Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01014683.1 Corchorus capsularis cultivar CVL-1 contig14704, 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: 91642
ACGTcount: A:0.31, C:0.18, G:0.19, T:0.33
Found at i:896 original size:12 final size:13
Alignment explanation
Indices: 855--899 Score: 74
Period size: 13 Copynumber: 3.5 Consensus size: 13
845 AATTATTGTT
855 TGCTTTATTAATC
1 TGCTTTATTAATC
*
868 TGCTTTATTAATT
1 TGCTTTATTAATC
881 TGCTTTA-TAATC
1 TGCTTTATTAATC
893 TGCTTTA
1 TGCTTTA
900 GATTTAGATT
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
12 11 0.37
13 19 0.63
ACGTcount: A:0.22, C:0.13, G:0.09, T:0.56
Consensus pattern (13 bp):
TGCTTTATTAATC
Found at i:907 original size:6 final size:6
Alignment explanation
Indices: 896--928 Score: 66
Period size: 6 Copynumber: 5.5 Consensus size: 6
886 TATAATCTGC
896 TTTAGA TTTAGA TTTAGA TTTAGA TTTAGA TTT
1 TTTAGA TTTAGA TTTAGA TTTAGA TTTAGA TTT
929 GCTTTGCTTT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 27 1.00
ACGTcount: A:0.30, C:0.00, G:0.15, T:0.55
Consensus pattern (6 bp):
TTTAGA
Found at i:6924 original size:102 final size:98
Alignment explanation
Indices: 6760--6951 Score: 262
Period size: 102 Copynumber: 1.9 Consensus size: 98
6750 TACCCGACAA
*
6760 TCAAAGTCCTCAAACACAAGGGCATTCATAAGCCCCTAAACATAGAGGAATCTATATCAAAGTCC
1 TCAAAGTCCTCAAACACAAGGGCATCCATAAGCCCCTAAACATAGAGGAATCTATATCAAAGTCC
*
6825 CCAAACACATATAACACAGGGGCAACTCTCTTT
66 CCAAACACATATAACACAAGGGCAACTCTCTTT
* * *
6858 TCAAAGTCCTCAAGCACAAGGGCATCCATACTAAAGTCCCTAAACATAGAGGCA-C-ATATACTA
1 TCAAAGTCCTCAAACACAAGGGCATCC--A-T-AAGCCCCTAAACATAGAGGAATCTATAT-C-A
*
6921 AAGTCCCTAAACACATATAACACAAGGGCAA
60 AAGTCCCCAAACACATATAACACAAGGGCAA
6952 TTTTCTTCTT
Statistics
Matches: 82, Mismatches: 6, Indels: 8
0.85 0.06 0.08
Matches are distributed among these distances:
98 25 0.30
100 5 0.06
101 3 0.04
102 49 0.60
ACGTcount: A:0.41, C:0.27, G:0.14, T:0.19
Consensus pattern (98 bp):
TCAAAGTCCTCAAACACAAGGGCATCCATAAGCCCCTAAACATAGAGGAATCTATATCAAAGTCC
CCAAACACATATAACACAAGGGCAACTCTCTTT
Found at i:12432 original size:93 final size:93
Alignment explanation
Indices: 12273--12458 Score: 363
Period size: 93 Copynumber: 2.0 Consensus size: 93
12263 AAAAAAAATG
12273 AGTGTTAGTAACCCCTAAATCATGAACACTTCTAAGGTTAGTAACATTGTTTTCTTAAAAATAAG
1 AGTGTTAGTAACCCCTAAATCATGAACACTTCTAAGGTTAGTAACATTGTTTTCTTAAAAATAAG
*
12338 CCATCCTTTTTAAACCTATTCTAATTTT
66 CCATCCTTTTTAAACCCATTCTAATTTT
12366 AGTGTTAGTAACCCCTAAATCATGAACACTTCTAAGGTTAGTAACATTGTTTTCTTAAAAATAAG
1 AGTGTTAGTAACCCCTAAATCATGAACACTTCTAAGGTTAGTAACATTGTTTTCTTAAAAATAAG
12431 CCATCCTTTTTAAACCCATTCTAATTTT
66 CCATCCTTTTTAAACCCATTCTAATTTT
12459 TGATAAATAT
Statistics
Matches: 92, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
93 92 1.00
ACGTcount: A:0.33, C:0.19, G:0.10, T:0.38
Consensus pattern (93 bp):
AGTGTTAGTAACCCCTAAATCATGAACACTTCTAAGGTTAGTAACATTGTTTTCTTAAAAATAAG
CCATCCTTTTTAAACCCATTCTAATTTT
Found at i:21813 original size:19 final size:18
Alignment explanation
Indices: 21789--21828 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
21779 TTGAAGATTT
*
21789 ATTGAAGATAATTTGAAGA
1 ATTGAAGACAA-TTGAAGA
*
21808 ATTGAAGACCATTGAAGA
1 ATTGAAGACAATTGAAGA
21826 ATT
1 ATT
21829 ATTTCACGAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
18 10 0.53
19 9 0.47
ACGTcount: A:0.45, C:0.05, G:0.20, T:0.30
Consensus pattern (18 bp):
ATTGAAGACAATTGAAGA
Found at i:26948 original size:10 final size:10
Alignment explanation
Indices: 26933--26957 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
26923 GTTTCTGCAC
26933 AATTCCAGAA
1 AATTCCAGAA
26943 AATTCCAGAA
1 AATTCCAGAA
26953 AATTC
1 AATTC
26958 TAGAGTCCTC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.48, C:0.20, G:0.08, T:0.24
Consensus pattern (10 bp):
AATTCCAGAA
Found at i:27903 original size:6 final size:6
Alignment explanation
Indices: 27892--27924 Score: 66
Period size: 6 Copynumber: 5.5 Consensus size: 6
27882 ATTAATCTGC
27892 TTTAGA TTTAGA TTTAGA TTTAGA TTTAGA TTT
1 TTTAGA TTTAGA TTTAGA TTTAGA TTTAGA TTT
27925 GCTTTGCTTT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 27 1.00
ACGTcount: A:0.30, C:0.00, G:0.15, T:0.55
Consensus pattern (6 bp):
TTTAGA
Found at i:32522 original size:23 final size:25
Alignment explanation
Indices: 32483--32529 Score: 71
Period size: 24 Copynumber: 2.0 Consensus size: 25
32473 ATATGCTCAT
32483 ATTGATCGATTGATTTG-ATTTTTG
1 ATTGATCGATTGATTTGAATTTTTG
*
32507 ATTGAT-GATTGCTTTGAATTTTT
1 ATTGATCGATTGATTTGAATTTTT
32530 AAGAATGTTT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 9 0.43
24 12 0.57
ACGTcount: A:0.21, C:0.04, G:0.19, T:0.55
Consensus pattern (25 bp):
ATTGATCGATTGATTTGAATTTTTG
Found at i:46236 original size:197 final size:196
Alignment explanation
Indices: 45883--46278 Score: 668
Period size: 197 Copynumber: 2.0 Consensus size: 196
45873 GCTTTAATTG
* * *
45883 CGAAGGATTGAAGACAAGCCCTGAAGAAGCCCATAAGCTATGGAATTTTGGATATTTCATATGGG
1 CGAAGAATTGAAGACAAGCCCTGAAGAAGCCCAGAAGCTATGGAATTTTGGATATTTCATATGCG
*
45948 ATAATACTCAGCCCATAGAAGCCTACAATTGGAGTTAAAATCCCAATTTGTGCCACCTATATCCA
66 ATAATACTCAGCCCATAGAAGCCCACAATTGGAGTTAAAATCCCAATTTGTGCCACCTATATCCA
46013 AGGAAATATCCAACTTCCATAATAATCCCGATACTAGTCCTAGTTGGATTAGGATTCAGCGCAGT
131 AGGAAATATCCAACTTCCA-AATAATCCCGATACTAGTCCTAGTTGGATTAGGATTCAGCGCAGT
46078 CT
195 CT
* * *
46080 CGAAGAATTGAAGACAAGCCCTGAAGAGGCCCGGAAGCTATGGAATTTTGGATATTTTATATGCG
1 CGAAGAATTGAAGACAAGCCCTGAAGAAGCCCAGAAGCTATGGAATTTTGGATATTTCATATGCG
*
46145 ATAATACTCAGCCCATATAAGCCCACAATTGGAGTTAAAATCCCAATTTGTGCCACCTATATCCA
66 ATAATACTCAGCCCATAGAAGCCCACAATTGGAGTTAAAATCCCAATTTGTGCCACCTATATCCA
* *
46210 AGGAAATATCCAATCTTCGC-AATAATCCTGATAGTAGTCCTAGTTGGATTAGGATTCAGCGCAG
131 AGGAAATATCCAA-CTTC-CAAATAATCCCGATACTAGTCCTAGTTGGATTAGGATTCAGCGCAG
46274 TCT
194 TCT
46277 CG
1 CG
46279 GTAAAAAAGT
Statistics
Matches: 187, Mismatches: 10, Indels: 4
0.93 0.05 0.02
Matches are distributed among these distances:
197 182 0.97
198 4 0.02
199 1 0.01
ACGTcount: A:0.33, C:0.21, G:0.19, T:0.27
Consensus pattern (196 bp):
CGAAGAATTGAAGACAAGCCCTGAAGAAGCCCAGAAGCTATGGAATTTTGGATATTTCATATGCG
ATAATACTCAGCCCATAGAAGCCCACAATTGGAGTTAAAATCCCAATTTGTGCCACCTATATCCA
AGGAAATATCCAACTTCCAAATAATCCCGATACTAGTCCTAGTTGGATTAGGATTCAGCGCAGTC
T
Found at i:54335 original size:19 final size:19
Alignment explanation
Indices: 54311--54349 Score: 60
Period size: 19 Copynumber: 2.1 Consensus size: 19
54301 TTTTTTCCTA
54311 TAAATGATTGAAAGTATTT
1 TAAATGATTGAAAGTATTT
* *
54330 TAAATGATTGGAAGTGTTT
1 TAAATGATTGAAAGTATTT
54349 T
1 T
54350 GTTGTTTGTA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.36, C:0.00, G:0.21, T:0.44
Consensus pattern (19 bp):
TAAATGATTGAAAGTATTT
Found at i:56412 original size:38 final size:38
Alignment explanation
Indices: 56366--56455 Score: 164
Period size: 38 Copynumber: 2.4 Consensus size: 38
56356 GACACGATCA
56366 GGGTTAAACTGTTGGTAAGAGTGGACCCGTGCCTCAGG
1 GGGTTAAACTGTTGGTAAGAGTGGACCCGTGCCTCAGG
*
56404 GGGTTAAACTGTTAGTAAGAGTGGACCCGTGCCTCAGG
1 GGGTTAAACTGTTGGTAAGAGTGGACCCGTGCCTCAGG
56442 GGGTT-AACTGTTGG
1 GGGTTAAACTGTTGG
56456 CTAGATTGTG
Statistics
Matches: 50, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
37 8 0.16
38 42 0.84
ACGTcount: A:0.21, C:0.17, G:0.37, T:0.26
Consensus pattern (38 bp):
GGGTTAAACTGTTGGTAAGAGTGGACCCGTGCCTCAGG
Found at i:56477 original size:6 final size:6
Alignment explanation
Indices: 56459--56489 Score: 53
Period size: 6 Copynumber: 5.2 Consensus size: 6
56449 CTGTTGGCTA
*
56459 GATTGT GACTGT GATTGT GATTGT GATTGT G
1 GATTGT GATTGT GATTGT GATTGT GATTGT G
56490 GTGCAGTCTG
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.16, C:0.03, G:0.35, T:0.45
Consensus pattern (6 bp):
GATTGT
Found at i:59638 original size:15 final size:16
Alignment explanation
Indices: 59618--59651 Score: 52
Period size: 15 Copynumber: 2.2 Consensus size: 16
59608 GTTTTCAAAG
*
59618 ATTATATGTATTAT-A
1 ATTATATGAATTATGA
59633 ATTATATGAATTATGA
1 ATTATATGAATTATGA
59649 ATT
1 ATT
59652 CTTTTATGGA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 13 0.76
16 4 0.24
ACGTcount: A:0.41, C:0.00, G:0.09, T:0.50
Consensus pattern (16 bp):
ATTATATGAATTATGA
Found at i:59935 original size:38 final size:38
Alignment explanation
Indices: 59849--60034 Score: 302
Period size: 38 Copynumber: 4.9 Consensus size: 38
59839 GGCTGTGCAT
*
59849 AGTGGACCCGTGCCTTAGGGGGTTAAACTGATTGGTAAG
1 AGTGGACCCGTGCCTCAGGGGGTTAAACTG-TTGGTAAG
*
59888 AGTGGACCCGTGCCTCAGGGGGTTAAACTGTTGCTAAG
1 AGTGGACCCGTGCCTCAGGGGGTTAAACTGTTGGTAAG
**
59926 AGTGGACCCGTGCCTCAGGGAATTAAACTGTTGGTAAG
1 AGTGGACCCGTGCCTCAGGGGGTTAAACTGTTGGTAAG
* *
59964 AGTGGACTCGTGCCTCAGGGGGTTAAATTGTTGGTAAG
1 AGTGGACCCGTGCCTCAGGGGGTTAAACTGTTGGTAAG
60002 AGTGGACCCGTGCCTCAGGGGGTT-AACTGTTGG
1 AGTGGACCCGTGCCTCAGGGGGTTAAACTGTTGG
60035 CTAGATTGTG
Statistics
Matches: 136, Mismatches: 11, Indels: 2
0.91 0.07 0.01
Matches are distributed among these distances:
37 8 0.06
38 99 0.73
39 29 0.21
ACGTcount: A:0.22, C:0.18, G:0.35, T:0.25
Consensus pattern (38 bp):
AGTGGACCCGTGCCTCAGGGGGTTAAACTGTTGGTAAG
Found at i:60049 original size:6 final size:6
Alignment explanation
Indices: 60038--60068 Score: 62
Period size: 6 Copynumber: 5.2 Consensus size: 6
60028 CTGTTGGCTA
60038 GATTGT GATTGT GATTGT GATTGT GATTGT G
1 GATTGT GATTGT GATTGT GATTGT GATTGT G
60069 GTGCAGCCTG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 25 1.00
ACGTcount: A:0.16, C:0.00, G:0.35, T:0.48
Consensus pattern (6 bp):
GATTGT
Found at i:60313 original size:12 final size:12
Alignment explanation
Indices: 60296--60329 Score: 68
Period size: 12 Copynumber: 2.8 Consensus size: 12
60286 TGATGATTGA
60296 GCATTGGGGATT
1 GCATTGGGGATT
60308 GCATTGGGGATT
1 GCATTGGGGATT
60320 GCATTGGGGA
1 GCATTGGGGA
60330 GAGTGATCGT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 22 1.00
ACGTcount: A:0.18, C:0.09, G:0.44, T:0.29
Consensus pattern (12 bp):
GCATTGGGGATT
Found at i:61746 original size:19 final size:19
Alignment explanation
Indices: 61722--61758 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
61712 CCTATGTTGG
61722 AGGTTTCTTTCATATATTT
1 AGGTTTCTTTCATATATTT
*
61741 AGGTTTCTTTTATATATT
1 AGGTTTCTTTCATATATT
61759 GATTTAGATT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.22, C:0.08, G:0.11, T:0.59
Consensus pattern (19 bp):
AGGTTTCTTTCATATATTT
Found at i:63881 original size:19 final size:18
Alignment explanation
Indices: 63857--63892 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
63847 TGAAGATTTC
63857 TTGAAGATAATTTGAAGAT
1 TTGAAGATAA-TTGAAGAT
*
63876 TTGAAGATCATTGAAGA
1 TTGAAGATAATTGAAGA
63893 ATTATTTCAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 7 0.44
19 9 0.56
ACGTcount: A:0.42, C:0.03, G:0.22, T:0.33
Consensus pattern (18 bp):
TTGAAGATAATTGAAGAT
Found at i:65187 original size:13 final size:14
Alignment explanation
Indices: 65169--65198 Score: 53
Period size: 13 Copynumber: 2.2 Consensus size: 14
65159 TCTTGATTGC
65169 TTACTTAGTTA-AT
1 TTACTTAGTTAGAT
65182 TTACTTAGTTAGAT
1 TTACTTAGTTAGAT
65196 TTA
1 TTA
65199 ATTTTAATTC
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 11 0.69
14 5 0.31
ACGTcount: A:0.30, C:0.07, G:0.10, T:0.53
Consensus pattern (14 bp):
TTACTTAGTTAGAT
Found at i:79773 original size:50 final size:50
Alignment explanation
Indices: 79695--82403 Score: 2636
Period size: 50 Copynumber: 54.7 Consensus size: 50
79685 AAGGTGCTGC
* * * *
79695 TTCCAAAAATGCCCCTTCCTGGTCTGAAGGTCCCTGTTTTCTTTCTTTGT
1 TTCCCAAAATGCCCCTTCCCGGTCGGAAGGTCCCTGTTTTCTTTATTTGT
* * ** * *
79745 TTCCCAAAATGCCCCTTCCCGGTCTGAAGGACTTTGTCTTCTTTGTTTGT
1 TTCCCAAAATGCCCCTTCCCGGTCGGAAGGTCCCTGTTTTCTTTATTTGT
* * *
79795 TTCCCAAAATGCCCCTTCTCGGTCGGAAGATCCCTGTTTTCTTTGTTTGT
1 TTCCCAAAATGCCCCTTCCCGGTCGGAAGGTCCCTGTTTTCTTTATTTGT
* * *
79845 TTCCCAAGATGCCCCTTCCCGGTCGGAAGGTCCCTGTTTTGTTTGTTTGT
1 TTCCCAAAATGCCCCTTCCCGGTCGGAAGGTCCCTGTTTTCTTTATTTGT
** * * **
79895 TTCCCAAAATGCCCCTTCCAAGTCAGAAGGTCCCTGATTTCTTTATTCCT
1 TTCCCAAAATGCCCCTTCCCGGTCGGAAGGTCCCTGTTTTCTTTATTTGT
* * *
79945 TTCCCAAGATGCCCCTACCCGGTCGGAAGGTCCCTGTTCTCTTTATTTGT
1 TTCCCAAAATGCCCCTTCCCGGTCGGAAGGTCCCTGTTTTCTTTATTTGT
* * * ** *
79995 TTCCAAAAATGCCCCTTGCCGGTCGGAAGGACTTTGTTCTCTTTATTTGT
1 TTCCCAAAATGCCCCTTCCCGGTCGGAAGGTCCCTGTTTTCTTTATTTGT
*
80045 TTCCCAAAATGCCCCTTCCCGGTCGGAAGG-CCCTTGTTTTCTTTGTTTG-
1 TTCCCAAAATGCCCCTTCCCGGTCGGAAGGTCCC-TGTTTTCTTTATTTGT
* * * * **
80094 TTCCCTAAAATGCCACTTCCCGGTCGGAAGGTCCTTGTGATTC--AAAATG-
1 TTCCC-AAAATGCCCCTTCCCGGTCGGAAGGTCCCTGT-TTTCTTTATTTGT
* * * ** ** ** * * *
80143 -ACCC----TTCTCGGT--CGG-AAG-A-TCCCTGT-TTTCTCACTT-TGT-T
1 TTCCCAAAATGCCCCTTCCCGGTCGGAAGGTCC-CTGTTT-TC-TTTATTTGT
* * *** * * * *** * * ** ** * * *
80183 TCCCAAAATGCCCCTTCCCGGTCGGAAGGTCCTTGTGTTCTCTGT-TTG-T
1 TTCCCAAAATGCCCCTTCCCGGTCGGAAGGTC-CCTGTTTTCTTTATTTGT
* * * * * * *
80232 TTCCAAAAATGCCCCTTCCTGGTTGGAAGGTCTCTGTTCTCTTTGTTAGT
1 TTCCCAAAATGCCCCTTCCCGGTCGGAAGGTCCCTGTTTTCTTTATTTGT
**
80282 TTCCCAAAATGCCCCTTCAAGGTCGGAAGGTCCCTGTTTTCTTTATTTGT
1 TTCCCAAAATGCCCCTTCCCGGTCGGAAGGTCCCTGTTTTCTTTATTTGT
* * *
80332 TT-CCAAAACTGCCCCTTCCCGGTCGGAAGGTCTCTCTTCTCTTTATTTGT
1 TTCCCAAAA-TGCCCCTTCCCGGTCGGAAGGTCCCTGTTTTCTTTATTTGT
* ** * *
80382 TTCCCAAAATACCCCTTCCCGGTCAAAAGGACCCTGTTTTCTTTGTTTGT
1 TTCCCAAAATGCCCCTTCCCGGTCGGAAGGTCCCTGTTTTCTTTATTTGT
* * * *
80432 TTCCCGAAATGCCCCTT-CCGGTCGGAAGGTCCTTGTTTTCTCTGTTTGT
1 TTCCCAAAATGCCCCTTCCCGGTCGGAAGGTCCCTGTTTTCTTTATTTGT
* * * * ** *
80481 TTCCAAAAATGCCCCTTCCTGGTTGGAAGGTCTCTGTTCACTTTCTTTGT
1 TTCCCAAAATGCCCCTTCCCGGTCGGAAGGTCCCTGTTTTCTTTATTTGT
* * * *
80531 TTCCCGAAATGCCCCTTCCTGGTCGGAAGGTCTCTGTTCTCTTTATTTGT
1 TTCCCAAAATGCCCCTTCCCGGTCGGAAGGTCCCTGTTTTCTTTATTTGT
* ** ** * *
80581 TTCGCAAAATGTACCTTCCCGGTCAAAAGGTCCCTGTTTTATTTGTTTGT
1 TTCCCAAAATGCCCCTTCCCGGTCGGAAGGTCCCTGTTTTCTTTATTTGT
* * * * *
80631 TTCCCAAAATGCCCCTTCCCGGTCGGATGGTCCTTATGTTCTTTGTTTGT
1 TTCCCAAAATGCCCCTTCCCGGTCGGAAGGTCCCTGTTTTCTTTATTTGT
* * *
80681 TT-CCAAAATGCCACTTCCCGGTCGGAAGATCCCTGTTTTCTTTCTTTGT
1 TTCCCAAAATGCCCCTTCCCGGTCGGAAGGTCCCTGTTTTCTTTATTTGT
* *
80730 TTCCCAAAATGCCCCTTCCCGGTCGGAAGGTCCTTGTTTTCTCTATTTGT
1 TTCCCAAAATGCCCCTTCCCGGTCGGAAGGTCCCTGTTTTCTTTATTTGT
* * * * *
80780 TTCCAAAAATGCCCCTTCCTGGTTGGAAGGTCTCTGTTCTCTTTATTTGT
1 TTCCCAAAATGCCCCTTCCCGGTCGGAAGGTCCCTGTTTTCTTTATTTGT
*
80830 TT-CAAATAATG-CCCTTCCCGGTCGGAAGGTCCCTGTTTTCTTTATTTGT
1 TTCCCAA-AATGCCCCTTCCCGGTCGGAAGGTCCCTGTTTTCTTTATTTGT
* * * * *
80879 TTCCCGAAATGCCCCTTCCCGGTCGGAAGGTTCTTGTTTTCTCTGTTTGT
1 TTCCCAAAATGCCCCTTCCCGGTCGGAAGGTCCCTGTTTTCTTTATTTGT
* * * * * *
80929 TTCCAAAAACGCCCCTTCCTGGTTGGAAGGTCTCTGTTCTCTTTATTTGT
1 TTCCCAAAATGCCCCTTCCCGGTCGGAAGGTCCCTGTTTTCTTTATTTGT
* * * *
80979 TTCCCAAAATGTCCCTTCCCGGACGAAAGGTCCCTGTTTTGTTTATTTGT
1 TTCCCAAAATGCCCCTTCCCGGTCGGAAGGTCCCTGTTTTCTTTATTTGT
* ** * * * *
81029 TTCCAAAAATGTTCCTTCCCAGTCGGATGGTCTCTGTTCTCTTTATTTGT
1 TTCCCAAAATGCCCCTTCCCGGTCGGAAGGTCCCTGTTTTCTTTATTTGT
* * * * * * ** * * *
81079 TTCGCAAAATGCCGCATACCAGT-TGAAACTACCCTGTTTTCCTTGTTTAT
1 TTCCCAAAATGCCCCTTCCCGGTCGGAAGGT-CCCTGTTTTCTTTATTTGT
* * ***
81129 TTCCCAAAAT-CCCTCTTCCCGGTCGGAAGGTCCTTGTGTTCTTTGCATGT
1 TTCCCAAAATGCCC-CTTCCCGGTCGGAAGGTCCCTGTTTTCTTTATTTGT
* * * ** * *
81179 TT-CCAAAATGCCCATTCCCGGTCGTAAGATTGCTGTTTACTTTTTTTGT
1 TTCCCAAAATGCCCCTTCCCGGTCGGAAGGTCCCTGTTTTCTTTATTTGT
* *
81228 TTCCCAAAATGCCCCTTCCCGGTCGGAAGGTCCTTGTTTTCTCTGA-TTGT
1 TTCCCAAAATGCCCCTTCCCGGTCGGAAGGTCCCTGTTTTCT-TTATTTGT
* * * * *
81278 TTCCAAAAATGCCCCTTCCAGGTTGGAAGGTCTCTGTTCTCTTTATTTGT
1 TTCCCAAAATGCCCCTTCCCGGTCGGAAGGTCCCTGTTTTCTTTATTTGT
* *
81328 TTCCCAAAATGCCCCTTCCCGGTCGGAATGTCTCTGTTTTCTTTATTTGT
1 TTCCCAAAATGCCCCTTCCCGGTCGGAAGGTCCCTGTTTTCTTTATTTGT
* * * *
81378 TTCCCAAAACGCCCCTTCCCAGTCGGAAGGTCCTTGTTTTCTTTGTTTGT
1 TTCCCAAAATGCCCCTTCCCGGTCGGAAGGTCCCTGTTTTCTTTATTTGT
* * * *
81428 TTCCCAAGATGCTCCTTCCCGGTCGGAAGGTCCCTATTTTCTTTATTTAT
1 TTCCCAAAATGCCCCTTCCCGGTCGGAAGGTCCCTGTTTTCTTTATTTGT
* * * * * *
81478 TTCCAAAAATGCCCATTCCCCGTCTGAAGGTCGCTGTTCTCTTTATTTGT
1 TTCCCAAAATGCCCCTTCCCGGTCGGAAGGTCCCTGTTTTCTTTATTTGT
* * * **
81528 TTCCCTAAATGCCTCTTCCCGGTCAGAAAATCCCTGTTTTCTTTATTTGT
1 TTCCCAAAATGCCCCTTCCCGGTCGGAAGGTCCCTGTTTTCTTTATTTGT
* * * * *
81578 TTCCCAAAACGCCCTTTCCCGGTCGGAAGGTTCTTGTTTTCTTTGTTTGT
1 TTCCCAAAATGCCCCTTCCCGGTCGGAAGGTCCCTGTTTTCTTTATTTGT
* * *
81628 TTCCCAAGATGCCCCTTCCCGGTCGGAAGGTCCCTATTTTCTTTGTTTGT
1 TTCCCAAAATGCCCCTTCCCGGTCGGAAGGTCCCTGTTTTCTTTATTTGT
* * * * * *
81678 TACCCAAAATTCCCCTTCCAGGTCAG-AGGTCCCTATTTTCTTTATTCGT
1 TTCCCAAAATGCCCCTTCCCGGTCGGAAGGTCCCTGTTTTCTTTATTTGT
* *
81727 TTCCCAAAATGACCCTTCCCGGTCAGAAGGTCCCTGTTTTCTTTATTTGT
1 TTCCCAAAATGCCCCTTCCCGGTCGGAAGGTCCCTGTTTTCTTTATTTGT
* * * ** *
81777 TTCCAAAAATACGCCTTCCCGGTCAAAAGGTCCCTGTTCTCTTTATTTGT
1 TTCCCAAAATGCCCCTTCCCGGTCGGAAGGTCCCTGTTTTCTTTATTTGT
* ** * *
81827 TTCCCAAAATTCCCCTTCCCGGTCAAAAGGTCCCTGTTTTATTTGTTTGT
1 TTCCCAAAATGCCCCTTCCCGGTCGGAAGGTCCCTGTTTTCTTTATTTGT
* * * *
81877 TTCCCAAAATGCCCCTTCCCGGTCGGAAGGTCCTTATGTTCTTTGTTTGT
1 TTCCCAAAATGCCCCTTCCCGGTCGGAAGGTCCCTGTTTTCTTTATTTGT
* * *
81927 TT-CCAAAATGCCACTTCCCGGTCGGAAGATCCCTGTTTTCTTTCTTTGT
1 TTCCCAAAATGCCCCTTCCCGGTCGGAAGGTCCCTGTTTTCTTTATTTGT
* *
81976 TTCCCAAAATGCCCCTTCCCGGTCGGAAGGTCCTTGTTTT-TCTATTTGT
1 TTCCCAAAATGCCCCTTCCCGGTCGGAAGGTCCCTGTTTTCTTTATTTGT
* * * * *
82025 TTCCAAAAATGCCCCTTCCTGGTTGGAAGGTCTCTGTTCTCTTTATTTGT
1 TTCCCAAAATGCCCCTTCCCGGTCGGAAGGTCCCTGTTTTCTTTATTTGT
* *
82075 TT-CAAATAATGCCCCTTCCCGGTCGGAAGGTCTCTGTTTTCTTTATTTGT
1 TTCCCAA-AATGCCCCTTCCCGGTCGGAAGGTCCCTGTTTTCTTTATTTGT
* ** *
82125 GTCCCAAAATGCCCCTTCCCGGTCGGAAGGTCCCTACTTTCTTTATTT-A
1 TTCCCAAAATGCCCCTTCCCGGTCGGAAGGTCCCTGTTTTCTTTATTTGT
* * *
82174 TTCCAAAAATGCCCCTTCCCAGTCAGAAGGTCCCTGTTTTC--T-TTTGT
1 TTCCCAAAATGCCCCTTCCCGGTCGGAAGGTCCCTGTTTTCTTTATTTGT
* * *
82221 TTCCAAAAATGCCCCTTCCCGGTCGGAAGGTCCATGTTTTCTTTATTCGT
1 TTCCCAAAATGCCCCTTCCCGGTCGGAAGGTCCCTGTTTTCTTTATTTGT
* *
82271 TTCCTAAAATGCCCCTTCCCGGTCGGAAGGTCCCTG--TTGTTTACTTTTGT
1 TTCCCAAAATGCCCCTTCCCGGTCGGAAGGTCCCTGTTTTCTTTA--TTTGT
* * * * * * *
82321 TT-CCAAAACAGCCCATTCCTGGTTGGAATGTCCCAGTTTTCTTTCTTTGT
1 TTCCCAAAA-TGCCCCTTCCCGGTCGGAAGGTCCCTGTTTTCTTTATTTGT
* *
82371 TCCCCAAAATGCCCCTTCCCGGTAGGAAGGTCC
1 TTCCCAAAATGCCCCTTCCCGGTCGGAAGGTCC
82404 AGTTTTCGCT
Statistics
Matches: 2174, Mismatches: 432, Indels: 106
0.80 0.16 0.04
Matches are distributed among these distances:
37 1 0.00
38 5 0.00
39 2 0.00
40 2 0.00
41 5 0.00
43 3 0.00
45 2 0.00
46 3 0.00
47 40 0.02
48 19 0.01
49 378 0.17
50 1682 0.77
51 27 0.01
52 5 0.00
ACGTcount: A:0.16, C:0.28, G:0.18, T:0.38
Consensus pattern (50 bp):
TTCCCAAAATGCCCCTTCCCGGTCGGAAGGTCCCTGTTTTCTTTATTTGT
Found at i:79836 original size:100 final size:100
Alignment explanation
Indices: 79695--82403 Score: 2943
Period size: 100 Copynumber: 27.3 Consensus size: 100
79685 AAGGTGCTGC
* * * *
79695 TTCCAAAAATGCCCCTTCCTGGTCTGAAGGTCCCTGTTTTCTTTCTTTGTTTCCCAAAATGCCCC
1 TTCCCAAAATGCCCCTTCCCGGTCGGAAGGTCCCTGTTTTCTTTATTTGTTTCCCAAAATGCCCC
* * ** * *
79760 TTCCCGGTCTGAAGGACTTTGTCTTCTTTGTTTGT
66 TTCCCGGTCGGAAGGTCCCTGTTTTCTTTATTTGT
* * * *
79795 TTCCCAAAATGCCCCTTCTCGGTCGGAAGATCCCTGTTTTCTTTGTTTGTTTCCCAAGATGCCCC
1 TTCCCAAAATGCCCCTTCCCGGTCGGAAGGTCCCTGTTTTCTTTATTTGTTTCCCAAAATGCCCC
* *
79860 TTCCCGGTCGGAAGGTCCCTGTTTTGTTTGTTTGT
66 TTCCCGGTCGGAAGGTCCCTGTTTTCTTTATTTGT
** * * ** *
79895 TTCCCAAAATGCCCCTTCCAAGTCAGAAGGTCCCTGATTTCTTTATTCCTTTCCCAAGATGCCCC
1 TTCCCAAAATGCCCCTTCCCGGTCGGAAGGTCCCTGTTTTCTTTATTTGTTTCCCAAAATGCCCC
* *
79960 TACCCGGTCGGAAGGTCCCTGTTCTCTTTATTTGT
66 TTCCCGGTCGGAAGGTCCCTGTTTTCTTTATTTGT
* * * ** *
79995 TTCCAAAAATGCCCCTTGCCGGTCGGAAGGACTTTGTTCTCTTTATTTGTTTCCCAAAATGCCCC
1 TTCCCAAAATGCCCCTTCCCGGTCGGAAGGTCCCTGTTTTCTTTATTTGTTTCCCAAAATGCCCC
*
80060 TTCCCGGTCGGAAGG-CCCTTGTTTTCTTTGTTTG-
66 TTCCCGGTCGGAAGGTCCC-TGTTTTCTTTATTTGT
* * * *
80094 TTCCCTAAAATGCCACTTCCCGGTCGGAAGGT--C------C--T-TGTGATT--CAAAATGACC
1 TTCCC-AAAATGCCCCTTCCCGGTCGGAAGGTCCCTGTTTTCTTTATTTGTTTCCCAAAATGCCC
* * *
80146 CTTCTCGGTCGGAAGATCCCTGTTTTC-TCACTTTGT
65 CTTCCCGGTCGGAAGGTCCCTGTTTTCTTTA-TTTGT
* * * * *
80182 TTCCCAAAATGCCCCTTCCCGGTCGGAAGGTCCTTGTGTTCTCTGTTTGTTTCCAAAAATGCCCC
1 TTCCCAAAATGCCCCTTCCCGGTCGGAAGGTCCCTGTTTTCTTTATTTGTTTCCCAAAATGCCCC
* * * * * *
80247 TTCCTGGTTGGAAGGTCTCTGTTCTCTTTGTTAGT
66 TTCCCGGTCGGAAGGTCCCTGTTTTCTTTATTTGT
**
80282 TTCCCAAAATGCCCCTTCAAGGTCGGAAGGTCCCTGTTTTCTTTATTTGTTT-CCAAAACTGCCC
1 TTCCCAAAATGCCCCTTCCCGGTCGGAAGGTCCCTGTTTTCTTTATTTGTTTCCCAAAA-TGCCC
* * *
80346 CTTCCCGGTCGGAAGGTCTCTCTTCTCTTTATTTGT
65 CTTCCCGGTCGGAAGGTCCCTGTTTTCTTTATTTGT
* ** * * *
80382 TTCCCAAAATACCCCTTCCCGGTCAAAAGGACCCTGTTTTCTTTGTTTGTTTCCCGAAATGCCCC
1 TTCCCAAAATGCCCCTTCCCGGTCGGAAGGTCCCTGTTTTCTTTATTTGTTTCCCAAAATGCCCC
* * *
80447 TT-CCGGTCGGAAGGTCCTTGTTTTCTCTGTTTGT
66 TTCCCGGTCGGAAGGTCCCTGTTTTCTTTATTTGT
* * * * ** * *
80481 TTCCAAAAATGCCCCTTCCTGGTTGGAAGGTCTCTGTTCACTTTCTTTGTTTCCCGAAATGCCCC
1 TTCCCAAAATGCCCCTTCCCGGTCGGAAGGTCCCTGTTTTCTTTATTTGTTTCCCAAAATGCCCC
* * *
80546 TTCCTGGTCGGAAGGTCTCTGTTCTCTTTATTTGT
66 TTCCCGGTCGGAAGGTCCCTGTTTTCTTTATTTGT
* ** ** * *
80581 TTCGCAAAATGTACCTTCCCGGTCAAAAGGTCCCTGTTTTATTTGTTTGTTTCCCAAAATGCCCC
1 TTCCCAAAATGCCCCTTCCCGGTCGGAAGGTCCCTGTTTTCTTTATTTGTTTCCCAAAATGCCCC
* * * * *
80646 TTCCCGGTCGGATGGTCCTTATGTTCTTTGTTTGT
66 TTCCCGGTCGGAAGGTCCCTGTTTTCTTTATTTGT
* * *
80681 TT-CCAAAATGCCACTTCCCGGTCGGAAGATCCCTGTTTTCTTTCTTTGTTTCCCAAAATGCCCC
1 TTCCCAAAATGCCCCTTCCCGGTCGGAAGGTCCCTGTTTTCTTTATTTGTTTCCCAAAATGCCCC
* *
80745 TTCCCGGTCGGAAGGTCCTTGTTTTCTCTATTTGT
66 TTCCCGGTCGGAAGGTCCCTGTTTTCTTTATTTGT
* * * * * *
80780 TTCCAAAAATGCCCCTTCCTGGTTGGAAGGTCTCTGTTCTCTTTATTTGTTT-CAAATAATG-CC
1 TTCCCAAAATGCCCCTTCCCGGTCGGAAGGTCCCTGTTTTCTTTATTTGTTTCCCAA-AATGCCC
80843 CTTCCCGGTCGGAAGGTCCCTGTTTTCTTTATTTGT
65 CTTCCCGGTCGGAAGGTCCCTGTTTTCTTTATTTGT
* * * * * * *
80879 TTCCCGAAATGCCCCTTCCCGGTCGGAAGGTTCTTGTTTTCTCTGTTTGTTTCCAAAAACGCCCC
1 TTCCCAAAATGCCCCTTCCCGGTCGGAAGGTCCCTGTTTTCTTTATTTGTTTCCCAAAATGCCCC
* * * *
80944 TTCCTGGTTGGAAGGTCTCTGTTCTCTTTATTTGT
66 TTCCCGGTCGGAAGGTCCCTGTTTTCTTTATTTGT
* * * * * **
80979 TTCCCAAAATGTCCCTTCCCGGACGAAAGGTCCCTGTTTTGTTTATTTGTTTCCAAAAATGTTCC
1 TTCCCAAAATGCCCCTTCCCGGTCGGAAGGTCCCTGTTTTCTTTATTTGTTTCCCAAAATGCCCC
* * * *
81044 TTCCCAGTCGGATGGTCTCTGTTCTCTTTATTTGT
66 TTCCCGGTCGGAAGGTCCCTGTTTTCTTTATTTGT
* * * * * * ** * * *
81079 TTCGCAAAATGCCGCATACCAGT-TGAAACTACCCTGTTTTCCTTGTTTATTTCCCAAAAT-CCC
1 TTCCCAAAATGCCCCTTCCCGGTCGGAAGGT-CCCTGTTTTCTTTATTTGTTTCCCAAAATGCCC
* * ***
81142 TCTTCCCGGTCGGAAGGTCCTTGTGTTCTTTGCATGT
65 -CTTCCCGGTCGGAAGGTCCCTGTTTTCTTTATTTGT
* * * ** * *
81179 TT-CCAAAATGCCCATTCCCGGTCGTAAGATTGCTGTTTACTTTTTTTGTTTCCCAAAATGCCCC
1 TTCCCAAAATGCCCCTTCCCGGTCGGAAGGTCCCTGTTTTCTTTATTTGTTTCCCAAAATGCCCC
* *
81243 TTCCCGGTCGGAAGGTCCTTGTTTTCTCTGA-TTGT
66 TTCCCGGTCGGAAGGTCCCTGTTTTCT-TTATTTGT
* * * * *
81278 TTCCAAAAATGCCCCTTCCAGGTTGGAAGGTCTCTGTTCTCTTTATTTGTTTCCCAAAATGCCCC
1 TTCCCAAAATGCCCCTTCCCGGTCGGAAGGTCCCTGTTTTCTTTATTTGTTTCCCAAAATGCCCC
* *
81343 TTCCCGGTCGGAATGTCTCTGTTTTCTTTATTTGT
66 TTCCCGGTCGGAAGGTCCCTGTTTTCTTTATTTGT
* * * * * *
81378 TTCCCAAAACGCCCCTTCCCAGTCGGAAGGTCCTTGTTTTCTTTGTTTGTTTCCCAAGATGCTCC
1 TTCCCAAAATGCCCCTTCCCGGTCGGAAGGTCCCTGTTTTCTTTATTTGTTTCCCAAAATGCCCC
* *
81443 TTCCCGGTCGGAAGGTCCCTATTTTCTTTATTTAT
66 TTCCCGGTCGGAAGGTCCCTGTTTTCTTTATTTGT
* * * * * * * *
81478 TTCCAAAAATGCCCATTCCCCGTCTGAAGGTCGCTGTTCTCTTTATTTGTTTCCCTAAATGCCTC
1 TTCCCAAAATGCCCCTTCCCGGTCGGAAGGTCCCTGTTTTCTTTATTTGTTTCCCAAAATGCCCC
* **
81543 TTCCCGGTCAGAAAATCCCTGTTTTCTTTATTTGT
66 TTCCCGGTCGGAAGGTCCCTGTTTTCTTTATTTGT
* * * * * *
81578 TTCCCAAAACGCCCTTTCCCGGTCGGAAGGTTCTTGTTTTCTTTGTTTGTTTCCCAAGATGCCCC
1 TTCCCAAAATGCCCCTTCCCGGTCGGAAGGTCCCTGTTTTCTTTATTTGTTTCCCAAAATGCCCC
* *
81643 TTCCCGGTCGGAAGGTCCCTATTTTCTTTGTTTGT
66 TTCCCGGTCGGAAGGTCCCTGTTTTCTTTATTTGT
* * * * * * *
81678 TACCCAAAATTCCCCTTCCAGGTCAG-AGGTCCCTATTTTCTTTATTCGTTTCCCAAAATGACCC
1 TTCCCAAAATGCCCCTTCCCGGTCGGAAGGTCCCTGTTTTCTTTATTTGTTTCCCAAAATGCCCC
*
81742 TTCCCGGTCAGAAGGTCCCTGTTTTCTTTATTTGT
66 TTCCCGGTCGGAAGGTCCCTGTTTTCTTTATTTGT
* * * ** * *
81777 TTCCAAAAATACGCCTTCCCGGTCAAAAGGTCCCTGTTCTCTTTATTTGTTTCCCAAAATTCCCC
1 TTCCCAAAATGCCCCTTCCCGGTCGGAAGGTCCCTGTTTTCTTTATTTGTTTCCCAAAATGCCCC
** * *
81842 TTCCCGGTCAAAAGGTCCCTGTTTTATTTGTTTGT
66 TTCCCGGTCGGAAGGTCCCTGTTTTCTTTATTTGT
* * * * *
81877 TTCCCAAAATGCCCCTTCCCGGTCGGAAGGTCCTTATGTTCTTTGTTTGTTT-CCAAAATGCCAC
1 TTCCCAAAATGCCCCTTCCCGGTCGGAAGGTCCCTGTTTTCTTTATTTGTTTCCCAAAATGCCCC
* *
81941 TTCCCGGTCGGAAGATCCCTGTTTTCTTTCTTTGT
66 TTCCCGGTCGGAAGGTCCCTGTTTTCTTTATTTGT
* * *
81976 TTCCCAAAATGCCCCTTCCCGGTCGGAAGGTCCTTGTTTT-TCTATTTGTTTCCAAAAATGCCCC
1 TTCCCAAAATGCCCCTTCCCGGTCGGAAGGTCCCTGTTTTCTTTATTTGTTTCCCAAAATGCCCC
* * * *
82040 TTCCTGGTTGGAAGGTCTCTGTTCTCTTTATTTGT
66 TTCCCGGTCGGAAGGTCCCTGTTTTCTTTATTTGT
* * *
82075 TT-CAAATAATGCCCCTTCCCGGTCGGAAGGTCTCTGTTTTCTTTATTTGTGTCCCAAAATGCCC
1 TTCCCAA-AATGCCCCTTCCCGGTCGGAAGGTCCCTGTTTTCTTTATTTGTTTCCCAAAATGCCC
** *
82139 CTTCCCGGTCGGAAGGTCCCTACTTTCTTTATTT-A
65 CTTCCCGGTCGGAAGGTCCCTGTTTTCTTTATTTGT
* * * *
82174 TTCCAAAAATGCCCCTTCCCAGTCAGAAGGTCCCTGTTTTC--T-TTTGTTTCCAAAAATGCCCC
1 TTCCCAAAATGCCCCTTCCCGGTCGGAAGGTCCCTGTTTTCTTTATTTGTTTCCCAAAATGCCCC
* *
82236 TTCCCGGTCGGAAGGTCCATGTTTTCTTTATTCGT
66 TTCCCGGTCGGAAGGTCCCTGTTTTCTTTATTTGT
* * *
82271 TTCCTAAAATGCCCCTTCCCGGTCGGAAGGTCCCTG--TTGTTTACTTTTGTTT-CCAAAACAGC
1 TTCCCAAAATGCCCCTTCCCGGTCGGAAGGTCCCTGTTTTCTTTA--TTTGTTTCCCAAAA-TGC
* * * * * *
82333 CCATTCCTGGTTGGAATGTCCCAGTTTTCTTTCTTTGT
63 CCCTTCCCGGTCGGAAGGTCCCTGTTTTCTTTATTTGT
* *
82371 TCCCCAAAATGCCCCTTCCCGGTAGGAAGGTCC
1 TTCCCAAAATGCCCCTTCCCGGTCGGAAGGTCC
82404 AGTTTTCGCT
Statistics
Matches: 2162, Mismatches: 402, Indels: 90
0.81 0.15 0.03
Matches are distributed among these distances:
86 1 0.00
87 59 0.03
88 8 0.00
89 5 0.00
90 1 0.00
92 1 0.00
95 3 0.00
96 47 0.02
97 36 0.02
98 17 0.01
99 609 0.28
100 1369 0.63
101 6 0.00
ACGTcount: A:0.16, C:0.28, G:0.18, T:0.38
Consensus pattern (100 bp):
TTCCCAAAATGCCCCTTCCCGGTCGGAAGGTCCCTGTTTTCTTTATTTGTTTCCCAAAATGCCCC
TTCCCGGTCGGAAGGTCCCTGTTTTCTTTATTTGT
Found at i:80200 original size:87 final size:87
Alignment explanation
Indices: 80049--80219 Score: 247
Period size: 87 Copynumber: 2.0 Consensus size: 87
80039 ATTTGTTTCC
* ***
80049 CAAAATGCCCCTTCCCGGTCGGAAGGCCCTTGTTTTCTTTGTTTGTTCCCTAAAATGCCACTTCC
1 CAAAATGACCCTTCCCGGTCGGAAGGCCCTTGTTTTCTCACTTTGTTCCCTAAAATGCCACTTCC
80114 CGGTCGGAAGGTCCTTGTGATT
66 CGGTCGGAAGGTCCTTGTGATT
* * *
80136 CAAAATGACCCTTCTCGGTCGGAAGATCCC-TGTTTTCTCACTTTGTTTCCC-AAAATGCCCCTT
1 CAAAATGACCCTTCCCGGTCGGAAG-GCCCTTGTTTTCTCACTTTG-TTCCCTAAAATGCCACTT
80199 CCCGGTCGGAAGGTCCTTGTG
64 CCCGGTCGGAAGGTCCTTGTG
80220 TTCTCTGTTT
Statistics
Matches: 75, Mismatches: 7, Indels: 4
0.87 0.08 0.05
Matches are distributed among these distances:
87 67 0.89
88 8 0.11
ACGTcount: A:0.17, C:0.30, G:0.21, T:0.32
Consensus pattern (87 bp):
CAAAATGACCCTTCCCGGTCGGAAGGCCCTTGTTTTCTCACTTTGTTCCCTAAAATGCCACTTCC
CGGTCGGAAGGTCCTTGTGATT
Found at i:80483 original size:249 final size:248
Alignment explanation
Indices: 80136--82403 Score: 2590
Period size: 249 Copynumber: 9.1 Consensus size: 248
80126 CCTTGTGATT
* * * * ***
80136 CAAAATGACCCTTCTCGGTCGGAAGATCCCTGTTTTCTCACTTTGTTTCCCAAAATGCCCCTTCC
1 CAAAATGCCCCTTCCCGGTCGGAAGGTCCTTGTTTTCTTTGTTTGTTTCCCAAAATGCCCCTTCC
* * * * * * *
80201 CGGTCGGAAGGTCCTTGTGTTCTCTGTTTGTTTCCAAAAATGCCCCTTCCTGGTTGGAAGGTCTC
66 CGGTCGGAAGGTCCCTGTTTTCTTTATTTGTTTCCCAAAATGCCCCTTCCCGGTCGGAAGGTC-C
* * * * * * *
80266 TGTTCTCTTTGTTAGTTTCCCAAAATGCCCCTTCAAGGTCGGAAGGTCCCTGTTTTCTTTATTTG
130 TGTTTTCTTTATTTGTTTCCAAAAATGCCCCTTCCAGGTCGGAAGGTCTCTGTTCTCTTTATTTG
* * *
80331 TTTCCAAAACTGCCCCTTCCCGGTCGGAAGGTCTCTCTTCTCTTTATTTGTTTCC
195 TTTCCAAAA-TGCCCCTTCCCGGTCGGAAGGTCCCTGTTTTCTTTATTTGTTTCC
* ** * * *
80386 CAAAATACCCCTTCCCGGTCAAAAGGACCCTGTTTTCTTTGTTTGTTTCCCGAAATGCCCCTT-C
1 CAAAATGCCCCTTCCCGGTCGGAAGGTCCTTGTTTTCTTTGTTTGTTTCCCAAAATGCCCCTTCC
* * * * * *
80450 CGGTCGGAAGGTCCTTGTTTTCTCTGTTTGTTTCCAAAAATGCCCCTTCCTGGTTGGAAGGTCTC
66 CGGTCGGAAGGTCCCTGTTTTCTTTATTTGTTTCCCAAAATGCCCCTTCCCGGTCGGAAGGTC-C
** * ** *
80515 TGTTCACTTTCTTTGTTTCCCGAAATGCCCCTTCCTGGTCGGAAGGTCTCTGTTCTCTTTATTTG
130 TGTTTTCTTTATTTGTTTCCAAAAATGCCCCTTCCAGGTCGGAAGGTCTCTGTTCTCTTTATTTG
** ** * *
80580 TTTCGCAAAATGTACCTTCCCGGTCAAAAGGTCCCTGTTTTATTTGTTTGTTTCC
195 TTTC-CAAAATGCCCCTTCCCGGTCGGAAGGTCCCTGTTTTCTTTATTTGTTTCC
* * * *
80635 CAAAATGCCCCTTCCCGGTCGGATGGTCCTTATGTTCTTTGTTTGTTT-CCAAAATGCCACTTCC
1 CAAAATGCCCCTTCCCGGTCGGAAGGTCCTTGTTTTCTTTGTTTGTTTCCCAAAATGCCCCTTCC
* *
80699 CGGTCGGAAGATCCCTGTTTTCTTTCTTTGTTTCCCAAAATGCCCCTTCCCGGTCGGAAGGTCCT
66 CGGTCGGAAGGTCCCTGTTTTCTTTATTTGTTTCCCAAAATGCCCCTTCCCGGTCGGAAGGTCC-
* * *
80764 TGTTTTCTCTATTTGTTTCCAAAAATGCCCCTTCCTGGTTGGAAGGTCTCTGTTCTCTTTATTTG
130 TGTTTTCTTTATTTGTTTCCAAAAATGCCCCTTCCAGGTCGGAAGGTCTCTGTTCTCTTTATTTG
*
80829 TTTCAAATAATG-CCCTTCCCGGTCGGAAGGTCCCTGTTTTCTTTATTTGTTTCC
195 TTTCCAA-AATGCCCCTTCCCGGTCGGAAGGTCCCTGTTTTCTTTATTTGTTTCC
* * * * *
80883 CGAAATGCCCCTTCCCGGTCGGAAGGTTCTTGTTTTCTCTGTTTGTTTCCAAAAACGCCCCTTCC
1 CAAAATGCCCCTTCCCGGTCGGAAGGTCCTTGTTTTCTTTGTTTGTTTCCCAAAATGCCCCTTCC
* * * * * * *
80948 TGGTTGGAAGGTCTCTGTTCTCTTTATTTGTTTCCCAAAATGTCCCTTCCCGGACGAAAGGTCCC
66 CGGTCGGAAGGTCCCTGTTTTCTTTATTTGTTTCCCAAAATGCCCCTTCCCGGTCGGAAGGT-CC
* ** *
81013 TGTTTTGTTTATTTGTTTCCAAAAATGTTCCTTCCCA-GTCGGATGGTCTCTGTTCTCTTTATTT
130 TGTTTTCTTTATTTGTTTCCAAAAATGCCCCTT-CCAGGTCGGAAGGTCTCTGTTCTCTTTATTT
* * * * * ** * * *
81077 GTTTCGCAAAATGCCGCATACCAGT-TGAAACTACCCTGTTTTCCTTGTTTATTTCC
194 GTTTC-CAAAATGCCCCTTCCCGGTCGGAAGGT-CCCTGTTTTCTTTATTTGTTTCC
* ** *
81133 CAAAAT-CCCTCTTCCCGGTCGGAAGGTCCTTGTGTTCTTTGCATGTTT-CCAAAATGCCCATTC
1 CAAAATGCCC-CTTCCCGGTCGGAAGGTCCTTGTTTTCTTTGTTTGTTTCCCAAAATGCCCCTTC
* * ** * *
81196 CCGGTCGTAAGATTGCTGTTTACTTTTTTTGTTTCCCAAAATGCCCCTTCCCGGTCGGAAGGTCC
65 CCGGTCGGAAGGTCCCTGTTTTCTTTATTTGTTTCCCAAAATGCCCCTTCCCGGTCGGAAGGTCC
* *
81261 TTGTTTTCTCTGA-TTGTTTCCAAAAATGCCCCTTCCAGGTTGGAAGGTCTCTGTTCTCTTTATT
130 -TGTTTTCT-TTATTTGTTTCCAAAAATGCCCCTTCCAGGTCGGAAGGTCTCTGTTCTCTTTATT
* *
81325 TGTTTCCCAAAATGCCCCTTCCCGGTCGGAATGTCTCTGTTTTCTTTATTTGTTTCC
193 TGTTT-CCAAAATGCCCCTTCCCGGTCGGAAGGTCCCTGTTTTCTTTATTTGTTTCC
* * * *
81382 CAAAACGCCCCTTCCCAGTCGGAAGGTCCTTGTTTTCTTTGTTTGTTTCCCAAGATGCTCCTTCC
1 CAAAATGCCCCTTCCCGGTCGGAAGGTCCTTGTTTTCTTTGTTTGTTTCCCAAAATGCCCCTTCC
* * * * * *
81447 CGGTCGGAAGGTCCCTATTTTCTTTATTTATTTCCAAAAATGCCCATTCCCCGTCTGAAGGTCGC
66 CGGTCGGAAGGTCCCTGTTTTCTTTATTTGTTTCCCAAAATGCCCCTTCCCGGTCGGAAGGTC-C
* ** * * * ** * *
81512 TGTTCTCTTTATTTGTTTCCCTAAATGCCTCTTCCCGGTCAGAAAATCCCTGTTTTCTTTATTTG
130 TGTTTTCTTTATTTGTTTCCAAAAATGCCCCTTCCAGGTCGGAAGGTCTCTGTTCTCTTTATTTG
* * * * *
81577 TTTCCCAAAACGCCCTTTCCCGGTCGGAAGGTTCTTGTTTTCTTTGTTTGTTTCC
195 TTT-CCAAAATGCCCCTTCCCGGTCGGAAGGTCCCTGTTTTCTTTATTTGTTTCC
* * * * *
81632 CAAGATGCCCCTTCCCGGTCGGAAGGTCCCTATTTTCTTTGTTTGTTACCCAAAATTCCCCTTCC
1 CAAAATGCCCCTTCCCGGTCGGAAGGTCCTTGTTTTCTTTGTTTGTTTCCCAAAATGCCCCTTCC
* * * * * *
81697 AGGTCAG-AGGTCCCTATTTTCTTTATTCGTTTCCCAAAATGACCCTTCCCGGTCAGAAGGTCCC
66 CGGTCGGAAGGTCCCTGTTTTCTTTATTTGTTTCCCAAAATGCCCCTTCCCGGTCGGAAGGT-CC
* * * ** *
81761 TGTTTTCTTTATTTGTTTCCAAAAATACGCCTTCCCGGTCAAAAGGTCCCTGTTCTCTTTATTTG
130 TGTTTTCTTTATTTGTTTCCAAAAATGCCCCTTCCAGGTCGGAAGGTCTCTGTTCTCTTTATTTG
* ** * *
81826 TTTCCCAAAATTCCCCTTCCCGGTCAAAAGGTCCCTGTTTTATTTGTTTGTTTCC
195 TTT-CCAAAATGCCCCTTCCCGGTCGGAAGGTCCCTGTTTTCTTTATTTGTTTCC
* * *
81881 CAAAATGCCCCTTCCCGGTCGGAAGGTCCTTATGTTCTTTGTTTGTTT-CCAAAATGCCACTTCC
1 CAAAATGCCCCTTCCCGGTCGGAAGGTCCTTGTTTTCTTTGTTTGTTTCCCAAAATGCCCCTTCC
* *
81945 CGGTCGGAAGATCCCTGTTTTCTTTCTTTGTTTCCCAAAATGCCCCTTCCCGGTCGGAAGGTCCT
66 CGGTCGGAAGGTCCCTGTTTTCTTTATTTGTTTCCCAAAATGCCCCTTCCCGGTCGGAAGGTCC-
* * *
82010 TGTTTT-TCTATTTGTTTCCAAAAATGCCCCTTCCTGGTTGGAAGGTCTCTGTTCTCTTTATTTG
130 TGTTTTCTTTATTTGTTTCCAAAAATGCCCCTTCCAGGTCGGAAGGTCTCTGTTCTCTTTATTTG
* * *
82074 TTTCAAATAATGCCCCTTCCCGGTCGGAAGGTCTCTGTTTTCTTTATTTGTGTCC
195 TTTCCAA-AATGCCCCTTCCCGGTCGGAAGGTCCCTGTTTTCTTTATTTGTTTCC
* ** * * *
82129 CAAAATGCCCCTTCCCGGTCGGAAGGTCCCTACTTTCTTTATTT-ATTCCAAAAATGCCCCTTCC
1 CAAAATGCCCCTTCCCGGTCGGAAGGTCCTTGTTTTCTTTGTTTGTTTCCCAAAATGCCCCTTCC
* * *
82193 CAGTCAGAAGGTCCCTGTTTTC--T-TTTGTTTCCAAAAATGCCCCTTCCCGGTCGGAAGGTCCA
66 CGGTCGGAAGGTCCCTGTTTTCTTTATTTGTTTCCCAAAATGCCCCTTCCCGGTCGGAAGGTCC-
* * * * *
82255 TGTTTTCTTTATTCGTTTCCTAAAATGCCCCTTCCCGGTCGGAAGGTCCCTG-T-TGTTTACTTT
130 TGTTTTCTTTATTTGTTTCCAAAAATGCCCCTTCCAGGTCGGAAGGTCTCTGTTCTCTTTA--TT
* * * * * * * *
82318 TGTTTCCAAAACAGCCCATTCCTGGTTGGAATGTCCCAGTTTTCTTTCTTTGTTCCC
193 TGTTTCCAAAA-TGCCCCTTCCCGGTCGGAAGGTCCCTGTTTTCTTTATTTGTTTCC
*
82375 CAAAATGCCCCTTCCCGGTAGGAAGGTCC
1 CAAAATGCCCCTTCCCGGTCGGAAGGTCC
82404 AGTTTTCGCT
Statistics
Matches: 1720, Mismatches: 269, Indels: 62
0.84 0.13 0.03
Matches are distributed among these distances:
244 5 0.00
245 46 0.03
246 113 0.07
247 5 0.00
248 286 0.17
249 902 0.52
250 362 0.21
251 1 0.00
ACGTcount: A:0.16, C:0.28, G:0.18, T:0.39
Consensus pattern (248 bp):
CAAAATGCCCCTTCCCGGTCGGAAGGTCCTTGTTTTCTTTGTTTGTTTCCCAAAATGCCCCTTCC
CGGTCGGAAGGTCCCTGTTTTCTTTATTTGTTTCCCAAAATGCCCCTTCCCGGTCGGAAGGTCCT
GTTTTCTTTATTTGTTTCCAAAAATGCCCCTTCCAGGTCGGAAGGTCTCTGTTCTCTTTATTTGT
TTCCAAAATGCCCCTTCCCGGTCGGAAGGTCCCTGTTTTCTTTATTTGTTTCC
Found at i:86999 original size:11 final size:11
Alignment explanation
Indices: 86985--87018 Score: 61
Period size: 11 Copynumber: 3.2 Consensus size: 11
86975 AATTGCTGCC
86985 AAATTCCAGAA
1 AAATTCCAGAA
86996 AAATTCCAG-A
1 AAATTCCAGAA
87006 AAATTCCAGAA
1 AAATTCCAGAA
87017 AA
1 AA
87019 TTCTAGAGTC
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
10 10 0.45
11 12 0.55
ACGTcount: A:0.56, C:0.18, G:0.09, T:0.18
Consensus pattern (11 bp):
AAATTCCAGAA
Found at i:87010 original size:10 final size:10
Alignment explanation
Indices: 86985--87021 Score: 65
Period size: 10 Copynumber: 3.6 Consensus size: 10
86975 AATTGCTGCC
86985 AAATTCCAGAA
1 AAATTCCAG-A
86996 AAATTCCAGA
1 AAATTCCAGA
87006 AAATTCCAGA
1 AAATTCCAGA
87016 AAATTC
1 AAATTC
87022 TAGAGTCCTC
Statistics
Matches: 26, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
10 17 0.65
11 9 0.35
ACGTcount: A:0.51, C:0.19, G:0.08, T:0.22
Consensus pattern (10 bp):
AAATTCCAGA
Found at i:87889 original size:6 final size:6
Alignment explanation
Indices: 87878--87904 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
87868 TATATTCTGC
87878 TTTAGA TTTAGA TTTAGA TTTAGA TTT
1 TTTAGA TTTAGA TTTAGA TTTAGA TTT
87905 GCTTTGCTTT
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:0.30, C:0.00, G:0.15, T:0.56
Consensus pattern (6 bp):
TTTAGA
Found at i:89858 original size:10 final size:11
Alignment explanation
Indices: 89820--89861 Score: 52
Period size: 10 Copynumber: 3.9 Consensus size: 11
89810 AAATTATGCA
89820 TATTTTTATAGC
1 TATTTTTATA-C
89832 TATTTTTATA-
1 TATTTTTATAC
*
89842 TACTTTT-TAC
1 TATTTTTATAC
89852 TATTTTTATA
1 TATTTTTATA
89862 TGTGTTTTTA
Statistics
Matches: 26, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
9 2 0.08
10 12 0.46
11 2 0.08
12 10 0.38
ACGTcount: A:0.26, C:0.07, G:0.02, T:0.64
Consensus pattern (11 bp):
TATTTTTATAC
Found at i:91367 original size:6 final size:6
Alignment explanation
Indices: 91356--91388 Score: 66
Period size: 6 Copynumber: 5.5 Consensus size: 6
91346 TTAATTCTGC
91356 TTTAGA TTTAGA TTTAGA TTTAGA TTTAGA TTT
1 TTTAGA TTTAGA TTTAGA TTTAGA TTTAGA TTT
91389 GCTTTGCTTT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 27 1.00
ACGTcount: A:0.30, C:0.00, G:0.15, T:0.55
Consensus pattern (6 bp):
TTTAGA
Done.