Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007940.1 Hibiscus syriacus cultivar Beakdansim tig00110356_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: 1348078
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 5 of 5
Found at i:1222006 original size:17 final size:17
Alignment explanation
Indices: 1221984--1222040 Score: 60
Period size: 17 Copynumber: 3.4 Consensus size: 17
1221974 AAAATGAAAC
1221984 TAAAAGATACAATATAG
1 TAAAAGATACAATATAG
* * * *
1222001 TAAAAGATATAGTAAAT
1 TAAAAGATACAATATAG
*
1222018 TAAAAGATACATTATAG
1 TAAAAGATACAATATAG
*
1222035 TGAAAG
1 TAAAAG
1222041 GAACAATACA
Statistics
Matches: 31, Mismatches: 9, Indels: 0
0.77 0.22 0.00
Matches are distributed among these distances:
17 31 1.00
ACGTcount: A:0.56, C:0.04, G:0.14, T:0.26
Consensus pattern (17 bp):
TAAAAGATACAATATAG
Found at i:1234899 original size:2 final size:2
Alignment explanation
Indices: 1234892--1234947 Score: 112
Period size: 2 Copynumber: 28.0 Consensus size: 2
1234882 ATTCCAACCC
1234892 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1234934 AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT
1234948 CCTAAAACTT
Statistics
Matches: 54, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 54 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1242637 original size:20 final size:20
Alignment explanation
Indices: 1242612--1242764 Score: 109
Period size: 20 Copynumber: 7.7 Consensus size: 20
1242602 AAATGACCAA
1242612 CAAATTCGCAACGCGAAAGT
1 CAAATTCGCAACGCGAAAGT
* *
1242632 CAAATTCGCAATGCG-AACT
1 CAAATTCGCAACGCGAAAGT
* * ***
1242651 CCAATTTCGCAAC-CCAGTTT
1 -CAAATTCGCAACGCGAAAGT
*
1242671 CCAATTTCGCAACGCG-AA-T
1 -CAAATTCGCAACGCGAAAGT
* *
1242690 CTATAAATCGCAACAC-AGAAGT
1 C-A-AATTCGCAACGCGA-AAGT
* *
1242712 CAAATTCGCAACACAAAAGT
1 CAAATTCGCAACGCGAAAGT
*
1242732 CAAATTCGCAACGCGATAGT
1 CAAATTCGCAACGCGAAAGT
1242752 CAAATTCGCAACG
1 CAAATTCGCAACG
1242765 TGAATAATAA
Statistics
Matches: 106, Mismatches: 18, Indels: 18
0.75 0.13 0.13
Matches are distributed among these distances:
18 1 0.01
19 6 0.06
20 92 0.87
21 5 0.05
22 2 0.02
ACGTcount: A:0.38, C:0.27, G:0.15, T:0.20
Consensus pattern (20 bp):
CAAATTCGCAACGCGAAAGT
Found at i:1242761 original size:60 final size:59
Alignment explanation
Indices: 1242612--1242763 Score: 139
Period size: 60 Copynumber: 2.5 Consensus size: 59
1242602 AAATGACCAA
** * * ***
1242612 CAAATTCGCAACGCGAAAGTCAAATTCGCAATGCGAACTCCAATTTCGCAACCCAGTTTC
1 CAAATTCGCAACGCG-AAGTCAAATTCGCAACACGAACTCCAAATTCGCAACCAAAAGTC
* * *
1242672 CAATTTCGCAACGCGAA-TCTATAAATCGCAACACAGAAGT-CAAATTCGCAACACAAAAGT-
1 CAAATTCGCAACGCGAAGTC-A-AATTCGCAACAC-GAACTCCAAATTCGCAAC-CAAAAGTC
1242732 CAAATTCGCAACGCGATAGTCAAATTCGCAAC
1 CAAATTCGCAACGCGA-AGTCAAATTCGCAAC
1242764 GTGAATAATA
Statistics
Matches: 74, Mismatches: 12, Indels: 12
0.76 0.12 0.12
Matches are distributed among these distances:
58 2 0.03
59 3 0.04
60 58 0.78
61 9 0.12
62 2 0.03
ACGTcount: A:0.38, C:0.28, G:0.14, T:0.20
Consensus pattern (59 bp):
CAAATTCGCAACGCGAAGTCAAATTCGCAACACGAACTCCAAATTCGCAACCAAAAGTC
Found at i:1242788 original size:21 final size:21
Alignment explanation
Indices: 1242758--1242805 Score: 62
Period size: 21 Copynumber: 2.3 Consensus size: 21
1242748 TAGTCAAATT
1242758 CGCAACGTGAATAATAAAAAG
1 CGCAACGTGAATAATAAAAAG
* * *
1242779 CGCAATGTGAATAGT-AAAAT
1 CGCAACGTGAATAATAAAAAG
1242799 CGCAACG
1 CGCAACG
1242806 AATCTATATG
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
20 10 0.43
21 13 0.57
ACGTcount: A:0.46, C:0.17, G:0.21, T:0.17
Consensus pattern (21 bp):
CGCAACGTGAATAATAAAAAG
Found at i:1243200 original size:20 final size:20
Alignment explanation
Indices: 1243177--1243225 Score: 89
Period size: 20 Copynumber: 2.5 Consensus size: 20
1243167 AAATTCGCGT
1243177 TGCGATTTTACTATTCACGC
1 TGCGATTTTACTATTCACGC
1243197 TGCGATTTTACTATTCACGC
1 TGCGATTTTACTATTCACGC
*
1243217 TACGATTTT
1 TGCGATTTT
1243226 GGAAACTGAG
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 28 1.00
ACGTcount: A:0.20, C:0.22, G:0.14, T:0.43
Consensus pattern (20 bp):
TGCGATTTTACTATTCACGC
Found at i:1245553 original size:28 final size:28
Alignment explanation
Indices: 1245521--1245596 Score: 71
Period size: 30 Copynumber: 2.6 Consensus size: 28
1245511 ATCTTTTTAA
* *
1245521 TTTTGAATATTAAAAGATAATTATATAT
1 TTTTGAATATTAAAAGAAAATAATATAT
* **
1245549 TTTTGTATATTTCAAATTAAAATAATATAT
1 TTTTGAATA-TT-AAAAGAAAATAATATAT
* *
1245579 GTTTGAATAGTAAAAGAA
1 TTTTGAATATTAAAAGAA
1245597 TTTTACTTTT
Statistics
Matches: 36, Mismatches: 10, Indels: 4
0.72 0.20 0.08
Matches are distributed among these distances:
28 13 0.36
29 3 0.08
30 20 0.56
ACGTcount: A:0.46, C:0.01, G:0.09, T:0.43
Consensus pattern (28 bp):
TTTTGAATATTAAAAGAAAATAATATAT
Found at i:1245749 original size:23 final size:23
Alignment explanation
Indices: 1245714--1245768 Score: 74
Period size: 23 Copynumber: 2.3 Consensus size: 23
1245704 ACTGAATATT
* *
1245714 TATATATATGTTTCGAATTATAA
1 TATATATAAGTTTCGAATTAAAA
*
1245737 TATATTTAAGTTTCGAATTAAAA
1 TATATATAAGTTTCGAATTAAAA
1245760 TAATATATA
1 T-ATATATA
1245769 TTTAAGTTTG
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
23 21 0.78
24 6 0.22
ACGTcount: A:0.44, C:0.04, G:0.07, T:0.45
Consensus pattern (23 bp):
TATATATAAGTTTCGAATTAAAA
Found at i:1250038 original size:4 final size:4
Alignment explanation
Indices: 1250029--1250059 Score: 53
Period size: 4 Copynumber: 7.8 Consensus size: 4
1250019 ATGATCTTAT
*
1250029 ATAC ATAC ATAC ATAT ATAC ATAC ATAC ATA
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATA
1250060 TAAAATGAGA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
4 25 1.00
ACGTcount: A:0.52, C:0.19, G:0.00, T:0.29
Consensus pattern (4 bp):
ATAC
Found at i:1250047 original size:16 final size:16
Alignment explanation
Indices: 1250026--1250061 Score: 72
Period size: 16 Copynumber: 2.2 Consensus size: 16
1250016 ATAATGATCT
1250026 TATATACATACATACA
1 TATATACATACATACA
1250042 TATATACATACATACA
1 TATATACATACATACA
1250058 TATA
1 TATA
1250062 AAATGAGATT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.50, C:0.17, G:0.00, T:0.33
Consensus pattern (16 bp):
TATATACATACATACA
Found at i:1253587 original size:4 final size:4
Alignment explanation
Indices: 1253580--1253619 Score: 80
Period size: 4 Copynumber: 10.0 Consensus size: 4
1253570 TAACGAAAAG
1253580 AGAA AGAA AGAA AGAA AGAA AGAA AGAA AGAA AGAA AGAA
1 AGAA AGAA AGAA AGAA AGAA AGAA AGAA AGAA AGAA AGAA
1253620 TTACCTTGAG
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 36 1.00
ACGTcount: A:0.75, C:0.00, G:0.25, T:0.00
Consensus pattern (4 bp):
AGAA
Found at i:1254287 original size:2 final size:2
Alignment explanation
Indices: 1254280--1254318 Score: 71
Period size: 2 Copynumber: 20.0 Consensus size: 2
1254270 TTAACCATTA
1254280 AT AT AT AT AT AT AT -T AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1254319 CTTTATGCTA
Statistics
Matches: 36, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.03
2 35 0.97
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
AT
Found at i:1254410 original size:31 final size:31
Alignment explanation
Indices: 1254334--1254411 Score: 88
Period size: 31 Copynumber: 2.5 Consensus size: 31
1254324 TGCTACTCAA
*
1254334 AAAATATCAATTTGACTATTAAAATTTAAAT
1 AAAATATCAATTTGACTATTAAAATTCAAAT
* * *
1254365 AAAAT-TCTAGTTTGATCT-TTTAAATTCAGAT
1 AAAATATC-AATTTGA-CTATTAAAATTCAAAT
1254396 AAAATATCAATTTGAC
1 AAAATATCAATTTGAC
1254412 CTCTTAATTA
Statistics
Matches: 39, Mismatches: 5, Indels: 7
0.76 0.10 0.14
Matches are distributed among these distances:
30 3 0.08
31 32 0.82
32 4 0.10
ACGTcount: A:0.45, C:0.09, G:0.06, T:0.40
Consensus pattern (31 bp):
AAAATATCAATTTGACTATTAAAATTCAAAT
Found at i:1261437 original size:4 final size:4
Alignment explanation
Indices: 1261428--1261458 Score: 62
Period size: 4 Copynumber: 7.8 Consensus size: 4
1261418 CAAAAACATA
1261428 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATG
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATG
1261459 CATTTGCCTT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 27 1.00
ACGTcount: A:0.26, C:0.00, G:0.26, T:0.48
Consensus pattern (4 bp):
ATGT
Found at i:1269248 original size:20 final size:20
Alignment explanation
Indices: 1269212--1269249 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
1269202 ATCTTATTAC
**
1269212 CTGATAATCTTTTATTCCCA
1 CTGATAATCTTACATTCCCA
1269232 CTGATAATCTTACATTCC
1 CTGATAATCTTACATTCC
1269250 GTTAACCAAA
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:0.26, C:0.26, G:0.05, T:0.42
Consensus pattern (20 bp):
CTGATAATCTTACATTCCCA
Found at i:1269653 original size:28 final size:28
Alignment explanation
Indices: 1269613--1269668 Score: 103
Period size: 28 Copynumber: 2.0 Consensus size: 28
1269603 TTCTAATGAA
1269613 ATATTTTATTAAAACTCATCAAATCGAC
1 ATATTTTATTAAAACTCATCAAATCGAC
*
1269641 ATATTTTATTAAAACTCATCAAGTCGAC
1 ATATTTTATTAAAACTCATCAAATCGAC
1269669 GTGATAAGTT
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
28 27 1.00
ACGTcount: A:0.41, C:0.18, G:0.05, T:0.36
Consensus pattern (28 bp):
ATATTTTATTAAAACTCATCAAATCGAC
Found at i:1270148 original size:15 final size:15
Alignment explanation
Indices: 1270128--1270157 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
1270118 CACTTTTATT
1270128 TCATTTTGGTCACCC
1 TCATTTTGGTCACCC
1270143 TCATTTTGGTCACCC
1 TCATTTTGGTCACCC
1270158 AGCTATATTT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.13, C:0.33, G:0.13, T:0.40
Consensus pattern (15 bp):
TCATTTTGGTCACCC
Found at i:1272524 original size:2 final size:2
Alignment explanation
Indices: 1272517--1272543 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
1272507 TTCATTCAAT
1272517 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 T
1272544 TAAATATTTG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:1272690 original size:2 final size:2
Alignment explanation
Indices: 1272683--1272709 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
1272673 TTCATTCAAT
1272683 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 T
1272710 TAAATATTTG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:1272801 original size:164 final size:166
Alignment explanation
Indices: 1272487--1272817 Score: 648
Period size: 166 Copynumber: 2.0 Consensus size: 166
1272477 ATAGCTCCCC
1272487 TCCACAAATAATATAAATCCTTCATTCAATTATATATATATATATATATATATATATTAAATATT
1 TCCACAAATAATATAAATCCTTCATTCAATTATATATATATATATATATATATATATTAAATATT
1272552 TGGGTAAACTATAAATTTAGTACCTAAATTATCAATTTTGGTATGTTTTAGTACCAAAACTTTTA
66 TGGGTAAACTATAAATTTAGTACCTAAATTATCAATTTTGGTATGTTTTAGTACCAAAACTTTTA
1272617 ATTTTTTCAAAAATATACCTAAAGTTTAGTTTTTAT
131 ATTTTTTCAAAAATATACCTAAAGTTTAGTTTTTAT
1272653 TCCACAAATAATATAAATCCTTCATTCAATTATATATATATATATATATATATATATTAAATATT
1 TCCACAAATAATATAAATCCTTCATTCAATTATATATATATATATATATATATATATTAAATATT
1272718 T-GGTAAACTATAAATTTAGTACCTAAATTATCAATTTTGGTATGTTTTAGTACCAAAACTTTTA
66 TGGGTAAACTATAAATTTAGTACCTAAATTATCAATTTTGGTATGTTTTAGTACCAAAACTTTTA
1272782 A-TTTTTCAAAAATATACCTAAAGTTTAGTTTTTAT
131 ATTTTTTCAAAAATATACCTAAAGTTTAGTTTTTAT
1272817 T
1 T
1272818 TTATTTAGTA
Statistics
Matches: 165, Mismatches: 0, Indels: 2
0.99 0.00 0.01
Matches are distributed among these distances:
164 35 0.21
165 64 0.39
166 66 0.40
ACGTcount: A:0.40, C:0.10, G:0.06, T:0.44
Consensus pattern (166 bp):
TCCACAAATAATATAAATCCTTCATTCAATTATATATATATATATATATATATATATTAAATATT
TGGGTAAACTATAAATTTAGTACCTAAATTATCAATTTTGGTATGTTTTAGTACCAAAACTTTTA
ATTTTTTCAAAAATATACCTAAAGTTTAGTTTTTAT
Found at i:1276066 original size:16 final size:16
Alignment explanation
Indices: 1276045--1276097 Score: 65
Period size: 16 Copynumber: 3.4 Consensus size: 16
1276035 TAAAAAAAAT
1276045 ATTAAAATAAATTAAA
1 ATTAAAATAAATTAAA
*
1276061 ATTAAAATAATTTAAA
1 ATTAAAATAAATTAAA
*
1276077 A-TAAAA-AAATATTAA
1 ATTAAAATAAAT-TAAA
1276092 ATTAAA
1 ATTAAA
1276098 GGGTAAACTA
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
14 3 0.09
15 9 0.28
16 20 0.62
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (16 bp):
ATTAAAATAAATTAAA
Found at i:1276090 original size:26 final size:27
Alignment explanation
Indices: 1276037--1276092 Score: 71
Period size: 26 Copynumber: 2.1 Consensus size: 27
1276027 ATTAACTTTA
*
1276037 AAAAAAATATTAAAATAAATTAAAATT
1 AAAAAAATATTAAAATAAATAAAAATT
*
1276064 AAAATAAT-TTAAAATAAA-AAAATATT
1 AAAAAAATATTAAAATAAATAAAA-ATT
1276090 AAA
1 AAA
1276093 TTAAAGGGTA
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
25 3 0.12
26 16 0.62
27 7 0.27
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (27 bp):
AAAAAAATATTAAAATAAATAAAAATT
Found at i:1277099 original size:14 final size:14
Alignment explanation
Indices: 1277080--1277119 Score: 53
Period size: 14 Copynumber: 2.9 Consensus size: 14
1277070 ATAAAATATG
* *
1277080 GTATGAACTGTACT
1 GTATGAACAGTACC
1277094 GTATGAACAGTACC
1 GTATGAACAGTACC
*
1277108 GTATAAACAGTA
1 GTATGAACAGTA
1277120 TCCCAAATGT
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
14 23 1.00
ACGTcount: A:0.38, C:0.15, G:0.20, T:0.28
Consensus pattern (14 bp):
GTATGAACAGTACC
Found at i:1282206 original size:36 final size:36
Alignment explanation
Indices: 1282159--1282435 Score: 491
Period size: 36 Copynumber: 7.7 Consensus size: 36
1282149 CAAATGTTTG
* *
1282159 TTCCGATTCAAGTCGAACGGAGGGAAGCATCTGCAC
1 TTCCGATTCAAGTCGAACGGAAGGAAGCATCGGCAC
*
1282195 TTCCGATTCAAGTCGAACGGAGGGAAGCATCGGCAC
1 TTCCGATTCAAGTCGAACGGAAGGAAGCATCGGCAC
*
1282231 TTCCGATTCAAGTCGAACGGAGGGAAGCATCGGCAC
1 TTCCGATTCAAGTCGAACGGAAGGAAGCATCGGCAC
*
1282267 TTCCGATTCAAGTCGAACGGAAGGAAGCATCGACAC
1 TTCCGATTCAAGTCGAACGGAAGGAAGCATCGGCAC
*
1282303 TTCCGATTCAAGTCGAACGGAAGGAAGCATCGACAC
1 TTCCGATTCAAGTCGAACGGAAGGAAGCATCGGCAC
*
1282339 TTCCGATTCAAGTCGAACGGAAGGAAGCATTGGCAC
1 TTCCGATTCAAGTCGAACGGAAGGAAGCATCGGCAC
1282375 TTCCGATTCAAGTCGAACGGAAGGAAGCATCGGCAC
1 TTCCGATTCAAGTCGAACGGAAGGAAGCATCGGCAC
1282411 TTCCGATTCAAGTCGAACGGAAGGA
1 TTCCGATTCAAGTCGAACGGAAGGA
1282436 TGTGTCTTAC
Statistics
Matches: 235, Mismatches: 6, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
36 235 1.00
ACGTcount: A:0.30, C:0.24, G:0.28, T:0.18
Consensus pattern (36 bp):
TTCCGATTCAAGTCGAACGGAAGGAAGCATCGGCAC
Found at i:1282716 original size:17 final size:17
Alignment explanation
Indices: 1282694--1282727 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
1282684 AAGAGAAAGT
*
1282694 AGTAAAACGTTTATTGA
1 AGTAAAACATTTATTGA
1282711 AGTAAAACATTTATTGA
1 AGTAAAACATTTATTGA
1282728 TACTCTGATT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.44, C:0.06, G:0.15, T:0.35
Consensus pattern (17 bp):
AGTAAAACATTTATTGA
Found at i:1282961 original size:36 final size:36
Alignment explanation
Indices: 1282905--1283048 Score: 137
Period size: 36 Copynumber: 3.8 Consensus size: 36
1282895 AGATGAACAA
*
1282905 TTGAGTCGAAAGTGCTGATGCTTCCTTCCGTTCACT
1 TTGAATCGAAAGTGCTGATGCTTCCTTCCGTTCACT
* *
1282941 TTGAATCGAAAGTGTCGATGCTTTCGATGCTTCCTTTCGTTC-TT
1 TTGAATCGAAA-----G-TGC--T-GATGCTTCCTTCCGTTCACT
* *
1282985 CTTGAACCGAAAGTGCCGATGCTTCCTTCCGTTCACT
1 -TTGAATCGAAAGTGCTGATGCTTCCTTCCGTTCACT
*
1283022 TTGAATCGAAAGTGCTTATGCTTCCTT
1 TTGAATCGAAAGTGCTGATGCTTCCTT
1283049 TCGTACTTCT
Statistics
Matches: 87, Mismatches: 10, Indels: 22
0.73 0.08 0.18
Matches are distributed among these distances:
36 50 0.57
37 1 0.01
39 3 0.03
40 1 0.01
41 1 0.01
42 3 0.03
44 2 0.02
45 26 0.30
ACGTcount: A:0.18, C:0.24, G:0.20, T:0.38
Consensus pattern (36 bp):
TTGAATCGAAAGTGCTGATGCTTCCTTCCGTTCACT
Found at i:1290487 original size:39 final size:40
Alignment explanation
Indices: 1290421--1290522 Score: 134
Period size: 39 Copynumber: 2.6 Consensus size: 40
1290411 TCCGTTATTT
* *
1290421 ATTAAATGAATGAATATGAATAAGATTTTATGTCCGTTTA
1 ATTAAATGAATGAACATGAACAAGATTTTATGTCCGTTTA
* * * *
1290461 ATTAAAT-AAAGAACATGAACATGATTTTGTGTTCGTTTA
1 ATTAAATGAATGAACATGAACAAGATTTTATGTCCGTTTA
*
1290500 ATTAAATGAATGAACACGAACAA
1 ATTAAATGAATGAACATGAACAA
1290523 ATGATTTACT
Statistics
Matches: 52, Mismatches: 9, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
39 33 0.63
40 19 0.37
ACGTcount: A:0.43, C:0.08, G:0.15, T:0.34
Consensus pattern (40 bp):
ATTAAATGAATGAACATGAACAAGATTTTATGTCCGTTTA
Found at i:1298497 original size:22 final size:20
Alignment explanation
Indices: 1298448--1298498 Score: 57
Period size: 22 Copynumber: 2.4 Consensus size: 20
1298438 AGATATTTAA
* *
1298448 ATAATATATTTAAATATAAT
1 ATAATATATATAAAAATAAT
1298468 ATAGATATATCATAAAAATAAT
1 ATA-ATATAT-ATAAAAATAAT
1298490 ATTAATATA
1 A-TAATATA
1298499 AATATTATAT
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
20 3 0.12
21 6 0.23
22 15 0.58
23 2 0.08
ACGTcount: A:0.57, C:0.02, G:0.02, T:0.39
Consensus pattern (20 bp):
ATAATATATATAAAAATAAT
Found at i:1298533 original size:20 final size:20
Alignment explanation
Indices: 1298485--1298544 Score: 75
Period size: 20 Copynumber: 2.9 Consensus size: 20
1298475 TATCATAAAA
*
1298485 ATAATATTAATATAAATATTAT
1 ATAATATT-ATTTAAATA-TAT
*
1298507 ATTATATTATTTAAATATAT
1 ATAATATTATTTAAATATAT
*
1298527 ATAATATCATTTAAATAT
1 ATAATATTATTTAAATAT
1298545 CAATTTAATA
Statistics
Matches: 34, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
20 19 0.56
21 8 0.24
22 7 0.21
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (20 bp):
ATAATATTATTTAAATATAT
Found at i:1304292 original size:7 final size:8
Alignment explanation
Indices: 1304276--1304301 Score: 52
Period size: 8 Copynumber: 3.2 Consensus size: 8
1304266 TTAAAAGATG
1304276 TTTTATTT
1 TTTTATTT
1304284 TTTTATTT
1 TTTTATTT
1304292 TTTTATTT
1 TTTTATTT
1304300 TT
1 TT
1304302 ATACCATATA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 18 1.00
ACGTcount: A:0.12, C:0.00, G:0.00, T:0.88
Consensus pattern (8 bp):
TTTTATTT
Found at i:1305292 original size:21 final size:21
Alignment explanation
Indices: 1305248--1305292 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
1305238 GCTTAACGCA
* *
1305248 TTTAGTATTTAAACTATCAGT
1 TTTAGTAATTAAACTATCAAT
* *
1305269 TTTAGTAATTAAACTTTTAAT
1 TTTAGTAATTAAACTATCAAT
1305290 TTT
1 TTT
1305293 TTCAAAACTT
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.33, C:0.07, G:0.07, T:0.53
Consensus pattern (21 bp):
TTTAGTAATTAAACTATCAAT
Found at i:1310043 original size:20 final size:21
Alignment explanation
Indices: 1310018--1310060 Score: 61
Period size: 20 Copynumber: 2.1 Consensus size: 21
1310008 ACGATTATAG
*
1310018 AATTAAATTTAT-TAAATTAA
1 AATTAAATTGATATAAATTAA
*
1310038 AATTAAATTGATATAATTTAA
1 AATTAAATTGATATAAATTAA
1310059 AA
1 AA
1310061 ATAATAAAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
20 11 0.55
21 9 0.45
ACGTcount: A:0.56, C:0.00, G:0.02, T:0.42
Consensus pattern (21 bp):
AATTAAATTGATATAAATTAA
Found at i:1310771 original size:21 final size:20
Alignment explanation
Indices: 1310732--1310778 Score: 67
Period size: 21 Copynumber: 2.3 Consensus size: 20
1310722 TAAGTATAAA
*
1310732 TATAATTTAAATATTATATT
1 TATAATTTAAATATAATATT
*
1310752 TTTAATTTATAATATAATATT
1 TATAATTTA-AATATAATATT
1310773 TATAAT
1 TATAAT
1310779 AGATATTTTA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
20 8 0.35
21 15 0.65
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (20 bp):
TATAATTTAAATATAATATT
Found at i:1317050 original size:25 final size:25
Alignment explanation
Indices: 1317016--1317064 Score: 71
Period size: 25 Copynumber: 2.0 Consensus size: 25
1317006 TAGTTAATTA
* *
1317016 TATTCAATTAATTTAAATTTATATG
1 TATTCAATTAATTCAAAATTATATG
*
1317041 TATTTAATTAATTCAAAATTATAT
1 TATTCAATTAATTCAAAATTATAT
1317065 ACATAGTTAT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
25 21 1.00
ACGTcount: A:0.43, C:0.04, G:0.02, T:0.51
Consensus pattern (25 bp):
TATTCAATTAATTCAAAATTATATG
Found at i:1319067 original size:28 final size:28
Alignment explanation
Indices: 1319027--1319091 Score: 114
Period size: 28 Copynumber: 2.4 Consensus size: 28
1319017 TATTGTATGA
1319027 TATTTA-TATTTTATCTTACATTTAAAT
1 TATTTATTATTTTATCTTACATTTAAAT
*
1319054 TATTTATTATTTTATCTTATATTTAAAT
1 TATTTATTATTTTATCTTACATTTAAAT
1319082 TATTTATTAT
1 TATTTATTAT
1319092 AATGATCAAA
Statistics
Matches: 36, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
27 6 0.17
28 30 0.83
ACGTcount: A:0.32, C:0.05, G:0.00, T:0.63
Consensus pattern (28 bp):
TATTTATTATTTTATCTTACATTTAAAT
Found at i:1325989 original size:23 final size:23
Alignment explanation
Indices: 1325955--1325998 Score: 70
Period size: 23 Copynumber: 1.9 Consensus size: 23
1325945 ATTTCAAGTC
* *
1325955 CATCTACTGTTTGTTGACTGGAT
1 CATCTACCGTTTATTGACTGGAT
1325978 CATCTACCGTTTATTGACTGG
1 CATCTACCGTTTATTGACTGG
1325999 TTCAGCTGCT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.18, C:0.20, G:0.20, T:0.41
Consensus pattern (23 bp):
CATCTACCGTTTATTGACTGGAT
Found at i:1328683 original size:2 final size:2
Alignment explanation
Indices: 1328676--1328714 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
1328666 CACAAAGAAT
1328676 TA TA TA 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 TA TA TA T
1328715 TTGAGTTGCC
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:1337596 original size:2 final size:2
Alignment explanation
Indices: 1337589--1337613 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
1337579 AAATAAAGGA
1337589 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
1337614 ACCTCCAAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1344364 original size:42 final size:36
Alignment explanation
Indices: 1344281--1344364 Score: 141
Period size: 36 Copynumber: 2.3 Consensus size: 36
1344271 GGTTGATTTG
1344281 ACCGGTGCCGGTGCTGCTGATATCATCCATGAAAGT
1 ACCGGTGCCGGTGCTGCTGATATCATCCATGAAAGT
*
1344317 ACCGGTGCCGGTGCTGCTGATATTATCCATGAAAGT
1 ACCGGTGCCGGTGCTGCTGATATCATCCATGAAAGT
* *
1344353 AGCAGTGCCGGT
1 ACCGGTGCCGGT
1344365 TCCGGATGAA
Statistics
Matches: 45, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
36 45 1.00
ACGTcount: A:0.21, C:0.24, G:0.30, T:0.25
Consensus pattern (36 bp):
ACCGGTGCCGGTGCTGCTGATATCATCCATGAAAGT
Found at i:1345674 original size:14 final size:16
Alignment explanation
Indices: 1345640--1345683 Score: 56
Period size: 14 Copynumber: 2.9 Consensus size: 16
1345630 AAATTAAAAA
1345640 TTTAAATACTAAATAG
1 TTTAAATACTAAATAG
*
1345656 ATTAAA-ACT-AATAG
1 TTTAAATACTAAATAG
*
1345670 TTTAAGTACTAAAT
1 TTTAAATACTAAAT
1345684 GTGTAGTTTA
Statistics
Matches: 23, Mismatches: 3, Indels: 4
0.77 0.10 0.13
Matches are distributed among these distances:
14 9 0.39
15 6 0.26
16 8 0.35
ACGTcount: A:0.50, C:0.07, G:0.07, T:0.36
Consensus pattern (16 bp):
TTTAAATACTAAATAG
Found at i:1346860 original size:23 final size:21
Alignment explanation
Indices: 1346797--1346860 Score: 60
Period size: 23 Copynumber: 2.9 Consensus size: 21
1346787 TTAATTATAA
*
1346797 TATAAATTTATTATATA-TCT
1 TATAAATTTATTTTATATTCT
1346817 TATTAAATTTTTATTTT-TATTCTT
1 TA-TAAA--TTTATTTTATATTC-T
1346841 TATAAATTTAATTTTATATT
1 TATAAATTT-ATTTTATATT
1346861 ATATACAAAA
Statistics
Matches: 36, Mismatches: 1, Indels: 11
0.75 0.02 0.23
Matches are distributed among these distances:
20 2 0.06
21 7 0.19
22 7 0.19
23 17 0.47
24 3 0.08
ACGTcount: A:0.34, C:0.03, G:0.00, T:0.62
Consensus pattern (21 bp):
TATAAATTTATTTTATATTCT
Done.