Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01001000.1 Hibiscus syriacus cultivar Beakdansim tig00002000_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: 72292
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.34
Found at i:10799 original size:21 final size:21
Alignment explanation
Indices: 10757--10808 Score: 52
Period size: 21 Copynumber: 2.5 Consensus size: 21
10747 ACTCCGGGAG
* * *
10757 CTAGTTCCTCACGAGCTGCTC
1 CTAGCTCCTCTCGAGCTCCTC
*
10778 CTAGCTCCTCTCGTGCTCCTC
1 CTAGCTCCTCTCGAGCTCCTC
*
10799 CT-CCTCCTCT
1 CTAGCTCCTCT
10809 TCCGGCTCCA
Statistics
Matches: 26, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
20 7 0.27
21 19 0.73
ACGTcount: A:0.08, C:0.46, G:0.13, T:0.33
Consensus pattern (21 bp):
CTAGCTCCTCTCGAGCTCCTC
Found at i:12067 original size:65 final size:64
Alignment explanation
Indices: 11937--12096 Score: 196
Period size: 65 Copynumber: 2.5 Consensus size: 64
11927 AATTAAATTG
* * *
11937 AACATCGAATGCATTTCATGCATCGATGCACATACCATGCACCGATGCACTAAGGATTTTATGAA
1 AACATCGAATGCATTTGATGCATCGATGCACAAACCATGCACCGATACACTAAGGATTTTATG-A
* * ** *
12002 AACATCAAATGCATTTGATGCATCGATGCACAAACCATGCATCGATACACTCTGGCTATTT-TGA
1 AACATCGAATGCATTTGATGCATCGATGCACAAACCATGCACCGATACACTAAGGAT-TTTATGA
* * *
12066 AACATTGAATGCACTTGATGCATTGATGCAC
1 AACATCGAATGCATTTGATGCATCGATGCAC
12097 TCTTAGTGCA
Statistics
Matches: 82, Mismatches: 12, Indels: 3
0.85 0.12 0.03
Matches are distributed among these distances:
64 28 0.34
65 51 0.62
66 3 0.04
ACGTcount: A:0.33, C:0.23, G:0.17, T:0.28
Consensus pattern (64 bp):
AACATCGAATGCATTTGATGCATCGATGCACAAACCATGCACCGATACACTAAGGATTTTATGA
Found at i:14132 original size:12 final size:12
Alignment explanation
Indices: 14117--14144 Score: 56
Period size: 12 Copynumber: 2.3 Consensus size: 12
14107 CGGTTTTGAG
14117 ATTGTGTTTGGT
1 ATTGTGTTTGGT
14129 ATTGTGTTTGGT
1 ATTGTGTTTGGT
14141 ATTG
1 ATTG
14145 GAAATGTGGT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 16 1.00
ACGTcount: A:0.11, C:0.00, G:0.32, T:0.57
Consensus pattern (12 bp):
ATTGTGTTTGGT
Found at i:14745 original size:394 final size:397
Alignment explanation
Indices: 14005--14797 Score: 1394
Period size: 394 Copynumber: 2.0 Consensus size: 397
13995 CTGACTAGTA
*
14005 CTCACAATTTTTTCTGTTGGCTCATCATCGTTTAACTGGTCAATACAAAAATAAGAATTTGGTGC
1 CTCACAATTTTTTCTGTTGGCTCATCATCGTTTAACTGGTCAATACAAAAACAAGAATTTGGTGC
14070 TGAAAGTTGATTGGGATTTGGATTAGGGAAAGATTGTCGGTTTTGAGATTGTGTTTGGTATTGTG
66 TGAAAGTTGATTGGGATTTGGATTAGGGAAAGATTGTCGGTTTT-AGA-------T-GTATTGTG
*
14135 TTTGGTATTGGAAATGTGGTGAAACAAAATTTTCTTGGTGATGAAATTGTGCTGGAACCATTAAA
122 TTTGGTATTGGAAATGTGGTGAAACAAAATTTTCTTGGTGATGAAATTGTGCTGGAACCACTAAA
14200 TTTTGAGGTTGATAACAACGTTGTAAATTGTGAGCACCATAAACTGGGGTTGAAGAACTTAGTTA
187 TTTTGAGGTTGATAACAACGTTGTAAATTGTGAGCACCATAAACTGGGGTTGAAGAACTTAGTTA
14265 ATTACTACCCGCTACTGACCCAACTTCACTACTTCTAGGTTCAACAACATACAATTTAACATCAT
252 ATTACTACCCGCTACTGACCCAACTTCACTACTTCTAGGTTCAACAACATACAATTTAACATCAT
14330 CTTGCGAAACACTAATGTAAGCAATGAATAGTTCAACATCTTCATTGTCGGTTAACAAATAAACT
317 CTTGCGAAACACTAATGTAAGCAATGAATAGTTCAACATCTTCATTGTCGGTTAACAAATAAACT
14395 TTACCTTTTCTGTTGG
382 TTACCTTTTCTGTTGG
* * * *
14411 CTCACAATTTTTTTTGTTGGCTCATCATCGTTTAATTGGTCAATACGAAAACATGAATTTGGTGC
1 CTCACAATTTTTTCTGTTGGCTCATCATCGTTTAACTGGTCAATACAAAAACAAGAATTTGGTGC
*
14476 TGAAAGTTGATTGGGATTTGGATTAGGGAAAGGTTGTCGGTTTT-GA-G-ATTGTGTTTGGTATT
66 TGAAAGTTGATTGGGATTTGGATTAGGGAAAGATTGTCGGTTTTAGATGTATTGTGTTTGGTATT
14538 GGAAATGTGGTGAAACAAAATTTTCTTGGTGATGAAATTGTGCTGGAACCACTAAATTTTGAGGT
131 GGAAATGTGGTGAAACAAAATTTTCTTGGTGATGAAATTGTGCTGGAACCACTAAATTTTGAGGT
* *
14603 TGATAACAATGTTGTAAATTGTGAGCACCATAAACTGGGGTTGAAGCACTTAGTTAATTACTACC
196 TGATAACAACGTTGTAAATTGTGAGCACCATAAACTGGGGTTGAAGAACTTAGTTAATTACTACC
*
14668 CGCTACTGACCCAACTTCACTACTTTTAGGTTCAACAACATACAATTTAACATCATCTTGCGAAA
261 CGCTACTGACCCAACTTCACTACTTCTAGGTTCAACAACATACAATTTAACATCATCTTGCGAAA
14733 CACTAATGTAAGCAATGAATAGTTCAACATCTTCATTGTCGGTTAACAAATAAACTTTACCTTTT
326 CACTAATGTAAGCAATGAATAGTTCAACATCTTCATTGTCGGTTAACAAATAAACTTTACCTTTT
14798 ATCTGATAAG
Statistics
Matches: 377, Mismatches: 10, Indels: 12
0.94 0.03 0.03
Matches are distributed among these distances:
394 271 0.72
395 1 0.00
404 2 0.01
406 103 0.27
ACGTcount: A:0.30, C:0.15, G:0.20, T:0.35
Consensus pattern (397 bp):
CTCACAATTTTTTCTGTTGGCTCATCATCGTTTAACTGGTCAATACAAAAACAAGAATTTGGTGC
TGAAAGTTGATTGGGATTTGGATTAGGGAAAGATTGTCGGTTTTAGATGTATTGTGTTTGGTATT
GGAAATGTGGTGAAACAAAATTTTCTTGGTGATGAAATTGTGCTGGAACCACTAAATTTTGAGGT
TGATAACAACGTTGTAAATTGTGAGCACCATAAACTGGGGTTGAAGAACTTAGTTAATTACTACC
CGCTACTGACCCAACTTCACTACTTCTAGGTTCAACAACATACAATTTAACATCATCTTGCGAAA
CACTAATGTAAGCAATGAATAGTTCAACATCTTCATTGTCGGTTAACAAATAAACTTTACCTTTT
CTGTTGG
Found at i:15166 original size:14 final size:15
Alignment explanation
Indices: 15130--15167 Score: 51
Period size: 16 Copynumber: 2.5 Consensus size: 15
15120 GATATCATTG
15130 AAAAATTATATAGAA
1 AAAAATTATATAGAA
*
15145 ATAAAATTATGTA-AA
1 A-AAAATTATATAGAA
15160 AAAAATTA
1 AAAAATTA
15168 GAGATGGGGA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
14 7 0.33
15 4 0.19
16 10 0.48
ACGTcount: A:0.66, C:0.00, G:0.05, T:0.29
Consensus pattern (15 bp):
AAAAATTATATAGAA
Found at i:15204 original size:22 final size:22
Alignment explanation
Indices: 15175--15227 Score: 90
Period size: 22 Copynumber: 2.5 Consensus size: 22
15165 TTAGAGATGG
*
15175 GGAA-GGATGCCGTTGGATATT
1 GGAACGGATGACGTTGGATATT
15196 GGAACGGATGACGTTGGATATT
1 GGAACGGATGACGTTGGATATT
15218 GGAACGGATG
1 GGAACGGATG
15228 TCACCGGAGA
Statistics
Matches: 30, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
21 4 0.13
22 26 0.87
ACGTcount: A:0.26, C:0.09, G:0.40, T:0.25
Consensus pattern (22 bp):
GGAACGGATGACGTTGGATATT
Found at i:15371 original size:20 final size:19
Alignment explanation
Indices: 15327--15435 Score: 80
Period size: 20 Copynumber: 5.6 Consensus size: 19
15317 CAAAACATTT
* *
15327 GTGTTGCGAAAATAAAAGC
1 GTGTTGCGAAATTAAAATC
15346 -TGTTGCGAAATTAAAATTC
1 GTGTTGCGAAATTAAAA-TC
15365 GTGTTGCG-AATTCGAAAATC
1 GTGTTGCGAAATT--AAAATC
* **
15385 GAGTTGCGAAAACAAAATTC
1 GTGTTGCGAAATTAAAA-TC
*
15405 GTGTTGCG-ATTTAGAAAATC
1 GTGTTGCGAAATT--AAAATC
*
15425 TTGTTGCGAAA
1 GTGTTGCGAAA
15436 AGAAACTTGT
Statistics
Matches: 70, Mismatches: 11, Indels: 16
0.72 0.11 0.16
Matches are distributed among these distances:
18 15 0.21
19 10 0.14
20 34 0.49
21 11 0.16
ACGTcount: A:0.36, C:0.12, G:0.23, T:0.29
Consensus pattern (19 bp):
GTGTTGCGAAATTAAAATC
Found at i:15402 original size:40 final size:40
Alignment explanation
Indices: 15347--15436 Score: 126
Period size: 40 Copynumber: 2.2 Consensus size: 40
15337 AATAAAAGCT
** *
15347 GTTGCGAAATTAAAATTCGTGTTGCGAATTCGAAAATCGA
1 GTTGCGAAAACAAAATTCGTGTTGCGAATTAGAAAATCGA
* **
15387 GTTGCGAAAACAAAATTCGTGTTGCGATTTAGAAAATCTT
1 GTTGCGAAAACAAAATTCGTGTTGCGAATTAGAAAATCGA
15427 GTTGCGAAAA
1 GTTGCGAAAA
15437 GAAACTTGTG
Statistics
Matches: 44, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
40 44 1.00
ACGTcount: A:0.36, C:0.12, G:0.22, T:0.30
Consensus pattern (40 bp):
GTTGCGAAAACAAAATTCGTGTTGCGAATTAGAAAATCGA
Found at i:15517 original size:21 final size:20
Alignment explanation
Indices: 15458--15558 Score: 77
Period size: 20 Copynumber: 5.0 Consensus size: 20
15448 TATGAAAAAT
15458 AAATTCGCGTTGCGAATTTG
1 AAATTCGCGTTGCGAATTTG
15478 AAATTC-CATGTTGCG-ATTT-
1 AAATTCGC--GTTGCGAATTTG
15497 ACATATTCGCGTTGCGAATTTG
1 A-A-ATTCGCGTTGCGAATTTG
* * * *
15519 GAA-CCTGTGTTGCGAAATTG
1 AAATTC-GCGTTGCGAATTTG
15539 AAGA-TCGCGTTGCGAATTTG
1 AA-ATTCGCGTTGCGAATTTG
15559 TTGGTCATTT
Statistics
Matches: 64, Mismatches: 8, Indels: 18
0.71 0.09 0.20
Matches are distributed among these distances:
19 3 0.05
20 43 0.67
21 17 0.27
22 1 0.02
ACGTcount: A:0.25, C:0.16, G:0.25, T:0.35
Consensus pattern (20 bp):
AAATTCGCGTTGCGAATTTG
Found at i:19521 original size:42 final size:42
Alignment explanation
Indices: 19474--19568 Score: 165
Period size: 42 Copynumber: 2.3 Consensus size: 42
19464 TTCCCCGAAA
19474 TCTCGTGTTTGTTTCACGTAATTC-TTTTTTCGGAAAATGTTT
1 TCTCGTGTTTGTTTCACGTAATTCGTTTTTT-GGAAAATGTTT
19516 TCTCGTGTTTGTTTCACGTAATTCGTTTTTTGGAAAATGTTT
1 TCTCGTGTTTGTTTCACGTAATTCGTTTTTTGGAAAATGTTT
*
19558 TCTAGTGTTTG
1 TCTCGTGTTTG
19569 GTTGGAGGAA
Statistics
Matches: 51, Mismatches: 1, Indels: 2
0.94 0.02 0.04
Matches are distributed among these distances:
42 45 0.88
43 6 0.12
ACGTcount: A:0.16, C:0.13, G:0.19, T:0.53
Consensus pattern (42 bp):
TCTCGTGTTTGTTTCACGTAATTCGTTTTTTGGAAAATGTTT
Found at i:19827 original size:22 final size:23
Alignment explanation
Indices: 19766--19843 Score: 72
Period size: 22 Copynumber: 3.4 Consensus size: 23
19756 ATTTTAATCA
*
19766 AATATTAATATTAAAATATT-TAA-
1 AATA-TAATATTAATAT-TTCTAAT
*
19789 AATATATTTATTAATATTTCTAAT
1 AATATA-ATATTAATATTTCTAAT
*
19813 AATATAATATT-ATATTTTTAAT
1 AATATAATATTAATATTTCTAAT
*
19835 ATTATAATA
1 AATATAATA
19844 AAATAATCAA
Statistics
Matches: 47, Mismatches: 5, Indels: 7
0.80 0.08 0.12
Matches are distributed among these distances:
22 22 0.47
23 19 0.40
24 6 0.13
ACGTcount: A:0.49, C:0.01, G:0.00, T:0.50
Consensus pattern (23 bp):
AATATAATATTAATATTTCTAAT
Found at i:19857 original size:32 final size:32
Alignment explanation
Indices: 19791--19870 Score: 92
Period size: 32 Copynumber: 2.5 Consensus size: 32
19781 ATATTTAAAA
* *
19791 TATATTTATTAATATTTCTAATAATATAATAT
1 TATATTTATTAATATTTATAATAAAATAATAT
19823 TATATTT-TTAATA-TTATAATAAAATAATCAAT
1 TATATTTATTAATATTTATAATAAAATAAT--AT
*
19855 TATATTATAATAATAT
1 TATATT-TATTAATAT
19871 AAGATATTAT
Statistics
Matches: 40, Mismatches: 3, Indels: 7
0.80 0.06 0.14
Matches are distributed among these distances:
30 13 0.32
31 6 0.15
32 15 0.38
33 1 0.03
34 5 0.12
ACGTcount: A:0.47, C:0.03, G:0.00, T:0.50
Consensus pattern (32 bp):
TATATTTATTAATATTTATAATAAAATAATAT
Found at i:19862 original size:23 final size:23
Alignment explanation
Indices: 19833--19885 Score: 72
Period size: 23 Copynumber: 2.3 Consensus size: 23
19823 TATATTTTTA
19833 ATATTATAATAAAATAATCA-ATT
1 ATATTATAATAAAATAA-CATATT
* *
19856 ATATTATAATAATATAAGATATT
1 ATATTATAATAAAATAACATATT
19879 ATATTAT
1 ATATTAT
19886 TATTTTAATA
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
22 1 0.04
23 26 0.96
ACGTcount: A:0.53, C:0.02, G:0.02, T:0.43
Consensus pattern (23 bp):
ATATTATAATAAAATAACATATT
Found at i:19932 original size:21 final size:20
Alignment explanation
Indices: 19877--19936 Score: 57
Period size: 21 Copynumber: 2.9 Consensus size: 20
19867 ATATAAGATA
*
19877 TTATATTATTATTTTAATAAT
1 TTATATTATT-TATTAATAAT
* * *
19898 ATATAATAAATTATTAATAAAT
1 TTAT-ATTATTTATTAAT-AAT
19920 TTATATTATTTATTAAT
1 TTATATTATTTATTAAT
19937 TTCATAGAAA
Statistics
Matches: 30, Mismatches: 7, Indels: 4
0.73 0.17 0.10
Matches are distributed among these distances:
21 20 0.67
22 10 0.33
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (20 bp):
TTATATTATTTATTAATAAT
Found at i:20048 original size:23 final size:23
Alignment explanation
Indices: 20022--20066 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
20012 AATAATATTT
20022 TAATAAAGATATTTAAAATATAC
1 TAATAAAGATATTTAAAATATAC
* * *
20045 TAATTAATATTTTTAAAATATA
1 TAATAAAGATATTTAAAATATA
20067 ATATAACATT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.53, C:0.02, G:0.02, T:0.42
Consensus pattern (23 bp):
TAATAAAGATATTTAAAATATAC
Found at i:20440 original size:14 final size:14
Alignment explanation
Indices: 20421--20479 Score: 55
Period size: 14 Copynumber: 4.1 Consensus size: 14
20411 CCAGAAATGT
*
20421 AATTCATTTTCCAG
1 AATTCAATTTCCAG
* *
20435 AATTCAAATTCGAG
1 AATTCAATTTCCAG
* * *
20449 TAATTCATTTTTCAA
1 -AATTCAATTTCCAG
20464 AATTCAATTTCCAG
1 AATTCAATTTCCAG
20478 AA
1 AA
20480 AACCAGTTAC
Statistics
Matches: 33, Mismatches: 11, Indels: 2
0.72 0.24 0.04
Matches are distributed among these distances:
14 24 0.73
15 9 0.27
ACGTcount: A:0.37, C:0.17, G:0.07, T:0.39
Consensus pattern (14 bp):
AATTCAATTTCCAG
Found at i:20444 original size:20 final size:20
Alignment explanation
Indices: 20405--20445 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
20395 TTCCGGGAAA
**
20405 CATTTTCCAGAAATGTAATT
1 CATTTTCCAGAAATCAAATT
*
20425 CATTTTCCAGAATTCAAATT
1 CATTTTCCAGAAATCAAATT
20445 C
1 C
20446 GAGTAATTCA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.34, C:0.20, G:0.07, T:0.39
Consensus pattern (20 bp):
CATTTTCCAGAAATCAAATT
Found at i:20591 original size:21 final size:20
Alignment explanation
Indices: 20551--20599 Score: 62
Period size: 21 Copynumber: 2.4 Consensus size: 20
20541 TTACCCTAGC
**
20551 AAAAGGATCAATCCTTTTGA
1 AAAAGGATCAATCCCCTTGA
*
20571 CCAAAGGATCAATCCCCTTGA
1 -AAAAGGATCAATCCCCTTGA
20592 AAAAGGAT
1 AAAAGGAT
20600 TGATCCCTTA
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
20 7 0.29
21 17 0.71
ACGTcount: A:0.41, C:0.20, G:0.16, T:0.22
Consensus pattern (20 bp):
AAAAGGATCAATCCCCTTGA
Found at i:23556 original size:19 final size:20
Alignment explanation
Indices: 23517--23566 Score: 75
Period size: 19 Copynumber: 2.5 Consensus size: 20
23507 GCCTGAGTGT
*
23517 ATCGATGCATAGTCTTGTGC
1 ATCGATGCATAGTCATGTGC
*
23537 ATCGATGCATGGT-ATGTGC
1 ATCGATGCATAGTCATGTGC
23556 ATCGATGCATA
1 ATCGATGCATA
23567 AAATGCATTC
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
19 15 0.56
20 12 0.44
ACGTcount: A:0.24, C:0.18, G:0.26, T:0.32
Consensus pattern (20 bp):
ATCGATGCATAGTCATGTGC
Found at i:23605 original size:84 final size:84
Alignment explanation
Indices: 23468--23630 Score: 224
Period size: 84 Copynumber: 1.9 Consensus size: 84
23458 TGCACTAAGA
* *
23468 GTGCATCGATGCATAAAATGCATTCGATGTTTTGAAAAAGCCTGAGTGTATCGATGCATAG-TCT
1 GTGCATCGATGCATAAAATGCATTCGATGTTTTGAAAAAACCTGAGTGCATCGATGCATAGAT-T
23532 TGTGCATCGATGCATGGTAT
65 TGTGCATCGATGCATGGTAT
** *
23552 GTGCATCGATGCATAAAATGCATTCGATG-TTTGAAAAATTATTTG-GTGCATCGATGCATGGAT
1 GTGCATCGATGCATAAAATGCATTCGATGTTTTGAAAAA--ACCTGAGTGCATCGATGCATAGAT
*
23615 TTGTGCATCGGTGCAT
64 TTGTGCATCGATGCAT
23631 CACTTTGAAA
Statistics
Matches: 70, Mismatches: 6, Indels: 6
0.85 0.07 0.07
Matches are distributed among these distances:
83 9 0.13
84 58 0.83
85 3 0.04
ACGTcount: A:0.27, C:0.15, G:0.25, T:0.33
Consensus pattern (84 bp):
GTGCATCGATGCATAAAATGCATTCGATGTTTTGAAAAAACCTGAGTGCATCGATGCATAGATTT
GTGCATCGATGCATGGTAT
Found at i:23622 original size:20 final size:21
Alignment explanation
Indices: 23592--23630 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 21
23582 TTGAAAAATT
23592 ATTTGGTGCATCGATGCATGG
1 ATTTGGTGCATCGATGCATGG
*
23613 ATTT-GTGCATCGGTGCAT
1 ATTTGGTGCATCGATGCAT
23631 CACTTTGAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 13 0.76
21 4 0.24
ACGTcount: A:0.18, C:0.15, G:0.31, T:0.36
Consensus pattern (21 bp):
ATTTGGTGCATCGATGCATGG
Found at i:24345 original size:20 final size:20
Alignment explanation
Indices: 24316--24373 Score: 89
Period size: 20 Copynumber: 2.9 Consensus size: 20
24306 TTTCAAAGTG
* * *
24316 ATGCACCGATGCATCAATCT
1 ATGCATCGATGCACCAATCC
24336 ATGCATCGATGCACCAATCC
1 ATGCATCGATGCACCAATCC
24356 ATGCATCGATGCACCAAT
1 ATGCATCGATGCACCAAT
24374 TAATTTTTCA
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 35 1.00
ACGTcount: A:0.31, C:0.31, G:0.16, T:0.22
Consensus pattern (20 bp):
ATGCATCGATGCACCAATCC
Found at i:24442 original size:45 final size:46
Alignment explanation
Indices: 24393--24483 Score: 139
Period size: 45 Copynumber: 2.0 Consensus size: 46
24383 AAACATCGAA
* * *
24393 TGCATTTTATGCATCGATGCAC-ATACCATGCATCGATGCACTCAG
1 TGCATTTGATGCATCGATGCACAAGACCATGCAACGATGCACTCAG
*
24438 TGCATTTGATGCATCGATGCACAAGACTATGCAACGATGCACTCAG
1 TGCATTTGATGCATCGATGCACAAGACCATGCAACGATGCACTCAG
24484 GCTTTTTCAA
Statistics
Matches: 41, Mismatches: 4, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
45 21 0.51
46 20 0.49
ACGTcount: A:0.29, C:0.25, G:0.20, T:0.26
Consensus pattern (46 bp):
TGCATTTGATGCATCGATGCACAAGACCATGCAACGATGCACTCAG
Found at i:29256 original size:11 final size:11
Alignment explanation
Indices: 29240--29302 Score: 51
Period size: 11 Copynumber: 5.9 Consensus size: 11
29230 AAAATTACAT
29240 TATTAAAAATA
1 TATTAAAAATA
29251 TATTAAAAATA
1 TATTAAAAATA
* * ***
29262 CACTATTGATA
1 TATTAAAAATA
29273 -ATTATAAAAT-
1 TATTA-AAAATA
29283 T-TTAAAAATA
1 TATTAAAAATA
29293 TATTAAAAAT
1 TATTAAAAAT
29303 TCTATAATAC
Statistics
Matches: 39, Mismatches: 9, Indels: 8
0.70 0.16 0.14
Matches are distributed among these distances:
9 5 0.13
10 7 0.18
11 27 0.69
ACGTcount: A:0.57, C:0.03, G:0.02, T:0.38
Consensus pattern (11 bp):
TATTAAAAATA
Found at i:29594 original size:25 final size:24
Alignment explanation
Indices: 29566--29614 Score: 64
Period size: 25 Copynumber: 2.0 Consensus size: 24
29556 TTAATAAAAA
29566 AATAT-TTATCTAATGAAAAATATTT
1 AATATATT-TCTAATG-AAAATATTT
*
29591 AATATATTTCTAATGATAATATTT
1 AATATATTTCTAATGAAAATATTT
29615 TTAATTAACT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
24 8 0.36
25 12 0.55
26 2 0.09
ACGTcount: A:0.45, C:0.04, G:0.04, T:0.47
Consensus pattern (24 bp):
AATATATTTCTAATGAAAATATTT
Found at i:31502 original size:22 final size:22
Alignment explanation
Indices: 31477--31553 Score: 82
Period size: 22 Copynumber: 3.5 Consensus size: 22
31467 TCTTGGCTAA
* * *
31477 GATTTGAGCTTAATTTGAGCTT
1 GATTCGAGTTTAATTCGAGCTT
*
31499 GATTCGAGTTTGATTCGAGCTT
1 GATTCGAGTTTAATTCGAGCTT
*
31521 GATTCGAGTTTAAAATCGAGCTT
1 GATTCGAGTTT-AATTCGAGCTT
* *
31544 TAATCGAGTT
1 GATTCGAGTT
31554 CGAGTCTCGA
Statistics
Matches: 46, Mismatches: 8, Indels: 1
0.84 0.15 0.02
Matches are distributed among these distances:
22 29 0.63
23 17 0.37
ACGTcount: A:0.25, C:0.12, G:0.23, T:0.40
Consensus pattern (22 bp):
GATTCGAGTTTAATTCGAGCTT
Found at i:31511 original size:11 final size:11
Alignment explanation
Indices: 31497--31531 Score: 61
Period size: 11 Copynumber: 3.2 Consensus size: 11
31487 TAATTTGAGC
31497 TTGATTCGAGT
1 TTGATTCGAGT
*
31508 TTGATTCGAGC
1 TTGATTCGAGT
31519 TTGATTCGAGT
1 TTGATTCGAGT
31530 TT
1 TT
31532 AAAATCGAGC
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
11 22 1.00
ACGTcount: A:0.17, C:0.11, G:0.26, T:0.46
Consensus pattern (11 bp):
TTGATTCGAGT
Found at i:43046 original size:24 final size:24
Alignment explanation
Indices: 43019--43069 Score: 59
Period size: 24 Copynumber: 2.1 Consensus size: 24
43009 ATAAAGAACC
*
43019 AAAAA-AAAACTTAAATATACCATT
1 AAAAATAAAACTTAAACA-ACCATT
**
43043 AAAAATAAAGTTTAAACAACCATT
1 AAAAATAAAACTTAAACAACCATT
43067 AAA
1 AAA
43070 TCAACCACCA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
24 14 0.61
25 9 0.39
ACGTcount: A:0.63, C:0.12, G:0.02, T:0.24
Consensus pattern (24 bp):
AAAAATAAAACTTAAACAACCATT
Found at i:44620 original size:27 final size:27
Alignment explanation
Indices: 44582--44661 Score: 88
Period size: 27 Copynumber: 3.0 Consensus size: 27
44572 AATATCCATC
* * *
44582 ATTCAATTATTAATATCCATCATATTA
1 ATTCAAATATTAATATCAATCACATTA
*
44609 ATTCAAATATTAATATTAATCACATTA
1 ATTCAAATATTAATATCAATCACATTA
* * * *
44636 ATTCAACTATTGATATTATTCACATT
1 ATTCAAATATTAATATCAATCACATT
44662 TCTTTTTCTA
Statistics
Matches: 46, Mismatches: 7, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
27 46 1.00
ACGTcount: A:0.41, C:0.14, G:0.01, T:0.44
Consensus pattern (27 bp):
ATTCAAATATTAATATCAATCACATTA
Found at i:44751 original size:27 final size:27
Alignment explanation
Indices: 44719--44797 Score: 104
Period size: 27 Copynumber: 2.9 Consensus size: 27
44709 AAATATCCAA
*
44719 CATATTAATTCAATTATTGATATTAAT
1 CATATTAATTCAACTATTGATATTAAT
* *
44746 CGTATTAATTCAACTATTGATATTATT
1 CATATTAATTCAACTATTGATATTAAT
* * *
44773 CACATTCATTCAACTAATGATATTA
1 CATATTAATTCAACTATTGATATTA
44798 TCCATAATAT
Statistics
Matches: 45, Mismatches: 7, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
27 45 1.00
ACGTcount: A:0.38, C:0.13, G:0.05, T:0.44
Consensus pattern (27 bp):
CATATTAATTCAACTATTGATATTAAT
Found at i:46289 original size:46 final size:44
Alignment explanation
Indices: 46233--46326 Score: 109
Period size: 45 Copynumber: 2.1 Consensus size: 44
46223 TGCACTTACC
* *
46233 ATGCACCGATGCACTGAGG-ATTTTATGAAAACATCGAATGCATTTG
1 ATGCACCGATGCACTCAGGCA-TTT-TG-AAACATCGAATGCACTTG
* *
46279 ATGCATCGATGCACTCTGGCCATTTTGAAACATCGAATGCACTTG
1 ATGCACCGATGCACTCAGG-CATTTTGAAACATCGAATGCACTTG
46324 ATG
1 ATG
46327 TACTCTTAGT
Statistics
Matches: 42, Mismatches: 4, Indels: 5
0.82 0.08 0.10
Matches are distributed among these distances:
45 20 0.48
46 18 0.43
47 3 0.07
48 1 0.02
ACGTcount: A:0.30, C:0.20, G:0.21, T:0.29
Consensus pattern (44 bp):
ATGCACCGATGCACTCAGGCATTTTGAAACATCGAATGCACTTG
Found at i:46421 original size:21 final size:21
Alignment explanation
Indices: 46395--46442 Score: 87
Period size: 21 Copynumber: 2.3 Consensus size: 21
46385 TAATGCACCA
46395 ATGCACCATGGGTATACATCG
1 ATGCACCATGGGTATACATCG
*
46416 ATGCACCATGGGTATGCATCG
1 ATGCACCATGGGTATACATCG
46437 ATGCAC
1 ATGCAC
46443 TGACGCTCCC
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.27, C:0.25, G:0.25, T:0.23
Consensus pattern (21 bp):
ATGCACCATGGGTATACATCG
Found at i:49034 original size:38 final size:38
Alignment explanation
Indices: 48935--49048 Score: 142
Period size: 38 Copynumber: 3.0 Consensus size: 38
48925 TGCAACAACC
* *
48935 AACCACCAACCTACCCGGGA-TATTAATGGATAATTAAT
1 AACCACCAACCTA-CCTGAATTATTAATGGATAATTAAT
* * *
48973 AACCACCAACCTACCTGAGTTATTAAAGGATAATTATT
1 AACCACCAACCTACCTGAATTATTAATGGATAATTAAT
*
49011 AACCACCAACCTA-TTGATATTATTAATGGATAATTAAT
1 AACCACCAACCTACCTGA-ATTATTAATGGATAATTAAT
49049 GTTGCATTTA
Statistics
Matches: 65, Mismatches: 9, Indels: 4
0.83 0.12 0.05
Matches are distributed among these distances:
37 6 0.09
38 59 0.91
ACGTcount: A:0.40, C:0.20, G:0.11, T:0.29
Consensus pattern (38 bp):
AACCACCAACCTACCTGAATTATTAATGGATAATTAAT
Found at i:57747 original size:21 final size:22
Alignment explanation
Indices: 57721--57779 Score: 75
Period size: 24 Copynumber: 2.6 Consensus size: 22
57711 GGGAGCGTTA
57721 CAGATTCTTAGGCTG-ATTAGG
1 CAGATTCTTAGGCTGTATTAGG
*
57742 CAGATTCTTAGGTTGATTATTAGG
1 CAGATTCTTAGGCTG--TATTAGG
*
57766 TAGATTCTTAGGCT
1 CAGATTCTTAGGCT
57780 AATCACTTTT
Statistics
Matches: 32, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
21 14 0.44
24 18 0.56
ACGTcount: A:0.24, C:0.12, G:0.25, T:0.39
Consensus pattern (22 bp):
CAGATTCTTAGGCTGTATTAGG
Found at i:57752 original size:12 final size:12
Alignment explanation
Indices: 57721--57778 Score: 50
Period size: 12 Copynumber: 5.1 Consensus size: 12
57711 GGGAGCGTTA
57721 CAGATTCTTAGG
1 CAGATTCTTAGG
*
57733 CTGA---TTAGG
1 CAGATTCTTAGG
57742 CAGATTCTTAGG
1 CAGATTCTTAGG
** *
57754 TTGATTATTAGG
1 CAGATTCTTAGG
*
57766 TAGATTCTTAGG
1 CAGATTCTTAGG
57778 C
1 C
57779 TAATCACTTT
Statistics
Matches: 35, Mismatches: 8, Indels: 6
0.71 0.16 0.12
Matches are distributed among these distances:
9 8 0.23
12 27 0.77
ACGTcount: A:0.24, C:0.12, G:0.26, T:0.38
Consensus pattern (12 bp):
CAGATTCTTAGG
Found at i:66286 original size:24 final size:24
Alignment explanation
Indices: 66259--66305 Score: 58
Period size: 24 Copynumber: 2.0 Consensus size: 24
66249 ATTTGAATTC
66259 TGTTATGATACCTGACCTGGATTT
1 TGTTATGATACCTGACCTGGATTT
* ** *
66283 TGTTCTGATTTCTGATCTGGATT
1 TGTTATGATACCTGACCTGGATT
66306 ATATTCTGAT
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
24 19 1.00
ACGTcount: A:0.17, C:0.15, G:0.21, T:0.47
Consensus pattern (24 bp):
TGTTATGATACCTGACCTGGATTT
Found at i:66312 original size:24 final size:24
Alignment explanation
Indices: 66270--66315 Score: 65
Period size: 24 Copynumber: 1.9 Consensus size: 24
66260 GTTATGATAC
* *
66270 CTGACCTGGATTTTGTTCTGATTT
1 CTGACCTGGATTATATTCTGATTT
*
66294 CTGATCTGGATTATATTCTGAT
1 CTGACCTGGATTATATTCTGAT
66316 ATCTTATTTG
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 19 1.00
ACGTcount: A:0.17, C:0.15, G:0.20, T:0.48
Consensus pattern (24 bp):
CTGACCTGGATTATATTCTGATTT
Found at i:68986 original size:22 final size:24
Alignment explanation
Indices: 68947--68991 Score: 58
Period size: 22 Copynumber: 2.0 Consensus size: 24
68937 ATAAATATTT
*
68947 AAAATATATTTACTAATAATTTTC
1 AAAATATATATACTAATAATTTTC
*
68971 AAAATATA-ATAC-AATATTTTT
1 AAAATATATATACTAATAATTTT
68992 ATTTATTATT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
22 8 0.42
23 3 0.16
24 8 0.42
ACGTcount: A:0.49, C:0.07, G:0.00, T:0.44
Consensus pattern (24 bp):
AAAATATATATACTAATAATTTTC
Found at i:69014 original size:18 final size:19
Alignment explanation
Indices: 68991--69029 Score: 55
Period size: 18 Copynumber: 2.1 Consensus size: 19
68981 ACAATATTTT
68991 TATTTATTATT-ATAA-TAA
1 TATTTATT-TTAATAATTAA
69009 TATTTATTTTAATAATTAA
1 TATTTATTTTAATAATTAA
69028 TA
1 TA
69030 ATATAATATT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
17 2 0.11
18 12 0.63
19 5 0.26
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (19 bp):
TATTTATTTTAATAATTAA
Found at i:69064 original size:25 final size:23
Alignment explanation
Indices: 69003--69071 Score: 77
Period size: 25 Copynumber: 3.0 Consensus size: 23
68993 TTTATTATTA
69003 TAATAATA-TTTATTTTAATAAT
1 TAATAATATTTTATTTTAATAAT
** *
69025 TAATAATATAATATTCTTATATGAT
1 TAATAATATTTTATT-TTA-ATAAT
*
69050 TTATAATATTTTATTTTAATAA
1 TAATAATATTTTATTTTAATAA
69072 AATATAATAG
Statistics
Matches: 37, Mismatches: 7, Indels: 5
0.76 0.14 0.10
Matches are distributed among these distances:
22 8 0.22
23 7 0.19
24 6 0.16
25 16 0.43
ACGTcount: A:0.43, C:0.01, G:0.01, T:0.54
Consensus pattern (23 bp):
TAATAATATTTTATTTTAATAAT
Found at i:69079 original size:48 final size:51
Alignment explanation
Indices: 68971--69080 Score: 131
Period size: 48 Copynumber: 2.2 Consensus size: 51
68961 AATAATTTTC
* *
68971 AAAATATAATACAATATTTTTATTTATTATTATAATAATATTTATTTTAAT
1 AAAATATAATACAATATTCTTATTGATTATTATAATAATATTTATTTTAAT
* *
69022 -AATTAATAATATAATATTCTTATATGA-T-TTATAAT-AT-TTTATTTTAAT
1 AAAAT-ATAATACAATATTCTTAT-TGATTATTATAATAATATTTATTTTAAT
69070 AAAATATAATA
1 AAAATATAATA
69081 GTCTTAATAT
Statistics
Matches: 51, Mismatches: 5, Indels: 9
0.78 0.08 0.14
Matches are distributed among these distances:
48 17 0.33
49 5 0.10
50 10 0.20
51 17 0.33
52 2 0.04
ACGTcount: A:0.46, C:0.02, G:0.01, T:0.51
Consensus pattern (51 bp):
AAAATATAATACAATATTCTTATTGATTATTATAATAATATTTATTTTAAT
Found at i:69144 original size:15 final size:15
Alignment explanation
Indices: 69110--69152 Score: 54
Period size: 13 Copynumber: 2.9 Consensus size: 15
69100 TAAAATATGG
*
69110 AAATAATATTTA-AT
1 AAATAATATTGATAT
69124 -AATAATATTGATAT
1 AAATAATATTGATAT
69138 AAATAATATTAGATA
1 AAATAATATT-GATA
69153 AATTATTTTT
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
13 10 0.40
14 2 0.08
15 9 0.36
16 4 0.16
ACGTcount: A:0.56, C:0.00, G:0.05, T:0.40
Consensus pattern (15 bp):
AAATAATATTGATAT
Done.