Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold1722
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: 64342
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.35
Found at i:897 original size:52 final size:52
Alignment explanation
Indices: 812--936 Score: 223
Period size: 52 Copynumber: 2.4 Consensus size: 52
802 ATATGAAAAG
*
812 TTGCCTGCATGTATCGATACATTTAATAGTGTATCGATACATCTGGGCAAAT
1 TTGCCTGCATGTATCGATACATTTAATAATGTATCGATACATCTGGGCAAAT
*
864 TTGCCTGCATGTATCGATACATTTTATAATGTATCGATACATCTGGGCAAAT
1 TTGCCTGCATGTATCGATACATTTAATAATGTATCGATACATCTGGGCAAAT
*
916 TTGCTTGCATGTATCGATACA
1 TTGCCTGCATGTATCGATACA
937 AAGATCAGTG
Statistics
Matches: 70, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
52 70 1.00
ACGTcount: A:0.28, C:0.18, G:0.18, T:0.36
Consensus pattern (52 bp):
TTGCCTGCATGTATCGATACATTTAATAATGTATCGATACATCTGGGCAAAT
Found at i:949 original size:52 final size:51
Alignment explanation
Indices: 812--956 Score: 211
Period size: 52 Copynumber: 2.8 Consensus size: 51
802 ATATGAAAAG
812 TTGCCTGCATGTATCGATACATTTAATAGTGTATCGATACATCTGGGCAAAT
1 TTGCCTGCATGTATCGATACA-TTAATAGTGTATCGATACATCTGGGCAAAT
* *
864 TTGCCTGCATGTATCGATACATTTTATAATGTATCGATACATCTGGGCAAAT
1 TTGCCTGCATGTATCGATACA-TTAATAGTGTATCGATACATCTGGGCAAAT
* *
916 TTGCTTGCATGTATCGATACA-AAGATCAGTGTATCGATACA
1 TTGCCTGCATGTATCGATACATTA-AT-AGTGTATCGATACA
957 ATGTATCGAT
Statistics
Matches: 85, Mismatches: 6, Indels: 4
0.89 0.06 0.04
Matches are distributed among these distances:
51 2 0.02
52 83 0.98
ACGTcount: A:0.30, C:0.17, G:0.19, T:0.34
Consensus pattern (51 bp):
TTGCCTGCATGTATCGATACATTAATAGTGTATCGATACATCTGGGCAAAT
Found at i:963 original size:13 final size:13
Alignment explanation
Indices: 945--969 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
935 CAAAGATCAG
945 TGTATCGATACAA
1 TGTATCGATACAA
958 TGTATCGATACA
1 TGTATCGATACA
970 TTTGAGTAAT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:2712 original size:13 final size:13
Alignment explanation
Indices: 2694--2719 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
2684 CAATTTTTTG
2694 TGTATCGATACAT
1 TGTATCGATACAT
2707 TGTATCGATACAT
1 TGTATCGATACAT
2720 ACTTGGTGTA
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:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:2734 original size:32 final size:33
Alignment explanation
Indices: 2674--2737 Score: 94
Period size: 32 Copynumber: 2.0 Consensus size: 33
2664 TACAAGTCAA
** *
2674 TGTATCGATACAATTTTTTGTGTATCGATACAT
1 TGTATCGATACAATACTTGGTGTATCGATACAT
2707 TGTATCGATAC-ATACTTGGTGTATCGATACA
1 TGTATCGATACAATACTTGGTGTATCGATACA
2738 AGTTTGGCTA
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
32 17 0.61
33 11 0.39
ACGTcount: A:0.28, C:0.14, G:0.17, T:0.41
Consensus pattern (33 bp):
TGTATCGATACAATACTTGGTGTATCGATACAT
Found at i:3337 original size:21 final size:21
Alignment explanation
Indices: 3296--3339 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
3286 CTCCCCTTTA
* *
3296 TCTCCCCCGTTTATTAATAAT
1 TCTCCCCCGTTAATCAATAAT
3317 TCTCCCCC-TTAATCAAGTAAT
1 TCTCCCCCGTTAATCAA-TAAT
3338 TC
1 TC
3340 ATATCAAAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
20 6 0.30
21 14 0.70
ACGTcount: A:0.25, C:0.32, G:0.05, T:0.39
Consensus pattern (21 bp):
TCTCCCCCGTTAATCAATAAT
Found at i:3432 original size:112 final size:112
Alignment explanation
Indices: 3235--3466 Score: 446
Period size: 112 Copynumber: 2.1 Consensus size: 112
3225 TAATTTTAAC
*
3235 AAATTTGTACATTCTCCCCCTTAATAAGATAATTGTAGCAATTTACGCATTCTCCCCTTTATCTC
1 AAATTTATACATTCTCCCCCTTAATAAGATAATTGTAGCAATTTACGCATTCTCCCCTTTATCTC
3300 CCCCGTTTATTAATAATTCTCCCCCTTAATCAAGTAATTCATATCAA
66 CCCCGTTTATTAATAATTCTCCCCCTTAATCAAGTAATTCATATCAA
*
3347 AAATTTATGCATTCTCCCCCTTAATAAGATAATTGTAGCAATTTACGCATTCTCCCCTTTATCTC
1 AAATTTATACATTCTCCCCCTTAATAAGATAATTGTAGCAATTTACGCATTCTCCCCTTTATCTC
3412 CCCCGTTTATTAATAATTCTCCCCCTTAATCAAGTAATTCATATCAA
66 CCCCGTTTATTAATAATTCTCCCCCTTAATCAAGTAATTCATATCAA
3459 AAATTTAT
1 AAATTTAT
3467 TTGCACATAT
Statistics
Matches: 118, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
112 118 1.00
ACGTcount: A:0.30, C:0.26, G:0.06, T:0.38
Consensus pattern (112 bp):
AAATTTATACATTCTCCCCCTTAATAAGATAATTGTAGCAATTTACGCATTCTCCCCTTTATCTC
CCCCGTTTATTAATAATTCTCCCCCTTAATCAAGTAATTCATATCAA
Found at i:3449 original size:21 final size:21
Alignment explanation
Indices: 3408--3451 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
3398 CTCCCCTTTA
* *
3408 TCTCCCCCGTTTATTAATAAT
1 TCTCCCCCGTTAATCAATAAT
3429 TCTCCCCC-TTAATCAAGTAAT
1 TCTCCCCCGTTAATCAA-TAAT
3450 TC
1 TC
3452 ATATCAAAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
20 6 0.30
21 14 0.70
ACGTcount: A:0.25, C:0.32, G:0.05, T:0.39
Consensus pattern (21 bp):
TCTCCCCCGTTAATCAATAAT
Found at i:5271 original size:13 final size:13
Alignment explanation
Indices: 5253--5278 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
5243 ATAATCACCC
5253 TGTATCGATACAA
1 TGTATCGATACAA
5266 TGTATCGATACAA
1 TGTATCGATACAA
5279 AGAAAAATGT
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:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:7371 original size:15 final size:16
Alignment explanation
Indices: 7346--7380 Score: 54
Period size: 15 Copynumber: 2.2 Consensus size: 16
7336 ATCAATTTCG
*
7346 TTTGAAGCTTCTTCAT
1 TTTGAAGCTTCCTCAT
7362 TTTG-AGCTTCCTCAT
1 TTTGAAGCTTCCTCAT
7377 TTTG
1 TTTG
7381 GACATTTTTA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 14 0.78
16 4 0.22
ACGTcount: A:0.14, C:0.20, G:0.14, T:0.51
Consensus pattern (16 bp):
TTTGAAGCTTCCTCAT
Found at i:9213 original size:21 final size:21
Alignment explanation
Indices: 9184--9228 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 21
9174 AAGTTTTCAT
*
9184 TTTTCTTAGCTAAC-TCATTA
1 TTTTCTTAGCCAACTTCATTA
*
9204 TTTTCATTAGCCAACTTCTTTA
1 TTTTC-TTAGCCAACTTCATTA
9226 TTT
1 TTT
9229 CATCTTGCAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 5 0.24
21 8 0.38
22 8 0.38
ACGTcount: A:0.22, C:0.20, G:0.04, T:0.53
Consensus pattern (21 bp):
TTTTCTTAGCCAACTTCATTA
Found at i:11462 original size:13 final size:13
Alignment explanation
Indices: 11444--11469 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
11434 CAATTTTTTG
11444 TGTATCGATACAT
1 TGTATCGATACAT
11457 TGTATCGATACAT
1 TGTATCGATACAT
11470 ACTTGGTGTA
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:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:11484 original size:32 final size:33
Alignment explanation
Indices: 11424--11487 Score: 94
Period size: 32 Copynumber: 2.0 Consensus size: 33
11414 TACAAGCCAA
** *
11424 TGTATCGATACAATTTTTTGTGTATCGATACAT
1 TGTATCGATACAATACTTGGTGTATCGATACAT
11457 TGTATCGATAC-ATACTTGGTGTATCGATACA
1 TGTATCGATACAATACTTGGTGTATCGATACA
11488 AGTTTGGCTA
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
32 17 0.61
33 11 0.39
ACGTcount: A:0.28, C:0.14, G:0.17, T:0.41
Consensus pattern (33 bp):
TGTATCGATACAATACTTGGTGTATCGATACAT
Found at i:15853 original size:17 final size:17
Alignment explanation
Indices: 15823--15887 Score: 58
Period size: 19 Copynumber: 3.5 Consensus size: 17
15813 AAACAAAAGC
15823 ACAAAAAATGAAAGAAAAA
1 ACAAAAAA--AAAGAAAAA
*
15842 ACAAAAAAAAAGCAAAA
1 ACAAAAAAAAAGAAAAA
* *
15859 GCAAAATAAAAAAGAGAACA
1 AC-AAA-AAAAAAGA-AAAA
15879 ACAAAAAAA
1 ACAAAAAAA
15888 TGAGGACATG
Statistics
Matches: 38, Mismatches: 5, Indels: 7
0.76 0.10 0.14
Matches are distributed among these distances:
17 9 0.24
18 7 0.18
19 18 0.47
20 4 0.11
ACGTcount: A:0.78, C:0.09, G:0.09, T:0.03
Consensus pattern (17 bp):
ACAAAAAAAAAGAAAAA
Found at i:15886 original size:38 final size:36
Alignment explanation
Indices: 15811--15887 Score: 95
Period size: 37 Copynumber: 2.1 Consensus size: 36
15801 TGAAAAAGTC
15811 AAAAACAAAAGCACAAAAAATGAAAGAAAAAACAAAA
1 AAAAACAAAAGCACAAAAAA-GAAAGAAAAAACAAAA
*
15848 AAAAAGCAAAAGCA-AAATAAA-AAAGAGAACAACAAAA
1 AAAAA-CAAAAGCACAAA-AAAGAAAGA-AAAAACAAAA
15885 AAA
1 AAA
15888 TGAGGACATG
Statistics
Matches: 36, Mismatches: 1, Indels: 6
0.84 0.02 0.14
Matches are distributed among these distances:
36 5 0.14
37 20 0.56
38 11 0.31
ACGTcount: A:0.78, C:0.10, G:0.09, T:0.03
Consensus pattern (36 bp):
AAAAACAAAAGCACAAAAAAGAAAGAAAAAACAAAA
Found at i:17346 original size:27 final size:27
Alignment explanation
Indices: 17223--18153 Score: 749
Period size: 27 Copynumber: 33.7 Consensus size: 27
17213 AACTTCTTCA
* ** *
17223 AAGTCCACAACTCTGCAGCAGCCTTTTT
1 AAGTCCACAACTCCGTGGCA-CCCTTTT
* * *
17251 AAGTCCACAACTTCATGGCACTCTTTT
1 AAGTCCACAACTCCGTGGCACCCTTTT
*
17278 AAAGTCCACAAGTCCGTGGCACCCTTTT
1 -AAGTCCACAACTCCGTGGCACCCTTTT
** *
17306 AAAGTCCATGACTCCGTGGCATCCTTTT
1 -AAGTCCACAACTCCGTGGCACCCTTTT
* * * *
17334 AAGTCCATAACTCTGTGGTATCCTTTT
1 AAGTCCACAACTCCGTGGCACCCTTTT
* *
17361 AAAGTCCACAACTCTGTGGCATCCTTTT
1 -AAGTCCACAACTCCGTGGCACCCTTTT
* *
17389 AAAGTCCACAACTCTGTGGCATCCTTTT
1 -AAGTCCACAACTCCGTGGCACCCTTTT
* *
17417 --GTCCACAACTCTGTGGCATCCTTTT
1 AAGTCCACAACTCCGTGGCACCCTTTT
* * * * *
17442 AAGTCAACAACTCCGTCGTATCTTTTT
1 AAGTCCACAACTCCGTGGCACCCTTTT
* *
17469 AAAGTCCACAACTCCGTGGCATCTTTTT
1 -AAGTCCACAACTCCGTGGCACCCTTTT
* * *
17497 AAGTCCACAACTCGGTGGCATCCTTTA
1 AAGTCCACAACTCCGTGGCACCCTTTT
* * *
17524 AAGTCCACAACTCTGTGACACCCTTTA
1 AAGTCCACAACTCCGTGGCACCCTTTT
* *
17551 AAGTCCACAACTCCGTGACACCCTTTA
1 AAGTCCACAACTCCGTGGCACCCTTTT
*
17578 AAATCCACAAC-CTCGTGGCACCCTTTT
1 AAGTCCACAACTC-CGTGGCACCCTTTT
* ** * *
17605 AAGCCCACAACTTTGTGGCATCCATTT
1 AAGTCCACAACTCCGTGGCACCCTTTT
* *
17632 AAGTCCACAACTCCATGGCATCCTTTT
1 AAGTCCACAACTCCGTGGCACCCTTTT
* *
17659 AAGTCCACAACTCTGTGGCATCCTACCTTTCCA
1 AAGTCCACAACTCCGTGGCA--C--CCTTT--T
* * **
17692 AAGCCCACAAGTCAATGGCATCCCTTTTT
1 AAGTCCACAACTCCGTGGCA-CCC-TTTT
** * ** **
17721 AAACCCACAAGTTAGTGGCACCCTTCCA
1 AAGTCCACAACTCCGTGGCACCCTT-TT
* * * * *
17749 AAGCCCACAAGTCAGTAGCACCCATTTC
1 AAGTCCACAACTCCGTGGCACCC-TTTT
** * * *
17777 AAAACCTACAAGTCAGTGGCATCCTTTTT
1 AAGTCC-ACAACTCCGTGGCA-CCCTTTT
* * ** *
17806 AAGCCCACAAGTTAGGGGCACCCCTTTTT
1 AAGTCCACAACTCCGTGGCA-CCC-TTTT
** * * *
17835 AAACCCCCAACTCCATGGCACCCTTTA
1 AAGTCCACAACTCCGTGGCACCCTTTT
*
17862 AATTCCACAACTCCGTGGCA-CCTTTT
1 AAGTCCACAACTCCGTGGCACCCTTTT
17888 AAAGTCCACAACTCCGTGGCACCCTTTT
1 -AAGTCCACAACTCCGTGGCACCCTTTT
*
17916 AAGTCCACAATTCCGTGGCACCCTTTT
1 AAGTCCACAACTCCGTGGCACCCTTTT
* * *
17943 AGGTCCATAACTCCATGGCA-CCTTTT
1 AAGTCCACAACTCCGTGGCACCCTTTT
*
17969 AAAAGTCTACAACTCCGTGGCACCCTTTT
1 --AAGTCCACAACTCCGTGGCACCCTTTT
*
17998 AAGTCCACAACTCCGTGGCACTCTTTT
1 AAGTCCACAACTCCGTGGCACCCTTTT
* *
18025 AAAGTCCACTACTCCATGGCACCCTTTT
1 -AAGTCCACAACTCCGTGGCACCCTTTT
18053 AAGTCCACAACTCCGTGGCA-CCTATTT
1 AAGTCCACAACTCCGTGGCACCCT-TTT
18080 AAGTCCACAACTCCGTGGCACCCTTTT
1 AAGTCCACAACTCCGTGGCACCCTTTT
* * * *
18107 AAGTCTATAACTCTGTGGCACCCTTTA
1 AAGTCCACAACTCCGTGGCACCCTTTT
* **
18134 AAGTCTACAGGTCCGTGGCA
1 AAGTCCACAACTCCGTGGCA
18154 TCATTTCAAA
Statistics
Matches: 758, Mismatches: 118, Indels: 55
0.81 0.13 0.06
Matches are distributed among these distances:
25 25 0.03
26 15 0.02
27 395 0.52
28 232 0.31
29 62 0.08
30 4 0.01
31 8 0.01
32 1 0.00
33 16 0.02
ACGTcount: A:0.26, C:0.32, G:0.14, T:0.28
Consensus pattern (27 bp):
AAGTCCACAACTCCGTGGCACCCTTTT
Found at i:17728 original size:29 final size:28
Alignment explanation
Indices: 17695--18461 Score: 213
Period size: 28 Copynumber: 27.6 Consensus size: 28
17685 CTTTCCAAAG
*
17695 CCCACAAGTCAATGGCATCCCTTTTTAAA
1 CCCACAAGTCAGTGGCA-CCCTTTTTAAA
* **
17724 CCCACAAGTTAGTGGCACCC-TTCCAAA
1 CCCACAAGTCAGTGGCACCCTTTTTAAA
* **
17751 GCCCACAAGTCAGTAGCACCCATTTCAAAA
1 -CCCACAAGTCAGTGGCACCC-TTTTTAAA
* * *
17781 CCTACAAGTCAGTGGCATCCTTTTTAAG
1 CCCACAAGTCAGTGGCACCCTTTTTAAA
* *
17809 CCCACAAGTTAGGGGCACCCCTTTTTAAA
1 CCCACAAGTCAGTGGCA-CCCTTTTTAAA
* *
17838 CCCCCAACTCCA-TGGCACCC--TTTAAA
1 CCCACAAGT-CAGTGGCACCCTTTTTAAA
* * *
17864 TTCCACAACTCCGTGGCA-CC-TTTTAAA
1 -CCCACAAGTCAGTGGCACCCTTTTTAAA
* * * *
17891 GTCCACAACTCCGTGGCACCC-TTTTAAG
1 -CCCACAAGTCAGTGGCACCCTTTTTAAA
* * * **
17919 TCCACAATTCCGTGGCACCC-TTTTAGG
1 CCCACAAGTCAGTGGCACCCTTTTTAAA
* * * *
17946 TCCATAACTCCA-TGGCA-CCTTTTAAAA
1 CCCACAAGT-CAGTGGCACCCTTTTTAAA
* * * * *
17973 GTCTACAACTCCGTGGCACCC-TTTTAAG
1 -CCCACAAGTCAGTGGCACCCTTTTTAAA
* * * *
18001 TCCACAACTCCGTGGCACTC-TTTTAAA
1 CCCACAAGTCAGTGGCACCCTTTTTAAA
* * * *
18028 GTCCACTACTCCA-TGGCACCC-TTTTAAG
1 -CCCACAAGT-CAGTGGCACCCTTTTTAAA
* * * * *
18056 TCCACAACTCCGTGGCA-CCTATTTAAG
1 CCCACAAGTCAGTGGCACCCTTTTTAAA
* * * *
18083 TCCACAACTCCGTGGCACCC-TTTTAAG
1 CCCACAAGTCAGTGGCACCCTTTTTAAA
* * * * *
18110 TCTATAACTCTGTGGCACCC--TTTAAA
1 CCCACAAGTCAGTGGCACCCTTTTTAAA
* * * * * * *
18136 GTCTACAGGTCCGTGGCA-TCATTTCAAA
1 -CCCACAAGTCAGTGGCACCCTTTTTAAA
* *
18164 TCCCACAAGTCAGTGGCATCC-TTTCAAA
1 -CCCACAAGTCAGTGGCACCCTTTTTAAA
* * *
18192 GCCCACAAGTCCA-TGGCA-TCATTTCAAA
1 -CCCACAAGT-CAGTGGCACCCTTTTTAAA
* * * *
18220 GCCCAGAAGTCAGTGGCA-TCATTTCAAA
1 -CCCACAAGTCAGTGGCACCCTTTTTAAA
* *
18248 GCCCACAAGTCAGTGGCA-CCATTTCAAA
1 -CCCACAAGTCAGTGGCACCCTTTTTAAA
* * * * *
18276 GCCCATAAGTCAATGGCA-TCATTTCAAA
1 -CCCACAAGTCAGTGGCACCCTTTTTAAA
* * *
18304 GCCCACAAGTTAGTGGCA-CCATTTCAAA
1 -CCCACAAGTCAGTGGCACCCTTTTTAAA
* ** * *
18332 GCCCATAAGTCAGTGGC-GTCATTTCAAA
1 -CCCACAAGTCAGTGGCACCCTTTTTAAA
* ** * *
18360 GCCCATAAGTCAGTGGC-TTCATTTCAAA
1 -CCCACAAGTCAGTGGCACCCTTTTTAAA
* * **
18388 GCCCATAAGTCAGTGGCATCCTTTCAAAA
1 -CCCACAAGTCAGTGGCACCCTTTTTAAA
* * * **
18417 CCCACAAGTCCGTGGCATCATTTCAAAA
1 CCCACAAGTCAGTGGCACCCTTTTTAAA
*
18445 CCCACAAGTCGGTGGCA
1 CCCACAAGTCAGTGGCA
18462 ACTCATTTCA
Statistics
Matches: 619, Mismatches: 91, Indels: 57
0.81 0.12 0.07
Matches are distributed among these distances:
26 20 0.03
27 181 0.29
28 346 0.56
29 65 0.11
30 7 0.01
ACGTcount: A:0.28, C:0.31, G:0.16, T:0.25
Consensus pattern (28 bp):
CCCACAAGTCAGTGGCACCCTTTTTAAA
Found at i:17761 original size:57 final size:56
Alignment explanation
Indices: 17687--18480 Score: 287
Period size: 56 Copynumber: 14.2 Consensus size: 56
17677 CATCCTACCT
* *
17687 TTCCAAAGCCCACAAGTCAATGGCATCCCTTTTTAAACCCACAAGTTAGTGGCACCC
1 TTCCAAAGCCCACAAGTCAGTGGCA-CCCTTTTTAAACCCACAAGTCAGTGGCACCC
* ** * *
17744 TTCCAAAGCCCACAAGTCAGTAGCACCCATTTCAAAACCTACAAGTCAGTGGCATCC
1 TTCCAAAGCCCACAAGTCAGTGGCACCC-TTTTTAAACCCACAAGTCAGTGGCACCC
*** * * * *
17801 TTTTTAAGCCCACAAGTTAGGGGCACCCCTTTTTAAACCCCCAACTCCA-TGGCACCC
1 TTCCAAAGCCCACAAGTCAGTGGCA-CCCTTTTTAAACCCACAAGT-CAGTGGCACCC
* ** * * * * *
17858 TT-TAAATTCCACAACTCCGTGGCA-CC-TTTTAAAGTCCACAACTCCGTGGCACCC
1 TTCCAAAGCCCACAAGTCAGTGGCACCCTTTTTAAA-CCCACAAGTCAGTGGCACCC
** * * * *** * * *
17912 TT-TTAAGTCCACAATTCCGTGGCACCC-TTTTAGGTCCATAACTCCA-TGGCACCT
1 TTCCAAAGCCCACAAGTCAGTGGCACCCTTTTTAAACCCACAAGT-CAGTGGCACCC
** * * * * ** * * *
17966 TTTAAAAGTCTACAACTCCGTGGCACCC-TTTTAAGTCCACAACTCCGTGGCACTC
1 TTCCAAAGCCCACAAGTCAGTGGCACCCTTTTTAAACCCACAAGTCAGTGGCACCC
** * * * ** * *
18021 TTTTAAAGTCCACTACTCCA-TGGCACCC-TTTTAAGTCCACAACTCCGTGGCA-CC
1 TTCCAAAGCCCACAAGT-CAGTGGCACCCTTTTTAAACCCACAAGTCAGTGGCACCC
** * * * ** * * * *
18075 TAT-TTAAGTCCACAACTCCGTGGCACCC-TTTTAAGTCTATAACTCTGTGGCACCC
1 T-TCCAAAGCCCACAAGTCAGTGGCACCCTTTTTAAACCCACAAGTCAGTGGCACCC
* * * * * * * * *
18130 TT-TAAAGTCTACAGGTCCGTGGCA-TCATTTCAAATCCCACAAGTCAGTGGCATCC
1 TTCCAAAGCCCACAAGTCAGTGGCACCCTTTTTAAA-CCCACAAGTCAGTGGCACCC
* * * * * * *
18185 TTTCAAAGCCCACAAGTCCA-TGGCA-TCATTTCAAAGCCCAGAAGTCAGTGGCATCA
1 TTCCAAAGCCCACAAGT-CAGTGGCACCCTTTTTAAA-CCCACAAGTCAGTGGCACCC
* * * * * * *
18241 TTTCAAAGCCCACAAGTCAGTGGCA-CCATTTCAAAGCCCATAAGTCAATGGCATCA
1 TTCCAAAGCCCACAAGTCAGTGGCACCCTTTTTAAA-CCCACAAGTCAGTGGCACCC
* * * * * ** *
18297 TTTCAAAGCCCACAAGTTAGTGGCA-CCATTTCAAAGCCCATAAGTCAGTGGCGTCA
1 TTCCAAAGCCCACAAGTCAGTGGCACCCTTTTTAAA-CCCACAAGTCAGTGGCACCC
* * ** * * * *
18353 TTTCAAAGCCCATAAGTCAGTGGC-TTCATTTCAAAGCCCATAAGTCAGTGGCATCC
1 TTCCAAAGCCCACAAGTCAGTGGCACCCTTTTTAAA-CCCACAAGTCAGTGGCACCC
* * * * * ** * *
18409 TTTCAAAACCCACAAGTCCGTGGCATCATTTCAAAACCCACAAGTCGGTGGCAACTCA
1 TTCCAAAGCCCACAAGTCAGTGGCACCCTTTTTAAACCCACAAGTCAGTGGC-AC-CC
*
18467 TTTCAAAGCCCACA
1 TTCCAAAGCCCACA
18481 CAAGTTGGTG
Statistics
Matches: 613, Mismatches: 102, Indels: 43
0.81 0.13 0.06
Matches are distributed among these distances:
53 10 0.02
54 123 0.20
55 117 0.19
56 250 0.41
57 94 0.15
58 19 0.03
ACGTcount: A:0.28, C:0.31, G:0.15, T:0.25
Consensus pattern (56 bp):
TTCCAAAGCCCACAAGTCAGTGGCACCCTTTTTAAACCCACAAGTCAGTGGCACCC
Found at i:18188 original size:28 final size:28
Alignment explanation
Indices: 18148--18512 Score: 471
Period size: 28 Copynumber: 12.8 Consensus size: 28
18138 CTACAGGTCC
*
18148 GTGGCATCATTTCAAATCCCACAAGTCA
1 GTGGCATCATTTCAAAGCCCACAAGTCA
*
18176 GTGGCATCCTTTCAAAGCCCACAAGTCCA
1 GTGGCATCATTTCAAAGCCCACAAGT-CA
*
18205 -TGGCATCATTTCAAAGCCCAGAAGTCA
1 GTGGCATCATTTCAAAGCCCACAAGTCA
18232 GTGGCATCATTTCAAAGCCCACAAGTCA
1 GTGGCATCATTTCAAAGCCCACAAGTCA
* *
18260 GTGGCACCATTTCAAAGCCCATAAGTCA
1 GTGGCATCATTTCAAAGCCCACAAGTCA
* *
18288 ATGGCATCATTTCAAAGCCCACAAGTTA
1 GTGGCATCATTTCAAAGCCCACAAGTCA
* *
18316 GTGGCACCATTTCAAAGCCCATAAGTCA
1 GTGGCATCATTTCAAAGCCCACAAGTCA
* *
18344 GTGGCGTCATTTCAAAGCCCATAAGTCA
1 GTGGCATCATTTCAAAGCCCACAAGTCA
* *
18372 GTGGCTTCATTTCAAAGCCCATAAGTCA
1 GTGGCATCATTTCAAAGCCCACAAGTCA
* * *
18400 GTGGCATCCTTTCAAAACCCACAAGTCC
1 GTGGCATCATTTCAAAGCCCACAAGTCA
* *
18428 GTGGCATCATTTCAAAACCCACAAGTCG
1 GTGGCATCATTTCAAAGCCCACAAGTCA
**
18456 GTGGCAACTCATTTCAAAGCCCACACAAGTTG
1 GTGGC-A-TCATTTCAAAG-CC-CACAAGTCA
*
18488 GTGGCAACCCATTTCAAAGCCCACA
1 GTGGC-A-TCATTTCAAAGCCCACA
18513 CAAGTCGGTG
Statistics
Matches: 303, Mismatches: 28, Indels: 10
0.89 0.08 0.03
Matches are distributed among these distances:
27 2 0.01
28 254 0.84
29 3 0.01
30 14 0.05
31 4 0.01
32 26 0.09
ACGTcount: A:0.31, C:0.29, G:0.17, T:0.22
Consensus pattern (28 bp):
GTGGCATCATTTCAAAGCCCACAAGTCA
Found at i:18491 original size:32 final size:32
Alignment explanation
Indices: 18154--18620 Score: 261
Period size: 28 Copynumber: 15.9 Consensus size: 32
18144 GTCCGTGGCA
* *
18154 TCATTTCAAA-TCC-CACAAGTCAGTGGC-A-
1 TCATTTCAAAGCCCACACAAGTCGGTGGCAAC
* **
18182 TCCTTTCAAAG-CC-CACAAGTCCATGGC-A-
1 TCATTTCAAAGCCCACACAAGTCGGTGGCAAC
* *
18210 TCATTTCAAAG-CC-CAGAAGTCAGTGGC-A-
1 TCATTTCAAAGCCCACACAAGTCGGTGGCAAC
*
18238 TCATTTCAAAG-CC-CACAAGTCAGTGGC-AC
1 TCATTTCAAAGCCCACACAAGTCGGTGGCAAC
* **
18267 -CATTTCAAAG-CC-CATAAGTCAATGGC-A-
1 TCATTTCAAAGCCCACACAAGTCGGTGGCAAC
**
18294 TCATTTCAAAG-CC-CACAAGTTAGTGGC-AC
1 TCATTTCAAAGCCCACACAAGTCGGTGGCAAC
* * *
18323 -CATTTCAAAG-CC-CATAAGTCAGTGGC--G
1 TCATTTCAAAGCCCACACAAGTCGGTGGCAAC
* * *
18350 TCATTTCAAAG-CC-CATAAGTCAGTGGC--T
1 TCATTTCAAAGCCCACACAAGTCGGTGGCAAC
* *
18378 TCATTTCAAAG-CC-CATAAGTCAGTGGC-A-
1 TCATTTCAAAGCCCACACAAGTCGGTGGCAAC
* * *
18406 TCCTTTCAAA-ACC-CACAAGTCCGTGGC-A-
1 TCATTTCAAAGCCCACACAAGTCGGTGGCAAC
*
18434 TCATTTCAAA-ACC-CACAAGTCGGTGGCAAC
1 TCATTTCAAAGCCCACACAAGTCGGTGGCAAC
*
18464 TCATTTCAAAGCCCACACAAGTTGGTGGCAAC
1 TCATTTCAAAGCCCACACAAGTCGGTGGCAAC
*
18496 CCATTTCAAAGCCCACACAAGTCGGTGGCAAC
1 TCATTTCAAAGCCCACACAAGTCGGTGGCAAC
* * * *
18528 CCTTTTCAAACCCCACACAAATCGGTAGG-AACC
1 TCATTTCAAAGCCCACACAAGTCGGT-GGCAA-C
* *
18561 TC-TCTCAAAGCCCGCACAAGTCGGTGTG-AAC
1 TCATTTCAAAGCCCACACAAGTCGGTG-GCAAC
* * *
18592 -CCTTTTAAAGCCCACACAAGTTGGTGGCA
1 TCATTTCAAAGCCCACACAAGTCGGTGGCA
18621 TCGTTTTTCA
Statistics
Matches: 385, Mismatches: 38, Indels: 29
0.85 0.08 0.06
Matches are distributed among these distances:
28 250 0.65
29 1 0.00
30 12 0.03
31 25 0.06
32 93 0.24
33 4 0.01
ACGTcount: A:0.31, C:0.30, G:0.18, T:0.22
Consensus pattern (32 bp):
TCATTTCAAAGCCCACACAAGTCGGTGGCAAC
Found at i:18688 original size:127 final size:128
Alignment explanation
Indices: 18447--18688 Score: 285
Period size: 127 Copynumber: 1.9 Consensus size: 128
18437 TTTCAAAACC
18447 CACAAGTCGGTGGCAACTCATTTCAAAGCCCACACAAGTTGGTGGCAACCCATTTCAAAGCCCAC
1 CACAAGTCGGTGGCAACTCATTTCAAAGCCCACACAAGTTGGTGGCAACCCATTTCAAAGCCCAC
* * * *
18512 ACAAGTCGGTGGCAACCCTTTTCAAACCCCACACAAATCGGTAGGAACCTCTCTCAAAGCCCG
66 ACAAGTCGGTGGCAACACTTTTCAAAACCCACACAAACCAGTAGGAACCTCTCTCAAAGCCCG
* * * *** *
18575 CACAAGTCGGTGTG-AAC-CCTTTTAAAGCCCACACAAGTTGGTGGCATCGTTTTTCAAAAGTCC
1 CACAAGTCGGTG-GCAACTCATTTCAAAGCCCACACAAGTTGGTGGCAACCCATTTC-AAAGCCC
** * * *
18638 ACAC-TTTCGGTGGCAACACTTTTTAAAACCCACGCAAGCCAGT-GGCAACCT
64 ACACAAGTCGGTGGCAACACTTTTCAAAACCCACACAAACCAGTAGG-AACCT
18689 TTTTCAAGTC
Statistics
Matches: 95, Mismatches: 16, Indels: 7
0.81 0.14 0.06
Matches are distributed among these distances:
126 2 0.02
127 67 0.71
128 25 0.26
129 1 0.01
ACGTcount: A:0.29, C:0.31, G:0.19, T:0.21
Consensus pattern (128 bp):
CACAAGTCGGTGGCAACTCATTTCAAAGCCCACACAAGTTGGTGGCAACCCATTTCAAAGCCCAC
ACAAGTCGGTGGCAACACTTTTCAAAACCCACACAAACCAGTAGGAACCTCTCTCAAAGCCCG
Found at i:19147 original size:18 final size:17
Alignment explanation
Indices: 19124--19157 Score: 59
Period size: 17 Copynumber: 1.9 Consensus size: 17
19114 GACTTATTTA
19124 AAAAAATACAAAAAAAAT
1 AAAAAATA-AAAAAAAAT
19142 AAAAAATAAAAAAAAA
1 AAAAAATAAAAAAAAA
19158 GAAAGAAAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 8 0.50
18 8 0.50
ACGTcount: A:0.88, C:0.03, G:0.00, T:0.09
Consensus pattern (17 bp):
AAAAAATAAAAAAAAAT
Found at i:22901 original size:29 final size:29
Alignment explanation
Indices: 22844--22900 Score: 78
Period size: 30 Copynumber: 1.9 Consensus size: 29
22834 TATCCAAACA
**
22844 AAAAATTTTAAATTTATTAATTTGAAAAT
1 AAAAATTTTAAATTTAAGAATTTGAAAAT
*
22873 AAAAATTTTCAAATTTAAGATTTTGAAA
1 AAAAATTTT-AAATTTAAGAATTTGAAA
22901 TTTAAATCCA
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
29 9 0.38
30 15 0.62
ACGTcount: A:0.51, C:0.02, G:0.05, T:0.42
Consensus pattern (29 bp):
AAAAATTTTAAATTTAAGAATTTGAAAAT
Found at i:23247 original size:13 final size:13
Alignment explanation
Indices: 23229--23276 Score: 62
Period size: 13 Copynumber: 3.7 Consensus size: 13
23219 AAACTAAAGT
23229 TATTTTTTATTTA
1 TATTTTTTATTTA
*
23242 TATTTTTTATATA
1 TATTTTTTATTTA
23255 -ATATTTTTATTTA
1 TAT-TTTTTATTTA
*
23268 AATTTTTTA
1 TATTTTTTA
23277 AATATTAAAT
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
12 2 0.06
13 27 0.87
14 2 0.06
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (13 bp):
TATTTTTTATTTA
Found at i:23847 original size:2 final size:2
Alignment explanation
Indices: 23840--23873 Score: 59
Period size: 2 Copynumber: 16.5 Consensus size: 2
23830 GTGAAATCTT
23840 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TGA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T-A TA T
23874 TTGATTTTCT
Statistics
Matches: 31, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
2 29 0.94
3 2 0.06
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (2 bp):
TA
Found at i:24324 original size:22 final size:19
Alignment explanation
Indices: 24278--24326 Score: 55
Period size: 22 Copynumber: 2.5 Consensus size: 19
24268 TTATAATAAA
24278 ATATTAAA-ATTTATTTTT
1 ATATTAAATATTTATTTTT
*
24296 ATGTTAAATATTTATATATTTT
1 ATATTAAATA-TT-TAT-TTTT
24318 ATATTAAAT
1 ATATTAAAT
24327 TATAAAATAA
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
18 7 0.28
19 1 0.04
20 2 0.08
21 3 0.12
22 12 0.48
ACGTcount: A:0.41, C:0.00, G:0.02, T:0.57
Consensus pattern (19 bp):
ATATTAAATATTTATTTTT
Found at i:29965 original size:13 final size:13
Alignment explanation
Indices: 29947--29972 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
29937 TACAGCAAGT
29947 ATGTATCGATACA
1 ATGTATCGATACA
29960 ATGTATCGATACA
1 ATGTATCGATACA
29973 CAAAAAATTG
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:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:30494 original size:34 final size:35
Alignment explanation
Indices: 30431--30497 Score: 102
Period size: 37 Copynumber: 1.9 Consensus size: 35
30421 CTAAGTGATT
30431 GAGAGGTTCTATCTTAGCCTTTGAAAAAGATAGAGA
1 GAGAGGTTCTATCTTAGCCTTTG-AAAAGATAGAGA
30467 GAGAGGTTTCTATCTTAGCC-TTG-AAAGATAG
1 GAGAGG-TTCTATCTTAGCCTTTGAAAAGATAG
30498 TGTTGTAAGG
Statistics
Matches: 30, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
34 8 0.27
36 9 0.30
37 13 0.43
ACGTcount: A:0.33, C:0.12, G:0.25, T:0.30
Consensus pattern (35 bp):
GAGAGGTTCTATCTTAGCCTTTGAAAAGATAGAGA
Found at i:33684 original size:13 final size:13
Alignment explanation
Indices: 33666--33690 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
33656 TTTTCCAGAT
33666 TGTATCGATACAA
1 TGTATCGATACAA
33679 TGTATCGATACA
1 TGTATCGATACA
33691 TTGCTTCAGT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:35589 original size:13 final size:13
Alignment explanation
Indices: 35571--35596 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
35561 TACAGCAAGT
35571 ATGTATCGATACA
1 ATGTATCGATACA
35584 ATGTATCGATACA
1 ATGTATCGATACA
35597 CAAAAAATTG
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:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:36118 original size:34 final size:35
Alignment explanation
Indices: 36055--36121 Score: 102
Period size: 37 Copynumber: 1.9 Consensus size: 35
36045 CTAAGTGATT
36055 GAGAGGTTCTATCTTAGCCTTTGAAAAAGATAGAGA
1 GAGAGGTTCTATCTTAGCCTTTG-AAAAGATAGAGA
36091 GAGAGGTTTCTATCTTAGCC-TTG-AAAGATAG
1 GAGAGG-TTCTATCTTAGCCTTTGAAAAGATAG
36122 TGTTGTAAGG
Statistics
Matches: 30, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
34 8 0.27
36 9 0.30
37 13 0.43
ACGTcount: A:0.33, C:0.12, G:0.25, T:0.30
Consensus pattern (35 bp):
GAGAGGTTCTATCTTAGCCTTTGAAAAGATAGAGA
Found at i:37136 original size:48 final size:48
Alignment explanation
Indices: 37081--37529 Score: 264
Period size: 48 Copynumber: 9.2 Consensus size: 48
37071 TAAAAATATG
*
37081 GAGGAGGAGGTGAAGAAGATGGTGGAGGTGGGGACTTGTAGATGTAAGGAA
1 GAGGAGGAGGTGAAGAAGATGGTGGAGGTGGGGACTTGTAGATAT-A--AA
* * * * * *
37132 GAGGAGAAGGTGATGGAGATGGAGGAGGTGGGGACTTGTAGACATAAG
1 GAGGAGGAGGTGAAGAAGATGGTGGAGGTGGGGACTTGTAGATATAAA
* * * *
37180 GAGGAAGAGGTGAA-AGATATAGTGGAGGTGGGGACTTGTAGACATAAA
1 GAGGAGGAGGTGAAGA-AGATGGTGGAGGTGGGGACTTGTAGATATAAA
* * * * *
37228 GA--A-GAGGTAAAGGAGATGGTGGAGGTGGGGAATTGTGGATCTAAA
1 GAGGAGGAGGTGAAGAAGATGGTGGAGGTGGGGACTTGTAGATATAAA
* * * * * * *
37273 GAGGAGGGGGTGAGGGAGATGGTGGGGGAGGGAACTTATAGATATAAA
1 GAGGAGGAGGTGAAGAAGATGGTGGAGGTGGGGACTTGTAGATATAAA
* * * * * **
37321 GAGGAGGAAGTGAAGAAGATGGAGGTGGTGGTGGTGGGGCCTAGTAGACATATG
1 GAGGAGGAGGTGAAG-A-A--GA--TGGTGGAGGTGGGGACTTGTAGATATAAA
* * * * * ** *
37375 GTA-GAGGTGGTGATGGAGATGGAGGAGTTGGGGACTTAAAGACATAAA
1 G-AGGAGGAGGTGAAGAAGATGGTGGAGGTGGGGACTTGTAGATATAAA
* * * * * * *
37423 GAGGA-AAGGCTGAGGGAGATGATGGAGGTGTGGACTTGTAG-TTTAAG
1 GAGGAGGAGG-TGAAGAAGATGGTGGAGGTGGGGACTTGTAGATATAAA
* * * * * * * *
37470 GAGGAGGGGGTGAGGGAGATAGTGAAGGAGGGGACTTATAGATATAAG
1 GAGGAGGAGGTGAAGAAGATGGTGGAGGTGGGGACTTGTAGATATAAA
37518 GAGGAGGAGGTG
1 GAGGAGGAGGTG
37530 GTGATGGAGA
Statistics
Matches: 301, Mismatches: 81, Indels: 35
0.72 0.19 0.08
Matches are distributed among these distances:
45 35 0.12
46 1 0.00
47 37 0.12
48 151 0.50
50 4 0.01
51 39 0.13
52 3 0.01
54 30 0.10
55 1 0.00
ACGTcount: A:0.32, C:0.03, G:0.47, T:0.18
Consensus pattern (48 bp):
GAGGAGGAGGTGAAGAAGATGGTGGAGGTGGGGACTTGTAGATATAAA
Found at i:37274 original size:45 final size:45
Alignment explanation
Indices: 37087--37263 Score: 167
Period size: 51 Copynumber: 3.7 Consensus size: 45
37077 TATGGAGGAG
* * **
37087 GAGGTGAAGAAGATGGTGGAGGTGGGGACTTGTAGATGTAAGGAAGAGGA
1 GAGGTAAAGGAGATGGTGGAGGTGGGGACTTGTAGACAT-A--AAGA--A
* * *
37137 GAAGGTGATGGAGATGGAGGAGGTGGGGACTTGTAGACATAAGGAGGAA
1 G-AGGTAAAGGAGATGGTGGAGGTGGGGACTTGTAGACATAA--A-GAA
* *
37186 GAGGTGAAA-GATATAGTGGAGGTGGGGACTTGTAGACATAAAGAA
1 GAGGT-AAAGGAGATGGTGGAGGTGGGGACTTGTAGACATAAAGAA
*
37231 GAGGTAAAGGAGATGGTGGAGGTGGGGAATTGT
1 GAGGTAAAGGAGATGGTGGAGGTGGGGACTTGT
37264 GGATCTAAAG
Statistics
Matches: 108, Mismatches: 13, Indels: 17
0.78 0.09 0.12
Matches are distributed among these distances:
44 3 0.03
45 29 0.27
46 1 0.01
48 34 0.31
49 3 0.03
50 3 0.03
51 35 0.32
ACGTcount: A:0.33, C:0.03, G:0.46, T:0.19
Consensus pattern (45 bp):
GAGGTAAAGGAGATGGTGGAGGTGGGGACTTGTAGACATAAAGAA
Found at i:37320 original size:93 final size:93
Alignment explanation
Indices: 37146--37327 Score: 204
Period size: 93 Copynumber: 2.0 Consensus size: 93
37136 AGAAGGTGAT
* * * *
37146 GGAGATGGAGGAGGTGGGGACTTGTAGACATAAGGAGGAAGAGGTGAAAGATATAGTGGAGGTGG
1 GGAGATGGAGGAGGTGGGGAATTGTAGACATAAAGAGGAAGAGGTGAAAGAGATAGTGGAGGAGG
* *
37211 GGACTTGTAGACATAAAGAAGAGGTAAA
66 GAACTTATAGACATAAAGAAGAGGTAAA
* * * * ** * *
37239 GGAGATGGTGGAGGTGGGGAATTGTGGATC-TAAAGAGGAGGGGGTGAGGGAGATGGTGGGGGAG
1 GGAGATGGAGGAGGTGGGGAATTGTAGA-CATAAAGAGGAAGAGGTGAAAGAGATAGTGGAGGAG
* *
37303 GGAACTTATAGATATAAAGAGGAGG
65 GGAACTTATAGACATAAAGAAGAGG
37328 AAGTGAAGAA
Statistics
Matches: 72, Mismatches: 16, Indels: 2
0.80 0.18 0.02
Matches are distributed among these distances:
93 71 0.99
94 1 0.01
ACGTcount: A:0.33, C:0.03, G:0.46, T:0.18
Consensus pattern (93 bp):
GGAGATGGAGGAGGTGGGGAATTGTAGACATAAAGAGGAAGAGGTGAAAGAGATAGTGGAGGAGG
GAACTTATAGACATAAAGAAGAGGTAAA
Found at i:37487 original size:47 final size:48
Alignment explanation
Indices: 37404--37529 Score: 123
Period size: 47 Copynumber: 2.6 Consensus size: 48
37394 TGGAGGAGTT
* * * * * *
37404 GGGGACTTAAAGACATAAAGAGGA-AAGGCTGAGGGAGAT-GATGGAGGT
1 GGGGACTTATAGATATAAGGAGGAGGAGG-TGAGGGAGATAG-TGAAGGA
* * * *
37452 GTGGACTTGTAG-TTTAAGGAGGAGGGGGTGAGGGAGATAGTGAAGGA
1 GGGGACTTATAGATATAAGGAGGAGGAGGTGAGGGAGATAGTGAAGGA
37499 GGGGACTTATAGATATAAGGAGGAGGAGGTG
1 GGGGACTTATAGATATAAGGAGGAGGAGGTG
37530 GTGATGGAGA
Statistics
Matches: 61, Mismatches: 14, Indels: 6
0.75 0.17 0.07
Matches are distributed among these distances:
47 33 0.54
48 28 0.46
ACGTcount: A:0.33, C:0.04, G:0.45, T:0.18
Consensus pattern (48 bp):
GGGGACTTATAGATATAAGGAGGAGGAGGTGAGGGAGATAGTGAAGGA
Found at i:37547 original size:48 final size:47
Alignment explanation
Indices: 37377--37547 Score: 127
Period size: 48 Copynumber: 3.5 Consensus size: 47
37367 GACATATGGT
* * *
37377 AGAGGTGGTGATGGAGATGGAGGAGTTGGGGACTTAAAGACATAAAGAGG
1 AGAGGTGGTGATGGAGATGGAGGA---GGGGACTTATAGATATAAGGAGG
* * * * * *
37427 AAAGGCTGAGGGA--GATGATGGAGGTGTGGACTTGTAG-TTTAAGGAGG
1 AGAGG-TG-GTGATGGA-GATGGAGGAGGGGACTTATAGATATAAGGAGG
*
37474 AG-GG-GGTGAGGGAGATAGTGAAGGAGGGGACTTATAGATATAAGGAGG
1 AGAGGTGGTGATGGAGAT-G-G-AGGAGGGGACTTATAGATATAAGGAGG
37522 AGGAGGTGGTGATGGAGATGGAGGAG
1 A-GAGGTGGTGATGGAGATGGAGGAG
37548 ATAAGGGCTT
Statistics
Matches: 93, Mismatches: 16, Indels: 26
0.69 0.12 0.19
Matches are distributed among these distances:
43 3 0.03
44 4 0.04
45 3 0.03
46 3 0.03
47 21 0.23
48 24 0.26
49 2 0.02
50 9 0.10
51 21 0.23
52 3 0.03
ACGTcount: A:0.31, C:0.03, G:0.47, T:0.19
Consensus pattern (47 bp):
AGAGGTGGTGATGGAGATGGAGGAGGGGACTTATAGATATAAGGAGG
Found at i:39237 original size:30 final size:32
Alignment explanation
Indices: 39203--39271 Score: 74
Period size: 30 Copynumber: 2.2 Consensus size: 32
39193 CAAATTTTCA
*
39203 TATTTTTTA-AATTTTTTTGA-ATTTTA-TTTT
1 TATTTTTTATAAGTTTTTT-ATATTTTATTTTT
* *
39233 TA-TTTCTATAAGTTTTTTATTTTTTATTTTT
1 TATTTTTTATAAGTTTTTTATATTTTATTTTT
39264 TATTTTTT
1 TATTTTTT
39272 TAATAATGAC
Statistics
Matches: 31, Mismatches: 4, Indels: 6
0.76 0.10 0.15
Matches are distributed among these distances:
29 6 0.19
30 15 0.48
31 6 0.19
32 4 0.13
ACGTcount: A:0.20, C:0.01, G:0.03, T:0.75
Consensus pattern (32 bp):
TATTTTTTATAAGTTTTTTATATTTTATTTTT
Found at i:39273 original size:8 final size:7
Alignment explanation
Indices: 39245--39271 Score: 54
Period size: 7 Copynumber: 3.9 Consensus size: 7
39235 TTTCTATAAG
39245 TTTTTTA
1 TTTTTTA
39252 TTTTTTA
1 TTTTTTA
39259 TTTTTTA
1 TTTTTTA
39266 TTTTTT
1 TTTTTT
39272 TAATAATGAC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 20 1.00
ACGTcount: A:0.11, C:0.00, G:0.00, T:0.89
Consensus pattern (7 bp):
TTTTTTA
Found at i:39943 original size:24 final size:23
Alignment explanation
Indices: 39915--39979 Score: 69
Period size: 23 Copynumber: 2.8 Consensus size: 23
39905 TTAAGATATG
39915 AATATAATATAAAA-AAATAATTAA
1 AATATAATATAAAATAAAT-A-TAA
*
39939 AATATGATATAAAATAAATATAA
1 AATATAATATAAAATAAATATAA
* * *
39962 AATAAAAAATAACATAAA
1 AATATAATATAAAATAAA
39980 CACAATATAT
Statistics
Matches: 35, Mismatches: 5, Indels: 3
0.81 0.12 0.07
Matches are distributed among these distances:
23 17 0.49
24 14 0.40
25 4 0.11
ACGTcount: A:0.71, C:0.02, G:0.02, T:0.26
Consensus pattern (23 bp):
AATATAATATAAAATAAATATAA
Found at i:39959 original size:11 final size:11
Alignment explanation
Indices: 39915--39967 Score: 54
Period size: 11 Copynumber: 4.5 Consensus size: 11
39905 TTAAGATATG
39915 AATATAATATAA
1 AATA-AATATAA
39927 AA-AAATAATTAA
1 AATAAAT-A-TAA
*
39939 AATATGATATAA
1 AATA-AATATAA
39951 AATAAATATAA
1 AATAAATATAA
39962 AATAAA
1 AATAAA
39968 AAATAACATA
Statistics
Matches: 35, Mismatches: 2, Indels: 9
0.76 0.04 0.20
Matches are distributed among these distances:
10 3 0.09
11 14 0.40
12 14 0.40
13 2 0.06
14 2 0.06
ACGTcount: A:0.70, C:0.00, G:0.02, T:0.28
Consensus pattern (11 bp):
AATAAATATAA
Found at i:40067 original size:20 final size:21
Alignment explanation
Indices: 40042--40087 Score: 60
Period size: 20 Copynumber: 2.2 Consensus size: 21
40032 ATCAAAATTT
*
40042 ATATAATATATAATAT-CAAAA
1 ATATAAT-TAAAATATGCAAAA
40063 -TATAATTAAAATATGCAAAA
1 ATATAATTAAAATATGCAAAA
40083 ATATA
1 ATATA
40088 CATACGATAC
Statistics
Matches: 22, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
19 7 0.32
20 11 0.50
21 4 0.18
ACGTcount: A:0.61, C:0.04, G:0.02, T:0.33
Consensus pattern (21 bp):
ATATAATTAAAATATGCAAAA
Found at i:40076 original size:24 final size:24
Alignment explanation
Indices: 40030--40076 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 24
40020 AATTATTGAC
* *
40030 ATATCAAAATTTATATAATATATA
1 ATATCAAAATTAATATAAAATATA
40054 ATATCAAAATATAAT-TAAAATAT
1 ATATCAAAAT-TAATATAAAATAT
40077 GCAAAAATAT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
24 17 0.85
25 3 0.15
ACGTcount: A:0.57, C:0.04, G:0.00, T:0.38
Consensus pattern (24 bp):
ATATCAAAATTAATATAAAATATA
Found at i:41874 original size:11 final size:12
Alignment explanation
Indices: 41825--41875 Score: 54
Period size: 11 Copynumber: 4.4 Consensus size: 12
41815 AATTAACAAG
41825 TATTTATAAATAT
1 TATTTA-AAATAT
*
41838 TAATTAAAA-AT
1 TATTTAAAATAT
*
41849 TATTT-AATTAT
1 TATTTAAAATAT
41860 TATTTAAAATA-
1 TATTTAAAATAT
41871 TATTT
1 TATTT
41876 TATATTTGAT
Statistics
Matches: 32, Mismatches: 4, Indels: 6
0.76 0.10 0.14
Matches are distributed among these distances:
10 2 0.06
11 18 0.56
12 7 0.22
13 5 0.16
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (12 bp):
TATTTAAAATAT
Found at i:42657 original size:21 final size:21
Alignment explanation
Indices: 42631--42691 Score: 70
Period size: 21 Copynumber: 2.8 Consensus size: 21
42621 AAAAAATTAA
42631 AAATATTTTAT-ATTAATATTT
1 AAATATTTTATAATTAA-ATTT
*
42652 ATATATTTTATAATTAAATTT
1 AAATATTTTATAATTAAATTT
*
42673 AAATAATTTTTTTAATTAA
1 AAAT-A-TTTTATAATTAA
42692 TAAATATCAA
Statistics
Matches: 34, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
21 17 0.50
22 6 0.18
23 11 0.32
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (21 bp):
AAATATTTTATAATTAAATTT
Found at i:43583 original size:18 final size:18
Alignment explanation
Indices: 43560--43664 Score: 67
Period size: 18 Copynumber: 5.8 Consensus size: 18
43550 ATTTAAAATA
43560 TTTAATATTTATATAATT
1 TTTAATATTTATATAATT
*
43578 TTTAATATATCA-ATAATT
1 TTTAATAT-TTATATAATT
* * *
43596 TCTATTATATA-AT-ATT
1 TTTAATATTTATATAATT
43612 TTTAGATATTTATAT-ATT
1 TTTA-ATATTTATATAATT
*
43630 TATATCATATTTATTATATATT
1 T-T-TAATATTTA-TATA-ATT
*
43652 TTTCATA-TTATAT
1 TTTAATATTTATAT
43665 TTTATTTCGT
Statistics
Matches: 70, Mismatches: 9, Indels: 16
0.74 0.09 0.17
Matches are distributed among these distances:
16 6 0.09
17 8 0.11
18 29 0.41
19 13 0.19
20 9 0.13
21 1 0.01
22 4 0.06
ACGTcount: A:0.37, C:0.04, G:0.01, T:0.58
Consensus pattern (18 bp):
TTTAATATTTATATAATT
Found at i:43967 original size:4 final size:4
Alignment explanation
Indices: 43958--43984 Score: 54
Period size: 4 Copynumber: 6.8 Consensus size: 4
43948 TAATCTTCCC
43958 TTTA TTTA TTTA TTTA TTTA TTTA TTT
1 TTTA TTTA TTTA TTTA TTTA TTTA TTT
43985 TTTTTTGGTA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 23 1.00
ACGTcount: A:0.22, C:0.00, G:0.00, T:0.78
Consensus pattern (4 bp):
TTTA
Found at i:44067 original size:3 final size:3
Alignment explanation
Indices: 44059--44085 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
44049 TCAAAGAACA
44059 ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT
44086 TTAGATTCTT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
ATT
Found at i:44454 original size:11 final size:12
Alignment explanation
Indices: 44433--44457 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
44423 CCTTTATTTC
44433 TTTGTTTTTTTT
1 TTTGTTTTTTTT
44445 TTTGTTTTTTTT
1 TTTGTTTTTTTT
44457 T
1 T
44458 AATTTCCTTT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.00, C:0.00, G:0.08, T:0.92
Consensus pattern (12 bp):
TTTGTTTTTTTT
Found at i:44694 original size:16 final size:16
Alignment explanation
Indices: 44666--44707 Score: 59
Period size: 16 Copynumber: 2.6 Consensus size: 16
44656 TAAATTCATT
44666 AAATAATATATTTT-AA
1 AAATAATA-ATTTTGAA
44682 AAATTAATAATTTTGAA
1 AAA-TAATAATTTTGAA
44699 AAATAATAA
1 AAATAATAA
44708 CGTGAAATAA
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
16 14 0.58
17 10 0.42
ACGTcount: A:0.60, C:0.00, G:0.02, T:0.38
Consensus pattern (16 bp):
AAATAATAATTTTGAA
Found at i:46736 original size:37 final size:37
Alignment explanation
Indices: 46688--46764 Score: 127
Period size: 37 Copynumber: 2.1 Consensus size: 37
46678 CCTTATTATA
*
46688 TTTAAAATTAAGATAAAAAAGATATTTTTTATCATCT
1 TTTAAAATTAAGATAAAAAAGATACTTTTTATCATCT
* *
46725 TTTAAAGTTAAGATAAAAAAGATACTTTTTATCATTT
1 TTTAAAATTAAGATAAAAAAGATACTTTTTATCATCT
46762 TTT
1 TTT
46765 TTCGTTCTTA
Statistics
Matches: 37, Mismatches: 3, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
37 37 1.00
ACGTcount: A:0.43, C:0.05, G:0.06, T:0.45
Consensus pattern (37 bp):
TTTAAAATTAAGATAAAAAAGATACTTTTTATCATCT
Found at i:47326 original size:18 final size:17
Alignment explanation
Indices: 47282--47328 Score: 51
Period size: 18 Copynumber: 2.7 Consensus size: 17
47272 AATTATATCG
47282 ATTAAATTTTA-AATTA
1 ATTAAATTTTATAATTA
* *
47298 TTTATAATTTTATATTTAA
1 ATTA-AATTTTATAATT-A
47317 ATTAAATTTTAT
1 ATTAAATTTTAT
47329 TTATTTATTA
Statistics
Matches: 25, Mismatches: 3, Indels: 4
0.78 0.09 0.12
Matches are distributed among these distances:
16 3 0.12
17 7 0.28
18 11 0.44
19 4 0.16
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (17 bp):
ATTAAATTTTATAATTA
Found at i:50969 original size:2 final size:2
Alignment explanation
Indices: 50957--50993 Score: 56
Period size: 2 Copynumber: 18.0 Consensus size: 2
50947 ACACTTTTCT
*
50957 TA TA AA TA TA TA TA TA TA TA TA TA TA TA TA TA CTA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA -TA TA
50994 GAATACAATA
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
2 30 0.94
3 2 0.06
ACGTcount: A:0.51, C:0.03, G:0.00, T:0.46
Consensus pattern (2 bp):
TA
Found at i:51167 original size:22 final size:22
Alignment explanation
Indices: 51139--51183 Score: 74
Period size: 22 Copynumber: 2.0 Consensus size: 22
51129 TTTTTAAAAA
51139 ATATATTTTTAT-ATTAATATTT
1 ATATATTTTTATAATTAAT-TTT
51161 ATATATTTTTATAATTAATTTT
1 ATATATTTTTATAATTAATTTT
51183 A
1 A
51184 AATAAAAATT
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
22 16 0.73
23 6 0.27
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (22 bp):
ATATATTTTTATAATTAATTTT
Found at i:51383 original size:17 final size:17
Alignment explanation
Indices: 51363--51424 Score: 53
Period size: 15 Copynumber: 3.8 Consensus size: 17
51353 TATATAACAC
51363 AAATATATAAAATATT-
1 AAATATATAAAATATTA
51379 AAA-ATATAAAATA-TA
1 AAATATATAAAATATTA
*
51394 AATTAT-TAATAA-ATTA
1 AAATATATAA-AATATTA
*
51410 AAATTTATATAAATA
1 AAATATATA-AAATA
51425 AATATACAAT
Statistics
Matches: 36, Mismatches: 3, Indels: 12
0.71 0.06 0.24
Matches are distributed among these distances:
14 1 0.03
15 16 0.44
16 13 0.36
17 4 0.11
18 2 0.06
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (17 bp):
AAATATATAAAATATTA
Found at i:51442 original size:21 final size:21
Alignment explanation
Indices: 51387--51452 Score: 63
Period size: 21 Copynumber: 3.4 Consensus size: 21
51377 TTAAAATATA
51387 AAATATA-AATTAT--T-AAT
1 AAATATACAATTATAATAAAT
*
51404 AAAT-TAAAATT-TATATAAAT
1 AAATATACAATTATA-ATAAAT
51424 AAATATACAATTATAATAAAT
1 AAATATACAATTATAATAAAT
*
51445 AAAAATAC
1 AAATATAC
51453 GCATGCCCAT
Statistics
Matches: 40, Mismatches: 2, Indels: 10
0.77 0.04 0.19
Matches are distributed among these distances:
16 3 0.08
17 8 0.20
19 1 0.03
20 7 0.17
21 19 0.47
22 2 0.05
ACGTcount: A:0.62, C:0.03, G:0.00, T:0.35
Consensus pattern (21 bp):
AAATATACAATTATAATAAAT
Found at i:52901 original size:18 final size:19
Alignment explanation
Indices: 52880--52916 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
52870 ATTTAATTTT
52880 TTATT-TAAATACTTTTAA
1 TTATTATAAATACTTTTAA
*
52898 TTATTATATATACTTTTAA
1 TTATTATAAATACTTTTAA
52917 ACTGAATGAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 5 0.29
19 12 0.71
ACGTcount: A:0.38, C:0.05, G:0.00, T:0.57
Consensus pattern (19 bp):
TTATTATAAATACTTTTAA
Found at i:52902 original size:36 final size:36
Alignment explanation
Indices: 52814--52903 Score: 84
Period size: 36 Copynumber: 2.6 Consensus size: 36
52804 TTAATTTAAA
52814 TTTTAAATATTA-A-A--ATTAAAATTTAAATTATT
1 TTTTAAATATTATATATTATTAAAATTTAAATTATT
* * *
52846 TTTTAAGTATTATATTTTATTAAAATTT-AATTTTT
1 TTTTAAATATTATATATTATTAAAATTTAAATTATT
*
52881 TATTTAAATACTTTTA-ATTATTA
1 T-TTTAAATA-TTATATATTATTA
52904 TATATACTTT
Statistics
Matches: 46, Mismatches: 6, Indels: 8
0.77 0.10 0.13
Matches are distributed among these distances:
32 11 0.24
33 1 0.02
35 7 0.15
36 23 0.50
37 4 0.09
ACGTcount: A:0.41, C:0.01, G:0.01, T:0.57
Consensus pattern (36 bp):
TTTTAAATATTATATATTATTAAAATTTAAATTATT
Found at i:53682 original size:17 final size:16
Alignment explanation
Indices: 53659--53747 Score: 53
Period size: 17 Copynumber: 5.6 Consensus size: 16
53649 ATTTTTATAT
53659 TTTAAATAAATTTTAA
1 TTTAAATAAATTTTAA
*
53675 TCT---TAAA-TTTATA
1 TTTAAATAAATTTTA-A
* *
53688 CTTAAATAAATTTTTA
1 TTTAAATAAATTTTAA
* * *
53704 TAATAATTAACTTTTAA
1 T-TTAAATAAATTTTAA
53721 TTTAAAATAAAATTTTAA
1 TTT-AAAT-AAATTTTAA
53739 -TTAAATAAA
1 TTTAAATAAA
53748 AATCAAATGA
Statistics
Matches: 53, Mismatches: 12, Indels: 17
0.65 0.15 0.21
Matches are distributed among these distances:
12 4 0.08
13 6 0.11
15 3 0.06
16 12 0.23
17 20 0.38
18 8 0.15
ACGTcount: A:0.49, C:0.03, G:0.00, T:0.47
Consensus pattern (16 bp):
TTTAAATAAATTTTAA
Found at i:53746 original size:16 final size:16
Alignment explanation
Indices: 53679--53748 Score: 52
Period size: 16 Copynumber: 4.2 Consensus size: 16
53669 TTTTAATCTT
*
53679 AAATTTATACTTAAAT-
1 AAATTT-TAATTAAATA
* * *
53695 AAATTTTTATAATAATT
1 AAATTTTAATTA-AATA
*
53712 AACTTTTAATTTAAAATA
1 AAATTTTAA-TT-AAATA
53730 AAATTTTAATTAAATA
1 AAATTTTAATTAAATA
53746 AAA
1 AAA
53749 ATCAAATGAT
Statistics
Matches: 42, Mismatches: 8, Indels: 8
0.72 0.14 0.14
Matches are distributed among these distances:
15 3 0.07
16 17 0.40
17 9 0.21
18 12 0.29
19 1 0.02
ACGTcount: A:0.53, C:0.03, G:0.00, T:0.44
Consensus pattern (16 bp):
AAATTTTAATTAAATA
Found at i:53750 original size:17 final size:18
Alignment explanation
Indices: 53715--53748 Score: 54
Period size: 16 Copynumber: 2.0 Consensus size: 18
53705 AATAATTAAC
53715 TTTTAATTTAAAATAAAA
1 TTTTAATTTAAAATAAAA
53733 TTTTAA-TT-AAATAAAA
1 TTTTAATTTAAAATAAAA
53749 ATCAAATGAT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 8 0.50
17 2 0.12
18 6 0.38
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (18 bp):
TTTTAATTTAAAATAAAA
Found at i:53888 original size:31 final size:32
Alignment explanation
Indices: 53818--53888 Score: 78
Period size: 29 Copynumber: 2.3 Consensus size: 32
53808 AATATTTTAA
53818 TATTTTAATCTTTTATATTTAGATAAAAAAAT
1 TATTTTAATCTTTTATATTTAGATAAAAAAAT
* *
53850 T-TATTAAT-TTTT-TATTTA-ATAATTAAAAT
1 TATTTTAATCTTTTATATTTAGATAA-AAAAAT
53879 TAATTTTAAT
1 T-ATTTTAAT
53889 AATGAAATGA
Statistics
Matches: 33, Mismatches: 3, Indels: 7
0.77 0.07 0.16
Matches are distributed among these distances:
28 4 0.12
29 12 0.36
30 4 0.12
31 12 0.36
32 1 0.03
ACGTcount: A:0.42, C:0.01, G:0.01, T:0.55
Consensus pattern (32 bp):
TATTTTAATCTTTTATATTTAGATAAAAAAAT
Found at i:55163 original size:18 final size:16
Alignment explanation
Indices: 55140--55174 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 16
55130 ATATGTTTAA
55140 ATTTTTAATTAATTTTTT
1 ATTTTTAA-T-ATTTTTT
55158 ATTTTTAATATTTTTT
1 ATTTTTAATATTTTTT
55174 A
1 A
55175 AAAATATTTG
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 8 0.47
17 1 0.06
18 8 0.47
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (16 bp):
ATTTTTAATATTTTTT
Found at i:55310 original size:11 final size:11
Alignment explanation
Indices: 55289--55328 Score: 55
Period size: 11 Copynumber: 3.5 Consensus size: 11
55279 ATTCTATATA
55289 TTTTTCGTTTTC
1 TTTTTC-TTTTC
55301 TTTTTCTTTTC
1 TTTTTCTTTTC
55312 TTTTT-TTTTAC
1 TTTTTCTTTT-C
55323 TTTTTC
1 TTTTTC
55329 CATGTTAAAA
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
10 4 0.15
11 16 0.62
12 6 0.23
ACGTcount: A:0.03, C:0.15, G:0.03, T:0.80
Consensus pattern (11 bp):
TTTTTCTTTTC
Found at i:55514 original size:48 final size:46
Alignment explanation
Indices: 55449--55540 Score: 109
Period size: 48 Copynumber: 2.0 Consensus size: 46
55439 GATGAATCAA
*
55449 TATAATTATTAATTTAAAATTT-ATTAAAA-ATTATTTTATATTAATATT
1 TATAATTAATAATTT-AAATTTAATTAAAATA-T-TTTTA-ATTAATATT
55497 TATAATTTAATAA-TTAAATTTAATTAAAATATTTTTAATTAATA
1 TATAA-TTAATAATTTAAATTTAATTAAAATATTTTTAATTAATA
55541 AATAATAATT
Statistics
Matches: 40, Mismatches: 1, Indels: 8
0.82 0.02 0.16
Matches are distributed among these distances:
46 7 0.17
47 11 0.28
48 15 0.38
49 7 0.17
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (46 bp):
TATAATTAATAATTTAAATTTAATTAAAATATTTTTAATTAATATT
Found at i:55776 original size:6 final size:6
Alignment explanation
Indices: 55765--55817 Score: 52
Period size: 6 Copynumber: 8.2 Consensus size: 6
55755 TTATGTTTAA
* *
55765 AAATTT AAATTT AAATTT AGATTA AAATTTT AAAATTTT AAATTTT AAATTT
1 AAATTT AAATTT AAATTT AAATTT AAA-TTT -AAA-TTT AAA-TTT AAATTT
55817 A
1 A
55818 TGATCTTTAA
Statistics
Matches: 41, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
6 22 0.54
7 12 0.29
8 7 0.17
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (6 bp):
AAATTT
Found at i:56584 original size:2 final size:2
Alignment explanation
Indices: 56577--56613 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
56567 GATTTTGATT
56577 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
56614 AAAAAATCCC
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.00, C:0.49, G:0.00, T:0.51
Consensus pattern (2 bp):
TC
Done.