Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01015968.1 Corchorus capsularis cultivar CVL-1 contig15989, 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: 39641
ACGTcount: A:0.31, C:0.18, G:0.20, T:0.31
Found at i:4641 original size:31 final size:31
Alignment explanation
Indices: 4590--4651 Score: 90
Period size: 31 Copynumber: 2.0 Consensus size: 31
4580 AGTTTTGTAA
4590 AACTTTTAAATCACCCATTATACCCTTATTT
1 AACTTTTAAATCACCCATTATACCCTTATTT
* *
4621 AACTTTTGAAAT-ACCTATTATATCCTTATTT
1 AACTTTT-AAATCACCCATTATACCCTTATTT
4652 TTCTAACATA
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
31 24 0.86
32 4 0.14
ACGTcount: A:0.32, C:0.21, G:0.02, T:0.45
Consensus pattern (31 bp):
AACTTTTAAATCACCCATTATACCCTTATTT
Found at i:9547 original size:226 final size:226
Alignment explanation
Indices: 9153--9604 Score: 823
Period size: 226 Copynumber: 2.0 Consensus size: 226
9143 AATTAGGCTT
*
9153 ATAGAAATTACAACGTCAACAACTCATGTCTTGTCCACATTAGTAATGTGGTGGTGAAAAGTTTC
1 ATAGAAATTACAACGTCAACAACTCATGTCTTGTCCACATTAGTAATGTGGTGGCGAAAAGTTTC
* *
9218 AATAAATTTGAGTAATATATACTTTTTTTGTAGAAAAAATTTAGTAAGGAGAGACTGTCGCAGTT
66 AATAAATTTGAGTAATATATACTTTTTTGGTAGAAAAAATTTAGTAAGGAGAGACTATCGCAGTT
9283 CAGGGACAGGGTATGCTACAGACCTCAGAGAGAACTTATAGTTGTTCTTACAAATCATTTACCAA
131 CAGGGACAGGGTATGCTACAGACCTCAGAGAGAACTTATAGTTGTTCTTACAAATCATTTACCAA
*
9348 TAAGAATTGTTGTCACGATTCAAACCACAAA
196 TAAGAACTGTTGTCACGATTCAAACCACAAA
9379 ATAGAAATTACAACGTCAACAACTCATGTCTTGTCCACATTAGTAATGTGGTGGCGAAAAGTTTC
1 ATAGAAATTACAACGTCAACAACTCATGTCTTGTCCACATTAGTAATGTGGTGGCGAAAAGTTTC
9444 AATAAATTTGAGTAATATATACTTTTTTGGTAGAAAAAATTTAGTAAGGAGAGACTATCGCAGTT
66 AATAAATTTGAGTAATATATACTTTTTTGGTAGAAAAAATTTAGTAAGGAGAGACTATCGCAGTT
* ** *
9509 CAGGGATAGGGTATGCTACAGGTCTCAGAGAGAACTTATAGTTGTTCTTACAAATCATTTACTAA
131 CAGGGACAGGGTATGCTACAGACCTCAGAGAGAACTTATAGTTGTTCTTACAAATCATTTACCAA
*
9574 TAAGAACTGTTGTCACGATTCAAATCACAAA
196 TAAGAACTGTTGTCACGATTCAAACCACAAA
9605 CATTATAAAC
Statistics
Matches: 217, Mismatches: 9, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
226 217 1.00
ACGTcount: A:0.36, C:0.15, G:0.18, T:0.31
Consensus pattern (226 bp):
ATAGAAATTACAACGTCAACAACTCATGTCTTGTCCACATTAGTAATGTGGTGGCGAAAAGTTTC
AATAAATTTGAGTAATATATACTTTTTTGGTAGAAAAAATTTAGTAAGGAGAGACTATCGCAGTT
CAGGGACAGGGTATGCTACAGACCTCAGAGAGAACTTATAGTTGTTCTTACAAATCATTTACCAA
TAAGAACTGTTGTCACGATTCAAACCACAAA
Found at i:12548 original size:10 final size:10
Alignment explanation
Indices: 12533--12557 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
12523 AGTCCTTCAA
12533 AATAAATATC
1 AATAAATATC
12543 AATAAATATC
1 AATAAATATC
12553 AATAA
1 AATAA
12558 CTTTACAATT
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:0.64, C:0.08, G:0.00, T:0.28
Consensus pattern (10 bp):
AATAAATATC
Found at i:13266 original size:5 final size:5
Alignment explanation
Indices: 13248--13281 Score: 50
Period size: 5 Copynumber: 6.6 Consensus size: 5
13238 GAAGGAGAAG
*
13248 AAAGA AAAGGA AAAAA AAAGA AAAGA AAAGA AAA
1 AAAGA AAA-GA AAAGA AAAGA AAAGA AAAGA AAA
13282 AGAACGCAGA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
5 21 0.81
6 5 0.19
ACGTcount: A:0.82, C:0.00, G:0.18, T:0.00
Consensus pattern (5 bp):
AAAGA
Found at i:13269 original size:16 final size:16
Alignment explanation
Indices: 13243--13285 Score: 61
Period size: 16 Copynumber: 2.6 Consensus size: 16
13233 TAAAAGAAGG
13243 AGAAGAAAGAAAAGGAAA
1 AGAA-AAAGAAAA-GAAA
13261 A-AAAAAGAAAAGAAA
1 AGAAAAAGAAAAGAAA
13276 AGAAAAAGAA
1 AGAAAAAGAA
13286 CGCAGATGAA
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
15 5 0.21
16 16 0.67
17 2 0.08
18 1 0.04
ACGTcount: A:0.79, C:0.00, G:0.21, T:0.00
Consensus pattern (16 bp):
AGAAAAAGAAAAGAAA
Found at i:14077 original size:22 final size:22
Alignment explanation
Indices: 14033--14095 Score: 58
Period size: 22 Copynumber: 2.9 Consensus size: 22
14023 GAATTTCGAG
* * *
14033 AACCTTTTTAT-AATTTTTTTT
1 AACCTTCTTATGAAATTTTGTT
14054 AACCTTCTTATGAAATTTTGTT
1 AACCTTCTTATGAAATTTTGTT
* *
14076 AA-CTTCCTTAAGGAATTTTG
1 AACCTT-CTTATGAAATTTTG
14096 AAGATCTCAA
Statistics
Matches: 35, Mismatches: 5, Indels: 3
0.81 0.12 0.07
Matches are distributed among these distances:
21 13 0.37
22 22 0.63
ACGTcount: A:0.27, C:0.13, G:0.08, T:0.52
Consensus pattern (22 bp):
AACCTTCTTATGAAATTTTGTT
Found at i:14185 original size:22 final size:22
Alignment explanation
Indices: 14053--14578 Score: 194
Period size: 22 Copynumber: 24.4 Consensus size: 22
14043 TAATTTTTTT
* * *
14053 TAACCTTCTTATGAAATTTTGT
1 TAACCTCCATATGAAATTTTGA
* * * *
14075 TAACTTCCTTAAGGAATTTTGA
1 TAACCTCCATATGAAATTTTGA
* *
14097 -AGATCTCAATATGAAATTTTGA
1 TA-ACCTCCATATGAAATTTTGA
*
14119 TAACTTCCCA-ATGAAATTTTGA
1 TAACCT-CCATATGAAATTTTGA
** * *
14141 TAACCAACACTATGAGATGTTGA
1 TAACCTCCA-TATGAAATTTTGA
* *
14164 TAACCTCCATATGATATATTGA
1 TAACCTCCATATGAAATTTTGA
* ** *
14186 TAACCACGTTATGAGAA-TTTAA
1 TAACCTCCATATGA-AATTTTGA
*
14208 AAACCTCCATATG-AATTGTT-A
1 TAACCTCCATATGAAATT-TTGA
*
14229 GTAA--TCACACTCTGAAATTTTGA
1 -TAACCTC-CA-TATGAAATTTTGA
* *
14252 TAA--TAACACTATGAAATTGTGA
1 TAACCT-CCA-TATGAAATTTTGA
14274 TAACCTCGC-TATGAAATTTTGA
1 TAACCTC-CATATGAAATTTTGA
* *
14296 TAAATCTTCC-TATAAAATTTTGA
1 T-AA-CCTCCATATGAAATTTTGA
*
14319 TAAACCTCCCA-ATAAAATTTTGA
1 T-AACCT-CCATATGAAATTTTGA
* *** *
14342 TAACTTTTTTATGAAATCTTGA
1 TAACCTCCATATGAAATTTTGA
* *
14364 TAA----C-TA-CAAACTTTGA
1 TAACCTCCATATGAAATTTTGA
* ** *
14380 TAACCTCCCTATGATTTTTTAA
1 TAACCTCCATATGAAATTTTGA
*
14402 TAACCT-CATTATGAAATTTTGT
1 TAACCTCCA-TATGAAATTTTGA
* *
14424 TAATCTCCCTATGAAATTTTGA
1 TAACCTCCATATGAAATTTTGA
* *
14446 TAACCTTCTTATGAAATTTTGA
1 TAACCTCCATATGAAATTTTGA
* **
14468 -AAACTAAACTATGAAATTTTGA
1 TAACCTCCA-TATGAAATTTTGA
* *
14490 TATCCTCC--CTGAAATTTTGA
1 TAACCTCCATATGAAATTTTGA
* * *
14510 TTA-CTCCATAATGAAAGTTTAA
1 TAACCTCCAT-ATGAAATTTTGA
14532 TAACCTTCC---T--AA-TTTGA
1 TAACC-TCCATATGAAATTTTGA
*
14549 TAACCATAC-TATGAAATTTTGA
1 TAACC-TCCATATGAAATTTTGA
14571 TAACCTCC
1 TAACCTCC
14579 CCAGAAATAC
Statistics
Matches: 374, Mismatches: 88, Indels: 85
0.68 0.16 0.16
Matches are distributed among these distances:
16 10 0.03
17 13 0.03
18 2 0.01
19 5 0.01
20 18 0.05
21 18 0.05
22 235 0.63
23 65 0.17
24 8 0.02
ACGTcount: A:0.36, C:0.16, G:0.10, T:0.38
Consensus pattern (22 bp):
TAACCTCCATATGAAATTTTGA
Found at i:14313 original size:23 final size:23
Alignment explanation
Indices: 14260--14344 Score: 100
Period size: 23 Copynumber: 3.7 Consensus size: 23
14250 GATAATAACA
* * *
14260 CTATGAAATTGTGAT-AACCTCG
1 CTATAAAATTTTGATAAACCTCC
* * *
14282 CTATGAAATTTTGATAAATCTTC
1 CTATAAAATTTTGATAAACCTCC
14305 CTATAAAATTTTGATAAACCTCC
1 CTATAAAATTTTGATAAACCTCC
*
14328 CAATAAAATTTTGATAA
1 CTATAAAATTTTGATAA
14345 CTTTTTTATG
Statistics
Matches: 54, Mismatches: 8, Indels: 1
0.86 0.13 0.02
Matches are distributed among these distances:
22 14 0.26
23 40 0.74
ACGTcount: A:0.39, C:0.15, G:0.09, T:0.36
Consensus pattern (23 bp):
CTATAAAATTTTGATAAACCTCC
Found at i:14365 original size:45 final size:45
Alignment explanation
Indices: 14260--14366 Score: 110
Period size: 45 Copynumber: 2.4 Consensus size: 45
14250 GATAATAACA
* * *
14260 CTATGAAATTGTGAT-AACCTCGCTATGAAATTTTGATAAATCTTC
1 CTATGAAATT-TGATAAACCTCCCAATAAAATTTTGATAAATCTTC
* * *
14305 CTATAAAATTTTGATAAACCTCCCAATAAAATTTTGATAACT-TTT
1 CTATGAAA-TTTGATAAACCTCCCAATAAAATTTTGATAAATCTTC
*
14350 TTATGAAATCTTGATAA
1 CTATGAAAT-TTGATAA
14367 CTACAAACTT
Statistics
Matches: 51, Mismatches: 8, Indels: 6
0.78 0.12 0.09
Matches are distributed among these distances:
44 1 0.02
45 26 0.51
46 24 0.47
ACGTcount: A:0.37, C:0.14, G:0.09, T:0.39
Consensus pattern (45 bp):
CTATGAAATTTGATAAACCTCCCAATAAAATTTTGATAAATCTTC
Found at i:14641 original size:22 final size:23
Alignment explanation
Indices: 14616--14686 Score: 67
Period size: 22 Copynumber: 3.2 Consensus size: 23
14606 AATCACATTT
*
14616 TGAAAATTT-GATAACCTCTTTA
1 TGAAAATTTCGATAACCTCTCTA
*
14638 TG-AAATTTCTATAACCTCTCTA
1 TGAAAATTTCGATAACCTCTCTA
* * * *
14660 T-AAAATTTTGTTGACCCCTCTA
1 TGAAAATTTCGATAACCTCTCTA
14682 TGAAA
1 TGAAA
14687 TTATGATAAT
Statistics
Matches: 39, Mismatches: 7, Indels: 5
0.76 0.14 0.10
Matches are distributed among these distances:
21 6 0.15
22 30 0.77
23 3 0.08
ACGTcount: A:0.34, C:0.18, G:0.08, T:0.39
Consensus pattern (23 bp):
TGAAAATTTCGATAACCTCTCTA
Found at i:14889 original size:22 final size:22
Alignment explanation
Indices: 14847--14964 Score: 73
Period size: 22 Copynumber: 5.4 Consensus size: 22
14837 AAATTGAGAC
* * *
14847 TTTT-ATAACCTTCATAAGAAA
1 TTTTGATAACCTCCCTATGAAA
*
14868 TTTTGATAACCTCCCCATGAAA
1 TTTTGATAACCTCCCTATGAAA
* *
14890 TATT-AGTAACCT-GCTAATGAAA
1 TTTTGA-TAACCTCCCT-ATGAAA
* * *
14912 TTTTGTTAACCACACTATGAAA
1 TTTTGATAACCTCCCTATGAAA
* * *
14934 TTCTT-ATAACATCGCTATGACA
1 TT-TTGATAACCTCCCTATGAAA
14956 TTTTGATAA
1 TTTTGATAA
14965 TCTCTTTGAT
Statistics
Matches: 74, Mismatches: 16, Indels: 13
0.72 0.16 0.13
Matches are distributed among these distances:
21 8 0.11
22 62 0.84
23 4 0.05
ACGTcount: A:0.36, C:0.18, G:0.09, T:0.36
Consensus pattern (22 bp):
TTTTGATAACCTCCCTATGAAA
Found at i:15061 original size:24 final size:22
Alignment explanation
Indices: 15000--15086 Score: 68
Period size: 22 Copynumber: 3.9 Consensus size: 22
14990 TTGTGATAAT
* *
15000 TAACCACCCTATGAAATTTCAA
1 TAACCAACCTATGAAATTTAAA
*
15022 TAACCAACCTAAGAAATTTAAA
1 TAACCAACCTATGAAATTTAAA
* * ***
15044 TAATCTGATCCTATGAAATTTTGG
1 TAA-C-CAACCTATGAAATTTAAA
15068 TAACC-ACACTATGAAATTT
1 TAACCAAC-CTATGAAATTT
15087 TGATAACTTC
Statistics
Matches: 51, Mismatches: 11, Indels: 6
0.75 0.16 0.09
Matches are distributed among these distances:
21 1 0.02
22 33 0.65
23 2 0.04
24 15 0.29
ACGTcount: A:0.41, C:0.20, G:0.08, T:0.31
Consensus pattern (22 bp):
TAACCAACCTATGAAATTTAAA
Found at i:15072 original size:46 final size:44
Alignment explanation
Indices: 15007--15151 Score: 125
Period size: 44 Copynumber: 3.2 Consensus size: 44
14997 AATTAACCAC
***
15007 CCTATGAAATTTCAATAACCAAC-CTAAGAAATTTAAATAATCTGAT
1 CCTATGAAATTTTGGTAACCAACACTAAGAAATTTAAATAA-CT--T
* **
15053 CCTATGAAATTTTGGTAACC-ACACTATGAAATTTTGATAACTT
1 CCTATGAAATTTTGGTAACCAACACTAAGAAATTTAAATAACTT
* * ** *
15096 CCATATGAAATTTTGGTAACC-ACAATATGAAATTTTGATAACCT
1 CC-TATGAAATTTTGGTAACCAACACTAAGAAATTTAAATAACTT
15140 CCTCATGAAATT
1 CCT-ATGAAATT
15152 ATAATAACCA
Statistics
Matches: 88, Mismatches: 8, Indels: 8
0.85 0.08 0.08
Matches are distributed among these distances:
43 4 0.05
44 49 0.56
45 4 0.05
46 31 0.35
ACGTcount: A:0.39, C:0.17, G:0.10, T:0.34
Consensus pattern (44 bp):
CCTATGAAATTTTGGTAACCAACACTAAGAAATTTAAATAACTT
Found at i:15087 original size:22 final size:22
Alignment explanation
Indices: 15054--15185 Score: 137
Period size: 22 Copynumber: 6.0 Consensus size: 22
15044 TAATCTGATC
*
15054 CTATGAAATTTTGGTAACCACA
1 CTATGAAATTTTGATAACCACA
15076 CTATGAAATTTTGATAACTTC-CA
1 CTATGAAATTTTGATAAC--CACA
*
15099 -TATGAAATTTTGGTAACCACA
1 CTATGAAATTTTGATAACCACA
* *
15120 ATATGAAATTTTGATAACCTC-
1 CTATGAAATTTTGATAACCACA
* *
15141 CTCATGAAATTATAATAACCATC-
1 CT-ATGAAATTTTGATAACCA-CA
*
15164 TTATGAAATTTTGATAACCACA
1 CTATGAAATTTTGATAACCACA
15186 TAGAGACAAG
Statistics
Matches: 92, Mismatches: 11, Indels: 14
0.79 0.09 0.12
Matches are distributed among these distances:
20 1 0.01
21 4 0.04
22 82 0.89
23 4 0.04
24 1 0.01
ACGTcount: A:0.39, C:0.17, G:0.10, T:0.35
Consensus pattern (22 bp):
CTATGAAATTTTGATAACCACA
Found at i:15111 original size:44 final size:43
Alignment explanation
Indices: 15052--15182 Score: 174
Period size: 44 Copynumber: 3.0 Consensus size: 43
15042 AATAATCTGA
* *
15052 TCCTATGAAATTTTGGTAACCACACTATGAAATTTTGATAACT
1 TCCTATGAAATTTTGGTAACCACAATATGAAATTTTGATAACC
15095 TCCATATGAAATTTTGGTAACCACAATATGAAATTTTGATAACC
1 TCC-TATGAAATTTTGGTAACCACAATATGAAATTTTGATAACC
* ** *
15139 TCCTCATGAAATTATAATAACCATC-TTATGAAATTTTGATAACC
1 TCCT-ATGAAATTTTGGTAACCA-CAATATGAAATTTTGATAACC
15183 ACATAGAGAC
Statistics
Matches: 79, Mismatches: 6, Indels: 5
0.88 0.07 0.06
Matches are distributed among these distances:
43 4 0.05
44 74 0.94
45 1 0.01
ACGTcount: A:0.37, C:0.17, G:0.10, T:0.36
Consensus pattern (43 bp):
TCCTATGAAATTTTGGTAACCACAATATGAAATTTTGATAACC
Found at i:15149 original size:66 final size:66
Alignment explanation
Indices: 15055--15185 Score: 167
Period size: 66 Copynumber: 2.0 Consensus size: 66
15045 AATCTGATCC
* * * * *
15055 TATGAAATTTTGGTAACCACACTATGAAATTTTGATAA-CTTCCATATGAAATTTTGGTAACCAC
1 TATGAAATTTTGATAACCACACTATGAAATTATAATAACCAT-CATATGAAATTTTGATAACCAC
15119 AA
65 AA
* *
15121 TATGAAATTTTGATAACCTC-CTCATGAAATTATAATAACCATCTTATGAAATTTTGATAACCAC
1 TATGAAATTTTGATAACCACACT-ATGAAATTATAATAACCATCATATGAAATTTTGATAACCAC
15185 A
65 A
15186 TAGAGACAAG
Statistics
Matches: 56, Mismatches: 7, Indels: 4
0.84 0.10 0.06
Matches are distributed among these distances:
65 2 0.04
66 52 0.93
67 2 0.04
ACGTcount: A:0.39, C:0.16, G:0.10, T:0.35
Consensus pattern (66 bp):
TATGAAATTTTGATAACCACACTATGAAATTATAATAACCATCATATGAAATTTTGATAACCACA
A
Found at i:15380 original size:19 final size:20
Alignment explanation
Indices: 15349--15386 Score: 53
Period size: 19 Copynumber: 1.9 Consensus size: 20
15339 TATTGACATT
15349 TAAAAATTGAAATT-AAAAG
1 TAAAAATTGAAATTCAAAAG
15368 TAAAATATT-AAATTCAAAA
1 TAAAA-ATTGAAATTCAAAA
15387 AATAATAGTA
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
19 10 0.59
20 7 0.41
ACGTcount: A:0.63, C:0.03, G:0.05, T:0.29
Consensus pattern (20 bp):
TAAAAATTGAAATTCAAAAG
Found at i:15858 original size:28 final size:28
Alignment explanation
Indices: 15827--15885 Score: 100
Period size: 28 Copynumber: 2.1 Consensus size: 28
15817 GGTCACCTAA
15827 GGGCATTTTGGTCATTTGCATGTTCAGG
1 GGGCATTTTGGTCATTTGCATGTTCAGG
* *
15855 GGGCGTTTTGGTCATTTGCATGTTCGGG
1 GGGCATTTTGGTCATTTGCATGTTCAGG
15883 GGG
1 GGG
15886 GGGGGGGGCA
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
28 29 1.00
ACGTcount: A:0.10, C:0.14, G:0.39, T:0.37
Consensus pattern (28 bp):
GGGCATTTTGGTCATTTGCATGTTCAGG
Found at i:21466 original size:360 final size:357
Alignment explanation
Indices: 20807--21532 Score: 1373
Period size: 360 Copynumber: 2.0 Consensus size: 357
20797 CTGTGGAACC
20807 GAATGGAAGAAAAACTCAAAGGATTAGTTGGTAGCCAGCCATATTTCAAGGGAGTGGATAAGGTG
1 GAATGGAAGAAAAACTCAAAGGATTAGTTGGTAGCCAGCCATATTTCAAGGGAGTGGATAAGGTG
20872 TCACTAGTTACGGATTTAGTGTTGCCACGTAAGTTCAAAGTCCCGGAGTTTGAAAAGTTTGATGG
66 TCACTAGTTACGGATTTAGTGTTGCCACGTAAGTTCAAAGTCCCGGAGTTTGAAAAGTTTGATGG
*
20937 TAGTAGATCCCCAGAAGACGTTAACACATATGTGCGCCAAATGCAGCCTTACACCTCAGATGATA
131 TACTAGATCCCCAGAAGACGTTAACACATATGTGCGCCAAATGCAGCCTTACACCTCAGATGATA
*
21002 TGCTCATGCATTACTTTCAGAGGAGTCTCACGGGTTCATCTTTTAAATGGTACAATAGATTGGAT
196 TGATCATGCATTACTTTCAGAGGAGTCTCACGGGTTCATCTTTTAAATGGTACAATAGATTGGAT
*
21067 TCTAGCCAGATCAAGTCATTGAATGACATGGCTAATGCTTTTATAGCACAGTACAAATACATTGA
261 TCTAGCCAGATCAAGTCATGGAATGACATGGCTAATGCTTTTATAGCACAGTACAAATACATTGA
21132 TGAGTTGGCTTCTTCCCGTGAAACACTGTTGA
326 TGAGTTGGCTTCTTCCCGTGAAACACTGTTGA
21164 GAATGGAAGAAAAACTCAAAGGATTAGTTGGTAGCCAGCCATATTTCAAGGGAGTGGATAAGGTG
1 GAATGGAAGAAAAACTCAAAGGATTAGTTGGTAGCCAGCCATATTTCAAGGGAGTGGATAAGGTG
21229 TCACTAGTTACGGATTTAGTGTTGCCACGTAAGTTCAAAGTCCCGGAGTTTGAAAAGTTTGATGG
66 TCACTAGTTACGGATTTAGTGTTGCCACGTAAGTTCAAAGTCCCGGAGTTTGAAAAGTTTGATGG
21294 TACTAGATCCCCAGAAGACCATGTTAACACATATGTGCGCCAAATGCAGCCTTACACCTCAGATG
131 TACTAGATCCCCAGAAGA-C--GTTAACACATATGTGCGCCAAATGCAGCCTTACACCTCAGATG
*
21359 ATATGATCATGCATTACTTTCAGAGGAGTCTCACGGGTTCATCTTTTAAATGGTACAATAGCTTG
193 ATATGATCATGCATTACTTTCAGAGGAGTCTCACGGGTTCATCTTTTAAATGGTACAATAGATTG
21424 GATTCTAGCCAGATCAAGTCATGGAATGACATGGCTAATGCTTTTATAGCACAGTACAAATACAT
258 GATTCTAGCCAGATCAAGTCATGGAATGACATGGCTAATGCTTTTATAGCACAGTACAAATACAT
21489 TGATGAGTTGGCTTCTTCCCGTGAAACACTGTTGA
323 TGATGAGTTGGCTTCTTCCCGTGAAACACTGTTGA
*
21524 GCAT-GAAGA
1 GAATGGAAGA
21533 GGAAGCCGGG
Statistics
Matches: 361, Mismatches: 5, Indels: 4
0.98 0.01 0.01
Matches are distributed among these distances:
357 147 0.41
358 1 0.00
359 5 0.01
360 208 0.58
ACGTcount: A:0.31, C:0.18, G:0.23, T:0.28
Consensus pattern (357 bp):
GAATGGAAGAAAAACTCAAAGGATTAGTTGGTAGCCAGCCATATTTCAAGGGAGTGGATAAGGTG
TCACTAGTTACGGATTTAGTGTTGCCACGTAAGTTCAAAGTCCCGGAGTTTGAAAAGTTTGATGG
TACTAGATCCCCAGAAGACGTTAACACATATGTGCGCCAAATGCAGCCTTACACCTCAGATGATA
TGATCATGCATTACTTTCAGAGGAGTCTCACGGGTTCATCTTTTAAATGGTACAATAGATTGGAT
TCTAGCCAGATCAAGTCATGGAATGACATGGCTAATGCTTTTATAGCACAGTACAAATACATTGA
TGAGTTGGCTTCTTCCCGTGAAACACTGTTGA
Found at i:25092 original size:14 final size:13
Alignment explanation
Indices: 25070--25149 Score: 70
Period size: 13 Copynumber: 5.6 Consensus size: 13
25060 GTCATGGTTA
25070 TCAAAAATGTTTT
1 TCAAAAATGTTTT
*
25083 TCTCAAAATGTTTT
1 TC-AAAAATGTTTT
25097 TCAAAAATGTTTTTTT
1 TCAAAAATG---TTTT
*
25113 TAAAAAAAATGTTTTT
1 T--CAAAAATG-TTTT
*
25129 TCAAAAATGTTTC
1 TCAAAAATGTTTT
25142 TCAAAAAT
1 TCAAAAAT
25150 AATTTTCGAA
Statistics
Matches: 56, Mismatches: 5, Indels: 12
0.77 0.07 0.16
Matches are distributed among these distances:
13 19 0.34
14 19 0.34
16 11 0.20
18 7 0.12
ACGTcount: A:0.40, C:0.09, G:0.06, T:0.45
Consensus pattern (13 bp):
TCAAAAATGTTTT
Found at i:25135 original size:18 final size:18
Alignment explanation
Indices: 25099--25135 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
25089 AATGTTTTTC
**
25099 AAAAATGTTTTTTTTAAA
1 AAAAATGTTTTTTCAAAA
25117 AAAAATGTTTTTTCAAAA
1 AAAAATGTTTTTTCAAAA
25135 A
1 A
25136 TGTTTCTCAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.49, C:0.03, G:0.05, T:0.43
Consensus pattern (18 bp):
AAAAATGTTTTTTCAAAA
Found at i:25462 original size:6 final size:6
Alignment explanation
Indices: 25448--25485 Score: 53
Period size: 6 Copynumber: 6.5 Consensus size: 6
25438 ATAAAGATGC
25448 AAAAA- AAAAAG AAAAAG AAAAA- AAAGAAG AAAAAG AAA
1 AAAAAG AAAAAG AAAAAG AAAAAG AAA-AAG AAAAAG AAA
25486 TGAAAAAATG
Statistics
Matches: 30, Mismatches: 0, Indels: 5
0.86 0.00 0.14
Matches are distributed among these distances:
5 8 0.27
6 19 0.63
7 3 0.10
ACGTcount: A:0.87, C:0.00, G:0.13, T:0.00
Consensus pattern (6 bp):
AAAAAG
Found at i:25462 original size:9 final size:9
Alignment explanation
Indices: 25448--25485 Score: 51
Period size: 9 Copynumber: 4.3 Consensus size: 9
25438 ATAAAGATGC
25448 AAAAAAAA-
1 AAAAAAAAG
*
25456 AAGAAAAAG
1 AAAAAAAAG
25465 AAAAAAAAG
1 AAAAAAAAG
*
25474 AAGAAAAAG
1 AAAAAAAAG
25483 AAA
1 AAA
25486 TGAAAAAATG
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
8 7 0.28
9 18 0.72
ACGTcount: A:0.87, C:0.00, G:0.13, T:0.00
Consensus pattern (9 bp):
AAAAAAAAG
Found at i:25469 original size:18 final size:18
Alignment explanation
Indices: 25448--25485 Score: 67
Period size: 18 Copynumber: 2.1 Consensus size: 18
25438 ATAAAGATGC
25448 AAAAAAAAAAGAAAAAGA
1 AAAAAAAAAAGAAAAAGA
*
25466 AAAAAAAGAAGAAAAAGA
1 AAAAAAAAAAGAAAAAGA
25484 AA
1 AA
25486 TGAAAAAATG
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.87, C:0.00, G:0.13, T:0.00
Consensus pattern (18 bp):
AAAAAAAAAAGAAAAAGA
Found at i:25775 original size:27 final size:27
Alignment explanation
Indices: 25738--25802 Score: 89
Period size: 27 Copynumber: 2.4 Consensus size: 27
25728 TTGGCAAAAT
*
25738 GTTTTG-GTCAAAACTTTCGAAAGGA-
1 GTTTTGAGTCAAAACTTTCGAAAAGAG
*
25763 GTTTTCGAGTCAAAACTTTTGAAAAGAG
1 GTTTT-GAGTCAAAACTTTCGAAAAGAG
25791 GTTTTGAGTCAA
1 GTTTTGAGTCAA
25803 TTAAGAGTTT
Statistics
Matches: 35, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
25 5 0.14
26 1 0.03
27 24 0.69
28 5 0.14
ACGTcount: A:0.32, C:0.11, G:0.23, T:0.34
Consensus pattern (27 bp):
GTTTTGAGTCAAAACTTTCGAAAAGAG
Found at i:25855 original size:16 final size:16
Alignment explanation
Indices: 25824--25862 Score: 53
Period size: 15 Copynumber: 2.4 Consensus size: 16
25814 CAACTGCAAT
25824 GAAAAAATGAAAAAGAA
1 GAAAAAATGAAAAAG-A
*
25841 GAAAAAA-GAAGAAGA
1 GAAAAAATGAAAAAGA
25856 GAAAAAA
1 GAAAAAA
25863 AAAACGAAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
15 8 0.38
16 6 0.29
17 7 0.33
ACGTcount: A:0.77, C:0.00, G:0.21, T:0.03
Consensus pattern (16 bp):
GAAAAAATGAAAAAGA
Found at i:25865 original size:18 final size:16
Alignment explanation
Indices: 25825--25878 Score: 54
Period size: 19 Copynumber: 3.1 Consensus size: 16
25815 AACTGCAATG
*
25825 AAAAAATGAAAAAGAA
1 AAAAAAAGAAAAAGAA
*
25841 GAAAAAAGAAGAAGAGAAA
1 AAAAAAAGAA-AA-AG-AA
25860 AAAAAAACGAAAAAGAA
1 AAAAAAA-GAAAAAGAA
25877 AA
1 AA
25879 GCAGCTCTAG
Statistics
Matches: 31, Mismatches: 3, Indels: 7
0.76 0.07 0.17
Matches are distributed among these distances:
16 8 0.26
17 6 0.19
18 4 0.13
19 10 0.32
20 3 0.10
ACGTcount: A:0.80, C:0.02, G:0.17, T:0.02
Consensus pattern (16 bp):
AAAAAAAGAAAAAGAA
Found at i:27109 original size:38 final size:38
Alignment explanation
Indices: 27054--27213 Score: 154
Period size: 38 Copynumber: 4.3 Consensus size: 38
27044 AAATTATTAA
* *
27054 AGGTCAT-TTTCCA-AATTATCAA-AGTTGATTGGAAAC
1 AGGTCATCTTTCAACAATTATCAAGA-TTGACTGGAAAC
* * * *
27090 AGGTCCTCTTTCAGCAATTAT----TTTCGACCGGAAAC
1 AGGTCATCTTTCAACAATTATCAAGATT-GACTGGAAAC
**
27125 AGGTCATCTTTCAACAATTATCAAGACCGACTGGAAAC
1 AGGTCATCTTTCAACAATTATCAAGATTGACTGGAAAC
* * *
27163 AGGTCGTCTTTCAACACTTATCAAGATTGACTGGAAAT
1 AGGTCATCTTTCAACAATTATCAAGATTGACTGGAAAC
27201 AGGTCATCTTTCA
1 AGGTCATCTTTCA
27214 GTGGCTTTCA
Statistics
Matches: 99, Mismatches: 18, Indels: 12
0.77 0.14 0.09
Matches are distributed among these distances:
34 2 0.02
35 27 0.27
36 6 0.06
37 4 0.04
38 60 0.61
ACGTcount: A:0.32, C:0.21, G:0.17, T:0.31
Consensus pattern (38 bp):
AGGTCATCTTTCAACAATTATCAAGATTGACTGGAAAC
Found at i:27345 original size:19 final size:19
Alignment explanation
Indices: 27292--27339 Score: 87
Period size: 19 Copynumber: 2.5 Consensus size: 19
27282 CAAAAGGAGA
27292 CATTCCAACAACTTTTCAG
1 CATTCCAACAACTTTTCAG
*
27311 CATTCCAACAACTTTTTAG
1 CATTCCAACAACTTTTCAG
27330 CATTCCAACA
1 CATTCCAACA
27340 GGTTTTCAGT
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
19 28 1.00
ACGTcount: A:0.33, C:0.31, G:0.04, T:0.31
Consensus pattern (19 bp):
CATTCCAACAACTTTTCAG
Found at i:27423 original size:41 final size:43
Alignment explanation
Indices: 27330--27432 Score: 138
Period size: 41 Copynumber: 2.4 Consensus size: 43
27320 AACTTTTTAG
**
27330 CATTCCAACAGGTTTTCAGTTTTCAGCTACTCCCAAAAGGAGA
1 CATTCCAACAACTTTTCAGTTTTCAGCTACTCCCAAAAGGAGA
* * * *
27373 CATTCCAACAACTTTTCAGTTTTTAGC-AGT-CTAGAAGGAGA
1 CATTCCAACAACTTTTCAGTTTTCAGCTACTCCCAAAAGGAGA
27414 CATTCCAACAACTTTTCAG
1 CATTCCAACAACTTTTCAG
27433 CATTCCAACA
Statistics
Matches: 54, Mismatches: 6, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
41 28 0.52
42 2 0.04
43 24 0.44
ACGTcount: A:0.31, C:0.24, G:0.15, T:0.30
Consensus pattern (43 bp):
CATTCCAACAACTTTTCAGTTTTCAGCTACTCCCAAAAGGAGA
Found at i:27514 original size:50 final size:48
Alignment explanation
Indices: 27441--27577 Score: 161
Period size: 50 Copynumber: 2.8 Consensus size: 48
27431 AGCATTCCAA
*
27441 CAACGTTACAGTTTTCAGGTGCTCACAATGAGGGGCATTATAATAGTTTC
1 CAACGTTACAGTTTTCA-GTGCTCACAATG-GGGGCATTATAACAGTTTC
* * *
27491 CAACTTTACAGTTTTCAGTTGCTCACAATGGGGGGGCATTATAGCAGTTTT
1 CAACGTTACAGTTTTCAG-TGCTCACAAT--GGGGGCATTATAACAGTTTC
*
27542 CAACGTTGCA-TTTTCAGTGCTCACGAA-GGGGGCATT
1 CAACGTTACAGTTTTCAGTGCTCAC-AATGGGGGCATT
27578 CCAACAGCTT
Statistics
Matches: 77, Mismatches: 6, Indels: 11
0.82 0.06 0.12
Matches are distributed among these distances:
47 9 0.12
49 8 0.10
50 35 0.45
51 24 0.31
52 1 0.01
ACGTcount: A:0.25, C:0.19, G:0.24, T:0.32
Consensus pattern (48 bp):
CAACGTTACAGTTTTCAGTGCTCACAATGGGGGCATTATAACAGTTTC
Found at i:28043 original size:28 final size:28
Alignment explanation
Indices: 27985--28043 Score: 91
Period size: 28 Copynumber: 2.1 Consensus size: 28
27975 GATCACCTAA
*
27985 GGGCATTTTGGTCATTTGCATGTTCAGG
1 GGGCATTTTGGTCATTTGCATGTTCAAG
* *
28013 GGGCGTTTTGGTCATTTGCATGTTTAAG
1 GGGCATTTTGGTCATTTGCATGTTCAAG
28041 GGG
1 GGG
28044 GGGGGGGGGG
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
28 28 1.00
ACGTcount: A:0.14, C:0.12, G:0.36, T:0.39
Consensus pattern (28 bp):
GGGCATTTTGGTCATTTGCATGTTCAAG
Found at i:29749 original size:28 final size:29
Alignment explanation
Indices: 29688--29766 Score: 83
Period size: 29 Copynumber: 2.7 Consensus size: 29
29678 TAAGGTCATC
29688 CAGGAGCATTTTGGTCA--TTTTCACATCAT
1 CAGG-GCATTTTGGTCATTTTTTCACAT-AT
* *
29717 AAGGGCATTTTGGTCATTTTTTTACAT-T
1 CAGGGCATTTTGGTCATTTTTTCACATAT
*
29745 CAGGGGTATTTTGGTCATTTTT
1 CA-GGGCATTTTGGTCATTTTT
29767 AGTCCATTTT
Statistics
Matches: 43, Mismatches: 4, Indels: 6
0.81 0.08 0.11
Matches are distributed among these distances:
28 14 0.33
29 21 0.49
30 8 0.19
ACGTcount: A:0.20, C:0.14, G:0.20, T:0.46
Consensus pattern (29 bp):
CAGGGCATTTTGGTCATTTTTTCACATAT
Found at i:34350 original size:21 final size:21
Alignment explanation
Indices: 34299--34341 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
34289 GCAAAAGAAG
34299 GAATGGCTGATGGAAAATCGAC
1 GAAT-GCTGATGGAAAATCGAC
*
34321 TAATGCTGATGGAAAAGTCGA
1 GAATGCTGATGGAAAA-TCGA
34342 GAACTCTGAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
21 12 0.63
22 7 0.37
ACGTcount: A:0.37, C:0.12, G:0.30, T:0.21
Consensus pattern (21 bp):
GAATGCTGATGGAAAATCGAC
Found at i:36815 original size:44 final size:44
Alignment explanation
Indices: 36762--36905 Score: 216
Period size: 44 Copynumber: 3.2 Consensus size: 44
36752 AAGAGCAACG
36762 ATGGTTTTCAAAAAGAGTCGTGGTTTTCAAAAGGTTTTGATAAA
1 ATGGTTTTCAAAAAGAGTCGTGGTTTTCAAAAGGTTTTGATAAA
36806 ATGGTTTTCAAAAAGAGTCGTGGTTTTCAAAAGGTTTTGATAAA
1 ATGGTTTTCAAAAAGAGTCGTGGTTTTCAAAAGGTTTTGATAAA
* * * * *
36850 ATGTTTTTTTCAAGAAGAATCATGGTTTTCAAGAGGGTTTTGATAAA
1 ATG--GTTTTCAAAAAGAGTCGTGGTTTTCAA-AAGGTTTTGATAAA
36897 ATGGTTTTC
1 ATGGTTTTC
36906 CAAAGTTGCA
Statistics
Matches: 91, Mismatches: 6, Indels: 5
0.89 0.06 0.05
Matches are distributed among these distances:
44 47 0.52
45 5 0.05
46 23 0.25
47 16 0.18
ACGTcount: A:0.32, C:0.07, G:0.22, T:0.39
Consensus pattern (44 bp):
ATGGTTTTCAAAAAGAGTCGTGGTTTTCAAAAGGTTTTGATAAA
Found at i:37279 original size:31 final size:31
Alignment explanation
Indices: 37241--37299 Score: 82
Period size: 31 Copynumber: 1.9 Consensus size: 31
37231 AAAGATAAAA
**
37241 AAAAAAAAAAGTGAAAATTGAAAGTGAAGTG
1 AAAAAAAAAAGTGAAAAAAGAAAGTGAAGTG
**
37272 AAAAAAAAATTTGAAAAAAGAAAGTGAA
1 AAAAAAAAAAGTGAAAAAAGAAAGTGAA
37300 AGGAAAGGTG
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
31 24 1.00
ACGTcount: A:0.66, C:0.00, G:0.19, T:0.15
Consensus pattern (31 bp):
AAAAAAAAAAGTGAAAAAAGAAAGTGAAGTG
Found at i:37623 original size:5 final size:5
Alignment explanation
Indices: 37613--37655 Score: 54
Period size: 5 Copynumber: 8.6 Consensus size: 5
37603 AAAAAAATAG
37613 AAAGA AAAGA AAAGA AAAGA AAA-A AGAAG- AAAGAA AAAGA AAA
1 AAAGA AAAGA AAAGA AAAGA AAAGA A-AAGA AAAG-A AAAGA AAA
37656 ATGAATGATG
Statistics
Matches: 34, Mismatches: 0, Indels: 8
0.81 0.00 0.19
Matches are distributed among these distances:
4 5 0.15
5 25 0.74
6 4 0.12
ACGTcount: A:0.81, C:0.00, G:0.19, T:0.00
Consensus pattern (5 bp):
AAAGA
Found at i:37642 original size:20 final size:19
Alignment explanation
Indices: 37601--37656 Score: 60
Period size: 20 Copynumber: 2.8 Consensus size: 19
37591 CAAGTGCATT
* *
37601 GAAAAAAAATAGAAAGAAAA
1 GAAAAGAAA-AGAAAAAAAA
37621 GAAAAGAAAAGAAAAAAGAA
1 GAAAAGAAAAGAAAAAA-AA
37641 G-AAAGAAAAAGAAAAA
1 GAAAAG-AAAAGAAAAA
37657 TGAATGATGA
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
19 11 0.34
20 21 0.66
ACGTcount: A:0.80, C:0.00, G:0.18, T:0.02
Consensus pattern (19 bp):
GAAAAGAAAAGAAAAAAAA
Found at i:37642 original size:25 final size:25
Alignment explanation
Indices: 37601--37656 Score: 71
Period size: 25 Copynumber: 2.2 Consensus size: 25
37591 CAAGTGCATT
*
37601 GAAAAAAAATAGAAAGAAA-AGAAAA
1 GAAAAAAAAAAGAAAGAAAGA-AAAA
37626 GAAAAGAAAAAAG-AAGAAAGAAAAA
1 GAAAA-AAAAAAGAAAGAAAGAAAAA
37651 GAAAAA
1 GAAAAA
37657 TGAATGATGA
Statistics
Matches: 28, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
24 1 0.04
25 20 0.71
26 7 0.25
ACGTcount: A:0.80, C:0.00, G:0.18, T:0.02
Consensus pattern (25 bp):
GAAAAAAAAAAGAAAGAAAGAAAAA
Found at i:38884 original size:36 final size:36
Alignment explanation
Indices: 38835--38942 Score: 121
Period size: 35 Copynumber: 3.0 Consensus size: 36
38825 CAGTTCACCC
*
38835 AGGGTGGGT-TTTCTTTAGTTTATGTCGGAATGATCG
1 AGGGT-GGTCTTTCTTTAGTTTATGTCAGAATGATCG
* * * * *
38871 AGGGTGGTCTTTCTTTAGCTTATTTCAG-TTGACCC
1 AGGGTGGTCTTTCTTTAGTTTATGTCAGAATGATCG
**
38906 AGGGTGGTCTTTCTCCAGTTTATGTCAGAATGATCG
1 AGGGTGGTCTTTCTTTAGTTTATGTCAGAATGATCG
38942 A
1 A
38943 TTCAGTTGAC
Statistics
Matches: 57, Mismatches: 13, Indels: 4
0.77 0.18 0.05
Matches are distributed among these distances:
35 31 0.54
36 26 0.46
ACGTcount: A:0.18, C:0.15, G:0.28, T:0.40
Consensus pattern (36 bp):
AGGGTGGTCTTTCTTTAGTTTATGTCAGAATGATCG
Found at i:38914 original size:35 final size:35
Alignment explanation
Indices: 38823--38919 Score: 106
Period size: 35 Copynumber: 2.7 Consensus size: 35
38813 GAATGATCGA
* *
38823 TTCAGTTCACCCAGGGTGGGT-TTTCTTTAGTTTAT
1 TTCAGTTGACCCAGGGT-GGTCTTTCTTTAGCTTAT
* * * * *
38858 GTCGGAATGATCGAGGGTGGTCTTTCTTTAGCTTAT
1 TTCAG-TTGACCCAGGGTGGTCTTTCTTTAGCTTAT
38894 TTCAGTTGACCCAGGGTGGTCTTTCT
1 TTCAGTTGACCCAGGGTGGTCTTTCT
38920 CCAGTTTATG
Statistics
Matches: 48, Mismatches: 12, Indels: 4
0.75 0.19 0.06
Matches are distributed among these distances:
35 24 0.50
36 24 0.50
ACGTcount: A:0.14, C:0.18, G:0.27, T:0.41
Consensus pattern (35 bp):
TTCAGTTGACCCAGGGTGGTCTTTCTTTAGCTTAT
Found at i:38989 original size:35 final size:35
Alignment explanation
Indices: 38943--39017 Score: 114
Period size: 35 Copynumber: 2.1 Consensus size: 35
38933 GAATGATCGA
* *
38943 TTCAGTTGACCCAGGGTGGTCTTTCTTAAGTTTAT
1 TTCAGTTGACCCAGGGCGGTCTTTCTCAAGTTTAT
*
38978 TTCAGTTGACCCAGGGCGGTCTTTCTCCAGTTTAT
1 TTCAGTTGACCCAGGGCGGTCTTTCTCAAGTTTAT
*
39013 GTCAG
1 TTCAG
39018 AATGATTGAT
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
35 36 1.00
ACGTcount: A:0.16, C:0.21, G:0.24, T:0.39
Consensus pattern (35 bp):
TTCAGTTGACCCAGGGCGGTCTTTCTCAAGTTTAT
Found at i:39012 original size:84 final size:84
Alignment explanation
Indices: 38871--39058 Score: 313
Period size: 84 Copynumber: 2.2 Consensus size: 84
38861 GGAATGATCG
* * *
38871 AGGGTGGTCTTTCTTTAGCTTATTTCAGTTGACCCAGGGTGGTCTTTCTCCAGTTTATGTCAGAA
1 AGGGTGGTCTTTCTTAAGTTTATTTCAGTTGACCCAGGGCGGTCTTTCTCCAGTTTATGTCAGAA
*
38936 TGATCGATTCAGTTGACCC
66 TGATCGATTCAGTCGACCC
38955 AGGGTGGTCTTTCTTAAGTTTATTTCAGTTGACCCAGGGCGGTCTTTCTCCAGTTTATGTCAGAA
1 AGGGTGGTCTTTCTTAAGTTTATTTCAGTTGACCCAGGGCGGTCTTTCTCCAGTTTATGTCAGAA
*
39020 TGATTGATTCAGTCGACCC
66 TGATCGATTCAGTCGACCC
* *
39039 AGGGCGGTCTTTCTTCAGTT
1 AGGGTGGTCTTTCTTAAGTT
39059 GTTTTCAAGT
Statistics
Matches: 97, Mismatches: 7, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
84 97 1.00
ACGTcount: A:0.18, C:0.20, G:0.24, T:0.38
Consensus pattern (84 bp):
AGGGTGGTCTTTCTTAAGTTTATTTCAGTTGACCCAGGGCGGTCTTTCTCCAGTTTATGTCAGAA
TGATCGATTCAGTCGACCC
Found at i:39183 original size:70 final size:71
Alignment explanation
Indices: 39006--39339 Score: 469
Period size: 71 Copynumber: 4.7 Consensus size: 71
38996 GTCTTTCTCC
* * *
39006 AGTTTATGTCAGAATGATTGATTCAGTCGACCCAGGGCGGTCTTTCTTCAGTTGTTTTCAAGTTT
1 AGTTTATGTCAGAATGATCGATTCAGTCGACCCAGGGCGGTCTTTCTTCAGTAGTTTCCAAGTTT
39071 ATTCCA
66 ATTCCA
* * * *
39077 AGTTTATGTCAGAATGATCAAATCAGTCGACCCAGGGCGGTCTTTCTTTAGTAGCTTCCACA-TT
1 AGTTTATGTCAGAATGATCGATTCAGTCGACCCAGGGCGGTCTTTCTTCAGTAGTTTCCA-AGTT
39141 TA-TCCA
65 TATTCCA
* * * *
39147 AGTTTATGTCAGAATGATCGATTCGGTCAACCCAGGGCGGTCTTTCTTCAGTTGTTTTCAAGTTT
1 AGTTTATGTCAGAATGATCGATTCAGTCGACCCAGGGCGGTCTTTCTTCAGTAGTTTCCAAGTTT
*
39212 ATTCGA
66 ATTCCA
* *
39218 AGTTTATGTCAGAATGATCGATTCAGTTGACCCAGGGCGGTCTTTCTTTAGTAGTTTCCAAGTTT
1 AGTTTATGTCAGAATGATCGATTCAGTCGACCCAGGGCGGTCTTTCTTCAGTAGTTTCCAAGTTT
39283 A-TCCA
66 ATTCCA
* * *
39288 AGTTTATGTTAGAATGATCGATTCAGTTGACCCAGGGTGGT-TCTTCTTCAGT
1 AGTTTATGTCAGAATGATCGATTCAGTCGACCCAGGGCGGTCT-TTCTTCAGT
39340 TCATGTCAGA
Statistics
Matches: 233, Mismatches: 26, Indels: 9
0.87 0.10 0.03
Matches are distributed among these distances:
69 2 0.01
70 110 0.47
71 120 0.52
72 1 0.00
ACGTcount: A:0.22, C:0.19, G:0.22, T:0.37
Consensus pattern (71 bp):
AGTTTATGTCAGAATGATCGATTCAGTCGACCCAGGGCGGTCTTTCTTCAGTAGTTTCCAAGTTT
ATTCCA
Found at i:39260 original size:141 final size:141
Alignment explanation
Indices: 39006--39340 Score: 539
Period size: 141 Copynumber: 2.4 Consensus size: 141
38996 GTCTTTCTCC
*
39006 AGTTTATGTCAGAATGATTGATTCAGTCGACCCAGGGCGGTCTTTCTTCAGTTGTTTTCAAGTTT
1 AGTTTATGTCAGAATGATCGATTCAGTCGACCCAGGGCGGTCTTTCTTCAGTTGTTTTCAAGTTT
39071 ATTCCAAGTTTATGTCAGAATGATCAAATCAGTCGACCCAGGGCGGTCTTTCTTTAGTAGCTTCC
66 ATTCCAAGTTTATGTCAGAATGATCAAATCAGTCGACCCAGGGCGGTCTTTCTTTAGTAGCTTCC
39136 ACA-TTTATCCA
131 A-AGTTTATCCA
* *
39147 AGTTTATGTCAGAATGATCGATTCGGTCAACCCAGGGCGGTCTTTCTTCAGTTGTTTTCAAGTTT
1 AGTTTATGTCAGAATGATCGATTCAGTCGACCCAGGGCGGTCTTTCTTCAGTTGTTTTCAAGTTT
* * * * *
39212 ATTCGAAGTTTATGTCAGAATGATCGATTCAGTTGACCCAGGGCGGTCTTTCTTTAGTAGTTTCC
66 ATTCCAAGTTTATGTCAGAATGATCAAATCAGTCGACCCAGGGCGGTCTTTCTTTAGTAGCTTCC
39277 AAGTTTATCCA
131 AAGTTTATCCA
* * *
39288 AGTTTATGTTAGAATGATCGATTCAGTTGACCCAGGGTGGT-TCTTCTTCAGTT
1 AGTTTATGTCAGAATGATCGATTCAGTCGACCCAGGGCGGTCT-TTCTTCAGTT
39341 CATGTCAGAA
Statistics
Matches: 179, Mismatches: 13, Indels: 4
0.91 0.07 0.02
Matches are distributed among these distances:
140 2 0.01
141 177 0.99
ACGTcount: A:0.22, C:0.19, G:0.21, T:0.37
Consensus pattern (141 bp):
AGTTTATGTCAGAATGATCGATTCAGTCGACCCAGGGCGGTCTTTCTTCAGTTGTTTTCAAGTTT
ATTCCAAGTTTATGTCAGAATGATCAAATCAGTCGACCCAGGGCGGTCTTTCTTTAGTAGCTTCC
AAGTTTATCCA
Found at i:39370 original size:49 final size:49
Alignment explanation
Indices: 39288--39388 Score: 141
Period size: 49 Copynumber: 2.1 Consensus size: 49
39278 AGTTTATCCA
* * * *
39288 AGTTTATGTTAGAATGATCGATTCAGTTGACCCAGGGTGGT-TCTTCTTC
1 AGTTCATGTCAGAATGATCGACTCAGTCGACCCAGGGTGGTCT-TTCTTC
*
39337 AGTTCATGTCAGAATGATCGACTCGGTCGACCCAGGGTGGTCTTTCTTC
1 AGTTCATGTCAGAATGATCGACTCAGTCGACCCAGGGTGGTCTTTCTTC
39386 AGT
1 AGT
39389 AGTTTCCACG
Statistics
Matches: 46, Mismatches: 5, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
49 45 0.98
50 1 0.02
ACGTcount: A:0.20, C:0.20, G:0.26, T:0.35
Consensus pattern (49 bp):
AGTTCATGTCAGAATGATCGACTCAGTCGACCCAGGGTGGTCTTTCTTC
Found at i:39434 original size:119 final size:119
Alignment explanation
Indices: 39218--39459 Score: 394
Period size: 119 Copynumber: 2.0 Consensus size: 119
39208 GTTTATTCGA
* * * *
39218 AGTTTATGTCAGAATGATCGATTCAGTTGACCCAGGGCGGTCTTTCTTTAGTAGTTTCCAAGTTT
1 AGTTCATGTCAGAATGATCGACTCAGTCGACCCAGGGCGGTCTTTCTTCAGTAGTTTCCAAGTTT
* *
39283 ATCCAAGTTTATGTTAGAATGATCGATTCAGTTGACCCAGGGTGGTTCTTCTTC
66 ATCCAAGTTTATGTTAGAATGATCGATTCAGTTGACCCAGGGCGGTTCTTCATC
* * *
39337 AGTTCATGTCAGAATGATCGACTCGGTCGACCCAGGGTGGTCTTTCTTCAGTAGTTTCCACGTTT
1 AGTTCATGTCAGAATGATCGACTCAGTCGACCCAGGGCGGTCTTTCTTCAGTAGTTTCCAAGTTT
*
39402 ATCCAAGTTTATGTTAGAATGATCGATTCAGTTGACCCAGGGCGGTTTTTCATC
66 ATCCAAGTTTATGTTAGAATGATCGATTCAGTTGACCCAGGGCGGTTCTTCATC
39456 AGTT
1 AGTT
39460 GTTTCCGGTT
Statistics
Matches: 113, Mismatches: 10, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
119 113 1.00
ACGTcount: A:0.21, C:0.19, G:0.23, T:0.36
Consensus pattern (119 bp):
AGTTCATGTCAGAATGATCGACTCAGTCGACCCAGGGCGGTCTTTCTTCAGTAGTTTCCAAGTTT
ATCCAAGTTTATGTTAGAATGATCGATTCAGTTGACCCAGGGCGGTTCTTCATC
Done.