Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold1724
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: 75563
ACGTcount: A:0.33, C:0.17, G:0.16, T:0.33
Found at i:4786 original size:21 final size:21
Alignment explanation
Indices: 4746--4786 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
4736 TTAAGTATAA
*
4746 ATATTTTTCAAGCTATAAATC
1 ATATTTTTCAAGCTAAAAATC
4767 ATATGTTTTCAAG-TAAAAAT
1 ATAT-TTTTCAAGCTAAAAAT
4787 AATCCAAAGT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 10 0.56
22 8 0.44
ACGTcount: A:0.41, C:0.10, G:0.07, T:0.41
Consensus pattern (21 bp):
ATATTTTTCAAGCTAAAAATC
Found at i:6815 original size:118 final size:118
Alignment explanation
Indices: 6599--6829 Score: 311
Period size: 118 Copynumber: 2.0 Consensus size: 118
6589 ACCAGAACAG
* * * *
6599 AAACCTTTTTTTCTCTCTTTTTTTGCTAATTAACAATAAGGAAAAGAGAAAATTCAAGCCATCTT
1 AAACCTTTTTTTCTCTCTTTTCTTGCTAATTAACAACAAGGAAAAAAGAAAATTCAAGCCATCTC
* *
6664 TGCTGCTCTAATAACTTAGCCAAAAGCTGGAGCTTTGTTGGTATAATTTACAA
66 TGCTGCTCTAATAACTTAGCCAAAAGCTAGAGCTTTGTTAGTATAATTTACAA
* * * *
6717 AAACC-TTTTTTCTTTCTTTTCTTGGTAATTAACAACAAGGAAAAAAGAAAAATTGAGGCCATCT
1 AAACCTTTTTTTCTCTCTTTTCTTGCTAATTAACAACAAGGAAAAAAG-AAAATTCAAGCCATCT
* * * * *
6781 CTGCTGTTCTAATCACTTGGCCAAAGGCTAGAGCTTTGTTATTATAATT
65 CTGCTGCTCTAATAACTTAGCCAAAAGCTAGAGCTTTGTTAGTATAATT
6830 CCTACTTAAT
Statistics
Matches: 97, Mismatches: 15, Indels: 2
0.85 0.13 0.02
Matches are distributed among these distances:
117 37 0.38
118 60 0.62
ACGTcount: A:0.32, C:0.17, G:0.14, T:0.36
Consensus pattern (118 bp):
AAACCTTTTTTTCTCTCTTTTCTTGCTAATTAACAACAAGGAAAAAAGAAAATTCAAGCCATCTC
TGCTGCTCTAATAACTTAGCCAAAAGCTAGAGCTTTGTTAGTATAATTTACAA
Found at i:11625 original size:164 final size:163
Alignment explanation
Indices: 11327--11869 Score: 544
Period size: 164 Copynumber: 3.3 Consensus size: 163
11317 AATCTCTATC
* * * * * *
11327 AAATCAATTTTGAACAATTCTTTTATTTTCATGAGTTTTTAATTTTTTTCTTGAAATTCTCTT-T
1 AAATCAGTTTTCAAAAATTCATTCATTTTCATGAGTTTTTAATTTTTTTCTTAAAATTC-CTTAT
* ** * ** * *
11391 TTTTCGAAA-CCGGTGTTTTCTACTTTGTAATTTTTTTTTAAGAGA-TTTTCGAGGTTTTCAATT
65 TTTT-GAAATACGGTGTTTTCTACTCCGTAAATTTTTTCGAAGGGATTTTTC-CGGTTTTCAA-T
*
11454 TTTAAAATTCATCAAACATCATTATTTGTTTCATAAT
127 TTTAAAATTCATCAAACATCATTATTTGTTTCATATT
* * * * * *
11491 AATTTAGTTTTTAAAAATTCATTCATTTTCATGAATTTTTAATTGTTTTCTTAAAACTCCTATAT
1 AAATCAGTTTTCAAAAATTCATTCATTTTCATGAGTTTTTAATTTTTTTCTTAAAATTCCT-TAT
* * *
11556 TTTTGAAATACGGTGTTTTCTACACCGTAAATTTTCTCGAAGGGATTTTTCTCGGTTTTCAA-AT
65 TTTTGAAATACGGTGTTTTCTACTCCGTAAATTTTTTCGAAGGGATTTTTC-CGGTTTTCAATTT
* *
11620 TAAAATTCATCAAACATCATCATTTGATTCATATT
129 TAAAATTCATCAAACATCATTATTTGTTTCATATT
* * *
11655 AAATCAGTTTTCAAAAAGTT-ATTCATTTTCATGAGTTTTTCATTTTTTTCCATGAAATTTTCC-
1 AAATCAGTTTTCAAAAA-TTCATTCATTTTCATGAGTTTTTAATTTTTTT-C-TTAAA-ATTCCT
*** * *
11718 TATTTTTGAAATACAAAGTTTTCTACTCGGT-AATTTTTTCG-AGGGCATTTTTCCTGGTTTTTA
62 TATTTTTGAAATACGGTGTTTTCTACTCCGTAAATTTTTTCGAAGGG-ATTTTTCC-GGTTTTCA
* * *
11781 ATTTTTAAAATTCATCAAATATTATTATTTATTTCATATT
125 A-TTTTAAAATTCATCAAACATCATTATTTGTTTCATATT
* * * *
11821 AAATCAGTTTTCAAAAATTCGTTTATTTTCTTGAGTTTTAAATTTTTTT
1 AAATCAGTTTTCAAAAATTCATTCATTTTCATGAGTTTTTAATTTTTTT
11870 TCTTTGAAAT
Statistics
Matches: 313, Mismatches: 53, Indels: 24
0.80 0.14 0.06
Matches are distributed among these distances:
163 7 0.02
164 150 0.48
165 63 0.20
166 90 0.29
167 3 0.01
ACGTcount: A:0.29, C:0.12, G:0.09, T:0.50
Consensus pattern (163 bp):
AAATCAGTTTTCAAAAATTCATTCATTTTCATGAGTTTTTAATTTTTTTCTTAAAATTCCTTATT
TTTGAAATACGGTGTTTTCTACTCCGTAAATTTTTTCGAAGGGATTTTTCCGGTTTTCAATTTTA
AAATTCATCAAACATCATTATTTGTTTCATATT
Found at i:13598 original size:17 final size:15
Alignment explanation
Indices: 13565--13599 Score: 52
Period size: 15 Copynumber: 2.2 Consensus size: 15
13555 GAAATTTTTG
13565 AAAATAAAAAATAAT
1 AAAATAAAAAATAAT
13580 AAAATAAAATAACTAAT
1 AAAATAAAA-AA-TAAT
13597 AAA
1 AAA
13600 TTCTTTTTCA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
15 9 0.50
16 2 0.11
17 7 0.39
ACGTcount: A:0.77, C:0.03, G:0.00, T:0.20
Consensus pattern (15 bp):
AAAATAAAAAATAAT
Found at i:14402 original size:156 final size:154
Alignment explanation
Indices: 14145--14509 Score: 391
Period size: 156 Copynumber: 2.4 Consensus size: 154
14135 TCTCTTAGGG
* * * ** *
14145 GTATCGGGTACTTTTACATCAAAGGTATCCCCTAGGGGTATTTTCATAATTTTTTAGAACCAACT
1 GTATCGGGTACTTATACATCGAAGGTATCACCTAAAGGCATTTTCATAATTTTTTAGAACCAACT
* * * * * * ** *
14210 CCTAGGTCATCGTCGGGTCCTCTTTTATGTCGAAGGTAGATGTTTAGGATAGGTTCATCCC-TTC
66 CCTAAGTCATCATCGAGTCCGCTTTTATCTCAAAGGTAGACATTTAGGATACGTTCATCCCATTC
* *
14274 TATATCCTTTTTAAGTCCTTTA-GG
131 TA-ATCATTTTTAAGTCCTTTATGA
*
14298 GT-TACTGGGATACTT-TCACATCGAAGTTAT-ACCTATAGAGGCATTTTCATAATTTTTTAGAA
1 GTAT-C-GGG-TACTTAT-ACATCGAAGGTATCACCTA-A-AGGCATTTTCATAATTTTTTAGAA
* * *
14360 CCAACTCTTAAGTCATCATCGAGTCCGCTTTTATACT-AAAGGTGGGCATTTAGGATACGTTCAT
60 CCAACTCCTAAGTCATCATCGAGTCCGCTTTTAT-CTCAAAGGTAGACATTTAGGATACGTTCAT
*
14424 CCCATTTCTAATCATTTTTAAGTCTTTTATGA
124 CCCA-TTCTAATCATTTTTAAGTCCTTTATGA
* *
14456 GTATCGGGTACTTATACGTCGAAGGTATCCCCTAAAGGCATTTTCATAATTTTT
1 GTATCGGGTACTTATACATCGAAGGTATCACCTAAAGGCATTTTCATAATTTTT
14510 CTTAAACTTA
Statistics
Matches: 175, Mismatches: 24, Indels: 24
0.78 0.11 0.11
Matches are distributed among these distances:
152 1 0.01
153 3 0.02
154 8 0.05
155 35 0.20
156 92 0.53
157 26 0.15
158 9 0.05
159 1 0.01
ACGTcount: A:0.25, C:0.19, G:0.18, T:0.38
Consensus pattern (154 bp):
GTATCGGGTACTTATACATCGAAGGTATCACCTAAAGGCATTTTCATAATTTTTTAGAACCAACT
CCTAAGTCATCATCGAGTCCGCTTTTATCTCAAAGGTAGACATTTAGGATACGTTCATCCCATTC
TAATCATTTTTAAGTCCTTTATGA
Found at i:16464 original size:163 final size:161
Alignment explanation
Indices: 16048--16681 Score: 554
Period size: 164 Copynumber: 3.9 Consensus size: 161
16038 TCTATTATCG
* ** * * *
16048 AAATACGGAGTTTTCCACTATGTAAATGTTTGTAGGTGGATTTTTCTTAGTTTATAATTTTTAAA
1 AAATACGGAGTTTTCTACTCCGTAAATATTT-TTGGGGGATTTTTCTTAGTTTATAATTTTTAAA
* * *
16113 ATTCATCTAATATCATC-----A-TC-TATTAAATCAGTTTTGAAAAATTCATTTATTTTCTTGA
65 ATTCATCAAATATCATCATTTAATTCATATTAAATCAGTTTTGAAAAATTCATTTA-TCTCATGA
* * * *
16171 GTTTTTCATTTTTTTTCCTTAAAATTTTCTTATTTCCA
129 -TTTTTCA--TTTTTT--TTGAAATTCTCATAGTTCCA
* * ** *
16209 AAATACAGAGTTTTATACTCCGTAAATATTTGCGGGGAGATTTTTCTTGGTTTATAATTTTTAAA
1 AAATACGGAGTTTTCTACTCCGTAAATATTTTTGGGG-GATTTTTCTTAGTTTATAATTTTTAAA
* ** * *
16274 ATGCATCAAATATCATCACATAATTCATATTAAATTAGTTTTGAAAAATTCCTTTTATCTCATGC
65 ATTCATCAAATATCATCATTTAATTCATATTAAATCAGTTTTGAAAAATT-CATTTATCTCATG-
* *
16339 ATTGTTCATTTTTTTTGAAATTCTCCTAGTTCCA
128 ATTTTTCATTTTTTTTGAAATTCTCATAGTTCCA
* * * * *
16373 AAATATGGAGTTTTCTACTCCGTAAATGTTTTTTGGTGGATTTTT-TTTGTTTGTAATTTTTAAA
1 AAATACGGAGTTTTCTACTCCGTAAAT-ATTTTTGGGGGATTTTTCTTAGTTTATAATTTTTAAA
* *
16437 ATTCATCAAATATCATCATTTAATTCATAGTAAATCAGTTTTGAAAAAATT-ATTTATGTTCACA
65 ATTCATCAAATATCATCATTTAATTCATATTAAATCAGTTTTG-AAAAATTCATTTA---TCTCA
*
16501 TG-TTTTTCATTTTTCTTTGAAATTCTCAT-GTTTCTA
126 TGATTTTTCATTTTT-TTTGAAATTCTCATAG-TTCCA
* ** * * * * *
16537 AAAAATTGAGTTTTCTATTCCATAAATATTTTTGGAGGGATTTTTCTCAATTTAAAATTTTTAAA
1 AAATACGGAGTTTTCTACTCCGTAAATATTTTTGG-GGGATTTTTCTTAGTTTATAATTTTTAAA
* ** * * * * *
16602 ATTTATCAAATATTGTCATTAAATTGACATTAAATCAG-TTTGAGAAAATTACATTTATTTTATG
65 ATTCATCAAATATCATCATTTAATTCATATTAAATCAGTTTTGA-AAAATT-CATTTATCTCATG
16666 AATTTTTCATTTTTTT
128 -ATTTTTCATTTTTTT
16682 CATATAATAA
Statistics
Matches: 388, Mismatches: 61, Indels: 45
0.79 0.12 0.09
Matches are distributed among these distances:
160 3 0.01
161 66 0.17
162 4 0.01
163 79 0.20
164 114 0.29
165 69 0.18
166 12 0.03
167 2 0.01
168 33 0.09
169 6 0.02
ACGTcount: A:0.31, C:0.11, G:0.10, T:0.48
Consensus pattern (161 bp):
AAATACGGAGTTTTCTACTCCGTAAATATTTTTGGGGGATTTTTCTTAGTTTATAATTTTTAAAA
TTCATCAAATATCATCATTTAATTCATATTAAATCAGTTTTGAAAAATTCATTTATCTCATGATT
TTTCATTTTTTTTGAAATTCTCATAGTTCCA
Found at i:16636 original size:328 final size:323
Alignment explanation
Indices: 16048--16681 Score: 688
Period size: 328 Copynumber: 1.9 Consensus size: 323
16038 TCTATTATCG
*
16048 AAATACGGAGTTTTCCACTATGTAAATGTTTGTAGGTGGATTTTTCTTAGTTTATAATTTTTAAA
1 AAATACGGAGTTTTCCACTACGTAAATGTTTGTAGGTGGATTTTTCTTAGTTTATAATTTTTAAA
* * * **
16113 ATTCATCTAATATCATCATCTATTAAATCAGTTTTGAAAAATTCATTTATTTTCTTGAGTTTTTC
66 ATTCATCAAATATCATCATCTAGTAAATCAGTTTTGAAAAATTCATTTATGTTCTACAGTTTTTC
* * * *
16178 ATTTTTTTTCCTTAAAATTTTCTTATTTCCAAAATACAGAGTTTTATACTCCGTAAATATTTGCG
131 A--TTTTTTCCTTAAAATTCTCATATTTCCAAAAAACAGAGTTTTATACTCCATAAATATTTGCG
*** * *
16243 GGGAGATTTTTCTTGGTTTATAATTTTTAAAATGCATCAAATATCATCACATAATTCATATTAAA
194 GGGAGATTTTTCTCAATTTAAAATTTTTAAAATGCATCAAATATCATCACATAATTCACATTAAA
* * * *
16308 TTAGTTTTGA-AAAATTCCTTTTATCTCATGCATTGTTCATTTTTTTTGAAATTCTCCTAGTTCC
259 TCAG-TTTGAGAAAATTACATTTATCTCATGAATTGTTCATTTTTTTTGAAATTCTCCTAGTTCC
16372 A
323 A
* * * * * * *
16373 AAATATGGAGTTTTCTACTCCGTAAATGTTTTTTGGTGGATTTTT-TTTGTTTGTAATTTTTAAA
1 AAATACGGAGTTTTCCACTACGTAAATGTTTGTAGGTGGATTTTTCTTAGTTTATAATTTTTAAA
16437 ATTCATCAAATATCATCATTTAATTCATAGTAAATCAGTTTTGAAAAAATT-ATTTATGTTC-AC
66 ATTCATCAAATATCATC-----A-TC-TAGTAAATCAGTTTTG-AAAAATTCATTTATGTTCTAC
* * * * ** * *
16500 ATGTTTTTCA-TTTTTCTTTGAAATTCTCATGTTTCTAAAAAATTGAGTTTTCTATTCCATAAAT
123 A-GTTTTTCATTTTTTCCTTAAAATTCTCATATTTCCAAAAAACAGAGTTTTATACTCCATAAAT
** ** ** *
16564 ATTTTTGGAGG-GATTTTTCTCAATTTAAAATTTTTAAAATTTATCAAATATTGTCA-TTAAATT
187 ATTTGCGG-GGAGATTTTTCTCAATTTAAAATTTTTAAAATGCATCAAATATCATCACAT-AATT
* * * *
16627 GACATTAAATCAGTTTGAGAAAATTACATTTATTTTATGAATTTTTCATTTTTTT
250 CACATTAAATCAGTTTGAGAAAATTACATTTATCTCATGAATTGTTCATTTTTTT
16682 CATATAATAA
Statistics
Matches: 252, Mismatches: 45, Indels: 21
0.79 0.14 0.07
Matches are distributed among these distances:
324 33 0.13
325 39 0.15
327 6 0.02
328 129 0.51
329 3 0.01
330 3 0.01
331 32 0.13
332 7 0.03
ACGTcount: A:0.31, C:0.11, G:0.10, T:0.48
Consensus pattern (323 bp):
AAATACGGAGTTTTCCACTACGTAAATGTTTGTAGGTGGATTTTTCTTAGTTTATAATTTTTAAA
ATTCATCAAATATCATCATCTAGTAAATCAGTTTTGAAAAATTCATTTATGTTCTACAGTTTTTC
ATTTTTTCCTTAAAATTCTCATATTTCCAAAAAACAGAGTTTTATACTCCATAAATATTTGCGGG
GAGATTTTTCTCAATTTAAAATTTTTAAAATGCATCAAATATCATCACATAATTCACATTAAATC
AGTTTGAGAAAATTACATTTATCTCATGAATTGTTCATTTTTTTTGAAATTCTCCTAGTTCCA
Found at i:17960 original size:14 final size:14
Alignment explanation
Indices: 17941--17990 Score: 57
Period size: 14 Copynumber: 3.6 Consensus size: 14
17931 GTACATACTT
17941 TTTAATTTTTACAA
1 TTTAATTTTTACAA
** *
17955 TTTAATCCTTATAA
1 TTTAATTTTTACAA
17969 -TTAATTTTTACAA
1 TTTAATTTTTACAA
*
17982 TATAATTTT
1 TTTAATTTT
17991 ACGAATTAAT
Statistics
Matches: 28, Mismatches: 7, Indels: 2
0.76 0.19 0.05
Matches are distributed among these distances:
13 10 0.36
14 18 0.64
ACGTcount: A:0.36, C:0.08, G:0.00, T:0.56
Consensus pattern (14 bp):
TTTAATTTTTACAA
Found at i:17997 original size:27 final size:27
Alignment explanation
Indices: 17942--18000 Score: 75
Period size: 27 Copynumber: 2.2 Consensus size: 27
17932 TACATACTTT
* *
17942 TTAATTTTTACAATTTAATCCTTATAA
1 TTAATTTTTACAATATAATCCTTAGAA
*
17969 TTAATTTTTACAATATAAT-TTTACGAA
1 TTAATTTTTACAATATAATCCTTA-GAA
17996 TTAAT
1 TTAAT
18001 ATAAATATCT
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
26 3 0.11
27 25 0.89
ACGTcount: A:0.39, C:0.08, G:0.02, T:0.51
Consensus pattern (27 bp):
TTAATTTTTACAATATAATCCTTAGAA
Found at i:18300 original size:20 final size:21
Alignment explanation
Indices: 18275--18315 Score: 57
Period size: 22 Copynumber: 2.0 Consensus size: 21
18265 CCTTCCATGC
*
18275 ATAAAAAGA-AAGAAAAAAAT
1 ATAAAAACACAAGAAAAAAAT
18295 ATAAAAACACTAAGAAAAAAA
1 ATAAAAACAC-AAGAAAAAAA
18316 ATCAATTTTT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 8 0.44
22 10 0.56
ACGTcount: A:0.78, C:0.05, G:0.07, T:0.10
Consensus pattern (21 bp):
ATAAAAACACAAGAAAAAAAT
Found at i:19075 original size:9 final size:9
Alignment explanation
Indices: 19061--19094 Score: 59
Period size: 9 Copynumber: 3.7 Consensus size: 9
19051 ATGATATCTA
19061 TTTAATATG
1 TTTAATATG
19070 TTTAATATG
1 TTTAATATG
19079 TTTAATATG
1 TTTAATATG
19088 TTATAAT
1 TT-TAAT
19095 GAAAATTTCC
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
9 20 0.83
10 4 0.17
ACGTcount: A:0.35, C:0.00, G:0.09, T:0.56
Consensus pattern (9 bp):
TTTAATATG
Found at i:20170 original size:155 final size:152
Alignment explanation
Indices: 19844--20282 Score: 473
Period size: 155 Copynumber: 2.9 Consensus size: 152
19834 CTAGGTTCAT
* * * * *
19844 TTTTATGCCAAAGGTGGGTATTTA-GATAGTTTCATCCTATCTATAATCCTTTTTAAGTTCTTTA
1 TTTTATGTCGAAGGTGGGTATTTAGGATAGTTTCATCCCATCTATAATCCTTTTAAAGTCCTTTA
* * * * * *
19908 AGGGTATCGAGCAC--TT-CG---AATGTACCTTTAATGGTATTTTTGTAATTTTTCAAAATTGA
66 AGGGTATCG-GCACTTTTACGTCAAAAGTACCCTTAA-GGCATTTTCGTAATTTTTTAAAATCGA
**
19967 GTCTTAGGTTATCACCGAGTCTGC
129 GTCTTAGGCCATCACCGAGTCTGC
*
19991 TTTTATGTCGAAAGTGGGTATTTAGGATAGTTTCATCCCATCTATAATCCTTTTAAAGTCCTTTA
1 TTTTATGTCGAAGGTGGGTATTTAGGATAGTTTCATCCCATCTATAATCCTTTTAAAGTCCTTTA
* * * *
20056 CGGGTATCGGCCACTTTTACGTCAAAGGTATCCCTTAAGAGCATTTTCATAATTTTTTATAATCG
66 AGGGTATCGG-CACTTTTACGTCAAAAGTA-CCCTTAAG-GCATTTTCGTAATTTTTTAAAATCG
* *
20121 AGTCCTAGGCCGTCACCGAGT-TCGC
128 AGTCTTAGGCCATCACCGAGTCT-GC
* * * *
20146 TTTTATGTGGAAGGTAGGTATTTAGGATAGGTTCATCCCATCTATAATCCTTTTAAAGTCTTTTA
1 TTTTATGTCGAAGGTGGGTATTTAGGATAGTTTCATCCCATCTATAATCCTTTTAAAGTCCTTTA
** * * * *
20211 AGGGTATTAAGCACTTCTATGTCAAAAGTACCCTCTAGGGCATTTTCGTAA-TTTTTAGAATCGA
66 AGGGTA-TCGGCACTTTTACGTCAAAAGTACCCT-TAAGGCATTTTCGTAATTTTTTAAAATCGA
20275 GTCTTAGG
129 GTCTTAGG
20283 TTGTTGCTTT
Statistics
Matches: 245, Mismatches: 34, Indels: 20
0.82 0.11 0.07
Matches are distributed among these distances:
147 22 0.09
148 48 0.20
150 2 0.01
151 2 0.01
153 19 0.08
154 22 0.09
155 128 0.52
156 2 0.01
ACGTcount: A:0.26, C:0.17, G:0.18, T:0.39
Consensus pattern (152 bp):
TTTTATGTCGAAGGTGGGTATTTAGGATAGTTTCATCCCATCTATAATCCTTTTAAAGTCCTTTA
AGGGTATCGGCACTTTTACGTCAAAAGTACCCTTAAGGCATTTTCGTAATTTTTTAAAATCGAGT
CTTAGGCCATCACCGAGTCTGC
Found at i:31495 original size:152 final size:153
Alignment explanation
Indices: 31309--32093 Score: 538
Period size: 163 Copynumber: 5.0 Consensus size: 153
31299 TTAAACCGAG
*
31309 AAAAATCTCCCCCAAAAAAAATTACGGAG-AAAAAACT-T-AATTTCTCGAAAAAA-AAGGGATT
1 AAAAATCTCCCCCAAAAAAAATTACGGAGAAAAAAACTCTGAATTT-T--AAAAAAGAA--GAAT
* *
31370 TTCAAAG-AAAAATTCAAAACTCATGAAAATAAAAT-AATTTTTTAAAAATAATTTAATATGAAA
61 TTCAAAGAAAAAATTCAAAACTCATGAAAAT-AAATGAATTTTTGAAAAATAAATTAATATGAAA
*
31433 TATATAATAATATTTGATGAATTTAAAAA
125 TAAATAATAATATTTGATGAATTTAAAAA
* * * * * *
31462 AAAAATC-CCTCCGAAAAAATTTACGGGGTAAAAAACTCTGTATTTTAAAAAAGAAGAATTTCAA
1 AAAAATCTCCCCCAAAAAAAATTACGGAGAAAAAAACTCTGAATTTTAAAAAAGAAGAATTTCAA
* * * * *
31526 GGAAAAAATTCAAAACTTATGAAAATGAATGAATTTTTGAAAACTAAATTAATGTGAAATAAATA
66 AGAAAAAATTCAAAACTCATGAAAATAAATGAATTTTTGAAAAATAAATTAATATGAAATAAATA
31591 ATAATATTTGATGAATTTTAAAAA
131 ATAATATTTGATGAA-TTTAAAAA
* * * * * *
31615 TTAAAAACCTAGAAAAAGGCTCCCTAAAAAATTTAC--AGAATAGAAAACTCTGTATTTTGGAAA
1 --AAAAATCT---------CCCCCAAAAAAAATTACGGAGAA-A-AAAACTCTGAATTTT-AAAA
* * * * ** * *
31678 AAGAAAAATTTCAAGGAAAAAATTCAAAATTTATTTAAATGAATGAATTTTTGAAAACTAAATTA
52 AAGAAGAATTTCAAAGAAAAAATTCAAAACTCATGAAAATAAATGAATTTTTGAAAAATAAATTA
*
31743 ATGTGAAATAAATAATAATATTTGATGAATTTTAAAAATAAGAAA
117 ATATGAAATAAATAATAATATTTGATGAA--TT-----TAA-AAA
** ** * * ** *
31788 AAGAAAAATCCCCCTGAAAAATTTACGAACTAAAAAACTCT-ATATTTCAGAAAAA-AGAGAATT
1 AA-AAATCTCCCCCAAAAAAAATTACGGAGAAAAAAACTCTGA-ATTTTA-AAAAAGA-AGAATT
* * * * * * *
31851 TC-AAGAAAAAAATTTAAAATTCATGGAAATGAATGAATTTTTGAAAACTAAATTAATGTAAAAT
62 TCAAAG-AAAAAATTCAAAACTCATGAAAATAAATGAATTTTTGAAAAATAAATTAATATGAAAT
31915 AAATAATAATATTTGATGAATTTTAAAAGTAA
126 AAATAATAATATTTGATGAA-TTT-AAA--AA
* * * * * * * * *
31947 AAAAATC-CCTCC-AAAAAATTTACGGAGTAGAAAACTTTGTATTTCGGAAAAAGGAA-AATTTT
1 AAAAATCTCCCCCAAAAAAAATTACGGAGAAAAAAACTCTGAATTT--TAAAAAAGAAGAATTTC
* * * * * * *
32009 AAGGAAAAAATTCTAAATTCATGGAAATGAATGAATTTTTGAAAACTGAATTAATATGAAATAAA
64 AAAGAAAAAATTCAAAACTCATGAAAATAAATGAATTTTTGAAAAATAAATTAATATGAAATAAA
*
32074 TAATAATATTTGGTGAATTT
129 TAATAATATTTGATGAATTT
32094 TATAAATCAA
Statistics
Matches: 528, Mismatches: 60, Indels: 86
0.78 0.09 0.13
Matches are distributed among these distances:
151 12 0.02
152 89 0.17
153 25 0.05
154 2 0.00
155 13 0.02
156 102 0.19
157 13 0.02
158 7 0.01
159 4 0.01
162 6 0.01
163 114 0.22
164 2 0.00
165 31 0.06
166 93 0.18
167 3 0.01
171 2 0.00
172 7 0.01
173 3 0.01
ACGTcount: A:0.51, C:0.08, G:0.11, T:0.30
Consensus pattern (153 bp):
AAAAATCTCCCCCAAAAAAAATTACGGAGAAAAAAACTCTGAATTTTAAAAAAGAAGAATTTCAA
AGAAAAAATTCAAAACTCATGAAAATAAATGAATTTTTGAAAAATAAATTAATATGAAATAAATA
ATAATATTTGATGAATTTAAAAA
Found at i:31701 original size:166 final size:162
Alignment explanation
Indices: 31457--32172 Score: 837
Period size: 166 Copynumber: 4.4 Consensus size: 162
31447 TGATGAATTT
* * ** * ** *
31457 AAAAA-AAAAATCCCTCCGAAAAAATTTACGGGGTAAAAAACTCTGTATTT-TAAAAAAGAAGAA
1 AAAAAGAAAAATCTC-CCTAAAAAATTTAC-GAATAGAAAACTCTGTATTTCGGAAAAAGAAAAA
*
31520 TTTCAAGGAAAAAATTCAAAACTT-ATGAAAATGAATGAATTTTTGAAAACTAAATTAATGTGAA
64 TTTCAAGGAAAAAATTCAAAA-TTCATGGAAATGAATGAATTTTTGAAAACTAAATTAATGTGAA
31584 ATAAATAATAATATTTGATGAATTTTAAAAATTAA
128 ATAAATAATAATATTTGATGAATTTTAAAAATTAA
* * *
31619 AAACCTAGAAAAAGGCTCCCTAAAAAATTTACAGAATAGAAAACTCTGTATTTTGGAAAAAGAAA
1 AAA--AAGAAAAA-TCTCCCTAAAAAATTTAC-GAATAGAAAACTCTGTATTTCGGAAAAAGAAA
* **
31684 AATTTCAAGGAAAAAATTCAAAATTTATTTAAATGAATGAATTTTTGAAAACTAAATTAATGTGA
62 AATTTCAAGGAAAAAATTCAAAATTCATGGAAATGAATGAATTTTTGAAAACTAAATTAATGTGA
31749 AATAAATAATAATATTTGATGAATTTTAAAAA-TAA
127 AATAAATAATAATATTTGATGAATTTTAAAAATTAA
* * * * * *
31784 GAAAAAGAAAAATCCCCCTGAAAAATTTACGAACTAAAAAACTCTATATTTCAGAAAAA-AGAGA
1 -AAAAAGAAAAATCTCCCTAAAAAATTTACGAA-TAGAAAACTCTGTATTTCGGAAAAAGA-AAA
* * *
31848 ATTTCAAGAAAAAAATTTAAAATTCATGGAAATGAATGAATTTTTGAAAACTAAATTAATGTAAA
63 ATTTCAAGGAAAAAATTCAAAATTCATGGAAATGAATGAATTTTTGAAAACTAAATTAATGTGAA
*
31913 ATAAATAATAATATTTGATGAATTTT-AAAAGT--
128 ATAAATAATAATATTTGATGAATTTTAAAAATTAA
* * * *
31945 ---AA-AAAAATC-CCTCCAAAAAATTTACGGAGTAGAAAACTTTGTATTTCGGAAAAAGGAAAA
1 AAAAAGAAAAATCTCC-CTAAAAAATTTAC-GAATAGAAAACTCTGTATTTCGGAAAAAGAAAAA
* * * *
32005 TTTTAAGGAAAAAATTCTAAATTCATGGAAATGAATGAATTTTTGAAAACTGAATTAATATGAAA
64 TTTCAAGGAAAAAATTCAAAATTCATGGAAATGAATGAATTTTTGAAAACTAAATTAATGTGAAA
* * *
32070 TAAATAATAATATTTGGTGAATTTTATAAATCAA
129 TAAATAATAATATTTGATGAATTTTAAAAATTAA
* * * *
32104 AGAACAAGCAAAATCTCTCTGAAAAAATTTACGAAGTAGAGAACTCTGTATTTCGGAAAAAGTAA
1 A-AA-AAGAAAAATCTCCCT-AAAAAATTTACGAA-TAGAAAACTCTGTATTTCGGAAAAAGAAA
32169 AATT
62 AATT
32173 CTAAAAGAAA
Statistics
Matches: 474, Mismatches: 55, Indels: 46
0.82 0.10 0.08
Matches are distributed among these distances:
155 2 0.00
156 124 0.26
157 7 0.01
162 11 0.02
163 124 0.26
164 10 0.02
165 49 0.10
166 147 0.31
ACGTcount: A:0.51, C:0.08, G:0.12, T:0.29
Consensus pattern (162 bp):
AAAAAGAAAAATCTCCCTAAAAAATTTACGAATAGAAAACTCTGTATTTCGGAAAAAGAAAAATT
TCAAGGAAAAAATTCAAAATTCATGGAAATGAATGAATTTTTGAAAACTAAATTAATGTGAAATA
AATAATAATATTTGATGAATTTTAAAAATTAA
Found at i:32063 original size:319 final size:327
Alignment explanation
Indices: 31369--32165 Score: 953
Period size: 319 Copynumber: 2.5 Consensus size: 327
31359 AAAAAGGGAT
* * * * * * *
31369 TTTCAAAG-AAAAATTCAAAACTCATGAAAATAAAAT-AATTTTTTAAAAATAATTTAATATGAA
1 TTTCAAGGAAAAAATTCAAAATTCATGGAAAT-GAATGAATTTTTGAAAACTAAATTAATATGAA
*
31432 ATATATAATAATATTTGATGAA--TT-----T----AAAAA-AAAAATCCCTCC-GAAAAAATTT
65 ATAAATAATAATATTTGATGAATTTTAAAAATAAAGAAAAAGAAAAATCCC-CCTGAAAAAATTT
** * *
31484 ACGGGGTAAAAAACTCTGTATTT-TAAAAAAGAAGAATTTCAAGGAAAAAATTCAAAACTTATGA
129 ACGAAGTAAAAAACTCTGTATTTCGAAAAAAGAAGAATTTCAAGAAAAAAATTCAAAACTTATGA
*
31548 AAATGAATGAATTTTTGAAAACTAAATTAATGTGAAATAAATAATAATATTTGATGAATTTTAAA
194 AAATGAATGAATTTTTGAAAACTAAATTAATGTAAAATAAATAATAATATTTGATGAATTTTAAA
* ** *
31613 AATTAAAAACCTAGAAAAAGGCTCCCTAAAAAATTTACAGAATAGAAAACTCTGTATTTTGGAAA
259 AAGT--AAA-C-AGAAAAACCCTCCCTAAAAAATTTACAGAATAGAAAACTCTGTATTTCGGAAA
31678 AAGAAAAA
320 AAGAAAAA
* ** *
31686 TTTCAAGGAAAAAATTCAAAATTTATTTAAATGAATGAATTTTTGAAAACTAAATTAATGTGAAA
1 TTTCAAGGAAAAAATTCAAAATTCATGGAAATGAATGAATTTTTGAAAACTAAATTAATATGAAA
31751 TAAATAATAATATTTGATGAATTTTAAAAAT-AAGAAAAAGAAAAATCCCCCTG-AAAAATTTAC
66 TAAATAATAATATTTGATGAATTTTAAAAATAAAGAAAAAGAAAAATCCCCCTGAAAAAATTTAC
* * * *
31814 GAACTAAAAAACTCTATATTTCAGAAAAAAG-AGAATTTCAAGAAAAAAATTTAAAA-TTCATGG
131 GAAGTAAAAAACTCTGTATTTC-GAAAAAAGAAGAATTTCAAGAAAAAAATTCAAAACTT-ATGA
31877 AAATGAATGAATTTTTGAAAACTAAATTAATGTAAAATAAATAATAATATTTGATGAATTTT-AA
194 AAATGAATGAATTTTTGAAAACTAAATTAATGTAAAATAAATAATAATATTTGATGAATTTTAAA
* * * * *
31941 AAGT-AA-A-AAAATCCCT-CC-AAAAAATTTACGGAGTAGAAAACTTTGTATTTCGGAAAAAGG
259 AAGTAAACAGAAAAACCCTCCCTAAAAAATTTACAGAATAGAAAACTCTGTATTTCGGAAAAAGA
32001 AAAA
324 AAAA
* * *
32005 TTTTAAGGAAAAAATTCTAAATTCATGGAAATGAATGAATTTTTGAAAACTGAATTAATATGAAA
1 TTTCAAGGAAAAAATTCAAAATTCATGGAAATGAATGAATTTTTGAAAACTAAATTAATATGAAA
* * * * * *
32070 TAAATAATAATATTTGGTGAATTTTATAAATCAAAGAACAAGCAAAATCTCTCTGAAAAAATTTA
66 TAAATAATAATATTTGATGAATTTTAAAAAT-AAAGAAAAAGAAAAATCCCCCTGAAAAAATTTA
* * *
32135 CGAAGTAGAGAACTCTGTATTTCGGAAAAAG
130 CGAAGTAAAAAACTCTGTATTTCGAAAAAAG
32166 TAAAATTCTA
Statistics
Matches: 413, Mismatches: 47, Indels: 36
0.83 0.09 0.07
Matches are distributed among these distances:
317 10 0.02
318 63 0.15
319 128 0.31
320 4 0.01
321 31 0.08
322 29 0.07
325 3 0.01
328 41 0.10
329 97 0.23
330 7 0.02
ACGTcount: A:0.51, C:0.08, G:0.11, T:0.30
Consensus pattern (327 bp):
TTTCAAGGAAAAAATTCAAAATTCATGGAAATGAATGAATTTTTGAAAACTAAATTAATATGAAA
TAAATAATAATATTTGATGAATTTTAAAAATAAAGAAAAAGAAAAATCCCCCTGAAAAAATTTAC
GAAGTAAAAAACTCTGTATTTCGAAAAAAGAAGAATTTCAAGAAAAAAATTCAAAACTTATGAAA
ATGAATGAATTTTTGAAAACTAAATTAATGTAAAATAAATAATAATATTTGATGAATTTTAAAAA
GTAAACAGAAAAACCCTCCCTAAAAAATTTACAGAATAGAAAACTCTGTATTTCGGAAAAAGAAA
AA
Found at i:33691 original size:78 final size:76
Alignment explanation
Indices: 33513--34051 Score: 466
Period size: 78 Copynumber: 6.9 Consensus size: 76
33503 CAGGGTTGGA
* * *
33513 GAAAAATTTAATATTTTAGAAATAAAAACGGGGTTGGAGTATCCCTTAGAAATAATAGGA-TTAG
1 GAAAAATTTAATATTTCA-AAATAAAAACGGGGTTGGAGTATCCCTCAGAAAT-A-AGGAGTTGG
*
33577 AGTAT-CCCAAGAT
63 AGTATCCCCGAGAT
* * * **
33590 GAAAACTTTAATATTTTGAAAATATAAATAGGGTTGGAGTATCTCCTCAGAAATAATGGAGTTGG
1 GAAAAATTTAATA-TTTCAAAATAAAAACGGGGTTGGAGTATC-CCTCAGAAATAA-GGAGTTGG
33655 AGTATCCCCGAGAT
63 AGTATCCCCGAGAT
* * **
33669 GAAAATTTTAATATTTCAAAATAAAAACGGGGTTGGAGTATCCCTTCGGAAATAACAAGGTTGGA
1 GAAAAATTTAATATTTCAAAATAAAAACGGGGTTGGAGTATCCC-TCAGAAATAAGGA-GTTGGA
*
33734 ATA-CTCCCGAGAT
64 GTATC-CCCGAGAT
* * *
33747 GAAAAATTTAATATTTCAAAAATAAAAATGGGGTTGGAGTATCTCCTCAAAAATAACGG-GATTA
1 GAAAAATTTAATATTTC-AAAATAAAAACGGGGTTGGAGTATC-CCTCAGAAATAA-GGAG-TTG
* *
33811 GACTATCCCCAAGAT
62 GAGTATCCCCGAGAT
* * * *
33826 GAAAAATTTGATATTTCAAAATAAAAATGGGGTTGGAGTATCCCTCAAAAATAACGGGGTTGGAG
1 GAAAAATTTAATATTTCAAAATAAAAACGGGGTTGGAGTATCCCTCAGAAATAA-GGAGTTGGAG
33891 TA-CCCCTGAGAT
65 TATCCCC-GAGAT
* * *** * * *
33903 GAAAATTTTAATATTTTGAAAATAAAAACGACATTAGACTATCGCTC-GAAAATAACAGG-GTTG
1 GAAAAATTTAATA-TTTCAAAATAAAAACGGGGTTGGAGTATCCCTCAG-AAAT-A-AGGAGTTG
*
33966 GAATA-CCTCCGAGAT
62 GAGTATCC-CCGAGAT
* ** * *
33981 GAAAATTTTAATATTTCAAAAATAAAAACAAGGTTGGAGTATCTCATC-GAAAATAACGAGATTG
1 GAAAAATTTAATATTTC-AAAATAAAAACGGGGTTGGAGTATC-CCTCAG-AAATAAGGAG-TTG
34045 GAGTATC
62 GAGTATC
34052 TCCTCAAAAA
Statistics
Matches: 385, Mismatches: 52, Indels: 47
0.80 0.11 0.10
Matches are distributed among these distances:
76 5 0.01
77 82 0.21
78 193 0.50
79 100 0.26
80 5 0.01
ACGTcount: A:0.41, C:0.12, G:0.19, T:0.28
Consensus pattern (76 bp):
GAAAAATTTAATATTTCAAAATAAAAACGGGGTTGGAGTATCCCTCAGAAATAAGGAGTTGGAGT
ATCCCCGAGAT
Found at i:33801 original size:157 final size:156
Alignment explanation
Indices: 33513--34054 Score: 585
Period size: 157 Copynumber: 3.5 Consensus size: 156
33503 CAGGGTTGGA
* * * *
33513 GAAAAATTTAATATTTTAGAAATAAAAACGGGGTTGGAGTATCCCTT-AGAAATAA-TAGGATTA
1 GAAAAATTTAATATTTCA-AAATAAAAACGGGGTTGGAGTATCCCTTCAAAAATAACGAGG-TTG
* * * * *
33576 GAGTA-TCCCAAGATGAAAACTTTAATATTTTGAAAATATAAATAGGGTTGGAGTATCTCCTCAG
64 GAGTACTCCCGAGATGAAAAATTTAATATTTTGAAAATAAAAATGGGGTTGGAGTATCTCCTCAA
* *
33640 AAATAATGGAGTTGGAGTATCCCCGAGAT
129 AAATAAAGG-GTTGGAATATCCCCGAGAT
* ** *
33669 GAAAATTTTAATATTTCAAAATAAAAACGGGGTTGGAGTATCCCTTCGGAAATAACAAGGTTGGA
1 GAAAAATTTAATATTTCAAAATAAAAACGGGGTTGGAGTATCCCTTCAAAAATAACGAGGTTGGA
* **
33734 ATACTCCCGAGATGAAAAATTTAATATTTCAAAAATAAAAATGGGGTTGGAGTATCTCCTCAAAA
66 GTACTCCCGAGATGAAAAATTTAATATTTTGAAAATAAAAATGGGGTTGGAGTATCTCCTCAAAA
* * * *
33799 ATAACGGGATTAGACTATCCCCAAGAT
131 ATAAAGGG-TTGGAATATCCCCGAGAT
* * *
33826 GAAAAATTTGATATTTCAAAATAAAAATGGGGTTGGAGTATCCC-TCAAAAATAACGGGGTTGGA
1 GAAAAATTTAATATTTCAAAATAAAAACGGGGTTGGAGTATCCCTTCAAAAATAACGAGGTTGGA
* * *** * * * *
33890 GTAC-CCCTGAGATGAAAATTTTAATATTTTGAAAATAAAAACGACATTAGACTATC-GCTCGAA
66 GTACTCCC-GAGATGAAAAATTTAATATTTTGAAAATAAAAATGGGGTTGGAGTATCTCCTCAAA
33953 AATAACAGGGTTGGAATA-CCTCCGAGAT
130 AATAA-AGGGTTGGAATATCC-CCGAGAT
* ** * * * *
33981 GAAAATTTTAATATTTCAAAAATAAAAACAAGGTTGGAGTATCTCATCGAAAATAACGAGATTGG
1 GAAAAATTTAATATTTC-AAAATAAAAACGGGGTTGGAGTATCCCTTCAAAAATAACGAGGTTGG
34046 AGTATCTCC
65 AGTA-CTCC
34055 TCAAAAATAA
Statistics
Matches: 326, Mismatches: 49, Indels: 19
0.83 0.12 0.05
Matches are distributed among these distances:
154 2 0.01
155 68 0.21
156 114 0.35
157 139 0.43
158 1 0.00
159 2 0.01
ACGTcount: A:0.41, C:0.13, G:0.19, T:0.28
Consensus pattern (156 bp):
GAAAAATTTAATATTTCAAAATAAAAACGGGGTTGGAGTATCCCTTCAAAAATAACGAGGTTGGA
GTACTCCCGAGATGAAAAATTTAATATTTTGAAAATAAAAATGGGGTTGGAGTATCTCCTCAAAA
ATAAAGGGTTGGAATATCCCCGAGAT
Found at i:33958 original size:234 final size:235
Alignment explanation
Indices: 33513--34043 Score: 705
Period size: 234 Copynumber: 2.3 Consensus size: 235
33503 CAGGGTTGGA
* * * * **
33513 GAAAAATTTAATATTTTAGAAATAAAAACGGGGTTGGAGTATC-CCTTAGAAATAATAGGATTAG
1 GAAAAATTTAATATTTCAAAAATAAAAACGGGGTTGGAGTATCTCCTCAAAAATAACGGGATTAG
* * * * *
33577 AGTATCCCAAGATGAAAACTTTAATATTTTGAAAATATAAATAGGGTTGGAGTATCTCCTCAGAA
66 ACTATCCCAAGATGAAAAATTTAATATTTTCAAAATAAAAATAGGGTTGGAGTATCTCCTCAAAA
* *** * *
33642 ATAATGGAGTTGGAGTATCCCCGAGATGAAAATTTTAATATTTCAAAATAAAAACGGGGTTGGAG
131 ATAACGGAGTTGGAGTATCCCCGAGATGAAAATTTTAATATTTCAAAATAAAAACGACATTAGAC
*
33707 TATCCCTTCGGAAATAACAAGGTTGGAATA-CTCCCGAGAT
196 TATCCCTTCGAAAATAACAAGGTTGGAATACCT-CCGAGAT
*
33747 GAAAAATTTAATATTTCAAAAATAAAAATGGGGTTGGAGTATCTCCTCAAAAATAACGGGATTAG
1 GAAAAATTTAATATTTCAAAAATAAAAACGGGGTTGGAGTATCTCCTCAAAAATAACGGGATTAG
* *
33812 ACTATCCCCAAGATGAAAAATTTGATA-TTTCAAAATAAAAATGGGGTTGGAGTATC-CCTCAAA
66 ACTAT-CCCAAGATGAAAAATTTAATATTTTCAAAATAAAAATAGGGTTGGAGTATCTCCTCAAA
* *
33875 AATAACGGGGTTGGAGTA-CCCCTGAGATGAAAATTTTAATATTTTGAAAATAAAAACGACATTA
130 AATAACGGAGTTGGAGTATCCCC-GAGATGAAAATTTTAATA-TTTCAAAATAAAAACGACATTA
* *
33939 GACTATCGC-TCGAAAATAACAGGGTTGGAATACCTCCGAGAT
193 GACTATCCCTTCGAAAATAACAAGGTTGGAATACCTCCGAGAT
* ** * * *
33981 GAAAATTTTAATATTTCAAAAATAAAAACAAGGTTGGAGTATCTCATCGAAAATAACGAGATT
1 GAAAAATTTAATATTTCAAAAATAAAAACGGGGTTGGAGTATCTCCTCAAAAATAACGGGATT
34044 GGAGTATCTC
Statistics
Matches: 260, Mismatches: 32, Indels: 10
0.86 0.11 0.03
Matches are distributed among these distances:
233 4 0.02
234 164 0.63
235 73 0.28
236 19 0.07
ACGTcount: A:0.41, C:0.12, G:0.19, T:0.28
Consensus pattern (235 bp):
GAAAAATTTAATATTTCAAAAATAAAAACGGGGTTGGAGTATCTCCTCAAAAATAACGGGATTAG
ACTATCCCAAGATGAAAAATTTAATATTTTCAAAATAAAAATAGGGTTGGAGTATCTCCTCAAAA
ATAACGGAGTTGGAGTATCCCCGAGATGAAAATTTTAATATTTCAAAATAAAAACGACATTAGAC
TATCCCTTCGAAAATAACAAGGTTGGAATACCTCCGAGAT
Found at i:34822 original size:13 final size:13
Alignment explanation
Indices: 34804--34829 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
34794 GAAAAATATC
34804 AAAAAAATTCAAA
1 AAAAAAATTCAAA
34817 AAAAAAATTCAAA
1 AAAAAAATTCAAA
34830 TTTTTAAAAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.77, C:0.08, G:0.00, T:0.15
Consensus pattern (13 bp):
AAAAAAATTCAAA
Found at i:37121 original size:20 final size:20
Alignment explanation
Indices: 37098--37222 Score: 88
Period size: 20 Copynumber: 5.7 Consensus size: 20
37088 AAGTACCCAG
*
37098 ATGTATCAATACATTTTTCA
1 ATGTATCGATACATTTTTCA
* * * * *
37118 ATGTATTGATAGATGTATGA
1 ATGTATCGATACATTTTTCA
*
37138 ATGTATCGATACATTCTTCA
1 ATGTATCGATACATTTTTCA
37158 ATGTATCGATACATTCTATCTTTTTACCCA
1 ATGTATCGAT--A--C-A--TTTTT---CA
37188 GATGTATCGATACATTTTTCA
1 -ATGTATCGATACATTTTTCA
37209 ATGTATCGATACAT
1 ATGTATCGATACAT
37223 CTAGTTAAAA
Statistics
Matches: 81, Mismatches: 13, Indels: 22
0.70 0.11 0.19
Matches are distributed among these distances:
20 52 0.64
21 2 0.02
22 1 0.01
24 6 0.07
25 1 0.01
26 1 0.01
27 5 0.06
29 1 0.01
30 2 0.02
31 10 0.12
ACGTcount: A:0.31, C:0.15, G:0.12, T:0.42
Consensus pattern (20 bp):
ATGTATCGATACATTTTTCA
Found at i:41442 original size:20 final size:20
Alignment explanation
Indices: 41404--41444 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
41394 GAGGGCCTAC
*
41404 TTTTTTTTATTGATGTTCAT
1 TTTTTTTTATTGATATTCAT
* *
41424 TTTTTTTTCTTGCTATTCAT
1 TTTTTTTTATTGATATTCAT
41444 T
1 T
41445 CTTATTATTT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.12, C:0.10, G:0.07, T:0.71
Consensus pattern (20 bp):
TTTTTTTTATTGATATTCAT
Found at i:52368 original size:28 final size:28
Alignment explanation
Indices: 52313--53283 Score: 906
Period size: 28 Copynumber: 33.2 Consensus size: 28
52303 CATCATTCGA
* * *
52313 CCCACAAGTCACTGGCACCCTTTTAAAG
1 CCCACAAGTCAGTGGCATCCTTTCAAAG
* * *
52341 CCCACAAGTTAGTGACATCATTTCAAAG
1 CCCACAAGTCAGTGGCATCCTTTCAAAG
* * *
52369 CCCACACAAGTC-GATGTCAACTCATTTGAAAG
1 -CC-CACAAGTCAG-TGGC-A-TCCTTTCAAAG
*
52401 CCCACACAAGTCAGTGGCATCATTTCAAAG
1 -CC-CACAAGTCAGTGGCATCCTTTCAAAG
*
52431 CCCACACAAGTCAGTGGCATCATTTCAAAG
1 -CC-CACAAGTCAGTGGCATCCTTTCAAAG
* *
52461 CCCACACAAGTCGGTGGCAACTCATTTCAAAG
1 -CC-CACAAGTCAGTGGC-A-TCCTTTCAAAG
** *
52493 CCCACATAAGTTGGTGGCAACCTATTTCAAAG
1 CCCAC--AAGTCAGTGGCATCC--TTTCAAAG
** *
52525 CCCACACAAGTTGGTGGCAACCCATTTCAAAG
1 -CC-CACAAGTCAGTGGC-ATCC-TTTCAAAG
** *
52557 CCCACACAAGTTGGTGGCAACCCATTTCAAAG
1 -CC-CACAAGTCAGTGGC-ATCC-TTTCAAAG
* *
52589 CCCACACAAGTCAATGGCACCCTTTCAAAG
1 -CC-CACAAGTCAGTGGCATCCTTTCAAAG
52619 CCCACAAGTCAGTGGCATCCTTTCAAAG
1 CCCACAAGTCAGTGGCATCCTTTCAAAG
* ** *
52647 TCCACAAGTTGGTGGCATCTTTTCAAAG
1 CCCACAAGTCAGTGGCATCCTTTCAAAG
*
52675 CCCATAAGTCAGTGGCATCCTTTCAAAG
1 CCCACAAGTCAGTGGCATCCTTTCAAAG
*
52703 CCCACAAGTCAGTGGCACCCTTTCAAAG
1 CCCACAAGTCAGTGGCATCCTTTCAAAG
* * *
52731 CCCACGAGTCGGTGGCAACTCTTTTCAAAG
1 CCCACAAGTCAGTGGC-A-TCCTTTCAAAG
* * * **
52761 CCAAGAAATTGGTGGCATCCTTTCAAAG
1 CCCACAAGTCAGTGGCATCCTTTCAAAG
* *
52789 TCCACAAGTC-GATGGCATCTTTTCAAAG
1 CCCACAAGTCAG-TGGCATCCTTTCAAAG
*
52817 CCCACAAGTTAGTGGCATCCTTTCAAAG
1 CCCACAAGTCAGTGGCATCCTTTCAAAG
*
52845 CCCACAAGTCAGTGGCACCCTTTCAAAG
1 CCCACAAGTCAGTGGCATCCTTTCAAAG
*
52873 CCCACAAGTTAGTGGCATCCTTTCAAAG
1 CCCACAAGTCAGTGGCATCCTTTCAAAG
* *
52901 TCCACAAGTC-GATGGCATCTTTTCAAAG
1 CCCACAAGTCAG-TGGCATCCTTTCAAAG
*
52929 CCCACAAGTTAGTGGCATCCTTTCAAAG
1 CCCACAAGTCAGTGGCATCCTTTCAAAG
52957 CCCACAAGTCAGTGGCATCCTTTCAAAG
1 CCCACAAGTCAGTGGCATCCTTTCAAAG
*
52985 CCCACAAGTCAGTGGCACCCTTTCAAAG
1 CCCACAAGTCAGTGGCATCCTTTCAAAG
*
53013 CCCACAAGTCAGTGGCACCCTTTCAAAG
1 CCCACAAGTCAGTGGCATCCTTTCAAAG
*
53041 CCCACAAGTCAGTGGCACCCTTTCAAAG
1 CCCACAAGTCAGTGGCATCCTTTCAAAG
* *
53069 CCCACAAGTTAGTGGCACCCTTTCAAAG
1 CCCACAAGTCAGTGGCATCCTTTCAAAG
* * * *
53097 CCTACAAGTCAGTTGTACCCTTTCAAAG
1 CCCACAAGTCAGTGGCATCCTTTCAAAG
**
53125 CCCACAAGTCAGTGGCACTATTTTCAAAG
1 CCCACAAGTCAGTGGCA-TCCTTTCAAAG
* * * *
53154 CTCACAAGTTAGTGGTAACTCTTTTCAAAG
1 CCCACAAGTCAGTGG-CA-TCCTTTCAAAG
*
53184 CCCACACAAGTC-GATGGCGACTCTTTTCAAAG
1 -CC-CACAAGTCAG-TGGC-A-TCCTTTCAAAG
* * * *
53216 CTCACAAGCCAGTGGTAACTCTTTTCAAAG
1 CCCACAAGTCAGTGG-CA-TCCTTTCAAAG
*
53246 CCCACATGAGTCAGTGGCGACTCTTTTCAAAG
1 CCCACA--AGTCAGTGGC-A-TCCTTTCAAAG
53278 CCCACA
1 CCCACA
53284 CAAGTTAATG
Statistics
Matches: 824, Mismatches: 87, Indels: 60
0.85 0.09 0.06
Matches are distributed among these distances:
27 2 0.00
28 459 0.56
29 30 0.04
30 139 0.17
31 14 0.02
32 171 0.21
33 6 0.01
34 3 0.00
ACGTcount: A:0.30, C:0.30, G:0.18, T:0.23
Consensus pattern (28 bp):
CCCACAAGTCAGTGGCATCCTTTCAAAG
Found at i:54200 original size:20 final size:20
Alignment explanation
Indices: 54175--54251 Score: 102
Period size: 20 Copynumber: 3.9 Consensus size: 20
54165 AAGTACCCAG
54175 ATGTATCGATACATTCTTCA
1 ATGTATCGATACATTCTTCA
* *
54195 ATGTATCGATACATGT-ATGA
1 ATGTATCGATACAT-TCTTCA
54215 ATGTATCGATACATTCTTCA
1 ATGTATCGATACATTCTTCA
* *
54235 ATGTATTGAAACATTCT
1 ATGTATCGATACATTCT
54252 GTCTTTTTAC
Statistics
Matches: 49, Mismatches: 6, Indels: 4
0.83 0.10 0.07
Matches are distributed among these distances:
19 1 0.02
20 47 0.96
21 1 0.02
ACGTcount: A:0.32, C:0.16, G:0.13, T:0.39
Consensus pattern (20 bp):
ATGTATCGATACATTCTTCA
Found at i:58437 original size:121 final size:120
Alignment explanation
Indices: 58219--58466 Score: 460
Period size: 121 Copynumber: 2.1 Consensus size: 120
58209 GAAAGGATCT
*
58219 CCAAGATCACGAGCAACACAAGTGTCTTACTTCAACGATAATCCACATAGATAGCTTTTAAAACC
1 CCAAAATCACGAGCAACACAAGTGTCTTACTTCAACGATAATCCACATAGATAGCTTTTAAAACC
58284 TTTAGAAAAGTCTAGTGGTTCTTTGGTGCTAGCTAGAAGACTCAAGAAACTTGAA
66 TTTAGAAAAGTCTAGTGGTTCTTTGGTGCTAGCTAGAAGACTCAAGAAACTTGAA
* *
58339 CCAAAATCACGAGCAACACAAGTGTCTTACTTCTAACGATGATCCATATAGATAGCTTTTAAAAC
1 CCAAAATCACGAGCAACACAAGTGTCTTACTTC-AACGATAATCCACATAGATAGCTTTTAAAAC
58404 CTTTAGAAAAGTCTAGTGGTTCTTTGGTGCTAGCTAGAAGACTCAAGAAACTTGAA
65 CTTTAGAAAAGTCTAGTGGTTCTTTGGTGCTAGCTAGAAGACTCAAGAAACTTGAA
58460 CCAAAAT
1 CCAAAAT
58467 GAAAGATACA
Statistics
Matches: 124, Mismatches: 3, Indels: 1
0.97 0.02 0.01
Matches are distributed among these distances:
120 32 0.26
121 92 0.74
ACGTcount: A:0.36, C:0.20, G:0.17, T:0.27
Consensus pattern (120 bp):
CCAAAATCACGAGCAACACAAGTGTCTTACTTCAACGATAATCCACATAGATAGCTTTTAAAACC
TTTAGAAAAGTCTAGTGGTTCTTTGGTGCTAGCTAGAAGACTCAAGAAACTTGAA
Found at i:59160 original size:11 final size:11
Alignment explanation
Indices: 59139--59171 Score: 50
Period size: 11 Copynumber: 3.1 Consensus size: 11
59129 TTACCTTACA
59139 TAAAT-ATTAT
1 TAAATAATTAT
59149 TAAATAATTAT
1 TAAATAATTAT
*
59160 TAAATAGTTAT
1 TAAATAATTAT
59171 T
1 T
59172 CAATTTGCTA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
10 5 0.24
11 16 0.76
ACGTcount: A:0.48, C:0.00, G:0.03, T:0.48
Consensus pattern (11 bp):
TAAATAATTAT
Found at i:63265 original size:15 final size:16
Alignment explanation
Indices: 63214--63271 Score: 50
Period size: 16 Copynumber: 3.6 Consensus size: 16
63204 TAATATAAAC
63214 TAAATTAATTTTGTATA
1 TAAATTAATTTT-TATA
*
63231 TTAGCA-TAATTTTTATA
1 -TA-AATTAATTTTTATA
63248 T-AATTAATATTTTA-A
1 TAAATTAAT-TTTTATA
63263 TAAATTAAT
1 TAAATTAAT
63272 CGTTGAATTT
Statistics
Matches: 34, Mismatches: 2, Indels: 10
0.74 0.04 0.22
Matches are distributed among these distances:
14 1 0.03
15 6 0.18
16 13 0.38
17 4 0.12
18 9 0.26
19 1 0.03
ACGTcount: A:0.43, C:0.02, G:0.03, T:0.52
Consensus pattern (16 bp):
TAAATTAATTTTTATA
Found at i:63268 original size:16 final size:17
Alignment explanation
Indices: 63239--63271 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
63229 TATTAGCATA
*
63239 ATTTTTATATAATTAAT
1 ATTTTAATATAATTAAT
63256 ATTTTAATA-AATTAAT
1 ATTTTAATATAATTAAT
63272 CGTTGAATTT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 7 0.47
17 8 0.53
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (17 bp):
ATTTTAATATAATTAAT
Found at i:63371 original size:14 final size:14
Alignment explanation
Indices: 63322--63372 Score: 50
Period size: 14 Copynumber: 3.7 Consensus size: 14
63312 AATTTTTAAA
*
63322 TTAATTTATTATTT
1 TTAATATATTATTT
* * *
63336 TTATTATATCA-AT
1 TTAATATATTATTT
*
63349 TTAAAATATTATTT
1 TTAATATATTATTT
63363 TTAATATATT
1 TTAATATATT
63373 TTTAATAATT
Statistics
Matches: 27, Mismatches: 9, Indels: 2
0.71 0.24 0.05
Matches are distributed among these distances:
13 9 0.33
14 18 0.67
ACGTcount: A:0.37, C:0.02, G:0.00, T:0.61
Consensus pattern (14 bp):
TTAATATATTATTT
Found at i:63500 original size:22 final size:21
Alignment explanation
Indices: 63475--63515 Score: 64
Period size: 22 Copynumber: 1.9 Consensus size: 21
63465 AATATGATAC
*
63475 TTAAATTAAAAATATATATAGA
1 TTAAATAAAAAAT-TATATAGA
63497 TTAAATAAAAAATTATATA
1 TTAAATAAAAAATTATATA
63516 ATAATATAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 6 0.33
22 12 0.67
ACGTcount: A:0.61, C:0.00, G:0.02, T:0.37
Consensus pattern (21 bp):
TTAAATAAAAAATTATATAGA
Found at i:63858 original size:36 final size:37
Alignment explanation
Indices: 63792--63877 Score: 97
Period size: 35 Copynumber: 2.4 Consensus size: 37
63782 TTGTTTTCAT
*
63792 ATAAATAT-ATTTATAATAATTTTTAATTATTATTTAAC
1 ATAAATATAATTTATAATAATTATT-ATTATTATTT-AC
* *
63830 ATAAATATAATTTATAATTA-TATT-TTATTATTTAT
1 ATAAATATAATTTATAATAATTATTATTATTATTTAC
*
63865 ATAAATAAAATTT
1 ATAAATATAATTT
63878 TTATTATCTA
Statistics
Matches: 43, Mismatches: 4, Indels: 5
0.83 0.08 0.10
Matches are distributed among these distances:
35 13 0.30
36 9 0.21
38 11 0.26
39 10 0.23
ACGTcount: A:0.47, C:0.01, G:0.00, T:0.52
Consensus pattern (37 bp):
ATAAATATAATTTATAATAATTATTATTATTATTTAC
Found at i:63866 original size:29 final size:29
Alignment explanation
Indices: 63798--63868 Score: 72
Period size: 29 Copynumber: 2.4 Consensus size: 29
63788 TCATATAAAT
*
63798 ATATTTATAATAATTTTTAATTATTATTTA
1 ATATTTAT-ATAATTTATAATTATTATTTA
* **
63828 ACATAAATATAATTTATAATTA-TATTTTA
1 ATATTTATATAATTTATAATTATTA-TTTA
*
63857 TTATTTATATAA
1 ATATTTATATAA
63869 ATAAAATTTT
Statistics
Matches: 32, Mismatches: 8, Indels: 3
0.74 0.19 0.07
Matches are distributed among these distances:
28 2 0.06
29 25 0.78
30 5 0.16
ACGTcount: A:0.44, C:0.01, G:0.00, T:0.55
Consensus pattern (29 bp):
ATATTTATATAATTTATAATTATTATTTA
Found at i:63873 original size:39 final size:38
Alignment explanation
Indices: 63792--63881 Score: 105
Period size: 39 Copynumber: 2.4 Consensus size: 38
63782 TTGTTTTCAT
*
63792 ATAAATATATTTATAATAATTTTTAATTATTATTTAAC
1 ATAAATATATTTATAATAATTTTTAATTATTATATAAC
*
63830 ATAAATATAATTTATAATTATATTTT-ATTATTTATATAA-
1 ATAAATAT-ATTTATAATAAT-TTTTAATTA-TTATATAAC
*
63869 ATAAA-ATTTTTAT
1 ATAAATATATTTAT
63882 TATCTATTTG
Statistics
Matches: 46, Mismatches: 3, Indels: 7
0.82 0.05 0.12
Matches are distributed among these distances:
37 5 0.11
38 10 0.22
39 20 0.43
40 11 0.24
ACGTcount: A:0.46, C:0.01, G:0.00, T:0.53
Consensus pattern (38 bp):
ATAAATATATTTATAATAATTTTTAATTATTATATAAC
Found at i:68487 original size:4 final size:4
Alignment explanation
Indices: 68480--68504 Score: 50
Period size: 4 Copynumber: 6.2 Consensus size: 4
68470 TAAACCAAGT
68480 AGAC AGAC AGAC AGAC AGAC AGAC A
1 AGAC AGAC AGAC AGAC AGAC AGAC A
68505 AGGTTTATAG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 21 1.00
ACGTcount: A:0.52, C:0.24, G:0.24, T:0.00
Consensus pattern (4 bp):
AGAC
Found at i:68742 original size:3 final size:3
Alignment explanation
Indices: 68736--68765 Score: 60
Period size: 3 Copynumber: 10.0 Consensus size: 3
68726 CTTATTATTA
68736 TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG
1 TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG
68766 CATTTATTAC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.00, C:0.00, G:0.33, T:0.67
Consensus pattern (3 bp):
TTG
Found at i:69481 original size:88 final size:88
Alignment explanation
Indices: 69332--69499 Score: 237
Period size: 88 Copynumber: 1.9 Consensus size: 88
69322 AGATATCTCA
* ** *
69332 TTTTGTTCGGGTTAATTTTTGATAACTTGAGGCCTGCTTAGTAAATGAATGATCGAAGATGTGTA
1 TTTTGTTCGGGCTAATTTCCGACAACTTGAGGCCTGCTTAGTAAATGAATGATCGAAGATGTGTA
69397 GGGACGAAGATCGCCGAGTACCG
66 GGGACGAAGATCGCCGAGTACCG
* *** * * *
69420 TTTTGTTCGGGCTAATTTCCGACAACTTGAGGTCTGCTTAGTTGGTGGATGATTGAAGATGTGTG
1 TTTTGTTCGGGCTAATTTCCGACAACTTGAGGCCTGCTTAGTAAATGAATGATCGAAGATGTGTA
69485 GGGACGAAGATCGCC
66 GGGACGAAGATCGCC
69500 AAGTGCCAAC
Statistics
Matches: 69, Mismatches: 11, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
88 69 1.00
ACGTcount: A:0.23, C:0.14, G:0.30, T:0.32
Consensus pattern (88 bp):
TTTTGTTCGGGCTAATTTCCGACAACTTGAGGCCTGCTTAGTAAATGAATGATCGAAGATGTGTA
GGGACGAAGATCGCCGAGTACCG
Found at i:69733 original size:21 final size:21
Alignment explanation
Indices: 69709--69778 Score: 63
Period size: 21 Copynumber: 3.4 Consensus size: 21
69699 AATTTGTACT
69709 GATACAAACATTAAATGTATC
1 GATACAAACATTAAATGTATC
* * *
69730 GATACATA-AGTGAATGTATC
1 GATACAAACATTAAATGTATC
* **
69750 TATACATGC-TTAAAATGTATC
1 GATACAAACATT-AAATGTATC
69771 GATACAAA
1 GATACAAA
69779 ATCACCCTAT
Statistics
Matches: 37, Mismatches: 10, Indels: 4
0.73 0.20 0.08
Matches are distributed among these distances:
20 17 0.46
21 20 0.54
ACGTcount: A:0.44, C:0.13, G:0.13, T:0.30
Consensus pattern (21 bp):
GATACAAACATTAAATGTATC
Found at i:69871 original size:20 final size:20
Alignment explanation
Indices: 69826--69883 Score: 57
Period size: 20 Copynumber: 2.9 Consensus size: 20
69816 TTAATAAATG
*
69826 TATCGATACATGCTTCTAGTTG
1 TATCGATACAT--TTCTAGTTA
69848 TATCGATACATTTCTCA-TTA
1 TATCGATACATTTCT-AGTTA
*
69868 TATCGAAACA-TTCTAG
1 TATCGATACATTTCTAG
69884 GCTTTTGACC
Statistics
Matches: 32, Mismatches: 2, Indels: 7
0.78 0.05 0.17
Matches are distributed among these distances:
18 1 0.03
19 4 0.12
20 15 0.47
21 1 0.03
22 11 0.34
ACGTcount: A:0.29, C:0.19, G:0.12, T:0.40
Consensus pattern (20 bp):
TATCGATACATTTCTAGTTA
Found at i:72533 original size:22 final size:22
Alignment explanation
Indices: 72506--72550 Score: 81
Period size: 22 Copynumber: 2.0 Consensus size: 22
72496 TTTTCTTTTC
72506 TCTCCCCCTTAATAAAAAAATT
1 TCTCCCCCTTAATAAAAAAATT
*
72528 TCTCCCCCTTAATAAAATAATT
1 TCTCCCCCTTAATAAAAAAATT
72550 T
1 T
72551 AACAATTTCG
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.38, C:0.27, G:0.00, T:0.36
Consensus pattern (22 bp):
TCTCCCCCTTAATAAAAAAATT
Done.