Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01005044.1 Hibiscus syriacus cultivar Beakdansim tig00011322_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: 46059
ACGTcount: A:0.32, C:0.18, G:0.16, T:0.33
Found at i:438 original size:21 final size:21
Alignment explanation
Indices: 379--488 Score: 70
Period size: 21 Copynumber: 5.4 Consensus size: 21
369 ATGAATCGGG
* *
379 CTCTTGAA-TGTGGGAGGGAC
1 CTCTTGAACGGTGGGAGGGGC
* * **
399 CTCTTCAACGATGACAGGGGC
1 CTCTTGAACGGTGGGAGGGGC
*
420 CTCTTGAACGGTGGGAGGGGA
1 CTCTTGAACGGTGGGAGGGGC
*
441 CTCTTG-A-GG-GATGATGGGGC
1 CTCTTGAACGGTG-GGA-GGGGC
* *
461 CTCTTGAACGATAGGA--GGC
1 CTCTTGAACGGTGGGAGGGGC
480 CTCTTGAAC
1 CTCTTGAAC
489 AATGACAGTG
Statistics
Matches: 68, Mismatches: 16, Indels: 13
0.70 0.16 0.13
Matches are distributed among these distances:
18 1 0.01
19 16 0.24
20 18 0.26
21 30 0.44
22 3 0.04
ACGTcount: A:0.21, C:0.20, G:0.36, T:0.23
Consensus pattern (21 bp):
CTCTTGAACGGTGGGAGGGGC
Found at i:1094 original size:20 final size:20
Alignment explanation
Indices: 1065--1102 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
1055 ATGAACTAAA
*
1065 TTCGCGTTGCAATTTTCATT
1 TTCGCATTGCAATTTTCATT
*
1085 TTCGCATTGCGATTTTCA
1 TTCGCATTGCAATTTTCA
1103 CGTTGCGATT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.16, C:0.21, G:0.16, T:0.47
Consensus pattern (20 bp):
TTCGCATTGCAATTTTCATT
Found at i:1126 original size:33 final size:33
Alignment explanation
Indices: 1069--1144 Score: 91
Period size: 33 Copynumber: 2.3 Consensus size: 33
1059 ACTAAATTCG
* *
1069 CGTTGCAATTTTCATTTTCGCATTGCGATTTTC
1 CGTTGCGATTTTCATTTTCGCATTGCGATTATC
* *
1102 ACGTTGCGATTTTTA-TTTCGCATTGTGATTATC
1 -CGTTGCGATTTTCATTTTCGCATTGCGATTATC
1135 CTGTTGCGAT
1 C-GTTGCGAT
1145 AGTCAAATTC
Statistics
Matches: 37, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
32 1 0.03
33 24 0.65
34 12 0.32
ACGTcount: A:0.16, C:0.18, G:0.18, T:0.47
Consensus pattern (33 bp):
CGTTGCGATTTTCATTTTCGCATTGCGATTATC
Found at i:1271 original size:99 final size:102
Alignment explanation
Indices: 1114--1305 Score: 336
Period size: 99 Copynumber: 1.9 Consensus size: 102
1104 GTTGCGATTT
* *
1114 TTATTTCGCATTGTGATTATCCTGTTGCGATAGTCAAATTCGCGTTGCGATAGTCATTTCCGTGT
1 TTATTTCGCATTGCGATTATCCTGTTGCGATAGTCAAATTCACGTTGCGATAGTCATTTCCGTGT
1179 TGCGATAGTCATTTTCGC-TTGCGATTTGTTATATTG
66 TGCGATAGTCATTTTCGCATTGCGATTTGTTATATTG
*
1215 TTATTTCGCA-TGCGATTATCTTGTTGCGATAGTC-AATTCACGTTGCGATAGTCATTTCCGTGT
1 TTATTTCGCATTGCGATTATCCTGTTGCGATAGTCAAATTCACGTTGCGATAGTCATTTCCGTGT
1278 TGCGATAGTCATTTTCGCATTGCGATTT
66 TGCGATAGTCATTTTCGCATTGCGATTT
1306 TAAGTTTCGT
Statistics
Matches: 87, Mismatches: 3, Indels: 3
0.94 0.03 0.03
Matches are distributed among these distances:
99 46 0.53
100 31 0.36
101 10 0.11
ACGTcount: A:0.18, C:0.18, G:0.21, T:0.43
Consensus pattern (102 bp):
TTATTTCGCATTGCGATTATCCTGTTGCGATAGTCAAATTCACGTTGCGATAGTCATTTCCGTGT
TGCGATAGTCATTTTCGCATTGCGATTTGTTATATTG
Found at i:1281 original size:20 final size:20
Alignment explanation
Indices: 1236--1291 Score: 80
Period size: 19 Copynumber: 2.9 Consensus size: 20
1226 GCGATTATCT
*
1236 TGTTGCGATAGTCAATTCAC
1 TGTTGCGATAGTCATTTCAC
1256 -GTTGCGATAGTCATTTC-C
1 TGTTGCGATAGTCATTTCAC
1274 GTGTTGCGATAGTCATTT
1 -TGTTGCGATAGTCATTT
1292 TCGCATTGCG
Statistics
Matches: 33, Mismatches: 1, Indels: 4
0.87 0.03 0.11
Matches are distributed among these distances:
18 1 0.03
19 16 0.48
20 16 0.48
ACGTcount: A:0.20, C:0.18, G:0.23, T:0.39
Consensus pattern (20 bp):
TGTTGCGATAGTCATTTCAC
Found at i:1300 original size:20 final size:20
Alignment explanation
Indices: 1137--1303 Score: 101
Period size: 20 Copynumber: 8.4 Consensus size: 20
1127 TGATTATCCT
**
1137 GTTGCGATAGTCAAATTCGC
1 GTTGCGATAGTCATTTTCGC
* *
1157 GTTGCGATAGTCATTTCCGT
1 GTTGCGATAGTCATTTTCGC
1177 GTTGCGATAGTCATTTTCGC
1 GTTGCGATAGTCATTTTCGC
* * * *
1197 -TTGCGATTTGTTATATT-GTT
1 GTTGCGA-TAGTCATTTTCG-C
* * * **
1217 ATTTCGCAT-G-CGATTATCTT
1 GTTGCG-ATAGTC-ATTTTCGC
* *
1237 GTTGCGATAGTCA-ATTCAC
1 GTTGCGATAGTCATTTTCGC
* *
1256 GTTGCGATAGTCATTTCCGT
1 GTTGCGATAGTCATTTTCGC
1276 GTTGCGATAGTCATTTTCGC
1 GTTGCGATAGTCATTTTCGC
*
1296 ATTGCGAT
1 GTTGCGAT
1304 TTTAAGTTTC
Statistics
Matches: 110, Mismatches: 28, Indels: 18
0.71 0.18 0.12
Matches are distributed among these distances:
19 24 0.22
20 79 0.72
21 6 0.05
22 1 0.01
ACGTcount: A:0.19, C:0.18, G:0.23, T:0.41
Consensus pattern (20 bp):
GTTGCGATAGTCATTTTCGC
Found at i:3218 original size:20 final size:20
Alignment explanation
Indices: 3161--3210 Score: 82
Period size: 20 Copynumber: 2.5 Consensus size: 20
3151 TCTGAAACTT
3161 AAATCGCAACACGAAAATGA
1 AAATCGCAACACGAAAATGA
3181 AAATCGCAACACGAAAATGA
1 AAATCGCAACACGAAAATGA
**
3201 CTATCGCAAC
1 AAATCGCAAC
3211 GAGAAAATAG
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
20 28 1.00
ACGTcount: A:0.50, C:0.24, G:0.14, T:0.12
Consensus pattern (20 bp):
AAATCGCAACACGAAAATGA
Found at i:3636 original size:22 final size:22
Alignment explanation
Indices: 3606--3656 Score: 93
Period size: 22 Copynumber: 2.3 Consensus size: 22
3596 GATGGAGATA
3606 GACGGATTTCGTCGGAGATGGG
1 GACGGATTTCGTCGGAGATGGG
*
3628 GAGGGATTTCGTCGGAGATGGG
1 GACGGATTTCGTCGGAGATGGG
3650 GACGGAT
1 GACGGAT
3657 GTCGGCCGTA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
22 27 1.00
ACGTcount: A:0.20, C:0.12, G:0.47, T:0.22
Consensus pattern (22 bp):
GACGGATTTCGTCGGAGATGGG
Found at i:3853 original size:20 final size:20
Alignment explanation
Indices: 3802--3956 Score: 136
Period size: 20 Copynumber: 7.7 Consensus size: 20
3792 GCGCTTTGAA
*
3802 AATCGCATTGCGATTATGT-AT
1 AATCGCATTGCGA-TA-GTCAG
* *
3823 TATCGCATTGCGATAGACAG
1 AATCGCATTGCGATAGTCAG
*
3843 AATCGCGTTGCGATAGTCAG
1 AATCGCATTGCGATAGTCAG
*
3863 AATCGCATTGCGATTATGT-AT
1 AATCGCATTGCGA-TA-GTCAG
* *
3884 TATCGCGTTGCGATAGTCAG
1 AATCGCATTGCGATAGTCAG
* *
3904 AATCGCATTGCGAT-TTACAT
1 AATCGCATTGCGATAGT-CAG
* *
3924 ATTCGCATTGCGATAGTCAA
1 AATCGCATTGCGATAGTCAG
*
3944 AATCGCGTTGCGA
1 AATCGCATTGCGA
3957 ATCTGGAAAC
Statistics
Matches: 108, Mismatches: 20, Indels: 13
0.77 0.14 0.09
Matches are distributed among these distances:
19 4 0.04
20 75 0.69
21 27 0.25
22 2 0.02
ACGTcount: A:0.27, C:0.19, G:0.23, T:0.31
Consensus pattern (20 bp):
AATCGCATTGCGATAGTCAG
Found at i:3889 original size:41 final size:39
Alignment explanation
Indices: 3824--3956 Score: 158
Period size: 40 Copynumber: 3.3 Consensus size: 39
3814 ATTATGTATT
** *
3824 ATCGCATTGCGATAGACAGAATCGCGTTGCGATAGTCAGA
1 ATCGCATTGCGATTTACA-TATCGCGTTGCGATAGTCAGA
**
3864 ATCGCATTGCGATTATGTATTATCGCGTTGCGATAGTCAGA
1 ATCGCATTGCGATT-TACA-TATCGCGTTGCGATAGTCAGA
* *
3905 ATCGCATTGCGATTTACATATTCGCATTGCGATAGTCAAA
1 ATCGCATTGCGATTTACATA-TCGCGTTGCGATAGTCAGA
*
3945 ATCGCGTTGCGA
1 ATCGCATTGCGA
3957 ATCTGGAAAC
Statistics
Matches: 80, Mismatches: 11, Indels: 4
0.84 0.12 0.04
Matches are distributed among these distances:
39 2 0.03
40 43 0.54
41 35 0.44
ACGTcount: A:0.27, C:0.20, G:0.24, T:0.29
Consensus pattern (39 bp):
ATCGCATTGCGATTTACATATCGCGTTGCGATAGTCAGA
Found at i:3937 original size:61 final size:61
Alignment explanation
Indices: 3802--3917 Score: 205
Period size: 61 Copynumber: 1.9 Consensus size: 61
3792 GCGCTTTGAA
*
3802 AATCGCATTGCGATTATGTATTATCGCATTGCGATAGACAGAATCGCGTTGCGATAGTCAG
1 AATCGCATTGCGATTATGTATTATCGCATTGCGATAGACAGAATCGCATTGCGATAGTCAG
* *
3863 AATCGCATTGCGATTATGTATTATCGCGTTGCGATAGTCAGAATCGCATTGCGAT
1 AATCGCATTGCGATTATGTATTATCGCATTGCGATAGACAGAATCGCATTGCGAT
3918 TTACATATTC
Statistics
Matches: 52, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
61 52 1.00
ACGTcount: A:0.27, C:0.18, G:0.24, T:0.31
Consensus pattern (61 bp):
AATCGCATTGCGATTATGTATTATCGCATTGCGATAGACAGAATCGCATTGCGATAGTCAG
Found at i:3994 original size:20 final size:19
Alignment explanation
Indices: 3971--4016 Score: 56
Period size: 19 Copynumber: 2.4 Consensus size: 19
3961 GGAAACTGAT
* *
3971 TTGCGATACTGGAGATCGCG
1 TTGCGAT-CTAGAGATCGCA
*
3991 TTGCGATTTAGAGATCGCA
1 TTGCGATCTAGAGATCGCA
4010 TTGCGAT
1 TTGCGAT
4017 TTTGTTGGTC
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
19 16 0.70
20 7 0.30
ACGTcount: A:0.22, C:0.17, G:0.30, T:0.30
Consensus pattern (19 bp):
TTGCGATCTAGAGATCGCA
Found at i:4006 original size:19 final size:19
Alignment explanation
Indices: 3982--4018 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
3972 TGCGATACTG
*
3982 GAGATCGCGTTGCGATTTA
1 GAGATCGCATTGCGATTTA
4001 GAGATCGCATTGCGATTT
1 GAGATCGCATTGCGATTT
4019 TGTTGGTCAT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.22, C:0.16, G:0.30, T:0.32
Consensus pattern (19 bp):
GAGATCGCATTGCGATTTA
Found at i:5725 original size:6 final size:6
Alignment explanation
Indices: 5715--5859 Score: 87
Period size: 6 Copynumber: 24.2 Consensus size: 6
5705 CCTGGCGGTG
* * * * * * *
5715 GCTGTT CCTGTT CCTGTT -CTTGTT CCTGTT GCTGTG GCTGTG GCTATG
1 GCTGTT GCTGTT GCTGTT GC-TGTT GCTGTT GCTGTT GCTGTT GCTGTT
* * * * * * *
5763 GCTGTG GCTGTG GCTGTT GCTGTT -CTTGTT CCTGAT CCTGAT CCTGTT
1 GCTGTT GCTGTT GCTGTT GCTGTT GC-TGTT GCTGTT GCTGTT GCTGTT
* * * * *
5811 CCTGTT CCTGTT GTTGTT GCTGTG GCTGTT GCTGTT CCTGTT GCTGTT
1 GCTGTT GCTGTT GCTGTT GCTGTT GCTGTT GCTGTT GCTGTT GCTGTT
5859 G
1 G
5860 TTTCAAAAGT
Statistics
Matches: 120, Mismatches: 15, Indels: 8
0.84 0.10 0.06
Matches are distributed among these distances:
5 2 0.02
6 116 0.97
7 2 0.02
ACGTcount: A:0.02, C:0.22, G:0.30, T:0.46
Consensus pattern (6 bp):
GCTGTT
Found at i:5828 original size:18 final size:18
Alignment explanation
Indices: 5690--5859 Score: 114
Period size: 18 Copynumber: 9.6 Consensus size: 18
5680 ATTTTGTTGC
*
5690 GTTGCTATTGCTGTTCCT
1 GTTGCTGTTGCTGTTCCT
* *
5708 G--GCGGTGGCTGTTCCT
1 GTTGCTGTTGCTGTTCCT
*
5724 GTTCCTGTT-CTTGTTCCT
1 GTTGCTGTTGC-TGTTCCT
* **
5742 GTTGCTGTGGCTGTGGCT
1 GTTGCTGTTGCTGTTCCT
* * * **
5760 ATGGCTGTGGCTGTGGCT
1 GTTGCTGTTGCTGTTCCT
5778 GTTGCTGTT-CTTGTTCCT
1 GTTGCTGTTGC-TGTTCCT
* * * *
5796 GATCCTGATCCTGTTCCT
1 GTTGCTGTTGCTGTTCCT
* * *
5814 GTTCCTGTTGTTGTTGCT
1 GTTGCTGTTGCTGTTCCT
*
5832 GTGGCTGTTGCTGTTCCT
1 GTTGCTGTTGCTGTTCCT
5850 GTTGCTGTTG
1 GTTGCTGTTG
5860 TTTCAAAAGT
Statistics
Matches: 116, Mismatches: 30, Indels: 12
0.73 0.19 0.08
Matches are distributed among these distances:
16 13 0.11
17 2 0.02
18 99 0.85
19 2 0.02
ACGTcount: A:0.02, C:0.22, G:0.31, T:0.45
Consensus pattern (18 bp):
GTTGCTGTTGCTGTTCCT
Found at i:9336 original size:20 final size:21
Alignment explanation
Indices: 9311--9357 Score: 69
Period size: 21 Copynumber: 2.3 Consensus size: 21
9301 AACCAACTAA
9311 AAATTATATAT-AATATGCAT
1 AAATTATATATCAATATGCAT
* *
9331 AAATTATATATCTATATGCGT
1 AAATTATATATCAATATGCAT
9352 AAATTA
1 AAATTA
9358 ATAAAAATTA
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
20 11 0.46
21 13 0.54
ACGTcount: A:0.47, C:0.06, G:0.06, T:0.40
Consensus pattern (21 bp):
AAATTATATATCAATATGCAT
Found at i:9442 original size:17 final size:17
Alignment explanation
Indices: 9391--9445 Score: 56
Period size: 17 Copynumber: 3.1 Consensus size: 17
9381 ATATAAGTGT
9391 TACGCATGTTATATATA
1 TACGCATGTTATATATA
*** *
9408 TAAAAATAATTATAATATA
1 TACGCAT-GTTAT-ATATA
9427 TACGCATGTTATATATA
1 TACGCATGTTATATATA
9444 TA
1 TA
9446 TTACATAATG
Statistics
Matches: 28, Mismatches: 8, Indels: 4
0.70 0.20 0.10
Matches are distributed among these distances:
17 11 0.39
18 8 0.29
19 9 0.32
ACGTcount: A:0.45, C:0.07, G:0.07, T:0.40
Consensus pattern (17 bp):
TACGCATGTTATATATA
Found at i:9529 original size:22 final size:22
Alignment explanation
Indices: 9480--9546 Score: 52
Period size: 22 Copynumber: 3.1 Consensus size: 22
9470 TACATTCTAC
9480 ATAC-TAT-ATAATATATATAAT
1 ATACTTATAATAATATATAT-AT
*
9501 ACACTTA-AATAATATAATATAT
1 ATACTTATAATAATAT-ATATAT
* *
9523 ATGCTTATAA-AATATGTTATAT
1 ATACTTATAATAATAT-ATATAT
9545 AT
1 AT
9547 CGTATGTTTC
Statistics
Matches: 37, Mismatches: 5, Indels: 7
0.76 0.10 0.14
Matches are distributed among these distances:
21 3 0.08
22 28 0.76
23 6 0.16
ACGTcount: A:0.49, C:0.06, G:0.03, T:0.42
Consensus pattern (22 bp):
ATACTTATAATAATATATATAT
Found at i:11423 original size:113 final size:113
Alignment explanation
Indices: 11190--11845 Score: 1011
Period size: 113 Copynumber: 5.8 Consensus size: 113
11180 TTCAGGGAAT
*
11190 ATTGAATCAGGGTAGACTTGTTCCACTTACTCTGAAGGGAATATCAAATCTTGGAAAAAAAGAGA
1 ATTGAATCAGGGTAGACTTGTTCCACTTACTCTGAAGGGAATATCAAATCTTGG-AAAAGAGAGA
* * * * * *
11255 TATGTTCTGCTTACTCTGAAGGGAATATCATATTTTGGGGAGTTAATCC
65 CATGTTCCGCTTACTCTGAAGGGAATATCAGATCTGGGGGAGTTGATCC
* *
11304 ATTGAATCTA-GGTAGACTTGTTCCACTTACTCTGAATGGAATATCAAATCTTGGAAAAAAGAGA
1 ATTGAATC-AGGGTAGACTTGTTCCACTTACTCTGAAGGGAATATCAAATCTTGGAAAAGAGAGA
* *
11368 CATGTTCCGCTTACTCTGAAGGGAATATCATATCTGGGGGAATTGATCC
65 CATGTTCCGCTTACTCTGAAGGGAATATCAGATCTGGGGGAGTTGATCC
* * *
11417 ATTGAATCATGGTAGACTTGTTCCACTTACTCTGAAGGGAATATCAAATCTTGGAAAAGAGATAT
1 ATTGAATCAGGGTAGACTTGTTCCACTTACTCTGAAGGGAATATCAAATCTTGGAAAAGAGAGAC
* *
11482 ATGTTCCGCTTACTCTGAAGGGAATATCAGATCT-GGGGAATTGATCA
66 ATGTTCCGCTTACTCTGAAGGGAATATCAGATCTGGGGGAGTTGATCC
* *
11529 ATTGAATCAGGGTAGACTTGCTCCACTTACTCTGAAGGGAATATCAAATCTTGGATAAGAGAGAC
1 ATTGAATCAGGGTAGACTTGTTCCACTTACTCTGAAGGGAATATCAAATCTTGGAAAAGAGAGAC
* *
11594 CTGTTCCGCTTACTCTGAAGGGAATATCAGATCTGGGGGAGTTGATTC
66 ATGTTCCGCTTACTCTGAAGGGAATATCAGATCTGGGGGAGTTGATCC
11642 ATTGAATC-GAGGTAGACTTGTTCCACTTACTCTGAAGGGAATATCAAATCTT-G-AAAGAGAGA
1 ATTGAATCAG-GGTAGACTTGTTCCACTTACTCTGAAGGGAATATCAAATCTTGGAAAAGAGAGA
* *
11704 CCTGTTCCGCTTACTCTGAAGGGAATATCAGATCTGGAGGAGTTGATCC
65 CATGTTCCGCTTACTCTGAAGGGAATATCAGATCTGGGGGAGTTGATCC
* *
11753 ATTGAATC-GAGGAAGACTTGTTCCACTTACTCTGAAGGGAATATCAAATCTTAG-AAAGAGAGA
1 ATTGAATCAG-GGTAGACTTGTTCCACTTACTCTGAAGGGAATATCAAATCTTGGAAAAGAGAGA
11816 CATGTTCCGCTTACTCTGAAGGGAATATCA
65 CATGTTCCGCTTACTCTGAAGGGAATATCA
11846 TATTCTGAAG
Statistics
Matches: 509, Mismatches: 28, Indels: 12
0.93 0.05 0.02
Matches are distributed among these distances:
111 106 0.21
112 147 0.29
113 204 0.40
114 51 0.10
115 1 0.00
ACGTcount: A:0.31, C:0.16, G:0.23, T:0.29
Consensus pattern (113 bp):
ATTGAATCAGGGTAGACTTGTTCCACTTACTCTGAAGGGAATATCAAATCTTGGAAAAGAGAGAC
ATGTTCCGCTTACTCTGAAGGGAATATCAGATCTGGGGGAGTTGATCC
Found at i:11601 original size:225 final size:223
Alignment explanation
Indices: 11190--11848 Score: 1029
Period size: 225 Copynumber: 2.9 Consensus size: 223
11180 TTCAGGGAAT
*
11190 ATTGAATCAGGGTAGACTTGTTCCACTTACTCTGAAGGGAATATCAAATCTTGGAAAAAAAGAGA
1 ATTGAATCA-GGTAGACTTGTTCCACTTACTCTGAAGGGAATATCAAATCTTGG-AAAAGAGAGA
* * * *
11255 TATGTTCTGCTTACTCTGAAGGGAATATCATATTTTGGGGAGTTAATCCATTGAATCTA-GGTAG
64 TATGTTCCGCTTACTCTGAAGGGAATATCAGA-TCTGGGGAGTTGATCCATTGAATC-AGGGTAG
* *
11319 ACTTGTTCCACTTACTCTGAATGGAATATCAAATCTTGGAAAAAAGAGACATGTTCCGCTTACTC
127 ACTTGTTCCACTTACTCTGAAGGGAATATCAAATCTTGG-AAAGAGAGACATGTTCCGCTTACTC
11384 TGAAGGGAATATCATATCTGGGGGAATTGATCC
191 TGAAGGGAATATCATATCTGGGGGAATTGATCC
*
11417 ATTGAATCATGGTAGACTTGTTCCACTTACTCTGAAGGGAATATCAAATCTTGGAAAAGAGATAT
1 ATTGAATCA-GGTAGACTTGTTCCACTTACTCTGAAGGGAATATCAAATCTTGGAAAAGAGAGAT
* *
11482 ATGTTCCGCTTACTCTGAAGGGAATATCAGATCTGGGGAATTGATCAATTGAATCAGGGTAGACT
65 ATGTTCCGCTTACTCTGAAGGGAATATCAGATCTGGGGAGTTGATCCATTGAATCAGGGTAGACT
* *
11547 TGCTCCACTTACTCTGAAGGGAATATCAAATCTTGGATAAGAGAGACCTGTTCCGCTTACTCTGA
130 TGTTCCACTTACTCTGAAGGGAATATCAAATCTTGGA-AAGAGAGACATGTTCCGCTTACTCTGA
* * *
11612 AGGGAATATCAGATCTGGGGGAGTTGATTC
194 AGGGAATATCATATCTGGGGGAATTGATCC
*
11642 ATTGAATCGAGGTAGACTTGTTCCACTTACTCTGAAGGGAATATCAAATCTT-G-AAAGAGAGAC
1 ATTGAATC-AGGTAGACTTGTTCCACTTACTCTGAAGGGAATATCAAATCTTGGAAAAGAGAGAT
* *
11705 CTGTTCCGCTTACTCTGAAGGGAATATCAGATCTGGAGGAGTTGATCCATTGAATC-GAGGAAGA
65 ATGTTCCGCTTACTCTGAAGGGAATATCAGATCTGG-GGAGTTGATCCATTGAATCAG-GGTAGA
*
11769 CTTGTTCCACTTACTCTGAAGGGAATATCAAATCTTAGAAAGAGAGACATGTTCCGCTTACTCTG
128 CTTGTTCCACTTACTCTGAAGGGAATATCAAATCTTGGAAAGAGAGACATGTTCCGCTTACTCTG
11834 AAGGGAATATCATAT
193 AAGGGAATATCATAT
11849 TCTGAAGGGA
Statistics
Matches: 401, Mismatches: 26, Indels: 14
0.91 0.06 0.03
Matches are distributed among these distances:
223 83 0.21
224 62 0.15
225 164 0.41
226 39 0.10
227 53 0.13
ACGTcount: A:0.31, C:0.16, G:0.23, T:0.29
Consensus pattern (223 bp):
ATTGAATCAGGTAGACTTGTTCCACTTACTCTGAAGGGAATATCAAATCTTGGAAAAGAGAGATA
TGTTCCGCTTACTCTGAAGGGAATATCAGATCTGGGGAGTTGATCCATTGAATCAGGGTAGACTT
GTTCCACTTACTCTGAAGGGAATATCAAATCTTGGAAAGAGAGACATGTTCCGCTTACTCTGAAG
GGAATATCATATCTGGGGGAATTGATCC
Found at i:18269 original size:8 final size:8
Alignment explanation
Indices: 18258--18291 Score: 59
Period size: 8 Copynumber: 4.2 Consensus size: 8
18248 ATATTTTATA
18258 TATTTAAT
1 TATTTAAT
18266 TATTTAAT
1 TATTTAAT
*
18274 TATTTAAC
1 TATTTAAT
18282 TATTTAAT
1 TATTTAAT
18290 TA
1 TA
18292 CTTATCCGTA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
8 24 1.00
ACGTcount: A:0.38, C:0.03, G:0.00, T:0.59
Consensus pattern (8 bp):
TATTTAAT
Found at i:27415 original size:21 final size:22
Alignment explanation
Indices: 27391--27439 Score: 66
Period size: 21 Copynumber: 2.3 Consensus size: 22
27381 AACTAAAAAT
27391 ATTAATATAT-AATATGCATAA
1 ATTAATATATCAATATGCATAA
* *
27412 ATT-ATATATCTATATGCGTAA
1 ATTAATATATCAATATGCATAA
27433 ATTAATA
1 ATTAATA
27440 AAAATTATTA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
20 6 0.25
21 15 0.62
22 3 0.12
ACGTcount: A:0.47, C:0.06, G:0.06, T:0.41
Consensus pattern (22 bp):
ATTAATATATCAATATGCATAA
Found at i:27609 original size:22 final size:22
Alignment explanation
Indices: 27560--27626 Score: 52
Period size: 22 Copynumber: 3.1 Consensus size: 22
27550 TACATTCTAC
27560 ATAC-TAT-ATAATATATATAAT
1 ATACTTATAATAATATATAT-AT
*
27581 ACACTTA-AATAATATAATATAT
1 ATACTTATAATAATAT-ATATAT
* *
27603 ATGCTTATAA-AATATGTTATAT
1 ATACTTATAATAATAT-ATATAT
27625 AT
1 AT
27627 CGTATGTTTC
Statistics
Matches: 37, Mismatches: 5, Indels: 7
0.76 0.10 0.14
Matches are distributed among these distances:
21 3 0.08
22 28 0.76
23 6 0.16
ACGTcount: A:0.49, C:0.06, G:0.03, T:0.42
Consensus pattern (22 bp):
ATACTTATAATAATATATATAT
Found at i:29497 original size:15 final size:16
Alignment explanation
Indices: 29464--29498 Score: 54
Period size: 15 Copynumber: 2.2 Consensus size: 16
29454 CCATATTTCA
29464 TGTTTGATATGTATTT
1 TGTTTGATATGTATTT
*
29480 TGTTTGATA-GTGTTT
1 TGTTTGATATGTATTT
29495 TGTT
1 TGTT
29499 AACAGTATGA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 9 0.50
16 9 0.50
ACGTcount: A:0.14, C:0.00, G:0.23, T:0.63
Consensus pattern (16 bp):
TGTTTGATATGTATTT
Found at i:29686 original size:33 final size:33
Alignment explanation
Indices: 29649--29714 Score: 123
Period size: 33 Copynumber: 2.0 Consensus size: 33
29639 ACAAATGCAC
*
29649 GTTAGAATATGCACATCTGTTCTTTATTACAGT
1 GTTAGAATATGCACATATGTTCTTTATTACAGT
29682 GTTAGAATATGCACATATGTTCTTTATTACAGT
1 GTTAGAATATGCACATATGTTCTTTATTACAGT
29715 ATTTGGATAA
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 32 1.00
ACGTcount: A:0.29, C:0.14, G:0.15, T:0.42
Consensus pattern (33 bp):
GTTAGAATATGCACATATGTTCTTTATTACAGT
Found at i:30083 original size:21 final size:21
Alignment explanation
Indices: 30059--30100 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
30049 AGTTTATTAT
30059 TGAGAAGATGCTATAGCAGGG
1 TGAGAAGATGCTATAGCAGGG
* * *
30080 TGAGAAGTTGTTGTAGCAGGG
1 TGAGAAGATGCTATAGCAGGG
30101 GCTTGAGATG
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.29, C:0.07, G:0.40, T:0.24
Consensus pattern (21 bp):
TGAGAAGATGCTATAGCAGGG
Found at i:31498 original size:20 final size:20
Alignment explanation
Indices: 31475--31519 Score: 63
Period size: 20 Copynumber: 2.2 Consensus size: 20
31465 CTTTAGTACT
*
31475 GATATTGAATCCTCAGTATC
1 GATATTGAACCCTCAGTATC
**
31495 GATATTGAACCCTTGGTATC
1 GATATTGAACCCTCAGTATC
31515 GATAT
1 GATAT
31520 CAACATGTTG
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.29, C:0.18, G:0.18, T:0.36
Consensus pattern (20 bp):
GATATTGAACCCTCAGTATC
Found at i:31530 original size:20 final size:20
Alignment explanation
Indices: 31507--31578 Score: 126
Period size: 20 Copynumber: 3.6 Consensus size: 20
31497 TATTGAACCC
*
31507 TTGGTATCGATATCAACATG
1 TTGGTATCGATATCCACATG
31527 TTGGTATCGATATCCACATG
1 TTGGTATCGATATCCACATG
*
31547 TTGGTATCGATACCCACATG
1 TTGGTATCGATATCCACATG
31567 TTGGTATCGATA
1 TTGGTATCGATA
31579 CCTTCTAACT
Statistics
Matches: 50, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 50 1.00
ACGTcount: A:0.26, C:0.18, G:0.21, T:0.35
Consensus pattern (20 bp):
TTGGTATCGATATCCACATG
Found at i:31534 original size:40 final size:40
Alignment explanation
Indices: 31490--31578 Score: 108
Period size: 40 Copynumber: 2.2 Consensus size: 40
31480 TGAATCCTCA
* *
31490 GTATCGATATTGAAC-CCTTGGTATCGATATCAACATGTTG
1 GTATCGATA-TCAACACCTTGGTATCGATACCAACATGTTG
* ** *
31530 GTATCGATATCCACATGTTGGTATCGATACCCACATGTTG
1 GTATCGATATCAACACCTTGGTATCGATACCAACATGTTG
31570 GTATCGATA
1 GTATCGATA
31579 CCTTCTAACT
Statistics
Matches: 42, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
39 3 0.07
40 39 0.93
ACGTcount: A:0.27, C:0.19, G:0.20, T:0.34
Consensus pattern (40 bp):
GTATCGATATCAACACCTTGGTATCGATACCAACATGTTG
Found at i:37494 original size:2 final size:2
Alignment explanation
Indices: 37487--37541 Score: 110
Period size: 2 Copynumber: 27.5 Consensus size: 2
37477 TTTAAACATT
37487 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
37529 TA TA TA TA TA TA T
1 TA TA TA TA TA TA T
37542 CATGAGTTTT
Statistics
Matches: 53, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 53 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:39068 original size:38 final size:38
Alignment explanation
Indices: 39025--39102 Score: 120
Period size: 38 Copynumber: 2.1 Consensus size: 38
39015 TAACATGTTA
* * *
39025 TTAAAGTGTATTATTTTATTAGTTTTCTACTTTATTAG
1 TTAAAGTGTATTACTTTATTAATTTACTACTTTATTAG
*
39063 TTAAAGTGTATTACTTTATTAATTTACTATTTTATTAG
1 TTAAAGTGTATTACTTTATTAATTTACTACTTTATTAG
39101 TT
1 TT
39103 TAGAAATTGA
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
38 36 1.00
ACGTcount: A:0.28, C:0.05, G:0.09, T:0.58
Consensus pattern (38 bp):
TTAAAGTGTATTACTTTATTAATTTACTACTTTATTAG
Found at i:39098 original size:16 final size:16
Alignment explanation
Indices: 39074--39194 Score: 102
Period size: 16 Copynumber: 7.6 Consensus size: 16
39064 TAAAGTGTAT
*
39074 TACTTTATTAATTTAC
1 TACTTTATTAGTTTAC
* *
39090 TATTTTATTAGTTTAG
1 TACTTTATTAGTTTAC
* * * * *
39106 AAATTGATTAATTTAT
1 TACTTTATTAGTTTAC
**
39122 TACTCAATTAGTTTTA-
1 TACTTTATTAG-TTTAC
39138 TAC-TTATTAGTTTAC
1 TACTTTATTAGTTTAC
* *
39153 TACTTAATTAGTTTAA
1 TACTTTATTAGTTTAC
39169 TACTTTATTAGTTTAC
1 TACTTTATTAGTTTAC
*
39185 TATTTTATTA
1 TACTTTATTA
39195 ATTACTGTTT
Statistics
Matches: 82, Mismatches: 20, Indels: 6
0.76 0.19 0.06
Matches are distributed among these distances:
14 4 0.05
15 8 0.10
16 66 0.80
17 4 0.05
ACGTcount: A:0.31, C:0.07, G:0.06, T:0.55
Consensus pattern (16 bp):
TACTTTATTAGTTTAC
Found at i:39182 original size:32 final size:32
Alignment explanation
Indices: 39074--39186 Score: 122
Period size: 32 Copynumber: 3.6 Consensus size: 32
39064 TAAAGTGTAT
* *
39074 TACTTTATTAATTTACTATTTTATTAGTTTAGA
1 TACTTTATTAATTTACTACTTAATTAGTTTA-A
* * * * *
39107 -AATTGATTAATTTATTACTCAATTAGTTTTA
1 TACTTTATTAATTTACTACTTAATTAGTTTAA
*
39138 TAC-TTATTAGTTTACTACTTAATTAGTTTAA
1 TACTTTATTAATTTACTACTTAATTAGTTTAA
*
39169 TACTTTATTAGTTTACTA
1 TACTTTATTAATTTACTA
39187 TTTTATTAAT
Statistics
Matches: 65, Mismatches: 13, Indels: 5
0.78 0.16 0.06
Matches are distributed among these distances:
31 27 0.42
32 38 0.58
ACGTcount: A:0.32, C:0.08, G:0.06, T:0.54
Consensus pattern (32 bp):
TACTTTATTAATTTACTACTTAATTAGTTTAA
Found at i:39183 original size:8 final size:8
Alignment explanation
Indices: 39033--39194 Score: 55
Period size: 8 Copynumber: 20.6 Consensus size: 8
39023 TATTAAAGTG
*
39033 TATTATTT
1 TATTAGTT
39041 TATTAGTT
1 TATTAGTT
*
39049 T-TCTACTT
1 TAT-TAGTT
39057 TATTAG-T
1 TATTAGTT
* *
39064 TA-AAGTG
1 TATTAGTT
*
39071 TATTACTT
1 TATTAGTT
*
39079 TATTAATT
1 TATTAGTT
* *
39087 TACTATTT
1 TATTAGTT
39095 TATTAGTT
1 TATTAGTT
** *
39103 TAGAAATT
1 TATTAGTT
* *
39111 GATTAATT
1 TATTAGTT
* *
39119 TATTACTC
1 TATTAGTT
*
39127 AATTAGTT
1 TATTAGTT
*
39135 T-TATA-CT
1 TAT-TAGTT
39142 TATTAGTT
1 TATTAGTT
* *
39150 TACTACTT
1 TATTAGTT
*
39158 AATTAGTT
1 TATTAGTT
* *
39166 TAATACTT
1 TATTAGTT
39174 TATTAGTT
1 TATTAGTT
* *
39182 TACTATTT
1 TATTAGTT
39190 TATTA
1 TATTA
39195 ATTACTGTTT
Statistics
Matches: 106, Mismatches: 41, Indels: 14
0.66 0.25 0.09
Matches are distributed among these distances:
6 2 0.02
7 11 0.10
8 92 0.87
9 1 0.01
ACGTcount: A:0.30, C:0.07, G:0.07, T:0.56
Consensus pattern (8 bp):
TATTAGTT
Found at i:39467 original size:40 final size:40
Alignment explanation
Indices: 39407--39493 Score: 138
Period size: 40 Copynumber: 2.2 Consensus size: 40
39397 TGTCCATAGA
* * *
39407 AACACAATGTACGCAGAACATTTTTGTCCACAAAATCATC
1 AACACAATGTACACAAAACATTTATGTCCACAAAATCATC
*
39447 AACACAATGTACACAAAACATTTATGTTCACAAAATCATC
1 AACACAATGTACACAAAACATTTATGTCCACAAAATCATC
39487 AACACAA
1 AACACAA
39494 ATATCTACAG
Statistics
Matches: 43, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
40 43 1.00
ACGTcount: A:0.46, C:0.24, G:0.07, T:0.23
Consensus pattern (40 bp):
AACACAATGTACACAAAACATTTATGTCCACAAAATCATC
Found at i:40133 original size:19 final size:19
Alignment explanation
Indices: 40092--40134 Score: 50
Period size: 19 Copynumber: 2.3 Consensus size: 19
40082 GGAAGAGAAT
* *
40092 AAACTCTTTTAGACAATCA
1 AAACCCTTTTAGACAACCA
* *
40111 AAACCCTTTTTGACAACCG
1 AAACCCTTTTAGACAACCA
40130 AAACC
1 AAACC
40135 TTACTCTAAC
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.40, C:0.28, G:0.07, T:0.26
Consensus pattern (19 bp):
AAACCCTTTTAGACAACCA
Found at i:43069 original size:23 final size:24
Alignment explanation
Indices: 43043--43087 Score: 56
Period size: 23 Copynumber: 1.9 Consensus size: 24
43033 ATTTAATTTT
*
43043 TTTTTCATATT-TAACTTGATTGG
1 TTTTACATATTCTAACTTGATTGG
* *
43066 TTTTACTTATTCTAATTTGATT
1 TTTTACATATTCTAACTTGATT
43088 TTTCTTTTTA
Statistics
Matches: 18, Mismatches: 3, Indels: 1
0.82 0.14 0.05
Matches are distributed among these distances:
23 9 0.50
24 9 0.50
ACGTcount: A:0.22, C:0.09, G:0.09, T:0.60
Consensus pattern (24 bp):
TTTTACATATTCTAACTTGATTGG
Found at i:43843 original size:32 final size:32
Alignment explanation
Indices: 43806--43875 Score: 122
Period size: 32 Copynumber: 2.2 Consensus size: 32
43796 TTCCATTCTC
43806 CTGAAAACATGGTACTCTGAATGTTTTATGAA
1 CTGAAAACATGGTACTCTGAATGTTTTATGAA
* *
43838 TTGAAAACATGGTACTCTGAATGTTTTATTAA
1 CTGAAAACATGGTACTCTGAATGTTTTATGAA
43870 CTGAAA
1 CTGAAA
43876 TCTTCATTAC
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
32 35 1.00
ACGTcount: A:0.36, C:0.11, G:0.17, T:0.36
Consensus pattern (32 bp):
CTGAAAACATGGTACTCTGAATGTTTTATGAA
Found at i:45168 original size:18 final size:18
Alignment explanation
Indices: 45147--45181 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
45137 ATGACCATTG
45147 CCAGCATTAGACCCACTA
1 CCAGCATTAGACCCACTA
* *
45165 CCAGTATTTGACCCACT
1 CCAGCATTAGACCCACT
45182 GGTAGCATTC
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.29, C:0.37, G:0.11, T:0.23
Consensus pattern (18 bp):
CCAGCATTAGACCCACTA
Found at i:45242 original size:11 final size:11
Alignment explanation
Indices: 45224--45285 Score: 54
Period size: 11 Copynumber: 5.5 Consensus size: 11
45214 TAAATAGATT
45224 AAATGTTATTA
1 AAATGTTATTA
*
45235 ACATGTTATTA
1 AAATGTTATTA
*
45246 AGGAATATT-TTA
1 A--AATGTTATTA
* *
45258 ATATATTATTA
1 AAATGTTATTA
*
45269 ACATGTTATTA
1 AAATGTTATTA
45280 AAATGT
1 AAATGT
45286 ATCATTTTAT
Statistics
Matches: 41, Mismatches: 7, Indels: 6
0.76 0.13 0.11
Matches are distributed among these distances:
10 5 0.12
11 28 0.68
12 4 0.10
13 4 0.10
ACGTcount: A:0.42, C:0.03, G:0.10, T:0.45
Consensus pattern (11 bp):
AAATGTTATTA
Done.