Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008321.1 Hibiscus syriacus cultivar Beakdansim tig00111024_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: 74815
ACGTcount: A:0.33, C:0.16, G:0.19, T:0.32
Found at i:445 original size:17 final size:17
Alignment explanation
Indices: 423--466 Score: 79
Period size: 17 Copynumber: 2.6 Consensus size: 17
413 AATTATGACT
423 TTATTTTGAAAAATTGA
1 TTATTTTGAAAAATTGA
440 TTATTTTGAAAAATTGA
1 TTATTTTGAAAAATTGA
*
457 TGATTTTGAA
1 TTATTTTGAA
467 TTAATTTGGA
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
17 26 1.00
ACGTcount: A:0.39, C:0.00, G:0.14, T:0.48
Consensus pattern (17 bp):
TTATTTTGAAAAATTGA
Found at i:558 original size:18 final size:18
Alignment explanation
Indices: 537--571 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
527 TTTTAAAACA
537 ATTTTTAAGAAAAAAATC
1 ATTTTTAAGAAAAAAATC
* *
555 ATTTTTTAGACAAAAAT
1 ATTTTTAAGAAAAAAAT
572 AGGTATGTGT
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:0.51, C:0.06, G:0.06, T:0.37
Consensus pattern (18 bp):
ATTTTTAAGAAAAAAATC
Found at i:2406 original size:21 final size:21
Alignment explanation
Indices: 2380--2420 Score: 73
Period size: 21 Copynumber: 2.0 Consensus size: 21
2370 TTACAAGTTT
2380 GATAATTGAAACAAAGTTTAC
1 GATAATTGAAACAAAGTTTAC
*
2401 GATAATTGAAATAAAGTTTA
1 GATAATTGAAACAAAGTTTA
2421 AAAATAAACT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.49, C:0.05, G:0.15, T:0.32
Consensus pattern (21 bp):
GATAATTGAAACAAAGTTTAC
Found at i:4824 original size:27 final size:26
Alignment explanation
Indices: 4794--4849 Score: 69
Period size: 27 Copynumber: 2.1 Consensus size: 26
4784 GGGTTTTTCC
*
4794 CAAATCTGGT-TTCGGATATTTTTTGTG
1 CAAATCGGGTATTCGG--ATTTTTTGTG
4821 CAAAATCGGGTATTCGGATTTTTTGTG
1 C-AAATCGGGTATTCGGATTTTTTGTG
4848 CA
1 CA
4850 CCTCTACTCA
Statistics
Matches: 26, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
26 1 0.04
27 12 0.46
28 8 0.31
29 5 0.19
ACGTcount: A:0.21, C:0.12, G:0.23, T:0.43
Consensus pattern (26 bp):
CAAATCGGGTATTCGGATTTTTTGTG
Found at i:6007 original size:2 final size:2
Alignment explanation
Indices: 6000--6040 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
5990 CTCTATTTCA
6000 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
6041 GTTTGTGTTC
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.00, C:0.49, G:0.00, T:0.51
Consensus pattern (2 bp):
TC
Found at i:9054 original size:2 final size:2
Alignment explanation
Indices: 9049--9097 Score: 89
Period size: 2 Copynumber: 24.5 Consensus size: 2
9039 AGAATTAGAC
*
9049 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TG
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
9091 TA TA TA T
1 TA TA TA T
9098 GATTTTCAAT
Statistics
Matches: 45, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
2 45 1.00
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.51
Consensus pattern (2 bp):
TA
Found at i:13636 original size:17 final size:18
Alignment explanation
Indices: 13613--13660 Score: 62
Period size: 17 Copynumber: 2.7 Consensus size: 18
13603 GTTTGAGTAC
13613 ATTTATTTCTATACAAGT
1 ATTTATTTCTATACAAGT
* *
13631 -TTTATTTATATTCAAGT
1 ATTTATTTCTATACAAGT
*
13648 ATTTATCTCTATA
1 ATTTATTTCTATA
13661 AATAAATATT
Statistics
Matches: 24, Mismatches: 5, Indels: 2
0.77 0.16 0.06
Matches are distributed among these distances:
17 15 0.62
18 9 0.38
ACGTcount: A:0.31, C:0.10, G:0.04, T:0.54
Consensus pattern (18 bp):
ATTTATTTCTATACAAGT
Found at i:17555 original size:19 final size:20
Alignment explanation
Indices: 17526--17568 Score: 63
Period size: 19 Copynumber: 2.2 Consensus size: 20
17516 TTACTCAATC
17526 ATTAGTTTAATTATAAAT-TT
1 ATTAGTTTAATTA-AAATATT
17546 ATTA-TTTAATTAAAATATT
1 ATTAGTTTAATTAAAATATT
17565 ATTA
1 ATTA
17569 CAATTTGCTT
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
18 4 0.18
19 14 0.64
20 4 0.18
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.53
Consensus pattern (20 bp):
ATTAGTTTAATTAAAATATT
Found at i:18806 original size:64 final size:64
Alignment explanation
Indices: 18738--18962 Score: 267
Period size: 64 Copynumber: 3.5 Consensus size: 64
18728 TTGTTTGAAG
** **
18738 GTGCATCGATGCATTGGTAGTGCATCGATGCA-CTCTTTTAA-AATAAATACATCGAATGCAATT
1 GTGCATCGATGCATAAGTAGTGCATCGATGCATC-CCATTAATAATAAA-ACATCGAATGCAATT
18801 T
64 T
** *
18802 GTGCATCGATGCATAAGTAGTGCATCGATGCATCCCATTAATAAGGAAACATCGAATGCAATTA
1 GTGCATCGATGCATAAGTAGTGCATCGATGCATCCCATTAATAATAAAACATCGAATGCAATTT
* * * * *
18866 GTGCATCGATGCATAAGGCA-TGCATCGATGCATCCCAGTAATAATACAACATCGAATACATTTT
1 GTGCATCGATGCATAA-GTAGTGCATCGATGCATCCCATTAATAATAAAACATCGAATGCAATTT
* * *
18930 ATGCACCGATGCATCAGTAGTGCATCGATGCAT
1 GTGCATCGATGCATAAGTAGTGCATCGATGCAT
18963 ACCTTCATTA
Statistics
Matches: 138, Mismatches: 19, Indels: 8
0.84 0.12 0.05
Matches are distributed among these distances:
63 2 0.01
64 129 0.93
65 7 0.05
ACGTcount: A:0.33, C:0.20, G:0.20, T:0.28
Consensus pattern (64 bp):
GTGCATCGATGCATAAGTAGTGCATCGATGCATCCCATTAATAATAAAACATCGAATGCAATTT
Found at i:19837 original size:103 final size:103
Alignment explanation
Indices: 19714--19936 Score: 437
Period size: 103 Copynumber: 2.2 Consensus size: 103
19704 TTCGAGGGTC
*
19714 TATGTGGTCATTCGGGATATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
1 TATGTGGTCCTTCGGGATATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
19779 TTGATCCCTAGTATATGTATATGATTCTTAAGGAGTGA
66 TTGATCCCTAGTATATGTATATGATTCTTAAGGAGTGA
19817 TATGTGGTCCTTCGGGATATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
1 TATGTGGTCCTTCGGGATATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
19882 TTGATCCCTAGTATATGTATATGATTCTTAAGGAGTGA
66 TTGATCCCTAGTATATGTATATGATTCTTAAGGAGTGA
19920 TATGTGGTCCTTCGGGA
1 TATGTGGTCCTTCGGGA
19937 CATTATTATA
Statistics
Matches: 119, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
103 119 1.00
ACGTcount: A:0.26, C:0.13, G:0.25, T:0.37
Consensus pattern (103 bp):
TATGTGGTCCTTCGGGATATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
TTGATCCCTAGTATATGTATATGATTCTTAAGGAGTGA
Found at i:19981 original size:23 final size:23
Alignment explanation
Indices: 19948--20010 Score: 99
Period size: 23 Copynumber: 2.7 Consensus size: 23
19938 ATTATTATAT
19948 GGCACTACGGTGCAATTCTACGC
1 GGCACTACGGTGCAATTCTACGC
* *
19971 GGCACTCCGGTGCAATTCTACGT
1 GGCACTACGGTGCAATTCTACGC
*
19994 GGCACTTCGGTGCAATT
1 GGCACTACGGTGCAATT
20011 ATATGAGCTG
Statistics
Matches: 37, Mismatches: 3, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
23 37 1.00
ACGTcount: A:0.19, C:0.29, G:0.27, T:0.25
Consensus pattern (23 bp):
GGCACTACGGTGCAATTCTACGC
Found at i:24544 original size:19 final size:19
Alignment explanation
Indices: 24520--24571 Score: 104
Period size: 19 Copynumber: 2.7 Consensus size: 19
24510 AATGCAATTT
24520 GTGCATCGATGCATAAGTA
1 GTGCATCGATGCATAAGTA
24539 GTGCATCGATGCATAAGTA
1 GTGCATCGATGCATAAGTA
24558 GTGCATCGATGCAT
1 GTGCATCGATGCAT
24572 CCCATTAATA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 33 1.00
ACGTcount: A:0.29, C:0.17, G:0.27, T:0.27
Consensus pattern (19 bp):
GTGCATCGATGCATAAGTA
Found at i:24638 original size:64 final size:64
Alignment explanation
Indices: 24537--24699 Score: 181
Period size: 64 Copynumber: 2.5 Consensus size: 64
24527 GATGCATAAG
* * *
24537 TAGTGCATCGATGCATAAGTAGTGCATCGATGCATCCCATTAATAAGGA-AACATCGAATGCAAT
1 TAGTGAATCGATGCATAAGCAGTGCATCGATGCATCCCAGTAATAA-GACAACATCGAATGCAAT
* * *
24601 TAGTGAATCGATGCATAAGGCA-TGCATCGATGCATCCCAGTAATAATACAACATCGAATACATT
1 TAGTGAATCGATGCATAA-GCAGTGCATCGATGCATCCCAGTAATAAGACAACATCGAATGCA-A
24665 T
64 T
* * *
24666 TA-TGCACCGATGCATCAA-TAGTGCATCGATGCAT
1 TAGTGAATCGATGCAT-AAGCAGTGCATCGATGCAT
24700 ACCTTCATTA
Statistics
Matches: 85, Mismatches: 9, Indels: 10
0.82 0.09 0.10
Matches are distributed among these distances:
63 2 0.02
64 76 0.89
65 7 0.08
ACGTcount: A:0.35, C:0.20, G:0.19, T:0.26
Consensus pattern (64 bp):
TAGTGAATCGATGCATAAGCAGTGCATCGATGCATCCCAGTAATAAGACAACATCGAATGCAAT
Found at i:25574 original size:103 final size:103
Alignment explanation
Indices: 25451--25673 Score: 437
Period size: 103 Copynumber: 2.2 Consensus size: 103
25441 TTCGAGGGTC
*
25451 TATGTGGTCTTTCGGGATATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
1 TATGTGGTCCTTCGGGATATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
25516 TTGATCCCTAGTATATGTATATGATTCTTAAGGAGTGA
66 TTGATCCCTAGTATATGTATATGATTCTTAAGGAGTGA
25554 TATGTGGTCCTTCGGGATATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
1 TATGTGGTCCTTCGGGATATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
25619 TTGATCCCTAGTATATGTATATGATTCTTAAGGAGTGA
66 TTGATCCCTAGTATATGTATATGATTCTTAAGGAGTGA
25657 TATGTGGTCCTTCGGGA
1 TATGTGGTCCTTCGGGA
25674 CATTATTATA
Statistics
Matches: 119, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
103 119 1.00
ACGTcount: A:0.25, C:0.13, G:0.25, T:0.37
Consensus pattern (103 bp):
TATGTGGTCCTTCGGGATATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
TTGATCCCTAGTATATGTATATGATTCTTAAGGAGTGA
Found at i:25724 original size:23 final size:23
Alignment explanation
Indices: 25685--25747 Score: 81
Period size: 23 Copynumber: 2.7 Consensus size: 23
25675 ATTATTATAT
* *
25685 GGCACTACGGTGAAATTCTACGC
1 GGCACTCCGGTGCAATTCTACGC
* *
25708 GGTACTCCGGTGCAATTCTACGT
1 GGCACTCCGGTGCAATTCTACGC
*
25731 GGCACTTCGGTGCAATT
1 GGCACTCCGGTGCAATT
25748 ATATGAGCTG
Statistics
Matches: 34, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
23 34 1.00
ACGTcount: A:0.21, C:0.25, G:0.27, T:0.27
Consensus pattern (23 bp):
GGCACTCCGGTGCAATTCTACGC
Found at i:30297 original size:64 final size:64
Alignment explanation
Indices: 30229--30449 Score: 218
Period size: 64 Copynumber: 3.5 Consensus size: 64
30219 TTGAAGGTGT
* ** * *
30229 ATCGATGCATTGGTAGTGCATCGATGCA-CTCTTTTAA-AATAAATACATCGAATGCAATTTGTG
1 ATCGATGCATAGGTAGTGCATCGATGCATC-CCATTAATAAGAAA-ACATCGAATGCAATTAGTG
30292 C
64 C
* *
30293 ATCGATGCATAAGTAGTGCATCGATGCATCCCATTAATAAGGAAACATCGAATGCAATTAGTGC
1 ATCGATGCATAGGTAGTGCATCGATGCATCCCATTAATAAGAAAACATCGAATGCAATTAGTGC
* * * * * *
30357 ATCGATGCATAAGGCA-TGCATCGATGCATCCCAGTAATAATACAACATCGAATACATTTTA-TG
1 ATCGATGCAT-AGGTAGTGCATCGATGCATCCCATTAATAAGAAAACATCGAATGCA-ATTAGTG
*
30420 T
64 C
* *
30421 ACCGATACATCA-GTAGTGCATCGATGCAT
1 ATCGATGCAT-AGGTAGTGCATCGATGCAT
30450 ACCTTCATTA
Statistics
Matches: 132, Mismatches: 20, Indels: 10
0.81 0.12 0.06
Matches are distributed among these distances:
63 2 0.02
64 119 0.90
65 11 0.08
ACGTcount: A:0.34, C:0.19, G:0.19, T:0.28
Consensus pattern (64 bp):
ATCGATGCATAGGTAGTGCATCGATGCATCCCATTAATAAGAAAACATCGAATGCAATTAGTGC
Found at i:31324 original size:103 final size:103
Alignment explanation
Indices: 31200--31422 Score: 446
Period size: 103 Copynumber: 2.2 Consensus size: 103
31190 GTCGAGGGTC
31200 TATGTGGTCCTTCGGGATATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
1 TATGTGGTCCTTCGGGATATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
31265 TTGATCCCTAGTATATGTATATGATTCTTAAGGAGTGA
66 TTGATCCCTAGTATATGTATATGATTCTTAAGGAGTGA
31303 TATGTGGTCCTTCGGGATATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
1 TATGTGGTCCTTCGGGATATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
31368 TTGATCCCTAGTATATGTATATGATTCTTAAGGAGTGA
66 TTGATCCCTAGTATATGTATATGATTCTTAAGGAGTGA
31406 TATGTGGTCCTTCGGGA
1 TATGTGGTCCTTCGGGA
31423 CATTATTATA
Statistics
Matches: 120, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
103 120 1.00
ACGTcount: A:0.25, C:0.13, G:0.25, T:0.37
Consensus pattern (103 bp):
TATGTGGTCCTTCGGGATATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
TTGATCCCTAGTATATGTATATGATTCTTAAGGAGTGA
Found at i:31475 original size:23 final size:23
Alignment explanation
Indices: 31434--31496 Score: 72
Period size: 23 Copynumber: 2.7 Consensus size: 23
31424 ATTATTATAT
* *
31434 GGCACTACGGTGCAATTCTACGC
1 GGCACTCCGGCGCAATTCTACGC
* *
31457 GGTACTCCGGCGCAATTCTACGT
1 GGCACTCCGGCGCAATTCTACGC
* *
31480 GGCACTTCGGTGCAATT
1 GGCACTCCGGCGCAATT
31497 ATATGAGCTG
Statistics
Matches: 33, Mismatches: 7, Indels: 0
0.82 0.17 0.00
Matches are distributed among these distances:
23 33 1.00
ACGTcount: A:0.19, C:0.29, G:0.27, T:0.25
Consensus pattern (23 bp):
GGCACTCCGGCGCAATTCTACGC
Found at i:35469 original size:29 final size:29
Alignment explanation
Indices: 35435--35493 Score: 118
Period size: 29 Copynumber: 2.0 Consensus size: 29
35425 CCTAAATTAA
35435 TTTGATGTCATTGCTTACATCAATTTAGT
1 TTTGATGTCATTGCTTACATCAATTTAGT
35464 TTTGATGTCATTGCTTACATCAATTTAGT
1 TTTGATGTCATTGCTTACATCAATTTAGT
35493 T
1 T
35494 AGGTGAAAAT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 30 1.00
ACGTcount: A:0.24, C:0.14, G:0.14, T:0.49
Consensus pattern (29 bp):
TTTGATGTCATTGCTTACATCAATTTAGT
Found at i:40149 original size:29 final size:29
Alignment explanation
Indices: 40115--40173 Score: 118
Period size: 29 Copynumber: 2.0 Consensus size: 29
40105 CCTAAATTAA
40115 TTTGATGTCATTGCTTACATCAATTTAGT
1 TTTGATGTCATTGCTTACATCAATTTAGT
40144 TTTGATGTCATTGCTTACATCAATTTAGT
1 TTTGATGTCATTGCTTACATCAATTTAGT
40173 T
1 T
40174 AGGTGAAAAT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 30 1.00
ACGTcount: A:0.24, C:0.14, G:0.14, T:0.49
Consensus pattern (29 bp):
TTTGATGTCATTGCTTACATCAATTTAGT
Found at i:44469 original size:38 final size:37
Alignment explanation
Indices: 44388--44515 Score: 122
Period size: 38 Copynumber: 3.5 Consensus size: 37
44378 TATATACACA
* * * *
44388 TATATATTATATAGTTTACAAATTGTTTTTGAAAATACA
1 TATATAATATATAGTTTA-AAAATATTTTTGAAAATA-T
44427 TATATAATATATAGTTTAAAACAT-TTTTTGAAAATAT
1 TATATAATATATAGTTTAAAA-ATATTTTTGAAAATAT
*
44464 GTATAT--TATATAGTTTTTAAAATATTTTTG-AAA-AT
1 -TATATAATATATAG-TTTAAAAATATTTTTGAAAATAT
*
44499 TACATAATATATAGTTT
1 TATATAATATATAGTTT
44516 TTGAAAGCGT
Statistics
Matches: 78, Mismatches: 5, Indels: 16
0.79 0.05 0.16
Matches are distributed among these distances:
34 4 0.05
35 5 0.06
36 19 0.24
37 12 0.15
38 20 0.26
39 18 0.23
ACGTcount: A:0.42, C:0.03, G:0.07, T:0.48
Consensus pattern (37 bp):
TATATAATATATAGTTTAAAAATATTTTTGAAAATAT
Found at i:44510 original size:36 final size:37
Alignment explanation
Indices: 44413--44613 Score: 173
Period size: 36 Copynumber: 5.4 Consensus size: 37
44403 TTACAAATTG
44413 TTTTTGAAAATACATATATAATATATAG--TTTAAAACA
1 TTTTTGAAAAT--ATATATAATATATAGTTTTTAAAACA
* * *
44450 TTTTTTGAAAATATGTATATTATATAGTTTTTAAAATA
1 -TTTTTGAAAATATATATAATATATAGTTTTTAAAACA
* *
44488 TTTTTGAAAAT-TACATAATATATAGTTTTTGAAAGC-
1 TTTTTGAAAATATATATAATATATAGTTTTT-AAAACA
* * *
44524 GTTTT-AAAATATATATAATATATACTTTTGAAAAC-
1 TTTTTGAAAATATATATAATATATAGTTTTTAAAACA
* * * *
44559 GTTATGAAAACATTTATATAATATATAATTTTTAAAAACCA
1 TTTTTG-AAA-ATATATATAATATATAGTTTTT-AAAA-CA
44600 -TTTTGAAAATATAT
1 TTTTTGAAAATATAT
44614 TTTTTGAAAA
Statistics
Matches: 134, Mismatches: 19, Indels: 20
0.77 0.11 0.12
Matches are distributed among these distances:
35 13 0.10
36 49 0.37
37 17 0.13
38 43 0.32
39 7 0.05
40 5 0.04
ACGTcount: A:0.44, C:0.04, G:0.07, T:0.44
Consensus pattern (37 bp):
TTTTTGAAAATATATATAATATATAGTTTTTAAAACA
Found at i:44577 original size:38 final size:35
Alignment explanation
Indices: 44494--44595 Score: 98
Period size: 38 Copynumber: 2.8 Consensus size: 35
44484 AATATTTTTG
* * * *
44494 AAAAT-TACATAATATATAGTTTTTGAAAGCGTTTT
1 AAAATATATATAATATATA-ATTTTGAAAACGTTTA
*
44529 AAAATATATATAATATATACTTTTGAAAACGTTATGA
1 AAAATATATATAATATATAATTTTGAAAACGTT-T-A
* *
44566 AAACATTTATATAATATATAATTTTTAAAA
1 AAA-ATATATATAATATATAATTTTGAAAA
44596 ACCATTTTGA
Statistics
Matches: 56, Mismatches: 7, Indels: 5
0.82 0.10 0.07
Matches are distributed among these distances:
35 17 0.30
36 13 0.23
37 3 0.05
38 23 0.41
ACGTcount: A:0.47, C:0.05, G:0.07, T:0.41
Consensus pattern (35 bp):
AAAATATATATAATATATAATTTTGAAAACGTTTA
Found at i:44620 original size:15 final size:16
Alignment explanation
Indices: 44600--44629 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
44590 TTAAAAACCA
44600 TTTTGAAAA-TATATT
1 TTTTGAAAATTATATT
44615 TTTTGAAAATTATAT
1 TTTTGAAAATTATAT
44630 AATATATAGT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 9 0.64
16 5 0.36
ACGTcount: A:0.40, C:0.00, G:0.07, T:0.53
Consensus pattern (16 bp):
TTTTGAAAATTATATT
Found at i:44636 original size:25 final size:25
Alignment explanation
Indices: 44572--44648 Score: 73
Period size: 25 Copynumber: 3.0 Consensus size: 25
44562 ATGAAAACAT
*
44572 TTATATAATATATAATTTTTAAAAA
1 TTATATAATATATAATTTTTGAAAA
** * * *
44597 CCATTTTGAAAATATATTTTTTGAAAA
1 TTA-TAT-AATATATAATTTTTGAAAA
*
44624 TTATATAATATATAGTTTTTGAAAA
1 TTATATAATATATAATTTTTGAAAA
44649 CGTTTTTAAA
Statistics
Matches: 39, Mismatches: 11, Indels: 4
0.72 0.20 0.07
Matches are distributed among these distances:
25 18 0.46
26 4 0.10
27 17 0.44
ACGTcount: A:0.45, C:0.03, G:0.05, T:0.47
Consensus pattern (25 bp):
TTATATAATATATAATTTTTGAAAA
Found at i:45504 original size:21 final size:21
Alignment explanation
Indices: 45478--45522 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
45468 GATTTCTGGG
* *
45478 CAAGGGGAATCGGTACCCATT
1 CAAGGGGAACCGATACCCATT
*
45499 CAAGGGGAACCGATACCCCTT
1 CAAGGGGAACCGATACCCATT
45520 CAA
1 CAA
45523 ACGACAGAAT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.31, C:0.29, G:0.24, T:0.16
Consensus pattern (21 bp):
CAAGGGGAACCGATACCCATT
Found at i:46427 original size:31 final size:31
Alignment explanation
Indices: 46389--46542 Score: 256
Period size: 31 Copynumber: 5.0 Consensus size: 31
46379 GGGTCGAGGG
46389 TTACCTATGTTCTTCGGAACATATGGACTGT
1 TTACCTATGTTCTTCGGAACATATGGACTGT
46420 TTACCTATGTTCTTCGGAACATATGGACTGT
1 TTACCTATGTTCTTCGGAACATATGGACTGT
46451 TTACCTATGTTCTTCGGAACATATGGACTGT
1 TTACCTATGTTCTTCGGAACATATGGACTGT
* * *
46482 TTACCTATGTCCTTCGGGACATATGGACTGA
1 TTACCTATGTTCTTCGGAACATATGGACTGT
*
46513 TTACCTAGGTTCTTCGGAATC-TATGGACTG
1 TTACCTATGTTCTTCGGAA-CATATGGACTG
46543 GTCCTTCGGG
Statistics
Matches: 116, Mismatches: 6, Indels: 2
0.94 0.05 0.02
Matches are distributed among these distances:
31 115 0.99
32 1 0.01
ACGTcount: A:0.22, C:0.20, G:0.21, T:0.37
Consensus pattern (31 bp):
TTACCTATGTTCTTCGGAACATATGGACTGT
Found at i:49531 original size:21 final size:21
Alignment explanation
Indices: 49505--49549 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
49495 GATTTCTGGG
* *
49505 CAAGGGGAATCGGTACCCATT
1 CAAGGGGAACCGATACCCATT
*
49526 CAAGGGGAACCGATACCCCTT
1 CAAGGGGAACCGATACCCATT
49547 CAA
1 CAA
49550 ACGACAGAAT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.31, C:0.29, G:0.24, T:0.16
Consensus pattern (21 bp):
CAAGGGGAACCGATACCCATT
Found at i:50452 original size:31 final size:31
Alignment explanation
Indices: 50414--50567 Score: 256
Period size: 31 Copynumber: 5.0 Consensus size: 31
50404 GGGTCGAGGG
50414 TTACCTATGTTCTTCGGAACATATGGACTGT
1 TTACCTATGTTCTTCGGAACATATGGACTGT
50445 TTACCTATGTTCTTCGGAACATATGGACTGT
1 TTACCTATGTTCTTCGGAACATATGGACTGT
50476 TTACCTATGTTCTTCGGAACATATGGACTGT
1 TTACCTATGTTCTTCGGAACATATGGACTGT
* * *
50507 TTACCTATGTCCTTCGGGACATATGGACTGA
1 TTACCTATGTTCTTCGGAACATATGGACTGT
*
50538 TTACCTAGGTTCTTCGGAATC-TATGGACTG
1 TTACCTATGTTCTTCGGAA-CATATGGACTG
50568 GTCCTTCGGG
Statistics
Matches: 116, Mismatches: 6, Indels: 2
0.94 0.05 0.02
Matches are distributed among these distances:
31 115 0.99
32 1 0.01
ACGTcount: A:0.22, C:0.20, G:0.21, T:0.37
Consensus pattern (31 bp):
TTACCTATGTTCTTCGGAACATATGGACTGT
Found at i:53976 original size:26 final size:26
Alignment explanation
Indices: 53940--54002 Score: 117
Period size: 26 Copynumber: 2.4 Consensus size: 26
53930 GCATTAAGGA
*
53940 AACGAAGACTAATTAATAAAGTTGGC
1 AACGTAGACTAATTAATAAAGTTGGC
53966 AACGTAGACTAATTAATAAAGTTGGC
1 AACGTAGACTAATTAATAAAGTTGGC
53992 AACGTAGACTA
1 AACGTAGACTA
54003 CAAACATTGA
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
26 36 1.00
ACGTcount: A:0.44, C:0.13, G:0.19, T:0.24
Consensus pattern (26 bp):
AACGTAGACTAATTAATAAAGTTGGC
Found at i:55475 original size:3 final size:3
Alignment explanation
Indices: 55456--55525 Score: 79
Period size: 3 Copynumber: 22.3 Consensus size: 3
55446 AGCCCCTGCA
**
55456 AAT AAT AA- AAT TTT AAT AAT AAT AAT AAT AAT AAAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT -AAT AAT AAT AAT
55501 AAT AAT AAT AAAT AAAT AAAT AAT A
1 AAT AAT AAT -AAT -AAT -AAT AAT A
55526 TTTTTTAAAT
Statistics
Matches: 60, Mismatches: 4, Indels: 6
0.86 0.06 0.09
Matches are distributed among these distances:
2 2 0.03
3 44 0.73
4 14 0.23
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:55497 original size:22 final size:22
Alignment explanation
Indices: 55469--55525 Score: 96
Period size: 22 Copynumber: 2.5 Consensus size: 22
55459 AATAAAATTT
55469 TAATAATAATAATAATAATAAA
1 TAATAATAATAATAATAATAAA
55491 TAATAATAATAATAATAATAAA
1 TAATAATAATAATAATAATAAA
55513 TAAATAAATAATA
1 T-AAT-AATAATA
55526 TTTTTTAAAT
Statistics
Matches: 33, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
22 23 0.70
23 3 0.09
24 7 0.21
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (22 bp):
TAATAATAATAATAATAATAAA
Found at i:55515 original size:19 final size:19
Alignment explanation
Indices: 55470--55508 Score: 78
Period size: 19 Copynumber: 2.1 Consensus size: 19
55460 ATAAAATTTT
55470 AATAATAATAATAATAATA
1 AATAATAATAATAATAATA
55489 AATAATAATAATAATAATA
1 AATAATAATAATAATAATA
55508 A
1 A
55509 TAAATAAATA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (19 bp):
AATAATAATAATAATAATA
Found at i:55813 original size:23 final size:23
Alignment explanation
Indices: 55787--55834 Score: 69
Period size: 23 Copynumber: 2.1 Consensus size: 23
55777 ATAAAGTACA
*
55787 ATAACATACTAGGTAGCGCTTAT
1 ATAACATAATAGGTAGCGCTTAT
**
55810 ATAATGTAATAGGTAGCGCTTAT
1 ATAACATAATAGGTAGCGCTTAT
55833 AT
1 AT
55835 TTACCTATTT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.35, C:0.12, G:0.19, T:0.33
Consensus pattern (23 bp):
ATAACATAATAGGTAGCGCTTAT
Found at i:56482 original size:333 final size:334
Alignment explanation
Indices: 55874--56538 Score: 1269
Period size: 333 Copynumber: 2.0 Consensus size: 334
55864 TTATACCGAT
55874 AGCATTGCAAATTTACCTATTACATTATATTATATTGAAAGTGTCCATACTTTTTATAAAAAGGA
1 AGCATTGCAAATTTACCTATTACATTATATTATATTGAAAGTGTCCATACTTTTTATAAAAAGGA
*
55939 TCGATATTTCTTTTAAAGTTATGTAATTTATGTTTCAATTTTTTTTAATAGTGTTTCATGTTTTC
66 TCGATACTTCTTTTAAAGTTATGTAATTTATGTTTCAA-TTTTTTTAATAGTGTTTCATGTTTTC
56004 CACCTACAATATTAATTTAATAATTTCATTTGCACAAAAAATTATTTGATTGTTTTGATATTTTA
130 CACCTACAATATTAATTTAATAATTTCATTTGCACAAAAAATTATTTGATTGTTTTGATATTTTA
* * *
56069 TAAAATATTATTTAGAATTTTTAATTTAATAATAATATATATTGTAACGTAAAAAATAAATCATT
195 TAAAATAATATTTAGAATTTTTAATTTAATAATAATATATATCGTAACGTAAAAAATAAACCATT
56134 AGACGCCTATAATTACTAAATTAATATCTTAAAACTCACTCAAAAGATAACCTTAAATTAATGTT
260 AGACGCCTATAATTACTAAATTAATATCTTAAAACTCACTCAAAAGATAACCTTAAATTAATGTT
56199 TTCCACATTG
325 TTCCACATTG
56209 AGCATTGCAAATTTACCTATTACATTATATTATATTGAAAGTGTCCATACTTTTTATAAAAAGGA
1 AGCATTGCAAATTTACCTATTACATTATATTATATTGAAAGTGTCCATACTTTTTATAAAAAGGA
56274 TCGATACTTCTTTTAAAGTTATGTAATTTATGTTTCAA-TTTTTTAATAGTGTTTCATGTTTTCC
66 TCGATACTTCTTTTAAAGTTATGTAATTTATGTTTCAATTTTTTTAATAGTGTTTCATGTTTTCC
56338 ACCTACAATATTAATTTAATAATTTCATTTGCACAAAAAATTATTTGATTGTTTTGATATTTTAT
131 ACCTACAATATTAATTTAATAATTTCATTTGCACAAAAAATTATTTGATTGTTTTGATATTTTAT
56403 AAAATAATATTTAGAATTTTTAATTTAATAATAATATATATCGTAACGTAAAAAATAAACCATTA
196 AAAATAATATTTAGAATTTTTAATTTAATAATAATATATATCGTAACGTAAAAAATAAACCATTA
*
56468 GACGCCTATAATTACTAAATTAATATCTTAAAACTCACTTAAAAGATAACCTTAAATTAATGTTT
261 GACGCCTATAATTACTAAATTAATATCTTAAAACTCACTCAAAAGATAACCTTAAATTAATGTTT
56533 TCCACA
326 TCCACA
56539 GTGAAAAAAG
Statistics
Matches: 325, Mismatches: 5, Indels: 2
0.98 0.02 0.01
Matches are distributed among these distances:
333 223 0.69
335 102 0.31
ACGTcount: A:0.38, C:0.11, G:0.08, T:0.43
Consensus pattern (334 bp):
AGCATTGCAAATTTACCTATTACATTATATTATATTGAAAGTGTCCATACTTTTTATAAAAAGGA
TCGATACTTCTTTTAAAGTTATGTAATTTATGTTTCAATTTTTTTAATAGTGTTTCATGTTTTCC
ACCTACAATATTAATTTAATAATTTCATTTGCACAAAAAATTATTTGATTGTTTTGATATTTTAT
AAAATAATATTTAGAATTTTTAATTTAATAATAATATATATCGTAACGTAAAAAATAAACCATTA
GACGCCTATAATTACTAAATTAATATCTTAAAACTCACTCAAAAGATAACCTTAAATTAATGTTT
TCCACATTG
Found at i:56648 original size:23 final size:23
Alignment explanation
Indices: 56585--56657 Score: 83
Period size: 23 Copynumber: 3.2 Consensus size: 23
56575 ACACTTTACA
* *
56585 ATATAACCACTACCTATTACATT
1 ATATAAACGCTACCTATTACATT
* *
56608 ATATAAACGATACATATTACATT
1 ATATAAACGCTACCTATTACATT
** *
56631 ATATAAGGGCTACCTATTACATC
1 ATATAAACGCTACCTATTACATT
56654 ATAT
1 ATAT
56658 GTTTACCTAT
Statistics
Matches: 41, Mismatches: 9, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
23 41 1.00
ACGTcount: A:0.41, C:0.19, G:0.05, T:0.34
Consensus pattern (23 bp):
ATATAAACGCTACCTATTACATT
Found at i:57058 original size:25 final size:25
Alignment explanation
Indices: 57001--57066 Score: 87
Period size: 25 Copynumber: 2.6 Consensus size: 25
56991 CACTCAAAAG
*
57001 ATGTATATACCTAAATATGTAGTTA
1 ATGTACATACCTAAATATGTAGTTA
***
57026 ACAAACATACCTAAATATGTAGTTA
1 ATGTACATACCTAAATATGTAGTTA
*
57051 TTGTACATACCTAAAT
1 ATGTACATACCTAAAT
57067 TTAATGATAA
Statistics
Matches: 33, Mismatches: 8, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
25 33 1.00
ACGTcount: A:0.42, C:0.14, G:0.09, T:0.35
Consensus pattern (25 bp):
ATGTACATACCTAAATATGTAGTTA
Found at i:59875 original size:183 final size:183
Alignment explanation
Indices: 59567--60231 Score: 1267
Period size: 183 Copynumber: 3.6 Consensus size: 183
59557 ACACATTTTA
*
59567 GACATAAAGTACCGACACAATATTAAAAAGTGTCGATATAGGTTGTAAACCTATTCGCGCATAAA
1 GACATAAAGTACCGACACAATATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCGCATAAA
59632 ACCGGTATATTTATACCGGTTATATTACAAAATTATCTATTACATTATAATTATGGGTTCCGATG
66 ACCGGTATATTTATACCGGTTATATTACAAAATTATCTATTACATTATAATTATGGGTTCCGATG
59697 TGTAAATGTCGACACTTTTTTAAATCGTATCGACACATTTTTCTTCCAATATG
131 TGTAAATGTCGACACTTTTTTAAATCGTATCGACACATTTTTCTTCCAATATG
*
59750 GACATAAAGTACCGACACAATATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCGCATACA
1 GACATAAAGTACCGACACAATATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCGCATAAA
59815 ACCGGTATATTTATACCGGTTATATTACAAAATTATCTATTACATTATAATTATGGGTTCCGATG
66 ACCGGTATATTTATACCGGTTATATTACAAAATTATCTATTACATTATAATTATGGGTTCCGATG
59880 TGTAAATGTCGACACTTTTTTAAATCGTATCGACACATTTTTCTTCCAATATG
131 TGTAAATGTCGACACTTTTTTAAATCGTATCGACACATTTTTCTTCCAATATG
59933 GACATAAAGTACCGACACAATATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCGCATAAA
1 GACATAAAGTACCGACACAATATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCGCATAAA
59998 ACCGGTATATTTATACCGGTTATATTACAAAATTATCTATTACATTATAATTATGGGTTCCGATG
66 ACCGGTATATTTATACCGGTTATATTACAAAATTATCTATTACATTATAATTATGGGTTCCGATG
60063 TGTAAATGTCGACACTTTTTTAAATCGTATCGACACATTTTTCTTCCAATATG
131 TGTAAATGTCGACACTTTTTTAAATCGTATCGACACATTTTTCTTCCAATATG
60116 GACATAAAGTACCGACACAATATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCGCATAAA
1 GACATAAAGTACCGACACAATATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCGCATAAA
* * * **
60181 ACCGGTATATTTATACCGGTTATATTGCAAATTTACCTATTTTATTATAAT
66 ACCGGTATATTTATACCGGTTATATTACAAAATTATCTATTACATTATAAT
60232 ATGTTGAAAG
Statistics
Matches: 474, Mismatches: 8, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
183 474 1.00
ACGTcount: A:0.34, C:0.16, G:0.15, T:0.35
Consensus pattern (183 bp):
GACATAAAGTACCGACACAATATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCGCATAAA
ACCGGTATATTTATACCGGTTATATTACAAAATTATCTATTACATTATAATTATGGGTTCCGATG
TGTAAATGTCGACACTTTTTTAAATCGTATCGACACATTTTTCTTCCAATATG
Found at i:61442 original size:3 final size:3
Alignment explanation
Indices: 61434--61508 Score: 60
Period size: 3 Copynumber: 25.0 Consensus size: 3
61424 ACTTGTTTGG
* * * ** * *
61434 ATC ATC ATC TTC ATC ATC ATC ATC GTC ATC ATC TTC ATC GCC AGC TTC
1 ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC
* * *
61482 ATC GTC ATC ATC ATC GTC ATC TTC ATC
1 ATC ATC ATC ATC ATC ATC ATC ATC ATC
61509 GTCAGCTTCA
Statistics
Matches: 53, Mismatches: 19, Indels: 0
0.74 0.26 0.00
Matches are distributed among these distances:
3 53 1.00
ACGTcount: A:0.23, C:0.35, G:0.07, T:0.36
Consensus pattern (3 bp):
ATC
Found at i:61451 original size:12 final size:12
Alignment explanation
Indices: 61438--61520 Score: 94
Period size: 12 Copynumber: 6.9 Consensus size: 12
61428 GTTTGGATCA
*
61438 TCATCTTCATCA
1 TCATCTTCATCG
* * *
61450 TCATCATCGTCA
1 TCATCTTCATCG
61462 TCATCTTCATCG
1 TCATCTTCATCG
* *
61474 CCAGCTTCATCG
1 TCATCTTCATCG
*
61486 TCATCATCATCG
1 TCATCTTCATCG
61498 TCATCTTCATCG
1 TCATCTTCATCG
*
61510 TCAGCTTCATC
1 TCATCTTCATC
61521 TTCTGCGACC
Statistics
Matches: 59, Mismatches: 12, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
12 59 1.00
ACGTcount: A:0.20, C:0.35, G:0.08, T:0.36
Consensus pattern (12 bp):
TCATCTTCATCG
Found at i:61482 original size:36 final size:36
Alignment explanation
Indices: 61442--61520 Score: 122
Period size: 36 Copynumber: 2.2 Consensus size: 36
61432 GGATCATCAT
*
61442 CTTCATCATCATCATCGTCATCATCTTCATCGCCAG
1 CTTCATCATCATCATCATCATCATCTTCATCGCCAG
* * *
61478 CTTCATCGTCATCATCATCGTCATCTTCATCGTCAG
1 CTTCATCATCATCATCATCATCATCTTCATCGCCAG
61514 CTTCATC
1 CTTCATC
61521 TTCTGCGACC
Statistics
Matches: 39, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
36 39 1.00
ACGTcount: A:0.20, C:0.35, G:0.09, T:0.35
Consensus pattern (36 bp):
CTTCATCATCATCATCATCATCATCTTCATCGCCAG
Found at i:61521 original size:18 final size:18
Alignment explanation
Indices: 61462--61523 Score: 79
Period size: 18 Copynumber: 3.4 Consensus size: 18
61452 ATCATCGTCA
*
61462 TCATCTTCATCGCCAGCT
1 TCATCTTCATCGTCAGCT
* * * *
61480 TCATCGTCATCATCATCG
1 TCATCTTCATCGTCAGCT
61498 TCATCTTCATCGTCAGCT
1 TCATCTTCATCGTCAGCT
61516 TCATCTTC
1 TCATCTTC
61524 TGCGACCGCT
Statistics
Matches: 35, Mismatches: 9, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
18 35 1.00
ACGTcount: A:0.18, C:0.35, G:0.10, T:0.37
Consensus pattern (18 bp):
TCATCTTCATCGTCAGCT
Found at i:61523 original size:6 final size:6
Alignment explanation
Indices: 61438--61523 Score: 64
Period size: 6 Copynumber: 14.3 Consensus size: 6
61428 GTTTGGATCA
* * * * * * * *
61438 TCATCT TCATCA TCATCA TCGTCA TCATCT TCATCG CCAGCT TCATCG
1 TCATCT TCATCT TCATCT TCATCT TCATCT TCATCT TCATCT TCATCT
* * * *
61486 TCATCA TCATCG TCATCT TCATCG TCAGCT TCATCT TC
1 TCATCT TCATCT TCATCT TCATCT TCATCT TCATCT TC
61524 TGCGACCGCT
Statistics
Matches: 62, Mismatches: 18, Indels: 0
0.77 0.22 0.00
Matches are distributed among these distances:
6 62 1.00
ACGTcount: A:0.20, C:0.35, G:0.08, T:0.37
Consensus pattern (6 bp):
TCATCT
Found at i:63300 original size:198 final size:198
Alignment explanation
Indices: 62962--64045 Score: 2098
Period size: 198 Copynumber: 5.5 Consensus size: 198
62952 TTTAAATTAG
* *
62962 TATCGACACAAACTCTATTAGTGTCGACACATTATTTAGATATATTCTCACATAAAACCGGTATA
1 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTCTCACATAAAACCGGTATA
63027 ATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
66 ATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
63092 CGACACTTTTTATATATGGATCGACACTTTATGGGTGCACCCTGTTTTCCATTCATTCTGGAAA-
131 CGACACTTTTTATATATGGATCGACACTTTATGGGTGCACCCTGTTTTCCATTCATTCTGGAAAT
63156 ACAA
196 A-AA
63160 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTCTCACATAAAACCGGTATA
1 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTCTCACATAAAACCGGTATA
63225 ATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
66 ATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
63290 CGACACTTTTTATATATGGATCGACACTTTATGGGTGCACCCTGTTTTCCATTCATTCTGGAAAT
131 CGACACTTTTTATATATGGATCGACACTTTATGGGTGCACCCTGTTTTCCATTCATTCTGGAAAT
63355 AAA
196 AAA
*
63358 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTATA
1 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTCTCACATAAAACCGGTATA
63423 ATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
66 ATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
63488 CGACACTTTTTATATATGGATCGACACTTTATGGGTGCACCCTGTTTTCCATTCATTCTGGAAAT
131 CGACACTTTTTATATATGGATCGACACTTTATGGGTGCACCCTGTTTTCCATTCATTCTGGAAAT
63553 AAA
196 AAA
*
63556 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTATA
1 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTCTCACATAAAACCGGTATA
63621 ATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
66 ATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
*
63686 CGACACTTTTTATATATGGATCGACACTTTATGGGTGCACCCTGTTTTCCATTCATTCTGGAAAA
131 CGACACTTTTTATATATGGATCGACACTTTATGGGTGCACCCTGTTTTCCATTCATTCTGGAAAT
63751 AAA
196 AAA
63754 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTCTCACATAAAACCGGTATA
1 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTCTCACATAAAACCGGTATA
63819 ATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
66 ATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
63884 CGACACTTTTTATATATGGATCGACACTTTATGGGTGCACCCTGTTTTCCATTCATTCTGGAAAT
131 CGACACTTTTTATATATGGATCGACACTTTATGGGTGCACCCTGTTTTCCATTCATTCTGGAAAT
63949 AAA
196 AAA
*
63952 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTATA
1 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTCTCACATAAAACCGGTATA
64017 ATTGTACCGGTTAGATTGAAAAATTACAT
66 ATTGTACCGGTTAGATTGAAAAATTACAT
64046 CCTTTTGGCC
Statistics
Matches: 878, Mismatches: 7, Indels: 2
0.99 0.01 0.00
Matches are distributed among these distances:
198 877 1.00
199 1 0.00
ACGTcount: A:0.32, C:0.17, G:0.15, T:0.36
Consensus pattern (198 bp):
TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTCTCACATAAAACCGGTATA
ATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
CGACACTTTTTATATATGGATCGACACTTTATGGGTGCACCCTGTTTTCCATTCATTCTGGAAAT
AAA
Found at i:64216 original size:19 final size:19
Alignment explanation
Indices: 64170--64218 Score: 80
Period size: 19 Copynumber: 2.6 Consensus size: 19
64160 TTATATTCAC
*
64170 ATACAAAAATATAAATCGT
1 ATACAAAATTATAAATCGT
*
64189 ATACAAAATTATAAATCTT
1 ATACAAAATTATAAATCGT
64208 ATACAAAATTA
1 ATACAAAATTA
64219 ACCCTACATT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
19 28 1.00
ACGTcount: A:0.57, C:0.10, G:0.02, T:0.31
Consensus pattern (19 bp):
ATACAAAATTATAAATCGT
Found at i:66046 original size:33 final size:33
Alignment explanation
Indices: 66009--66074 Score: 105
Period size: 33 Copynumber: 2.0 Consensus size: 33
65999 CATCTTAATA
*
66009 TCACCCCTTAACACCCCAACTTCTTTCACCACT
1 TCACCCCTCAACACCCCAACTTCTTTCACCACT
* *
66042 TCACCCCTCAACACCTCTACTTCTTTCACCACT
1 TCACCCCTCAACACCCCAACTTCTTTCACCACT
66075 CCATCTATTT
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.23, C:0.48, G:0.00, T:0.29
Consensus pattern (33 bp):
TCACCCCTCAACACCCCAACTTCTTTCACCACT
Found at i:66148 original size:21 final size:21
Alignment explanation
Indices: 66108--66172 Score: 69
Period size: 21 Copynumber: 3.1 Consensus size: 21
66098 CCCCTTATGC
* *
66108 CTCTCGAGTGTATCTTCGACT
1 CTCTCGAGTTTCTCTTCGACT
*
66129 CTCTCGAGTTTCTCTACGACT
1 CTCTCGAGTTTCTCTTCGACT
* *
66150 -TGATCAAGTTTCTCTTCGACT
1 CT-CTCGAGTTTCTCTTCGACT
66171 CT
1 CT
66173 TGATTGTCTT
Statistics
Matches: 36, Mismatches: 6, Indels: 3
0.80 0.13 0.07
Matches are distributed among these distances:
20 1 0.03
21 34 0.94
22 1 0.03
ACGTcount: A:0.15, C:0.29, G:0.15, T:0.40
Consensus pattern (21 bp):
CTCTCGAGTTTCTCTTCGACT
Found at i:68420 original size:17 final size:18
Alignment explanation
Indices: 68398--68440 Score: 61
Period size: 20 Copynumber: 2.3 Consensus size: 18
68388 ATATATCCGG
68398 TATCATTT-TACCGGTTT
1 TATCATTTATACCGGTTT
68415 TATCATTTTGATACCGGTTT
1 TATCA-TTT-ATACCGGTTT
68435 TATCAT
1 TATCAT
68441 ATTTTTACCT
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
17 5 0.22
18 3 0.13
19 1 0.04
20 14 0.61
ACGTcount: A:0.21, C:0.16, G:0.12, T:0.51
Consensus pattern (18 bp):
TATCATTTATACCGGTTT
Found at i:68458 original size:20 final size:19
Alignment explanation
Indices: 68403--68449 Score: 67
Period size: 20 Copynumber: 2.4 Consensus size: 19
68393 TCCGGTATCA
68403 TTTTACCGGTTTTATCATT
1 TTTTACCGGTTTTATCATT
*
68422 TTGATACCGGTTTTATCATAT
1 TT-TTACCGGTTTTATCAT-T
68443 TTTTACC
1 TTTTACC
68450 TGTTATATCG
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
19 2 0.08
20 19 0.79
21 3 0.12
ACGTcount: A:0.19, C:0.17, G:0.11, T:0.53
Consensus pattern (19 bp):
TTTTACCGGTTTTATCATT
Found at i:68597 original size:20 final size:20
Alignment explanation
Indices: 68571--68616 Score: 76
Period size: 20 Copynumber: 2.3 Consensus size: 20
68561 CACTTTTAAA
68571 TTTACCGGTTTTATCAT-TT
1 TTTACCGGTTTTATCATATT
68590 TGTTACCGGTTTTATCATATT
1 T-TTACCGGTTTTATCATATT
68611 TTTACC
1 TTTACC
68617 TGGTATATCG
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
19 1 0.04
20 21 0.84
21 3 0.12
ACGTcount: A:0.17, C:0.17, G:0.11, T:0.54
Consensus pattern (20 bp):
TTTACCGGTTTTATCATATT
Found at i:73728 original size:33 final size:34
Alignment explanation
Indices: 73662--73730 Score: 131
Period size: 34 Copynumber: 2.1 Consensus size: 34
73652 CTGGTTCAAG
73662 CTATCAAAGTTATTTGCATAGTGAAAAAACTTAC
1 CTATCAAAGTTATTTGCATAGTGAAAAAACTTAC
73696 CTATCAAAGTTATTTGCATAGTG-AAAAACTTAC
1 CTATCAAAGTTATTTGCATAGTGAAAAAACTTAC
73729 CT
1 CT
73731 GTATAAGACC
Statistics
Matches: 35, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
33 12 0.34
34 23 0.66
ACGTcount: A:0.39, C:0.16, G:0.12, T:0.33
Consensus pattern (34 bp):
CTATCAAAGTTATTTGCATAGTGAAAAAACTTAC
Done.