
Period size: 19 Copynumber: 2.1 Consensus size: 19
833965 TCGAATGCAT
833975 TCCATGCACCGATGCACTC
1 TCCATGCACCGATGCACTC
*
833994 TCCATGCATCGATGCACTC
1 TCCATGCACCGATGCACTC
834013 T
1 T
834014 GAATACTTTC
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.21, C:0.38, G:0.15, T:0.26
Consensus pattern (19 bp):
TCCATGCACCGATGCACTC
Found at i:834030 original size:65 final size:64
Alignment explanation
Indices: 833912--834121 Score: 205
Period size: 65 Copynumber: 3.2 Consensus size: 64
833902 TATTCAAAGG
* *
833912 CATGCACCGATGCA-TCAGTCCATGCATCGATGCA-TCGATGAATTAATT-GAACATCGAATGCA
1 CATGCACCGATGCACTC--TCCATGCATCGATGCACTC-ATGAA-TATTTCAAACATCGAATGCA
*
833974 TTC
62 TTT
833977 CATGCACCGATGCACTCTCCATGCATCGATGCACTC-TGAATACTTTCAAAACATCGAATGCATT
1 CATGCACCGATGCACTCTCCATGCATCGATGCACTCATGAATA-TTTC-AAACATCGAATGCATT
834041 T
64 T
* * *** * * *
834042 GATGCATCGATGCACAAGCCATGCATCGATGCAC-CAGGCTATTTTTTCAAACATCGAATGCATT
1 CATGCACCGATGCACTCTCCATGCATCGATGCACTCATG--AATATTTCAAACATCGAATGCATT
834106 T
64 T
*
834107 CATGCATCGATGCAC
1 CATGCACCGATGCAC
834122 ACTTGGTGCA
Statistics
Matches: 125, Mismatches: 12, Indels: 16
0.82 0.08 0.10
Matches are distributed among these distances:
62 2 0.02
63 6 0.05
64 17 0.14
65 92 0.74
66 6 0.05
67 2 0.02
ACGTcount: A:0.30, C:0.27, G:0.17, T:0.27
Consensus pattern (64 bp):
CATGCACCGATGCACTCTCCATGCATCGATGCACTCATGAATATTTCAAACATCGAATGCATTT
Found at i:836924 original size:175 final size:178
Alignment explanation
Indices: 836632--836992 Score: 665
Period size: 175 Copynumber: 2.0 Consensus size: 178
836622 TATGCCTATT
836632 GGAAAAATATAATGATGTACTTTATTCAAGCAAGTGACATGGGAGCATGGAATGTCGTAGAAGAA
1 GGAAAAATATAATGATGTACTTTATTCAAGCAAGTGACATGGGAGCATGGAATGTCGTAGAAGAA
836697 GGATACTTCAAGCCTCTCACTCATCCAAGATTATGGAGTGAAGGAGAAACAAAAATGTTCCAGCT
66 GGATACTTCAAGCCTCTCACTCATCCAAGATTATGGAGTGAAGGAGAAACAAAAATGTTCCAGCT
836762 CAACTTC-AG-CCATATTATATTTTGTGCTCTTGGACCAGATGAATAC
131 CAACTTCAAGCCCATATTATATTTTGTGCTCTTGGACCAGATGAATAC
836808 GGAAAAATATAATGATGTAC-TTATTCAAGCAAGTGACATGGGAGCATGGAATGTCGTAGAAGAA
1 GGAAAAATATAATGATGTACTTTATTCAAGCAAGTGACATGGGAGCATGGAATGTCGTAGAAGAA
836872 GGATACTTCAAGCCTCTCACTCATCCAAGATTATGGAGTGAAGGAGAAACAAAAATGTTCCAGCT
66 GGATACTTCAAGCCTCTCACTCATCCAAGATTATGGAGTGAAGGAGAAACAAAAATGTTCCAGCT
836937 CAACTTCAAAGCCATCCATATTATATTTTGTGCTCTTGGACCAGATGAATAC
131 CAACTTC-AAG-C--CCATATTATATTTTGTGCTCTTGGACCAGATGAATAC
836989 GGAA
1 GGAA
836993 GAGTTTCATC
Statistics
Matches: 179, Mismatches: 0, Indels: 7
0.96 0.00 0.04
Matches are distributed among these distances:
175 116 0.65
176 20 0.11
177 2 0.01
181 41 0.23
ACGTcount: A:0.36, C:0.17, G:0.21, T:0.26
Consensus pattern (178 bp):
GGAAAAATATAATGATGTACTTTATTCAAGCAAGTGACATGGGAGCATGGAATGTCGTAGAAGAA
GGATACTTCAAGCCTCTCACTCATCCAAGATTATGGAGTGAAGGAGAAACAAAAATGTTCCAGCT
CAACTTCAAGCCCATATTATATTTTGTGCTCTTGGACCAGATGAATAC
Found at i:838561 original size:19 final size:19
Alignment explanation
Indices: 838537--838575 Score: 69
Period size: 19 Copynumber: 2.1 Consensus size: 19
838527 TCGAATGCAT
838537 TCCATGCACCGATGCACTC
1 TCCATGCACCGATGCACTC
*
838556 TCCATGCATCGATGCACTC
1 TCCATGCACCGATGCACTC
838575 T
1 T
838576 GAATACTTTC
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.21, C:0.38, G:0.15, T:0.26
Consensus pattern (19 bp):
TCCATGCACCGATGCACTC
Found at i:838700 original size:64 final size:65
Alignment explanation
Indices: 838524--838685 Score: 211
Period size: 65 Copynumber: 2.5 Consensus size: 65
838514 AATTAATTGT
* * * *
838524 ACATCGAATGCATTCCATGCACCGATGCACTCTCCATGCATCGATGCACTCTGAATACTTTCAAA
1 ACATCGAATGCATTTCATGCATCGATGCACACTCCATGCATCGATGCACTCAGAATACTTTCAAA
* ** ** *
838589 ACATCGAATGCATTTGATGCATCGATGCACAAGCCATGCATCGATGCAC-CAGGCTATTTTTC-A
1 ACATCGAATGCATTTCATGCATCGATGCACACTCCATGCATCGATGCACTCAGAATA-CTTTCAA
838652 A
65 A
838653 ACATCGAATGCATTTCATGCATCGATGCACACT
1 ACATCGAATGCATTTCATGCATCGATGCACACT
838686 TGGTGCACCG
Statistics
Matches: 83, Mismatches: 13, Indels: 3
0.84 0.13 0.03
Matches are distributed among these distances:
64 36 0.43
65 47 0.57
ACGTcount: A:0.30, C:0.28, G:0.16, T:0.27
Consensus pattern (65 bp):
ACATCGAATGCATTTCATGCATCGATGCACACTCCATGCATCGATGCACTCAGAATACTTTCAAA
Found at i:843831 original size:65 final size:66
Alignment explanation
Indices: 843726--843856 Score: 246
Period size: 65 Copynumber: 2.0 Consensus size: 66
843716 ATTATCTACC
843726 ACTGAAGCGGAATACATTTCAGCCGGTAGTTGTTGGGCACAAGTTTTATGGACGAAACAA-AACT
1 ACTGAAGCGGAATACATTTCAGCCGGTAGTTGTTGGGCACAAGTTTTATGGACGAAACAACAACT
843790 T
66 T
*
843791 ACTGAAGCGGAATACATTTCAGCCGGTAGTTGTTGTGCACAAGTTTTATGGACGAAACAACAACT
1 ACTGAAGCGGAATACATTTCAGCCGGTAGTTGTTGGGCACAAGTTTTATGGACGAAACAACAACT
843856 T
66 T
843857 TTTGATTATG
Statistics
Matches: 64, Mismatches: 1, Indels: 1
0.97 0.02 0.02
Matches are distributed among these distances:
65 59 0.92
66 5 0.08
ACGTcount: A:0.32, C:0.18, G:0.24, T:0.27
Consensus pattern (66 bp):
ACTGAAGCGGAATACATTTCAGCCGGTAGTTGTTGGGCACAAGTTTTATGGACGAAACAACAACT
T
Found at i:845910 original size:19 final size:19
Alignment explanation
Indices: 845886--845924 Score: 69
Period size: 19 Copynumber: 2.1 Consensus size: 19
845876 TCGAATGCAT
845886 TCCATGCACCGATGCACTC
1 TCCATGCACCGATGCACTC
*
845905 TCCATGCATCGATGCACTC
1 TCCATGCACCGATGCACTC
845924 T
1 T
845925 GAATACTTTC
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.21, C:0.38, G:0.15, T:0.26
Consensus pattern (19 bp):
TCCATGCACCGATGCACTC
Found at i:846032 original size:64 final size:65
Alignment explanation
Indices: 845872--846032 Score: 200
Period size: 65 Copynumber: 2.5 Consensus size: 65
845862 GAATTAATTG
* * *** *
845872 AACATCGAATGCATTCCATGCACCGATGCACTCTCCATGCATCGATGCACTCTGAATACTTTCAA
1 AACATCGAATGCATTTCATGCATCGATGCACAAGCCATGCATCGATGCACTCAGAATACTTTCAA
* ** *
845937 AACATCGAATGCATTTGATGCATCGATGCACAAGCCATGCATCGATGCAC-CAGGCTATTTTTC-
1 AACATCGAATGCATTTCATGCATCGATGCACAAGCCATGCATCGATGCACTCAGAATA-CTTTCA
846000 A
65 A
*
846001 AACATCAAATGCATTTCATGCATCGATGCACA
1 AACATCGAATGCATTTCATGCATCGATGCACA
846033 CTTGGTGCAC
Statistics
Matches: 83, Mismatches: 12, Indels: 3
0.85 0.12 0.03
Matches are distributed among these distances:
64 35 0.42
65 48 0.58
ACGTcount: A:0.31, C:0.27, G:0.16, T:0.26
Consensus pattern (65 bp):
AACATCGAATGCATTTCATGCATCGATGCACAAGCCATGCATCGATGCACTCAGAATACTTTCAA
Found at i:857008 original size:105 final size:105
Alignment explanation
Indices: 856801--857023 Score: 250
Period size: 105 Copynumber: 2.1 Consensus size: 105
856791 GATTGTCCAT
* * * * * *
856801 AATGACCACATA-TAAATTTCTTAAGAACCATATACATATACCAAGGATCAAGTAAGTGTCTCAA
1 AATGACCACGTAGAAAATTCCTTAAGAACCATATACATATACCAAGGACCAAATAAGTGTCGCAA
856865 AAGACCTCATACAGGCTCCAAAGAATACATATACGTCCCG
66 AAGACCTCATACAGGCTCCAAAGAATACATATACGTCCCG
** * * *
856905 AATGACCACGTAGAAAATTCCTTAAGAATTATATACATATGCTAAGGACCAAATACGTGTCGCAA
1 AATGACCACGTAGAAAATTCCTTAAGAACCATATACATATACCAAGGACCAAATAAGTGTCGCAA
* * * * * * * *
856970 AGGACCTCATAGATGTTCCATAGGATACCTATATGTCCCG
66 AAGACCTCATACAGGCTCCAAAGAATACATATACGTCCCG
* *
857010 AAGGACCGCGTAGA
1 AATGACCACGTAGA
857024 CCCTCGACTC
Statistics
Matches: 97, Mismatches: 21, Indels: 1
0.82 0.18 0.01
Matches are distributed among these distances:
104 11 0.11
105 86 0.89
ACGTcount: A:0.39, C:0.22, G:0.16, T:0.23
Consensus pattern (105 bp):
AATGACCACGTAGAAAATTCCTTAAGAACCATATACATATACCAAGGACCAAATAAGTGTCGCAA
AAGACCTCATACAGGCTCCAAAGAATACATATACGTCCCG
Found at i:858546 original size:21 final size:21
Alignment explanation
Indices: 858520--858560 Score: 82
Period size: 21 Copynumber: 2.0 Consensus size: 21
858510 CAATTCCTGT
858520 TTGAATGGGTACCGATTCCCA
1 TTGAATGGGTACCGATTCCCA
858541 TTGAATGGGTACCGATTCCC
1 TTGAATGGGTACCGATTCCC
858561 CTAGCCCAGA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.22, C:0.24, G:0.24, T:0.29
Consensus pattern (21 bp):
TTGAATGGGTACCGATTCCCA
Found at i:861748 original size:231 final size:231
Alignment explanation
Indices: 861345--861802 Score: 871
Period size: 231 Copynumber: 2.0 Consensus size: 231
861335 CCTTTGGGTT
* *
861345 TTTTTTTTTACAGAAGCACACATACATTTCATACATACAAAGAGAAGGTTGTTTTTTTTATTTCA
1 TTTTTTTTGACAGAAGCACACATACATTTCATACATACAAAGAGAAGGTTGTTTTTGTTATTTCA
*
861410 ATAACGGCGGAAGCAAAGGTAATGACAGTGTCCCATGAATCATAAACAACACTAGTTTTCCAGTC
66 ATAACGGCGGAAGCAAAGGTAATGACAGTGTCCCATGAATCATAAACAACACTAGTGTTCCAGTC
861475 AGCATATACTTTACCCAAATCCACCTGCTTCCATACCCAGAAATGACCTTGAATCTGAATTGCAA
131 AGCATATACTTTACCCAAATCCACCTGCTTCCATACCCAGAAATGACCTTGAATCTGAATTGCAA
*
861540 GGCACCATTGTTTGCATCTCAAACGGCCCCATGGGG
196 GGCACCATTGTTTGCATCTCAAACAGCCCCATGGGG
*
861576 TTTTTTTTGACAGAAGCACACATACATTTCATATATACAAAGAGAAGGTTGTTTTTGTTATTTCA
1 TTTTTTTTGACAGAAGCACACATACATTTCATACATACAAAGAGAAGGTTGTTTTTGTTATTTCA
861641 ATAACGGCGGAAGCAAAGGTAATGACAGTGTCCCATGAATCATAAACAACACTAGTGTTCCAGTC
66 ATAACGGCGGAAGCAAAGGTAATGACAGTGTCCCATGAATCATAAACAACACTAGTGTTCCAGTC
861706 AGCATATACTTTACCCAAATCCACCTGCTTCCATACCCAGAAATGACCTTGAATCTGAATTGCAA
131 AGCATATACTTTACCCAAATCCACCTGCTTCCATACCCAGAAATGACCTTGAATCTGAATTGCAA
861771 GGCACCATTGTTTGCATCTCAAACAGCCCCAT
196 GGCACCATTGTTTGCATCTCAAACAGCCCCAT
861803 AGCTCGAAGA
Statistics
Matches: 222, Mismatches: 5, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
231 222 1.00
ACGTcount: A:0.33, C:0.23, G:0.16, T:0.29
Consensus pattern (231 bp):
TTTTTTTTGACAGAAGCACACATACATTTCATACATACAAAGAGAAGGTTGTTTTTGTTATTTCA
ATAACGGCGGAAGCAAAGGTAATGACAGTGTCCCATGAATCATAAACAACACTAGTGTTCCAGTC
AGCATATACTTTACCCAAATCCACCTGCTTCCATACCCAGAAATGACCTTGAATCTGAATTGCAA
GGCACCATTGTTTGCATCTCAAACAGCCCCATGGGG
Found at i:863378 original size:27 final size:27
Alignment explanation
Indices: 863348--863436 Score: 144
Period size: 27 Copynumber: 3.3 Consensus size: 27
863338 GATAGGCACA
863348 AATAAAATTTTCAGAGTTGGCACCATC
1 AATAAAATTTTCAGAGTTGGCACCATC
*
863375 AATAAAATTTTCAGA-TTGAACACCATC
1 AATAAAATTTTCAGAGTTG-GCACCATC
*
863402 AATAAAATTTTCAGAGTGGGCACCATC
1 AATAAAATTTTCAGAGTTGGCACCATC
863429 AATAAAAT
1 AATAAAAT
863437 AAACAGCTAA
Statistics
Matches: 57, Mismatches: 3, Indels: 4
0.89 0.05 0.06
Matches are distributed among these distances:
26 3 0.05
27 52 0.91
28 2 0.04
ACGTcount: A:0.43, C:0.17, G:0.12, T:0.28
Consensus pattern (27 bp):
AATAAAATTTTCAGAGTTGGCACCATC
Found at i:865611 original size:34 final size:34
Alignment explanation
Indices: 865566--865656 Score: 128
Period size: 34 Copynumber: 2.7 Consensus size: 34
865556 TGCAATACAT
* *
865566 TTTTATTAATCAAGGAATTCTTGGTAATAAGACA
1 TTTTCTTAATCAAGGAATTCTTGGCAATAAGACA
* * *
865600 TTTTCTTAATCAAGGAATTCTTGGCAGTAATATA
1 TTTTCTTAATCAAGGAATTCTTGGCAATAAGACA
*
865634 TTTTCTTAATCAAGGAACTCTTG
1 TTTTCTTAATCAAGGAATTCTTG
865657 TAACGAAACT
Statistics
Matches: 51, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
34 51 1.00
ACGTcount: A:0.33, C:0.12, G:0.14, T:0.41
Consensus pattern (34 bp):
TTTTCTTAATCAAGGAATTCTTGGCAATAAGACA
Found at i:867871 original size:24 final size:24
Alignment explanation
Indices: 867843--867921 Score: 113
Period size: 24 Copynumber: 3.3 Consensus size: 24
867833 TCTTAAACTT
*
867843 AACTCGATTAAAGTCTCAAACTCA
1 AACTCGATTGAAGTCTCAAACTCA
* *
867867 AACTCTATTGAAGTCTTAAACTCA
1 AACTCGATTGAAGTCTCAAACTCA
* *
867891 AACTCCATTGAAGTCTCAAACTCG
1 AACTCGATTGAAGTCTCAAACTCA
867915 AACTCGA
1 AACTCGA
867922 ACCTTAAATA
Statistics
Matches: 48, Mismatches: 7, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 48 1.00
ACGTcount: A:0.38, C:0.25, G:0.10, T:0.27
Consensus pattern (24 bp):
AACTCGATTGAAGTCTCAAACTCA
Found at i:868528 original size:2 final size:2
Alignment explanation
Indices: 868481--868511 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
868471 TTTAAATTTA
868481 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 A
868512 AATTAAAGAT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:868742 original size:19 final size:19
Alignment explanation
Indices: 868718--868754 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
868708 ATACTTATAC
868718 CTTTTATAATTTCATAGAA
1 CTTTTATAATTTCATAGAA
*
868737 CTTTTATAATTTTATAGA
1 CTTTTATAATTTCATAGA
868755 TTTATGAAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.35, C:0.08, G:0.05, T:0.51
Consensus pattern (19 bp):
CTTTTATAATTTCATAGAA
Found at i:870909 original size:60 final size:58
Alignment explanation
Indices: 870796--870953 Score: 147
Period size: 60 Copynumber: 2.6 Consensus size: 58
870786 ACATATAGTT
* * * * * * *
870796 GGGATGAAATTATAATGTTCAAAAAGTTTGGGGTCCAATTTAGAATGCAAGTCATAGTTTG
1 GGGATGAAATTA-AATGTT-TAAAA-TTTAGGGACTAATCTAGAATGCAAGTCATAGCTTA
870857 GGGATGAAATTGAAATGTTTAAAACTTTAGGGACTAATCTAGAATG-ATAGTCATAGCTTA
1 GGGATGAAATT-AAATGTTTAAAA-TTTAGGGACTAATCTAGAATGCA-AGTCATAGCTTA
** * *
870917 ATGATGAAATTAAAATATTTAAAATTTAGGGATTAAT
1 GGGATGAAATT-AAATGTTTAAAATTTAGGGACTAAT
870954 TTAAAATGTG
Statistics
Matches: 82, Mismatches: 13, Indels: 6
0.81 0.13 0.06
Matches are distributed among these distances:
59 13 0.16
60 51 0.62
61 17 0.21
62 1 0.01
ACGTcount: A:0.39, C:0.06, G:0.21, T:0.34
Consensus pattern (58 bp):
GGGATGAAATTAAATGTTTAAAATTTAGGGACTAATCTAGAATGCAAGTCATAGCTTA
Found at i:894080 original size:21 final size:22
Alignment explanation
Indices: 894069--894158 Score: 84
Period size: 21 Copynumber: 4.3 Consensus size: 22
894059 ATTTTGGACT
894069 ATCGCAACGCGAACTTGGAATAA
1 ATCGCAACGCGAACTTGGAAT-A
*
894092 ATCGCAA--CGAATTTGGAATAA
1 ATCGCAACGCGAACTTGGAAT-A
* *
894113 ATCGCAACGCGAACTTCGACT-
1 ATCGCAACGCGAACTTGGAATA
*
894134 ATCGCAA--CGAATTTGGAA-A
1 ATCGCAACGCGAACTTGGAATA
894153 ATCGCA
1 ATCGCA
894159 TTGCGATAGT
Statistics
Matches: 57, Mismatches: 7, Indels: 10
0.77 0.09 0.14
Matches are distributed among these distances:
19 14 0.25
21 27 0.47
23 16 0.28
ACGTcount: A:0.38, C:0.22, G:0.20, T:0.20
Consensus pattern (22 bp):
ATCGCAACGCGAACTTGGAATA
Found at i:894099 original size:23 final size:23
Alignment explanation
Indices: 894069--894128 Score: 97
Period size: 21 Copynumber: 2.7 Consensus size: 23
894059 ATTTTGGACT
894069 ATCGCAACGCGAACTTGGAATAA
1 ATCGCAACGCGAACTTGGAATAA
*
894092 ATCGCAA--CGAATTTGGAATAA
1 ATCGCAACGCGAACTTGGAATAA
894113 ATCGCAACGCGAACTT
1 ATCGCAACGCGAACTT
894129 CGACTATCGC
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
21 20 0.61
23 13 0.39
ACGTcount: A:0.38, C:0.22, G:0.20, T:0.20
Consensus pattern (23 bp):
ATCGCAACGCGAACTTGGAATAA
Found at i:894108 original size:42 final size:41
Alignment explanation
Indices: 894061--894158 Score: 128
Period size: 42 Copynumber: 2.4 Consensus size: 41
894051 TCGTTGCGAT
* *
894061 TTTGGACT-ATCGCAACGCGAACTTGGAATAAATCGCAACGAA
1 TTTGGAATAATCGCAACGCGAACTTCGAAT--ATCGCAACGAA
*
894103 TTTGGAATAAATCGCAACGCGAACTTCGACTATCGCAACGAA
1 TTTGGAAT-AATCGCAACGCGAACTTCGAATATCGCAACGAA
894145 TTTGGAA-AATCGCA
1 TTTGGAATAATCGCA
894159 TTGCGATAGT
Statistics
Matches: 51, Mismatches: 3, Indels: 6
0.85 0.05 0.10
Matches are distributed among these distances:
40 7 0.14
42 25 0.49
44 19 0.37
ACGTcount: A:0.36, C:0.21, G:0.20, T:0.22
Consensus pattern (41 bp):
TTTGGAATAATCGCAACGCGAACTTCGAATATCGCAACGAA
Found at i:894123 original size:44 final size:40
Alignment explanation
Indices: 894069--894158 Score: 126
Period size: 44 Copynumber: 2.1 Consensus size: 40
894059 ATTTTGGACT
*
894069 ATCGCAACGCGAACTTGGAATAAATCGCAACGAATTTGGAATAA
1 ATCGCAACGCGAACTTCGAAT--ATCGCAACGAATTTGG-A-AA
*
894113 ATCGCAACGCGAACTTCGACTATCGCAACGAATTTGGAAA
1 ATCGCAACGCGAACTTCGAATATCGCAACGAATTTGGAAA
894153 ATCGCA
1 ATCGCA
894159 TTGCGATAGT
Statistics
Matches: 44, Mismatches: 2, Indels: 4
0.88 0.04 0.08
Matches are distributed among these distances:
40 8 0.18
41 1 0.02
42 16 0.36
44 19 0.43
ACGTcount: A:0.38, C:0.22, G:0.20, T:0.20
Consensus pattern (40 bp):
ATCGCAACGCGAACTTCGAATATCGCAACGAATTTGGAAA
Found at i:898735 original size:2 final size:2
Alignment explanation
Indices: 898728--898756 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
898718 TTCTTTTAAA
898728 AC AC AC AC AC AC AC AC AC AC AC AC AC AC A
1 AC AC AC AC AC AC AC AC AC AC AC AC AC AC A
898757 TATATATATA
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:0.52, C:0.48, G:0.00, T:0.00
Consensus pattern (2 bp):
AC
Found at i:898761 original size:2 final size:2
Alignment explanation
Indices: 898756--898797 Score: 77
Period size: 2 Copynumber: 21.5 Consensus size: 2
898746 ACACACACAC
898756 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A- 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
898797 A
1 A
898798 CCCCCATCCG
Statistics
Matches: 39, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.03
2 38 0.97
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:898985 original size:24 final size:24
Alignment explanation
Indices: 898958--899068 Score: 89
Period size: 24 Copynumber: 4.7 Consensus size: 24
898948 TATATCAAAA
* *
898958 ATCAAAACATATTTCAGGTCAAGT
1 ATCAAAACAGAATTCAGGTCAAGT
* * *
898982 ATCATATCAGAATTCAGGTCATGT
1 ATCAAAACAGAATTCAGGTCAAGT
* * * *
899006 ATCAGATCAGAATCCATGTCAA-T
1 ATCAAAACAGAATTCAGGTCAAGT
* * * *
899029 ATCAGATCAGAATCCAGGTCAGGT
1 ATCAAAACAGAATTCAGGTCAAGT
*
899053 ATCATAACAGAATTCA
1 ATCAAAACAGAATTCA
899069 AATCGGAAAT
Statistics
Matches: 72, Mismatches: 14, Indels: 2
0.82 0.16 0.02
Matches are distributed among these distances:
23 21 0.29
24 51 0.71
ACGTcount: A:0.39, C:0.19, G:0.15, T:0.27
Consensus pattern (24 bp):
ATCAAAACAGAATTCAGGTCAAGT
Found at i:899035 original size:23 final size:23
Alignment explanation
Indices: 898972--899049 Score: 102
Period size: 24 Copynumber: 3.3 Consensus size: 23
898962 AAACATATTT
* *
898972 CAGGTCAAGTATCATATCAGAATT
1 CAGGTCAA-TATCAGATCAGAATC
*
898996 CAGGTCATGTATCAGATCAGAATC
1 CAGGTCA-ATATCAGATCAGAATC
*
899020 CATGTCAATATCAGATCAGAATC
1 CAGGTCAATATCAGATCAGAATC
899043 CAGGTCA
1 CAGGTCA
899050 GGTATCATAA
Statistics
Matches: 47, Mismatches: 6, Indels: 3
0.84 0.11 0.05
Matches are distributed among these distances:
23 21 0.45
24 26 0.55
ACGTcount: A:0.36, C:0.21, G:0.18, T:0.26
Consensus pattern (23 bp):
CAGGTCAATATCAGATCAGAATC
Found at i:899047 original size:47 final size:48
Alignment explanation
Indices: 898975--899065 Score: 130
Period size: 47 Copynumber: 1.9 Consensus size: 48
898965 CATATTTCAG
* * * *
898975 GTCAAGTATCATATCAGAATTCAGGTCATGTATCAGATCAGAATCCAT
1 GTCAAGTATCAGATCAGAATCCAGGTCAGGTATCAGAACAGAATCCAT
*
899023 GTCAA-TATCAGATCAGAATCCAGGTCAGGTATCATAACAGAAT
1 GTCAAGTATCAGATCAGAATCCAGGTCAGGTATCAGAACAGAAT
899066 TCAAATCGGA
Statistics
Matches: 38, Mismatches: 5, Indels: 1
0.86 0.11 0.02
Matches are distributed among these distances:
47 33 0.87
48 5 0.13
ACGTcount: A:0.37, C:0.19, G:0.18, T:0.26
Consensus pattern (48 bp):
GTCAAGTATCAGATCAGAATCCAGGTCAGGTATCAGAACAGAATCCAT
Found at i:900329 original size:23 final size:23
Alignment explanation
Indices: 900303--900347 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
900293 CACCACAGCT
*
900303 CGTATAAATGCACCGAAGTGCCC
1 CGTAGAAATGCACCGAAGTGCCC
* *
900326 CGTAGAATTGCACCGTAGTGCC
1 CGTAGAAATGCACCGAAGTGCC
900348 ATATAATGAT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.27, C:0.29, G:0.24, T:0.20
Consensus pattern (23 bp):
CGTAGAAATGCACCGAAGTGCCC
Found at i:901542 original size:22 final size:23
Alignment explanation
Indices: 901517--901562 Score: 67
Period size: 23 Copynumber: 2.0 Consensus size: 23
901507 TAATTCAATT
*
901517 TCATATAAC-TCCTATAATCTTC
1 TCATATAACTTCATATAATCTTC
*
901539 TCATATAACTTCATATAATTTTC
1 TCATATAACTTCATATAATCTTC
901562 T
1 T
901563 ATCATACAAC
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
22 9 0.43
23 12 0.57
ACGTcount: A:0.33, C:0.22, G:0.00, T:0.46
Consensus pattern (23 bp):
TCATATAACTTCATATAATCTTC
Found at i:902262 original size:21 final size:21
Alignment explanation
Indices: 902232--902276 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
902222 ATTCTGTCGT
* *
902232 TTGAAGGGGTATCGGTTCCCC
1 TTGAAGGGGTACCGATTCCCC
*
902253 TTGAATGGGTACCGATTCCCC
1 TTGAAGGGGTACCGATTCCCC
902274 TTG
1 TTG
902277 CCCAGAAATC
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.16, C:0.24, G:0.29, T:0.31
Consensus pattern (21 bp):
TTGAAGGGGTACCGATTCCCC
Found at i:905482 original size:23 final size:23
Alignment explanation
Indices: 905456--905500 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
905446 CACCACAGCT
*
905456 CGTATAAATGCACCGAAGTGCCC
1 CGTAGAAATGCACCGAAGTGCCC
* *
905479 CGTAGAATTGCACCGTAGTGCC
1 CGTAGAAATGCACCGAAGTGCC
905501 ATATAATGAT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.27, C:0.29, G:0.24, T:0.20
Consensus pattern (23 bp):
CGTAGAAATGCACCGAAGTGCCC
Found at i:905738 original size:149 final size:149
Alignment explanation
Indices: 905479--905780 Score: 568
Period size: 149 Copynumber: 2.0 Consensus size: 149
905469 CGAAGTGCCC
* *
905479 CGTAGAATTGCACCGTAGTGCCATATAATGATGTCCATAAGGACCACGTAGAATTCTTTAAGAAT
1 CGTAGAATTGCACCGTAGTGCCATATAATAATGTCCATAAGGACCACATAGAATTCTTTAAGAAT
905544 CATATACATATGCTAGGGATCAAGTATGTGTCTTTCCAGACTTCACACATGTTCCAAAGAATATA
66 CATATACATATGCTAGGGATCAAGTATGTGTCTTTCCAGACTTCACACATGTTCCAAAGAATATA
905609 CATATGTCCCGAAGAACCG
131 CATATGTCCCGAAGAACCG
*
905628 CGTAGAATTGCACCTTAGTGCCATATAATAATGTCCATAAGGACCACATAGAATTCTTTAAGAAT
1 CGTAGAATTGCACCGTAGTGCCATATAATAATGTCCATAAGGACCACATAGAATTCTTTAAGAAT
905693 CATATACATATGCTAGGGATCAAGTATGTGTCTTTCCAGACTTCACACATGTTCCAAAGAATATA
66 CATATACATATGCTAGGGATCAAGTATGTGTCTTTCCAGACTTCACACATGTTCCAAAGAATATA
*
905758 CATATGTCTCGAAGAACCG
131 CATATGTCCCGAAGAACCG
905777 CGTA
1 CGTA
905781 ACCCTCGACT
Statistics
Matches: 149, Mismatches: 4, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
149 149 1.00
ACGTcount: A:0.34, C:0.21, G:0.17, T:0.28
Consensus pattern (149 bp):
CGTAGAATTGCACCGTAGTGCCATATAATAATGTCCATAAGGACCACATAGAATTCTTTAAGAAT
CATATACATATGCTAGGGATCAAGTATGTGTCTTTCCAGACTTCACACATGTTCCAAAGAATATA
CATATGTCCCGAAGAACCG
Found at i:906427 original size:2 final size:2
Alignment explanation
Indices: 906420--906452 Score: 59
Period size: 2 Copynumber: 17.0 Consensus size: 2
906410 TCTCTTAGAC
906420 AT AT AT AT AT AT AT AT AT AT A- AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
906453 TCACATGTCG
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 29 0.97
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:907419 original size:21 final size:21
Alignment explanation
Indices: 907389--907433 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
907379 ATTCTGTCGT
* *
907389 TTGAAGGGGTATCGGTTCCCC
1 TTGAAGGGGTACCGATTCCCC
*
907410 TTGAATGGGTACCGATTCCCC
1 TTGAAGGGGTACCGATTCCCC
907431 TTG
1 TTG
907434 CCCAGAAATC
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.16, C:0.24, G:0.29, T:0.31
Consensus pattern (21 bp):
TTGAAGGGGTACCGATTCCCC
Found at i:910282 original size:20 final size:20
Alignment explanation
Indices: 910259--910302 Score: 70
Period size: 20 Copynumber: 2.2 Consensus size: 20
910249 TTCTTTTCCA
910259 CAACGCGAATATGTAAATCG
1 CAACGCGAATATGTAAATCG
* *
910279 CAACGCGAATTTGTAATTCG
1 CAACGCGAATATGTAAATCG
910299 CAAC
1 CAAC
910303 ACAGAAGTCA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.36, C:0.23, G:0.18, T:0.23
Consensus pattern (20 bp):
CAACGCGAATATGTAAATCG
Found at i:910893 original size:20 final size:20
Alignment explanation
Indices: 910858--910916 Score: 102
Period size: 20 Copynumber: 3.0 Consensus size: 20
910848 AATTTGCAAC
*
910858 GCGATTTT-AGTTTCGCGTT
1 GCGATTTTCATTTTCGCGTT
910877 GCGATTTTCATTTTCGCGTT
1 GCGATTTTCATTTTCGCGTT
910897 GCGATTTTCATTTTCGCGTT
1 GCGATTTTCATTTTCGCGTT
910917 ACGAATTTAA
Statistics
Matches: 38, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
19 8 0.21
20 30 0.79
ACGTcount: A:0.10, C:0.19, G:0.22, T:0.49
Consensus pattern (20 bp):
GCGATTTTCATTTTCGCGTT
Found at i:910931 original size:20 final size:20
Alignment explanation
Indices: 910861--910931 Score: 79
Period size: 20 Copynumber: 3.5 Consensus size: 20
910851 TTGCAACGCG
*
910861 ATTTTAGTTTCGCGTTGCGA
1 ATTTCAGTTTCGCGTTGCGA
* *
910881 TTTTCATTTTCGCGTTGCGA
1 ATTTCAGTTTCGCGTTGCGA
* * *
910901 TTTTCATTTTCGCGTTACGA
1 ATTTCAGTTTCGCGTTGCGA
*
910921 ATTTAAGTTTC
1 ATTTCAGTTTC
910932 CAAAACTACT
Statistics
Matches: 44, Mismatches: 7, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 44 1.00
ACGTcount: A:0.15, C:0.17, G:0.18, T:0.49
Consensus pattern (20 bp):
ATTTCAGTTTCGCGTTGCGA
Found at i:911851 original size:21 final size:21
Alignment explanation
Indices: 911826--911877 Score: 95
Period size: 21 Copynumber: 2.5 Consensus size: 21
911816 ACTTATTTAT
911826 GAGGACCTAATATTATTGGTA
1 GAGGACCTAATATTATTGGTA
911847 GAGGACCTAATATTATTGGTA
1 GAGGACCTAATATTATTGGTA
*
911868 GATGACCTAA
1 GAGGACCTAA
911878 ATGCATGGAA
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 30 1.00
ACGTcount: A:0.35, C:0.12, G:0.23, T:0.31
Consensus pattern (21 bp):
GAGGACCTAATATTATTGGTA
Found at i:912698 original size:21 final size:21
Alignment explanation
Indices: 912674--912715 Score: 50
Period size: 21 Copynumber: 2.0 Consensus size: 21
912664 TGGTGCATGG
912674 CGTGATGAAGTACGAT-TTTTA
1 CGTGATGAAGTA-GATGTTTTA
* *
912695 CGTGGTGAGGTAGATGTTTTA
1 CGTGATGAAGTAGATGTTTTA
912716 TACGATGACA
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
20 3 0.17
21 15 0.83
ACGTcount: A:0.24, C:0.07, G:0.31, T:0.38
Consensus pattern (21 bp):
CGTGATGAAGTAGATGTTTTA
Found at i:912889 original size:4 final size:4
Alignment explanation
Indices: 912880--912917 Score: 58
Period size: 4 Copynumber: 9.5 Consensus size: 4
912870 TTTTTCGGTA
* *
912880 TTAT TTAT TTAT TTAT TAAT TTAT TTAT TAAT TTAT TT
1 TTAT TTAT TTAT TTAT TTAT TTAT TTAT TTAT TTAT TT
912918 TTAGTGGCCC
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
4 30 1.00
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (4 bp):
TTAT
Found at i:912901 original size:12 final size:12
Alignment explanation
Indices: 912880--912917 Score: 67
Period size: 12 Copynumber: 3.2 Consensus size: 12
912870 TTTTTCGGTA
*
912880 TTATTTATTTAT
1 TTATTAATTTAT
912892 TTATTAATTTAT
1 TTATTAATTTAT
912904 TTATTAATTTAT
1 TTATTAATTTAT
912916 TT
1 TT
912918 TTAGTGGCCC
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
12 25 1.00
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (12 bp):
TTATTAATTTAT
Found at i:913093 original size:21 final size:21
Alignment explanation
Indices: 913067--913179 Score: 151
Period size: 21 Copynumber: 5.4 Consensus size: 21
913057 CCTGTCATCA
913067 TTCAAGAGGCCCCTCCTATCG
1 TTCAAGAGGCCCCTCCTATCG
913088 TTCAAGAGGCCCCT-CTCATCG
1 TTCAAGAGGCCCCTCCT-ATCG
* *
913109 TTCAAGAGGCCCCTCCCACCG
1 TTCAAGAGGCCCCTCCTATCG
913130 TTCAAGAGGCCCCT-CTCATCG
1 TTCAAGAGGCCCCTCCT-ATCG
*
913151 TTCAAGAGGTCCCTCAC-ATCG
1 TTCAAGAGGCCCCTC-CTATCG
913172 TTCAAGAG
1 TTCAAGAG
913180 CCCGATTCAC
Statistics
Matches: 82, Mismatches: 5, Indels: 10
0.85 0.05 0.10
Matches are distributed among these distances:
20 3 0.04
21 77 0.94
22 1 0.01
23 1 0.01
ACGTcount: A:0.21, C:0.37, G:0.19, T:0.22
Consensus pattern (21 bp):
TTCAAGAGGCCCCTCCTATCG
Found at i:913113 original size:42 final size:41
Alignment explanation
Indices: 913061--913179 Score: 184
Period size: 42 Copynumber: 2.8 Consensus size: 41
913051 GATTCACCTG
*
913061 TCATCATTCAAGAGGCCCCTCCTATCGTTCAAGAGGCCCCTC
1 TCATCGTTCAAGAGGCCCCTCC-ATCGTTCAAGAGGCCCCTC
*
913103 TCATCGTTCAAGAGGCCCCTCCCACCGTTCAAGAGGCCCCTC
1 TCATCGTTCAAGAGGCCCCT-CCATCGTTCAAGAGGCCCCTC
*
913145 TCATCGTTCAAGAGGTCCCTCACATCGTTCAAGAG
1 TCATCGTTCAAGAGGCCCCTC-CATCGTTCAAGAG
913180 CCCGATTCAC
Statistics
Matches: 71, Mismatches: 4, Indels: 4
0.90 0.05 0.05
Matches are distributed among these distances:
41 1 0.01
42 68 0.96
43 2 0.03
ACGTcount: A:0.22, C:0.37, G:0.18, T:0.23
Consensus pattern (41 bp):
TCATCGTTCAAGAGGCCCCTCCATCGTTCAAGAGGCCCCTC
Found at i:914783 original size:18 final size:18
Alignment explanation
Indices: 914760--914795 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
914750 AAGCCGGTTG
*
914760 TGATTGGGATTTTGATTT
1 TGATTGCGATTTTGATTT
914778 TGATTGCGATTTTGATTT
1 TGATTGCGATTTTGATTT
914796 CCTTTTACTT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.17, C:0.03, G:0.25, T:0.56
Consensus pattern (18 bp):
TGATTGCGATTTTGATTT
Found at i:918091 original size:20 final size:20
Alignment explanation
Indices: 918065--918233 Score: 92
Period size: 20 Copynumber: 8.4 Consensus size: 20
918055 AAATAAAAGC
918065 TGTTGCGAATTCGAAAATCG
1 TGTTGCGAATTCGAAAATCG
* **
918085 AGTTGCGAAAAC-AAAATTCG
1 TGTTGCGAATTCGAAAA-TCG
* * *
918105 TGTTGCGATTTAGAAAATCT
1 TGTTGCGAATTCGAAAATCG
*** * *
918125 TGTTGCGAAAAGGAAACTTG
1 TGTTGCGAATTCGAAAATCG
*** * *
918145 TGTTGCGAAAAAGAAATTTG
1 TGTTGCGAATTCGAAAATCG
*
918165 CGTTGCGAATTCCG-AAATCG
1 TGTTGCGAATT-CGAAAATCG
* * *
918185 AGTTGTGAATT-GAAATTCG
1 TGTTGCGAATTCGAAAATCG
*
918204 TTGTTGCGAATTTGGAAAATCG
1 -TGTTGCGAA-TTCGAAAATCG
918226 TGTTGCGA
1 TGTTGCGA
918234 GAAAGAAAGT
Statistics
Matches: 112, Mismatches: 30, Indels: 13
0.72 0.19 0.08
Matches are distributed among these distances:
18 1 0.01
19 9 0.08
20 80 0.71
21 15 0.13
22 7 0.06
ACGTcount: A:0.32, C:0.12, G:0.25, T:0.31
Consensus pattern (20 bp):
TGTTGCGAATTCGAAAATCG
Found at i:918121 original size:40 final size:40
Alignment explanation
Indices: 918048--918153 Score: 110
Period size: 40 Copynumber: 2.7 Consensus size: 40
918038 AAACATTTGT
* * *
918048 GTTGCGAAAATAAAA-GC-TGTTGCGAATTCGAAAATCGA
1 GTTGCGAAAACAAAATTCGTGTTGCGAATTAGAAAATCGA
* **
918086 GTTGCGAAAACAAAATTCGTGTTGCGATTTAGAAAATCTT
1 GTTGCGAAAACAAAATTCGTGTTGCGAATTAGAAAATCGA
* *
918126 GTTGCGAAAAGGAAACTT-GTGTTGCGAA
1 GTTGCGAAAA-CAAAATTCGTGTTGCGAA
918154 AAAGAAATTT
Statistics
Matches: 56, Mismatches: 9, Indels: 4
0.81 0.13 0.06
Matches are distributed among these distances:
38 14 0.25
39 1 0.02
40 36 0.64
41 5 0.09
ACGTcount: A:0.36, C:0.12, G:0.25, T:0.27
Consensus pattern (40 bp):
GTTGCGAAAACAAAATTCGTGTTGCGAATTAGAAAATCGA
Found at i:918250 original size:41 final size:39
Alignment explanation
Indices: 918144--918253 Score: 103
Period size: 41 Copynumber: 2.7 Consensus size: 39
918134 AAGGAAACTT
* *
918144 GTGTTGCGAAAAAGAAATTTGCGTTGCGAATTCCGAAATC
1 GTGTTGCG-AAAAGAAATTCGTGTTGCGAATTCCGAAATC
* * ** **
918184 GAGTTGTGAATTGAAATTCGTTGTTGCGAATTTGGAAAATC
1 GTGTTGCGAAAAGAAATTCG-TGTTGCGAATTCCG-AAATC
*
918225 GTGTTGCGAGAAAGAAAGTCGTGTTGCGA
1 GTGTTGCGA-AAAGAAATTCGTGTTGCGA
918254 TTGCAGAAAC
Statistics
Matches: 54, Mismatches: 13, Indels: 5
0.75 0.18 0.07
Matches are distributed among these distances:
39 9 0.17
40 17 0.31
41 20 0.37
42 8 0.15
ACGTcount: A:0.30, C:0.11, G:0.29, T:0.30
Consensus pattern (39 bp):
GTGTTGCGAAAAGAAATTCGTGTTGCGAATTCCGAAATC
Found at i:924961 original size:50 final size:50
Alignment explanation
Indices: 924842--924967 Score: 171
Period size: 50 Copynumber: 2.5 Consensus size: 50
924832 GTAGCAGTAA
* *
924842 AGCGCGCCCCCTGAACCACGCTATACGCTGATTTGGCACCACGTGGGTAT
1 AGCGCGCCCCCTGAACCGCGCTATACGCTGATCTGGCACCACGTGGGTAT
* * ** * *
924892 AGCACGCCCCTTGCCCCGCGATATACGGTGATCTGGCACCACGTGGGTAT
1 AGCGCGCCCCCTGAACCGCGCTATACGCTGATCTGGCACCACGTGGGTAT
*
924942 AGCGCGCCCCCTGATCCGCGCTATAC
1 AGCGCGCCCCCTGAACCGCGCTATAC
924968 CTGGGTATCT
Statistics
Matches: 63, Mismatches: 13, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
50 63 1.00
ACGTcount: A:0.18, C:0.37, G:0.26, T:0.19
Consensus pattern (50 bp):
AGCGCGCCCCCTGAACCGCGCTATACGCTGATCTGGCACCACGTGGGTAT
Found at i:925105 original size:10 final size:10
Alignment explanation
Indices: 925090--925129 Score: 55
Period size: 10 Copynumber: 4.0 Consensus size: 10
925080 TTTATCACAC
925090 CAAATTCTCT
1 CAAATTCTCT
925100 CAAATTCTCT
1 CAAATTCTCT
925110 -AAATTTCTCT
1 CAAA-TTCTCT
*
925120 CAAATACTCT
1 CAAATTCTCT
925130 ATCTTTTTAA
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
9 3 0.11
10 21 0.78
11 3 0.11
ACGTcount: A:0.33, C:0.28, G:0.00, T:0.40
Consensus pattern (10 bp):
CAAATTCTCT
Found at i:925448 original size:111 final size:111
Alignment explanation
Indices: 925254--925475 Score: 381
Period size: 111 Copynumber: 2.0 Consensus size: 111
925244 TAGAAATCAT
*
925254 ATATCTCTACACTTTACTGATACAGTAACATTTTAACGTTTTAATTTAATTTAAATTATTAGTAA
1 ATATCTCGACACTTTACTGATACAGTAACATTTTAACGTTTTAATTTAATTTAAATTATTAGTAA
* *
925319 TATTTAGTTGATTTATTTAATGCATTATTATTAGATTAAGAATTAA
66 TAATTAGTTGATTTATTTAATGCATGATTATTAGATTAAGAATTAA
** * *
925365 ATATCTCGACACTTTGTTGATACGGTAACATTTTAACGTTTTAATTTAATTTAAATTATTAGTGA
1 ATATCTCGACACTTTACTGATACAGTAACATTTTAACGTTTTAATTTAATTTAAATTATTAGTAA
925430 TAATTAGTTGATTTATTTAATGCATGATTATTAGATTAAGAATTAA
66 TAATTAGTTGATTTATTTAATGCATGATTATTAGATTAAGAATTAA
925476 TTTTTGTAAT
Statistics
Matches: 104, Mismatches: 7, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
111 104 1.00
ACGTcount: A:0.36, C:0.08, G:0.10, T:0.46
Consensus pattern (111 bp):
ATATCTCGACACTTTACTGATACAGTAACATTTTAACGTTTTAATTTAATTTAAATTATTAGTAA
TAATTAGTTGATTTATTTAATGCATGATTATTAGATTAAGAATTAA
Found at i:927080 original size:12 final size:12
Alignment explanation
Indices: 927063--927099 Score: 51
Period size: 12 Copynumber: 3.2 Consensus size: 12
927053 ATTTATAATA
927063 GAGGAGAGATGC
1 GAGGAGAGATGC
*
927075 GA-G-GAGATGT
1 GAGGAGAGATGC
927085 GAGGAGAGATGC
1 GAGGAGAGATGC
927097 GAG
1 GAG
927100 AACATGAGGT
Statistics
Matches: 21, Mismatches: 2, Indels: 4
0.78 0.07 0.15
Matches are distributed among these distances:
10 8 0.38
11 2 0.10
12 11 0.52
ACGTcount: A:0.32, C:0.05, G:0.51, T:0.11
Consensus pattern (12 bp):
GAGGAGAGATGC
Found at i:927201 original size:271 final size:271
Alignment explanation
Indices: 926871--927413 Score: 1006
Period size: 273 Copynumber: 2.0 Consensus size: 271
926861 CCGCTTTTCA
926871 ATTTTACAAACATAAAAATTAATTAAATAATTAGTATAATATTTTTTTCAAATATGATAATAAAC
1 ATTTTACAAACATAAAAATTAATTAAATAATTAGTATAATATTTTTTTCAAATATGATAATAAAC
926936 AATAA-TATAATT-AAAAATTATAACAAAATTACCTTATAACGAAAAATCGCACGAAC-TCTAAA
66 AATAAGTATAATTAAAAAATTATAACAAAATTACCTTATAACGAAAAATCGCACGAACTTCTAAA
926998 TTCAAATATAAGAATATTGCCAGAATTATTACTCGTAAACGGAATTGTTGTATTAATTTATAATA
131 -TCAAATATAAGAATATTGCCAGAATTATTACTCGTAAACGGAATTGTTGTATTAATTTATAATA
927063 GAGGAGAGATGCGAGGAGATGTGAGGAGAGATGCGAGAACATGAGGTATTTATAAACATATAAGG
195 GAGGAGAGATGCGAGGAGATGTGAGGAGAGATGCGAGAACATGAGGTATTTATAAACATATAAGG
927128 CGCAGTAACCTCC
260 CGCAGT-ACCTCC
927141 ATTTTACAAACAT-AAAATTAATTAAAAATAATTAGTATAATA-TTTTTTCAAATAATGATAATA
1 ATTTTACAAACATAAAAATTAATT--AAATAATTAGTATAATATTTTTTTCAAAT-ATGATAATA
927204 AACAATAAGTATAATTAAAAAATTATAACAAAATTACCTTATAACGAAAAATCGCACGAACTTCT
63 AACAATAAGTATAATTAAAAAATTATAACAAAATTACCTTATAACGAAAAATCGCACGAACTTCT
927269 AAATCAAATATAAGAATATTGCCAGAATTATTACTCGTAAACGGAATTGTTGTATTAATTTATAA
128 AAATCAAATATAAGAATATTGCCAGAATTATTACTCGTAAACGGAATTGTTGTATTAATTTATAA
927334 TAGAGGAGAGATGCGAGGAGATGTGAGGAGAGATGCGAGAACATGAGGTATTTATAAACATATAA
193 TAGAGGAGAGATGCGAGGAGATGTGAGGAGAGATGCGAGAACATGAGGTATTTATAAACATATAA
927399 GGCGCAGTACCTCC
258 GGCGCAGTACCTCC
927413 A
1 A
927414 CCGCGTTATA
Statistics
Matches: 267, Mismatches: 0, Indels: 10
0.96 0.00 0.04
Matches are distributed among these distances:
269 10 0.04
270 24 0.09
271 34 0.13
272 14 0.05
273 179 0.67
274 6 0.02
ACGTcount: A:0.45, C:0.11, G:0.15, T:0.30
Consensus pattern (271 bp):
ATTTTACAAACATAAAAATTAATTAAATAATTAGTATAATATTTTTTTCAAATATGATAATAAAC
AATAAGTATAATTAAAAAATTATAACAAAATTACCTTATAACGAAAAATCGCACGAACTTCTAAA
TCAAATATAAGAATATTGCCAGAATTATTACTCGTAAACGGAATTGTTGTATTAATTTATAATAG
AGGAGAGATGCGAGGAGATGTGAGGAGAGATGCGAGAACATGAGGTATTTATAAACATATAAGGC
GCAGTACCTCC
Found at i:927353 original size:12 final size:12
Alignment explanation
Indices: 927336--927372 Score: 51
Period size: 12 Copynumber: 3.2 Consensus size: 12
927326 ATTTATAATA
927336 GAGGAGAGATGC
1 GAGGAGAGATGC
*
927348 GA-G-GAGATGT
1 GAGGAGAGATGC
927358 GAGGAGAGATGC
1 GAGGAGAGATGC
927370 GAG
1 GAG
927373 AACATGAGGT
Statistics
Matches: 21, Mismatches: 2, Indels: 4
0.78 0.07 0.15
Matches are distributed among these distances:
10 8 0.38
11 2 0.10
12 11 0.52
ACGTcount: A:0.32, C:0.05, G:0.51, T:0.11
Consensus pattern (12 bp):
GAGGAGAGATGC
Found at i:929860 original size:2 final size:2
Alignment explanation
Indices: 929853--929886 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
929843 TTTTTACAAA
929853 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
929887 TGTATCAAAT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:930399 original size:32 final size:31
Alignment explanation
Indices: 930353--930433 Score: 90
Period size: 32 Copynumber: 2.5 Consensus size: 31
930343 AGTTCCAGAC
* *
930353 ATGTAATGACTATTTTACAATAATTTGATAAA
1 ATGTAATGATTATTTTACAATAAATTG-TAAA
* * *
930385 TTTTAATGATTATTTTATAATAAATTGTAAA
1 ATGTAATGATTATTTTACAATAAATTGTAAA
*
930416 ATGTAATGACTAATTTTA
1 ATGTAATGA-TTATTTTA
930434 ATTTTGTAAA
Statistics
Matches: 40, Mismatches: 8, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
31 11 0.28
32 29 0.73
ACGTcount: A:0.42, C:0.04, G:0.09, T:0.46
Consensus pattern (31 bp):
ATGTAATGATTATTTTACAATAAATTGTAAA
Found at i:930713 original size:24 final size:27
Alignment explanation
Indices: 930692--930751 Score: 68
Period size: 27 Copynumber: 2.3 Consensus size: 27
930682 CGGCAATGGA
*
930692 ACAA-TTCTCCTCCTTACAAATGATAG
1 ACAATTTCTCCTCCTTACAAATGAGAG
* * *
930718 AGAATTTTTCCTCCTTACAAATGATAG
1 ACAATTTCTCCTCCTTACAAATGAGAG
*
930745 AGAATTT
1 ACAATTT
930752 TCGAGTTCAA
Statistics
Matches: 31, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
26 3 0.10
27 28 0.90
ACGTcount: A:0.35, C:0.20, G:0.10, T:0.35
Consensus pattern (27 bp):
ACAATTTCTCCTCCTTACAAATGAGAG
Found at i:930733 original size:27 final size:27
Alignment explanation
Indices: 930699--930752 Score: 108
Period size: 27 Copynumber: 2.0 Consensus size: 27
930689 GGAACAATTC
930699 TCCTCCTTACAAATGATAGAGAATTTT
1 TCCTCCTTACAAATGATAGAGAATTTT
930726 TCCTCCTTACAAATGATAGAGAATTTT
1 TCCTCCTTACAAATGATAGAGAATTTT
930753 CGAGTTCAAT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 27 1.00
ACGTcount: A:0.33, C:0.19, G:0.11, T:0.37
Consensus pattern (27 bp):
TCCTCCTTACAAATGATAGAGAATTTT
Found at i:933656 original size:60 final size:60
Alignment explanation
Indices: 933563--933682 Score: 197
Period size: 60 Copynumber: 2.0 Consensus size: 60
933553 AGATTTCAAG
*
933563 TTGTTGATGTCAATGTTAGGAGTGTACTAGTTTGGAGGATATTTATTGGTTATTGTTCTA
1 TTGTTGATGTCAATGTTAGGAGTGTACAAGTTTGGAGGATATTTATTGGTTATTGTTCTA
* *
933623 TTGTTGATGT-AAGTGTTTGGAGTGTACAAGTTTGGAGGATATTTGTTGGTTATTGTTCTA
1 TTGTTGATGTCAA-TGTTAGGAGTGTACAAGTTTGGAGGATATTTATTGGTTATTGTTCTA
933683 AAGTCAGCTT
Statistics
Matches: 56, Mismatches: 3, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
59 2 0.04
60 54 0.96
ACGTcount: A:0.21, C:0.04, G:0.28, T:0.47
Consensus pattern (60 bp):
TTGTTGATGTCAATGTTAGGAGTGTACAAGTTTGGAGGATATTTATTGGTTATTGTTCTA
Found at i:937197 original size:12 final size:12
Alignment explanation
Indices: 937180--937204 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
937170 TGCCTCTTCC
937180 TCGGTCCATCCT
1 TCGGTCCATCCT
937192 TCGGTCCATCCT
1 TCGGTCCATCCT
937204 T
1 T
937205 GCATGCATAC
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:0.08, C:0.40, G:0.16, T:0.36
Consensus pattern (12 bp):
TCGGTCCATCCT
Found at i:943780 original size:19 final size:19
Alignment explanation
Indices: 943748--943790 Score: 52
Period size: 19 Copynumber: 2.3 Consensus size: 19
943738 TAAACTTTTA
943748 AAAATTATAAAATTA-TCAT
1 AAAATTATAAAATTACT-AT
**
943767 AAAATTATTGAATTACTAT
1 AAAATTATAAAATTACTAT
943786 AAAAT
1 AAAAT
943791 AATTATTGTA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
19 20 0.95
20 1 0.05
ACGTcount: A:0.56, C:0.05, G:0.02, T:0.37
Consensus pattern (19 bp):
AAAATTATAAAATTACTAT
Found at i:943819 original size:32 final size:32
Alignment explanation
Indices: 943751--943855 Score: 101
Period size: 32 Copynumber: 3.3 Consensus size: 32
943741 ACTTTTAAAA
* * *
943751 ATTATAAAATTATCA-TAA-AATTATTGAATT
1 ATTATAAAATAATCATTAATATTTATCGAATT
* * *
943781 ACTATAAAATAATTATT-GTATTTTATCGAATT
1 ATTATAAAATAATCATTAATA-TTTATCGAATT
*
943813 ATTATAAAATAATCGTTAATATTTATC-ACATT
1 ATTATAAAATAATCATTAATATTTATCGA-ATT
943845 ATTATAAAATA
1 ATTATAAAATA
943856 TTCAATAAAT
Statistics
Matches: 60, Mismatches: 10, Indels: 8
0.77 0.13 0.10
Matches are distributed among these distances:
30 12 0.20
31 3 0.05
32 43 0.72
33 2 0.03
ACGTcount: A:0.47, C:0.06, G:0.04, T:0.44
Consensus pattern (32 bp):
ATTATAAAATAATCATTAATATTTATCGAATT
Found at i:943862 original size:29 final size:31
Alignment explanation
Indices: 943802--943862 Score: 74
Period size: 32 Copynumber: 2.0 Consensus size: 31
943792 ATTATTGTAT
*
943802 TTTATCGAATTATTATAAAATAATCGTTAATA
1 TTTATCGAATTATTATAAAATAATC-TCAATA
943834 TTTATC-ACATTATTATAAAAT-AT-TCAATA
1 TTTATCGA-ATTATTATAAAATAATCTCAATA
943863 AATTAAATCA
Statistics
Matches: 27, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
29 5 0.19
31 3 0.11
32 19 0.70
ACGTcount: A:0.44, C:0.08, G:0.03, T:0.44
Consensus pattern (31 bp):
TTTATCGAATTATTATAAAATAATCTCAATA
Found at i:960101 original size:14 final size:14
Alignment explanation
Indices: 960084--960117 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
960074 TTACGTAATT
*
960084 TATTTTTTGGAAAA
1 TATTTTTCGGAAAA
960098 TATTTTTCGGAAAA
1 TATTTTTCGGAAAA
*
960112 TGTTTT
1 TATTTT
960118 CCCGTGTTTG
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.29, C:0.03, G:0.15, T:0.53
Consensus pattern (14 bp):
TATTTTTCGGAAAA
Found at i:960404 original size:26 final size:24
Alignment explanation
Indices: 960368--960445 Score: 99
Period size: 23 Copynumber: 3.3 Consensus size: 24
960358 TTTTAATCAA
960368 AATATTAATTATTAAAATTTTTAA-
1 AATA-TAATTATTAAAATTTTTAAT
*
960392 AATATATTTATTAAAATTTTTAAT
1 AATATAATTATTAAAATTTTTAAT
*
960416 AATATAA-TATT-ATATTTTTAAT
1 AATATAATTATTAAAATTTTTAAT
*
960438 ATTATAAT
1 AATATAAT
960446 AAAATAATTA
Statistics
Matches: 48, Mismatches: 4, Indels: 5
0.84 0.07 0.09
Matches are distributed among these distances:
22 16 0.33
23 22 0.46
24 10 0.21
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (24 bp):
AATATAATTATTAAAATTTTTAAT
Found at i:960420 original size:22 final size:24
Alignment explanation
Indices: 960368--960443 Score: 83
Period size: 22 Copynumber: 3.4 Consensus size: 24
960358 TTTTAATCAA
960368 AATAT-TA-ATTATTAAAATTTTT
1 AATATATATATTATTAAAATTTTT
*
960390 AAAATATAT-TTATTAAAATTTTT
1 AATATATATATTATTAAAATTTTT
* *
960413 AATA-ATATAATATT-ATATTTTT
1 AATATATATATTATTAAAATTTTT
960435 AATAT-TATA
1 AATATATATA
960444 ATAAAATAAT
Statistics
Matches: 46, Mismatches: 4, Indels: 8
0.79 0.07 0.14
Matches are distributed among these distances:
22 23 0.50
23 23 0.50
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (24 bp):
AATATATATATTATTAAAATTTTT
Found at i:960453 original size:30 final size:34
Alignment explanation
Indices: 960394--960463 Score: 85
Period size: 32 Copynumber: 2.2 Consensus size: 34
960384 ATTTTTAAAA
* *
960394 TATATTTATTAAAATTTTTAATAATATAA-T-AT
1 TATATTTATTAAAATTTATAATAAAATAATTAAT
*
960426 TATATTT-TTAATA-TTATAATAAAATAATTAAT
1 TATATTTATTAAAATTTATAATAAAATAATTAAT
960458 TATATT
1 TATATT
960464 ATAATAATAT
Statistics
Matches: 33, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
30 12 0.36
31 6 0.18
32 15 0.45
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (34 bp):
TATATTTATTAAAATTTATAATAAAATAATTAAT
Found at i:960482 original size:23 final size:23
Alignment explanation
Indices: 960436--960486 Score: 68
Period size: 23 Copynumber: 2.2 Consensus size: 23
960426 TATATTTTTA
*
960436 ATATTATAATAAAATAATTAATT
1 ATATTATAATAAAATAAATAATT
*
960459 ATATTATAATAATATAAGAT-ATT
1 ATATTATAATAAAATAA-ATAATT
960482 ATATT
1 ATATT
960487 TTTATTTTAA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
23 24 0.96
24 1 0.04
ACGTcount: A:0.53, C:0.00, G:0.02, T:0.45
Consensus pattern (23 bp):
ATATTATAATAAAATAAATAATT
Found at i:960514 original size:31 final size:32
Alignment explanation
Indices: 960431--960514 Score: 79
Period size: 31 Copynumber: 2.8 Consensus size: 32
960421 AATATTATAT
*
960431 TTTTAAT-AT-TATAATAAAATA-ATTAATTA
1 TTTTAATAATATATAATAAATTATATTAATTA
* * * *
960460 TATT-ATAATAATATAAGATATTATATT-TTTA
1 TTTTAATAAT-ATATAATAAATTATATTAATTA
960491 TTTTAATAATATATAATAAATTAT
1 TTTTAATAATATATAATAAATTAT
960515 TAATAAAATT
Statistics
Matches: 42, Mismatches: 8, Indels: 8
0.72 0.14 0.14
Matches are distributed among these distances:
28 2 0.05
29 5 0.12
31 27 0.64
32 8 0.19
ACGTcount: A:0.49, C:0.00, G:0.01, T:0.50
Consensus pattern (32 bp):
TTTTAATAATATATAATAAATTATATTAATTA
Found at i:960565 original size:24 final size:26
Alignment explanation
Indices: 960546--960611 Score: 78
Period size: 27 Copynumber: 2.4 Consensus size: 26
960536 TTAATTTCAT
960546 ATAAATAATATTATTAAATTATTAATA
1 ATAAATAATATTATT-AATTATTAATA
*
960573 ATAAATAATATTATTTATATATTTAATA
1 ATAAATAATATTATTAAT-TA-TTAATA
*
960601 TTAACATAATA
1 ATAA-ATAATA
960612 ATATAATAAT
Statistics
Matches: 34, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
26 2 0.06
27 17 0.50
28 9 0.26
29 6 0.18
ACGTcount: A:0.53, C:0.02, G:0.00, T:0.45
Consensus pattern (26 bp):
ATAAATAATATTATTAATTATTAATA
Found at i:960576 original size:27 final size:27
Alignment explanation
Indices: 960495--960587 Score: 93
Period size: 27 Copynumber: 3.4 Consensus size: 27
960485 TTTTTATTTT
*
960495 AATAATATATAATAAATTATTAATAA-A
1 AATAATAT-TATTAAATTATTAATAATA
* * * *
960522 ATTTATATTATT-TATTAATTTCAT-ATA
1 AATAATATTATTAAATT-A-TTAATAATA
960549 AATAATATTATTAAATTATTAATAATA
1 AATAATATTATTAAATTATTAATAATA
960576 AATAATATTATT
1 AATAATATTATT
960588 TATATATTTA
Statistics
Matches: 52, Mismatches: 9, Indels: 10
0.73 0.13 0.14
Matches are distributed among these distances:
25 3 0.06
26 9 0.17
27 37 0.71
28 3 0.06
ACGTcount: A:0.52, C:0.01, G:0.00, T:0.47
Consensus pattern (27 bp):
AATAATATTATTAAATTATTAATAATA
Found at i:960638 original size:54 final size:54
Alignment explanation
Indices: 960309--960632 Score: 148
Period size: 54 Copynumber: 6.1 Consensus size: 54
960299 TAAATACTCA
* * * ** *
960309 AAATAATTTTATTTTATGAATTTAATATTAATAA-AATATTTTAATATCATTTTAAT
1 AAATAATATTA-TTTATTAATTTAATATAAATAATAATATAATAATAT--TATTAAT
* * * * * * *
960365 CAA-AATATTAATTATTAAAATTT-TTA-AAAT-AT-ATTTATTAAAATTTTTAAT
1 AAATAATATTATTTATT--AATTTAATATAAATAATAATATAATAATATTATTAAT
* *
960416 AATATAATATTATATTTTTAATATT-ATA-ATAA-AATAAT-TAATTATATTA-TAAT
1 AA-ATAATATTAT-TTATTAAT-TTAATATA-AATAATAATATAATAATATTATTAAT
* * *
960469 AATATAAGA-TATTATATT--TTT-ATTTTAATAAT-ATATAATAA-ATTATTAAT
1 AA-ATAATATTATT-TATTAATTTAATATAAATAATAATATAATAATATTATTAAT
* * * * *
960519 AAAATTTATATTATTTATTAATTTCATATAAATAATATTATTAA-ATTATTAATAAT
1 -AAA-TAATATTATTTATTAATTTAATATAAATAATAATA-TAATAATATTATTAAT
960575 AAATAATATTATTTA-TATATTTAATATTAACATAATAATATAATAATATT-TTAAT
1 AAATAATATTATTTATTA-ATTTAATA-TAA-ATAATAATATAATAATATTATTAAT
960630 AAA
1 AAA
960633 GATATTTAAA
Statistics
Matches: 206, Mismatches: 34, Indels: 57
0.69 0.11 0.19
Matches are distributed among these distances:
49 12 0.06
50 14 0.07
51 18 0.09
52 14 0.07
53 39 0.19
54 49 0.24
55 29 0.14
56 31 0.15
ACGTcount: A:0.49, C:0.01, G:0.01, T:0.49
Consensus pattern (54 bp):
AAATAATATTATTTATTAATTTAATATAAATAATAATATAATAATATTATTAAT
Found at i:960652 original size:23 final size:23
Alignment explanation
Indices: 960626--960670 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
960616 AATAATATTT
960626 TAATAAAGATATTTAAAATATAC
1 TAATAAAGATATTTAAAATATAC
* * *
960649 TAATTAATATTTTTAAAATATA
1 TAATAAAGATATTTAAAATATA
960671 ATATAACACT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.53, C:0.02, G:0.02, T:0.42
Consensus pattern (23 bp):
TAATAAAGATATTTAAAATATAC
Found at i:961042 original size:20 final size:20
Alignment explanation
Indices: 961005--961042 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
960995 TCGGAAAACG
*
961005 TTTTTCATAAATCTAATTCA
1 TTTTTCATAAATCAAATTCA
961025 TTTTTCA-AAATTCAAATT
1 TTTTTCATAAA-TCAAATT
961043 TCAGTAATTC
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
19 3 0.19
20 13 0.81
ACGTcount: A:0.37, C:0.13, G:0.00, T:0.50
Consensus pattern (20 bp):
TTTTTCATAAATCAAATTCA
Found at i:969035 original size:21 final size:20
Alignment explanation
Indices: 969005--969049 Score: 63
Period size: 21 Copynumber: 2.2 Consensus size: 20
968995 AATTATATGC
* *
969005 TATAAGTATTCCTCTTTGTT
1 TATAAGTATTCCCCTATGTT
969025 TATAATGTATTCCCCTATGTT
1 TATAA-GTATTCCCCTATGTT
969046 TATA
1 TATA
969050 TTGTCTTGCA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
20 5 0.23
21 17 0.77
ACGTcount: A:0.24, C:0.16, G:0.09, T:0.51
Consensus pattern (20 bp):
TATAAGTATTCCCCTATGTT
Found at i:974251 original size:16 final size:16
Alignment explanation
Indices: 974230--974262 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
974220 TAATAAATAG
974230 ACGAACATAAACGAAC
1 ACGAACATAAACGAAC
974246 ACGAACATAAACGAAC
1 ACGAACATAAACGAAC
974262 A
1 A
974263 AATTTTTTTT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.58, C:0.24, G:0.12, T:0.06
Consensus pattern (16 bp):
ACGAACATAAACGAAC
Found at i:974344 original size:10 final size:10
Alignment explanation
Indices: 974329--974403 Score: 61
Period size: 10 Copynumber: 7.7 Consensus size: 10
974319 CATTTAATAA
974329 ATAAACGAAC
1 ATAAACGAAC
974339 ATAAACGAAC
1 ATAAACGAAC
974349 ----ACGAAC
1 ATAAACGAAC
974355 ATAAACGAAC
1 ATAAACGAAC
** *
974365 ACGAAC-ATAA
1 ATAAACGA-AC
974375 ATGAACACGAAC
1 AT-AA-ACGAAC
974387 ATAAACGAAC
1 ATAAACGAAC
974397 ATAAACG
1 ATAAACG
974404 TTGGAGACCC
Statistics
Matches: 51, Mismatches: 6, Indels: 16
0.70 0.08 0.22
Matches are distributed among these distances:
6 6 0.12
9 1 0.02
10 35 0.69
11 3 0.06
12 5 0.10
13 1 0.02
ACGTcount: A:0.57, C:0.21, G:0.12, T:0.09
Consensus pattern (10 bp):
ATAAACGAAC
Found at i:974354 original size:16 final size:16
Alignment explanation
Indices: 974333--974397 Score: 121
Period size: 16 Copynumber: 4.1 Consensus size: 16
974323 TAATAAATAA
974333 ACGAACATAAACGAAC
1 ACGAACATAAACGAAC
974349 ACGAACATAAACGAAC
1 ACGAACATAAACGAAC
*
974365 ACGAACATAAATGAAC
1 ACGAACATAAACGAAC
974381 ACGAACATAAACGAAC
1 ACGAACATAAACGAAC
974397 A
1 A
974398 TAAACGTTGG
Statistics
Matches: 47, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
16 47 1.00
ACGTcount: A:0.57, C:0.23, G:0.12, T:0.08
Consensus pattern (16 bp):
ACGAACATAAACGAAC
Found at i:975199 original size:14 final size:14
Alignment explanation
Indices: 975151--975206 Score: 66
Period size: 14 Copynumber: 4.3 Consensus size: 14
975141 AATGAACATA
**
975151 AACGAACATATTCG
1 AACGAACATAACCG
975165 AACGAACAT-A---
1 AACGAACATAACCG
975175 AACGAACATAACCG
1 AACGAACATAACCG
975189 AACGAACATAACCG
1 AACGAACATAACCG
975203 AACG
1 AACG
975207 TTCACGAACG
Statistics
Matches: 37, Mismatches: 1, Indels: 8
0.80 0.02 0.17
Matches are distributed among these distances:
10 9 0.24
11 1 0.03
14 27 0.73
ACGTcount: A:0.50, C:0.25, G:0.14, T:0.11
Consensus pattern (14 bp):
AACGAACATAACCG
Found at i:975205 original size:10 final size:10
Alignment explanation
Indices: 975144--975191 Score: 51
Period size: 10 Copynumber: 4.4 Consensus size: 10
975134 ATAAATGAAT
975144 GAACATAAAC
1 GAACATAAAC
975154 GAACATATTCGAAC
1 GAACATA----AAC
975168 GAACATAAAC
1 GAACATAAAC
*
975178 GAACATAACC
1 GAACATAAAC
975188 GAAC
1 GAAC
975192 GAACATAACC
Statistics
Matches: 33, Mismatches: 1, Indels: 8
0.79 0.02 0.19
Matches are distributed among these distances:
10 23 0.70
14 10 0.30
ACGTcount: A:0.52, C:0.23, G:0.12, T:0.12
Consensus pattern (10 bp):
GAACATAAAC
Found at i:975216 original size:24 final size:24
Alignment explanation
Indices: 975144--975205 Score: 97
Period size: 24 Copynumber: 2.6 Consensus size: 24
975134 ATAAATGAAT
**
975144 GAACATAAACGAACATATTCGAAC
1 GAACATAAACGAACATAACCGAAC
975168 GAACATAAACGAACATAACCGAAC
1 GAACATAAACGAACATAACCGAAC
*
975192 GAACATAACCGAAC
1 GAACATAAACGAAC
975206 GTTCACGAAC
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
24 35 1.00
ACGTcount: A:0.52, C:0.24, G:0.13, T:0.11
Consensus pattern (24 bp):
GAACATAAACGAACATAACCGAAC
Found at i:975887 original size:61 final size:58
Alignment explanation
Indices: 975766--975887 Score: 136
Period size: 58 Copynumber: 2.1 Consensus size: 58
975756 GTCCCCTAAC
* * * * * * *
975766 TATAAGGTGTTGCTTTATTGATTCCTCTGACTTAAAAGTTACAAAATAGTCCCCCGAT
1 TATAAGATGTTGCTTTATTAATTCCACTAACTTAAAAGTTACAAAATAGTCACACAAT
* *
975824 TATAAGATGTTGCTTTTTTAATTCCACTAACAATTAAAAAGTTACAAAATGGTCACACAAT
1 TATAAGATGTTGCTTTATTAATTCCACTAAC--TT-AAAAGTTACAAAATAGTCACACAAT
975885 TAT
1 TAT
975888 TCATTGTGTT
Statistics
Matches: 52, Mismatches: 9, Indels: 3
0.81 0.14 0.05
Matches are distributed among these distances:
58 26 0.50
60 2 0.04
61 24 0.46
ACGTcount: A:0.35, C:0.16, G:0.12, T:0.36
Consensus pattern (58 bp):
TATAAGATGTTGCTTTATTAATTCCACTAACTTAAAAGTTACAAAATAGTCACACAAT
Found at i:982075 original size:115 final size:115
Alignment explanation
Indices: 981872--982079 Score: 382
Period size: 115 Copynumber: 1.8 Consensus size: 115
981862 TTCATATTAT
981872 TCTAATTGAGAAAATAATTTTTCTTTCCCCATGTGAGCAATTCTTTTTTTTTTCCCATGATATTA
1 TCTAATTGAGAAAATAATTTTTCTTTCCCCATGTGAGCAATTCTTTTTTTTTT-CCATGATATTA
981937 TCTATGGAAAATTGCCCATCTTTCCTACTCATTACACCTACATTTGACAAC
65 TCTATGGAAAATTGCCCATCTTTCCTACTCATTACACCTACATTTGACAAC
981988 TCTAATTGAGAAAATAATTTTTCTTTACCCCATGTGAGCAATTCTTTTTTTTTT-CATGATATTA
1 TCTAATTGAGAAAATAATTTTTCTTT-CCCCATGTGAGCAATTCTTTTTTTTTTCCATGATATTA
*
982052 TCTATGGAGAATTGCCCATCTTTCCTAC
65 TCTATGGAAAATTGCCCATCTTTCCTAC
982080 ATTTGACATA
Statistics
Matches: 90, Mismatches: 1, Indels: 3
0.96 0.01 0.03
Matches are distributed among these distances:
115 37 0.41
116 26 0.29
117 27 0.30
ACGTcount: A:0.27, C:0.21, G:0.10, T:0.43
Consensus pattern (115 bp):
TCTAATTGAGAAAATAATTTTTCTTTCCCCATGTGAGCAATTCTTTTTTTTTTCCATGATATTAT
CTATGGAAAATTGCCCATCTTTCCTACTCATTACACCTACATTTGACAAC
Found at i:1005004 original size:21 final size:22
Alignment explanation
Indices: 1004980--1005026 Score: 60
Period size: 22 Copynumber: 2.2 Consensus size: 22
1004970 GTTGACATGC
**
1004980 ATGAG-CTATTTTTCATTTAAT
1 ATGAGACTATTTTAAATTTAAT
*
1005001 ATGAGATTATTTTAAATTTAAT
1 ATGAGACTATTTTAAATTTAAT
1005023 ATGA
1 ATGA
1005027 ATTATGAATC
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
21 5 0.23
22 17 0.77
ACGTcount: A:0.36, C:0.04, G:0.11, T:0.49
Consensus pattern (22 bp):
ATGAGACTATTTTAAATTTAAT
Found at i:1007310 original size:59 final size:58
Alignment explanation
Indices: 1007200--1007310 Score: 145
Period size: 59 Copynumber: 1.9 Consensus size: 58
1007190 ACATACATAG
* *
1007200 AGTTTGGGATGAAATCGGAATGTTCAAAAAGTTTGGGAACCAATTAGAATGAACTCAT
1 AGTTTGGGATGAAATCGAAATGTTCAAAAAGTTTGGGAACCAATTAAAATGAACTCAT
* *
1007258 AGTTTGGGAATGAAATTGAAATGTTC-AAAAGTTTGAGG-ACTAATTTAAAATGA
1 AGTTTGGG-ATGAAATCGAAATGTTCAAAAAGTTTG-GGAACCAA-TTAAAATGA
1007311 TAGTTATAAT
Statistics
Matches: 46, Mismatches: 4, Indels: 5
0.84 0.07 0.09
Matches are distributed among these distances:
58 21 0.46
59 25 0.54
ACGTcount: A:0.40, C:0.07, G:0.23, T:0.30
Consensus pattern (58 bp):
AGTTTGGGATGAAATCGAAATGTTCAAAAAGTTTGGGAACCAATTAAAATGAACTCAT
Found at i:1007551 original size:59 final size:59
Alignment explanation
Indices: 1007458--1007569 Score: 156
Period size: 59 Copynumber: 1.9 Consensus size: 59
1007448 ACATACATAG
* *
1007458 AGTTTGGGATGAAATCGGAATGTTCAAAAAGTTTG-GGAACCAATTTAGAATGAACTCAT
1 AGTTTGGGATGAAATCGAAATGTTCAAAAAGTTTGAGG-ACCAATTTAAAATGAACTCAT
* *
1007517 AGTTTGGGAATGAAATTGAAATGTTC-AAAAGTTTGAGGACTAATTTAAAATGA
1 AGTTTGGG-ATGAAATCGAAATGTTCAAAAAGTTTGAGGACCAATTTAAAATGA
1007570 TAGTTATAAT
Statistics
Matches: 47, Mismatches: 4, Indels: 4
0.85 0.07 0.07
Matches are distributed among these distances:
59 30 0.64
60 17 0.36
ACGTcount: A:0.39, C:0.07, G:0.23, T:0.30
Consensus pattern (59 bp):
AGTTTGGGATGAAATCGAAATGTTCAAAAAGTTTGAGGACCAATTTAAAATGAACTCAT
Found at i:1007574 original size:259 final size:255
Alignment explanation
Indices: 1007077--1007591 Score: 994
Period size: 259 Copynumber: 2.0 Consensus size: 255
1007067 AAAACTTTTG
1007077 AATCTTCTAATTTCATCCCCAACTTCATTCAAGTATGCAATTATTTCAAACCTAAATTTTATTTT
1 AATCTTCTAATTTCATCCCCAACTTCATTCAAGTATGCAATTATTTCAAACCTAAATTTTATTTT
1007142 CTTTCAAACATATAGACCTAACAATTTTATACAAGGGATGCGATTATTACATACATAGAGTTTGG
66 CTTTCAAACATATAGACCTAACAATTTTATACAAGGGATGCGATTATTACATACATAGAGTTTGG
1007207 GATGAAATCGGAATGTTCAAAAAGTTTGGGAACCAATTAGAATGAACTCATAGTTTGGGAATGAA
131 GATGAAATCGGAATGTTCAAAAAGTTTGGGAACCAATTAGAATGAACTCATAGTTTGGGAATGAA
1007272 ATTGAAATGTTCAAAAGTTTGAGGACTAATTTAAAATGATAGTTATAATTCAAGGATGAA
196 ATTGAAATGTTCAAAAGTTTGAGGACTAATTTAAAATGATAGTTATAATTCAAGGATGAA
1007332 AATCTTCTAATTTCATCCCCAACTTCATTCAAGTATGCAATTAGTTTCAAACCTAAATTTTATTT
1 AATCTTCTAATTTCATCCCCAACTTCATTCAAGTATGCAATTA-TTTCAAACCTAAATTTTATTT
1007397 TCTTTCAAACATATAGACCTAACAATTTTATTAACAAGGGATGCGATTATTACATACATAGAGTT
65 TCTTTCAAACATATAGACCTAACAATTTTA-T-ACAAGGGATGCGATTATTACATACATAGAGTT
1007462 TGGGATGAAATCGGAATGTTCAAAAAGTTTGGGAACCAATTTAGAATGAACTCATAGTTTGGGAA
128 TGGGATGAAATCGGAATGTTCAAAAAGTTTGGGAACCAA-TTAGAATGAACTCATAGTTTGGGAA
1007527 TGAAATTGAAATGTTCAAAAGTTTGAGGACTAATTTAAAATGATAGTTATAATTCAAGGATGAA
192 TGAAATTGAAATGTTCAAAAGTTTGAGGACTAATTTAAAATGATAGTTATAATTCAAGGATGAA
1007591 A
1 A
1007592 TTGAAGCATT
Statistics
Matches: 256, Mismatches: 0, Indels: 4
0.98 0.00 0.02
Matches are distributed among these distances:
255 43 0.17
256 51 0.20
257 1 0.00
258 71 0.28
259 90 0.35
ACGTcount: A:0.38, C:0.13, G:0.15, T:0.34
Consensus pattern (255 bp):
AATCTTCTAATTTCATCCCCAACTTCATTCAAGTATGCAATTATTTCAAACCTAAATTTTATTTT
CTTTCAAACATATAGACCTAACAATTTTATACAAGGGATGCGATTATTACATACATAGAGTTTGG
GATGAAATCGGAATGTTCAAAAAGTTTGGGAACCAATTAGAATGAACTCATAGTTTGGGAATGAA
ATTGAAATGTTCAAAAGTTTGAGGACTAATTTAAAATGATAGTTATAATTCAAGGATGAA
Found at i:1012308 original size:19 final size:19
Alignment explanation
Indices: 1012284--1012320 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
1012274 ATGACCAACA
*
1012284 AAATCGCAATGCGATCTCT
1 AAATCGCAACGCGATCTCT
1012303 AAATCGCAACGCGATCTC
1 AAATCGCAACGCGATCTC
1012321 CAGTATCGCA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.32, C:0.30, G:0.16, T:0.22
Consensus pattern (19 bp):
AAATCGCAACGCGATCTCT
Found at i:1012434 original size:21 final size:21
Alignment explanation
Indices: 1012383--1012436 Score: 99
Period size: 21 Copynumber: 2.6 Consensus size: 21
1012373 GCGAATATGT
*
1012383 AAATCGCAACGCGATAATACA
1 AAATCGCAATGCGATAATACA
1012404 AAATCGCAATGCGATAATACA
1 AAATCGCAATGCGATAATACA
1012425 AAATCGCAATGC
1 AAATCGCAATGC
1012437 AATTTTCCAA
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 32 1.00
ACGTcount: A:0.46, C:0.22, G:0.15, T:0.17
Consensus pattern (21 bp):
AAATCGCAATGCGATAATACA
Found at i:1012900 original size:19 final size:19
Alignment explanation
Indices: 1012876--1012912 Score: 74
Period size: 19 Copynumber: 1.9 Consensus size: 19
1012866 TTATTTTGGA
1012876 TTTTTCACTATCGCAACAC
1 TTTTTCACTATCGCAACAC
1012895 TTTTTCACTATCGCAACA
1 TTTTTCACTATCGCAACA
1012913 ATACGTTTTT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.27, C:0.30, G:0.05, T:0.38
Consensus pattern (19 bp):
TTTTTCACTATCGCAACAC
Found at i:1013510 original size:60 final size:60
Alignment explanation
Indices: 1013392--1013566 Score: 160
Period size: 60 Copynumber: 2.9 Consensus size: 60
1013382 AAGTAATAAT
* ** * *
1013392 TCTCATTTTAAATTGGTCCTTAACCTTTTGAATATTCCAATTTCATCCTCAAATTATGAC
1 TCTCATTCTAAATTAATCCTTAAACTTTTGAACATTCCAATTTCATCCTCAAATTATGAC
** *
1013452 TCTCATTCTAAATTAATCCTTAAACTTTTGAACATTTTAATTTCATCCT-TAATATATGAC
1 TCTCATTCTAAATTAATCCTTAAACTTTTGAACATTCCAATTTCATCCTCAAAT-TATGAC
* ** * * *
1013512 -CAT-ATTTCTAAATGAATCCCCAAACTTTTTAATATTCCAATTCCATGCC-CAAATT
1 TC-TCA-TTCTAAATTAATCCTTAAACTTTTGAACATTCCAATTTCAT-CCTCAAATT
1013567 CATCCAAATA
Statistics
Matches: 93, Mismatches: 17, Indels: 10
0.77 0.14 0.08
Matches are distributed among these distances:
59 5 0.05
60 83 0.89
61 5 0.05
ACGTcount: A:0.32, C:0.22, G:0.05, T:0.42
Consensus pattern (60 bp):
TCTCATTCTAAATTAATCCTTAAACTTTTGAACATTCCAATTTCATCCTCAAATTATGAC
Found at i:1013821 original size:60 final size:59
Alignment explanation
Indices: 1013688--1013864 Score: 171
Period size: 60 Copynumber: 2.9 Consensus size: 59
1013678 GTATATGCAT
* * *
1013688 ATAGTTTGGGATGGAATTAGAATGTTTAAAAAGTTTGGGGGACTAATTTAAAAT-AAAGGTT
1 ATAGTTTGGGATGAAATTAGAATG-TTAAAAAGTTT-GAGGACTAATTTAAAATGAAA-GTC
* * *
1013749 ATAATTTGGGGATGAAATT-GAAGTGTTCAAAAGTTTGAGAACTAATTTAAAATGATAA-TC
1 ATAGTTT-GGGATGAAATTAGAA-TGTTAAAAAGTTTGAGGACTAATTTAAAATGA-AAGTC
* * * * *
1013809 ATAGTTTAGGGATAAAATTGGAATATTAAAAAGTTTAAGGACCAATTTAAAATGAA
1 ATAGTTT-GGGATGAAATTAGAATGTTAAAAAGTTTGAGGACTAATTTAAAATGAA
1013865 TGTTATACTT
Statistics
Matches: 97, Mismatches: 14, Indels: 12
0.79 0.11 0.10
Matches are distributed among these distances:
59 1 0.01
60 59 0.61
61 23 0.24
62 14 0.14
ACGTcount: A:0.42, C:0.03, G:0.21, T:0.33
Consensus pattern (59 bp):
ATAGTTTGGGATGAAATTAGAATGTTAAAAAGTTTGAGGACTAATTTAAAATGAAAGTC
Found at i:1018191 original size:2 final size:2
Alignment explanation
Indices: 1018184--1018210 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
1018174 AAGTGCATCC
1018184 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 A
1018211 GCTAAGAGTT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1023539 original size:27 final size:26
Alignment explanation
Indices: 1023509--1023564 Score: 69
Period size: 25 Copynumber: 2.2 Consensus size: 26
1023499 TATAATTTTA
1023509 TAACCGTTCAAAAATTTTAATGAATAT
1 TAACCGTTCAAAAA-TTTAATGAATAT
* **
1023536 TAA-CTTTTGAAAATTTAATGAATAT
1 TAACCGTTCAAAAATTTAATGAATAT
1023561 TAAC
1 TAAC
1023565 ATAATTTAAT
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
25 15 0.60
26 7 0.28
27 3 0.12
ACGTcount: A:0.45, C:0.09, G:0.07, T:0.39
Consensus pattern (26 bp):
TAACCGTTCAAAAATTTAATGAATAT
Found at i:1032358 original size:6 final size:6
Alignment explanation
Indices: 1032342--1032376 Score: 54
Period size: 6 Copynumber: 5.8 Consensus size: 6
1032332 TAAGAAGCAA
1032342 AAAAAT AAAAAAT AAAAAT AAAAAT -AAAAT AAAAA
1 AAAAAT -AAAAAT AAAAAT AAAAAT AAAAAT AAAAA
1032377 AATATTGAAT
Statistics
Matches: 27, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
5 5 0.19
6 16 0.59
7 6 0.22
ACGTcount: A:0.86, C:0.00, G:0.00, T:0.14
Consensus pattern (6 bp):
AAAAAT
Found at i:1032364 original size:12 final size:12
Alignment explanation
Indices: 1032342--1032376 Score: 54
Period size: 11 Copynumber: 2.9 Consensus size: 12
1032332 TAAGAAGCAA
1032342 AAAAATAAAAAAT
1 AAAAAT-AAAAAT
1032355 AAAAATAAAAAT
1 AAAAATAAAAAT
1032367 -AAAATAAAAA
1 AAAAATAAAAA
1032377 AATATTGAAT
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
11 10 0.45
12 6 0.27
13 6 0.27
ACGTcount: A:0.86, C:0.00, G:0.00, T:0.14
Consensus pattern (12 bp):
AAAAATAAAAAT
Found at i:1032366 original size:19 final size:19
Alignment explanation
Indices: 1032342--1032380 Score: 62
Period size: 19 Copynumber: 2.1 Consensus size: 19
1032332 TAAGAAGCAA
1032342 AAAAATAAAA-AATAAAAAT
1 AAAAATAAAATAA-AAAAAT
1032361 AAAAATAAAATAAAAAAAT
1 AAAAATAAAATAAAAAAAT
1032380 A
1 A
1032381 TTGAATTCTA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 17 0.89
20 2 0.11
ACGTcount: A:0.85, C:0.00, G:0.00, T:0.15
Consensus pattern (19 bp):
AAAAATAAAATAAAAAAAT
Found at i:1032378 original size:13 final size:13
Alignment explanation
Indices: 1032343--1032380 Score: 53
Period size: 12 Copynumber: 3.1 Consensus size: 13
1032333 AAGAAGCAAA
1032343 AAAAT-AAAAAAT
1 AAAATAAAAAAAT
*
1032355 AAAA-ATAAAAAT
1 AAAATAAAAAAAT
1032367 AAAATAAAAAAAT
1 AAAATAAAAAAAT
1032380 A
1 A
1032381 TTGAATTCTA
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
12 14 0.64
13 8 0.36
ACGTcount: A:0.84, C:0.00, G:0.00, T:0.16
Consensus pattern (13 bp):
AAAATAAAAAAAT
Done.