Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007598.1 Hibiscus syriacus cultivar Beakdansim tig00021967_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: 152705
ACGTcount: A:0.36, C:0.14, G:0.14, T:0.36
Found at i:2807 original size:2 final size:2
Alignment explanation
Indices: 2800--2833 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
2790 CAGAAAACAA
2800 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
2834 TTCAAGAATT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:5732 original size:31 final size:29
Alignment explanation
Indices: 5692--5758 Score: 71
Period size: 29 Copynumber: 2.2 Consensus size: 29
5682 AATTCTTATA
* * *
5692 ATATGATATTATTCTTTAATATTATAATGAT
1 ATATAATATTATACTTT--TATTATAATAAT
* *
5723 ATATAATATTGTACTTTTATTTTAATAAT
1 ATATAATATTATACTTTTATTATAATAAT
5752 ATATAAT
1 ATATAAT
5759 GATTTTTCAA
Statistics
Matches: 31, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
29 17 0.55
31 14 0.45
ACGTcount: A:0.40, C:0.03, G:0.04, T:0.52
Consensus pattern (29 bp):
ATATAATATTATACTTTTATTATAATAAT
Found at i:18161 original size:11 final size:11
Alignment explanation
Indices: 18145--18172 Score: 56
Period size: 11 Copynumber: 2.5 Consensus size: 11
18135 TTATTATACT
18145 ATTTTATTAAA
1 ATTTTATTAAA
18156 ATTTTATTAAA
1 ATTTTATTAAA
18167 ATTTTA
1 ATTTTA
18173 ATTATTAAAT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 17 1.00
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (11 bp):
ATTTTATTAAA
Found at i:21068 original size:11 final size:11
Alignment explanation
Indices: 21052--21079 Score: 56
Period size: 11 Copynumber: 2.5 Consensus size: 11
21042 TTATTATACT
21052 ATTTTATTAAA
1 ATTTTATTAAA
21063 ATTTTATTAAA
1 ATTTTATTAAA
21074 ATTTTA
1 ATTTTA
21080 ATTATTAAAT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 17 1.00
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (11 bp):
ATTTTATTAAA
Found at i:36874 original size:24 final size:24
Alignment explanation
Indices: 36847--36893 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 24
36837 ATTTTTCAAT
36847 AAAAATATATTATTCA-TAAATTAC
1 AAAAATATATTATT-ATTAAATTAC
* *
36871 AAAACTTTATTATTATTAAATTA
1 AAAAATATATTATTATTAAATTA
36894 TTTAATATTT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
23 1 0.05
24 19 0.95
ACGTcount: A:0.51, C:0.06, G:0.00, T:0.43
Consensus pattern (24 bp):
AAAAATATATTATTATTAAATTAC
Found at i:38140 original size:2 final size:2
Alignment explanation
Indices: 38133--38168 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
38123 TTTCTTGGAA
38133 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
38169 TAGAATGCTG
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:42023 original size:24 final size:24
Alignment explanation
Indices: 41996--42043 Score: 62
Period size: 24 Copynumber: 2.0 Consensus size: 24
41986 CGAATTTTCA
41996 ATAAAAATAATATTCA-TAAATTAT
1 ATAAAAATAATATT-ATTAAATTAT
* *
42020 ATAAAATTATTATTATTAAATTAT
1 ATAAAAATAATATTATTAAATTAT
42044 TTAATATTTA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
23 1 0.05
24 20 0.95
ACGTcount: A:0.54, C:0.02, G:0.00, T:0.44
Consensus pattern (24 bp):
ATAAAAATAATATTATTAAATTAT
Found at i:44683 original size:18 final size:18
Alignment explanation
Indices: 44660--44695 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
44650 TTGAGGACTT
*
44660 TTATATTATTTATAAAAA
1 TTATATTATTTAGAAAAA
*
44678 TTATATTTTTTAGAAAAA
1 TTATATTATTTAGAAAAA
44696 AATAATATAT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (18 bp):
TTATATTATTTAGAAAAA
Found at i:44705 original size:2 final size:2
Alignment explanation
Indices: 44700--44735 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
44690 GAAAAAAATA
44700 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
44736 CAAGAATTAA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:45580 original size:24 final size:24
Alignment explanation
Indices: 45551--45616 Score: 80
Period size: 24 Copynumber: 2.8 Consensus size: 24
45541 GAGATATCAG
*
45551 AAATCAAAACAGAATTCAGA-AAA
1 AAATCAGAACAGAATTCAGATAAA
* * *
45574 AATATCAGAACAGAATCCAGATCAG
1 AA-ATCAGAACAGAATTCAGATAAA
45599 AAATCAGAACAGAATTCA
1 AAATCAGAACAGAATTCA
45617 AGTCATGTAT
Statistics
Matches: 36, Mismatches: 5, Indels: 3
0.82 0.11 0.07
Matches are distributed among these distances:
23 2 0.06
24 31 0.86
25 3 0.08
ACGTcount: A:0.56, C:0.17, G:0.12, T:0.15
Consensus pattern (24 bp):
AAATCAGAACAGAATTCAGATAAA
Found at i:45594 original size:12 final size:11
Alignment explanation
Indices: 45552--45613 Score: 52
Period size: 12 Copynumber: 5.3 Consensus size: 11
45542 AGATATCAGA
*
45552 AATCAAAACAG
1 AATCAGAACAG
* *
45563 AATTCAGAAAAA
1 AA-TCAGAACAG
45575 ATATCAGAACAG
1 A-ATCAGAACAG
*
45587 AATCCAGATCAG
1 AAT-CAGAACAG
45599 AAATCAGAACAG
1 -AATCAGAACAG
45611 AAT
1 AAT
45614 TCAAGTCATG
Statistics
Matches: 40, Mismatches: 7, Indels: 8
0.73 0.13 0.15
Matches are distributed among these distances:
11 7 0.17
12 29 0.73
13 4 0.10
ACGTcount: A:0.56, C:0.16, G:0.13, T:0.15
Consensus pattern (11 bp):
AATCAGAACAG
Found at i:45628 original size:24 final size:24
Alignment explanation
Indices: 45575--45654 Score: 83
Period size: 24 Copynumber: 3.3 Consensus size: 24
45565 TTCAGAAAAA
*
45575 ATATCAGAACAGAA-TCCAGATCAG
1 ATATCAGAACAGAATTCAAG-TCAG
*
45599 AAATCAGAACAGAATTCAAGTCATG
1 ATATCAGAACAGAATTCAAGTCA-G
* *
45624 -TATCATAACAAAATTCAAGTCAG
1 ATATCAGAACAGAATTCAAGTCAG
*
45647 AAATCAGA
1 ATATCAGA
45655 TAAAATATTT
Statistics
Matches: 46, Mismatches: 7, Indels: 6
0.78 0.12 0.10
Matches are distributed among these distances:
23 1 0.02
24 40 0.87
25 5 0.11
ACGTcount: A:0.49, C:0.17, G:0.14, T:0.20
Consensus pattern (24 bp):
ATATCAGAACAGAATTCAAGTCAG
Found at i:49942 original size:59 final size:58
Alignment explanation
Indices: 49879--50138 Score: 199
Period size: 58 Copynumber: 4.4 Consensus size: 58
49869 ATACCATTAG
** * *
49879 TATGATTTTGTTACCATTTTAGCACATAATATGCCCTATCTGGAAATCCATATTTTAAA
1 TATGATTTCCTTACCA-TTTAGCACATAATATGCCCTATCTGGAAATCCATAATTTCAA
* * * * ** * * *
49938 TATGATTTCTTTATCATTTAGCGCCCT--TAGTGCTTTATCTGGAAACCCATACA-CTCAG
1 TATGATTTCCTTACCATTTAGC-ACATAATA-TGCCCTATCTGGAAATCCATA-ATTTCAA
* *
49996 TATGATTCCCTTACCATTTTAGCACATAATATTCCCTATCTGGAAATCCATAATTTCAA
1 TATGATTTCCTTACCA-TTTAGCACATAATATGCCCTATCTGGAAATCCATAATTTCAA
* * * * * *
50055 TATGATTTCCTTATCATTTAGCACACTCA-GTGCTCC-ATATGGAAATCCATACACTT-AG
1 TATGATTTCCTTACCATTTAGCACA-TAATATGC-CCTATCTGGAAATCCATA-ATTTCAA
*
50113 TATGATTTCCTTATCATTATAGCACA
1 TATGATTTCCTTACCATT-TAGCACA
50139 CAAAGTGCCA
Statistics
Matches: 159, Mismatches: 31, Indels: 22
0.75 0.15 0.10
Matches are distributed among these distances:
57 2 0.01
58 86 0.54
59 69 0.43
60 2 0.01
ACGTcount: A:0.30, C:0.22, G:0.10, T:0.38
Consensus pattern (58 bp):
TATGATTTCCTTACCATTTAGCACATAATATGCCCTATCTGGAAATCCATAATTTCAA
Found at i:49998 original size:117 final size:117
Alignment explanation
Indices: 49877--50138 Score: 371
Period size: 117 Copynumber: 2.2 Consensus size: 117
49867 CCATACCATT
** *
49877 AGTATGATTTTGTTACCATTTTAGCACATAATATGCCCTATCTGGAAATCCATATTTTAAATATG
1 AGTATGATTTCCTTACCATTTTAGCACATAATATGCCCTATCTGGAAATCCATAATTTAAATATG
* * * * ** *
49942 ATTTCTTTATCATTTAGCGCCCTTAGTGCTTTATCTGGAAACCCATACACTC
66 ATTTCCTTATCATTTAGCACACTCAGTGCTCCATATGGAAACCCATACACTC
* * *
49994 AGTATGATTCCCTTACCATTTTAGCACATAATATTCCCTATCTGGAAATCCATAATTTCAATATG
1 AGTATGATTTCCTTACCATTTTAGCACATAATATGCCCTATCTGGAAATCCATAATTTAAATATG
* *
50059 ATTTCCTTATCATTTAGCACACTCAGTGCTCCATATGGAAATCCATACACTT
66 ATTTCCTTATCATTTAGCACACTCAGTGCTCCATATGGAAACCCATACACTC
* *
50111 AGTATGATTTCCTTATCATTATAGCACA
1 AGTATGATTTCCTTACCATTTTAGCACA
50139 CAAAGTGCCA
Statistics
Matches: 127, Mismatches: 18, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
117 127 1.00
ACGTcount: A:0.30, C:0.22, G:0.11, T:0.38
Consensus pattern (117 bp):
AGTATGATTTCCTTACCATTTTAGCACATAATATGCCCTATCTGGAAATCCATAATTTAAATATG
ATTTCCTTATCATTTAGCACACTCAGTGCTCCATATGGAAACCCATACACTC
Found at i:50633 original size:19 final size:19
Alignment explanation
Indices: 50609--50679 Score: 124
Period size: 19 Copynumber: 3.7 Consensus size: 19
50599 TATTTAGGTG
*
50609 TGCATCGATGCACTACTTA
1 TGCATCGATGCACCACTTA
50628 TGCATCGATGCACCACTTA
1 TGCATCGATGCACCACTTA
*
50647 TGCATCGATGTACCACTTA
1 TGCATCGATGCACCACTTA
50666 TGCATCGATGCACC
1 TGCATCGATGCACC
50680 TTACCTAGAA
Statistics
Matches: 49, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 49 1.00
ACGTcount: A:0.25, C:0.30, G:0.17, T:0.28
Consensus pattern (19 bp):
TGCATCGATGCACCACTTA
Found at i:53401 original size:12 final size:12
Alignment explanation
Indices: 53375--53407 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
53365 TTATTATACT
*
53375 ATTTT-ATTAAC
1 ATTTTAATTAAA
53386 ATTTTAATTAAA
1 ATTTTAATTAAA
53398 ATTTTAATTA
1 ATTTTAATTA
53408 TTAAATTATA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
11 5 0.25
12 15 0.75
ACGTcount: A:0.42, C:0.03, G:0.00, T:0.55
Consensus pattern (12 bp):
ATTTTAATTAAA
Found at i:60621 original size:65 final size:64
Alignment explanation
Indices: 60457--60642 Score: 189
Period size: 65 Copynumber: 2.9 Consensus size: 64
60447 TGACCGCTGG
* * **
60457 ATCCTTAGTGCATCGGTGCACTAAG-AGTGCATCGATGCATCATGTGCATTCGATG-TTTCAAAA
1 ATCCTCAGTGCATCGGTGCA-T-GGTAGTGCATCGATGCATCAAATGCATTCGATGTTTTCAAAA
60520 T
64 T
* ** * * *
60521 AGCCAGAGTGTATCGATGCATGGCTGGTGCATCGATGCATCAAATGCATTCGATGTTTTCATAAA
1 ATCCTCAGTGCATCGGTGCATGG-TAGTGCATCGATGCATCAAATGCATTCGATGTTTTCA-AAA
60586 -
64 T
* * *
60586 ATCCTCAGTGCATCGGTGCATGGTATGTGCATCGATGCGTGAAATACATTCGATGTT
1 ATCCTCAGTGCATCGGTGCATGGTA-GTGCATCGATGCATCAAATGCATTCGATGTT
60643 CAATTTAATT
Statistics
Matches: 99, Mismatches: 18, Indels: 9
0.79 0.14 0.07
Matches are distributed among these distances:
62 1 0.01
63 1 0.01
64 43 0.43
65 51 0.52
66 3 0.03
ACGTcount: A:0.26, C:0.19, G:0.24, T:0.31
Consensus pattern (64 bp):
ATCCTCAGTGCATCGGTGCATGGTAGTGCATCGATGCATCAAATGCATTCGATGTTTTCAAAAT
Found at i:60681 original size:65 final size:63
Alignment explanation
Indices: 60483--60692 Score: 178
Period size: 65 Copynumber: 3.3 Consensus size: 63
60473 TGCACTAAGA
** * * * *
60483 GTGCATCGATGCATCATGTGCATTCGATGTTTCA-AAATAGC-CAGAGTGTATCGATGCATGGCT
1 GTGCATCGATGCATCAAATACATTCGATGTTTCATAAA-ATCTC--AGTGCATCGATGCATGGTT
60546 G
63 G
* *
60547 GTGCATCGATGCATCAAATGCATTCGATGTTTTCATAAAATCCTCAGTGCATCGGTGCATGGTAT
1 GTGCATCGATGCATCAAATACATTCGATG-TTTCATAAAAT-CTCAGTGCATCGATGCATGGT-T
60612 -
63 G
* * **
60612 GTGCATCGATGCGTGAAATACATTCGATG-TTCAATTTAAT-TCATGGTGCATCGATGCATGGAT
1 GTGCATCGATGCATCAAATACATTCGATGTTTC-ATAAAATCTCA--GTGCATCGATGCATGG-T
60675 TG
62 TG
*
60677 GTGCATCGGTGCATCA
1 GTGCATCGATGCATCA
60693 CTCTGAAACA
Statistics
Matches: 121, Mismatches: 15, Indels: 19
0.78 0.10 0.12
Matches are distributed among these distances:
62 3 0.02
63 3 0.02
64 48 0.40
65 61 0.50
66 5 0.04
67 1 0.01
ACGTcount: A:0.25, C:0.19, G:0.25, T:0.31
Consensus pattern (63 bp):
GTGCATCGATGCATCAAATACATTCGATGTTTCATAAAATCTCAGTGCATCGATGCATGGTTG
Found at i:63395 original size:23 final size:23
Alignment explanation
Indices: 63369--63413 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 23
63359 ATAAAAATAA
63369 TATTATTCA-TAAATTAAATAATG
1 TATTATT-ATTAAATTAAATAATG
*
63392 TATTATTATTAAATTATATAAT
1 TATTATTATTAAATTAAATAAT
63414 ATTTATAACA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
22 1 0.05
23 19 0.95
ACGTcount: A:0.47, C:0.02, G:0.02, T:0.49
Consensus pattern (23 bp):
TATTATTATTAAATTAAATAATG
Found at i:67584 original size:43 final size:43
Alignment explanation
Indices: 67523--67619 Score: 176
Period size: 43 Copynumber: 2.3 Consensus size: 43
67513 GAAGTTAGAT
* *
67523 AAAGGGACCTGGGGAAACTGTAAGGCTTACCCTTGCACATAGC
1 AAAGGGACCTGGGGAAACTGTAAGGCTTACCCTTGCACACAAC
67566 AAAGGGACCTGGGGAAACTGTAAGGCTTACCCTTGCACACAAC
1 AAAGGGACCTGGGGAAACTGTAAGGCTTACCCTTGCACACAAC
67609 AAAGGGACCTG
1 AAAGGGACCTG
67620 TTGTAATGGT
Statistics
Matches: 52, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
43 52 1.00
ACGTcount: A:0.32, C:0.24, G:0.28, T:0.16
Consensus pattern (43 bp):
AAAGGGACCTGGGGAAACTGTAAGGCTTACCCTTGCACACAAC
Found at i:70501 original size:22 final size:21
Alignment explanation
Indices: 70474--70518 Score: 56
Period size: 22 Copynumber: 2.1 Consensus size: 21
70464 TTATACAATT
70474 ATTTACA-AAACTAACACCCGAA
1 ATTTACACAAA-TAACACCC-AA
*
70496 ATTTACACAAATAGCACCCAA
1 ATTTACACAAATAACACCCAA
70517 AT
1 AT
70519 AAAAATTAAT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
21 4 0.19
22 14 0.67
23 3 0.14
ACGTcount: A:0.49, C:0.27, G:0.04, T:0.20
Consensus pattern (21 bp):
ATTTACACAAATAACACCCAA
Found at i:72679 original size:2 final size:2
Alignment explanation
Indices: 72672--72710 Score: 69
Period size: 2 Copynumber: 19.5 Consensus size: 2
72662 TTTCTTTGAA
*
72672 AT AT AT AT AT AT AC 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 AT AT AT AT AT AT AT A
72711 AGATATTTTT
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.51, C:0.03, G:0.00, T:0.46
Consensus pattern (2 bp):
AT
Found at i:77571 original size:20 final size:20
Alignment explanation
Indices: 77535--77572 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
77525 TTATACTTTT
*
77535 ATTTTAATAATATATAATGA
1 ATTTTAATAATAAATAATGA
77555 ATTTTCAATAA-AAATAAT
1 ATTTT-AATAATAAATAAT
77573 ACTAATAATA
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
20 11 0.69
21 5 0.31
ACGTcount: A:0.53, C:0.03, G:0.03, T:0.42
Consensus pattern (20 bp):
ATTTTAATAATAAATAATGA
Found at i:83322 original size:18 final size:18
Alignment explanation
Indices: 83269--83326 Score: 57
Period size: 18 Copynumber: 3.2 Consensus size: 18
83259 ATATTTACTC
* *
83269 ATAATTCTA-ATAATATG
1 ATAATTATATATAATATT
83286 AT-ATTATATTATGTAATATT
1 ATAATTATA-TA--TAATATT
83306 ATAATTATATATAATATT
1 ATAATTATATATAATATT
83324 ATA
1 ATA
83327 CTTTTATTTT
Statistics
Matches: 34, Mismatches: 2, Indels: 9
0.76 0.04 0.20
Matches are distributed among these distances:
16 5 0.15
17 2 0.06
18 11 0.32
20 10 0.29
21 6 0.18
ACGTcount: A:0.47, C:0.02, G:0.03, T:0.48
Consensus pattern (18 bp):
ATAATTATATATAATATT
Found at i:83572 original size:22 final size:19
Alignment explanation
Indices: 83536--83579 Score: 52
Period size: 22 Copynumber: 2.2 Consensus size: 19
83526 ATTATTATTA
*
83536 TTATTAAATTTAATATAAT
1 TTATTAAATTTAATAAAAT
83555 TTATTCAAAGTTTCAATAAAAT
1 TTATT-AAA-TTT-AATAAAAT
83577 TTA
1 TTA
83580 ATAATCTTAA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
19 5 0.24
20 3 0.14
21 3 0.14
22 10 0.48
ACGTcount: A:0.45, C:0.05, G:0.02, T:0.48
Consensus pattern (19 bp):
TTATTAAATTTAATAAAAT
Found at i:86068 original size:2 final size:2
Alignment explanation
Indices: 86061--86086 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
86051 CATAAAAATA
86061 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
86087 GTCAGGAATT
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):
AT
Found at i:94999 original size:24 final size:24
Alignment explanation
Indices: 94958--95065 Score: 119
Period size: 24 Copynumber: 4.5 Consensus size: 24
94948 GAATGTTTTA
*
94958 TCTGATTT-TCGATTTGAATTCTGT
1 TCTGATTTCT-GATCTGAATTCTGT
* * * *
94982 TATGATTTCTTATATGAATCCTGT
1 TCTGATTTCTGATCTGAATTCTGT
* *
95006 TCTGATTTCTGATCTGGATTTTGT
1 TCTGATTTCTGATCTGAATTCTGT
*
95030 TCTGATATCTGATCTGAATTCTGT
1 TCTGATTTCTGATCTGAATTCTGT
*
95054 TTTGATTTCTGA
1 TCTGATTTCTGA
95066 CATCTCTGTG
Statistics
Matches: 68, Mismatches: 15, Indels: 2
0.80 0.18 0.02
Matches are distributed among these distances:
24 67 0.99
25 1 0.01
ACGTcount: A:0.19, C:0.13, G:0.17, T:0.52
Consensus pattern (24 bp):
TCTGATTTCTGATCTGAATTCTGT
Found at i:98813 original size:2 final size:2
Alignment explanation
Indices: 98806--98847 Score: 84
Period size: 2 Copynumber: 21.0 Consensus size: 2
98796 CATAAAAATA
98806 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
98848 CAAGAATTAA
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:104203 original size:22 final size:22
Alignment explanation
Indices: 104155--104203 Score: 66
Period size: 20 Copynumber: 2.3 Consensus size: 22
104145 TAAGAAAAAT
104155 GGGGAGAAGGTGTGTTATAGTAA
1 GGGG-GAAGGTGTGTTATAGTAA
*
104178 --GGGAATGTGTGTTATAGTAA
1 GGGGGAAGGTGTGTTATAGTAA
104198 GGGGGA
1 GGGGGA
104204 GTAATTTTGG
Statistics
Matches: 23, Mismatches: 1, Indels: 5
0.79 0.03 0.17
Matches are distributed among these distances:
20 17 0.74
21 2 0.09
22 4 0.17
ACGTcount: A:0.29, C:0.00, G:0.45, T:0.27
Consensus pattern (22 bp):
GGGGGAAGGTGTGTTATAGTAA
Found at i:107019 original size:8 final size:9
Alignment explanation
Indices: 107006--107058 Score: 58
Period size: 8 Copynumber: 6.0 Consensus size: 9
106996 CAGTTTACTT
107006 TTATT-TTA
1 TTATTATTA
107014 TTATT-TTAA
1 TTATTATT-A
107023 TTATTATTA
1 TTATTATTA
107032 -TATTATTA
1 TTATTATTA
*
107040 TTATTGTTA
1 TTATTATTA
107049 TATATTATTA
1 T-TATTATTA
107059 ATAAATTAAA
Statistics
Matches: 39, Mismatches: 2, Indels: 6
0.83 0.04 0.13
Matches are distributed among these distances:
8 15 0.38
9 15 0.38
10 9 0.23
ACGTcount: A:0.32, C:0.00, G:0.02, T:0.66
Consensus pattern (9 bp):
TTATTATTA
Found at i:107026 original size:17 final size:19
Alignment explanation
Indices: 107006--107060 Score: 64
Period size: 17 Copynumber: 3.1 Consensus size: 19
106996 CAGTTTACTT
107006 TTATT-TTATTATT-TTAA
1 TTATTATTATTATTATTAA
107023 TTATTATTA-TATTATT-A
1 TTATTATTATTATTATTAA
*
107040 TTATTGTTATATATTATTAA
1 TTATTATTAT-TATTATTAA
107060 T
1 T
107061 AAATTAAAAA
Statistics
Matches: 32, Mismatches: 1, Indels: 7
0.80 0.03 0.17
Matches are distributed among these distances:
17 18 0.56
18 5 0.16
19 7 0.22
20 2 0.06
ACGTcount: A:0.33, C:0.00, G:0.02, T:0.65
Consensus pattern (19 bp):
TTATTATTATTATTATTAA
Found at i:107028 original size:3 final size:3
Alignment explanation
Indices: 107006--107058 Score: 58
Period size: 3 Copynumber: 18.0 Consensus size: 3
106996 CAGTTTACTT
*
107006 TTA TT- TTA TTA TT- TTAA TTA TTA TTA -TA TTA TTA TTA TTG TTA
1 TTA TTA TTA TTA TTA TT-A TTA TTA TTA TTA TTA TTA TTA TTA TTA
107049 TATA TTA TTA
1 T-TA TTA TTA
107059 ATAAATTAAA
Statistics
Matches: 43, Mismatches: 2, Indels: 10
0.78 0.04 0.18
Matches are distributed among these distances:
2 6 0.14
3 32 0.74
4 5 0.12
ACGTcount: A:0.32, C:0.00, G:0.02, T:0.66
Consensus pattern (3 bp):
TTA
Found at i:107035 original size:20 final size:20
Alignment explanation
Indices: 107006--107058 Score: 65
Period size: 20 Copynumber: 2.7 Consensus size: 20
106996 CAGTTTACTT
*
107006 TTATTTTATTATT-TTAATTA
1 TTATTATATTATTATT-ATTA
*
107026 TTATTATATTATTATTATTG
1 TTATTATATTATTATTATTA
107046 TTA-TATATTATTA
1 TTATTATATTATTA
107059 ATAAATTAAA
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
19 10 0.33
20 18 0.60
21 2 0.07
ACGTcount: A:0.32, C:0.00, G:0.02, T:0.66
Consensus pattern (20 bp):
TTATTATATTATTATTATTA
Found at i:108092 original size:13 final size:13
Alignment explanation
Indices: 108074--108098 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
108064 ATGAGCCTTG
108074 TAATTCAGTTTTC
1 TAATTCAGTTTTC
108087 TAATTCAGTTTT
1 TAATTCAGTTTT
108099 ATTATAATTT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.24, C:0.12, G:0.08, T:0.56
Consensus pattern (13 bp):
TAATTCAGTTTTC
Found at i:108676 original size:33 final size:34
Alignment explanation
Indices: 108615--108684 Score: 83
Period size: 33 Copynumber: 2.1 Consensus size: 34
108605 AAATATCCTA
*
108615 TTTTATAAATTATATTTTAATATATTA-TTATTAT
1 TTTTATAAATAATATTTTAATATATTATTTATT-T
*
108649 TTTTATAAA-AATGTTTTAAT-TATTTATTTATTT
1 TTTTATAAATAATATTTTAATATA-TTATTTATTT
108682 TTT
1 TTT
108685 AATATCGAAG
Statistics
Matches: 32, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
32 2 0.06
33 16 0.50
34 14 0.44
ACGTcount: A:0.34, C:0.00, G:0.01, T:0.64
Consensus pattern (34 bp):
TTTTATAAATAATATTTTAATATATTATTTATTT
Found at i:109239 original size:20 final size:21
Alignment explanation
Indices: 109216--109266 Score: 61
Period size: 21 Copynumber: 2.5 Consensus size: 21
109206 AGAAATTAAA
109216 AATTCATTTT-TTT-AATTTTT
1 AATT-ATTTTCTTTCAATTTTT
109236 AATTATTTTCTTTCAATTTTT
1 AATTATTTTCTTTCAATTTTT
* *
109257 TATGATTTTC
1 AATTATTTTC
109267 ATAATATTAT
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
19 5 0.19
20 7 0.26
21 15 0.56
ACGTcount: A:0.24, C:0.08, G:0.02, T:0.67
Consensus pattern (21 bp):
AATTATTTTCTTTCAATTTTT
Found at i:111649 original size:7 final size:7
Alignment explanation
Indices: 111614--111654 Score: 57
Period size: 7 Copynumber: 5.9 Consensus size: 7
111604 TTTTCATATA
111614 TGCATTT
1 TGCATTT
111621 T-CATTT
1 TGCATTT
111627 TGCATCTT
1 TGCAT-TT
111635 TGCATTT
1 TGCATTT
*
111642 TTCATTT
1 TGCATTT
111649 TGCATT
1 TGCATT
111655 CATACTTTTA
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
6 6 0.20
7 17 0.57
8 7 0.23
ACGTcount: A:0.15, C:0.17, G:0.10, T:0.59
Consensus pattern (7 bp):
TGCATTT
Found at i:116012 original size:114 final size:114
Alignment explanation
Indices: 115812--116031 Score: 377
Period size: 114 Copynumber: 1.9 Consensus size: 114
115802 CACGTTCTCG
* * *
115812 TAGTAGAAATAAGGAGACCCAATAGTATCTTCTGGAAGTGTTCTTTGAGTTATCTGATTTGATTT
1 TAGTAGAAATAAGGAGACCCAATAGAATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGATTC
* *
115877 GGTATGAACCCCAAAACCAATCATTGGATTTGAAAGATGAATTTGCTCA
66 GGTAGGAACCCCAAAACCAATCATTGGAATTGAAAGATGAATTTGCTCA
* *
115926 TAGTAGAAATAAGGAGACCGAATAGAATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTC
1 TAGTAGAAATAAGGAGACCCAATAGAATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGATTC
115991 GGTAGGAACCCCAAAACCAATCATTGGAATTGAAAGATGAA
66 GGTAGGAACCCCAAAACCAATCATTGGAATTGAAAGATGAA
116032 CTGCATGATC
Statistics
Matches: 99, Mismatches: 7, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
114 99 1.00
ACGTcount: A:0.34, C:0.14, G:0.22, T:0.30
Consensus pattern (114 bp):
TAGTAGAAATAAGGAGACCCAATAGAATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGATTC
GGTAGGAACCCCAAAACCAATCATTGGAATTGAAAGATGAATTTGCTCA
Found at i:118594 original size:22 final size:22
Alignment explanation
Indices: 118562--118616 Score: 74
Period size: 22 Copynumber: 2.5 Consensus size: 22
118552 ATCTACACTC
* *
118562 TTCAAAGATGATAGATTTTCTT
1 TTCAAAGATGATACATTCTCTT
* *
118584 TTTAAATATGATACATTCTCTT
1 TTCAAAGATGATACATTCTCTT
118606 TTCAAAGATGA
1 TTCAAAGATGA
118617 AAGCTTTATG
Statistics
Matches: 27, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
22 27 1.00
ACGTcount: A:0.35, C:0.11, G:0.11, T:0.44
Consensus pattern (22 bp):
TTCAAAGATGATACATTCTCTT
Found at i:119696 original size:75 final size:76
Alignment explanation
Indices: 119448--120011 Score: 940
Period size: 75 Copynumber: 7.5 Consensus size: 76
119438 CTATTTCCCA
*
119448 CATCTGTAAGTCCTGCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGC-TTTTGATGTTTTCAA
1 CATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
*
119512 AACCTTAGGGT
66 AGCCTTAGGGT
119523 CATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCA
1 CATCTGTAAGTCCTACAGTGCATGATGTTTCC-AAAAAGCCTTCGGGAGCTTTTTGATGTTTTCA
119588 AAGCCTTAGGGT
65 AAGCCTTAGGGT
* *
119600 CATCTGTAAGTCCTGCAGTGCATGATGTTTCCAAAAAGCCTTTGGGAGCTTTTTGATGTTTTC-A
1 CATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
*
119664 AGCCTTCGGGT
66 AGCCTTAGGGT
*
119675 CATCTGTAAGTCCTACAGTGCATAATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTC-A
1 CATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
*
119739 AGCCTTCGGGT
66 AGCCTTAGGGT
* *
119750 CATCTGTAAGTCCTGCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAACTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
119815 AGCCTTAGGGT
66 AGCCTTAGGGT
*
119826 CATCTGTAAGTCCTA-AGTGCATGATGTTTCCAAAAAGCCTTCAGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
119890 AGCCTTAGGGT
66 AGCCTTAGGGT
119901 CATCTGTAAGTCCTACAGTGCATGATGTTTCC-AAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTC-A
* *
119965 AAACCTTCGGGT
65 AAGCCTTAGGGT
* * *
119977 CATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAA
1 CATCTGTAAGTCCTACAGTGCATGATGTTTCCAAA
120012 CATTTTCATC
Statistics
Matches: 462, Mismatches: 21, Indels: 10
0.94 0.04 0.02
Matches are distributed among these distances:
75 276 0.60
76 128 0.28
77 58 0.13
ACGTcount: A:0.24, C:0.20, G:0.22, T:0.34
Consensus pattern (76 bp):
CATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
AGCCTTAGGGT
Found at i:120161 original size:14 final size:15
Alignment explanation
Indices: 120138--120193 Score: 57
Period size: 14 Copynumber: 3.9 Consensus size: 15
120128 AGTTTACTTT
120138 TATT-TTATTATTTA
1 TATTATTATTATTTA
*
120152 -ATTGTTATTA-TTA
1 TATTATTATTATTTA
120165 TATTATTATTA-TTA
1 TATTATTATTATTTA
120179 TTATTATATATTATT
1 -TATTAT-TATTATT
120194 AATAAATAAA
Statistics
Matches: 36, Mismatches: 1, Indels: 7
0.82 0.02 0.16
Matches are distributed among these distances:
13 6 0.17
14 18 0.50
15 6 0.17
16 5 0.14
17 1 0.03
ACGTcount: A:0.32, C:0.00, G:0.02, T:0.66
Consensus pattern (15 bp):
TATTATTATTATTTA
Found at i:120162 original size:3 final size:3
Alignment explanation
Indices: 120137--120194 Score: 68
Period size: 3 Copynumber: 20.0 Consensus size: 3
120127 CAGTTTACTT
* *
120137 TTA TT- TTA TTA TT- TAA TTG TTA TTA TTA -TA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
120182 TTA TATA TTA TTA
1 TTA T-TA TTA TTA
120195 ATAAATAAAT
Statistics
Matches: 47, Mismatches: 4, Indels: 8
0.80 0.07 0.14
Matches are distributed among these distances:
2 5 0.11
3 39 0.83
4 3 0.06
ACGTcount: A:0.33, C:0.00, G:0.02, T:0.66
Consensus pattern (3 bp):
TTA
Found at i:120162 original size:17 final size:16
Alignment explanation
Indices: 120137--120194 Score: 66
Period size: 17 Copynumber: 3.6 Consensus size: 16
120127 CAGTTTACTT
120137 TTATT-TTATTATTTAA
1 TTATTATTATTATTT-A
*
120153 TTGTTATTATTATATTA
1 TTATTATTATTAT-TTA
120170 TTATTATTATTA-TTA
1 TTATTATTATTATTTA
120185 TATATTATTA
1 T-TATTATTA
120195 ATAAATAAAT
Statistics
Matches: 37, Mismatches: 2, Indels: 6
0.82 0.04 0.13
Matches are distributed among these distances:
15 4 0.11
16 12 0.32
17 19 0.51
18 2 0.05
ACGTcount: A:0.33, C:0.00, G:0.02, T:0.66
Consensus pattern (16 bp):
TTATTATTATTATTTA
Found at i:120163 original size:22 final size:21
Alignment explanation
Indices: 120137--120193 Score: 62
Period size: 22 Copynumber: 2.6 Consensus size: 21
120127 CAGTTTACTT
*
120137 TTATTTTATTATTTAATTGTTA
1 TTATTTTATTATTT-ATTATTA
*
120159 TTATTATATTA-TTATTATTA
1 TTATTTTATTATTTATTATTA
120179 TTATTATATATTATT
1 TTATT-T-TATTATT
120194 AATAAATAAA
Statistics
Matches: 29, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
20 11 0.38
21 2 0.07
22 15 0.52
23 1 0.03
ACGTcount: A:0.32, C:0.00, G:0.02, T:0.67
Consensus pattern (21 bp):
TTATTTTATTATTTATTATTA
Found at i:121893 original size:19 final size:22
Alignment explanation
Indices: 121869--121910 Score: 63
Period size: 21 Copynumber: 2.0 Consensus size: 22
121859 ATATTTCTAA
121869 ATAAA-TAA-ATATTTT-AAAT
1 ATAAATTAATATATTTTGAAAT
121888 ATAAATTAATATATTTTGAAAT
1 ATAAATTAATATATTTTGAAAT
121910 A
1 A
121911 ATAGGATTAT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
19 5 0.25
20 3 0.15
21 7 0.35
22 5 0.25
ACGTcount: A:0.55, C:0.00, G:0.02, T:0.43
Consensus pattern (22 bp):
ATAAATTAATATATTTTGAAAT
Found at i:121898 original size:23 final size:22
Alignment explanation
Indices: 121866--121910 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 22
121856 CTGATATTTC
121866 TAAATAAATAAATATTTT-AAATA
1 TAAATAAAT--ATATTTTGAAATA
*
121889 TAAATTAATATATTTTGAAATA
1 TAAATAAATATATTTTGAAATA
121911 ATAGGATTAT
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
21 7 0.35
22 5 0.25
23 8 0.40
ACGTcount: A:0.56, C:0.00, G:0.02, T:0.42
Consensus pattern (22 bp):
TAAATAAATATATTTTGAAATA
Found at i:123792 original size:19 final size:21
Alignment explanation
Indices: 123755--123794 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
123745 AATAATCAAG
*
123755 AATATATTATTATACTTAAAA
1 AATATATAATTATACTTAAAA
123776 AATATATAATT-TA-TTAAAA
1 AATATATAATTATACTTAAAA
123795 GTTTCAATAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
19 6 0.33
20 2 0.11
21 10 0.56
ACGTcount: A:0.55, C:0.03, G:0.00, T:0.42
Consensus pattern (21 bp):
AATATATAATTATACTTAAAA
Found at i:126283 original size:2 final size:2
Alignment explanation
Indices: 126278--126313 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
126268 AGAAAAAATA
126278 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
126314 CAAGAATAAA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:133038 original size:24 final size:24
Alignment explanation
Indices: 133011--133141 Score: 140
Period size: 24 Copynumber: 5.5 Consensus size: 24
133001 TCGATTTGAT
133011 TTCTGATCTGATACTTGACATGGA
1 TTCTGATCTGATACTTGACATGGA
*
133035 TTCTGATCTGATA-TCTGATATGGA
1 TTCTGATCTGATACT-TGACATGGA
* *
133059 TTCTGATCTGATACTTAACTTGGA
1 TTCTGATCTGATACTTGACATGGA
* *
133083 TTCTGATATGATACTTGACCTGGA
1 TTCTGATCTGATACTTGACATGGA
* * * *
133107 TTTTGATATGAAAC-TGACATGAA
1 TTCTGATCTGATACTTGACATGGA
* *
133130 TTATGATTTGAT
1 TTCTGATCTGAT
133142 TTTTTATATC
Statistics
Matches: 91, Mismatches: 14, Indels: 5
0.83 0.13 0.05
Matches are distributed among these distances:
23 17 0.19
24 73 0.80
25 1 0.01
ACGTcount: A:0.27, C:0.13, G:0.19, T:0.40
Consensus pattern (24 bp):
TTCTGATCTGATACTTGACATGGA
Found at i:133136 original size:23 final size:24
Alignment explanation
Indices: 133086--133136 Score: 59
Period size: 23 Copynumber: 2.2 Consensus size: 24
133076 ACTTGGATTC
* * * *
133086 TGATATGATACTTGACCTGGATTT
1 TGATATGAAACTTGACATGAATTA
133110 TGATATGAAAC-TGACATGAATTA
1 TGATATGAAACTTGACATGAATTA
133133 TGAT
1 TGAT
133137 TTGATTTTTT
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
23 13 0.57
24 10 0.43
ACGTcount: A:0.33, C:0.10, G:0.20, T:0.37
Consensus pattern (24 bp):
TGATATGAAACTTGACATGAATTA
Found at i:140379 original size:2 final size:2
Alignment explanation
Indices: 140374--140399 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
140364 TCAGAAAAAA
140374 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
140400 CAAGAATTAA
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):
AT
Found at i:146651 original size:2 final size:2
Alignment explanation
Indices: 146646--146671 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
146636 GAAAAAATAA
146646 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
146672 CAAGAATTAA
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):
AT
Found at i:147337 original size:10 final size:10
Alignment explanation
Indices: 147324--147371 Score: 51
Period size: 10 Copynumber: 4.6 Consensus size: 10
147314 GAATATATTA
*
147324 TAATAAAAAT
1 TAATAAAATT
*
147334 TAATATAATT
1 TAATAAAATT
*
147344 TATTAAAAGTT
1 TAATAAAA-TT
147355 TCAATAAAATT
1 T-AATAAAATT
147366 TAATAA
1 TAATAA
147372 TCTTAATATT
Statistics
Matches: 31, Mismatches: 5, Indels: 4
0.77 0.12 0.10
Matches are distributed among these distances:
10 19 0.61
11 6 0.19
12 6 0.19
ACGTcount: A:0.56, C:0.02, G:0.02, T:0.40
Consensus pattern (10 bp):
TAATAAAATT
Found at i:150259 original size:18 final size:18
Alignment explanation
Indices: 150238--150272 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
150228 TTTACTCATA
150238 ATTCTATAATATGATATT
1 ATTCTATAATATGATATT
* *
150256 ATTCTTTAATATTATAT
1 ATTCTATAATATGATAT
150273 GATATATATT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.37, C:0.06, G:0.03, T:0.54
Consensus pattern (18 bp):
ATTCTATAATATGATATT
Found at i:150289 original size:27 final size:25
Alignment explanation
Indices: 150243--150305 Score: 72
Period size: 27 Copynumber: 2.4 Consensus size: 25
150233 TCATAATTCT
*
150243 ATAATATGATATTATTCTTTAATATTA
1 ATAATAT-ATATTATACTTTAAT-TTA
* *
150270 TATGATATATATTATACTTTTATTTA
1 -ATAATATATATTATACTTTAATTTA
150296 ATAATATATA
1 ATAATATATA
150306 ATGATTTTTC
Statistics
Matches: 31, Mismatches: 4, Indels: 3
0.82 0.11 0.08
Matches are distributed among these distances:
25 9 0.29
26 3 0.10
27 13 0.42
28 6 0.19
ACGTcount: A:0.41, C:0.03, G:0.03, T:0.52
Consensus pattern (25 bp):
ATAATATATATTATACTTTAATTTA
Found at i:151760 original size:16 final size:16
Alignment explanation
Indices: 151739--151772 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
151729 AGTTTGATGG
151739 TTTATTTCATTTAAAA
1 TTTATTTCATTTAAAA
* *
151755 TTTATTTTATTTATAA
1 TTTATTTCATTTAAAA
151771 TT
1 TT
151773 ACAAAATAAT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.32, C:0.03, G:0.00, T:0.65
Consensus pattern (16 bp):
TTTATTTCATTTAAAA
Done.