Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01003837.1 Hibiscus syriacus cultivar Beakdansim tig00008224_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: 83779
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.32
Found at i:2451 original size:39 final size:38
Alignment explanation
Indices: 2354--2468 Score: 112
Period size: 39 Copynumber: 3.1 Consensus size: 38
2344 TATTATATTT
* * * *
2354 TAATTTTCAAT-TCTCAAATTATTTAACTCTAACATCC
1 TAATTTTTAATATCTTAAATTATTTTACTCTAACATTC
*
2391 TAAATTTTTAATATCTTAAATTATTTTACTATAACATTC
1 T-AATTTTTAATATCTTAAATTATTTTACTCTAACATTC
* *
2430 TAATTTCTTGAT-TTTTAAAATTATTTT--TCTAACATTC
1 TAATTT-TTAATATCTT-AAATTATTTTACTCTAACATTC
2467 TA
1 TA
2469 TGTTATTTTA
Statistics
Matches: 66, Mismatches: 8, Indels: 8
0.80 0.10 0.10
Matches are distributed among these distances:
37 12 0.18
38 17 0.26
39 37 0.56
ACGTcount: A:0.35, C:0.14, G:0.01, T:0.50
Consensus pattern (38 bp):
TAATTTTTAATATCTTAAATTATTTTACTCTAACATTC
Found at i:3833 original size:13 final size:13
Alignment explanation
Indices: 3815--3844 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
3805 CAAGTATACA
*
3815 TTTTTATAATCAC
1 TTTTTAAAATCAC
3828 TTTTTAAAATCAC
1 TTTTTAAAATCAC
3841 TTTT
1 TTTT
3845 GAGATGACAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.30, C:0.13, G:0.00, T:0.57
Consensus pattern (13 bp):
TTTTTAAAATCAC
Found at i:5008 original size:17 final size:18
Alignment explanation
Indices: 4971--5014 Score: 72
Period size: 17 Copynumber: 2.5 Consensus size: 18
4961 AAATGGGTAC
*
4971 CGATACCCTACCCAGTAT
1 CGATACCCTACCCAATAT
4989 CGATACCCTA-CCAATAT
1 CGATACCCTACCCAATAT
5006 CGATACCCT
1 CGATACCCT
5015 TACATATAGT
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
17 15 0.60
18 10 0.40
ACGTcount: A:0.30, C:0.39, G:0.09, T:0.23
Consensus pattern (18 bp):
CGATACCCTACCCAATAT
Found at i:28068 original size:17 final size:18
Alignment explanation
Indices: 28046--28086 Score: 57
Period size: 17 Copynumber: 2.3 Consensus size: 18
28036 CATAATTCTA
* *
28046 TATTAAAACCTT-TAATT
1 TATTAAAACATTATAAAT
28063 TATTAAAACATTATAAAT
1 TATTAAAACATTATAAAT
28081 TATTAA
1 TATTAA
28087 TATACTAGAA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
17 11 0.52
18 10 0.48
ACGTcount: A:0.49, C:0.07, G:0.00, T:0.44
Consensus pattern (18 bp):
TATTAAAACATTATAAAT
Found at i:32427 original size:570 final size:570
Alignment explanation
Indices: 31348--32953 Score: 2584
Period size: 570 Copynumber: 2.8 Consensus size: 570
31338 TGGCTTTGGT
*
31348 TTTCAGTGATAATACATAAATAAATATATTTTTTATTTGCAGGTTTCATGTCCTGCCTTGGAGAC
1 TTTCAGTGATAATACATAAATAAATATATTTTTCATTTGCAGGTTTCATGTCCTGCCTTGGAGAC
*
31413 GTTG-GAAGT-GATGGGATGCCATAAGTTGAAGTGTGTGTTTAGTTCATCTACGGTTAAAAGCTT
66 GTTGAG-AGTGGA-GGAATGCCATAAGTTGAAGTGTGTGTTTAGTTCATCTACGGTTAAAAGCTT
*
31476 TGTTCAACTCGAAGATCTTATAGTTTCTGATTGTGATGAACTGGAAGAGATGATACAAGGAATAT
129 TGTTCAACTCGAAGATCTTATAGTTTCTGATTGTGATGAACTGGAAGAGGTGATACAAGGAATAT
*
31541 TAGGAGAAGAAGAAAGGATTAGCAGCTGCATAAGTGTGTTTCCAAAACTTGACTCCTTGAAATTC
194 TAGGAGAAGAAGAAAGGATTAGCAGCTGCATAAGTCTGTTTCCAAAACTTGACTCCTTGAAATTC
* *
31606 AACAAACTTCCCAAACTCGGAAGGTTTTGCAGTGGAACTGATATTTCGATTAAATTTACTTCTCT
259 AACAAACTTCCCAAACTCGGAAGGTTTTGCAGTGGAACTGATATTTCGATTGAATTTACCTCTCT
* * *
31671 AAGGAAATT-GTATATA-GGGAAATGTTGTGGTTTGAGCACTTTCCATTTGAATAGTACAAATGT
324 AAGGTATTTAG-ATATACGGG-AATGTCGTGGTTTGAGCACTTTCCATTTGAATAGTACAAATGT
* * *
31734 TGTTAGAAAGAGCAG-AGGTAACATCTCACTTGAT-AGGTCACAACATATCTTCAATGAAAAGGT
387 TGTTGGAAAGAGCAGCA-GTAACATCTCACTTGATCA-GTCACAACATCTCTTCCATGAAAAGGT
* *
31797 ATGTATTAATATCCAATATTGGATATTTAAATAACGTACAAGAATTTTGGATATTTCAATGATAG
450 ATGTATTAATATCCAATCTTGGATATTTAAATAACGTACAAGAATCTTGGATATTTCAATGATAG
*
31862 TAAAAACTAGTACTTAATATTTTAATTAAAGAAAAATTTATATAAATAATTATCAA
515 TAAAAACTAGTACTTAATATTTTAATTAAAGAAAAATTGATATAAATAATTATCAA
* *
31918 TTTCAGTGATAATACAAAAATAAATACATTTTTCATTTGCAGGTTTCATGTCCTGCCTTGGAGAC
1 TTTCAGTGATAATACATAAATAAATATATTTTTCATTTGCAGGTTTCATGTCCTGCCTTGGAGAC
31983 GTTGAGAGTGGAGGAATGCCATAAGTTGAAGTGTGTGTTTAGTTCATCTACGGTTAAAAGCTTTG
66 GTTGAGAGTGGAGGAATGCCATAAGTTGAAGTGTGTGTTTAGTTCATCTACGGTTAAAAGCTTTG
*
32048 TTCAACTCGAAGATCTTGTAGTTTCTGATTGTGATGAACTGGAAGAGGTGATACAAGGAATATTA
131 TTCAACTCGAAGATCTTATAGTTTCTGATTGTGATGAACTGGAAGAGGTGATACAAGGAATATTA
* *
32113 GGAGAAGAAGAAAGGATTAGCAACTGCATAAGTTTGTTTCCAAAACTTGACTCCTTGAAATTCAA
196 GGAGAAGAAGAAAGGATTAGCAGCTGCATAAGTCTGTTTCCAAAACTTGACTCCTTGAAATTCAA
*
32178 CAAACTTCCCAAACTCGGAAGGTTTTGTAGTGGAACTGATATTTCGATTGAATTTACCTCTCTAA
261 CAAACTTCCCAAACTCGGAAGGTTTTGCAGTGGAACTGATATTTCGATTGAATTTACCTCTCTAA
* * * *
32243 GGTATTTAGATATACTGGAATGTCATAGTTTGAGCACTTTTCATTTGAATAGTACAAATGTTGTT
326 GGTATTTAGATATACGGGAATGTCGTGGTTTGAGCACTTTCCATTTGAATAGTACAAATGTTGTT
32308 GGAAAGAGCAGCAGTAACATCTCACTTGATCAGTCACAACATCTCTTCCATGAAAAGGTATGTAT
391 GGAAAGAGCAGCAGTAACATCTCACTTGATCAGTCACAACATCTCTTCCATGAAAAGGTATGTAT
* *
32373 TAATATCCAATCTTGGATATTTAAATAACGTACACGAATCTTGGATATTTCAATGATGGTAAAAA
456 TAATATCCAATCTTGGATATTTAAATAACGTACAAGAATCTTGGATATTTCAATGATAGTAAAAA
*
32438 CTAGTACTTAATATTTTAATTAAAGAAAAATTGATATAAATAATTATCCA
521 CTAGTACTTAATATTTTAATTAAAGAAAAATTGATATAAATAATTATCAA
32488 TTTCAGTGATAATACATAAATAAATATATTTTTCATTTGCAGGTTTCATGTCCTGCCTTGGAGAC
1 TTTCAGTGATAATACATAAATAAATATATTTTTCATTTGCAGGTTTCATGTCCTGCCTTGGAGAC
* * *
32553 GTTGAGAGTGGGGGAATGCCATAAGTCGAAGTGTGTGTTTAGTTCATCTACTGTTAAAAGCTTTG
66 GTTGAGAGTGGAGGAATGCCATAAGTTGAAGTGTGTGTTTAGTTCATCTACGGTTAAAAGCTTTG
* * * * * * *
32618 TTCAACTCAAAGAACTTAAAGTTTCTTATTGTGATGAACTGGAAGAGGTAATACGAGGAGTATTA
131 TTCAACTCGAAGATCTTATAGTTTCTGATTGTGATGAACTGGAAGAGGTGATACAAGGAATATTA
* * * * * * ****
32683 -G-G-AGAAGAAATGATTAGCAGCTTCACAAGTCTGCTTCCTAAACTAGACTCCTTGCTGCTCGA
196 GGAGAAGAAGAAAGGATTAGCAGCTGCATAAGTCTGTTTCCAAAACTTGACTCCTTGAAATTC-A
* * *
32745 AC-GACTTCCCAAACTCAGAAGGTTTTGCAGTGTAACTGATATTTCGATTGAATTTACCTCTCTA
260 ACAAACTTCCCAAACTCGGAAGGTTTTGCAGTGGAACTGATATTTCGATTGAATTTACCTCTCTA
* *
32809 AGGTATTTACATATACGGGGATGTCGTGGTTTGAGCACTTTCCATTTGAATAGTACAAATGTTGT
325 AGGTATTTAGATATACGGGAATGTCGTGGTTTGAGCACTTTCCATTTGAATAGTACAAATGTTGT
* *
32874 TGGAAAGAGCAGCGGTAACATCTCACTTGATCAGTCTCAACATCTCTTCCATGAAAAGGTATGTA
390 TGGAAAGAGCAGCAGTAACATCTCACTTGATCAGTCACAACATCTCTTCCATGAAAAGGTATGTA
32939 TTAATATCCAATCTT
455 TTAATATCCAATCTT
32954 AGTTAAATCT
Statistics
Matches: 965, Mismatches: 64, Indels: 17
0.92 0.06 0.02
Matches are distributed among these distances:
567 241 0.25
568 4 0.00
569 1 0.00
570 711 0.74
571 8 0.01
ACGTcount: A:0.33, C:0.14, G:0.19, T:0.33
Consensus pattern (570 bp):
TTTCAGTGATAATACATAAATAAATATATTTTTCATTTGCAGGTTTCATGTCCTGCCTTGGAGAC
GTTGAGAGTGGAGGAATGCCATAAGTTGAAGTGTGTGTTTAGTTCATCTACGGTTAAAAGCTTTG
TTCAACTCGAAGATCTTATAGTTTCTGATTGTGATGAACTGGAAGAGGTGATACAAGGAATATTA
GGAGAAGAAGAAAGGATTAGCAGCTGCATAAGTCTGTTTCCAAAACTTGACTCCTTGAAATTCAA
CAAACTTCCCAAACTCGGAAGGTTTTGCAGTGGAACTGATATTTCGATTGAATTTACCTCTCTAA
GGTATTTAGATATACGGGAATGTCGTGGTTTGAGCACTTTCCATTTGAATAGTACAAATGTTGTT
GGAAAGAGCAGCAGTAACATCTCACTTGATCAGTCACAACATCTCTTCCATGAAAAGGTATGTAT
TAATATCCAATCTTGGATATTTAAATAACGTACAAGAATCTTGGATATTTCAATGATAGTAAAAA
CTAGTACTTAATATTTTAATTAAAGAAAAATTGATATAAATAATTATCAA
Found at i:54684 original size:41 final size:42
Alignment explanation
Indices: 54582--54700 Score: 222
Period size: 42 Copynumber: 2.9 Consensus size: 42
54572 TTTCCCCGAA
*
54582 TTCCCGTGTTTGTTTCACGTAATTCGTTTTCCGGAAAATGTT
1 TTCCCGTGTTTGTTTCACGTAATTCGTTTTCCGGAAAACGTT
54624 TTCCCGTGTTTGTTTCACGTAATTCGTTTTCCGGAAAACGTT
1 TTCCCGTGTTTGTTTCACGTAATTCGTTTTCCGGAAAACGTT
54666 TT-CCGTGTTTGTTTCACGTAATTCGTTTTCCGGAA
1 TTCCCGTGTTTGTTTCACGTAATTCGTTTTCCGGAA
54701 TGTAATTCAT
Statistics
Matches: 76, Mismatches: 1, Indels: 1
0.97 0.01 0.01
Matches are distributed among these distances:
41 33 0.43
42 43 0.57
ACGTcount: A:0.16, C:0.20, G:0.19, T:0.45
Consensus pattern (42 bp):
TTCCCGTGTTTGTTTCACGTAATTCGTTTTCCGGAAAACGTT
Found at i:54915 original size:21 final size:22
Alignment explanation
Indices: 54889--54949 Score: 61
Period size: 22 Copynumber: 2.8 Consensus size: 22
54879 TAATTATTAA
*
54889 AATATTTAAAAT-ATATTTATT
1 AATATTTAAAATAATATATATT
*
54910 AATATTTATAATAATATATATT
1 AATATTTAAAATAATATATATT
* * * *
54932 TATTTTTAATATTATATA
1 AATATTTAAAATAATATA
54950 AAATAATCAA
Statistics
Matches: 32, Mismatches: 7, Indels: 1
0.80 0.17 0.03
Matches are distributed among these distances:
21 11 0.34
22 21 0.66
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (22 bp):
AATATTTAAAATAATATATATT
Found at i:54931 original size:22 final size:22
Alignment explanation
Indices: 54889--54949 Score: 65
Period size: 20 Copynumber: 2.9 Consensus size: 22
54879 TAATTATTAA
* *
54889 AATATTTAAAAT-ATATTTATT
1 AATATTTATAATAATATATATT
54910 AATATTTATAATAATATATATT
1 AATATTTATAATAATATATATT
* *
54932 --TATTTTTAATATTATATA
1 AATATTTATAATAATATATA
54950 AAATAATCAA
Statistics
Matches: 35, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
20 16 0.46
21 11 0.31
22 8 0.23
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (22 bp):
AATATTTATAATAATATATATT
Found at i:54972 original size:30 final size:31
Alignment explanation
Indices: 54900--54977 Score: 74
Period size: 30 Copynumber: 2.5 Consensus size: 31
54890 ATATTTAAAA
*
54900 TATATTTATTAATATT-TATAATAATATATATT
1 TATA-TTA-TAATATTATATAATAATATATAAT
*
54932 TAT-TTTTAATATTATATAA-AATA-ATCAAT
1 TATATTATAATATTATATAATAATATAT-AAT
*
54961 TATATTATAATAATATA
1 TATATTATAATATTATA
54978 AGATATTATA
Statistics
Matches: 39, Mismatches: 4, Indels: 8
0.76 0.08 0.16
Matches are distributed among these distances:
28 2 0.05
29 16 0.41
30 18 0.46
32 3 0.08
ACGTcount: A:0.47, C:0.01, G:0.00, T:0.51
Consensus pattern (31 bp):
TATATTATAATATTATATAATAATATATAAT
Found at i:55049 original size:28 final size:29
Alignment explanation
Indices: 54961--55062 Score: 93
Period size: 29 Copynumber: 3.5 Consensus size: 29
54951 AATAATCAAT
* * * *
54961 TATATTATAATAATATAAGATATTATATTTT
1 TATATT-TAATAATAGAATAAATT-TATTTA
* *
54992 TAT-TTTAATAATATAATAAATTTTTTTA
1 TATATTTAATAATAGAATAAATTTATTTA
55020 TATATTTAATAAT-GAAT-AATATTATTTA
1 TATATTTAATAATAGAATAAAT-TTATTTA
55048 TATATTTTAATAATA
1 TATA-TTTAATAATA
55063 TTTTAGTAAA
Statistics
Matches: 61, Mismatches: 6, Indels: 9
0.80 0.08 0.12
Matches are distributed among these distances:
27 3 0.05
28 20 0.33
29 33 0.54
30 2 0.03
31 3 0.05
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.53
Consensus pattern (29 bp):
TATATTTAATAATAGAATAAATTTATTTA
Found at i:55254 original size:20 final size:20
Alignment explanation
Indices: 55229--55296 Score: 127
Period size: 20 Copynumber: 3.4 Consensus size: 20
55219 TTTCCAGATG
55229 TTTTCCAGAAATGTAATTCA
1 TTTTCCAGAAATGTAATTCA
55249 TTTTCCAGAAATGTAATTCA
1 TTTTCCAGAAATGTAATTCA
*
55269 TTTTACAGAAATGTAATTCA
1 TTTTCCAGAAATGTAATTCA
55289 TTTTCCAG
1 TTTTCCAG
55297 TAATTCAAAT
Statistics
Matches: 46, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 46 1.00
ACGTcount: A:0.34, C:0.15, G:0.10, T:0.41
Consensus pattern (20 bp):
TTTTCCAGAAATGTAATTCA
Found at i:55301 original size:15 final size:15
Alignment explanation
Indices: 55281--55323 Score: 68
Period size: 15 Copynumber: 2.9 Consensus size: 15
55271 TTACAGAAAT
55281 GTAATTCATTTTCCA
1 GTAATTCATTTTCCA
**
55296 GTAATTCAAATTCCA
1 GTAATTCATTTTCCA
55311 GTAATTCATTTTC
1 GTAATTCATTTTC
55324 TGGAAAACCA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
15 24 1.00
ACGTcount: A:0.30, C:0.19, G:0.07, T:0.44
Consensus pattern (15 bp):
GTAATTCATTTTCCA
Found at i:55467 original size:17 final size:18
Alignment explanation
Indices: 55445--55484 Score: 64
Period size: 18 Copynumber: 2.3 Consensus size: 18
55435 ATAATTCTAA
*
55445 ATTAAAACCTT-TAATTT
1 ATTAAAACATTATAATTT
55462 ATTAAAACATTATAATTT
1 ATTAAAACATTATAATTT
55480 ATTAA
1 ATTAA
55485 TATACTAGAA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
17 10 0.48
18 11 0.52
ACGTcount: A:0.47, C:0.07, G:0.00, T:0.45
Consensus pattern (18 bp):
ATTAAAACATTATAATTT
Found at i:55810 original size:32 final size:31
Alignment explanation
Indices: 55774--55833 Score: 84
Period size: 32 Copynumber: 1.9 Consensus size: 31
55764 ATTCATATTT
55774 AAATTCATATAAAAAATAAATCTTTATAATAA
1 AAATTCATATAAAAAATAAATC-TTATAATAA
* * *
55806 AAATTTATATTATAAATAAATCTTATAA
1 AAATTCATATAAAAAATAAATCTTATAA
55834 AATTTTTCTT
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
31 6 0.24
32 19 0.76
ACGTcount: A:0.57, C:0.05, G:0.00, T:0.38
Consensus pattern (31 bp):
AAATTCATATAAAAAATAAATCTTATAATAA
Found at i:55831 original size:18 final size:18
Alignment explanation
Indices: 55780--55832 Score: 60
Period size: 15 Copynumber: 3.2 Consensus size: 18
55770 ATTTAAATTC
*
55780 ATATAAAAAATAAATCTT
1 ATATAATAAATAAATCTT
55798 -TATAAT-AA-AAAT-TT
1 ATATAATAAATAAATCTT
*
55812 ATATTATAAATAAATCTT
1 ATATAATAAATAAATCTT
55830 ATA
1 ATA
55833 AAATTTTTCT
Statistics
Matches: 29, Mismatches: 2, Indels: 8
0.74 0.05 0.21
Matches are distributed among these distances:
14 2 0.07
15 9 0.31
16 4 0.14
17 9 0.31
18 5 0.17
ACGTcount: A:0.57, C:0.04, G:0.00, T:0.40
Consensus pattern (18 bp):
ATATAATAAATAAATCTT
Found at i:67017 original size:3 final size:3
Alignment explanation
Indices: 67009--67127 Score: 168
Period size: 3 Copynumber: 39.3 Consensus size: 3
66999 AATATATATA
*
67009 TAT TAT TAT AAT TACT TAT TAT TAT TAAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TA-T TAT TAT TAT T-AT TAT TAT TAT TAT TAT TAT
* * * *
67056 TA- TAT TAT TAT TAT TAT TAA TAT TTT TAT TTT TAT TAT TAT TAT TAA
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
67103 TAT TAT TAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT T
67128 TTTGCAGGGT
Statistics
Matches: 103, Mismatches: 10, Indels: 6
0.87 0.08 0.05
Matches are distributed among these distances:
2 2 0.02
3 95 0.92
4 6 0.06
ACGTcount: A:0.34, C:0.01, G:0.00, T:0.65
Consensus pattern (3 bp):
TAT
Found at i:68141 original size:14 final size:14
Alignment explanation
Indices: 68124--68167 Score: 54
Period size: 15 Copynumber: 3.1 Consensus size: 14
68114 ACCCATAGTT
68124 TTGTTTT-TTATATA
1 TTGTTTTATTAT-TA
68138 TTGTTTTATTATTA
1 TTGTTTTATTATTA
*
68152 TTATTATTATTATTA
1 TTGTT-TTATTATTA
68167 T
1 T
68168 AAATTTTTAC
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
14 13 0.48
15 14 0.52
ACGTcount: A:0.25, C:0.00, G:0.05, T:0.70
Consensus pattern (14 bp):
TTGTTTTATTATTA
Found at i:68151 original size:3 final size:3
Alignment explanation
Indices: 68143--68167 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
68133 ATATATTGTT
68143 TTA TTA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA T
68168 AAATTTTTAC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:70654 original size:3 final size:3
Alignment explanation
Indices: 70634--70701 Score: 50
Period size: 3 Copynumber: 23.0 Consensus size: 3
70624 GAGAATAAAA
* * * * *
70634 ATT A-T ATT ATA ATA ATT ATT A-T ATT ATA ATT ATA ATT ATT ATAA
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT-T
* *
70678 ATT ATT ATT ATT AGT ATT AAT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT
70702 CTGTTTATTT
Statistics
Matches: 50, Mismatches: 12, Indels: 6
0.74 0.18 0.09
Matches are distributed among these distances:
2 4 0.08
3 44 0.88
4 2 0.04
ACGTcount: A:0.44, C:0.00, G:0.01, T:0.54
Consensus pattern (3 bp):
ATT
Found at i:70671 original size:17 final size:17
Alignment explanation
Indices: 70627--70672 Score: 65
Period size: 17 Copynumber: 2.7 Consensus size: 17
70617 TTTGTCCGAG
*
70627 AATAAAAATTATATTAT
1 AATAATAATTATATTAT
*
70644 AATAATTATTATATTAT
1 AATAATAATTATATTAT
*
70661 AATTATAATTAT
1 AATAATAATTAT
70673 TATAAATTAT
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
17 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (17 bp):
AATAATAATTATATTAT
Found at i:76198 original size:81 final size:79
Alignment explanation
Indices: 76081--76236 Score: 249
Period size: 81 Copynumber: 1.9 Consensus size: 79
76071 GTCTCTTGCA
* * *
76081 CAACTGGCTCGGTAGCTTCCTGCTACACCTCTGTGAGAGCTTGTCGATCCGCCATTTCGTGTGCG
1 CAACCGGCTCAGTAACTTCCTGCTACACCTCTGTGAGAGCTTGTCGATCCGCCATTTCGTGTGCG
76146 AACCATTCTTGGTG
66 AACCATTCTTGGTG
* *
76160 CAACCGGCTCAGTAACTTCCTGCTCTACACCTCTGTGAGAGCTTGTTGCTCCGCCATTTCGTGTG
1 CAACCGGCTCAGTAACTTCCTG--CTACACCTCTGTGAGAGCTTGTCGATCCGCCATTTCGTGTG
76225 CGAACCATTCTT
64 CGAACCATTCTT
76237 TGTAACTCGC
Statistics
Matches: 70, Mismatches: 5, Indels: 2
0.91 0.06 0.03
Matches are distributed among these distances:
79 19 0.27
81 51 0.73
ACGTcount: A:0.16, C:0.31, G:0.22, T:0.31
Consensus pattern (79 bp):
CAACCGGCTCAGTAACTTCCTGCTACACCTCTGTGAGAGCTTGTCGATCCGCCATTTCGTGTGCG
AACCATTCTTGGTG
Found at i:76391 original size:55 final size:56
Alignment explanation
Indices: 76330--76596 Score: 261
Period size: 55 Copynumber: 4.8 Consensus size: 56
76320 GAATCCATAG
* * *
76330 CACCTCTGTGCTAG-AATTAACGATTGAGCACCTCTATGCTTCAATCGAGAGCTGA
1 CACCTCTGTGCTAGCAATAAATGATTGAGCACCTCTGTGCTTCAATCGAGAGCTGA
* *
76385 CACCTCTGTG-TAGCCAA-AAGTGATTGAGCACCTCTGTGCTTCAATCGAGAACTGA
1 CACCTCTGTGCTAG-CAATAAATGATTGAGCACCTCTGTGCTTCAATCGAGAGCTGA
* * * * * *
76440 CACCTCTGTGC-AGTTAAAAAAATGACTGAGCACCTCTGTGCTTC-AGCTGGGAGTTGA
1 CACCTCTGTGCTAG--CAATAAATGATTGAGCACCTCTGTGCTTCAATC-GAGAGCTGA
*
76497 CACCTCTGTG-TAGC--TAAGATGATTGAGCACCTCTGTGCTTCAATTGAG-GACTGA
1 CACCTCTGTGCTAGCAATAA-ATGATTGAGCACCTCTGTGCTTCAATCGAGAG-CTGA
*
76551 CACCTCTGTGC-AGCCAACT--ATGACTGAGCACCTCTGTGCTTCAATC
1 CACCTCTGTGCTAG-CAA-TAAATGATTGAGCACCTCTGTGCTTCAATC
76597 TAAATTCTGG
Statistics
Matches: 175, Mismatches: 22, Indels: 30
0.77 0.10 0.13
Matches are distributed among these distances:
53 3 0.02
54 42 0.24
55 82 0.47
56 6 0.03
57 41 0.23
58 1 0.01
ACGTcount: A:0.25, C:0.26, G:0.22, T:0.27
Consensus pattern (56 bp):
CACCTCTGTGCTAGCAATAAATGATTGAGCACCTCTGTGCTTCAATCGAGAGCTGA
Found at i:76554 original size:27 final size:28
Alignment explanation
Indices: 76328--76595 Score: 112
Period size: 27 Copynumber: 9.7 Consensus size: 28
76318 CTGAATCCAT
** * * *
76328 AGCACCTCTGTGCTAGAATTAACGATTG
1 AGCACCTCTGTGCTTCAATTGAGGACTG
* *
76356 AGCACCTCTATGCTTCAATCGA-GAGCTG
1 AGCACCTCTGTGCTTCAATTGAGGA-CTG
* * *
76384 A-CACCTCTGTG-TAGCCAA--AAGTGATTG
1 AGCACCTCTGTGCT--TCAATTGAG-GACTG
* *
76411 AGCACCTCTGTGCTTCAATCGAGAACTG
1 AGCACCTCTGTGCTTCAATTGAGGACTG
* *** *
76439 A-CACCTCTGTGCAGTTAAAAAAATGACTG
1 AGCACCTCTGTGC--TTCAATTGAGGACTG
** *
76468 AGCACCTCTGTGCTTCAGCTG-GGAGTTG
1 AGCACCTCTGTGCTTCAATTGAGGA-CTG
* * *
76496 A-CACCTCTGTG-TAGCTAA--GATGATTG
1 AGCACCTCTGTGCT-TC-AATTGAGGACTG
76522 AGCACCTCTGTGCTTCAATTGAGGACTG
1 AGCACCTCTGTGCTTCAATTGAGGACTG
** * *
76550 A-CACCTCTGTGCAGCCAACT-ATGACTG
1 AGCACCTCTGTGC-TTCAATTGAGGACTG
76577 AGCACCTCTGTGCTTCAAT
1 AGCACCTCTGTGCTTCAAT
76596 CTAAATTCTG
Statistics
Matches: 178, Mismatches: 40, Indels: 45
0.68 0.15 0.17
Matches are distributed among these distances:
26 10 0.06
27 75 0.42
28 69 0.39
29 13 0.07
30 11 0.06
ACGTcount: A:0.26, C:0.25, G:0.22, T:0.27
Consensus pattern (28 bp):
AGCACCTCTGTGCTTCAATTGAGGACTG
Found at i:76640 original size:54 final size:55
Alignment explanation
Indices: 76351--76654 Score: 251
Period size: 55 Copynumber: 5.5 Consensus size: 55
76341 TAGAATTAAC
* * * * *
76351 GATTGAGCACCTCTATGCTTCAATCGAGAG-CTGACACCTCTGTGTAGCCAAAAGT
1 GATTGAGCACCTCTGTGCTTCAATCTAAAGACTGACACCTCTGTGCAGCCAACA-T
* * ** *
76406 GATTGAGCACCTCTGTGCTTCAATCGAGA-ACTGACACCTCTGTGCAGTTAAAAAAAT
1 GATTGAGCACCTCTGTGCTTCAATCTAAAGACTGACACCTCTGTGCAG---CCAACAT
* * ** * * * *
76463 GACTGAGCACCTCTGTGCTTC-AGCT-GGGAGTTGACACCTCTGTGTAGCTAAGAT
1 GATTGAGCACCTCTGTGCTTCAATCTAAAGA-CTGACACCTCTGTGCAGCCAACAT
* *
76517 GATTGAGCACCTCTGTGCTTCAAT-TGAGGACTGACACCTCTGTGCAGCCAACTAT
1 GATTGAGCACCTCTGTGCTTCAATCTAAAGACTGACACCTCTGTGCAGCCAAC-AT
* ** * ****
76572 GACTGAGCACCTCTGTGCTTCAATCTAAATTCTGGCACCTCTGTGCATTGGA-AT
1 GATTGAGCACCTCTGTGCTTCAATCTAAAGACTGACACCTCTGTGCAGCCAACAT
*
76626 GATTGAGCACCTCTGTGCTACAATCTAAA
1 GATTGAGCACCTCTGTGCTTCAATCTAAA
76655 ATCAAGCACC
Statistics
Matches: 207, Mismatches: 32, Indels: 21
0.80 0.12 0.08
Matches are distributed among these distances:
54 72 0.35
55 74 0.36
56 21 0.10
57 36 0.17
58 4 0.02
ACGTcount: A:0.26, C:0.25, G:0.22, T:0.28
Consensus pattern (55 bp):
GATTGAGCACCTCTGTGCTTCAATCTAAAGACTGACACCTCTGTGCAGCCAACAT
Found at i:76642 original size:109 final size:110
Alignment explanation
Indices: 76354--76650 Score: 307
Period size: 109 Copynumber: 2.7 Consensus size: 110
76344 AATTAACGAT
* * * * * * *
76354 TGAGCACCTCTATGCTTCA-ATCGAGAGCTGACACCTCTGTGTAGCCAAAAGTGATTGAGCACCT
1 TGAGCACCTCTGTGCTTCAGCT-GAAAGTTGACACCTCTGTGCAGCTAAGA-TGATTGAGCACCT
76418 CTGTGCTTCAATCGAGAACTGACACCTCTGTGCAGTTAAAAAAATGAC
64 CTGTGCTTCAATCGAGAACTGACACCTCTGTGCAG-TAAAAAAATGAC
** *
76466 TGAGCACCTCTGTGCTTCAGCTGGGAGTTGACACCTCTGTGTAGCTAAGATGATTGAGCACCTCT
1 TGAGCACCTCTGTGCTTCAGCTGAAAGTTGACACCTCTGTGCAGCTAAGATGATTGAGCACCTCT
* * ** **
76531 GTGCTTCAATTGAGGACTGACACCTCTGTGCAG-CCAACTATGAC
66 GTGCTTCAATCGAGAACTGACACCTCTGTGCAGTAAAAAAATGAC
* * * **
76575 TGAGCACCTCTGTGCTTCAATCT-AAATTCTGGCACCTCTGTGCA--TTGGAATGATTGAGCACC
1 TGAGCACCTCTGTGCTTC-AGCTGAAAGT-TGACACCTCTGTGCAGCTAAG-ATGATTGAGCACC
*
76637 TCTGTGCTACAATC
63 TCTGTGCTTCAATC
76651 TAAAATCAAG
Statistics
Matches: 159, Mismatches: 22, Indels: 11
0.83 0.11 0.06
Matches are distributed among these distances:
108 2 0.01
109 52 0.33
110 16 0.10
111 46 0.29
112 42 0.26
113 1 0.01
ACGTcount: A:0.25, C:0.26, G:0.22, T:0.28
Consensus pattern (110 bp):
TGAGCACCTCTGTGCTTCAGCTGAAAGTTGACACCTCTGTGCAGCTAAGATGATTGAGCACCTCT
GTGCTTCAATCGAGAACTGACACCTCTGTGCAGTAAAAAAATGAC
Found at i:79882 original size:15 final size:17
Alignment explanation
Indices: 79848--79882 Score: 70
Period size: 17 Copynumber: 2.1 Consensus size: 17
79838 TTCCGAACTT
79848 GAGATTGCAAAGGAAGA
1 GAGATTGCAAAGGAAGA
79865 GAGATTGCAAAGGAAGA
1 GAGATTGCAAAGGAAGA
79882 G
1 G
79883 TTCGAAGCTG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.46, C:0.06, G:0.37, T:0.11
Consensus pattern (17 bp):
GAGATTGCAAAGGAAGA
Found at i:83597 original size:30 final size:31
Alignment explanation
Indices: 83561--83635 Score: 100
Period size: 31 Copynumber: 2.5 Consensus size: 31
83551 TGTGAATTGA
*
83561 GTTAAATTAATCTTTTAT-TTAAAG-TTAAGG
1 GTTAAATTAATATTTTATCTT-AAGTTTAAGG
* *
83591 GTTAAATTGATATTTTATCTTAAGTTTAGGG
1 GTTAAATTAATATTTTATCTTAAGTTTAAGG
83622 GTTAAATTAATATT
1 GTTAAATTAATATT
83636 CGGGATGATT
Statistics
Matches: 39, Mismatches: 4, Indels: 3
0.85 0.09 0.07
Matches are distributed among these distances:
30 19 0.49
31 20 0.51
ACGTcount: A:0.35, C:0.03, G:0.15, T:0.48
Consensus pattern (31 bp):
GTTAAATTAATATTTTATCTTAAGTTTAAGG
Done.