Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01001185.1 Hibiscus syriacus cultivar Beakdansim tig00002352_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: 70743
ACGTcount: A:0.35, C:0.16, G:0.16, T:0.34
Found at i:7871 original size:31 final size:30
Alignment explanation
Indices: 7818--7875 Score: 73
Period size: 31 Copynumber: 1.9 Consensus size: 30
7808 GTTACGTTGG
**
7818 GGACCATATTGCAAAAAGACTAAATGTTAGA
1 GGACCATATCACAAAAAGACT-AATGTTAGA
7849 GGACCATATCACAAACAA-ACTAATGTT
1 GGACCATATCACAAA-AAGACTAATGTT
7876 GGGGACTGTA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
30 6 0.25
31 16 0.67
32 2 0.08
ACGTcount: A:0.45, C:0.17, G:0.16, T:0.22
Consensus pattern (30 bp):
GGACCATATCACAAAAAGACTAATGTTAGA
Found at i:9667 original size:64 final size:64
Alignment explanation
Indices: 9594--9825 Score: 231
Period size: 64 Copynumber: 3.6 Consensus size: 64
9584 TGTTTGAATG
* * **
9594 TGCACCGATGCATTGGTAGTGCATCGATGCA-CTCTTTTAA-AATAAATACATCGAATGCAATTC
1 TGCATCGATGCATAGGTAGTGCATCGATGCATC-CCATTAATAATAAA-ACATCGAATGCAATTC
9657 A
64 A
* * **
9658 TGCATCGATGCATAAGTAGTGCATCGATGCATCCCATTAATAATGAAACATCGAATGCAATTGG
1 TGCATCGATGCATAGGTAGTGCATCGATGCATCCCATTAATAATAAAACATCGAATGCAATTCA
** ** * ** *
9722 TGCATCGATGCATAAGG-AGTGCATCGATGCATCCCAGCAATAATATTACATCGAATACCTTTTA
1 TGCATCGATGCAT-AGGTAGTGCATCGATGCATCCCATTAATAATAAAACATCGAATGCAATTCA
* *
9786 TGCACCGATGCATCA-GTAGTGCATCGATGCATACC-TTAAT
1 TGCATCGATGCAT-AGGTAGTGCATCGATGCATCCCATTAAT
9826 TAAAAGATGA
Statistics
Matches: 140, Mismatches: 24, Indels: 9
0.81 0.14 0.05
Matches are distributed among these distances:
63 4 0.03
64 128 0.91
65 8 0.06
ACGTcount: A:0.32, C:0.21, G:0.19, T:0.28
Consensus pattern (64 bp):
TGCATCGATGCATAGGTAGTGCATCGATGCATCCCATTAATAATAAAACATCGAATGCAATTCA
Found at i:10866 original size:31 final size:31
Alignment explanation
Indices: 10757--10878 Score: 131
Period size: 31 Copynumber: 3.9 Consensus size: 31
10747 GAGGGTATAA
*
10757 CTATGTTCTACGGAACATATGGACAGAATTAC
1 CTATGTTCTACGGAACATATGGACAG-TTTAC
* *
10789 CTATG-TCTTTC-GAGACATATGGACAGTATAC
1 CTATGTTC-TACGGA-ACATATGGACAGTTTAC
* *
10820 CTATGCTCTAAGGAACATATGGACAGTTTAC
1 CTATGTTCTACGGAACATATGGACAGTTTAC
* * *
10851 CTAGGTTCTTCGGAACCTATGGACAGTT
1 CTATGTTCTACGGAACATATGGACAGTT
10879 GCCAAGGATC
Statistics
Matches: 75, Mismatches: 11, Indels: 9
0.79 0.12 0.09
Matches are distributed among these distances:
31 52 0.69
32 23 0.31
ACGTcount: A:0.30, C:0.20, G:0.20, T:0.30
Consensus pattern (31 bp):
CTATGTTCTACGGAACATATGGACAGTTTAC
Found at i:11788 original size:25 final size:25
Alignment explanation
Indices: 11754--11803 Score: 91
Period size: 25 Copynumber: 2.0 Consensus size: 25
11744 TACGTTGGGG
*
11754 ACCATATTGCAAACGGACTAAATGT
1 ACCATATTGCAAACGAACTAAATGT
11779 ACCATATTGCAAACGAACTAAATGT
1 ACCATATTGCAAACGAACTAAATGT
11804 TGGAGGATTG
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.42, C:0.20, G:0.14, T:0.24
Consensus pattern (25 bp):
ACCATATTGCAAACGAACTAAATGT
Found at i:12097 original size:20 final size:20
Alignment explanation
Indices: 12072--12125 Score: 74
Period size: 20 Copynumber: 2.7 Consensus size: 20
12062 GACCAACAAA
12072 TTCGCAACGCGAATTCCAAT
1 TTCGCAACGCGAATTCCAAT
* *
12092 TTCGCAAC-CCAGTTTCCAAT
1 TTCGCAACGCGA-ATTCCAAT
12112 TTCGCAACGCGAAT
1 TTCGCAACGCGAAT
12126 ATGTAAATCG
Statistics
Matches: 28, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
19 2 0.07
20 24 0.86
21 2 0.07
ACGTcount: A:0.28, C:0.31, G:0.15, T:0.26
Consensus pattern (20 bp):
TTCGCAACGCGAATTCCAAT
Found at i:12136 original size:20 final size:20
Alignment explanation
Indices: 12113--12180 Score: 73
Period size: 20 Copynumber: 3.4 Consensus size: 20
12103 GTTTCCAATT
*
12113 TCGCAACGCGAATATGTAAA
1 TCGCAACGCGAATTTGTAAA
** * **
12133 TCGCATTGCGATTTTCCAAA
1 TCGCAACGCGAATTTGTAAA
12153 TTCGCAACGCGAATTTGTAAA
1 -TCGCAACGCGAATTTGTAAA
12174 TCGCAAC
1 TCGCAAC
12181 ACATAAGTCA
Statistics
Matches: 36, Mismatches: 11, Indels: 2
0.73 0.22 0.04
Matches are distributed among these distances:
20 21 0.58
21 15 0.42
ACGTcount: A:0.32, C:0.24, G:0.18, T:0.26
Consensus pattern (20 bp):
TCGCAACGCGAATTTGTAAA
Found at i:12197 original size:20 final size:20
Alignment explanation
Indices: 12174--12213 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
12164 AATTTGTAAA
12174 TCGCAACAC-ATAAGTCAAAT
1 TCGCAACACGA-AAGTCAAAT
*
12194 TCGCAACGCGAAAGTCAAAT
1 TCGCAACACGAAAGTCAAAT
12214 GTTTTTACAC
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 17 0.94
21 1 0.06
ACGTcount: A:0.42, C:0.25, G:0.15, T:0.17
Consensus pattern (20 bp):
TCGCAACACGAAAGTCAAAT
Found at i:12692 original size:19 final size:20
Alignment explanation
Indices: 12655--12694 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 20
12645 ACCAAATTCA
12655 CAACGCGAAAATGAAAATCG
1 CAACGCGAAAATGAAAATCG
*
12675 CAACGCGAAACT-AAAATCG
1 CAACGCGAAAATGAAAATCG
12694 C
1 C
12695 GTTGCAAATT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 8 0.42
20 11 0.58
ACGTcount: A:0.47, C:0.25, G:0.17, T:0.10
Consensus pattern (20 bp):
CAACGCGAAAATGAAAATCG
Found at i:14886 original size:21 final size:21
Alignment explanation
Indices: 14845--14940 Score: 79
Period size: 21 Copynumber: 4.6 Consensus size: 21
14835 GATGCACCTA
* **
14845 TCATCATTCAAGAGGTGCCTC
1 TCATCGTTCAAGAGGCCCCTC
14866 -CTATCGTTCAAGAGGCCCCTC
1 TC-ATCGTTCAAGAGGCCCCTC
* *
14887 TCATC-ATCGAAGAAGCCCCTC
1 TCATCGTTC-AAGAGGCCCCTC
* * * *
14908 CCACCGTTTAAGAGGCCCCTA
1 TCATCGTTCAAGAGGCCCCTC
14929 TCATCGTTCAAG
1 TCATCGTTCAAG
14941 TGGTCTCGTC
Statistics
Matches: 57, Mismatches: 14, Indels: 8
0.72 0.18 0.10
Matches are distributed among these distances:
20 3 0.05
21 52 0.91
22 2 0.04
ACGTcount: A:0.24, C:0.34, G:0.18, T:0.24
Consensus pattern (21 bp):
TCATCGTTCAAGAGGCCCCTC
Found at i:14892 original size:42 final size:42
Alignment explanation
Indices: 14841--14940 Score: 112
Period size: 42 Copynumber: 2.4 Consensus size: 42
14831 GCCCGATGCA
* ** * *
14841 CCTATCATCATTCAAGAGGTGCCTCCTATCGTTCAAGAGGCC
1 CCTATCATCATTCAAGAAGCCCCTCCCACCGTTCAAGAGGCC
* *
14883 CCTCTCATCA-TCGAAGAAGCCCCTCCCACCGTTTAAGAGGCC
1 CCTATCATCATTC-AAGAAGCCCCTCCCACCGTTCAAGAGGCC
*
14925 CCTATCATCGTTCAAG
1 CCTATCATCATTCAAG
14941 TGGTCTCGTC
Statistics
Matches: 47, Mismatches: 9, Indels: 4
0.78 0.15 0.07
Matches are distributed among these distances:
41 2 0.04
42 43 0.91
43 2 0.04
ACGTcount: A:0.24, C:0.35, G:0.17, T:0.24
Consensus pattern (42 bp):
CCTATCATCATTCAAGAAGCCCCTCCCACCGTTCAAGAGGCC
Found at i:16385 original size:14 final size:14
Alignment explanation
Indices: 16366--16407 Score: 57
Period size: 14 Copynumber: 3.0 Consensus size: 14
16356 TTTTTTGATT
16366 AATTGATTTGTAAA
1 AATTGATTTGTAAA
**
16380 AATTGATTTGTTTA
1 AATTGATTTGTAAA
*
16394 ATTTGATTTGTAAA
1 AATTGATTTGTAAA
16408 TAAGAATTAT
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
14 23 1.00
ACGTcount: A:0.36, C:0.00, G:0.14, T:0.50
Consensus pattern (14 bp):
AATTGATTTGTAAA
Found at i:16400 original size:61 final size:65
Alignment explanation
Indices: 16321--16456 Score: 165
Period size: 65 Copynumber: 2.2 Consensus size: 65
16311 ACATTGAAAG
16321 TTGATTTG-TTACAATTGATGAGGAAATAAG-ATT-TATTTT-TTGATTAATTGATTTGTAAAAA
1 TTGATTTGTTTACAATTGATGAGGAAATAAGAATTATATTTTCTTGATTAATTGATTTGTAAAAA
* ** * * *
16382 TTGATTTGTTTA-ATTTGATTTGTAAATAAGAATTATTTTTTGCTTGTTTAATTGATTTGTAAAA
1 TTGATTTGTTTACAATTGATGAGGAAATAAGAATTATATTTT-CTTGATTAATTGATTTGTAAAA
*
16446 G
65 A
16447 TTGATTTGTT
1 TTGATTTGTT
16457 ATTTCTAAAA
Statistics
Matches: 63, Mismatches: 7, Indels: 6
0.83 0.09 0.08
Matches are distributed among these distances:
61 22 0.35
62 6 0.10
63 5 0.08
65 30 0.48
ACGTcount: A:0.31, C:0.01, G:0.16, T:0.51
Consensus pattern (65 bp):
TTGATTTGTTTACAATTGATGAGGAAATAAGAATTATATTTTCTTGATTAATTGATTTGTAAAAA
Found at i:16597 original size:20 final size:20
Alignment explanation
Indices: 16572--16621 Score: 82
Period size: 20 Copynumber: 2.5 Consensus size: 20
16562 GCAACGCTTA
16572 TTTCGCGTTGCAAATTTGAC
1 TTTCGCGTTGCAAATTTGAC
*
16592 TTTCGCGTTGCGAATTTGAC
1 TTTCGCGTTGCAAATTTGAC
*
16612 TTTCACGTTG
1 TTTCGCGTTG
16622 ATCGCAACAT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
20 28 1.00
ACGTcount: A:0.16, C:0.20, G:0.22, T:0.42
Consensus pattern (20 bp):
TTTCGCGTTGCAAATTTGAC
Found at i:17168 original size:24 final size:24
Alignment explanation
Indices: 17141--17204 Score: 76
Period size: 24 Copynumber: 2.7 Consensus size: 24
17131 AGTGGAGCCG
17141 AAATTTATATTGAAATTCAAACTC
1 AAATTTATATTGAAATTCAAACTC
* * *
17165 AAATTGAAATTTAAATTCAAACTC
1 AAATTTATATTGAAATTCAAACTC
*
17189 CAA-TTATATATGAAAT
1 AAATTTATAT-TGAAAT
17205 GAATTTGAAA
Statistics
Matches: 32, Mismatches: 7, Indels: 2
0.78 0.17 0.05
Matches are distributed among these distances:
23 4 0.12
24 28 0.88
ACGTcount: A:0.48, C:0.11, G:0.05, T:0.36
Consensus pattern (24 bp):
AAATTTATATTGAAATTCAAACTC
Found at i:17172 original size:18 final size:18
Alignment explanation
Indices: 17149--17185 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
17139 CGAAATTTAT
17149 ATTGAAATTCAAACTCAA
1 ATTGAAATTCAAACTCAA
* *
17167 ATTGAAATTTAAATTCAA
1 ATTGAAATTCAAACTCAA
17185 A
1 A
17186 CTCCAATTAT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.51, C:0.11, G:0.05, T:0.32
Consensus pattern (18 bp):
ATTGAAATTCAAACTCAA
Found at i:17563 original size:25 final size:25
Alignment explanation
Indices: 17529--17578 Score: 82
Period size: 25 Copynumber: 2.0 Consensus size: 25
17519 ATTATTTTTC
*
17529 CAAATAATGTACCCATAAAAATGTT
1 CAAATAATGTACCCACAAAAATGTT
*
17554 CAAATAATGTACCCACAACAATGTT
1 CAAATAATGTACCCACAAAAATGTT
17579 TAATTGATTT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
25 23 1.00
ACGTcount: A:0.46, C:0.20, G:0.08, T:0.26
Consensus pattern (25 bp):
CAAATAATGTACCCACAAAAATGTT
Found at i:17989 original size:18 final size:18
Alignment explanation
Indices: 17966--18001 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
17956 AAGCCGGTTG
*
17966 TGATTGGGATTTTGATTT
1 TGATTGCGATTTTGATTT
17984 TGATTGCGATTTTGATTT
1 TGATTGCGATTTTGATTT
18002 CCTTTTTCTT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.17, C:0.03, G:0.25, T:0.56
Consensus pattern (18 bp):
TGATTGCGATTTTGATTT
Found at i:20291 original size:24 final size:24
Alignment explanation
Indices: 20257--20310 Score: 90
Period size: 24 Copynumber: 2.2 Consensus size: 24
20247 CCATCACATC
20257 ATCAAAATCCGAGTATTGACCAAG
1 ATCAAAATCCGAGTATTGACCAAG
* *
20281 ATCAAAGTCCGGGTATTGACCAAG
1 ATCAAAATCCGAGTATTGACCAAG
20305 ATCAAA
1 ATCAAA
20311 TTTTGAATAC
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.41, C:0.20, G:0.19, T:0.20
Consensus pattern (24 bp):
ATCAAAATCCGAGTATTGACCAAG
Found at i:20454 original size:12 final size:12
Alignment explanation
Indices: 20437--20470 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
20427 GGTTGTGGGT
20437 TTTGATATTGTG
1 TTTGATATTGTG
*
20449 TTTGATATTATG
1 TTTGATATTGTG
*
20461 TTTGGTATTG
1 TTTGATATTG
20471 GAAATGTGGT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.18, C:0.00, G:0.24, T:0.59
Consensus pattern (12 bp):
TTTGATATTGTG
Found at i:21239 original size:19 final size:20
Alignment explanation
Indices: 21215--21325 Score: 97
Period size: 20 Copynumber: 5.7 Consensus size: 20
21205 ACTAAAACCT
21215 GTTGCGAAATT-AAATTCGC
1 GTTGCGAAATTGAAATTCGC
* *
21234 GTTGCGAATTTGAAATTC-A
1 GTTGCGAAATTGAAATTCGC
*
21253 GTTGCG--ATTTACAACTTCGC
1 GTTGCGAAATTGA-AA-TTCGC
* *
21273 GTTGCGAAATTGGAAACT-GG
1 GTTGCGAAATT-GAAATTCGC
*
21293 GTTGCGAAATTGGAATTCGC
1 GTTGCGAAATTGAAATTCGC
*
21313 GTTGCGAATTTGA
1 GTTGCGAAATTGA
21326 GACCGCATTG
Statistics
Matches: 71, Mismatches: 13, Indels: 15
0.72 0.13 0.15
Matches are distributed among these distances:
17 3 0.04
18 2 0.03
19 23 0.32
20 36 0.51
21 1 0.01
22 5 0.07
23 1 0.01
ACGTcount: A:0.27, C:0.14, G:0.26, T:0.32
Consensus pattern (20 bp):
GTTGCGAAATTGAAATTCGC
Found at i:21251 original size:20 final size:20
Alignment explanation
Indices: 21215--21343 Score: 99
Period size: 19 Copynumber: 6.6 Consensus size: 20
21205 ACTAAAACCT
*
21215 GTTGCGAAATT-AAATTCGC
1 GTTGCGAATTTGAAATTCGC
*
21234 GTTGCGAATTTGAAATTC-A
1 GTTGCGAATTTGAAATTCGC
21253 GTTGCG-ATTT-ACAACTTCGC
1 GTTGCGAATTTGA-AA-TTCGC
* * *
21273 GTTGCGAAATTGGAAACT-GG
1 GTTGCG-AATTTGAAATTCGC
* *
21293 GTTGCGAAATTGGAATTCGC
1 GTTGCGAATTTGAAATTCGC
* *
21313 GTTGCGAATTTGAGA-CCGC
1 GTTGCGAATTTGAAATTCGC
*
21332 ATTGCGAATTTG
1 GTTGCGAATTTG
21344 TTGGTCATTT
Statistics
Matches: 86, Mismatches: 16, Indels: 16
0.73 0.14 0.14
Matches are distributed among these distances:
17 1 0.01
18 6 0.07
19 40 0.47
20 32 0.37
21 1 0.01
22 5 0.06
23 1 0.01
ACGTcount: A:0.26, C:0.16, G:0.26, T:0.32
Consensus pattern (20 bp):
GTTGCGAATTTGAAATTCGC
Found at i:21312 original size:40 final size:39
Alignment explanation
Indices: 21215--21320 Score: 117
Period size: 40 Copynumber: 2.7 Consensus size: 39
21205 ACTAAAACCT
* *
21215 GTTGCGAAATTAAATTCGCGTTGCG-AATTTGAAATTCA
1 GTTGCGAAATTAAATTCGCGTTGCGAAATTGGAAACTCA
* **
21253 GTTGCG-ATTTACAACTTCGCGTTGCGAAATTGGAAACTGG
1 GTTGCGAAATTA-AA-TTCGCGTTGCGAAATTGGAAACTCA
*
21293 GTTGCGAAATTGGAATTCGCGTTGCGAA
1 GTTGCGAAATT-AAATTCGCGTTGCGAA
21321 TTTGAGACCG
Statistics
Matches: 56, Mismatches: 7, Indels: 8
0.79 0.10 0.11
Matches are distributed among these distances:
37 4 0.07
38 8 0.14
39 11 0.20
40 28 0.50
41 5 0.09
ACGTcount: A:0.27, C:0.15, G:0.26, T:0.31
Consensus pattern (39 bp):
GTTGCGAAATTAAATTCGCGTTGCGAAATTGGAAACTCA
Found at i:21876 original size:19 final size:20
Alignment explanation
Indices: 21841--21878 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
21831 TTTCTCATAT
21841 ATATAAAATACAATTATTTA
1 ATATAAAATACAATTATTTA
*
21861 ATATTAAATA-AATTATTT
1 ATATAAAATACAATTATTT
21879 TTAAGCAGAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 8 0.47
20 9 0.53
ACGTcount: A:0.53, C:0.03, G:0.00, T:0.45
Consensus pattern (20 bp):
ATATAAAATACAATTATTTA
Found at i:23137 original size:2 final size:2
Alignment explanation
Indices: 23130--23196 Score: 134
Period size: 2 Copynumber: 33.5 Consensus size: 2
23120 ACTTTAATTA
23130 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
23172 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
23197 GAGAGAGAGA
Statistics
Matches: 65, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 65 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:23201 original size:2 final size:2
Alignment explanation
Indices: 23196--23236 Score: 73
Period size: 2 Copynumber: 20.5 Consensus size: 2
23186 ATATATATAT
*
23196 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG GG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
23237 ATAATATGAT
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.49, C:0.00, G:0.51, T:0.00
Consensus pattern (2 bp):
AG
Found at i:24715 original size:29 final size:27
Alignment explanation
Indices: 24682--24772 Score: 65
Period size: 29 Copynumber: 3.1 Consensus size: 27
24672 ATTGGTTTTT
24682 AAACTTTTAAATATTCTAATTTCATTCCC
1 AAACTTTTAAATATTCTAATTT-A-TCCC
* * ** * *
24711 AAACTATGACCCTCTTTCTAAATTAATCCTC
1 AAACTTTTA-AAT-ATTCT-AATTTATCC-C
24742 AAACTTTTAAATATTCTAATTTTATCCC
1 AAACTTTTAAATATTCTAA-TTTATCCC
24770 AAA
1 AAA
24773 TTCATCCAAA
Statistics
Matches: 45, Mismatches: 12, Indels: 11
0.66 0.18 0.16
Matches are distributed among these distances:
28 6 0.13
29 17 0.38
30 5 0.11
31 13 0.29
32 4 0.09
ACGTcount: A:0.36, C:0.22, G:0.01, T:0.41
Consensus pattern (27 bp):
AAACTTTTAAATATTCTAATTTATCCC
Found at i:27684 original size:27 final size:28
Alignment explanation
Indices: 27617--27685 Score: 79
Period size: 27 Copynumber: 2.5 Consensus size: 28
27607 AATTTAAAAT
* *
27617 AAATTCTTATTTATTTTTTAAATGTCAA
1 AAATTCTAATTTATTTTTTAAATATCAA
* *
27645 TAATT-TAATTTATTTTTTTAATAT-AA
1 AAATTCTAATTTATTTTTTAAATATCAA
*
27671 AAATTCTAACTTATT
1 AAATTCTAATTTATT
27686 ACTTAAAAGT
Statistics
Matches: 34, Mismatches: 6, Indels: 3
0.79 0.14 0.07
Matches are distributed among these distances:
26 6 0.18
27 24 0.71
28 4 0.12
ACGTcount: A:0.38, C:0.06, G:0.01, T:0.55
Consensus pattern (28 bp):
AAATTCTAATTTATTTTTTAAATATCAA
Found at i:32792 original size:2 final size:2
Alignment explanation
Indices: 32785--32810 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
32775 TTTATTTCCT
32785 TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA
32811 ATCTTAAATT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:39300 original size:77 final size:77
Alignment explanation
Indices: 39132--39286 Score: 283
Period size: 77 Copynumber: 2.0 Consensus size: 77
39122 ATATGATGAT
*
39132 TAAAAAAATTAAATATTGTATATTCTCAAATAAAAAATTAGCACATTAACTTACTTTTGTAAATA
1 TAAAAAAATTAAATATTGTATATTCTCAAATAAAAAATTAGCACATTAACTTACTTCTGTAAATA
*
39197 TAGAATATATTA
66 TAAAATATATTA
*
39209 TAAAAAAATTAAATATTGTATATTCTCAAATAAAAAATTAGTACATTAACTTACTTCTGTAAATA
1 TAAAAAAATTAAATATTGTATATTCTCAAATAAAAAATTAGCACATTAACTTACTTCTGTAAATA
39274 TAAAATATATTA
66 TAAAATATATTA
39286 T
1 T
39287 TAAATTTTAA
Statistics
Matches: 75, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
77 75 1.00
ACGTcount: A:0.50, C:0.08, G:0.05, T:0.38
Consensus pattern (77 bp):
TAAAAAAATTAAATATTGTATATTCTCAAATAAAAAATTAGCACATTAACTTACTTCTGTAAATA
TAAAATATATTA
Found at i:41527 original size:21 final size:22
Alignment explanation
Indices: 41501--41544 Score: 63
Period size: 21 Copynumber: 2.0 Consensus size: 22
41491 TCACTCATTC
41501 ACTAAAAATCAAGGAA-AAAAA
1 ACTAAAAATCAAGGAAGAAAAA
* *
41522 ACTAAAAATGATGGAAGAAAAA
1 ACTAAAAATCAAGGAAGAAAAA
41544 A
1 A
41545 ACTTACCTCG
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
21 14 0.70
22 6 0.30
ACGTcount: A:0.68, C:0.07, G:0.14, T:0.11
Consensus pattern (22 bp):
ACTAAAAATCAAGGAAGAAAAA
Found at i:43868 original size:20 final size:21
Alignment explanation
Indices: 43845--43883 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 21
43835 TAAAATCCAA
*
43845 ACAATATAATTTA-AATAACT
1 ACAATAAAATTTATAATAACT
43865 ACAATAAAATTTATAATAA
1 ACAATAAAATTTATAATAA
43884 AAAACATATA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 12 0.71
21 5 0.29
ACGTcount: A:0.59, C:0.08, G:0.00, T:0.33
Consensus pattern (21 bp):
ACAATAAAATTTATAATAACT
Found at i:44785 original size:16 final size:17
Alignment explanation
Indices: 44745--44786 Score: 52
Period size: 16 Copynumber: 2.5 Consensus size: 17
44735 TTCAAATTAG
44745 AATTAAATAATATCATA
1 AATTAAATAATATCATA
44762 ATATTAAA-AATAT-ATA
1 A-ATTAAATAATATCATA
44778 CAATTAAAT
1 -AATTAAAT
44787 TTAAATTTAA
Statistics
Matches: 22, Mismatches: 0, Indels: 6
0.79 0.00 0.21
Matches are distributed among these distances:
16 9 0.41
17 7 0.32
18 6 0.27
ACGTcount: A:0.60, C:0.05, G:0.00, T:0.36
Consensus pattern (17 bp):
AATTAAATAATATCATA
Found at i:53652 original size:173 final size:171
Alignment explanation
Indices: 53357--53682 Score: 505
Period size: 173 Copynumber: 1.9 Consensus size: 171
53347 GAAAGAGTTC
* *
53357 CATAATTTTCAATATCAACAAACTATTTACAATGTTAAAAAAAGATCTAAAATGACATGAGATCA
1 CATAATATTCAATATCAACAAACTA-TTACAATGTTAAAAAAAGATCTAAAATGAAATGAGATCA
*
53422 GTTCTCAAAAGTTGTTCAGTGCAATTTTTAGGTAGTCAATAAGAAAACAACAAATTAAAAAAGAA
65 GTTCTCAAAAGTTGTTCAGTGCAATTTTTAGGTAGCCAATAAGAAAACAACAAATTAAAAAAGAA
*
53487 ACATTTATGACTGGAAA-TTCTAATAAAAAAAAGGACAGATAT
130 ACAATTATGACT-GAAATTTCTAATAAAAAAAAGGACAGATAT
*
53529 CATAATATTCAATATCAAC-AACTA-TACAGTGCTTAAAAAAAAGGATCTAAAAATGAAATGAGA
1 CATAATATTCAATATCAACAAACTATTACAATG-TT-AAAAAAA-GATCT-AAAATGAAATGAGA
* *
53592 TCAGTTCTCAAAAGTTGTTCATTGCAATTTTTAGGTAGCCAATAAGAAAATAACAAATTAAAAAA
62 TCAGTTCTCAAAAGTTGTTCAGTGCAATTTTTAGGTAGCCAATAAGAAAACAACAAATTAAAAAA
*
53657 GACACAATTATGACTGAAATTTCTAA
127 GAAACAATTATGACTGAAATTTCTAA
53683 AAGACTAATC
Statistics
Matches: 141, Mismatches: 8, Indels: 9
0.89 0.05 0.06
Matches are distributed among these distances:
169 6 0.04
170 2 0.01
171 12 0.09
172 27 0.19
173 94 0.67
ACGTcount: A:0.48, C:0.12, G:0.12, T:0.28
Consensus pattern (171 bp):
CATAATATTCAATATCAACAAACTATTACAATGTTAAAAAAAGATCTAAAATGAAATGAGATCAG
TTCTCAAAAGTTGTTCAGTGCAATTTTTAGGTAGCCAATAAGAAAACAACAAATTAAAAAAGAAA
CAATTATGACTGAAATTTCTAATAAAAAAAAGGACAGATAT
Found at i:56908 original size:2 final size:2
Alignment explanation
Indices: 56901--56948 Score: 96
Period size: 2 Copynumber: 24.0 Consensus size: 2
56891 TTCAAACATC
56901 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
56943 AT AT AT
1 AT AT AT
56949 GAATGTGTTT
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 46 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:64588 original size:13 final size:13
Alignment explanation
Indices: 64570--64595 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
64560 TACTTTAAAG
64570 ATATATATATATA
1 ATATATATATATA
64583 ATATATATATATA
1 ATATATATATATA
64596 TTGAAATAGT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (13 bp):
ATATATATATATA
Found at i:65861 original size:24 final size:24
Alignment explanation
Indices: 65829--65882 Score: 99
Period size: 24 Copynumber: 2.2 Consensus size: 24
65819 TCTTATTATT
*
65829 TTTGACAATAGTTCCAAATCATCA
1 TTTGTCAATAGTTCCAAATCATCA
65853 TTTGTCAATAGTTCCAAATCATCA
1 TTTGTCAATAGTTCCAAATCATCA
65877 TTTGTC
1 TTTGTC
65883 CTTTTTAATC
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
24 29 1.00
ACGTcount: A:0.31, C:0.20, G:0.09, T:0.39
Consensus pattern (24 bp):
TTTGTCAATAGTTCCAAATCATCA
Found at i:66547 original size:20 final size:20
Alignment explanation
Indices: 66524--66562 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
66514 GAACAGTAAT
* *
66524 GTGAACATTGTTACAGTGCC
1 GTGAACAGTGCTACAGTGCC
*
66544 GTGAATAGTGCTACAGTGC
1 GTGAACAGTGCTACAGTGC
66563 ATCGATGCAT
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.26, C:0.18, G:0.28, T:0.28
Consensus pattern (20 bp):
GTGAACAGTGCTACAGTGCC
Found at i:67200 original size:24 final size:24
Alignment explanation
Indices: 67173--67245 Score: 66
Period size: 24 Copynumber: 3.2 Consensus size: 24
67163 AACTCGTATA
67173 AATTTGCACCGAAGTGCCACGTAG
1 AATTTGCACCGAAGTGCCACGTAG
*
67197 AATTTGTC-CCGAAG-GACCGCGTAG
1 AATTTG-CACCGAAGTG-CCACGTAG
* *
67221 AA-TTGTATCGAAGTGCCA--TAG
1 AATTTGCACCGAAGTGCCACGTAG
67242 AATT
1 AATT
67246 GCATCGTAGT
Statistics
Matches: 40, Mismatches: 4, Indels: 12
0.71 0.07 0.21
Matches are distributed among these distances:
21 5 0.12
22 1 0.03
23 11 0.28
24 22 0.55
25 1 0.03
ACGTcount: A:0.30, C:0.21, G:0.25, T:0.25
Consensus pattern (24 bp):
AATTTGCACCGAAGTGCCACGTAG
Found at i:67244 original size:21 final size:21
Alignment explanation
Indices: 67218--67257 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
67208 AAGGACCGCG
*
67218 TAGAATTGTATCGAAGTGCCA
1 TAGAATTGCATCGAAGTGCCA
*
67239 TAGAATTGCATCGTAGTGC
1 TAGAATTGCATCGAAGTGC
67258 AATATAATAT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.30, C:0.15, G:0.25, T:0.30
Consensus pattern (21 bp):
TAGAATTGCATCGAAGTGCCA
Found at i:67629 original size:25 final size:25
Alignment explanation
Indices: 67600--67658 Score: 64
Period size: 25 Copynumber: 2.3 Consensus size: 25
67590 AATTCATATG
** *
67600 ATATGAATTCTGGTCATGTATCATA
1 ATATGAATTCTCATCATGTATCAAA
* *
67625 ATATGAAATGTCATCATGTATCAAA
1 ATATGAATTCTCATCATGTATCAAA
67650 ATATTGAAT
1 ATA-TGAAT
67659 CTAGACTTAT
Statistics
Matches: 27, Mismatches: 6, Indels: 1
0.79 0.18 0.03
Matches are distributed among these distances:
25 23 0.85
26 4 0.15
ACGTcount: A:0.39, C:0.10, G:0.14, T:0.37
Consensus pattern (25 bp):
ATATGAATTCTCATCATGTATCAAA
Found at i:68793 original size:11 final size:11
Alignment explanation
Indices: 68777--68803 Score: 54
Period size: 11 Copynumber: 2.5 Consensus size: 11
68767 CCGTTAAATA
68777 ATATATATTAT
1 ATATATATTAT
68788 ATATATATTAT
1 ATATATATTAT
68799 ATATA
1 ATATA
68804 ATCTATGAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 16 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (11 bp):
ATATATATTAT
Found at i:69618 original size:21 final size:23
Alignment explanation
Indices: 69578--69619 Score: 61
Period size: 21 Copynumber: 1.9 Consensus size: 23
69568 ATTTTTGTAG
69578 AAAAATCATCCCCAAACGGCTCC
1 AAAAATCATCCCCAAACGGCTCC
*
69601 AAAAA-CATTCCC-AACGGCT
1 AAAAATCATCCCCAAACGGCT
69620 ATATCGACTT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 7 0.39
22 6 0.33
23 5 0.28
ACGTcount: A:0.40, C:0.36, G:0.10, T:0.14
Consensus pattern (23 bp):
AAAAATCATCCCCAAACGGCTCC
Done.