Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01012907.1 Corchorus capsularis cultivar CVL-1 contig12928, 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: 96549
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Found at i:7083 original size:10 final size:10
Alignment explanation
Indices: 7068--7092 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
7058 GAGGACTCTA
7068 GAATTTTCTG
1 GAATTTTCTG
7078 GAATTTTCTG
1 GAATTTTCTG
7088 GAATT
1 GAATT
7093 GTGCAGCAAC
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:0.24, C:0.08, G:0.20, T:0.48
Consensus pattern (10 bp):
GAATTTTCTG
Found at i:9017 original size:15 final size:15
Alignment explanation
Indices: 8998--9036 Score: 51
Period size: 15 Copynumber: 2.5 Consensus size: 15
8988 GAAAATCCTA
*
8998 AAAAAAAAAAGAAAAG
1 AAAAATAAAA-AAAAG
*
9014 AAAAATAAAACAAAG
1 AAAAATAAAAAAAAG
9029 AAAAATAA
1 AAAAATAA
9037 GGGTTAGTGA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
15 12 0.57
16 9 0.43
ACGTcount: A:0.85, C:0.03, G:0.08, T:0.05
Consensus pattern (15 bp):
AAAAATAAAAAAAAG
Found at i:9293 original size:12 final size:13
Alignment explanation
Indices: 9278--9312 Score: 54
Period size: 12 Copynumber: 2.8 Consensus size: 13
9268 ATTCTAAATC
9278 TAAAGCAGATT-A
1 TAAAGCAGATTAA
*
9290 TAAAGCAAATTAA
1 TAAAGCAGATTAA
9303 TAAAGCAGAT
1 TAAAGCAGAT
9313 AAAGCAAACA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
12 10 0.50
13 10 0.50
ACGTcount: A:0.54, C:0.09, G:0.14, T:0.23
Consensus pattern (13 bp):
TAAAGCAGATTAA
Found at i:14702 original size:28 final size:28
Alignment explanation
Indices: 14667--14720 Score: 83
Period size: 28 Copynumber: 1.9 Consensus size: 28
14657 CCCTGATTTT
14667 AAAAACGGAAAAATAAT-TTTTTTTTAGA
1 AAAAACGGAAAAA-AATCTTTTTTTTAGA
*
14695 AAAAACGGAAAAAACTCTTTTTTTTA
1 AAAAACGGAAAAAAATCTTTTTTTTA
14721 TCGACGCAAA
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
27 2 0.08
28 22 0.92
ACGTcount: A:0.48, C:0.07, G:0.09, T:0.35
Consensus pattern (28 bp):
AAAAACGGAAAAAAATCTTTTTTTTAGA
Found at i:16028 original size:10 final size:10
Alignment explanation
Indices: 16013--16037 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
16003 GAGGACTCTA
16013 GAATTTTCTG
1 GAATTTTCTG
16023 GAATTTTCTG
1 GAATTTTCTG
16033 GAATT
1 GAATT
16038 GTGCAGCAAC
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:0.24, C:0.08, G:0.20, T:0.48
Consensus pattern (10 bp):
GAATTTTCTG
Found at i:21855 original size:137 final size:136
Alignment explanation
Indices: 21529--22157 Score: 528
Period size: 136 Copynumber: 4.5 Consensus size: 136
21519 CGCCAGGATG
* * *
21529 CCGATCTGGAGCAGGACATTTGAGGGGCAGGAGCCTGTCATTATAGTGCAACCCTCCCATGTGAA
1 CCGATCTGGAGCAGGACACTTGGGGGGCAGGAGCCTGTCATTACAGTGCAACCCTCCCATGTGAA
* * * * *
21594 CCTCCAGTCGGACGAACGCGGGTATCTAGTTGGACGAGCCTCCCCCACGGGACCTCCACCTCAGT
66 CCTCTAGTCAGACGAACGCGGGTATCCAGTTGGACGAGCCTCCCCCACGGAACCTCCACCTCAGC
*
21659 GAGACG
131 GAGACA
* * *
21665 CCGATTTGGAGTAGGACACTTGGGGGGCAGGAGCCTGTCATTACAGTGTAACCCTCCCATGTGAA
1 CCGATCTGGAGCAGGACACTTGGGGGGCAGGAGCCTGTCATTACAGTGCAACCCTCCCATGTGAA
* * * *
21730 CCTCTAGTCAGACGAACGCGGGTATCCAGTTGGACGGGCGTCTCCCACGGAAACCTCCACTTCAG
66 CCTCTAGTCAGACGAACGCGGGTATCCAGTTGGACGAGCCTCCCCCACGG-AACCTCCACCTCAG
**
21795 CGATCCA
130 CGAGACA
*
21802 CCGATCTGGAGCAGGACACTTGGGGGGCAGGAGCCTGTCAATACAGTGCAACCCTCCCATGTGAA
1 CCGATCTGGAGCAGGACACTTGGGGGGCAGGAGCCTGTCATTACAGTGCAACCCTCCCATGTGAA
* * ** * * * *
21867 CCTCCTA-TCAGATGAACGCGATCGCCTAATTACCAACGCACAAGCTGACGAACGTCTCCAACGG
66 CCT-CTAGTCAGACGAACGCG---G-GT-A-T-CC-A-G---TTG--GACGAGCCTCCCCCACGG
*
21931 AGACCTCCGCCTCAGCGAGACA
116 A-ACCTCCACCTCAGCGAGACA
* * * * *
21953 CCGATATGGGGCAGGACACTTGGGGGGCAGGAGCTTGTCATTATAGTGCAACCCTCCTATGTGAA
1 CCGATCTGGAGCAGGACACTTGGGGGGCAGGAGCCTGTCATTACAGTGCAACCCTCCCATGTGAA
* * * * * * * * * * * * * *
22018 CC-CGCAATCGGACGAATGC-AGTCATCCAATT-GATGAACGTCTCCGACGGAGACTTCCGCCTT
66 CCTC-TAGTCAGACGAACGCGGGT-ATCCAGTTGGACGAGCCTCCCCCACGGA-ACCTCCACCTC
** *
22080 AGTAAGGCA
128 AGCGAGACA
* * * * * * * *
22089 CCGATCTAGAGCAGAAGACTTGGGGGACAGGAGCCTGTCATCACAGAGCAATCCTCCCATTTGAA
1 CCGATCTGGAGCAGGACACTTGGGGGGCAGGAGCCTGTCATTACAGTGCAACCCTCCCATGTGAA
22154 CCTC
66 CCTC
22158 CAATCGGACG
Statistics
Matches: 404, Mismatches: 69, Indels: 39
0.79 0.13 0.08
Matches are distributed among these distances:
136 190 0.47
137 92 0.23
138 3 0.01
140 1 0.00
141 1 0.00
142 1 0.00
143 2 0.00
144 4 0.01
145 2 0.00
146 3 0.01
149 2 0.00
150 2 0.00
151 101 0.25
ACGTcount: A:0.25, C:0.30, G:0.27, T:0.19
Consensus pattern (136 bp):
CCGATCTGGAGCAGGACACTTGGGGGGCAGGAGCCTGTCATTACAGTGCAACCCTCCCATGTGAA
CCTCTAGTCAGACGAACGCGGGTATCCAGTTGGACGAGCCTCCCCCACGGAACCTCCACCTCAGC
GAGACA
Found at i:22257 original size:16 final size:16
Alignment explanation
Indices: 22236--22273 Score: 67
Period size: 16 Copynumber: 2.4 Consensus size: 16
22226 CCGAACTGGA
22236 GCAGGACACTTAGGGG
1 GCAGGACACTTAGGGG
*
22252 GCAGGACACTTGGGGG
1 GCAGGACACTTAGGGG
22268 GCAGGA
1 GCAGGA
22274 GCCTGTCATT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 21 1.00
ACGTcount: A:0.24, C:0.18, G:0.47, T:0.11
Consensus pattern (16 bp):
GCAGGACACTTAGGGG
Found at i:22453 original size:39 final size:38
Alignment explanation
Indices: 22408--22537 Score: 125
Period size: 39 Copynumber: 3.3 Consensus size: 38
22398 ACTGAGTGAT
*
22408 TAGACTGGCACCCCTGTATAATTCTGACGGCTGAGCACC
1 TAGACTGGCACCCCTGT-TAATTCTGACGGCTGAGCGCC
* * * *
22447 TAGACTGTCGCCCCCGTTTAACTCATTGACGGCTGAGCGCC
1 TAGACTGGCACCCCTG-TTAATTC--TGACGGCTGAGCGCC
* * * * *
22488 TAGACTGGCGCCCCTGCTCAATGCTGACGGTTGAGTGCC
1 TAGACTGGCACCCCTG-TTAATTCTGACGGCTGAGCGCC
22527 TAGACTGGCAC
1 TAGACTGGCAC
22538 TCACGTTTAA
Statistics
Matches: 74, Mismatches: 14, Indels: 6
0.79 0.15 0.06
Matches are distributed among these distances:
39 41 0.55
40 1 0.01
41 32 0.43
ACGTcount: A:0.19, C:0.32, G:0.26, T:0.23
Consensus pattern (38 bp):
TAGACTGGCACCCCTGTTAATTCTGACGGCTGAGCGCC
Found at i:22622 original size:76 final size:76
Alignment explanation
Indices: 22519--22702 Score: 210
Period size: 77 Copynumber: 2.4 Consensus size: 76
22509 TGCTGACGGT
* * * * * *
22519 TGAGTGCCTAGACTGGCACTCACGTTTAACTG-GCAGCGAGGCCGAGCGTCCA-CGCAGATGCCC
1 TGAGTGCCTAGACTGGCAC-CCCGTTTAACTGAGAAGCGAGGCAGAGCGTCCACCGCAAACGCCA
*
22582 CTCGCGGACGCCC
65 CTCACGGACG-CC
* * * *
22595 TGAGTGCCTAGACTGGCGCCCCTGTTTAATTGATAAGTGAGGCAGAGCGTCCACCGCAAACGCCA
1 TGAGTGCCTAGACTGGCACCCC-GTTTAACTGAGAAGCGAGGCAGAGCGTCCACCGCAAACGCCA
*
22660 CTCACGGACGGC
65 CTCACGGACGCC
22672 TGAGTGCCTAGACTGGCACCCCCGTTTAACT
1 TGAGTGCCTAGACTGGCA-CCCCGTTTAACT
22703 AGCAATAAGG
Statistics
Matches: 90, Mismatches: 14, Indels: 7
0.81 0.13 0.06
Matches are distributed among these distances:
75 2 0.02
76 26 0.29
77 41 0.46
78 21 0.23
ACGTcount: A:0.21, C:0.33, G:0.28, T:0.18
Consensus pattern (76 bp):
TGAGTGCCTAGACTGGCACCCCGTTTAACTGAGAAGCGAGGCAGAGCGTCCACCGCAAACGCCAC
TCACGGACGCC
Found at i:27341 original size:3 final size:3
Alignment explanation
Indices: 27333--27394 Score: 115
Period size: 3 Copynumber: 20.7 Consensus size: 3
27323 ACCACTAAAC
*
27333 CTT CTT CTT TTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT
1 CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT
27381 CTT CTT CTT CTT CT
1 CTT CTT CTT CTT CT
27395 GTTCTGTTTT
Statistics
Matches: 57, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
3 57 1.00
ACGTcount: A:0.00, C:0.32, G:0.00, T:0.68
Consensus pattern (3 bp):
CTT
Found at i:28089 original size:12 final size:13
Alignment explanation
Indices: 28067--28100 Score: 54
Period size: 12 Copynumber: 2.8 Consensus size: 13
28057 ATACTTAATC
28067 TATATGTATACTG
1 TATATGTATACTG
28080 TATA-GTATACTG
1 TATATGTATACTG
28092 TA-ATGTATA
1 TATATGTATA
28101 GTATACTATA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
11 1 0.05
12 15 0.75
13 4 0.20
ACGTcount: A:0.35, C:0.06, G:0.15, T:0.44
Consensus pattern (13 bp):
TATATGTATACTG
Found at i:28104 original size:29 final size:28
Alignment explanation
Indices: 28051--28107 Score: 80
Period size: 29 Copynumber: 2.0 Consensus size: 28
28041 ATTCTATATG
28051 GTATGTATACTTAATCTATATGTATACT
1 GTATGTATACTTAATCTATATGTATACT
*
28079 GTATAGTATACTGTAATGTATA-GTATACT
1 GTAT-GTATACT-TAATCTATATGTATACT
28108 ATAAGTACAT
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
28 4 0.15
29 14 0.54
30 8 0.31
ACGTcount: A:0.33, C:0.09, G:0.14, T:0.44
Consensus pattern (28 bp):
GTATGTATACTTAATCTATATGTATACT
Found at i:28260 original size:21 final size:21
Alignment explanation
Indices: 28209--28260 Score: 77
Period size: 21 Copynumber: 2.5 Consensus size: 21
28199 GATAAGTTTC
*
28209 AATTTCTAATTTGTTTTGATA
1 AATTTCTAATCTGTTTTGATA
*
28230 AATATCTAATCTGTTTTGATA
1 AATTTCTAATCTGTTTTGATA
*
28251 AATTTGTAAT
1 AATTTCTAAT
28261 GAAGTCAATC
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.33, C:0.06, G:0.10, T:0.52
Consensus pattern (21 bp):
AATTTCTAATCTGTTTTGATA
Found at i:29482 original size:13 final size:14
Alignment explanation
Indices: 29458--29489 Score: 50
Period size: 13 Copynumber: 2.4 Consensus size: 14
29448 GAATTATAAT
29458 TAAATCTAACTAAG
1 TAAATCTAACTAAG
29472 TAAAT-TAACTAAG
1 TAAATCTAACTAAG
29485 -AAATC
1 TAAATC
29490 AATCAAGAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
12 4 0.24
13 8 0.47
14 5 0.29
ACGTcount: A:0.53, C:0.12, G:0.06, T:0.28
Consensus pattern (14 bp):
TAAATCTAACTAAG
Found at i:30797 original size:19 final size:18
Alignment explanation
Indices: 30764--30799 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
30754 TCGAAATAAT
30764 TCTTCAATGATCTTCAAA
1 TCTTCAATGATCTTCAAA
*
30782 TCTTCAAATTATCTTCAA
1 TCTTC-AATGATCTTCAA
30800 GAAATCTTCA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 5 0.31
19 11 0.69
ACGTcount: A:0.33, C:0.22, G:0.03, T:0.42
Consensus pattern (18 bp):
TCTTCAATGATCTTCAAA
Found at i:31001 original size:20 final size:21
Alignment explanation
Indices: 30963--31001 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 21
30953 TATAAAATAA
*
30963 GGTAAAAATGCATATAAAAGT
1 GGTAAAAATGCATAGAAAAGT
*
30984 GGTAAAAA-GTATAGAAAA
1 GGTAAAAATGCATAGAAAA
31002 ATAGCTATAA
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 8 0.50
21 8 0.50
ACGTcount: A:0.56, C:0.03, G:0.21, T:0.21
Consensus pattern (21 bp):
GGTAAAAATGCATAGAAAAGT
Found at i:32329 original size:13 final size:12
Alignment explanation
Indices: 32311--32353 Score: 54
Period size: 10 Copynumber: 3.7 Consensus size: 12
32301 TGAAACTTGA
32311 AAAATAAAGACAT
1 AAAATAAAG-CAT
32324 AAAATAAAG-A-
1 AAAATAAAGCAT
32334 AAAATAAAGCAT
1 AAAATAAAGCAT
*
32346 AAACTAAA
1 AAAATAAA
32354 TAGCTAAACC
Statistics
Matches: 27, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
10 9 0.33
11 2 0.07
12 7 0.26
13 9 0.33
ACGTcount: A:0.72, C:0.07, G:0.07, T:0.14
Consensus pattern (12 bp):
AAAATAAAGCAT
Found at i:32346 original size:22 final size:23
Alignment explanation
Indices: 32309--32353 Score: 74
Period size: 23 Copynumber: 2.0 Consensus size: 23
32299 AATGAAACTT
32309 GAAAAATAAAGACATAAAATAAA
1 GAAAAATAAAGACATAAAATAAA
*
32332 GAAAAATAAAG-CATAAACTAAA
1 GAAAAATAAAGACATAAAATAAA
32354 TAGCTAAACC
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
22 10 0.48
23 11 0.52
ACGTcount: A:0.71, C:0.07, G:0.09, T:0.13
Consensus pattern (23 bp):
GAAAAATAAAGACATAAAATAAA
Found at i:40785 original size:19 final size:18
Alignment explanation
Indices: 40752--40787 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
40742 TTGAAATAAT
40752 TCTTCAATGATCTTCAAA
1 TCTTCAATGATCTTCAAA
*
40770 TCTTCAAATTATCTTCAA
1 TCTTC-AATGATCTTCAA
40788 GAAATCTTCA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 5 0.31
19 11 0.69
ACGTcount: A:0.33, C:0.22, G:0.03, T:0.42
Consensus pattern (18 bp):
TCTTCAATGATCTTCAAA
Found at i:40989 original size:20 final size:21
Alignment explanation
Indices: 40951--40989 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 21
40941 TATAAAATAA
*
40951 GGTAAAAATGCATATAAAAGT
1 GGTAAAAATGCATAGAAAAGT
*
40972 GGTAAAAA-GTATAGAAAA
1 GGTAAAAATGCATAGAAAA
40990 ATAGCCATAA
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 8 0.50
21 8 0.50
ACGTcount: A:0.56, C:0.03, G:0.21, T:0.21
Consensus pattern (21 bp):
GGTAAAAATGCATAGAAAAGT
Found at i:46066 original size:15 final size:16
Alignment explanation
Indices: 46046--46079 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
46036 GATTTCTCTC
*
46046 TTAGTTA-ATTTACTT
1 TTAGTTAGATTTAATT
46061 TTAGTTAGATTTAATT
1 TTAGTTAGATTTAATT
46077 TTA
1 TTA
46080 ATTCTTCTTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 7 0.41
16 10 0.59
ACGTcount: A:0.29, C:0.03, G:0.09, T:0.59
Consensus pattern (16 bp):
TTAGTTAGATTTAATT
Found at i:56461 original size:18 final size:18
Alignment explanation
Indices: 56427--56461 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
56417 AAAGGTTTTC
*
56427 CAAAAAATCCAAAAAAAT
1 CAAAAAATCAAAAAAAAT
*
56445 CAAAAATTCAAAAAAAA
1 CAAAAAATCAAAAAAAA
56462 AAGGAATTTC
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.74, C:0.14, G:0.00, T:0.11
Consensus pattern (18 bp):
CAAAAAATCAAAAAAAAT
Found at i:61150 original size:14 final size:14
Alignment explanation
Indices: 61127--61177 Score: 86
Period size: 14 Copynumber: 3.6 Consensus size: 14
61117 AGAGTCATGG
61127 TTTTCAAAAATGCTT
1 TTTTCAAAAATG-TT
61142 TTTTCAAAAATGTT
1 TTTTCAAAAATGTT
61156 TTTTCAAAAATG-T
1 TTTTCAAAAATGTT
61169 TTTTCAAAA
1 TTTTCAAAA
61178 GAGAGTCATG
Statistics
Matches: 36, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
13 10 0.28
14 14 0.39
15 12 0.33
ACGTcount: A:0.37, C:0.10, G:0.06, T:0.47
Consensus pattern (14 bp):
TTTTCAAAAATGTT
Found at i:61222 original size:14 final size:14
Alignment explanation
Indices: 61205--61246 Score: 50
Period size: 14 Copynumber: 3.0 Consensus size: 14
61195 AAAATGATTT
61205 TTTTTTTCAAAATG-
1 TTTTTTTCAAAA-GA
*
61219 TTTTCTTCAAAAGA
1 TTTTTTTCAAAAGA
*
61233 TGTTTTTCAAAAGA
1 TTTTTTTCAAAAGA
61247 GAGTCATGGT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
13 1 0.04
14 23 0.96
ACGTcount: A:0.33, C:0.10, G:0.10, T:0.48
Consensus pattern (14 bp):
TTTTTTTCAAAAGA
Found at i:61306 original size:67 final size:65
Alignment explanation
Indices: 61115--61299 Score: 234
Period size: 67 Copynumber: 2.8 Consensus size: 65
61105 CTGGAATATT
* * *
61115 AGAGAGTCATGGTTTTC--AAAAATG-CTTTTTTCAAAAATGTTTTTTCAAAAATGTTTTTCAAA
1 AGAGAGTCATGGTTTTCAAAAAAAAGTTTTTTTTCCAAAATGTTTTTTCAAAAATGTTTTTCAAA
** * *
61177 AGAGAGTCATGGTTTTCAAAAATGATTTTTTTTTTCAAAATGTTTTCTTCAAAAGATGTTTTTCA
1 AGAGAGTCATGGTTTTCAAAAAAAAGTTTTTTTTCCAAAATGTTTT-TTCAAAA-ATGTTTTTCA
61242 AA
64 AA
*
61244 AGAGAGTCATGGTTTTCAAAAAAAAAAGTTTTTTTTCCAAGATG-TTTTTCAAAAAT
1 AGAGAGTCATGGTTTTC--AAAAAAAAGTTTTTTTTCCAAAATGTTTTTTCAAAAAT
61300 AATTTTTGAA
Statistics
Matches: 104, Mismatches: 12, Indels: 10
0.83 0.10 0.08
Matches are distributed among these distances:
62 17 0.16
64 3 0.03
65 16 0.15
66 9 0.09
67 36 0.35
68 3 0.03
69 20 0.19
ACGTcount: A:0.36, C:0.09, G:0.14, T:0.42
Consensus pattern (65 bp):
AGAGAGTCATGGTTTTCAAAAAAAAGTTTTTTTTCCAAAATGTTTTTTCAAAAATGTTTTTCAAA
Found at i:62906 original size:16 final size:16
Alignment explanation
Indices: 62885--62915 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
62875 TTTCAATTAG
*
62885 CTTCAATTCTTCAATC
1 CTTCAATGCTTCAATC
62901 CTTCAATGCTTCAAT
1 CTTCAATGCTTCAAT
62916 ATATATCAAA
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:0.26, C:0.29, G:0.03, T:0.42
Consensus pattern (16 bp):
CTTCAATGCTTCAATC
Found at i:63062 original size:8 final size:8
Alignment explanation
Indices: 63051--63131 Score: 71
Period size: 8 Copynumber: 10.5 Consensus size: 8
63041 CTAATTATTT
63051 AATTCTTC
1 AATTCTTC
63059 AATTCTTC
1 AATTCTTC
*
63067 AATACTTC
1 AATTCTTC
*
63075 AATACTTC
1 AATTCTTC
63083 AA-T-TT-
1 AATTCTTC
*
63088 ATTTCTTC
1 AATTCTTC
63096 AATTCTTC
1 AATTCTTC
*
63104 AATTATT-
1 AATTCTTC
*
63111 TATTGCTTC
1 AATT-CTTC
*
63120 AATCCTTC
1 AATTCTTC
63128 AATT
1 AATT
63132 ACATAAAGCT
Statistics
Matches: 58, Mismatches: 10, Indels: 10
0.74 0.13 0.13
Matches are distributed among these distances:
5 1 0.02
6 3 0.05
7 5 0.09
8 47 0.81
9 2 0.03
ACGTcount: A:0.28, C:0.21, G:0.01, T:0.49
Consensus pattern (8 bp):
AATTCTTC
Found at i:63062 original size:16 final size:16
Alignment explanation
Indices: 63043--63110 Score: 54
Period size: 16 Copynumber: 4.4 Consensus size: 16
63033 CTCTTCGACT
*
63043 AATTATTTAATTCTTC
1 AATTATTCAATTCTTC
* *
63059 AATTCTTCAATACTTC
1 AATTATTCAATTCTTC
63075 AA-TACTTCAA-T-TT-
1 AATTA-TTCAATTCTTC
* *
63088 ATTTCTTCAATTCTTC
1 AATTATTCAATTCTTC
63104 AATTATT
1 AATTATT
63111 TATTGCTTCA
Statistics
Matches: 38, Mismatches: 9, Indels: 10
0.67 0.16 0.18
Matches are distributed among these distances:
13 6 0.16
14 4 0.11
15 3 0.08
16 25 0.66
ACGTcount: A:0.31, C:0.18, G:0.00, T:0.51
Consensus pattern (16 bp):
AATTATTCAATTCTTC
Found at i:63119 original size:24 final size:24
Alignment explanation
Indices: 63051--63132 Score: 80
Period size: 24 Copynumber: 3.5 Consensus size: 24
63041 CTAATTATTT
* * *
63051 AATTCTTCAATTCTTCAATACTTC
1 AATTCTTCAATTATTTATTACTTC
* *
63075 AATACTTC-A--ATTTATTTCTTC
1 AATTCTTCAATTATTTATTACTTC
*
63096 AATTCTTCAATTATTTATTGCTTC
1 AATTCTTCAATTATTTATTACTTC
*
63120 AATCCTTCAATTA
1 AATTCTTCAATTA
63133 CATAAAGCTT
Statistics
Matches: 47, Mismatches: 8, Indels: 6
0.77 0.13 0.10
Matches are distributed among these distances:
21 15 0.32
22 1 0.02
23 1 0.02
24 30 0.64
ACGTcount: A:0.29, C:0.21, G:0.01, T:0.49
Consensus pattern (24 bp):
AATTCTTCAATTATTTATTACTTC
Found at i:63142 original size:24 final size:24
Alignment explanation
Indices: 63092--63145 Score: 63
Period size: 24 Copynumber: 2.2 Consensus size: 24
63082 CAATTTATTT
* ** **
63092 CTTCAATTCTTCAATTATTTATTG
1 CTTCAATCCTTCAATTACATAAAG
63116 CTTCAATCCTTCAATTACATAAAG
1 CTTCAATCCTTCAATTACATAAAG
63140 CTTCAA
1 CTTCAA
63146 CTCTTCCATT
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.31, C:0.22, G:0.04, T:0.43
Consensus pattern (24 bp):
CTTCAATCCTTCAATTACATAAAG
Found at i:63204 original size:59 final size:58
Alignment explanation
Indices: 63141--63273 Score: 153
Period size: 58 Copynumber: 2.3 Consensus size: 58
63131 TACATAAAGC
* * *
63141 TTCAACTCTTCCATTCACTTTCAATGACCCAGGGTGGTCTTTCTT-CGTTTCTTCAATTA
1 TTCAACTCTTCAATTCAC-TTCAATGACACAGGGTGGTCTTTCTTCCGTTCCTT-AATTA
** * *
63200 TTCAA-TACTTCAATTTGCTTCAATGATACATGGTGGTCTTTCTTCCGTTCCTTAATTA
1 TTCAACT-CTTCAATTCACTTCAATGACACAGGGTGGTCTTTCTTCCGTTCCTTAATTA
*
63258 TTCAACTCCTCAATTC
1 TTCAACTCTTCAATTC
63274 CAAATCTTCA
Statistics
Matches: 62, Mismatches: 9, Indels: 7
0.79 0.12 0.09
Matches are distributed among these distances:
58 41 0.66
59 21 0.34
ACGTcount: A:0.21, C:0.26, G:0.11, T:0.43
Consensus pattern (58 bp):
TTCAACTCTTCAATTCACTTCAATGACACAGGGTGGTCTTTCTTCCGTTCCTTAATTA
Found at i:63292 original size:22 final size:22
Alignment explanation
Indices: 63267--63531 Score: 116
Period size: 22 Copynumber: 11.8 Consensus size: 22
63257 ATTCAACTCC
*
63267 TCAATTCCAAATCTTCAATGCT
1 TCAATTTCAAATCTTCAATGCT
* * *
63289 TCAATTTCAATTCTCCAATGTT
1 TCAATTTCAAATCTTCAATGCT
* *
63311 TC--TTTCAATTCTTTAATGCT
1 TCAATTTCAAATCTTCAATGCT
* *
63331 TCAGTTTCAATAT-TTCAATGCC
1 TCAATTTCAA-ATCTTCAATGCT
* *
63353 TCAATTTCAGTAT-TTCAATGTTT
1 TCAATTTCA-AATCTTCAATG-CT
* **
63376 TCAATTTCAATTCTTCAATATT
1 TCAATTTCAAATCTTCAATGCT
* ** *
63398 TCAATGCTCCGAT-TTCAATTCT
1 TCAAT-TTCAAATCTTCAATGCT
* * * *
63420 TCAAGTTC-AGTCCTTCTATGTT
1 TCAATTTCAAAT-CTTCAATGCT
* *
63442 TCAATTTGAATTCTTCAAATTCAGTTCT
1 TCAATTTCAAATCTTC-AA-T--G--CT
63470 TCAATTTC-AATACTTCAATGCT
1 TCAATTTCAAAT-CTTCAATGCT
*
63492 TCGATTTCAATAT-TTCAATG-T
1 TCAATTTCAA-ATCTTCAATGCT
*
63513 TCCAATTTCAATTCTTCAA
1 T-CAATTTCAAATCTTCAA
63532 ATTCCAAATT
Statistics
Matches: 182, Mismatches: 40, Indels: 42
0.69 0.15 0.16
Matches are distributed among these distances:
20 18 0.10
21 5 0.03
22 114 0.63
23 23 0.13
24 4 0.02
26 2 0.01
27 4 0.02
28 12 0.07
ACGTcount: A:0.27, C:0.21, G:0.06, T:0.45
Consensus pattern (22 bp):
TCAATTTCAAATCTTCAATGCT
Found at i:63523 original size:36 final size:36
Alignment explanation
Indices: 63389--64017 Score: 162
Period size: 36 Copynumber: 17.0 Consensus size: 36
63379 ATTTCAATTC
* * * *
63389 TTCAATATTTCAATGCTCCGATTTCAATTCTTCAAG
1 TTCAATATTTCAATGTTTCAATTTCAATTCTTCAAT
* ** * * *
63425 TTCAGTCCTTCTATGTTTCAATTTGAATTCTTCAAA
1 TTCAATATTTCAATGTTTCAATTTCAATTCTTCAAT
* * *
63461 TTCAGT-TCTTCAA--TTTCAATACTTCAATGCTTCGAT
1 TTCAATAT-TTCAATGTTTCAAT--TTCAATTCTTCAAT
*
63497 TTCAATATTTCAATGTTCCAATTTCAATTCTTCAAAT
1 TTCAATATTTCAATGTTTCAATTTCAATTCTTC-AAT
* *
63534 TCCAA-ATTTCAATGTTTCAATATTTTAATTCTTCAAAT
1 TTCAATATTTCAATGTTTC-A-ATTTCAATTCTTC-AAT
** * * *
63572 GCTTC-A-GGTTCAAT-TCTCCAAATTCAATCCTTCAACT
1 --TTCAATATTTCAATGT-TTCAATTTCAATTCTTCAA-T
**
63609 ATTCAATCCTTCAAT-TGTTCAATGCTTCAATTTACTTCAAT
1 -TTCAATATTTCAATGT-TTCAAT--TTCAA-TT-CTTCAAT
** * * * *
63650 GACCCAGGGTA-GTC--TTTCTTCAATTCTTCAATTATTCAA-
1 --TTCA--ATATTTCAATGT-TTCAA-T-TTCAATTCTTCAAT
* * * * *
63689 ATCAAT-TCTTCAATGGTTCAATTTGAATTCTGCAAA
1 TTCAATAT-TTCAATGTTTCAATTTCAATTCTTCAAT
* *
63725 TTCAA-ATCCTTCAATGTTTCAAATTCAATTCTTCGAT
1 TTCAATAT--TTCAATGTTTCAATTTCAATTCTTCAAT
* *
63762 GCTTC-A-ATTTCAAT-TCTTCAAATTCAATCCTTCAAT
1 --TTCAATATTTCAATGT-TTCAATTTCAATTCTTCAAT
* * *
63798 TTC-A-ACTTCAA--TTTCGATTCTTCAATACTTCAAT
1 TTCAATATTTCAATGTTTC-AAT-TTCAATTCTTCAAT
* * *
63832 TTCCAT-TTTCCAATATTTCAATTTCAATCCTTCAAAT
1 TTCAATATTT-CAATGTTTCAATTTCAATTCTTC-AAT
* * *
63869 TCCAA-ATGTCAATGCTTCAATATTTCAATTCTTCAAT
1 TTCAATATTTCAATGTTTC-A-ATTTCAATTCTTCAAT
* * *
63906 TTCAAT-TCCTCAA--ATTCAATCCCTCAATGT-TTCAATT
1 TTCAATAT-TTCAATGTTTCAAT--TTCAAT-TCTTCAA-T
* * * *
63943 ATTCAATGTTTCAATGCTTCAATTTCAATTCCTCAAA
1 -TTCAATATTTCAATGTTTCAATTTCAATTCTTCAAT
**
63980 TTCAATCCTTCAATTGTTTCAATTTCAATGT-TTCAAT
1 TTCAATATTTCAA-TGTTTCAATTTCAAT-TCTTCAAT
64017 T
1 T
64018 CTTCAATTTC
Statistics
Matches: 447, Mismatches: 88, Indels: 115
0.69 0.14 0.18
Matches are distributed among these distances:
32 3 0.01
33 2 0.00
34 35 0.08
35 16 0.04
36 160 0.36
37 91 0.20
38 79 0.18
39 13 0.03
40 18 0.04
41 5 0.01
42 21 0.05
43 3 0.01
44 1 0.00
ACGTcount: A:0.29, C:0.22, G:0.06, T:0.43
Consensus pattern (36 bp):
TTCAATATTTCAATGTTTCAATTTCAATTCTTCAAT
Found at i:63541 original size:22 final size:22
Alignment explanation
Indices: 63471--63557 Score: 81
Period size: 22 Copynumber: 4.0 Consensus size: 22
63461 TTCAGTTCTT
* *
63471 CAATTTCAATACTTCAATGCTT-
1 CAATTTCAATATTTCAAT-ATTC
* *
63493 CGATTTCAATATTTCAATGTTC
1 CAATTTCAATATTTCAATATTC
63515 CAATTTCAAT-TCTTCAA-ATTC
1 CAATTTCAATAT-TTCAATATTC
*
63536 CAAATTTCAATGTTTCAATATT
1 C-AATTTCAATATTTCAATATT
63558 TTAATTCTTC
Statistics
Matches: 55, Mismatches: 5, Indels: 9
0.80 0.07 0.13
Matches are distributed among these distances:
21 7 0.13
22 44 0.80
23 4 0.07
ACGTcount: A:0.32, C:0.20, G:0.05, T:0.44
Consensus pattern (22 bp):
CAATTTCAATATTTCAATATTC
Found at i:63639 original size:16 final size:16
Alignment explanation
Indices: 63593--63640 Score: 69
Period size: 16 Copynumber: 3.0 Consensus size: 16
63583 AATTCTCCAA
*
63593 ATTCAATCCTTCAACT
1 ATTCAATCCTTCAATT
63609 ATTCAATCCTTCAATT
1 ATTCAATCCTTCAATT
* *
63625 GTTCAATGCTTCAATT
1 ATTCAATCCTTCAATT
63641 TACTTCAATG
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
16 29 1.00
ACGTcount: A:0.29, C:0.25, G:0.04, T:0.42
Consensus pattern (16 bp):
ATTCAATCCTTCAATT
Found at i:63678 original size:8 final size:8
Alignment explanation
Indices: 63665--64200 Score: 113
Period size: 8 Copynumber: 71.8 Consensus size: 8
63655 AGGGTAGTCT
63665 TTCTTCAA
1 TTCTTCAA
63673 TTCTTCAA
1 TTCTTCAA
*
63681 TTATTCAA
1 TTCTTCAA
*
63689 ---ATCAA
1 TTCTTCAA
63694 TTCTTCAA
1 TTCTTCAA
**
63702 TGGTTCAA
1 TTCTTCAA
*
63710 -T-TTGAA
1 TTCTTCAA
*
63716 TTCTGCAAA
1 TTCTTC-AA
*
63725 TTC--AAA
1 TTCTTCAA
*
63731 TCCTTCAA
1 TTCTTCAA
63739 TGT-TTCAA
1 T-TCTTCAA
*
63747 AT-T-CAA
1 TTCTTCAA
*
63753 TTCTTCGA
1 TTCTTCAA
*
63761 TGCTTCAA
1 TTCTTCAA
63769 -T-TTCAA
1 TTCTTCAA
63775 TTCTTCAA
1 TTCTTCAA
*
63783 --ATTCAA
1 TTCTTCAA
*
63789 TCCTTCAA
1 TTCTTCAA
63797 -T-TTCAA
1 TTCTTCAA
63803 --CTTCAA
1 TTCTTCAA
*
63809 -T-TTCGA
1 TTCTTCAA
63815 TTCTTCAA
1 TTCTTCAA
*
63823 TACTTCAA
1 TTCTTCAA
*
63831 -T-TTCCA
1 TTCTTCAA
63837 TT-TTCCAA
1 TTCTT-CAA
63845 TAT-TTCAA
1 T-TCTTCAA
63853 -T-TTCAA
1 TTCTTCAA
*
63859 TCCTTCAAA
1 TTCTTC-AA
63868 TTC--CAA
1 TTCTTCAA
* *
63874 AT-GTCAA
1 TTCTTCAA
*
63881 TGCTTCAA
1 TTCTTCAA
63889 TAT-TTCAA
1 T-TCTTCAA
63897 TTCTTCAA
1 TTCTTCAA
63905 -T-TTCAA
1 TTCTTCAA
*
63911 TTCCTCAA
1 TTCTTCAA
*
63919 --ATTCAA
1 TTCTTCAA
* *
63925 TCCCTCAA
1 TTCTTCAA
63933 TGT-TTCAA
1 T-TCTTCAA
*
63941 TTATTCAA
1 TTCTTCAA
63949 TGT-TTCAA
1 T-TCTTCAA
*
63957 TGCTTCAA
1 TTCTTCAA
63965 -T-TTCAA
1 TTCTTCAA
*
63971 TTCCTCAA
1 TTCTTCAA
*
63979 --ATTCAA
1 TTCTTCAA
*
63985 TCCTTCAA
1 TTCTTCAA
*
63993 TTGTTTCAA
1 TT-CTTCAA
64002 -T-TTCAA
1 TTCTTCAA
64008 TGT-TTCAA
1 T-TCTTCAA
64016 TTCTTCAA
1 TTCTTCAA
64024 -T-TTCAA
1 TTCTTCAA
*
64030 TCCTTCAA
1 TTCTTCAA
64038 TGT-TTCAA
1 T-TCTTCAA
64046 -T-TTCAA
1 TTCTTCAA
64052 TAT-TTCAA
1 T-TCTTCAA
*
64060 TGCTTCAA
1 TTCTTCAA
64068 -T-TTCAA
1 TTCTTCAA
64074 TTCTTCAA
1 TTCTTCAA
64082 -TCATTCAA
1 TTC-TTCAA
**
64090 CGCTTCAA
1 TTCTTCAA
*
64098 TT-TGGTC-T
1 TTCT--TCAA
64106 TTCTTCAA
1 TTCTTCAA
*
64114 TTATTCAA
1 TTCTTCAA
*
64122 TTCTTTAAA
1 TTC-TTCAA
*
64131 TTATTCAA
1 TTCTTCAA
* *
64139 TTATTCCA
1 TTCTTCAA
64147 TGT-TTCAA
1 T-TCTTCAA
*
64155 TTCCTCAA
1 TTCTTCAA
*
64163 TTATTC-A
1 TTCTTCAA
*
64170 TTGTTTCAA
1 TT-CTTCAA
* *
64179 TTATTTAA
1 TTCTTCAA
64187 TTCTTCAA
1 TTCTTCAA
64195 TTCTTC
1 TTCTTC
64201 GGTATCTCAA
Statistics
Matches: 389, Mismatches: 74, Indels: 130
0.66 0.12 0.22
Matches are distributed among these distances:
5 4 0.01
6 88 0.23
7 30 0.08
8 235 0.60
9 32 0.08
ACGTcount: A:0.29, C:0.21, G:0.04, T:0.45
Consensus pattern (8 bp):
TTCTTCAA
Found at i:63767 original size:22 final size:22
Alignment explanation
Indices: 63721--63978 Score: 90
Period size: 22 Copynumber: 11.8 Consensus size: 22
63711 TTGAATTCTG
* *
63721 CAAATTCAAATCCTTCAATGTTT
1 CAAATTC-AATTCTTCAATGCTT
*
63744 CAAATTCAATTCTTCGATGCTT
1 CAAATTCAATTCTTCAATGCTT
* *
63766 CAATTTCAATTCTTCAA--ATT
1 CAAATTCAATTCTTCAATGCTT
*
63786 CAATCCTTCAA-T-TTCAA--CTT
1 CAA--ATTCAATTCTTCAATGCTT
* * *
63806 CAATTTCGATTCTTCAATACTT
1 CAAATTCAATTCTTCAATGCTT
* * **
63828 CAATTTCCATT-TTCCAATATTT
1 CAAATTCAATTCTT-CAATGCTT
* * *
63850 CAATTTCAATCCTTCAAAT--TC
1 CAAATTCAATTCTTC-AATGCTT
* **
63871 CAAATGTCAATGCTTCAATATTT
1 CAAAT-TCAATTCTTCAATGCTT
* * *
63894 CAATTCTTCAA-T-TTCAATTCCT
1 CAA--ATTCAATTCTTCAATGCTT
* * *
63916 CAAATTCAATCCCTCAATGTTT
1 CAAATTCAATTCTTCAATGCTT
63938 CAATTATTCAATGT-TTCAATGCTT
1 CAA--ATTCAAT-TCTTCAATGCTT
* *
63962 CAATTTCAATTCCTCAA
1 CAAATTCAATTCTTCAA
63979 ATTCAATCCT
Statistics
Matches: 181, Mismatches: 34, Indels: 41
0.71 0.13 0.16
Matches are distributed among these distances:
18 4 0.02
19 1 0.01
20 25 0.14
21 12 0.07
22 100 0.55
23 16 0.09
24 22 0.12
25 1 0.01
ACGTcount: A:0.31, C:0.24, G:0.03, T:0.42
Consensus pattern (22 bp):
CAAATTCAATTCTTCAATGCTT
Found at i:63768 original size:59 final size:57
Alignment explanation
Indices: 63668--63832 Score: 194
Period size: 59 Copynumber: 2.9 Consensus size: 57
63658 GTAGTCTTTC
* * * *
63668 TTCAATTCTTCAATTATTCAAA-TCAATTCTTCAATGGTTCAATTTGAATTCTGCAAA
1 TTCAATCCTTCAATT-TTCAAATTCAATTCTTCGATGCTTCAATTTCAATTCTGCAAA
*
63725 TTCAAATCCTTCAATGTTTCAAATTCAATTCTTCGATGCTTCAATTTCAATTCTTCAAA
1 TTC-AATCCTTCAAT-TTTCAAATTCAATTCTTCGATGCTTCAATTTCAATTCTGCAAA
* *
63784 TTCAATCCTTCAA-TTTCAACTTCAA-T-TTCGATTCTTCAATACTTCAATT
1 TTCAATCCTTCAATTTTCAAATTCAATTCTTCGATGCTTCAAT--TTCAATT
63833 TCCATTTTCC
Statistics
Matches: 96, Mismatches: 7, Indels: 11
0.84 0.06 0.10
Matches are distributed among these distances:
54 13 0.14
55 1 0.01
56 18 0.19
57 3 0.03
58 26 0.27
59 35 0.36
ACGTcount: A:0.31, C:0.21, G:0.05, T:0.43
Consensus pattern (57 bp):
TTCAATCCTTCAATTTTCAAATTCAATTCTTCGATGCTTCAATTTCAATTCTGCAAA
Found at i:63782 original size:14 final size:14
Alignment explanation
Indices: 63763--64082 Score: 184
Period size: 14 Copynumber: 22.5 Consensus size: 14
63753 TTCTTCGATG
63763 CTTCAATTTCAATT
1 CTTCAATTTCAATT
* *
63777 CTTCAAATTCAATC
1 CTTCAATTTCAATT
63791 CTTCAATTTCAA--
1 CTTCAATTTCAATT
*
63803 CTTCAATTTCGATT
1 CTTCAATTTCAATT
63817 CTTCAATACTTCAATT
1 CTTCAAT--TTCAATT
* *
63833 -TCCATTTTCCAATAT
1 CTTCAATTT-CAAT-T
*
63848 -TTCAATTTCAATC
1 CTTCAATTTCAATT
63861 CTTC-A----AATT
1 CTTCAATTTCAATT
* *
63870 C--CAAATGTCAATG
1 CTTC-AATTTCAATT
63883 CTTCAATATTTCAATT
1 CTTC-A-ATTTCAATT
63899 CTTCAATTTCAATT
1 CTTCAATTTCAATT
* * *
63913 CCTCAAATTCAATC
1 CTTCAATTTCAATT
*
63927 CCTCAATGTTTCAATT
1 CTTCAA--TTTCAATT
* *
63943 ATTCAATGTTTCAATG
1 CTTCAA--TTTCAATT
63959 CTTCAATTTCAATT
1 CTTCAATTTCAATT
* * *
63973 CCTCAAATTCAATC
1 CTTCAATTTCAATT
63987 CTTCAATTGTTTCAA-T
1 CTTCAA---TTTCAATT
64003 -TTCAATGTTTCAATT
1 CTTCAA--TTTCAATT
*
64018 CTTCAATTTCAATC
1 CTTCAATTTCAATT
64032 CTTCAATGTTTCAA-T
1 CTTCAA--TTTCAATT
*
64047 -TTCAATATTTCAATG
1 CTTC-A-ATTTCAATT
64062 CTTCAATTTCAATT
1 CTTCAATTTCAATT
64076 CTTCAAT
1 CTTCAAT
64083 CATTCAACGC
Statistics
Matches: 243, Mismatches: 34, Indels: 58
0.73 0.10 0.17
Matches are distributed among these distances:
7 1 0.00
9 5 0.02
12 11 0.05
13 7 0.03
14 135 0.56
15 23 0.09
16 56 0.23
17 5 0.02
ACGTcount: A:0.30, C:0.23, G:0.03, T:0.44
Consensus pattern (14 bp):
CTTCAATTTCAATT
Found at i:63858 original size:62 final size:61
Alignment explanation
Indices: 63742--64082 Score: 186
Period size: 60 Copynumber: 5.3 Consensus size: 61
63732 CCTTCAATGT
* *
63742 TTCAAATTCAATTCTTCGATGCTTCAATTTCAATTCTTCAAATTCAATCCTTCAATTTCAAC
1 TTCAAATTCAATTCTTCAATACTTCAATTTCAATTCTTCAAATTCAAT-CTTCAATTTCAAC
* * *
63804 TTCAATTTCGATTCTTCAATACTTCAATTTCCATT-TTCCAATATTTCAAT-TTCAATCCTTCAA
1 TTCAAATTCAATTCTTCAATACTTCAATTTCAATTCTT-CAA-A-TTCAATCTTCAAT--TTCAA
*
63867 A
61 C
* * *
63868 TTCCAAATGTCAATGCTTCAATATTTCAATTCTTCAATTTCAATTCCTCAAATTCAATCCCTCAA
1 TT-CAAAT-TCAA---TTC-----TTCAATACTTCAATTTCAATTCTTCAAATTCAAT-CTTCAA
63933 TGTTTCAA-
55 --TTTCAAC
* *
63941 TT---ATTCAATGT-TTCAATGCTTCAATTTCAATTCCTCAAATTCAATCCTTCAATTGT----
1 TTCAAATTCAAT-TCTTCAATACTTCAATTTCAATTCTTCAAATTCAAT-CTTCAATT-TCAAC
* * * *
63997 TTCAATTTCAATGT-TTCAATTCTTCAATTTCAATCCTTCAATGTTTCAAT-TTCAATATTTCAA
1 TTCAAATTCAAT-TCTTCAATACTTCAATTTCAATTCTTCAA--ATTCAATCTTC-A-ATTTCAA
64060 TGC
61 --C
*
64063 TTCAATTTCAATTCTTCAAT
1 TTCAAATTCAATTCTTCAAT
64083 CATTCAACGC
Statistics
Matches: 224, Mismatches: 19, Indels: 68
0.72 0.06 0.22
Matches are distributed among these distances:
56 2 0.01
58 2 0.01
59 36 0.16
60 41 0.18
61 11 0.05
62 39 0.17
63 1 0.00
64 13 0.06
65 6 0.03
66 22 0.10
68 4 0.02
69 5 0.02
72 6 0.03
73 3 0.01
74 31 0.14
75 1 0.00
76 1 0.00
ACGTcount: A:0.30, C:0.23, G:0.04, T:0.44
Consensus pattern (61 bp):
TTCAAATTCAATTCTTCAATACTTCAATTTCAATTCTTCAAATTCAATCTTCAATTTCAAC
Found at i:63963 original size:60 final size:59
Alignment explanation
Indices: 63884--64030 Score: 242
Period size: 60 Copynumber: 2.5 Consensus size: 59
63874 ATGTCAATGC
*
63884 TTCAATATTTCAATTCTTCAATTTCAATTCCTCAAATTCAATCCCTCAA-TGTTTCAATT
1 TTCAATGTTTCAATTCTTCAATTTCAATTCCTCAAATTCAATCCCTCAATTGTTTCAA-T
* *
63943 ATTCAATGTTTCAATGCTTCAATTTCAATTCCTCAAATTCAATCCTTCAATTGTTTCAAT
1 -TTCAATGTTTCAATTCTTCAATTTCAATTCCTCAAATTCAATCCCTCAATTGTTTCAAT
64003 TTCAATGTTTCAATTCTTCAATTTCAAT
1 TTCAATGTTTCAATTCTTCAATTTCAAT
64031 CCTTCAATGT
Statistics
Matches: 82, Mismatches: 4, Indels: 3
0.92 0.04 0.03
Matches are distributed among these distances:
59 27 0.33
60 47 0.57
61 8 0.10
ACGTcount: A:0.30, C:0.22, G:0.03, T:0.45
Consensus pattern (59 bp):
TTCAATGTTTCAATTCTTCAATTTCAATTCCTCAAATTCAATCCCTCAATTGTTTCAAT
Found at i:63991 original size:22 final size:22
Alignment explanation
Indices: 63966--64082 Score: 128
Period size: 22 Copynumber: 5.3 Consensus size: 22
63956 ATGCTTCAAT
* *
63966 TTCAATTCCTCAAATTCAATCC
1 TTCAATTCTTCAATTTCAATCC
* **
63988 TTCAATTGTTTCAATTTCAATGT
1 TTCAATT-CTTCAATTTCAATCC
64011 TTCAATTCTTCAATTTCAATCC
1 TTCAATTCTTCAATTTCAATCC
**
64033 TTCAATGT-TTCAATTTCAATAT
1 TTCAAT-TCTTCAATTTCAATCC
* *
64055 TTCAATGCTTCAATTTCAATTC
1 TTCAATTCTTCAATTTCAATCC
64077 TTCAAT
1 TTCAAT
64083 CATTCAACGC
Statistics
Matches: 79, Mismatches: 13, Indels: 6
0.81 0.13 0.06
Matches are distributed among these distances:
22 61 0.77
23 18 0.23
ACGTcount: A:0.29, C:0.21, G:0.03, T:0.46
Consensus pattern (22 bp):
TTCAATTCTTCAATTTCAATCC
Found at i:64196 original size:16 final size:16
Alignment explanation
Indices: 63877--64196 Score: 161
Period size: 16 Copynumber: 20.9 Consensus size: 16
63867 ATTCCAAATG
*
63877 TCAATGCTTCAA-TATT
1 TCAATTCTTCAATTA-T
63893 TCAATTCTTCAA-T-T
1 TCAATTCTTCAATTAT
*
63907 TCAATTCCTCAA--AT
1 TCAATTCTTCAATTAT
* *
63921 TCAATCCCTCAATGT-T
1 TCAATTCTTCAAT-TAT
*
63937 TCAATTATTCAATGT-T
1 TCAATTCTTCAAT-TAT
*
63953 TCAATGCTTCAA-T-T
1 TCAATTCTTCAATTAT
*
63967 TCAATTCCTCAA--AT
1 TCAATTCTTCAATTAT
* *
63981 TCAATCCTTCAATTGTT
1 TCAATTCTTCAATT-AT
63998 TCAA-T-TTCAATGT-T
1 TCAATTCTTCAAT-TAT
64012 TCAATTCTTCAA-T-T
1 TCAATTCTTCAATTAT
*
64026 TCAATCCTTCAATGT-T
1 TCAATTCTTCAAT-TAT
64042 TCAA-T-TTCAA-TATT
1 TCAATTCTTCAATTA-T
*
64056 TCAATGCTTCAA-T-T
1 TCAATTCTTCAATTAT
*
64070 TCAATTCTTCAATCAT
1 TCAATTCTTCAATTAT
**
64086 TCAACGCTTCAATT-T
1 TCAATTCTTCAATTAT
*
64101 GGTC-TTTCTTCAATTAT
1 --TCAATTCTTCAATTAT
*
64118 TCAATTCTTTAAATTAT
1 TCAATTC-TTCAATTAT
* *
64135 TCAATTATTCCATGT-T
1 TCAATTCTTCAAT-TAT
*
64151 TCAATTCCTCAATTAT
1 TCAATTCTTCAATTAT
*
64167 TC-ATTGTTTCAATTAT
1 TCAATT-CTTCAATTAT
*
64183 TTAATTCTTCAATT
1 TCAATTCTTCAATT
64197 CTTCGGTATC
Statistics
Matches: 239, Mismatches: 37, Indels: 56
0.72 0.11 0.17
Matches are distributed among these distances:
12 1 0.00
14 87 0.36
15 14 0.06
16 111 0.46
17 26 0.11
ACGTcount: A:0.29, C:0.21, G:0.04, T:0.47
Consensus pattern (16 bp):
TCAATTCTTCAATTAT
Found at i:67849 original size:11 final size:11
Alignment explanation
Indices: 67835--67869 Score: 61
Period size: 11 Copynumber: 3.2 Consensus size: 11
67825 TTAACTATTA
67835 ATTAATTAGAT
1 ATTAATTAGAT
*
67846 ATTAATTAGCT
1 ATTAATTAGAT
67857 ATTAATTAGAT
1 ATTAATTAGAT
67868 AT
1 AT
67870 AGTATAATGG
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
11 22 1.00
ACGTcount: A:0.43, C:0.03, G:0.09, T:0.46
Consensus pattern (11 bp):
ATTAATTAGAT
Found at i:67864 original size:15 final size:15
Alignment explanation
Indices: 67820--67864 Score: 53
Period size: 15 Copynumber: 3.3 Consensus size: 15
67810 TTTATTCATT
*
67820 ATTAATTAACTATTA
1 ATTAATTAGCTATTA
67835 ATTAATTAG--A-T-
1 ATTAATTAGCTATTA
67846 ATTAATTAGCTATTA
1 ATTAATTAGCTATTA
67861 ATTA
1 ATTA
67865 GATATAGTAT
Statistics
Matches: 25, Mismatches: 1, Indels: 8
0.74 0.03 0.24
Matches are distributed among these distances:
11 9 0.36
12 1 0.04
13 2 0.08
14 1 0.04
15 12 0.48
ACGTcount: A:0.44, C:0.04, G:0.04, T:0.47
Consensus pattern (15 bp):
ATTAATTAGCTATTA
Found at i:83821 original size:601 final size:602
Alignment explanation
Indices: 82508--84259 Score: 3202
Period size: 601 Copynumber: 2.9 Consensus size: 602
82498 TGGTAAACCA
* *
82508 AGTAGTGTGATTATAGATGGAGAGAGTTGTACAAACATAGTTAATGATTATTTGGTAAAAGAGTT
1 AGTAGTGTGATTATAGATGGAGAGAGTTGTACAAACATAGTTAGTGATTATTTGGTGAAAGAGTT
* *
82573 ACAACTACCTACTTCTAAACATCCTAAACCCTATAGCTTAGGTTGGTTCAATGATAGAGAGGAGA
66 ACAACTACCTACTTCTAAACATCCTAAACCCTATAGCTTAGGTTGGTTCAATGATAGAGAAGAAA
* * * * *
82638 TTAGGGTTAACAAACAAGTTTTGGTTACTCTTTCTTTGGGTAGGTACAAAGAGGATGTCTTGTGT
131 TTAGGGTTAACAAACAAGTTTTGGTTACTCTTTCTTTGTGCAAGTACAAAGAGGATGTTTTGTGC
* * * *
82703 GACGTGCTACCAATGCGAGCTTGTCATGTTTTGCTTGGGAAGCCTTGGAAATATGACAACAAGGT
196 GATGTGCTACCAATGCGAGCATGTCATGTTTTGCTTGGGAAACCTTGGCAATATGACAACAAGGT
*
82768 GAAACATGATGGTGAGACAAACAAGTACTCTTTTAAGTGTGGTAAGATTCCTATAAATTTAGTTC
261 GAAACATGATGGTGAGACAAACAAGTACTCTTTTAAGTGTGGTAAGATTCCTATAACTTTAGTTC
82833 CTTTATCACTTCAAGAAGCTTTAAAAGATCAAATTAAATTGAGAGATGATGTTGCTAAATTGGAT
326 CTTTATCACTTCAAGAAGCTTTAAAAGATCAAATTAAATTGAGAGATGATGTTGCTAAATTGGAT
* *
82898 GTTGAATTTAGGGCTAAAGAAAAGAGTAAATCTGAACCTGAAATTGATGATTGTTTTGATGATAA
391 GTTGAATTTAGGGCTAAAG-AAAGAGTAAATCGGAACCTAAAATTGATGATTGTTTTGATGATAA
82963 AACAACCTTAGTTGCAAAGAGTGTTTTAGAAGTTGTTTGCGATGATACTAAACCTAATTTGAGTG
455 AACAACCTTAGTTGCAAAGAGTGTTTTAGAAGTTGTTTGCGATGATACTAAACCTAATTTGAGTG
*
83028 TTGTTTGCGATGACACTAAATCTGTTTTGGATGCTAATTGTGATGTAAACAAATCTGTTTTGGTT
520 TTGTTTGCGATGACACTAAATCTGTTTTGGATGCTAATTGTGATGAAAACAAATCTGTTTTGGTT
83093 GATCATACCATTGAAAAT
585 GATCATACCATTGAAAAT
*
83111 AGTAGTGTGATTATAGATGGAGAGAGTTGTACAAACATAATTAGTGATTATTTGGTGAAAGAGTT
1 AGTAGTGTGATTATAGATGGAGAGAGTTGTACAAACATAGTTAGTGATTATTTGGTGAAAGAGTT
*
83176 ACAACTACCTACTTCTAAACATCCCAAACCCTATAGCTTAGGTTGGTTCAATGATAGAGAAGAAA
66 ACAACTACCTACTTCTAAACATCCTAAACCCTATAGCTTAGGTTGGTTCAATGATAGAGAAGAAA
83241 TTAGGGTTAACAAACAAGTTTTGGTTACTCTTTCTTTGTGCAAGTACAAAGAGGATGTTTTGTGC
131 TTAGGGTTAACAAACAAGTTTTGGTTACTCTTTCTTTGTGCAAGTACAAAGAGGATGTTTTGTGC
* *
83306 GATGTGCTACCAATGCGAGCATGTCATGTTTTGCTTGGGAAATCTTGGCAATATGACAACAGGGT
196 GATGTGCTACCAATGCGAGCATGTCATGTTTTGCTTGGGAAACCTTGGCAATATGACAACAAGGT
83371 GAAACATGATGGTGAGACAAACAAGTACTCTTTTAAGTGTGGTAAGATTCCTATAACTTTAGTTC
261 GAAACATGATGGTGAGACAAACAAGTACTCTTTTAAGTGTGGTAAGATTCCTATAACTTTAGTTC
*
83436 CTTTATCACTTTAAGAAGCTTTAAAAGATCAAATTAAATTGAGAGATGATGTTGCTAAATTGGAT
326 CTTTATCACTTCAAGAAGCTTTAAAAGATCAAATTAAATTGAGAGATGATGTTGCTAAATTGGAT
83501 GTTGAATTTAGGGCTAAAG-AAGAGTAAATCGGAACCTAAAATTGATGATTGTTTTGATGATAAA
391 GTTGAATTTAGGGCTAAAGAAAGAGTAAATCGGAACCTAAAATTGATGATTGTTTTGATGATAAA
83565 ACAACCTTAGTTGCAAAGAGTGTTTTAGAAGTTGTTTGCGATGATACTAAACCTAATTTGAGTGT
456 ACAACCTTAGTTGCAAAGAGTGTTTTAGAAGTTGTTTGCGATGATACTAAACCTAATTTGAGTGT
83630 TGTTTGCGATGACACTAAATCTGTTTTGGATGCTAATTGTGATGAAAACAAATCTGTTTTGGTTG
521 TGTTTGCGATGACACTAAATCTGTTTTGGATGCTAATTGTGATGAAAACAAATCTGTTTTGGTTG
83695 ATCATACCATTGAAAAT
586 ATCATACCATTGAAAAT
*
83712 AGTAGTGTGATTATAGATGGAGAGAGTTGTATAAACATAGTTAGTGATTATTTGGTGAAAGAGTT
1 AGTAGTGTGATTATAGATGGAGAGAGTTGTACAAACATAGTTAGTGATTATTTGGTGAAAGAGTT
83777 ACAACTACCTACTTCTAAACATCCTAAACCCTATAGCTTAGGTTGGTTCAATGATAGAGAAGAAA
66 ACAACTACCTACTTCTAAACATCCTAAACCCTATAGCTTAGGTTGGTTCAATGATAGAGAAGAAA
*
83842 TTAGGGTTAACAAACAAGTTTTGGTTACTCTTTCTTTGTGCAAGTACAAAGATGATGTTTTGTGC
131 TTAGGGTTAACAAACAAGTTTTGGTTACTCTTTCTTTGTGCAAGTACAAAGAGGATGTTTTGTGC
83907 GATGTGCTACCAATGCGAGCATGTCATGTTTTGCTTGGGAAACCTTGGCAATATGACAACAAGGT
196 GATGTGCTACCAATGCGAGCATGTCATGTTTTGCTTGGGAAACCTTGGCAATATGACAACAAGGT
*
83972 GAAACATGATGGTGAGACAAACAAGTACTCTTTTAAGTGTGGTAA-AGTTCCTATCACTTTAGTT
261 GAAACATGATGGTGAGACAAACAAGTACTCTTTTAAGTGTGGTAAGA-TTCCTATAACTTTAGTT
*
84036 CCTTTATCACTTCAAGAAGCTTTAAAAGATCAAATTAAATTGAGAGATGATTTTGCTAAATTGGA
325 CCTTTATCACTTCAAGAAGCTTTAAAAGATCAAATTAAATTGAGAGATGATGTTGCTAAATTGGA
*
84101 TGCTGAATTTAGGGCTAAAGAAAAGAGTAAATCGGAACCTAAAATTGATGATTGTTTTGATGATA
390 TGTTGAATTTAGGGCTAAAG-AAAGAGTAAATCGGAACCTAAAATTGATGATTGTTTTGATGATA
* *
84166 AAACAACCTTAGTTGCAAAGAGTGTTTTAGATGTTGTTTGCAATGATACTAAACCTAATTTGAGT
454 AAACAACCTTAGTTGCAAAGAGTGTTTTAGAAGTTGTTTGCGATGATACTAAACCTAATTTGAGT
84231 GTTGTTTGCGATGACACTAAATCTGTTTT
519 GTTGTTTGCGATGACACTAAATCTGTTTT
84260 AGGTGTTGTT
Statistics
Matches: 1112, Mismatches: 34, Indels: 6
0.97 0.03 0.01
Matches are distributed among these distances:
600 1 0.00
601 586 0.53
603 525 0.47
ACGTcount: A:0.33, C:0.12, G:0.21, T:0.33
Consensus pattern (602 bp):
AGTAGTGTGATTATAGATGGAGAGAGTTGTACAAACATAGTTAGTGATTATTTGGTGAAAGAGTT
ACAACTACCTACTTCTAAACATCCTAAACCCTATAGCTTAGGTTGGTTCAATGATAGAGAAGAAA
TTAGGGTTAACAAACAAGTTTTGGTTACTCTTTCTTTGTGCAAGTACAAAGAGGATGTTTTGTGC
GATGTGCTACCAATGCGAGCATGTCATGTTTTGCTTGGGAAACCTTGGCAATATGACAACAAGGT
GAAACATGATGGTGAGACAAACAAGTACTCTTTTAAGTGTGGTAAGATTCCTATAACTTTAGTTC
CTTTATCACTTCAAGAAGCTTTAAAAGATCAAATTAAATTGAGAGATGATGTTGCTAAATTGGAT
GTTGAATTTAGGGCTAAAGAAAGAGTAAATCGGAACCTAAAATTGATGATTGTTTTGATGATAAA
ACAACCTTAGTTGCAAAGAGTGTTTTAGAAGTTGTTTGCGATGATACTAAACCTAATTTGAGTGT
TGTTTGCGATGACACTAAATCTGTTTTGGATGCTAATTGTGATGAAAACAAATCTGTTTTGGTTG
ATCATACCATTGAAAAT
Found at i:84266 original size:33 final size:33
Alignment explanation
Indices: 84188--84292 Score: 122
Period size: 33 Copynumber: 3.2 Consensus size: 33
84178 TTGCAAAGAG
* * * *
84188 TGTTTTAGATGTTGTTTGCAATGATACTAAACC
1 TGTTTTAGGTGTTGTTTGCGATGACACTAAATC
**
84221 TAATTT-GAGTGTTGTTTGCGATGACACTAAATC
1 TGTTTTAG-GTGTTGTTTGCGATGACACTAAATC
* *
84254 TGTTTTAGGTGTTGTTTGTGATTACACTAAATC
1 TGTTTTAGGTGTTGTTTGCGATGACACTAAATC
84287 TGTTTT
1 TGTTTT
84293 GGATGCTAAT
Statistics
Matches: 60, Mismatches: 10, Indels: 4
0.81 0.14 0.05
Matches are distributed among these distances:
32 1 0.02
33 58 0.97
34 1 0.02
ACGTcount: A:0.24, C:0.10, G:0.20, T:0.46
Consensus pattern (33 bp):
TGTTTTAGGTGTTGTTTGCGATGACACTAAATC
Found at i:84306 original size:33 final size:33
Alignment explanation
Indices: 84240--84328 Score: 94
Period size: 33 Copynumber: 2.7 Consensus size: 33
84230 TGTTGTTTGC
* **
84240 GATG-ACACTAAATCTGTTTTAGGTGTTGTTTGT
1 GATGAACACTAAATCTGTTTT-GGTGCTAATTGT
*
84273 GAT-TACACTAAATCTGTTTTGGATGCTAATTGT
1 GATGAACACTAAATCTGTTTTGG-TGCTAATTGT
*
84306 GATGAAAAC-AAATCTGTTTTGGT
1 GATGAACACTAAATCTGTTTTGGT
84329 TCATCATAGC
Statistics
Matches: 48, Mismatches: 5, Indels: 7
0.80 0.08 0.12
Matches are distributed among these distances:
32 3 0.06
33 42 0.88
34 3 0.06
ACGTcount: A:0.27, C:0.10, G:0.21, T:0.42
Consensus pattern (33 bp):
GATGAACACTAAATCTGTTTTGGTGCTAATTGT
Found at i:87503 original size:16 final size:16
Alignment explanation
Indices: 87480--87565 Score: 104
Period size: 16 Copynumber: 5.4 Consensus size: 16
87470 TGGATTTGGG
87480 TCAGGTTAATTCGGGT
1 TCAGGTTAATTCGGGT
* *
87496 TCATGTTAATTTGGG-
1 TCAGGTTAATTCGGGT
87511 TCAGGTTAATTCGGGT
1 TCAGGTTAATTCGGGT
* *
87527 TCGGGTTGAATTTGGG-
1 TCAGGTT-AATTCGGGT
87543 TCAGGTTAATTCGGGT
1 TCAGGTTAATTCGGGT
*
87559 TCGGGTT
1 TCAGGTT
87566 CTGTTTGGGT
Statistics
Matches: 58, Mismatches: 9, Indels: 6
0.79 0.12 0.08
Matches are distributed among these distances:
15 20 0.34
16 31 0.53
17 7 0.12
ACGTcount: A:0.16, C:0.10, G:0.34, T:0.40
Consensus pattern (16 bp):
TCAGGTTAATTCGGGT
Found at i:87544 original size:32 final size:32
Alignment explanation
Indices: 87458--87565 Score: 173
Period size: 32 Copynumber: 3.4 Consensus size: 32
87448 TAGGCTTGAG
* *
87458 TCGGATTCGGGTTGGATTTGGGTCAGGTTAAT
1 TCGGGTTCGGGTTGAATTTGGGTCAGGTTAAT
**
87490 TCGGGTTCATGTT-AATTTGGGTCAGGTTAAT
1 TCGGGTTCGGGTTGAATTTGGGTCAGGTTAAT
87521 TCGGGTTCGGGTTGAATTTGGGTCAGGTTAAT
1 TCGGGTTCGGGTTGAATTTGGGTCAGGTTAAT
87553 TCGGGTTCGGGTT
1 TCGGGTTCGGGTT
87566 CTGTTTGGGT
Statistics
Matches: 69, Mismatches: 6, Indels: 2
0.90 0.08 0.03
Matches are distributed among these distances:
31 28 0.41
32 41 0.59
ACGTcount: A:0.15, C:0.10, G:0.36, T:0.39
Consensus pattern (32 bp):
TCGGGTTCGGGTTGAATTTGGGTCAGGTTAAT
Found at i:87734 original size:16 final size:16
Alignment explanation
Indices: 87713--87834 Score: 127
Period size: 16 Copynumber: 7.6 Consensus size: 16
87703 TTTTCATAAA
*
87713 TTTTCGGATTCGGGTT
1 TTTTCGGGTTCGGGTT
* * *
87729 TTTTCGGGTTTGAGCT
1 TTTTCGGGTTCGGGTT
87745 TTTTCGGGTTCGGGTT
1 TTTTCGGGTTCGGGTT
* * *
87761 TTTTCGGGTTTGAGCT
1 TTTTCGGGTTCGGGTT
87777 TTTTCGGGTTCGGGTT
1 TTTTCGGGTTCGGGTT
* * *
87793 TTTTCGGGTTTGAGCT
1 TTTTCGGGTTCGGGTT
* **
87809 TTTTCGAGTTCGTATT
1 TTTTCGGGTTCGGGTT
87825 TTTTCGGGTT
1 TTTTCGGGTT
87835 GAGGCGGATT
Statistics
Matches: 84, Mismatches: 22, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
16 84 1.00
ACGTcount: A:0.05, C:0.12, G:0.31, T:0.52
Consensus pattern (16 bp):
TTTTCGGGTTCGGGTT
Found at i:87757 original size:32 final size:32
Alignment explanation
Indices: 87713--87834 Score: 208
Period size: 32 Copynumber: 3.8 Consensus size: 32
87703 TTTTCATAAA
*
87713 TTTTCGGATTCGGGTTTTTTCGGGTTTGAGCT
1 TTTTCGGGTTCGGGTTTTTTCGGGTTTGAGCT
87745 TTTTCGGGTTCGGGTTTTTTCGGGTTTGAGCT
1 TTTTCGGGTTCGGGTTTTTTCGGGTTTGAGCT
87777 TTTTCGGGTTCGGGTTTTTTCGGGTTTGAGCT
1 TTTTCGGGTTCGGGTTTTTTCGGGTTTGAGCT
* **
87809 TTTTCGAGTTCGTATTTTTTCGGGTT
1 TTTTCGGGTTCGGGTTTTTTCGGGTT
87835 GAGGCGGATT
Statistics
Matches: 86, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
32 86 1.00
ACGTcount: A:0.05, C:0.12, G:0.31, T:0.52
Consensus pattern (32 bp):
TTTTCGGGTTCGGGTTTTTTCGGGTTTGAGCT
Found at i:87847 original size:64 final size:64
Alignment explanation
Indices: 87715--87849 Score: 191
Period size: 64 Copynumber: 2.1 Consensus size: 64
87705 TTCATAAATT
* * ***
87715 TTCGGATTCGGGTTTTTTCGGGTTTGAGCTTTTTCGGGTTCGGGTTTTTTCGGGTTTGAGCTTT
1 TTCGGATTCGGGTTTTTTCGGGTTTGAGCTTTTTCGAGTTCGGATTTTTTCGGGTTTGAGCGGA
* *
87779 TTCGGGTTCGGGTTTTTTCGGGTTTGAGCTTTTTCGAGTTCGTATTTTTTCGGG-TTGAGGCGGA
1 TTCGGATTCGGGTTTTTTCGGGTTTGAGCTTTTTCGAGTTCGGATTTTTTCGGGTTTGA-GCGGA
87843 TTCGGAT
1 TTCGGAT
87850 AGTTGATTTT
Statistics
Matches: 62, Mismatches: 8, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
63 4 0.06
64 58 0.94
ACGTcount: A:0.07, C:0.13, G:0.33, T:0.47
Consensus pattern (64 bp):
TTCGGATTCGGGTTTTTTCGGGTTTGAGCTTTTTCGAGTTCGGATTTTTTCGGGTTTGAGCGGA
Found at i:88800 original size:30 final size:30
Alignment explanation
Indices: 88766--88822 Score: 80
Period size: 30 Copynumber: 1.9 Consensus size: 30
88756 CTTCTTTCTC
*
88766 CTTGAAATATTTCTTCAATGAA-CTTCATGA
1 CTTGAAAT-TATCTTCAATGAATCTTCATGA
*
88796 CTTGAAATTATCTTCAATTAATCTTCA
1 CTTGAAATTATCTTCAATGAATCTTCA
88823 ATCACGAACT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
29 11 0.46
30 13 0.54
ACGTcount: A:0.33, C:0.18, G:0.07, T:0.42
Consensus pattern (30 bp):
CTTGAAATTATCTTCAATGAATCTTCATGA
Found at i:92166 original size:240 final size:240
Alignment explanation
Indices: 91720--92426 Score: 1389
Period size: 240 Copynumber: 3.0 Consensus size: 240
91710 TAGGAGCCTT
91720 CAATTTGGAACCCTAACTATGGCATTTTGCATTTTGTCTTATTTTTCTAATCATCCAGCACTAGT
1 CAATTTGGAACCCTAACTATGGCATTTTGCATTTTGTCTTATTTTTCTAATCATCCAGCACTAGT
91785 AAGCTTTCATTCATTGACTCTTTTCATTTGTAAATTTT-GAGCTTAGTTATAGTTTCAATGACCT
66 AAGCTTTCATTCATTGACTCTTTTCATTTGTAAATTTTGGAGCTTAGTTATAGTTTCAATGACCT
91849 TTTATTGTAAGGAGTTGCTCTACCTCTATTGTGTAGCACTTTGCAGCCAAATGTTTCTAACTTCA
131 TTTATTGTAAGGAGTTGCTCTACCTCTATTGTGTAGCACTTTGCAGCCAAATGTTTCTAACTTCA
91914 ACATGGTTAATAACGATGGCTCTCCAAGATCTCCTCGAACTCTAG
196 ACATGGTTAATAACGATGGCTCTCCAAGATCTCCTCGAACTCTAG
91959 CAATTTGGAACCCTAACTATGGCATTTTGCATTTTGTCTTATTTTTCTAATCATCCAGCACTAGT
1 CAATTTGGAACCCTAACTATGGCATTTTGCATTTTGTCTTATTTTTCTAATCATCCAGCACTAGT
92024 AAGCTTTCATTCATTGACTCTTTTCATTTGTAAATTTTGGAGCTTAGTTATAGTTTCAATGACCT
66 AAGCTTTCATTCATTGACTCTTTTCATTTGTAAATTTTGGAGCTTAGTTATAGTTTCAATGACCT
92089 TTTATTGTAAGGAGTTGCTCTACCTCTATTGTGTAGCACTTTGCAGCCAAATGTTTCTAACTTCA
131 TTTATTGTAAGGAGTTGCTCTACCTCTATTGTGTAGCACTTTGCAGCCAAATGTTTCTAACTTCA
92154 ACATGGTTAATAACGATGGCTCTCCAAGATCTCCTCGAACTCTAG
196 ACATGGTTAATAACGATGGCTCTCCAAGATCTCCTCGAACTCTAG
92199 CAATTTGGAACCCTAACTATGGCATTTTGCATTTTGTCTTATTTTTCTAATCATCCAGCACTAGT
1 CAATTTGGAACCCTAACTATGGCATTTTGCATTTTGTCTTATTTTTCTAATCATCCAGCACTAGT
92264 AAGCTTTCATTCATTGACTCTTTTCATTTGTAAATTTTGGAGCTTAGTTATAGTTTCAATGACCT
66 AAGCTTTCATTCATTGACTCTTTTCATTTGTAAATTTTGGAGCTTAGTTATAGTTTCAATGACCT
*
92329 TTTATTGTAAGGAGTTGCACTACCTCTATTGTGTAGCACTTTGCAGCCAAATGTTTCTAACTTCA
131 TTTATTGTAAGGAGTTGCTCTACCTCTATTGTGTAGCACTTTGCAGCCAAATGTTTCTAACTTCA
*
92394 ACATGGTTAATAACCATGGCTCTCCAAGATCTC
196 ACATGGTTAATAACGATGGCTCTCCAAGATCTC
92427 GAACTCTACC
Statistics
Matches: 465, Mismatches: 2, Indels: 1
0.99 0.00 0.00
Matches are distributed among these distances:
239 103 0.22
240 362 0.78
ACGTcount: A:0.25, C:0.20, G:0.15, T:0.40
Consensus pattern (240 bp):
CAATTTGGAACCCTAACTATGGCATTTTGCATTTTGTCTTATTTTTCTAATCATCCAGCACTAGT
AAGCTTTCATTCATTGACTCTTTTCATTTGTAAATTTTGGAGCTTAGTTATAGTTTCAATGACCT
TTTATTGTAAGGAGTTGCTCTACCTCTATTGTGTAGCACTTTGCAGCCAAATGTTTCTAACTTCA
ACATGGTTAATAACGATGGCTCTCCAAGATCTCCTCGAACTCTAG
Found at i:94517 original size:22 final size:22
Alignment explanation
Indices: 94489--94540 Score: 104
Period size: 22 Copynumber: 2.4 Consensus size: 22
94479 GACGAGTTGT
94489 GACAAACAATTGAAATAATTGC
1 GACAAACAATTGAAATAATTGC
94511 GACAAACAATTGAAATAATTGC
1 GACAAACAATTGAAATAATTGC
94533 GACAAACA
1 GACAAACA
94541 TGGTCTCTAT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 30 1.00
ACGTcount: A:0.52, C:0.15, G:0.13, T:0.19
Consensus pattern (22 bp):
GACAAACAATTGAAATAATTGC
Done.