Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01006838.1 Corchorus capsularis cultivar CVL-1 contig06859, 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: 20995
ACGTcount: A:0.31, C:0.19, G:0.20, T:0.31
Found at i:1612 original size:33 final size:32
Alignment explanation
Indices: 1517--1623 Score: 108
Period size: 33 Copynumber: 3.2 Consensus size: 32
1507 AGCACTAGTG
* *
1517 ACCGGCCATGCGACTTGGAGAAGTCCGGCCAAC
1 ACCGGCCACGCGAC-TGGAGATGTCCGGCCAAC
* * *
1550 ACTGGCCACGTGACTCGGAGATGCCCGGCCAAC
1 ACCGGCCACGCGACT-GGAGATGTCCGGCCAAC
* *
1583 ACCGGCCACGCGACATGGACATGTACGGCC-AC
1 ACCGGCCACGCGAC-TGGAGATGTCCGGCCAAC
1615 AACCGGCCA
1 -ACCGGCCA
1624 TCGCTAGGCG
Statistics
Matches: 61, Mismatches: 10, Indels: 6
0.79 0.13 0.08
Matches are distributed among these distances:
32 3 0.05
33 57 0.93
34 1 0.02
ACGTcount: A:0.24, C:0.36, G:0.29, T:0.10
Consensus pattern (32 bp):
ACCGGCCACGCGACTGGAGATGTCCGGCCAAC
Found at i:4126 original size:198 final size:201
Alignment explanation
Indices: 3739--4192 Score: 612
Period size: 198 Copynumber: 2.3 Consensus size: 201
3729 AAGATAAGAA
* * * *
3739 TCAACTTTCTTGCATTTAGGTTCTAGTTTTCCTAAAACGCCCTTTCGGACAAAGGGTTAGTTTTG
1 TCAAATTTCTTGCATTTAGGTTCTAGTTTTCCTAAAACGCCCTTTCAGACAAAGGGCTAGTTCTG
* *
3804 TCACATTCCAGTATCCAAGTTCAGCATTTTCAATTCCCCAAAACGCCCTTTCGGACAAAGGGTTA
66 TCACATTCCAGTATCCAAGTTCAGCATATTCAATTCCCCAAAACACCCTTTCGGACAAAGGGTTA
* * *
3869 GTTTTGTAAAATTTCTTGCATTTAGGTTCTAGTTTTCCCAAAATGCCCTTTCGGACAAAGGGTTA
131 GTTTTCTAAAATTTCTTGCATTTAGGTTCTAGTTTTCCCAAAACGCCCTTTCAGACAAAGGGTTA
**
3934 GTTTTG
196 GTTTAC
* ** * * *
3940 TCAAATTTCTTGCATTGAGACTCTAGTTTTCCCAAAACACCC-TTCAAACAAAGGGCTAGTTCTG
1 TCAAATTTCTTGCATTTAGGTTCTAGTTTTCCTAAAACGCCCTTTCAGACAAAGGGCTAGTTCTG
* * * * *
4004 TCACATTCCATTATCTAAGTTCA-CAATATTCGATT-CCCAAAATACCCTTTCGGACATAGGGTT
66 TCACATTCCAGTATCCAAGTTCAGC-ATATTCAATTCCCCAAAACACCCTTTCGGACAAAGGGTT
* * * *
4067 AGTTTTCTCATA-TTCTTGTATTTAGGTTCTAGTTTTCCTAAAACGCCCTTTCAGACAAAGGGTT
130 AGTTTTCTAAAATTTCTTGCATTTAGGTTCTAGTTTTCCCAAAACGCCCTTTCAGACAAAGGGTT
4131 AGTTTAC
195 AGTTTAC
* *
4138 TCATA-TTCTTGCATTTAGGTTCTAGATTTCCTAAAACGCCCTTTCAGACAAAGGG
1 TCAAATTTCTTGCATTTAGGTTCTAGTTTTCCTAAAACGCCCTTTCAGACAAAGGG
4193 TTGGTTTTGT
Statistics
Matches: 217, Mismatches: 34, Indels: 7
0.84 0.13 0.03
Matches are distributed among these distances:
197 30 0.14
198 69 0.32
199 35 0.16
200 47 0.22
201 36 0.17
ACGTcount: A:0.26, C:0.22, G:0.16, T:0.36
Consensus pattern (201 bp):
TCAAATTTCTTGCATTTAGGTTCTAGTTTTCCTAAAACGCCCTTTCAGACAAAGGGCTAGTTCTG
TCACATTCCAGTATCCAAGTTCAGCATATTCAATTCCCCAAAACACCCTTTCGGACAAAGGGTTA
GTTTTCTAAAATTTCTTGCATTTAGGTTCTAGTTTTCCCAAAACGCCCTTTCAGACAAAGGGTTA
GTTTAC
Found at i:4154 original size:64 final size:64
Alignment explanation
Indices: 3840--4661 Score: 526
Period size: 64 Copynumber: 12.8 Consensus size: 64
3830 TTTTCAATTC
* * *
3840 CCCAAAACGCCCTTTCGGACAAAGGGTTAGTTTTGTAAAATTTCTTGCATTTAGGTTCTAGTTTT
1 CCCAAAACGCCCTTTCGGACAAAGGGTTAGTTTTCTCACA-TTCTTGCATTTAGGTTCTAGTTTT
* * * * **
3905 CCCAAAATGCCCTTTCGGACAAAGGGTTAGTTTTGTCAAATTTCTTGCATTGAGACTCTAGTTTT
1 CCCAAAACGCCCTTTCGGACAAAGGGTTAGTTTTCTCACA-TTCTTGCATTTAGGTTCTAGTTTT
* ** * * * * *
3970 CCCAAAACACCC-TTCAAACAAAGGGCTAGTTCTGTCACATTCCATT--ATCTAAGTTCACAATA
1 CCCAAAACGCCCTTTCGGACAAAGGGTTAGTTTTCTCACATT-C-TTGCATTTAGGTT--C--TA
4032 -TTCGATT
60 GTT---TT
** * * *
4039 CCCAAAATACCCTTTCGGACATAGGGTTAGTTTTCTCATATTCTTGTATTTAGGTTCTAGTTTT
1 CCCAAAACGCCCTTTCGGACAAAGGGTTAGTTTTCTCACATTCTTGCATTTAGGTTCTAGTTTT
* * * * *
4103 CCTAAAACGCCCTTTCAGACAAAGGGTTAGTTTACTCATATTCTTGCATTTAGGTTCTAGATTT
1 CCCAAAACGCCCTTTCGGACAAAGGGTTAGTTTTCTCACATTCTTGCATTTAGGTTCTAGTTTT
* * * * * * *
4167 CCTAAAACGCCCTTTCAGACAAAGGGTTGGTTTTGTCA-TTTCTTGCATTGAAGTTCTAGTTTT
1 CCCAAAACGCCCTTTCGGACAAAGGGTTAGTTTTCTCACATTCTTGCATTTAGGTTCTAGTTTT
* * ** * * *
4230 CGCAAAACGCCCTTTCGGACAAA-GGTCTAGTTTTGTCACATTCCAGTATCTAAGTTC-AGCATT
1 CCCAAAACGCCCTTTCGGACAAAGGGT-TAGTTTTCTCACATTCTTGCATTTAGGTTCTAG----
4293 TTTATTT
61 --T-TTT
** * * *
4300 CCCAAAATACCCTTTCGGACAAAGGGTTAG-TTTCTTCAAATTCCTGCATTTAGGATCTAGTTTT
1 CCCAAAACGCCCTTTCGGACAAAGGGTTAGTTTTC-TCACATTCTTGCATTTAGGTTCTAGTTTT
* * * * * *
4364 CCCAAACCGCCCTTTCAGACAAAGGGCT-GATTTCTCACATTCTTGCATTTAAGTT-TAGTATT
1 CCCAAAACGCCCTTTCGGACAAAGGGTTAGTTTTCTCACATTCTTGCATTTAGGTTCTAGTTTT
** * * * * *
4426 CCCAAAATACCCTTTTGGACAAAGGGTCAG-TTTCTTCACATTCCTGCACTTAGATTCTAG--TT
1 CCCAAAACGCCCTTTCGGACAAAGGGTTAGTTTTC-TCACATTCTTGCATTTAGGTTCTAGTTTT
** ** * * * * * * *
4488 CCCAAAATACCCTTTCAAACAAAGGGTCAGATTTGTCACATTCTCGCATATAGTTTC-A-ATTT
1 CCCAAAACGCCCTTTCGGACAAAGGGTTAGTTTTCTCACATTCTTGCATTTAGGTTCTAGTTTT
* ** * ** * ** ** *
4550 CCCAGAATACCCTTTCGGACAAAGGGTCAGTTTAGTCACACTCCCGCATTTAATTTCT-GATTT
1 CCCAAAACGCCCTTTCGGACAAAGGGTTAGTTTTCTCACATTCTTGCATTTAGGTTCTAGTTTT
* * * * * * *
4613 CCCCAGATGCCCTTTCAGACAAAGGATCAATTTTCTCACA-TCTCTGCAT
1 CCCAAAACGCCCTTTCGGACAAAGGGTTAGTTTTCTCACATTCT-TGCAT
4662 ACAAGTTTAA
Statistics
Matches: 610, Mismatches: 112, Indels: 72
0.77 0.14 0.09
Matches are distributed among these distances:
61 1 0.00
62 132 0.22
63 137 0.22
64 161 0.26
65 74 0.12
66 4 0.01
67 4 0.01
68 3 0.00
69 18 0.03
70 71 0.12
71 5 0.01
ACGTcount: A:0.26, C:0.23, G:0.15, T:0.35
Consensus pattern (64 bp):
CCCAAAACGCCCTTTCGGACAAAGGGTTAGTTTTCTCACATTCTTGCATTTAGGTTCTAGTTTT
Found at i:4314 original size:261 final size:260
Alignment explanation
Indices: 3840--4530 Score: 791
Period size: 261 Copynumber: 2.6 Consensus size: 260
3830 TTTTCAATTC
* * * *
3840 CCCAAAACGCCCTTTCGGACAAAGGGTTAGTTTTGTAAAATTTCTTGCATTTAGGTTCTAGTTTT
1 CCCAAAACGCCCTTTCAGACAAAGGGTTAG-TTTCTCAAA-TTCTTGCATTTAGGTTCTAGATTT
* *
3905 CCCAAAATGCCCTTTCGGACAAAGGGTTAGTTTTGTCAAATTTCTTGCATTGAGACTCTAGTTTT
64 CCCAAAACGCCCTTTCAGACAAAGGGTTAGTTTTGTC-AATTTCTTGCATTGAGACTCTAGTTTT
*
3970 CCCAAAACACCCTTCAAACAAAGGGCTAGTTCTGTCACATTCCATTATCTAAGTTCACAATATTC
128 CCCAAAACACCCTTCAAACAAAGGGCTAGTTCTGTCACATTCCAGTATCTAAGTTCACAATATTC
* * * * *
4035 GATTCCCAAAATACCCTTTCGGACATAGGGTTAGTTT-TCTCATATTCTTGTATTTAGGTTCTAG
193 GATTCCCAAAATACCCTTTCGGACAAAGGGTTAGTTTCT-TCAAATTCCTGCATTTAGGATCTAG
4099 TTTT
257 TTTT
* *
4103 CCTAAAACGCCCTTTCAGACAAAGGGTTAGTTTACTCATATTCTTGCATTTAGGTTCTAGATTTC
1 CCCAAAACGCCCTTTCAGACAAAGGGTTAGTTT-CTCAAATTCTTGCATTTAGGTTCTAGATTTC
* * *
4168 CTAAAACGCCCTTTCAGACAAAGGGTTGGTTTTGTC-ATTTCTTGCATTGA-AGTTCTAGTTTTC
65 CCAAAACGCCCTTTCAGACAAAGGGTTAGTTTTGTCAATTTCTTGCATTGAGA-CTCTAGTTTTC
* * ** * *
4231 GCAAAACGCCCTTTCGGACAAAGGTCTAGTTTTGTCACATTCCAGTATCTAAGTTCAGC-AT-TT
129 CCAAAACACCC-TTCAAACAAAGGGCTAGTTCTGTCACATTCCAGTATCTAAGTTCA-CAATATT
**
4294 TTATTTCCCAAAATACCCTTTCGGACAAAGGGTTAGTTTCTTCAAATTCCTGCATTTAGGATCTA
192 CGA-TTCCCAAAATACCCTTTCGGACAAAGGGTTAGTTTCTTCAAATTCCTGCATTTAGGATCTA
4359 GTTTT
256 GTTTT
* * * *
4364 CCCAAACCGCCCTTTCAGACAAAGGGCT-GATTTCTCACATTCTTGCATTTAAGTT-TAG-TATT
1 CCCAAAACGCCCTTTCAGACAAAGGGTTAG-TTTCTCAAATTCTTGCATTTAGGTTCTAGAT-TT
** ** * * *
4426 CCCAAAATACCCTTTTGGACAAAGGGTCAGTTTCT-TCACA-TTCCTGCACTT-AGATTCTAG--
64 CCCAAAACGCCCTTTCAGACAAAGGGTTAGTTT-TGTCA-ATTTCTTGCA-TTGAGACTCTAGTT
*
4486 TTCCCAAAATACCCTTTCAAACAAAGGG-TCAGATT-TGTCACATTC
126 TTCCCAAAACACCC-TTCAAACAAAGGGCT-AG-TTCTGTCACATTC
4531 TCGCATATAG
Statistics
Matches: 369, Mismatches: 44, Indels: 35
0.82 0.10 0.08
Matches are distributed among these distances:
257 1 0.00
258 35 0.09
259 36 0.10
260 72 0.20
261 133 0.36
262 61 0.17
263 31 0.08
ACGTcount: A:0.26, C:0.22, G:0.15, T:0.36
Consensus pattern (260 bp):
CCCAAAACGCCCTTTCAGACAAAGGGTTAGTTTCTCAAATTCTTGCATTTAGGTTCTAGATTTCC
CAAAACGCCCTTTCAGACAAAGGGTTAGTTTTGTCAATTTCTTGCATTGAGACTCTAGTTTTCCC
AAAACACCCTTCAAACAAAGGGCTAGTTCTGTCACATTCCAGTATCTAAGTTCACAATATTCGAT
TCCCAAAATACCCTTTCGGACAAAGGGTTAGTTTCTTCAAATTCCTGCATTTAGGATCTAGTTTT
Found at i:4323 original size:197 final size:196
Alignment explanation
Indices: 4112--4469 Score: 490
Period size: 197 Copynumber: 1.8 Consensus size: 196
4102 TCCTAAAACG
* * * *
4112 CCCTTTCAGACAAAGGGTTAGTTTAC-TCATATTCTTGCATTTAGGTTCTAGATTTCCTAAAACG
1 CCCTTTCAGACAAAGGGTTAGTTT-CTTCAAATTCCTGCATTTAGGATCTAGATTTCCCAAAACG
* * * * * * *
4176 CCCTTTCAGACAAAGGGTTGGTTTTGTCA-TTTCTTGCATTGAAGTTCTAGTTTTCGCAAAACGC
65 CCCTTTCAGACAAAGGGCT-GATTTCTCACATTCTTGCATTGAAGTT-TAGTATTCCCAAAACAC
4240 CCTTTCGGACAAA-GGTCTAGTTT-TGTCACATTCCAGTATCTAAGTTCAGCATTTTTATTTCCC
128 CCTTTCGGACAAAGGGTC-AGTTTCT-TCACATTCCAGTATCTAAGTTCAGCATTTTTATTTCCC
4303 AAAATA
191 AAAATA
* * *
4309 CCCTTTCGGACAAAGGGTTAGTTTCTTCAAATTCCTGCATTTAGGATCTAGTTTTCCCAAACCGC
1 CCCTTTCAGACAAAGGGTTAGTTTCTTCAAATTCCTGCATTTAGGATCTAGATTTCCCAAAACGC
* *
4374 CCTTTCAGACAAAGGGCTGATTTCTCACATTCTTGCATTTAAGTTTAGTATTCCCAAAATACCCT
66 CCTTTCAGACAAAGGGCTGATTTCTCACATTCTTGCATTGAAGTTTAGTATTCCCAAAACACCCT
*
4439 TTTGGACAAAGGGTCAGTTTCTTCACATTCC
131 TTCGGACAAAGGGTCAGTTTCTTCACATTCC
4470 TGCACTTAGA
Statistics
Matches: 140, Mismatches: 17, Indels: 9
0.84 0.10 0.05
Matches are distributed among these distances:
196 47 0.34
197 93 0.66
ACGTcount: A:0.25, C:0.23, G:0.16, T:0.36
Consensus pattern (196 bp):
CCCTTTCAGACAAAGGGTTAGTTTCTTCAAATTCCTGCATTTAGGATCTAGATTTCCCAAAACGC
CCTTTCAGACAAAGGGCTGATTTCTCACATTCTTGCATTGAAGTTTAGTATTCCCAAAACACCCT
TTCGGACAAAGGGTCAGTTTCTTCACATTCCAGTATCTAAGTTCAGCATTTTTATTTCCCAAAAT
A
Found at i:4447 original size:62 final size:62
Alignment explanation
Indices: 4293--4637 Score: 276
Period size: 62 Copynumber: 5.5 Consensus size: 62
4283 GTTCAGCATT
* *
4293 TTTA-TTTCCCAAAATACCCTTTCGGACAAAGGGTTAGTTTCTTCAAATTCCTGCATTTAGGA
1 TTTAGTTTCCCAAAATACCCTTTCGGACAAAGGGTGAGTTTCTTCACATTCCTGCATTTA-GA
* *** * *
4355 TCTAGTTTTCCCAAACCGCCCTTTCAGACAAAGGGCTGA-TTTC-TCACATTCTTGCATTTA-A
1 TTTAG-TTTCCCAAAATACCCTTTCGGACAAAGGG-TGAGTTTCTTCACATTCCTGCATTTAGA
* * *
4416 GTTTAGTATTCCCAAAATACCCTTTTGGACAAAGGGTCAGTTTCTTCACATTCCTGCACTTAGA
1 -TTTAGT-TTCCCAAAATACCCTTTCGGACAAAGGGTGAGTTTCTTCACATTCCTGCATTTAGA
** * * *
4480 TTCTAG-TTCCCAAAATACCCTTTCAAACAAAGGGTCAGATTT-GTCACATT-CTCGCATATAG-
1 TT-TAGTTTCCCAAAATACCCTTTCGGACAAAGGGTGAG-TTTCTTCACATTCCT-GCATTTAGA
* * * ** * *
4541 TTTCAATTTCCCAGAATACCCTTTCGGACAAAGGGTCAGTTTAGTCACACTCCCGCATTTA-A
1 TTT-AGTTTCCCAAAATACCCTTTCGGACAAAGGGTGAGTTTCTTCACATTCCTGCATTTAGA
* * * * *
4603 TTTCTGATTTCCCCAGATGCCCTTTCAGACAAAGG
1 TTT-AG-TTTCCCAAAATACCCTTTCGGACAAAGG
4638 ATCAATTTTC
Statistics
Matches: 229, Mismatches: 37, Indels: 33
0.77 0.12 0.11
Matches are distributed among these distances:
60 1 0.00
61 12 0.05
62 122 0.53
63 59 0.26
64 33 0.14
65 2 0.01
ACGTcount: A:0.27, C:0.25, G:0.14, T:0.33
Consensus pattern (62 bp):
TTTAGTTTCCCAAAATACCCTTTCGGACAAAGGGTGAGTTTCTTCACATTCCTGCATTTAGA
Found at i:4570 original size:124 final size:123
Alignment explanation
Indices: 4296--4714 Score: 416
Period size: 124 Copynumber: 3.3 Consensus size: 123
4286 CAGCATTTTT
* *
4296 ATTTCCCAAAATACCCTTTCGGACAAAGGGTTAGTTTCTTCAAATTCCTGCATTTAGGA-TCTAG
1 ATTTCCCAAAATACCCTTTCGGACAAAGGGTCAGTTTCTTCACATTCCTGCATTTA-GATTCTAG
** * * *
4360 TTTTCCCAAACCGCCCTTTCAGACAAAGGG-CTGATTTCTCACATTCTTGCATTTAAGTTTA
65 --TTCCCAAAATGCCCTTTCAGACAAAGGGTCAGATTTCTCACATTCTCGCATAT-AGTTTA
* * *
4421 GTATTCCCAAAATACCCTTTTGGACAAAGGGTCAGTTTCTTCACATTCCTGCACTTAGATTCTAG
1 AT-TTCCCAAAATACCCTTTCGGACAAAGGGTCAGTTTCTTCACATTCCTGCATTTAGATTCTAG
* * *
4486 TTCCCAAAATACCCTTTCAAACAAAGGGTCAGATTTGTCACATTCTCGCATATAGTTTCA
65 TTCCCAAAATGCCCTTTCAGACAAAGGGTCAGATTTCTCACATTCTCGCATATAGTTT-A
* ** * *
4546 ATTTCCCAGAATACCCTTTCGGACAAAGGGTCAGTTTAGTCACACTCCCGCATTTA-ATTTCTGA
1 ATTTCCCAAAATACCCTTTCGGACAAAGGGTCAGTTTCTTCACATTCCTGCATTTAGA-TTCT-A
* * * * *
4610 TTTCCCCAGATGCCCTTTCAGACAAAGGATCA-ATTTTCTCACA-TCTCTGCATACAAGTTTA
64 GTTCCCAAAATGCCCTTTCAGACAAAGGGTCAGA-TTTCTCACATTCTC-GCATA-TAGTTTA
* * *
4671 ATCTTGGTTTCCTAGAATACCCTTTCGGACAAAGGGTCAATTTC
1 A------TTTCCCAAAATACCCTTTCGGACAAAGGGTCAGTTTC
4715 GCCATCCTGC
Statistics
Matches: 247, Mismatches: 32, Indels: 24
0.82 0.11 0.08
Matches are distributed among these distances:
123 1 0.00
124 85 0.34
125 67 0.27
126 60 0.24
131 34 0.14
ACGTcount: A:0.27, C:0.25, G:0.14, T:0.33
Consensus pattern (123 bp):
ATTTCCCAAAATACCCTTTCGGACAAAGGGTCAGTTTCTTCACATTCCTGCATTTAGATTCTAGT
TCCCAAAATGCCCTTTCAGACAAAGGGTCAGATTTCTCACATTCTCGCATATAGTTTA
Found at i:4652 original size:63 final size:62
Alignment explanation
Indices: 4424--4713 Score: 180
Period size: 62 Copynumber: 4.6 Consensus size: 62
4414 AAGTTTAGTA
* ** * * * * *
4424 TTCCCAAAATACCCTTTTGGACAAAGGGTCAGTTTCT-TCACATTCCTGCACT-TAGA-TTCTAG
1 TTCCCAGAATACCCTTTCAGACAAAGGGTCAATTT-TGTCACACTCCCGCA-TATA-ATTTCAAT
* * * * *
4486 TTCCCAAAATACCCTTTCAAACAAAGGGTCAGA-TTTGTCACATTCTCGCATATAGTTTCAAT
1 TTCCCAGAATACCCTTTCAGACAAAGGGTCA-ATTTTGTCACACTCCCGCATATAATTTCAAT
* * * * *
4548 TTCCCAGAATACCCTTTCGGACAAAGGGTCAGTTTAGTCACACTCCCGCATTTAATTTCTGAT
1 TTCCCAGAATACCCTTTCAGACAAAGGGTCAATTTTGTCACACTCCCGCATATAATTTC-AAT
* * * * *
4611 TTCCCCAG-ATGCCCTTTCAGACAAAGGATCAATTTTCTCACA-TCTCTGCATACAAGTTT-AAT
1 TT-CCCAGAATACCCTTTCAGACAAAGGGTCAATTTTGTCACACTC-CCGCATATAA-TTTCAA-
4673 CTTGGT
62 -----T
* *
4679 TTCCTAGAATACCCTTTCGGACAAAGGGTCAATTT
1 TTCCCAGAATACCCTTTCAGACAAAGGGTCAATTT
4714 CGCCATCCTG
Statistics
Matches: 179, Mismatches: 33, Indels: 26
0.75 0.14 0.11
Matches are distributed among these distances:
61 2 0.01
62 99 0.55
63 39 0.22
64 8 0.04
67 4 0.02
68 27 0.15
ACGTcount: A:0.28, C:0.26, G:0.14, T:0.33
Consensus pattern (62 bp):
TTCCCAGAATACCCTTTCAGACAAAGGGTCAATTTTGTCACACTCCCGCATATAATTTCAAT
Found at i:6927 original size:42 final size:42
Alignment explanation
Indices: 6826--6927 Score: 134
Period size: 42 Copynumber: 2.4 Consensus size: 42
6816 CATGGAGCAA
** *
6826 CCGGCCATGACCGGCCAACGCAGGGGACATCGCACGAGCCAT
1 CCGGCCACAACCGGCCATCGCAGGGGACATCGCACGAGCCAT
* * *
6868 CCGGCCACAACCGGCCATCGCACGGGG-CATTGCATGGGCCAT
1 CCGGCCACAACCGGCCATCGCA-GGGGACATCGCACGAGCCAT
6910 CCGGCCACAACCGGCCAT
1 CCGGCCACAACCGGCCAT
6928 TCGATCCATT
Statistics
Matches: 53, Mismatches: 6, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
42 49 0.92
43 4 0.08
ACGTcount: A:0.22, C:0.40, G:0.29, T:0.09
Consensus pattern (42 bp):
CCGGCCACAACCGGCCATCGCAGGGGACATCGCACGAGCCAT
Found at i:8906 original size:155 final size:156
Alignment explanation
Indices: 8616--8918 Score: 484
Period size: 155 Copynumber: 1.9 Consensus size: 156
8606 TTAGGGTCAT
* *
8616 CTTGGCCAAATTTCATCTCAATTGGACTTAAGATGAAAAACTTATGCACGTTTTTCAGTTAAGGA
1 CTTGGCCAAATTTCAGCTCAATTAGACTTAAGATGAAAAACTTATGCACGTTTTTCAGTTAAGGA
* *
8681 CAGTTTGCGGTGAGAAACCAAGTTCACCATCAAGGAGAGCTCGGTTTTACTTAGAATTTTTTGCA
66 CAGTTTGCGGTGAGAAACCAAGTTCACCATCAAGGAGAGCTCGGTTTTACATAGAATTTTTTCCA
8746 CAATCTTGTGGAGATAATATAAGCCA
131 CAATCTTGTGGAGATAATATAAGCCA
* *
8772 CTTGG-CAAATTTCAGCTCAATTAGA-TTTAGAATGAAAAACTTATGCACGTTTTTCAGTTAAGT
1 CTTGGCCAAATTTCAGCTCAATTAGACTTAAG-ATGAAAAACTTATGCACGTTTTTCAGTTAAGG
* * *
8835 ATAGTTTGGGGTGAGAAACCAAGTTCACCATGAAGGAGAGCTCGGTTTTACATAGAATTTTTTCC
65 ACAGTTTGCGGTGAGAAACCAAGTTCACCATCAAGGAGAGCTCGGTTTTACATAGAATTTTTTCC
* *
8900 ATAATCTTGTGTAGATAAT
130 ACAATCTTGTGGAGATAAT
8919 TGTCGCAATG
Statistics
Matches: 135, Mismatches: 11, Indels: 3
0.91 0.07 0.02
Matches are distributed among these distances:
154 4 0.03
155 126 0.93
156 5 0.04
ACGTcount: A:0.32, C:0.16, G:0.20, T:0.33
Consensus pattern (156 bp):
CTTGGCCAAATTTCAGCTCAATTAGACTTAAGATGAAAAACTTATGCACGTTTTTCAGTTAAGGA
CAGTTTGCGGTGAGAAACCAAGTTCACCATCAAGGAGAGCTCGGTTTTACATAGAATTTTTTCCA
CAATCTTGTGGAGATAATATAAGCCA
Found at i:9547 original size:20 final size:18
Alignment explanation
Indices: 9522--9563 Score: 57
Period size: 18 Copynumber: 2.2 Consensus size: 18
9512 GAATGAATTT
9522 TTTTGATTTTGGTTTTTGAA
1 TTTTGATTTT--TTTTTGAA
*
9542 TTTTGATTTTTTTTTGGA
1 TTTTGATTTTTTTTTGAA
9560 TTTT
1 TTTT
9564 TGAAAACCTT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
18 11 0.52
20 10 0.48
ACGTcount: A:0.12, C:0.00, G:0.17, T:0.71
Consensus pattern (18 bp):
TTTTGATTTTTTTTTGAA
Found at i:13264 original size:35 final size:35
Alignment explanation
Indices: 13225--13292 Score: 127
Period size: 35 Copynumber: 1.9 Consensus size: 35
13215 TTTTAACTAT
*
13225 CCAAATTTTAAGCTCAAACCCATTACTAAGTTTCA
1 CCAAATTTTAAACTCAAACCCATTACTAAGTTTCA
13260 CCAAATTTTAAACTCAAACCCATTACTAAGTTT
1 CCAAATTTTAAACTCAAACCCATTACTAAGTTT
13293 TACCTTATAA
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
35 32 1.00
ACGTcount: A:0.38, C:0.25, G:0.04, T:0.32
Consensus pattern (35 bp):
CCAAATTTTAAACTCAAACCCATTACTAAGTTTCA
Found at i:13749 original size:26 final size:28
Alignment explanation
Indices: 13699--13759 Score: 90
Period size: 26 Copynumber: 2.2 Consensus size: 28
13689 TGTGACCAGG
13699 CAGAGGGAGAATTTTCCATCACCCATAC
1 CAGAGGGAGAATTTTCCATCACCCATAC
* *
13727 CAGAGGGA-AA-TTTCCGTCTCCCATAC
1 CAGAGGGAGAATTTTCCATCACCCATAC
13753 CAGAGGG
1 CAGAGGG
13760 TGACATCCTG
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
26 21 0.68
27 2 0.06
28 8 0.26
ACGTcount: A:0.30, C:0.28, G:0.23, T:0.20
Consensus pattern (28 bp):
CAGAGGGAGAATTTTCCATCACCCATAC
Found at i:14673 original size:30 final size:30
Alignment explanation
Indices: 14637--14696 Score: 102
Period size: 30 Copynumber: 2.0 Consensus size: 30
14627 CAAAGGACCA
14637 AATGGCATCTTTGGTGCGAATCCTACATCC
1 AATGGCATCTTTGGTGCGAATCCTACATCC
* *
14667 AATGGCATCTTTGGTGCGATTCCTCCATCC
1 AATGGCATCTTTGGTGCGAATCCTACATCC
14697 TTTGATATCT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 28 1.00
ACGTcount: A:0.20, C:0.28, G:0.20, T:0.32
Consensus pattern (30 bp):
AATGGCATCTTTGGTGCGAATCCTACATCC
Found at i:14707 original size:30 final size:30
Alignment explanation
Indices: 14637--14716 Score: 88
Period size: 30 Copynumber: 2.7 Consensus size: 30
14627 CAAAGGACCA
* *
14637 AATGGCATCTTTGGTGCGAATCCTACATCC
1 AATGACATCTTTGGTGCGATTCCTACATCC
* *
14667 AATGGCATCTTTGGTGCGATTCCTCCATCC
1 AATGACATCTTTGGTGCGATTCCTACATCC
** * *
14697 TTTGATATCTTCGGTGCGAT
1 AATGACATCTTTGGTGCGAT
14717 CCCATCTCCT
Statistics
Matches: 43, Mismatches: 7, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
30 43 1.00
ACGTcount: A:0.19, C:0.25, G:0.21, T:0.35
Consensus pattern (30 bp):
AATGACATCTTTGGTGCGATTCCTACATCC
Done.