Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01005546.1 Hibiscus syriacus cultivar Beakdansim tig00012840_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: 1755203
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 5 of 8
Found at i:879996 original size:337 final size:339
Alignment explanation
Indices: 879320--880001 Score: 1341
Period size: 337 Copynumber: 2.0 Consensus size: 339
879310 CTACAAATGA
*
879320 TAAAGAAATTAATGAATTATCTCATGGTTCTCATTCTTACCAACCAAATTCATGTTATCCACCTT
1 TAAAAAAATTAATGAATTATCTCATGGTTCTCATTCTTACCAACCAAATTCATGTTATCCACCTT
879385 ACCTTGAACAAAATCCAAGTTATGGATTTTTTTTGTCAACATTTATCATACAACATGTTTCCTAC
66 ACCTTGAACAAAATCCAAGTTATGGATTTTTTTTGTCAACATTTATCATACAACATGTTTCCTAC
879450 CAATGATGCATCTTATGATGCACATAATGTGATGTCTTCTTCATATGAAATATGAAAGAATCAAA
131 CAATGATGCATCTTATGATGCACATAATGTGATGTCTTCTTCATATGAAATATGAAAGAATCAAA
879515 ATTAAGACAATGACGAAGATGAAAATGCTTAAGATCCGTCACGCCATTCATTTTAGTAGTGAAGT
196 ATTAAGACAATGACGAAGATGAAAATGCTTAAGATCCGTCACGCCATTCATTTTAGTAGTGAAGT
879580 GTAAGATATAAAATTTTATATTTGTAGTTATATATTATTTTTATTTTTTTTAAGTTATGTAAAAT
261 GTAAGATATAAAATTTTATATTTGTAGTTATATATTATTTTTATTTTTTTTAAGTTATGTAAAAT
879645 GAATATTTTTATAT
326 GAATATTTTTATAT
879659 TAAAAAAATTAATGAATTATCTCATGGTTCTCATTCTTACCAACCAAATTCATGTTATCCACCTT
1 TAAAAAAATTAATGAATTATCTCATGGTTCTCATTCTTACCAACCAAATTCATGTTATCCACCTT
879724 ACCTTGAACAAAATCCAAGTTATGGATTTTTTTTGTCAACATTTATCATACAACATGTTTCCTAC
66 ACCTTGAACAAAATCCAAGTTATGGATTTTTTTTGTCAACATTTATCATACAACATGTTTCCTAC
879789 CAATGATGCATCTTATGATGCACATAATGT-ATGTCTTCTTCATATGAAATATG-AAGAATCAAA
131 CAATGATGCATCTTATGATGCACATAATGTGATGTCTTCTTCATATGAAATATGAAAGAATCAAA
879852 ATTAAGACAATGACGAAGATGAAAATGCTTAAGATCCGTCACGCCATTCATTTTAGTAGTGAAGT
196 ATTAAGACAATGACGAAGATGAAAATGCTTAAGATCCGTCACGCCATTCATTTTAGTAGTGAAGT
879917 GTAAGATATAAAATTTTATATTTGTAGTTATATATTATTTTTATTTTTTTTAAGTTATGTAAAAT
261 GTAAGATATAAAATTTTATATTTGTAGTTATATATTATTTTTATTTTTTTTAAGTTATGTAAAAT
879982 GAATATTTTTATAT
326 GAATATTTTTATAT
879996 TAAAAA
1 TAAAAA
880002 TTTGATATGA
Statistics
Matches: 342, Mismatches: 1, Indels: 2
0.99 0.00 0.01
Matches are distributed among these distances:
337 160 0.47
338 23 0.07
339 159 0.46
ACGTcount: A:0.36, C:0.13, G:0.12, T:0.39
Consensus pattern (339 bp):
TAAAAAAATTAATGAATTATCTCATGGTTCTCATTCTTACCAACCAAATTCATGTTATCCACCTT
ACCTTGAACAAAATCCAAGTTATGGATTTTTTTTGTCAACATTTATCATACAACATGTTTCCTAC
CAATGATGCATCTTATGATGCACATAATGTGATGTCTTCTTCATATGAAATATGAAAGAATCAAA
ATTAAGACAATGACGAAGATGAAAATGCTTAAGATCCGTCACGCCATTCATTTTAGTAGTGAAGT
GTAAGATATAAAATTTTATATTTGTAGTTATATATTATTTTTATTTTTTTTAAGTTATGTAAAAT
GAATATTTTTATAT
Found at i:890069 original size:325 final size:325
Alignment explanation
Indices: 889479--890120 Score: 1284
Period size: 325 Copynumber: 2.0 Consensus size: 325
889469 CATCCGGTTG
889479 TGTTACGCCTTGGCGAGAATTATTCAGCTGTTCTCCCCCAAACTTGTCATCTTGATCAACTTGTT
1 TGTTACGCCTTGGCGAGAATTATTCAGCTGTTCTCCCCCAAACTTGTCATCTTGATCAACTTGTT
889544 TTCCACTCCTTAGCATAATTACATTGCATTGCTCCTTCCCATGATGCTTAGTGAATTCAGTATCA
66 TTCCACTCCTTAGCATAATTACATTGCATTGCTCCTTCCCATGATGCTTAGTGAATTCAGTATCA
889609 CTAGGGAGATTTCCGTGTGGGTGAGAATGTAATTCCGTGGTAATCTATCCCACTTGATTCTCCAA
131 CTAGGGAGATTTCCGTGTGGGTGAGAATGTAATTCCGTGGTAATCTATCCCACTTGATTCTCCAA
889674 TACTCTGAGAGATGAACTATGGCTTTGCAAAAGTGTTGCCTGGCTTTGTAACAAATTTCCTTGAT
196 TACTCTGAGAGATGAACTATGGCTTTGCAAAAGTGTTGCCTGGCTTTGTAACAAATTTCCTTGAT
889739 TTTTTATTGTTGCAGAATGTTCATGCATCAAGGTTTTTGTAGATGCCATGAAATCTTGATCAACT
261 TTTTTATTGTTGCAGAATGTTCATGCATCAAGGTTTTTGTAGATGCCATGAAATCTTGATCAACT
889804 TGTTACGCCTTGGCGAGAATTATTCAGCTGTTCTCCCCCAAACTTGTCATCTTGATCAACTTGTT
1 TGTTACGCCTTGGCGAGAATTATTCAGCTGTTCTCCCCCAAACTTGTCATCTTGATCAACTTGTT
889869 TTCCACTCCTTAGCATAATTACATTGCATTGCTCCTTCCCATGATGCTTAGTGAATTCAGTATCA
66 TTCCACTCCTTAGCATAATTACATTGCATTGCTCCTTCCCATGATGCTTAGTGAATTCAGTATCA
889934 CTAGGGAGATTTCCGTGTGGGTGAGAATGTAATTCCGTGGTAATCTATCCCACTTGATTCTCCAA
131 CTAGGGAGATTTCCGTGTGGGTGAGAATGTAATTCCGTGGTAATCTATCCCACTTGATTCTCCAA
889999 TACTCTGAGAGATGAACTATGGCTTTGCAAAAGTGTTGCCTGGCTTTGTAACAAATTTCCTTGAT
196 TACTCTGAGAGATGAACTATGGCTTTGCAAAAGTGTTGCCTGGCTTTGTAACAAATTTCCTTGAT
890064 TTTTTATTGTTGCAGAATGTTCATGCATCAAGGTTTTTGTAGATGCCATGAAATCTT
261 TTTTTATTGTTGCAGAATGTTCATGCATCAAGGTTTTTGTAGATGCCATGAAATCTT
890121 TTGTCGAGGC
Statistics
Matches: 317, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
325 317 1.00
ACGTcount: A:0.24, C:0.21, G:0.19, T:0.37
Consensus pattern (325 bp):
TGTTACGCCTTGGCGAGAATTATTCAGCTGTTCTCCCCCAAACTTGTCATCTTGATCAACTTGTT
TTCCACTCCTTAGCATAATTACATTGCATTGCTCCTTCCCATGATGCTTAGTGAATTCAGTATCA
CTAGGGAGATTTCCGTGTGGGTGAGAATGTAATTCCGTGGTAATCTATCCCACTTGATTCTCCAA
TACTCTGAGAGATGAACTATGGCTTTGCAAAAGTGTTGCCTGGCTTTGTAACAAATTTCCTTGAT
TTTTTATTGTTGCAGAATGTTCATGCATCAAGGTTTTTGTAGATGCCATGAAATCTTGATCAACT
Found at i:891691 original size:21 final size:19
Alignment explanation
Indices: 891653--891698 Score: 58
Period size: 20 Copynumber: 2.3 Consensus size: 19
891643 AATTAATCCT
891653 ACTAAGTATTAAAGCTAAGA
1 ACTAA-TATTAAAGCTAAGA
891673 ACTAATATTAAGGAGCTAAGA
1 ACTAATATTAA--AGCTAAGA
891694 A-TAAT
1 ACTAAT
891699 GATTCAATGA
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
19 6 0.25
20 9 0.38
21 9 0.38
ACGTcount: A:0.50, C:0.09, G:0.15, T:0.26
Consensus pattern (19 bp):
ACTAATATTAAAGCTAAGA
Found at i:892877 original size:19 final size:19
Alignment explanation
Indices: 892850--892896 Score: 76
Period size: 19 Copynumber: 2.5 Consensus size: 19
892840 GGCGAGATAA
*
892850 ATCTACTCCTCACATTCTC
1 ATCTGCTCCTCACATTCTC
*
892869 ATCTGCTCCTCACATTCTT
1 ATCTGCTCCTCACATTCTC
892888 ATCTGCTCC
1 ATCTGCTCC
892897 ATTGGCCTTT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
19 26 1.00
ACGTcount: A:0.17, C:0.40, G:0.04, T:0.38
Consensus pattern (19 bp):
ATCTGCTCCTCACATTCTC
Found at i:894253 original size:13 final size:13
Alignment explanation
Indices: 894237--894269 Score: 50
Period size: 13 Copynumber: 2.5 Consensus size: 13
894227 TTTTTTAGGA
894237 TTTTTTT-TATTT
1 TTTTTTTGTATTT
894249 TTTTTTTGTATTT
1 TTTTTTTGTATTT
894262 TTTATTTT
1 TTT-TTTT
894270 CTGTAATATA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
12 7 0.37
13 8 0.42
14 4 0.21
ACGTcount: A:0.09, C:0.00, G:0.03, T:0.88
Consensus pattern (13 bp):
TTTTTTTGTATTT
Found at i:895023 original size:2 final size:2
Alignment explanation
Indices: 895016--895041 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
895006 ATATTATACT
895016 TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA
895042 ATTTTAAAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:904903 original size:31 final size:32
Alignment explanation
Indices: 904862--904925 Score: 103
Period size: 31 Copynumber: 2.0 Consensus size: 32
904852 TATATATTTT
*
904862 CTACATATATAACAAGCTAAT-AAACACATTC
1 CTACAGATATAACAAGCTAATAAAACACATTC
*
904893 CTACAGATATAACAAGCTATTAAAACACATTC
1 CTACAGATATAACAAGCTAATAAAACACATTC
904925 C
1 C
904926 CCATAATTTG
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
31 19 0.63
32 11 0.37
ACGTcount: A:0.47, C:0.23, G:0.05, T:0.25
Consensus pattern (32 bp):
CTACAGATATAACAAGCTAATAAAACACATTC
Found at i:907144 original size:43 final size:44
Alignment explanation
Indices: 907053--907159 Score: 121
Period size: 43 Copynumber: 2.5 Consensus size: 44
907043 AGCAAATAAA
*** *
907053 TTCCCAAAATCAAACCGATACCCAAAAATCACAATGGAATGCAC
1 TTCCCAAAATCAAACATCTACCCAAAAATCACAATGGAATACAC
*
907097 -TCCCAAAATCAAACATCTACCCAAAAATCA-AGATTGAATAC-C
1 TTCCCAAAATCAAACATCTACCCAAAAATCACA-ATGGAATACAC
**
907139 TTCCCAAAATCGGACATCTAC
1 TTCCCAAAATCAAACATCTAC
907160 AAAGAAATCG
Statistics
Matches: 54, Mismatches: 7, Indels: 5
0.82 0.11 0.08
Matches are distributed among these distances:
42 2 0.04
43 52 0.96
ACGTcount: A:0.44, C:0.30, G:0.07, T:0.19
Consensus pattern (44 bp):
TTCCCAAAATCAAACATCTACCCAAAAATCACAATGGAATACAC
Found at i:908164 original size:51 final size:50
Alignment explanation
Indices: 908083--908233 Score: 178
Period size: 51 Copynumber: 3.0 Consensus size: 50
908073 TATTAATGAG
*
908083 ATTGGTCTTGAAGAGGAAATTACTGAAATTGAAGTTGTAAACAATGTGGAC
1 ATTGGTCTTGAAGAGGAAAATACTG-AATTGAAGTTGTAAACAATGTGGAC
* * *
908134 ATTGGTCTTGAAGAGAAAAAAACTAGAATTGAAGTTGTAAACATTGTGGAC
1 ATTGGTCTTGAAGAGGAAAATACT-GAATTGAAGTTGTAAACAATGTGGAC
* * * **
908185 ACTGCTATTGAAGAGGAAAATGTTGGAATT-AATGTTGTAAACAATGTGG
1 ATTGGTCTTGAAGAGGAAAATACT-GAATTGAA-GTTGTAAACAATGTGG
908234 TCTGTAATGA
Statistics
Matches: 85, Mismatches: 13, Indels: 4
0.83 0.13 0.04
Matches are distributed among these distances:
50 2 0.02
51 82 0.96
52 1 0.01
ACGTcount: A:0.38, C:0.07, G:0.25, T:0.29
Consensus pattern (50 bp):
ATTGGTCTTGAAGAGGAAAATACTGAATTGAAGTTGTAAACAATGTGGAC
Found at i:912582 original size:15 final size:15
Alignment explanation
Indices: 912559--912603 Score: 81
Period size: 15 Copynumber: 3.0 Consensus size: 15
912549 CCTAAATCAG
*
912559 TTTCCCTCTCTTCCC
1 TTTCACTCTCTTCCC
912574 TTTCACTCTCTTCCC
1 TTTCACTCTCTTCCC
912589 TTTCACTCTCTTCCC
1 TTTCACTCTCTTCCC
912604 ATTCCTTCTA
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
15 29 1.00
ACGTcount: A:0.04, C:0.49, G:0.00, T:0.47
Consensus pattern (15 bp):
TTTCACTCTCTTCCC
Found at i:912752 original size:48 final size:48
Alignment explanation
Indices: 912681--912776 Score: 192
Period size: 48 Copynumber: 2.0 Consensus size: 48
912671 GAATGATAAA
912681 TTGTTACTACCAAAGCGAACCAAAAAATCGATTCCTTTCTCGATTCTT
1 TTGTTACTACCAAAGCGAACCAAAAAATCGATTCCTTTCTCGATTCTT
912729 TTGTTACTACCAAAGCGAACCAAAAAATCGATTCCTTTCTCGATTCTT
1 TTGTTACTACCAAAGCGAACCAAAAAATCGATTCCTTTCTCGATTCTT
912777 ATAGCCTACA
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
48 48 1.00
ACGTcount: A:0.31, C:0.25, G:0.10, T:0.33
Consensus pattern (48 bp):
TTGTTACTACCAAAGCGAACCAAAAAATCGATTCCTTTCTCGATTCTT
Found at i:917791 original size:230 final size:230
Alignment explanation
Indices: 917344--917797 Score: 648
Period size: 230 Copynumber: 2.0 Consensus size: 230
917334 AAAACACTAG
* *
917344 TTTTTTAGTATTACAGTAATCGGAAATAAGGGTTAGATTTATGGGTTTAGGGGTTTTGAAGTAAA
1 TTTTTTAGTATTACAATAATCGAAAATAAGGGTTAGATTTATGGGTTTAGGGGTTTTGAAGTAAA
* ** *
917409 GAAGCATTTAAGACCGGTTACAGGTAGAAAGTGATATTCTAGGTAGAAAATAAATATCGATACTT
66 GAAGCATTCAAGACCAATTACAGGTAGAAAGTGATATTCTAGGAAGAAAATAAATATCGATACTT
* *
917474 TTATATAATATTATAGGTAGAAAATGATATTGTAGGTTGTATAAATATATCGATACTTGTAGTAG
131 TTATATAATATTATAGGTAGAAAATGATATTGTAGGTTGTACAAATATATCGATACTTATAGTAG
* * *
917539 AGAGTGTTCTCATTCCTTTGAA-GAAACCCTAGTT
196 AGAGTATTCACATTCATTTGAAGGAAACCCTAGTT
* *
917573 TTTTTTAGTATTACAATATTTGAAAAT-AGGGATTAGGGA-TTATGGGTTT-GGGGTTTTCGAAG
1 TTTTTTAGTATTACAATAATCGAAAATAAGGG-TTA--GATTTATGGGTTTAGGGGTTTT-GAAG
* * ** *
917635 TAAAGAAGGATTCGAGACCAATTAGTGTTAGAAAGTGATATTCTAGGAAGAAAATAAATATCGAT
62 TAAAGAAGCATTCAAGACCAATTACAGGTAGAAAGTGATATTCTAGGAAGAAAATAAATATCGAT
* *
917700 ACTTTTATATAATATTATAGGTAGAAAATGATATTTTAGGTTGTACAAATGTAAT-GATACTTAT
127 ACTTTTATATAATATTATAGGTAGAAAATGATATTGTAGGTTGTACAAATAT-ATCGATACTTAT
917764 AGTAGAGAGTATTCACATTCATTTGAAGGAAACC
191 AGTAGAGAGTATTCACATTCATTTGAAGGAAACC
917798 GTTTTACTAT
Statistics
Matches: 199, Mismatches: 20, Indels: 10
0.87 0.09 0.04
Matches are distributed among these distances:
228 4 0.02
229 34 0.17
230 151 0.76
231 10 0.05
ACGTcount: A:0.36, C:0.07, G:0.21, T:0.35
Consensus pattern (230 bp):
TTTTTTAGTATTACAATAATCGAAAATAAGGGTTAGATTTATGGGTTTAGGGGTTTTGAAGTAAA
GAAGCATTCAAGACCAATTACAGGTAGAAAGTGATATTCTAGGAAGAAAATAAATATCGATACTT
TTATATAATATTATAGGTAGAAAATGATATTGTAGGTTGTACAAATATATCGATACTTATAGTAG
AGAGTATTCACATTCATTTGAAGGAAACCCTAGTT
Found at i:919366 original size:12 final size:12
Alignment explanation
Indices: 919346--919402 Score: 71
Period size: 12 Copynumber: 4.8 Consensus size: 12
919336 GAAGAGGAAA
*
919346 AAGAGAATGAAG
1 AAGAAAATGAAG
919358 AAGAAAATGAAG
1 AAGAAAATGAAG
*
919370 AAGATAATGAAG
1 AAGAAAATGAAG
919382 AAGAGAAA-GAAG
1 AAGA-AAATGAAG
*
919394 AAGAGAATG
1 AAGAAAATG
919403 TAGTAGGGGA
Statistics
Matches: 39, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
11 2 0.05
12 35 0.90
13 2 0.05
ACGTcount: A:0.61, C:0.00, G:0.30, T:0.09
Consensus pattern (12 bp):
AAGAAAATGAAG
Found at i:919378 original size:24 final size:24
Alignment explanation
Indices: 919346--919402 Score: 89
Period size: 24 Copynumber: 2.4 Consensus size: 24
919336 GAAGAGGAAA
919346 AAGAGAATGAAGAAGA-AAATGAAG
1 AAGAGAATGAAGAAGAGAAA-GAAG
*
919370 AAGATAATGAAGAAGAGAAAGAAG
1 AAGAGAATGAAGAAGAGAAAGAAG
919394 AAGAGAATG
1 AAGAGAATG
919403 TAGTAGGGGA
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
24 27 0.90
25 3 0.10
ACGTcount: A:0.61, C:0.00, G:0.30, T:0.09
Consensus pattern (24 bp):
AAGAGAATGAAGAAGAGAAAGAAG
Found at i:921315 original size:18 final size:18
Alignment explanation
Indices: 921274--921322 Score: 62
Period size: 19 Copynumber: 2.7 Consensus size: 18
921264 GATGTAAGGC
* *
921274 AAATTTTTTATGTGAATT
1 AAATTTTGTATGTGAATG
921292 ATAATTTTGTATGTGAATG
1 A-AATTTTGTATGTGAATG
*
921311 AAATTATGTATG
1 AAATTTTGTATG
921323 AGATGATCAA
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
18 11 0.41
19 16 0.59
ACGTcount: A:0.35, C:0.00, G:0.16, T:0.49
Consensus pattern (18 bp):
AAATTTTGTATGTGAATG
Found at i:924270 original size:200 final size:200
Alignment explanation
Indices: 923922--924633 Score: 1013
Period size: 200 Copynumber: 3.6 Consensus size: 200
923912 CAACATTTTT
**
923922 TTACTTTAAAGTAAT-GTGTAAATTTACAATGTAAGAGGTAAAAATATACTAATTTAATGACAAA
1 TTACTTTAAAGTAATAG-GTAAATTTACAATGTAAGAGGTAAAAATATACCGATTTAATGACAAA
* * * * * * *
923986 ATGCGTAAACACAAAGTTTAGATACTTTTTTTATATGTATTGATACTTTGGGTCCATAATGT--T
65 ATACGTAAACATAAAGTTTCGATACTTTTTGTATATGTATCGATACTTTTGGT-C-TAGTGTGCT
* * *
924049 TCCCAAACAAGATGTACCCAGAAAGTATCGATACACGTATCAGAAGTATCGATTCTTACAA-TTT
128 TCCCAAACGAGATGCACCCAGAAAGTATCGATACACGTATCACAAGTATCGATTCTTACAACTTT
**
924113 CGAAAATGA
193 -GAAACCGA
* *
924122 TTACTTTAAAGTAATAGGTAAATTTACAATGTAAGAGATAAAAATATACCGGTTTAATGACAAAA
1 TTACTTTAAAGTAATAGGTAAATTTACAATGTAAGAGGTAAAAATATACCGATTTAATGACAAAA
924187 TACGTAAACATAAAGTTTCGATACTTTTTGTATATGTATCGATACTTTTGGTCTAGTGTGCTTCC
66 TACGTAAACATAAAGTTTCGATACTTTTTGTATATGTATCGATACTTTTGGTCTAGTGTGCTTCC
* ** *
924252 CAAATGAGATGCACCCAGAAAG--TCGATACACGTATCACAAGTATAAATTCTTAGAACTTTGAA
131 CAAACGAGATGCACCCAGAAAGTATCGATACACGTATCACAAGTATCGATTCTTACAACTTTGAA
924315 ACCGA
196 ACCGA
* * *
924320 TTAATTTAAAGTAATAGGTAAATTTACAATGTAAGAGGTAAAAATATGCCGGTTTAATGACAAAA
1 TTACTTTAAAGTAATAGGTAAATTTACAATGTAAGAGGTAAAAATATACCGATTTAATGACAAAA
* * * * * *
924385 TGCGTAAACATAAAGTTTCGATACTTTTTCTATATGTTTCGATACTTTTGGTCCAGTATGCTTCG
66 TACGTAAACATAAAGTTTCGATACTTTTTGTATATGTATCGATACTTTTGGTCTAGTGTGCTTCC
* * *
924450 CAAACGAGATGCACACAGAAAGTATCGATACACGTATCACAAGTATCGATTCTTATAACTTTTAA
131 CAAACGAGATGCACCCAGAAAGTATCGATACACGTATCACAAGTATCGATTCTTACAACTTTGAA
924515 ACCGA
196 ACCGA
* *
924520 TTACTTTAAAGTAATAGGTAAATTTACAATGTAAGCGGTAAAAATATATCGATTTAATGACAAAA
1 TTACTTTAAAGTAATAGGTAAATTTACAATGTAAGAGGTAAAAATATACCGATTTAATGACAAAA
* * *
924585 TACTTAAACATAAAGTTTTGATAATTTTTGTATATGTATCGATACTTTT
66 TACGTAAACATAAAGTTTCGATACTTTTTGTATATGTATCGATACTTTT
924634 AGCCCAATAT
Statistics
Matches: 460, Mismatches: 46, Indels: 12
0.89 0.09 0.02
Matches are distributed among these distances:
198 182 0.40
199 4 0.01
200 273 0.59
201 1 0.00
ACGTcount: A:0.38, C:0.13, G:0.15, T:0.34
Consensus pattern (200 bp):
TTACTTTAAAGTAATAGGTAAATTTACAATGTAAGAGGTAAAAATATACCGATTTAATGACAAAA
TACGTAAACATAAAGTTTCGATACTTTTTGTATATGTATCGATACTTTTGGTCTAGTGTGCTTCC
CAAACGAGATGCACCCAGAAAGTATCGATACACGTATCACAAGTATCGATTCTTACAACTTTGAA
ACCGA
Found at i:924345 original size:18 final size:20
Alignment explanation
Indices: 924322--924361 Score: 57
Period size: 20 Copynumber: 2.1 Consensus size: 20
924312 GAAACCGATT
*
924322 AATTTA-AA-GTAATAGGTA
1 AATTTACAATGTAAGAGGTA
924340 AATTTACAATGTAAGAGGTA
1 AATTTACAATGTAAGAGGTA
924360 AA
1 AA
924362 AATATGCCGG
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
18 6 0.32
19 2 0.11
20 11 0.58
ACGTcount: A:0.50, C:0.03, G:0.17, T:0.30
Consensus pattern (20 bp):
AATTTACAATGTAAGAGGTA
Found at i:925090 original size:17 final size:18
Alignment explanation
Indices: 925068--925109 Score: 68
Period size: 17 Copynumber: 2.4 Consensus size: 18
925058 CAAGGCACAG
925068 TTCTTCTCAACCAAAC-C
1 TTCTTCTCAACCAAACTC
*
925085 TTCTTCTCAACCAAGCTC
1 TTCTTCTCAACCAAACTC
925103 TTCTTCT
1 TTCTTCT
925110 GATGTAAGGG
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
17 15 0.65
18 8 0.35
ACGTcount: A:0.21, C:0.38, G:0.02, T:0.38
Consensus pattern (18 bp):
TTCTTCTCAACCAAACTC
Found at i:937084 original size:6 final size:6
Alignment explanation
Indices: 937077--937140 Score: 78
Period size: 6 Copynumber: 10.8 Consensus size: 6
937067 TGTAGTTTTC
* *
937077 AATTTC AATTTG AGA-TTG AATTTC AATTTG AATTTG AATTTG AATTT-
1 AATTTG AATTTG A-ATTTG AATTTG AATTTG AATTTG AATTTG AATTTG
*
937124 AATTTG AGTTTG AATTT
1 AATTTG AATTTG AATTT
937141 CAAATTCGGC
Statistics
Matches: 50, Mismatches: 5, Indels: 6
0.82 0.08 0.10
Matches are distributed among these distances:
5 6 0.12
6 43 0.86
7 1 0.02
ACGTcount: A:0.33, C:0.03, G:0.14, T:0.50
Consensus pattern (6 bp):
AATTTG
Found at i:938218 original size:18 final size:18
Alignment explanation
Indices: 938195--938232 Score: 76
Period size: 18 Copynumber: 2.1 Consensus size: 18
938185 ATGGTCGGGA
938195 TTTCCCTCACGTTTCATG
1 TTTCCCTCACGTTTCATG
938213 TTTCCCTCACGTTTCATG
1 TTTCCCTCACGTTTCATG
938231 TT
1 TT
938233 GGTTGATTGC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.11, C:0.32, G:0.11, T:0.47
Consensus pattern (18 bp):
TTTCCCTCACGTTTCATG
Found at i:940924 original size:2 final size:2
Alignment explanation
Indices: 940917--940958 Score: 84
Period size: 2 Copynumber: 21.0 Consensus size: 2
940907 TACACATACA
940917 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
940959 TCCATACATA
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:945785 original size:21 final size:21
Alignment explanation
Indices: 945761--945809 Score: 89
Period size: 21 Copynumber: 2.3 Consensus size: 21
945751 CAAGATTCAA
945761 GTGAAGAGGTGGATGAAGACG
1 GTGAAGAGGTGGATGAAGACG
945782 GTGAAGAGGTGGATGAAGACG
1 GTGAAGAGGTGGATGAAGACG
*
945803 ATGAAGA
1 GTGAAGA
945810 AGAAGAGATG
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.37, C:0.04, G:0.45, T:0.14
Consensus pattern (21 bp):
GTGAAGAGGTGGATGAAGACG
Found at i:946237 original size:19 final size:19
Alignment explanation
Indices: 946213--946249 Score: 74
Period size: 19 Copynumber: 1.9 Consensus size: 19
946203 TGAAAATGAT
946213 TTGATTTTGAAAATCAAAG
1 TTGATTTTGAAAATCAAAG
946232 TTGATTTTGAAAATCAAA
1 TTGATTTTGAAAATCAAA
946250 ATGAAATTTT
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:0.43, C:0.05, G:0.14, T:0.38
Consensus pattern (19 bp):
TTGATTTTGAAAATCAAAG
Found at i:946260 original size:20 final size:19
Alignment explanation
Indices: 946214--946264 Score: 68
Period size: 19 Copynumber: 2.6 Consensus size: 19
946204 GAAAATGATT
*
946214 TGATTTTGAAAATCAAAGT
1 TGATTTTGAAAATCAAAGA
946233 TGATTTTGAAAATCAAA-A
1 TGATTTTGAAAATCAAAGA
946251 TGAAATTTTGAAAA
1 TG--ATTTTGAAAA
946265 ATGATTTAGA
Statistics
Matches: 29, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
18 2 0.07
19 17 0.59
20 10 0.34
ACGTcount: A:0.47, C:0.04, G:0.14, T:0.35
Consensus pattern (19 bp):
TGATTTTGAAAATCAAAGA
Found at i:946609 original size:9 final size:9
Alignment explanation
Indices: 946595--946620 Score: 52
Period size: 9 Copynumber: 2.9 Consensus size: 9
946585 CAATGGTGAT
946595 GAAATTGAA
1 GAAATTGAA
946604 GAAATTGAA
1 GAAATTGAA
946613 GAAATTGA
1 GAAATTGA
946621 GATGCTCTAG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 17 1.00
ACGTcount: A:0.54, C:0.00, G:0.23, T:0.23
Consensus pattern (9 bp):
GAAATTGAA
Found at i:948882 original size:226 final size:226
Alignment explanation
Indices: 948488--948930 Score: 751
Period size: 226 Copynumber: 2.0 Consensus size: 226
948478 ATCTTAACAT
* *
948488 CAAATCAAATAATTAACCGGTTATGTTATTGTCGGATTTCTAAGGCTCCATCAGCTTAGACTTTG
1 CAAATCAAATAATTAACCGGTTATGTTATCGTCGGATTTCTAAGGCTCCATCAGCTTAAACTTTG
* *
948553 GTAACATTTTAGCCTTTACCTAATATGTTGATAATACTCATAACAAATTAAGTAATTAACCTATT
66 GTAACATTTTAGCCGTTACCTAATATGTTGATAATACTCATAACAAATTAAGTAATTAACATATT
* * * * * *
948618 TTGTTATCGTCGGATTTCTAAGGCCCCGTCATCTTTAAAAAGGTGCTACCTATTACGTTACATAA
131 TTGTTATCGTCAGATTTCTAAGGCCCCATCAGCTTTAAAAAAGCGCTACCAATTACGTTACATAA
948683 GCGCTACCTAATATGTTATTATGGTTGATAA
196 GCGCTACCTAATATGTTATTATGGTTGATAA
*
948714 CAAATCAAGTAATTAACCGGTTATGTTATCGTCGGATTTCTAAGGCTCCATCAGCTTAAACTTTG
1 CAAATCAAATAATTAACCGGTTATGTTATCGTCGGATTTCTAAGGCTCCATCAGCTTAAACTTTG
* * * *
948779 GTAACATTTTAGGCGTTACCTAGTATGTTGATAATACTGATAACAAATTAAGTAATTAACATGTT
66 GTAACATTTTAGCCGTTACCTAATATGTTGATAATACTCATAACAAATTAAGTAATTAACATATT
948844 TTGTTATCGTCAGATTTCTAAGGCCCCATCAGCTTTAAAAAAGCGCTACCAATTACGTTACATAA
131 TTGTTATCGTCAGATTTCTAAGGCCCCATCAGCTTTAAAAAAGCGCTACCAATTACGTTACATAA
948909 GCGCTACCTAATATGTTATTAT
196 GCGCTACCTAATATGTTATTAT
948931 TTTTTTATAA
Statistics
Matches: 202, Mismatches: 15, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
226 202 1.00
ACGTcount: A:0.32, C:0.18, G:0.15, T:0.36
Consensus pattern (226 bp):
CAAATCAAATAATTAACCGGTTATGTTATCGTCGGATTTCTAAGGCTCCATCAGCTTAAACTTTG
GTAACATTTTAGCCGTTACCTAATATGTTGATAATACTCATAACAAATTAAGTAATTAACATATT
TTGTTATCGTCAGATTTCTAAGGCCCCATCAGCTTTAAAAAAGCGCTACCAATTACGTTACATAA
GCGCTACCTAATATGTTATTATGGTTGATAA
Found at i:955375 original size:17 final size:17
Alignment explanation
Indices: 955315--955378 Score: 53
Period size: 17 Copynumber: 3.9 Consensus size: 17
955305 GATCTAATGT
*
955315 TTTTAGGTATTTTAGGG
1 TTTTAGGAATTTTAGGG
*
955332 -TTTA--AAGTTTAGGG
1 TTTTAGGAATTTTAGGG
* * * *
955346 TATAATGATTTTTAGGG
1 TTTTAGGAATTTTAGGG
955363 TTTTAGGAATTTTAGG
1 TTTTAGGAATTTTAGG
955379 ATTAAGGGTT
Statistics
Matches: 34, Mismatches: 10, Indels: 6
0.68 0.20 0.12
Matches are distributed among these distances:
14 8 0.24
15 2 0.06
16 4 0.12
17 20 0.59
ACGTcount: A:0.25, C:0.00, G:0.27, T:0.48
Consensus pattern (17 bp):
TTTTAGGAATTTTAGGG
Found at i:955486 original size:25 final size:25
Alignment explanation
Indices: 955431--955507 Score: 90
Period size: 24 Copynumber: 3.2 Consensus size: 25
955421 TTTTAATATA
*
955431 TTTTAGGTTGAAGTGGA-TTAA-GGT
1 TTTTAGGTTAAAGT-GATTTAAGGGT
*
955455 TTTTAGGTTAAAATTG-TTTAAGGGT
1 TTTTAGGTT-AAAGTGATTTAAGGGT
955480 TTTTAGGTTAAAGTGATTT-AGGGT
1 TTTTAGGTTAAAGTGATTTAAGGGT
955504 TTTT
1 TTTT
955508 TAGGGTTTAG
Statistics
Matches: 46, Mismatches: 3, Indels: 8
0.81 0.05 0.14
Matches are distributed among these distances:
24 28 0.61
25 18 0.39
ACGTcount: A:0.25, C:0.00, G:0.27, T:0.48
Consensus pattern (25 bp):
TTTTAGGTTAAAGTGATTTAAGGGT
Found at i:955683 original size:25 final size:25
Alignment explanation
Indices: 955582--955676 Score: 109
Period size: 25 Copynumber: 3.8 Consensus size: 25
955572 GGTTAATATA
* *
955582 TTTTAGGTTAAAGTGTTTTAGAATTT
1 TTTTAGGTTAAAGTGGTTTAG-AGTT
* *
955608 TTTTAGGTTAAATTTGTTTAGAGTT
1 TTTTAGGTTAAAGTGGTTTAGAGTT
* * * *
955633 GTTTAGGTTAAAGTAGTTAAGGGTT
1 TTTTAGGTTAAAGTGGTTTAGAGTT
955658 TTTTAGGTTAAAGTGGTTT
1 TTTTAGGTTAAAGTGGTTT
955677 GGGGTTTATT
Statistics
Matches: 57, Mismatches: 12, Indels: 1
0.81 0.17 0.01
Matches are distributed among these distances:
25 39 0.68
26 18 0.32
ACGTcount: A:0.25, C:0.00, G:0.24, T:0.51
Consensus pattern (25 bp):
TTTTAGGTTAAAGTGGTTTAGAGTT
Found at i:956023 original size:27 final size:29
Alignment explanation
Indices: 955993--956145 Score: 115
Period size: 25 Copynumber: 5.7 Consensus size: 29
955983 AAAAAAATGG
955993 AAAATACACATACATTGAAAAATATTTA-A
1 AAAATACACATACATTGAAAAATA-TTAGA
956022 AAAATACA-ATTACATTG--AAATATTAGA
1 AAAATACACA-TACATTGAAAAATATTAGA
956049 AACAA-ACACATACATTG--AAATATTAG-
1 AA-AATACACATACATTGAAAAATATTAGA
*
956075 AAAATA-AGATTACATTG--AAATATTAG-
1 AAAATACACA-TACATTGAAAAATATTAGA
*
956101 AAAAGA-ACATACATTG--AAATATTAG-
1 AAAATACACATACATTGAAAAATATTAGA
* *
956126 AAAA-GCACATACATAGAAAA
1 AAAATACACATACATTGAAAA
956146 TACAATTACA
Statistics
Matches: 110, Mismatches: 5, Indels: 20
0.81 0.04 0.15
Matches are distributed among these distances:
25 33 0.30
26 29 0.26
27 29 0.26
28 4 0.04
29 15 0.14
ACGTcount: A:0.57, C:0.10, G:0.08, T:0.25
Consensus pattern (29 bp):
AAAATACACATACATTGAAAAATATTAGA
Found at i:956091 original size:53 final size:52
Alignment explanation
Indices: 955992--956129 Score: 190
Period size: 53 Copynumber: 2.6 Consensus size: 52
955982 CAAAAAAATG
* *
955992 GAAAATACACATACATTGAAAAATATTTAAAAAATACAATTACATTGAAATATTA
1 GAAAAAACACATACATTG--AAATA-TTAGAAAATACAATTACATTGAAATATTA
956047 GAAACAAACACATACATTGAAATATTAGAAAATA-AGATTACATTGAAATATTA
1 GAAA-AAACACATACATTGAAATATTAGAAAATACA-ATTACATTGAAATATTA
*
956100 GAAAAGA-ACATACATTGAAATATTAGAAAA
1 GAAAAAACACATACATTGAAATATTAGAAAA
956130 GCACATACAT
Statistics
Matches: 78, Mismatches: 3, Indels: 8
0.88 0.03 0.09
Matches are distributed among these distances:
51 23 0.29
52 3 0.04
53 30 0.38
54 5 0.06
55 4 0.05
56 13 0.17
ACGTcount: A:0.57, C:0.09, G:0.09, T:0.26
Consensus pattern (52 bp):
GAAAAAACACATACATTGAAATATTAGAAAATACAATTACATTGAAATATTA
Found at i:956095 original size:26 final size:26
Alignment explanation
Indices: 955992--956129 Score: 149
Period size: 27 Copynumber: 5.2 Consensus size: 26
955982 CAAAAAAATG
955992 GAAAATACACA-TACATTGAAAAATATTTA
1 GAAAATA-ACATTACATTG--AAATA-TTA
*
956021 AAAAAT-ACAATTACATTGAAATATTA
1 GAAAATAAC-ATTACATTGAAATATTA
*
956047 GAAACA-AACACATACATTGAAATATTA
1 GAAA-ATAACA-TTACATTGAAATATTA
*
956074 GAAAATAAGATTACATTGAAATATTA
1 GAAAATAACATTACATTGAAATATTA
*
956100 GAAAAGAACA-TACATTGAAATATTA
1 GAAAATAACATTACATTGAAATATTA
956125 GAAAA
1 GAAAA
956130 GCACATACAT
Statistics
Matches: 96, Mismatches: 7, Indels: 16
0.81 0.06 0.13
Matches are distributed among these distances:
25 20 0.21
26 31 0.32
27 32 0.33
28 1 0.01
29 12 0.12
ACGTcount: A:0.57, C:0.09, G:0.09, T:0.26
Consensus pattern (26 bp):
GAAAATAACATTACATTGAAATATTA
Found at i:956119 original size:25 final size:25
Alignment explanation
Indices: 956032--956144 Score: 154
Period size: 25 Copynumber: 4.4 Consensus size: 25
956022 AAAATACAAT
*
956032 TACATTGAAATATTAGAAACAAACACA
1 TACATTGAAATATTAGAAA-AGA-ACA
* *
956059 TACATTGAAATATTAGAAAATAAGA
1 TACATTGAAATATTAGAAAAGAACA
956084 TTACATTGAAATATTAGAAAAGAACA
1 -TACATTGAAATATTAGAAAAGAACA
*
956110 TACATTGAAATATTAGAAAAGCACA
1 TACATTGAAATATTAGAAAAGAACA
*
956135 TACATAGAAA
1 TACATTGAAA
956145 ATACAATTAC
Statistics
Matches: 79, Mismatches: 6, Indels: 4
0.89 0.07 0.04
Matches are distributed among these distances:
25 35 0.44
26 25 0.32
27 19 0.24
ACGTcount: A:0.55, C:0.10, G:0.11, T:0.25
Consensus pattern (25 bp):
TACATTGAAATATTAGAAAAGAACA
Found at i:956147 original size:51 final size:53
Alignment explanation
Indices: 955998--956144 Score: 160
Period size: 51 Copynumber: 2.8 Consensus size: 53
955988 AATGGAAAAT
*
955998 ACACATACATTGAAAAATATTTA-AAAA-ATACAATTACATTGAAATATTAGAAACAA
1 ACACATACATTG--AAATA-TTAGAAAAGA-AC-ATTACATAGAAATATTAGAAACAA
* * * *
956054 ACACATACATTGAAATATTAGAAAATAAGATTACATTGAAATATTAGAAA-AG
1 ACACATACATTGAAATATTAGAAAAGAACATTACATAGAAATATTAGAAACAA
*
956106 A-ACATACATTGAAATATTAGAAAAGCACA-TACATAGAAA
1 ACACATACATTGAAATATTAGAAAAGAACATTACATAGAAA
956145 ATACAATTAC
Statistics
Matches: 83, Mismatches: 6, Indels: 10
0.84 0.06 0.10
Matches are distributed among these distances:
50 9 0.11
51 25 0.30
52 2 0.02
53 24 0.29
54 10 0.12
55 1 0.01
56 12 0.14
ACGTcount: A:0.56, C:0.10, G:0.09, T:0.25
Consensus pattern (53 bp):
ACACATACATTGAAATATTAGAAAAGAACATTACATAGAAATATTAGAAACAA
Found at i:960967 original size:16 final size:16
Alignment explanation
Indices: 960916--960970 Score: 60
Period size: 16 Copynumber: 3.3 Consensus size: 16
960906 ATACGGTAAA
960916 AATTTTAAATTTTATTTT
1 AATTTT-AA-TTTATTTT
960934 AATTTTAA-TTATTGTT
1 AATTTTAATTTATT-TT
960950 AATATTTAATTTA-TTT
1 AAT-TTTAATTTATTTT
960966 AATTT
1 AATTT
960971 GTTTAGTATT
Statistics
Matches: 34, Mismatches: 0, Indels: 9
0.79 0.00 0.21
Matches are distributed among these distances:
15 7 0.21
16 10 0.29
17 8 0.24
18 9 0.26
ACGTcount: A:0.35, C:0.00, G:0.02, T:0.64
Consensus pattern (16 bp):
AATTTTAATTTATTTT
Found at i:962535 original size:90 final size:91
Alignment explanation
Indices: 962381--962559 Score: 270
Period size: 90 Copynumber: 2.0 Consensus size: 91
962371 CCTAACACAC
* * *
962381 CCTTTTATAGCCAAGTTACCCTAGTCATATTAGGGTTTTTTATTATTTAAAATTAATTAAATCTA
1 CCTTTTATAGCCAAGTTACCCTAATCATATCAGGGTATTTTATTATTTAAAATTAATTAAATCTA
* *
962446 TATTTAATTAATTGGAATTTAATAAT
66 TATTTAATTAATTGAAATTAAATAAT
* * * *
962472 CCTTTTATATCCAAGTTATCCTAATCATATCATGG-ATTTTATTATTTCAAATTAATTAAATCTA
1 CCTTTTATAGCCAAGTTACCCTAATCATATCAGGGTATTTTATTATTTAAAATTAATTAAATCTA
962536 TATTTAATTAATTGAAATTAAATA
66 TATTTAATTAATTGAAATTAAATA
962560 TTCGAGATTA
Statistics
Matches: 79, Mismatches: 9, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
90 49 0.62
91 30 0.38
ACGTcount: A:0.37, C:0.11, G:0.07, T:0.46
Consensus pattern (91 bp):
CCTTTTATAGCCAAGTTACCCTAATCATATCAGGGTATTTTATTATTTAAAATTAATTAAATCTA
TATTTAATTAATTGAAATTAAATAAT
Found at i:969408 original size:90 final size:90
Alignment explanation
Indices: 969254--969429 Score: 291
Period size: 90 Copynumber: 2.0 Consensus size: 90
969244 CCTAACCCAC
* * * *
969254 CCTTTTATAGCCAAGTTACCCTAGTCATATTAGGGTTTTTTATTATTTCAAATTAATTAAATCTA
1 CCTTTTATAGCCAAGTTACCCTAATCATATCAGAGTATTTTATTATTTCAAATTAATTAAATCTA
969319 TATTTAATTAATTGGAAATTAATAAT
66 TATTTAATTAATT-GAAATTAATAAT
*
969345 CCTTTTATATCCAAGTTACCCTAATCATATCAGAG-ATTTTATTATTTCAAATTAATTAAATCTA
1 CCTTTTATAGCCAAGTTACCCTAATCATATCAGAGTATTTTATTATTTCAAATTAATTAAATCTA
969409 TATTTAATTAATTGAAATTAA
66 TATTTAATTAATTGAAATTAA
969430 ATATTTGGGA
Statistics
Matches: 80, Mismatches: 5, Indels: 2
0.92 0.06 0.02
Matches are distributed among these distances:
89 8 0.10
90 41 0.51
91 31 0.39
ACGTcount: A:0.37, C:0.12, G:0.07, T:0.44
Consensus pattern (90 bp):
CCTTTTATAGCCAAGTTACCCTAATCATATCAGAGTATTTTATTATTTCAAATTAATTAAATCTA
TATTTAATTAATTGAAATTAATAAT
Found at i:979691 original size:35 final size:35
Alignment explanation
Indices: 979632--979700 Score: 86
Period size: 35 Copynumber: 2.0 Consensus size: 35
979622 GTTATTCAAG
* *
979632 GGGTATCAATACCTAAGGGGTAGTATCGATACCAA
1 GGGTATCAATACCTAAGGGCTAGTAGCGATACCAA
* *
979667 GGGTATCGATACCATAA-GGCTAGTAGCGGTACCA
1 GGGTATCAATACC-TAAGGGCTAGTAGCGATACCA
979701 TTTTGAAATA
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
35 26 0.90
36 3 0.10
ACGTcount: A:0.32, C:0.19, G:0.28, T:0.22
Consensus pattern (35 bp):
GGGTATCAATACCTAAGGGCTAGTAGCGATACCAA
Found at i:980456 original size:21 final size:21
Alignment explanation
Indices: 980408--980467 Score: 75
Period size: 21 Copynumber: 2.9 Consensus size: 21
980398 CGAGGGTTAT
*
980408 ATGAGGTCCTTCGGGACATAT
1 ATGAGGTCCTTCGGGACATAC
**
980429 ACAAGGTCCTTCGGGACATAC
1 ATGAGGTCCTTCGGGACATAC
* *
980450 ATGAGGTTCTACGGGACA
1 ATGAGGTCCTTCGGGACA
980468 AATTTTATAT
Statistics
Matches: 32, Mismatches: 7, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
21 32 1.00
ACGTcount: A:0.27, C:0.22, G:0.28, T:0.23
Consensus pattern (21 bp):
ATGAGGTCCTTCGGGACATAC
Found at i:981298 original size:18 final size:19
Alignment explanation
Indices: 981275--981331 Score: 55
Period size: 18 Copynumber: 3.0 Consensus size: 19
981265 TATAATATTA
981275 TTATAAATATATAA-AATT
1 TTATAAATATATAACAATT
**
981293 TTATAAAT-TAATAATTATT
1 TTATAAATAT-ATAACAATT
*
981312 TTATAATAAATATAACAATT
1 TTATAA-ATATATAACAATT
981332 AATAAATTTA
Statistics
Matches: 31, Mismatches: 4, Indels: 6
0.76 0.10 0.15
Matches are distributed among these distances:
17 1 0.03
18 12 0.39
19 9 0.29
20 8 0.26
21 1 0.03
ACGTcount: A:0.53, C:0.02, G:0.00, T:0.46
Consensus pattern (19 bp):
TTATAAATATATAACAATT
Found at i:981310 original size:43 final size:40
Alignment explanation
Indices: 981242--981325 Score: 98
Period size: 43 Copynumber: 2.0 Consensus size: 40
981232 AACAATATTC
* *
981242 ATAAAATTATTATAAATAACCATTATAATATTATTATAAATAT
1 ATAAAATTATTATAAATAACAATTAT--T-TTATAATAAATAT
*
981285 ATAAAATT-TTATAAATTAATAATTATTTTATAATAAATAT
1 ATAAAATTATTATAAA-TAACAATTATTTTATAATAAATAT
981325 A
1 A
981326 ACAATTAATA
Statistics
Matches: 37, Mismatches: 3, Indels: 5
0.82 0.07 0.11
Matches are distributed among these distances:
40 13 0.35
41 1 0.03
42 7 0.19
43 16 0.43
ACGTcount: A:0.54, C:0.02, G:0.00, T:0.44
Consensus pattern (40 bp):
ATAAAATTATTATAAATAACAATTATTTTATAATAAATAT
Found at i:981352 original size:39 final size:40
Alignment explanation
Indices: 981272--981353 Score: 105
Period size: 39 Copynumber: 2.1 Consensus size: 40
981262 CATTATAATA
* *
981272 TTATTATAAATATATAAAATTTTATAAATTAATAATTATT
1 TTATAATAAATATATAAAATTTAATAAATTAATAATTATT
* *
981312 TTATAATAAATATA-ACAA-TTAATAAATTTAATGATTATT
1 TTATAATAAATATATAAAATTTAATAAA-TTAATAATTATT
981351 TTA
1 TTA
981354 AGTAAATGTA
Statistics
Matches: 37, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
38 7 0.19
39 17 0.46
40 13 0.35
ACGTcount: A:0.50, C:0.01, G:0.01, T:0.48
Consensus pattern (40 bp):
TTATAATAAATATATAAAATTTAATAAATTAATAATTATT
Found at i:981983 original size:24 final size:25
Alignment explanation
Indices: 981941--981988 Score: 62
Period size: 24 Copynumber: 2.0 Consensus size: 25
981931 ATTATTAATT
**
981941 TTTTAAACATAAATGATAGATAGAA
1 TTTTAAACATAAACAATAGATAGAA
*
981966 TTTTAAA-ATAAACAATAGTTAGA
1 TTTTAAACATAAACAATAGATAGA
981989 TGATTAAAAC
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
24 13 0.65
25 7 0.35
ACGTcount: A:0.52, C:0.04, G:0.10, T:0.33
Consensus pattern (25 bp):
TTTTAAACATAAACAATAGATAGAA
Found at i:982413 original size:7 final size:7
Alignment explanation
Indices: 982401--982426 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
982391 TATTTATCAT
982401 ATATTTA
1 ATATTTA
982408 ATATTTA
1 ATATTTA
982415 ATATTTA
1 ATATTTA
982422 ATATT
1 ATATT
982427 AAATGAGATA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (7 bp):
ATATTTA
Found at i:982670 original size:20 final size:20
Alignment explanation
Indices: 982618--982671 Score: 90
Period size: 20 Copynumber: 2.7 Consensus size: 20
982608 TTGTTCTCAA
* *
982618 TATTTAGAATATCTAAGATT
1 TATTTAAAATATTTAAGATT
982638 TATTTAAAATATTTAAGATT
1 TATTTAAAATATTTAAGATT
982658 TATTTAAAATATTT
1 TATTTAAAATATTT
982672 GTATACATAA
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 32 1.00
ACGTcount: A:0.43, C:0.02, G:0.06, T:0.50
Consensus pattern (20 bp):
TATTTAAAATATTTAAGATT
Found at i:983728 original size:23 final size:23
Alignment explanation
Indices: 983702--983750 Score: 64
Period size: 23 Copynumber: 2.1 Consensus size: 23
983692 TTTTTATTTG
983702 AAAA-AATATAATTTTTAATCCAA
1 AAAAGAATATAA-TTTTAATCCAA
* *
983725 AAAAGTATATGATTTTAATCCAA
1 AAAAGAATATAATTTTAATCCAA
983748 AAA
1 AAA
983751 TTCATCGTAA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
23 18 0.78
24 5 0.22
ACGTcount: A:0.55, C:0.08, G:0.04, T:0.33
Consensus pattern (23 bp):
AAAAGAATATAATTTTAATCCAA
Found at i:984558 original size:23 final size:25
Alignment explanation
Indices: 984507--984562 Score: 71
Period size: 28 Copynumber: 2.2 Consensus size: 25
984497 TAACGGAATG
984507 AAACGTTAGGCACTAAACTGGAACGAAA
1 AAACGTTAGGCACTAAACT---ACGAAA
984535 AAACGTTAGGCACTAAACT-C-AAA
1 AAACGTTAGGCACTAAACTACGAAA
984558 AAACG
1 AAACG
984563 GTCATACGTT
Statistics
Matches: 28, Mismatches: 0, Indels: 5
0.85 0.00 0.15
Matches are distributed among these distances:
23 8 0.29
24 1 0.04
28 19 0.68
ACGTcount: A:0.48, C:0.20, G:0.18, T:0.14
Consensus pattern (25 bp):
AAACGTTAGGCACTAAACTACGAAA
Found at i:984945 original size:17 final size:17
Alignment explanation
Indices: 984925--984961 Score: 56
Period size: 17 Copynumber: 2.2 Consensus size: 17
984915 ATGTGTTACA
*
984925 TTTAGGGATTTAGGATT
1 TTTAGGGATTTAGCATT
*
984942 TTTATGGATTTAGCATT
1 TTTAGGGATTTAGCATT
984959 TTT
1 TTT
984962 TTGTAATTTA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.22, C:0.03, G:0.22, T:0.54
Consensus pattern (17 bp):
TTTAGGGATTTAGCATT
Found at i:988688 original size:39 final size:38
Alignment explanation
Indices: 988640--988748 Score: 130
Period size: 39 Copynumber: 2.8 Consensus size: 38
988630 TAATTTGAGA
*
988640 AATAATTTAGATAGTT-TGGGTGAAATAATTTAACAAATT
1 AATAATTTAGATA-TTAT-GGTGAAATAATTTAAAAAATT
988679 AATAATTTAGAATATTATGGTGAAATAATTTAAAAAATT
1 AATAATTTAG-ATATTATGGTGAAATAATTTAAAAAATT
** * *
988718 AGGAATTTAGAATGTTATGATGAAATAATTT
1 AATAATTTAG-ATATTATGGTGAAATAATTT
988749 GGGAATTAAG
Statistics
Matches: 63, Mismatches: 5, Indels: 4
0.88 0.07 0.06
Matches are distributed among these distances:
39 59 0.94
40 4 0.06
ACGTcount: A:0.46, C:0.01, G:0.15, T:0.39
Consensus pattern (38 bp):
AATAATTTAGATATTATGGTGAAATAATTTAAAAAATT
Found at i:989583 original size:20 final size:20
Alignment explanation
Indices: 989448--989797 Score: 338
Period size: 20 Copynumber: 17.3 Consensus size: 20
989438 GATTCTGACT
* **
989448 ATCGCATTGCGATTTCCCAA
1 ATCGCATTGCGATTTACGTA
* * *
989468 ATTCGCGTTGCGATTTTCCTA
1 A-TCGCATTGCGATTTACGTA
* *
989489 ATTCGCAATGCGA-ATACGTAA
1 A-TCGCATTGCGATTTACGT-A
* *
989510 ATCGCAATGCGAATTACGTAA
1 ATCGCATTGCGATTTACGT-A
*
989531 ATCGCAATGCGA-TTACGTA
1 ATCGCATTGCGATTTACGTA
989550 GATCGCATTGCGA-TTACGTA
1 -ATCGCATTGCGATTTACGTA
*
989570 GATCGCATTGCGA-TTATGTA
1 -ATCGCATTGCGATTTACGTA
*
989590 TTCGCATTGCGATTTACGTA
1 ATCGCATTGCGATTTACGTA
* *
989610 ATCGC-TTGCGATTTTCCTA
1 ATCGCATTGCGATTTACGTA
*
989629 ATTCGTATTGCGATTTACGTA
1 A-TCGCATTGCGATTTACGTA
*
989650 ACCGCATTGCGATTTACGTA
1 ATCGCATTGCGATTTACGTA
989670 A-CTGCATTGCGATTTACGTA
1 ATC-GCATTGCGATTTACGTA
* *
989690 ATCGCATTGCGATTTTCCTA
1 ATCGCATTGCGATTTACGTA
989710 ATTCGCATTGCGATTTACGTA
1 A-TCGCATTGCGATTTACGTA
* * *
989731 ATCACATTGCGATTTTCCTA
1 ATCGCATTGCGATTTACGTA
989751 ATTCGCACTT-CGATTTACGTA
1 A-TCGCA-TTGCGATTTACGTA
989772 ATCGCATTGCGATTTA-GTAA
1 ATCGCATTGCGATTTACGT-A
989792 ATCGCA
1 ATCGCA
989798 ATGAGATTCT
Statistics
Matches: 285, Mismatches: 31, Indels: 28
0.83 0.09 0.08
Matches are distributed among these distances:
19 30 0.11
20 159 0.56
21 94 0.33
22 2 0.01
ACGTcount: A:0.25, C:0.21, G:0.19, T:0.35
Consensus pattern (20 bp):
ATCGCATTGCGATTTACGTA
Found at i:989730 original size:41 final size:41
Alignment explanation
Indices: 989448--989786 Score: 363
Period size: 41 Copynumber: 8.4 Consensus size: 41
989438 GATTCTGACT
* * * * *
989448 ATCGCATTGCGATTTCCCAAATTCGCGTTGCGATTTTCCTA
1 ATCGCATTGCGATTTTCCTAATTCGCATTGCGATTTACGTA
* * * * * * *
989489 ATTCGCAATGCGA-ATACGTAAATCGCAATGCGAATTACGTAA
1 A-TCGCATTGCGATTTTCCTAATTCGCATTGCGATTTACGT-A
* * *
989531 ATCGCAATGCGA-TTACGTAGA-TCGCATTGCGA-TTACGTA
1 ATCGCATTGCGATTTTCCTA-ATTCGCATTGCGATTTACGTA
* *
989570 GATCGCATTGCGATTAT-GT-ATTCGCATTGCGATTTACGTA
1 -ATCGCATTGCGATTTTCCTAATTCGCATTGCGATTTACGTA
*
989610 ATCGC-TTGCGATTTTCCTAATTCGTATTGCGATTTACGTA
1 ATCGCATTGCGATTTTCCTAATTCGCATTGCGATTTACGTA
* * * *
989650 ACCGCATTGCGATTTACGTAACT-GCATTGCGATTTACGTA
1 ATCGCATTGCGATTTTCCTAATTCGCATTGCGATTTACGTA
989690 ATCGCATTGCGATTTTCCTAATTCGCATTGCGATTTACGTA
1 ATCGCATTGCGATTTTCCTAATTCGCATTGCGATTTACGTA
*
989731 ATCACATTGCGATTTTCCTAATTCGCACTT-CGATTTACGTA
1 ATCGCATTGCGATTTTCCTAATTCGCA-TTGCGATTTACGTA
989772 ATCGCATTGCGATTT
1 ATCGCATTGCGATTT
989787 AGTAAATCGC
Statistics
Matches: 256, Mismatches: 30, Indels: 24
0.83 0.10 0.08
Matches are distributed among these distances:
38 10 0.04
39 18 0.07
40 85 0.33
41 128 0.50
42 15 0.06
ACGTcount: A:0.25, C:0.22, G:0.19, T:0.35
Consensus pattern (41 bp):
ATCGCATTGCGATTTTCCTAATTCGCATTGCGATTTACGTA
Found at i:990687 original size:24 final size:24
Alignment explanation
Indices: 990660--990713 Score: 81
Period size: 24 Copynumber: 2.2 Consensus size: 24
990650 GTATTCGAAA
*
990660 TTTGTTCTTGGTCAATACCCGGAC
1 TTTGATCTTGGTCAATACCCGGAC
* *
990684 TTTGATCTTGGTCAATACTCGGAT
1 TTTGATCTTGGTCAATACCCGGAC
990708 TTTGAT
1 TTTGAT
990714 GATTTTTCAG
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.19, C:0.19, G:0.20, T:0.43
Consensus pattern (24 bp):
TTTGATCTTGGTCAATACCCGGAC
Found at i:993250 original size:20 final size:20
Alignment explanation
Indices: 993183--993275 Score: 66
Period size: 20 Copynumber: 4.7 Consensus size: 20
993173 GGCATTCATT
993183 TGACTATCGCAACACGGAAA
1 TGACTATCGCAACACGGAAA
**
993203 TGACGT-TCGCAATCATC-TTAA
1 TGAC-TATCGCAA-CA-CGGAAA
* *
993224 TGTCTATCGCAACGCGGAAA
1 TGACTATCGCAACACGGAAA
* *
993244 TGACTATCGTAATAC-GAAA
1 TGACTATCGCAACACGGAAA
**
993263 TGAAAATCGCAAC
1 TGACTATCGCAAC
993276 TAGAGAATCG
Statistics
Matches: 54, Mismatches: 14, Indels: 11
0.68 0.18 0.14
Matches are distributed among these distances:
19 14 0.26
20 25 0.46
21 14 0.26
22 1 0.02
ACGTcount: A:0.37, C:0.23, G:0.18, T:0.23
Consensus pattern (20 bp):
TGACTATCGCAACACGGAAA
Found at i:993300 original size:33 final size:33
Alignment explanation
Indices: 993249--993375 Score: 182
Period size: 33 Copynumber: 3.8 Consensus size: 33
993239 GGAAATGACT
* * * *
993249 ATCGTAATACGAAATGAAAATCGCAACTAGAGA
1 ATCGCAATGCGAAATGAAAATCACAACGAGAGA
993282 ATCGCAATGCGAAATGAAAATCACAACGAGAGA
1 ATCGCAATGCGAAATGAAAATCACAACGAGAGA
* *
993315 ATCGCAATGCGAAATGAAAATCGCAACGAGGGA
1 ATCGCAATGCGAAATGAAAATCACAACGAGAGA
* *
993348 ATCACAAAGCGAAATGAAAATCACAACG
1 ATCGCAATGCGAAATGAAAATCACAACG
993376 CGAATTTAGT
Statistics
Matches: 85, Mismatches: 9, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
33 85 1.00
ACGTcount: A:0.48, C:0.18, G:0.20, T:0.13
Consensus pattern (33 bp):
ATCGCAATGCGAAATGAAAATCACAACGAGAGA
Found at i:993338 original size:19 final size:19
Alignment explanation
Indices: 993281--993340 Score: 67
Period size: 19 Copynumber: 3.4 Consensus size: 19
993271 GCAACTAGAG
993281 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
* *
993300 AATCACAA--CG--A-GAG
1 AATCGCAATGCGAAATGAA
993314 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
993333 AATCGCAA
1 AATCGCAA
993341 CGAGGGAATC
Statistics
Matches: 32, Mismatches: 4, Indels: 10
0.70 0.09 0.22
Matches are distributed among these distances:
14 9 0.28
15 1 0.03
16 2 0.06
17 2 0.06
18 1 0.03
19 17 0.53
ACGTcount: A:0.48, C:0.18, G:0.20, T:0.13
Consensus pattern (19 bp):
AATCGCAATGCGAAATGAA
Found at i:994731 original size:19 final size:19
Alignment explanation
Indices: 994707--994773 Score: 63
Period size: 20 Copynumber: 3.7 Consensus size: 19
994697 TAAATCGCAA
994707 TTGCGATTTTCATTTCGCG
1 TTGCGATTTTCATTTCGCG
994726 TTGCGATTTTC---T--CG
1 TTGCGATTTTCATTTCGCG
**
994740 TTGCGATAGTCATTTCCGCG
1 TTGCGATTTTCATTT-CGCG
*
994760 TTGTGATTTTCATT
1 TTGCGATTTTCATT
994774 CTCGAAACTA
Statistics
Matches: 37, Mismatches: 5, Indels: 11
0.70 0.09 0.21
Matches are distributed among these distances:
14 11 0.30
16 1 0.03
17 1 0.03
19 11 0.30
20 13 0.35
ACGTcount: A:0.12, C:0.19, G:0.21, T:0.48
Consensus pattern (19 bp):
TTGCGATTTTCATTTCGCG
Found at i:994753 original size:33 final size:34
Alignment explanation
Indices: 994707--994770 Score: 94
Period size: 34 Copynumber: 1.9 Consensus size: 34
994697 TAAATCGCAA
**
994707 TTGCGATTTTCATTT-CGCGTTGCGATTTTCTCG
1 TTGCGATAGTCATTTCCGCGTTGCGATTTTCTCG
*
994740 TTGCGATAGTCATTTCCGCGTTGTGATTTTC
1 TTGCGATAGTCATTTCCGCGTTGCGATTTTC
994771 ATTCTCGAAA
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
33 13 0.48
34 14 0.52
ACGTcount: A:0.11, C:0.20, G:0.22, T:0.47
Consensus pattern (34 bp):
TTGCGATAGTCATTTCCGCGTTGCGATTTTCTCG
Found at i:995340 original size:20 final size:20
Alignment explanation
Indices: 995317--995410 Score: 116
Period size: 20 Copynumber: 4.7 Consensus size: 20
995307 CGATAGTCAG
995317 ATTCGCATTGCGATTTACGT
1 ATTCGCATTGCGATTTACGT
* *
995337 ATTCGCATTGCGATTTTCCT
1 ATTCGCATTGCGATTTACGT
* * *
995357 AATTCACATTGCAATTTACTT
1 -ATTCGCATTGCGATTTACGT
* *
995378 AATCGCGTTGCGATTTACGT
1 ATTCGCATTGCGATTTACGT
995398 ATTCGCATTGCGA
1 ATTCGCATTGCGA
995411 ATTAGGGAAA
Statistics
Matches: 60, Mismatches: 13, Indels: 2
0.80 0.17 0.03
Matches are distributed among these distances:
20 44 0.73
21 16 0.27
ACGTcount: A:0.22, C:0.21, G:0.17, T:0.39
Consensus pattern (20 bp):
ATTCGCATTGCGATTTACGT
Found at i:995431 original size:21 final size:21
Alignment explanation
Indices: 995407--995473 Score: 116
Period size: 21 Copynumber: 3.2 Consensus size: 21
995397 TATTCGCATT
*
995407 GCGAATTAGGGAAATCGCAAC
1 GCGAATTTGGGAAATCGCAAC
995428 GCGAATTTGGGAAATCGCAAC
1 GCGAATTTGGGAAATCGCAAC
*
995449 GCGAATTTGGGAAATCGCAAT
1 GCGAATTTGGGAAATCGCAAC
995470 GCGA
1 GCGA
995474 TAGTCAGAAT
Statistics
Matches: 44, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 44 1.00
ACGTcount: A:0.34, C:0.18, G:0.30, T:0.18
Consensus pattern (21 bp):
GCGAATTTGGGAAATCGCAAC
Found at i:996577 original size:19 final size:19
Alignment explanation
Indices: 996555--996611 Score: 62
Period size: 19 Copynumber: 3.0 Consensus size: 19
996545 GTAAACCAAA
* *
996555 TTTTAAGTTAGAAATATTT
1 TTTTAAGTTGGAAATATGT
**
996574 TTTTTGGTTGGAAACT-TGT
1 TTTTAAGTTGGAAA-TATGT
996593 TTTTAAGTTGGAAATATGT
1 TTTTAAGTTGGAAATATGT
996612 GTTATAACTT
Statistics
Matches: 30, Mismatches: 6, Indels: 4
0.75 0.15 0.10
Matches are distributed among these distances:
18 1 0.03
19 28 0.93
20 1 0.03
ACGTcount: A:0.28, C:0.02, G:0.19, T:0.51
Consensus pattern (19 bp):
TTTTAAGTTGGAAATATGT
Found at i:1000411 original size:36 final size:36
Alignment explanation
Indices: 1000205--1000412 Score: 132
Period size: 36 Copynumber: 5.7 Consensus size: 36
1000195 ATGACAAATA
* *
1000205 ACTACTGATGATTATATGCATGATCTATATATGCGCTT
1 ACTACTGATGATTATATGCATGA--TATACATGTGCTT
* * * * *
1000243 TCCAGC-GACGATGATATGCATGATATACATGCGCTT
1 ACTA-CTGATGATTATATGCATGATATACATGTGCTT
* * ** ** **
1000279 GCTAATGATGACAATATGCAAAATATACATGCACTT
1 ACTACTGATGATTATATGCATGATATACATGTGCTT
* * * * * *
1000315 TCTAATGATGATGATATGCATAATATATATGTGTTT
1 ACTACTGATGATTATATGCATGATATACATGTGCTT
* *
1000351 ACTACTGATGATTAAAAG-ATTGATATACATGTGCTT
1 ACTACTGATGATTATATGCA-TGATATACATGTGCTT
* **
1000387 AGTTTTGATGATTATATGCATGATAT
1 ACTACTGATGATTATATGCATGATAT
1000413 TTCACCCATG
Statistics
Matches: 131, Mismatches: 35, Indels: 10
0.74 0.20 0.06
Matches are distributed among these distances:
35 1 0.01
36 111 0.85
37 1 0.01
38 17 0.13
39 1 0.01
ACGTcount: A:0.33, C:0.13, G:0.17, T:0.37
Consensus pattern (36 bp):
ACTACTGATGATTATATGCATGATATACATGTGCTT
Found at i:1004012 original size:2 final size:2
Alignment explanation
Indices: 1004005--1004029 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
1003995 GGTGCTACAT
1004005 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 T
1004030 TAGGGCTTTA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:1004240 original size:16 final size:16
Alignment explanation
Indices: 1004219--1004260 Score: 50
Period size: 16 Copynumber: 2.6 Consensus size: 16
1004209 ATAAGTATGC
1004219 ATATATTTTTATAT-CT
1 ATATATTTTTAT-TCCT
*
1004235 ATATATTTCTATTCCT
1 ATATATTTTTATTCCT
*
1004251 AAATATTTTT
1 ATATATTTTT
1004261 CATCATTATT
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
15 1 0.05
16 21 0.95
ACGTcount: A:0.31, C:0.10, G:0.00, T:0.60
Consensus pattern (16 bp):
ATATATTTTTATTCCT
Found at i:1004694 original size:15 final size:15
Alignment explanation
Indices: 1004674--1004709 Score: 63
Period size: 15 Copynumber: 2.4 Consensus size: 15
1004664 GTATGATATG
1004674 GATTGAATCTTTGGC
1 GATTGAATCTTTGGC
1004689 GATTGAATCTTTGGC
1 GATTGAATCTTTGGC
*
1004704 GTTTGA
1 GATTGA
1004710 CTTGCACGTA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 20 1.00
ACGTcount: A:0.19, C:0.11, G:0.28, T:0.42
Consensus pattern (15 bp):
GATTGAATCTTTGGC
Found at i:1007720 original size:20 final size:20
Alignment explanation
Indices: 1007695--1007735 Score: 73
Period size: 20 Copynumber: 2.0 Consensus size: 20
1007685 ACCCGCACGT
*
1007695 GTGGCTTGTTTTGGTCCAGG
1 GTGGCTTGTTTTAGTCCAGG
1007715 GTGGCTTGTTTTAGTCCAGG
1 GTGGCTTGTTTTAGTCCAGG
1007735 G
1 G
1007736 AATTTTCCAG
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.07, C:0.15, G:0.39, T:0.39
Consensus pattern (20 bp):
GTGGCTTGTTTTAGTCCAGG
Found at i:1011699 original size:11 final size:11
Alignment explanation
Indices: 1011680--1011714 Score: 52
Period size: 11 Copynumber: 3.2 Consensus size: 11
1011670 TAATCTATTC
*
1011680 ATATAAAATTA
1 ATATTAAATTA
1011691 ATATTAAATTA
1 ATATTAAATTA
*
1011702 ATATTAGATTA
1 ATATTAAATTA
1011713 AT
1 AT
1011715 CTATTCATAT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
11 22 1.00
ACGTcount: A:0.54, C:0.00, G:0.03, T:0.43
Consensus pattern (11 bp):
ATATTAAATTA
Found at i:1015820 original size:46 final size:46
Alignment explanation
Indices: 1015759--1016107 Score: 587
Period size: 46 Copynumber: 7.7 Consensus size: 46
1015749 TATGGGGTTT
* *
1015759 CATGCAATTTAACCATTCAAAAATAAAACATAAATAATAGGGTTAG
1 CATGTAATTTTACCATTCAAAAATAAAACATAAATAATAGGGTTAG
* *
1015805 CAAGTAATTTTACCATTCAAAAATAAAACATAAATAATAGTGTTAG
1 CATGTAATTTTACCATTCAAAAATAAAACATAAATAATAGGGTTAG
*
1015851 CATGTAATTTTACCATTGAAAAATAAAACATAAATAATAGGGTTAG
1 CATGTAATTTTACCATTCAAAAATAAAACATAAATAATAGGGTTAG
*
1015897 CATGTAA-TTTACCATTAAAAAATAAAACATAAATAATAGGGTTAG
1 CATGTAATTTTACCATTCAAAAATAAAACATAAATAATAGGGTTAG
1015942 CATGTAA-TTTACCATTCAAAAATAAAACATAAATAATAGGGTTAG
1 CATGTAATTTTACCATTCAAAAATAAAACATAAATAATAGGGTTAG
* * *
1015987 CATGTAATTTAATCATTGAAAAATAAAACATAAATAATAGGGTTAG
1 CATGTAATTTTACCATTCAAAAATAAAACATAAATAATAGGGTTAG
*
1016033 CATGTAATTTTATCATT-AAAAATAAAACATAAATAATAGGGTTAG
1 CATGTAATTTTACCATTCAAAAATAAAACATAAATAATAGGGTTAG
1016078 CATGTAATTTTACCATTCAAAAATAAAACA
1 CATGTAATTTTACCATTCAAAAATAAAACA
1016108 AGTCCTCATC
Statistics
Matches: 287, Mismatches: 14, Indels: 4
0.94 0.05 0.01
Matches are distributed among these distances:
45 132 0.46
46 155 0.54
ACGTcount: A:0.50, C:0.10, G:0.11, T:0.30
Consensus pattern (46 bp):
CATGTAATTTTACCATTCAAAAATAAAACATAAATAATAGGGTTAG
Found at i:1016009 original size:91 final size:92
Alignment explanation
Indices: 1015759--1016107 Score: 587
Period size: 91 Copynumber: 3.8 Consensus size: 92
1015749 TATGGGGTTT
* * *
1015759 CATGCAATTTAACCATTCAAAAATAAAACATAAATAATAGGGTTAGCAAGTAATTTTACCATTCA
1 CATGTAATTTTACCATTCAAAAATAAAACATAAATAATAGGGTTAGCATGTAATTTTACCATTCA
*
1015824 AAAATAAAACATAAATAATAGTGTTAG
66 AAAATAAAACATAAATAATAGGGTTAG
* *
1015851 CATGTAATTTTACCATTGAAAAATAAAACATAAATAATAGGGTTAGCATGTAA-TTTACCATTAA
1 CATGTAATTTTACCATTCAAAAATAAAACATAAATAATAGGGTTAGCATGTAATTTTACCATTCA
1015915 AAAATAAAACATAAATAATAGGGTTAG
66 AAAATAAAACATAAATAATAGGGTTAG
* * *
1015942 CATGTAA-TTTACCATTCAAAAATAAAACATAAATAATAGGGTTAGCATGTAATTTAATCATTGA
1 CATGTAATTTTACCATTCAAAAATAAAACATAAATAATAGGGTTAGCATGTAATTTTACCATTCA
1016006 AAAATAAAACATAAATAATAGGGTTAG
66 AAAATAAAACATAAATAATAGGGTTAG
*
1016033 CATGTAATTTTATCATT-AAAAATAAAACATAAATAATAGGGTTAGCATGTAATTTTACCATTCA
1 CATGTAATTTTACCATTCAAAAATAAAACATAAATAATAGGGTTAGCATGTAATTTTACCATTCA
1016097 AAAATAAAACA
66 AAAATAAAACA
1016108 AGTCCTCATC
Statistics
Matches: 241, Mismatches: 14, Indels: 5
0.93 0.05 0.02
Matches are distributed among these distances:
90 44 0.18
91 140 0.58
92 57 0.24
ACGTcount: A:0.50, C:0.10, G:0.11, T:0.30
Consensus pattern (92 bp):
CATGTAATTTTACCATTCAAAAATAAAACATAAATAATAGGGTTAGCATGTAATTTTACCATTCA
AAAATAAAACATAAATAATAGGGTTAG
Found at i:1018425 original size:20 final size:21
Alignment explanation
Indices: 1018400--1018441 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
1018390 CAGCTTATCT
* *
1018400 TCCAAC-AATGTTAGCTACTC
1 TCCAACTAATGTCAACTACTC
1018420 TCCAACTAATGTCAACTACTC
1 TCCAACTAATGTCAACTACTC
1018441 T
1 T
1018442 TTATATCCTT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
20 6 0.32
21 13 0.68
ACGTcount: A:0.31, C:0.31, G:0.07, T:0.31
Consensus pattern (21 bp):
TCCAACTAATGTCAACTACTC
Found at i:1018595 original size:30 final size:30
Alignment explanation
Indices: 1018515--1018595 Score: 110
Period size: 30 Copynumber: 2.7 Consensus size: 30
1018505 GATGTATTTT
*
1018515 AGCT-TCCACTAGTTGCCATAAAAAGAGTG
1 AGCTATCCACAAGTTGCCATAAAAAGAGTG
* * * *
1018544 AACTATCCACACGCTGTCATAAAAAGAGTG
1 AGCTATCCACAAGTTGCCATAAAAAGAGTG
1018574 AGCTATCCACAAGTTGCCATAA
1 AGCTATCCACAAGTTGCCATAA
1018596 TGATCCTTAG
Statistics
Matches: 42, Mismatches: 9, Indels: 1
0.81 0.17 0.02
Matches are distributed among these distances:
29 3 0.07
30 39 0.93
ACGTcount: A:0.37, C:0.23, G:0.17, T:0.22
Consensus pattern (30 bp):
AGCTATCCACAAGTTGCCATAAAAAGAGTG
Found at i:1020384 original size:19 final size:19
Alignment explanation
Indices: 1020367--1020425 Score: 57
Period size: 19 Copynumber: 3.1 Consensus size: 19
1020357 TGAAAAGATT
1020367 TAATAAAATAAAATAGATAA
1 TAAT-AAATAAAATAGATAA
** *
1020387 TAATAAATAAAAGGGAAAA
1 TAATAAATAAAATAGATAA
* *
1020406 TAATAAA-ATAATAAATAA
1 TAATAAATAAAATAGATAA
1020424 TA
1 TA
1020426 GTAGTAAAAA
Statistics
Matches: 31, Mismatches: 8, Indels: 2
0.76 0.20 0.05
Matches are distributed among these distances:
18 8 0.26
19 19 0.61
20 4 0.13
ACGTcount: A:0.69, C:0.00, G:0.07, T:0.24
Consensus pattern (19 bp):
TAATAAATAAAATAGATAA
Found at i:1020392 original size:20 final size:20
Alignment explanation
Indices: 1020367--1020416 Score: 66
Period size: 19 Copynumber: 2.5 Consensus size: 20
1020357 TGAAAAGATT
* *
1020367 TAATAAAATAAAATAGATAA
1 TAATAAAATAAAAGAGAAAA
*
1020387 TAAT-AAATAAAAGGGAAAA
1 TAATAAAATAAAAGAGAAAA
1020406 TAATAAAATAA
1 TAATAAAATAA
1020417 TAAATAATAG
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
19 16 0.62
20 10 0.38
ACGTcount: A:0.70, C:0.00, G:0.08, T:0.22
Consensus pattern (20 bp):
TAATAAAATAAAAGAGAAAA
Found at i:1022207 original size:27 final size:29
Alignment explanation
Indices: 1022173--1022226 Score: 85
Period size: 27 Copynumber: 1.9 Consensus size: 29
1022163 TTTCTTTCTC
*
1022173 TGTTCGAAACAATGAAC-ATTT-TTTTGT
1 TGTTCGAAACAATAAACAATTTGTTTTGT
1022200 TGTTCGAAACAATAAACAATTTGTTTT
1 TGTTCGAAACAATAAACAATTTGTTTT
1022227 TTTTCTTCAA
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
27 16 0.67
28 4 0.17
29 4 0.17
ACGTcount: A:0.33, C:0.11, G:0.13, T:0.43
Consensus pattern (29 bp):
TGTTCGAAACAATAAACAATTTGTTTTGT
Found at i:1027380 original size:9 final size:9
Alignment explanation
Indices: 1027366--1027392 Score: 54
Period size: 9 Copynumber: 3.0 Consensus size: 9
1027356 TAATAACTCG
1027366 GATATTTCT
1 GATATTTCT
1027375 GATATTTCT
1 GATATTTCT
1027384 GATATTTCT
1 GATATTTCT
1027393 ACCCATACTT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 18 1.00
ACGTcount: A:0.22, C:0.11, G:0.11, T:0.56
Consensus pattern (9 bp):
GATATTTCT
Found at i:1030674 original size:15 final size:16
Alignment explanation
Indices: 1030640--1030681 Score: 50
Period size: 15 Copynumber: 2.7 Consensus size: 16
1030630 TATTCAGAGA
1030640 AAAAATAAAATTAATG
1 AAAAATAAAATTAATG
** *
1030656 -AAAATAAAATTCGTT
1 AAAAATAAAATTAATG
1030671 AAAAATAAAAT
1 AAAAATAAAAT
1030682 AAAAAATAAA
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
15 12 0.55
16 10 0.45
ACGTcount: A:0.67, C:0.02, G:0.05, T:0.26
Consensus pattern (16 bp):
AAAAATAAAATTAATG
Found at i:1036593 original size:20 final size:20
Alignment explanation
Indices: 1036568--1036617 Score: 66
Period size: 19 Copynumber: 2.5 Consensus size: 20
1036558 TGAAAATATT
** *
1036568 TAATAAAATAAAATTGATAA
1 TAATAAAATAAAAGGGAAAA
1036588 TAAT-AAATAAAAGGGAAAA
1 TAATAAAATAAAAGGGAAAA
1036607 TAATAAAATAA
1 TAATAAAATAA
1036618 TAAATAATAG
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
19 16 0.62
20 10 0.38
ACGTcount: A:0.68, C:0.00, G:0.08, T:0.24
Consensus pattern (20 bp):
TAATAAAATAAAAGGGAAAA
Found at i:1036640 original size:27 final size:25
Alignment explanation
Indices: 1036551--1036641 Score: 60
Period size: 24 Copynumber: 3.5 Consensus size: 25
1036541 AGAATTCCAC
* * *
1036551 GTAAAGTTGAAAATATTTAATAAAA-
1 GTAAAATT-AAAATAATAAATAAAAG
*
1036576 -TAAAATTGATAATAATAAATAAAAG
1 GTAAAATT-AAAATAATAAATAAAAG
* *
1036601 GGAAAATAATAAAATAATAAATAATAG
1 GTAAAAT--TAAAATAATAAATAAAAG
1036628 TAGTAAAATTAAAA
1 --GTAAAATTAAAA
1036642 AAAGTTTTTA
Statistics
Matches: 52, Mismatches: 8, Indels: 10
0.74 0.11 0.14
Matches are distributed among these distances:
24 20 0.38
26 5 0.10
27 20 0.38
28 1 0.02
29 6 0.12
ACGTcount: A:0.63, C:0.00, G:0.10, T:0.27
Consensus pattern (25 bp):
GTAAAATTAAAATAATAAATAAAAG
Found at i:1039874 original size:21 final size:22
Alignment explanation
Indices: 1039845--1039900 Score: 53
Period size: 21 Copynumber: 2.6 Consensus size: 22
1039835 GGTCACTTAT
* *
1039845 CTAGATAGGTACCT-TATGTAG
1 CTAGCTAGGTACCTGTAGGTAG
* *
1039866 CTAGCTAGGCA-GTGTAGGTAG
1 CTAGCTAGGTACCTGTAGGTAG
*
1039887 CTAGCTCGGTACCT
1 CTAGCTAGGTACCT
1039901 AGTGTCACTC
Statistics
Matches: 26, Mismatches: 7, Indels: 3
0.72 0.19 0.08
Matches are distributed among these distances:
20 1 0.04
21 24 0.92
22 1 0.04
ACGTcount: A:0.23, C:0.20, G:0.29, T:0.29
Consensus pattern (22 bp):
CTAGCTAGGTACCTGTAGGTAG
Found at i:1040457 original size:59 final size:59
Alignment explanation
Indices: 1040362--1040482 Score: 206
Period size: 59 Copynumber: 2.1 Consensus size: 59
1040352 GAACATGTCA
* * *
1040362 TGAAGAAAGTTGGTGCTAGACAGGATCACATTACATATGAAAATAATGTAAAGACAAAT
1 TGAAGAAAGTTGGTGCTAGACAGAATCACATCACATATGAAAATAATGCAAAGACAAAT
*
1040421 TGAAGAAAGTTGGTGCTAGACAGAATCATATCACATATGAAAATAATGCAAAGACAAAT
1 TGAAGAAAGTTGGTGCTAGACAGAATCACATCACATATGAAAATAATGCAAAGACAAAT
1040480 TGA
1 TGA
1040483 TGATTTATGA
Statistics
Matches: 58, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
59 58 1.00
ACGTcount: A:0.46, C:0.11, G:0.20, T:0.23
Consensus pattern (59 bp):
TGAAGAAAGTTGGTGCTAGACAGAATCACATCACATATGAAAATAATGCAAAGACAAAT
Found at i:1041424 original size:17 final size:15
Alignment explanation
Indices: 1041393--1041421 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
1041383 ACTTAGTTCA
1041393 ATGTCATATTTTTTG
1 ATGTCATATTTTTTG
1041408 ATGTCATATTTTTT
1 ATGTCATATTTTTT
1041422 TTGTATAATC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.21, C:0.07, G:0.10, T:0.62
Consensus pattern (15 bp):
ATGTCATATTTTTTG
Found at i:1047734 original size:81 final size:81
Alignment explanation
Indices: 1047590--1048311 Score: 897
Period size: 81 Copynumber: 8.9 Consensus size: 81
1047580 TTTCCTTTAG
* ** ** * * *
1047590 TCTTTTACCCAAAGACATTTAGTCTTTCATCTAACTTGCATGATTTACACCTTTCTATCAAATGC
1 TCTTTTACTCAAAGGTATTTAACCTTTCATCTAACTGGCATGATTGACACCTTTCTGTCAAATGC
*
1047655 ACAACTAGGCTATTAA
66 ACAGCTAGGCTATTAA
* * *
1047671 TCTCTTACTCAAAGGTATTTAACCTTTCATCTAACTGGCATAATTGACACTTTTCTGTCAAATGC
1 TCTTTTACTCAAAGGTATTTAACCTTTCATCTAACTGGCATGATTGACACCTTTCTGTCAAATGC
* *
1047736 ATAGCTAGGCCATTAA
66 ACAGCTAGGCTATTAA
* * * * * * ** * *
1047752 TCTTTTACTCAATGGTACTTAATCGTTCATCTAACTGGCTTAATTGACATTTTTCTGCCAAATAC
1 TCTTTTACTCAAAGGTATTTAACCTTTCATCTAACTGGCATGATTGACACCTTTCTGTCAAATGC
* * *
1047817 ACAACTAGGTTATAAA
66 ACAGCTAGGCTATTAA
* * *
1047833 TCTTTTACTCAAAGGTATTTAACCTTTCATCTAACTTGCATGATTGACACCTTTTTTTCAAATGC
1 TCTTTTACTCAAAGGTATTTAACCTTTCATCTAACTGGCATGATTGACACCTTTCTGTCAAATGC
*
1047898 ACAGCTAGGATATTAA
66 ACAGCTAGGCTATTAA
* * * * *
1047914 TCTTTTACTCAAAGGTATTTAACCTTTCATCTAATTCGAATGATTGACACATTTCTGTCAAATAC
1 TCTTTTACTCAAAGGTATTTAACCTTTCATCTAACTGGCATGATTGACACCTTTCTGTCAAATGC
* *
1047979 ACAGTTAGTCTATT-A
66 ACAGCTAGGCTATTAA
* * * *
1047994 TCTCTTACTCAAAGGTATTTAACCTTTCATCTAACTGGCATAATTGACACTTTTCTATCAAATGC
1 TCTTTTACTCAAAGGTATTTAACCTTTCATCTAACTGGCATGATTGACACCTTTCTGTCAAATGC
* *
1048059 ACAGCTAGGCCATTCA
66 ACAGCTAGGCTATTAA
* * * * * * * * *
1048075 TCTTTTACTCAACGGTACTTAATCGTTCTTCTGACTGGCATAATTGACACCTTTATGCCAAATGC
1 TCTTTTACTCAAAGGTATTTAACCTTTCATCTAACTGGCATGATTGACACCTTTCTGTCAAATGC
* *
1048140 ATAGCTAGGCTATAAA
66 ACAGCTAGGCTATTAA
* * * *
1048156 TCTTTTACTCAAAGGTATTTAACCTTTCATCTAATTTGCATGATTGACACCGTTCTGTCAAATGT
1 TCTTTTACTCAAAGGTATTTAACCTTTCATCTAACTGGCATGATTGACACCTTTCTGTCAAATGC
1048221 ACAGCTAGGCTATTAA
66 ACAGCTAGGCTATTAA
1048237 TCTTTTACTCAAAGGTATTTAACCTTTCATCTAACTGGCATGATTGACACCTTTCTGTCAAATGC
1 TCTTTTACTCAAAGGTATTTAACCTTTCATCTAACTGGCATGATTGACACCTTTCTGTCAAATGC
*
1048302 ACAGTTAGGC
66 ACAGCTAGGC
1048312 CTCAAAGGCA
Statistics
Matches: 540, Mismatches: 100, Indels: 2
0.84 0.16 0.00
Matches are distributed among these distances:
80 69 0.13
81 471 0.87
ACGTcount: A:0.30, C:0.21, G:0.12, T:0.37
Consensus pattern (81 bp):
TCTTTTACTCAAAGGTATTTAACCTTTCATCTAACTGGCATGATTGACACCTTTCTGTCAAATGC
ACAGCTAGGCTATTAA
Found at i:1048258 original size:323 final size:323
Alignment explanation
Indices: 1047590--1048311 Score: 1104
Period size: 323 Copynumber: 2.2 Consensus size: 323
1047580 TTTCCTTTAG
* ** ** * *
1047590 TCTTTTACCCAAAGACATTTAGTCTTTCATCTAACTTGCATGATTTACACCTTTCTATCAAATGC
1 TCTTTTACTCAAAGGTATTTAACCTTTCATCTAA-TTGCATGATTGACACCTTTCTGTCAAATGC
**
1047655 ACAACTAGGCTATTAATCTCTTACTCAAAGGTATTTAACCTTTCATCTAACTGGCATAATTGACA
65 ACAGTTAGGCTATTAATCTCTTACTCAAAGGTATTTAACCTTTCATCTAACTGGCATAATTGACA
* * *
1047720 CTTTTCTGTCAAATGCATAGCTAGGCCATTAATCTTTTACTCAATGGTACTTAATCGTTCATCTA
130 CTTTTCTATCAAATGCACAGCTAGGCCATTAATCTTTTACTCAACGGTACTTAATCGTTCATCTA
* ** * *
1047785 ACTGGCTTAATTGACATTTTTCTGCCAAATACACAACTAGGTTATAAATCTTTTACTCAAAGGTA
195 ACTGGCATAATTGACACCTTTATGCCAAATACACAACTAGGCTATAAATCTTTTACTCAAAGGTA
* * *
1047850 TTTAACCTTTCATCTAACTTGCATGATTGACACCTTTTTTTCAAATGCACAGCTAGGATATTAA
260 TTTAACCTTTCATCTAACTTGCATGATTGACACCGTTCTGTCAAATGCACAGCTAGGATATTAA
* * *
1047914 TCTTTTACTCAAAGGTATTTAACCTTTCATCTAATTCGAATGATTGACACATTTCTGTCAAATAC
1 TCTTTTACTCAAAGGTATTTAACCTTTCATCTAATT-GCATGATTGACACCTTTCTGTCAAATGC
*
1047979 ACAGTTAGTCTATT-ATCTCTTACTCAAAGGTATTTAACCTTTCATCTAACTGGCATAATTGACA
65 ACAGTTAGGCTATTAATCTCTTACTCAAAGGTATTTAACCTTTCATCTAACTGGCATAATTGACA
* * *
1048043 CTTTTCTATCAAATGCACAGCTAGGCCATTCATCTTTTACTCAACGGTACTTAATCGTTCTTCTG
130 CTTTTCTATCAAATGCACAGCTAGGCCATTAATCTTTTACTCAACGGTACTTAATCGTTCATCTA
* * *
1048108 ACTGGCATAATTGACACCTTTATGCCAAATGCATAGCTAGGCTATAAATCTTTTACTCAAAGGTA
195 ACTGGCATAATTGACACCTTTATGCCAAATACACAACTAGGCTATAAATCTTTTACTCAAAGGTA
* * *
1048173 TTTAACCTTTCATCTAATTTGCATGATTGACACCGTTCTGTCAAATGTACAGCTAGGCTATTAA
260 TTTAACCTTTCATCTAACTTGCATGATTGACACCGTTCTGTCAAATGCACAGCTAGGATATTAA
*
1048237 TCTTTTACTCAAAGGTATTTAACCTTTCATCTAACTGGCATGATTGACACCTTTCTGTCAAATGC
1 TCTTTTACTCAAAGGTATTTAACCTTTCATCTAA-TTGCATGATTGACACCTTTCTGTCAAATGC
1048302 ACAGTTAGGC
65 ACAGTTAGGC
1048312 CTCAAAGGCA
Statistics
Matches: 358, Mismatches: 38, Indels: 5
0.89 0.09 0.01
Matches are distributed among these distances:
323 294 0.82
324 64 0.18
ACGTcount: A:0.30, C:0.21, G:0.12, T:0.37
Consensus pattern (323 bp):
TCTTTTACTCAAAGGTATTTAACCTTTCATCTAATTGCATGATTGACACCTTTCTGTCAAATGCA
CAGTTAGGCTATTAATCTCTTACTCAAAGGTATTTAACCTTTCATCTAACTGGCATAATTGACAC
TTTTCTATCAAATGCACAGCTAGGCCATTAATCTTTTACTCAACGGTACTTAATCGTTCATCTAA
CTGGCATAATTGACACCTTTATGCCAAATACACAACTAGGCTATAAATCTTTTACTCAAAGGTAT
TTAACCTTTCATCTAACTTGCATGATTGACACCGTTCTGTCAAATGCACAGCTAGGATATTAA
Found at i:1048353 original size:68 final size:68
Alignment explanation
Indices: 1048244--1048381 Score: 213
Period size: 68 Copynumber: 2.0 Consensus size: 68
1048234 TAATCTTTTA
* * * *
1048244 CTCAAAGGTATTTAACCTTTCATCTAACTGGCATGATTGACACCTTTCTGTCAAATGCACAGTTA
1 CTCAAAGGCACTTAACCTTTCATCTAACTGGCATGATTGACACATTTCTGTCAAATGCACAATTA
1048309 GGC
66 GGC
* *
1048312 CTCAAAGGCACTTAGCCTTTCATCTAACTTGCATGATTGACACATTTCTGTCAAATGCACAATTA
1 CTCAAAGGCACTTAACCTTTCATCTAACTGGCATGATTGACACATTTCTGTCAAATGCACAATTA
*
1048377 TGC
66 GGC
1048380 CT
1 CT
1048382 TTATATTGTA
Statistics
Matches: 63, Mismatches: 7, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
68 63 1.00
ACGTcount: A:0.28, C:0.25, G:0.14, T:0.33
Consensus pattern (68 bp):
CTCAAAGGCACTTAACCTTTCATCTAACTGGCATGATTGACACATTTCTGTCAAATGCACAATTA
GGC
Found at i:1048664 original size:57 final size:57
Alignment explanation
Indices: 1048585--1048745 Score: 252
Period size: 57 Copynumber: 2.8 Consensus size: 57
1048575 TAAAGTTCTT
* * * * *
1048585 ATACATAAATTCATAAACAAATTATGAATTTCTTATCTTTTCGCACCCGAAGTACCC
1 ATACAGAAATTCATAAACAAATTATGAATTTCTTAACTTTTTGCACACAAAGTACCC
1048642 ATAC-GAAATTTCATAAACAAATTATGAATTTCTTAACTTTTTGCACACAAAGTACCC
1 ATACAGAAA-TTCATAAACAAATTATGAATTTCTTAACTTTTTGCACACAAAGTACCC
*
1048699 ATACAGAAATTCATAAACAAATTATAAATTTCTTAACTTTTTGCACA
1 ATACAGAAATTCATAAACAAATTATGAATTTCTTAACTTTTTGCACA
1048746 TTCAGTGCCA
Statistics
Matches: 96, Mismatches: 6, Indels: 4
0.91 0.06 0.04
Matches are distributed among these distances:
56 3 0.03
57 89 0.93
58 4 0.04
ACGTcount: A:0.40, C:0.19, G:0.06, T:0.34
Consensus pattern (57 bp):
ATACAGAAATTCATAAACAAATTATGAATTTCTTAACTTTTTGCACACAAAGTACCC
Found at i:1049208 original size:20 final size:20
Alignment explanation
Indices: 1049185--1049222 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
1049175 TCGATACCTT
*
1049185 CCCTTCTGTATCAATACTCC
1 CCCTTCGGTATCAATACTCC
*
1049205 CCCTTCGGTATCGATACT
1 CCCTTCGGTATCAATACT
1049223 GATTGAATCA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.18, C:0.37, G:0.11, T:0.34
Consensus pattern (20 bp):
CCCTTCGGTATCAATACTCC
Found at i:1051494 original size:2 final size:2
Alignment explanation
Indices: 1051489--1051523 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
1051479 ATTAAATTGA
1051489 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1051524 ACAAGTCAAT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:1051624 original size:29 final size:29
Alignment explanation
Indices: 1051545--1051652 Score: 87
Period size: 29 Copynumber: 3.7 Consensus size: 29
1051535 TTCCTATTTT
** *
1051545 AACAGAAAGTATAGAAAGTGATATCATATC
1 AACAGAAAACATA-AAAGTGATATCATATA
* *
1051575 AACAGGAACCATAAATA-TGATATCATATA
1 AACAGAAAACATAAA-AGTGATATCATATA
* * *
1051604 AATATAAAACATAAAAGTGATA--ATTTA
1 AACAGAAAACATAAAAGTGATATCATATA
*
1051631 AACAGAAAGCATAGAAAGTGAT
1 AACAGAAAACATA-AAAGTGAT
1051653 CCTATAAAGT
Statistics
Matches: 63, Mismatches: 12, Indels: 8
0.76 0.14 0.10
Matches are distributed among these distances:
27 14 0.22
28 9 0.14
29 29 0.46
30 11 0.17
ACGTcount: A:0.54, C:0.09, G:0.14, T:0.23
Consensus pattern (29 bp):
AACAGAAAACATAAAAGTGATATCATATA
Found at i:1052084 original size:19 final size:18
Alignment explanation
Indices: 1052044--1052082 Score: 60
Period size: 18 Copynumber: 2.2 Consensus size: 18
1052034 TCTATCTTTG
1052044 TTTCCTCACAATTCCCCT
1 TTTCCTCACAATTCCCCT
* *
1052062 TTTCCTCGCAATTTCCCT
1 TTTCCTCACAATTCCCCT
1052080 TTT
1 TTT
1052083 TCTCTCAAAC
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.13, C:0.38, G:0.03, T:0.46
Consensus pattern (18 bp):
TTTCCTCACAATTCCCCT
Found at i:1055386 original size:12 final size:12
Alignment explanation
Indices: 1055369--1055398 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
1055359 AAGACATGAA
1055369 GTCTTCTTCTTC
1 GTCTTCTTCTTC
1055381 GTCTTCTTCTTC
1 GTCTTCTTCTTC
*
1055393 TTCTTC
1 GTCTTC
1055399 ATCATCTTAT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.00, C:0.33, G:0.07, T:0.60
Consensus pattern (12 bp):
GTCTTCTTCTTC
Found at i:1057858 original size:14 final size:14
Alignment explanation
Indices: 1057839--1057866 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
1057829 ATATTTTACC
1057839 AAATTATAAATATT
1 AAATTATAAATATT
1057853 AAATTATAAATATT
1 AAATTATAAATATT
1057867 TGAATGAATT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (14 bp):
AAATTATAAATATT
Found at i:1058041 original size:60 final size:60
Alignment explanation
Indices: 1057973--1058085 Score: 147
Period size: 60 Copynumber: 1.9 Consensus size: 60
1057963 ATGGTCTCAC
* * * *
1057973 GACTATA-GGATACAGCTTTCTTGAGTCTCTCGGCTCTTAAAAGTTGCAAAATGATCTTAT
1 GACTATAGGGA-ACAGCTTTCTTCAGTCCCTCGGCTATTAAAAGTTACAAAATGATCTTAT
** *
1058033 GACTATAGGGAATTGCTTTGTTCAGTCCCTCGGCTATTAAAAGTTACAAAATG
1 GACTATAGGGAACAGCTTTCTTCAGTCCCTCGGCTATTAAAAGTTACAAAATG
1058086 GTCACCTAAC
Statistics
Matches: 45, Mismatches: 7, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
60 42 0.93
61 3 0.07
ACGTcount: A:0.29, C:0.18, G:0.19, T:0.34
Consensus pattern (60 bp):
GACTATAGGGAACAGCTTTCTTCAGTCCCTCGGCTATTAAAAGTTACAAAATGATCTTAT
Found at i:1058760 original size:3 final size:3
Alignment explanation
Indices: 1058752--1058777 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
1058742 ACTCTTTGTA
1058752 TAT TAT TAT TAT TAT TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TA
1058778 AATTTATAAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (3 bp):
TAT
Found at i:1066318 original size:28 final size:28
Alignment explanation
Indices: 1066278--1066334 Score: 105
Period size: 28 Copynumber: 2.0 Consensus size: 28
1066268 ACACATATCA
*
1066278 AATAACGATCAAATTTAATAGTCATTAC
1 AATAACGATCAAATTTAACAGTCATTAC
1066306 AATAACGATCAAATTTAACAGTCATTAC
1 AATAACGATCAAATTTAACAGTCATTAC
1066334 A
1 A
1066335 TTACAGATAC
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
28 28 1.00
ACGTcount: A:0.47, C:0.16, G:0.07, T:0.30
Consensus pattern (28 bp):
AATAACGATCAAATTTAACAGTCATTAC
Found at i:1069511 original size:17 final size:18
Alignment explanation
Indices: 1069474--1069514 Score: 66
Period size: 18 Copynumber: 2.3 Consensus size: 18
1069464 ATATTATGTA
*
1069474 TTTAATTTATTTAAGTAT
1 TTTACTTTATTTAAGTAT
1069492 TTTACTTTATTTAA-TAT
1 TTTACTTTATTTAAGTAT
1069509 TTTACT
1 TTTACT
1069515 AATATAAGTT
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
17 9 0.41
18 13 0.59
ACGTcount: A:0.29, C:0.05, G:0.02, T:0.63
Consensus pattern (18 bp):
TTTACTTTATTTAAGTAT
Found at i:1071556 original size:3 final size:3
Alignment explanation
Indices: 1071548--1071603 Score: 51
Period size: 3 Copynumber: 18.7 Consensus size: 3
1071538 ACCTGCTCAG
* * * * *
1071548 GAC GAC GAC GAT GAC GAC GAC GAC GAT GAC GAT GA- TAGT GAC GAC
1 GAC GAC GAC GAC GAC GAC GAC GAC GAC GAC GAC GAC GA-C GAC GAC
1071593 GAC GAC GAC GA
1 GAC GAC GAC GA
1071604 TGATGGTGAT
Statistics
Matches: 43, Mismatches: 8, Indels: 4
0.78 0.15 0.07
Matches are distributed among these distances:
2 1 0.02
3 41 0.95
4 1 0.02
ACGTcount: A:0.34, C:0.23, G:0.34, T:0.09
Consensus pattern (3 bp):
GAC
Found at i:1071590 original size:24 final size:24
Alignment explanation
Indices: 1071548--1071612 Score: 82
Period size: 24 Copynumber: 2.8 Consensus size: 24
1071538 ACCTGCTCAG
*
1071548 GACGACGACGATG--A-CGACGAC
1 GACGACGACGATGATAGTGACGAC
*
1071569 GACGATGACGATGATAGTGACGAC
1 GACGACGACGATGATAGTGACGAC
*
1071593 GACGACGACGATGATGGTGA
1 GACGACGACGATGATAGTGA
1071613 TGATGATGAA
Statistics
Matches: 37, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
21 12 0.32
23 1 0.03
24 24 0.65
ACGTcount: A:0.32, C:0.20, G:0.35, T:0.12
Consensus pattern (24 bp):
GACGACGACGATGATAGTGACGAC
Found at i:1077747 original size:12 final size:12
Alignment explanation
Indices: 1077730--1077754 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
1077720 TTACAAAATG
1077730 ATGATGATGATA
1 ATGATGATGATA
1077742 ATGATGATGATA
1 ATGATGATGATA
1077754 A
1 A
1077755 GAAATATTTT
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:0.44, C:0.00, G:0.24, T:0.32
Consensus pattern (12 bp):
ATGATGATGATA
Found at i:1079783 original size:17 final size:16
Alignment explanation
Indices: 1079745--1079785 Score: 55
Period size: 16 Copynumber: 2.5 Consensus size: 16
1079735 TAAGCATTCT
* *
1079745 AAATATTGATTTTAAT
1 AAATAATGATTTTAAA
1079761 AAATAATGATTTTCAAA
1 AAATAATGATTTT-AAA
1079778 AAATAATG
1 AAATAATG
1079786 TATATCGATT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
16 12 0.55
17 10 0.45
ACGTcount: A:0.51, C:0.02, G:0.07, T:0.39
Consensus pattern (16 bp):
AAATAATGATTTTAAA
Found at i:1085834 original size:13 final size:13
Alignment explanation
Indices: 1085790--1085834 Score: 56
Period size: 13 Copynumber: 3.4 Consensus size: 13
1085780 TACTTTCTAT
1085790 ATTAATTATAATC
1 ATTAATTATAATC
*
1085803 CTTATATTATAAATC
1 ATTA-ATTAT-AATC
1085818 -TTAATTATAATC
1 ATTAATTATAATC
1085830 ATTAA
1 ATTAA
1085835 ATTAATTCTA
Statistics
Matches: 28, Mismatches: 1, Indels: 6
0.80 0.03 0.17
Matches are distributed among these distances:
12 4 0.14
13 12 0.43
14 8 0.29
15 4 0.14
ACGTcount: A:0.44, C:0.09, G:0.00, T:0.47
Consensus pattern (13 bp):
ATTAATTATAATC
Found at i:1085978 original size:2 final size:2
Alignment explanation
Indices: 1085971--1086013 Score: 86
Period size: 2 Copynumber: 21.5 Consensus size: 2
1085961 AAAATTTTAA
1085971 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
1086013 A
1 A
1086014 AGAAGAATTT
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:1087742 original size:22 final size:22
Alignment explanation
Indices: 1087688--1087729 Score: 75
Period size: 22 Copynumber: 1.9 Consensus size: 22
1087678 TAAATATCAT
*
1087688 TAAATAATAAATTTAAAATAAA
1 TAAATAATAAACTTAAAATAAA
1087710 TAAATAATAAACTTAAAATA
1 TAAATAATAAACTTAAAATA
1087730 TATACTAATT
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:0.67, C:0.02, G:0.00, T:0.31
Consensus pattern (22 bp):
TAAATAATAAACTTAAAATAAA
Found at i:1091307 original size:36 final size:37
Alignment explanation
Indices: 1091236--1091320 Score: 120
Period size: 37 Copynumber: 2.3 Consensus size: 37
1091226 ATCCTATTAT
*
1091236 CATTTTTC-AACAAACATCTACCAAACTTTGAAAAAC
1 CATTTTTCAAAGAAACATCTACCAAACTTTGAAAAAC
* *
1091272 TATTTTTCAAAGAAACATTTACCAAACTTTG-AAAAC
1 CATTTTTCAAAGAAACATCTACCAAACTTTGAAAAAC
1091308 CATTTTTCCAAAG
1 CATTTTT-CAAAG
1091321 TTGGTTGCCA
Statistics
Matches: 43, Mismatches: 4, Indels: 3
0.86 0.08 0.06
Matches are distributed among these distances:
36 18 0.42
37 25 0.58
ACGTcount: A:0.42, C:0.21, G:0.05, T:0.32
Consensus pattern (37 bp):
CATTTTTCAAAGAAACATCTACCAAACTTTGAAAAAC
Found at i:1095555 original size:103 final size:103
Alignment explanation
Indices: 1095330--1095547 Score: 391
Period size: 103 Copynumber: 2.1 Consensus size: 103
1095320 GTCGAGGGTC
* *
1095330 TATGTGGTCCTTCGGGATATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
1 TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTCTGAAGTCTGGTGAGACACATAC
* *
1095395 TTGATCCTTGGCATATGTATATGATTCTTAAGGAATGA
66 TTGATCCCTAGCATATGTATATGATTCTTAAGGAATGA
1095433 TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTCTGAAGTCTGGTGAGACACATAC
1 TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTCTGAAGTCTGGTGAGACACATAC
*
1095498 TTGATCCCTAGTATATGTATATGATTCTTAAGGAATGA
66 TTGATCCCTAGCATATGTATATGATTCTTAAGGAATGA
1095536 TATGTGGTCCTT
1 TATGTGGTCCTT
1095548 ATGGACATTA
Statistics
Matches: 110, Mismatches: 5, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
103 110 1.00
ACGTcount: A:0.26, C:0.14, G:0.23, T:0.37
Consensus pattern (103 bp):
TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTCTGAAGTCTGGTGAGACACATAC
TTGATCCCTAGCATATGTATATGATTCTTAAGGAATGA
Found at i:1095613 original size:23 final size:23
Alignment explanation
Indices: 1095587--1095631 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
1095577 AATTCTACGC
1095587 GGCACTCCGACGCAATTATATGT
1 GGCACTCCGACGCAATTATATGT
* **
1095610 GGCACTTCGGTGCAATTATATG
1 GGCACTCCGACGCAATTATATG
1095632 AGCTGTGGTG
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:0.24, C:0.22, G:0.24, T:0.29
Consensus pattern (23 bp):
GGCACTCCGACGCAATTATATGT
Found at i:1100372 original size:18 final size:17
Alignment explanation
Indices: 1100349--1100394 Score: 65
Period size: 18 Copynumber: 2.6 Consensus size: 17
1100339 AATTTAAATA
*
1100349 CATCGAATGCAAGTAGTG
1 CATCG-ATGCAAGTAGTC
1100367 CATCGATGCTAAGTAGTC
1 CATCGATGC-AAGTAGTC
1100385 CATCGATGCA
1 CATCGATGCA
1100395 TCCCAGTAAT
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
17 5 0.19
18 21 0.81
ACGTcount: A:0.30, C:0.22, G:0.24, T:0.24
Consensus pattern (17 bp):
CATCGATGCAAGTAGTC
Found at i:1101387 original size:103 final size:103
Alignment explanation
Indices: 1101203--1101420 Score: 382
Period size: 103 Copynumber: 2.1 Consensus size: 103
1101193 GTCGAGGGTC
*
1101203 TATGTGGTCCTTCGAGATATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
1 TATGTGGTCCTTCGAGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
* *
1101268 TTGATCCTTGGCATATGTATATGATTCTTAAGAAATGA
66 TTGATCCCTAGCATATGTATATGATTCTTAAGAAATGA
*
1101306 TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
1 TATGTGGTCCTTCGAGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
* *
1101371 TTGATCCCTAGTATATGTATATGATTCTTAAGGAATGA
66 TTGATCCCTAGCATATGTATATGATTCTTAAGAAATGA
1101409 TATGTGGTCCTT
1 TATGTGGTCCTT
1101421 ATGGACATTA
Statistics
Matches: 109, Mismatches: 6, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
103 109 1.00
ACGTcount: A:0.27, C:0.13, G:0.23, T:0.37
Consensus pattern (103 bp):
TATGTGGTCCTTCGAGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
TTGATCCCTAGCATATGTATATGATTCTTAAGAAATGA
Found at i:1101472 original size:23 final size:23
Alignment explanation
Indices: 1101427--1101504 Score: 86
Period size: 23 Copynumber: 3.3 Consensus size: 23
1101417 CCTTATGGAC
*
1101427 ATTATTATATGGCACTACGGTGCA
1 ATTA-TATGTGGCACTACGGTGCA
* * *
1101451 ATTCTACT-TGGCACTCCAGTGCA
1 ATTATA-TGTGGCACTACGGTGCA
*
1101474 ATTATATGTGGCACTTCGGTGCA
1 ATTATATGTGGCACTACGGTGCA
1101497 ATTATATG
1 ATTATATG
1101505 AGCTGTGGTG
Statistics
Matches: 46, Mismatches: 6, Indels: 5
0.81 0.11 0.09
Matches are distributed among these distances:
22 1 0.02
23 41 0.89
24 4 0.09
ACGTcount: A:0.26, C:0.19, G:0.21, T:0.35
Consensus pattern (23 bp):
ATTATATGTGGCACTACGGTGCA
Found at i:1103398 original size:73 final size:72
Alignment explanation
Indices: 1103315--1103460 Score: 258
Period size: 73 Copynumber: 2.0 Consensus size: 72
1103305 AATTAAAGCT
*
1103315 CGATCTTCATCATCAAATTCAATTTCCATTGAACTCAACT-GGGTTGGTGTTGTGTTGAGTTCAT
1 CGATCTTCATCATCAAATTCAATTTCCATTGAACTCAACTGGGGTT-G-ATTGTGTTGAGTTCAT
1103379 TTTGTTGTG
64 TTTGTTGTG
1103388 CGATCTTCATCATCAAATTCAATTTCCATTGAACTCAACTGGGGTTGATTGTGTTGAGTTCATTT
1 CGATCTTCATCATCAAATTCAATTTCCATTGAACTCAACTGGGGTTGATTGTGTTGAGTTCATTT
1103453 TGTTGTG
66 TGTTGTG
1103460 C
1 C
1103461 CGGGATAACG
Statistics
Matches: 71, Mismatches: 1, Indels: 3
0.95 0.01 0.04
Matches are distributed among these distances:
72 25 0.35
73 41 0.58
74 5 0.07
ACGTcount: A:0.21, C:0.17, G:0.20, T:0.42
Consensus pattern (72 bp):
CGATCTTCATCATCAAATTCAATTTCCATTGAACTCAACTGGGGTTGATTGTGTTGAGTTCATTT
TGTTGTG
Found at i:1103763 original size:16 final size:16
Alignment explanation
Indices: 1103742--1103772 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
1103732 ACCTCGCAAA
1103742 AAATTCACTATTCATG
1 AAATTCACTATTCATG
1103758 AAATTCACTATTCAT
1 AAATTCACTATTCAT
1103773 ATGAATAGTA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.39, C:0.19, G:0.03, T:0.39
Consensus pattern (16 bp):
AAATTCACTATTCATG
Found at i:1104237 original size:35 final size:35
Alignment explanation
Indices: 1104170--1104278 Score: 184
Period size: 35 Copynumber: 3.1 Consensus size: 35
1104160 CCATTATCAT
* *
1104170 TTTTC-AACAAACATCTACCAAACTTTGAAAAACCA
1 TTTTCAAAGAAACATTTACCAAACTTTG-AAAACCA
1104205 TTTTCAAAGAAACATTTACCAAACTTTGAAAACCA
1 TTTTCAAAGAAACATTTACCAAACTTTGAAAACCA
1104240 TTTTCAAAGAAACATTTACCAAACTTTGAAAACCA
1 TTTTCAAAGAAACATTTACCAAACTTTGAAAACCA
1104275 TTTT
1 TTTT
1104279 TCCAAAGTTG
Statistics
Matches: 71, Mismatches: 2, Indels: 2
0.95 0.03 0.03
Matches are distributed among these distances:
35 51 0.72
36 20 0.28
ACGTcount: A:0.44, C:0.21, G:0.05, T:0.30
Consensus pattern (35 bp):
TTTTCAAAGAAACATTTACCAAACTTTGAAAACCA
Found at i:1104241 original size:21 final size:21
Alignment explanation
Indices: 1104217--1104277 Score: 64
Period size: 21 Copynumber: 3.2 Consensus size: 21
1104207 TTCAAAGAAA
1104217 CATTTACCAAACTTTGAAAAC
1 CATTTACCAAACTTTGAAAAC
*
1104238 CATTT-TCAAA----G-AAA-
1 CATTTACCAAACTTTGAAAAC
1104252 CATTTACCAAACTTTGAAAAC
1 CATTTACCAAACTTTGAAAAC
1104273 CATTT
1 CATTT
1104278 TTCCAAAGTT
Statistics
Matches: 31, Mismatches: 2, Indels: 14
0.66 0.04 0.30
Matches are distributed among these distances:
14 5 0.16
15 7 0.23
16 1 0.03
19 1 0.03
20 7 0.23
21 10 0.32
ACGTcount: A:0.43, C:0.21, G:0.05, T:0.31
Consensus pattern (21 bp):
CATTTACCAAACTTTGAAAAC
Found at i:1112425 original size:14 final size:15
Alignment explanation
Indices: 1112414--1112446 Score: 57
Period size: 15 Copynumber: 2.2 Consensus size: 15
1112404 TGGTGGTATT
1112414 GCAGTGGAGGTACTA
1 GCAGTGGAGGTACTA
*
1112429 GCAATGGAGGTACTA
1 GCAGTGGAGGTACTA
1112444 GCA
1 GCA
1112447 TCTCCTCGTC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.30, C:0.15, G:0.36, T:0.18
Consensus pattern (15 bp):
GCAGTGGAGGTACTA
Found at i:1112438 original size:15 final size:15
Alignment explanation
Indices: 1112418--1112446 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
1112408 GGTATTGCAG
1112418 TGGAGGTACTAGCAA
1 TGGAGGTACTAGCAA
1112433 TGGAGGTACTAGCA
1 TGGAGGTACTAGCA
1112447 TCTCCTCGTC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.31, C:0.14, G:0.34, T:0.21
Consensus pattern (15 bp):
TGGAGGTACTAGCAA
Found at i:1112678 original size:10 final size:10
Alignment explanation
Indices: 1112663--1112696 Score: 50
Period size: 10 Copynumber: 3.2 Consensus size: 10
1112653 TTCACGAGAT
1112663 AAAAAAAATA
1 AAAAAAAATA
1112673 AAAAAAAATA
1 AAAAAAAATA
1112683 AAATAAAGAATA
1 AAA-AAA-AATA
1112695 AA
1 AA
1112697 TTTATTATTT
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
10 13 0.59
11 3 0.14
12 6 0.27
ACGTcount: A:0.85, C:0.00, G:0.03, T:0.12
Consensus pattern (10 bp):
AAAAAAAATA
Found at i:1118091 original size:25 final size:25
Alignment explanation
Indices: 1118057--1118109 Score: 88
Period size: 25 Copynumber: 2.1 Consensus size: 25
1118047 CTTAGTTCTT
*
1118057 TTTTTGATAATAATAGGTTGAAATA
1 TTTTTGATAAAAATAGGTTGAAATA
*
1118082 TTTTTGATAAAAATTGGTTGAAATA
1 TTTTTGATAAAAATAGGTTGAAATA
1118107 TTT
1 TTT
1118110 GTTGTCATGG
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
25 26 1.00
ACGTcount: A:0.38, C:0.00, G:0.15, T:0.47
Consensus pattern (25 bp):
TTTTTGATAAAAATAGGTTGAAATA
Found at i:1118731 original size:101 final size:101
Alignment explanation
Indices: 1118514--1118816 Score: 502
Period size: 101 Copynumber: 3.0 Consensus size: 101
1118504 TCACAAGATG
*
1118514 ACTCTACCTGACTAGCTC-GGGGTGGAAGGTATGCTCCTTTTCACTTAGAGTGTGGGATGATAGT
1 ACTCTACCTGACTAGCTCGGGGGTGGAAGGTATGCTCCCTTTCACTTAGAGTGTGGGATGATAGT
*
1118578 GTGATGAGTTGAC-CCCCTTAAAGTATGCTAAAAAA
66 GTGATGAGCTGACTCCCCTTAAAGTATGCTAAAAAA
* * * *
1118613 ATTCTACATGACTAGCTCGGGGGTGGAAGGTATGCTCCCTTTGACTTAGAGTGTGGGATGGTAGT
1 ACTCTACCTGACTAGCTCGGGGGTGGAAGGTATGCTCCCTTTCACTTAGAGTGTGGGATGATAGT
*
1118678 GTGATGAGCTGACTCCCATTAAAGTATGCTAAAAAA
66 GTGATGAGCTGACTCCCCTTAAAGTATGCTAAAAAA
1118714 ACTCTACCTGACTAGCTCGGGGGTGGAAGGTATGCTCCCTTTCACTTAGAGTGTGGGATGATAGT
1 ACTCTACCTGACTAGCTCGGGGGTGGAAGGTATGCTCCCTTTCACTTAGAGTGTGGGATGATAGT
* *
1118779 GTGACGAGCTAACTCCCCTTAAAGTATGCTTAAAAAA
66 GTGATGAGCTGACTCCCCTTAAAGTATGC-TAAAAAA
1118816 A
1 A
1118817 GAGTTGAAGT
Statistics
Matches: 187, Mismatches: 14, Indels: 3
0.92 0.07 0.01
Matches are distributed among these distances:
99 16 0.09
100 55 0.29
101 108 0.58
102 8 0.04
ACGTcount: A:0.27, C:0.18, G:0.27, T:0.28
Consensus pattern (101 bp):
ACTCTACCTGACTAGCTCGGGGGTGGAAGGTATGCTCCCTTTCACTTAGAGTGTGGGATGATAGT
GTGATGAGCTGACTCCCCTTAAAGTATGCTAAAAAA
Found at i:1127264 original size:4 final size:4
Alignment explanation
Indices: 1127255--1127293 Score: 55
Period size: 4 Copynumber: 10.0 Consensus size: 4
1127245 CTACTAATTC
1127255 ATTT ATTT ATTT -TATT -TTT ATTT ATTT ATTT ATTT ATTT
1 ATTT ATTT ATTT AT-TT ATTT ATTT ATTT ATTT ATTT ATTT
1127294 TATTAGTTTT
Statistics
Matches: 33, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
3 3 0.09
4 30 0.91
ACGTcount: A:0.23, C:0.00, G:0.00, T:0.77
Consensus pattern (4 bp):
ATTT
Found at i:1128820 original size:10 final size:10
Alignment explanation
Indices: 1128805--1128846 Score: 50
Period size: 10 Copynumber: 4.1 Consensus size: 10
1128795 AGTGACTAAA
1128805 ATGAAAATTT
1 ATGAAAATTT
1128815 ATG-AAATTT
1 ATGAAAATTT
*
1128824 AGGGAACAATTT
1 A-TGAA-AATTT
1128836 ATGAAAATTT
1 ATGAAAATTT
1128846 A
1 A
1128847 AAAGTTCAAG
Statistics
Matches: 27, Mismatches: 2, Indels: 6
0.77 0.06 0.17
Matches are distributed among these distances:
9 7 0.26
10 10 0.37
11 4 0.15
12 6 0.22
ACGTcount: A:0.48, C:0.02, G:0.14, T:0.36
Consensus pattern (10 bp):
ATGAAAATTT
Found at i:1151282 original size:28 final size:29
Alignment explanation
Indices: 1151237--1151326 Score: 71
Period size: 27 Copynumber: 3.2 Consensus size: 29
1151227 ATAAGTTACC
* * *
1151237 TCTTCATTTCTTTACTTTCATTTTCCTTT
1 TCTTCAATCCTTTTCTTTCATTTTCCTTT
**
1151266 TCTTCAA-CCTTTTCTTTC-TTTTTATTT
1 TCTTCAATCCTTTTCTTTCATTTTCCTTT
* *
1151293 TCTTGAATCC-TTTCTTCTACA-TTTCCATT
1 TCTTCAATCCTTTTCTT-T-CATTTTCCTTT
1151322 TCTTC
1 TCTTC
1151327 TTTTCCTTTC
Statistics
Matches: 47, Mismatches: 10, Indels: 8
0.72 0.15 0.12
Matches are distributed among these distances:
27 19 0.40
28 12 0.26
29 16 0.34
ACGTcount: A:0.12, C:0.26, G:0.01, T:0.61
Consensus pattern (29 bp):
TCTTCAATCCTTTTCTTTCATTTTCCTTT
Found at i:1152121 original size:151 final size:151
Alignment explanation
Indices: 1151925--1152223 Score: 500
Period size: 151 Copynumber: 2.0 Consensus size: 151
1151915 GTGATGTTGT
1151925 TCCAATGATGCTCATATACTCCTATTAAGCCTTGGTAGTTTGATAAAAAGGTTGTTCATGATGGT
1 TCCAATGATGCTCATATACTCCTATTAAGCCTTGGTAGTTTGATAAAAAGGTTGTTCATGATGGT
1151990 TTCAC-AACCA-A-C-TT-TTCACAATGAAAGGAAATTCATCTTCACTCCACTTTCACCAAACCA
66 TTCACAAACCAGACCTTTCTTCACAATGAAAGGAAA-TCATCTTCACTCC-CTTTCACCAAACCA
1152050 AGTATATGAAGATCAAGACTTTG
129 AGTATATGAAGATCAAGACTTTG
1152073 TCCAATGAATGCTCCATATACTCCTATTAAGACCTTGGTAGTTTGATAAAAAGGTTGTTCATGAT
1 TCCAATG-ATGCT-CATATACTCCTATTAAG-CCTTGGTAGTTTGATAAAAAGGTTGTTCATGAT
1152138 GGTTTCACAAACCAGTACTCTTTCTTCACAATGAAAGGAAATCATCTTCACTCCCTTTCACCAAA
63 GGTTTCACAAACCAG-AC-CTTTCTTCACAATGAAAGGAAATCATCTTCACTCCCTTTCACCAAA
1152203 CCAAGTATATGAAGATCAAGA
126 CCAAGTATATGAAGATCAAGA
1152224 AACTTTGGAA
Statistics
Matches: 141, Mismatches: 0, Indels: 12
0.92 0.00 0.08
Matches are distributed among these distances:
148 7 0.05
149 5 0.04
150 17 0.12
151 41 0.29
152 5 0.04
154 1 0.01
156 33 0.23
157 15 0.11
158 17 0.12
ACGTcount: A:0.33, C:0.21, G:0.14, T:0.31
Consensus pattern (151 bp):
TCCAATGATGCTCATATACTCCTATTAAGCCTTGGTAGTTTGATAAAAAGGTTGTTCATGATGGT
TTCACAAACCAGACCTTTCTTCACAATGAAAGGAAATCATCTTCACTCCCTTTCACCAAACCAAG
TATATGAAGATCAAGACTTTG
Done.