Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01001845.1 Hibiscus syriacus cultivar Beakdansim tig00003740_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: 100316
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.34
Found at i:6433 original size:27 final size:27
Alignment explanation
Indices: 6402--6467 Score: 71
Period size: 27 Copynumber: 2.4 Consensus size: 27
6392 AGATTTTTGG
*
6402 TTTTTGTTTTTTTTACTTTCT-TTTGTTA
1 TTTTT-TTTCTTTTACTTT-TATTTGTTA
*
6430 TTTTTTTTCTTTTTCTTTTATTTGTTA
1 TTTTTTTTCTTTTACTTTTATTTGTTA
*
6457 TATTATTTTCT
1 T-TTTTTTTCT
6468 CTTATTCTAC
Statistics
Matches: 33, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
26 1 0.03
27 19 0.58
28 13 0.39
ACGTcount: A:0.09, C:0.08, G:0.05, T:0.79
Consensus pattern (27 bp):
TTTTTTTTCTTTTACTTTTATTTGTTA
Found at i:6683 original size:24 final size:24
Alignment explanation
Indices: 6655--6714 Score: 93
Period size: 24 Copynumber: 2.5 Consensus size: 24
6645 AAATATTAAT
6655 AAAACTCAAACAACATTTTAACCA
1 AAAACTCAAACAACATTTTAACCA
*
6679 AAAACTCAAACAACATTTTAACTA
1 AAAACTCAAACAACATTTTAACCA
* *
6703 ACAACCCAAACA
1 AAAACTCAAACA
6715 CAAAATACTA
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
24 33 1.00
ACGTcount: A:0.55, C:0.27, G:0.00, T:0.18
Consensus pattern (24 bp):
AAAACTCAAACAACATTTTAACCA
Found at i:7809 original size:102 final size:103
Alignment explanation
Indices: 7572--7879 Score: 537
Period size: 102 Copynumber: 3.0 Consensus size: 103
7562 TATGGATACA
* * *
7572 AAGAAGAAGAACAAAATACAATACCATCGGAGTAACTAGCAATTACCATTGAAGACCAGTTCAAA
1 AAGAAGAAGAACAAAATACAGTACCATCGGAGTAACTAACAATTACCATTCAAGACCAGTTCAAA
7637 CCAAATGCAGATTTTAAGAAGGAACAAAACTCACCAAG
66 CCAAATGCAGATTTTAAGAAGGAACAAAACTCACCAAG
*
7675 AAGAAGAAGAACAAAATACAGTACCATCGGAGTAACTAACAATTACCATACAAGACCAGTTCAAA
1 AAGAAGAAGAACAAAATACAGTACCATCGGAGTAACTAACAATTACCATTCAAGACCAGTTCAAA
* *
7740 CCAAATGCAGA-TTGAAGAAGGAACAAAACTAACCAAG
66 CCAAATGCAGATTTTAAGAAGGAACAAAACTCACCAAG
*
7777 AAGAAGAAGAACAAAATACAGTACAATCGGAGTAACTAACAATTACCATTCAAGACCAGTTCAAA
1 AAGAAGAAGAACAAAATACAGTACCATCGGAGTAACTAACAATTACCATTCAAGACCAGTTCAAA
*
7842 CCAAACGCAGATTTTAAGAAGGAACAAAACTCACCAAG
66 CCAAATGCAGATTTTAAGAAGGAACAAAACTCACCAAG
7880 CATAAACAAA
Statistics
Matches: 193, Mismatches: 11, Indels: 2
0.94 0.05 0.01
Matches are distributed among these distances:
102 97 0.50
103 96 0.50
ACGTcount: A:0.50, C:0.20, G:0.15, T:0.15
Consensus pattern (103 bp):
AAGAAGAAGAACAAAATACAGTACCATCGGAGTAACTAACAATTACCATTCAAGACCAGTTCAAA
CCAAATGCAGATTTTAAGAAGGAACAAAACTCACCAAG
Found at i:16651 original size:2 final size:2
Alignment explanation
Indices: 16644--16669 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
16634 CCCAAGTAAT
16644 TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC
16670 ATTTGGGGTT
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:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
TC
Found at i:33092 original size:139 final size:144
Alignment explanation
Indices: 32759--33111 Score: 522
Period size: 139 Copynumber: 2.5 Consensus size: 144
32749 ATGTTCAATG
* * * *
32759 ATCCTAA-TGATTATGTATGTTTATAGAATATAAACCATCAGTTAATTATGGGATCATTCCTTTT
1 ATCCTAATTGATTATATATGTTTATAGAATTTACACCATCATTTAATTATGGGATCATTCCTTTT
* *
32823 AGATTTTTTTTACTCTGAATGAATATAATATAATATAATACATATTTAAAGATTTTTAACTATTT
66 AGA-TTTGTTTACTCTGAA-GAATAGAATATAATATAATACATATTTAAAGATTTTTAACTATTT
* *
32888 GATAATAAACGGTCAT
129 GAAAATAAACGGTAAT
32904 ATCCTAATTGATTATATATGTTTATAGAATTTACACCATCATTTAATTATGGGATCATTCCTTTT
1 ATCCTAATTGATTATATATGTTTATAGAATTTACACCATCATTTAATTATGGGATCATTCCTTTT
* *
32969 AGATTTGTTTACTC-G-A-AAT-GAATATAATATAATACATGTTTAAAGATTTTTAA-TCGTTTG
66 AGATTTGTTTACTCTGAAGAATAGAATATAATATAATACATATTTAAAGATTTTTAACT-ATTTG
* *
33029 AAAATAATCGTTAAT
130 AAAATAAACGGTAAT
33044 AT-CTAATTGATTATATATGTTTATAGAATTTACACCATCATTTAATTATGGGATCATTCCTTTT
1 ATCCTAATTGATTATATATGTTTATAGAATTTACACCATCATTTAATTATGGGATCATTCCTTTT
33108 AGAT
66 AGAT
33112 ATAAAGATTT
Statistics
Matches: 194, Mismatches: 12, Indels: 10
0.90 0.06 0.05
Matches are distributed among these distances:
139 67 0.35
140 49 0.25
141 3 0.02
143 1 0.01
144 1 0.01
145 17 0.09
146 56 0.29
ACGTcount: A:0.36, C:0.10, G:0.10, T:0.44
Consensus pattern (144 bp):
ATCCTAATTGATTATATATGTTTATAGAATTTACACCATCATTTAATTATGGGATCATTCCTTTT
AGATTTGTTTACTCTGAAGAATAGAATATAATATAATACATATTTAAAGATTTTTAACTATTTGA
AAATAAACGGTAAT
Found at i:34663 original size:2 final size:2
Alignment explanation
Indices: 34658--34695 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
34648 ATTGATCCTA
34658 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
34696 TATTCCTTAC
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:35814 original size:81 final size:82
Alignment explanation
Indices: 35706--35884 Score: 195
Period size: 81 Copynumber: 2.2 Consensus size: 82
35696 TTGTAGCGGC
* * * *
35706 GTTTTTAGAACAAACGCCGTTAAAGACTCGT-ACTATAGCGGCGTTTTTATAAAAATGACGCTA-
1 GTTTTTA-TACAAACGCCGCTAAAGACTCGTGA-TATAGCGGCATTTTTATAAAAACGACGCTAT
35769 AAAAT-GTACTTTAGTGGCAT
64 AAAATAGTACTTTAGTGG--T
* * * * * *
35789 -TTTTTATACAAACGCCGCTATAGACTCGTGATTTAGTGGCATTTTTATATAAACGCCGCTATAG
1 GTTTTTATACAAACGCCGCTAAAGACTCGTGATATAGCGGCATTTTTATAAAAACGACGCTATAA
*
35853 ACTAGTACTTTAGTGGT
66 AATAGTACTTTAGTGGT
35870 GTTTTTATACAAACG
1 GTTTTTATACAAACG
35885 ATGCTAAAAA
Statistics
Matches: 81, Mismatches: 11, Indels: 9
0.80 0.11 0.09
Matches are distributed among these distances:
81 45 0.56
82 24 0.30
83 12 0.15
ACGTcount: A:0.31, C:0.16, G:0.18, T:0.35
Consensus pattern (82 bp):
GTTTTTATACAAACGCCGCTAAAGACTCGTGATATAGCGGCATTTTTATAAAAACGACGCTATAA
AATAGTACTTTAGTGGT
Found at i:35961 original size:124 final size:124
Alignment explanation
Indices: 35812--36039 Score: 291
Period size: 124 Copynumber: 1.8 Consensus size: 124
35802 GCCGCTATAG
* * * *
35812 ACTCGTGATTTAGTGGCATTTTTATATAAACGCCGCTATAGACTAGTACTTTAGTGGTGTTTTTA
1 ACTCGTGATTTAGTGGCACTTTTATATAAACGCCGCTAAAGACTA-TACTTTAATGGTGTTTTAA
* *
35877 -TACAAACGATGCTAAA-AACTCATACTTTAGTGGCGTTTTAAGCCCAAACGCCTCCAAAT
65 GCACAAACGACGCTAAATAA-TCATACTTTAGTGGCGTTTTAAGCCCAAACGCCTCCAAAT
* * * * *
35936 ACTCGT-ACTTTAGTGTCACTTTTATATAAATGCCGCTAAATATTATAGTTTAATGGTGTTTTAA
1 ACTCGTGA-TTTAGTGGCACTTTTATATAAACGCCGCTAAAGACTATACTTTAATGGTGTTTTAA
* *
36000 GCACAAACGCCGCTAAATAATCATTCTTTAGTGGCGTTTT
65 GCACAAACGACGCTAAATAATCATACTTTAGTGGCGTTTT
36040 TATACAAATG
Statistics
Matches: 88, Mismatches: 13, Indels: 6
0.82 0.12 0.06
Matches are distributed among these distances:
123 17 0.19
124 69 0.78
125 2 0.02
ACGTcount: A:0.29, C:0.18, G:0.16, T:0.36
Consensus pattern (124 bp):
ACTCGTGATTTAGTGGCACTTTTATATAAACGCCGCTAAAGACTATACTTTAATGGTGTTTTAAG
CACAAACGACGCTAAATAATCATACTTTAGTGGCGTTTTAAGCCCAAACGCCTCCAAAT
Found at i:36047 original size:41 final size:41
Alignment explanation
Indices: 35703--36047 Score: 198
Period size: 41 Copynumber: 8.4 Consensus size: 41
35693 CATTTGTAGC
* * * * * *
35703 GGCGTTTTTAGAACAAACGCCGTTAAAGACTCGTACTATAGC
1 GGCGTTTTTA-TACAAACGCCGCTAAAGAATCATACTTTAGT
* * * *
35745 GGCGTTTTTATAAAAATGACGCTAAA-AAT-GTACTTTAGT
1 GGCGTTTTTATACAAACGCCGCTAAAGAATCATACTTTAGT
* * * *
35784 GGCATTTTTTATACAAACGCCGCTATAGACTCGTGA-TTTAGT
1 GGC-GTTTTTATACAAACGCCGCTAAAGAATCAT-ACTTTAGT
* * * *
35826 GGCATTTTTATATAAACGCCGCTATAGACT-AGTACTTTAGT
1 GGCGTTTTTATACAAACGCCGCTAAAGAATCA-TACTTTAGT
* **
35867 GGTGTTTTTATACAAACGATGCTAAA-AACTCATACTTTAGT
1 GGCGTTTTTATACAAACGCCGCTAAAGAA-TCATACTTTAGT
* ** * * * * *
35908 GGCGTTTTAAGCCCAAACGCCTCCAAATACTCGTACTTTAGT
1 GGCGTTTTTA-TACAAACGCCGCTAAAGAATCATACTTTAGT
* ** * * * * * *
35950 GTCACTTTTATATAAATGCCGCTAAA-TATTATAGTTTAAT
1 GGCGTTTTTATACAAACGCCGCTAAAGAATCATACTTTAGT
* * * * *
35990 GGTGTTTTAAGCACAAACGCCGCTAAATAATCATTCTTTAGT
1 GGCGTTTTTA-TACAAACGCCGCTAAAGAATCATACTTTAGT
36032 GGCGTTTTTATACAAA
1 GGCGTTTTTATACAAA
36048 TGTTGCTATA
Statistics
Matches: 225, Mismatches: 66, Indels: 25
0.71 0.21 0.08
Matches are distributed among these distances:
39 11 0.05
40 35 0.16
41 111 0.49
42 66 0.29
43 2 0.01
ACGTcount: A:0.31, C:0.18, G:0.17, T:0.34
Consensus pattern (41 bp):
GGCGTTTTTATACAAACGCCGCTAAAGAATCATACTTTAGT
Found at i:39545 original size:21 final size:22
Alignment explanation
Indices: 39521--39580 Score: 77
Period size: 21 Copynumber: 2.8 Consensus size: 22
39511 TGATTTATTA
*
39521 TTATGGATTTCAATTTTCTTG-
1 TTATGGATTTCAAGTTTCTTGT
* *
39542 TTATGGATTTTAAGTTTGTTGT
1 TTATGGATTTCAAGTTTCTTGT
*
39564 TTATGGATGTCAAGTTT
1 TTATGGATTTCAAGTTT
39581 ATTGGAAAAT
Statistics
Matches: 33, Mismatches: 5, Indels: 1
0.85 0.13 0.03
Matches are distributed among these distances:
21 18 0.55
22 15 0.45
ACGTcount: A:0.20, C:0.05, G:0.20, T:0.55
Consensus pattern (22 bp):
TTATGGATTTCAAGTTTCTTGT
Found at i:39864 original size:43 final size:43
Alignment explanation
Indices: 39780--39915 Score: 132
Period size: 43 Copynumber: 3.2 Consensus size: 43
39770 GATCTTTTGT
** *
39780 GGCATTT-GTGGGAAAAACATCGCTAAATCTCAAGACCTATTGC
1 GGCATTTGGT-GGAAAAACGCCGCTAAATATCAAGACCTATTGC
* * * *
39823 GGCGTTTGGTGGACAAACGCCGCTAAATATCAACG-CTTATTGT
1 GGCATTTGGTGGAAAAACGCCGCTAAATATCAA-GACCTATTGC
* * ***
39866 GGCATTTGTTGGAAAAACGCCGCTATATATCGTTACCTATTGC
1 GGCATTTGGTGGAAAAACGCCGCTAAATATCAAGACCTATTGC
39909 GGCATTT
1 GGCATTT
39916 TTTGTTACCA
Statistics
Matches: 74, Mismatches: 16, Indels: 6
0.77 0.17 0.06
Matches are distributed among these distances:
43 71 0.96
44 3 0.04
ACGTcount: A:0.27, C:0.21, G:0.23, T:0.29
Consensus pattern (43 bp):
GGCATTTGGTGGAAAAACGCCGCTAAATATCAAGACCTATTGC
Found at i:42274 original size:7 final size:8
Alignment explanation
Indices: 42236--42271 Score: 65
Period size: 8 Copynumber: 4.6 Consensus size: 8
42226 ATTAAACACA
42236 TATTTTAT
1 TATTTTAT
42244 TATTTTAT
1 TATTTTAT
42252 TATTTTAT
1 TATTTTAT
42260 TA-TTTAT
1 TATTTTAT
42267 TATTT
1 TATTT
42272 ATTTTATTTC
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
7 7 0.26
8 20 0.74
ACGTcount: A:0.25, C:0.00, G:0.00, T:0.75
Consensus pattern (8 bp):
TATTTTAT
Found at i:42279 original size:19 final size:16
Alignment explanation
Indices: 42236--42271 Score: 65
Period size: 15 Copynumber: 2.3 Consensus size: 16
42226 ATTAAACACA
42236 TATTTTATTATTTTAT
1 TATTTTATTATTTTAT
42252 TATTTTATTA-TTTAT
1 TATTTTATTATTTTAT
42267 TATTT
1 TATTT
42272 ATTTTATTTC
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
15 10 0.50
16 10 0.50
ACGTcount: A:0.25, C:0.00, G:0.00, T:0.75
Consensus pattern (16 bp):
TATTTTATTATTTTAT
Found at i:43630 original size:3 final size:3
Alignment explanation
Indices: 43624--43661 Score: 51
Period size: 3 Copynumber: 12.3 Consensus size: 3
43614 ACTCTTGTTT
43624 TTA TTA TTA TCTA -TA TTA TTA TTA TATA TTA TTA TTA T
1 TTA TTA TTA T-TA TTA TTA TTA TTA T-TA TTA TTA TTA T
43662 ATATATTACT
Statistics
Matches: 32, Mismatches: 0, Indels: 6
0.84 0.00 0.16
Matches are distributed among these distances:
2 2 0.06
3 25 0.78
4 5 0.16
ACGTcount: A:0.34, C:0.03, G:0.00, T:0.63
Consensus pattern (3 bp):
TTA
Found at i:43642 original size:15 final size:14
Alignment explanation
Indices: 43624--43669 Score: 67
Period size: 15 Copynumber: 3.2 Consensus size: 14
43614 ACTCTTGTTT
43624 TTATTATTATCTATA
1 TTATTATTAT-TATA
43639 TTATTATTA-TATA
1 TTATTATTATTATA
43652 TTATTATTATATATA
1 TTATTATTAT-TATA
43667 TTA
1 TTA
43670 CTAACCAAAC
Statistics
Matches: 29, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
13 13 0.45
15 16 0.55
ACGTcount: A:0.37, C:0.02, G:0.00, T:0.61
Consensus pattern (14 bp):
TTATTATTATTATA
Found at i:45115 original size:14 final size:14
Alignment explanation
Indices: 45096--45132 Score: 60
Period size: 13 Copynumber: 2.8 Consensus size: 14
45086 TCCTTTACCA
45096 TTTATTTATTTATT
1 TTTATTTATTTATT
45110 TTTATTTA-TTATT
1 TTTATTTATTTATT
45123 TTT-TTTATTT
1 TTTATTTATTT
45133 CTATTTTACT
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
12 4 0.18
13 10 0.45
14 8 0.36
ACGTcount: A:0.19, C:0.00, G:0.00, T:0.81
Consensus pattern (14 bp):
TTTATTTATTTATT
Found at i:55595 original size:105 final size:105
Alignment explanation
Indices: 55413--56290 Score: 1567
Period size: 105 Copynumber: 8.3 Consensus size: 105
55403 AGGTTTTACC
* *
55413 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGATTCCAGACAACGCAAGTTCAACTTCATG
1 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
*
55478 ACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAATTT
66 ACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAAATT
55518 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
1 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
* *
55583 ACGAAGGGACCGCTGGTTGTCAACAAATATTTCTCAATTT
66 ACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAAATT
* *
55623 CAGAGCCAATTTTAACTTCACAACGAATGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
1 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
55688 ACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAAATT
66 ACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAAATT
*
55728 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAATTCAACTTCACG
1 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
*
55793 ACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAGATT
66 ACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAAATT
*
55833 CAGAGTCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
1 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
55898 ACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAAATT
66 ACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAAATT
*
55938 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAATTTCACG
1 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
56003 ACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAAATT
66 ACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAAATT
*
56043 CAGAGCCAATTTCAACTTCACAATGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
1 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
56108 ACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAAATT
66 ACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAAATT
*
56148 CAGAGCCAATTTCAACTTCACAACGAATGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
1 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
* * *
56213 ACGAAGGGACTGCTGGTTGTCAACAAACAATTTCCCAATTT
66 ACGAAGGGACCGCTGGTTGTCAACAAAC-ATTTCTCAAATT
* * *
56254 CAGGAGCCAATTTCAACTTCATAGCGAAAGATATTGG
1 CA-GAGCCAATTTCAACTTCACAACGAAGGATATTGG
56291 CCTCGAAACA
Statistics
Matches: 745, Mismatches: 26, Indels: 2
0.96 0.03 0.00
Matches are distributed among these distances:
105 702 0.94
106 12 0.02
107 31 0.04
ACGTcount: A:0.34, C:0.25, G:0.18, T:0.23
Consensus pattern (105 bp):
CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
ACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAAATT
Found at i:58456 original size:4 final size:4
Alignment explanation
Indices: 58442--58543 Score: 52
Period size: 4 Copynumber: 26.0 Consensus size: 4
58432 ATTTTTTCCC
* * *
58442 TTAT CTTAT TTAT TTAG TTAT CTAT TTAT TTA- TT-T TTCT TTA- TT-T
1 TTAT -TTAT TTAT TTAT TTAT TTAT TTAT TTAT TTAT TTAT TTAT TTAT
* * * * * **
58487 TTCT TTAT CT-T TGAT TTAT TTACT CATAT TTGT TTAT TTAT TTAT CCAT
1 TTAT TTAT TTAT TTAT TTAT TTA-T -TTAT TTAT TTAT TTAT TTAT TTAT
58536 TTAT TTAT
1 TTAT TTAT
58544 GTATATTGTC
Statistics
Matches: 72, Mismatches: 18, Indels: 15
0.69 0.17 0.14
Matches are distributed among these distances:
3 9 0.12
4 55 0.76
5 6 0.08
6 2 0.03
ACGTcount: A:0.21, C:0.09, G:0.03, T:0.68
Consensus pattern (4 bp):
TTAT
Found at i:58485 original size:10 final size:10
Alignment explanation
Indices: 58470--58494 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
58460 TATCTATTTA
58470 TTTATTTTTC
1 TTTATTTTTC
58480 TTTATTTTTC
1 TTTATTTTTC
58490 TTTAT
1 TTTAT
58495 CTTTGATTTA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.12, C:0.08, G:0.00, T:0.80
Consensus pattern (10 bp):
TTTATTTTTC
Found at i:59962 original size:16 final size:17
Alignment explanation
Indices: 59941--59975 Score: 54
Period size: 16 Copynumber: 2.1 Consensus size: 17
59931 TTTTATTATT
*
59941 ATTTAATATAAA-AATA
1 ATTTAAAATAAATAATA
59957 ATTTAAAATAAATAATA
1 ATTTAAAATAAATAATA
59974 AT
1 AT
59976 AAAATTATTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 11 0.65
17 6 0.35
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (17 bp):
ATTTAAAATAAATAATA
Found at i:62376 original size:2 final size:2
Alignment explanation
Indices: 62369--62394 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
62359 GTCATTTCTG
62369 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
62395 GCTTAAATTT
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:65406 original size:45 final size:45
Alignment explanation
Indices: 65342--65523 Score: 310
Period size: 45 Copynumber: 4.0 Consensus size: 45
65332 TGGTATTGTG
*
65342 GGGATGGATGGCATGGTTGGCAATGTTGGCATACTAGGAAGTGGA
1 GGGATGGATGGCATGGTAGGCAATGTTGGCATACTAGGAAGTGGA
*
65387 GGGATGGATGGCATGGTTGGCAATGTTGGCATACTAGGAAGTGGA
1 GGGATGGATGGCATGGTAGGCAATGTTGGCATACTAGGAAGTGGA
* *
65432 GGGATGGATGGCATGGTAGGCAATATTGGCATGCTAGGAAGTGGA
1 GGGATGGATGGCATGGTAGGCAATGTTGGCATACTAGGAAGTGGA
**
65477 GGGATGGATGGCATGGTAGGCAATGTTGGCATGGTAGGAAGTGGA
1 GGGATGGATGGCATGGTAGGCAATGTTGGCATACTAGGAAGTGGA
65522 GG
1 GG
65524 TAGAGCTCCA
Statistics
Matches: 132, Mismatches: 5, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
45 132 1.00
ACGTcount: A:0.25, C:0.08, G:0.44, T:0.23
Consensus pattern (45 bp):
GGGATGGATGGCATGGTAGGCAATGTTGGCATACTAGGAAGTGGA
Found at i:72625 original size:54 final size:54
Alignment explanation
Indices: 72543--72646 Score: 208
Period size: 54 Copynumber: 1.9 Consensus size: 54
72533 GTTCTGACCT
72543 AATACTTGACTCGAATCAACTTATCATAGACTTCAACTAAATTTAAACCAGGTC
1 AATACTTGACTCGAATCAACTTATCATAGACTTCAACTAAATTTAAACCAGGTC
72597 AATACTTGACTCGAATCAACTTATCATAGACTTCAACTAAATTTAAACCA
1 AATACTTGACTCGAATCAACTTATCATAGACTTCAACTAAATTTAAACCA
72647 AATTTGATTT
Statistics
Matches: 50, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
54 50 1.00
ACGTcount: A:0.40, C:0.22, G:0.08, T:0.30
Consensus pattern (54 bp):
AATACTTGACTCGAATCAACTTATCATAGACTTCAACTAAATTTAAACCAGGTC
Found at i:81484 original size:127 final size:128
Alignment explanation
Indices: 81143--81745 Score: 1074
Period size: 127 Copynumber: 4.7 Consensus size: 128
81133 ACTATTTACA
*
81143 TGAAGGCGCGTTCCCGGGGGAGCGCCTTCCATTA-TTTGTCAGAGAATATGTTATCATTGCCCTA
1 TGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTTGTCAGAGAATATGTTATCATTGCCCTA
* * *
81207 TTATGTCACTCATGTCCCTCGGGGATACTATTCATACCAGTACCTATTATTTCTCATGGGACT
66 TTATGTCACTCATGTCCCTCGGGGACACTATTCATATCAGTACCTATTATTTCTCAGGGGACT
*
81270 TGAAGGCGCGTTCCCGGGGGGGGCGCCTTCCATTATTTTGTCAGAGAATATGTTATCATTGCCCT
1 TGAAGGCGCGTTCCC-GGGGGCGCGCCTTCCATTATTTTGTCAGAGAATATGTTATCATTGCCCT
*
81335 A-TATGTCACTCATGTCCATCGGGGACACTATTCATATCAGTACCTATTA-TTCTCAGGGGACT
65 ATTATGTCACTCATGTCCCTCGGGGACACTATTCATATCAGTACCTATTATTTCTCAGGGGACT
81397 TGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTTGTCAGAGAATATGTTATCATTGCCCTA
1 TGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTTGTCAGAGAATATGTTATCATTGCCCTA
*
81462 TTATGTCACTCATGTCCCTCGGGGACACTATTTATATCAGTACCTATTA-TTCTCAGGGGACT
66 TTATGTCACTCATGTCCCTCGGGGACACTATTCATATCAGTACCTATTATTTCTCAGGGGACT
81524 TGAAGGCGCGTTCCCGAGGGG-GCGCCTTCCATTATTTTGTCAGAGAATATGTTATCATTGCCCT
1 TGAAGGCGCGTTCCCG-GGGGCGCGCCTTCCATTATTTTGTCAGAGAATATGTTATCATTGCCCT
*
81588 ATTATGTCACTCATGTCCCTCAGGGACACTATTCATATCAGTACCTATTATTTCTCAGGGGACT
65 ATTATGTCACTCATGTCCCTCGGGGACACTATTCATATCAGTACCTATTATTTCTCAGGGGACT
81652 TGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTTGTCAGA-AATATGTTATCATTGCCCTA
1 TGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTTGTCAGAGAATATGTTATCATTGCCCTA
81716 TTATGTCACTCATGTCCCTCGGGGACACTA
66 TTATGTCACTCATGTCCCTCGGGGACACTA
81746 GATGGATGCG
Statistics
Matches: 459, Mismatches: 11, Indels: 12
0.95 0.02 0.02
Matches are distributed among these distances:
126 49 0.11
127 261 0.57
128 119 0.26
129 30 0.07
ACGTcount: A:0.21, C:0.25, G:0.22, T:0.32
Consensus pattern (128 bp):
TGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTTGTCAGAGAATATGTTATCATTGCCCTA
TTATGTCACTCATGTCCCTCGGGGACACTATTCATATCAGTACCTATTATTTCTCAGGGGACT
Found at i:82230 original size:33 final size:34
Alignment explanation
Indices: 82139--82244 Score: 142
Period size: 34 Copynumber: 3.1 Consensus size: 34
82129 TAAGTTGAAA
* *
82139 TTTAATGTTAAATTTCGAATACTATAATTTATAT
1 TTTAATTTTAAATTTCGAATAATATAATTTATAT
* *
82173 TTTAATTTTAAATTTCGAATAATATTATTTTTAT
1 TTTAATTTTAAATTTCGAATAATATAATTTATAT
* * *
82207 TTTTATTTTAAA-TTCGAACAATATAATTTGTAT
1 TTTAATTTTAAATTTCGAATAATATAATTTATAT
82240 TTTAA
1 TTTAA
82245 AAACATTTAT
Statistics
Matches: 63, Mismatches: 9, Indels: 1
0.86 0.12 0.01
Matches are distributed among these distances:
33 22 0.35
34 41 0.65
ACGTcount: A:0.37, C:0.05, G:0.05, T:0.54
Consensus pattern (34 bp):
TTTAATTTTAAATTTCGAATAATATAATTTATAT
Found at i:82774 original size:21 final size:21
Alignment explanation
Indices: 82750--82848 Score: 109
Period size: 21 Copynumber: 4.9 Consensus size: 21
82740 TAAAAACCCT
*
82750 GCGGGCTAGGCATGTAACCTG
1 GCGGGCTAGGAATGTAACCTG
82771 GCGGGCTAGGAATGTAACCCT-
1 GCGGGCTAGGAATGTAA-CCTG
*
82792 GCGGGCTCGGAATGTAACCTG
1 GCGGGCTAGGAATGTAACCTG
* *
82813 GTGGGCTAGGAA--TAACCCG
1 GCGGGCTAGGAATGTAACCTG
*
82832 GC-GGCT-CGAATGTAACC
1 GCGGGCTAGGAATGTAACC
82849 CTACGGAGAT
Statistics
Matches: 67, Mismatches: 7, Indels: 10
0.80 0.08 0.12
Matches are distributed among these distances:
17 3 0.04
18 4 0.06
19 12 0.18
20 3 0.04
21 42 0.63
22 3 0.04
ACGTcount: A:0.22, C:0.24, G:0.35, T:0.18
Consensus pattern (21 bp):
GCGGGCTAGGAATGTAACCTG
Found at i:82807 original size:42 final size:40
Alignment explanation
Indices: 82744--82848 Score: 142
Period size: 42 Copynumber: 2.6 Consensus size: 40
82734 ATGGTATAAA
* *
82744 AACCCTGCGGGCTAGGCATGTAACCTGGCGGGCTAGGAATGT
1 AACCCTGCGGGCTCGGAATGTAACCTGGCGGGCTAGGAA--T
*
82786 AACCCTGCGGGCTCGGAATGTAACCTGGTGGGCTAGGAAT
1 AACCCTGCGGGCTCGGAATGTAACCTGGCGGGCTAGGAAT
*
82826 AACCCGGC-GGCTC-GAATGTAACC
1 AACCCTGCGGGCTCGGAATGTAACC
82849 CTACGGAGAT
Statistics
Matches: 59, Mismatches: 4, Indels: 4
0.88 0.06 0.06
Matches are distributed among these distances:
38 10 0.17
39 5 0.08
40 8 0.14
42 36 0.61
ACGTcount: A:0.23, C:0.26, G:0.33, T:0.18
Consensus pattern (40 bp):
AACCCTGCGGGCTCGGAATGTAACCTGGCGGGCTAGGAAT
Found at i:82883 original size:20 final size:20
Alignment explanation
Indices: 82858--82903 Score: 65
Period size: 20 Copynumber: 2.3 Consensus size: 20
82848 CCTACGGAGA
*
82858 TGGCATATGACTGGTGGGCT
1 TGGCATATGACTGGAGGGCT
*
82878 TGGCATATGAGTGGAGGGCT
1 TGGCATATGACTGGAGGGCT
*
82898 GGGCAT
1 TGGCAT
82904 GTACCCCTGC
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.17, C:0.13, G:0.43, T:0.26
Consensus pattern (20 bp):
TGGCATATGACTGGAGGGCT
Found at i:84446 original size:18 final size:17
Alignment explanation
Indices: 84415--84464 Score: 55
Period size: 18 Copynumber: 2.9 Consensus size: 17
84405 ATAAAATATT
* * *
84415 AAAATTAATATAAATTC
1 AAAATAAATTTAAATTA
*
84432 ATAATAAACTTTAAATTA
1 AAAATAAA-TTTAAATTA
84450 AAAATAAATTTAAAT
1 AAAATAAATTTAAAT
84465 ATTAACATTA
Statistics
Matches: 27, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
17 13 0.48
18 14 0.52
ACGTcount: A:0.60, C:0.04, G:0.00, T:0.36
Consensus pattern (17 bp):
AAAATAAATTTAAATTA
Found at i:84633 original size:25 final size:25
Alignment explanation
Indices: 84605--84671 Score: 62
Period size: 25 Copynumber: 2.6 Consensus size: 25
84595 ATTCTAAATA
* *
84605 AATAATAATTATATAAATATATTTT
1 AATAATAATAATATAAATATATTAT
* **
84630 AATAAAAATAATATTTATATATTAT
1 AATAATAATAATATAAATATATTAT
* *
84655 ATTAATATAAAATATAA
1 AATAATA-ATAATATAA
84672 TAACTATTTA
Statistics
Matches: 31, Mismatches: 10, Indels: 1
0.74 0.24 0.02
Matches are distributed among these distances:
25 25 0.81
26 6 0.19
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (25 bp):
AATAATAATAATATAAATATATTAT
Found at i:86703 original size:8 final size:8
Alignment explanation
Indices: 86680--86709 Score: 51
Period size: 8 Copynumber: 3.6 Consensus size: 8
86670 CTTAAATTTA
86680 ATTATAAT
1 ATTATAAT
86688 ATTTATAAT
1 A-TTATAAT
86697 ATTATAAT
1 ATTATAAT
86705 ATTAT
1 ATTAT
86710 TTTATTCTAA
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
8 13 0.62
9 8 0.38
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (8 bp):
ATTATAAT
Found at i:87544 original size:17 final size:18
Alignment explanation
Indices: 87504--87551 Score: 62
Period size: 19 Copynumber: 2.7 Consensus size: 18
87494 ATAAACGTTT
87504 TATGAATAGTACTATACGG
1 TATGAATAGTACTATA-GG
*
87523 TATGAATAGTACTAT-TG
1 TATGAATAGTACTATAGG
*
87540 TATGAACAGTAC
1 TATGAATAGTAC
87552 CGTGAACAAA
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
17 12 0.44
19 15 0.56
ACGTcount: A:0.38, C:0.10, G:0.19, T:0.33
Consensus pattern (18 bp):
TATGAATAGTACTATAGG
Found at i:87581 original size:22 final size:22
Alignment explanation
Indices: 87541--87582 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
87531 GTACTATTGT
*
87541 ATGAACAGTACCGTGAACAAAA
1 ATGAACAGTACCATGAACAAAA
* *
87563 ATGAATAGTACCATTAACAA
1 ATGAACAGTACCATGAACAA
87583 TAACTTCAGC
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 17 1.00
ACGTcount: A:0.50, C:0.17, G:0.14, T:0.19
Consensus pattern (22 bp):
ATGAACAGTACCATGAACAAAA
Found at i:89417 original size:15 final size:15
Alignment explanation
Indices: 89397--89434 Score: 67
Period size: 15 Copynumber: 2.5 Consensus size: 15
89387 ATGGAAAATT
89397 CTACGTGAAAGTAAA
1 CTACGTGAAAGTAAA
89412 CTACGTGAAAGTAAA
1 CTACGTGAAAGTAAA
*
89427 CTAAGTGA
1 CTACGTGA
89435 CTATGTGATC
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
15 22 1.00
ACGTcount: A:0.45, C:0.13, G:0.21, T:0.21
Consensus pattern (15 bp):
CTACGTGAAAGTAAA
Found at i:90593 original size:23 final size:24
Alignment explanation
Indices: 90566--90611 Score: 67
Period size: 23 Copynumber: 2.0 Consensus size: 24
90556 TAATTTTGCA
*
90566 CCGAAGTACCGAGTAG-AATTTGT
1 CCGAAGAACCGAGTAGAAATTTGT
*
90589 CCGAAGAACCGCGTAGAAATTTG
1 CCGAAGAACCGAGTAGAAATTTG
90612 CACCGTGTGC
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
23 14 0.70
24 6 0.30
ACGTcount: A:0.33, C:0.20, G:0.26, T:0.22
Consensus pattern (24 bp):
CCGAAGAACCGAGTAGAAATTTGT
Found at i:90636 original size:19 final size:22
Alignment explanation
Indices: 90599--90641 Score: 65
Period size: 20 Copynumber: 2.1 Consensus size: 22
90589 CCGAAGAACC
90599 GCGTAGAAATTTGCACCGT-GT
1 GCGTAGAAATTTGCACCGTAGT
90620 GCGTAG-AATTT-CACCGTAGT
1 GCGTAGAAATTTGCACCGTAGT
90640 GC
1 GC
90642 CATATAAGAT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
19 6 0.29
20 9 0.43
21 6 0.29
ACGTcount: A:0.23, C:0.21, G:0.28, T:0.28
Consensus pattern (22 bp):
GCGTAGAAATTTGCACCGTAGT
Found at i:90790 original size:23 final size:23
Alignment explanation
Indices: 90760--90815 Score: 85
Period size: 23 Copynumber: 2.4 Consensus size: 23
90750 CATATATGTC
90760 CCGAAGGACCACGTAGAATTGTA
1 CCGAAGGACCACGTAGAATTGTA
* *
90783 CCGAAGGATCACGTAGAATTGTC
1 CCGAAGGACCACGTAGAATTGTA
*
90806 CCGAATGACC
1 CCGAAGGACC
90816 GTAGACCCTC
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 29 1.00
ACGTcount: A:0.32, C:0.25, G:0.25, T:0.18
Consensus pattern (23 bp):
CCGAAGGACCACGTAGAATTGTA
Found at i:92919 original size:8 final size:8
Alignment explanation
Indices: 92906--92940 Score: 70
Period size: 8 Copynumber: 4.4 Consensus size: 8
92896 AGTTTACCAA
92906 TATGAATT
1 TATGAATT
92914 TATGAATT
1 TATGAATT
92922 TATGAATT
1 TATGAATT
92930 TATGAATT
1 TATGAATT
92938 TAT
1 TAT
92941 AGAGATTGGA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 27 1.00
ACGTcount: A:0.37, C:0.00, G:0.11, T:0.51
Consensus pattern (8 bp):
TATGAATT
Found at i:93620 original size:16 final size:16
Alignment explanation
Indices: 93599--93639 Score: 57
Period size: 16 Copynumber: 2.6 Consensus size: 16
93589 TAAAATTAAG
93599 TAATTTTTTATAT-AAT
1 TAATTTTTTA-ATGAAT
*
93615 TAATTTTTTAATGATT
1 TAATTTTTTAATGAAT
93631 TAATTTTTT
1 TAATTTTTT
93640 TTACAAAGAT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
15 2 0.09
16 21 0.91
ACGTcount: A:0.32, C:0.00, G:0.02, T:0.66
Consensus pattern (16 bp):
TAATTTTTTAATGAAT
Found at i:93747 original size:2 final size:2
Alignment explanation
Indices: 93740--93792 Score: 90
Period size: 2 Copynumber: 27.0 Consensus size: 2
93730 TAATATCTTC
93740 AT AT AT AT AT AT AT AT AT AT AT AT AT AT -T 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
*
93781 AG AT AT AT AT AT
1 AT AT AT AT AT AT
93793 TGATGAAATA
Statistics
Matches: 48, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
1 1 0.02
2 47 0.98
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (2 bp):
AT
Found at i:94320 original size:30 final size:29
Alignment explanation
Indices: 94285--94341 Score: 87
Period size: 30 Copynumber: 1.9 Consensus size: 29
94275 AACTTAAAAG
* *
94285 AGTTTTGCAATACTGAGATTTAAATAATTT
1 AGTTTTACAATACTGAAATTT-AATAATTT
94315 AGTTTTACAATACTGAAATTTAATAAT
1 AGTTTTACAATACTGAAATTTAATAAT
94342 CCATATAACT
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
29 6 0.24
30 19 0.76
ACGTcount: A:0.40, C:0.07, G:0.11, T:0.42
Consensus pattern (29 bp):
AGTTTTACAATACTGAAATTTAATAATTT
Found at i:94385 original size:30 final size:29
Alignment explanation
Indices: 94351--94675 Score: 125
Period size: 22 Copynumber: 12.2 Consensus size: 29
94341 TCCATATAAC
94351 TACAATAAATTATTTAAAATAAATCAAT-CA
1 TACAATAAA-TA-TTAAAATAAATCAATCCA
94381 TACAAATAAATATTAAAATAAATCAATCCA
1 TAC-AATAAATATTAAAATAAATCAATCCA
*
94411 TACAACTACA-A-T--AATAAATCAATCCA
1 TACAA-TAAATATTAAAATAAATCAATCCA
*
94437 T---AT---T-TTAAAATAAATCAATTCA
1 TACAATAAATATTAAAATAAATCAATCCA
* * *
94459 TACTAATAAATTATTTAAATAAATAAATCAA
1 TAC-AATAAA-TATTAAAATAAATCAATCCA
* *
94490 T-CTATACAA-ATACAAAATAAATCAATCCA
1 TACAATA-AATAT-TAAAATAAATCAATCCA
* * *
94519 T---AT---T-TTAAAATCAATCCATAC-
1 TACAATAAATATTAAAATAAATCAATCCA
*
94540 TA-ATA-AATTATTAAAATAAATCAATCCA
1 TACA-ATAAATATTAAAATAAATCAATCCA
94568 T---AT---T-TTAAAATAAATCAATCCA
1 TACAATAAATATTAAAATAAATCAATCCA
* *
94590 TACTAATAATTATTTAAATAAATCAATCCA
1 TAC-AATAAATATTAAAATAAATCAATCCA
* *
94620 T---AT---T-TTAAAATAAATTAATACA
1 TACAATAAATATTAAAATAAATCAATCCA
* *
94642 TACTAATAAATTTTAAAA-AAATCAATCTA
1 TAC-AATAAATATTAAAATAAATCAATCCA
94671 TACAA
1 TACAA
94676 CTACAATAAT
Statistics
Matches: 226, Mismatches: 25, Indels: 90
0.66 0.07 0.26
Matches are distributed among these distances:
20 1 0.00
21 1 0.00
22 62 0.27
23 4 0.02
24 1 0.00
25 1 0.00
26 24 0.11
27 16 0.07
28 6 0.03
29 48 0.21
30 41 0.18
31 21 0.09
ACGTcount: A:0.54, C:0.13, G:0.00, T:0.33
Consensus pattern (29 bp):
TACAATAAATATTAAAATAAATCAATCCA
Found at i:94399 original size:29 final size:32
Alignment explanation
Indices: 94354--94415 Score: 103
Period size: 29 Copynumber: 2.0 Consensus size: 32
94344 ATATAACTAC
94354 AATAAATTATTTAAAATAAATCAAT-CATACA
1 AATAAATTATTTAAAATAAATCAATCCATACA
94385 AATAAA-TA-TTAAAATAAATCAATCCATACA
1 AATAAATTATTTAAAATAAATCAATCCATACA
94415 A
1 A
94416 CTACAATAAT
Statistics
Matches: 30, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
29 15 0.50
30 9 0.30
31 6 0.20
ACGTcount: A:0.60, C:0.11, G:0.00, T:0.29
Consensus pattern (32 bp):
AATAAATTATTTAAAATAAATCAATCCATACA
Found at i:94528 original size:82 final size:83
Alignment explanation
Indices: 94363--94565 Score: 275
Period size: 78 Copynumber: 2.6 Consensus size: 83
94353 CAATAAATTA
* *
94363 TTTAAAATAAATCAA-TCATACAAATAAA-TA-TT--A-AAATAAATCAATCCATACAACTACAA
1 TTTAAAATAAATCAATTCATACTAATAAATTATTTAAATAAATAAATCAATCCATACAAATACAA
94422 TAATAAATCAATCCATAT
66 TAATAAATCAATCCATAT
*
94440 TTTAAAATAAATCAATTCATACTAATAAATTATTTAAATAAATAAATCAATCTATACAAATACAA
1 TTTAAAATAAATCAATTCATACTAATAAATTATTTAAATAAATAAATCAATCCATACAAATACAA
94505 -AATAAATCAATCCATAT
66 TAATAAATCAATCCATAT
* * *
94522 TTT---A-AAATCAATCCATACTAATAAATTATTAAAATAAATCAATC
1 TTTAAAATAAATCAATTCATACTAATAAATTATTTAAATAAATAAATC
94566 CATATTTTAA
Statistics
Matches: 114, Mismatches: 6, Indels: 11
0.87 0.05 0.08
Matches are distributed among these distances:
77 15 0.13
78 49 0.43
79 3 0.03
80 2 0.02
82 21 0.18
83 24 0.21
ACGTcount: A:0.55, C:0.14, G:0.00, T:0.32
Consensus pattern (83 bp):
TTTAAAATAAATCAATTCATACTAATAAATTATTTAAATAAATAAATCAATCCATACAAATACAA
TAATAAATCAATCCATAT
Found at i:94623 original size:52 final size:52
Alignment explanation
Indices: 94504--94668 Score: 241
Period size: 52 Copynumber: 3.2 Consensus size: 52
94494 TACAAATACA
*
94504 AAATAAATCAATCCATATTTT---A-AAATCAATCCATACTAATAAATTATTA
1 AAATAAATCAATCCATATTTTAAAATAAATCAATCCATACTAAT-AATTATTT
94553 AAATAAATCAATCCATATTTTAAAATAAATCAATCCATACTAATAATTATTT
1 AAATAAATCAATCCATATTTTAAAATAAATCAATCCATACTAATAATTATTT
* * *
94605 AAATAAATCAATCCATATTTTAAAATAAATTAATACATACTAATAAAT-TTT
1 AAATAAATCAATCCATATTTTAAAATAAATCAATCCATACTAATAATTATTT
*
94656 AAAAAAATCAATC
1 AAATAAATCAATC
94669 TATACAACTA
Statistics
Matches: 107, Mismatches: 5, Indels: 6
0.91 0.04 0.05
Matches are distributed among these distances:
49 21 0.20
51 15 0.14
52 53 0.50
53 18 0.17
ACGTcount: A:0.53, C:0.13, G:0.00, T:0.35
Consensus pattern (52 bp):
AAATAAATCAATCCATATTTTAAAATAAATCAATCCATACTAATAATTATTT
Found at i:94655 original size:131 final size:129
Alignment explanation
Indices: 94363--95062 Score: 494
Period size: 131 Copynumber: 5.4 Consensus size: 129
94353 CAATAAATTA
* * * *
94363 TTTAAAATAAATCAATCATACAAATAAATATTAAAATAAATCAATCCATACAACTACAATAATAA
1 TTTAAAATAAATTAATCATACTAATAAATTTTAAAATAAATCAATCTATACAACTACAATAATAA
*
94428 ATCAATCCATATTTTAAAATAAATCAATTCATACTAATAAATTATTTAAATAAATAAAT-CA-AT
66 ATCAATCCATATTTTAAAATAAATCAA-TCATACTAATAAATTATTTAAATAAATCAATCCATAT
* * * * * *
94491 CTATACAAATACAA--AAT-A-AATCAATCCATATTTTAAAATCAATCCATACTAATA-AATTAT
1 -TTTA-AAATA-AATTAATCATACT-AAT--AAATTTTAAAATAAATCAAT-CT-ATACAACTA-
*
94551 TAA-AATAAATCAATCCATATTTTAAAATAAATCAATCCATACTAAT-AATTATTTAAATAAATC
57 CAATAATAAATCAATCCATATTTTAAAATAAATCAAT-CATACTAATAAATTATTTAAATAAATC
94614 AATCCATAT
121 AATCCATAT
94623 TTTAAAATAAATTAATACATACTAATAAATTTTAAAA-AAATCAATCTATACAACTACAATAATA
1 TTTAAAATAAATTAAT-CATACTAATAAATTTTAAAATAAATCAATCTATACAACTACAATAATA
* *
94687 AATTAATTCATA-TTT-AAATAAATCAAT-AT-CTATATAAATTATTTAAAATAAATCAATCCAT
65 AATCAATCCATATTTTAAAATAAATCAATCATACTA-ATAAATTATTT-AAATAAATCAATCCAT
94748 AT
128 AT
* * * **
94750 TTT-AAATAAATTAAT-ATACTAATAAATTATT-TAATAAATCAATCCAT---ATTTTAA-AATA
1 TTTAAAATAAATTAATCATACTAATAAATT-TTAAAATAAATCAATCTATACAACTACAATAATA
* * **
94808 AATCAATTCACTAATAAATTATTTAAAATAAATCAAT-ATA-T-ACAAACTA-CAATAATAAATC
65 AATCAA-TC-C--AT--A-T-TTTAAAATAAATCAATCATACTAATAAATTATTTA-AATAAATC
*
94869 AATCTAT-T
121 AATCCATAT
* * *** *
94877 TTTAAAATAAATCAATTCATACTAATAAATTATTTAAAATAAATCAATCGATA-TTTTAAAATAA
1 TTTAAAATAAATTAA-TCATACTAATAAA-T-TTTAAAATAAATCAATCTATACAACTACAAT-A
* ** *
94941 ATCAATTCATATTAATAAACTATTTAAAATAAATCAATCCATAC-AACTACA--A--T-AATAAA
62 AT-AAATCA-ATCCAT--A-T-TTTAAAATAAATCAAT-CATACTAA-TAAATTATTTAAATAAA
*
95000 TCAATCCATGT
119 TCAATCCATAT
* *
95011 TTTAAAATAAATCAATCCATACTAATAAATATTTAAAATAATTCAATCTATA
1 TTTAAAATAAATTAAT-CATACTAATAAAT-TTTAAAATAAATCAATCTATA
95063 TTTTAAAATA
Statistics
Matches: 469, Mismatches: 48, Indels: 104
0.76 0.08 0.17
Matches are distributed among these distances:
121 9 0.02
122 5 0.01
123 1 0.00
124 18 0.04
125 19 0.04
126 20 0.04
127 40 0.09
128 36 0.08
129 35 0.07
130 66 0.14
131 84 0.18
132 22 0.05
133 40 0.09
134 57 0.12
136 7 0.01
137 7 0.01
138 3 0.01
ACGTcount: A:0.53, C:0.12, G:0.00, T:0.35
Consensus pattern (129 bp):
TTTAAAATAAATTAATCATACTAATAAATTTTAAAATAAATCAATCTATACAACTACAATAATAA
ATCAATCCATATTTTAAAATAAATCAATCATACTAATAAATTATTTAAATAAATCAATCCATAT
Found at i:94724 original size:20 final size:20
Alignment explanation
Indices: 94683--94725 Score: 52
Period size: 20 Copynumber: 2.1 Consensus size: 20
94673 CAACTACAAT
* *
94683 AATAAATTAATTCATATTTA
1 AATAAATCAATTCATATATA
94703 AATAAATCAATATC-TATATA
1 AATAAATCAAT-TCATATATA
94723 AAT
1 AAT
94726 TATTTAAAAT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
20 18 0.90
21 2 0.10
ACGTcount: A:0.53, C:0.07, G:0.00, T:0.40
Consensus pattern (20 bp):
AATAAATCAATTCATATATA
Found at i:94916 original size:32 final size:31
Alignment explanation
Indices: 94877--94984 Score: 108
Period size: 32 Copynumber: 3.7 Consensus size: 31
94867 TCAATCTATT
94877 TTTAAAATAAATCAATTCATACTAATAAATTA
1 TTTAAAATAAATCAATTCATACTAATAAA-TA
*
94909 TTTAAAATAAATC-A---AT-C-GAT--AT-
1 TTTAAAATAAATCAATTCATACTAATAAATA
*
94931 TTTAAAATAAATCAATTCATATTAATAAACTA
1 TTTAAAATAAATCAATTCATACTAATAAA-TA
*
94963 TTTAAAATAAATCAATCCATAC
1 TTTAAAATAAATCAATTCATAC
94985 AACTACAATA
Statistics
Matches: 61, Mismatches: 5, Indels: 20
0.71 0.06 0.23
Matches are distributed among these distances:
22 13 0.21
23 2 0.03
24 1 0.02
26 4 0.07
27 1 0.02
28 4 0.07
30 1 0.02
31 2 0.03
32 33 0.54
ACGTcount: A:0.52, C:0.11, G:0.01, T:0.36
Consensus pattern (31 bp):
TTTAAAATAAATCAATTCATACTAATAAATA
Found at i:94942 original size:54 final size:53
Alignment explanation
Indices: 94861--94979 Score: 202
Period size: 54 Copynumber: 2.2 Consensus size: 53
94851 AAACTACAAT
* *
94861 AATAAATCAATCTATTTTTAAAATAAATCAATTCATACTAATAAATTATTTAA
1 AATAAATCAATCGATTTTTAAAATAAATCAATTCATACTAATAAACTATTTAA
*
94914 AATAAATCAATCGATATTTTAAAATAAATCAATTCATATTAATAAACTATTTAA
1 AATAAATCAATCGAT-TTTTAAAATAAATCAATTCATACTAATAAACTATTTAA
94968 AATAAATCAATC
1 AATAAATCAATC
94980 CATACAACTA
Statistics
Matches: 62, Mismatches: 3, Indels: 1
0.94 0.05 0.02
Matches are distributed among these distances:
53 14 0.23
54 48 0.77
ACGTcount: A:0.52, C:0.10, G:0.01, T:0.37
Consensus pattern (53 bp):
AATAAATCAATCGATTTTTAAAATAAATCAATTCATACTAATAAACTATTTAA
Found at i:95041 original size:22 final size:23
Alignment explanation
Indices: 94965--95039 Score: 73
Period size: 22 Copynumber: 3.2 Consensus size: 23
94955 ATAAACTATT
94965 TAAAATAAATCAATCCATAC-AA
1 TAAAATAAATCAATCCATACTAA
* **
94987 CTACAATAATAAATCAATCCAT-GTTT
1 -T--AA-AATAAATCAATCCATACTAA
95013 TAAAATAAATCAATCCATACTAA
1 TAAAATAAATCAATCCATACTAA
95036 TAAA
1 TAAA
95040 TATTTAAAAT
Statistics
Matches: 41, Mismatches: 6, Indels: 10
0.72 0.11 0.18
Matches are distributed among these distances:
22 15 0.37
23 8 0.20
25 3 0.07
26 15 0.37
ACGTcount: A:0.53, C:0.17, G:0.01, T:0.28
Consensus pattern (23 bp):
TAAAATAAATCAATCCATACTAA
Found at i:95122 original size:54 final size:54
Alignment explanation
Indices: 94683--95212 Score: 454
Period size: 53 Copynumber: 10.1 Consensus size: 54
94673 CAACTACAAT
* *
94683 AATAAATTAATTCATA-TTT-AAATAAATCAAT--AT-CTATATAAATTATTTAA
1 AATAAATCAATCCATATTTTAAAATAAATCAATCCATACTA-ATAAATTATTTAA
*
94733 AATAAATCAATCCATATTTT-AAATAAATTAAT--ATACTAATAAATTATTT--
1 AATAAATCAATCCATATTTTAAAATAAATCAATCCATACTAATAAATTATTTAA
*
94782 AATAAATCAATCCATATTTTAAAATAAATCAATTC--ACTAATAAATTATTTAA
1 AATAAATCAATCCATATTTTAAAATAAATCAATCCATACTAATAAATTATTTAA
** * ** **
94834 AATAAATCAAT--ATA-TACAAACTACAAT-AATAAAT-C-AATCTATT-TTTAA
1 AATAAATCAATCCATATTTTAAAATA-AATCAATCCATACTAATAAATTATTTAA
* ** * ** *
94882 AATAAATCAATTCATACTAATAAATTATTTAAAATAAATCAATCGATA-TTTTAAAATAAATCA
1 AATAAATCAA-TC---C--AT--A-T-TTTAAAATAAATCAATCCATACTAATAAATTATTTAA
* * * ** *
94945 ATTCATATTAATAAACTA-TTTAAAATAAATCAATCCATAC-AACTACA--A--T--
1 AAT-AAATCAATCCA-TATTTTAAAATAAATCAATCCATACTAA-TAAATTATTTAA
*
94994 AATAAATCAATCCATGTTTTAAAATAAATCAATCCATACTAATAAA-TATTTAA
1 AATAAATCAATCCATATTTTAAAATAAATCAATCCATACTAATAAATTATTTAA
* * *
95047 AATAATTCAATCTATATTTTAAAATAAATCAATCGATACTAATAAATTATTTAA
1 AATAAATCAATCCATATTTTAAAATAAATCAATCCATACTAATAAATTATTTAA
95101 AATAAATCAATCCATATTTTAAAATAAATCAATCCATACTAATAAATTATTT-A
1 AATAAATCAATCCATATTTTAAAATAAATCAATCCATACTAATAAATTATTTAA
*
95154 AATAAATCAATCCATATTTTAAAATAAATCAATCCATACTAATAAATCATTTAA
1 AATAAATCAATCCATATTTTAAAATAAATCAATCCATACTAATAAATTATTTAA
95208 AATAA
1 AATAA
95213 TTATTTTAAA
Statistics
Matches: 392, Mismatches: 48, Indels: 76
0.76 0.09 0.15
Matches are distributed among these distances:
47 1 0.00
48 47 0.12
49 41 0.10
50 47 0.12
51 29 0.07
52 14 0.04
53 95 0.24
54 82 0.21
55 3 0.01
56 2 0.01
57 1 0.00
58 2 0.01
59 1 0.00
60 3 0.01
61 11 0.03
62 3 0.01
63 5 0.01
64 5 0.01
ACGTcount: A:0.52, C:0.11, G:0.01, T:0.36
Consensus pattern (54 bp):
AATAAATCAATCCATATTTTAAAATAAATCAATCCATACTAATAAATTATTTAA
Found at i:95123 original size:107 final size:108
Alignment explanation
Indices: 94683--95212 Score: 449
Period size: 107 Copynumber: 5.0 Consensus size: 108
94673 CAACTACAAT
* *
94683 AATAAATTAATTCATA-TTT-AAATAAATCAAT--AT-CTATATAAATTATTTAAAATAAATCAA
1 AATAAATCAATCCATATTTTAAAATAAATCAATCCATACTA-ATAAATTATTTAAAATAAATCAA
* *
94743 TCCATATTTT-AAATAAATTAAT--ATACTAATAAATTATTT--
65 TCTATATTTTAAAATAAATCAATCCATACTAATAAATTATTTAA
*
94782 AATAAATCAATCCATATTTTAAAATAAATCAATTC--ACTAATAAATTATTTAAAATAAATCAA-
1 AATAAATCAATCCATATTTTAAAATAAATCAATCCATACTAATAAATTATTTAAAATAAATCAAT
** * ** **
94844 -TATA-TACAAACTACAAT-AATAAAT-C-AATCTATT-TTTAA
66 CTATATTTTAAAATA-AATCAATCCATACTAATAAATTATTTAA
* * * *
94882 AATAAATCAATTCATACTAATAAATTATTTAAAATAAATCAATCGATATTTTAAAATAAATCAAT
1 AATAAATCAA-TC---C--AT--A-T-TTTAAAATAAATCAATCCATA--CT--AATAAATTATT
* * * * *
94947 TCATATTAAT-AAAC--TA-TTTAAAATAAATCAATCCATAC-AACTACA--A--T--
52 TAAAATAAATCAATCTATATTTTAAAATAAATCAATCCATACTAA-TAAATTATTTAA
* *
94994 AATAAATCAATCCATGTTTTAAAATAAATCAATCCATACTAATAAA-TATTTAAAATAATTCAAT
1 AATAAATCAATCCATATTTTAAAATAAATCAATCCATACTAATAAATTATTTAAAATAAATCAAT
*
95058 CTATATTTTAAAATAAATCAATCGATACTAATAAATTATTTAA
66 CTATATTTTAAAATAAATCAATCCATACTAATAAATTATTTAA
95101 AATAAATCAATCCATATTTTAAAATAAATCAATCCATACTAATAAATTATTT-AAATAAATCAAT
1 AATAAATCAATCCATATTTTAAAATAAATCAATCCATACTAATAAATTATTTAAAATAAATCAAT
* *
95165 CCATATTTTAAAATAAATCAATCCATACTAATAAATCATTTAA
66 CTATATTTTAAAATAAATCAATCCATACTAATAAATTATTTAA
95208 AATAA
1 AATAA
95213 TTATTTTAAA
Statistics
Matches: 346, Mismatches: 40, Indels: 82
0.74 0.09 0.18
Matches are distributed among these distances:
97 8 0.02
98 13 0.04
99 30 0.09
100 20 0.06
101 63 0.18
102 25 0.07
103 2 0.01
104 1 0.00
105 1 0.00
106 4 0.01
107 101 0.29
108 7 0.02
109 1 0.00
110 16 0.05
111 2 0.01
112 11 0.03
114 5 0.01
115 15 0.04
116 19 0.05
117 2 0.01
ACGTcount: A:0.52, C:0.11, G:0.01, T:0.36
Consensus pattern (108 bp):
AATAAATCAATCCATATTTTAAAATAAATCAATCCATACTAATAAATTATTTAAAATAAATCAAT
CTATATTTTAAAATAAATCAATCCATACTAATAAATTATTTAA
Found at i:95147 original size:22 final size:22
Alignment explanation
Indices: 95098--95146 Score: 71
Period size: 22 Copynumber: 2.2 Consensus size: 22
95088 ATAAATTATT
**
95098 TAAAATAAATCAATCCATATTT
1 TAAAATAAATCAATCCATATAA
95120 TAAAATAAATCAATCCATACTAA
1 TAAAATAAATCAATCCATA-TAA
95143 TAAA
1 TAAA
95147 TTATTTAAAT
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
22 19 0.79
23 5 0.21
ACGTcount: A:0.55, C:0.14, G:0.00, T:0.31
Consensus pattern (22 bp):
TAAAATAAATCAATCCATATAA
Found at i:95191 original size:22 final size:22
Alignment explanation
Indices: 95096--95138 Score: 86
Period size: 22 Copynumber: 2.0 Consensus size: 22
95086 TAATAAATTA
95096 TTTAAAATAAATCAATCCATAT
1 TTTAAAATAAATCAATCCATAT
95118 TTTAAAATAAATCAATCCATA
1 TTTAAAATAAATCAATCCATA
95139 CTAATAAATT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.51, C:0.14, G:0.00, T:0.35
Consensus pattern (22 bp):
TTTAAAATAAATCAATCCATAT
Found at i:95200 original size:22 final size:21
Alignment explanation
Indices: 95152--95200 Score: 62
Period size: 22 Copynumber: 2.2 Consensus size: 21
95142 ATAAATTATT
**
95152 TAAATAAATCAATCCATATTT
1 TAAATAAATCAATCCATATAA
95173 TAAAATAAATCAATCCATACTAA
1 T-AAATAAATCAATCCATA-TAA
95196 TAAAT
1 TAAAT
95201 CATTTAAAAT
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
21 1 0.04
22 21 0.88
23 2 0.08
ACGTcount: A:0.53, C:0.14, G:0.00, T:0.33
Consensus pattern (21 bp):
TAAATAAATCAATCCATATAA
Found at i:95254 original size:15 final size:15
Alignment explanation
Indices: 95194--95263 Score: 63
Period size: 15 Copynumber: 4.5 Consensus size: 15
95184 AATCCATACT
*
95194 AATAAATCA-TTTAA
1 AATAAATTATTTTAA
95208 AAT-AATTATTTTAAAA
1 AATAAATTATTTT--AA
*
95224 AATCAATCCATATTTTAA
1 AATAAAT---TATTTTAA
95242 AATAAATTATTTTAA
1 AATAAATTATTTTAA
95257 AATAAAT
1 AATAAAT
95264 AACCTTATTA
Statistics
Matches: 47, Mismatches: 2, Indels: 13
0.76 0.03 0.21
Matches are distributed among these distances:
13 4 0.09
14 6 0.13
15 15 0.32
16 5 0.11
17 3 0.06
18 8 0.17
20 6 0.13
ACGTcount: A:0.54, C:0.06, G:0.00, T:0.40
Consensus pattern (15 bp):
AATAAATTATTTTAA
Found at i:99048 original size:50 final size:46
Alignment explanation
Indices: 98975--99070 Score: 129
Period size: 50 Copynumber: 2.0 Consensus size: 46
98965 AATGTCATTC
*
98975 AATAAATTCTTACATATATAGTTTATACTTAGTATATCAATTATTA
1 AATAAATTCTTACATATATAGTTTATACTTAGTATATCAAATATTA
* *
99021 AATAAATTCTATTAACATTATATAGTTTATATTTAGTATATGAAATATTA
1 AATAAATTC--TT-ACA-TATATAGTTTATACTTAGTATATCAAATATTA
99071 TTCTTAACGA
Statistics
Matches: 43, Mismatches: 3, Indels: 4
0.86 0.06 0.08
Matches are distributed among these distances:
46 9 0.21
48 2 0.05
49 3 0.07
50 29 0.67
ACGTcount: A:0.43, C:0.06, G:0.05, T:0.46
Consensus pattern (46 bp):
AATAAATTCTTACATATATAGTTTATACTTAGTATATCAAATATTA
Done.