Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008779.1 Hibiscus syriacus cultivar Beakdansim tig00111904_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: 82390
ACGTcount: A:0.33, C:0.16, G:0.18, T:0.34
Found at i:1584 original size:8 final size:8
Alignment explanation
Indices: 1573--1642 Score: 131
Period size: 8 Copynumber: 8.8 Consensus size: 8
1563 TTTGGTGATT
*
1573 AAAGTGGA
1 AAAGTTGA
1581 AAAGTTGA
1 AAAGTTGA
1589 AAAGTTGA
1 AAAGTTGA
1597 AAAGTTGA
1 AAAGTTGA
1605 AAAGTTGA
1 AAAGTTGA
1613 AAAGTTGA
1 AAAGTTGA
1621 AAAGTTGA
1 AAAGTTGA
1629 AAAGTTGA
1 AAAGTTGA
1637 AAAGTT
1 AAAGTT
1643 CAATGATTTA
Statistics
Matches: 61, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
8 61 1.00
ACGTcount: A:0.50, C:0.00, G:0.26, T:0.24
Consensus pattern (8 bp):
AAAGTTGA
Found at i:7143 original size:19 final size:19
Alignment explanation
Indices: 7119--7155 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
7109 ATAACCAACA
*
7119 AAATCGCAATGCGATCTCT
1 AAATCGCAACGCGATCTCT
7138 AAATCGCAACGCGATCTC
1 AAATCGCAACGCGATCTC
7156 CAGTATCGCA
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:0.32, C:0.30, G:0.16, T:0.22
Consensus pattern (19 bp):
AAATCGCAACGCGATCTCT
Found at i:8903 original size:2 final size:2
Alignment explanation
Indices: 8896--8931 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
8886 ATGTTTTAAA
8896 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
8932 TACCCCAATC
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:9120 original size:24 final size:24
Alignment explanation
Indices: 9093--9199 Score: 63
Period size: 24 Copynumber: 4.5 Consensus size: 24
9083 AAACGGAGAT
*
9093 ATCAGAAATCAAAACATAATTCAG
1 ATCAGAAATCAAAACAGAATTCAG
** * *
9117 ATCAGCTATCATAACAGAATCCATG
1 ATCAGAAATCAAAACAGAATTCA-G
* * * * * *
9142 TTAAGAAA-CAGAACATATTTCAT
1 ATCAGAAATCAAAACAGAATTCAG
** *
9165 ATCAGATGTCAAAACAGAATTCAA
1 ATCAGAAATCAAAACAGAATTCAG
*
9189 ATAAGAAATCA
1 ATCAGAAATCA
9200 GATAAAATAT
Statistics
Matches: 56, Mismatches: 25, Indels: 4
0.66 0.29 0.05
Matches are distributed among these distances:
23 4 0.07
24 47 0.84
25 5 0.09
ACGTcount: A:0.50, C:0.17, G:0.10, T:0.23
Consensus pattern (24 bp):
ATCAGAAATCAAAACAGAATTCAG
Found at i:13594 original size:17 final size:18
Alignment explanation
Indices: 13572--13607 Score: 56
Period size: 17 Copynumber: 2.1 Consensus size: 18
13562 TTTTAAGTTT
13572 TTTAAAAATA-TAAAATA
1 TTTAAAAATACTAAAATA
*
13589 TTTAAAATTACTAAAATA
1 TTTAAAAATACTAAAATA
13607 T
1 T
13608 GACACGTGTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 9 0.53
18 8 0.47
ACGTcount: A:0.58, C:0.03, G:0.00, T:0.39
Consensus pattern (18 bp):
TTTAAAAATACTAAAATA
Found at i:18065 original size:2 final size:2
Alignment explanation
Indices: 18058--18090 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
18048 CCATGTCCAG
18058 TA TA TA TA 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 TA TA TA TA T
18091 CTGCAATGAG
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:24299 original size:27 final size:25
Alignment explanation
Indices: 24243--24310 Score: 102
Period size: 27 Copynumber: 2.6 Consensus size: 25
24233 AATTTTTTTT
24243 TTATTAAAT-TTATTATTATTATTA
1 TTATTAAATATTATTATTATTATTA
24267 TTATTAAATATTATTATTAGTGTATTA
1 TTATTAAATATTATTATTA-T-TATTA
24294 TTATTAAATAATTATTA
1 TTATTAAAT-ATTATTA
24311 CAAGCCCAAA
Statistics
Matches: 40, Mismatches: 0, Indels: 4
0.91 0.00 0.09
Matches are distributed among these distances:
24 9 0.22
25 9 0.22
26 1 0.03
27 14 0.35
28 7 0.17
ACGTcount: A:0.40, C:0.00, G:0.03, T:0.57
Consensus pattern (25 bp):
TTATTAAATATTATTATTATTATTA
Found at i:24310 original size:3 final size:3
Alignment explanation
Indices: 24252--24299 Score: 60
Period size: 3 Copynumber: 15.0 Consensus size: 3
24242 TTTATTAAAT
*
24252 TTA TTA TTA TTA TTA TTA TTAA ATA TTA TTA TTA GTGTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TT-A TTA TTA TTA TTA -T-TA TTA TTA TTA
24300 AATAATTATT
Statistics
Matches: 40, Mismatches: 2, Indels: 6
0.83 0.04 0.12
Matches are distributed among these distances:
3 34 0.85
4 4 0.10
5 2 0.05
ACGTcount: A:0.35, C:0.00, G:0.04, T:0.60
Consensus pattern (3 bp):
TTA
Found at i:26247 original size:20 final size:21
Alignment explanation
Indices: 26224--26275 Score: 56
Period size: 20 Copynumber: 2.6 Consensus size: 21
26214 AGAAATTAAA
26224 AATTCATTTATTT-AATTTTT
1 AATTCATTTATTTAAATTTTT
* *
26244 AATTCTTTTCTTTCAAATTTTT
1 AATTCATTTATTT-AAATTTTT
26266 -ATT-ATTTATT
1 AATTCATTTATT
26276 ATTTTTATAT
Statistics
Matches: 26, Mismatches: 4, Indels: 4
0.76 0.12 0.12
Matches are distributed among these distances:
20 16 0.62
21 3 0.12
22 7 0.27
ACGTcount: A:0.27, C:0.08, G:0.00, T:0.65
Consensus pattern (21 bp):
AATTCATTTATTTAAATTTTT
Found at i:26294 original size:14 final size:16
Alignment explanation
Indices: 26260--26301 Score: 52
Period size: 14 Copynumber: 2.8 Consensus size: 16
26250 TTTCTTTCAA
*
26260 ATTTTTATTATTTATT
1 ATTTTTATTATTTAAT
26276 ATTTTTA-TA-TTAAT
1 ATTTTTATTATTTAAT
*
26290 ATTTTTTTTATT
1 ATTTTTATTATT
26302 CAGGTATTAA
Statistics
Matches: 22, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
14 10 0.45
15 4 0.18
16 8 0.36
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (16 bp):
ATTTTTATTATTTAAT
Found at i:35249 original size:22 final size:23
Alignment explanation
Indices: 35198--35253 Score: 69
Period size: 23 Copynumber: 2.5 Consensus size: 23
35188 ATCTACACTC
* *
35198 TTCAAAGATGATAGATTCCCTTT
1 TTCAAAGATGACAAATTCCCTTT
* *
35221 TTAAAAGATGACAAATTCTC-TT
1 TTCAAAGATGACAAATTCCCTTT
35243 TTCAAAGATGA
1 TTCAAAGATGA
35254 AAGCTTTATG
Statistics
Matches: 28, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
22 12 0.43
23 16 0.57
ACGTcount: A:0.38, C:0.14, G:0.12, T:0.36
Consensus pattern (23 bp):
TTCAAAGATGACAAATTCCCTTT
Found at i:36127 original size:76 final size:76
Alignment explanation
Indices: 35928--36564 Score: 1132
Period size: 76 Copynumber: 8.3 Consensus size: 76
35918 CTATTTCCCA
35928 CATCTGTAAGT-CTTGCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCA
1 CATCTGTAAGTCCTT-CAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTC-
* *
35992 AAAACCTTAGGGT
64 AAAGCCTTCGGGT
36005 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
36070 AGCCTTCGGGT
66 AGCCTTCGGGT
36081 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
36146 AGCCTTCGGGT
66 AGCCTTCGGGT
36157 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTC-A
* *
36222 AAACCTTAGGGT
65 AAGCCTTCGGGT
36234 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
36299 AGCCTTCGGGT
66 AGCCTTCGGGT
*
36310 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCATCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTC-A
* *
36375 AAACCTTAGGGT
65 AAGCCTTCGGGT
36387 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
*
36452 AGTCTTCGGGT
66 AGCCTTCGGGT
* *
36463 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGACTTCGGGAGTTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
*
36528 AGTCTTCGGGT
66 AGCCTTCGGGT
36539 CATCTGTAAGTCCTTCAGTGCATGAT
1 CATCTGTAAGTCCTTCAGTGCATGAT
36565 CTTTTCTAAA
Statistics
Matches: 542, Mismatches: 15, Indels: 7
0.96 0.03 0.01
Matches are distributed among these distances:
76 333 0.61
77 206 0.38
78 3 0.01
ACGTcount: A:0.23, C:0.20, G:0.22, T:0.36
Consensus pattern (76 bp):
CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
AGCCTTCGGGT
Found at i:36329 original size:229 final size:230
Alignment explanation
Indices: 35928--36564 Score: 1163
Period size: 229 Copynumber: 2.8 Consensus size: 230
35918 CTATTTCCCA
35928 CATCTGTAAGT-CTTGCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCA
1 CATCTGTAAGTCCTT-CAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCA
35992 AAAACCTTAGGGTCATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTT
65 AAAACCTTAGGGTCATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTT
*
36057 TTGATGTTTTCAAAGCCTTCGGGTCATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCT
130 TTGATGTTTTCAAAGCCTTCGGGTCATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCA
* *
36122 TCGGGAGCTTTTTGATGTTTTC-AAAGCCTTCGGGT
195 TCGGGAGCTTTTTGATGTTTTCAAAAACCTTAGGGT
36157 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
36222 AAACCTTAGGGTCATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTT
66 AAACCTTAGGGTCATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTT
36287 TGATGTTTTCAAAGCCTTCGGGTCATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCAT
131 TGATGTTTTCAAAGCCTTCGGGTCATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCAT
36352 CGGGAGCTTTTTGATGTTTTCAAAAACCTTAGGGT
196 CGGGAGCTTTTTGATGTTTTCAAAAACCTTAGGGT
36387 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTC-A
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
** * * *
36451 AAGTCTTCGGGTCATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGACTTCGGGAGTTTTT
66 AAACCTTAGGGTCATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTT
*
36516 TGATGTTTTCAAAGTCTTCGGGTCATCTGTAAGTCCTTCAGTGCATGAT
131 TGATGTTTTCAAAGCCTTCGGGTCATCTGTAAGTCCTTCAGTGCATGAT
36565 CTTTTCTAAA
Statistics
Matches: 397, Mismatches: 9, Indels: 4
0.97 0.02 0.01
Matches are distributed among these distances:
229 320 0.81
230 77 0.19
ACGTcount: A:0.23, C:0.20, G:0.22, T:0.36
Consensus pattern (230 bp):
CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
AAACCTTAGGGTCATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTT
TGATGTTTTCAAAGCCTTCGGGTCATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCAT
CGGGAGCTTTTTGATGTTTTCAAAAACCTTAGGGT
Found at i:36576 original size:153 final size:153
Alignment explanation
Indices: 35928--36564 Score: 1136
Period size: 153 Copynumber: 4.2 Consensus size: 153
35918 CTATTTCCCA
35928 CATCTGTAAGT-CTTGCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCA
1 CATCTGTAAGTCCTT-CAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTC-
* *
35992 AAAACCTTAGGGTCATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTT
64 AAAGCCTTCGGGTCATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTT
* *
36057 TTGATGTTTTC-AAAGCCTTCGGGT
129 TTGATGTTTTCAAAAACCTTAGGGT
36081 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
36146 AGCCTTCGGGTCATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTT
66 AGCCTTCGGGTCATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTT
36211 GATGTTTTCAAAAACCTTAGGGT
131 GATGTTTTCAAAAACCTTAGGGT
36234 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
*
36299 AGCCTTCGGGTCATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCATCGGGAGCTTTTT
66 AGCCTTCGGGTCATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTT
36364 GATGTTTTCAAAAACCTTAGGGT
131 GATGTTTTCAAAAACCTTAGGGT
36387 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
* * *
36452 AGTCTTCGGGTCATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGACTTCGGGAGTTTTTT
66 AGCCTTCGGGTCATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTT
** *
36517 GATGTTTTC-AAAGTCTTCGGGT
131 GATGTTTTCAAAAACCTTAGGGT
36539 CATCTGTAAGTCCTTCAGTGCATGAT
1 CATCTGTAAGTCCTTCAGTGCATGAT
36565 CTTTTCTAAA
Statistics
Matches: 470, Mismatches: 12, Indels: 5
0.97 0.02 0.01
Matches are distributed among these distances:
152 110 0.23
153 357 0.76
154 3 0.01
ACGTcount: A:0.23, C:0.20, G:0.22, T:0.36
Consensus pattern (153 bp):
CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
AGCCTTCGGGTCATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTT
GATGTTTTCAAAAACCTTAGGGT
Found at i:37703 original size:65 final size:65
Alignment explanation
Indices: 37543--37703 Score: 204
Period size: 64 Copynumber: 2.5 Consensus size: 65
37533 TTGTTTAAGG
* * * **
37543 TGCATCGATGCACATGCAGTGCATCGATGCAT--GAATTTAAATAGAAAACATCGAATAGGATTT
1 TGCATCGATGCATAAGGAGTGCATCGATGCATCCCCA-TTAAATAGAAAACATCGAATAGGATTT
37606 A
65 A
*
37607 TGCATCGATGCATAAGGAGTGCATCGATGCATCCCCATTAAATA-CAAACATCGAATAGGATTTA
1 TGCATCGATGCATAAGGAGTGCATCGATGCATCCCCATTAAATAGAAAACATCGAATAGGATTTA
*
37671 TGCATCGATGCAT-GGTGTAGTGCATCGATGCAT
1 TGCATCGATGCATAAG-G-AGTGCATCGATGCAT
37704 ACCTTCATTA
Statistics
Matches: 86, Mismatches: 7, Indels: 7
0.86 0.07 0.07
Matches are distributed among these distances:
63 1 0.01
64 62 0.72
65 22 0.26
66 1 0.01
ACGTcount: A:0.34, C:0.18, G:0.22, T:0.27
Consensus pattern (65 bp):
TGCATCGATGCATAAGGAGTGCATCGATGCATCCCCATTAAATAGAAAACATCGAATAGGATTTA
Found at i:39522 original size:154 final size:149
Alignment explanation
Indices: 39078--39537 Score: 839
Period size: 149 Copynumber: 3.1 Consensus size: 149
39068 GAGTCGAGGG
*
39078 TCTACGCGGTCCTTCGGGATATATATATATTCTGTGGAACATGTGTGAAGTCTTGAAAGACACAT
1 TCTACGCGGTCCTTCGGGATATATATATATTCTGTGGAACATGTGTGAAGTCTTGAAAGATACAT
39143 ACTTGATCCCTAGTATATGTATATGATTCTTAAGGAATAATATGTGGTCCTTATGGACATTATTA
66 ACTTGATCCCTAGTATATGTATATGATTCTTAAGGAATAATATGTGGTCCTTATGGACATTATTA
39208 TATGGCACTACGGTGCAAT
131 TATGGCACTACGGTGCAAT
39227 TCTACGCGGTCCTTCGGGATATATATATATTCTGTGGAACATGTGTGAAGTCTTGAAAGATACAT
1 TCTACGCGGTCCTTCGGGATATATATATATTCTGTGGAACATGTGTGAAGTCTTGAAAGATACAT
*
39292 ACTTGGTCCCTAGTATATGTATATGATTCTTAAGGAATAATATGTGGTCCTTATGGACATTATTA
66 ACTTGATCCCTAGTATATGTATATGATTCTTAAGGAATAATATGTGGTCCTTATGGACATTATTA
39357 TATGGCACTACGGTGCAAT
131 TATGGCACTACGGTGCAAT
*
39376 TCTACGCGGTCCTTCGGGATATATATATATATATATATGTGGAACATGTGTGAAGTCTTGAAAGA
1 TCTACGCGGTCCTTCGGG----ATATATATATAT-TCTGTGGAACATGTGTGAAGTCTTGAAAGA
*
39441 TAAATACTTGATCCCTAGTATATGTATATGATTCTTAAGGAATAATATGTGGTCCTTATGGACAT
61 TACATACTTGATCCCTAGTATATGTATATGATTCTTAAGGAATAATATGTGGTCCTTATGGACAT
39506 TATTATATGGCACTACGGTGCAAT
126 TATTATATGGCACTACGGTGCAAT
39530 TCTACGCG
1 TCTACGCG
39538 CACTTTGGTG
Statistics
Matches: 301, Mismatches: 5, Indels: 5
0.97 0.02 0.02
Matches are distributed among these distances:
149 165 0.55
153 12 0.04
154 124 0.41
ACGTcount: A:0.29, C:0.15, G:0.21, T:0.35
Consensus pattern (149 bp):
TCTACGCGGTCCTTCGGGATATATATATATTCTGTGGAACATGTGTGAAGTCTTGAAAGATACAT
ACTTGATCCCTAGTATATGTATATGATTCTTAAGGAATAATATGTGGTCCTTATGGACATTATTA
TATGGCACTACGGTGCAAT
Found at i:43041 original size:65 final size:65
Alignment explanation
Indices: 42881--43041 Score: 204
Period size: 64 Copynumber: 2.5 Consensus size: 65
42871 TTGTTTAAGG
* * * **
42881 TGCATCGATGCACATGCAGTGCATCGATGCAT--GAATTTAAATAGAAAACATCGAATAGGATTT
1 TGCATCGATGCATAAGGAGTGCATCGATGCATCCCCA-TTAAATAGAAAACATCGAATAGGATTT
42944 A
65 A
*
42945 TGCATCGATGCATAAGGAGTGCATCGATGCATCCCCATTAAATA-CAAACATCGAATAGGATTTA
1 TGCATCGATGCATAAGGAGTGCATCGATGCATCCCCATTAAATAGAAAACATCGAATAGGATTTA
*
43009 TGCATCGATGCAT-GGTGTAGTGCATCGATGCAT
1 TGCATCGATGCATAAG-G-AGTGCATCGATGCAT
43042 ACCTTCATTA
Statistics
Matches: 86, Mismatches: 7, Indels: 7
0.86 0.07 0.07
Matches are distributed among these distances:
63 1 0.01
64 62 0.72
65 22 0.26
66 1 0.01
ACGTcount: A:0.34, C:0.18, G:0.22, T:0.27
Consensus pattern (65 bp):
TGCATCGATGCATAAGGAGTGCATCGATGCATCCCCATTAAATAGAAAACATCGAATAGGATTTA
Found at i:44815 original size:151 final size:149
Alignment explanation
Indices: 44412--44877 Score: 844
Period size: 149 Copynumber: 3.1 Consensus size: 149
44402 GAGTCGAGGG
* *
44412 TCTACGCAGTCCTTCGGGATATATATATATTCTGTGGAACATGTGTGAAGTCTTGAAAGACACAT
1 TCTACGCGGTCCTTCGGGATATATATATATTCTGTGGAACATGTGTGAAGTCTTGAAAGATACAT
*
44477 ACTTGATCCCTAGTATATGTATATGATTATTAAGGAATAATATGTGGTCCTTATGGACATTATTA
66 ACTTGATCCCTAGTATATGTATATGATTCTTAAGGAATAATATGTGGTCCTTATGGACATTATTA
44542 TATGGCACTACGGTGCAAT
131 TATGGCACTACGGTGCAAT
*
44561 TCTACGCGATCCTTCGGGATATATATATATTCTGTGGAACATGTGTGAAGTCTTGAAAGATACAT
1 TCTACGCGGTCCTTCGGGATATATATATATTCTGTGGAACATGTGTGAAGTCTTGAAAGATACAT
44626 ACTTGATCCCTAGTATATGTATATGATTCTTAAGGAATAATATGTGGTCCTTATGGACATTATTA
66 ACTTGATCCCTAGTATATGTATATGATTCTTAAGGAATAATATGTGGTCCTTATGGACATTATTA
44691 TATGGCACTACGGTGCAAT
131 TATGGCACTACGGTGCAAT
44710 TCTACGCGGTCCTTCGGGATATATATATATATTCTGTGGAACATGTGTGAAGTCTTGAAAGATAC
1 TCTACGCGGTCCTTCGGG--ATATATATATATTCTGTGGAACATGTGTGAAGTCTTGAAAGATAC
*
44775 ATACTTGATCCCTAGTATATGTATATGATTCTTAATGAATAATATGTGGTCCTTATGGACATTAT
64 ATACTTGATCCCTAGTATATGTATATGATTCTTAAGGAATAATATGTGGTCCTTATGGACATTAT
*
44840 TATATGGCACTACGGTGTAAT
129 TATATGGCACTACGGTGCAAT
44861 TCTACGCGG-CACTTCGG
1 TCTACGCGGTC-CTTCGG
44878 TGCAATTATA
Statistics
Matches: 307, Mismatches: 7, Indels: 4
0.97 0.02 0.01
Matches are distributed among these distances:
149 162 0.53
150 1 0.00
151 144 0.47
ACGTcount: A:0.29, C:0.15, G:0.20, T:0.35
Consensus pattern (149 bp):
TCTACGCGGTCCTTCGGGATATATATATATTCTGTGGAACATGTGTGAAGTCTTGAAAGATACAT
ACTTGATCCCTAGTATATGTATATGATTCTTAAGGAATAATATGTGGTCCTTATGGACATTATTA
TATGGCACTACGGTGCAAT
Found at i:44878 original size:23 final size:23
Alignment explanation
Indices: 44845--44889 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
44835 ATTATTATAT
* *
44845 GGCACTACGGTGTAATTCTACGC
1 GGCACTACGGTGCAATTATACGC
*
44868 GGCACTTCGGTGCAATTATACG
1 GGCACTACGGTGCAATTATACG
44890 AGCTGTGGTG
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.22, C:0.24, G:0.27, T:0.27
Consensus pattern (23 bp):
GGCACTACGGTGCAATTATACGC
Found at i:48232 original size:14 final size:14
Alignment explanation
Indices: 48213--48239 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
48203 AACAAGTCTT
48213 ATCATTCATTAAAG
1 ATCATTCATTAAAG
48227 ATCATTCATTAAA
1 ATCATTCATTAAA
48240 TTTTAAAACA
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:0.44, C:0.15, G:0.04, T:0.37
Consensus pattern (14 bp):
ATCATTCATTAAAG
Found at i:48609 original size:43 final size:43
Alignment explanation
Indices: 48543--48813 Score: 294
Period size: 43 Copynumber: 6.3 Consensus size: 43
48533 TGGTAACAAA
*** * *
48543 AAACGCCGCAATAGGTAACGATATATAGCGGCGTTTGTCCAAC
1 AAACGCCGCAATAGGTGTTGATATTTAGCGGCGTTTTTCCAAC
* * * *
48586 AAATGTCGCAATAGGTGTTGATATTTGGCGGCATTTTTCCAAC
1 AAACGCCGCAATAGGTGTTGATATTTAGCGGCGTTTTTCCAAC
* * *
48629 AAACGCCGCAATAGATGTTGAGATTTAGCGGCGTTTTTCCCAC
1 AAACGCCGCAATAGGTGTTGATATTTAGCGGCGTTTTTCCAAC
48672 AAACGCCGCAATAGGTGTTGATATTTAGCGGCGTTTTTTTCC-AC
1 AAACGCCGCAATAGGTGTTGATATTTAGCGGCG--TTTTTCCAAC
* *
48716 AAACGCCGCAATAGGTGTTGATATTTAGCGACGTTTTTCCCAC
1 AAACGCCGCAATAGGTGTTGATATTTAGCGGCGTTTTTCCAAC
* * * * * * **
48759 AAACACCGCAAAAGAT-ATGGTATATAGCGGCGTTTTTTTAGAAC
1 AAACGCCGCAATAGGTGTTGATATTTAGCGGCG--TTTTTCCAAC
48803 AAACGCCGCAA
1 AAACGCCGCAA
48814 AATGTCATAT
Statistics
Matches: 193, Mismatches: 30, Indels: 9
0.83 0.13 0.04
Matches are distributed among these distances:
42 19 0.10
43 116 0.60
44 51 0.26
45 7 0.04
ACGTcount: A:0.29, C:0.21, G:0.22, T:0.28
Consensus pattern (43 bp):
AAACGCCGCAATAGGTGTTGATATTTAGCGGCGTTTTTCCAAC
Found at i:48992 original size:21 final size:21
Alignment explanation
Indices: 48966--49024 Score: 73
Period size: 21 Copynumber: 2.8 Consensus size: 21
48956 ATTTTCCAAT
*
48966 AAACTTGACATCCATAACAAC
1 AAACTTGAAATCCATAACAAC
* *
48987 AAACTTAAAATCCATAACAAG
1 AAACTTGAAATCCATAACAAC
**
49008 AAAAATGAAATCCATAA
1 AAACTTGAAATCCATAA
49025 TAATAAATCA
Statistics
Matches: 32, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 32 1.00
ACGTcount: A:0.56, C:0.20, G:0.05, T:0.19
Consensus pattern (21 bp):
AAACTTGAAATCCATAACAAC
Found at i:52971 original size:52 final size:52
Alignment explanation
Indices: 52903--53061 Score: 300
Period size: 52 Copynumber: 3.1 Consensus size: 52
52893 TAACAACAAA
52903 ATACATTATAATTTAGAAACATTAAAGTACTTATGCATAAACAGTCTTCACC
1 ATACATTATAATTTAGAAACATTAAAGTACTTATGCATAAACAGTCTTCACC
*
52955 ATACATTATAATTTAGAAACATTAAAGTACTTATGCATAAACAGTCTTCAAC
1 ATACATTATAATTTAGAAACATTAAAGTACTTATGCATAAACAGTCTTCACC
*
53007 ATACATTATAATTTAGAAATATTAAAGTACTTATGCATAAACAGTCTTCACC
1 ATACATTATAATTTAGAAACATTAAAGTACTTATGCATAAACAGTCTTCACC
53059 ATA
1 ATA
53062 TTGTTCAGTA
Statistics
Matches: 104, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
52 104 1.00
ACGTcount: A:0.43, C:0.16, G:0.08, T:0.33
Consensus pattern (52 bp):
ATACATTATAATTTAGAAACATTAAAGTACTTATGCATAAACAGTCTTCACC
Found at i:54203 original size:42 final size:40
Alignment explanation
Indices: 54157--54263 Score: 103
Period size: 39 Copynumber: 2.6 Consensus size: 40
54147 ATTTACCACC
54157 ATATTGCGGCGTTTTTGGTATAAACGCCACTAAATGT-TAAAT
1 ATATTGCGGCGTTTTT--TATAAACGCCACTAAATGTCT-AAT
* * * *
54199 ATATTACGGCG--TTTTACTAAACACCACTACATGTCTACT
1 ATATTGCGGCGTTTTTTA-TAAACGCCACTAAATGTCTAAT
54238 ATATTGCGGCGTTTTTACTATAAACG
1 ATATTGCGGCGTTTTT--TATAAACG
54264 TCGCTATTGT
Statistics
Matches: 53, Mismatches: 6, Indels: 12
0.75 0.08 0.17
Matches are distributed among these distances:
38 2 0.04
39 27 0.51
40 4 0.08
41 3 0.06
42 15 0.28
43 2 0.04
ACGTcount: A:0.30, C:0.19, G:0.16, T:0.36
Consensus pattern (40 bp):
ATATTGCGGCGTTTTTTATAAACGCCACTAAATGTCTAAT
Found at i:56556 original size:15 final size:15
Alignment explanation
Indices: 56536--56569 Score: 68
Period size: 15 Copynumber: 2.3 Consensus size: 15
56526 TAAAGATGTC
56536 ACATCAACTTTACAA
1 ACATCAACTTTACAA
56551 ACATCAACTTTACAA
1 ACATCAACTTTACAA
56566 ACAT
1 ACAT
56570 TCACTGATCA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.47, C:0.26, G:0.00, T:0.26
Consensus pattern (15 bp):
ACATCAACTTTACAA
Found at i:57331 original size:24 final size:25
Alignment explanation
Indices: 57285--57339 Score: 69
Period size: 24 Copynumber: 2.3 Consensus size: 25
57275 CAGAATTTTC
* *
57285 TTAT-TTTATTCTCATTTTCCATTT
1 TTATATTTATTCACATATTCCATTT
57309 TTATATTTATTCACATATT-CATTT
1 TTATATTTATTCACATATTCCATTT
*
57333 TCATATT
1 TTATATT
57340 CCATGTTCAT
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
24 15 0.56
25 12 0.44
ACGTcount: A:0.24, C:0.15, G:0.00, T:0.62
Consensus pattern (25 bp):
TTATATTTATTCACATATTCCATTT
Found at i:57476 original size:19 final size:19
Alignment explanation
Indices: 57393--57488 Score: 111
Period size: 19 Copynumber: 5.1 Consensus size: 19
57383 AGAATCGGAA
* *
57393 CTTATTTCCAGATTCATAA
1 CTTATTTTCAGATTCATAG
* *
57412 CTTATTTCCAGACTCATAG
1 CTTATTTTCAGATTCATAG
* *
57431 CTTACTGTCAGATTCATAG
1 CTTATTTTCAGATTCATAG
*
57450 CTTATTTTCAAATTCATAG
1 CTTATTTTCAGATTCATAG
* *
57469 CTTATTTTTAAATTCATAG
1 CTTATTTTCAGATTCATAG
57488 C
1 C
57489 CCAATGCATA
Statistics
Matches: 67, Mismatches: 10, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
19 67 1.00
ACGTcount: A:0.29, C:0.20, G:0.08, T:0.43
Consensus pattern (19 bp):
CTTATTTTCAGATTCATAG
Found at i:60413 original size:3 final size:3
Alignment explanation
Indices: 60405--60449 Score: 81
Period size: 3 Copynumber: 14.7 Consensus size: 3
60395 ACATATTAAA
60405 AAT AAT AAT ATAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT A-AT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
60450 CATCCGGATG
Statistics
Matches: 41, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
3 38 0.93
4 3 0.07
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:60848 original size:20 final size:20
Alignment explanation
Indices: 60825--60887 Score: 51
Period size: 20 Copynumber: 3.2 Consensus size: 20
60815 CTTGAGAGAG
60825 AATTGCCTCGAGTGAGGCAA
1 AATTGCCTCGAGTGAGGCAA
* ** *
60845 AATTTTCCT--TTTGAGAG-AG
1 AA-TTGCCTCGAGTGAG-GCAA
60864 AATTGCCTCGAGTGAGGCAA
1 AATTGCCTCGAGTGAGGCAA
60884 AATT
1 AATT
60888 TGTTTAAATT
Statistics
Matches: 30, Mismatches: 8, Indels: 10
0.62 0.17 0.21
Matches are distributed among these distances:
18 5 0.17
19 8 0.27
20 12 0.40
21 5 0.17
ACGTcount: A:0.30, C:0.16, G:0.25, T:0.29
Consensus pattern (20 bp):
AATTGCCTCGAGTGAGGCAA
Found at i:60859 original size:39 final size:39
Alignment explanation
Indices: 60804--60888 Score: 152
Period size: 39 Copynumber: 2.2 Consensus size: 39
60794 TAAGAGATAA
*
60804 AAAAATTTCCTCTTGAGAGAGAATTGCCTCGAGTGAGGC
1 AAAATTTTCCTCTTGAGAGAGAATTGCCTCGAGTGAGGC
*
60843 AAAATTTTCCTTTTGAGAGAGAATTGCCTCGAGTGAGGC
1 AAAATTTTCCTCTTGAGAGAGAATTGCCTCGAGTGAGGC
60882 AAAATTT
1 AAAATTT
60889 GTTTAAATTT
Statistics
Matches: 44, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
39 44 1.00
ACGTcount: A:0.32, C:0.15, G:0.24, T:0.29
Consensus pattern (39 bp):
AAAATTTTCCTCTTGAGAGAGAATTGCCTCGAGTGAGGC
Found at i:62104 original size:16 final size:16
Alignment explanation
Indices: 62065--62105 Score: 50
Period size: 15 Copynumber: 2.7 Consensus size: 16
62055 GATTTGGTTG
*
62065 CAGAAATGA-TGATGA
1 CAGAAATGACTAATGA
*
62080 CA-CAATGACTAATGA
1 CAGAAATGACTAATGA
62095 CAGAAATGACT
1 CAGAAATGACT
62106 TCACCGACTA
Statistics
Matches: 21, Mismatches: 3, Indels: 3
0.78 0.11 0.11
Matches are distributed among these distances:
14 5 0.24
15 9 0.43
16 7 0.33
ACGTcount: A:0.46, C:0.15, G:0.20, T:0.20
Consensus pattern (16 bp):
CAGAAATGACTAATGA
Found at i:65247 original size:12 final size:12
Alignment explanation
Indices: 65232--65256 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
65222 ATATATCTGA
65232 TAAAATATTATT
1 TAAAATATTATT
65244 TAAAATATTATT
1 TAAAATATTATT
65256 T
1 T
65257 TTTTATCAAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (12 bp):
TAAAATATTATT
Found at i:73679 original size:97 final size:97
Alignment explanation
Indices: 73513--73707 Score: 390
Period size: 97 Copynumber: 2.0 Consensus size: 97
73503 TTATTAAAAA
73513 TCTGTCTTTTATTTACTTCAGTTTGACTTAACCAATCTTGATATTGTTAACGGGTTGCTAAATAT
1 TCTGTCTTTTATTTACTTCAGTTTGACTTAACCAATCTTGATATTGTTAACGGGTTGCTAAATAT
73578 TTATTTTTCTTTCCTTCCAGAATTTCTGAATG
66 TTATTTTTCTTTCCTTCCAGAATTTCTGAATG
73610 TCTGTCTTTTATTTACTTCAGTTTGACTTAACCAATCTTGATATTGTTAACGGGTTGCTAAATAT
1 TCTGTCTTTTATTTACTTCAGTTTGACTTAACCAATCTTGATATTGTTAACGGGTTGCTAAATAT
73675 TTATTTTTCTTTCCTTCCAGAATTTCTGAATG
66 TTATTTTTCTTTCCTTCCAGAATTTCTGAATG
73707 T
1 T
73708 AGATGATGAT
Statistics
Matches: 98, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
97 98 1.00
ACGTcount: A:0.23, C:0.16, G:0.12, T:0.49
Consensus pattern (97 bp):
TCTGTCTTTTATTTACTTCAGTTTGACTTAACCAATCTTGATATTGTTAACGGGTTGCTAAATAT
TTATTTTTCTTTCCTTCCAGAATTTCTGAATG
Found at i:81544 original size:24 final size:24
Alignment explanation
Indices: 81515--81564 Score: 66
Period size: 24 Copynumber: 2.1 Consensus size: 24
81505 TGGTGGTTGA
*
81515 TTTAATGGT-TGTTTAAACTTTATT
1 TTTAATGGTATATTT-AACTTTATT
*
81539 TTTAATGGTATATTTAAGTTTATT
1 TTTAATGGTATATTTAACTTTATT
81563 TT
1 TT
81565 GGTTCTTTAT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
24 19 0.83
25 4 0.17
ACGTcount: A:0.26, C:0.02, G:0.12, T:0.60
Consensus pattern (24 bp):
TTTAATGGTATATTTAACTTTATT
Found at i:82072 original size:19 final size:19
Alignment explanation
Indices: 82034--82071 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 19
82024 TCACGTGAGG
82034 ATTATTTTCTTCTTATTTT
1 ATTATTTTCTTCTTATTTT
*
82053 ATTATTTATCTTTTTATTT
1 ATTATTT-TCTTCTTATTT
82072 ACTGTTTTTA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 7 0.41
20 10 0.59
ACGTcount: A:0.18, C:0.08, G:0.00, T:0.74
Consensus pattern (19 bp):
ATTATTTTCTTCTTATTTT
Done.