Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008817.1 Hibiscus syriacus cultivar Beakdansim tig00111983_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: 1047399
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.33
File 4 of 4
Found at i:805239 original size:31 final size:29
Alignment explanation
Indices: 805203--805267 Score: 85
Period size: 29 Copynumber: 2.2 Consensus size: 29
805193 GGTTCAGTAG
*
805203 TATAATTGAAACAAAAATCAAAGTTTAGTGA
1 TATAATTG--ACAAAAATAAAAGTTTAGTGA
* *
805234 TATAATTGATAAAATTAAAAGTTTAGTGA
1 TATAATTGACAAAAATAAAAGTTTAGTGA
805263 TATAA
1 TATAA
805268 CGATATAATG
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
29 23 0.74
31 8 0.26
ACGTcount: A:0.51, C:0.03, G:0.12, T:0.34
Consensus pattern (29 bp):
TATAATTGACAAAAATAAAAGTTTAGTGA
Found at i:824117 original size:33 final size:31
Alignment explanation
Indices: 824076--824139 Score: 83
Period size: 33 Copynumber: 2.0 Consensus size: 31
824066 TTTAGAACCT
*
824076 AAAATCTTAAATCTTCCTTCAGAACAAAAAAA
1 AAAATCTTAAATCATCCTTCAG-ACAAAAAAA
* *
824108 AAAAGTCTTAAGTCATCCTTCAGATAAAAAAA
1 AAAA-TCTTAAATCATCCTTCAGACAAAAAAA
824140 CTTAATCTTC
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
32 12 0.43
33 16 0.57
ACGTcount: A:0.52, C:0.17, G:0.06, T:0.25
Consensus pattern (31 bp):
AAAATCTTAAATCATCCTTCAGACAAAAAAA
Found at i:825756 original size:30 final size:30
Alignment explanation
Indices: 825720--825780 Score: 104
Period size: 30 Copynumber: 2.0 Consensus size: 30
825710 TTGATGATAA
**
825720 ACCAATTACATAAGACTTAAGTACACTCCT
1 ACCAATTACATAAGACTTAAACACACTCCT
825750 ACCAATTACATAAGACTTAAACACACTCCT
1 ACCAATTACATAAGACTTAAACACACTCCT
825780 A
1 A
825781 TTACACATTT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
30 29 1.00
ACGTcount: A:0.43, C:0.28, G:0.05, T:0.25
Consensus pattern (30 bp):
ACCAATTACATAAGACTTAAACACACTCCT
Found at i:833880 original size:38 final size:38
Alignment explanation
Indices: 833840--834019 Score: 177
Period size: 38 Copynumber: 4.8 Consensus size: 38
833830 TAATGTTTTG
* *
833840 TTATTTAAGAATTTATATTCAATTAAAATTCAAATATG
1 TTATTTAAGAATTTATATTCAATTAAAATACAAATATA
** * * * **
833878 TTATTTTTGCATTTATATTCTATTGAAATAGGAATATA
1 TTATTTAAGAATTTATATTCAATTAAAATACAAATATA
* **
833916 TTATTTAAAAATTTATATTTTATT-AAATACAAATATA
1 TTATTTAAGAATTTATATTCAATTAAAATACAAATATA
* **
833953 TTATTTATGAATTTATATTCAATTAAAATATGAATATA
1 TTATTTAAGAATTTATATTCAATTAAAATACAAATATA
* *
833991 TTA-TTACA-AATTTATATTCGAGTAAAATA
1 TTATTTA-AGAATTTATATTCAATTAAAATA
834020 TAGTATTGTA
Statistics
Matches: 115, Mismatches: 25, Indels: 5
0.79 0.17 0.03
Matches are distributed among these distances:
37 53 0.46
38 62 0.54
ACGTcount: A:0.43, C:0.04, G:0.06, T:0.47
Consensus pattern (38 bp):
TTATTTAAGAATTTATATTCAATTAAAATACAAATATA
Found at i:833933 original size:19 final size:18
Alignment explanation
Indices: 833911--834007 Score: 52
Period size: 19 Copynumber: 5.2 Consensus size: 18
833901 TGAAATAGGA
833911 ATATATTATTTAAAAATTT
1 ATATATTA-TTAAAAATTT
* * ***
833930 ATATTTTATTAAATACAA
1 ATATATTATTAAAAATTT
**
833948 ATATATTATTTATGAATTT
1 ATATATTA-TTAAAAATTT
* **
833967 ATAT-TCAATTAAAATATGA
1 ATATAT-TATTAAAA-ATTT
*
833986 ATATATTATTACAAATTT
1 ATATATTATTAAAAATTT
834004 ATAT
1 ATAT
834008 TCGAGTAAAA
Statistics
Matches: 53, Mismatches: 21, Indels: 9
0.64 0.25 0.11
Matches are distributed among these distances:
18 24 0.45
19 28 0.53
20 1 0.02
ACGTcount: A:0.46, C:0.03, G:0.02, T:0.48
Consensus pattern (18 bp):
ATATATTATTAAAAATTT
Found at i:833982 original size:75 final size:76
Alignment explanation
Indices: 833840--834019 Score: 229
Period size: 75 Copynumber: 2.4 Consensus size: 76
833830 TAATGTTTTG
* * * * * * *
833840 TTATTTAAGAATTTATATTCAATTAAAATTCAAATATGTTATTTTTGCATTTATATTCTATTGAA
1 TTATTTAAAAATTTATATTCAATTAAAATACAAATATATTATTTATGAATTTATATTCAATTAAA
833905 ATAGGAATATA
66 ATAGGAATATA
**
833916 TTATTTAAAAATTTATATTTTATT-AAATACAAATATATTATTTATGAATTTATATTCAATTAAA
1 TTATTTAAAAATTTATATTCAATTAAAATACAAATATATTATTTATGAATTTATATTCAATTAAA
*
833980 ATATGAATATA
66 ATAGGAATATA
* * *
833991 TTA-TTACAAATTTATATTCGAGTAAAATA
1 TTATTTAAAAATTTATATTCAATTAAAATA
834020 TAGTATTGTA
Statistics
Matches: 89, Mismatches: 14, Indels: 3
0.84 0.13 0.03
Matches are distributed among these distances:
74 16 0.18
75 52 0.58
76 21 0.24
ACGTcount: A:0.43, C:0.04, G:0.06, T:0.47
Consensus pattern (76 bp):
TTATTTAAAAATTTATATTCAATTAAAATACAAATATATTATTTATGAATTTATATTCAATTAAA
ATAGGAATATA
Found at i:844340 original size:22 final size:19
Alignment explanation
Indices: 844289--844327 Score: 78
Period size: 19 Copynumber: 2.1 Consensus size: 19
844279 TGTGATAGGT
844289 TTTTAGTATGTCAAGTTCA
1 TTTTAGTATGTCAAGTTCA
844308 TTTTAGTATGTCAAGTTCA
1 TTTTAGTATGTCAAGTTCA
844327 T
1 T
844328 CATTTCAGTA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.26, C:0.10, G:0.15, T:0.49
Consensus pattern (19 bp):
TTTTAGTATGTCAAGTTCA
Found at i:847406 original size:2 final size:2
Alignment explanation
Indices: 847399--847429 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
847389 TAAAATCGTA
847399 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
847430 AAATGATAAT
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:854955 original size:41 final size:39
Alignment explanation
Indices: 854872--854974 Score: 113
Period size: 41 Copynumber: 2.6 Consensus size: 39
854862 TATATTTACG
* * *
854872 TTTTAAA-TTATTATCTT-TATTTATATTAATCTTTAAAT
1 TTTTAAATTTATTATCTTAT-TTTAAATTAATCTTCAAAC
854910 TTTTAATATTTATTACTCTTATTTTAAATTAATCTTCAAAC
1 TTTTAA-ATTTATTA-TCTTATTTTAAATTAATCTTCAAAC
854951 TTTTAAATATT-TTAATCTTATTTT
1 TTTTAAAT-TTATT-ATCTTATTTT
854975 TCGACCTATG
Statistics
Matches: 56, Mismatches: 3, Indels: 10
0.81 0.04 0.14
Matches are distributed among these distances:
38 6 0.11
39 1 0.02
40 19 0.34
41 29 0.52
42 1 0.02
ACGTcount: A:0.33, C:0.08, G:0.00, T:0.59
Consensus pattern (39 bp):
TTTTAAATTTATTATCTTATTTTAAATTAATCTTCAAAC
Found at i:858389 original size:23 final size:23
Alignment explanation
Indices: 858355--858419 Score: 85
Period size: 23 Copynumber: 2.8 Consensus size: 23
858345 CACCACAGCT
*
858355 CGTATAAATGCACCGAAGTGCCA
1 CGTAGAAATGCACCGAAGTGCCA
* * *
858378 CGTAGAATTGCACCGTAGTGCCG
1 CGTAGAAATGCACCGAAGTGCCA
*
858401 CGTAGAAATGCACAGAAGT
1 CGTAGAAATGCACCGAAGT
858420 TCCATATAAT
Statistics
Matches: 35, Mismatches: 7, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
23 35 1.00
ACGTcount: A:0.32, C:0.23, G:0.26, T:0.18
Consensus pattern (23 bp):
CGTAGAAATGCACCGAAGTGCCA
Found at i:859864 original size:21 final size:21
Alignment explanation
Indices: 859840--859884 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
859830 TTTTGTTCGT
* *
859840 TTGAAGGGGTATCGGTTCCCC
1 TTGAAGGGGTACCGATTCCCC
*
859861 TTGAATGGGTACCGATTCCCC
1 TTGAAGGGGTACCGATTCCCC
859882 TTG
1 TTG
859885 CCCATAAATC
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:877009 original size:18 final size:20
Alignment explanation
Indices: 876986--877022 Score: 60
Period size: 18 Copynumber: 1.9 Consensus size: 20
876976 TGTATCAAAG
876986 TTTATAAAA-AA-TATTTAT
1 TTTATAAAAGAATTATTTAT
877004 TTTATAAAAGAATTATTTA
1 TTTATAAAAGAATTATTTA
877023 GAATCAATTC
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 9 0.53
19 2 0.12
20 6 0.35
ACGTcount: A:0.49, C:0.00, G:0.03, T:0.49
Consensus pattern (20 bp):
TTTATAAAAGAATTATTTAT
Found at i:881164 original size:16 final size:16
Alignment explanation
Indices: 881143--881175 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
881133 TATTACCTCG
881143 TTTATAAAATTTAAAA
1 TTTATAAAATTTAAAA
*
881159 TTTATAAAATTTTAAA
1 TTTATAAAATTTAAAA
881175 T
1 T
881176 AATTTATCAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (16 bp):
TTTATAAAATTTAAAA
Found at i:885900 original size:2 final size:2
Alignment explanation
Indices: 885893--885923 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
885883 AAACCTTTCC
885893 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
885924 AAGAGGGGAT
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:888398 original size:24 final size:24
Alignment explanation
Indices: 888369--888415 Score: 76
Period size: 24 Copynumber: 2.0 Consensus size: 24
888359 ATCTTTGACA
* *
888369 AACCCATGTTACCTACTAGAATTG
1 AACCCATGTGACCTACTAAAATTG
888393 AACCCATGTGACCTACTAAAATT
1 AACCCATGTGACCTACTAAAATT
888416 AAATTTTCTA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.36, C:0.26, G:0.11, T:0.28
Consensus pattern (24 bp):
AACCCATGTGACCTACTAAAATTG
Found at i:898530 original size:76 final size:76
Alignment explanation
Indices: 898404--898555 Score: 304
Period size: 76 Copynumber: 2.0 Consensus size: 76
898394 TCGGTTTCGG
898404 TTCTGGTAAACGGTTCCCCTTCGGAAGAGTTTACTATGGCTAAAGGACTAAGACAAGGTTGTAGT
1 TTCTGGTAAACGGTTCCCCTTCGGAAGAGTTTACTATGGCTAAAGGACTAAGACAAGGTTGTAGT
898469 CTCTCTCCGCT
66 CTCTCTCCGCT
898480 TTCTGGTAAACGGTTCCCCTTCGGAAGAGTTTACTATGGCTAAAGGACTAAGACAAGGTTGTAGT
1 TTCTGGTAAACGGTTCCCCTTCGGAAGAGTTTACTATGGCTAAAGGACTAAGACAAGGTTGTAGT
898545 CTCTCTCCGCT
66 CTCTCTCCGCT
898556 CTTATTTAAT
Statistics
Matches: 76, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
76 76 1.00
ACGTcount: A:0.24, C:0.22, G:0.24, T:0.30
Consensus pattern (76 bp):
TTCTGGTAAACGGTTCCCCTTCGGAAGAGTTTACTATGGCTAAAGGACTAAGACAAGGTTGTAGT
CTCTCTCCGCT
Found at i:900785 original size:66 final size:68
Alignment explanation
Indices: 900679--900813 Score: 256
Period size: 66 Copynumber: 2.0 Consensus size: 68
900669 CCACTACTTG
900679 ATCCTTTCTATTAGGAAAGGGTCAACTATGAGGGAGG-TTTTAACGAGGC-TCCTATTTCTATCA
1 ATCCTTTCTATTAGGAAAGGGTCAACTATGAGGGAGGTTTTTAACGAGGCTTCCTATTTCTATCA
900742 AAA
66 AAA
900745 ATCCTTTCTATTAGGAAAGGGTCAACTATGAGGGAGGTTTTTAACGAGGCTTCCTATTTCTATCA
1 ATCCTTTCTATTAGGAAAGGGTCAACTATGAGGGAGGTTTTTAACGAGGCTTCCTATTTCTATCA
900810 AAA
66 AAA
900813 A
1 A
900814 AAAAAAAATG
Statistics
Matches: 67, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
66 37 0.55
67 12 0.18
68 18 0.27
ACGTcount: A:0.30, C:0.16, G:0.21, T:0.33
Consensus pattern (68 bp):
ATCCTTTCTATTAGGAAAGGGTCAACTATGAGGGAGGTTTTTAACGAGGCTTCCTATTTCTATCA
AAA
Found at i:901319 original size:4 final size:4
Alignment explanation
Indices: 901312--901353 Score: 84
Period size: 4 Copynumber: 10.5 Consensus size: 4
901302 ATATATATAT
901312 ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG AT
1 ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG AT
901354 TGATGTTAAA
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 38 1.00
ACGTcount: A:0.50, C:0.00, G:0.24, T:0.26
Consensus pattern (4 bp):
ATAG
Found at i:908751 original size:16 final size:17
Alignment explanation
Indices: 908719--908752 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
908709 CATTAGATTT
*
908719 AATATTAAAAAATATAA
1 AATATCAAAAAATATAA
908736 AATATCAAAAAA-ATAA
1 AATATCAAAAAATATAA
908752 A
1 A
908753 TTTAAAAATA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 5 0.31
17 11 0.69
ACGTcount: A:0.74, C:0.03, G:0.00, T:0.24
Consensus pattern (17 bp):
AATATCAAAAAATATAA
Found at i:909733 original size:231 final size:229
Alignment explanation
Indices: 909321--909771 Score: 794
Period size: 231 Copynumber: 2.0 Consensus size: 229
909311 GTAAATTATC
* * *
909321 TATCCTTTTTATAAAAGTGTCCATACTTATTTCACTGTGAAAATATATTTATTATTATCTTTAGT
1 TATCATTTTTATAAAAGTGTCCATACTTATTTCACTGTGAAAACATATTTATTATTATATTTAGT
**
909386 TAATATTGTTAAATTTAAAATCTAAATAATATTTTATAAAATATCAAAACAATCAAATAATTTTT
66 TAATATTGTTAAATTTAAAATCTAAATAATATTTTATAAAATATCAAAACAATCAAATAAAATTT
*
909451 TGTGTAAATGAAATTATTAAATTAATATTGTAGGTGGAAAACATGAAACACTATTAAAAAAATTG
131 TGTGTAAATGAAATTATTAAATTAATATTGTAGGTGGAAAACATAAAACACTATTAAAAAAATTG
909516 AAACATAAATTACATAACTTTCAAAAAAGTATATA
196 AAACATAAATTACATAACTTT-AAAAAAGTATATA
*
909551 TATCATTTTTATAAAAGTGTCCATACTTATTTCACTGTTGAAAACATATTTATTATTATATTTGG
1 TATCATTTTTATAAAAGTGTCCATACTTATTTCACTG-TGAAAACATATTTATTATTATATTTAG
*
909616 TTAATATTGTTAAATTTAAATTCTAAATAATATTTTATAAAATATCAAAACAATCAAATAAAATT
65 TTAATATTGTTAAATTTAAAATCTAAATAATATTTTATAAAATATCAAAACAATCAAATAAAATT
* *
909681 TTGTGTAAATTAAATTATTAAATTAATATTGTAGGTGGAAAACATAAAACACTATTAAATAAATT
130 TTGTGTAAATGAAATTATTAAATTAATATTGTAGGTGGAAAACATAAAACACTATTAAAAAAATT
909746 GAAACATAAATTACATAACTTTAAAA
195 GAAACATAAATTACATAACTTTAAAA
909772 GCAGTTTTAA
Statistics
Matches: 210, Mismatches: 10, Indels: 2
0.95 0.05 0.01
Matches are distributed among these distances:
230 40 0.19
231 170 0.81
ACGTcount: A:0.45, C:0.08, G:0.07, T:0.39
Consensus pattern (229 bp):
TATCATTTTTATAAAAGTGTCCATACTTATTTCACTGTGAAAACATATTTATTATTATATTTAGT
TAATATTGTTAAATTTAAAATCTAAATAATATTTTATAAAATATCAAAACAATCAAATAAAATTT
TGTGTAAATGAAATTATTAAATTAATATTGTAGGTGGAAAACATAAAACACTATTAAAAAAATTG
AAACATAAATTACATAACTTTAAAAAAGTATATA
Found at i:909860 original size:20 final size:19
Alignment explanation
Indices: 909837--909883 Score: 76
Period size: 20 Copynumber: 2.4 Consensus size: 19
909827 CGATATACCA
909837 GGTAAAAATATGATAAAACC
1 GGTAAAAA-ATGATAAAACC
909857 GGTAACAAAATGATAAAACC
1 GGTAA-AAAATGATAAAACC
909877 GGTAAAA
1 GGTAAAA
909884 TTAAAAGTGT
Statistics
Matches: 26, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
19 2 0.08
20 21 0.81
21 3 0.12
ACGTcount: A:0.55, C:0.11, G:0.17, T:0.17
Consensus pattern (19 bp):
GGTAAAAAATGATAAAACC
Found at i:910027 original size:20 final size:18
Alignment explanation
Indices: 910004--910049 Score: 56
Period size: 20 Copynumber: 2.4 Consensus size: 18
909994 CGATATAACA
910004 GGTAAAAATATGATAAAACC
1 GGTAAAAA-ATGATAAAA-C
*
910024 GGTATCAAAATGATAAAAC
1 GGTA-AAAAATGATAAAAC
910043 GGTAAAA
1 GGTAAAA
910050 TGATACCGGA
Statistics
Matches: 23, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
18 2 0.09
19 5 0.22
20 13 0.57
21 3 0.13
ACGTcount: A:0.54, C:0.09, G:0.17, T:0.20
Consensus pattern (18 bp):
GGTAAAAAATGATAAAAC
Found at i:912390 original size:33 final size:33
Alignment explanation
Indices: 912348--912413 Score: 96
Period size: 33 Copynumber: 2.0 Consensus size: 33
912338 AAATAGAAGG
*
912348 AGTGGTGAAAGAAGTAGAGGTGTTGAGGGGTGA
1 AGTGGTGAAAGAAGTAGAGGTGTTAAGGGGTGA
***
912381 AGTGGTGAAAGAAGTTTCGGTGTTAAGGGGTGA
1 AGTGGTGAAAGAAGTAGAGGTGTTAAGGGGTGA
912414 TATTAAGATG
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 29 1.00
ACGTcount: A:0.29, C:0.02, G:0.45, T:0.24
Consensus pattern (33 bp):
AGTGGTGAAAGAAGTAGAGGTGTTAAGGGGTGA
Found at i:914251 original size:19 final size:19
Alignment explanation
Indices: 914207--914250 Score: 72
Period size: 19 Copynumber: 2.4 Consensus size: 19
914197 AATGTCGAGT
914207 TAATTTTGTATAAGATTTA
1 TAATTTTGTATAAGATTTA
*
914226 TAATTTTGTATACGATTTA
1 TAATTTTGTATAAGATTTA
914245 T-ATTTT
1 TAATTTT
914251 TTTATGTGAA
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
18 5 0.21
19 19 0.79
ACGTcount: A:0.32, C:0.02, G:0.09, T:0.57
Consensus pattern (19 bp):
TAATTTTGTATAAGATTTA
Found at i:914772 original size:198 final size:198
Alignment explanation
Indices: 914333--915551 Score: 2327
Period size: 198 Copynumber: 6.1 Consensus size: 198
914323 TTAAGGGTCA
*
914333 TGTCGATACTAATATAGTTTGTGTCGATATTTTTTTTCCAGAATGAATTAAAAACAAGGTGCATC
1 TGTCGACACTAATATAGTTTGTGTCGATA-TTTTTTTCCAGAATGAATTAAAAACAAGGTGCATC
914398 AATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAATG
65 AATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAATG
914463 TAATATGTAATTTTTTAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATAAGTCTAAAT
130 TAATATGTAATTTTTTAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATAAGTCTAAAT
914528 AATG
195 AATG
914532 TGTCGACACTAATATAGTTTGTGTCGATATTTTTTTCCAGAATGAATTAAAAACAAGGTGCATCA
1 TGTCGACACTAATATAGTTTGTGTCGATATTTTTTTCCAGAATGAATTAAAAACAAGGTGCATCA
914597 ATAAAGTGTCGATCCATATAT-AAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAATGT
66 ATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAATGT
*
914661 AATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATAAGTCTAAATA
131 AATATGTAATTTTTTAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATAAGTCTAAATA
914726 ATG
196 ATG
*
914729 TGTCGACACTAATATAGTTTGTGTCGATATTTTTTTCCCAGAATGAATTAAAAACAAGGTGCACC
1 TGTCGACACTAATATAGTTTGTGTCGATATTTTTTT-CCAGAATGAATTAAAAACAAGGTGCATC
*
914794 CATAAAGTGTCGATCCATATATAAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAAT
65 AATAAAGTGTCGATCCATATAT-AAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAAT
914859 GTAATATGTAATTTTTTAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATAAGTCTAAA
129 GTAATATGTAATTTTTTAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATAAGTCTAAA
914924 TAATG
194 TAATG
914929 TGTCGACACTAATATAGTTTGTGTCGATATTGTTTTTCCAGAATGAATTAAAAACAAGGTGCATC
1 TGTCGACACTAATATAGTTTGTGTCGATATT-TTTTTCCAGAATGAATTAAAAACAAGGTGCATC
914994 AATAAAGTGTCGATCCATATA-AAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAATG
65 AATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAATG
915058 TAATATGTAATTTTTTAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATAAGTCTAAAT
130 TAATATGTAATTTTTTAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATAAGTCTAAAT
915123 AATG
195 AATG
915127 TGTCGACACTAATATAGTTTGTGTCGATATTTTTTTCCAGAATGAATTAAAAACAAGGTGCATCA
1 TGTCGACACTAATATAGTTTGTGTCGATATTTTTTTCCAGAATGAATTAAAAACAAGGTGCATCA
915192 ATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAATGT
66 ATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAATGT
915257 AATATGTAATTTTTTAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATAAGTCTAAATA
131 AATATGTAATTTTTTAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATAAGTCTAAATA
915322 ATG
196 ATG
915325 TGTCGACACTAATATAGTTTGTGTCGATATTTTTTTTCCAGAATGAATTAAAAACAAGGTGCATC
1 TGTCGACACTAATATAGTTTGTGTCGATA-TTTTTTTCCAGAATGAATTAAAAACAAGGTGCATC
915390 AAT-AAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAATG
65 AATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAATG
*
915454 TAATATGTAATTTTTGAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATAAGTCTAAAT
130 TAATATGTAATTTTTTAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATAAGTCTAAAT
915519 AATG
195 AATG
915523 TGTCGACACTAATATAGTTTGTGTCGATA
1 TGTCGACACTAATATAGTTTGTGTCGATA
915552 CTAATTTAAA
Statistics
Matches: 1006, Mismatches: 8, Indels: 13
0.98 0.01 0.01
Matches are distributed among these distances:
197 200 0.20
198 547 0.54
199 66 0.07
200 188 0.19
201 5 0.00
ACGTcount: A:0.38, C:0.14, G:0.15, T:0.32
Consensus pattern (198 bp):
TGTCGACACTAATATAGTTTGTGTCGATATTTTTTTCCAGAATGAATTAAAAACAAGGTGCATCA
ATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAATGT
AATATGTAATTTTTTAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATAAGTCTAAATA
ATG
Found at i:917038 original size:18 final size:18
Alignment explanation
Indices: 917015--917097 Score: 55
Period size: 21 Copynumber: 4.4 Consensus size: 18
917005 ATCGGTCGCA
917015 GAAGATGAAGCTGACGAT
1 GAAGATGAAGCTGACGAT
* *
917033 GAAGATGACGATGATGATGAT
1 GAAGATGA--A-GCTGACGAT
*
917054 GATGACGATGAAGCTGGCGAT
1 GA--A-GATGAAGCTGACGAT
917075 GAAGAT---GCTGACGAT
1 GAAGATGAAGCTGACGAT
*
917090 GATGATGA
1 GAAGATGA
917098 TGATGATGAA
Statistics
Matches: 50, Mismatches: 7, Indels: 17
0.68 0.09 0.23
Matches are distributed among these distances:
15 13 0.26
18 11 0.22
19 1 0.02
20 1 0.02
21 17 0.34
22 1 0.02
23 1 0.02
24 5 0.10
ACGTcount: A:0.35, C:0.10, G:0.35, T:0.20
Consensus pattern (18 bp):
GAAGATGAAGCTGACGAT
Found at i:917039 original size:6 final size:6
Alignment explanation
Indices: 917015--917112 Score: 61
Period size: 6 Copynumber: 16.3 Consensus size: 6
917005 ATCGGTCGCA
* * * * * *
917015 GAAGAT GAAGCT GACGAT GAAGAT GACGAT GATGAT GATGAT GACGAT
1 GAAGAT GAAGAT GAAGAT GAAGAT GAAGAT GAAGAT GAAGAT GAAGAT
* ** ** * * * *
917063 GAAGCT GGCGAT GAAGAT GCTGAC GATGAT GATGAT GATGAT GAAGAT
1 GAAGAT GAAGAT GAAGAT GAAGAT GAAGAT GAAGAT GAAGAT GAAGAT
917111 GA
1 GA
917113 TGATCCAAAC
Statistics
Matches: 72, Mismatches: 20, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
6 72 1.00
ACGTcount: A:0.36, C:0.08, G:0.35, T:0.21
Consensus pattern (6 bp):
GAAGAT
Found at i:917050 original size:3 final size:3
Alignment explanation
Indices: 917030--917116 Score: 75
Period size: 3 Copynumber: 29.0 Consensus size: 3
917020 TGAAGCTGAC
* * * * * ** *
917030 GAT GAA GAT GAC GAT GAT GAT GAT GAT GAC GAT GAA GCT GGC GAT GAA
1 GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT
* * *
917078 GAT GCT GAC GAT GAT GAT GAT GAT GAT GAA GAT GAT GAT
1 GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT
917117 CCAAACAAGT
Statistics
Matches: 63, Mismatches: 21, Indels: 0
0.75 0.25 0.00
Matches are distributed among these distances:
3 63 1.00
ACGTcount: A:0.34, C:0.07, G:0.34, T:0.24
Consensus pattern (3 bp):
GAT
Found at i:917065 original size:42 final size:42
Alignment explanation
Indices: 917018--917108 Score: 139
Period size: 42 Copynumber: 2.2 Consensus size: 42
917008 GGTCGCAGAA
*
917018 GATGAAGCTGACGATGAAGATGAC-GATGATGATGATGATGAC
1 GATGAAGCTGACGATGAAGATG-CTGACGATGATGATGATGAC
* *
917060 GATGAAGCTGGCGATGAAGATGCTGACGATGATGATGATGAT
1 GATGAAGCTGACGATGAAGATGCTGACGATGATGATGATGAC
917102 GATGAAG
1 GATGAAG
917109 ATGATGATCC
Statistics
Matches: 45, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
41 1 0.02
42 44 0.98
ACGTcount: A:0.34, C:0.09, G:0.35, T:0.22
Consensus pattern (42 bp):
GATGAAGCTGACGATGAAGATGCTGACGATGATGATGATGAC
Found at i:918897 original size:184 final size:184
Alignment explanation
Indices: 918588--919443 Score: 1613
Period size: 184 Copynumber: 4.7 Consensus size: 184
918578 CTTTCAACAT
**
918588 ATTATAATAAAATAGATAATTTTGTAATATAACCGGTATAAATATACCGGTCTTATGCGCGAATA
1 ATTATAATGTAATAGATAATTTTGTAATATAACCGGTATAAATATACCGGTCTTATGCGCGAATA
*
918653 GGTCTACAACCTATATCGACACTTTTTAATATTGTGTCGGTACTTTATGTCCATATTGGAAAAAA
66 GGTCTACAACCTATATCGACACTTTTTAATATTGTGTCGGTACTTTATGTCCATATTGGAAGAAA
* *
918718 AATGTATCGATACAATTTAAAAAAGTGTCGACATTTTACACATCGGAACCCATA
131 AATGTGTCGATACGATTTAAAAAAGTGTCGACATTTTACACATCGGAACCCATA
*
918772 ATTATAATGTAATAGATAATTTTGTAATATAACCGATATAAATATACCGGTCTTATGCGCGAATA
1 ATTATAATGTAATAGATAATTTTGTAATATAACCGGTATAAATATACCGGTCTTATGCGCGAATA
918837 GGTCTACAACCTATATCGACACTTTTTAATATTGTGTCGGTACTTTATGTCCATATTGGAAGAAA
66 GGTCTACAACCTATATCGACACTTTTTAATATTGTGTCGGTACTTTATGTCCATATTGGAAGAAA
918902 AATGTGTCGATACGATTTAAAAAAGTGTCGACATTTTACACATCGGAACCCATA
131 AATGTGTCGATACGATTTAAAAAAGTGTCGACATTTTACACATCGGAACCCATA
918956 ATTATAATGTAATAGATAATTTTGTAATATAACCGGTATAAATATACCGGTCTTATGCGCGAATA
1 ATTATAATGTAATAGATAATTTTGTAATATAACCGGTATAAATATACCGGTCTTATGCGCGAATA
*
919021 GGTCTACAACCTATATCGACATTTTTTAATATTGTGTCGGTACTTTATGTCCATATTGGAAGAAA
66 GGTCTACAACCTATATCGACACTTTTTAATATTGTGTCGGTACTTTATGTCCATATTGGAAGAAA
919086 AATGTGTCGATACGATTTAAAAAAGTGTCGACATTTTACACATCGGAACCCATA
131 AATGTGTCGATACGATTTAAAAAAGTGTCGACATTTTACACATCGGAACCCATA
919140 ATTATAATGTAATAGATAATTTTGTAATATAACCGGTATAAATATACCGGTCTTATGCGCGAATA
1 ATTATAATGTAATAGATAATTTTGTAATATAACCGGTATAAATATACCGGTCTTATGCGCGAATA
919205 GGTCTACAACCTATATCGACACTTTTTAATATTGTGTCGGTACTTTATGTCCATATTGGAAGAAA
66 GGTCTACAACCTATATCGACACTTTTTAATATTGTGTCGGTACTTTATGTCCATATTGGAAGAAA
*
919270 AATGTGTCAATACGATTTAAAAAAGTGTCGACATTTTACACATCGGAACCCATA
131 AATGTGTCGATACGATTTAAAAAAGTGTCGACATTTTACACATCGGAACCCATA
* *
919324 ATTATAATGTAATAGATAATTTTGTAATATAACCGGTATAAATATACCGGTTTTATGAGCGAATA
1 ATTATAATGTAATAGATAATTTTGTAATATAACCGGTATAAATATACCGGTCTTATGCGCGAATA
*
919389 GGTCTACAACCTATATCGACACTTTATAATATTGTGTCGGTACTTTATGTCCATA
66 GGTCTACAACCTATATCGACACTTTTTAATATTGTGTCGGTACTTTATGTCCATA
919444 CCATTTAAAA
Statistics
Matches: 659, Mismatches: 13, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
184 659 1.00
ACGTcount: A:0.36, C:0.15, G:0.15, T:0.34
Consensus pattern (184 bp):
ATTATAATGTAATAGATAATTTTGTAATATAACCGGTATAAATATACCGGTCTTATGCGCGAATA
GGTCTACAACCTATATCGACACTTTTTAATATTGTGTCGGTACTTTATGTCCATATTGGAAGAAA
AATGTGTCGATACGATTTAAAAAAGTGTCGACATTTTACACATCGGAACCCATA
Found at i:922032 original size:23 final size:23
Alignment explanation
Indices: 922001--922063 Score: 90
Period size: 23 Copynumber: 2.7 Consensus size: 23
921991 ATAGGTAAAC
*
922001 ATATGATGTAATAGGTAGCCCTT
1 ATATAATGTAATAGGTAGCCCTT
* **
922024 ATATAATGTAATAGGTATCGTTT
1 ATATAATGTAATAGGTAGCCCTT
922047 ATATAATGTAATAGGTA
1 ATATAATGTAATAGGTA
922064 ATGGTTATAT
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 36 1.00
ACGTcount: A:0.37, C:0.06, G:0.19, T:0.38
Consensus pattern (23 bp):
ATATAATGTAATAGGTAGCCCTT
Found at i:922071 original size:23 final size:23
Alignment explanation
Indices: 922001--922073 Score: 85
Period size: 23 Copynumber: 3.2 Consensus size: 23
921991 ATAGGTAAAC
* * **
922001 ATATGATGTAATAGGTAGCCCTT
1 ATATAATGTAATAGGTATCGGTT
*
922024 ATATAATGTAATAGGTATCGTTT
1 ATATAATGTAATAGGTATCGGTT
922047 ATATAATGTAATAGGTAAT-GGTT
1 ATATAATGTAATAGGT-ATCGGTT
922070 ATAT
1 ATAT
922074 TGTAAAGTGT
Statistics
Matches: 44, Mismatches: 5, Indels: 2
0.86 0.10 0.04
Matches are distributed among these distances:
23 42 0.95
24 2 0.05
ACGTcount: A:0.36, C:0.05, G:0.19, T:0.40
Consensus pattern (23 bp):
ATATAATGTAATAGGTATCGGTT
Found at i:922463 original size:23 final size:23
Alignment explanation
Indices: 922432--922494 Score: 90
Period size: 23 Copynumber: 2.7 Consensus size: 23
922422 ATAGGTAAAC
*
922432 ATATGATGTAATAGGTAGCCCTT
1 ATATAATGTAATAGGTAGCCCTT
* **
922455 ATATAATGTAATAGGTATCGTTT
1 ATATAATGTAATAGGTAGCCCTT
922478 ATATAATGTAATAGGTA
1 ATATAATGTAATAGGTA
922495 ATGGTTATAT
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 36 1.00
ACGTcount: A:0.37, C:0.06, G:0.19, T:0.38
Consensus pattern (23 bp):
ATATAATGTAATAGGTAGCCCTT
Found at i:922502 original size:23 final size:23
Alignment explanation
Indices: 922432--922504 Score: 85
Period size: 23 Copynumber: 3.2 Consensus size: 23
922422 ATAGGTAAAC
* * **
922432 ATATGATGTAATAGGTAGCCCTT
1 ATATAATGTAATAGGTATCGGTT
*
922455 ATATAATGTAATAGGTATCGTTT
1 ATATAATGTAATAGGTATCGGTT
922478 ATATAATGTAATAGGTAAT-GGTT
1 ATATAATGTAATAGGT-ATCGGTT
922501 ATAT
1 ATAT
922505 TGTAAAGTGT
Statistics
Matches: 44, Mismatches: 5, Indels: 2
0.86 0.10 0.04
Matches are distributed among these distances:
23 42 0.95
24 2 0.05
ACGTcount: A:0.36, C:0.05, G:0.19, T:0.40
Consensus pattern (23 bp):
ATATAATGTAATAGGTATCGGTT
Found at i:924762 original size:33 final size:33
Alignment explanation
Indices: 924720--924788 Score: 120
Period size: 33 Copynumber: 2.1 Consensus size: 33
924710 CAATGAAAAC
*
924720 AAATTTTAAATAAATAAATATGATCGGAATTGT
1 AAATTTTAAATAAATAAATATGATCAGAATTGT
*
924753 AAATTTTAAATAAATAAATATGATCAGACTTGT
1 AAATTTTAAATAAATAAATATGATCAGAATTGT
924786 AAA
1 AAA
924789 AGCCATTTAT
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
33 34 1.00
ACGTcount: A:0.51, C:0.04, G:0.10, T:0.35
Consensus pattern (33 bp):
AAATTTTAAATAAATAAATATGATCAGAATTGT
Found at i:932580 original size:14 final size:14
Alignment explanation
Indices: 932561--932587 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
932551 TTTGGTCAAA
932561 AATGGCAAATGGGG
1 AATGGCAAATGGGG
932575 AATGGCAAATGGG
1 AATGGCAAATGGG
932588 CGGCTAATTC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.37, C:0.07, G:0.41, T:0.15
Consensus pattern (14 bp):
AATGGCAAATGGGG
Found at i:938435 original size:2 final size:2
Alignment explanation
Indices: 938424--938457 Score: 61
Period size: 2 Copynumber: 17.5 Consensus size: 2
938414 ATTTAAATTT
938424 TA TA -A TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
938458 TTGAAAATTA
Statistics
Matches: 31, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 30 0.97
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:951278 original size:24 final size:24
Alignment explanation
Indices: 951246--951301 Score: 96
Period size: 24 Copynumber: 2.3 Consensus size: 24
951236 AAAACCGAAT
951246 TAAATGGGTTGGGTTCAGGG-ATGA
1 TAAATGGGTTGGGTTC-GGGAATGA
951270 TAAATGGGTTGGGTTCGGGAATGA
1 TAAATGGGTTGGGTTCGGGAATGA
951294 TAAATGGG
1 TAAATGGG
951302 GACGGAGACG
Statistics
Matches: 31, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
23 3 0.10
24 28 0.90
ACGTcount: A:0.27, C:0.04, G:0.41, T:0.29
Consensus pattern (24 bp):
TAAATGGGTTGGGTTCGGGAATGA
Found at i:955159 original size:16 final size:16
Alignment explanation
Indices: 955138--955168 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
955128 ATAAATTAAT
955138 TTAACGGTACTCATCG
1 TTAACGGTACTCATCG
955154 TTAACGGTACTCATC
1 TTAACGGTACTCATC
955169 CAGCCAACAT
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:0.26, C:0.26, G:0.16, T:0.32
Consensus pattern (16 bp):
TTAACGGTACTCATCG
Found at i:974812 original size:28 final size:28
Alignment explanation
Indices: 974780--974843 Score: 112
Period size: 28 Copynumber: 2.3 Consensus size: 28
974770 ATATGTGTGG
974780 ATTGTTAT-TTTGGTGTTTAGACTTTGAA
1 ATTGTT-TCTTTGGTGTTTAGACTTTGAA
974808 ATTGTTTCTTTGGTGTTTAGACTTTGAA
1 ATTGTTTCTTTGGTGTTTAGACTTTGAA
974836 ATTGTTTC
1 ATTGTTTC
974844 ATACATTTTT
Statistics
Matches: 35, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
27 1 0.03
28 34 0.97
ACGTcount: A:0.19, C:0.06, G:0.20, T:0.55
Consensus pattern (28 bp):
ATTGTTTCTTTGGTGTTTAGACTTTGAA
Found at i:975020 original size:32 final size:30
Alignment explanation
Indices: 974979--975039 Score: 86
Period size: 31 Copynumber: 2.0 Consensus size: 30
974969 GAGCATCGAG
*
974979 TTTAACGAGCAACAAGTCGAACAACAATTTTT
1 TTTAACGAGC-ACAAGTAGAACAA-AATTTTT
*
975011 TTTAACGAGCACGAGTAGAACAAAATTTT
1 TTTAACGAGCACAAGTAGAACAAAATTTT
975040 AATAAGCTTA
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
30 6 0.22
31 11 0.41
32 10 0.37
ACGTcount: A:0.41, C:0.16, G:0.15, T:0.28
Consensus pattern (30 bp):
TTTAACGAGCACAAGTAGAACAAAATTTTT
Found at i:976481 original size:24 final size:24
Alignment explanation
Indices: 976449--976505 Score: 87
Period size: 24 Copynumber: 2.4 Consensus size: 24
976439 GGATTGTGGG
* *
976449 ATTCTCATGAGATGGGAATCTCAC
1 ATTCTCATGAGATGAGAATCCCAC
*
976473 ATTCTCATGGGATGAGAATCCCAC
1 ATTCTCATGAGATGAGAATCCCAC
976497 ATTCTCATG
1 ATTCTCATG
976506 TTTAGTTGGC
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 30 1.00
ACGTcount: A:0.28, C:0.23, G:0.19, T:0.30
Consensus pattern (24 bp):
ATTCTCATGAGATGAGAATCCCAC
Found at i:977089 original size:20 final size:20
Alignment explanation
Indices: 977053--977090 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
977043 ATCCTATTCC
**
977053 CTGGTAATCTTTTATTCCCA
1 CTGGTAATCTTACATTCCCA
977073 CTGGTAATCTTACATTCC
1 CTGGTAATCTTACATTCC
977091 GTGAACCAAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.21, C:0.26, G:0.11, T:0.42
Consensus pattern (20 bp):
CTGGTAATCTTACATTCCCA
Found at i:982764 original size:37 final size:37
Alignment explanation
Indices: 982721--982801 Score: 94
Period size: 36 Copynumber: 2.2 Consensus size: 37
982711 GCTCGATTCG
* *
982721 ACTCGAAAAGCTCACTAA-TTTAAAATTTTCAATCTTA
1 ACTCGAAAAGCTCAC-AACCTTAAAATTTTCAAGCTTA
* * *
982758 ACTCG-AAAGCTCGCAACCTTAAACTTTTCAAGCTTG
1 ACTCGAAAAGCTCACAACCTTAAAATTTTCAAGCTTA
982794 ACTCGAAA
1 ACTCGAAA
982802 TAAAAAAAAT
Statistics
Matches: 37, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
35 2 0.05
36 28 0.76
37 7 0.19
ACGTcount: A:0.37, C:0.23, G:0.10, T:0.30
Consensus pattern (37 bp):
ACTCGAAAAGCTCACAACCTTAAAATTTTCAAGCTTA
Found at i:985765 original size:45 final size:45
Alignment explanation
Indices: 985716--985811 Score: 140
Period size: 45 Copynumber: 2.1 Consensus size: 45
985706 GGAACTTATG
985716 TAGAATGGGATCAAAATAAAATAATTT-ATAATTTATGAACCAATT
1 TAGAATGGGATCAAAATAAAATAATTTGA-AATTTATGAACCAATT
* * *
985761 TAGAATGGGGTCATAATAAAATAATTTGAAATTTATGAACTAATT
1 TAGAATGGGATCAAAATAAAATAATTTGAAATTTATGAACCAATT
*
985806 TGGAAT
1 TAGAAT
985812 AGTAACTATA
Statistics
Matches: 46, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
45 45 0.98
46 1 0.02
ACGTcount: A:0.46, C:0.05, G:0.15, T:0.34
Consensus pattern (45 bp):
TAGAATGGGATCAAAATAAAATAATTTGAAATTTATGAACCAATT
Found at i:987697 original size:16 final size:16
Alignment explanation
Indices: 987665--987705 Score: 66
Period size: 16 Copynumber: 2.6 Consensus size: 16
987655 GTTTACTCCA
*
987665 GAATGATT-AAGTGCT
1 GAATGATTCAAATGCT
987680 GAATGATTCAAATGCT
1 GAATGATTCAAATGCT
987696 GAATGATTCA
1 GAATGATTCA
987706 GAGGCTCTGA
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
15 8 0.33
16 16 0.67
ACGTcount: A:0.37, C:0.10, G:0.22, T:0.32
Consensus pattern (16 bp):
GAATGATTCAAATGCT
Found at i:990315 original size:21 final size:23
Alignment explanation
Indices: 990291--990341 Score: 67
Period size: 21 Copynumber: 2.4 Consensus size: 23
990281 GTCACAAAGC
990291 AATTATTAAAA-TTT-ATTAAAT
1 AATTATTAAAATTTTAATTAAAT
990312 AATTA-TAAAATTTTAATTAAAT
1 AATTATTAAAATTTTAATTAAAT
990334 --TTATTAAA
1 AATTATTAAA
990342 CTTCTACATT
Statistics
Matches: 27, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
20 8 0.30
21 12 0.44
22 7 0.26
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (23 bp):
AATTATTAAAATTTTAATTAAAT
Found at i:997307 original size:24 final size:25
Alignment explanation
Indices: 997274--997324 Score: 95
Period size: 24 Copynumber: 2.1 Consensus size: 25
997264 AGCATTTCAT
997274 ACACTTAACAAAAATTGTTAACAGA
1 ACACTTAACAAAAATTGTTAACAGA
997299 ACAC-TAACAAAAATTGTTAACAGA
1 ACACTTAACAAAAATTGTTAACAGA
997323 AC
1 AC
997325 TAGTAAATAA
Statistics
Matches: 26, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
24 22 0.85
25 4 0.15
ACGTcount: A:0.53, C:0.18, G:0.08, T:0.22
Consensus pattern (25 bp):
ACACTTAACAAAAATTGTTAACAGA
Found at i:1004095 original size:22 final size:22
Alignment explanation
Indices: 1004070--1004112 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 22
1004060 CGGTTGCAAT
* *
1004070 CTATCCAACTTAAAAGGTTACG
1 CTATCCAACCTAAAAAGTTACG
1004092 CTATCCAACCTAAAAAGTTAC
1 CTATCCAACCTAAAAAGTTAC
1004113 ACTCTTGATA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.40, C:0.26, G:0.09, T:0.26
Consensus pattern (22 bp):
CTATCCAACCTAAAAAGTTACG
Found at i:1023740 original size:21 final size:21
Alignment explanation
Indices: 1023705--1023745 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 21
1023695 TATATGTTTT
*
1023705 TAAAAAATTATTTTTTAAAAAA
1 TAAAAAATTA-ATTTTAAAAAA
1023727 TAAAAAA-TAATTTTAAAAA
1 TAAAAAATTAATTTTAAAAA
1023746 CATTTTAAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 9 0.50
21 2 0.11
22 7 0.39
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (21 bp):
TAAAAAATTAATTTTAAAAAA
Found at i:1023959 original size:29 final size:30
Alignment explanation
Indices: 1023924--1023996 Score: 78
Period size: 30 Copynumber: 2.5 Consensus size: 30
1023914 TATGGTCAAA
**
1023924 AATTAATGTGACCA-CCGAACT-TTCAATTG
1 AATTAATCAGACCATCC-AACTATTCAATTG
*
1023953 AATTAATCAGACCATCCAACTATTTAATTG
1 AATTAATCAGACCATCCAACTATTCAATTG
* *
1023983 AATCAATCATACCA
1 AATTAATCAGACCA
1023997 CCGGCCGTTA
Statistics
Matches: 37, Mismatches: 5, Indels: 3
0.82 0.11 0.07
Matches are distributed among these distances:
29 16 0.43
30 21 0.57
ACGTcount: A:0.40, C:0.22, G:0.08, T:0.30
Consensus pattern (30 bp):
AATTAATCAGACCATCCAACTATTCAATTG
Found at i:1024200 original size:23 final size:23
Alignment explanation
Indices: 1024168--1024211 Score: 63
Period size: 23 Copynumber: 1.9 Consensus size: 23
1024158 ATGATTGGAA
*
1024168 TATTTTATTT-ATGAATTTTTTAT
1 TATTTAATTTAAT-AATTTTTTAT
1024191 TATTTAATTTAATAATTTTTT
1 TATTTAATTTAATAATTTTTT
1024212 TATCTAATCA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
23 17 0.89
24 2 0.11
ACGTcount: A:0.30, C:0.00, G:0.02, T:0.68
Consensus pattern (23 bp):
TATTTAATTTAATAATTTTTTAT
Found at i:1025757 original size:24 final size:24
Alignment explanation
Indices: 1025707--1025757 Score: 57
Period size: 24 Copynumber: 2.1 Consensus size: 24
1025697 GTTCGTGAAC
* * *
1025707 GTTCGATTATGTTCGTTCGGTTCT
1 GTTCGATTATGTTCATTCAGTTAT
* *
1025731 GTTCGTTTATGTTCATTCATTTAT
1 GTTCGATTATGTTCATTCAGTTAT
1025755 GTT
1 GTT
1025758 TAACATAATA
Statistics
Matches: 22, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.12, C:0.14, G:0.20, T:0.55
Consensus pattern (24 bp):
GTTCGATTATGTTCATTCAGTTAT
Found at i:1026868 original size:16 final size:16
Alignment explanation
Indices: 1026849--1026885 Score: 56
Period size: 16 Copynumber: 2.3 Consensus size: 16
1026839 TTCGTGTTTA
*
1026849 TTTATGCTCGTGTTCG
1 TTTATGCTCATGTTCG
*
1026865 TTTATGTTCATGTTCG
1 TTTATGCTCATGTTCG
1026881 TTTAT
1 TTTAT
1026886 TTATTAAATG
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.11, C:0.14, G:0.19, T:0.57
Consensus pattern (16 bp):
TTTATGCTCATGTTCG
Found at i:1040243 original size:10 final size:10
Alignment explanation
Indices: 1040228--1040256 Score: 58
Period size: 10 Copynumber: 2.9 Consensus size: 10
1040218 TTTTCGAAAT
1040228 ATATATATAG
1 ATATATATAG
1040238 ATATATATAG
1 ATATATATAG
1040248 ATATATATA
1 ATATATATA
1040257 TATTTTGTTT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 19 1.00
ACGTcount: A:0.52, C:0.00, G:0.07, T:0.41
Consensus pattern (10 bp):
ATATATATAG
Found at i:1040274 original size:2 final size:2
Alignment explanation
Indices: 1040226--1040259 Score: 50
Period size: 2 Copynumber: 17.0 Consensus size: 2
1040216 ATTTTTCGAA
* *
1040226 AT AT AT AT AT AG AT AT AT AT AG AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1040260 TTTGTTTTTA
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.06, T:0.44
Consensus pattern (2 bp):
AT
Found at i:1040290 original size:21 final size:21
Alignment explanation
Indices: 1040248--1040289 Score: 75
Period size: 22 Copynumber: 2.0 Consensus size: 21
1040238 ATATATATAG
1040248 ATATATATATATTTTGTTTTT
1 ATATATATATATTTTGTTTTT
1040269 ATATATTATATATTTTGTTTT
1 ATATA-TATATATTTTGTTTT
1040290 AACCAAACAT
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
21 5 0.25
22 15 0.75
ACGTcount: A:0.29, C:0.00, G:0.05, T:0.67
Consensus pattern (21 bp):
ATATATATATATTTTGTTTTT
Found at i:1040711 original size:57 final size:58
Alignment explanation
Indices: 1040650--1040764 Score: 214
Period size: 57 Copynumber: 2.0 Consensus size: 58
1040640 ATTAAACTAT
1040650 ATAGACTAAATTCTAAATTGAAGCATTATGAAGGGACCAAAAC-AAATTTGAACTTGG
1 ATAGACTAAATTCTAAATTGAAGCATTATGAAGGGACCAAAACAAAATTTGAACTTGG
*
1040707 ATAGACTAAATTCTAAATTGAAGCATTATGAAGGGACCAAACCAAAATTTGAACTTGG
1 ATAGACTAAATTCTAAATTGAAGCATTATGAAGGGACCAAAACAAAATTTGAACTTGG
1040765 TTTTTTATTC
Statistics
Matches: 56, Mismatches: 1, Indels: 1
0.97 0.02 0.02
Matches are distributed among these distances:
57 42 0.75
58 14 0.25
ACGTcount: A:0.43, C:0.13, G:0.17, T:0.26
Consensus pattern (58 bp):
ATAGACTAAATTCTAAATTGAAGCATTATGAAGGGACCAAAACAAAATTTGAACTTGG
Found at i:1040759 original size:31 final size:30
Alignment explanation
Indices: 1040667--1040759 Score: 72
Period size: 30 Copynumber: 3.2 Consensus size: 30
1040657 AAATTCTAAA
1040667 TTGAAGCATTATGAAGGGACCAAAACAAAT
1 TTGAAGCATTATGAAGGGACCAAAACAAAT
* * *
1040697 TTGAA-C-TT-GGATA--GACTAAATTCTAAA-
1 TTGAAGCATTATGA-AGGGACCAAA-AC-AAAT
*
1040724 TTGAAGCATTATGAAGGGACCAAACCAAAAT
1 TTGAAGCATTATGAAGGGACCAAAAC-AAAT
1040755 TTGAA
1 TTGAA
1040760 CTTGGTTTTT
Statistics
Matches: 47, Mismatches: 7, Indels: 17
0.66 0.10 0.24
Matches are distributed among these distances:
26 6 0.13
27 8 0.17
28 7 0.15
29 4 0.09
30 11 0.23
31 11 0.23
ACGTcount: A:0.44, C:0.13, G:0.18, T:0.25
Consensus pattern (30 bp):
TTGAAGCATTATGAAGGGACCAAAACAAAT
Found at i:1043321 original size:17 final size:15
Alignment explanation
Indices: 1043291--1043324 Score: 50
Period size: 17 Copynumber: 2.1 Consensus size: 15
1043281 CTATAAAACA
1043291 ATTTATAAAATAATT
1 ATTTATAAAATAATT
1043306 ATTTAGTAAAATTAATT
1 ATTTA-TAAAA-TAATT
1043323 AT
1 AT
1043325 ACATGTAGAG
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 5 0.29
16 5 0.29
17 7 0.41
ACGTcount: A:0.50, C:0.00, G:0.03, T:0.47
Consensus pattern (15 bp):
ATTTATAAAATAATT
Done.