Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008747.1 Hibiscus syriacus cultivar Beakdansim tig00111837_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: 12616935
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 41 of 51
Found at i:10282367 original size:20 final size:21
Alignment explanation
Indices: 10282320--10282376 Score: 62
Period size: 23 Copynumber: 2.7 Consensus size: 21
10282310 AGTAATTTTA
*
10282320 AAATTTATTTTTAAAAAAATT
1 AAATTTATTTATAAAAAAATT
*
10282341 AAAAATTTATTTATAAAAAACTT
1 --AAATTTATTTATAAAAAAATT
*
10282364 -AATTTATCTATAA
1 AAATTTATTTATAA
10282377 TTATAAAAAC
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
20 12 0.39
23 19 0.61
ACGTcount: A:0.53, C:0.04, G:0.00, T:0.44
Consensus pattern (21 bp):
AAATTTATTTATAAAAAAATT
Found at i:10291852 original size:13 final size:13
Alignment explanation
Indices: 10291834--10291858 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
10291824 TTATATTTTT
10291834 GGTTAATTCGGTC
1 GGTTAATTCGGTC
10291847 GGTTAATTCGGT
1 GGTTAATTCGGT
10291859 TAAAACCAAA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.16, C:0.12, G:0.32, T:0.40
Consensus pattern (13 bp):
GGTTAATTCGGTC
Found at i:10298653 original size:2 final size:2
Alignment explanation
Indices: 10298646--10298673 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
10298636 CGGTTTTATG
10298646 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
10298674 TTATCGTATG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:10301073 original size:11 final size:11
Alignment explanation
Indices: 10301057--10301087 Score: 53
Period size: 11 Copynumber: 2.8 Consensus size: 11
10301047 TGTACGTAGG
10301057 AATTTTTCCAA
1 AATTTTTCCAA
10301068 AATTTTTCCAA
1 AATTTTTCCAA
*
10301079 AATATTTCC
1 AATTTTTCC
10301088 GACCCCTAGA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
11 19 1.00
ACGTcount: A:0.35, C:0.19, G:0.00, T:0.45
Consensus pattern (11 bp):
AATTTTTCCAA
Found at i:10301195 original size:23 final size:23
Alignment explanation
Indices: 10301165--10301213 Score: 98
Period size: 23 Copynumber: 2.1 Consensus size: 23
10301155 GAAATTGGGT
10301165 CGACCCGTCTACCTGACCCGACC
1 CGACCCGTCTACCTGACCCGACC
10301188 CGACCCGTCTACCTGACCCGACC
1 CGACCCGTCTACCTGACCCGACC
10301211 CGA
1 CGA
10301214 ACCAAACCGG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 26 1.00
ACGTcount: A:0.18, C:0.51, G:0.18, T:0.12
Consensus pattern (23 bp):
CGACCCGTCTACCTGACCCGACC
Found at i:10302055 original size:39 final size:39
Alignment explanation
Indices: 10302001--10302133 Score: 176
Period size: 39 Copynumber: 3.4 Consensus size: 39
10301991 TCTATGACTT
* *
10302001 GTAAGACCTTACCGCAAGCTCCTTTGCTTTGTGCTCAGG
1 GTAAGTCCTTACCGCAAGCTCCTCTGCTTTGTGCTCAGG
* * * **
10302040 GTAAGTCCTTGCCGCAAACTCCTCTGCTTTGTGCTTAAA
1 GTAAGTCCTTACCGCAAGCTCCTCTGCTTTGTGCTCAGG
* * *
10302079 GTAAGTCCTTACCGTAGGCTCCTCTGCCTTGTGCTCAGG
1 GTAAGTCCTTACCGCAAGCTCCTCTGCTTTGTGCTCAGG
10302118 GTAAGTCCTTACCGCA
1 GTAAGTCCTTACCGCA
10302134 GGTCCTTATG
Statistics
Matches: 78, Mismatches: 16, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
39 78 1.00
ACGTcount: A:0.18, C:0.29, G:0.22, T:0.31
Consensus pattern (39 bp):
GTAAGTCCTTACCGCAAGCTCCTCTGCTTTGTGCTCAGG
Found at i:10302380 original size:15 final size:15
Alignment explanation
Indices: 10302360--10302397 Score: 67
Period size: 15 Copynumber: 2.5 Consensus size: 15
10302350 TTTCATATAA
10302360 TAGCAGACCGTAGGC
1 TAGCAGACCGTAGGC
10302375 TAGCAGACCGTAGGC
1 TAGCAGACCGTAGGC
*
10302390 TAGAAGAC
1 TAGCAGAC
10302398 TCGGCATTAA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
15 22 1.00
ACGTcount: A:0.32, C:0.24, G:0.32, T:0.13
Consensus pattern (15 bp):
TAGCAGACCGTAGGC
Found at i:10311817 original size:16 final size:15
Alignment explanation
Indices: 10311798--10311828 Score: 53
Period size: 16 Copynumber: 2.0 Consensus size: 15
10311788 TTATTCATAC
10311798 TATTAATTATATTTAA
1 TATTAATTAT-TTTAA
10311814 TATTAATTATTTTAA
1 TATTAATTATTTTAA
10311829 GAAATTTCAG
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 5 0.33
16 10 0.67
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (15 bp):
TATTAATTATTTTAA
Found at i:10314068 original size:11 final size:11
Alignment explanation
Indices: 10314037--10314070 Score: 52
Period size: 11 Copynumber: 3.2 Consensus size: 11
10314027 TTCCTCATCC
10314037 TTTTGATTCGA
1 TTTTGATTCGA
*
10314048 TTTTG-CTCGA
1 TTTTGATTCGA
10314058 TTTTGATTCGA
1 TTTTGATTCGA
10314069 TT
1 TT
10314071 CAAGCATGAA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
10 9 0.45
11 11 0.55
ACGTcount: A:0.15, C:0.12, G:0.18, T:0.56
Consensus pattern (11 bp):
TTTTGATTCGA
Found at i:10315046 original size:31 final size:31
Alignment explanation
Indices: 10315005--10315093 Score: 101
Period size: 31 Copynumber: 2.9 Consensus size: 31
10314995 CTTTTTAAGA
* *
10315005 TTACACTTTAGTCTCTAAACTTTTCCAAAGT
1 TTACACTTTAGTCACTAAACTTTTCCAAAAT
* *
10315036 TTATACTTTAGCCACTAAACTTTT--AAAAT
1 TTACACTTTAGTCACTAAACTTTTCCAAAAT
* * *
10315065 TTACATTTTGGTCACTTAACTTTTCCAAA
1 TTACACTTTAGTCACTAAACTTTTCCAAA
10315094 TCCATTCATG
Statistics
Matches: 47, Mismatches: 9, Indels: 4
0.78 0.15 0.07
Matches are distributed among these distances:
29 23 0.49
31 24 0.51
ACGTcount: A:0.31, C:0.20, G:0.06, T:0.43
Consensus pattern (31 bp):
TTACACTTTAGTCACTAAACTTTTCCAAAAT
Found at i:10317757 original size:19 final size:19
Alignment explanation
Indices: 10317730--10317766 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
10317720 GTTTAAATAG
10317730 TGCAAAAAAAAAAATGCAA
1 TGCAAAAAAAAAAATGCAA
* *
10317749 TGCAGAAAAAACAATGCA
1 TGCAAAAAAAAAAATGCA
10317767 TAATTTTTAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.62, C:0.14, G:0.14, T:0.11
Consensus pattern (19 bp):
TGCAAAAAAAAAAATGCAA
Found at i:10326950 original size:111 final size:114
Alignment explanation
Indices: 10326767--10327022 Score: 311
Period size: 114 Copynumber: 2.2 Consensus size: 114
10326757 TAGTAAGATA
* *
10326767 ATGTTGAGGTCGAACAAACTCTCCTATATGAACTTCTTCTTCCTTGATCGTTTCCTCCTATATGG
1 ATGTTGAGGTCGAACAAGCTCTCCTATATGAA--TCTTCTTCCTTGATCGCTTCCTCCTATATGG
* * * * * *
10326832 AACGAGTAG-GAGCTCTCCTATATAAGCTCCCTATTCTCCC-TTAAAGGCC
64 AACGAGTAGAAAACTCTCCTATATAAGCTCCATATTATCCCATAAAAGACC
* * * *
10326881 ATGTTGAGGTCGAATAAGCTTTCCTATATTAA-CTTCTTCCTTGATTGCTTCCTCCTATATGGAA
1 ATGTTGAGGTCGAACAAGCTCTCCTATATGAATCTTCTTCCTTGATCGCTTCCTCCTATATGGAA
* * *
10326945 TGAGTAGACAAACTCTCCTATATAAGTTCTATATTATCCCATAAAAGACC
66 CGAGTAGA-AAACTCTCCTATATAAGCTCCATATTATCCCATAAAAGACC
* *
10326995 ATGTTGAGGTTGAACAAGCTCTCATATA
1 ATGTTGAGGTCGAACAAGCTCTCCTATA
10327023 GGAAAATTTT
Statistics
Matches: 120, Mismatches: 19, Indels: 6
0.83 0.13 0.04
Matches are distributed among these distances:
111 36 0.30
113 25 0.21
114 59 0.49
ACGTcount: A:0.27, C:0.23, G:0.15, T:0.34
Consensus pattern (114 bp):
ATGTTGAGGTCGAACAAGCTCTCCTATATGAATCTTCTTCCTTGATCGCTTCCTCCTATATGGAA
CGAGTAGAAAACTCTCCTATATAAGCTCCATATTATCCCATAAAAGACC
Found at i:10328302 original size:20 final size:21
Alignment explanation
Indices: 10328277--10328321 Score: 58
Period size: 19 Copynumber: 2.2 Consensus size: 21
10328267 ATATAATAAG
10328277 ATATTTTTAAAAAACTATA-T
1 ATATTTTTAAAAAACTATAGT
* *
10328297 ATA-TTTTACAAACCTATAGT
1 ATATTTTTAAAAAACTATAGT
10328317 ATATT
1 ATATT
10328322 ATATATGTTT
Statistics
Matches: 21, Mismatches: 2, Indels: 3
0.81 0.08 0.12
Matches are distributed among these distances:
19 13 0.62
20 7 0.33
21 1 0.05
ACGTcount: A:0.44, C:0.09, G:0.02, T:0.44
Consensus pattern (21 bp):
ATATTTTTAAAAAACTATAGT
Found at i:10328344 original size:14 final size:14
Alignment explanation
Indices: 10328325--10328355 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
10328315 GTATATTATA
*
10328325 TATGTTTTTAAAAC
1 TATGTTTTCAAAAC
10328339 TATGTTTTCAAAAC
1 TATGTTTTCAAAAC
10328353 TAT
1 TAT
10328356 ATATATATTT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.35, C:0.10, G:0.06, T:0.48
Consensus pattern (14 bp):
TATGTTTTCAAAAC
Found at i:10328358 original size:61 final size:61
Alignment explanation
Indices: 10328287--10328402 Score: 171
Period size: 61 Copynumber: 1.9 Consensus size: 61
10328277 ATATTTTTAA
* * * *
10328287 AAAACTATATATAT-TTTACAAACCTATAGTATATTATATATGTTTTTAAAACTATGTTTTC
1 AAAACTATATATATATTTACAAAACTATA-TACATTATATATGTATTCAAAACTATGTTTTC
*
10328348 AAAACTATATATATATTTTCAAAACTATATACATTATATATGTATTCAAAACTAT
1 AAAACTATATATATATTTACAAAACTATATACATTATATATGTATTCAAAACTAT
10328403 ATTATATATA
Statistics
Matches: 49, Mismatches: 5, Indels: 2
0.88 0.09 0.04
Matches are distributed among these distances:
61 37 0.76
62 12 0.24
ACGTcount: A:0.43, C:0.10, G:0.03, T:0.43
Consensus pattern (61 bp):
AAAACTATATATATATTTACAAAACTATATACATTATATATGTATTCAAAACTATGTTTTC
Found at i:10328385 original size:25 final size:24
Alignment explanation
Indices: 10328356--10328545 Score: 155
Period size: 25 Copynumber: 8.0 Consensus size: 24
10328346 TCAAAACTAT
10328356 ATATATATTTTCAAAACTATATAC
1 ATATATATTTTCAAAACTATATAC
*
10328380 ATTATATATGTATTCAAAACTATAT-T
1 A-TATATAT-T-TTCAAAACTATATAC
10328406 ATATATATTTTTCAAAACTATATATC
1 ATATATA-TTTTCAAAACTATATA-C
*
10328432 ATATATGTTTTTCAAAAC--TAT--
1 ATATAT-ATTTTCAAAACTATATAC
*
10328453 ATATATGTTTTCAAAA-T-TATAC
1 ATATATATTTTCAAAACTATATAC
*
10328475 ATATATGTTTTTCAAAA-T-TATAC
1 ATATAT-ATTTTCAAAACTATATAC
* * * *
10328498 GTATATGTTTTTAAAACTATATATT
1 ATATATATTTTCAAAACTATATA-C
* *
10328523 ACATATATTTTCAAAACTGTATA
1 ATATATATTTTCAAAACTATATA
10328546 TATACTATTA
Statistics
Matches: 138, Mismatches: 14, Indels: 27
0.77 0.08 0.15
Matches are distributed among these distances:
20 12 0.09
21 6 0.04
22 14 0.10
23 21 0.15
24 21 0.15
25 32 0.23
26 19 0.14
27 13 0.09
ACGTcount: A:0.41, C:0.09, G:0.04, T:0.46
Consensus pattern (24 bp):
ATATATATTTTCAAAACTATATAC
Found at i:10328396 original size:47 final size:45
Alignment explanation
Indices: 10328339--10328549 Score: 221
Period size: 47 Copynumber: 4.5 Consensus size: 45
10328329 TTTTTAAAAC
10328339 TATGTTTTCAAAACTATATATATATTTTCAAAACTATATACATTATA
1 TATGTTTTCAAAACTATATATATATTTTCAAAACTATAT--ATTATA
* *
10328386 TATGTATTCAAAACTATATTATATATATTTTTCAAAACTATATATCATA
1 TATGTTTTCAAAAC--TA-TATATATA-TTTTCAAAACTATATATTATA
* *
10328435 TATGTTTTTCAAAACTATATATATGTTTTCAAAA-T-TATA-CATA
1 TATG-TTTTCAAAACTATATATATATTTTCAAAACTATATATTATA
* * * *
10328478 TATGTTTTTCAAAATTATACGTATATGTTTTTAAAACTATATATTACA
1 TATG-TTTTCAAAACTATA--TATATATTTTCAAAACTATATATTATA
* *
10328526 TATATTTTCAAAACTGTATATATA
1 TATGTTTTCAAAACTATATATATA
10328550 CTATTATAAT
Statistics
Matches: 142, Mismatches: 12, Indels: 22
0.81 0.07 0.12
Matches are distributed among these distances:
43 22 0.15
44 4 0.03
45 20 0.14
46 10 0.07
47 36 0.25
48 7 0.05
49 11 0.08
50 17 0.12
51 15 0.11
ACGTcount: A:0.41, C:0.09, G:0.04, T:0.46
Consensus pattern (45 bp):
TATGTTTTCAAAACTATATATATATTTTCAAAACTATATATTATA
Found at i:10328406 original size:23 final size:22
Alignment explanation
Indices: 10328339--10328549 Score: 169
Period size: 22 Copynumber: 9.1 Consensus size: 22
10328329 TTTTTAAAAC
10328339 TATGTTTTCAAAACTATATATA
1 TATGTTTTCAAAACTATATATA
10328361 TA--TTTTCAAAACTATATACATTATA
1 TATGTTTTCAAAAC--TAT--A-TATA
*
10328386 TATGTATTCAAAACTATATTATA
1 TATGTTTTCAAAACTATA-TATA
*
10328409 TATATTTTTCAAAACTATATATCATA
1 TAT-GTTTTCAAAAC--TATAT-ATA
10328435 TATGTTTTTCAAAAC--TATATA
1 TATG-TTTTCAAAACTATATATA
* *
10328456 TATGTTTTCAAAATTATACATA
1 TATGTTTTCAAAACTATATATA
* **
10328478 TATGTTTTTCAAAATTATACGTA
1 TATG-TTTTCAAAACTATATATA
*
10328501 TATGTTTTTAAAACTATATATTACA
1 TATGTTTTCAAAACTATATA-T--A
* *
10328526 TATATTTTCAAAACTGTATATA
1 TATGTTTTCAAAACTATATATA
10328548 TA
1 TA
10328550 CTATTATAAT
Statistics
Matches: 157, Mismatches: 14, Indels: 36
0.76 0.07 0.17
Matches are distributed among these distances:
20 19 0.12
21 7 0.04
22 32 0.20
23 31 0.20
24 11 0.07
25 28 0.18
26 20 0.13
27 9 0.06
ACGTcount: A:0.41, C:0.09, G:0.04, T:0.46
Consensus pattern (22 bp):
TATGTTTTCAAAACTATATATA
Found at i:10328456 original size:43 final size:44
Alignment explanation
Indices: 10328407--10328546 Score: 137
Period size: 43 Copynumber: 3.2 Consensus size: 44
10328397 AACTATATTA
10328407 TATATAT-TTTTCAAAACTATATATCATATATGTTTTTCAAAAC
1 TATATATGTTTTCAAAACTATATATCATATATGTTTTTCAAAAC
*
10328450 TATATATATGTTTTCAAAA-T-TATA-CATATATGTTTTTCAAAATTA
1 --TATATATGTTTTCAAAACTATATATCATATATGTTTTTCAAAA--C
* * * *
10328495 TACGTATATGTTTTTAAAACTATATATTACATAT-ATTTTCAAAAC
1 TA--TATATGTTTTCAAAACTATATATCATATATGTTTTTCAAAAC
*
10328540 TGTATAT
1 TATATAT
10328547 ATACTATTAT
Statistics
Matches: 80, Mismatches: 7, Indels: 18
0.76 0.07 0.17
Matches are distributed among these distances:
43 25 0.31
44 4 0.05
45 23 0.29
46 10 0.12
47 13 0.16
48 5 0.06
ACGTcount: A:0.39, C:0.09, G:0.04, T:0.47
Consensus pattern (44 bp):
TATATATGTTTTCAAAACTATATATCATATATGTTTTTCAAAAC
Found at i:10328546 original size:25 final size:24
Alignment explanation
Indices: 10328355--10328546 Score: 134
Period size: 23 Copynumber: 8.0 Consensus size: 24
10328345 TTCAAAACTA
10328355 TATATATATTTTCAAAACTATATACAT
1 TATATATATTTTCAAAACT-TAT--AT
* *
10328382 TATATATGTATTCAAAAC-TATAT
1 TATATATATTTTCAAAACTTATAT
10328405 TATATATATTTTTCAAAACTATATAT
1 TATATATA-TTTTCAAAACT-TATAT
* *
10328431 CATATATGTTTTTCAAAAC---TA-
1 TATATAT-ATTTTCAAAACTTATAT
*
10328452 TATATATGTTTTCAAAA-TTATA-
1 TATATATATTTTCAAAACTTATAT
* * *
10328474 CATATATGTTTTTCAAAA-TTATACG
1 TATATAT-ATTTTCAAAACTTATA-T
*
10328499 TATATGT-TTTT-AAAACTATATAT
1 TATATATATTTTCAAAACT-TATAT
*
10328522 TACATATATTTTCAAAACTGTATAT
1 TATATATATTTTCAAAACT-TATAT
10328547 ATACTATTAT
Statistics
Matches: 135, Mismatches: 16, Indels: 30
0.75 0.09 0.17
Matches are distributed among these distances:
20 9 0.07
21 6 0.04
22 14 0.10
23 33 0.24
24 17 0.13
25 19 0.14
26 21 0.16
27 16 0.12
ACGTcount: A:0.41, C:0.09, G:0.04, T:0.46
Consensus pattern (24 bp):
TATATATATTTTCAAAACTTATAT
Found at i:10330667 original size:9 final size:9
Alignment explanation
Indices: 10330646--10330676 Score: 53
Period size: 9 Copynumber: 3.3 Consensus size: 9
10330636 TAAACTCTCA
10330646 TTTTTCTTCT
1 TTTTTCTT-T
10330656 TTTTTCTTT
1 TTTTTCTTT
10330665 TTTTTCTTT
1 TTTTTCTTT
10330674 TTT
1 TTT
10330677 ACATATAGTG
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
9 13 0.62
10 8 0.38
ACGTcount: A:0.00, C:0.13, G:0.00, T:0.87
Consensus pattern (9 bp):
TTTTTCTTT
Found at i:10330671 original size:16 final size:16
Alignment explanation
Indices: 10330646--10330676 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
10330636 TAAACTCTCA
10330646 TTTTTCTTCTTTTTTC
1 TTTTTCTTCTTTTTTC
*
10330662 TTTTTTTTCTTTTTT
1 TTTTTCTTCTTTTTT
10330677 ACATATAGTG
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.00, C:0.13, G:0.00, T:0.87
Consensus pattern (16 bp):
TTTTTCTTCTTTTTTC
Found at i:10332591 original size:18 final size:18
Alignment explanation
Indices: 10332563--10332612 Score: 55
Period size: 18 Copynumber: 2.7 Consensus size: 18
10332553 ATAAGATTAA
*
10332563 TTATAATATTAGTATACTT
1 TTAT-ATATTAGTATAATT
*
10332582 TTATATATTAGGATAATT
1 TTATATATTAGTATAATT
*
10332600 TAATATATATAGT
1 TTATATAT-TAGT
10332613 TTTAATATTT
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
18 19 0.73
19 7 0.27
ACGTcount: A:0.40, C:0.02, G:0.08, T:0.50
Consensus pattern (18 bp):
TTATATATTAGTATAATT
Found at i:10338372 original size:20 final size:20
Alignment explanation
Indices: 10338347--10338468 Score: 154
Period size: 20 Copynumber: 6.1 Consensus size: 20
10338337 TTTTCCAAGA
* *
10338347 ATTTATAAAACCTTCGGGTC
1 ATTTGTAAATCCTTCGGGTC
* *
10338367 ATTTATAAATCCTTCAGGTC
1 ATTTGTAAATCCTTCGGGTC
*
10338387 ATTTGTAAATCATTCGGGTC
1 ATTTGTAAATCCTTCGGGTC
*
10338407 ATTTGTAAATCCTCCGGGTC
1 ATTTGTAAATCCTTCGGGTC
* * *
10338427 ATTGGTAAATCATCCGGGTC
1 ATTTGTAAATCCTTCGGGTC
*
10338447 ATTTGTAAATCCTTTGGGTC
1 ATTTGTAAATCCTTCGGGTC
10338467 AT
1 AT
10338469 CTGTCAGTCT
Statistics
Matches: 89, Mismatches: 13, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 89 1.00
ACGTcount: A:0.25, C:0.19, G:0.18, T:0.38
Consensus pattern (20 bp):
ATTTGTAAATCCTTCGGGTC
Found at i:10338613 original size:41 final size:41
Alignment explanation
Indices: 10338562--10338746 Score: 203
Period size: 41 Copynumber: 4.5 Consensus size: 41
10338552 TAAATGTGAT
10338562 CTTCACGGAAGAGTAGTGAAACAGGTTCTTCTTAAACCAAC
1 CTTCACGGAAGAGTAGTGAAACAGGTTCTTCTTAAACCAAC
* *
10338603 CTTCACGGAAGAGTAGTGAAATAGGTTCTTCTTAAATCAAC
1 CTTCACGGAAGAGTAGTGAAACAGGTTCTTCTTAAACCAAC
* ** ** * ** *
10338644 CTTCACGGAAGAGTAATGAAGTA--TTCCAACCTTGAATCTGAT
1 CTTCACGGAAGAGTAGTGAAACAGGTT-C-TTCTT-AAACCAAC
* *
10338686 CTTCACGGAAGAGTAGTGAAACAGATTCTTCTTAAATCAAC
1 CTTCACGGAAGAGTAGTGAAACAGGTTCTTCTTAAACCAAC
*
10338727 CTTCACGGAAGAATAGTGAA
1 CTTCACGGAAGAGTAGTGAA
10338747 GTATTCCAAC
Statistics
Matches: 117, Mismatches: 22, Indels: 10
0.79 0.15 0.07
Matches are distributed among these distances:
39 2 0.02
40 1 0.01
41 85 0.73
42 26 0.22
43 1 0.01
44 2 0.02
ACGTcount: A:0.35, C:0.19, G:0.19, T:0.26
Consensus pattern (41 bp):
CTTCACGGAAGAGTAGTGAAACAGGTTCTTCTTAAACCAAC
Found at i:10338693 original size:83 final size:83
Alignment explanation
Indices: 10338603--10338807 Score: 331
Period size: 83 Copynumber: 2.5 Consensus size: 83
10338593 TTAAACCAAC
* * *
10338603 CTTCACGGAAGAGTAGTGAAATAGGTTCTTCTTAAATCAACCTTCACGGAAGAGTAATGAAGTAT
1 CTTCACGGAAGAGTAGTGAAACAGATTCTTCTTAAATCAACCTTCACGGAAGAATAATGAAGTAT
*
10338668 TCCAACCTTGAATCTGAT
66 TCCAACCATGAATCTGAT
*
10338686 CTTCACGGAAGAGTAGTGAAACAGATTCTTCTTAAATCAACCTTCACGGAAGAATAGTGAAGTAT
1 CTTCACGGAAGAGTAGTGAAACAGATTCTTCTTAAATCAACCTTCACGGAAGAATAATGAAGTAT
*
10338751 TCCAACCATGAGTCTGAT
66 TCCAACCATGAATCTGAT
*
10338769 CTTCACGAAAGAGTAGTGAAACAGATTCTT-TTCAAATCA
1 CTTCACGGAAGAGTAGTGAAACAGATTCTTCTT-AAATCA
10338808 TTATTAGCCT
Statistics
Matches: 114, Mismatches: 7, Indels: 2
0.93 0.06 0.02
Matches are distributed among these distances:
82 2 0.02
83 112 0.98
ACGTcount: A:0.35, C:0.19, G:0.19, T:0.28
Consensus pattern (83 bp):
CTTCACGGAAGAGTAGTGAAACAGATTCTTCTTAAATCAACCTTCACGGAAGAATAATGAAGTAT
TCCAACCATGAATCTGAT
Found at i:10338786 original size:42 final size:42
Alignment explanation
Indices: 10338644--10338788 Score: 145
Period size: 42 Copynumber: 3.5 Consensus size: 42
10338634 TTAAATCAAC
*
10338644 CTTCACGGAAGAGTAATGAAGTATTCCAACCTTGAATCTGAT
1 CTTCACGGAAGAGTAGTGAAGTATTCCAACCTTGAATCTGAT
** * * *
10338686 CTTCACGGAAGAGTAGTGAAACAG-ATT-C-TTCTTAAATC-AAC
1 CTTCACGGAAGAGTAGTG--A-AGTATTCCAACCTTGAATCTGAT
* * *
10338727 CTTCACGGAAGAATAGTGAAGTATTCCAACCATGAGTCTGAT
1 CTTCACGGAAGAGTAGTGAAGTATTCCAACCTTGAATCTGAT
*
10338769 CTTCACGAAAGAGTAGTGAA
1 CTTCACGGAAGAGTAGTGAA
10338789 ACAGATTCTT
Statistics
Matches: 80, Mismatches: 16, Indels: 14
0.73 0.15 0.13
Matches are distributed among these distances:
38 2 0.03
39 4 0.05
40 1 0.01
41 23 0.29
42 43 0.54
43 1 0.01
44 4 0.05
45 2 0.03
ACGTcount: A:0.35, C:0.19, G:0.20, T:0.26
Consensus pattern (42 bp):
CTTCACGGAAGAGTAGTGAAGTATTCCAACCTTGAATCTGAT
Found at i:10338908 original size:89 final size:89
Alignment explanation
Indices: 10338815--10338978 Score: 231
Period size: 90 Copynumber: 1.8 Consensus size: 89
10338805 TCATTATTAG
* * * *
10338815 CCTTCACAGAAGAGTAGTGAAG-AAGAGCAAGATCAAAATTCGCTCTCTACAGAAGAGTAGTGGA
1 CCTTCACAGAAGAGTAGTGAAGCAAGAGCAAGATCAAAATTAGATCTCCACAAAAGAGTAGTGGA
*
10338879 ACAGATTTTTCAGCAAAGTATGAGA
66 AC-GAATTTTCAGCAAAGTATGAGA
* * * *
10338904 CCTTCACGGAAGAGTAGTGAAGCAAGAGCAAGATTAAAGTTAGATCTCCACAAAATAGTAGTGGA
1 CCTTCACAGAAGAGTAGTGAAGCAAGAGCAAGATCAAAATTAGATCTCCACAAAAGAGTAGTGGA
10338969 ACGAATTTTC
66 ACGAATTTTC
10338979 CATCAAAGCA
Statistics
Matches: 65, Mismatches: 9, Indels: 2
0.86 0.12 0.03
Matches are distributed among these distances:
89 28 0.43
90 37 0.57
ACGTcount: A:0.39, C:0.16, G:0.23, T:0.22
Consensus pattern (89 bp):
CCTTCACAGAAGAGTAGTGAAGCAAGAGCAAGATCAAAATTAGATCTCCACAAAAGAGTAGTGGA
ACGAATTTTCAGCAAAGTATGAGA
Found at i:10343752 original size:20 final size:21
Alignment explanation
Indices: 10343714--10343753 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 21
10343704 TTTTTTGGTC
*
10343714 AAGTCAACAGTCAATGAGTCA
1 AAGTCAACAGTCAACGAGTCA
*
10343735 AAGTCAA-AGTTAACGAGTC
1 AAGTCAACAGTCAACGAGTC
10343754 TGGTTAACGG
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 10 0.59
21 7 0.41
ACGTcount: A:0.42, C:0.17, G:0.20, T:0.20
Consensus pattern (21 bp):
AAGTCAACAGTCAACGAGTCA
Found at i:10350545 original size:43 final size:42
Alignment explanation
Indices: 10350457--10350545 Score: 112
Period size: 44 Copynumber: 2.1 Consensus size: 42
10350447 GTTTTTGTCC
10350457 GTTTATATTATTATATATTTAATTATATATATTAATTGTATAT
1 GTTTATATTATTATATATTTAATTATATATATTAA-TGTATAT
10350500 GTTTATATATATTATATATTAATAATTAGTAT-TATTAA-GTA-AT
1 GTTTATAT-TATTATATATT--TAATTA-TATATATTAATGTATAT
10350543 GTT
1 GTT
10350546 ACAAGTAAAG
Statistics
Matches: 42, Mismatches: 0, Indels: 8
0.84 0.00 0.16
Matches are distributed among these distances:
43 13 0.31
44 14 0.33
46 12 0.29
47 3 0.07
ACGTcount: A:0.38, C:0.00, G:0.07, T:0.55
Consensus pattern (42 bp):
GTTTATATTATTATATATTTAATTATATATATTAATGTATAT
Found at i:10353256 original size:16 final size:17
Alignment explanation
Indices: 10353235--10353267 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
10353225 GTGTCAAGAA
*
10353235 TAGAT-GTTTAGTGTTG
1 TAGATGGTTTAATGTTG
10353251 TAGATGGTTTAATGTTG
1 TAGATGGTTTAATGTTG
10353268 AGGCAATAAG
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 5 0.33
17 10 0.67
ACGTcount: A:0.21, C:0.00, G:0.30, T:0.48
Consensus pattern (17 bp):
TAGATGGTTTAATGTTG
Found at i:10353846 original size:23 final size:23
Alignment explanation
Indices: 10353802--10353848 Score: 60
Period size: 23 Copynumber: 2.0 Consensus size: 23
10353792 ATAAAGAACC
*
10353802 AAAATAAACTTAAATATACCATT
1 AAAATAAACTTAAACATACCATT
*
10353825 AAAATAAAGTTTAAACAT-CCATT
1 AAAATAAA-CTTAAACATACCATT
10353848 A
1 A
10353849 CACAACCACC
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
23 14 0.67
24 7 0.33
ACGTcount: A:0.55, C:0.13, G:0.02, T:0.30
Consensus pattern (23 bp):
AAAATAAACTTAAACATACCATT
Found at i:10354971 original size:131 final size:127
Alignment explanation
Indices: 10354750--10355004 Score: 433
Period size: 131 Copynumber: 2.0 Consensus size: 127
10354740 AATTTCAACC
10354750 CTTAGAAAAATAGGCTTCAACATGTTACCTTACAAGAATTCAATCTTTTCCTAGGTCAAGATCCT
1 CTTAGAAAAATAGGCTTCAACATGTTACCTTACAAGAATTCAATCTTTTCCTAGGTCAAGATCCT
*
10354815 TTGTGTATTGTGTGTGGCTTGATTGTATCCAATCTATAC-TAGCAAATTTAGACAATTTTCT
66 TTGTGTATTGTGTGTGGCGTGATTGTATCCAATCTATACTTAGCAAATTTAGACAATTTTCT
10354876 CTTAGAAAAATAGGCTTCAACATGTTACACTTATCAAGAATTCAAGTACTTTTCCCTAGGTCAAG
1 CTTAGAAAAATAGGCTTCAACATGTTAC-CTTA-CAAGAATTCAA-T-CTTTT-CCTAGGTCAAG
10354941 ATCCTTTGTGGTATTGTGTGT-GCGTGATTGTATCCAATCTATACTTAGCAAATTTAGACAATTT
61 ATCCTTTGT-GTATTGTGTGTGGCGTGATTGTATCCAATCTATACTTAGCAAATTTAGACAATTT
10355005 CTAATCAAGT
Statistics
Matches: 121, Mismatches: 1, Indels: 8
0.93 0.01 0.06
Matches are distributed among these distances:
126 28 0.23
127 4 0.03
128 11 0.09
129 1 0.01
130 5 0.04
131 42 0.35
132 30 0.25
ACGTcount: A:0.30, C:0.17, G:0.16, T:0.37
Consensus pattern (127 bp):
CTTAGAAAAATAGGCTTCAACATGTTACCTTACAAGAATTCAATCTTTTCCTAGGTCAAGATCCT
TTGTGTATTGTGTGTGGCGTGATTGTATCCAATCTATACTTAGCAAATTTAGACAATTTTCT
Found at i:10355992 original size:24 final size:24
Alignment explanation
Indices: 10355956--10356008 Score: 70
Period size: 24 Copynumber: 2.2 Consensus size: 24
10355946 AGGCAGATAT
*
10355956 TCAGGGGTGTCAGAACGGTGCAGA
1 TCAGGGGTCTCAGAACGGTGCAGA
* **
10355980 TCAGGTGTCTCAGAACGGTGGTGA
1 TCAGGGGTCTCAGAACGGTGCAGA
10356004 TCAGG
1 TCAGG
10356009 AGTCGGGTCA
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.23, C:0.17, G:0.40, T:0.21
Consensus pattern (24 bp):
TCAGGGGTCTCAGAACGGTGCAGA
Found at i:10365170 original size:57 final size:57
Alignment explanation
Indices: 10365082--10365195 Score: 228
Period size: 57 Copynumber: 2.0 Consensus size: 57
10365072 AAAGATAATG
10365082 TCATAAAGGAAGTTGCTGCCCAAGCAAGCAATGTGGCTCGTAAACTGATTGATTTAA
1 TCATAAAGGAAGTTGCTGCCCAAGCAAGCAATGTGGCTCGTAAACTGATTGATTTAA
10365139 TCATAAAGGAAGTTGCTGCCCAAGCAAGCAATGTGGCTCGTAAACTGATTGATTTAA
1 TCATAAAGGAAGTTGCTGCCCAAGCAAGCAATGTGGCTCGTAAACTGATTGATTTAA
10365196 ATGGTTTTAC
Statistics
Matches: 57, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
57 57 1.00
ACGTcount: A:0.33, C:0.18, G:0.23, T:0.26
Consensus pattern (57 bp):
TCATAAAGGAAGTTGCTGCCCAAGCAAGCAATGTGGCTCGTAAACTGATTGATTTAA
Found at i:10368663 original size:65 final size:65
Alignment explanation
Indices: 10368553--10368688 Score: 186
Period size: 65 Copynumber: 2.1 Consensus size: 65
10368543 AAAAACCTGG
* *
10368553 CAAGAGATCTGATTAAAAATTGAGACATTAAAGGAATTAGCATAAATCCTTCTTGTGAGT-TATT
1 CAAGAGATCTGATTAAAAATGGAGACATGAAAGGAATTAGCATAAATCCTTCTTGTGA-TATATT
10368617 T
65 T
* ** *
10368618 CAAGAGATCTGATTAGATGTGGAGACATGAAAGGAATTAAG-ATAAATCCTTCTTGTGATATGTT
1 CAAGAGATCTGATTAAAAATGGAGACATGAAAGGAATT-AGCATAAATCCTTCTTGTGATATATT
10368682 T
65 T
10368683 CAAGAG
1 CAAGAG
10368689 TCAAATAAGA
Statistics
Matches: 63, Mismatches: 6, Indels: 4
0.86 0.08 0.05
Matches are distributed among these distances:
64 1 0.02
65 60 0.95
66 2 0.03
ACGTcount: A:0.38, C:0.10, G:0.21, T:0.32
Consensus pattern (65 bp):
CAAGAGATCTGATTAAAAATGGAGACATGAAAGGAATTAGCATAAATCCTTCTTGTGATATATTT
Found at i:10369817 original size:249 final size:249
Alignment explanation
Indices: 10369343--10370251 Score: 1380
Period size: 249 Copynumber: 3.7 Consensus size: 249
10369333 TGAAAAAAAG
* * * *
10369343 TCTTACCCAGTAAAATATTTCTCATGAATTTA-TAAATCCTTCGGGTCATCTGTAAGT-CTTTCG
1 TCTTACTCAGTAAATTATTTATCACGAA-TTAGTAAATCCTTCGGGTCATCTGTAAGTCCTTT-G
** * *
10369406 AGCATGATGTTTAAATCCTTCGGGTCATCTGCCAGTCTTTCGAGCCAGATGATAAGTCCTTAGGG
64 AGCATGATGTTTAAATCCTTCGGGTCATCTGTAAGTCTTTCGAGCAAGATAATAAGTCCTTAGGG
* *
10369471 CCATCCGTCAAACCTTTGGGGAGGATGTTTACATC-TGATTTTCGCATGAAAATGAGATA-GATA
129 CCATCCGTCAAACCTTTGGGTAGGATGTTTACA-CATGATTTTCGCATGAAAATAAGATACGAT-
*
10369534 TTTCAAAGTTTCTCATTTAATGTTCTAGAAAATCAAATTTTTGAAAAAGTAAGAAGTC
192 TTTCAAAGTTTCTCATTTAATGTTCTACAAAATCAAATTTTTGAAAAAGTAAGAAGTC
*
10369592 TCTTACTCACTAAATTATTTATCACGAATTAGTAAATCCTTCGGGTCATCTGTAAGTCCTTTGAG
1 TCTTACTCAGTAAATTATTTATCACGAATTAGTAAATCCTTCGGGTCATCTGTAAGTCCTTTGAG
* * * * *
10369657 CATGATGTTTAAATCCTTCGGGTCGTTTGTCAGTCTTTCGAGCAATATAAT-AGTCCTTAGGGTC
66 CATGATGTTTAAATCCTTCGGGTCATCTGTAAGTCTTTCGAGCAAGATAATAAGTCCTTAGGGCC
*
10369721 ATCCGTCAAACCTTTGGGTAGGATGTTTACACATGATTTTTGCATGAAAATAAGATAGCGATTTT
131 ATCCGTCAAACCTTTGGGTAGGATGTTTACACATGATTTTCGCATGAAAATAAGATA-CGATTTT
*
10369786 CAAAGTTTCTCATTTAATGTTCTACAAAATCAAATTTTTGAGAAAGTAAGAAGTC
195 CAAAGTTTCTCATTTAATGTTCTACAAAATCAAATTTTTGAAAAAGTAAGAAGTC
*
10369841 TCTTACTCAGTAAATTATTTATCACGAATTAGTAAATCCTTCGGGTCATCTGTAAGCCCTTTGAG
1 TCTTACTCAGTAAATTATTTATCACGAATTAGTAAATCCTTCGGGTCATCTGTAAGTCCTTTGAG
* * * * * *
10369906 CATGATGTTTAAATCTTTCGGGTCGTTTGTAAGTTTTTCGAGCAATATAATAAGTCCTTAGGGTC
66 CATGATGTTTAAATCCTTCGGGTCATCTGTAAGTCTTTCGAGCAAGATAATAAGTCCTTAGGGCC
*
10369971 ATCCGTCAAACCTTTGGGTAGGATGTTTACACATGATTTTCGCATGAAAATAAGATAACGGTTTT
131 ATCCGTCAAACCTTTGGGTAGGATGTTTACACATGATTTTCGCATGAAAATAAGAT-ACGATTTT
* *
10370036 TAAAGTTTCTCATTTAATGTTCTACAAAATCAAATTTTTG-AAAAGTAAGAAATC
195 CAAAGTTTCTCATTTAATGTTCTACAAAATCAAATTTTTGAAAAAGTAAGAAGTC
* * * *
10370090 TCTTACTCAATAAATTATTTATCACGAATTTGTAAATCCTTCAGGTCATCTGTAAGTCCTTCGAG
1 TCTTACTCAGTAAATTATTTATCACGAATTAGTAAATCCTTCGGGTCATCTGTAAGTCCTTTGAG
* *
10370155 CATGATGTTTAAATCCTTCGGGTCATCTGTAAGTTTTTCGAGCAAGATGATAAGTCCTTAGGGCC
66 CATGATGTTTAAATCCTTCGGGTCATCTGTAAGTCTTTCGAGCAAGATAATAAGTCCTTAGGGCC
* * *
10370220 ATCCGTCAGACCTTTGGGCAAGATGTTTACAC
131 ATCCGTCAAACCTTTGGGTAGGATGTTTACAC
10370252 TCTTTAATTC
Statistics
Matches: 612, Mismatches: 41, Indels: 14
0.92 0.06 0.02
Matches are distributed among these distances:
247 1 0.00
248 67 0.11
249 423 0.69
250 120 0.20
251 1 0.00
ACGTcount: A:0.29, C:0.17, G:0.18, T:0.36
Consensus pattern (249 bp):
TCTTACTCAGTAAATTATTTATCACGAATTAGTAAATCCTTCGGGTCATCTGTAAGTCCTTTGAG
CATGATGTTTAAATCCTTCGGGTCATCTGTAAGTCTTTCGAGCAAGATAATAAGTCCTTAGGGCC
ATCCGTCAAACCTTTGGGTAGGATGTTTACACATGATTTTCGCATGAAAATAAGATACGATTTTC
AAAGTTTCTCATTTAATGTTCTACAAAATCAAATTTTTGAAAAAGTAAGAAGTC
Found at i:10370149 original size:20 final size:20
Alignment explanation
Indices: 10370120--10370186 Score: 62
Period size: 20 Copynumber: 3.2 Consensus size: 20
10370110 ATCACGAATT
10370120 TGTAAATCCTTCAGGTCATC
1 TGTAAATCCTTCAGGTCATC
* * * *
10370140 TGTAAGTCCTTCGAGCATGATG
1 TGTAAATCCTTC-AG-GTCATC
* *
10370162 TTTAAATCCTTCGGGTCATC
1 TGTAAATCCTTCAGGTCATC
10370182 TGTAA
1 TGTAA
10370187 GTTTTTCGAG
Statistics
Matches: 34, Mismatches: 11, Indels: 4
0.69 0.22 0.08
Matches are distributed among these distances:
20 18 0.53
21 3 0.09
22 13 0.38
ACGTcount: A:0.24, C:0.21, G:0.19, T:0.36
Consensus pattern (20 bp):
TGTAAATCCTTCAGGTCATC
Found at i:10370181 original size:42 final size:42
Alignment explanation
Indices: 10370122--10370203 Score: 128
Period size: 42 Copynumber: 2.0 Consensus size: 42
10370112 CACGAATTTG
*
10370122 TAAATCCTTCAGGTCATCTGTAAGTCCTTCGAGCATGATGTT
1 TAAATCCTTCAGGTCATCTGTAAGTCCTTCGAGCAAGATGTT
* **
10370164 TAAATCCTTCGGGTCATCTGTAAGTTTTTCGAGCAAGATG
1 TAAATCCTTCAGGTCATCTGTAAGTCCTTCGAGCAAGATG
10370204 ATAAGTCCTT
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
42 36 1.00
ACGTcount: A:0.24, C:0.20, G:0.21, T:0.35
Consensus pattern (42 bp):
TAAATCCTTCAGGTCATCTGTAAGTCCTTCGAGCAAGATGTT
Found at i:10370454 original size:14 final size:15
Alignment explanation
Indices: 10370413--10370455 Score: 52
Period size: 16 Copynumber: 2.9 Consensus size: 15
10370403 TGTTGGTTTA
10370413 TATTATTATATATAT
1 TATTATTATATATAT
* *
10370428 TATTAATTGTATATGT
1 TATT-ATTATATATAT
10370444 T-TTATTATATAT
1 TATTATTATATAT
10370456 TAAAAATATT
Statistics
Matches: 24, Mismatches: 3, Indels: 3
0.80 0.10 0.10
Matches are distributed among these distances:
14 8 0.33
15 6 0.25
16 10 0.42
ACGTcount: A:0.35, C:0.00, G:0.05, T:0.60
Consensus pattern (15 bp):
TATTATTATATATAT
Found at i:10370576 original size:16 final size:15
Alignment explanation
Indices: 10370555--10370593 Score: 51
Period size: 16 Copynumber: 2.5 Consensus size: 15
10370545 AATTCAGATT
*
10370555 CAGGCCCAGACCCATC
1 CAGGCCCAGACCCA-A
*
10370571 CAGGCCCAGATCCAA
1 CAGGCCCAGACCCAA
10370586 CAGGCCCA
1 CAGGCCCA
10370594 AGAGTGAACC
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
15 8 0.38
16 13 0.62
ACGTcount: A:0.28, C:0.46, G:0.21, T:0.05
Consensus pattern (15 bp):
CAGGCCCAGACCCAA
Found at i:10371702 original size:15 final size:15
Alignment explanation
Indices: 10371650--10371705 Score: 53
Period size: 15 Copynumber: 3.7 Consensus size: 15
10371640 TAGGTATACT
10371650 ATTTTAGATATTTTATA
1 ATTTTA-ATATTTT-TA
* *
10371667 A-TTTAAT-TCTTGA
1 ATTTTAATATTTTTA
*
10371680 ACTTTAATATTTTTA
1 ATTTTAATATTTTTA
10371695 ATTTTAATATT
1 ATTTTAATATT
10371706 ACTTTTATCT
Statistics
Matches: 32, Mismatches: 5, Indels: 6
0.74 0.12 0.14
Matches are distributed among these distances:
13 2 0.06
14 9 0.28
15 16 0.50
16 4 0.12
17 1 0.03
ACGTcount: A:0.34, C:0.04, G:0.04, T:0.59
Consensus pattern (15 bp):
ATTTTAATATTTTTA
Found at i:10373548 original size:19 final size:20
Alignment explanation
Indices: 10373521--10373558 Score: 60
Period size: 19 Copynumber: 1.9 Consensus size: 20
10373511 CTTTTTTTCT
*
10373521 TCTCTTCTTTCTGTTTTTTA
1 TCTCTTCTTTCTATTTTTTA
10373541 TCTC-TCTTTCTATTTTTT
1 TCTCTTCTTTCTATTTTTT
10373559 TGTGTCTTAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 13 0.76
20 4 0.24
ACGTcount: A:0.05, C:0.21, G:0.03, T:0.71
Consensus pattern (20 bp):
TCTCTTCTTTCTATTTTTTA
Found at i:10373559 original size:20 final size:19
Alignment explanation
Indices: 10373509--10373559 Score: 59
Period size: 20 Copynumber: 2.6 Consensus size: 19
10373499 TCACTCTCAC
10373509 TTCTTTTTTTCTTCTCTTCT
1 TTCTTTTTTT-TTCTCTTCT
*
10373529 TTCTGTTTTTTATCTC-TCT
1 TTCT-TTTTTTTTCTCTTCT
*
10373548 TTCTATTTTTTT
1 TTCTTTTTTTTT
10373560 GTGTCTTAAA
Statistics
Matches: 27, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
18 6 0.22
19 7 0.26
20 8 0.30
21 6 0.22
ACGTcount: A:0.04, C:0.20, G:0.02, T:0.75
Consensus pattern (19 bp):
TTCTTTTTTTTTCTCTTCT
Found at i:10383852 original size:3 final size:3
Alignment explanation
Indices: 10383846--10383876 Score: 62
Period size: 3 Copynumber: 10.3 Consensus size: 3
10383836 TATTATTAAT
10383846 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T
10383877 TATTATTATT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (3 bp):
TAA
Found at i:10384932 original size:18 final size:18
Alignment explanation
Indices: 10384909--10384962 Score: 58
Period size: 18 Copynumber: 3.0 Consensus size: 18
10384899 AATTTATTTC
*
10384909 TTATTTTTTA-TAGTTATT
1 TTATTTTTTATTACTTA-T
*
10384927 TTATTTATTATTACTTAT
1 TTATTTTTTATTACTTAT
10384945 TTATTTTTTTATTA-TTAT
1 TTA-TTTTTTATTACTTAT
10384963 CATTATCTTT
Statistics
Matches: 31, Mismatches: 3, Indels: 4
0.82 0.08 0.11
Matches are distributed among these distances:
18 17 0.55
19 14 0.45
ACGTcount: A:0.24, C:0.02, G:0.02, T:0.72
Consensus pattern (18 bp):
TTATTTTTTATTACTTAT
Found at i:10384973 original size:22 final size:22
Alignment explanation
Indices: 10384922--10384976 Score: 69
Period size: 22 Copynumber: 2.5 Consensus size: 22
10384912 TTTTTTATAG
*
10384922 TTATTTTATTTATTATTACTTAT
1 TTATTTT-TTTATTATTACTCAT
10384945 TTATTTTTTTATTATTA-TCA-
1 TTATTTTTTTATTATTACTCAT
10384965 TTATCTTTTTTA
1 TTAT-TTTTTTA
10384977 ACTCTAATTT
Statistics
Matches: 30, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
20 4 0.13
21 9 0.30
22 10 0.33
23 7 0.23
ACGTcount: A:0.24, C:0.05, G:0.00, T:0.71
Consensus pattern (22 bp):
TTATTTTTTTATTATTACTCAT
Found at i:10390887 original size:91 final size:92
Alignment explanation
Indices: 10390732--10390914 Score: 359
Period size: 91 Copynumber: 2.0 Consensus size: 92
10390722 ATAAGACTTA
10390732 AAATCCTCCAAAATGGACTGATTCCACAAGGTTGCTAAAACCCACACTAAACCCTTATGGAAAAC
1 AAATCCTCCAAAATGGACTGATTCCACAAGGTTGCTAAAACCCACACTAAACCCTTATGGAAAAC
10390797 TTTGGCCAAAGCTTAA-TTTGTGGGCT
66 TTTGGCCAAAGCTTAATTTTGTGGGCT
10390823 AAATCCTCCAAAATGGACTGATTCCACAAGGTTGCTAAAACCCACACTAAACCCTTATGGAAAAC
1 AAATCCTCCAAAATGGACTGATTCCACAAGGTTGCTAAAACCCACACTAAACCCTTATGGAAAAC
10390888 TTTGGCCAAAGCTTAATTTTGTGGGCT
66 TTTGGCCAAAGCTTAATTTTGTGGGCT
10390915 CAACTGGAAG
Statistics
Matches: 91, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
91 81 0.89
92 10 0.11
ACGTcount: A:0.34, C:0.24, G:0.16, T:0.26
Consensus pattern (92 bp):
AAATCCTCCAAAATGGACTGATTCCACAAGGTTGCTAAAACCCACACTAAACCCTTATGGAAAAC
TTTGGCCAAAGCTTAATTTTGTGGGCT
Found at i:10394329 original size:23 final size:24
Alignment explanation
Indices: 10394299--10394354 Score: 89
Period size: 23 Copynumber: 2.4 Consensus size: 24
10394289 GAGTCGAGGG
10394299 ATTT-ATAGTGGTCCTTCGGGAC-
1 ATTTCATAGTGGTCCTTCGGGACA
10394321 ATTTCATAGTGGTCCTTCGGGACAA
1 ATTTCATAGTGGTCCTTCGGGAC-A
10394346 ATTTCATAG
1 ATTTCATAG
10394355 CCCCTAGTGG
Statistics
Matches: 31, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
22 4 0.13
23 18 0.58
25 9 0.29
ACGTcount: A:0.23, C:0.18, G:0.23, T:0.36
Consensus pattern (24 bp):
ATTTCATAGTGGTCCTTCGGGACA
Found at i:10398813 original size:50 final size:50
Alignment explanation
Indices: 10398738--10398837 Score: 200
Period size: 50 Copynumber: 2.0 Consensus size: 50
10398728 TTTTGGTTAT
10398738 TTTGGTCAATTTATGTAAATAAACCGCTTTTATTTTAATGAAAGTTTTAA
1 TTTGGTCAATTTATGTAAATAAACCGCTTTTATTTTAATGAAAGTTTTAA
10398788 TTTGGTCAATTTATGTAAATAAACCGCTTTTATTTTAATGAAAGTTTTAA
1 TTTGGTCAATTTATGTAAATAAACCGCTTTTATTTTAATGAAAGTTTTAA
10398838 ATTTTCTTTG
Statistics
Matches: 50, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
50 50 1.00
ACGTcount: A:0.34, C:0.08, G:0.12, T:0.46
Consensus pattern (50 bp):
TTTGGTCAATTTATGTAAATAAACCGCTTTTATTTTAATGAAAGTTTTAA
Found at i:10402890 original size:27 final size:28
Alignment explanation
Indices: 10402838--10402899 Score: 90
Period size: 27 Copynumber: 2.2 Consensus size: 28
10402828 AGGTCTTGGA
10402838 GGTATTTTGCATCATTTTACACTTTAGG
1 GGTATTTTGCATCATTTTACACTTTAGG
* * *
10402866 GGTATTTTG-GTCATTTTATAGTTTAGG
1 GGTATTTTGCATCATTTTACACTTTAGG
10402893 GGTATTT
1 GGTATTT
10402900 CAGTCCTTTG
Statistics
Matches: 31, Mismatches: 3, Indels: 1
0.89 0.09 0.03
Matches are distributed among these distances:
27 22 0.71
28 9 0.29
ACGTcount: A:0.19, C:0.08, G:0.23, T:0.50
Consensus pattern (28 bp):
GGTATTTTGCATCATTTTACACTTTAGG
Found at i:10403893 original size:22 final size:25
Alignment explanation
Indices: 10403868--10403916 Score: 68
Period size: 26 Copynumber: 2.0 Consensus size: 25
10403858 ATCCAAGTTA
10403868 TTATTTCA-AA-TT-AATTAAATAT
1 TTATTTCATAATTTAAATTAAATAT
10403890 TTATTTCATTAATTTAAATTAAATAT
1 TTATTTCA-TAATTTAAATTAAATAT
10403916 T
1 T
10403917 CGGGATAATT
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
22 8 0.35
24 2 0.09
25 2 0.09
26 11 0.48
ACGTcount: A:0.43, C:0.04, G:0.00, T:0.53
Consensus pattern (25 bp):
TTATTTCATAATTTAAATTAAATAT
Found at i:10405251 original size:19 final size:19
Alignment explanation
Indices: 10405228--10405272 Score: 72
Period size: 19 Copynumber: 2.4 Consensus size: 19
10405218 TCAGCTTGAC
10405228 CCAGTTCAGTATGACTGGA
1 CCAGTTCAGTATGACTGGA
* *
10405247 TCAGTTCAGTCTGACTGGA
1 CCAGTTCAGTATGACTGGA
10405266 CCAGTTC
1 CCAGTTC
10405273 CAGAAAGCTC
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
19 23 1.00
ACGTcount: A:0.22, C:0.24, G:0.24, T:0.29
Consensus pattern (19 bp):
CCAGTTCAGTATGACTGGA
Found at i:10406729 original size:19 final size:19
Alignment explanation
Indices: 10406632--10406735 Score: 54
Period size: 19 Copynumber: 5.5 Consensus size: 19
10406622 TTAATCTAAA
10406632 TAGGTTTTAGTATTTTAAT
1 TAGGTTTTAGTATTTTAAT
* * **
10406651 TAAGTTTTAGGATTTATTTT
1 TAGGTTTTAGTATTT-TAAT
** * *
10406671 TATATTTTA-TCTTTGT-TT
1 TAGGTTTTAGTATTT-TAAT
* *
10406689 TAGGTATTT--TAGTTTAAA
1 TAGGT-TTTAGTATTTTAAT
10406707 TAGGTTTTAGTATTTTAAT
1 TAGGTTTTAGTATTTTAAT
*
10406726 TAGGATTTAG
1 TAGGTTTTAG
10406736 AATATTATTT
Statistics
Matches: 62, Mismatches: 18, Indels: 10
0.69 0.20 0.11
Matches are distributed among these distances:
17 4 0.06
18 13 0.21
19 36 0.58
20 9 0.15
ACGTcount: A:0.26, C:0.01, G:0.15, T:0.58
Consensus pattern (19 bp):
TAGGTTTTAGTATTTTAAT
Found at i:10406774 original size:75 final size:75
Alignment explanation
Indices: 10406618--10406774 Score: 176
Period size: 75 Copynumber: 2.1 Consensus size: 75
10406608 TTTATCTTTG
* * * * **
10406618 TATTTTAATCTAAATAGGTTTTAGTATTTTAATTAAGTTTTAGGATTTATTTTTATATTTTATCT
1 TATTTTAGTTTAAATAGGTTTTAGTATTTTAATTAAGATTTAGAATTTATTTTTATATGGTATCT
**
10406683 TTGTTTTAGG
66 TTGTTTTAAA
* *
10406693 TATTTTAGTTTAAATAGGTTTTAGTATTTTAATTAGGATTTAGAATATTATTTTTTTA-GGTAT-
1 TATTTTAGTTTAAATAGGTTTTAGTATTTTAATTAAGATTTAGAAT-TTATTTTTATATGGTATC
10406756 TTTAG-TTTAAA
65 TTT-GTTTTAAA
10406767 TAGTTTTA
1 TA-TTTTA
10406775 AGTGTTTTAA
Statistics
Matches: 69, Mismatches: 10, Indels: 6
0.81 0.12 0.07
Matches are distributed among these distances:
74 9 0.13
75 50 0.72
76 10 0.14
ACGTcount: A:0.29, C:0.01, G:0.13, T:0.57
Consensus pattern (75 bp):
TATTTTAGTTTAAATAGGTTTTAGTATTTTAATTAAGATTTAGAATTTATTTTTATATGGTATCT
TTGTTTTAAA
Found at i:10407390 original size:18 final size:17
Alignment explanation
Indices: 10407367--10407418 Score: 68
Period size: 18 Copynumber: 2.9 Consensus size: 17
10407357 TCTTTATTTG
10407367 TTTATTTAATTATTTTCT
1 TTTATTTAATT-TTTTCT
*
10407385 TTTATTTAATTCTTATCT
1 TTTATTTAATT-TTTTCT
10407403 TTTATTTTAATTTTTT
1 TTTA-TTTAATTTTTT
10407419 TTAAAAAAAC
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
18 23 0.77
19 7 0.23
ACGTcount: A:0.21, C:0.06, G:0.00, T:0.73
Consensus pattern (17 bp):
TTTATTTAATTTTTTCT
Found at i:10407475 original size:16 final size:15
Alignment explanation
Indices: 10407433--10407494 Score: 52
Period size: 16 Copynumber: 3.9 Consensus size: 15
10407423 AAAAACCCCC
*
10407433 TTTTATATTTATTACT
1 TTTTAT-TTTATTATT
* *
10407449 ATTAATATTTATTATT
1 TTTTAT-TTTATTATT
* *
10407465 TTTATTTTTTATAATT
1 TTT-TATTTTATTATT
10407481 TTTTATTTTATTAT
1 TTTTATTTTATTAT
10407495 ACCTTTTATA
Statistics
Matches: 36, Mismatches: 9, Indels: 3
0.75 0.19 0.06
Matches are distributed among these distances:
15 9 0.25
16 26 0.72
17 1 0.03
ACGTcount: A:0.27, C:0.02, G:0.00, T:0.71
Consensus pattern (15 bp):
TTTTATTTTATTATT
Found at i:10407501 original size:18 final size:17
Alignment explanation
Indices: 10407463--10407501 Score: 51
Period size: 17 Copynumber: 2.2 Consensus size: 17
10407453 ATATTTATTA
*
10407463 TTTTTATTTTTTATAAT
1 TTTTTATTTTTTATAAC
*
10407480 TTTTTATTTTATTATACC
1 TTTTTATTTT-TTATAAC
10407498 TTTT
1 TTTT
10407502 ATACTTTACC
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
17 10 0.53
18 9 0.47
ACGTcount: A:0.21, C:0.05, G:0.00, T:0.74
Consensus pattern (17 bp):
TTTTTATTTTTTATAAC
Found at i:10410445 original size:5 final size:5
Alignment explanation
Indices: 10410435--10410514 Score: 52
Period size: 5 Copynumber: 15.2 Consensus size: 5
10410425 TTTTTTAGCC
** * * *
10410435 TATTT TATTT TATTT TATTT TATCA GATGCTT AATTT TATTT TATTT TAATT
1 TATTT TATTT TATTT TATTT TATTT TAT--TT TATTT TATTT TATTT TATTT
** *
10410487 TATCA GATGCTT TATTT TATTT TATTT T
1 TATTT TAT--TT TATTT TATTT TATTT T
10410515 TCTCTGAACA
Statistics
Matches: 56, Mismatches: 15, Indels: 8
0.71 0.19 0.10
Matches are distributed among these distances:
5 52 0.93
7 4 0.07
ACGTcount: A:0.24, C:0.05, G:0.05, T:0.66
Consensus pattern (5 bp):
TATTT
Found at i:10410472 original size:32 final size:32
Alignment explanation
Indices: 10410436--10410514 Score: 140
Period size: 32 Copynumber: 2.5 Consensus size: 32
10410426 TTTTTAGCCT
*
10410436 ATTTTATTTTATTTTATTTTATCAGATGCTTA
1 ATTTTATTTTATTTTAATTTATCAGATGCTTA
*
10410468 ATTTTATTTTATTTTAATTTATCAGATGCTTT
1 ATTTTATTTTATTTTAATTTATCAGATGCTTA
10410500 ATTTTATTTTATTTT
1 ATTTTATTTTATTTT
10410515 TCTCTGAACA
Statistics
Matches: 45, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
32 45 1.00
ACGTcount: A:0.24, C:0.05, G:0.05, T:0.66
Consensus pattern (32 bp):
ATTTTATTTTATTTTAATTTATCAGATGCTTA
Found at i:10421311 original size:18 final size:18
Alignment explanation
Indices: 10421288--10421330 Score: 68
Period size: 18 Copynumber: 2.4 Consensus size: 18
10421278 CTTTGACTTA
*
10421288 TTTATTTAATTATTTTCT
1 TTTATTTAATTATTATCT
*
10421306 TTTATTTAATTCTTATCT
1 TTTATTTAATTATTATCT
10421324 TTTATTT
1 TTTATTT
10421331 TAAAATCAAC
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.21, C:0.07, G:0.00, T:0.72
Consensus pattern (18 bp):
TTTATTTAATTATTATCT
Found at i:10422547 original size:19 final size:20
Alignment explanation
Indices: 10422525--10422565 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 20
10422515 TGTTATTTGC
10422525 AAATGAA-AATGTTGTGGCA
1 AAATGAAGAATGTTGTGGCA
*
10422544 AAATGAATGGATGTTGTGGCA
1 AAATGAA-GAATGTTGTGGCA
10422565 A
1 A
10422566 TTTTCTGATG
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
19 7 0.37
21 12 0.63
ACGTcount: A:0.39, C:0.05, G:0.29, T:0.27
Consensus pattern (20 bp):
AAATGAAGAATGTTGTGGCA
Found at i:10435375 original size:20 final size:20
Alignment explanation
Indices: 10435350--10435388 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
10435340 GCTATGGCTT
*
10435350 TGAAGTAAGGCGCCTTGATA
1 TGAAGTAAAGCGCCTTGATA
*
10435370 TGAAGTAAAGCTCCTTGAT
1 TGAAGTAAAGCGCCTTGAT
10435389 TCTTAATTGA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.31, C:0.15, G:0.26, T:0.28
Consensus pattern (20 bp):
TGAAGTAAAGCGCCTTGATA
Found at i:10440375 original size:12 final size:12
Alignment explanation
Indices: 10440358--10440386 Score: 58
Period size: 12 Copynumber: 2.4 Consensus size: 12
10440348 AGCTATCTAA
10440358 AAAAAGTAAAAT
1 AAAAAGTAAAAT
10440370 AAAAAGTAAAAT
1 AAAAAGTAAAAT
10440382 AAAAA
1 AAAAA
10440387 TGCTTTGACA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.79, C:0.00, G:0.07, T:0.14
Consensus pattern (12 bp):
AAAAAGTAAAAT
Found at i:10442595 original size:35 final size:35
Alignment explanation
Indices: 10442483--10442604 Score: 95
Period size: 34 Copynumber: 3.5 Consensus size: 35
10442473 ATCGCTTGAG
* * *
10442483 AAGTTTTCCCATGAAAATTTTCATCTCACTCGAGA
1 AAGTTTTCTCTTGAAAATTTTCATCTTACTCGAGA
* ** * *
10442518 AAATTGTTCTCTTGAAAAAAAATT-ATCTTGCTTGAGA
1 AAGTT-TTCTCTTG--AAAATTTTCATCTTACTCGAGA
* *
10442555 TAGTTTTCTCTTGAAAATTTTCATCTTACTCAAGA
1 AAGTTTTCTCTTGAAAATTTTCATCTTACTCGAGA
* *
10442590 CAG-TTTCTCTCGAAA
1 AAGTTTTCTCTTGAAA
10442605 CAAAAAATTT
Statistics
Matches: 66, Mismatches: 17, Indels: 9
0.72 0.18 0.10
Matches are distributed among these distances:
34 17 0.26
35 16 0.24
36 14 0.21
37 13 0.20
38 6 0.09
ACGTcount: A:0.32, C:0.18, G:0.11, T:0.39
Consensus pattern (35 bp):
AAGTTTTCTCTTGAAAATTTTCATCTTACTCGAGA
Found at i:10442634 original size:73 final size:73
Alignment explanation
Indices: 10442374--10443080 Score: 685
Period size: 73 Copynumber: 9.6 Consensus size: 73
10442364 TCTTAAAGAT
* * * * * ** * * *
10442374 GTTTCCCTTGAAACAAAAATTTTGTTTCACTTGAGATAGTTTTC-CATAAAACAAGTATCGTCTC
1 GTTTCTCTTGAAACAAAAAATTTATCTCGCTTGAGATAGTTTTCTC-TTGAA-AATTTTCATCTC
*
10442438 ACTCGAGACA
64 ACTCAAGACA
* ** * * *
10442448 GTTTTTCTTGAAACAAAATTTTTATATCGCTTGAGA-AGTTTTCCCATGAAAATTTTCATCTCAC
1 GTTTCTCTTGAAACAAAAAATTTATCTCGCTTGAGATAGTTTTCTCTTGAAAATTTTCATCTCAC
* *
10442512 TCGAGAAAA
66 TCAAG-ACA
* * *
10442521 TTGTTCTCTTG-AA-AAAAAA-TTATCTTGCTTGAGATAGTTTTCTCTTGAAAATTTTCATCTTA
1 GT-TTCTCTTGAAACAAAAAATTTATCTCGCTTGAGATAGTTTTCTCTTGAAAATTTTCATCTCA
10442583 CTCAAGACA
65 CTCAAGACA
* * *
10442592 GTTTCTCTCGAAACAAAAAATTTATCTCGCTTGAGATAGTTTTCTCTTGAAAATTTCCGTCTCAC
1 GTTTCTCTTGAAACAAAAAATTTATCTCGCTTGAGATAGTTTTCTCTTGAAAATTTTCATCTCAC
10442657 TCAAGACA
66 TCAAGACA
* ** * *
10442665 GTTTCTCTTAAAACAAAAAAAAAATACCTCTCTTGAGATAGTTTTCTCTTGAAAATTTT-ATCTC
1 GTTTCTCTTGAAAC--AAAAAATTTATCTCGCTTGAGATAGTTTTCTCTTGAAAATTTTCATCTC
*
10442729 ACTCGAGACAATA
64 ACTCAAGAC---A
* * * * *
10442742 TTTTCTCTTGAAACAAAAATTTTATCTCGCTTCAAATAATTTTCTCTTGAAAATTTTCATCTCAC
1 GTTTCTCTTGAAACAAAAAATTTATCTCGCTTGAGATAGTTTTCTCTTGAAAATTTTCATCTCAC
10442807 TCAAGACA
66 TCAAGACA
* * * * * *
10442815 GTTTCTCATGAAA-TAAAACTTTATCTCTCTTGAGATAGTTTTCTCTTGAAATTTTTCCTCTCAC
1 GTTTCTCTTGAAACAAAAAATTTATCTCGCTTGAGATAGTTTTCTCTTGAAAATTTTCATCTCAC
10442879 TCAAGACA
66 TCAAGACA
* * * ** *
10442887 ATTCTCTCTTAAAATAAAAAATTTATCTTACTTGAGATAGTTTTCTCTTGAAAATATTT-GTCTC
1 GTT-TCTCTTGAAACAAAAAATTTATCTCGCTTGAGATAGTTTTCTCTTGAAAAT-TTTCATCTC
*
10442951 GCTCAAGACA
64 ACTCAAGACA
* * * * **
10442961 ATTTCTGTTGAAACAAAAAATTTATCTCACTTGAGATAGTTTTCTCTTGAAATTTTTTGTCTCAC
1 GTTTCTCTTGAAACAAAAAATTTATCTCGCTTGAGATAGTTTTCTCTTGAAAATTTTCATCTCAC
*
10443026 TCGAGACCA
66 TCAAGA-CA
* * * *
10443035 TATTTCTCTTGAAACAAAAAAAATTATCTCACTTGAAATA-TTTTCT
1 -GTTTCTCTTGAAAC-AAAAAATTTATCTCGCTTGAGATAGTTTTCT
10443081 TTAAAGATTT
Statistics
Matches: 533, Mismatches: 80, Indels: 39
0.82 0.12 0.06
Matches are distributed among these distances:
70 7 0.01
71 18 0.03
72 111 0.21
73 151 0.28
74 103 0.19
75 95 0.18
76 35 0.07
77 13 0.02
ACGTcount: A:0.33, C:0.18, G:0.10, T:0.39
Consensus pattern (73 bp):
GTTTCTCTTGAAACAAAAAATTTATCTCGCTTGAGATAGTTTTCTCTTGAAAATTTTCATCTCAC
TCAAGACA
Found at i:10442803 original size:295 final size:294
Alignment explanation
Indices: 10442434--10443080 Score: 812
Period size: 295 Copynumber: 2.2 Consensus size: 294
10442424 ACAAGTATCG
* * * * * *
10442434 TCTCACTCGAGACA-GTTTT-TCTTGAAACAAAATTTTTATATCGCTTGAGA-AGTTTTCCCATG
1 TCTCACTCGAGACATATTTTCTCTTGAAACAAAAATTTTATCTCGCTTGAAATAATTTTCTCATG
* * *
10442496 AAAATTTTCATCTCACTCGAGAAAATTGTTCTCTTGAAA-AAAA-ATTATCT-TGCTTGAGATAG
66 AAAATTTTCATCTCACTCAAG-AAAGT-TTCTCATGAAATAAAACATTATCTCT-CTTGAGATAG
* * * *
10442558 TTTTCTCTTGAAAATTTTCATCTTACTCAAGACAGTT-TCTCTCGAAACAAAAAATTTATCTCGC
128 TTTTCTCTTGAAAATTTTCATCTCACTCAAGACAATTCTCTCTCAAAACAAAAAATTTATCTCAC
*
10442622 TTGAGATAGTTTTCTCTTGAAAAT-TTCCGTCTCACTCAAGACAGTTTCTCTTAAAACAAAAAAA
193 TTGAGATAGTTTTCTCTTGAAAATATT-CGTCTCACTCAAGACAATTTCTCTTAAAAC--AAAAA
*
10442686 AAATACCTCTCTTGAGATAGTTTTCTCTTGAAA-ATTTTA
255 AAATACCTCACTTGAGATAGTTTTCTCTTGAAATATTTTA
* *
10442725 TCTCACTCGAGACAATATTTTCTCTTGAAACAAAAATTTTATCTCGCTTCAAATAATTTTCTCTT
1 TCTCACTCGAGAC-ATATTTTCTCTTGAAACAAAAATTTTATCTCGCTTGAAATAATTTTCTCAT
* *
10442790 GAAAATTTTCATCTCACTCAAGACAGTTTCTCATGAAATAAAACTTTATCTCTCTTGAGATAGTT
65 GAAAATTTTCATCTCACTCAAGAAAGTTTCTCATGAAATAAAACATTATCTCTCTTGAGATAGTT
* * * * *
10442855 TTCTCTTGAAATTTTTCCTCTCACTCAAGACAATTCTCTCTTAAAATAAAAAATTTATCTTACTT
130 TTCTCTTGAAAATTTTCATCTCACTCAAGACAATTCTCTCTCAAAACAAAAAATTTATCTCACTT
* * * * **
10442920 GAGATAGTTTTCTCTTGAAAATATTTGTCTCGCTCAAGACAATTTCTGTTGAAACAAAAAATTTA
195 GAGATAGTTTTCTCTTGAAAATATTCGTCTCACTCAAGACAATTTCTCTTAAAACAAAAAAAATA
* * *
10442985 TCTCACTTGAGATAGTTTTCTCTTGAAATTTTTTG
260 CCTCACTTGAGATAGTTTTCTCTTGAAATATTTTA
** *
10443020 TCTCACTCGAGACCATA-TTTCTCTTGAAACAAAAAAAATTATCTCACTTGAAAT-ATTTTCT
1 TCTCACTCGAGA-CATATTTTCTCTTGAAAC-AAAAATTTTATCTCGCTTGAAATAATTTTCT
10443081 TTAAAGATTT
Statistics
Matches: 307, Mismatches: 37, Indels: 21
0.84 0.10 0.06
Matches are distributed among these distances:
291 13 0.04
292 1 0.00
293 14 0.05
294 88 0.29
295 116 0.38
296 73 0.24
297 2 0.01
ACGTcount: A:0.32, C:0.19, G:0.10, T:0.39
Consensus pattern (294 bp):
TCTCACTCGAGACATATTTTCTCTTGAAACAAAAATTTTATCTCGCTTGAAATAATTTTCTCATG
AAAATTTTCATCTCACTCAAGAAAGTTTCTCATGAAATAAAACATTATCTCTCTTGAGATAGTTT
TCTCTTGAAAATTTTCATCTCACTCAAGACAATTCTCTCTCAAAACAAAAAATTTATCTCACTTG
AGATAGTTTTCTCTTGAAAATATTCGTCTCACTCAAGACAATTTCTCTTAAAACAAAAAAAATAC
CTCACTTGAGATAGTTTTCTCTTGAAATATTTTA
Found at i:10443095 original size:147 final size:146
Alignment explanation
Indices: 10442434--10443080 Score: 673
Period size: 147 Copynumber: 4.4 Consensus size: 146
10442424 ACAAGTATCG
* * * ** * * * * *
10442434 TCTCACTCGAGACAGTTTTTCTTGAAACAAAATTTTTATATCGCTTGAGA-AGTTTTCCCATGAA
1 TCTCACTCAAGACAATTTCTCTTGAAACAAAAAATTTATCTCACTTGAAATAGTTTTCTCTTGAA
* * * *
10442498 AATTTTCATCTCACTCGAGAAAATTGTTCTCTTG--A-AAAAAAATTATCT-TGCTTGAGATAGT
66 AATTTTCGTCTCACTCAAG-ACAGT-TTCTCTTGAAACAAAAAAATTATCTCT-CTTGAGATAGT
*
10442559 TTTCTCTTGAAAATTTTCA
128 TTTCTCTTGAAATTTTTCA
* * * * *
10442578 TCTTACTCAAGACAGTTTCTCTCGAAACAAAAAATTTATCTCGCTTGAGATAGTTTTCTCTTGAA
1 TCTCACTCAAGACAATTTCTCTTGAAACAAAAAATTTATCTCACTTGAAATAGTTTTCTCTTGAA
* * * *
10442643 AATTTCCGTCTCACTCAAGACAGTTTCTCTTAAAACAAAAAAAAAATACCTCTCTTGAGATAGTT
66 AATTTTCGTCTCACTCAAGACAGTTTCTCTTGAAAC--AAAAAAATTATCTCTCTTGAGATAGTT
*
10442708 TTCTCTTGAAAATTTT-A
129 TTCTCTTGAAATTTTTCA
* * * * *
10442725 TCTCACTCGAGACAATATTTTCTCTTGAAACAAAAATTTTATCTCGCTTCAAATAATTTTCTCTT
1 TCTCACTCAAGAC-A-A-TTTCTCTTGAAACAAAAAATTTATCTCACTTGAAATAGTTTTCTCTT
* * * **
10442790 GAAAATTTTCATCTCACTCAAGACAGTTTCTCATGAAA-TAAAACTTTATCTCTCTTGAGATAGT
63 GAAAATTTTCGTCTCACTCAAGACAGTTTCTCTTGAAACAAAAAAATTATCTCTCTTGAGATAGT
*
10442854 TTTCTCTTGAAATTTTTCC
128 TTTCTCTTGAAATTTTTCA
* * * *
10442873 TCTCACTCAAGACAATTCTCTCTTAAAATAAAAAATTTATCTTACTTGAGATAGTTTTCTCTTGA
1 TCTCACTCAAGACAATT-TCTCTTGAAACAAAAAATTTATCTCACTTGAAATAGTTTTCTCTTGA
* * * * *
10442938 AAATATTT-GTCTCGCTCAAGACAATTTCTGTTGAAACAAAAAATTTATCTCACTTGAGATAGTT
65 AAAT-TTTCGTCTCACTCAAGACAGTTTCTCTTGAAACAAAAAAATTATCTCTCTTGAGATAGTT
**
10443002 TTCTCTTGAAATTTTTTG
129 TTCTCTTGAAATTTTTCA
* *
10443020 TCTCACTCGAGACCATATTTCTCTTGAAACAAAAAAAATTATCTCACTTGAAATA-TTTTCT
1 TCTCACTCAAGA-CA-ATTTCTCTTGAAAC-AAAAAATTTATCTCACTTGAAATAGTTTTCT
10443081 TTAAAGATTT
Statistics
Matches: 425, Mismatches: 61, Indels: 30
0.82 0.12 0.06
Matches are distributed among these distances:
143 7 0.02
144 46 0.11
145 31 0.07
146 67 0.16
147 104 0.24
148 69 0.16
149 25 0.06
150 76 0.18
ACGTcount: A:0.32, C:0.19, G:0.10, T:0.39
Consensus pattern (146 bp):
TCTCACTCAAGACAATTTCTCTTGAAACAAAAAATTTATCTCACTTGAAATAGTTTTCTCTTGAA
AATTTTCGTCTCACTCAAGACAGTTTCTCTTGAAACAAAAAAATTATCTCTCTTGAGATAGTTTT
CTCTTGAAATTTTTCA
Found at i:10443171 original size:36 final size:36
Alignment explanation
Indices: 10443061--10443207 Score: 137
Period size: 36 Copynumber: 4.2 Consensus size: 36
10443051 AAAAAAATTA
10443061 TCTCACTTGAAATATTTTCT-TTAAAGAT---TTTTG
1 TCTCACTTGAAATATTTTCTCTTAAA-ATAAATTTTG
* * *** *
10443094 TCGCACTTGAGATAGTTTT-TCCCCAAATAAAATTTTA
1 TCTCACTTGAAATA-TTTTCTCTTAAAAT-AAATTTTG
* *
10443131 TCTCACTTGAGATATTTTCTTTTAAAATAAATTTTG
1 TCTCACTTGAAATATTTTCTCTTAAAATAAATTTTG
*
10443167 TCTCACTTGAAATATTTTCTCTT-GAA-AAATTTTG
1 TCTCACTTGAAATATTTTCTCTTAAAATAAATTTTG
10443201 TCTCACT
1 TCTCACT
10443208 CGAGGCAGTT
Statistics
Matches: 92, Mismatches: 15, Indels: 13
0.77 0.12 0.11
Matches are distributed among these distances:
33 15 0.16
34 21 0.23
35 2 0.02
36 32 0.35
37 22 0.24
ACGTcount: A:0.29, C:0.16, G:0.09, T:0.46
Consensus pattern (36 bp):
TCTCACTTGAAATATTTTCTCTTAAAATAAATTTTG
Found at i:10443179 original size:17 final size:18
Alignment explanation
Indices: 10443159--10443207 Score: 52
Period size: 17 Copynumber: 2.8 Consensus size: 18
10443149 CTTTTAAAAT
10443159 AAATTTTGTCTCACTTG-
1 AAATTTTGTCTCACTTGA
10443176 AAATATTT-TCT--CTTGAA
1 AAAT-TTTGTCTCACTTG-A
10443193 AAATTTTGTCTCACT
1 AAATTTTGTCTCACT
10443208 CGAGGCAGTT
Statistics
Matches: 26, Mismatches: 0, Indels: 10
0.72 0.00 0.28
Matches are distributed among these distances:
15 4 0.15
16 3 0.12
17 14 0.54
18 3 0.12
19 2 0.08
ACGTcount: A:0.29, C:0.16, G:0.08, T:0.47
Consensus pattern (18 bp):
AAATTTTGTCTCACTTGA
Found at i:10445508 original size:39 final size:40
Alignment explanation
Indices: 10445454--10445534 Score: 146
Period size: 39 Copynumber: 2.0 Consensus size: 40
10445444 GAAATTAAAG
10445454 AAAACTTTTGAATAGGTAATTC-ATTTTTTTCCTTTGTTC
1 AAAACTTTTGAATAGGTAATTCGATTTTTTTCCTTTGTTC
*
10445493 AAAACTTTTGAATAGGTAATTCGTTTTTTTTCCTTTGTTC
1 AAAACTTTTGAATAGGTAATTCGATTTTTTTCCTTTGTTC
10445533 AA
1 AA
10445535 TTTCTTTTTT
Statistics
Matches: 40, Mismatches: 1, Indels: 1
0.95 0.02 0.02
Matches are distributed among these distances:
39 22 0.55
40 18 0.45
ACGTcount: A:0.26, C:0.12, G:0.11, T:0.51
Consensus pattern (40 bp):
AAAACTTTTGAATAGGTAATTCGATTTTTTTCCTTTGTTC
Found at i:10449661 original size:15 final size:15
Alignment explanation
Indices: 10449641--10449672 Score: 64
Period size: 15 Copynumber: 2.1 Consensus size: 15
10449631 GGAAATTAAA
10449641 AATAAAGATAAAGAT
1 AATAAAGATAAAGAT
10449656 AATAAAGATAAAGAT
1 AATAAAGATAAAGAT
10449671 AA
1 AA
10449673 AATACAATGC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.69, C:0.00, G:0.12, T:0.19
Consensus pattern (15 bp):
AATAAAGATAAAGAT
Found at i:10455416 original size:5 final size:5
Alignment explanation
Indices: 10455403--10455445 Score: 50
Period size: 5 Copynumber: 8.4 Consensus size: 5
10455393 TAATAATTTT
* **
10455403 CTCCT CTCCC CTCCC CTCCC CTCCC CTCAT CTCCC TCTCCC CT
1 CTCCC CTCCC CTCCC CTCCC CTCCC CTCCC CTCCC -CTCCC CT
10455446 TTTCCACCAT
Statistics
Matches: 32, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
5 27 0.84
6 5 0.16
ACGTcount: A:0.02, C:0.70, G:0.00, T:0.28
Consensus pattern (5 bp):
CTCCC
Found at i:10456104 original size:37 final size:36
Alignment explanation
Indices: 10456029--10456104 Score: 109
Period size: 36 Copynumber: 2.1 Consensus size: 36
10456019 TTTTTATATT
10456029 TTTAATTTTGTAAAAAAATTATATAAATATTATAAA
1 TTTAATTTTGTAAAAAAATTATATAAATATTATAAA
* *
10456065 TTTAATTTTTTAAAGAAAA-TATATAAATATTTTACAA
1 TTTAATTTTGTAAA-AAAATTATATAAATATTATA-AA
10456102 TTT
1 TTT
10456105 GTAATATTAT
Statistics
Matches: 36, Mismatches: 2, Indels: 3
0.88 0.05 0.07
Matches are distributed among these distances:
36 27 0.75
37 9 0.25
ACGTcount: A:0.49, C:0.01, G:0.03, T:0.47
Consensus pattern (36 bp):
TTTAATTTTGTAAAAAAATTATATAAATATTATAAA
Found at i:10456306 original size:20 final size:20
Alignment explanation
Indices: 10456249--10456299 Score: 102
Period size: 20 Copynumber: 2.5 Consensus size: 20
10456239 ATCCTATTCT
10456249 CTGGTAATCTTTTATTCCCA
1 CTGGTAATCTTTTATTCCCA
10456269 CTGGTAATCTTTTATTCCCA
1 CTGGTAATCTTTTATTCCCA
10456289 CTGGTAATCTT
1 CTGGTAATCTT
10456300 ACATTCCGTG
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.20, C:0.24, G:0.12, T:0.45
Consensus pattern (20 bp):
CTGGTAATCTTTTATTCCCA
Found at i:10457744 original size:18 final size:19
Alignment explanation
Indices: 10457723--10457764 Score: 59
Period size: 18 Copynumber: 2.3 Consensus size: 19
10457713 CACCAATTAA
10457723 AATTTTAAATA-AATATTT
1 AATTTTAAATATAATATTT
*
10457741 AATTATAAATATAATATTT
1 AATTTTAAATATAATATTT
*
10457760 TATTT
1 AATTT
10457765 ATTTGAAAAA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
18 10 0.50
19 10 0.50
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (19 bp):
AATTTTAAATATAATATTT
Found at i:10457836 original size:21 final size:19
Alignment explanation
Indices: 10457811--10457859 Score: 53
Period size: 21 Copynumber: 2.4 Consensus size: 19
10457801 GAATGAATAT
*
10457811 TATTTTAAAATTTTTGTAAA
1 TATTTTAAAATTTTTAT-AA
*
10457831 TGATTTTATATATTTTTATAA
1 T-ATTTTA-AAATTTTTATAA
10457852 TATTTTAA
1 TATTTTAA
10457860 TTTTAAATTA
Statistics
Matches: 25, Mismatches: 2, Indels: 5
0.78 0.06 0.16
Matches are distributed among these distances:
19 1 0.04
20 7 0.28
21 9 0.36
22 8 0.32
ACGTcount: A:0.37, C:0.00, G:0.04, T:0.59
Consensus pattern (19 bp):
TATTTTAAAATTTTTATAA
Found at i:10460489 original size:26 final size:27
Alignment explanation
Indices: 10460440--10460490 Score: 68
Period size: 26 Copynumber: 1.9 Consensus size: 27
10460430 ACCCAATGTA
* *
10460440 CCTCTAAGCCCTGAAATGACTAAATAC
1 CCTCTAAGCCCTGAAATAAATAAATAC
*
10460467 CCTC-AAGCTCTGAAATAAATAAAT
1 CCTCTAAGCCCTGAAATAAATAAAT
10460491 CAACCTCGAA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
26 17 0.81
27 4 0.19
ACGTcount: A:0.41, C:0.25, G:0.10, T:0.24
Consensus pattern (27 bp):
CCTCTAAGCCCTGAAATAAATAAATAC
Found at i:10468873 original size:22 final size:21
Alignment explanation
Indices: 10468831--10468870 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
10468821 GAGTTTATTT
*
10468831 TCATTTTTCAATTTTGAAACA
1 TCATTTTTCAATTTTAAAACA
10468852 TCATTTTT-ATATTTTAAAA
1 TCATTTTTCA-ATTTTAAAA
10468871 ACAATTTCTC
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 1 0.06
21 16 0.94
ACGTcount: A:0.35, C:0.10, G:0.03, T:0.53
Consensus pattern (21 bp):
TCATTTTTCAATTTTAAAACA
Found at i:10472043 original size:14 final size:15
Alignment explanation
Indices: 10472013--10472050 Score: 60
Period size: 14 Copynumber: 2.5 Consensus size: 15
10472003 TATTATTTTT
10472013 TATTATCAACTGAAAA
1 TATTAT-AACTGAAAA
10472029 TATTATAAC-GAAAA
1 TATTATAACTGAAAA
10472043 TATTATAA
1 TATTATAA
10472051 AAAGTTTGTA
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
14 13 0.59
15 3 0.14
16 6 0.27
ACGTcount: A:0.53, C:0.08, G:0.05, T:0.34
Consensus pattern (15 bp):
TATTATAACTGAAAA
Found at i:10480848 original size:6 final size:6
Alignment explanation
Indices: 10480839--10480875 Score: 74
Period size: 6 Copynumber: 6.2 Consensus size: 6
10480829 GGGATGATAA
10480839 ACGGGG ACGGGG ACGGGG ACGGGG ACGGGG ACGGGG A
1 ACGGGG ACGGGG ACGGGG ACGGGG ACGGGG ACGGGG A
10480876 AAACCCATTT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 31 1.00
ACGTcount: A:0.19, C:0.16, G:0.65, T:0.00
Consensus pattern (6 bp):
ACGGGG
Found at i:10480904 original size:6 final size:6
Alignment explanation
Indices: 10480893--10480919 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
10480883 TTTATTTTAA
10480893 ACGGGG ACGGGG ACGGGG ACGGGG ACG
1 ACGGGG ACGGGG ACGGGG ACGGGG ACG
10480920 AGTTTGGTAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.19, C:0.19, G:0.63, T:0.00
Consensus pattern (6 bp):
ACGGGG
Found at i:10480960 original size:12 final size:12
Alignment explanation
Indices: 10480932--10480968 Score: 56
Period size: 12 Copynumber: 3.0 Consensus size: 12
10480922 TTTGGTAATC
10480932 CCCGCCCCGATTA
1 CCCGCCCCGA-TA
10480945 CCCGCCCCGATA
1 CCCGCCCCGATA
*
10480957 CCCGACCCGATA
1 CCCGCCCCGATA
10480969 AATATTAAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
12 13 0.57
13 10 0.43
ACGTcount: A:0.19, C:0.54, G:0.16, T:0.11
Consensus pattern (12 bp):
CCCGCCCCGATA
Found at i:10480995 original size:2 final size:2
Alignment explanation
Indices: 10480988--10481045 Score: 109
Period size: 2 Copynumber: 29.5 Consensus size: 2
10480978 AATAATTATT
10480988 TA TA TA TA TA TA TA TA 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 TA TA TA TA TA TA TA TA
10481030 TA TA TA TA TA TA -A TA T
1 TA TA TA TA TA TA TA TA T
10481046 TAATAAATTT
Statistics
Matches: 55, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
1 1 0.02
2 54 0.98
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:10481139 original size:23 final size:24
Alignment explanation
Indices: 10481097--10481162 Score: 89
Period size: 23 Copynumber: 2.8 Consensus size: 24
10481087 ATATATATAT
* * *
10481097 ATACCCGGCCCGATTCCCGACCCA
1 ATACCCGACCCAATACCCGACCCA
10481121 ATA-CCGACCCAATACCCGACCCA
1 ATACCCGACCCAATACCCGACCCA
*
10481144 ATACCCGGCCCAATACCCG
1 ATACCCGACCCAATACCCG
10481163 TTTAAATAAC
Statistics
Matches: 37, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
23 20 0.54
24 17 0.46
ACGTcount: A:0.27, C:0.48, G:0.14, T:0.11
Consensus pattern (24 bp):
ATACCCGACCCAATACCCGACCCA
Found at i:10481141 original size:12 final size:12
Alignment explanation
Indices: 10481097--10481162 Score: 89
Period size: 12 Copynumber: 5.6 Consensus size: 12
10481087 ATATATATAT
* *
10481097 ATACCCGGCCCG
1 ATACCCGACCCA
*
10481109 ATTCCCGACCCA
1 ATACCCGACCCA
10481121 ATA-CCGACCCA
1 ATACCCGACCCA
10481132 ATACCCGACCCA
1 ATACCCGACCCA
*
10481144 ATACCCGGCCCA
1 ATACCCGACCCA
10481156 ATACCCG
1 ATACCCG
10481163 TTTAAATAAC
Statistics
Matches: 48, Mismatches: 5, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
11 11 0.23
12 37 0.77
ACGTcount: A:0.27, C:0.48, G:0.14, T:0.11
Consensus pattern (12 bp):
ATACCCGACCCA
Found at i:10483477 original size:358 final size:358
Alignment explanation
Indices: 10482813--10483527 Score: 1349
Period size: 358 Copynumber: 2.0 Consensus size: 358
10482803 AATAGCTAGA
* **
10482813 GTAGGAGGTAACTTGACATGCCTAAGAGGAACATTTTAGAGGGAGCAAAAGTATCTTGACACTCT
1 GTAGGAGGTAACTCGACACACCTAAGAGGAACATTTTAGAGGGAGCAAAAGTATCTTGACACTCT
*
10482878 TAGGTAGAGACATCTCAAAATTATGTGAGCATCATTAGAGAGACTCATAATTGTAGAATGAAGGC
66 TAGGTAGAGACATCTCAAAATTATGTGAGCATCAATAGAGAGACTCATAATTGTAGAATGAAGGC
*
10482943 ATCCTGACTCTAATTTGGCCAAACAATTAACTGGTGATAAGGAAATTCCTTTAAGTAAAGTGGAG
131 ATCCTGACTCTAATTTGGCCAAACAATCAACTGGTGATAAGGAAATTCCTTTAAGTAAAGTGGAG
10483008 CAGAGGTATCTCAATGCTTTTGGCCAGAGACGATGCAACTCGAAGACCTTAGAGAAACACTATAG
196 CAGAGGTATCTCAATGCTTTTGGCCAGAGACGATGCAACTCGAAGACCTTAGAGAAACACTATAG
*
10483073 AATGATTAGAGGCATCTCCATGCTCTCAAAGAAATATTGTAGTATGAGAAGAGGCATCTTCACCT
261 AATGATTAGAGGCATCTCCATGCTCTCAAAGAAATATTGCAGTATGAGAAGAGGCATCTTCACCT
10483138 TGGTTGCAGAAATGAGAGGATTCCCAGTGAAAC
326 TGGTTGCAGAAATGAGAGGATTCCCAGTGAAAC
*
10483171 GTAGGAGGTAACTCGACACACCTAAGAGGAACATTTTAGAGGTAGCAAAAGTATCTTGACACTCT
1 GTAGGAGGTAACTCGACACACCTAAGAGGAACATTTTAGAGGGAGCAAAAGTATCTTGACACTCT
10483236 TAGGTAGAGACATCTCAAAATTATGTGAGCATCAATAGAGAGACTCATAATTGTAGAATGAAGGC
66 TAGGTAGAGACATCTCAAAATTATGTGAGCATCAATAGAGAGACTCATAATTGTAGAATGAAGGC
10483301 ATCCTGACTCTAATTTGGCCAAACAATCAACTGGTGATAAGGAAATTCCTTTAAGTAAAGTGGAG
131 ATCCTGACTCTAATTTGGCCAAACAATCAACTGGTGATAAGGAAATTCCTTTAAGTAAAGTGGAG
*
10483366 CAGAGGTATCTCAATGCTTTTGGCCAGGGACGATGCAACTCGAAGACCTTAGAGAAACACTATAG
196 CAGAGGTATCTCAATGCTTTTGGCCAGAGACGATGCAACTCGAAGACCTTAGAGAAACACTATAG
10483431 AATGATTAGAGGCATCTCCATGCTCTCAAAGAAATATTGCAGTATGAGAAGAGGCATCTTCACCT
261 AATGATTAGAGGCATCTCCATGCTCTCAAAGAAATATTGCAGTATGAGAAGAGGCATCTTCACCT
*
10483496 TGGTTGTAGAAATGAGAGGATTCCCAGTGAAA
326 TGGTTGCAGAAATGAGAGGATTCCCAGTGAAA
10483528 AGTATCTAGA
Statistics
Matches: 348, Mismatches: 9, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
358 348 1.00
ACGTcount: A:0.35, C:0.17, G:0.23, T:0.25
Consensus pattern (358 bp):
GTAGGAGGTAACTCGACACACCTAAGAGGAACATTTTAGAGGGAGCAAAAGTATCTTGACACTCT
TAGGTAGAGACATCTCAAAATTATGTGAGCATCAATAGAGAGACTCATAATTGTAGAATGAAGGC
ATCCTGACTCTAATTTGGCCAAACAATCAACTGGTGATAAGGAAATTCCTTTAAGTAAAGTGGAG
CAGAGGTATCTCAATGCTTTTGGCCAGAGACGATGCAACTCGAAGACCTTAGAGAAACACTATAG
AATGATTAGAGGCATCTCCATGCTCTCAAAGAAATATTGCAGTATGAGAAGAGGCATCTTCACCT
TGGTTGCAGAAATGAGAGGATTCCCAGTGAAAC
Found at i:10490360 original size:22 final size:22
Alignment explanation
Indices: 10490308--10490371 Score: 69
Period size: 22 Copynumber: 2.9 Consensus size: 22
10490298 AATTAAACCC
* * *
10490308 TTATTAT-TTATATGTATATAT
1 TTATTATATTTTATTTATTTAT
10490329 TTAATTATATTTTATTTATTTAT
1 TT-ATTATATTTTATTTATTTAT
10490352 TTATTATATTTT-TTTCATTT
1 TTATTATATTTTATTT-ATTT
10490372 TTCTTTGCGT
Statistics
Matches: 37, Mismatches: 3, Indels: 5
0.82 0.07 0.11
Matches are distributed among these distances:
21 5 0.14
22 19 0.51
23 13 0.35
ACGTcount: A:0.28, C:0.02, G:0.02, T:0.69
Consensus pattern (22 bp):
TTATTATATTTTATTTATTTAT
Found at i:10490364 original size:23 final size:24
Alignment explanation
Indices: 10490312--10490364 Score: 65
Period size: 23 Copynumber: 2.3 Consensus size: 24
10490302 AAACCCTTAT
*
10490312 TATTTATATGTATATATTTAATTA
1 TATTTTTATGTATATATTTAATTA
* *
10490336 TA-TTTTATTTATTTATTT-ATTA
1 TATTTTTATGTATATATTTAATTA
10490358 TATTTTT
1 TATTTTT
10490365 TTCATTTTTC
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
22 6 0.24
23 17 0.68
24 2 0.08
ACGTcount: A:0.30, C:0.00, G:0.02, T:0.68
Consensus pattern (24 bp):
TATTTTTATGTATATATTTAATTA
Found at i:10490578 original size:16 final size:16
Alignment explanation
Indices: 10490538--10490594 Score: 55
Period size: 16 Copynumber: 3.6 Consensus size: 16
10490528 TTTTAGTTAA
*
10490538 TATTATATGTA-TATT
1 TATTATATTTAGTATT
* *
10490553 TATTTTTATTTATTA-T
1 TA-TTATATTTAGTATT
10490569 TATTACTATTTAGTATT
1 TATTA-TATTTAGTATT
10490586 TATTATATT
1 TATTATATT
10490595 ATACATACAT
Statistics
Matches: 34, Mismatches: 4, Indels: 7
0.76 0.09 0.16
Matches are distributed among these distances:
15 4 0.12
16 22 0.65
17 8 0.24
ACGTcount: A:0.30, C:0.02, G:0.04, T:0.65
Consensus pattern (16 bp):
TATTATATTTAGTATT
Found at i:10490629 original size:14 final size:13
Alignment explanation
Indices: 10490607--10490669 Score: 51
Period size: 12 Copynumber: 4.8 Consensus size: 13
10490597 ACATACATTT
*
10490607 TTATATTTTTATA
1 TTATATTTTTTTA
10490620 -TATATTTTTTTA
1 TTATATTTTTTTA
*
10490632 TTAT-TTTATTTA
1 TTATATTTTTTTA
10490644 -TACTAATTTATTTTCA
1 TTA-T-ATTT-TTTT-A
10490660 TTATATTTTT
1 TTATATTTTT
10490670 AGTTTCTTTG
Statistics
Matches: 40, Mismatches: 3, Indels: 13
0.71 0.05 0.23
Matches are distributed among these distances:
11 2 0.05
12 19 0.47
13 3 0.08
14 5 0.12
15 7 0.17
16 2 0.05
17 2 0.05
ACGTcount: A:0.27, C:0.03, G:0.00, T:0.70
Consensus pattern (13 bp):
TTATATTTTTTTA
Found at i:10490639 original size:22 final size:22
Alignment explanation
Indices: 10490584--10490646 Score: 65
Period size: 22 Copynumber: 2.9 Consensus size: 22
10490574 CTATTTAGTA
* *
10490584 TTTATTATATTATACATACATT
1 TTTATTATTTTATATATACATT
**
10490606 TTTA-TATTTTTATATATATTTT
1 TTTATTA-TTTTATATATACATT
*
10490628 TTTATTATTTTATTTATAC
1 TTTATTATTTTATATATAC
10490647 TAATTTATTT
Statistics
Matches: 33, Mismatches: 6, Indels: 4
0.77 0.14 0.09
Matches are distributed among these distances:
21 2 0.06
22 29 0.88
23 2 0.06
ACGTcount: A:0.30, C:0.05, G:0.00, T:0.65
Consensus pattern (22 bp):
TTTATTATTTTATATATACATT
Found at i:10491655 original size:20 final size:20
Alignment explanation
Indices: 10491630--10491674 Score: 65
Period size: 20 Copynumber: 2.2 Consensus size: 20
10491620 TAAGGGTCTG
10491630 GCAAG-CCAGAGGGGGCACCA
1 GCAAGCCCA-AGGGGGCACCA
*
10491650 GCAAGCCCAAGGGGGCACCG
1 GCAAGCCCAAGGGGGCACCA
10491670 GCAAG
1 GCAAG
10491675 GAGAACTCGA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
20 20 0.87
21 3 0.13
ACGTcount: A:0.29, C:0.31, G:0.40, T:0.00
Consensus pattern (20 bp):
GCAAGCCCAAGGGGGCACCA
Found at i:10495094 original size:16 final size:15
Alignment explanation
Indices: 10495054--10495124 Score: 74
Period size: 16 Copynumber: 4.7 Consensus size: 15
10495044 AGATTCAATC
*
10495054 AGAACAAAAAGGGAAA
1 AGAACAAAAA-AGAAA
* *
10495070 AAAATAAAAAAGAAA
1 AGAACAAAAAAGAAA
10495085 AGAAGCAAAAAAGAAGA
1 AGAA-CAAAAAAGAA-A
10495102 A-AACAAAAAA-AAA
1 AGAACAAAAAAGAAA
10495115 AGAACAAAAA
1 AGAACAAAAA
10495125 TCAAAAAGAA
Statistics
Matches: 47, Mismatches: 5, Indels: 8
0.78 0.08 0.13
Matches are distributed among these distances:
13 2 0.04
14 10 0.21
15 14 0.30
16 19 0.40
17 2 0.04
ACGTcount: A:0.79, C:0.06, G:0.14, T:0.01
Consensus pattern (15 bp):
AGAACAAAAAAGAAA
Found at i:10495103 original size:19 final size:19
Alignment explanation
Indices: 10495067--10495138 Score: 63
Period size: 19 Copynumber: 3.6 Consensus size: 19
10495057 ACAAAAAGGG
* *
10495067 AAAAAAATAAAAAAGAAAAG
1 AAAAAAA-AAAGAAGAAAAC
**
10495087 AAGCAAAAAAGAAGAAAAC
1 AAAAAAAAAAGAAGAAAAC
*
10495106 AAAAAAAAAAGAACAAAAATC
1 AAAAAAAAAAGAA-GAAAA-C
10495127 AAAAAGAAAAAG
1 AAAAA-AAAAAG
10495139 GGATAAAAAA
Statistics
Matches: 42, Mismatches: 7, Indels: 4
0.79 0.13 0.08
Matches are distributed among these distances:
19 21 0.50
20 9 0.21
21 6 0.14
22 6 0.14
ACGTcount: A:0.81, C:0.06, G:0.11, T:0.03
Consensus pattern (19 bp):
AAAAAAAAAAGAAGAAAAC
Found at i:10495130 original size:16 final size:14
Alignment explanation
Indices: 10495075--10495134 Score: 59
Period size: 16 Copynumber: 3.9 Consensus size: 14
10495065 GGAAAAAAAT
10495075 AAAAAAGAAAAGAAGC
1 AAAAAA-AAAAGAA-C
10495091 AAAAAAGAAGAA-AAC
1 AAAAAA-AA-AAGAAC
10495106 AAAAAAAAAAGAAC
1 AAAAAAAAAAGAAC
10495120 AAAAATCAAAAAGAA
1 AAAAA--AAAAAGAA
10495135 AAAGGGATAA
Statistics
Matches: 40, Mismatches: 0, Indels: 8
0.83 0.00 0.17
Matches are distributed among these distances:
13 2 0.05
14 10 0.25
15 7 0.17
16 19 0.47
17 2 0.05
ACGTcount: A:0.80, C:0.07, G:0.12, T:0.02
Consensus pattern (14 bp):
AAAAAAAAAAGAAC
Found at i:10495763 original size:22 final size:22
Alignment explanation
Indices: 10495738--10495792 Score: 101
Period size: 22 Copynumber: 2.5 Consensus size: 22
10495728 AGCACCCCAT
*
10495738 CAAACATTTGAGCATCAAATGC
1 CAAACCTTTGAGCATCAAATGC
10495760 CAAACCTTTGAGCATCAAATGC
1 CAAACCTTTGAGCATCAAATGC
10495782 CAAACCTTTGA
1 CAAACCTTTGA
10495793 CCAAACACAA
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
22 32 1.00
ACGTcount: A:0.38, C:0.25, G:0.13, T:0.24
Consensus pattern (22 bp):
CAAACCTTTGAGCATCAAATGC
Found at i:10496241 original size:18 final size:18
Alignment explanation
Indices: 10496206--10496241 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
10496196 TCAACATCAA
**
10496206 ATATTGGGGCATTTTTTG
1 ATATTGGGGCATCATTTG
10496224 ATATTGGGGCATCATTTG
1 ATATTGGGGCATCATTTG
10496242 GGGATTCAAC
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.19, C:0.08, G:0.28, T:0.44
Consensus pattern (18 bp):
ATATTGGGGCATCATTTG
Found at i:10496881 original size:106 final size:106
Alignment explanation
Indices: 10496758--10498028 Score: 1909
Period size: 106 Copynumber: 12.0 Consensus size: 106
10496748 GTGCCCCTCG
* * * * *
10496758 AGACAACACAAGTTCAACTTCACAACGAAGGGACGGCTGGTTGTCAACAAATAACTTCCCAAATT
1 AGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCCAATTT
*
10496823 CAGAGCCAATTTCAACTTCACCGCGAAGGATATTGGACTCC
66 CAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCC
* * * * *
10496864 AGACAACACAATTTCAACTTCACGACGAAGGGACCACTGGTTGTCAACAAACAACATCTCAATTT
1 AGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCCAATTT
* **
10496929 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTTT
66 CAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCC
* * * * * * *
10496970 AGACAACGTAAGTTCAACTTCACGACAAAGCGACAGCTGGTTGTCAATAAATAATTTCCCAATTT
1 AGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCCAATTT
*
10497035 CAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCA
66 CAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCC
* *
10497076 AGACAACGCAAGTTCAACTTCATGACGAAGGGACCGCTGGTTGTCAATAAACAACTTCCCAATTT
1 AGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCCAATTT
*
10497141 CAGAGCCAATTTCAACTTCATAGCGAAGGATATTGGACTCC
66 CAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCC
* *
10497182 AGACAACGCAAGTTCAACTTCACGACGAAGGGACTGCTGGTTGTCAACAAACAACTTCTCAATTT
1 AGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCCAATTT
*
10497247 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCC
66 CAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCC
*
10497288 AGACAATGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCCAATTT
1 AGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCCAATTT
*
10497353 CAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCG
66 CAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCC
* *
10497394 AGACAACGCAAGTTCAACTTCATGACGAAGGGACCGCTGGTTGTCAACAAACAATTTCCCAATTT
1 AGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCCAATTT
* * *
10497459 CGGAGCCAATTTCAACTCCACAGCGAAAGATATTGGACTCC
66 CAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCC
* *
10497500 AGACAACACAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAATTTCCCAATTT
1 AGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCCAATTT
*
10497565 C-GAAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCC
66 CAG-AGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCC
* * * *
10497606 AAACAATGCAAGTTCAACTTCACTACGAAGGGACCGCTGGTTGTCAACAAACAACTTCTCAATTT
1 AGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCCAATTT
* *
10497671 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCA
66 CAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCC
*
10497712 AGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTTCCAATTT
1 AGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCCAATTT
* *
10497777 CAGAACCAATTTCAACTTCACAGCGAAGGATATTGGACTCG
66 CAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCC
* * * * *
10497818 AGACAACACAAGTTCAACTTCACGACGAAGGGACCACTGGTTTTCAACAAATAATTTCCCAATTT
1 AGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCCAATTT
** * * *
10497883 TGGAGCCAATTTCAACTTCACAACAAAGGATATTGGACTCG
66 CAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCC
* * * * * * *
10497924 AGATAACACAAGTTCAACTTCACAACGAAGGGACAGCTGGTTGTCAACAAACAATTTCCCGATTC
1 AGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCCAATTT
*
10497989 CAGAGCCAATTTTAACTTCACGATG-G-AGGATATTGGACTC
66 CAGAGCCAATTTCAACTTCAC-A-GCGAAGGATATTGGACTC
10498029 GGAACAATCT
Statistics
Matches: 1063, Mismatches: 98, Indels: 8
0.91 0.08 0.01
Matches are distributed among these distances:
105 1 0.00
106 1060 1.00
107 2 0.00
ACGTcount: A:0.35, C:0.25, G:0.18, T:0.23
Consensus pattern (106 bp):
AGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCCAATTT
CAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCC
Found at i:10498830 original size:37 final size:37
Alignment explanation
Indices: 10498780--10498881 Score: 150
Period size: 37 Copynumber: 2.8 Consensus size: 37
10498770 TTTCATCCTA
*
10498780 CTAGGATTCAAACTCCTAAAAATAGGATAGAATTTTG
1 CTAGGATTCAAACTCCTAAAAATAGGATAGAATTCTG
*
10498817 CTAGGATTCAAACTCCTAAAAATAGGATAGAGTTCTG
1 CTAGGATTCAAACTCCTAAAAATAGGATAGAATTCTG
** * *
10498854 CTATTATTTAAACTCCTAAAGATAGGAT
1 CTAGGATTCAAACTCCTAAAAATAGGAT
10498882 CCACAAGCAT
Statistics
Matches: 59, Mismatches: 6, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
37 59 1.00
ACGTcount: A:0.39, C:0.15, G:0.16, T:0.30
Consensus pattern (37 bp):
CTAGGATTCAAACTCCTAAAAATAGGATAGAATTCTG
Found at i:10499312 original size:15 final size:14
Alignment explanation
Indices: 10499292--10499334 Score: 54
Period size: 12 Copynumber: 3.1 Consensus size: 14
10499282 TGTCTGTATA
10499292 TATTTAATTATATTT
1 TATTT-ATTATATTT
10499307 TATTTATT-TA-TT
1 TATTTATTATATTT
10499319 TATTTATTATAATTT
1 TATTTATTAT-ATTT
10499334 T
1 T
10499335 TTTCATTTTT
Statistics
Matches: 25, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
12 10 0.40
13 3 0.12
14 4 0.16
15 8 0.32
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (14 bp):
TATTTATTATATTT
Found at i:10499381 original size:2 final size:2
Alignment explanation
Indices: 10499374--10499398 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
10499364 ATTTTCCTAT
10499374 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
10499399 TATTTTTTAT
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:10499549 original size:26 final size:25
Alignment explanation
Indices: 10499520--10499641 Score: 81
Period size: 26 Copynumber: 4.7 Consensus size: 25
10499510 TTAGTTAATA
10499520 TTATATGTATATTTATTTTTTATTTT
1 TTATAT-TATATTTATTTTTTATTTT
* **
10499546 TTATTATTAT-TACTATTTAGTATTTT
1 TTA-TATTATAT-TTATTTTTTATTTT
** *
10499572 ATTATATTATACATACATTTTTATATTT
1 -TTATATTATATTTA-TTTTTTAT-TTT
10499600 TTATATATATATTT-TTTTTTATTTT
1 TTATAT-TATATTTATTTTTTATTTT
10499625 ATT-TA-TACTATTTATTT
1 -TTATATTA-TATTTATTT
10499642 ATTTTCATTA
Statistics
Matches: 75, Mismatches: 11, Indels: 21
0.70 0.10 0.20
Matches are distributed among these distances:
23 2 0.03
24 5 0.07
25 9 0.12
26 34 0.45
27 17 0.23
28 8 0.11
ACGTcount: A:0.28, C:0.03, G:0.02, T:0.67
Consensus pattern (25 bp):
TTATATTATATTTATTTTTTATTTT
Found at i:10499624 original size:23 final size:25
Alignment explanation
Indices: 10499483--10499643 Score: 73
Period size: 24 Copynumber: 6.2 Consensus size: 25
10499473 CTTTATTTTA
*
10499483 TTTTATATTTCTATGAT-TACTATTT
1 TTTTATATTTTTAT-ATATACTATTT
* * *
10499508 TTTTAGTTAATATTATATGTA-TATTT
1 TTTTA--TATTTTTATATATACTATTT
* *
10499534 ATTTTTTATTTTT-TAT-TATTATTACT
1 -TTTTATATTTTTATATATACTATT--T
* **
10499560 ATTTAGTATTTTATTATATTATACATACAT
1 TTTTA-TA-TTT-TTATA-TATAC-TATTT
10499590 TTTTATATTTTTATATATA-TATTT
1 TTTTATATTTTTATATATACTATTT
* *
10499614 TTTTTTA-TTTTATTTATACTATTT
1 TTTTATATTTTTATATATACTATTT
*
10499638 ATTTAT
1 TTTTAT
10499644 TTTCATTATA
Statistics
Matches: 103, Mismatches: 18, Indels: 31
0.68 0.12 0.20
Matches are distributed among these distances:
23 12 0.12
24 25 0.24
25 13 0.13
26 14 0.14
27 20 0.19
28 5 0.05
29 4 0.04
30 6 0.06
31 2 0.02
32 2 0.02
ACGTcount: A:0.28, C:0.04, G:0.02, T:0.66
Consensus pattern (25 bp):
TTTTATATTTTTATATATACTATTT
Found at i:10499655 original size:28 final size:27
Alignment explanation
Indices: 10499599--10499656 Score: 71
Period size: 28 Copynumber: 2.1 Consensus size: 27
10499589 TTTTTATATT
* * *
10499599 TTTATATATATATTTTTTTTTATTTTA
1 TTTATATATATATTTATTTTCATTATA
*
10499626 TTTATACTATTTATTTATTTTCATTATA
1 TTTATA-TATATATTTATTTTCATTATA
10499654 TTT
1 TTT
10499657 TTAGTTTCTT
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
27 6 0.23
28 20 0.77
ACGTcount: A:0.26, C:0.03, G:0.00, T:0.71
Consensus pattern (27 bp):
TTTATATATATATTTATTTTCATTATA
Found at i:10499766 original size:15 final size:15
Alignment explanation
Indices: 10499748--10499777 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
10499738 ATCTTCATTT
*
10499748 ATTTTATTTTTTTTA
1 ATTTCATTTTTTTTA
10499763 ATTTCATTTTTTTTA
1 ATTTCATTTTTTTTA
10499778 TCCAATTATT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.20, C:0.03, G:0.00, T:0.77
Consensus pattern (15 bp):
ATTTCATTTTTTTTA
Found at i:10504019 original size:29 final size:31
Alignment explanation
Indices: 10503982--10504052 Score: 92
Period size: 31 Copynumber: 2.4 Consensus size: 31
10503972 GTTTCGGAGA
*
10503982 ACATAGGTAACTT-TCCATATGTC-CCAAGG
1 ACATAGGTAACTTGTCCATATGTCTCCAAAG
* *
10504011 ACATAGGTAAATTGTCCATATGTCTCGAAAG
1 ACATAGGTAACTTGTCCATATGTCTCCAAAG
*
10504042 ATATAGGTAAC
1 ACATAGGTAAC
10504053 CCTCGACTCT
Statistics
Matches: 35, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
29 12 0.34
30 10 0.29
31 13 0.37
ACGTcount: A:0.35, C:0.18, G:0.18, T:0.28
Consensus pattern (31 bp):
ACATAGGTAACTTGTCCATATGTCTCCAAAG
Found at i:10509549 original size:29 final size:31
Alignment explanation
Indices: 10509512--10509582 Score: 92
Period size: 31 Copynumber: 2.4 Consensus size: 31
10509502 GTTTCGGAGA
*
10509512 ACATAGGTAACTT-TCCATATGTC-CCAAGG
1 ACATAGGTAACTTGTCCATATGTCTCCAAAG
* *
10509541 ACATAGGTAAATTGTCCATATGTCTCGAAAG
1 ACATAGGTAACTTGTCCATATGTCTCCAAAG
*
10509572 ATATAGGTAAC
1 ACATAGGTAAC
10509583 CCTCGACTCT
Statistics
Matches: 35, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
29 12 0.34
30 10 0.29
31 13 0.37
ACGTcount: A:0.35, C:0.18, G:0.18, T:0.28
Consensus pattern (31 bp):
ACATAGGTAACTTGTCCATATGTCTCCAAAG
Found at i:10509731 original size:16 final size:17
Alignment explanation
Indices: 10509710--10509753 Score: 56
Period size: 16 Copynumber: 2.7 Consensus size: 17
10509700 TATCTCATAT
10509710 CATATAACATGT-ATCA
1 CATATAACATGTAATCA
10509726 CATAT-ACATGTAATCA
1 CATATAACATGTAATCA
**
10509742 TGTATAACATGT
1 CATATAACATGT
10509754 CTCATAATTT
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
15 6 0.25
16 12 0.50
17 6 0.25
ACGTcount: A:0.41, C:0.16, G:0.09, T:0.34
Consensus pattern (17 bp):
CATATAACATGTAATCA
Found at i:10509758 original size:16 final size:16
Alignment explanation
Indices: 10509711--10509759 Score: 55
Period size: 16 Copynumber: 3.1 Consensus size: 16
10509701 ATCTCATATC
*
10509711 ATATAACATGTATCAC
1 ATATAACATGTATCAT
10509727 ATAT-ACATGTAATCAT
1 ATATAACATGT-ATCAT
* *
10509743 GTATAACATGTCTCAT
1 ATATAACATGTATCAT
10509759 A
1 A
10509760 ATTTATATTA
Statistics
Matches: 27, Mismatches: 4, Indels: 4
0.77 0.11 0.11
Matches are distributed among these distances:
15 6 0.22
16 15 0.56
17 6 0.22
ACGTcount: A:0.41, C:0.16, G:0.08, T:0.35
Consensus pattern (16 bp):
ATATAACATGTATCAT
Found at i:10515210 original size:16 final size:17
Alignment explanation
Indices: 10515189--10515232 Score: 56
Period size: 16 Copynumber: 2.7 Consensus size: 17
10515179 TATCTCATAT
10515189 CATATAACATGT-ATCA
1 CATATAACATGTAATCA
10515205 CATAT-ACATGTAATCA
1 CATATAACATGTAATCA
* *
10515221 CTTATATCATGT
1 CATATAACATGT
10515233 CTCATAGTTT
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
15 6 0.25
16 13 0.54
17 5 0.21
ACGTcount: A:0.39, C:0.18, G:0.07, T:0.36
Consensus pattern (17 bp):
CATATAACATGTAATCA
Found at i:10517453 original size:43 final size:43
Alignment explanation
Indices: 10517406--10517493 Score: 124
Period size: 43 Copynumber: 2.1 Consensus size: 43
10517396 TTTAAAAAGA
* *
10517406 TTTTTT-ATAGCTTATGCAATGGGTATTGAAGTTGGAGGATGG
1 TTTTTTGATAGCTTATGCAATAGGCATTGAAGTTGGAGGATGG
* * *
10517448 TTTTTTGGTAGCTTATGCAGTAGGCATTGAAGTTTGAGGATGG
1 TTTTTTGATAGCTTATGCAATAGGCATTGAAGTTGGAGGATGG
10517491 TTT
1 TTT
10517494 ATGCAATAGG
Statistics
Matches: 40, Mismatches: 5, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
42 6 0.15
43 34 0.85
ACGTcount: A:0.22, C:0.06, G:0.31, T:0.42
Consensus pattern (43 bp):
TTTTTTGATAGCTTATGCAATAGGCATTGAAGTTGGAGGATGG
Found at i:10517731 original size:33 final size:31
Alignment explanation
Indices: 10517673--10517748 Score: 107
Period size: 33 Copynumber: 2.4 Consensus size: 31
10517663 TTTTATTTTG
* *
10517673 ATGTTAATTATATAGATTTTGATGTTAATGTT
1 ATGTT-ATTTTATAGATTTTAATGTTAATGTT
10517705 ATGTTATTTTATAGATTTGTTAATGTTAATGTT
1 ATGTTATTTTATAGA-TT-TTAATGTTAATGTT
10517738 ATGTTATTTTA
1 ATGTTATTTTA
10517749 ATGTTCTATT
Statistics
Matches: 40, Mismatches: 2, Indels: 3
0.89 0.04 0.07
Matches are distributed among these distances:
31 9 0.22
32 7 0.17
33 24 0.60
ACGTcount: A:0.29, C:0.00, G:0.14, T:0.57
Consensus pattern (31 bp):
ATGTTATTTTATAGATTTTAATGTTAATGTT
Found at i:10517751 original size:16 final size:16
Alignment explanation
Indices: 10517697--10517753 Score: 64
Period size: 16 Copynumber: 3.5 Consensus size: 16
10517687 GATTTTGATG
10517697 TTAATGTTATGTTATT
1 TTAATGTTATGTTATT
*
10517713 TT-ATAGATT-TGTTAATG
1 TTAAT-G-TTATGTT-ATT
10517730 TTAATGTTATGTTATT
1 TTAATGTTATGTTATT
10517746 TTAATGTT
1 TTAATGTT
10517754 CTATTATGAT
Statistics
Matches: 34, Mismatches: 2, Indels: 10
0.74 0.04 0.22
Matches are distributed among these distances:
15 2 0.06
16 19 0.56
17 11 0.32
18 2 0.06
ACGTcount: A:0.26, C:0.00, G:0.14, T:0.60
Consensus pattern (16 bp):
TTAATGTTATGTTATT
Found at i:10520639 original size:24 final size:24
Alignment explanation
Indices: 10520574--10520639 Score: 89
Period size: 24 Copynumber: 2.8 Consensus size: 24
10520564 ATATATTCGA
*
10520574 CATTGGTTTCAGTATGTCCAACAT
1 CATTGGTTTCAGTATGTTCAACAT
*
10520598 CGTTGGTTTCAGTATGTTCAACAAT
1 CATTGGTTTCAGTATGTTCAAC-AT
*
10520623 -ATTGGATTCAGTATGTT
1 CATTGGTTTCAGTATGTT
10520640 TAGTATTTGT
Statistics
Matches: 37, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
24 35 0.95
25 2 0.05
ACGTcount: A:0.24, C:0.15, G:0.20, T:0.41
Consensus pattern (24 bp):
CATTGGTTTCAGTATGTTCAACAT
Found at i:10522414 original size:21 final size:22
Alignment explanation
Indices: 10522390--10522436 Score: 69
Period size: 22 Copynumber: 2.2 Consensus size: 22
10522380 TACAAAAGTT
10522390 ATTTGT-AAGAACCCCAAATTG
1 ATTTGTCAAGAACCCCAAATTG
**
10522411 ATTTGTCATTAACCCCAAATTG
1 ATTTGTCAAGAACCCCAAATTG
10522433 ATTT
1 ATTT
10522437 CGATAACTCA
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
21 6 0.26
22 17 0.74
ACGTcount: A:0.34, C:0.19, G:0.11, T:0.36
Consensus pattern (22 bp):
ATTTGTCAAGAACCCCAAATTG
Found at i:10526156 original size:36 final size:37
Alignment explanation
Indices: 10526115--10526185 Score: 108
Period size: 38 Copynumber: 1.9 Consensus size: 37
10526105 TTTTCCTTTT
10526115 TTAAAATATATTTT-CTTGTTTTCCCTTAGTTTTTAC
1 TTAAAATATATTTTCCTTGTTTTCCCTTAGTTTTTAC
* *
10526151 TTAAAATATTTTTTCCCTTGTTTTGCCTTAGTTTT
1 TTAAAATATATTTT-CCTTGTTTTCCCTTAGTTTT
10526186 ATGATAGGTA
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
36 13 0.42
38 18 0.58
ACGTcount: A:0.20, C:0.14, G:0.07, T:0.59
Consensus pattern (37 bp):
TTAAAATATATTTTCCTTGTTTTCCCTTAGTTTTTAC
Found at i:10527257 original size:20 final size:22
Alignment explanation
Indices: 10527227--10527268 Score: 61
Period size: 21 Copynumber: 2.0 Consensus size: 22
10527217 AAGTTGATAT
10527227 AGTGAATTTTC-GGGCATGAAC
1 AGTGAATTTTCTGGGCATGAAC
*
10527248 AGTG-ATTTTCTGGGCTTGAAC
1 AGTGAATTTTCTGGGCATGAAC
10527269 GAAAATTCCA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
20 6 0.32
21 13 0.68
ACGTcount: A:0.24, C:0.14, G:0.29, T:0.33
Consensus pattern (22 bp):
AGTGAATTTTCTGGGCATGAAC
Found at i:10528353 original size:24 final size:23
Alignment explanation
Indices: 10528326--10528371 Score: 65
Period size: 24 Copynumber: 2.0 Consensus size: 23
10528316 ATTTCTACGC
*
10528326 GGCACTTCAGTGCAAATTCTATGT
1 GGCACTACAGTGCAAATT-TATGT
*
10528350 GGCACTACGGTGCAAATTTATG
1 GGCACTACAGTGCAAATTTATG
10528372 CGAGCTGTGG
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
23 4 0.20
24 16 0.80
ACGTcount: A:0.26, C:0.20, G:0.24, T:0.30
Consensus pattern (23 bp):
GGCACTACAGTGCAAATTTATGT
Found at i:10529080 original size:22 final size:21
Alignment explanation
Indices: 10529039--10529081 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 21
10529029 GTAGCGGTAT
*
10529039 TGTAGCAGGGTATCGATTCCC
1 TGTAGCAGGGAATCGATTCCC
*
10529060 TGTAGCAGGGGAATCGGTTCCC
1 TGTAGCA-GGGAATCGATTCCC
10529082 CTAATATAAT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
21 7 0.37
22 12 0.63
ACGTcount: A:0.19, C:0.23, G:0.33, T:0.26
Consensus pattern (21 bp):
TGTAGCAGGGAATCGATTCCC
Done.