Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01006699.1 Hibiscus syriacus cultivar Beakdansim tig00016673_pilon, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 41468
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Found at i:1526 original size:20 final size:20
Alignment explanation
Indices: 1501--1543 Score: 77
Period size: 20 Copynumber: 2.1 Consensus size: 20
1491 TACGACGAGG
*
1501 AACCGCCTCGACTGCCAAGT
1 AACCGCCTCGACTGCCAACT
1521 AACCGCCTCGACTGCCAACT
1 AACCGCCTCGACTGCCAACT
1541 AAC
1 AAC
1544 GGTGAGGATG
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.28, C:0.42, G:0.16, T:0.14
Consensus pattern (20 bp):
AACCGCCTCGACTGCCAACT
Found at i:4263 original size:17 final size:18
Alignment explanation
Indices: 4243--4284 Score: 50
Period size: 17 Copynumber: 2.4 Consensus size: 18
4233 CGGTCATGTT
4243 GGGTCAGGTCA-ACGGTC
1 GGGTCAGGTCAGACGGTC
* * *
4260 GGGTCGGGTCAGTCGGTT
1 GGGTCAGGTCAGACGGTC
4278 GGGTCAG
1 GGGTCAG
4285 ACCGGTCAAA
Statistics
Matches: 20, Mismatches: 4, Indels: 1
0.80 0.16 0.04
Matches are distributed among these distances:
17 10 0.50
18 10 0.50
ACGTcount: A:0.12, C:0.19, G:0.48, T:0.21
Consensus pattern (18 bp):
GGGTCAGGTCAGACGGTC
Found at i:4268 original size:22 final size:22
Alignment explanation
Indices: 4227--4271 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
4217 GACGGTCAAC
* *
4227 GGTCAACGGTCATGTTGGGTCA
1 GGTCAACGGTCAGGTCGGGTCA
*
4249 GGTCAACGGTCGGGTCGGGTCA
1 GGTCAACGGTCAGGTCGGGTCA
4271 G
1 G
4272 TCGGTTGGGT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.16, C:0.20, G:0.42, T:0.22
Consensus pattern (22 bp):
GGTCAACGGTCAGGTCGGGTCA
Found at i:4313 original size:28 final size:30
Alignment explanation
Indices: 4281--4339 Score: 95
Period size: 28 Copynumber: 2.0 Consensus size: 30
4271 GTCGGTTGGG
4281 TCAGACCGGTC-AAACCGATCA-AACCGGT
1 TCAGACCGGTCAAAACCGATCAGAACCGGT
*
4309 TCAGACCGGTCAAAACCGGTCAGAACCGGT
1 TCAGACCGGTCAAAACCGATCAGAACCGGT
4339 T
1 T
4340 GAAAACCGGT
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
28 11 0.39
29 9 0.32
30 8 0.29
ACGTcount: A:0.31, C:0.31, G:0.24, T:0.15
Consensus pattern (30 bp):
TCAGACCGGTCAAAACCGATCAGAACCGGT
Found at i:4318 original size:10 final size:9
Alignment explanation
Indices: 4279--4358 Score: 70
Period size: 9 Copynumber: 8.3 Consensus size: 9
4269 CAGTCGGTTG
*
4279 GGTCAGACC
1 GGTCAAACC
4288 GGTCAAACC
1 GGTCAAACC
*
4297 GATCAAACC
1 GGTCAAACC
*
4306 GGTTCAGACC
1 GG-TCAAACC
4316 GGTCAAAACC
1 GGTC-AAACC
4326 GGTCAGAACC
1 GGTCA-AACC
*
4336 GGTTGAAAACC
1 GG-T-CAAACC
*
4347 GGTTAAACC
1 GGTCAAACC
4356 GGT
1 GGT
4359 TTCCAGCAGC
Statistics
Matches: 59, Mismatches: 7, Indels: 10
0.78 0.09 0.13
Matches are distributed among these distances:
9 28 0.47
10 23 0.39
11 7 0.12
12 1 0.02
ACGTcount: A:0.31, C:0.28, G:0.26, T:0.15
Consensus pattern (9 bp):
GGTCAAACC
Found at i:4326 original size:20 final size:22
Alignment explanation
Indices: 4301--4359 Score: 74
Period size: 20 Copynumber: 2.9 Consensus size: 22
4291 CAAACCGATC
4301 AAACCGGTTCAG-ACCGG-TCA
1 AAACCGGTTCAGAACCGGTTCA
*
4321 AAACCGG-TCAGAACCGGTTGA
1 AAACCGGTTCAGAACCGGTTCA
4342 AAACCGGTT-A-AACCGGTT
1 AAACCGGTTCAGAACCGGTT
4360 TCCAGCAGCC
Statistics
Matches: 35, Mismatches: 1, Indels: 6
0.83 0.02 0.14
Matches are distributed among these distances:
19 4 0.11
20 20 0.57
21 10 0.29
22 1 0.03
ACGTcount: A:0.32, C:0.25, G:0.25, T:0.17
Consensus pattern (22 bp):
AAACCGGTTCAGAACCGGTTCA
Found at i:6578 original size:21 final size:21
Alignment explanation
Indices: 6552--6691 Score: 169
Period size: 21 Copynumber: 6.7 Consensus size: 21
6542 ACGATTTTAA
6552 ACTATCGCAATGCGAACTTGG
1 ACTATCGCAATGCGAACTTGG
6573 ACTATCGCAATGCGAACTTGG
1 ACTATCGCAATGCGAACTTGG
*
6594 ACTATCGCAATGCGAA-TATGT
1 ACTATCGCAATGCGAACT-TGG
* * * *
6615 A-AATCGTAATGCGATA-GTCG
1 ACTATCGCAATGCGA-ACTTGG
6635 ACTATCGCAATGCGAACTTGG
1 ACTATCGCAATGCGAACTTGG
* *
6656 ACTATCGGAATGCGAACTTCG
1 ACTATCGCAATGCGAACTTGG
*
6677 ACTATCGCATTGCGA
1 ACTATCGCAATGCGA
6692 TTTACATATT
Statistics
Matches: 101, Mismatches: 14, Indels: 8
0.82 0.11 0.07
Matches are distributed among these distances:
20 15 0.15
21 86 0.85
ACGTcount: A:0.30, C:0.22, G:0.23, T:0.25
Consensus pattern (21 bp):
ACTATCGCAATGCGAACTTGG
Found at i:6622 original size:83 final size:83
Alignment explanation
Indices: 6535--6691 Score: 242
Period size: 83 Copynumber: 1.9 Consensus size: 83
6525 GTTTCCAGAT
** *
6535 TCGTAATACGATTTTAAACTATCGCAATGCGAACTTGGACTATCGCAATGCGAACTTGGACTATC
1 TCGTAATACGATAGTAAACTATCGCAATGCGAACTTGGACTATCGCAATGCGAACTTCGACTATC
6600 GCAATGCGAATATGTAAA
66 GCAATGCGAATATGTAAA
* ** *
6618 TCGTAATGCGATAGTCGACTATCGCAATGCGAACTTGGACTATCGGAATGCGAACTTCGACTATC
1 TCGTAATACGATAGTAAACTATCGCAATGCGAACTTGGACTATCGCAATGCGAACTTCGACTATC
*
6683 GCATTGCGA
66 GCAATGCGA
6692 TTTACATATT
Statistics
Matches: 66, Mismatches: 8, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
83 66 1.00
ACGTcount: A:0.31, C:0.21, G:0.22, T:0.27
Consensus pattern (83 bp):
TCGTAATACGATAGTAAACTATCGCAATGCGAACTTGGACTATCGCAATGCGAACTTCGACTATC
GCAATGCGAATATGTAAA
Found at i:6959 original size:21 final size:21
Alignment explanation
Indices: 6933--7000 Score: 109
Period size: 21 Copynumber: 3.2 Consensus size: 21
6923 CACCAGTCGT
6933 TGCGATTTTGGACTATCGCAA
1 TGCGATTTTGGACTATCGCAA
6954 TGCGATTTTGGACTATCGCAA
1 TGCGATTTTGGACTATCGCAA
** *
6975 TGCGAACTTCGACTATCGCAA
1 TGCGATTTTGGACTATCGCAA
6996 TGCGA
1 TGCGA
7001 ATATGTAAAT
Statistics
Matches: 44, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
21 44 1.00
ACGTcount: A:0.25, C:0.22, G:0.24, T:0.29
Consensus pattern (21 bp):
TGCGATTTTGGACTATCGCAA
Found at i:7040 original size:21 final size:21
Alignment explanation
Indices: 7010--7124 Score: 121
Period size: 21 Copynumber: 5.5 Consensus size: 21
7000 AATATGTAAA
*
7010 TCGCAATGCGATAGTCAAAGT
1 TCGCATTGCGATAGTCAAAGT
*
7031 TCGCATTGCGATAGTCCAAGT
1 TCGCATTGCGATAGTCAAAGT
* * *
7052 TTGCATTGCGAT-TTACATA-T
1 TCGCATTGCGATAGT-CAAAGT
7072 TCGCATTGCGATAGTTC-AAGT
1 TCGCATTGCGATAG-TCAAAGT
*
7093 TCGCATTGCGATAGTCCAAA-A
1 TCGCATTGCGATAGT-CAAAGT
7114 TCGCATTGCGA
1 TCGCATTGCGA
7125 ATCTAGAAAC
Statistics
Matches: 78, Mismatches: 10, Indels: 12
0.78 0.10 0.12
Matches are distributed among these distances:
20 15 0.19
21 60 0.77
22 3 0.04
ACGTcount: A:0.27, C:0.21, G:0.22, T:0.30
Consensus pattern (21 bp):
TCGCATTGCGATAGTCAAAGT
Found at i:7143 original size:62 final size:62
Alignment explanation
Indices: 7010--7164 Score: 156
Period size: 62 Copynumber: 2.5 Consensus size: 62
7000 AATATGTAAA
* ** * * * *
7010 TCGCAATGCGATAGTCAAAGTTCGCATTGCGATAGTCCAAGTTTGCATTGCGATTTACATAT
1 TCGCATTGCGATAGTCAAAGTTCGCATTGCGATAGTCCAAAATCGCATTGCGATCTACAAAC
*
7072 TCGCATTGCGATAGTTC-AAGTTCGCATTGCGATAGTCCAAAATCGCATTGCGAATCTAGAAAC
1 TCGCATTGCGATAG-TCAAAGTTCGCATTGCGATAGTCCAAAATCGCATTGCG-ATCTACAAAC
** *
7135 T-G-ATTTGCGATA-TCGGAGATCGCATTGCGA
1 TCGCA-TTGCGATAGTCAAAGTTCGCATTGCGA
7165 ATTATCGATC
Statistics
Matches: 79, Mismatches: 10, Indels: 9
0.81 0.10 0.09
Matches are distributed among these distances:
60 2 0.03
61 14 0.18
62 54 0.68
63 9 0.11
ACGTcount: A:0.28, C:0.20, G:0.23, T:0.30
Consensus pattern (62 bp):
TCGCATTGCGATAGTCAAAGTTCGCATTGCGATAGTCCAAAATCGCATTGCGATCTACAAAC
Found at i:8875 original size:46 final size:45
Alignment explanation
Indices: 8825--8974 Score: 246
Period size: 46 Copynumber: 3.3 Consensus size: 45
8815 GTAAATTGAT
*
8825 ATTTATCCAAATTATTTTGGGTTTACAAAAAAACTCATGATTAGTA
1 ATTTA-CCAAATTATTTTGGGTTTACAAAAAAACACATGATTAGTA
*
8871 ATTTACCTAAATTATTTTGGGTTTACAGAAAAACACATGATTAGTA
1 ATTTACC-AAATTATTTTGGGTTTACAAAAAAACACATGATTAGTA
*
8917 ATTTTCCCAAATTATTTTGGGTTTACAAAAAAACACATGATTAGTA
1 A-TTTACCAAATTATTTTGGGTTTACAAAAAAACACATGATTAGTA
8963 ATTTACCAAATT
1 ATTTACCAAATT
8975 CTAACAACAT
Statistics
Matches: 97, Mismatches: 5, Indels: 5
0.91 0.05 0.05
Matches are distributed among these distances:
45 12 0.12
46 80 0.82
47 5 0.05
ACGTcount: A:0.39, C:0.12, G:0.11, T:0.38
Consensus pattern (45 bp):
ATTTACCAAATTATTTTGGGTTTACAAAAAAACACATGATTAGTA
Found at i:9529 original size:19 final size:20
Alignment explanation
Indices: 9505--9551 Score: 60
Period size: 21 Copynumber: 2.4 Consensus size: 20
9495 AAAATTTTCC
9505 AAATTTCCCTCT-ATTCTCA
1 AAATTTCCCTCTAATTCTCA
*
9524 AAATTTTCCTCTAAATTCTCA
1 AAATTTCCCTCT-AATTCTCA
*
9545 AATTTTC
1 AAATTTC
9552 AAGTTCTCAA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
19 11 0.48
21 12 0.52
ACGTcount: A:0.30, C:0.26, G:0.00, T:0.45
Consensus pattern (20 bp):
AAATTTCCCTCTAATTCTCA
Found at i:9543 original size:21 final size:20
Alignment explanation
Indices: 9504--9551 Score: 64
Period size: 19 Copynumber: 2.5 Consensus size: 20
9494 CAAAATTTTC
*
9504 CAAATTTCCCTCT--ATTCT
1 CAAATTTTCCTCTAAATTCT
9522 CAAAATTTTCCTCTAAATTCT
1 C-AAATTTTCCTCTAAATTCT
9543 CAAATTTTC
1 CAAATTTTC
9552 AAGTTCTCAA
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
18 1 0.04
19 11 0.42
20 8 0.31
21 6 0.23
ACGTcount: A:0.29, C:0.27, G:0.00, T:0.44
Consensus pattern (20 bp):
CAAATTTTCCTCTAAATTCT
Found at i:18468 original size:56 final size:54
Alignment explanation
Indices: 18408--18537 Score: 152
Period size: 54 Copynumber: 2.4 Consensus size: 54
18398 CGAGACACTA
*
18408 GTGCAAGTGTCCGACAGGGAGGTTAAAGACAGAGGATCAGACTTGCCAAGACATTG
1 GTGCAAGTGTCCGACAAGGA-G-TAAAGACAGAGGATCAGACTTGCCAAGACATTG
** * * * * * *
18464 GTGCAAGTGTATGACAAGGAGTCATGATAGAGTATCGGGCTTGCCAAGACATTG
1 GTGCAAGTGTCCGACAAGGAGTAAAGACAGAGGATCAGACTTGCCAAGACATTG
*
18518 GTGCAAGTGTCCGAAAAGGA
1 GTGCAAGTGTCCGACAAGGA
18538 ATCTCAAGAT
Statistics
Matches: 62, Mismatches: 12, Indels: 2
0.82 0.16 0.03
Matches are distributed among these distances:
54 44 0.71
55 1 0.02
56 17 0.27
ACGTcount: A:0.32, C:0.16, G:0.32, T:0.20
Consensus pattern (54 bp):
GTGCAAGTGTCCGACAAGGAGTAAAGACAGAGGATCAGACTTGCCAAGACATTG
Found at i:18537 original size:54 final size:55
Alignment explanation
Indices: 18449--18565 Score: 157
Period size: 54 Copynumber: 2.1 Consensus size: 55
18439 GAGGATCAGA
* * * * *
18449 CTTGCCAAGACATTGGTGCAAGTGTATGACAAGG-A-GTCATGATAGAGTATCGGG
1 CTTGCCAAGACATTGGTGCAAGTGTACGAAAAGGAATCTCAAGATA-AATATCGGG
*
18503 CTTGCCAAGACATTGGTGCAAGTGTCCGAAAAGGAATCTCAAGATAAATATCGGG
1 CTTGCCAAGACATTGGTGCAAGTGTACGAAAAGGAATCTCAAGATAAATATCGGG
18558 CTTGCCAA
1 CTTGCCAA
18566 AGCCACCAGA
Statistics
Matches: 55, Mismatches: 6, Indels: 3
0.86 0.09 0.05
Matches are distributed among these distances:
54 31 0.56
55 17 0.31
56 7 0.13
ACGTcount: A:0.32, C:0.18, G:0.27, T:0.23
Consensus pattern (55 bp):
CTTGCCAAGACATTGGTGCAAGTGTACGAAAAGGAATCTCAAGATAAATATCGGG
Found at i:19989 original size:2 final size:2
Alignment explanation
Indices: 19984--20034 Score: 102
Period size: 2 Copynumber: 25.5 Consensus size: 2
19974 ACACATTACA
19984 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
20026 AT AT AT AT A
1 AT AT AT AT A
20035 ATACACCAAT
Statistics
Matches: 49, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 49 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:22133 original size:134 final size:133
Alignment explanation
Indices: 21877--23351 Score: 1821
Period size: 134 Copynumber: 11.1 Consensus size: 133
21867 CAACTCCATA
* *
21877 TGTGAT-GAATCGAGC-AAGAAGTTGACATTGATCCAACTCCTTCTGCGATGGATTTGAACGAAA
1 TGTGATAGAATCGAGCTAA-AAGTTGACACTGATCCAACTCCTTCTGCGATGGATTTGAGCGAAA
* * * * **
21940 ATAAAAATGTCGATCAACTTCCTTTTGTGATGGAAATTGAACGATATGTTAATGCTGATCTACCT
65 ATAAAAATGTCGATCCACCTCCTTCTGTGATGG-AATCGAACGATATGTCGATGCTGATCTACCT
22005 CATTC
129 CATTC
** *
22010 TGTGATAGAATCGAGCTAAAAGTTGACACTGATCCAACTCCTTCTGTAATTGATTTGAGCGAAAA
1 TGTGATAGAATCGAGCTAAAAGTTGACACTGATCCAACTCCTTCTGCGATGGATTTGAGCGAAAA
* * * * * *
22075 TAAAAATATCGATCCACCTCATTCTGTGATGGAAATCAAACGACATGTCAATGTTGATCTACCTC
66 TAAAAATGTCGATCCACCTCCTTCTGTGATGG-AATCGAACGATATGTCGATGCTGATCTACCTC
*
22140 CTTC
130 ATTC
* * *
22144 TGTGATAGAATCGAGCTAAAAGGTGACACTGATCCAACTCCTTCTACGATGGATTTGAGCAAAAA
1 TGTGATAGAATCGAGCTAAAAGTTGACACTGATCCAACTCCTTCTGCGATGGATTTGAGCGAAAA
* * *
22209 TAAAAATGTCGATCAACCTCCTTCTGTGATGGAAATCGAACGATATGTCAATGCTGATCTGCCTC
66 TAAAAATGTCGATCCACCTCCTTCTGTGATGG-AATCGAACGATATGTCGATGCTGATCTACCTC
22274 ATTC
130 ATTC
* * * *
22278 TGTGATAGAATCGAGTTAAAAGTTGACGCTGATCTAACTCCTTCTGTGATGGATTTGAGCGAAAA
1 TGTGATAGAATCGAGCTAAAAGTTGACACTGATCCAACTCCTTCTGCGATGGATTTGAGCGAAAA
* * * * *
22343 TAAAAGTATCGATCCACTTCCTTCTGTGATGGAATCGAACGAGATGTCGATGCTGATCTACCTCT
66 TAAAAATGTCGATCCACCTCCTTCTGTGATGGAATCGAACGATATGTCGATGCTGATCTACCTCA
22408 TTC
131 TTC
* * * *
22411 TGTGATAGAATCGAGCAAAAAGTTGACGCTGATCCAACTCCTTCTGCGATGAATTTGAGCGAAGA
1 TGTGATAGAATCGAGCTAAAAGTTGACACTGATCCAACTCCTTCTGCGATGGATTTGAGCGAAAA
* *
22476 TAAAAATTTCGATCCACCTCATTCTGTGATGGAAATCGAACGATATGTCGATGCTGATCTACCTC
66 TAAAAATGTCGATCCACCTCCTTCTGTGATGG-AATCGAACGATATGTCGATGCTGATCTACCTC
*
22541 TTTC
130 ATTC
* * * *
22545 TGTGATAGAATCAAGCTAAAAGTTGACGCTGATCCAACTCCTTCTGTGATGGATTTGAGCAAAAA
1 TGTGATAGAATCGAGCTAAAAGTTGACACTGATCCAACTCCTTCTGCGATGGATTTGAGCGAAAA
* * *
22610 TAAAAATGTCGATCCACCTCCTTTTGTAATGGAAATCGAACGATATGTCAATGCTGATCTACCTT
66 TAAAAATGTCGATCCACCTCCTTCTGTGATGG-AATCGAACGATATGTCGATGCTGATCTACC-T
22675 C-TTC
129 CATTC
** * * * *
22679 TGTGATAGAATCGAG-TAAAAAGTTGATGCTGATCCAACTTCTTCTGCAATGGATTTGAACGAAG
1 TGTGATAGAATCGAGCT-AAAAGTTGACACTGATCCAACTCCTTCTGCGATGGATTTGAGCGAAA
* *
22743 ATAAAAATGTCGATCCACCTCCTTCTGTGATGGAATCAAATGATATGTCGATGCTGATCTACCTC
65 ATAAAAATGTCGATCCACCTCCTTCTGTGATGGAATCGAACGATATGTCGATGCTGATCTACCTC
*
22808 CTTC
130 ATTC
* * *
22812 TGTGATATAATCTAG-TAAAAAGTTGA-AGCTGATCCAACTCCTTCTGCGATGGATTTGAGTG--
1 TGTGATAGAATCGAGCT-AAAAGTTGACA-CTGATCCAACTCCTTCTGCGATGGATTTGAGCGAA
* ** * *
22873 -A-ACAAATGTCGATCCACCTCCTTCTGTGATGGAATCGAGTGATATGTCGGTGATGATCTACCT
64 AATAAAAATGTCGATCCACCTCCTTCTGTGATGGAATCGAACGATATGTCGATGCTGATCTACCT
*
22936 CCTTC
129 CATTC
* * *
22941 TGTGATAGAATCGAGCTAAAAGTTGACACTGATCCAACTCCTCCTTCGATGGATTTGAGTGAAAA
1 TGTGATAGAATCGAGCTAAAAGTTGACACTGATCCAACTCCTTCTGCGATGGATTTGAGCGAAAA
* * * * *
23006 TAAAAAAGTCGATCCATCTCTTTCTGTGATAGAATCGAACGATATGTCGATGTTGATCTACCTCA
66 TAAAAATGTCGATCCACCTCCTTCTGTGATGGAATCGAACGATATGTCGATGCTGATCTACCTCA
23071 TTC
131 TTC
* *
23074 TGTGATA-AATTCAAGCTAAAAGTTGACACTGATCCAACTCCTTCTGCGATGGATTTGAGTGAAA
1 TGTGATAGAA-TCGAGCTAAAAGTTGACACTGATCCAACTCCTTCTGCGATGGATTTGAGCGAAA
** * * * * * *
23138 ATAAAAATGTCGATCCATTTCCTTTTGTGATGGAATTGAGCGAAATGTTGGTGCTGATCTACCTT
65 ATAAAAATGTCGATCCACCTCCTTCTGTGATGGAATCGAACGATATGTCGATGCTGATCTACC-T
23203 C-TTC
129 CATTC
* * ** ** * * *
23207 TATGATAGAAACGAGAAAAAAGTTGATGCAGATCTAACTCCTTCCGCGATGGATTTGAGCG---A
1 TGTGATAGAATCGAGCTAAAAGTTGACACTGATCCAACTCCTTCTGCGATGGATTTGAGCGAAAA
* * * * * * * * *
23269 -ACAAATGTCGATCCATCTTCTTCTGTGATGGAATCAAACAAAATATTGGTGCTGATCTACCTCA
66 TAAAAATGTCGATCCACCTCCTTCTGTGATGGAATCGAACGATATGTCGATGCTGATCTACCTCA
23333 TTC
131 TTC
23336 TGTGATAGAATCGAGC
1 TGTGATAGAATCGAGC
23352 AAACAATTGA
Statistics
Matches: 1182, Mismatches: 143, Indels: 38
0.87 0.10 0.03
Matches are distributed among these distances:
128 2 0.00
129 183 0.15
130 4 0.00
132 5 0.00
133 426 0.36
134 558 0.47
135 4 0.00
ACGTcount: A:0.30, C:0.19, G:0.20, T:0.31
Consensus pattern (133 bp):
TGTGATAGAATCGAGCTAAAAGTTGACACTGATCCAACTCCTTCTGCGATGGATTTGAGCGAAAA
TAAAAATGTCGATCCACCTCCTTCTGTGATGGAATCGAACGATATGTCGATGCTGATCTACCTCA
TTC
Found at i:22631 original size:401 final size:397
Alignment explanation
Indices: 21877--23351 Score: 1892
Period size: 401 Copynumber: 3.7 Consensus size: 397
21867 CAACTCCATA
* *
21877 TGTGAT-GAATCGAG-CAAGAAGTTGACATTGATCCAACTCCTTCTGCGATGGATTTGAACGAAA
1 TGTGATAGAATCGAGTTAA-AAGTTGACACTGATCCAACTCCTTCTGCGATGGATTTGAACGAAA
* * * **
21940 ATAAAAATGTCGATCAACTTCCTTTTGTGATGGAAATTGAACGATATGTTAATGCTGATCTACCT
65 ATAAAAATGTCGATCCACTTCCTTCTGTGATGG-AATCGAACGATATGTCGATGCTGATCTACCT
* * * ** *
22005 CATTCTGTGATAGAATCGAGCTAAAAGTTGACACTGATCCAACTCCTTCTGTAATTGATTTGAGC
129 CTTTCTGTGATAGAATCGAGCAAAAAGTTGACGCTGATCCAACTCCTTCTGCGATGGATTTGAGC
* * * * *
22070 GAAAATAAAAATATCGATCCACCTCATTCTGTGATGGAAATCAAACGACATGTCAATGTTGATCT
194 G-AGA-AAAAATGTCGATCCACCTCATTCTGTGATGG-AATCAAACGATATGTCGATGCTGATCT
* *
22135 ACCTCCTTCTGTGATAGAATCGAGCTAAAAGGTGACACTGATCCAACTCCTTCTACGATGGATTT
256 ACCTCCTTCTGTGATAGAATCGAGCTAAAAGTTGACACTGATCCAACTCCTTCT-TGATGGATTT
*
22200 GAGCAAAAATAAAAATGTCGATCAACCTCCTTCTGTGATGGAAATCGAACGATATGTCAATGCTG
320 GAGCAAAAATAAAAATGTCGATCCACCTCCTTCTGTGATGGAAATCGAACGATATGTCAATGCTG
*
22265 ATCTGCCTCATTC
385 ATCTACCTCATTC
* * * *
22278 TGTGATAGAATCGAGTTAAAAGTTGACGCTGATCTAACTCCTTCTGTGATGGATTTGAGCGAAAA
1 TGTGATAGAATCGAGTTAAAAGTTGACACTGATCCAACTCCTTCTGCGATGGATTTGAACGAAAA
* * *
22343 TAAAAGTATCGATCCACTTCCTTCTGTGATGGAATCGAACGAGATGTCGATGCTGATCTACCTCT
66 TAAAAATGTCGATCCACTTCCTTCTGTGATGGAATCGAACGATATGTCGATGCTGATCTACCTCT
*
22408 TTCTGTGATAGAATCGAGCAAAAAGTTGACGCTGATCCAACTCCTTCTGCGATGAATTTGAGCGA
131 TTCTGTGATAGAATCGAGCAAAAAGTTGACGCTGATCCAACTCCTTCTGCGATGGATTTGAGCG-
* *
22473 AGATAAAAATTTCGATCCACCTCATTCTGTGATGGAAATCGAACGATATGTCGATGCTGATCTAC
195 AGA-AAAAATGTCGATCCACCTCATTCTGTGATGG-AATCAAACGATATGTCGATGCTGATCTAC
* * *
22538 CTCTTTCTGTGATAGAATCAAGCTAAAAGTTGACGCTGATCCAACTCCTTCTGTGATGGATTTGA
258 CTCCTTCTGTGATAGAATCGAGCTAAAAGTTGACACTGATCCAACTCCTTCT-TGATGGATTTGA
* *
22603 GCAAAAATAAAAATGTCGATCCACCTCCTTTTGTAATGGAAATCGAACGATATGTCAATGCTGAT
322 GCAAAAATAAAAATGTCGATCCACCTCCTTCTGTGATGGAAATCGAACGATATGTCAATGCTGAT
22668 CTACCTTC-TTC
387 CTACC-TCATTC
* ** * * *
22679 TGTGATAGAATCGAGTAAAAAGTTGATGCTGATCCAACTTCTTCTGCAATGGATTTGAACGAAGA
1 TGTGATAGAATCGAGTTAAAAGTTGACACTGATCCAACTCCTTCTGCGATGGATTTGAACGAAAA
* * * *
22744 TAAAAATGTCGATCCACCTCCTTCTGTGATGGAATCAAATGATATGTCGATGCTGATCTACCTCC
66 TAAAAATGTCGATCCACTTCCTTCTGTGATGGAATCGAACGATATGTCGATGCTGATCTACCTCT
* * * * *
22809 TTCTGTGATATAATCTAGTAAAAAGTTGAAGCTGATCCAACTCCTTCTGCGATGGATTTGA--GT
131 TTCTGTGATAGAATCGAGCAAAAAGTTGACGCTGATCCAACTCCTTCTGCGATGGATTTGAGCGA
* * * ** * *
22872 GAACAAATGTCGATCCACCTCCTTCTGTGATGGAATCGAGTGATATGTCGGTGATGATCTACCTC
196 GAAAAAATGTCGATCCACCTCATTCTGTGATGGAATCAAACGATATGTCGATGCTGATCTACCTC
* **
22937 CTTCTGTGATAGAATCGAGCTAAAAGTTGACACTGATCCAACTCCTCCTTCGATGGATTTGAGTG
261 CTTCTGTGATAGAATCGAGCTAAAAGTTGACACTGATCCAACTCCTTCTT-GATGGATTTGAGCA
* * * * * *
23002 AAAATAAAAAAGTCGATCCATCTCTTTCTGTGATAG-AATCGAACGATATGTCGATGTTGATCTA
325 AAAATAAAAATGTCGATCCACCTCCTTCTGTGATGGAAATCGAACGATATGTCAATGCTGATCTA
23066 CCTCATTC
390 CCTCATTC
* * **
23074 TGTGATA-AATTCAAGCTAAAAGTTGACACTGATCCAACTCCTTCTGCGATGGATTTGAGTGAAA
1 TGTGATAGAA-TCGAGTTAAAAGTTGACACTGATCCAACTCCTTCTGCGATGGATTTGAACGAAA
* * * * * * *
23138 ATAAAAATGTCGATCCATTTCCTTTTGTGATGGAATTGAGCGAAATGTTGGTGCTGATCTACCT-
65 ATAAAAATGTCGATCCACTTCCTTCTGTGATGGAATCGAACGATATGTCGATGCTGATCTACCTC
* * * * * * *
23202 TCTTCTATGATAGAAACGAGAAAAAAGTTGATGCAGATCTAACTCCTTCCGCGATGGATTTGAGC
130 T-TTCTGTGATAGAATCGAGCAAAAAGTTGACGCTGATCCAACTCCTTCTGCGATGGATTTGAGC
* * * * * * *
23267 --GAACAAATGTCGATCCATCTTC-TTCTGTGATGGAATCAAACAAAATATTGGTGCTGATCTAC
194 GAGAAAAAATGTCGATCCA-CCTCATTCTGTGATGGAATCAAACGATATGTCGATGCTGATCTAC
*
23329 CTCATTCTGTGATAGAATCGAGC
258 CTCCTTCTGTGATAGAATCGAGC
23352 AAACAATTGA
Statistics
Matches: 945, Mismatches: 119, Indels: 26
0.87 0.11 0.02
Matches are distributed among these distances:
394 4 0.00
395 260 0.28
396 118 0.12
397 28 0.03
398 2 0.00
399 1 0.00
401 451 0.48
402 79 0.08
403 2 0.00
ACGTcount: A:0.30, C:0.19, G:0.20, T:0.31
Consensus pattern (397 bp):
TGTGATAGAATCGAGTTAAAAGTTGACACTGATCCAACTCCTTCTGCGATGGATTTGAACGAAAA
TAAAAATGTCGATCCACTTCCTTCTGTGATGGAATCGAACGATATGTCGATGCTGATCTACCTCT
TTCTGTGATAGAATCGAGCAAAAAGTTGACGCTGATCCAACTCCTTCTGCGATGGATTTGAGCGA
GAAAAAATGTCGATCCACCTCATTCTGTGATGGAATCAAACGATATGTCGATGCTGATCTACCTC
CTTCTGTGATAGAATCGAGCTAAAAGTTGACACTGATCCAACTCCTTCTTGATGGATTTGAGCAA
AAATAAAAATGTCGATCCACCTCCTTCTGTGATGGAAATCGAACGATATGTCAATGCTGATCTAC
CTCATTC
Found at i:22709 original size:44 final size:44
Alignment explanation
Indices: 22259--22982 Score: 252
Period size: 44 Copynumber: 16.4 Consensus size: 44
22249 CGATATGTCA
** * *
22259 ATGCTGATCTGCCTCATTCTGTGATAGAATCGAGTTAAAAGTTG
1 ATGCTGATCCACCTCCTTCTGTGATAGAATCGAGTAAAAAGTTG
* * * * * * * ***
22303 ACGCTGATCTAACTCCTTCTGTGATGGATTTGAGCGAAAATAAAAG
1 ATGCTGATCCACCTCCTTCTGTGATAGAATCGAG-TAAAA-AGTTG
* * *** * * *
22349 TAT-C-GATCCACTTCCTTCTGTGATGGAATCGAACGAGATGTCG
1 -ATGCTGATCCACCTCCTTCTGTGATAGAATCGAGTAAAAAGTTG
* * *
22392 ATGCTGATCTACCTCTTTCTGTGATAGAATCGAGCAAAAAGTTG
1 ATGCTGATCCACCTCCTTCTGTGATAGAATCGAGTAAAAAGTTG
* * *
22436 ACGCTGATCCAACTCCTTCTGCGAT-GAATTTGAGCGAAGATAAAAA-TT-
1 ATGCTGATCCACCTCCTTCTGTGATAGAA--T---CG-AG-TAAAAAGTTG
* * *** * * *
22484 -T-C-GATCCACCTCATTCTGTGATGGAAATCGAACGATATGTCG
1 ATGCTGATCCACCTCCTTCTGTGATAG-AATCGAGTAAAAAGTTG
* * *
22526 ATGCTGATCTACCTCTTTCTGTGATAGAATCAAGCT-AAAAGTTG
1 ATGCTGATCCACCTCCTTCTGTGATAGAATCGAG-TAAAAAGTTG
* * * * * * **
22570 ACGCTGATCCAACTCCTTCTGTGATGGATTTGAGCAAAAA-TAAAA
1 ATGCTGATCCACCTCCTTCTGTGATAGAATCGAGTAAAAAGT--TG
* * * *** * * **
22615 ATG-TCGATCCACCTCCTTTTGTAATGGAAATCGAACGATATGTCA
1 ATGCT-GATCCACCTCCTTCTGTGATAG-AATCGAGTAAAAAGTTG
* *
22660 ATGCTGATCTACCTTCTTCTGTGATAGAATCGAGTAAAAAGTTG
1 ATGCTGATCCACCTCCTTCTGTGATAGAATCGAGTAAAAAGTTG
* * *
22704 ATGCTGATCCAACTTCTTCTGCAATGGATTTGAA-CGAAGATAAAAA--TG
1 ATGCTGATCCACCTCCTTCTG---T-GA-TAGAATCG-AG-TAAAAAGTTG
* * * * * * *
22752 -T-C-GATCCACCTCCTTCTGTGATGGAATCAAATGATATGTCG
1 ATGCTGATCCACCTCCTTCTGTGATAGAATCGAGTAAAAAGTTG
* * *
22793 ATGCTGATCTACCTCCTTCTGTGATATAATCTAGTAAAAAGTTG
1 ATGCTGATCCACCTCCTTCTGTGATAGAATCGAGTAAAAAGTTG
* * * * * *
22837 AAGCTGATCCAACTCCTTCTGCGATGGATTTGAGTGAACAAA--TG
1 ATGCTGATCCACCTCCTTCTGTGATAGAATCGAGT-AA-AAAGTTG
* * * * *
22881 -T-C-GATCCACCTCCTTCTGTGATGGAATCGAGTGATATGTCG
1 ATGCTGATCCACCTCCTTCTGTGATAGAATCGAGTAAAAAGTTG
* * *
22922 GTGATGATCTACCTCCTTCTGTGATAGAATCGAGCT-AAAAGTTG
1 ATGCTGATCCACCTCCTTCTGTGATAGAATCGAG-TAAAAAGTTG
** *
22966 ACACTGATCCAACTCCT
1 ATGCTGATCCACCTCCT
22983 CCTTCGATGG
Statistics
Matches: 487, Mismatches: 145, Indels: 96
0.67 0.20 0.13
Matches are distributed among these distances:
39 4 0.01
40 8 0.02
41 33 0.07
42 8 0.02
43 8 0.02
44 251 0.52
45 123 0.25
46 17 0.03
47 6 0.01
48 8 0.02
49 10 0.02
50 11 0.02
ACGTcount: A:0.29, C:0.20, G:0.20, T:0.31
Consensus pattern (44 bp):
ATGCTGATCCACCTCCTTCTGTGATAGAATCGAGTAAAAAGTTG
Found at i:22776 original size:45 final size:45
Alignment explanation
Indices: 21905--22776 Score: 127
Period size: 45 Copynumber: 19.5 Consensus size: 45
21895 AAGTTGACAT
* * *
21905 TGATCCAACTCCTTCTGCGATGGATTTGAACGAAAATAAAAATGTC
1 TGATCCACCTCCTTCTGTGATGGATTTGAACG-AGATAAAAATGTC
* * * * * ***
21951 -GATCAACTTCCTTTTGTGATGGAAATTGAACGATATGTTAATG-C
1 TGATCCACCTCCTTCTGTGATGG-ATTTGAACGAGATAAAAATGTC
* * * * *
21995 TGATCTACCTCATTCTGTGAT--A---GAATCGAGCTAAAAGTTGACAC
1 TGATCCACCTCCTTCTGTGATGGATTTGAA-CGAGATAAAA-ATG--TC
* * * * * *
22039 TGATCCAACTCCTTCTGTAATTGATTTGAGCGAAAATAAAAATATC
1 TGATCCACCTCCTTCTGTGATGGATTTGAACG-AGATAAAAATGTC
* * ** * ***
22085 -GATCCACCTCATTCTGTGATGGAAATCAAACGACATGTCAATGT-
1 TGATCCACCTCCTTCTGTGATGG-ATTTGAACGAGATAAAAATGTC
* * * *
22129 TGATCTACCTCCTTCTGTGAT--A---GAATCGAGCTAAAAGGTGACAC
1 TGATCCACCTCCTTCTGTGATGGATTTGAA-CGAGATAAAA-ATG--TC
* ** * * *
22173 TGATCCAACTCCTTCTACGATGGATTTGAGCAAAAATAAAAATGTC
1 TGATCCACCTCCTTCTGTGATGGATTTGAAC-GAGATAAAAATGTC
* * * * ***
22219 -GATCAACCTCCTTCTGTGATGGAAATCGAACGATATGTCAATG-C
1 TGATCCACCTCCTTCTGTGATGG-ATTTGAACGAGATAAAAATGTC
** * * * *
22263 TGATCTGCCTCATTCTGTGAT--A---GAATCGAGTTAAAAGTTGACGC
1 TGATCCACCTCCTTCTGTGATGGATTTGAA-CGAGATAAAA-ATG--TC
* * * * * *
22307 TGATCTAACTCCTTCTGTGATGGATTTGAGCGAAAATAAAAGTATC
1 TGATCCACCTCCTTCTGTGATGGATTTGAACG-AGATAAAAATGTC
* * * ****
22353 -GATCCACTTCCTTCTGTGATGGAATCGAACGAGATGTCGATG-C
1 TGATCCACCTCCTTCTGTGATGGATTTGAACGAGATAAAAATGTC
* * * * * * ** *
22396 TGATCTACCTCTTTCTGTGATAGAATCGAGC-A-A-AAAGTTGACGC
1 TGATCCACCTCCTTCTGTGATGGATTTGAACGAGATAAAAATG--TC
* * * * *
22440 TGATCCAACTCCTTCTGCGATGAATTTGAGCGAAGATAAAAATTTC
1 TGATCCACCTCCTTCTGTGATGGATTTGAACG-AGATAAAAATGTC
* * * * ****
22486 -GATCCACCTCATTCTGTGATGGAAATCGAACGATATGTCGATG-C
1 TGATCCACCTCCTTCTGTGATGG-ATTTGAACGAGATAAAAATGTC
* * * * * *
22530 TGATCTACCTCTTTCTGTGAT--A---GAATCAAGCTAAAAGTTGACGC
1 TGATCCACCTCCTTCTGTGATGGATTTGAA-CGAGATAAAA-ATG--TC
* * * *
22574 TGATCCAACTCCTTCTGTGATGGATTTGAGCAAAAATAAAAATGTC
1 TGATCCACCTCCTTCTGTGATGGATTTGAAC-GAGATAAAAATGTC
* * * * * ***
22620 -GATCCACCTCCTTTTGTAATGGAAATCGAACGATATGTCAATG-C
1 TGATCCACCTCCTTCTGTGATGG-ATTTGAACGAGATAAAAATGTC
* *
22664 TGATCTACCTTCTTCTGTGAT--A---GAATCGAG-TAAAAAGTTGATGC
1 TGATCCACCTCCTTCTGTGATGGATTTGAA-CGAGATAAAAA--TG-T-C
* * **
22708 TGATCCAACTTCTTCTGCAATGGATTTGAACGAAGATAAAAATGTC
1 TGATCCACCTCCTTCTGTGATGGATTTGAACG-AGATAAAAATGTC
22754 -GATCCACCTCCTTCTGTGATGGA
1 TGATCCACCTCCTTCTGTGATGGA
22777 ATCAAATGAT
Statistics
Matches: 566, Mismatches: 185, Indels: 151
0.63 0.21 0.17
Matches are distributed among these distances:
39 17 0.03
40 21 0.04
41 13 0.02
42 6 0.01
43 2 0.00
44 148 0.26
45 252 0.45
46 41 0.07
47 2 0.00
48 20 0.04
49 38 0.07
50 6 0.01
ACGTcount: A:0.31, C:0.20, G:0.19, T:0.30
Consensus pattern (45 bp):
TGATCCACCTCCTTCTGTGATGGATTTGAACGAGATAAAAATGTC
Found at i:24140 original size:90 final size:90
Alignment explanation
Indices: 23983--24447 Score: 761
Period size: 90 Copynumber: 5.2 Consensus size: 90
23973 TGAAAATCAT
* * * *
23983 GCTTAGTTTCTAAAAACTCATTTGAAAACATCCTGCACTGAAGGTCTTATGGATGACTCGAAAGA
1 GCTTAGTTTCTAAAATCTCATTTGAAAACATCCTGCACTGAAGGTCTTATGGATGGCCCGAAGGA
24048 CTTACAAATTAAGAAACCCCCGAAG
66 CTTACAAATTAAGAAACCCCCGAAG
* * * *
24073 GCTCAGTTTCTATAATCTAATTTGAAAACATCCAGCACTGAAGGTCTTATGGATGGCCCGAAGGA
1 GCTTAGTTTCTAAAATCTCATTTGAAAACATCCTGCACTGAAGGTCTTATGGATGGCCCGAAGGA
*
24138 CTTACAAATCAAGAAACCCCCGAAG
66 CTTACAAATTAAGAAACCCCCGAAG
* *
24163 GCTTAGTTTCTAAAATCTCATTTGAAAACATCCTGCACTGAAAGTCTTATAGATGGCCCGAAGGA
1 GCTTAGTTTCTAAAATCTCATTTGAAAACATCCTGCACTGAAGGTCTTATGGATGGCCCGAAGGA
*
24228 CTTACAAATCAAGAAACCCCCGAAG
66 CTTACAAATTAAGAAACCCCCGAAG
* * *
24253 GCTTAGTTTCTAAAATCTTATTTGAAAACATCCTGCATTAAAGGTCTTATGGATGGCCCGAAGGA
1 GCTTAGTTTCTAAAATCTCATTTGAAAACATCCTGCACTGAAGGTCTTATGGATGGCCCGAAGGA
24318 CTTACAAATTAAGAAACCCCCGAAG
66 CTTACAAATTAAGAAACCCCCGAAG
* *
24343 GCTTAGTTTCTAAAATCTCATTTGAAAACATCATGCACTGAAGGTCTTATGGATGGCCCGAATGA
1 GCTTAGTTTCTAAAATCTCATTTGAAAACATCCTGCACTGAAGGTCTTATGGATGGCCCGAAGGA
24408 CTTACAAATCTAA-AAACCCCCGAAG
66 CTTACAAAT-TAAGAAACCCCCGAAG
24433 GCTTAGTTTCTAAAA
1 GCTTAGTTTCTAAAA
24448 AATCTTTTGA
Statistics
Matches: 348, Mismatches: 26, Indels: 2
0.93 0.07 0.01
Matches are distributed among these distances:
90 345 0.99
91 3 0.01
ACGTcount: A:0.35, C:0.22, G:0.17, T:0.26
Consensus pattern (90 bp):
GCTTAGTTTCTAAAATCTCATTTGAAAACATCCTGCACTGAAGGTCTTATGGATGGCCCGAAGGA
CTTACAAATTAAGAAACCCCCGAAG
Found at i:34955 original size:21 final size:21
Alignment explanation
Indices: 34937--34989 Score: 72
Period size: 21 Copynumber: 2.5 Consensus size: 21
34927 ATGAAGCAAG
34937 GGAAGCAGAGAGAGCAGCAGC
1 GGAAGCAGAGAGAGCAGCAGC
*
34958 GGAAGCA-ACCAGAGCAGCAGC
1 GGAAGCAGA-GAGAGCAGCAGC
*
34979 GGAAGTAGAGA
1 GGAAGCAGAGA
34990 AAAGAAGCAG
Statistics
Matches: 27, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
20 1 0.04
21 25 0.93
22 1 0.04
ACGTcount: A:0.40, C:0.19, G:0.40, T:0.02
Consensus pattern (21 bp):
GGAAGCAGAGAGAGCAGCAGC
Found at i:35018 original size:21 final size:21
Alignment explanation
Indices: 34992--35042 Score: 75
Period size: 21 Copynumber: 2.4 Consensus size: 21
34982 AGTAGAGAAA
*
34992 AGAAGCAGCGACAGCACAGAG
1 AGAAGCAGCGACAACACAGAG
* *
35013 AGAAGCAACGTCAACACAGAG
1 AGAAGCAGCGACAACACAGAG
35034 AGAAGCAGC
1 AGAAGCAGC
35043 ATATCAGCAG
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.45, C:0.24, G:0.29, T:0.02
Consensus pattern (21 bp):
AGAAGCAGCGACAACACAGAG
Found at i:35569 original size:43 final size:43
Alignment explanation
Indices: 35455--35792 Score: 342
Period size: 43 Copynumber: 7.9 Consensus size: 43
35445 TTTTTAGCAG
* * * * * * ** *
35455 AAACGCCGCAAAACATCAACACTTACTGCGGCGTATTAACAAA
1 AAACGCCGCTAAATATCAACACCTATTGCGGCGTTTTTATGAC
* ** * *
35498 AAACGCCGCTAAACATCATA-ATATATTGCGGC-TTTTGTCTGAG
1 AAACGCCGCTAAATATCA-ACACCTATTGCGGCGTTTT-TATGAC
* * * *
35541 AAACGCTGCTAAATATTAACACCAATTGCAGCGTTTTTATGAC
1 AAACGCCGCTAAATATCAACACCTATTGCGGCGTTTTTATGAC
* * * *
35584 AAACACCGCGAAATATCAACACCTATTGCGGCGTTTGT-TGAA
1 AAACGCCGCTAAATATCAACACCTATTGCGGCGTTTTTATGAC
* * *
35626 AAACGCTGTTAAATATCAACACCTATTGCGGTGTTTTTATGAC
1 AAACGCCGCTAAATATCAACACCTATTGCGGCGTTTTTATGAC
* *
35669 AAACTCCGCTAAATATCAACACCTATTGCGGCGTTTTTATAAC
1 AAACGCCGCTAAATATCAACACCTATTGCGGCGTTTTTATGAC
* * *
35712 AAACGCCACTAAATATCAACACCTATTGCGACGTTTTTCA-CAC
1 AAACGCCGCTAAATATCAACACCTATTGCGGCGTTTTT-ATGAC
*
35755 AAACGCCGCTAAATATCAATACCTATTGCGGCGTTTTT
1 AAACGCCGCTAAATATCAACACCTATTGCGGCGTTTTT
35793 TGTGAAAAAA
Statistics
Matches: 243, Mismatches: 46, Indels: 12
0.81 0.15 0.04
Matches are distributed among these distances:
42 39 0.16
43 198 0.81
44 6 0.02
ACGTcount: A:0.33, C:0.24, G:0.15, T:0.28
Consensus pattern (43 bp):
AAACGCCGCTAAATATCAACACCTATTGCGGCGTTTTTATGAC
Found at i:36649 original size:2 final size:2
Alignment explanation
Indices: 36642--36675 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
36632 CAATTTTTGA
36642 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
36676 TCACTTTATA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:37015 original size:60 final size:60
Alignment explanation
Indices: 36939--37053 Score: 212
Period size: 60 Copynumber: 1.9 Consensus size: 60
36929 TCGTATTCAC
*
36939 TTTGTTTTCTGGATCAACATATTCACTTTGATATGAACTAAAATGTTTAATAAGTGCACT
1 TTTGCTTTCTGGATCAACATATTCACTTTGATATGAACTAAAATGTTTAATAAGTGCACT
*
36999 TTTGCTTTCTGTATCAACATATTCACTTTGATATGAACTAAAATGTTTAATAAGT
1 TTTGCTTTCTGGATCAACATATTCACTTTGATATGAACTAAAATGTTTAATAAGT
37054 ACTCAACTAT
Statistics
Matches: 53, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
60 53 1.00
ACGTcount: A:0.32, C:0.13, G:0.12, T:0.43
Consensus pattern (60 bp):
TTTGCTTTCTGGATCAACATATTCACTTTGATATGAACTAAAATGTTTAATAAGTGCACT
Found at i:39431 original size:29 final size:29
Alignment explanation
Indices: 39389--39465 Score: 109
Period size: 29 Copynumber: 2.7 Consensus size: 29
39379 AACCCAACCA
* *
39389 TAGGTCGCCATGCACTCCCAGCGACCTCC
1 TAGGTCGCCATGCACGCCCAGCGACATCC
* **
39418 TAGGTCGCCATGCACGCCCGGCGACATGG
1 TAGGTCGCCATGCACGCCCAGCGACATCC
39447 TAGGTCGCCATGCACGCCC
1 TAGGTCGCCATGCACGCCC
39466 CACGACCTTG
Statistics
Matches: 43, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
29 43 1.00
ACGTcount: A:0.17, C:0.40, G:0.27, T:0.16
Consensus pattern (29 bp):
TAGGTCGCCATGCACGCCCAGCGACATCC
Found at i:39888 original size:17 final size:17
Alignment explanation
Indices: 39866--39901 Score: 72
Period size: 17 Copynumber: 2.1 Consensus size: 17
39856 ATTATAGTTT
39866 GTTAGTTTAGGGTTAGG
1 GTTAGTTTAGGGTTAGG
39883 GTTAGTTTAGGGTTAGG
1 GTTAGTTTAGGGTTAGG
39900 GT
1 GT
39902 AAAAAATTTA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.17, C:0.00, G:0.42, T:0.42
Consensus pattern (17 bp):
GTTAGTTTAGGGTTAGG
Found at i:40096 original size:30 final size:30
Alignment explanation
Indices: 40028--40132 Score: 133
Period size: 30 Copynumber: 3.5 Consensus size: 30
40018 TTTAGTTAAT
*
40028 TAGTTTTTTAGTAGTGAA-TTATAATTAAA-AA
1 TAGTTTATTAGT--TGAAGTTAT-ATTAAAGAA
* * *
40059 CATTTTATTAGTTTAAGTTATATTAAAGAA
1 TAGTTTATTAGTTGAAGTTATATTAAAGAA
40089 TAGTTTATTAGTTGAAGTTATATTAAAGAA
1 TAGTTTATTAGTTGAAGTTATATTAAAGAA
40119 TAGTTTATTAGTTG
1 TAGTTTATTAGTTG
40133 TTTAAAGAAA
Statistics
Matches: 65, Mismatches: 7, Indels: 5
0.84 0.09 0.06
Matches are distributed among these distances:
29 9 0.14
30 47 0.72
31 9 0.14
ACGTcount: A:0.38, C:0.01, G:0.14, T:0.47
Consensus pattern (30 bp):
TAGTTTATTAGTTGAAGTTATATTAAAGAA
Found at i:40097 original size:15 final size:16
Alignment explanation
Indices: 40074--40128 Score: 55
Period size: 15 Copynumber: 3.6 Consensus size: 16
40064 TATTAGTTTA
40074 AGTTATATTAAAGAAT
1 AGTTATATTAAAGAAT
**
40090 AGTT-TATTAGTTG-A-
1 AGTTATATTA-AAGAAT
40104 AGTTATATTAAAGAAT
1 AGTTATATTAAAGAAT
40120 AGTT-TATTA
1 AGTTATATTA
40129 GTTGTTTAAA
Statistics
Matches: 31, Mismatches: 4, Indels: 9
0.70 0.09 0.20
Matches are distributed among these distances:
14 5 0.16
15 17 0.55
16 9 0.29
ACGTcount: A:0.42, C:0.00, G:0.15, T:0.44
Consensus pattern (16 bp):
AGTTATATTAAAGAAT
Done.