Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01000257.1 Hibiscus syriacus cultivar Beakdansim tig00000470_pilon, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 89565
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:947 original size:25 final size:25
Alignment explanation
Indices: 897--947 Score: 68
Period size: 25 Copynumber: 2.0 Consensus size: 25
887 CTCAAATAAA
* *
897 TAGTTTAGTACAATATTTTAGTTTT
1 TAGTTTAGTACAATATTTCAGATTT
922 TAGTTTAGTACAAATATTTCA-ATTT
1 TAGTTTAGTAC-AATATTTCAGATTT
947 T
1 T
948 GAAGATTGAA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
25 15 0.65
26 8 0.35
ACGTcount: A:0.31, C:0.06, G:0.10, T:0.53
Consensus pattern (25 bp):
TAGTTTAGTACAATATTTCAGATTT
Found at i:947 original size:26 final size:25
Alignment explanation
Indices: 897--947 Score: 75
Period size: 26 Copynumber: 2.0 Consensus size: 25
887 CTCAAATAAA
* *
897 TAGTTTAGTACAATATTTTAGTTTT
1 TAGTTTAGTACAATATTTCAATTTT
922 TAGTTTAGTACAAATATTTCAATTTT
1 TAGTTTAGTAC-AATATTTCAATTTT
948 GAAGATTGAA
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
25 11 0.48
26 12 0.52
ACGTcount: A:0.31, C:0.06, G:0.10, T:0.53
Consensus pattern (25 bp):
TAGTTTAGTACAATATTTCAATTTT
Found at i:3271 original size:24 final size:24
Alignment explanation
Indices: 3246--3293 Score: 62
Period size: 24 Copynumber: 2.0 Consensus size: 24
3236 TCAAAATATA
3246 TTATAATTATAATATTATTA-ATTAT
1 TTATAATT-TAATATT-TTACATTAT
*
3271 TTATTATTTAATATTTTACATTA
1 TTATAATTTAATATTTTACATTA
3294 ATTTTCATTA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
23 3 0.14
24 11 0.52
25 7 0.33
ACGTcount: A:0.40, C:0.02, G:0.00, T:0.58
Consensus pattern (24 bp):
TTATAATTTAATATTTTACATTAT
Found at i:7635 original size:31 final size:31
Alignment explanation
Indices: 7595--7655 Score: 104
Period size: 31 Copynumber: 2.0 Consensus size: 31
7585 AACACCAAAT
*
7595 TATATATGAGTTTAGAGTGAGTTACATTTGG
1 TATAGATGAGTTTAGAGTGAGTTACATTTGG
*
7626 TATAGATGAGTTTAGAGTGAGTTACCTTTG
1 TATAGATGAGTTTAGAGTGAGTTACATTTG
7656 CTTACTAACT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
31 28 1.00
ACGTcount: A:0.28, C:0.05, G:0.26, T:0.41
Consensus pattern (31 bp):
TATAGATGAGTTTAGAGTGAGTTACATTTGG
Found at i:8364 original size:32 final size:32
Alignment explanation
Indices: 8301--8364 Score: 74
Period size: 32 Copynumber: 2.0 Consensus size: 32
8291 GGGCATTACA
* **
8301 CAGATAATGCACAACAGAGTCAGTGTTGCATT
1 CAGAAAATGCACAACAGAGTCAGTGACGCATT
** *
8333 CAGAAAATGCACATGAGTGTCAGTGACGCATT
1 CAGAAAATGCACAACAGAGTCAGTGACGCATT
8365 TAGGTAATGC
Statistics
Matches: 26, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
32 26 1.00
ACGTcount: A:0.34, C:0.19, G:0.23, T:0.23
Consensus pattern (32 bp):
CAGAAAATGCACAACAGAGTCAGTGACGCATT
Found at i:11362 original size:84 final size:84
Alignment explanation
Indices: 11044--11918 Score: 897
Period size: 84 Copynumber: 10.4 Consensus size: 84
11034 GAATTTGACA
* * * * * * **
11044 TGCCCTTGAGCTGAATGGAATCGAACTCGAAGGT-ATTTGTTGACAGATAACCCTTTTTACCTTG
1 TGCCTTTGAGCTGAGTGTAATCGAACTCGAAGGTCTTTTGTTGATAGATAACCCTTCTCGCCTTG
* * ** *
11108 AGTTATACTATAAATTTGATT
66 AGCTATGCTGCAAA--TGATG
* * * * ** * * *
11129 TACCTCTGAGCTGAATATAATCGAACTTAAAGGTC-TTGGCTGACAGATAACCCTTCTCGCCTTG
1 TGCCTTTGAGCTGAGTGTAATCGAACTCGAAGGTCTTTTGTTGATAGATAACCCTTCTCGCCTTG
* * **
11193 AGTTATGCTGTAAAATTGACA
66 AGCTATGCTG-CAAA-TGATG
* * *
11214 TGCCTTTGAGCTAAATGTAATCGAACTCGAAGGTCTTTTGTTG-TAGATAGCCCTTCTCGCCTTG
1 TGCCTTTGAGCTGAGTGTAATCGAACTCGAAGGTCTTTTGTTGATAGATAACCCTTCTCGCCTTG
*
11278 AGCTATGTTGCAAATGATG
66 AGCTATGCTGCAAATGATG
* ** * * *
11297 TGCATTTTTGCTGAGGGTAATCAAACTCGAAGGTCTTTAGTTGATAGATAACCCTTCTCGCCTTG
1 TGCCTTTGAGCTGAGTGTAATCGAACTCGAAGGTCTTTTGTTGATAGATAACCCTTCTCGCCTTG
* * *
11362 AGTTATGATGTAAATTGGATG
66 AGCTATGCTGCAAA-T-GATG
* **
11383 TGCCTTTGAGCTGAGTGTAATCGAACTCGAAGGTCTTTTGTTGGTAGATAACTGTTCTCGCCTTG
1 TGCCTTTGAGCTGAGTGTAATCGAACTCGAAGGTCTTTTGTTGATAGATAACCCTTCTCGCCTTG
11448 AGCTATGCTGCAAATGATG
66 AGCTATGCTGCAAATGATG
* * *
11467 TGCCTTTGAGCTGAGTGTAATCGAACTCGAAGGTC-TTGGTTAATAGATAACCCTTATCGCCTTG
1 TGCCTTTGAGCTGAGTGTAATCGAACTCGAAGGTCTTTTGTTGATAGATAACCCTTCTCGCCTTG
* **
11531 AGTTATGCTATAAATTAGATG
66 AGCTATGCTGCAAA-T-GATG
**
11552 TGCCTTTGAGCTGAGTGTAATCGAACTCGAAGGTCTTTTGTTGGCAGATAACCCTTCTCGCCTTG
1 TGCCTTTGAGCTGAGTGTAATCGAACTCGAAGGTCTTTTGTTGATAGATAACCCTTCTCGCCTTG
*
11617 AGCTATGTTGCAAATGATG
66 AGCTATGCTGCAAATGATG
* ** * * *
11636 TGCCTTTGAGCTGAGTGTAATCGAACTTGAAGGTCTTTTGTTGGCATATAGCCCTTCTCTCCTTG
1 TGCCTTTGAGCTGAGTGTAATCGAACTCGAAGGTCTTTTGTTGATAGATAACCCTTCTCGCCTTG
*
11701 AGCTATACTGCAAATGATG
66 AGCTATGCTGCAAATGATG
* * * *
11720 TGCCTTTGAGCTGAGTGTAATTGAACTCGAAGGTC-TTGGTTGATAGATAATCATTCTCGCCTTG
1 TGCCTTTGAGCTGAGTGTAATCGAACTCGAAGGTCTTTTGTTGATAGATAACCCTTCTCGCCTTG
* * *
11784 AGTTATGTTGTAAATTAGATG
66 AGCTATGCTGCAAA-T-GATG
* * * * *
11805 TTCTTTTGAGCTGAGTGTAATC-AA-AC-AA-GTCTTTTGTTGA-ACGATAACCCTTATCACCTT
1 TGCCTTTGAGCTGAGTGTAATCGAACTCGAAGGTCTTTTGTTGATA-GATAACCCTTCTCGCCTT
* ** * *
11865 TAGCTACACTACAAATGATA
65 GAGCTATGCTGCAAATGATG
*
11885 TGCCTTTGAGCTGAGTGTATTCGAACTCGAAGGT
1 TGCCTTTGAGCTGAGTGTAATCGAACTCGAAGGT
11919 TGTCCGCTCG
Statistics
Matches: 658, Mismatches: 115, Indels: 35
0.81 0.14 0.04
Matches are distributed among these distances:
80 22 0.03
81 7 0.01
82 32 0.05
83 106 0.16
84 194 0.29
85 184 0.28
86 113 0.17
ACGTcount: A:0.25, C:0.18, G:0.22, T:0.35
Consensus pattern (84 bp):
TGCCTTTGAGCTGAGTGTAATCGAACTCGAAGGTCTTTTGTTGATAGATAACCCTTCTCGCCTTG
AGCTATGCTGCAAATGATG
Found at i:11389 original size:169 final size:169
Alignment explanation
Indices: 11044--11918 Score: 896
Period size: 169 Copynumber: 5.2 Consensus size: 169
11034 GAATTTGACA
* * * * ** * **
11044 TGCCCTTGAGCTGAATGGAATCGAACTCGAAGGT-ATTTGTTGACAGATAACCCTTTTTACCTTG
1 TGCCTTTGAGCTGAGTGTAATCGAACTCGAAGGTCTTTTGTTGGTAGATAACCCTTCTCGCCTTG
* ** ** * * * * * * ** * *
11108 AGTTATACTATAAATTTGATTTACCTCTGAGCTGAATATAATCGAACTTAAAGGTC-TTGGCTGA
66 AGCTATGTTGCAAA--TGATGTGCCTTTGAGCTGAGTGTAATCAAACTCGAAGGTCTTTAGTTGA
* * **
11172 CAGATAACCCTTCTCGCCTTGAGTTATGCTGTAAAATTGACA
129 TAGATAACCCTTCTCGCCTTGAGTTATGATGT-AAATTGATG
* * *
11214 TGCCTTTGAGCTAAATGTAATCGAACTCGAAGGTCTTTTGTT-GTAGATAGCCCTTCTCGCCTTG
1 TGCCTTTGAGCTGAGTGTAATCGAACTCGAAGGTCTTTTGTTGGTAGATAACCCTTCTCGCCTTG
* ** *
11278 AGCTATGTTGCAAATGATGTGCATTTTTGCTGAGGGTAATCAAACTCGAAGGTCTTTAGTTGATA
66 AGCTATGTTGCAAATGATGTGCCTTTGAGCTGAGTGTAATCAAACTCGAAGGTCTTTAGTTGATA
11343 GATAACCCTTCTCGCCTTGAGTTATGATGTAAATTGGATG
131 GATAACCCTTCTCGCCTTGAGTTATGATGTAAATT-GATG
**
11383 TGCCTTTGAGCTGAGTGTAATCGAACTCGAAGGTCTTTTGTTGGTAGATAACTGTTCTCGCCTTG
1 TGCCTTTGAGCTGAGTGTAATCGAACTCGAAGGTCTTTTGTTGGTAGATAACCCTTCTCGCCTTG
* * * *
11448 AGCTATGCTGCAAATGATGTGCCTTTGAGCTGAGTGTAATCGAACTCGAAGGTC-TTGGTTAATA
66 AGCTATGTTGCAAATGATGTGCCTTTGAGCTGAGTGTAATCAAACTCGAAGGTCTTTAGTTGATA
* * *
11512 GATAACCCTTATCGCCTTGAGTTATGCTATAAATTAGATG
131 GATAACCCTTCTCGCCTTGAGTTATGATGTAAATT-GATG
*
11552 TGCCTTTGAGCTGAGTGTAATCGAACTCGAAGGTCTTTTGTTGGCAGATAACCCTTCTCGCCTTG
1 TGCCTTTGAGCTGAGTGTAATCGAACTCGAAGGTCTTTTGTTGGTAGATAACCCTTCTCGCCTTG
* * * **
11617 AGCTATGTTGCAAATGATGTGCCTTTGAGCTGAGTGTAATCGAACTTGAAGGTCTTTTGTTGGCA
66 AGCTATGTTGCAAATGATGTGCCTTTGAGCTGAGTGTAATCAAACTCGAAGGTCTTTAGTTGATA
* * * * *
11682 TATAGCCCTTCTCTCCTTGAGCTAT-ACTGCAAA-TGATG
131 GATAACCCTTCTCGCCTTGAGTTATGA-TGTAAATTGATG
* * * * *
11720 TGCCTTTGAGCTGAGTGTAATTGAACTCGAAGGTC-TTGGTTGATAGATAATCATTCTCGCCTTG
1 TGCCTTTGAGCTGAGTGTAATCGAACTCGAAGGTCTTTTGTTGGTAGATAACCCTTCTCGCCTTG
* * * * *
11784 AGTTATGTTGTAAATTAGATGTTCTTTTGAGCTGAGTGTAATCAAA--C-AA-GTCTTTTGTTGA
66 AGCTATGTTGCAAA-T-GATGTGCCTTTGAGCTGAGTGTAATCAAACTCGAAGGTCTTTAGTTGA
* * * * * * * *
11845 -ACGATAACCCTTATCACCTTTAGCTA-CA-CTACAAATGATA
129 TA-GATAACCCTTCTCGCCTTGAGTTATGATGTA-AATTGATG
*
11885 TGCCTTTGAGCTGAGTGTATTCGAACTCGAAGGT
1 TGCCTTTGAGCTGAGTGTAATCGAACTCGAAGGT
11919 TGTCCGCTCG
Statistics
Matches: 603, Mismatches: 90, Indels: 29
0.84 0.12 0.04
Matches are distributed among these distances:
163 1 0.00
164 3 0.00
165 67 0.11
166 2 0.00
167 36 0.06
168 72 0.12
169 263 0.44
170 153 0.25
171 6 0.01
ACGTcount: A:0.25, C:0.18, G:0.22, T:0.35
Consensus pattern (169 bp):
TGCCTTTGAGCTGAGTGTAATCGAACTCGAAGGTCTTTTGTTGGTAGATAACCCTTCTCGCCTTG
AGCTATGTTGCAAATGATGTGCCTTTGAGCTGAGTGTAATCAAACTCGAAGGTCTTTAGTTGATA
GATAACCCTTCTCGCCTTGAGTTATGATGTAAATTGATG
Found at i:11529 original size:253 final size:252
Alignment explanation
Indices: 11052--11918 Score: 959
Period size: 253 Copynumber: 3.4 Consensus size: 252
11042 CATGCCCTTG
* * * * * * *
11052 AGCTGAATGGAATCGAACTCGAAGGT-ATTTGTTGACAGATAACCCTTTTTACCTTGAGTTAT-A
1 AGCTGAGTGTAATCAAACTCGAAGGTCTTTTGTTGACAGATAACCCTTCTCACCTTGAGCTATGA
* * * * * * ** * * *
11115 CTATAAATTTGATTTACCTCTGAGCTGAATATAATCGAACTTAAAGGTC-TTGGCTGACAGATAA
66 -TGTAAA-TTGATGTGCCTTTGAGCTGAGTGTAATCGAACTCGAAGGTCTTTTGTTGGCAGATAA
* * ** * *
11179 CCCTTCTCGCCTTGAGTTATGCTGTAAAATTGACATGCCTTTGAGCTAAATGTAATCGAACTCGA
129 CCCTTCTCGCCTTGAGCTATGCTG-CAAA-TGATGTGCCTTTGAGCTGAGTGTAATCGAACTCGA
* * * * *
11244 AGGTCTTTTGTTGTAGATAGCCCTTCTCGCCTTGAGCTATGTTGCAAA-T-GATGTGCATTTT
192 AGGTC-TTGGTTATAGATAACCCTTCTCGCCTTGAGTTATGTTGTAAATTAGATGTGC-TTTT
* * * * * *
11305 TGCTGAGGGTAATCAAACTCGAAGGTCTTTAGTTGATAGATAACCCTTCTCGCCTTGAGTTATGA
1 AGCTGAGTGTAATCAAACTCGAAGGTCTTTTGTTGACAGATAACCCTTCTCACCTTGAGCTATGA
*
11370 TGTAAATTGGATGTGCCTTTGAGCTGAGTGTAATCGAACTCGAAGGTCTTTTGTTGGTAGATAAC
66 TGTAAATT-GATGTGCCTTTGAGCTGAGTGTAATCGAACTCGAAGGTCTTTTGTTGGCAGATAAC
**
11435 TGTTCTCGCCTTGAGCTATGCTGCAAATGATGTGCCTTTGAGCTGAGTGTAATCGAACTCGAAGG
130 CCTTCTCGCCTTGAGCTATGCTGCAAATGATGTGCCTTTGAGCTGAGTGTAATCGAACTCGAAGG
* * * *
11500 TCTTGGTTAATAGATAACCCTTATCGCCTTGAGTTATGCTATAAATTAGATGTGCCTTTG
195 TCTTGGTT-ATAGATAACCCTTCTCGCCTTGAGTTATGTTGTAAATTAGATGTG-CTTTT
* * * *
11560 AGCTGAGTGTAATCGAACTCGAAGGTCTTTTGTTGGCAGATAACCCTTCTCGCCTTGAGCTATGT
1 AGCTGAGTGTAATCAAACTCGAAGGTCTTTTGTTGACAGATAACCCTTCTCACCTTGAGCTATGA
* * * *
11625 TGCAAA-TGATGTGCCTTTGAGCTGAGTGTAATCGAACTTGAAGGTCTTTTGTTGGCATATAGCC
66 TGTAAATTGATGTGCCTTTGAGCTGAGTGTAATCGAACTCGAAGGTCTTTTGTTGGCAGATAACC
* * *
11689 CTTCTCTCCTTGAGCTATACTGCAAATGATGTGCCTTTGAGCTGAGTGTAATTGAACTCGAAGGT
131 CTTCTCGCCTTGAGCTATGCTGCAAATGATGTGCCTTTGAGCTGAGTGTAATCGAACTCGAAGGT
* * *
11754 CTTGGTTGATAGATAATCATTCTCGCCTTGAGTTATGTTGTAAATTAGATGTTCTTTT
196 CTTGGTT-ATAGATAACCCTTCTCGCCTTGAGTTATGTTGTAAATTAGATGTGCTTTT
* *
11812 GAGCTGAGTGTAATCAAA--C-AA-GTCTTTTGTTGA-ACGATAACCCTTATCACCTTTAGCTA-
1 -AGCTGAGTGTAATCAAACTCGAAGGTCTTTTGTTGACA-GATAACCCTTCTCACCTTGAGCTAT
* * * * *
11871 CA-CTACAAATGATATGCCTTTGAGCTGAGTGTATTCGAACTCGAAGGT
64 GATGTA-AATTGATGTGCCTTTGAGCTGAGTGTAATCGAACTCGAAGGT
11919 TGTCCGCTCG
Statistics
Matches: 524, Mismatches: 78, Indels: 28
0.83 0.12 0.04
Matches are distributed among these distances:
247 1 0.00
248 3 0.01
249 68 0.13
250 2 0.00
251 1 0.00
252 9 0.02
253 263 0.50
254 72 0.14
255 104 0.20
256 1 0.00
ACGTcount: A:0.25, C:0.18, G:0.22, T:0.35
Consensus pattern (252 bp):
AGCTGAGTGTAATCAAACTCGAAGGTCTTTTGTTGACAGATAACCCTTCTCACCTTGAGCTATGA
TGTAAATTGATGTGCCTTTGAGCTGAGTGTAATCGAACTCGAAGGTCTTTTGTTGGCAGATAACC
CTTCTCGCCTTGAGCTATGCTGCAAATGATGTGCCTTTGAGCTGAGTGTAATCGAACTCGAAGGT
CTTGGTTATAGATAACCCTTCTCGCCTTGAGTTATGTTGTAAATTAGATGTGCTTTT
Found at i:13927 original size:86 final size:86
Alignment explanation
Indices: 13779--13948 Score: 214
Period size: 86 Copynumber: 2.0 Consensus size: 86
13769 TCTTGGTTGA
** ** * * *
13779 CAGATAACCATTCTCGCCTTGAGTTATGCTGTAAATTGGATGTGTATTTGAGTTGAGTGTAATCA
1 CAGATAACCATTCTCGCCTTGAGCCATGCTACAAATTGGATGTGCATTTGAGCTGAGGGTAATCA
13844 AACTCGAAGGTCTTTTGTTAG
66 AACTCGAAGGTCTTTTGTTAG
* * * **
13865 CAGATAACCCTTCTCGCCTTGAGCCATGCTACAAATTTGATGTGCCTTTGAGCTGAGGGTAATTG
1 CAGATAACCATTCTCGCCTTGAGCCATGCTACAAATTGGATGTGCATTTGAGCTGAGGGTAATCA
* *
13930 AACTCGAATGTTTTTTGTT
66 AACTCGAAGGTCTTTTGTT
13949 GAAGATGCTT
Statistics
Matches: 70, Mismatches: 14, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
86 70 1.00
ACGTcount: A:0.24, C:0.17, G:0.22, T:0.36
Consensus pattern (86 bp):
CAGATAACCATTCTCGCCTTGAGCCATGCTACAAATTGGATGTGCATTTGAGCTGAGGGTAATCA
AACTCGAAGGTCTTTTGTTAG
Found at i:14958 original size:96 final size:96
Alignment explanation
Indices: 14789--14990 Score: 318
Period size: 96 Copynumber: 2.1 Consensus size: 96
14779 GGACAGATCA
* *
14789 ATAT-TATAATCACCTTTATCAGGCTAGCTGACTATTATCCATAAAGCCGGGGCGTTTAGCCAAT
1 ATATATATAATCACCTTTATCAGGCTAGCTGAATATTATCCATAAAGCCGGGGCGTTTAACCAAT
14853 TACATTAGAGGGACAACTCAAGCTTTATTGT
66 TACATTAGAGGGACAACTCAAGCTTTATTGT
* *
14884 AT-TATAATAATCACCTTTATCAGGCTAGCTGAATCTTATCCATAAAGCTGGGGCGTTTAACCAA
1 ATATAT-ATAATCACCTTTATCAGGCTAGCTGAATATTATCCATAAAGCCGGGGCGTTTAACCAA
* * *
14948 TTTCTTTAGAGGGACAGCTCAAGCTTTATTGT
65 TTACATTAGAGGGACAACTCAAGCTTTATTGT
14980 ATATATATAAT
1 ATATATATAAT
14991 ATTATAATAT
Statistics
Matches: 97, Mismatches: 7, Indels: 5
0.89 0.06 0.05
Matches are distributed among these distances:
94 1 0.01
95 3 0.03
96 90 0.93
97 3 0.03
ACGTcount: A:0.31, C:0.18, G:0.17, T:0.34
Consensus pattern (96 bp):
ATATATATAATCACCTTTATCAGGCTAGCTGAATATTATCCATAAAGCCGGGGCGTTTAACCAAT
TACATTAGAGGGACAACTCAAGCTTTATTGT
Found at i:22160 original size:22 final size:22
Alignment explanation
Indices: 22135--22184 Score: 57
Period size: 21 Copynumber: 2.3 Consensus size: 22
22125 TTCTCGACGG
22135 TGAAAATGAGTTTCTGAGATAA
1 TGAAAATGAGTTTCTGAGATAA
* * *
22157 TGAAGA-GAGTTTTTGGGATAA
1 TGAAAATGAGTTTCTGAGATAA
*
22178 AGAAAAT
1 TGAAAAT
22185 AAAAAGGAAA
Statistics
Matches: 22, Mismatches: 5, Indels: 2
0.76 0.17 0.07
Matches are distributed among these distances:
21 17 0.77
22 5 0.23
ACGTcount: A:0.42, C:0.02, G:0.26, T:0.30
Consensus pattern (22 bp):
TGAAAATGAGTTTCTGAGATAA
Found at i:23859 original size:61 final size:60
Alignment explanation
Indices: 23816--23941 Score: 207
Period size: 61 Copynumber: 2.1 Consensus size: 60
23806 ATGACACGTA
*
23816 ATCACACTGGGCACATGACAAAGTAATGTCATTACTTTTAGACATGTGACATGTAAGATAT
1 ATCACACTGGGCACATGACAAAGTAATGTCATTAC-TTTAGACACGTGACATGTAAGATAT
* * *
23877 ATCACATTGGGCACATGACAAAGTAATGTCATTACTTTAGACATGTGACATGTAAAATAT
1 ATCACACTGGGCACATGACAAAGTAATGTCATTACTTTAGACACGTGACATGTAAGATAT
23937 ATCAC
1 ATCAC
23942 TTTAGATAGA
Statistics
Matches: 63, Mismatches: 2, Indels: 1
0.95 0.03 0.02
Matches are distributed among these distances:
60 29 0.46
61 34 0.54
ACGTcount: A:0.37, C:0.17, G:0.17, T:0.29
Consensus pattern (60 bp):
ATCACACTGGGCACATGACAAAGTAATGTCATTACTTTAGACACGTGACATGTAAGATAT
Found at i:23926 original size:30 final size:30
Alignment explanation
Indices: 23831--23926 Score: 81
Period size: 30 Copynumber: 3.2 Consensus size: 30
23821 ACTGGGCACA
23831 TGACAAAGTAATGTCATTACTTTTAGACATG
1 TGACAAAGTAATGTCATTAC-TTTAGACATG
* * * * **
23862 TGAC-ATGTAA-GAT-ATATCACATTGGGCACA
1 TGACAAAGTAATG-TCAT-T-ACTTTAGACATG
23892 TGACAAAGTAATGTCATTACTTTAGACATG
1 TGACAAAGTAATGTCATTACTTTAGACATG
23922 TGACA
1 TGACA
23927 TGTAAAATAT
Statistics
Matches: 47, Mismatches: 12, Indels: 13
0.65 0.17 0.18
Matches are distributed among these distances:
29 3 0.06
30 28 0.60
31 13 0.28
32 3 0.06
ACGTcount: A:0.36, C:0.15, G:0.18, T:0.31
Consensus pattern (30 bp):
TGACAAAGTAATGTCATTACTTTAGACATG
Found at i:23944 original size:30 final size:30
Alignment explanation
Indices: 23852--23947 Score: 79
Period size: 30 Copynumber: 3.2 Consensus size: 30
23842 TGTCATTACT
*
23852 TTTAGACATGTGACATGTAAGATATATCAC
1 TTTAGACATGTGACATGTAAAATATATCAC
* * * ** * * *
23882 ATTGGGCACATGACAAAGT--AATGTCATTAC
1 TTTAGACATGTGAC-ATGTAAAATAT-ATCAC
23912 TTTAGACATGTGACATGTAAAATATATCAC
1 TTTAGACATGTGACATGTAAAATATATCAC
23942 TTTAGA
1 TTTAGA
23948 TAGATAACCT
Statistics
Matches: 45, Mismatches: 17, Indels: 8
0.64 0.24 0.11
Matches are distributed among these distances:
29 6 0.13
30 32 0.71
31 7 0.16
ACGTcount: A:0.38, C:0.14, G:0.17, T:0.32
Consensus pattern (30 bp):
TTTAGACATGTGACATGTAAAATATATCAC
Found at i:25482 original size:85 final size:85
Alignment explanation
Indices: 25383--25700 Score: 197
Period size: 87 Copynumber: 3.7 Consensus size: 85
25373 GCCATTCAAT
* * * *
25383 TTTTTAACTTTATAATTGAGG-TC-TAAAATTTTATCAATC-CTAGTTTTTATATTTATAATTGA
1 TTTTTAACTTTATAATTAAGGCCCTTAAAA-TTT-TCAATCTCT-CTTTTTACATTTATAATTGA
25445 -ATCCCTTAATTTTTTAATCTAAA
63 GATCCC-TAATTTTTTAATCTAAA
* *
25468 TTTTT-ACATTTATAATTAAGGCCCTTAAAATTTTCAATCTCTCTTTTTACCTTTATAATTGAGG
1 TTTTTAAC-TTTATAATTAAGGCCCTTAAAATTTTCAATCTCTCTTTTTACATTTATAATTGAGA
* * *
25532 TCCCTAATTTTTTTCAATATCAC
65 TCCCTAA-TTTTTT-AATCTAAA
* * * *** * * * *
25555 TTTCT-ACTTTTATAATTAAAGCCCCTAGTTTTTTTAATCTCACTTTTTACTTTTATAGTTGAGA
1 TTTTTAAC-TTTATAATTAAGGCCCTTAAAATTTTCAATCTCTCTTTTTACATTTATAATTGAGA
* * *
25619 -CTCCTAATTTTTTTAATTTCAC
65 TC-CCTAA-TTTTTTAATCTAAA
* * ** * *
25641 CTTTT-ACATTTATAATTGAA-TCCCTTAATTTTTTTAATCTAAT-TTTTTACATTTATAATT
1 TTTTTAAC-TTTATAATT-AAGGCCCTTAAAATTTTCAATCT-CTCTTTTTACATTTATAATT
25701 AAGGCCCTTA
Statistics
Matches: 191, Mismatches: 32, Indels: 19
0.79 0.13 0.08
Matches are distributed among these distances:
84 2 0.01
85 43 0.23
86 70 0.37
87 76 0.40
ACGTcount: A:0.29, C:0.15, G:0.05, T:0.52
Consensus pattern (85 bp):
TTTTTAACTTTATAATTAAGGCCCTTAAAATTTTCAATCTCTCTTTTTACATTTATAATTGAGAT
CCCTAATTTTTTAATCTAAA
Found at i:25523 original size:43 final size:43
Alignment explanation
Indices: 25434--25885 Score: 343
Period size: 43 Copynumber: 10.5 Consensus size: 43
25424 AGTTTTTATA
* * * *
25434 TTTATAATTGAA-TCCCTTAATTTTTT-AATCTAAATTTTTACA
1 TTTATAATT-AAGGCCCTTAATTTTTTCAATCTCACTTTTTACC
** *
25476 TTTATAATTAAGGCCCTTAAAATTTTCAATCTCTCTTTTTACC
1 TTTATAATTAAGGCCCTTAATTTTTTCAATCTCACTTTTTACC
* * * *
25519 TTTATAATTGAGGTCCC-TAATTTTTTTCAATATCACTTTCTACT
1 TTTATAATTAAGG-CCCTTAA-TTTTTTCAATCTCACTTTTTACC
* * * * *
25563 TTTATAATTAAAGCCCCTAGTTTTTTTAATCTCACTTTTTACT
1 TTTATAATTAAGGCCCTTAATTTTTTCAATCTCACTTTTTACC
* * * * * * *
25606 TTTATAGTTGAGACTCC-TAATTTTTTTAATTTCACCTTTTACA
1 TTTATAATTAAGGC-CCTTAATTTTTTCAATCTCACTTTTTACC
* * * * *
25649 TTTATAATTGAA-TCCCTTAATTTTTTTAATCTAATTTTTTACA
1 TTTATAATT-AAGGCCCTTAATTTTTTCAATCTCACTTTTTACC
* *
25692 TTTATAATTAAGGCCCTTAAATTTTTCAATCTCTCTTTTTTACC
1 TTTATAATTAAGGCCCTTAATTTTTTCAATCTCAC-TTTTTACC
* ** *
25736 TTTATAATTGAGG-TTTCTAATTTTTTCAATCTCACTTTCT-CC
1 TTTATAATTAAGGCCCT-TAATTTTTTCAATCTCACTTTTTACC
*
25778 TTTTATAATTGAA-GCCCTTGATTTTTT-AATCTCACTTTTTACC
1 -TTTATAATT-AAGGCCCTTAATTTTTTCAATCTCACTTTTTACC
* ** * * *
25821 TTCATAATTGAAATCCC-TAA-TTTTTCAATATAACTTTTTACT
1 TTTATAATT-AAGGCCCTTAATTTTTTCAATCTCACTTTTTACC
*
25863 TTTATAATTTAGGACCC-TAATTT
1 TTTATAATTAAGG-CCCTTAATTT
25886 AATCATTTTC
Statistics
Matches: 328, Mismatches: 63, Indels: 37
0.77 0.15 0.09
Matches are distributed among these distances:
41 8 0.02
42 78 0.24
43 169 0.52
44 73 0.22
ACGTcount: A:0.27, C:0.17, G:0.05, T:0.51
Consensus pattern (43 bp):
TTTATAATTAAGGCCCTTAATTTTTTCAATCTCACTTTTTACC
Found at i:25601 original size:87 final size:85
Alignment explanation
Indices: 25434--25885 Score: 365
Period size: 87 Copynumber: 5.3 Consensus size: 85
25424 AGTTTTTATA
** * * * * * **
25434 TTTATAATTGAATCCCTTAA-TTTTTTAATCTAAATTTTTACATTTATAATTAAGGCCCTTAAAA
1 TTTATAATTGAGGCCC-TAATTTTTTTAATCTCACTTTTTACCTTTATAATTAAAGCCCCTAATT
*
25498 TTTTCAATCTCTCTTTTTACC
65 TTTTCAATCTCACTTTTTACC
* * * *
25519 TTTATAATTGAGGTCCCTAATTTTTTTCAATATCACTTTCTACTTTTATAATTAAAGCCCCTAGT
1 TTTATAATTGAGG-CCCTAATTTTTTT-AATCTCACTTTTTACCTTTATAATTAAAGCCCCTAAT
* *
25584 TTTTTTAATCTCACTTTTTACT
64 TTTTTCAATCTCACTTTTTACC
* * * * * * * *
25606 TTTATAGTTGAGACTCCTAATTTTTTTAATTTCACCTTTTACATTTATAATTGAATCCCTTAATT
1 TTTATAATTGAGGC-CCTAATTTTTTTAATCTCACTTTTTACCTTTATAATTAAAGCCCCTAATT
* * * *
25671 TTTTTAATCTAATTTTTTACA
65 TTTTCAATCTCACTTTTTACC
* * * * * * ***
25692 TTTATAATTAAGGCCCTTAAATTTTTCAATCTCTCTTTTTTACCTTTATAATTGAGGTTTCTAAT
1 TTTATAATTGAGGCCC-TAATTTTTTTAATCTCAC-TTTTTACCTTTATAATTAAAGCCCCTAAT
*
25757 TTTTTCAATCTCACTTTCT-CC
64 TTTTTCAATCTCACTTTTTACC
* * * *
25778 TTTTATAATTGAAGCCCTTGA-TTTTTTAATCTCACTTTTTACCTTCATAATTGAAA-TCCCTAA
1 -TTTATAATTGAGGCCC-TAATTTTTTTAATCTCACTTTTTACCTTTATAATT-AAAGCCCCTAA
* * *
25841 -TTTTTCAATATAACTTTTTACT
63 TTTTTTCAATCTCACTTTTTACC
*
25863 TTTATAATTTAGGACCCTAATTT
1 TTTATAATTGAGG-CCCTAATTT
25886 AATCATTTTC
Statistics
Matches: 291, Mismatches: 65, Indels: 22
0.77 0.17 0.06
Matches are distributed among these distances:
84 29 0.10
85 43 0.15
86 97 0.33
87 122 0.42
ACGTcount: A:0.27, C:0.17, G:0.05, T:0.51
Consensus pattern (85 bp):
TTTATAATTGAGGCCCTAATTTTTTTAATCTCACTTTTTACCTTTATAATTAAAGCCCCTAATTT
TTTCAATCTCACTTTTTACC
Found at i:25653 original size:130 final size:127
Alignment explanation
Indices: 25426--25885 Score: 401
Period size: 130 Copynumber: 3.6 Consensus size: 127
25416 TCAATCCTAG
* * * * * * * * * *
25426 TTTTTATATTTATAATTGAATCCCTTAATTTTTTAATCTAAATTTTTACATTTATAATTAAGGC-
1 TTTTTACATTTATAATTAAAGCCCCTAATTTTTCAATCTCACTTTTTACTTTTATAATTGAGACT
** * * *
25490 CCTTAAAATTTTCAATCTCTCTTTTTACCTTTATAATTGAGGTCCC-TAATTTTTTTCAATATCA
66 CC-TAATTTTTTCAATCTCAC-TTTTACATTTATAATTGA-GTCCCTTAATTTTTTT-AATCTCA
25554 C
127 C
* * * * *
25555 TTTCTACTTTTATAATTAAAGCCCCTAGTTTTTTTAATCTCACTTTTTACTTTTATAGTTGAGAC
1 TTTTTACATTTATAATTAAAGCCCCTA-ATTTTTCAATCTCACTTTTTACTTTTATAATTGAGAC
* * * * *
25620 TCCTAATTTTTTTAATTTCACCTTTTACATTTATAATTGAATCCCTTAATTTTTTTAATCTAAT
65 TCCTAATTTTTTCAATCTCA-CTTTTACATTTATAATTGAGTCCCTTAATTTTTTTAATCTCAC
* * * * *
25684 TTTTTACATTTATAATTAAGGCCCTTAAATTTTTCAATCTCTCTTTTTTACCTTTATAATTGAGG
1 TTTTTACATTTATAATTAAAGCCCCT-AATTTTTCAATCTCAC-TTTTTACTTTTATAATTGAGA
* * * * *
25749 TTTCTAATTTTTTCAATCTCACTTTCTCCTTTTATAATTGAAG-CCCTTGA-TTTTTTAATCTCA
64 CTCCTAATTTTTTCAATCTCACTTT-TACATTTATAATTG-AGTCCCTTAATTTTTTTAATCTCA
25812 C
127 C
* * * * * *
25813 TTTTTACCTTCATAATTGAAA-TCCCTAATTTTTCAATATAACTTTTTACTTTTATAATTTAGGA
1 TTTTTACATTTATAATT-AAAGCCCCTAATTTTTCAATCTCACTTTTTACTTTTATAATTGA-GA
25877 C-CCTAATTT
64 CTCCTAATTT
25886 AATCATTTTC
Statistics
Matches: 265, Mismatches: 56, Indels: 22
0.77 0.16 0.06
Matches are distributed among these distances:
127 24 0.09
128 14 0.05
129 98 0.37
130 125 0.47
131 4 0.02
ACGTcount: A:0.27, C:0.17, G:0.05, T:0.51
Consensus pattern (127 bp):
TTTTTACATTTATAATTAAAGCCCCTAATTTTTCAATCTCACTTTTTACTTTTATAATTGAGACT
CCTAATTTTTTCAATCTCACTTTTACATTTATAATTGAGTCCCTTAATTTTTTTAATCTCAC
Found at i:34754 original size:20 final size:20
Alignment explanation
Indices: 34729--34779 Score: 75
Period size: 20 Copynumber: 2.5 Consensus size: 20
34719 TTAAGCAAAC
*
34729 CTTTAGATTTTTTGATCAAT
1 CTTTAGATTTTTAGATCAAT
* *
34749 CTTTAGATTTTTAGGTTAAT
1 CTTTAGATTTTTAGATCAAT
34769 CTTTAGATTTT
1 CTTTAGATTTT
34780 CAAGTCAACT
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 28 1.00
ACGTcount: A:0.24, C:0.08, G:0.12, T:0.57
Consensus pattern (20 bp):
CTTTAGATTTTTAGATCAAT
Found at i:34956 original size:64 final size:64
Alignment explanation
Indices: 34878--34998 Score: 242
Period size: 64 Copynumber: 1.9 Consensus size: 64
34868 TTTCACATTC
34878 TCAAATTTAAAGCTAGAAATTTTAATTTAATCGATCAAATCAATAAATCTTTAAAATCAAGAAT
1 TCAAATTTAAAGCTAGAAATTTTAATTTAATCGATCAAATCAATAAATCTTTAAAATCAAGAAT
34942 TCAAATTTAAAGCTAGAAATTTTAATTTAATCGATCAAATCAATAAATCTTTAAAAT
1 TCAAATTTAAAGCTAGAAATTTTAATTTAATCGATCAAATCAATAAATCTTTAAAAT
34999 AAAATTTTTT
Statistics
Matches: 57, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
64 57 1.00
ACGTcount: A:0.48, C:0.11, G:0.06, T:0.36
Consensus pattern (64 bp):
TCAAATTTAAAGCTAGAAATTTTAATTTAATCGATCAAATCAATAAATCTTTAAAATCAAGAAT
Found at i:35152 original size:2 final size:2
Alignment explanation
Indices: 35145--35169 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
35135 ATAAATGAGT
35145 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
35170 GATAAAAATA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:35760 original size:19 final size:19
Alignment explanation
Indices: 35736--35775 Score: 71
Period size: 19 Copynumber: 2.1 Consensus size: 19
35726 CAATTCATAC
35736 AATCATTAATTTTTAACAA
1 AATCATTAATTTTTAACAA
*
35755 AATCATTATTTTTTAACAA
1 AATCATTAATTTTTAACAA
35774 AA
1 AA
35776 CAAAATGAAT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.47, C:0.10, G:0.00, T:0.42
Consensus pattern (19 bp):
AATCATTAATTTTTAACAA
Found at i:35893 original size:29 final size:29
Alignment explanation
Indices: 35860--35924 Score: 69
Period size: 29 Copynumber: 2.2 Consensus size: 29
35850 ACAATATTCT
35860 ATAGTCGGATA-ACCATTATATAACTTTTG
1 ATAGTCGGA-AGACCATTATATAACTTTTG
* ** * *
35889 ATAGTTGGAAGATTATTTTGTAACTTTTG
1 ATAGTCGGAAGACCATTATATAACTTTTG
35918 ATAGTCG
1 ATAGTCG
35925 AGAGATTTCA
Statistics
Matches: 29, Mismatches: 6, Indels: 2
0.78 0.16 0.05
Matches are distributed among these distances:
28 1 0.03
29 28 0.97
ACGTcount: A:0.31, C:0.09, G:0.18, T:0.42
Consensus pattern (29 bp):
ATAGTCGGAAGACCATTATATAACTTTTG
Found at i:36012 original size:22 final size:22
Alignment explanation
Indices: 35971--36012 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
35961 TTTCATTAAA
*
35971 TTTATCATTTGTTGACTTTTTT
1 TTTATCATTTGTTGAATTTTTT
* *
35993 TTTATCATTTTTTTAATTTT
1 TTTATCATTTGTTGAATTTT
36013 GATTCATTAT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 17 1.00
ACGTcount: A:0.17, C:0.07, G:0.05, T:0.71
Consensus pattern (22 bp):
TTTATCATTTGTTGAATTTTTT
Found at i:39862 original size:41 final size:42
Alignment explanation
Indices: 39817--40032 Score: 173
Period size: 41 Copynumber: 5.4 Consensus size: 42
39807 TTTGTGGCGT
* *
39817 AAACGCCACTAAAGTACGAGTCTATAGCGACATTTATATAA-
1 AAACGCCACTAAAGTACGAGTCTATAGCGGCGTTTATATAAG
* *
39858 AAACGCCACTAAA-TACGAGTCTATAGCGGTGTTTGTA-AAG
1 AAACGCCACTAAAGTACGAGTCTATAGCGGCGTTTATATAAG
* * * * * *
39898 AAATGCCACTAAAGTATGAGTCTTTAGCGGCGTTTTTAGAAT
1 AAACGCCACTAAAGTACGAGTCTATAGCGGCGTTTATATAAG
* * * * *
39940 AAATGCCACTAAATTA-TAATCTTTAGCGGCGTTTATATAA-
1 AAACGCCACTAAAGTACGAGTCTATAGCGGCGTTTATATAAG
* * * *
39980 AAACGCTACT--AGTA-TAGTCTTTAGCGGTGTTTATA-AA-
1 AAACGCCACTAAAGTACGAGTCTATAGCGGCGTTTATATAAG
**
40017 AAACATCACTAAAGTA
1 AAACGCCACTAAAGTA
40033 TAAGTATTTA
Statistics
Matches: 147, Mismatches: 23, Indels: 12
0.81 0.13 0.07
Matches are distributed among these distances:
37 9 0.06
38 22 0.15
39 6 0.04
40 40 0.27
41 53 0.36
42 17 0.12
ACGTcount: A:0.37, C:0.16, G:0.17, T:0.30
Consensus pattern (42 bp):
AAACGCCACTAAAGTACGAGTCTATAGCGGCGTTTATATAAG
Found at i:40001 original size:38 final size:38
Alignment explanation
Indices: 39817--40051 Score: 166
Period size: 40 Copynumber: 5.9 Consensus size: 38
39807 TTTGTGGCGT
* * * *
39817 AAACGCCACTAAAGTACGAGTCTATAGCGACATTTATATAA
1 AAACGCCACT-AAGTA-TAGTCTTTAGCGGCGTTTATA-AA
* * * * *
39858 AAACGCCACTAAATACGAGTCTATAGCGGTGTTTGTAAA
1 AAACGCCACTAAGTA-TAGTCTTTAGCGGCGTTTATAAA
* *
39897 GAAATGCCACTAAAGTATGAGTCTTTAGCGGCGTTTTTAGAA
1 -AAACGCCACT-AAGTAT-AGTCTTTAGCGGCGTTTATA-AA
* * *
39939 TAAATGCCACTAAATTATAATCTTTAGCGGCGTTTATATAA
1 -AAACGCCACT-AAGTATAGTCTTTAGCGGCGTTTATA-AA
* *
39980 AAACGCTACT-AGTATAGTCTTTAGCGGTGTTTATAAA
1 AAACGCCACTAAGTATAGTCTTTAGCGGCGTTTATAAA
** * *
40017 AAACATCACTAAAGTATAAGTATTTAGCGGTGTTT
1 AAACGCCACT-AAGTAT-AGTCTTTAGCGGCGTTT
40052 GTTCTTAAAA
Statistics
Matches: 162, Mismatches: 25, Indels: 15
0.80 0.12 0.07
Matches are distributed among these distances:
37 9 0.06
38 22 0.14
39 7 0.04
40 55 0.34
41 51 0.31
42 18 0.11
ACGTcount: A:0.36, C:0.15, G:0.18, T:0.31
Consensus pattern (38 bp):
AAACGCCACTAAGTATAGTCTTTAGCGGCGTTTATAAA
Found at i:40071 original size:119 final size:121
Alignment explanation
Indices: 39816--40051 Score: 280
Period size: 122 Copynumber: 2.0 Consensus size: 121
39806 ATTTGTGGCG
* * * * * *
39816 TAAACGCCACTAAAGTACGAGTCTATAGCGACATTTATATAAAAACGCCACTAAATACGAGTCTA
1 TAAACGCCACTAAATTA-TAATCTTTAGCGGCGTTTATATAAAAACGCCACTAAATACGAGTCTA
* * * *
39881 TAGCGGTGTTTGTAAAGAAATGCCACTAAAGTATGAGTCTTTAGCGGCGTTTTTAGAA
65 TAGCGGTGTTTATAAAAAAAT-CCACTAAAGTATAAGTATTTAGCGGCGTTTTTAGAA
* * * * *
39939 TAAATGCCACTAAATTATAATCTTTAGCGGCGTTTATATAAAAACGCTACT-AGTA-TAGTCTTT
1 TAAACGCCACTAAATTATAATCTTTAGCGGCGTTTATATAAAAACGCCACTAAATACGAGTCTAT
*
40002 AGCGGTGTTTATAAAAAACAT-CACTAAAGTATAAGTATTTAGCGGTGTTT
66 AGCGGTGTTTATAAAAAA-ATCCACTAAAGTATAAGTATTTAGCGGCGTTT
40052 GTTCTTAAAA
Statistics
Matches: 96, Mismatches: 16, Indels: 6
0.81 0.14 0.05
Matches are distributed among these distances:
119 26 0.27
120 22 0.23
121 5 0.05
122 28 0.29
123 15 0.16
ACGTcount: A:0.36, C:0.15, G:0.18, T:0.31
Consensus pattern (121 bp):
TAAACGCCACTAAATTATAATCTTTAGCGGCGTTTATATAAAAACGCCACTAAATACGAGTCTAT
AGCGGTGTTTATAAAAAAATCCACTAAAGTATAAGTATTTAGCGGCGTTTTTAGAA
Found at i:41058 original size:2 final size:2
Alignment explanation
Indices: 41051--41112 Score: 124
Period size: 2 Copynumber: 31.0 Consensus size: 2
41041 AATTATTGTA
41051 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
41093 AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT
41113 GTGGATCCAT
Statistics
Matches: 60, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 60 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:45703 original size:20 final size:20
Alignment explanation
Indices: 45678--45829 Score: 144
Period size: 23 Copynumber: 7.2 Consensus size: 20
45668 CACAAAATAA
*
45678 TATATGAATAGTACCGATAC
1 TATATGAATAGTATCGATAC
*
45698 TATATGAACAGTA-CTGATAC
1 TATATGAATAGTATC-GATAC
*
45718 TATATGAATAATATCGATAC
1 TATATGAATAGTATCGATAC
*
45738 TGTATGAACAGTAGTATCGATAC
1 TATATG-A-A-TAGTATCGATAC
*
45761 TGTATGAACAATAGTATCGATAC
1 TATATG---AATAGTATCGATAC
45784 TATATGAACAATAGTATCGATAC
1 TATATG---AATAGTATCGATAC
* *
45807 TATATGAACAATATCGATAC
1 TATATGAATAGTATCGATAC
45827 TAT
1 TAT
45830 CAAGCCCAAC
Statistics
Matches: 116, Mismatches: 9, Indels: 14
0.83 0.06 0.10
Matches are distributed among these distances:
19 1 0.01
20 53 0.46
21 2 0.02
22 1 0.01
23 57 0.49
24 1 0.01
25 1 0.01
ACGTcount: A:0.41, C:0.13, G:0.14, T:0.32
Consensus pattern (20 bp):
TATATGAATAGTATCGATAC
Found at i:45758 original size:23 final size:23
Alignment explanation
Indices: 45684--45819 Score: 169
Period size: 23 Copynumber: 6.2 Consensus size: 23
45674 ATAATATATG
*
45684 AATAGTACCGATACTATATGAAC
1 AATAGTATCGATACTATATGAAC
45707 ---AGTA-CTGATACTATATG---
1 AATAGTATC-GATACTATATGAAC
* *
45724 AATAATATCGATACTGTATGAAC
1 AATAGTATCGATACTATATGAAC
* *
45747 AGTAGTATCGATACTGTATGAAC
1 AATAGTATCGATACTATATGAAC
45770 AATAGTATCGATACTATATGAAC
1 AATAGTATCGATACTATATGAAC
45793 AATAGTATCGATACTATATGAAC
1 AATAGTATCGATACTATATGAAC
45816 AATA
1 AATA
45820 TCGATACTAT
Statistics
Matches: 99, Mismatches: 6, Indels: 16
0.82 0.05 0.13
Matches are distributed among these distances:
19 1 0.01
20 28 0.28
21 1 0.01
23 69 0.70
ACGTcount: A:0.42, C:0.13, G:0.15, T:0.30
Consensus pattern (23 bp):
AATAGTATCGATACTATATGAAC
Found at i:47088 original size:23 final size:24
Alignment explanation
Indices: 47053--47097 Score: 65
Period size: 23 Copynumber: 1.9 Consensus size: 24
47043 GATTTCAAAA
**
47053 TTTAAAATTTAAAAT-GATTTTCT
1 TTTAAAAGCTAAAATGGATTTTCT
47076 TTTAAAAGCTAAAATGGATTTT
1 TTTAAAAGCTAAAATGGATTTT
47098 GAAAACCAAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
23 13 0.68
24 6 0.32
ACGTcount: A:0.40, C:0.04, G:0.09, T:0.47
Consensus pattern (24 bp):
TTTAAAAGCTAAAATGGATTTTCT
Found at i:48390 original size:20 final size:20
Alignment explanation
Indices: 48325--48392 Score: 66
Period size: 20 Copynumber: 3.2 Consensus size: 20
48315 TGAGCACAAA
**
48325 ATACTGTATGAACAAAACTG
1 ATACTGTATGAACAGTACTG
*
48345 ATATTGTATGAACAATAGTA-TCG
1 ATACTGTATGAAC---AGTACT-G
48368 ATACTGTATGAACAGTACTG
1 ATACTGTATGAACAGTACTG
48388 ATACT
1 ATACT
48393 CAAAATTCCA
Statistics
Matches: 39, Mismatches: 4, Indels: 10
0.74 0.08 0.19
Matches are distributed among these distances:
20 22 0.56
21 1 0.03
22 1 0.03
23 15 0.38
ACGTcount: A:0.40, C:0.13, G:0.16, T:0.31
Consensus pattern (20 bp):
ATACTGTATGAACAGTACTG
Found at i:51640 original size:23 final size:23
Alignment explanation
Indices: 51593--51744 Score: 204
Period size: 23 Copynumber: 6.8 Consensus size: 23
51583 TGGAGTCATT
*
51593 TGGTCCTTCGGGAC-A-TATATG
1 TGGTCCTTCGGGACAATTCTATG
51614 TGGTCCTTCGGGACAATTCTATG
1 TGGTCCTTCGGGACAATTCTATG
*
51637 TGGTCTTTCGGGACAATTCTATG
1 TGGTCCTTCGGGACAATTCTATG
* *
51660 TGGTCATTCGGGACATTTCTATG
1 TGGTCCTTCGGGACAATTCTATG
* *
51683 TGGTCATTCGGGACATTTCTATG
1 TGGTCCTTCGGGACAATTCTATG
* *
51706 TGGTCCTTCTGGAC-A-TATATG
1 TGGTCCTTCGGGACAATTCTATG
51727 TGGTCCTTCGGGACAATT
1 TGGTCCTTCGGGACAATT
51745 TTACGAGGTT
Statistics
Matches: 118, Mismatches: 9, Indels: 6
0.89 0.07 0.05
Matches are distributed among these distances:
21 32 0.27
22 2 0.02
23 84 0.71
ACGTcount: A:0.18, C:0.19, G:0.26, T:0.37
Consensus pattern (23 bp):
TGGTCCTTCGGGACAATTCTATG
Found at i:51670 original size:46 final size:46
Alignment explanation
Indices: 51593--51767 Score: 196
Period size: 46 Copynumber: 3.9 Consensus size: 46
51583 TGGAGTCATT
* *
51593 TGGTCCTTCGGGAC-A-TATATGTGGTCCTTCGGGACAATTCTATG
1 TGGTCCTTCGGGACAATTCTATGTGGTCATTCGGGACAATTCTATG
* *
51637 TGGTCTTTCGGGACAATTCTATGTGGTCATTCGGGACATTTCTATG
1 TGGTCCTTCGGGACAATTCTATGTGGTCATTCGGGACAATTCTATG
* * * * *
51683 TGGTCATTCGGGACATTTCTATGTGGTCCTTCTGGAC-A-TATATG
1 TGGTCCTTCGGGACAATTCTATGTGGTCATTCGGGACAATTCTATG
* * * * *
51727 TGGTCCTTCGGGACAATTTTACGAGGTTATTCGAGACAATT
1 TGGTCCTTCGGGACAATTCTATGTGGTCATTCGGGACAATT
51768 TTATATGGCA
Statistics
Matches: 108, Mismatches: 19, Indels: 6
0.81 0.14 0.05
Matches are distributed among these distances:
44 46 0.43
45 2 0.02
46 60 0.56
ACGTcount: A:0.19, C:0.18, G:0.26, T:0.37
Consensus pattern (46 bp):
TGGTCCTTCGGGACAATTCTATGTGGTCATTCGGGACAATTCTATG
Found at i:54456 original size:19 final size:18
Alignment explanation
Indices: 54422--54474 Score: 72
Period size: 19 Copynumber: 2.8 Consensus size: 18
54412 TATAAAATTC
54422 GAATTATAAATTTATTTAGT
1 GAATT-TAAATTTATTT-GT
54442 -AATTTAAATTGTATTTGT
1 GAATTTAAATT-TATTTGT
54460 GAATTTAAATTTATT
1 GAATTTAAATTTATT
54475 AAATAATTAA
Statistics
Matches: 31, Mismatches: 0, Indels: 6
0.84 0.00 0.16
Matches are distributed among these distances:
18 12 0.39
19 19 0.61
ACGTcount: A:0.38, C:0.00, G:0.09, T:0.53
Consensus pattern (18 bp):
GAATTTAAATTTATTTGT
Found at i:56941 original size:16 final size:16
Alignment explanation
Indices: 56920--56950 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
56910 CAAGAATCTT
56920 TGTTCAAAACCATTAG
1 TGTTCAAAACCATTAG
56936 TGTTCAAAACCATTA
1 TGTTCAAAACCATTA
56951 TTGTGAATTG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.39, C:0.19, G:0.10, T:0.32
Consensus pattern (16 bp):
TGTTCAAAACCATTAG
Found at i:64516 original size:37 final size:37
Alignment explanation
Indices: 64466--64770 Score: 149
Period size: 38 Copynumber: 8.6 Consensus size: 37
64456 TTAAATTGGT
*
64466 TTTTGAAACATATATATATAATATAATTTTTAAAAATA
1 TTTTGAAA-ATATATATATAATATAATTTTGAAAAATA
*
64504 TTTTGAAAATATATATA-ATATATAGTTTTGAAAATATA
1 TTTTGAAAATATATATATA-ATATAATTTTGAAAA-ATA
* * * *
64542 TATT----ATATAGT-TTTAA-AAACATTTT-TAAAA-A
1 TTTTGAAAATATA-TATATAATATA-ATTTTGAAAAATA
* * *
64573 -----AATATATATA-AT-ATATAGTTTTGGAAAATA
1 TTTTGAAAATATATATATAATATAATTTTGAAAAATA
*
64603 TTTTGAAAATGTATATA-ATATATAATTTTGAAAAATA
1 TTTTGAAAATATATATATA-ATATAATTTTGAAAAATA
* *
64640 TTTTTGGAAATGTATATA-ATATATAATTTTGAAAAATA
1 -TTTTGAAAATATATATATA-ATATAATTTTGAAAAATA
** **
64678 TTTTTCAAA-ATATAT-T-ATATGGTTTT-AAAAATAA
1 TTTTGAAAATATATATATAATATAATTTTGAAAAAT-A
* *
64712 TTTTTGAAAATATATAT-T-ATATAGTTTTGAAAATAAA
1 -TTTTGAAAATATATATATAATATAATTTTGAAAA-ATA
**
64749 TTTT-AAAA-GCATATATAATATA
1 TTTTGAAAATATATATATAATATA
64771 TGGTTTTAAA
Statistics
Matches: 211, Mismatches: 27, Indels: 60
0.71 0.09 0.20
Matches are distributed among these distances:
28 5 0.02
29 8 0.04
30 6 0.03
31 1 0.00
32 1 0.00
33 11 0.05
34 24 0.11
35 22 0.10
36 32 0.15
37 50 0.24
38 51 0.24
ACGTcount: A:0.48, C:0.01, G:0.07, T:0.44
Consensus pattern (37 bp):
TTTTGAAAATATATATATAATATAATTTTGAAAAATA
Found at i:64541 original size:21 final size:23
Alignment explanation
Indices: 64504--64560 Score: 78
Period size: 23 Copynumber: 2.4 Consensus size: 23
64494 TTTAAAAATA
*
64504 TTTTGAAAATATATATAATATATAG
1 TTTT-AAAA-ATATATATTATATAG
*
64529 TTTTGAAAATATATATTATATAG
1 TTTTAAAAATATATATTATATAG
64552 TTTTAAAAA
1 TTTTAAAAA
64561 CATTTTTAAA
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
23 22 0.76
24 3 0.10
25 4 0.14
ACGTcount: A:0.47, C:0.00, G:0.07, T:0.46
Consensus pattern (23 bp):
TTTTAAAAATATATATTATATAG
Found at i:64548 original size:23 final size:24
Alignment explanation
Indices: 64504--64560 Score: 89
Period size: 25 Copynumber: 2.4 Consensus size: 24
64494 TTTAAAAATA
64504 TTTTGAAAATATATATAATATATAG
1 TTTTGAAAATATATAT-ATATATAG
64529 TTTTGAAAATATATAT-TATATAG
1 TTTTGAAAATATATATATATATAG
*
64552 TTTTAAAAA
1 TTTTGAAAA
64561 CATTTTTAAA
Statistics
Matches: 31, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
23 15 0.48
25 16 0.52
ACGTcount: A:0.47, C:0.00, G:0.07, T:0.46
Consensus pattern (24 bp):
TTTTGAAAATATATATATATATAG
Found at i:64576 original size:62 final size:62
Alignment explanation
Indices: 64466--64603 Score: 183
Period size: 62 Copynumber: 2.2 Consensus size: 62
64456 TTAAATTGGT
* *
64466 TTTTGAAACATATATATATAATATAATTTTTAAAAATATTTTGAAAATATATATAATATATAG
1 TTTTGAAA-ATATATATATAATATAATTTTAAAAAATATTTTAAAAATATATATAATATATAG
*
64529 TTTTGAAAATATATAT-T-ATATAGTTTTAAAAACAT-TTTTAAAAAAATATATATAATATATAG
1 TTTTGAAAATATATATATAATATAATTTTAAAAA-ATATTTT--AAAAATATATATAATATATAG
64591 TTTTGGAAAATAT
1 TTTT-GAAAATAT
64604 TTTGAAAATG
Statistics
Matches: 68, Mismatches: 3, Indels: 8
0.86 0.04 0.10
Matches are distributed among these distances:
60 17 0.25
61 3 0.04
62 32 0.47
63 16 0.24
ACGTcount: A:0.49, C:0.01, G:0.06, T:0.44
Consensus pattern (62 bp):
TTTTGAAAATATATATATAATATAATTTTAAAAAATATTTTAAAAATATATATAATATATAG
Found at i:64654 original size:38 final size:37
Alignment explanation
Indices: 64529--64790 Score: 238
Period size: 38 Copynumber: 7.1 Consensus size: 37
64519 TAATATATAG
* *
64529 TTTTGAAA-ATATATATTATATAGTTTT-AAAAACAT
1 TTTTGAAATATATATAATATATAGTTTTGAAAAATAT
* *
64564 TTTTAAAAAAATATATATAATATATAGTTTTGGAAAATA-
1 TTTT---GAAATATATATAATATATAGTTTTGAAAAATAT
* *
64603 TTTTGAAAATGTATATAATATATAATTTTGAAAAATAT
1 TTTTG-AAATATATATAATATATAGTTTTGAAAAATAT
* *
64641 TTTTGGAAATGTATATAATATATAATTTTGAAAAATAT
1 TTTT-GAAATATATATAATATATAGTTTTGAAAAATAT
* *
64679 TTTTCAAA-ATATAT--TATATGGTTTT-AAAAATAAT
1 TTTTGAAATATATATAATATATAGTTTTGAAAAAT-AT
* *
64713 TTTTGAAA-ATATATATTATATAGTTTTG-AAAATAAA
1 TTTTGAAATATATATAATATATAGTTTTGAAAAAT-AT
* * *
64749 TTTTAAAAGCATATATAATATATGGTTTT-AAAAATGAT
1 TTTTGAAA-TATATATAATATATAGTTTTGAAAAAT-AT
64787 TTTT
1 TTTT
64791 ATTTTTATTA
Statistics
Matches: 192, Mismatches: 20, Indels: 27
0.80 0.08 0.11
Matches are distributed among these distances:
33 6 0.03
34 24 0.12
35 4 0.02
36 29 0.15
37 31 0.16
38 70 0.36
39 23 0.12
40 5 0.03
ACGTcount: A:0.46, C:0.01, G:0.08, T:0.45
Consensus pattern (37 bp):
TTTTGAAATATATATAATATATAGTTTTGAAAAATAT
Found at i:64828 original size:22 final size:21
Alignment explanation
Indices: 64789--64835 Score: 58
Period size: 22 Copynumber: 2.2 Consensus size: 21
64779 AAAATGATTT
64789 TTATTTTTATTATATATTATA
1 TTATTTTTATTATATATTATA
* * *
64810 TTATTTGTTTTTATTTATTATT
1 TTATTT-TTATTATATATTATA
64832 TTAT
1 TTAT
64836 GAATATTTTT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
21 6 0.27
22 16 0.73
ACGTcount: A:0.26, C:0.00, G:0.02, T:0.72
Consensus pattern (21 bp):
TTATTTTTATTATATATTATA
Found at i:65621 original size:13 final size:13
Alignment explanation
Indices: 65603--65636 Score: 59
Period size: 13 Copynumber: 2.6 Consensus size: 13
65593 CCCTTAGGTG
65603 TTTTGGCTCTCGA
1 TTTTGGCTCTCGA
*
65616 TTTTGGCTCTCGG
1 TTTTGGCTCTCGA
65629 TTTTGGCT
1 TTTTGGCT
65637 TATGGGTGAC
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 20 1.00
ACGTcount: A:0.03, C:0.21, G:0.26, T:0.50
Consensus pattern (13 bp):
TTTTGGCTCTCGA
Found at i:66207 original size:5 final size:5
Alignment explanation
Indices: 66186--66259 Score: 59
Period size: 5 Copynumber: 15.0 Consensus size: 5
66176 CCTTTTTTCT
* *
66186 TTTTA -TTTA GTTT- TTTTA TTTTA TTTTA TACTTA TTTTA -TTTA TTTTTA
1 TTTTA TTTTA TTTTA TTTTA TTTTA TTTTA T-TTTA TTTTA TTTTA -TTTTA
66235 TTTT- TTATT- TTTTA TTTTTA TTTTA
1 TTTTA TT-TTA TTTTA -TTTTA TTTTA
66260 ATATTTTAAT
Statistics
Matches: 58, Mismatches: 3, Indels: 16
0.75 0.04 0.21
Matches are distributed among these distances:
4 15 0.26
5 30 0.52
6 13 0.22
ACGTcount: A:0.19, C:0.01, G:0.01, T:0.78
Consensus pattern (5 bp):
TTTTA
Found at i:66207 original size:6 final size:6
Alignment explanation
Indices: 66179--66302 Score: 60
Period size: 6 Copynumber: 19.2 Consensus size: 6
66169 AATTTAACCT
* *
66179 TTTTTC TTTTTA TTTAGTT- TTTTTA -TTTTA TTTTATA CTTATTT- TATTTA
1 TTTTTA TTTTTA TTT--TTA TTTTTA TTTTTA TTTT-TA -TT-TTTA TTTTTA
66229 TTTTTA TTTTTTA TTTTTTA TTTTTA TTTTAATA TTTTAATA TTTTAATA
1 TTTTTA -TTTTTA -TTTTTA TTTTTA TTTT--TA TTTT--TA TTTT--TA
*
66279 TTTTT- TTTCTT- TTTTTA TATTTA T
1 TTTTTA TTT-TTA TTTTTA TTTTTA T
66303 ATATTTCACA
Statistics
Matches: 101, Mismatches: 4, Indels: 26
0.77 0.03 0.20
Matches are distributed among these distances:
5 15 0.15
6 39 0.39
7 18 0.18
8 27 0.27
9 2 0.02
ACGTcount: A:0.20, C:0.02, G:0.01, T:0.77
Consensus pattern (6 bp):
TTTTTA
Found at i:66225 original size:21 final size:18
Alignment explanation
Indices: 66197--66258 Score: 72
Period size: 20 Copynumber: 3.2 Consensus size: 18
66187 TTTATTTAGT
66197 TTTTTTATTTTATTTTATA
1 TTTTTTATTTTATTTT-TA
66216 CTTATTTTA-TTTATTTTTA
1 -TT-TTTTATTTTATTTTTA
66235 TTTTTTATTTTTTATTTTTA
1 TTTTTTA--TTTTATTTTTA
66255 TTTT
1 TTTT
66259 AATATTTTAA
Statistics
Matches: 38, Mismatches: 0, Indels: 8
0.83 0.00 0.17
Matches are distributed among these distances:
17 5 0.13
18 2 0.05
19 2 0.05
20 24 0.63
21 5 0.13
ACGTcount: A:0.18, C:0.02, G:0.00, T:0.81
Consensus pattern (18 bp):
TTTTTTATTTTATTTTTA
Found at i:66233 original size:51 final size:52
Alignment explanation
Indices: 66178--66292 Score: 125
Period size: 51 Copynumber: 2.2 Consensus size: 52
66168 AAATTTAACC
*
66178 TTTTTTCTTTTTATTTAGTT-TTTTTATTTT-AT-TTTATACTTATTTT-AT-TT
1 TTTTTTCTTTTTATTT-GTTATTTTTATTTTAATATTT-TA-ATATTTTAATATT
*
66228 ATTTTTAT-TTTTTATTTTTTATTTTTATTTTAATATTTTAATATTTTAATATT
1 -TTTTT-TCTTTTTATTTGTTATTTTTATTTTAATATTTTAATATTTTAATATT
66281 TTTTTTCTTTTT
1 TTTTTTCTTTTT
66293 TTATATTTAT
Statistics
Matches: 55, Mismatches: 2, Indels: 13
0.79 0.03 0.19
Matches are distributed among these distances:
50 2 0.04
51 31 0.56
52 17 0.31
53 5 0.09
ACGTcount: A:0.19, C:0.03, G:0.01, T:0.77
Consensus pattern (52 bp):
TTTTTTCTTTTTATTTGTTATTTTTATTTTAATATTTTAATATTTTAATATT
Found at i:66256 original size:35 final size:34
Alignment explanation
Indices: 66186--66302 Score: 91
Period size: 33 Copynumber: 3.5 Consensus size: 34
66176 CCTTTTTTCT
**
66186 TTTTATTTAGTTTTT-TTATTTTA-TTTTATACTTA
1 TTTTATTTA-TTTTTATT-TTTTATTTTTATTTTTA
66220 TTTTATTTATTTTTATTTTTTATTTTTTATTTTTA
1 TTTTATTTATTTTTATTTTTTA-TTTTTATTTTTA
* * * * *
66255 TTTTA-ATATTTTAATATTTTAATATTT-TTTTTC
1 TTTTATTTATTTTTAT-TTTTTATTTTTATTTTTA
*
66288 TTTT-TTTATATTTAT
1 TTTTATTTATTTTTAT
66303 ATATTTCACA
Statistics
Matches: 68, Mismatches: 10, Indels: 11
0.76 0.11 0.12
Matches are distributed among these distances:
33 26 0.38
34 23 0.34
35 19 0.28
ACGTcount: A:0.21, C:0.02, G:0.01, T:0.76
Consensus pattern (34 bp):
TTTTATTTATTTTTATTTTTTATTTTTATTTTTA
Found at i:66264 original size:8 final size:8
Alignment explanation
Indices: 66253--66282 Score: 60
Period size: 8 Copynumber: 3.8 Consensus size: 8
66243 TTTTTATTTT
66253 TATTTTAA
1 TATTTTAA
66261 TATTTTAA
1 TATTTTAA
66269 TATTTTAA
1 TATTTTAA
66277 TATTTT
1 TATTTT
66283 TTTTCTTTTT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 22 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (8 bp):
TATTTTAA
Found at i:66307 original size:35 final size:37
Alignment explanation
Indices: 66240--66308 Score: 92
Period size: 37 Copynumber: 1.9 Consensus size: 37
66230 TTTTATTTTT
66240 TATTTTTTATTTTTATTTTAATATTTTAATATTTTAA
1 TATTTTTTATTTTTATTTTAATATTTTAATATTTTAA
66277 TATTTTTT-TTCTTT-TTTT-ATA-TTTATATATTT
1 TATTTTTTATT-TTTATTTTAATATTTTA-ATATTT
66309 CACAATTTAA
Statistics
Matches: 30, Mismatches: 0, Indels: 6
0.83 0.00 0.17
Matches are distributed among these distances:
34 4 0.13
35 9 0.30
36 6 0.20
37 11 0.37
ACGTcount: A:0.25, C:0.01, G:0.00, T:0.74
Consensus pattern (37 bp):
TATTTTTTATTTTTATTTTAATATTTTAATATTTTAA
Found at i:66402 original size:12 final size:13
Alignment explanation
Indices: 66380--66408 Score: 51
Period size: 12 Copynumber: 2.3 Consensus size: 13
66370 CAAATCAAGT
66380 TTTTAAATTTTAA
1 TTTTAAATTTTAA
66393 TTTT-AATTTTAA
1 TTTTAAATTTTAA
66405 TTTT
1 TTTT
66409 CGCAATTAAG
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 12 0.75
13 4 0.25
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (13 bp):
TTTTAAATTTTAA
Found at i:67374 original size:16 final size:16
Alignment explanation
Indices: 67337--67374 Score: 51
Period size: 16 Copynumber: 2.3 Consensus size: 16
67327 TCTCACTAAC
67337 TTTTTCTTTTCATTTT
1 TTTTTCTTTTCATTTT
67353 TGTTTTC-TTTCATTTT
1 T-TTTTCTTTTCATTTT
67369 ATTTTT
1 -TTTTT
67375 ATCATTTACA
Statistics
Matches: 20, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
16 14 0.70
17 6 0.30
ACGTcount: A:0.08, C:0.11, G:0.03, T:0.79
Consensus pattern (16 bp):
TTTTTCTTTTCATTTT
Found at i:69164 original size:2 final size:2
Alignment explanation
Indices: 69157--69212 Score: 112
Period size: 2 Copynumber: 28.0 Consensus size: 2
69147 CATAAGATAG
69157 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
69199 AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT
69213 GTATGTTTAT
Statistics
Matches: 54, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 54 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:70774 original size:22 final size:22
Alignment explanation
Indices: 70749--70792 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
70739 ATGAGAAAGG
*
70749 ATATTGTTTTGTAAGAGTTTAA
1 ATATTGTTTTGTAAGAATTTAA
70771 ATATTGTTTTGTAAGAATTTAA
1 ATATTGTTTTGTAAGAATTTAA
70793 GAATGTATAC
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.34, C:0.00, G:0.16, T:0.50
Consensus pattern (22 bp):
ATATTGTTTTGTAAGAATTTAA
Found at i:73301 original size:2 final size:2
Alignment explanation
Indices: 73294--73331 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
73284 CATGCATAAG
73294 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
73332 GTTTATAGGA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:76884 original size:102 final size:101
Alignment explanation
Indices: 76698--76898 Score: 305
Period size: 102 Copynumber: 2.0 Consensus size: 101
76688 ACTTTTTTTC
* * *
76698 TTTTAACATACTTCAAGGGGAGTCAGCTCATCACACTACCATCTCACACTCTAAGTGAAAGGGAG
1 TTTTAACATACTTCAAGAGGAGTCAACTCATCACACTACCATCTCACACTCTAAGTGAAAGGGAA
*
76763 CATACCTTCCACCCTCGAGCTAGTAAGGTAGAGTTT
66 CATACCTTCCACCCCCGAGCTAGTAAGGTAGAGTTT
* * *
76799 TTTTAAGCATACTTTAATAGGAGTTAACTCATCACACTACCATC-CTACACTCTAAGTGAAAGGG
1 TTTTAA-CATACTTCAAGAGGAGTCAACTCATCACACTACCATCTC-ACACTCTAAGTGAAAGGG
*
76863 AACATACCTTCCACCCCCGAGCTAGTCAGGTAGAGT
64 AACATACCTTCCACCCCCGAGCTAGTAAGGTAGAGT
76899 CATCCCGTGA
Statistics
Matches: 90, Mismatches: 8, Indels: 3
0.89 0.08 0.03
Matches are distributed among these distances:
101 7 0.08
102 83 0.92
ACGTcount: A:0.31, C:0.26, G:0.17, T:0.26
Consensus pattern (101 bp):
TTTTAACATACTTCAAGAGGAGTCAACTCATCACACTACCATCTCACACTCTAAGTGAAAGGGAA
CATACCTTCCACCCCCGAGCTAGTAAGGTAGAGTTT
Found at i:81465 original size:4 final size:4
Alignment explanation
Indices: 81454--81506 Score: 54
Period size: 4 Copynumber: 13.0 Consensus size: 4
81444 CTTTCCTAAC
* * *
81454 ATTT -TTT ATTT ATAT ATGT GTTT ATTTT ATTT ATTT ATTT ATTT CATTT
1 ATTT ATTT ATTT ATTT ATTT ATTT A-TTT ATTT ATTT ATTT ATTT -ATTT
81503 ATTT
1 ATTT
81507 TCTACATAAC
Statistics
Matches: 41, Mismatches: 5, Indels: 6
0.79 0.10 0.12
Matches are distributed among these distances:
3 3 0.07
4 30 0.73
5 8 0.20
ACGTcount: A:0.23, C:0.02, G:0.04, T:0.72
Consensus pattern (4 bp):
ATTT
Found at i:81492 original size:13 final size:14
Alignment explanation
Indices: 81474--81507 Score: 54
Period size: 13 Copynumber: 2.6 Consensus size: 14
81464 TATATATGTG
81474 TTTATTTTATTT-A
1 TTTATTTTATTTCA
81487 TTTA-TTTATTTCA
1 TTTATTTTATTTCA
81500 TTTATTTT
1 TTTATTTT
81508 CTACATAACG
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
12 7 0.37
13 9 0.47
14 3 0.16
ACGTcount: A:0.21, C:0.03, G:0.00, T:0.76
Consensus pattern (14 bp):
TTTATTTTATTTCA
Found at i:81494 original size:17 final size:17
Alignment explanation
Indices: 81474--81506 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
81464 TATATATGTG
*
81474 TTTATTTTATTTATTTA
1 TTTATTTCATTTATTTA
81491 TTTATTTCATTTATTT
1 TTTATTTCATTTATTT
81507 TCTACATAAC
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.21, C:0.03, G:0.00, T:0.76
Consensus pattern (17 bp):
TTTATTTCATTTATTTA
Found at i:81945 original size:4 final size:4
Alignment explanation
Indices: 81896--81990 Score: 115
Period size: 4 Copynumber: 23.2 Consensus size: 4
81886 TTCCATTTAA
*
81896 TATT T-TT TCATT TATAT TA-T T-TT TATT TTTT TATAT ATATT ATATT
1 TATT TATT T-ATT TAT-T TATT TATT TATT TATT TAT-T -TATT -TATT
81942 TATT TATT TATT TATT TATT TATT TATT TATT TATT TATT TATT TATT
1 TATT TATT TATT TATT TATT TATT TATT TATT TATT TATT TATT TATT
81990 T
1 T
81991 GTTTTCACTT
Statistics
Matches: 82, Mismatches: 2, Indels: 14
0.84 0.02 0.14
Matches are distributed among these distances:
3 7 0.09
4 59 0.72
5 13 0.16
6 3 0.04
ACGTcount: A:0.25, C:0.01, G:0.00, T:0.74
Consensus pattern (4 bp):
TATT
Found at i:82014 original size:6 final size:7
Alignment explanation
Indices: 81896--82014 Score: 62
Period size: 8 Copynumber: 14.9 Consensus size: 7
81886 TTCCATTTAA
81896 TATTTTT
1 TATTTTT
81903 TCATTTATAT
1 T-ATTT-T-T
81913 TA-TTTT
1 TATTTTT
81919 TATTTTTT
1 TA-TTTTT
81927 TATATATATT
1 TAT-T-T-TT
81937 ATATTTATT
1 -TATTT-TT
81946 TATTTATT
1 TATTT-TT
81954 TATTTATT
1 TATTT-TT
81962 TATTTATT
1 TATTT-TT
81970 TATTTATT
1 TATTT-TT
81978 TATTTATT
1 TATTT-TT
81986 TATTTGTT
1 TATTT-TT
*
81994 T-TCACTTT
1 TAT--TTTT
82002 TATTTTT
1 TATTTTT
82009 TATTTT
1 TATTTT
82015 CATGCATATT
Statistics
Matches: 97, Mismatches: 3, Indels: 24
0.78 0.02 0.19
Matches are distributed among these distances:
6 3 0.03
7 13 0.13
8 64 0.66
9 9 0.09
10 5 0.05
11 3 0.03
ACGTcount: A:0.23, C:0.03, G:0.01, T:0.74
Consensus pattern (7 bp):
TATTTTT
Found at i:82014 original size:12 final size:13
Alignment explanation
Indices: 81896--82014 Score: 94
Period size: 12 Copynumber: 9.5 Consensus size: 13
81886 TTCCATTTAA
*
81896 TATTTT-TTCATT
1 TATTTTATTTATT
*
81908 TATATTA-TT-TT
1 TATTTTATTTATT
81919 TATTTT-TTTATAT
1 TATTTTATTTAT-T
*
81932 ATATTATATTTATT
1 -TATTTTATTTATT
81946 TA-TTTATTTATT
1 TATTTTATTTATT
81958 TA-TTTATTTATT
1 TATTTTATTTATT
81970 TA-TTTATTTATT
1 TATTTTATTTATT
*
81982 TA-TTTATTTGTTT
1 TATTTTATTT-ATT
81995 TCACTTTTATTT-TT
1 T-A-TTTTATTTATT
82009 TATTTT
1 TATTTT
82015 CATGCATATT
Statistics
Matches: 91, Mismatches: 6, Indels: 20
0.78 0.05 0.17
Matches are distributed among these distances:
11 9 0.10
12 53 0.58
13 7 0.08
14 10 0.11
15 5 0.05
16 7 0.08
ACGTcount: A:0.23, C:0.03, G:0.01, T:0.74
Consensus pattern (13 bp):
TATTTTATTTATT
Found at i:82142 original size:12 final size:13
Alignment explanation
Indices: 82125--82153 Score: 51
Period size: 12 Copynumber: 2.3 Consensus size: 13
82115 GAATCGAATT
82125 TTTTAATT-TTAA
1 TTTTAATTCTTAA
82137 TTTTAATTCTTAA
1 TTTTAATTCTTAA
82150 TTTT
1 TTTT
82154 TGCAATTAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 8 0.50
13 8 0.50
ACGTcount: A:0.28, C:0.03, G:0.00, T:0.69
Consensus pattern (13 bp):
TTTTAATTCTTAA
Found at i:85051 original size:18 final size:16
Alignment explanation
Indices: 85030--85116 Score: 77
Period size: 18 Copynumber: 5.1 Consensus size: 16
85020 AGATCCAATC
85030 AAGAACAAAAAAGAAAA
1 AAGAA-AAAAAAGAAAA
85047 GAAGAAAAAAAAGAGAAAA
1 -AAG-AAAAAAA-AGAAAA
*
85066 AAGAGAAAAAAGAGAAA
1 AAGAAAAAAAAGA-AAA
* *
85083 AA-AAACAAAAGGAAA
1 AAGAAAAAAAAGAAAA
85098 AAGAAATCAAAAAGAAAA
1 AAGAAA--AAAAAGAAAA
85116 A
1 A
85117 GGGACAAAAA
Statistics
Matches: 57, Mismatches: 6, Indels: 12
0.76 0.08 0.16
Matches are distributed among these distances:
15 5 0.09
16 13 0.23
17 11 0.19
18 20 0.35
19 8 0.14
ACGTcount: A:0.79, C:0.03, G:0.16, T:0.01
Consensus pattern (16 bp):
AAGAAAAAAAAGAAAA
Found at i:85060 original size:9 final size:9
Alignment explanation
Indices: 85030--85116 Score: 68
Period size: 9 Copynumber: 8.9 Consensus size: 9
85020 AGATCCAATC
85030 AAGAACAAAA
1 AAGAA-AAAA
*
85040 AAG-AAAAG
1 AAGAAAAAA
85048 AAGAAAAAA
1 AAGAAAAAA
85057 AAGAGAAAAA
1 AAGA-AAAAA
85067 AGAGAAAAAA
1 A-AGAAAAAA
*
85077 GAGAAAAAA
1 AAGAAAAAA
*
85086 AACAAAAGGAAA
1 AA-GAAA--AAA
85098 AAGAAATCAAA
1 AAGAAA--AAA
85109 AAGAAAAA
1 AAGAAAAA
85117 GGGACAAAAA
Statistics
Matches: 63, Mismatches: 8, Indels: 13
0.75 0.10 0.15
Matches are distributed among these distances:
8 6 0.10
9 20 0.32
10 17 0.27
11 15 0.24
12 5 0.08
ACGTcount: A:0.79, C:0.03, G:0.16, T:0.01
Consensus pattern (9 bp):
AAGAAAAAA
Found at i:85116 original size:17 final size:17
Alignment explanation
Indices: 85037--85117 Score: 62
Period size: 17 Copynumber: 4.7 Consensus size: 17
85027 ATCAAGAACA
85037 AAAAAGAAAAGAAGAAAA-
1 AAAAAG-AAA-AAGAAAAC
*
85055 AAAAGAGAAAAA-AGAGA-
1 AAAA-AGAAAAAGA-AAAC
85072 AAAAAGAGAAAA-AAAAC
1 AAAAAGA-AAAAGAAAAC
* *
85089 AAAAGGAAAAAGAAATC
1 AAAAAGAAAAAGAAAAC
85106 AAAAAGAAAAAG
1 AAAAAGAAAAAG
85118 GGACAAAAAG
Statistics
Matches: 53, Mismatches: 5, Indels: 11
0.77 0.07 0.16
Matches are distributed among these distances:
16 10 0.19
17 34 0.64
18 7 0.13
19 2 0.04
ACGTcount: A:0.79, C:0.02, G:0.17, T:0.01
Consensus pattern (17 bp):
AAAAAGAAAAAGAAAAC
Found at i:86703 original size:36 final size:36
Alignment explanation
Indices: 86663--86733 Score: 106
Period size: 36 Copynumber: 2.0 Consensus size: 36
86653 TTAAAAGAAG
* *
86663 ATTTTATCTCGCTTGAGATAGTTTCCCTTGAAACAA
1 ATTTTATCTCCCTTGAGACAGTTTCCCTTGAAACAA
* *
86699 ATTTTGTCTCCCTTGAGACAGTTTCTCTTGAAACA
1 ATTTTATCTCCCTTGAGACAGTTTCCCTTGAAACA
86734 TAAACTTTGA
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
36 31 1.00
ACGTcount: A:0.25, C:0.21, G:0.14, T:0.39
Consensus pattern (36 bp):
ATTTTATCTCCCTTGAGACAGTTTCCCTTGAAACAA
Found at i:87191 original size:106 final size:106
Alignment explanation
Indices: 87068--87593 Score: 733
Period size: 106 Copynumber: 5.0 Consensus size: 106
87058 ATCGTGCCAT
* *
87068 TCAAGACAACACAAGTTCAACTTCACAACGAAGGGACGACT-AGTTGTCAACAAACAATTTCCCA
1 TCAAGACAACACAAGCTCAACTTCACAACGAAGGGGCGACTGA-TTGTCAACAAACAATTTCCCA
*
87132 ATTTCAGAGCCAATTTCAACTTCACAGCAAAGGATATTGGAC
65 ATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGAC
* * * * *
87174 TCAAGACAACACAAGTTCAACTTCACAACGAAGGGACGGCTGGTTGTCAACAAACAATTTCCCAG
1 TCAAGACAACACAAGCTCAACTTCACAACGAAGGGGCGACTGATTGTCAACAAACAATTTCCCAA
87239 TTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGAC
66 TTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGAC
* * *
87280 TCAAGACAACACAAGCTCAACTTCACAGCGAAGGGGCGACTGACTGTCAACAAACAACTTCCCAA
1 TCAAGACAACACAAGCTCAACTTCACAACGAAGGGGCGACTGATTGTCAACAAACAATTTCCCAA
* * *
87345 TTTCATAGCCAATTTCAACTTCTCAGCGAAGGATCTTGGAC
66 TTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGAC
* * * *
87386 CCAAGACAACACAAGCTCAACTTCACGACGAAGGGGTGGCTGATTGTCAAC-AA-AATTT--C-A
1 TCAAGACAACACAAGCTCAACTTCACAACGAAGGGGCGACTGATTGTCAACAAACAATTTCCCAA
* *
87446 -TTCAGAGTCAATTTCAACTTCACAGCGAAGGATATTAGAC
66 TTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGAC
* * * * * *
87486 TCGAGACAGCACAAGCTCAACTTCACAGCGAAGGGGCGACTGACTGTCAGCAAACAATTTCCCAG
1 TCAAGACAACACAAGCTCAACTTCACAACGAAGGGGCGACTGATTGTCAACAAACAATTTCCCAA
* * *
87551 TTCCAGATCCAATTTCAACTTCACAGCGGAGGATATTGGAC
66 TTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGAC
87592 TC
1 TC
87594 GGAACAATAC
Statistics
Matches: 371, Mismatches: 42, Indels: 14
0.87 0.10 0.03
Matches are distributed among these distances:
100 77 0.21
101 3 0.01
102 6 0.02
104 5 0.01
105 2 0.01
106 278 0.75
ACGTcount: A:0.35, C:0.26, G:0.18, T:0.21
Consensus pattern (106 bp):
TCAAGACAACACAAGCTCAACTTCACAACGAAGGGGCGACTGATTGTCAACAAACAATTTCCCAA
TTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGAC
Found at i:89341 original size:18 final size:18
Alignment explanation
Indices: 89297--89353 Score: 53
Period size: 18 Copynumber: 3.2 Consensus size: 18
89287 CTTTCCTAAC
* * *
89297 ATTTTTTTATTTATATAT
1 ATTTATTTATTTTTATTT
* *
89315 ATGTGTTTATTTTTATTT
1 ATTTATTTATTTTTATTT
*
89333 ATTTATTTA-TTTCATTT
1 ATTTATTTATTTTTATTT
89350 ATTT
1 ATTT
89354 TCTACATAAC
Statistics
Matches: 32, Mismatches: 7, Indels: 1
0.80 0.17 0.03
Matches are distributed among these distances:
17 11 0.34
18 21 0.66
ACGTcount: A:0.23, C:0.02, G:0.04, T:0.72
Consensus pattern (18 bp):
ATTTATTTATTTTTATTT
Done.