Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01004121.1 Hibiscus syriacus cultivar Beakdansim tig00009019_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: 75099
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.34
Found at i:1154 original size:73 final size:72
Alignment explanation
Indices: 1076--1214 Score: 165
Period size: 73 Copynumber: 1.9 Consensus size: 72
1066 CATATATATA
* * * * *
1076 TATATATTATATAGTTTGCAAATGATTTTTTTAA-A-ATATATATAATATATAATTTTAAAATAT
1 TATATAATATATAATTTGCAAA-G-TGTTTTGAATATATATATATAATATA-AATTTTAAAAAAT
1139 TTTGAAAACT
63 TTTGAAAACT
** *
1149 TATATAATATATAATTTTTAAAGTGTTTTGAATATATATATATAATATAATTTTTAAAAAATTTT
1 TATATAATATATAATTTGCAAAGTGTTTTGAATATATATATATAATATAAATTTTAAAAAATTTT
1214 G
66 G
1215 GAAATAAATA
Statistics
Matches: 56, Mismatches: 8, Indels: 5
0.81 0.12 0.07
Matches are distributed among these distances:
71 7 0.12
72 17 0.30
73 32 0.57
ACGTcount: A:0.44, C:0.01, G:0.06, T:0.49
Consensus pattern (72 bp):
TATATAATATATAATTTGCAAAGTGTTTTGAATATATATATATAATATAAATTTTAAAAAATTTT
GAAAACT
Found at i:1251 original size:38 final size:36
Alignment explanation
Indices: 1113--1256 Score: 141
Period size: 36 Copynumber: 3.9 Consensus size: 36
1103 TTTTTAAAAT
* *
1113 ATATATAATATATAATTTTAAAATATTTTGAAA-AC
1 ATATATAATATATAATTTTTAAATATTTTGAAATAA
* * *
1148 TTATATAATATATAATTTTTAAAGTGTTTTG-AATAT
1 ATATATAATATATAATTTTTAAA-TATTTTGAAATAA
*
1184 ATATAT-ATAATATAATTTTTAAAAAATTTTGGAAATAA
1 ATATATAAT-ATATAATTTTT-AAATATTTT-GAAATAA
* *
1222 ATATAAAATATATAGTTTTTAAATCATTTTTGAAA
1 ATATATAATATATAATTTTTAAAT-A-TTTTGAAA
1257 ACATTTTTGA
Statistics
Matches: 89, Mismatches: 11, Indels: 15
0.77 0.10 0.13
Matches are distributed among these distances:
35 25 0.28
36 27 0.30
37 7 0.08
38 24 0.27
39 6 0.07
ACGTcount: A:0.47, C:0.01, G:0.06, T:0.46
Consensus pattern (36 bp):
ATATATAATATATAATTTTTAAATATTTTGAAATAA
Found at i:1263 original size:11 final size:12
Alignment explanation
Indices: 1237--1270 Score: 52
Period size: 12 Copynumber: 2.9 Consensus size: 12
1227 AAATATATAG
*
1237 TTTTT-AAATCA
1 TTTTTGAAAACA
1248 TTTTTGAAAACA
1 TTTTTGAAAACA
1260 TTTTTGAAAAC
1 TTTTTGAAAAC
1271 GTTTATATAA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
11 5 0.24
12 16 0.76
ACGTcount: A:0.38, C:0.09, G:0.06, T:0.47
Consensus pattern (12 bp):
TTTTTGAAAACA
Found at i:1324 original size:18 final size:17
Alignment explanation
Indices: 1301--1379 Score: 73
Period size: 18 Copynumber: 4.9 Consensus size: 17
1291 TTAAAAACAT
1301 TTTTGAAAATATATATAA
1 TTTTGAAAATATATAT-A
1319 TTTTGAAAAT-TA-AT-
1 TTTTGAAAATATATATA
1333 TTTT-AAAATATATATA
1 TTTTGAAAATATATATA
1349 GTTTTGAAAAT-TAT-T-
1 -TTTTGAAAATATATATA
**
1364 TTTAAAAAATATATAT
1 TTTTGAAAATATATAT
1380 TATATAGTTT
Statistics
Matches: 52, Mismatches: 2, Indels: 16
0.74 0.03 0.23
Matches are distributed among these distances:
13 5 0.10
14 14 0.27
15 5 0.10
16 4 0.08
17 9 0.17
18 15 0.29
ACGTcount: A:0.47, C:0.00, G:0.05, T:0.48
Consensus pattern (17 bp):
TTTTGAAAATATATATA
Found at i:1372 original size:75 final size:69
Alignment explanation
Indices: 1312--1490 Score: 270
Period size: 73 Copynumber: 2.5 Consensus size: 69
1302 TTTGAAAATA
* *
1312 TATATAATTTTGAAAATTAATTTTTAAAATATATATAGTTTTGAAAATTATTTTTAAAAAA-TAT
1 TATATAGTTTTGAAAATTATTTTTTAAAATATATATAGTTTTGAAAATTATTTTTAAAAAATTAT
1376 ATAT
66 ATAT
*
1380 TATATAGTTTTGAAAATTATTTTTTTAAACATATATAATATAGTTTTGAAAATTATTTTTTAAAA
1 TATATAGTTTTGAAAATTA-TTTTTT-AA-A-ATAT-ATATAGTTTTGAAAATTATTTTTAAAAA
1445 ATATATATAT
61 AT-TATATAT
1455 TATATAGTTTTGAAAATTATTTTTTAAAATATATAT
1 TATATAGTTTTGAAAATTATTTTTTAAAATATATAT
1491 TATATATTTT
Statistics
Matches: 101, Mismatches: 3, Indels: 12
0.87 0.03 0.10
Matches are distributed among these distances:
68 18 0.18
69 5 0.05
70 6 0.06
71 5 0.05
72 5 0.05
73 30 0.30
74 6 0.06
75 26 0.26
ACGTcount: A:0.44, C:0.01, G:0.05, T:0.50
Consensus pattern (69 bp):
TATATAGTTTTGAAAATTATTTTTTAAAATATATATAGTTTTGAAAATTATTTTTAAAAAATTAT
ATAT
Found at i:1421 original size:36 final size:36
Alignment explanation
Indices: 1309--1507 Score: 239
Period size: 36 Copynumber: 5.6 Consensus size: 36
1299 ATTTTTGAAA
* *
1309 ATAT-ATATAATTTTGAAAATTAATTTTT--AA-A-
1 ATATAATATAGTTTTGAAAATTATTTTTTAAAATAT
*
1340 ATAT-ATATAGTTTTGAAAATTATTTTTAAAAAATAT
1 ATATAATATAGTTTTGAAAATTATTTTT-TAAAATAT
* * *
1376 ATATTATATAGTTTTGAAAATTATTTTTTTAAACAT
1 ATATAATATAGTTTTGAAAATTATTTTTTAAAATAT
1412 ATATAATATAGTTTTGAAAATTATTTTTTAAAAATAT
1 ATATAATATAGTTTTGAAAATTATTTTTT-AAAATAT
1449 ATATATTATATAGTTTTGAAAATTATTTTTTAAAATAT
1 ATATA--ATATAGTTTTGAAAATTATTTTTTAAAATAT
* * *
1487 ATATTATATATTTTTTAAAAT
1 ATATAATATAGTTTTGAAAAT
1508 ATAATTTATA
Statistics
Matches: 147, Mismatches: 12, Indels: 13
0.85 0.07 0.08
Matches are distributed among these distances:
31 25 0.17
34 2 0.01
35 1 0.01
36 51 0.35
37 33 0.22
38 11 0.07
39 24 0.16
ACGTcount: A:0.44, C:0.01, G:0.05, T:0.51
Consensus pattern (36 bp):
ATATAATATAGTTTTGAAAATTATTTTTTAAAATAT
Found at i:1496 original size:75 final size:71
Alignment explanation
Indices: 1312--1507 Score: 272
Period size: 75 Copynumber: 2.7 Consensus size: 71
1302 TTTGAAAATA
* *
1312 TATATAATTTTGAAAATTAATTTTT-AAA-ATA-TATATAGTTTTGAAAATTATTTTTAAAAAAT
1 TATATAGTTTTGAAAATTATTTTTTAAAATATATTATATAGTTTTGAAAATTATTTTTAAAAAAT
1374 ATATAT
66 ATATAT
*
1380 TATATAGTTTTGAAAATTATTTTTTTAAACATATATAATATAGTTTTGAAAATTATTTTTTAAAA
1 TATATAGTTTTGAAAATTA-TTTTTTAAA-ATATATTATATAGTTTTGAAAATTA-TTTTTAAAA
1445 ATATATATAT
63 A-ATATATAT
* *
1455 TATATAGTTTTGAAAATTATTTTTTAAAATATATATTATATATTTTTTAAAAT
1 TATATAGTTTTGAAAATTATTTTTT-AAA-ATATATTATATAGTTTTGAAAAT
1508 ATAATTTATA
Statistics
Matches: 113, Mismatches: 7, Indels: 9
0.88 0.05 0.07
Matches are distributed among these distances:
68 18 0.16
69 5 0.04
70 2 0.02
71 1 0.01
72 3 0.03
73 18 0.16
74 16 0.14
75 50 0.44
ACGTcount: A:0.44, C:0.01, G:0.05, T:0.51
Consensus pattern (71 bp):
TATATAGTTTTGAAAATTATTTTTTAAAATATATTATATAGTTTTGAAAATTATTTTTAAAAAAT
ATATAT
Found at i:1531 original size:59 final size:61
Alignment explanation
Indices: 1433--1566 Score: 200
Period size: 59 Copynumber: 2.2 Consensus size: 61
1423 TTTTGAAAAT
*
1433 TATTTTTTAAAAATATATATATTATATAGTTTTGAAAATTATTTTTTAAAATATATATTATA
1 TATTTTTT-AAAATATATATATTATATAGTTTTGAAAATTATTTTTTAAAACATATATTATA
* *
1495 TATTTTTTAAAATATA-AT-TTATATATTTTTTAAAATTATTTTTTAAAACATATATTATA
1 TATTTTTTAAAATATATATATTATATAGTTTTGAAAATTATTTTTTAAAACATATATTATA
* *
1554 TAGTTTTAAAAAT
1 TATTTTTTAAAAT
1567 GTTTTTTATT
Statistics
Matches: 67, Mismatches: 5, Indels: 3
0.89 0.07 0.04
Matches are distributed among these distances:
59 49 0.73
60 2 0.03
61 8 0.12
62 8 0.12
ACGTcount: A:0.43, C:0.01, G:0.02, T:0.54
Consensus pattern (61 bp):
TATTTTTTAAAATATATATATTATATAGTTTTGAAAATTATTTTTTAAAACATATATTATA
Found at i:1534 original size:134 final size:141
Alignment explanation
Indices: 1312--1574 Score: 353
Period size: 134 Copynumber: 1.9 Consensus size: 141
1302 TTTGAAAATA
*
1312 TATATAATTTTGAAAATTAATTTTTAAAATATATATAGTTTTGAAAATTATTTTTAAAAAATATA
1 TATATAATTTTGAAAATTAATTTTTAAAATATATATAGTTAT-AAAATTATTTTTAAAAAATATA
* *
1377 TATTATATAGTTTTGAAAATTATTTTTTTAAACATATATAATATAGTTTTGAAAATTATTTTTTA
65 TATTATATAGTTTTGAAAATTATTTTTTAAAACATATATAATATAGTTTT-AAAAATATTTTTTA
1442 AAAATATATATAT
129 AAAATATATATAT
* * * *
1455 TATATAGTTTTGAAAATT-ATTTTTTAAA-ATATATA-TTAT-ATA-T-TTTTTAAAATATA-AT
1 TATATAATTTTGAAAATTAATTTTTAAAATATATATAGTTATAAAATTATTTTTAAAAAATATAT
* * * *
1513 -TTATATATTTTTTAAAATTATTTTTTAAAACATATATTATATAGTTTTAAAAATGTTTTTTA
66 ATTATATAGTTTTGAAAATTATTTTTTAAAACATATATAATATAGTTTTAAAAATATTTTTTA
1575 TTATATTTAT
Statistics
Matches: 109, Mismatches: 11, Indels: 10
0.84 0.08 0.08
Matches are distributed among these distances:
133 12 0.11
134 44 0.40
135 2 0.02
136 12 0.11
137 1 0.01
138 2 0.02
140 3 0.03
141 7 0.06
142 9 0.08
143 17 0.16
ACGTcount: A:0.43, C:0.01, G:0.04, T:0.52
Consensus pattern (141 bp):
TATATAATTTTGAAAATTAATTTTTAAAATATATATAGTTATAAAATTATTTTTAAAAAATATAT
ATTATATAGTTTTGAAAATTATTTTTTAAAACATATATAATATAGTTTTAAAAATATTTTTTAAA
AATATATATAT
Found at i:1535 original size:21 final size:22
Alignment explanation
Indices: 1472--1535 Score: 103
Period size: 23 Copynumber: 2.9 Consensus size: 22
1462 TTTTGAAAAT
1472 TATTTTTTAAAATATATATTATA
1 TATTTTTTAAAATATAT-TTATA
1495 TATTTTTTAAAATATAATTTATA
1 TATTTTTTAAAATAT-ATTTATA
1518 TATTTTTTAAAAT-TATTT
1 TATTTTTTAAAATATATTT
1536 TTTAAAACAT
Statistics
Matches: 40, Mismatches: 0, Indels: 4
0.91 0.00 0.09
Matches are distributed among these distances:
21 4 0.10
22 1 0.03
23 33 0.82
24 2 0.05
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (22 bp):
TATTTTTTAAAATATATTTATA
Found at i:1535 original size:36 final size:35
Alignment explanation
Indices: 1494--1574 Score: 101
Period size: 36 Copynumber: 2.3 Consensus size: 35
1484 TATATATTAT
* *
1494 ATATTTTTTAAAATATA-ATTTATATATTTTTTAAAA
1 ATATTTTTTAAAACATATA-TTATATA-GTTTTAAAA
*
1530 TTATTTTTTAAAACATATATTATATAGTTTTAAAA
1 ATATTTTTTAAAACATATATTATATAGTTTTAAAA
*
1565 ATGTTTTTTA
1 ATATTTTTTA
1575 TTATATTTAT
Statistics
Matches: 39, Mismatches: 5, Indels: 3
0.83 0.11 0.06
Matches are distributed among these distances:
35 16 0.41
36 22 0.56
37 1 0.03
ACGTcount: A:0.41, C:0.01, G:0.02, T:0.56
Consensus pattern (35 bp):
ATATTTTTTAAAACATATATTATATAGTTTTAAAA
Found at i:1587 original size:4 final size:4
Alignment explanation
Indices: 1571--1634 Score: 60
Period size: 4 Copynumber: 15.5 Consensus size: 4
1561 AAAAATGTTT
* *
1571 TTTA TTATA TTTA TTTA TTTA -TTA TTTT TCTTC TTT- TTTA TTTA TTTA
1 TTTA TT-TA TTTA TTTA TTTA TTTA TTTA T-TTA TTTA TTTA TTTA TTTA
1619 TTTTA TTTTA TTTA TT
1 -TTTA -TTTA TTTA TT
1635 ACTTATTATT
Statistics
Matches: 53, Mismatches: 2, Indels: 10
0.82 0.03 0.15
Matches are distributed among these distances:
3 6 0.11
4 31 0.58
5 16 0.30
ACGTcount: A:0.20, C:0.03, G:0.00, T:0.77
Consensus pattern (4 bp):
TTTA
Found at i:1645 original size:3 final size:3
Alignment explanation
Indices: 1616--1668 Score: 74
Period size: 3 Copynumber: 17.7 Consensus size: 3
1606 TTTTATTTAT
1616 TTA TT- TTA TT- TTA TTTA TTA CTTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA -TTA TTA -TTA TTA TTA TTA TTA TTA TTA TTA
1661 TTA TTA TT
1 TTA TTA TT
1669 TTCGTTTCAG
Statistics
Matches: 46, Mismatches: 0, Indels: 8
0.85 0.00 0.15
Matches are distributed among these distances:
2 4 0.09
3 36 0.78
4 6 0.13
ACGTcount: A:0.28, C:0.02, G:0.00, T:0.70
Consensus pattern (3 bp):
TTA
Found at i:2812 original size:5 final size:5
Alignment explanation
Indices: 2793--2906 Score: 54
Period size: 5 Copynumber: 21.8 Consensus size: 5
2783 CTTATTATTT
* * *
2793 TTTTA CTTTTG TTTTA TTTTA TCTTA TATTT- TTCTA TTTTA TTTT- TGGGTTTA
1 TTTTA -TTTTA TTTTA TTTTA TTTTA T-TTTA TTTTA TTTTA TTTTA T---TTTA
* ** * * *
2846 TTTAA TAATA TTATTA TTATTA TTAT- TTTTA TTTGTT TTTTA ATTTA
1 TTTTA TTTTA TT-TTA TT-TTA TTTTA TTTTA TTT-TA TTTTA TTTTA
2893 TTTTA TTTTA TTTT
1 TTTTA TTTTA TTTT
2907 TTCCTTTTCT
Statistics
Matches: 81, Mismatches: 18, Indels: 19
0.69 0.15 0.16
Matches are distributed among these distances:
4 6 0.07
5 51 0.63
6 20 0.25
7 3 0.04
8 1 0.01
ACGTcount: A:0.21, C:0.03, G:0.04, T:0.72
Consensus pattern (5 bp):
TTTTA
Found at i:2935 original size:14 final size:14
Alignment explanation
Indices: 2916--2942 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
2906 TTTCCTTTTC
2916 TTTATTTTTCCTTA
1 TTTATTTTTCCTTA
2930 TTTATTTTTCCTT
1 TTTATTTTTCCTT
2943 TTTTTATATT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.11, C:0.15, G:0.00, T:0.74
Consensus pattern (14 bp):
TTTATTTTTCCTTA
Found at i:6992 original size:95 final size:95
Alignment explanation
Indices: 6876--7168 Score: 462
Period size: 95 Copynumber: 3.1 Consensus size: 95
6866 AGATTATAAT
* * **
6876 ATTAT-ATACACAATAAAGCTTGAGCTGTCCCTCTAAAGCAATTGGTTAAACGCCCCAACTTTAT
1 ATTATAATATACAATAAAGCTTGAGTTGTCCCTCTAAAGCAATTGGTTAAACGCCCCGGCTTTAT
* *
6940 GTATAAGATTTAGCTAGCCTGATAAAGGTG
66 GGATAAGATTCAGCTAGCCTGATAAAGGTG
*
6970 ATTATAATATACAATAAAGCTTGAGTTGTCCCTCTAAAGCAATTAGTTAAACGCCCCGGCTTTAT
1 ATTATAATATACAATAAAGCTTGAGTTGTCCCTCTAAAGCAATTGGTTAAACGCCCCGGCTTTAT
* *
7035 GGATAAGATACAACTAGCCTGATAAAGGTG
66 GGATAAGATTCAGCTAGCCTGATAAAGGTG
* *
7065 ATTATAATATACAATAAAGCTCGAGTTGTCCCTCTAGAGCAATTGGTTAAACGCCCCGGCTTTAT
1 ATTATAATATACAATAAAGCTTGAGTTGTCCCTCTAAAGCAATTGGTTAAACGCCCCGGCTTTAT
* *
7130 GGATAATATTCAGGTAGCCTGATAAAGGTG
66 GGATAAGATTCAGCTAGCCTGATAAAGGTG
7160 ATTATAATA
1 ATTATAATA
7169 CAACGATATT
Statistics
Matches: 182, Mismatches: 16, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
94 5 0.03
95 177 0.97
ACGTcount: A:0.34, C:0.18, G:0.18, T:0.30
Consensus pattern (95 bp):
ATTATAATATACAATAAAGCTTGAGTTGTCCCTCTAAAGCAATTGGTTAAACGCCCCGGCTTTAT
GGATAAGATTCAGCTAGCCTGATAAAGGTG
Found at i:8364 original size:84 final size:84
Alignment explanation
Indices: 8237--8673 Score: 566
Period size: 84 Copynumber: 5.3 Consensus size: 84
8227 TGCGGTATAG
* * * * * *
8237 CTCAAGGCGAAAAGGGCTATCT-TCCAACAAAATACCTTTGAGTTCGATTACACTCAACTCCAAG
1 CTCAAGGCGAGAAGGGTTATCTGT-CAACAAAAGACCTTCGAGTTCGATTACACTCAGCTCAAAG
*
8301 GCACACCATTTACAGCATAA
65 GCACATCATTTACAGCATAA
* * * *
8321 CTCAAGGCGATAAGGGTTATATGTCAACAAAAGACCTTCGAGTTCGATTACACTCAACTCAAAAG
1 CTCAAGGCGAGAAGGGTTATCTGTCAACAAAAGACCTTCGAGTTCGATTACACTCAGCTCAAAGG
* *
8386 CACATCATTTATAACATAA
66 CACATCATTTACAGCATAA
* *
8405 CTCAAGGCGAGAAGGGTTATCTGTCCACCAAAG-CCTTCGAGTTCGATTACACTCAGCTCAAAGG
1 CTCAAGGCGAGAAGGGTTATCTGTCAACAAAAGACCTTCGAGTTCGATTACACTCAGCTCAAAGG
* * *
8469 CATATCATTTGCAACATAA
66 CACATCATTTACAGCATAA
* * * *
8488 CTTAAGGCTAGAAGGGTTATCTGTCAACACAAGACCTTCGAGTTCGATTACACTCAGCTCAAAAG
1 CTCAAGGCGAGAAGGGTTATCTGTCAACAAAAGACCTTCGAGTTCGATTACACTCAGCTCAAAGG
* *
8553 CACATCATTTGCAGCATAG
66 CACATCATTTACAGCATAA
*
8572 CTCAAGGCAAGAAGGGTTATCTG-C--C-AAAGACCTTCGAGTTCGATTACACTCAGCTCAAAGG
1 CTCAAGGCGAGAAGGGTTATCTGTCAACAAAAGACCTTCGAGTTCGATTACACTCAGCTCAAAGG
8633 CACATCA-TTACAGCA-AA
66 CACATCATTTACAGCATAA
*
8650 GCTCAAGGCAAGAAGGGTTATCTG
1 -CTCAAGGCGAGAAGGGTTATCTG
8674 CCAAAGACCT
Statistics
Matches: 316, Mismatches: 34, Indels: 11
0.88 0.09 0.03
Matches are distributed among these distances:
78 1 0.00
79 30 0.09
80 41 0.13
81 1 0.00
83 74 0.23
84 168 0.53
85 1 0.00
ACGTcount: A:0.34, C:0.24, G:0.18, T:0.23
Consensus pattern (84 bp):
CTCAAGGCGAGAAGGGTTATCTGTCAACAAAAGACCTTCGAGTTCGATTACACTCAGCTCAAAGG
CACATCATTTACAGCATAA
Found at i:8552 original size:167 final size:167
Alignment explanation
Indices: 8237--8673 Score: 582
Period size: 167 Copynumber: 2.6 Consensus size: 167
8227 TGCGGTATAG
* * * * * * *
8237 CTCAAGGCGAAAAGGGCTATCT-TCCAACAAAATACCTTTGAGTTCGATTACACTCAACTCCAAG
1 CTCAAGGCGAGAAGGGTTATCTGTCC-ACCAAA-GCCTTCGAGTTCGATTACACTCAGCTCAAAG
* * * *
8301 GCACACCATTTACAGCATAACTCAAGGCGATAAGGGTTATATGTCAACAAAAGACCTTCGAGTTC
64 GCACATCATTTACAGCATAACTCAAGGCAAGAAGGGTTATCTGTCAACAAAAGACCTTCGAGTTC
*
8366 GATTACACTCAACTCAAAAGCACATCATTTATAACATAA
129 GATTACACTCAACTCAAAAGCACATCATTTACAACATAA
8405 CTCAAGGCGAGAAGGGTTATCTGTCCACCAAAGCCTTCGAGTTCGATTACACTCAGCTCAAAGGC
1 CTCAAGGCGAGAAGGGTTATCTGTCCACCAAAGCCTTCGAGTTCGATTACACTCAGCTCAAAGGC
* * * * * *
8470 ATATCATTTGCAACATAACTTAAGGCTAGAAGGGTTATCTGTCAACACAAGACCTTCGAGTTCGA
66 ACATCATTTACAGCATAACTCAAGGCAAGAAGGGTTATCTGTCAACAAAAGACCTTCGAGTTCGA
* * * *
8535 TTACACTCAGCTCAAAAGCACATCATTTGCAGCATAG
131 TTACACTCAACTCAAAAGCACATCATTTACAACATAA
*
8572 CTCAAGGCAAGAAGGGTTATCTG----CCAAAGACCTTCGAGTTCGATTACACTCAGCTCAAAGG
1 CTCAAGGCGAGAAGGGTTATCTGTCCACCAAAG-CCTTCGAGTTCGATTACACTCAGCTCAAAGG
8633 CACATCA-TTACAGCA-AAGCTCAAGGCAAGAAGGGTTATCTG
65 CACATCATTTACAGCATAA-CTCAAGGCAAGAAGGGTTATCTG
8674 CCAAAGACCT
Statistics
Matches: 239, Mismatches: 27, Indels: 11
0.86 0.10 0.04
Matches are distributed among these distances:
162 2 0.01
163 33 0.14
164 37 0.15
167 139 0.58
168 25 0.10
169 3 0.01
ACGTcount: A:0.34, C:0.24, G:0.18, T:0.23
Consensus pattern (167 bp):
CTCAAGGCGAGAAGGGTTATCTGTCCACCAAAGCCTTCGAGTTCGATTACACTCAGCTCAAAGGC
ACATCATTTACAGCATAACTCAAGGCAAGAAGGGTTATCTGTCAACAAAAGACCTTCGAGTTCGA
TTACACTCAACTCAAAAGCACATCATTTACAACATAA
Found at i:16373 original size:64 final size:64
Alignment explanation
Indices: 16287--16428 Score: 194
Period size: 64 Copynumber: 2.2 Consensus size: 64
16277 ACCAAACATT
* * * * *
16287 GTAATCTTATATTCATGCTAAACGAACCAAACACAACAATACAACATTCTCAGTAATGTGTTTG
1 GTAATATTACATTCATGCTAAACGAACCAAACACAACAATACAACATTCCCAGTAATATGTTAG
* * * *
16351 GTAATGTTACATTCATGTTAAACGAACCAAACACAATAATATAACATTCCCAGTAATATGTTAG
1 GTAATATTACATTCATGCTAAACGAACCAAACACAACAATACAACATTCCCAGTAATATGTTAG
*
16415 ATAATATTACATTC
1 GTAATATTACATTC
16429 CGATAATCAT
Statistics
Matches: 68, Mismatches: 10, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
64 68 1.00
ACGTcount: A:0.41, C:0.18, G:0.10, T:0.31
Consensus pattern (64 bp):
GTAATATTACATTCATGCTAAACGAACCAAACACAACAATACAACATTCCCAGTAATATGTTAG
Found at i:18149 original size:14 final size:15
Alignment explanation
Indices: 18126--18164 Score: 53
Period size: 14 Copynumber: 2.7 Consensus size: 15
18116 AAGAAATATT
18126 TATTATAAAATAAAA
1 TATTATAAAATAAAA
*
18141 TATTA-AAAATAAGA
1 TATTATAAAATAAAA
*
18155 TATTTTAAAA
1 TATTATAAAA
18165 AATAAAAATA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
14 12 0.57
15 9 0.43
ACGTcount: A:0.62, C:0.00, G:0.03, T:0.36
Consensus pattern (15 bp):
TATTATAAAATAAAA
Found at i:28896 original size:20 final size:21
Alignment explanation
Indices: 28867--28920 Score: 58
Period size: 20 Copynumber: 2.6 Consensus size: 21
28857 CAAATATTCA
28867 AAAAAGTAAATATAAAATACT
1 AAAAAGTAAATATAAAATACT
* *
28888 AAAAA-TAAA-ATTAAATTATT
1 AAAAAGTAAATA-TAAAATACT
*
28908 AAAAATTAAATAT
1 AAAAAGTAAATAT
28921 TCATATTAAA
Statistics
Matches: 28, Mismatches: 2, Indels: 6
0.78 0.06 0.17
Matches are distributed among these distances:
19 1 0.04
20 16 0.57
21 10 0.36
22 1 0.04
ACGTcount: A:0.67, C:0.02, G:0.02, T:0.30
Consensus pattern (21 bp):
AAAAAGTAAATATAAAATACT
Found at i:29472 original size:24 final size:26
Alignment explanation
Indices: 29430--29482 Score: 83
Period size: 24 Copynumber: 2.1 Consensus size: 26
29420 TCTTAATTTA
29430 TTATGAGAAAAAAAGTAATCTCTAAC
1 TTATGAGAAAAAAAGTAATCTCTAAC
*
29456 TTATGAG-AAAAAA-TAATCTTTAAC
1 TTATGAGAAAAAAAGTAATCTCTAAC
29480 TTA
1 TTA
29483 GAAAAACACT
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
24 13 0.50
25 6 0.23
26 7 0.27
ACGTcount: A:0.49, C:0.09, G:0.09, T:0.32
Consensus pattern (26 bp):
TTATGAGAAAAAAAGTAATCTCTAAC
Found at i:30205 original size:47 final size:47
Alignment explanation
Indices: 30152--30242 Score: 164
Period size: 47 Copynumber: 1.9 Consensus size: 47
30142 TTATATGCTT
30152 GAACAAAATCATCTAATCATTTTAAATAAAATAAAAGATATACGCAA
1 GAACAAAATCATCTAATCATTTTAAATAAAATAAAAGATATACGCAA
* *
30199 GAACAAAATCATCTGATCATTTTAAATGAAATAAAAGATATACG
1 GAACAAAATCATCTAATCATTTTAAATAAAATAAAAGATATACG
30243 TAGTCTATAT
Statistics
Matches: 42, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
47 42 1.00
ACGTcount: A:0.53, C:0.12, G:0.09, T:0.26
Consensus pattern (47 bp):
GAACAAAATCATCTAATCATTTTAAATAAAATAAAAGATATACGCAA
Found at i:32504 original size:10 final size:11
Alignment explanation
Indices: 32470--32505 Score: 58
Period size: 10 Copynumber: 3.5 Consensus size: 11
32460 AAGCCACCTA
32470 ATTTTTTTTAC
1 ATTTTTTTTAC
32481 A-TTTTTTTAC
1 ATTTTTTTTAC
32491 ATTTTTTTTA-
1 ATTTTTTTTAC
32501 ATTTT
1 ATTTT
32506 ATATTATTTT
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
10 15 0.62
11 9 0.38
ACGTcount: A:0.19, C:0.06, G:0.00, T:0.75
Consensus pattern (11 bp):
ATTTTTTTTAC
Found at i:32515 original size:20 final size:20
Alignment explanation
Indices: 32468--32505 Score: 60
Period size: 21 Copynumber: 1.9 Consensus size: 20
32458 GGAAGCCACC
32468 TAATTTTTTTTACATTTTTT
1 TAATTTTTTTTACATTTTTT
32488 TACATTTTTTTTA-ATTTT
1 TA-ATTTTTTTTACATTTT
32506 ATATTATTTT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
20 7 0.41
21 10 0.59
ACGTcount: A:0.21, C:0.05, G:0.00, T:0.74
Consensus pattern (20 bp):
TAATTTTTTTTACATTTTTT
Found at i:39514 original size:29 final size:29
Alignment explanation
Indices: 39472--39540 Score: 129
Period size: 29 Copynumber: 2.4 Consensus size: 29
39462 TCTAAGGAGA
*
39472 AATAGAAAATATTCTAATATTTCCGATTC
1 AATAGAAAATATTCTAATATTTCCGATCC
39501 AATAGAAAATATTCTAATATTTCCGATCC
1 AATAGAAAATATTCTAATATTTCCGATCC
39530 AATAGAAAATA
1 AATAGAAAATA
39541 ATCCTAAAAT
Statistics
Matches: 39, Mismatches: 1, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
29 39 1.00
ACGTcount: A:0.46, C:0.13, G:0.07, T:0.33
Consensus pattern (29 bp):
AATAGAAAATATTCTAATATTTCCGATCC
Found at i:40072 original size:35 final size:35
Alignment explanation
Indices: 40031--40107 Score: 154
Period size: 35 Copynumber: 2.2 Consensus size: 35
40021 AAATTGACAT
40031 GGAAATGGAGGAAAAATAAAGCTTAATAAATTGAG
1 GGAAATGGAGGAAAAATAAAGCTTAATAAATTGAG
40066 GGAAATGGAGGAAAAATAAAGCTTAATAAATTGAG
1 GGAAATGGAGGAAAAATAAAGCTTAATAAATTGAG
40101 GGAAATG
1 GGAAATG
40108 TTGTAATCTA
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
35 42 1.00
ACGTcount: A:0.51, C:0.03, G:0.27, T:0.19
Consensus pattern (35 bp):
GGAAATGGAGGAAAAATAAAGCTTAATAAATTGAG
Found at i:42378 original size:139 final size:140
Alignment explanation
Indices: 42052--42582 Score: 672
Period size: 139 Copynumber: 3.8 Consensus size: 140
42042 TGTTGTTCTA
* * *
42052 ACTCCTTATGCGATGAAAACAAGCTAAGATTGAACAAGTTCTTCTCAGTATGAACTTCTTATCCC
1 ACTCCATATGCGATG-AATCAAGCTAAGATTGAACAAGTTCTTCTCATTATGAACTTCTTATCCC
*
42117 TCATCGGATGAGTTCTTCTCATTATGAACTCTCCCATTGGAAATGTTGATACCTCGAGTGAGGTG
65 TCATCGGATGAGTTCTTCTCATTATGAACTCTCCCATTGGAAATGTTGATCCCTCGAGTGAGGTG
* *
42182 TTACTCATTCG
130 TTGCTGATTCG
** *
42193 ACTCCATATGCGATGAATCAATTTAAGATTGAACAAGTTTTTCTCATTATGAACTTCTTATCCCT
1 ACTCCATATGCGATGAATCAAGCTAAGATTGAACAAGTTCTTCTCATTATGAACTTCTTATCCCT
* *
42258 CATCGTATGAGTTCTTCTTATTATGAACTCTCCCATTGGAAATGTT-ATCCCTCGAGTGAGGTGT
66 CATCGGATGAGTTCTTCTCATTATGAACTCTCCCATTGGAAATGTTGATCCCTCGAGTGAGGTGT
42322 TGCTGATTCG
131 TGCTGATTCG
* * * * * * * *
42332 AGTCCATATGCGATGAATCGAGTTAAGGTTGAACAAGTTTTTCTCATTATAAACTTATTCTCCCT
1 ACTCCATATGCGATGAATCAAGCTAAGATTGAACAAGTTCTTCTCATTATGAACTTCTTATCCCT
* * * * * * * * * * *
42397 CATCAGATAAGCTATTCTCATTATGAATTCT-CTACTAGAAATGTTGATCTCTCAAGTGAGTTGT
66 CATCGGATGAGTTCTTCTCATTATGAACTCTCCCATTGGAAATGTTGATCCCTCGAGTGAGGTGT
* *
42461 TGATGATTCA
131 TGCTGATTCG
* * * *
42471 ACTCCATATGTGATGAATCGAGCTAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTCCCT
1 ACTCCATATGCGATGAATCAAGCTAAGATTGAACAAGTTCTTCTCATTATGAACTTCTTATCCCT
* * * *
42536 CATTGGATGAGTTTTTCTCATTATGAACTCT-CCACTAGAAATGTTGA
66 CATCGGATGAGTTCTTCTCATTATGAACTCTCCCATTGGAAATGTTGA
42583 CTGGTTTATC
Statistics
Matches: 343, Mismatches: 46, Indels: 4
0.87 0.12 0.01
Matches are distributed among these distances:
138 11 0.03
139 229 0.67
140 89 0.26
141 14 0.04
ACGTcount: A:0.27, C:0.20, G:0.17, T:0.36
Consensus pattern (140 bp):
ACTCCATATGCGATGAATCAAGCTAAGATTGAACAAGTTCTTCTCATTATGAACTTCTTATCCCT
CATCGGATGAGTTCTTCTCATTATGAACTCTCCCATTGGAAATGTTGATCCCTCGAGTGAGGTGT
TGCTGATTCG
Found at i:43494 original size:41 final size:40
Alignment explanation
Indices: 43433--43561 Score: 116
Period size: 42 Copynumber: 3.1 Consensus size: 40
43423 CATTTGAAAA
* * *
43433 CATCTTGCCCGAAGGTCTTATGGATGGCCAGAAGGACTTAT
1 CATCTTGCTCGAAAGACTTAT-GATGGCCAGAAGGACTTAT
* * * *
43474 CATCTTGCTCGAAAGACTTATAGATGACCCGAAGGATTTAAG
1 CATCTTGCTCGAAAGACTTAT-GATGGCCAGAAGGACTT-AT
**
43516 CATCACGCTCGAAAGACTTACTGATGGCTCA-AAGGACTTACT
1 CATCTTGCTCGAAAGACTTA-TGATGGC-CAGAAGGACTTA-T
43558 CATC
1 CATC
43562 AAGAAACCCT
Statistics
Matches: 70, Mismatches: 14, Indels: 7
0.77 0.15 0.08
Matches are distributed among these distances:
41 33 0.47
42 35 0.50
43 2 0.03
ACGTcount: A:0.29, C:0.23, G:0.22, T:0.26
Consensus pattern (40 bp):
CATCTTGCTCGAAAGACTTATGATGGCCAGAAGGACTTAT
Found at i:43699 original size:55 final size:55
Alignment explanation
Indices: 43653--43811 Score: 239
Period size: 55 Copynumber: 2.9 Consensus size: 55
43643 AGCTTCTTTA
* * *
43653 AAAATTCATTTGAAAATCATCAAGGAACTTCTGAAAATGAGACTTAGTTTCATTG
1 AAAATTCATTTGAAAATCATCAAGAAACTTTTGAAAATCAGACTTAGTTTCATTG
*
43708 AAAATTCATTTAAAAAT-ATTCAAGAAACTTTTGAAAATCAGACTTAGTTTCATTG
1 AAAATTCATTTGAAAATCA-TCAAGAAACTTTTGAAAATCAGACTTAGTTTCATTG
* * *
43763 AAAGTTCATTTGAAAATCGTCAAGAAACTTTTGAAAATCATACTTAGTT
1 AAAATTCATTTGAAAATCATCAAGAAACTTTTGAAAATCAGACTTAGTT
43812 CCTAAAAAAA
Statistics
Matches: 94, Mismatches: 8, Indels: 4
0.89 0.08 0.04
Matches are distributed among these distances:
54 1 0.01
55 93 0.99
ACGTcount: A:0.42, C:0.12, G:0.12, T:0.35
Consensus pattern (55 bp):
AAAATTCATTTGAAAATCATCAAGAAACTTTTGAAAATCAGACTTAGTTTCATTG
Found at i:45126 original size:28 final size:28
Alignment explanation
Indices: 45087--45197 Score: 177
Period size: 28 Copynumber: 3.9 Consensus size: 28
45077 TTAGGTTGAC
45087 TTGGGAAGGTAATGTGTTTCAGGTTAATT
1 TTGGGAA-GTAATGTGTTTCAGGTTAATT
*
45116 TTGGGAAGTAACGTGTTTCAGGTTAATT
1 TTGGGAAGTAATGTGTTTCAGGTTAATT
*
45144 TTGAGAAGTAATGTGTTTCAGGTTAATT
1 TTGGGAAGTAATGTGTTTCAGGTTAATT
*
45172 TTGGAGAAGTAATGTGTTTCATGTTA
1 TTGG-GAAGTAATGTGTTTCAGGTTA
45198 GCTTCTTGCG
Statistics
Matches: 76, Mismatches: 5, Indels: 2
0.92 0.06 0.02
Matches are distributed among these distances:
28 49 0.64
29 27 0.36
ACGTcount: A:0.26, C:0.05, G:0.28, T:0.41
Consensus pattern (28 bp):
TTGGGAAGTAATGTGTTTCAGGTTAATT
Found at i:45859 original size:10 final size:10
Alignment explanation
Indices: 45844--45945 Score: 77
Period size: 10 Copynumber: 10.3 Consensus size: 10
45834 ATTTGATCGG
45844 TTTTTTTT-T
1 TTTTTTTTCT
45853 TTTTTTTTC-
1 TTTTTTTTCT
*
45862 -TCTTTTTCT
1 TTTTTTTTCT
*
45871 CTTTTTTTCT
1 TTTTTTTTCT
*
45881 CTTTTTTTCT
1 TTTTTTTTCT
45891 TTTTTATTTC-
1 TTTTT-TTTCT
* *
45901 TTTTTTATGT
1 TTTTTTTTCT
*
45911 TTTTATTTCT
1 TTTTTTTTCT
*
45921 TTTTTTCTCTCA
1 TTTTTT-T-TCT
*
45933 TTTTTTTTAT
1 TTTTTTTTCT
45943 TTT
1 TTT
45946 CTCTCTCTTT
Statistics
Matches: 74, Mismatches: 12, Indels: 13
0.75 0.12 0.13
Matches are distributed among these distances:
8 7 0.09
9 10 0.14
10 43 0.58
11 6 0.08
12 8 0.11
ACGTcount: A:0.05, C:0.12, G:0.01, T:0.82
Consensus pattern (10 bp):
TTTTTTTTCT
Found at i:45875 original size:18 final size:18
Alignment explanation
Indices: 45854--45905 Score: 77
Period size: 18 Copynumber: 2.8 Consensus size: 18
45844 TTTTTTTTTT
45854 TTTTTTTCTCTTTTTCTC
1 TTTTTTTCTCTTTTTCTC
*
45872 TTTTTTTCTCTTTTTTTC
1 TTTTTTTCTCTTTTTCTC
*
45890 TTTTTTATTTCTTTTT
1 TTTTTT-TCTCTTTTT
45906 TATGTTTTTA
Statistics
Matches: 31, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
18 23 0.74
19 8 0.26
ACGTcount: A:0.02, C:0.15, G:0.00, T:0.83
Consensus pattern (18 bp):
TTTTTTTCTCTTTTTCTC
Found at i:45927 original size:8 final size:8
Alignment explanation
Indices: 45846--45928 Score: 58
Period size: 9 Copynumber: 9.1 Consensus size: 8
45836 TTGATCGGTT
*
45846 TTTTTTTT
1 TTTTTTTC
45854 TTTTTTTC
1 TTTTTTTC
45862 TCTTTTTCTC
1 T-TTTTT-TC
45872 TTTTTTTCTC
1 -TTTTTT-TC
45882 TTTTTTTC
1 TTTTTTTC
45890 TTTTTTATTTC
1 --TTTT-TTTC
*
45901 TTTTTTATGT
1 TTTTTT-T-C
45911 TTTTATTTC
1 TTTT-TTTC
45920 TTTTTTTC
1 TTTTTTTC
45928 T
1 T
45929 CTCATTTTTT
Statistics
Matches: 63, Mismatches: 3, Indels: 18
0.75 0.04 0.21
Matches are distributed among these distances:
8 17 0.27
9 20 0.32
10 19 0.30
11 7 0.11
ACGTcount: A:0.04, C:0.12, G:0.01, T:0.83
Consensus pattern (8 bp):
TTTTTTTC
Found at i:63541 original size:44 final size:44
Alignment explanation
Indices: 63474--63561 Score: 167
Period size: 44 Copynumber: 2.0 Consensus size: 44
63464 TCTGAAGTAT
63474 GCATATTTAGGAGAAGAGAAAACTCTTCCGGTGATAATTTCCAA
1 GCATATTTAGGAGAAGAGAAAACTCTTCCGGTGATAATTTCCAA
*
63518 GCATATTTAGGAGAAGAGGAAACTCTTCCGGTGATAATTTCCAA
1 GCATATTTAGGAGAAGAGAAAACTCTTCCGGTGATAATTTCCAA
63562 CAAACTTTCT
Statistics
Matches: 43, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
44 43 1.00
ACGTcount: A:0.35, C:0.16, G:0.22, T:0.27
Consensus pattern (44 bp):
GCATATTTAGGAGAAGAGAAAACTCTTCCGGTGATAATTTCCAA
Done.