Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01005730.1 Hibiscus syriacus cultivar Beakdansim tig00013391_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: 91109
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:1060 original size:63 final size:63
Alignment explanation
Indices: 940--1060 Score: 154
Period size: 63 Copynumber: 1.9 Consensus size: 63
930 CAAATAAATG
* * *
940 AACATCGAATGCAATTAGTGCATCGATGCATAAGGAGTGCATCGATTCACCCCTTAAGATGAA
1 AACATCGAATGCAATTAGTGCACCGATGCATAAGGAGTGCATCGATGCACACCTTAAGATGAA
* * * * *
1003 AACATCGAATGGAATTTGTGTACCGATGCAT-AGATAGTGCATCGATGCACACGTTAAG
1 AACATCGAATGCAATTAGTGCACCGATGCATAAG-GAGTGCATCGATGCACACCTTAAG
1061 GGATGCATCG
Statistics
Matches: 49, Mismatches: 8, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
62 2 0.04
63 47 0.96
ACGTcount: A:0.34, C:0.19, G:0.22, T:0.25
Consensus pattern (63 bp):
AACATCGAATGCAATTAGTGCACCGATGCATAAGGAGTGCATCGATGCACACCTTAAGATGAA
Found at i:1080 original size:22 final size:23
Alignment explanation
Indices: 1040--1086 Score: 78
Period size: 22 Copynumber: 2.0 Consensus size: 23
1030 GCATAGATAG
1040 TGCATCGATGCACACGTTAAGGGA
1 TGCATCGATG-ACACGTTAAGGGA
1064 TGCATCGATG-CACGTTAAGGGA
1 TGCATCGATGACACGTTAAGGGA
1086 T
1 T
1087 TAATCGATAC
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
22 13 0.57
24 10 0.43
ACGTcount: A:0.28, C:0.19, G:0.30, T:0.23
Consensus pattern (23 bp):
TGCATCGATGACACGTTAAGGGA
Found at i:1092 original size:22 final size:23
Alignment explanation
Indices: 1043--1098 Score: 71
Period size: 22 Copynumber: 2.5 Consensus size: 23
1033 TAGATAGTGC
*
1043 ATCGATGCACACGTTAAGGGATGC
1 ATCGATG-ACACGTTAAGGGATGA
*
1067 ATCGATG-CACGTTAAGGGATTA
1 ATCGATGACACGTTAAGGGATGA
1089 ATCGAT-ACAC
1 ATCGATGACAC
1099 TGTAGAGTGC
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
22 22 0.76
24 7 0.24
ACGTcount: A:0.32, C:0.20, G:0.25, T:0.23
Consensus pattern (23 bp):
ATCGATGACACGTTAAGGGATGA
Found at i:2303 original size:21 final size:21
Alignment explanation
Indices: 2269--2309 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
2259 GAAATTTTAG
*
2269 TGCATCGATTCACTATAGCAA
1 TGCATCGATGCACTATAGCAA
* *
2290 TGCATTGATGCACTGTAGCA
1 TGCATCGATGCACTATAGCA
2310 CTGTTCACGG
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.29, C:0.22, G:0.20, T:0.29
Consensus pattern (21 bp):
TGCATCGATGCACTATAGCAA
Found at i:7925 original size:30 final size:28
Alignment explanation
Indices: 7874--7945 Score: 76
Period size: 28 Copynumber: 2.5 Consensus size: 28
7864 TTAACTTTTT
*
7874 AAAA-TTACATTTTTGTC-CTAAACTTTTC
1 AAAATTTACA-TTTTGCCACTAAAC-TTTC
* *
7902 TAAAGTTTATATTTTGCCACTAAACTTTC
1 -AAAATTTACATTTTGCCACTAAACTTTC
7931 AAAATTTACATTTTG
1 AAAATTTACATTTTG
7946 GTCACTAGAC
Statistics
Matches: 36, Mismatches: 5, Indels: 5
0.78 0.11 0.11
Matches are distributed among these distances:
28 13 0.36
29 13 0.36
30 10 0.28
ACGTcount: A:0.33, C:0.15, G:0.06, T:0.46
Consensus pattern (28 bp):
AAAATTTACATTTTGCCACTAAACTTTC
Found at i:7952 original size:29 final size:30
Alignment explanation
Indices: 7866--7952 Score: 94
Period size: 29 Copynumber: 3.0 Consensus size: 30
7856 GGGCCGAATT
7866 AACTTTT-TAAAA-TTACATTTTTGTC-CTA
1 AACTTTTCTAAAATTTACA-TTTTGTCACTA
* * *
7894 AACTTTTCTAAAGTTTATATTTTGCCACTA
1 AACTTTTCTAAAATTTACATTTTGTCACTA
7924 AAC-TTTC-AAAATTTACATTTTGGTCACTA
1 AACTTTTCTAAAATTTACATTTT-GTCACTA
7953 GACGAAATTT
Statistics
Matches: 49, Mismatches: 6, Indels: 7
0.79 0.10 0.11
Matches are distributed among these distances:
28 19 0.39
29 20 0.41
30 10 0.20
ACGTcount: A:0.32, C:0.16, G:0.06, T:0.46
Consensus pattern (30 bp):
AACTTTTCTAAAATTTACATTTTGTCACTA
Found at i:28210 original size:23 final size:23
Alignment explanation
Indices: 28184--28228 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 23
28174 TTTAAAATTT
*
28184 TAATTCTT-ATTTTATTTTGTAGA
1 TAATTCTTGATTTGA-TTTGTAGA
*
28207 TAATTTTTGATTTGATTTGTAG
1 TAATTCTTGATTTGATTTGTAG
28229 GGTCTACATT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
23 14 0.74
24 5 0.26
ACGTcount: A:0.24, C:0.02, G:0.13, T:0.60
Consensus pattern (23 bp):
TAATTCTTGATTTGATTTGTAGA
Found at i:33126 original size:56 final size:56
Alignment explanation
Indices: 33041--33449 Score: 649
Period size: 56 Copynumber: 7.3 Consensus size: 56
33031 TTCTTACTTT
*
33041 TTAG-TTTTGCAAACAAAGTGCCCATACGGAAATTCATAAACTCATTATGAATTTC
1 TTAGTTTTTGCACACAAAGTGCCCATACGGAAATTCATAAACTCATTATGAATTTC
* * *
33096 TTAGTTTTTGCACAGAAAGTGCCCATACGGAAATTCATAAACGCATTATAAATTTC
1 TTAGTTTTTGCACACAAAGTGCCCATACGGAAATTCATAAACTCATTATGAATTTC
* * *
33152 TTAGTTTTTGTACACAAAGTGCTCATATGGAAATTCATAAACTCATTATGAATTTC
1 TTAGTTTTTGCACACAAAGTGCCCATACGGAAATTCATAAACTCATTATGAATTTC
* **
33208 TTAGTTTTTGCACATAAAGTGCCCATACGGAAATTTGTAAACTCATTATGAATTTC
1 TTAGTTTTTGCACACAAAGTGCCCATACGGAAATTCATAAACTCATTATGAATTTC
33264 TTAGTTTTTGCACACAAAGTGCCCATACGGAAATTCATAAACTCATTATGAATTTC
1 TTAGTTTTTGCACACAAAGTGCCCATACGGAAATTCATAAACTCATTATGAATTTC
* * *
33320 TTATTTTTTGCACACAAATTGCCCATACAGAAATTCATAAACTCATTATGAATTTC
1 TTAGTTTTTGCACACAAAGTGCCCATACGGAAATTCATAAACTCATTATGAATTTC
* * *
33376 TTAGTTTTTGCAAATAAAGTGCCCATACAGAAATTCATAAACTCATTATGAATTTC
1 TTAGTTTTTGCACACAAAGTGCCCATACGGAAATTCATAAACTCATTATGAATTTC
* *
33432 ATAGTTTTTACACACAAA
1 TTAGTTTTTGCACACAAA
33450 TAGTGTCATT
Statistics
Matches: 323, Mismatches: 30, Indels: 1
0.91 0.08 0.00
Matches are distributed among these distances:
55 4 0.01
56 319 0.99
ACGTcount: A:0.35, C:0.17, G:0.12, T:0.35
Consensus pattern (56 bp):
TTAGTTTTTGCACACAAAGTGCCCATACGGAAATTCATAAACTCATTATGAATTTC
Found at i:43211 original size:21 final size:20
Alignment explanation
Indices: 43165--43203 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 20
43155 AATGAACACC
43165 AAAAT-TTCATTATTGGAAG
1 AAAATATTCATTATTGGAAG
43184 TAAAATATTCATTCATTGGA
1 -AAAATATTCATT-ATTGGA
43204 TAAAAATACC
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
20 5 0.29
21 6 0.35
22 6 0.35
ACGTcount: A:0.41, C:0.08, G:0.13, T:0.38
Consensus pattern (20 bp):
AAAATATTCATTATTGGAAG
Found at i:46626 original size:15 final size:15
Alignment explanation
Indices: 46606--46637 Score: 64
Period size: 15 Copynumber: 2.1 Consensus size: 15
46596 GATGACCGGC
46606 GACCGTTTAGCTTAG
1 GACCGTTTAGCTTAG
46621 GACCGTTTAGCTTAG
1 GACCGTTTAGCTTAG
46636 GA
1 GA
46638 AATTAAAATT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.22, C:0.19, G:0.28, T:0.31
Consensus pattern (15 bp):
GACCGTTTAGCTTAG
Found at i:48553 original size:44 final size:43
Alignment explanation
Indices: 48505--48614 Score: 109
Period size: 43 Copynumber: 2.5 Consensus size: 43
48495 TTTTTATCTA
* *
48505 TATAATTGAGTTCCTTAATTTTTTTAAATCCCACATTT-TACATT
1 TATAATTGAGATCC-TAATTTTTTTAAATCCCAC-TTTGCACATT
* * * *
48549 TATAATTAATGATCCTAA-GTTTTTCAATCCCACTTTGCACTTT
1 TATAATTGA-GATCCTAATTTTTTTAAATCCCACTTTGCACATT
48592 TATAATTGA-ACTCCTAATTTTTT
1 TATAATTGAGA-TCCTAATTTTTT
48615 CAATATTACT
Statistics
Matches: 54, Mismatches: 8, Indels: 9
0.76 0.11 0.13
Matches are distributed among these distances:
41 1 0.02
42 9 0.17
43 29 0.54
44 11 0.20
45 4 0.07
ACGTcount: A:0.29, C:0.17, G:0.05, T:0.48
Consensus pattern (43 bp):
TATAATTGAGATCCTAATTTTTTTAAATCCCACTTTGCACATT
Found at i:48626 original size:42 final size:42
Alignment explanation
Indices: 48505--48707 Score: 139
Period size: 42 Copynumber: 4.8 Consensus size: 42
48495 TTTTTATCTA
* * * * *
48505 TATAATTGAG-TTCCTTAATTTTTTTAAATCCCACATTTTACATT
1 TATAATTGAGACTCC-TAA-TTTTTTCAATCTCAC-TTTCACCTT
* * * *
48549 TATAATTAATGA-TCCTAAGTTTTTCAATCCCACTTTGCACTTT
1 TATAATTGA-GACTCCTAATTTTTTCAATCTCACTTT-CACCTT
* *
48592 TATAATTGA-ACTCCTAATTTTTTCAATATTACTTTCTACCTT
1 TATAATTGAGACTCCTAATTTTTTCAATCTCACTTTC-ACCTT
* *
48634 TATTATTGAGGC-CCTTAATTTTTT-AATCTCACTTTTCACCTT
1 TATAATTGAGACTCC-TAATTTTTTCAATCTCAC-TTTCACCTT
* * *
48676 TATAATTTGGGCCT-CTAATTTTCTCAATCTCA
1 TATAA-TTGAGACTCCTAATTTTTTCAATCTCA
48708 TTTTTACTTA
Statistics
Matches: 129, Mismatches: 19, Indels: 23
0.75 0.11 0.13
Matches are distributed among these distances:
41 2 0.02
42 60 0.47
43 52 0.40
44 11 0.09
45 4 0.03
ACGTcount: A:0.27, C:0.20, G:0.06, T:0.48
Consensus pattern (42 bp):
TATAATTGAGACTCCTAATTTTTTCAATCTCACTTTCACCTT
Found at i:48755 original size:43 final size:42
Alignment explanation
Indices: 48652--48812 Score: 128
Period size: 42 Copynumber: 3.7 Consensus size: 42
48642 AGGCCCTTAA
* * * *
48652 TTTTTTAATCTCACTTTTCACCTTTATAATTTGGGCCTCTAAT
1 TTTTTTAATCTCACTTTTTA-CTTTATAATTTAGGCCCCTATT
* * *
48695 TTTCTCAATCTCA-TTTTTACTTATATACTTTAGGCCCCTATT
1 TTTTTTAATCTCACTTTTTACTT-TATAATTTAGGCCCCTATT
* * * * *
48737 TTTTTTAATTTCACTTTTTTTCCTTTAAAATTAAGACCCCTAGTTT
1 TTTTTTAATCTCAC--TTTTTACTTTATAATTTAGGCCCCTA--TT
*
48783 TTTTTTAATTTCAC-TTTTACCTTTATAATT
1 TTTTTTAATCTCACTTTTTA-CTTTATAATT
48813 GTGGTCCGTA
Statistics
Matches: 94, Mismatches: 17, Indels: 13
0.76 0.14 0.10
Matches are distributed among these distances:
41 3 0.03
42 30 0.32
43 15 0.16
44 22 0.23
45 8 0.09
46 16 0.17
ACGTcount: A:0.22, C:0.19, G:0.04, T:0.54
Consensus pattern (42 bp):
TTTTTTAATCTCACTTTTTACTTTATAATTTAGGCCCCTATT
Found at i:49157 original size:27 final size:27
Alignment explanation
Indices: 49101--49157 Score: 69
Period size: 27 Copynumber: 2.1 Consensus size: 27
49091 TTCATAAAGA
* *
49101 TAAGACATGGTCACTTTCGTTGTTAAT
1 TAAGACATAGTCACTTTCATTGTTAAT
* * *
49128 TAAGATATAGTCACTTTCATTTTTATT
1 TAAGACATAGTCACTTTCATTGTTAAT
49155 TAA
1 TAA
49158 TTAATATGTG
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
27 25 1.00
ACGTcount: A:0.30, C:0.12, G:0.12, T:0.46
Consensus pattern (27 bp):
TAAGACATAGTCACTTTCATTGTTAAT
Found at i:49355 original size:24 final size:24
Alignment explanation
Indices: 49297--49373 Score: 91
Period size: 24 Copynumber: 3.1 Consensus size: 24
49287 AAATTTAAAG
* *
49297 TAAAATATTTTTAAAATATGTTAATAA
1 TAAAATATATTT--AATAAGTTAAT-A
49324 TAAAATATATTTAATAAGTTAATA
1 TAAAATATATTTAATAAGTTAATA
**
49348 TAAAATATATTTTTTAAGTTAATA
1 TAAAATATATTTAATAAGTTAATA
49372 TA
1 TA
49374 TATAAAATAT
Statistics
Matches: 46, Mismatches: 4, Indels: 3
0.87 0.08 0.06
Matches are distributed among these distances:
24 25 0.54
25 10 0.22
27 11 0.24
ACGTcount: A:0.51, C:0.00, G:0.04, T:0.45
Consensus pattern (24 bp):
TAAAATATATTTAATAAGTTAATA
Found at i:56070 original size:24 final size:24
Alignment explanation
Indices: 56037--56106 Score: 104
Period size: 24 Copynumber: 2.9 Consensus size: 24
56027 TCGAGGGTTT
*
56037 TACGCAGTCCTTCGGGACAAATTC
1 TACGCGGTCCTTCGGGACAAATTC
*
56061 TACGTGGTCCTTCGGGACAAATTC
1 TACGCGGTCCTTCGGGACAAATTC
* *
56085 TATGCGGTCCTTCGGTACAAAT
1 TACGCGGTCCTTCGGGACAAAT
56107 CTATATGGCA
Statistics
Matches: 41, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 41 1.00
ACGTcount: A:0.23, C:0.26, G:0.23, T:0.29
Consensus pattern (24 bp):
TACGCGGTCCTTCGGGACAAATTC
Found at i:58250 original size:55 final size:55
Alignment explanation
Indices: 58046--58716 Score: 903
Period size: 55 Copynumber: 12.1 Consensus size: 55
58036 TCATTATACT
* *
58046 TGCAAAACTAAGAAATTCATAATAAGTTTATGAATTTCCGTATAGACACTTTGTG
1 TGCAAAACTAAGAAATTCATAATAAGTTTATGAATTTCCGTATGGGCACTTTGTG
* * * *
58101 TGCAAAAGCTAAGAAATTCTTAATAAGTTTATGAATTTACATACGGGCACTTTGTG
1 TGCAAAA-CTAAGAAATTCATAATAAGTTTATGAATTTCCGTATGGGCACTTTGTG
* *
58157 TGCAAAAGCTAGGAAATTCATAATAAGTTTATGAATTTCCGTATGGGCACATTGTG
1 TGCAAAA-CTAAGAAATTCATAATAAGTTTATGAATTTCCGTATGGGCACTTTGTG
* *
58213 TGCACAACTATA-AAATTCATAATAAGTTTATGAATTTCCGTATGGCCACTTTGTG
1 TGCAAAACTA-AGAAATTCATAATAAGTTTATGAATTTCCGTATGGGCACTTTGTG
* * *
58268 TGCAAAAGCTAAAAAAATCATAATAAGTTTATGAATTTCCGTTTGGGCACTTTGTG
1 TGCAAAA-CTAAGAAATTCATAATAAGTTTATGAATTTCCGTATGGGCACTTTGTG
* * * * *
58324 TGCAAAACTAAGAAATTCATAAAAAATTTATGAATTTTCGTATGGTCACTTTATG
1 TGCAAAACTAAGAAATTCATAATAAGTTTATGAATTTCCGTATGGGCACTTTGTG
* ** *
58379 TGCAAAACTAAGAAATTCATAATAAATTTATGAATTTTTGTATGGGCACGTTGTG
1 TGCAAAACTAAGAAATTCATAATAAGTTTATGAATTTCCGTATGGGCACTTTGTG
* * * *
58434 TACAAAAGTTAATAAATTCATAATAAGTTTATGAATTTCCGTATGGGCAATTTGTG
1 TGCAAAA-CTAAGAAATTCATAATAAGTTTATGAATTTCCGTATGGGCACTTTGTG
* * *
58490 TGCAAAACTAAGAAATTCAGAATAAGTTTATAAATTTCCATATGGGCACTTTGTG
1 TGCAAAACTAAGAAATTCATAATAAGTTTATGAATTTCCGTATGGGCACTTTGTG
* * *
58545 TGCAAAATTAAGAAATTCATAATAAGATTATGAATTTTCGTATGGGCACTTTGTG
1 TGCAAAACTAAGAAATTCATAATAAGTTTATGAATTTCCGTATGGGCACTTTGTG
* *
58600 TGCAAAACTAAGAAATTCATAATAAGTTTATGAATTTCCGTATGGGTACTTTTTG
1 TGCAAAACTAAGAAATTCATAATAAGTTTATGAATTTCCGTATGGGCACTTTGTG
* * * * * * **
58655 TGTAAAAATTAAGAAAATCATATTAAGTTTATGAATTACCGTATTGGCACTACGTG
1 TG-CAAAACTAAGAAATTCATAATAAGTTTATGAATTTCCGTATGGGCACTTTGTG
58711 TGCAAA
1 TGCAAA
58717 CTATAGAGTT
Statistics
Matches: 540, Mismatches: 70, Indels: 12
0.87 0.11 0.02
Matches are distributed among these distances:
55 300 0.56
56 240 0.44
ACGTcount: A:0.37, C:0.12, G:0.17, T:0.35
Consensus pattern (55 bp):
TGCAAAACTAAGAAATTCATAATAAGTTTATGAATTTCCGTATGGGCACTTTGTG
Found at i:58268 original size:111 final size:110
Alignment explanation
Indices: 58046--58716 Score: 903
Period size: 111 Copynumber: 6.1 Consensus size: 110
58036 TCATTATACT
* *
58046 TGCAAAACTAAGAAATTCATAATAAGTTTATGAATTTCCGTATAGACACTTTGTGTGCAAAAGCT
1 TGCAAAACTAAGAAATTCATAATAAGTTTATGAATTTCCGTATGGGCACTTTGTGTGCAAAA-CT
* * * *
58111 AAGAAATTCTTAATAAGTTTATGAATTTACATACGGGCACTTTGTG
65 AAGAAATTCATAATAAGTTTATGAATTTCCGTATGGGCACTTTGTG
* * *
58157 TGCAAAAGCTAGGAAATTCATAATAAGTTTATGAATTTCCGTATGGGCACATTGTGTGCACAACT
1 TGCAAAA-CTAAGAAATTCATAATAAGTTTATGAATTTCCGTATGGGCACTTTGTGTGCAAAACT
*
58222 ATA-AAATTCATAATAAGTTTATGAATTTCCGTATGGCCACTTTGTG
65 A-AGAAATTCATAATAAGTTTATGAATTTCCGTATGGGCACTTTGTG
* * *
58268 TGCAAAAGCTAAAAAAATCATAATAAGTTTATGAATTTCCGTTTGGGCACTTTGTGTGCAAAACT
1 TGCAAAA-CTAAGAAATTCATAATAAGTTTATGAATTTCCGTATGGGCACTTTGTGTGCAAAACT
* * * * *
58333 AAGAAATTCATAAAAAATTTATGAATTTTCGTATGGTCACTTTATG
65 AAGAAATTCATAATAAGTTTATGAATTTCCGTATGGGCACTTTGTG
* ** * * *
58379 TGCAAAACTAAGAAATTCATAATAAATTTATGAATTTTTGTATGGGCACGTTGTGTACAAAAGTT
1 TGCAAAACTAAGAAATTCATAATAAGTTTATGAATTTCCGTATGGGCACTTTGTGTGCAAAA-CT
* *
58444 AATAAATTCATAATAAGTTTATGAATTTCCGTATGGGCAATTTGTG
65 AAGAAATTCATAATAAGTTTATGAATTTCCGTATGGGCACTTTGTG
* * * *
58490 TGCAAAACTAAGAAATTCAGAATAAGTTTATAAATTTCCATATGGGCACTTTGTGTGCAAAATTA
1 TGCAAAACTAAGAAATTCATAATAAGTTTATGAATTTCCGTATGGGCACTTTGTGTGCAAAACTA
* *
58555 AGAAATTCATAATAAGATTATGAATTTTCGTATGGGCACTTTGTG
66 AGAAATTCATAATAAGTTTATGAATTTCCGTATGGGCACTTTGTG
* * * *
58600 TGCAAAACTAAGAAATTCATAATAAGTTTATGAATTTCCGTATGGGTACTTTTTGTGTAAAAATT
1 TGCAAAACTAAGAAATTCATAATAAGTTTATGAATTTCCGTATGGGCACTTTGTGTG-CAAAACT
* * * * **
58665 AAGAAAATCATATTAAGTTTATGAATTACCGTATTGGCACTACGTG
65 AAGAAATTCATAATAAGTTTATGAATTTCCGTATGGGCACTTTGTG
58711 TGCAAA
1 TGCAAA
58717 CTATAGAGTT
Statistics
Matches: 492, Mismatches: 63, Indels: 10
0.87 0.11 0.02
Matches are distributed among these distances:
110 144 0.29
111 297 0.60
112 51 0.10
ACGTcount: A:0.37, C:0.12, G:0.17, T:0.35
Consensus pattern (110 bp):
TGCAAAACTAAGAAATTCATAATAAGTTTATGAATTTCCGTATGGGCACTTTGTGTGCAAAACTA
AGAAATTCATAATAAGTTTATGAATTTCCGTATGGGCACTTTGTG
Found at i:58457 original size:166 final size:166
Alignment explanation
Indices: 58046--58716 Score: 907
Period size: 166 Copynumber: 4.0 Consensus size: 166
58036 TCATTATACT
* * *
58046 TGCAAAACTAAGAAATTCATAATAAGTTTATGAATTTCCGTATAGACACTTTGTGTGCAAAAGCT
1 TGCAAAACTAAGAAATTCATAATAAATTTATGAATTTCCGTATGGGCACTTTGTGTGCAAAAGCT
* * * * *
58111 AAGAAATTCTTAATAAGTTTATGAATTTACATACGGGCACTTTGTGTGCAAAAGCTAGGAAATTC
66 AAGAAATTCATAATAAGTTTATGAATTTCCGTATGGGCACTTTGTGTGCAAAA-CTAAGAAATTC
*
58176 ATAATAAGTTTATGAATTTCCGTATGGGCACATTGTG
130 ATAATAAGTTTATGAATTTCCGTATGGGCACTTTGTG
* * *
58213 TGCACAACTATA-AAATTCATAATAAGTTTATGAATTTCCGTATGGCCACTTTGTGTGCAAAAGC
1 TGCAAAACTA-AGAAATTCATAATAAATTTATGAATTTCCGTATGGGCACTTTGTGTGCAAAAGC
* * *
58277 TAAAAAAATCATAATAAGTTTATGAATTTCCGTTTGGGCACTTTGTGTGCAAAACTAAGAAATTC
65 TAAGAAATTCATAATAAGTTTATGAATTTCCGTATGGGCACTTTGTGTGCAAAACTAAGAAATTC
* * * * *
58342 ATAAAAAATTTATGAATTTTCGTATGGTCACTTTATG
130 ATAATAAGTTTATGAATTTCCGTATGGGCACTTTGTG
** * * *
58379 TGCAAAACTAAGAAATTCATAATAAATTTATGAATTTTTGTATGGGCACGTTGTGTACAAAAGTT
1 TGCAAAACTAAGAAATTCATAATAAATTTATGAATTTCCGTATGGGCACTTTGTGTGCAAAAGCT
* *
58444 AATAAATTCATAATAAGTTTATGAATTTCCGTATGGGCAATTTGTGTGCAAAACTAAGAAATTCA
66 AAGAAATTCATAATAAGTTTATGAATTTCCGTATGGGCACTTTGTGTGCAAAACTAAGAAATTCA
* * *
58509 GAATAAGTTTATAAATTTCCATATGGGCACTTTGTG
131 TAATAAGTTTATGAATTTCCGTATGGGCACTTTGTG
* *
58545 TGCAAAATTAAGAAATTCATAATAAGA-TTATGAATTTTCGTATGGGCACTTTGTGTGCAAAA-C
1 TGCAAAACTAAGAAATTCATAATAA-ATTTATGAATTTCCGTATGGGCACTTTGTGTGCAAAAGC
* * * * *
58608 TAAGAAATTCATAATAAGTTTATGAATTTCCGTATGGGTACTTTTTGTGTAAAAATTAAGAAAAT
65 TAAGAAATTCATAATAAGTTTATGAATTTCCGTATGGGCACTTTGTGTG-CAAAACTAAGAAATT
* * * **
58673 CATATTAAGTTTATGAATTACCGTATTGGCACTACGTG
129 CATAATAAGTTTATGAATTTCCGTATGGGCACTTTGTG
58711 TGCAAA
1 TGCAAA
58717 CTATAGAGTT
Statistics
Matches: 443, Mismatches: 57, Indels: 9
0.87 0.11 0.02
Matches are distributed among these distances:
165 46 0.10
166 289 0.65
167 107 0.24
168 1 0.00
ACGTcount: A:0.37, C:0.12, G:0.17, T:0.35
Consensus pattern (166 bp):
TGCAAAACTAAGAAATTCATAATAAATTTATGAATTTCCGTATGGGCACTTTGTGTGCAAAAGCT
AAGAAATTCATAATAAGTTTATGAATTTCCGTATGGGCACTTTGTGTGCAAAACTAAGAAATTCA
TAATAAGTTTATGAATTTCCGTATGGGCACTTTGTG
Found at i:62376 original size:56 final size:55
Alignment explanation
Indices: 62179--62383 Score: 311
Period size: 55 Copynumber: 3.7 Consensus size: 55
62169 ATAGTCTTAT
*
62179 GAAATTCATAATAAGTTTATGAATTTCCGTATGGGCACTTTGTGTGCAAAACTAA
1 GAAATTCATAATAAGTTTATGAATTTCTGTATGGGCACTTTGTGTGCAAAACTAA
* * **
62234 GAAATTCATAATACGTTTATGAATTTTTGTATGGTTACTTTGTGTGCAAAACTAA
1 GAAATTCATAATAAGTTTATGAATTTCTGTATGGGCACTTTGTGTGCAAAACTAA
* * *
62289 GAAATTCATAATAAGTTTATGAATTTTTGTATGGGCACTCTGTGTGTAAAACCTAA
1 GAAATTCATAATAAGTTTATGAATTTCTGTATGGGCACTTTGTGTGCAAAA-CTAA
* *
62345 GAAATTCATAATAAGTTTATGAATTACTGTATTGGCACT
1 GAAATTCATAATAAGTTTATGAATTTCTGTATGGGCACT
62384 ACATGTACGA
Statistics
Matches: 136, Mismatches: 13, Indels: 1
0.91 0.09 0.01
Matches are distributed among these distances:
55 96 0.71
56 40 0.29
ACGTcount: A:0.34, C:0.11, G:0.17, T:0.38
Consensus pattern (55 bp):
GAAATTCATAATAAGTTTATGAATTTCTGTATGGGCACTTTGTGTGCAAAACTAA
Found at i:69941 original size:698 final size:698
Alignment explanation
Indices: 68605--70002 Score: 2760
Period size: 698 Copynumber: 2.0 Consensus size: 698
68595 GAAAGGGTCT
*
68605 AATAGCATCAGATTTAAAACAACTTTTTGAAGGGGATCCAGTTGTTATCCGGTCGACATGTCTTC
1 AATAGCAGCAGATTTAAAACAACTTTTTGAAGGGGATCCAGTTGTTATCCGGTCGACATGTCTTC
68670 TGGAAATACAACCGTCTGTCTCTTATCTTTCCAACGGTTCTTGAATCGAATCAATCCGATATCGG
66 TGGAAATACAACCGTCTGTCTCTTATCTTTCCAACGGTTCTTGAATCGAATCAATCCGATATCGG
68735 GAACTCAAAATATGGTCATTTTACTGAAGACGGTGCAGACAGGAAACCCTATACGGGATTAATAC
131 GAACTCAAAATATGGTCATTTTACTGAAGACGGTGCAGACAGGAAACCCTATACGGGATTAATAC
68800 GTTATTTTGTAAATATTACGAATTTTCAATATTTATATTGATTATTTGTAATATAATTTAATATA
196 GTTATTTTGTAAATATTACGAATTTTCAATATTTATATTGATTATTTGTAATATAATTTAATATA
68865 GGATGATTAATTATCTTTTAGGATCAGATTTATTATTTTATTAGGAATTAAGGTTGGGTTAAAAC
261 GGATGATTAATTATCTTTTAGGATCAGATTTATTATTTTATTAGGAATTAAGGTTGGGTTAAAAC
*
68930 AATATTTTTAGTTATTATTATTTTATTAGGAATTAGAGTTAAAATATGTTTAGTTTATTAATATT
326 AATATTTTTAGTTATTATTATTTTATTAGGAATTAGAGTTAAAACATGTTTAGTTTATTAATATT
68995 TTATTCTTTAGTTATTTAGAACCTTTAGAATTCAGCCCCTATATAAAGGAGGCTTCATTCAACTT
391 TTATTCTTTAGTTATTTAGAACCTTTAGAATTCAGCCCCTATATAAAGGAGGCTTCATTCAACTT
69060 TGTAAAACAGATTTCTTTGATTAATAATACAACGAGAGTTCGTTTTTGCAAGTGCTGATTGCCTT
456 TGTAAAACAGATTTCTTTGATTAATAATACAACGAGAGTTCGTTTTTGCAAGTGCTGATTGCCTT
69125 GTGCCTTCGAAGCTTCTTCTCCTTGAGTTCTTTCAAGTTCTTGTGAGGGAGATTAATCTTCACAC
521 GTGCCTTCGAAGCTTCTTCTCCTTGAGTTCTTTCAAGTTCTTGTGAGGGAGATTAATCTTCACAC
69190 TCCAATTTGCCTTTTCATCACGACTAGGAGGGTTGGTTAGAGCCATTTATCGTGTTTTCCTTTTC
586 TCCAATTTGCCTTTTCATCACGACTAGGAGGGTTGGTTAGAGCCATTTATCGTGTTTTCCTTTTC
69255 ATTGCGACTAGGAGGGCTCGATAGGACACTTATCCATCTATTATCCAC
651 ATTGCGACTAGGAGGGCTCGATAGGACACTTATCCATCTATTATCCAC
69303 AATAGCAGCAGATTTAAAACAACTTTTTGAAGGGGATCCAGTTGTTATCCGGTCGACATGTCTTC
1 AATAGCAGCAGATTTAAAACAACTTTTTGAAGGGGATCCAGTTGTTATCCGGTCGACATGTCTTC
69368 TGGAAATACAACCGTCTGTCTCTTATCTTTCCAACGGTTCTTGAATCGAATCAATCCGATATCGG
66 TGGAAATACAACCGTCTGTCTCTTATCTTTCCAACGGTTCTTGAATCGAATCAATCCGATATCGG
69433 GAACTCAAAATATGGTCATTTTACTGAAGACGGTGCAGACAGGAAACCCTATACGGGATTAATAC
131 GAACTCAAAATATGGTCATTTTACTGAAGACGGTGCAGACAGGAAACCCTATACGGGATTAATAC
69498 GTTATTTTGTAAATATTACGAATTTTCAATATTTATATTGATTATTTGTAATATAATTTAATATA
196 GTTATTTTGTAAATATTACGAATTTTCAATATTTATATTGATTATTTGTAATATAATTTAATATA
69563 GGATGATTAATTATCTTTTAGGATCAGATTTATTATTTTATTAGGAATTAAGGTTGGGTTAAAAC
261 GGATGATTAATTATCTTTTAGGATCAGATTTATTATTTTATTAGGAATTAAGGTTGGGTTAAAAC
69628 AATATTTTTAGTTATTATTATTTTATTAGGAATTAGAGTTAAAACATGTTTAGTTTATTAATATT
326 AATATTTTTAGTTATTATTATTTTATTAGGAATTAGAGTTAAAACATGTTTAGTTTATTAATATT
*
69693 TTATTCTTTAGTTATTTAGAACCTTTAGAATTCAGCCCCTATATAAAGGAGGTTTCATTCAACTT
391 TTATTCTTTAGTTATTTAGAACCTTTAGAATTCAGCCCCTATATAAAGGAGGCTTCATTCAACTT
*
69758 TGTAAAATAGATTTCTTTGATTAATAATACAACGAGAGTTCGTTTTTGCAAGTGCTGATTGCCTT
456 TGTAAAACAGATTTCTTTGATTAATAATACAACGAGAGTTCGTTTTTGCAAGTGCTGATTGCCTT
69823 GTGCCTTCGAAGCTTCTTCTCCTTGAGTTCTTTCAAGTTCTTGTGAGGGAGATTAATCTTCACAC
521 GTGCCTTCGAAGCTTCTTCTCCTTGAGTTCTTTCAAGTTCTTGTGAGGGAGATTAATCTTCACAC
69888 TCCAATTTGCCTTTTCATCACGACTAGGAGGGTTGGTTAGAGCCATTTATCGTGTTTTCCTTTTC
586 TCCAATTTGCCTTTTCATCACGACTAGGAGGGTTGGTTAGAGCCATTTATCGTGTTTTCCTTTTC
69953 ATTGCGACTAGGAGGGCTCGATAGGACACTTATCCATCTATTATCCAC
651 ATTGCGACTAGGAGGGCTCGATAGGACACTTATCCATCTATTATCCAC
70001 AA
1 AA
70003 ATCCATTCGC
Statistics
Matches: 696, Mismatches: 4, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
698 696 1.00
ACGTcount: A:0.29, C:0.15, G:0.17, T:0.39
Consensus pattern (698 bp):
AATAGCAGCAGATTTAAAACAACTTTTTGAAGGGGATCCAGTTGTTATCCGGTCGACATGTCTTC
TGGAAATACAACCGTCTGTCTCTTATCTTTCCAACGGTTCTTGAATCGAATCAATCCGATATCGG
GAACTCAAAATATGGTCATTTTACTGAAGACGGTGCAGACAGGAAACCCTATACGGGATTAATAC
GTTATTTTGTAAATATTACGAATTTTCAATATTTATATTGATTATTTGTAATATAATTTAATATA
GGATGATTAATTATCTTTTAGGATCAGATTTATTATTTTATTAGGAATTAAGGTTGGGTTAAAAC
AATATTTTTAGTTATTATTATTTTATTAGGAATTAGAGTTAAAACATGTTTAGTTTATTAATATT
TTATTCTTTAGTTATTTAGAACCTTTAGAATTCAGCCCCTATATAAAGGAGGCTTCATTCAACTT
TGTAAAACAGATTTCTTTGATTAATAATACAACGAGAGTTCGTTTTTGCAAGTGCTGATTGCCTT
GTGCCTTCGAAGCTTCTTCTCCTTGAGTTCTTTCAAGTTCTTGTGAGGGAGATTAATCTTCACAC
TCCAATTTGCCTTTTCATCACGACTAGGAGGGTTGGTTAGAGCCATTTATCGTGTTTTCCTTTTC
ATTGCGACTAGGAGGGCTCGATAGGACACTTATCCATCTATTATCCAC
Found at i:77863 original size:24 final size:24
Alignment explanation
Indices: 77819--77865 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 24
77809 ATAAAGAACC
*
77819 AAAATAAACTTAAATATACCATTA
1 AAAATAAACTTAAACATACCATTA
*
77843 AAAATAAAGTTTAAACA-ACCATT
1 AAAATAAA-CTTAAACATACCATT
77866 CAACCAACCA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
24 14 0.70
25 6 0.30
ACGTcount: A:0.57, C:0.13, G:0.02, T:0.28
Consensus pattern (24 bp):
AAAATAAACTTAAACATACCATTA
Found at i:81192 original size:20 final size:19
Alignment explanation
Indices: 81144--81192 Score: 53
Period size: 19 Copynumber: 2.5 Consensus size: 19
81134 AAGAAAGAGA
* *
81144 AAAGGTAAAATTTAAAATG
1 AAAGATAAAAATTAAAATG
*
81163 AAAGAGAAAAATTAATAATG
1 AAAGATAAAAATTAA-AATG
*
81183 AAATATAAAA
1 AAAGATAAAA
81193 GAAAAAGTTA
Statistics
Matches: 24, Mismatches: 5, Indels: 1
0.80 0.17 0.03
Matches are distributed among these distances:
19 12 0.50
20 12 0.50
ACGTcount: A:0.65, C:0.00, G:0.12, T:0.22
Consensus pattern (19 bp):
AAAGATAAAAATTAAAATG
Found at i:83770 original size:14 final size:14
Alignment explanation
Indices: 83751--83778 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
83741 ATCCATGAAG
83751 ATCTCCAGAAAATC
1 ATCTCCAGAAAATC
83765 ATCTCCAGAAAATC
1 ATCTCCAGAAAATC
83779 CTCAACCATA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.43, C:0.29, G:0.07, T:0.21
Consensus pattern (14 bp):
ATCTCCAGAAAATC
Found at i:88083 original size:23 final size:23
Alignment explanation
Indices: 88040--88085 Score: 58
Period size: 23 Copynumber: 2.0 Consensus size: 23
88030 ATAAAGAACC
*
88040 AAAATAAACTTAAATATACCATT
1 AAAATAAACTTAAACATACCATT
*
88063 AAAATAAAGTTTAAACA-ACCATT
1 AAAATAAA-CTTAAACATACCATT
88086 CACCAACCAC
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
23 14 0.70
24 6 0.30
ACGTcount: A:0.57, C:0.13, G:0.02, T:0.28
Consensus pattern (23 bp):
AAAATAAACTTAAACATACCATT
Done.