Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01005371.1 Hibiscus syriacus cultivar Beakdansim tig00012213_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: 362493
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.33
File 2 of 2
Found at i:268992 original size:7 final size:7
Alignment explanation
Indices: 268982--269031 Score: 77
Period size: 7 Copynumber: 7.4 Consensus size: 7
268972 GACCCTACCC
268982 GACCGTT
1 GACCGTT
268989 GACCGTT
1 GACCGTT
268996 GACCG-T
1 GACCGTT
269002 GACCGTT
1 GACCGTT
269009 GACCG-T
1 GACCGTT
269015 GACCGTT
1 GACCGTT
*
269022 AACCGTT
1 GACCGTT
269029 GAC
1 GAC
269032 TTTCTTTGAC
Statistics
Matches: 39, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
6 12 0.31
7 27 0.69
ACGTcount: A:0.18, C:0.30, G:0.28, T:0.24
Consensus pattern (7 bp):
GACCGTT
Found at i:269006 original size:13 final size:13
Alignment explanation
Indices: 268982--269027 Score: 74
Period size: 13 Copynumber: 3.5 Consensus size: 13
268972 GACCCTACCC
268982 GACCGTTGACCGTT
1 GACCG-TGACCGTT
268996 GACCGTGACCGTT
1 GACCGTGACCGTT
269009 GACCGTGACCGTT
1 GACCGTGACCGTT
*
269022 AACCGT
1 GACCGT
269028 TGACTTTCTT
Statistics
Matches: 31, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
13 26 0.84
14 5 0.16
ACGTcount: A:0.17, C:0.30, G:0.28, T:0.24
Consensus pattern (13 bp):
GACCGTGACCGTT
Found at i:269007 original size:20 final size:20
Alignment explanation
Indices: 268982--269031 Score: 75
Period size: 20 Copynumber: 2.5 Consensus size: 20
268972 GACCCTACCC
268982 GACCGTTGACCGTTGACCG-T
1 GACCGTTGACCG-TGACCGTT
269002 GACCGTTGACCGTGACCGTT
1 GACCGTTGACCGTGACCGTT
*
269022 AACCGTTGAC
1 GACCGTTGAC
269032 TTTCTTTGAC
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
19 6 0.21
20 22 0.79
ACGTcount: A:0.18, C:0.30, G:0.28, T:0.24
Consensus pattern (20 bp):
GACCGTTGACCGTGACCGTT
Found at i:275010 original size:24 final size:24
Alignment explanation
Indices: 274978--275025 Score: 96
Period size: 24 Copynumber: 2.0 Consensus size: 24
274968 AAGAAATAGG
274978 GTTAATATCTAGATTTGTGGACGT
1 GTTAATATCTAGATTTGTGGACGT
275002 GTTAATATCTAGATTTGTGGACGT
1 GTTAATATCTAGATTTGTGGACGT
275026 TACCTTATTG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.25, C:0.08, G:0.25, T:0.42
Consensus pattern (24 bp):
GTTAATATCTAGATTTGTGGACGT
Found at i:282749 original size:42 final size:41
Alignment explanation
Indices: 282677--282761 Score: 152
Period size: 42 Copynumber: 2.0 Consensus size: 41
282667 AGATTGGGGT
*
282677 AATGCTTAGGGTTTTCTTTAGGTGAAGGCAACTTCCATACG
1 AATGCTTAGGGTTTTCTTTAGGTAAAGGCAACTTCCATACG
282718 AATGCTTAGGGTTTTGCTTTAGGTAAAGGCAACTTCCATACG
1 AATGCTTAGGGTTTT-CTTTAGGTAAAGGCAACTTCCATACG
282760 AA
1 AA
282762 GCGATGGAAG
Statistics
Matches: 42, Mismatches: 1, Indels: 1
0.95 0.02 0.02
Matches are distributed among these distances:
41 15 0.36
42 27 0.64
ACGTcount: A:0.27, C:0.16, G:0.24, T:0.33
Consensus pattern (41 bp):
AATGCTTAGGGTTTTCTTTAGGTAAAGGCAACTTCCATACG
Found at i:283398 original size:2 final size:2
Alignment explanation
Indices: 283391--283435 Score: 90
Period size: 2 Copynumber: 22.5 Consensus size: 2
283381 TTGATAAGTT
283391 TA TA TA TA TA TA TA TA 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 TA TA TA TA TA TA TA TA
283433 TA T
1 TA T
283436 GTGTGTGTGT
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 43 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:284629 original size:2 final size:2
Alignment explanation
Indices: 284624--284650 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
284614 ATATAAAACA
284624 AT 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 A
284651 AAGAGGGAGA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:290988 original size:30 final size:31
Alignment explanation
Indices: 290954--291026 Score: 112
Period size: 31 Copynumber: 2.4 Consensus size: 31
290944 ATTTGTATAC
* *
290954 TTTTAGTCACTTA-GTTATTGTTTTATTAAA
1 TTTTAGTCACTTACGTAATCGTTTTATTAAA
290984 TTTTAGTCACTTACGTAATCGTTTTATTAAA
1 TTTTAGTCACTTACGTAATCGTTTTATTAAA
*
291015 TTTTAGTTACTT
1 TTTTAGTCACTT
291027 GAAAATGAGT
Statistics
Matches: 39, Mismatches: 3, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
30 13 0.33
31 26 0.67
ACGTcount: A:0.26, C:0.10, G:0.10, T:0.55
Consensus pattern (31 bp):
TTTTAGTCACTTACGTAATCGTTTTATTAAA
Found at i:293145 original size:16 final size:16
Alignment explanation
Indices: 293126--293156 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
293116 ATATAGTTAT
293126 ATTTATCTACTTATTA
1 ATTTATCTACTTATTA
*
293142 ATTTATCTATTTATT
1 ATTTATCTACTTATT
293157 TATACTTATA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.29, C:0.10, G:0.00, T:0.61
Consensus pattern (16 bp):
ATTTATCTACTTATTA
Found at i:302879 original size:2 final size:2
Alignment explanation
Indices: 302872--302908 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
302862 GCTAAAACTA
302872 AT AT AT AT AT AT 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 A
302909 ATCTAGCAAA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:316650 original size:34 final size:34
Alignment explanation
Indices: 316603--316673 Score: 90
Period size: 34 Copynumber: 2.1 Consensus size: 34
316593 AATTATTGGG
*
316603 TAAACTCAACATTTAGTA-TCTAGAGTATCAATTT
1 TAAACTCAACATTTAGGACT-TAGAGTATCAATTT
* * *
316637 TAAACTTAGCATTTAGGACTTAGAGTATCAGTTT
1 TAAACTCAACATTTAGGACTTAGAGTATCAATTT
316671 TAA
1 TAA
316674 TACCTAAATT
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
34 31 0.97
35 1 0.03
ACGTcount: A:0.37, C:0.13, G:0.13, T:0.38
Consensus pattern (34 bp):
TAAACTCAACATTTAGGACTTAGAGTATCAATTT
Found at i:320799 original size:15 final size:15
Alignment explanation
Indices: 320763--320791 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
320753 AATTGCCATC
320763 TATATTCTTTTTAAA
1 TATATTCTTTTTAAA
320778 TATATTCTTTTTAA
1 TATATTCTTTTTAA
320792 TTTAATTCAC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.31, C:0.07, G:0.00, T:0.62
Consensus pattern (15 bp):
TATATTCTTTTTAAA
Found at i:321150 original size:2 final size:2
Alignment explanation
Indices: 321143--321176 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
321133 AATAATACTC
321143 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
321177 TATTTTTTAA
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:321241 original size:20 final size:20
Alignment explanation
Indices: 321171--321243 Score: 71
Period size: 20 Copynumber: 3.6 Consensus size: 20
321161 ATATATATAT
321171 ATATATTA-TTTTTTAATTAA
1 ATATATTATTTTTTTAA-TAA
*
321191 ATCTA-TATTTTTATTGAATACA
1 ATATATTATTTTT-TT-AATA-A
*
321213 A-ATAATATTTTTTTAATAA
1 ATATATTATTTTTTTAATAA
321232 ATATATTATTTT
1 ATATATTATTTT
321244 GGACCGGGTT
Statistics
Matches: 44, Mismatches: 3, Indels: 12
0.75 0.05 0.20
Matches are distributed among these distances:
19 4 0.09
20 21 0.48
21 8 0.18
22 11 0.25
ACGTcount: A:0.40, C:0.03, G:0.01, T:0.56
Consensus pattern (20 bp):
ATATATTATTTTTTTAATAA
Found at i:321555 original size:17 final size:17
Alignment explanation
Indices: 321535--321569 Score: 70
Period size: 17 Copynumber: 2.1 Consensus size: 17
321525 ACCTCGGAAT
321535 GTGTCTAAACATTCCAG
1 GTGTCTAAACATTCCAG
321552 GTGTCTAAACATTCCAG
1 GTGTCTAAACATTCCAG
321569 G
1 G
321570 CGGGAGTGAC
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:0.29, C:0.23, G:0.20, T:0.29
Consensus pattern (17 bp):
GTGTCTAAACATTCCAG
Found at i:324932 original size:40 final size:40
Alignment explanation
Indices: 324877--324958 Score: 164
Period size: 40 Copynumber: 2.0 Consensus size: 40
324867 TGTTTCATGA
324877 GTATGTTCTGAGTGACAGGGTAGAGAGTAACCCTTACATC
1 GTATGTTCTGAGTGACAGGGTAGAGAGTAACCCTTACATC
324917 GTATGTTCTGAGTGACAGGGTAGAGAGTAACCCTTACATC
1 GTATGTTCTGAGTGACAGGGTAGAGAGTAACCCTTACATC
324957 GT
1 GT
324959 TCCTGAATCA
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
40 42 1.00
ACGTcount: A:0.27, C:0.17, G:0.28, T:0.28
Consensus pattern (40 bp):
GTATGTTCTGAGTGACAGGGTAGAGAGTAACCCTTACATC
Found at i:325925 original size:18 final size:18
Alignment explanation
Indices: 325902--325943 Score: 66
Period size: 18 Copynumber: 2.3 Consensus size: 18
325892 TTATTCACTC
*
325902 TATTGTGCTCTTCTCTTG
1 TATTGTGCTATTCTCTTG
325920 TATTGTGCTATTCTCTTG
1 TATTGTGCTATTCTCTTG
*
325938 CATTGT
1 TATTGT
325944 CCTTGTAGTC
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.10, C:0.19, G:0.17, T:0.55
Consensus pattern (18 bp):
TATTGTGCTATTCTCTTG
Found at i:328864 original size:23 final size:23
Alignment explanation
Indices: 328838--328887 Score: 59
Period size: 23 Copynumber: 2.2 Consensus size: 23
328828 TAGTTGATAG
328838 AAAAT-TTAAAATATATATTTTA-A
1 AAAATATT-AAATAT-TATTTTATA
*
328861 AAAATATTTAATATTATTTTATA
1 AAAATATTAAATATTATTTTATA
328884 AAAA
1 AAAA
328888 CCCACTACAA
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
22 7 0.29
23 15 0.62
24 2 0.08
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (23 bp):
AAAATATTAAATATTATTTTATA
Found at i:330053 original size:29 final size:29
Alignment explanation
Indices: 330008--330063 Score: 80
Period size: 29 Copynumber: 1.9 Consensus size: 29
329998 TTTTGTTTTG
330008 TTTTTTTTTTTACTTTTTCAAA-AAATTAT
1 TTTTTTTTTTTACTTTTT-AAATAAATTAT
330037 TTTTTATTTTTTA-TTTTTAAATAAATT
1 TTTTT-TTTTTTACTTTTTAAATAAATT
330064 CTCAAAAATT
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
28 3 0.12
29 15 0.60
30 7 0.28
ACGTcount: A:0.29, C:0.04, G:0.00, T:0.68
Consensus pattern (29 bp):
TTTTTTTTTTTACTTTTTAAATAAATTAT
Found at i:335722 original size:29 final size:29
Alignment explanation
Indices: 335633--335722 Score: 69
Period size: 29 Copynumber: 3.1 Consensus size: 29
335623 TTGGTCCTTG
*
335633 AACT-TTTGAATATTCCAATTTCATCCC-A
1 AACTATTT-AATATTTCAATTTCATCCCTA
** * * *
335661 AACTATGTATCTTATTTTAAATT-ACTCCTTA
1 AACTAT-T-TAATATTTCAATTTCA-TCCCTA
335692 AACTATTTAATATTTCAATTTCATCCCTA
1 AACTATTTAATATTTCAATTTCATCCCTA
335721 AA
1 AA
335723 ATGCAACCTT
Statistics
Matches: 45, Mismatches: 11, Indels: 11
0.67 0.16 0.16
Matches are distributed among these distances:
28 4 0.09
29 19 0.42
30 14 0.31
31 8 0.18
ACGTcount: A:0.34, C:0.20, G:0.02, T:0.43
Consensus pattern (29 bp):
AACTATTTAATATTTCAATTTCATCCCTA
Found at i:336037 original size:60 final size:59
Alignment explanation
Indices: 335969--336081 Score: 156
Period size: 60 Copynumber: 1.9 Consensus size: 59
335959 TATAGGGATG
* * * *
335969 AAAATGAAAT-TTTCAAAAGTTTAAGGACTAATTTAGAATCATAGTCATACTTTATGGGT
1 AAAATGAAATATTT-AAAACTTTAAGGACTAATTTAAAATAAGAGTCATACTTTATGGGT
*
336028 AAAATTGAAATATTTAAAACTTTAGGGACTAATTTAAAATAAGAGTCATACTTT
1 AAAA-TGAAATATTTAAAACTTTAAGGACTAATTTAAAATAAGAGTCATACTTT
336082 GATGACATGA
Statistics
Matches: 47, Mismatches: 5, Indels: 3
0.85 0.09 0.05
Matches are distributed among these distances:
59 4 0.09
60 40 0.85
61 3 0.06
ACGTcount: A:0.43, C:0.08, G:0.13, T:0.35
Consensus pattern (59 bp):
AAAATGAAATATTTAAAACTTTAAGGACTAATTTAAAATAAGAGTCATACTTTATGGGT
Found at i:337569 original size:26 final size:27
Alignment explanation
Indices: 337536--337588 Score: 81
Period size: 26 Copynumber: 2.0 Consensus size: 27
337526 CGAACCGGAT
* *
337536 TTTAACCCGATTCGAAAG-CACCCGAA
1 TTTAACCCGACTCGAAAGTAACCCGAA
337562 TTTAACCCGACTCGAAAGTAACCCGAA
1 TTTAACCCGACTCGAAAGTAACCCGAA
337589 CAAATTGAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
26 17 0.71
27 7 0.29
ACGTcount: A:0.36, C:0.30, G:0.15, T:0.19
Consensus pattern (27 bp):
TTTAACCCGACTCGAAAGTAACCCGAA
Found at i:337946 original size:19 final size:20
Alignment explanation
Indices: 337894--337946 Score: 54
Period size: 19 Copynumber: 2.6 Consensus size: 20
337884 TTTTTTAAAA
337894 TTTAATAAAAAAATATTAAATT
1 TTTAAT-AAAAAATA-TAAATT
* **
337916 TATAATTGAAAATA-AAATT
1 TTTAATAAAAAATATAAATT
337935 TTTAATAAAAAA
1 TTTAATAAAAAA
337947 ATTATTTCTT
Statistics
Matches: 25, Mismatches: 6, Indels: 3
0.74 0.18 0.09
Matches are distributed among these distances:
19 14 0.56
21 6 0.24
22 5 0.20
ACGTcount: A:0.60, C:0.00, G:0.02, T:0.38
Consensus pattern (20 bp):
TTTAATAAAAAATATAAATT
Found at i:339190 original size:32 final size:32
Alignment explanation
Indices: 339154--339233 Score: 101
Period size: 32 Copynumber: 2.5 Consensus size: 32
339144 TTGACCTAAA
*
339154 CCGAAAATCAACCGATCTAATATTGACCCGAC
1 CCGAAAATCAACCGATCTAATATTAACCCGAC
* *
339186 CCG-AAATCTAACCAATCTGATATTAACCCGAC
1 CCGAAAATC-AACCGATCTAATATTAACCCGAC
*
339218 CCAAAAATCAA-CGATC
1 CCGAAAATCAACCGATC
339234 CTGTATTGAC
Statistics
Matches: 41, Mismatches: 5, Indels: 5
0.80 0.10 0.10
Matches are distributed among these distances:
31 9 0.22
32 27 0.66
33 5 0.12
ACGTcount: A:0.40, C:0.31, G:0.10, T:0.19
Consensus pattern (32 bp):
CCGAAAATCAACCGATCTAATATTAACCCGAC
Found at i:343660 original size:65 final size:67
Alignment explanation
Indices: 343581--343711 Score: 239
Period size: 67 Copynumber: 2.0 Consensus size: 67
343571 TAAAATGAAA
*
343581 TGAAAACTAAACGTTAGGTATGGTTTTG-AAAAA-TTGAAAGTTTTGGTACTAAAATAGACCAAA
1 TGAAAACTAAACGTTAGGTATGGTTTTGAAAAAATTTGAAAGTTTAGGTACTAAAATAGACCAAA
343644 AC
66 AC
343646 TGAAAACTAAACGTTAGGTATGGTTTTGAAAAAATTTGAAAGTTTAGGTACTAAAATAGACCAAA
1 TGAAAACTAAACGTTAGGTATGGTTTTGAAAAAATTTGAAAGTTTAGGTACTAAAATAGACCAAA
343711 A
66 A
343712 TTGATAGTTG
Statistics
Matches: 63, Mismatches: 1, Indels: 2
0.95 0.02 0.03
Matches are distributed among these distances:
65 28 0.44
66 5 0.08
67 30 0.48
ACGTcount: A:0.44, C:0.08, G:0.18, T:0.29
Consensus pattern (67 bp):
TGAAAACTAAACGTTAGGTATGGTTTTGAAAAAATTTGAAAGTTTAGGTACTAAAATAGACCAAA
AC
Found at i:343784 original size:122 final size:122
Alignment explanation
Indices: 343646--344462 Score: 1124
Period size: 122 Copynumber: 6.7 Consensus size: 122
343636 AGACCAAAAC
* * * *
343646 TGAAAACTAAACGTTAGGTATGGTTTTGAAAAAATTTGAAAGTTTAGGTACTAAAATAGACCAAA
1 TGAAAACTAAACGTTAGGTATGATTTTGAAAAAAATTGAAAGTTTAGGTACTAAAACAAACCAAA
* * * * *
343711 ATTGATAGTTGAGGTACTAAACGCATTAAGTTTTTAACGACGAGTACTAAAATGAAA
66 ACTGATAGTTTAGGTACTAAACACATTAATTTTTTAACGACGGGTACTAAAATGAAA
* *
343768 TGAAAACTAAATGTTAGGTATGATTTT-AAAAAAATTGAAAGTTTAGGTACTAAAACAAACCACA
1 TGAAAACTAAACGTTAGGTATGATTTTGAAAAAAATTGAAAGTTTAGGTACTAAAACAAACCAAA
* * * *
343832 ACTGATAGTTTAGGTACTAAACACGTTAATTTTTTAACGGCGGGGTTCTAAAATAAAA
66 ACTGATAGTTTAGGTACTAAACACATTAATTTTTTAACGAC-GGGTACTAAAATGAAA
* * * * *
343890 TGAAAACTAAACATTAGATATGATTTTG-AAAAACTTAAAAGTTTAGGTACTAAAACAGACCAAA
1 TGAAAACTAAACGTTAGGTATGATTTTGAAAAAAATTGAAAGTTTAGGTACTAAAACAAACCAAA
* * * *
343954 AATGATAGTTTAGGTATTAAACGCATTAAATTTTTAACGACGGGTACTAAAATGAAA
66 ACTGATAGTTTAGGTACTAAACACATTAATTTTTTAACGACGGGTACTAAAATGAAA
*
344011 TGAAAACTAAACGTTAAGTATGATTTTGAAAAAAAATT-AAATGTTTAGGTACTAAAACAAACCA
1 TGAAAACTAAACGTTAGGTATGATTTTG-AAAAAAATTGAAA-GTTTAGGTACTAAAACAAACCA
* * *
344075 CAACTGATAGTTTAGGTATTAAACACATTAATTTTTTAACGACGGGGTACTAAAATGATA
64 AAACTGATAGTTTAGGTACTAAACACATTAATTTTTTAACGAC-GGGTACTAAAATGAAA
* *
344135 TGAAAACTAAACGTTAGGTATGGTTTTG-AAAAAATTGAAAGGTTAGGTACTAAAACAAACCAAA
1 TGAAAACTAAACGTTAGGTATGATTTTGAAAAAAATTGAAAGTTTAGGTACTAAAACAAACCAAA
* * * * *
344199 ATTGATAGTTTAGGTACTAAACGCATTAAGTTTTTAACAACGGGTACTTAAATGAAA
66 ACTGATAGTTTAGGTACTAAACACATTAATTTTTTAACGACGGGTACTAAAATGAAA
* *
344256 TGAAAACTAAACGTTAGATATGATTTTGAAAAAAATTGAAAGTTTAGGTACTAAAACAAACCACA
1 TGAAAACTAAACGTTAGGTATGATTTTGAAAAAAATTGAAAGTTTAGGTACTAAAACAAACCAAA
* *
344321 ACTGATATTTTAGGTACTAAATACATTAATTTTTTAACGACGAGGTACTAAAATGAAA
66 ACTGATAGTTTAGGTACTAAACACATTAATTTTTTAACGACG-GGTACTAAAATGAAA
** * * * *
344379 TGAAAACTAAACGTTAGACATGATTTT-AAAAAAA-TAAAAGTTTAGGTACTAAAATAGACCGAA
1 TGAAAACTAAACGTTAGGTATGATTTTGAAAAAAATTGAAAGTTTAGGTACTAAAACAAACCAAA
* *
344442 ATTGATAATTTAGGTACTAAA
66 ACTGATAGTTTAGGTACTAAA
344463 ACAAACTACA
Statistics
Matches: 616, Mismatches: 70, Indels: 19
0.87 0.10 0.03
Matches are distributed among these distances:
121 190 0.31
122 275 0.45
123 110 0.18
124 41 0.07
ACGTcount: A:0.45, C:0.10, G:0.16, T:0.30
Consensus pattern (122 bp):
TGAAAACTAAACGTTAGGTATGATTTTGAAAAAAATTGAAAGTTTAGGTACTAAAACAAACCAAA
ACTGATAGTTTAGGTACTAAACACATTAATTTTTTAACGACGGGTACTAAAATGAAA
Found at i:343819 original size:188 final size:188
Alignment explanation
Indices: 343496--343836 Score: 513
Period size: 188 Copynumber: 1.8 Consensus size: 188
343486 TAAATTTTAT
* * * * *
343496 AAAGTTTAGGTACTATAACAAACCACAATTGATAGTTTAGGTACTAAACGCTTTAATTTTTTAAC
1 AAAGTTTAGGTACTAAAACAAACCAAAATTGATAGTTGAGGTACTAAACGCATTAAGTTTTTAAC
** * * * *
343561 GGTGGTGTACTAAAATGAAATGAAAACTAAACGTTAGGTATGGTTTTGAAAAATTGAAAGTTTTG
66 GGACGAGTACTAAAATGAAATGAAAACTAAACGTTAGGTATGATTTTAAAAAATTGAAAGTTTAG
* *
343626 GTACTAAAATAGACCAAAACTGAAAACTAAACGTTAGGTATGGTTTTGAAAAAATTTG
131 GTACTAAAACAAACCAAAACTGAAAACTAAACGTTAGGTATGGTTTTGAAAAAATTTG
* *
343684 AAAGTTTAGGTACTAAAATAGACCAAAATTGATAGTTGAGGTACTAAACGCATTAAGTTTTTAAC
1 AAAGTTTAGGTACTAAAACAAACCAAAATTGATAGTTGAGGTACTAAACGCATTAAGTTTTTAAC
*
343749 -GACGAGTACTAAAATGAAATGAAAACTAAATGTTAGGTATGATTTTAAAAAAATTGAAAGTTTA
66 GGACGAGTACTAAAATGAAATGAAAACTAAACGTTAGGTATGATTTT-AAAAAATTGAAAGTTTA
*
343813 GGTACTAAAACAAACCACAACTGA
130 GGTACTAAAACAAACCAAAACTGA
343837 TAGTTTAGGT
Statistics
Matches: 135, Mismatches: 17, Indels: 2
0.88 0.11 0.01
Matches are distributed among these distances:
187 41 0.30
188 94 0.70
ACGTcount: A:0.43, C:0.10, G:0.17, T:0.30
Consensus pattern (188 bp):
AAAGTTTAGGTACTAAAACAAACCAAAATTGATAGTTGAGGTACTAAACGCATTAAGTTTTTAAC
GGACGAGTACTAAAATGAAATGAAAACTAAACGTTAGGTATGATTTTAAAAAATTGAAAGTTTAG
GTACTAAAACAAACCAAAACTGAAAACTAAACGTTAGGTATGGTTTTGAAAAAATTTG
Found at i:344164 original size:245 final size:244
Alignment explanation
Indices: 343646--344462 Score: 1264
Period size: 245 Copynumber: 3.3 Consensus size: 244
343636 AGACCAAAAC
* * * *
343646 TGAAAACTAAACGTTAGGTATGGTTTTGAAAAAATTTGAAAGTTTAGGTACTAAAATAGACCAAA
1 TGAAAACTAAACGTTAGATATGATTTTGAAAAAA-TTAAAAGTTTAGGTACTAAAACAGACCAAA
* *
343711 ATTGATAGTTGAGGTACTAAACGCATTAAGTTTTTAACGACGAGTACTAAAATGAAATGAAAACT
65 ATTGATAGTTTAGGTACTAAACGCATTAAGTTTTTAACGACGGGTACTAAAATGAAATGAAAACT
* *
343776 AAATGTTAGGTATGATTTT-AAAAAAATTGAAAGTTTAGGTACTAAAACAAACCACAACTGATAG
130 AAACGTTAAGTATGATTTTGAAAAAAATTGAAAGTTTAGGTACTAAAACAAACCACAACTGATAG
* * * *
343840 TTTAGGTACTAAACACGTTAATTTTTTAACGGCGGGGTTCTAAAATAAAA
195 TTTAGGTACTAAACACATTAATTTTTTAACGACGGGGTACTAAAATGAAA
* *
343890 TGAAAACTAAACATTAGATATGATTTTGAAAAACTTAAAAGTTTAGGTACTAAAACAGACCAAAA
1 TGAAAACTAAACGTTAGATATGATTTTGAAAAAATTAAAAGTTTAGGTACTAAAACAGACCAAAA
* * *
343955 ATGATAGTTTAGGTATTAAACGCATTAAATTTTTAACGACGGGTACTAAAATGAAATGAAAACTA
66 TTGATAGTTTAGGTACTAAACGCATTAAGTTTTTAACGACGGGTACTAAAATGAAATGAAAACTA
344020 AACGTTAAGTATGATTTTGAAAAAAAATT-AAATGTTTAGGTACTAAAACAAACCACAACTGATA
131 AACGTTAAGTATGATTTTG-AAAAAAATTGAAA-GTTTAGGTACTAAAACAAACCACAACTGATA
* *
344084 GTTTAGGTATTAAACACATTAATTTTTTAACGACGGGGTACTAAAATGATA
194 GTTTAGGTACTAAACACATTAATTTTTTAACGACGGGGTACTAAAATGAAA
* * * * *
344135 TGAAAACTAAACGTTAGGTATGGTTTTGAAAAAATTGAAAGGTTAGGTACTAAAACAAACCAAAA
1 TGAAAACTAAACGTTAGATATGATTTTGAAAAAATTAAAAGTTTAGGTACTAAAACAGACCAAAA
* *
344200 TTGATAGTTTAGGTACTAAACGCATTAAGTTTTTAACAACGGGTACTTAAATGAAATGAAAACTA
66 TTGATAGTTTAGGTACTAAACGCATTAAGTTTTTAACGACGGGTACTAAAATGAAATGAAAACTA
*
344265 AACGTT-AGATATGATTTTGAAAAAAATTGAAAGTTTAGGTACTAAAACAAACCACAACTGATAT
131 AACGTTAAG-TATGATTTTGAAAAAAATTGAAAGTTTAGGTACTAAAACAAACCACAACTGATAG
* *
344329 TTTAGGTACTAAATACATTAATTTTTTAACGACGAGGTACTAAAATGAAA
195 TTTAGGTACTAAACACATTAATTTTTTAACGACGGGGTACTAAAATGAAA
* * * *
344379 TGAAAACTAAACGTTAGACATGATTTT-AAAAAAATAAAAGTTTAGGTACTAAAATAGACCGAAA
1 TGAAAACTAAACGTTAGATATGATTTTGAAAAAATTAAAAGTTTAGGTACTAAAACAGACCAAAA
*
344443 TTGATAATTTAGGTACTAAA
66 TTGATAGTTTAGGTACTAAA
344463 ACAAACTACA
Statistics
Matches: 522, Mismatches: 46, Indels: 11
0.90 0.08 0.02
Matches are distributed among these distances:
243 155 0.30
244 145 0.28
245 222 0.43
ACGTcount: A:0.45, C:0.10, G:0.16, T:0.30
Consensus pattern (244 bp):
TGAAAACTAAACGTTAGATATGATTTTGAAAAAATTAAAAGTTTAGGTACTAAAACAGACCAAAA
TTGATAGTTTAGGTACTAAACGCATTAAGTTTTTAACGACGGGTACTAAAATGAAATGAAAACTA
AACGTTAAGTATGATTTTGAAAAAAATTGAAAGTTTAGGTACTAAAACAAACCACAACTGATAGT
TTAGGTACTAAACACATTAATTTTTTAACGACGGGGTACTAAAATGAAA
Found at i:344357 original size:367 final size:365
Alignment explanation
Indices: 343646--344462 Score: 1138
Period size: 367 Copynumber: 2.2 Consensus size: 365
343636 AGACCAAAAC
* * * * *
343646 TGAAAACTAAACGTTAGGTATGGTTTTGAAAAAATTTGAAAGTTTAGGTACTAAAATAGACCAAA
1 TGAAAACTAAACGTTAAGTATGATTTTGAAAAAAATT-AAAGTTTAGGTACTAAAACAAACCAAA
* *
343711 ATTGATAGTTGAGGTACTAAACGCATTAAGTTTTTAACGACGAGTACTAAAATGAAATGAAAACT
65 ACTGATAGTTGAGGTACTAAACACATTAAGTTTTTAACGACGAGTACTAAAATGAAATGAAAACT
* * *
343776 AAATGTTAGGTATGATTTTAAAAAAATTGAAAGTTTAGGTACTAAAACAAACCACAACTGATAGT
130 AAACGTTAGGTATGATTTTAAAAAAATTGAAAGGTTAGGTACTAAAACAAACCAAAACTGATAGT
* * ** *
343841 TTAGGTACTAAACACGTTAATTTTTTAACGGCGGGGTTCTAAAATAAAATGAAAACTAAACATTA
195 TTAGGTACTAAACACATTAAGTTTTTAACAACGGGGTACTAAAATAAAATGAAAACTAAACATTA
* * *
343906 GATATGATTTTGAAAAACTTAAAAGTTTAGGTACTAAAACAGACCAAAAATGATAGTTTAGGTAT
260 GATATGATTTTGAAAAAATTAAAAGTTTAGGTACTAAAACAAACCAAAAATGATAGTTTAGGTAC
*
343971 TAAACGCATTAAATTTTTAACGACG-GGTACTAAAATGAAA
325 TAAACACATTAAATTTTTAACGACGAGGTACTAAAATGAAA
*
344011 TGAAAACTAAACGTTAAGTATGATTTTGAAAAAAAATTAAATGTTTAGGTACTAAAACAAACCAC
1 TGAAAACTAAACGTTAAGTATGATTTTG-AAAAAAATTAAA-GTTTAGGTACTAAAACAAACCAA
* * * * *
344076 AACTGATAGTTTAGGTATTAAACACATTAATTTTTTAACGACGGGGTACTAAAATGATATGAAAA
64 AACTGATAGTTGAGGTACTAAACACATTAAGTTTTTAACGAC-GAGTACTAAAATGAAATGAAAA
* * *
344141 CTAAACGTTAGGTATGGTTTTGAAAAAATTGAAAGGTTAGGTACTAAAACAAACCAAAATTGATA
128 CTAAACGTTAGGTATGATTTTAAAAAAATTGAAAGGTTAGGTACTAAAACAAACCAAAACTGATA
* * * *
344206 GTTTAGGTACTAAACGCATTAAGTTTTTAACAAC-GGGTACTTAAATGAAATGAAAACTAAACGT
193 GTTTAGGTACTAAACACATTAAGTTTTTAACAACGGGGTACTAAAATAAAATGAAAACTAAACAT
* * * *
344270 TAGATATGATTTTGAAAAAAATTGAAAGTTTAGGTACTAAAACAAACCACAACTGATATTTTAGG
258 TAGATATGATTTTG-AAAAAATTAAAAGTTTAGGTACTAAAACAAACCAAAAATGATAGTTTAGG
* *
344335 TACTAAATACATTAATTTTTTAACGACGAGGTACTAAAATGAAA
322 TACTAAACACATTAAATTTTTAACGACGAGGTACTAAAATGAAA
* * * * *
344379 TGAAAACTAAACGTT-AGACATGATTTT-AAAAAAATAAAAGTTTAGGTACTAAAATAGACCGAA
1 TGAAAACTAAACGTTAAG-TATGATTTTGAAAAAAATTAAAGTTTAGGTACTAAAACAAACCAAA
* * *
344442 ATTGATAATTTAGGTACTAAA
65 ACTGATAGTTGAGGTACTAAA
344463 ACAAACTACA
Statistics
Matches: 399, Mismatches: 47, Indels: 12
0.87 0.10 0.03
Matches are distributed among these distances:
365 67 0.17
366 116 0.29
367 178 0.45
368 38 0.10
ACGTcount: A:0.45, C:0.10, G:0.16, T:0.30
Consensus pattern (365 bp):
TGAAAACTAAACGTTAAGTATGATTTTGAAAAAAATTAAAGTTTAGGTACTAAAACAAACCAAAA
CTGATAGTTGAGGTACTAAACACATTAAGTTTTTAACGACGAGTACTAAAATGAAATGAAAACTA
AACGTTAGGTATGATTTTAAAAAAATTGAAAGGTTAGGTACTAAAACAAACCAAAACTGATAGTT
TAGGTACTAAACACATTAAGTTTTTAACAACGGGGTACTAAAATAAAATGAAAACTAAACATTAG
ATATGATTTTGAAAAAATTAAAAGTTTAGGTACTAAAACAAACCAAAAATGATAGTTTAGGTACT
AAACACATTAAATTTTTAACGACGAGGTACTAAAATGAAA
Found at i:357265 original size:2 final size:2
Alignment explanation
Indices: 357258--357285 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
357248 TAAAACCTTT
357258 TA 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 TA
357286 GATTTAAAAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:357338 original size:2 final size:2
Alignment explanation
Indices: 357333--357380 Score: 96
Period size: 2 Copynumber: 24.0 Consensus size: 2
357323 AAAAAAACCT
357333 TA TA TA TA TA TA TA TA 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 TA TA TA TA TA TA TA TA
357375 TA TA TA
1 TA TA TA
357381 CTTACATGCA
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):
TA
Found at i:358256 original size:9 final size:9
Alignment explanation
Indices: 358244--358280 Score: 51
Period size: 9 Copynumber: 4.2 Consensus size: 9
358234 TTTTTATTTA
358244 TTTTTTTC-
1 TTTTTTTCT
358252 -TTTTTTCT
1 TTTTTTTCT
358260 TTTTTTTCT
1 TTTTTTTCT
358269 TTTTTCTTCT
1 TTTTT-TTCT
358279 TT
1 TT
358281 CTTCAGGAGA
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
7 7 0.27
9 13 0.50
10 6 0.23
ACGTcount: A:0.00, C:0.14, G:0.00, T:0.86
Consensus pattern (9 bp):
TTTTTTTCT
Found at i:358257 original size:7 final size:7
Alignment explanation
Indices: 358245--358283 Score: 51
Period size: 7 Copynumber: 5.3 Consensus size: 7
358235 TTTTATTTAT
358245 TTTTTTC
1 TTTTTTC
358252 TTTTTTC
1 TTTTTTC
358259 TTTTTTTTC
1 --TTTTTTC
358268 TTTTTTC
1 TTTTTTC
*
358275 TTCTTTC
1 TTTTTTC
358282 TT
1 TT
358284 CAGGAGAAGT
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
7 22 0.76
9 7 0.24
ACGTcount: A:0.00, C:0.15, G:0.00, T:0.85
Consensus pattern (7 bp):
TTTTTTC
Found at i:358265 original size:16 final size:16
Alignment explanation
Indices: 358244--358276 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
358234 TTTTTATTTA
358244 TTTTTTTCTTTTTTCT
1 TTTTTTTCTTTTTTCT
358260 TTTTTTTCTTTTTTCT
1 TTTTTTTCTTTTTTCT
358276 T
1 T
358277 CTTTCTTCAG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.00, C:0.12, G:0.00, T:0.88
Consensus pattern (16 bp):
TTTTTTTCTTTTTTCT
Found at i:358266 original size:19 final size:19
Alignment explanation
Indices: 358234--358280 Score: 51
Period size: 19 Copynumber: 2.5 Consensus size: 19
358224 TCGAATCCCC
*
358234 TTTTTATTTATTTT-TTTCT
1 TTTTTCTTTATTTTCTTT-T
*
358253 TTTTTCTTTTTTTTCTTTT
1 TTTTTCTTTATTTTCTTTT
*
358272 TTCTTCTTT
1 TTTTTCTTT
358281 CTTCAGGAGA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
19 21 0.88
20 3 0.12
ACGTcount: A:0.04, C:0.11, G:0.00, T:0.85
Consensus pattern (19 bp):
TTTTTCTTTATTTTCTTTT
Found at i:361302 original size:17 final size:18
Alignment explanation
Indices: 361264--361318 Score: 51
Period size: 17 Copynumber: 3.1 Consensus size: 18
361254 ATAATAATTA
* *
361264 ATTTAAATAAAATTGATA-
1 ATTTATATAAAA-TAATAG
*
361282 ATTTAT-TAAAATATTAG
1 ATTTATATAAAATAATAG
361299 ATTTATAATAAAATAATAG
1 ATTTAT-ATAAAATAATAG
361318 A
1 A
361319 AAGTTTAGAG
Statistics
Matches: 30, Mismatches: 4, Indels: 5
0.77 0.10 0.13
Matches are distributed among these distances:
16 3 0.10
17 11 0.37
18 5 0.17
19 11 0.37
ACGTcount: A:0.55, C:0.00, G:0.05, T:0.40
Consensus pattern (18 bp):
ATTTATATAAAATAATAG
Done.