Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01004655.1 Hibiscus syriacus cultivar Beakdansim tig00010435_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: 60378
ACGTcount: A:0.34, C:0.16, G:0.17, T:0.32
Found at i:1470 original size:11 final size:11
Alignment explanation
Indices: 1454--1496 Score: 86
Period size: 11 Copynumber: 3.9 Consensus size: 11
1444 CTTGAAGAAA
1454 AAAAGAAAAAT
1 AAAAGAAAAAT
1465 AAAAGAAAAAT
1 AAAAGAAAAAT
1476 AAAAGAAAAAT
1 AAAAGAAAAAT
1487 AAAAGAAAAA
1 AAAAGAAAAA
1497 AGAATAAAAG
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 32 1.00
ACGTcount: A:0.84, C:0.00, G:0.09, T:0.07
Consensus pattern (11 bp):
AAAAGAAAAAT
Found at i:1504 original size:15 final size:15
Alignment explanation
Indices: 1454--1519 Score: 78
Period size: 15 Copynumber: 4.2 Consensus size: 15
1444 CTTGAAGAAA
*
1454 AAAAGAAAAATAAAAGA
1 AAAAGAAAAA-AAAA-T
*
1471 AAAATAAAAGAAAAAT
1 AAAAGAAAA-AAAAAT
*
1487 AAAAGAAAAAAGAAT
1 AAAAGAAAAAAAAAT
1502 AAAAGAAAAAAAAAT
1 AAAAGAAAAAAAAAT
1517 AAA
1 AAA
1520 TAAATGAGGG
Statistics
Matches: 43, Mismatches: 5, Indels: 4
0.83 0.10 0.08
Matches are distributed among these distances:
15 22 0.51
16 8 0.19
17 12 0.28
18 1 0.02
ACGTcount: A:0.83, C:0.00, G:0.09, T:0.08
Consensus pattern (15 bp):
AAAAGAAAAAAAAAT
Found at i:3076 original size:138 final size:137
Alignment explanation
Indices: 2502--3130 Score: 740
Period size: 135 Copynumber: 4.6 Consensus size: 137
2492 AACTATGACT
* * * * * * *
2502 AGATCTCCTCAACACGTAGGAGCAGCATCATTCTCAGATAACCAGACTTCCTCTTCATATAAGAA
1 AGATCTCCTCAACACGTAGGAGCAGCGTCATCCTCAGACAATCAGACTT-CTCATCATGTAGGAA
* * *
2567 -TCGTGTTGTCTACAAATCATCCCTAAAGATAGCTAGACATCCTCATCACGTAGGAACAATGTCG
65 CT-GTGTTGTCTCCAAATCATCCCTAAAGATGGCTAGACATCCTCATCA-TTAGGAACAATGTCG
**
2631 TATACCGACC
128 TCCACCGACC
* * * * *
2641 ATATCTCCTC-A-AC--AGGAGTAGTGTCATTCTCAGACAATCAGACTTCCTCATCACGTAGGAA
1 AGATCTCCTCAACACGTAGGAGCAGCGTCATCCTCAGACAATCAGACTT-CTCATCATGTAGGAA
* * *
2702 CTGTGTTATCTCCAAATCATCCCTAAAGATGGCTATACATCCTCATCATATAGGAATAATGTCGT
65 CTGTGTTGTCTCCAAATCATCCCTAAAGATGGCTAGACATCCTCATCAT-TAGGAACAATGTCGT
2767 CCACCGACC
129 CCACCGACC
* * * * * *
2776 AGATCTCCTCAACACGTAGGAGCATCGTCATCCTCAAAAAATTAGACTTCGTCATCACGTAAGAA
1 AGATCTCCTCAACACGTAGGAGCAGCGTCATCCTCAGACAATCAGACTTC-TCATCATGTAGGAA
* * * *
2841 CTGTGTTGTCTCCAAATCATCCCTAAAGA--CCTATACA--CTCATCA--ATGAACATTGTCGTC
65 CTGTGTTGTCTCCAAATCATCCCTAAAGATGGCTAGACATCCTCATCATTAGGAACAATGTCGTC
*
2900 CACCGACT
130 CACCGACC
* *
2908 AGATCTCCTCAACACGTATGAGCAGTGTCATCCTCAGACAATCAGACTTCTCATCATGTAGGAAC
1 AGATCTCCTCAACACGTAGGAGCAGCGTCATCCTCAGACAATCAGACTTCTCATCATGTAGGAAC
*
2973 TGTGTTGTCTCCAAATCATCCCTAAAGATGGCTAGACGTCCTCATCACTTAGGAACAATGTCGTC
66 TGTGTTGTCTCCAAATCATCCCTAAAGATGGCTAGACATCCTCATCA-TTAGGAACAATGTCGTC
**
3038 CAGTGACC
130 CACCGACC
* * * *
3046 AGATATCCTCAACACGTATGAGCAGCGTCATCCTCAGATAACCAGACTTCTCATCATGTAGGAAC
1 AGATCTCCTCAACACGTAGGAGCAGCGTCATCCTCAGACAATCAGACTTCTCATCATGTAGGAAC
**
3111 CATGTTGTCTCCAAATCATC
66 TGTGTTGTCTCCAAATCATC
3131 TCCAAATGAC
Statistics
Matches: 421, Mismatches: 55, Indels: 29
0.83 0.11 0.06
Matches are distributed among these distances:
131 41 0.10
132 63 0.15
133 5 0.01
135 125 0.30
136 2 0.00
137 11 0.03
138 99 0.24
139 75 0.18
ACGTcount: A:0.31, C:0.28, G:0.15, T:0.26
Consensus pattern (137 bp):
AGATCTCCTCAACACGTAGGAGCAGCGTCATCCTCAGACAATCAGACTTCTCATCATGTAGGAAC
TGTGTTGTCTCCAAATCATCCCTAAAGATGGCTAGACATCCTCATCATTAGGAACAATGTCGTCC
ACCGACC
Found at i:3310 original size:3 final size:3
Alignment explanation
Indices: 3302--3374 Score: 98
Period size: 3 Copynumber: 24.7 Consensus size: 3
3292 CAGGTTTTAA
3302 ATT ATT ATT A-T ATT ATT ATT ATT ATT ATAT ATT ATT -TT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT AT-T ATT ATT ATT ATT ATT
*
3346 ACT ATT ATT ATT ATT ATT A-T ATAT ATT AT
1 ATT ATT ATT ATT ATT ATT ATT AT-T ATT AT
3375 ATTTTACATT
Statistics
Matches: 63, Mismatches: 2, Indels: 10
0.84 0.03 0.13
Matches are distributed among these distances:
2 6 0.10
3 51 0.81
4 6 0.10
ACGTcount: A:0.36, C:0.01, G:0.00, T:0.63
Consensus pattern (3 bp):
ATT
Found at i:3334 original size:27 final size:26
Alignment explanation
Indices: 3302--3374 Score: 110
Period size: 27 Copynumber: 2.7 Consensus size: 26
3292 CAGGTTTTAA
3302 ATTATTATTATATTATTATTATTATT
1 ATTATTATTATATTATTATTATTATT
* *
3328 ATATATTATTTTATTATTACTATTATT
1 AT-TATTATTATATTATTATTATTATT
3355 ATTATTATTATATATATTAT
1 ATTATTATTATAT-TATTAT
3375 ATTTTACATT
Statistics
Matches: 41, Mismatches: 4, Indels: 3
0.85 0.08 0.06
Matches are distributed among these distances:
26 12 0.29
27 29 0.71
ACGTcount: A:0.36, C:0.01, G:0.00, T:0.63
Consensus pattern (26 bp):
ATTATTATTATATTATTATTATTATT
Found at i:9835 original size:8 final size:8
Alignment explanation
Indices: 9822--9880 Score: 59
Period size: 8 Copynumber: 7.4 Consensus size: 8
9812 ATATACTTAA
9822 ATATATAC
1 ATATATAC
**
9830 ATATATTT
1 ATATATAC
9838 ATATATAC
1 ATATATAC
9846 ATATATAC
1 ATATATAC
*
9854 ATATAAAAC
1 ATAT-ATAC
9863 ATATAT-C
1 ATATATAC
9870 AT-TGATAC
1 ATAT-ATAC
9878 ATA
1 ATA
9881 ATTGTGAATA
Statistics
Matches: 41, Mismatches: 6, Indels: 7
0.76 0.11 0.13
Matches are distributed among these distances:
6 1 0.02
7 5 0.12
8 28 0.68
9 7 0.17
ACGTcount: A:0.49, C:0.10, G:0.02, T:0.39
Consensus pattern (8 bp):
ATATATAC
Found at i:9835 original size:24 final size:24
Alignment explanation
Indices: 9808--9858 Score: 68
Period size: 24 Copynumber: 2.1 Consensus size: 24
9798 ACACACATGC
9808 ATATATATACT-TAAATATATACAT
1 ATATATATA-TATAAATATATACAT
* *
9832 ATATTTATATATACATATATACAT
1 ATATATATATATAAATATATACAT
9856 ATA
1 ATA
9859 AAACATATAT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
23 1 0.04
24 23 0.96
ACGTcount: A:0.49, C:0.08, G:0.00, T:0.43
Consensus pattern (24 bp):
ATATATATATATAAATATATACAT
Found at i:21107 original size:89 final size:90
Alignment explanation
Indices: 20958--21183 Score: 413
Period size: 89 Copynumber: 2.5 Consensus size: 90
20948 ATCAAAAATA
* *
20958 TTGAAAACACCCTGC-C-GAAGGTCTTATGGATGGCCCGAAGGACTTACAAATCAAGAAACCCCT
1 TTGAAAACATCCTGCACTGAAGGTCTTATGGATGGCCCGAAGGACTTACAAATCAAGAAACCCCC
21021 GAAGGCTTAGTTTCT-AAATCTCAT
66 GAAGGCTTAGTTTCTAAAATCTCAT
21045 TTGAAAACATCCTGCACTGAAGGTCTTATGGATGGCCCGAAGGACTTACAAATCAAGAAACCCCC
1 TTGAAAACATCCTGCACTGAAGGTCTTATGGATGGCCCGAAGGACTTACAAATCAAGAAACCCCC
21110 GAAGGCTTAGTTTCTAAAATCTCAT
66 GAAGGCTTAGTTTCTAAAATCTCAT
21135 TTGAAAACATCCTGCACTGAAGGTCTTATGGATGGCCCGAAGGACTTAC
1 TTGAAAACATCCTGCACTGAAGGTCTTATGGATGGCCCGAAGGACTTAC
21184 GCATCATGCT
Statistics
Matches: 134, Mismatches: 2, Indels: 3
0.96 0.01 0.02
Matches are distributed among these distances:
87 14 0.10
88 1 0.01
89 61 0.46
90 58 0.43
ACGTcount: A:0.32, C:0.23, G:0.20, T:0.24
Consensus pattern (90 bp):
TTGAAAACATCCTGCACTGAAGGTCTTATGGATGGCCCGAAGGACTTACAAATCAAGAAACCCCC
GAAGGCTTAGTTTCTAAAATCTCAT
Found at i:21348 original size:127 final size:129
Alignment explanation
Indices: 21075--21351 Score: 405
Period size: 127 Copynumber: 2.1 Consensus size: 129
21065 AGGTCTTATG
*
21075 GATGGCCCGAAGGACTTACAAATCAAGAAACCCCCGAAGGCTTAGTTTCTAAAATCTCATTTGAA
1 GATGGCCCGAAGGACTTACAAACCAAGAAACCCCCGAAGGCTTAGTTTCTAAAA---CATTTGAA
* * *
21140 AACATCCTGCACTGAAGGTCTTATGGATGGCCCGAAGGACTTACGCATCATGCTCGAAAGATTTA
63 AACATCCTGCACTGAAGGTCTTATGGATGGCCCAAAGGACTTACACATCATGCTCGAAAGACTTA
21205 CT
128 CT
* ** * *
21207 GATGGCCCAAAGGACTTACAAACCAAGAAACCCTTGAAGGCTTAGTTTCT-TAA-ATTTGAAAAT
1 GATGGCCCGAAGGACTTACAAACCAAGAAACCCCCGAAGGCTTAGTTTCTAAAACATTTGAAAAC
*
21270 ATCCTGCACTGAAGGTCTTATGGATGGCCCAAAGGATTTACACATCATGCTCGAAAGACTTACT
66 ATCCTGCACTGAAGGTCTTATGGATGGCCCAAAGGACTTACACATCATGCTCGAAAGACTTACT
* *
21334 GATGGCCTGGAGGACTTA
1 GATGGCCCGAAGGACTTA
21352 ATCATTAAGA
Statistics
Matches: 132, Mismatches: 13, Indels: 5
0.88 0.09 0.03
Matches are distributed among these distances:
127 84 0.64
131 2 0.02
132 46 0.35
ACGTcount: A:0.32, C:0.22, G:0.21, T:0.25
Consensus pattern (129 bp):
GATGGCCCGAAGGACTTACAAACCAAGAAACCCCCGAAGGCTTAGTTTCTAAAACATTTGAAAAC
ATCCTGCACTGAAGGTCTTATGGATGGCCCAAAGGACTTACACATCATGCTCGAAAGACTTACT
Found at i:21453 original size:43 final size:43
Alignment explanation
Indices: 21392--21838 Score: 338
Period size: 43 Copynumber: 10.4 Consensus size: 43
21382 ATTTTCTTAG
* *
21392 TTGTCATCAAGGAACCCCTACATATCACGATGGTCCCTCAAAC
1 TTGTCCTCAAGAAACCCCTACATATCACGATGGTCCCTCAAAC
* * * * * * ** *
21435 TTGTCCTCAAGAAACCCCTAAAAATCATGCTTAGT--TTCTTAG
1 TTGTCCTCAAGAAACCCCTACATATCACG-ATGGTCCCTCAAAC
* * *
21477 TTGTCAC-CAATG-AACCCCTACATATCATGTTGGTCCCTCACA-
1 TTGTC-CTCAA-GAAACCCCTACATATCACGATGGTCCCTCAAAC
* * * *
21519 TGTATCATTAAGGAACCCCTACATATCACGATGGTCCCTCAAAC
1 T-TGTCCTCAAGAAACCCCTACATATCACGATGGTCCCTCAAAC
21563 TTGTCCTCAAGAAACCCCTACATATCACGATGGTCCCTCAAAC
1 TTGTCCTCAAGAAACCCCTACATATCACGATGGTCCCTCAAAC
* *
21606 TTGTCCTCAAGAAACCCCTACATATCACGATGGTCTCTCAAGC
1 TTGTCCTCAAGAAACCCCTACATATCACGATGGTCCCTCAAAC
* * * * * * * ** *
21649 TTTTCTTCAAGAAACCCCTGA-AAATCATGCTTAGT--TTCTTAG
1 TTGTCCTCAAGAAACCCCT-ACATATCACG-ATGGTCCCTCAAAC
* * *
21691 TTGTCAC-CAAGGAACCCCTACATATCACGTTGGTCCCTC-AAG
1 TTGTC-CTCAAGAAACCCCTACATATCACGATGGTCCCTCAAAC
* * * * ** *
21733 TGTGTCATCAAGGAACCCTTATATATCAAAATAGTCCCTCAAAC
1 T-TGTCCTCAAGAAACCCCTACATATCACGATGGTCCCTCAAAC
* * * *
21777 TTGTCCTCAAGAAACCTCTACATATCATGATGGTCTCTCAAGC
1 TTGTCCTCAAGAAACCCCTACATATCACGATGGTCCCTCAAAC
* *
21820 TTTTCTTCAAGAAACCCCT
1 TTGTCCTCAAGAAACCCCT
21839 GAAAATCAGG
Statistics
Matches: 317, Mismatches: 69, Indels: 36
0.75 0.16 0.09
Matches are distributed among these distances:
41 9 0.03
42 54 0.17
43 243 0.77
44 11 0.03
ACGTcount: A:0.30, C:0.30, G:0.13, T:0.28
Consensus pattern (43 bp):
TTGTCCTCAAGAAACCCCTACATATCACGATGGTCCCTCAAAC
Found at i:21501 original size:85 final size:84
Alignment explanation
Indices: 21370--21625 Score: 248
Period size: 85 Copynumber: 3.0 Consensus size: 84
21360 GAAACTCTTG
* * *
21370 AAAATCAAGCTCATTTTCTTAGTTGTCATCAAGGAACCCCTACATATCACGATGGTCCCTCAAAC
1 AAAATCAAGCTTAGTTTCTTAGTTGTCACCAA-GAACCCCTACATATCACGATGGTCCCTCAAAC
21435 TTGTCCTCAAGAAACCCCTA
65 TTGTCCTCAAGAAACCCCTA
* * * *
21455 AAAATCATGCTTAGTTTCTTAGTTGTCACCAATGAACCCCTACATATCATGTTGGTCCCTCACA-
1 AAAATCAAGCTTAGTTTCTTAGTTGTCACCAA-GAACCCCTACATATCACGATGGTCCCTCAAAC
* * * *
21519 TGTATCATTAAGGAACCCCTA
65 T-TGTCCTCAAGAAACCCCTA
* * * * * * ** *
21540 CATATCACG-ATGGTCCCTCAAACTTGTC-CTCAAGAAACCCCTACATATCACGATGGTCCCTCA
1 AAAATCAAGCTTAGT--TTCTTAGTTGTCAC-CAAG-AACCCCTACATATCACGATGGTCCCTCA
21603 AACTTGTCCTCAAGAAACCCCTA
62 AACTTGTCCTCAAGAAACCCCTA
21626 CATATCACGA
Statistics
Matches: 137, Mismatches: 28, Indels: 11
0.78 0.16 0.06
Matches are distributed among these distances:
84 4 0.03
85 79 0.58
86 53 0.39
87 1 0.01
ACGTcount: A:0.30, C:0.30, G:0.12, T:0.27
Consensus pattern (84 bp):
AAAATCAAGCTTAGTTTCTTAGTTGTCACCAAGAACCCCTACATATCACGATGGTCCCTCAAACT
TGTCCTCAAGAAACCCCTA
Found at i:21705 original size:171 final size:172
Alignment explanation
Indices: 21392--21858 Score: 570
Period size: 171 Copynumber: 2.7 Consensus size: 172
21382 ATTTTCTTAG
*
21392 TTGTCATCAAGGAACCCCTACATATCACGATGGTCCCTCAAACTTGTCCTCAAGAAACCCCTAAA
1 TTGTCATCAAGGAACCCCTACATATCACGATGGTCCCTCAAACTTGTCCTCAAGAAACCCCTACA
* * * * * * ** * * **
21457 AATCATGCTTAGTTTCT-TAG-TTGTCACCAATG-AACCCCT-ACATATCATG-TTGGTCCCTCA
66 TATCATG-ATGGTCTCTCAAGCTTTTCTTCAA-GAAACCCCTGA-AAATCATGCTTAGTTTCTCA
**
21517 CATGTATCATTAAGGAACCCCTACATATCACGATGGTCCCTCAAAC
128 CATGTATCACCAAGGAACCCCTACATATCACGATGGTCCCTC-AAC
* *
21563 TTGTCCTCAAGAAACCCCTACATATCACGATGGTCCCTCAAACTTGTCCTCAAGAAACCCCTACA
1 TTGTCATCAAGGAACCCCTACATATCACGATGGTCCCTCAAACTTGTCCTCAAGAAACCCCTACA
* * *
21628 TATCACGATGGTCTCTCAAGCTTTTCTTCAAGAAACCCCTGAAAATCATGCTTAGTTTCTTA-GT
66 TATCATGATGGTCTCTCAAGCTTTTCTTCAAGAAACCCCTGAAAATCATGCTTAGTTTCTCACAT
* * *
21692 -TGTCACCAAGGAACCCCTACATATCACGTTGGTCCCTCAAG
131 GTATCACCAAGGAACCCCTACATATCACGATGGTCCCTCAAC
* * ** * *
21733 TGTGTCATCAAGGAACCCTTATATATCAAAATAGTCCCTCAAACTTGTCCTCAAGAAACCTCTAC
1 T-TGTCATCAAGGAACCCCTACATATCACGATGGTCCCTCAAACTTGTCCTCAAGAAACCCCTAC
*
21798 ATATCATGATGGTCTCTCAAGCTTTTCTTCAAGAAACCCCTGAAAATCAGGCTTAGTTTCT
65 ATATCATGATGGTCTCTCAAGCTTTTCTTCAAGAAACCCCTGAAAATCATGCTTAGTTTCT
21859 AAAAATATTG
Statistics
Matches: 257, Mismatches: 33, Indels: 12
0.85 0.11 0.04
Matches are distributed among these distances:
170 9 0.04
171 218 0.85
172 22 0.09
173 8 0.03
ACGTcount: A:0.30, C:0.29, G:0.13, T:0.28
Consensus pattern (172 bp):
TTGTCATCAAGGAACCCCTACATATCACGATGGTCCCTCAAACTTGTCCTCAAGAAACCCCTACA
TATCATGATGGTCTCTCAAGCTTTTCTTCAAGAAACCCCTGAAAATCATGCTTAGTTTCTCACAT
GTATCACCAAGGAACCCCTACATATCACGATGGTCCCTCAAC
Found at i:21773 original size:214 final size:214
Alignment explanation
Indices: 21392--21838 Score: 680
Period size: 214 Copynumber: 2.1 Consensus size: 214
21382 ATTTTCTTAG
*
21392 TTGTCATCAAGGAACCCCTACATATCACGATGGTCCCTCAAACTTGTCCTCAAGAAACCCCTAAA
1 TTGTCATCAAGAAACCCCTACATATCACGATGGTCCCTCAAACTTGTCCTCAAGAAACCCCTAAA
* *
21457 AATCATGCTTAGTTTCTTAGTTGTCACCAATGAACCCCTACATATCATGTTGGTCCCTCACATGT
66 AATCATGCTTAGTTTCTTAGTTGTCACCAAGGAACCCCTACATATCACGTTGGTCCCTCACATGT
* ** *
21522 ATCATTAAGGAACCCCTACATATCACGATGGTCCCTCAAACTTGTCCTCAAGAAACCCCTACATA
131 ATCATCAAGGAACCCCTACATATCAAAATAGTCCCTCAAACTTGTCCTCAAGAAACCCCTACATA
21587 TCACGATGGTCCCTCAAAC
196 TCACGATGGTCCCTCAAAC
* * * * * *
21606 TTGTCCTCAAGAAACCCCTACATATCACGATGGTCTCTCAAGCTTTTCTTCAAGAAACCCCTGAA
1 TTGTCATCAAGAAACCCCTACATATCACGATGGTCCCTCAAACTTGTCCTCAAGAAACCCCTAAA
21671 AATCATGCTTAGTTTCTTAGTTGTCACCAAGGAACCCCTACATATCACGTTGGTCCCTCA-AGTG
66 AATCATGCTTAGTTTCTTAGTTGTCACCAAGGAACCCCTACATATCACGTTGGTCCCTCACA-TG
* * * *
21735 TGTCATCAAGGAACCCTTATATATCAAAATAGTCCCTCAAACTTGTCCTCAAGAAACCTCTACAT
130 TATCATCAAGGAACCCCTACATATCAAAATAGTCCCTCAAACTTGTCCTCAAGAAACCCCTACAT
* * *
21800 ATCATGATGGTCTCTCAAGC
195 ATCACGATGGTCCCTCAAAC
* *
21820 TTTTCTTCAAGAAACCCCT
1 TTGTCATCAAGAAACCCCT
21839 GAAAATCAGG
Statistics
Matches: 210, Mismatches: 22, Indels: 2
0.90 0.09 0.01
Matches are distributed among these distances:
213 1 0.00
214 209 1.00
ACGTcount: A:0.30, C:0.30, G:0.13, T:0.28
Consensus pattern (214 bp):
TTGTCATCAAGAAACCCCTACATATCACGATGGTCCCTCAAACTTGTCCTCAAGAAACCCCTAAA
AATCATGCTTAGTTTCTTAGTTGTCACCAAGGAACCCCTACATATCACGTTGGTCCCTCACATGT
ATCATCAAGGAACCCCTACATATCAAAATAGTCCCTCAAACTTGTCCTCAAGAAACCCCTACATA
TCACGATGGTCCCTCAAAC
Found at i:21956 original size:39 final size:39
Alignment explanation
Indices: 21880--21970 Score: 164
Period size: 39 Copynumber: 2.3 Consensus size: 39
21870 GTTTTGAGCA
21880 AAATTATCTCAAGCGAGATAAAATCTTCTGTTTCAAGTG
1 AAATTATCTCAAGCGAGATAAAATCTTCTGTTTCAAGTG
*
21919 AAATAATCTCAAGCGAGATAAAATCTTCTGTTTCAAGTG
1 AAATTATCTCAAGCGAGATAAAATCTTCTGTTTCAAGTG
*
21958 AAATTGTCTCAAG
1 AAATTATCTCAAG
21971 GCAGACTATC
Statistics
Matches: 49, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
39 49 1.00
ACGTcount: A:0.37, C:0.15, G:0.15, T:0.32
Consensus pattern (39 bp):
AAATTATCTCAAGCGAGATAAAATCTTCTGTTTCAAGTG
Found at i:22004 original size:15 final size:15
Alignment explanation
Indices: 21962--22005 Score: 61
Period size: 15 Copynumber: 2.9 Consensus size: 15
21952 CAAGTGAAAT
*
21962 TGTCTCAAGGCAGAC
1 TGTCTCAAGGGAGAC
* *
21977 TATCTCAATGGAGAC
1 TGTCTCAAGGGAGAC
21992 TGTCTCAAGGGAGA
1 TGTCTCAAGGGAGA
22006 TAAAATTTGT
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
15 24 1.00
ACGTcount: A:0.30, C:0.20, G:0.27, T:0.23
Consensus pattern (15 bp):
TGTCTCAAGGGAGAC
Found at i:22040 original size:36 final size:36
Alignment explanation
Indices: 21993--22078 Score: 127
Period size: 36 Copynumber: 2.4 Consensus size: 36
21983 AATGGAGACT
* **
21993 GTCTCAAGGGAGATAAAATTTGTTTCAAGGGAAACC
1 GTCTCAAGGGAGACAAAATTCCTTTCAAGGGAAACC
*
22029 GTCTCAAGGGAGACAAAATTCCTTTCAAGGGAAACT
1 GTCTCAAGGGAGACAAAATTCCTTTCAAGGGAAACC
*
22065 GTCTTAAGGGAGAC
1 GTCTCAAGGGAGAC
22079 TGTCTCAAGG
Statistics
Matches: 45, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
36 45 1.00
ACGTcount: A:0.35, C:0.16, G:0.26, T:0.23
Consensus pattern (36 bp):
GTCTCAAGGGAGACAAAATTCCTTTCAAGGGAAACC
Found at i:22091 original size:15 final size:15
Alignment explanation
Indices: 22053--22093 Score: 64
Period size: 15 Copynumber: 2.7 Consensus size: 15
22043 AAAATTCCTT
*
22053 TCAAGGGAAACTGTC
1 TCAAGGGAGACTGTC
*
22068 TTAAGGGAGACTGTC
1 TCAAGGGAGACTGTC
22083 TCAAGGGAGAC
1 TCAAGGGAGAC
22094 AAAATTTGTT
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
15 23 1.00
ACGTcount: A:0.32, C:0.17, G:0.32, T:0.20
Consensus pattern (15 bp):
TCAAGGGAGACTGTC
Found at i:22108 original size:72 final size:72
Alignment explanation
Indices: 22032--22177 Score: 222
Period size: 72 Copynumber: 2.0 Consensus size: 72
22022 GGAAACCGTC
* *
22032 TCAAGGGAGACAAAATTCCTTTCAAGGGAAACTGTCTTAAGGGAGACTGTCTCAAGGGAGAC-AA
1 TCAAGGGAGACAAAATTCCTTTCAAGGGAAACGGTCTCAAGGGAGACTGTCTCAAGGGAGACAAA
22096 AATTTGTT
66 AATTT-TT
** * *
22104 TCAAGGGAGACAAAATTTGTTTCAAGGGAAACGGTCTCGAGGGAGACTGTCTCAATGGAGACAAA
1 TCAAGGGAGACAAAATTCCTTTCAAGGGAAACGGTCTCAAGGGAGACTGTCTCAAGGGAGACAAA
22169 AATTTTT
66 AATTTTT
22176 TC
1 TC
22178 GGGAAACTGT
Statistics
Matches: 67, Mismatches: 6, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
72 60 0.90
73 7 0.10
ACGTcount: A:0.34, C:0.15, G:0.25, T:0.25
Consensus pattern (72 bp):
TCAAGGGAGACAAAATTCCTTTCAAGGGAAACGGTCTCAAGGGAGACTGTCTCAAGGGAGACAAA
AATTTTT
Found at i:22109 original size:21 final size:21
Alignment explanation
Indices: 22083--22132 Score: 100
Period size: 21 Copynumber: 2.4 Consensus size: 21
22073 GGAGACTGTC
22083 TCAAGGGAGACAAAATTTGTT
1 TCAAGGGAGACAAAATTTGTT
22104 TCAAGGGAGACAAAATTTGTT
1 TCAAGGGAGACAAAATTTGTT
22125 TCAAGGGA
1 TCAAGGGA
22133 AACGGTCTCG
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 29 1.00
ACGTcount: A:0.38, C:0.10, G:0.26, T:0.26
Consensus pattern (21 bp):
TCAAGGGAGACAAAATTTGTT
Found at i:23699 original size:25 final size:24
Alignment explanation
Indices: 23671--23717 Score: 60
Period size: 24 Copynumber: 1.9 Consensus size: 24
23661 CCTTTTTCTT
23671 TTTCTTCTT-TTTCTTTACTTTTTAG
1 TTTCTT-TTCTTT-TTTACTTTTTAG
*
23696 TTTCTTTTCTTTTTTCCTTTTT
1 TTTCTTTTCTTTTTTACTTTTT
23718 GCTCTTTGTT
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
24 11 0.55
25 9 0.45
ACGTcount: A:0.04, C:0.17, G:0.02, T:0.77
Consensus pattern (24 bp):
TTTCTTTTCTTTTTTACTTTTTAG
Found at i:24983 original size:26 final size:25
Alignment explanation
Indices: 24933--24983 Score: 68
Period size: 26 Copynumber: 2.0 Consensus size: 25
24923 AAATGCTTAA
24933 AAATGAAATGCAAATGAAAAGATGT
1 AAATGAAATGCAAATGAAAAGATGT
*
24958 AAATGAAGATGCAGATGCAAAA-ATGT
1 AAATGAA-ATGCAAATG-AAAAGATGT
24984 TGATCCCAAC
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
25 7 0.30
26 12 0.52
27 4 0.17
ACGTcount: A:0.53, C:0.06, G:0.22, T:0.20
Consensus pattern (25 bp):
AAATGAAATGCAAATGAAAAGATGT
Found at i:29350 original size:23 final size:24
Alignment explanation
Indices: 29295--29353 Score: 93
Period size: 24 Copynumber: 2.5 Consensus size: 24
29285 AAACAATTAG
*
29295 GGGAATTATCTTTTGTGATTTTTA
1 GGGAATTATCTTTTATGATTTTTA
*
29319 GGGATTTATCTTTTATGATTTTTA
1 GGGAATTATCTTTTATGATTTTTA
29343 -GGAATTATCTT
1 GGGAATTATCTT
29354 GAGCATTTTT
Statistics
Matches: 32, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
23 10 0.31
24 22 0.69
ACGTcount: A:0.22, C:0.05, G:0.19, T:0.54
Consensus pattern (24 bp):
GGGAATTATCTTTTATGATTTTTA
Found at i:36344 original size:42 final size:41
Alignment explanation
Indices: 36298--36952 Score: 330
Period size: 43 Copynumber: 15.2 Consensus size: 41
36288 TTATTTCTTT
* * *
36298 TTTATAATTGAGGCTTTAATTTTTATAAACTCATTTTTTATA
1 TTTATAATTGAGGCCTTAATTTTT-TAATCTCATTTTTTACA
* ** *
36340 TTTATAATTTAGGTTGTTAATTGTTTCAATCTCATTTTTTACA
1 TTTATAATTGAGG-CCTTAATT-TTTTAATCTCATTTTTTACA
* * *
36383 TTTATATTTGAGGCCCTAATTTTTTAATCTCATTTTTTACC
1 TTTATAATTGAGGCCTTAATTTTTTAATCTCATTTTTTACA
* * *
36424 TTTATAATTGAGGCACTTAATTTTTCCT-ATCTCACTTTCTACC
1 TTTATAATTGAGGC-CTTAATTTTT--TAATCTCATTTTTTACA
* * ** * *
36467 TTTATAATTAAAGTTTCTAATTTTTTTTTAATTTCACTTTTTACA
1 TTTATAATTGAGGCCT-TAA---TTTTTTAATCTCATTTTTTACA
* * * * *
36512 TTTATAATAGATGCCTTTAATTTTTTTTTCAATCCCACTTTTTACT
1 TTTATAATTGAGGCC-TTAA---TTTTTT-AATCTCATTTTTTACA
* * * * **
36558 TTTATAATGGATGCCCTAATTTTTTTCAATCTCACTTTTTATT
1 TTTATAATTGAGGCCTTAA-TTTTTT-AATCTCATTTTTTACA
* * * * *
36601 TTTATAATTGAGGCCCGCTATTTTTTTCAATCTCAATTTCTACC
1 TTTATAATTGAGG-CC-TTAATTTTTT-AATCTCATTTTTTACA
* * * * * *
36645 TTTATAATTAAAGCCCATGATTTTTTAATCTCACTTTTTACT
1 TTTATAATT-GAGGCCTTAATTTTTTAATCTCATTTTTTACA
* * * *
36687 TTTATAATTGAGGCTCCTAAATTTTTCAATCCCATTTTTTTACC
1 TTTATAATTGAGG--CCTTAATTTTTTAATCTCA-TTTTTTACA
** * * *
36731 TTTATAATTGAAACCCCTAATTTTTTTAATCTCACTTTTTA-T
1 TTTATAATTG-AGGCCTTAA-TTTTTTAATCTCATTTTTTACA
* * *
36773 TTTATAATTGAGGCCCCTAATTTTTTCAATCCCACTTTTTTACC
1 TTTATAATTGAGG-CCTTAATTTTTT-AATCTCA-TTTTTTACA
** * * *
36817 TTTATAATTGAAACACTTAAGTTTTTTCAATCTCACTTTCTACT
1 TTTATAATTGAGGC-CTTAA-TTTTTT-AATCTCATTTTTTACA
** * ***
36861 TTTATAATTGAAATCCCTAATTTTTT-ATCTTGCTTTTTATC-
1 TTTATAATTG-AGGCCTTAATTTTTTAATCTCATTTTTTA-CA
* * * * *
36902 TTTATAATTGAGATCCCTAATTTTTCAATC-CAACTTTTTACT
1 TTTATAATTGAG-GCCTTAATTTTTTAATCTC-ATTTTTTACA
36944 TTTATAATT
1 TTTATAATT
36953 TAAGCCCCTA
Statistics
Matches: 492, Mismatches: 89, Indels: 64
0.76 0.14 0.10
Matches are distributed among these distances:
40 1 0.00
41 73 0.15
42 91 0.18
43 135 0.27
44 100 0.20
45 59 0.12
46 33 0.07
ACGTcount: A:0.26, C:0.17, G:0.06, T:0.52
Consensus pattern (41 bp):
TTTATAATTGAGGCCTTAATTTTTTAATCTCATTTTTTACA
Found at i:36581 original size:44 final size:43
Alignment explanation
Indices: 36363--36966 Score: 427
Period size: 44 Copynumber: 14.0 Consensus size: 43
36353 TTGTTAATTG
* * * *
36363 TTTCAATCTCATTTTTTACATTTATATTTGAGGCCCTAA-TTT
1 TTTCAATCTCACTTTTTACTTTTATAATTGATGCCCTAATTTT
* * * *
36405 TTT-AATCTCATTTTTTACCTTTATAATTGAGGCACTTAA-TTT
1 TTTCAATCTCACTTTTTACTTTTATAATTGATGC-CCTAATTTT
* * * * * * **
36447 TTCCTATCTCACTTTCTACCTTTATAATTAAAGTTTCTAATTTTT
1 TTTCAATCTCACTTTTTACTTTTATAATTGATG-CCCTAA-TTTT
* * * * *
36492 TTTTAATTTCACTTTTTACATTTATAATAGATGCCTTTAATTTTTT
1 TTTCAATCTCACTTTTTACTTTTATAATTGATGCC-CTAA--TTTT
* *
36538 TTTCAATCCCACTTTTTACTTTTATAATGGATGCCCTAATTTT
1 TTTCAATCTCACTTTTTACTTTTATAATTGATGCCCTAATTTT
* *
36581 TTTCAATCTCACTTTTTATTTTTATAATTGAGGCCCGCT-ATTTT
1 TTTCAATCTCACTTTTTACTTTTATAATTGATG-CC-CTAATTTT
* * * * * *
36625 TTTCAATCTCAATTTCTACCTTTATAATTAAAGCCCATGA-TTT
1 TTTCAATCTCACTTTTTACTTTTATAATTGATGCCC-TAATTTT
* *
36668 TTT-AATCTCACTTTTTACTTTTATAATTGAGGCTCCTAA-ATT
1 TTTCAATCTCACTTTTTACTTTTATAATTGATGC-CCTAATTTT
* * * **
36710 TTTCAATCCCATTTTTTTACCTTTATAATTGAAACCCCTAATTTT
1 TTTCAATCTCA-CTTTTTACTTTTATAATTG-ATGCCCTAATTTT
*
36755 TTT-AATCTCACTTTTTA-TTTTATAATTGAGGCCCCTAA-TTT
1 TTTCAATCTCACTTTTTACTTTTATAATTGATG-CCCTAATTTT
* * ** * *
36796 TTTCAATCCCACTTTTTTACCTTTATAATTGAAACACTTAAGTTT
1 TTTCAATCTCAC-TTTTTACTTTTATAATTGATGC-CCTAATTTT
*
36841 TTTCAATCTCACTTTCTACTTTTATAATTGAAAT-CCCTAA-TTT
1 TTTCAATCTCACTTTTTACTTTTATAATTG--ATGCCCTAATTTT
**
36884 TTT--ATCTTGCTTTTTA-TCTTTATAATTGA-GATCCCTAA--TT
1 TTTCAATCTCACTTTTTACT-TTTATAATTGATG--CCCTAATTTT
* *
36924 TTTCAATC-CAACTTTTTACTTTTATAATTTAAGCCCCTAATTT
1 TTTCAATCTC-ACTTTTTACTTTTATAATTGATG-CCCTAATTT
36967 AATCATTTTT
Statistics
Matches: 452, Mismatches: 75, Indels: 68
0.76 0.13 0.11
Matches are distributed among these distances:
39 1 0.00
40 6 0.01
41 61 0.13
42 94 0.21
43 98 0.22
44 99 0.22
45 57 0.13
46 36 0.08
ACGTcount: A:0.26, C:0.18, G:0.05, T:0.51
Consensus pattern (43 bp):
TTTCAATCTCACTTTTTACTTTTATAATTGATGCCCTAATTTT
Found at i:36690 original size:86 final size:85
Alignment explanation
Indices: 36357--36966 Score: 534
Period size: 86 Copynumber: 7.1 Consensus size: 85
36347 TTTAGGTTGT
* * * * * * *
36357 TAATTGTTTCAATCTCATTTTTTACATTTATATTTGAGGCCCTAA-TTTTTTAATCTCATTTTTT
1 TAATTTTTTCAATCCCATTTTTTACCTTTATAATTAAAGCCCTAATTTTTTTAATCTCACTTTTT
* * *
36421 ACCTTTATAATTGAGGCACT
66 ACTTTTATAATTGAGGCCCC
* * * * * ** *
36441 TAATTTTTCCTATCTCACTTTCTACCTTTATAATTAAAGTTTCTAATTTTTTTTTAATTTCACTT
1 TAATTTTTTCAATCCCATTTTTTACCTTTATAATTAAAG-CCCTAA--TTTTTTTAATCTCACTT
* * * **
36506 TTTACATTTATAATAGATGCCTT
63 TTTACTTTTATAATTGAGGCCCC
* * ** *
36529 TAATTTTTTTTTCAATCCCACTTTTTACTTTTATAATGGATGCCCTAATTTTTTTCAATCTCACT
1 TAA---TTTTTTCAATCCCATTTTTTACCTTTATAATTAAAGCCCTAATTTTTTT-AATCTCACT
*
36594 TTTTATTTTTATAATTGAGGCCCGC
62 TTTTACTTTTATAATTGAGGCCC-C
* * * * *
36619 TATTTTTTTCAATCTCAATTTCTACCTTTATAATTAAAGCCCATGA-TTTTTTAATCTCACTTTT
1 TAATTTTTTCAATCCCATTTTTTACCTTTATAATTAAAGCCC-TAATTTTTTTAATCTCACTTTT
*
36683 TACTTTTATAATTGAGGCTCC
65 TACTTTTATAATTGAGGCCCC
* *
36704 TAAATTTTTCAATCCCATTTTTTTACCTTTATAATTGAAACCCCTAATTTTTTTAATCTCACTTT
1 TAATTTTTTCAATCCCA-TTTTTTACCTTTATAATT-AAAGCCCTAATTTTTTTAATCTCACTTT
36769 TTA-TTTTATAATTGAGGCCCC
64 TTACTTTTATAATTGAGGCCCC
* *
36790 TAATTTTTTCAATCCCACTTTTTTACCTTTATAATTGAAA-CACTTAAGTTTTTTCAATCTCACT
1 TAATTTTTTCAATCCCA-TTTTTTACCTTTATAATT-AAAGC-CCTAA-TTTTTTTAATCTCACT
* ***
36854 TTCTACTTTTATAATTGAAATCCC
62 TTTTACTTTTATAATTGAGGCCCC
**** * * * *
36878 TAATTTTTT--ATCTTGCTTTTTATCTTTATAATTGAGATCCCTAA-TTTTTCAATC-CAACTTT
1 TAATTTTTTCAATCCCATTTTTTACCTTTATAATT-AAAGCCCTAATTTTTTTAATCTC-ACTTT
* *
36939 TTACTTTTATAATTTAAGCCCC
64 TTACTTTTATAATTGAGGCCCC
36961 TAATTT
1 TAATTT
36967 AATCATTTTT
Statistics
Matches: 435, Mismatches: 73, Indels: 37
0.80 0.13 0.07
Matches are distributed among these distances:
82 1 0.00
83 39 0.09
84 30 0.07
85 43 0.10
86 111 0.26
87 83 0.19
88 68 0.16
89 26 0.06
90 6 0.01
91 28 0.06
ACGTcount: A:0.26, C:0.18, G:0.05, T:0.51
Consensus pattern (85 bp):
TAATTTTTTCAATCCCATTTTTTACCTTTATAATTAAAGCCCTAATTTTTTTAATCTCACTTTTT
ACTTTTATAATTGAGGCCCC
Found at i:44046 original size:36 final size:37
Alignment explanation
Indices: 43973--44046 Score: 98
Period size: 37 Copynumber: 2.0 Consensus size: 37
43963 TACTATAATT
* *
43973 AATTTATATATTTTCTTTTAAAAAATTAAATTCATAA
1 AATTTATATAATTTCTTTTAAAAAATTAAAATCATAA
*
44010 AATTTATATAATTT-TTTTATAAAATTGAAAAT-ATAA
1 AATTTATATAATTTCTTTTAAAAAATT-AAAATCATAA
44046 A
1 A
44047 TAGATTTAAT
Statistics
Matches: 33, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
36 16 0.48
37 17 0.52
ACGTcount: A:0.49, C:0.03, G:0.01, T:0.47
Consensus pattern (37 bp):
AATTTATATAATTTCTTTTAAAAAATTAAAATCATAA
Found at i:44605 original size:21 final size:22
Alignment explanation
Indices: 44554--44605 Score: 61
Period size: 21 Copynumber: 2.4 Consensus size: 22
44544 TAAATATAGC
44554 TATGTATTATAATATGATATTAA
1 TATG-ATTATAATATGATATTAA
* * *
44577 TTTAATTAT-ATATGATATTTA
1 TATGATTATAATATGATATTAA
44598 TATGATTA
1 TATGATTA
44606 ATGTTTTTAA
Statistics
Matches: 24, Mismatches: 5, Indels: 2
0.77 0.16 0.06
Matches are distributed among these distances:
21 17 0.71
22 5 0.21
23 2 0.08
ACGTcount: A:0.40, C:0.00, G:0.08, T:0.52
Consensus pattern (22 bp):
TATGATTATAATATGATATTAA
Found at i:44634 original size:12 final size:12
Alignment explanation
Indices: 44619--44644 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
44609 TTTTTAATTT
44619 TATTTTCTTAAA
1 TATTTTCTTAAA
44631 TATTTTCTTAAA
1 TATTTTCTTAAA
44643 TA
1 TA
44645 ATGTTGCATG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.35, C:0.08, G:0.00, T:0.58
Consensus pattern (12 bp):
TATTTTCTTAAA
Found at i:47088 original size:4 final size:4
Alignment explanation
Indices: 47081--47661 Score: 1017
Period size: 4 Copynumber: 148.2 Consensus size: 4
47071 TTACACACAC
* * *
47081 ACAT ACAT ACAT GCAT GCAT ACAT ATAT ACAT --AT ACAT ACAT ACAT
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
47127 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
47175 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
47223 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
47271 ACAT ACAT ACAT AC-- ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
47317 ACAT ACAT ACAT AC-T ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
*
47364 ACAT ACAT AC-- ACAT ACAT ACAT ACAT ACAT ACAT ACAT ATAT ACAT
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
*
47410 ACAT ACCAT ACAT ACAT --AT ATAT ACAT AC-T ACAT ACAT ACAT ACAT
1 ACAT A-CAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
47456 ACAT ACAT ACAT ACAT ACAT ACAT ACAT --AT ACAT ACAT ACAT ACAT
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
47502 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
47550 ACAT ACAT AC-T ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
47597 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
47645 ACAT ACAT ACAT ACAT A
1 ACAT ACAT ACAT ACAT A
47662 TATATATATA
Statistics
Matches: 556, Mismatches: 7, Indels: 28
0.94 0.01 0.05
Matches are distributed among these distances:
2 10 0.02
3 9 0.02
4 533 0.96
5 4 0.01
ACGTcount: A:0.49, C:0.25, G:0.00, T:0.26
Consensus pattern (4 bp):
ACAT
Found at i:47890 original size:20 final size:20
Alignment explanation
Indices: 47865--47910 Score: 83
Period size: 20 Copynumber: 2.3 Consensus size: 20
47855 TATTGTTCTT
47865 ACAGTATCGATACCTCATGA
1 ACAGTATCGATACCTCATGA
*
47885 ATAGTATCGATACCTCATGA
1 ACAGTATCGATACCTCATGA
47905 ACAGTA
1 ACAGTA
47911 CCAATACTGT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.37, C:0.22, G:0.15, T:0.26
Consensus pattern (20 bp):
ACAGTATCGATACCTCATGA
Found at i:47917 original size:20 final size:20
Alignment explanation
Indices: 47874--47917 Score: 61
Period size: 20 Copynumber: 2.2 Consensus size: 20
47864 TACAGTATCG
* * *
47874 ATACCTCATGAATAGTATCG
1 ATACCTCATGAACAGTACCA
47894 ATACCTCATGAACAGTACCA
1 ATACCTCATGAACAGTACCA
47914 ATAC
1 ATAC
47918 TGTTCATATG
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.39, C:0.25, G:0.11, T:0.25
Consensus pattern (20 bp):
ATACCTCATGAACAGTACCA
Found at i:53156 original size:2 final size:2
Alignment explanation
Indices: 53149--53182 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
53139 ACCAAACCAA
53149 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
53183 TAAGTTCAAA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:54036 original size:23 final size:22
Alignment explanation
Indices: 54002--54064 Score: 74
Period size: 21 Copynumber: 2.9 Consensus size: 22
53992 CATGGCCTTC
*
54002 TGCATCGATGCACATTCAAGGCG
1 TGCATCGATGCACATTCAACG-G
* *
54025 TGCATCGGTGCACCTTC-ACGG
1 TGCATCGATGCACATTCAACGG
*
54046 TGTATCGATGCACATTCAA
1 TGCATCGATGCACATTCAA
54065 AGGGATGCAT
Statistics
Matches: 33, Mismatches: 6, Indels: 3
0.79 0.14 0.07
Matches are distributed among these distances:
21 15 0.45
22 3 0.09
23 15 0.45
ACGTcount: A:0.24, C:0.27, G:0.24, T:0.25
Consensus pattern (22 bp):
TGCATCGATGCACATTCAACGG
Found at i:54932 original size:19 final size:19
Alignment explanation
Indices: 54908--54958 Score: 84
Period size: 19 Copynumber: 2.7 Consensus size: 19
54898 AAGGTGATTT
*
54908 GTGCATCGATTCATGAGTA
1 GTGCATCGATGCATGAGTA
*
54927 GTGCATCGATGGATGAGTA
1 GTGCATCGATGCATGAGTA
54946 GTGCATCGATGCA
1 GTGCATCGATGCA
54959 CATGTTAAGG
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
19 29 1.00
ACGTcount: A:0.25, C:0.16, G:0.31, T:0.27
Consensus pattern (19 bp):
GTGCATCGATGCATGAGTA
Found at i:55793 original size:23 final size:24
Alignment explanation
Indices: 55763--55816 Score: 74
Period size: 23 Copynumber: 2.2 Consensus size: 24
55753 TCCTTCGGGA
* *
55763 CATAGTGGTCCTTCGGGAC-ATTT
1 CATAGTGGTCATTCGAGACAATTT
55786 CATAGTGGTCATTCGAGACAAATTT
1 CATAGTGGTCATTCGAGAC-AATTT
55811 CATAGT
1 CATAGT
55817 CCCTAGTAGG
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
23 17 0.63
25 10 0.37
ACGTcount: A:0.26, C:0.19, G:0.22, T:0.33
Consensus pattern (24 bp):
CATAGTGGTCATTCGAGACAATTT
Found at i:59174 original size:33 final size:33
Alignment explanation
Indices: 59132--59196 Score: 121
Period size: 33 Copynumber: 2.0 Consensus size: 33
59122 AAAGTAAGAA
*
59132 TTTTCGGGCTCATATGGAATTTTTGGGTTGTGC
1 TTTTCGGGCTCAAATGGAATTTTTGGGTTGTGC
59165 TTTTCGGGCTCAAATGGAATTTTTGGGTTGTG
1 TTTTCGGGCTCAAATGGAATTTTTGGGTTGTG
59197 TGCATCGATG
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 31 1.00
ACGTcount: A:0.14, C:0.11, G:0.31, T:0.45
Consensus pattern (33 bp):
TTTTCGGGCTCAAATGGAATTTTTGGGTTGTGC
Found at i:60135 original size:18 final size:18
Alignment explanation
Indices: 60112--60156 Score: 81
Period size: 18 Copynumber: 2.5 Consensus size: 18
60102 GGGTCTACGC
60112 GGTCCTTCGGGACACAGT
1 GGTCCTTCGGGACACAGT
*
60130 GGTCCTTCGGGACATAGT
1 GGTCCTTCGGGACACAGT
60148 GGTCCTTCG
1 GGTCCTTCG
60157 AAATATTTCA
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
18 26 1.00
ACGTcount: A:0.13, C:0.27, G:0.33, T:0.27
Consensus pattern (18 bp):
GGTCCTTCGGGACACAGT
Done.