Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007929.1 Hibiscus syriacus cultivar Beakdansim tig00110336_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: 398994
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 1 of 3
Found at i:3900 original size:19 final size:19
Alignment explanation
Indices: 3848--3901 Score: 72
Period size: 19 Copynumber: 2.8 Consensus size: 19
3838 AAGTCAACCC
3848 GACCTGACCCGTTGACTTT
1 GACCTGACCCGTTGACTTT
* *
3867 GACCCGACCTGTTGACTTT
1 GACCTGACCCGTTGACTTT
* *
3886 GACCTAACCCATTGAC
1 GACCTGACCCGTTGAC
3902 CGTTGATCGG
Statistics
Matches: 29, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
19 29 1.00
ACGTcount: A:0.20, C:0.33, G:0.19, T:0.28
Consensus pattern (19 bp):
GACCTGACCCGTTGACTTT
Found at i:6560 original size:28 final size:30
Alignment explanation
Indices: 6508--6571 Score: 78
Period size: 29 Copynumber: 2.2 Consensus size: 30
6498 TTTTACTATG
* * *
6508 GTTTTAAAAATATGTTTTAAATTTTTA-TT
1 GTTTTAAAAAGATGTTGTAAATTTTCACTT
*
6537 GTTTTAAAAAGA-GTTGTACATTTTCACTT
1 GTTTTAAAAAGATGTTGTAAATTTTCACTT
6566 GTTTTA
1 GTTTTA
6572 TGGAAACACA
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
28 11 0.37
29 19 0.63
ACGTcount: A:0.31, C:0.05, G:0.11, T:0.53
Consensus pattern (30 bp):
GTTTTAAAAAGATGTTGTAAATTTTCACTT
Found at i:8598 original size:20 final size:22
Alignment explanation
Indices: 8575--8614 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
8565 ACCCAAACCG
8575 TTGACC-GT-TAACCGTTGACT
1 TTGACCGGTATAACCGTTGACT
8595 TTGACCGGTATAACCGTTGA
1 TTGACCGGTATAACCGTTGA
8615 ACGTTAACTT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 6 0.33
21 2 0.11
22 10 0.56
ACGTcount: A:0.23, C:0.23, G:0.23, T:0.33
Consensus pattern (22 bp):
TTGACCGGTATAACCGTTGACT
Found at i:12235 original size:15 final size:15
Alignment explanation
Indices: 12210--12254 Score: 56
Period size: 14 Copynumber: 3.0 Consensus size: 15
12200 AACTTATAAA
*
12210 AATTAATATTTTTAT
1 AATTTATATTTTTAT
*
12225 ATTTTATA-TTTTAT
1 AATTTATATTTTTAT
12239 AATTTATAATTTTTAT
1 AATTTAT-ATTTTTAT
12255 TGGAAAAGAT
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
14 12 0.48
15 7 0.28
16 6 0.24
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (15 bp):
AATTTATATTTTTAT
Found at i:15160 original size:20 final size:20
Alignment explanation
Indices: 15135--15174 Score: 80
Period size: 20 Copynumber: 2.0 Consensus size: 20
15125 ATTATAAGAA
15135 TCAATATAATAGATTTATAT
1 TCAATATAATAGATTTATAT
15155 TCAATATAATAGATTTATAT
1 TCAATATAATAGATTTATAT
15175 GACTACATGA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.45, C:0.05, G:0.05, T:0.45
Consensus pattern (20 bp):
TCAATATAATAGATTTATAT
Found at i:17464 original size:29 final size:29
Alignment explanation
Indices: 17429--17486 Score: 98
Period size: 29 Copynumber: 2.0 Consensus size: 29
17419 TTCTTTAATC
*
17429 GGTTTCTAATTTGTATCTTGTATTTATTT
1 GGTTTCTAATTTGTATCTTGTAATTATTT
*
17458 GGTTTCTAATTTGTATGTTGTAATTATTT
1 GGTTTCTAATTTGTATCTTGTAATTATTT
17487 CAGTCTATTG
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
29 27 1.00
ACGTcount: A:0.19, C:0.05, G:0.16, T:0.60
Consensus pattern (29 bp):
GGTTTCTAATTTGTATCTTGTAATTATTT
Found at i:20680 original size:23 final size:23
Alignment explanation
Indices: 20645--20737 Score: 116
Period size: 23 Copynumber: 4.0 Consensus size: 23
20635 CATCTTATAT
20645 GGCACTTCA-GTGCATTTCTACGA
1 GGCACTT-AGGTGCATTTCTACGA
*
20668 GGCACTTAGGTGCATTTCTACGC
1 GGCACTTAGGTGCATTTCTACGA
* * *
20691 GGTACTTAGGTGCAATTCTACGT
1 GGCACTTAGGTGCATTTCTACGA
* *
20714 GGCACTTCGGTGCATTTATACGA
1 GGCACTTAGGTGCATTTCTACGA
20737 G
1 G
20738 TTGTGGTGGC
Statistics
Matches: 60, Mismatches: 9, Indels: 2
0.85 0.13 0.03
Matches are distributed among these distances:
22 1 0.02
23 59 0.98
ACGTcount: A:0.20, C:0.23, G:0.26, T:0.31
Consensus pattern (23 bp):
GGCACTTAGGTGCATTTCTACGA
Found at i:22294 original size:41 final size:41
Alignment explanation
Indices: 22247--22344 Score: 108
Period size: 41 Copynumber: 2.4 Consensus size: 41
22237 GCGTTTTAAG
** *
22247 TACAAACGTCGCTAAAGTACTTGTA-TTTAACGATATTTTTA
1 TACAAACGTCGCTAAAG-ACACGTACTTTAACGACATTTTTA
* ** *
22288 TACAAACGTCGGTAAAGACACGTACTTTAGTGGCATTTTTA
1 TACAAACGTCGCTAAAGACACGTACTTTAACGACATTTTTA
*
22329 TACAAACGCCGCTAAA
1 TACAAACGTCGCTAAA
22345 AAGTTATACT
Statistics
Matches: 47, Mismatches: 9, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
40 5 0.11
41 42 0.89
ACGTcount: A:0.35, C:0.18, G:0.15, T:0.32
Consensus pattern (41 bp):
TACAAACGTCGCTAAAGACACGTACTTTAACGACATTTTTA
Found at i:22449 original size:42 final size:42
Alignment explanation
Indices: 22240--22471 Score: 181
Period size: 42 Copynumber: 5.6 Consensus size: 42
22230 ATTAGCAGCG
* * ** **
22240 TTTTAAGTACAAACGTCGCTAAAGTACTTGTA-TTTAACGATA
1 TTTTAAGTACAAACGCCGCTAAA-TAATTGTACTTTAGTGGCA
* * * * *
22282 TTTTTA-TACAAACGTCGGTAAAGACA-CGTACTTTAGTGGCA
1 TTTTAAGTACAAACGCCGCTAAATA-ATTGTACTTTAGTGGCA
* *
22323 TTTTTA-TACAAACGCCGCTAAA-AAGTTATACTTTAGTGGCA
1 TTTTAAGTACAAACGCCGCTAAATAA-TTGTACTTTAGTGGCA
** * *
22364 TTTTAAGTACAAACGCCGCTAAATGCTTGTACTTTAGTAGCG
1 TTTTAAGTACAAACGCCGCTAAATAATTGTACTTTAGTGGCA
* * *
22406 TTTTAAGCACAAACGCCGCTAAATAAATGTACTTTAGTGGCG
1 TTTTAAGTACAAACGCCGCTAAATAATTGTACTTTAGTGGCA
* *
22448 TTTGT-A-TATAAACACCGCTAAATA
1 TTT-TAAGTACAAACGCCGCTAAATA
22472 TTTAGTCTTT
Statistics
Matches: 156, Mismatches: 27, Indels: 15
0.79 0.14 0.08
Matches are distributed among these distances:
39 1 0.01
40 5 0.03
41 74 0.47
42 75 0.48
43 1 0.01
ACGTcount: A:0.34, C:0.17, G:0.16, T:0.33
Consensus pattern (42 bp):
TTTTAAGTACAAACGCCGCTAAATAATTGTACTTTAGTGGCA
Found at i:25509 original size:31 final size:31
Alignment explanation
Indices: 25463--25521 Score: 91
Period size: 31 Copynumber: 1.9 Consensus size: 31
25453 CAAATGACAT
*
25463 TAAATACACAGTCAATAGCGGCGTTTGTCAC
1 TAAATACACAATCAATAGCGGCGTTTGTCAC
* *
25494 TAAATATACAATCAATAGTGGCGTTTGT
1 TAAATACACAATCAATAGCGGCGTTTGT
25522 AAAGAAAAAC
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
31 25 1.00
ACGTcount: A:0.34, C:0.17, G:0.19, T:0.31
Consensus pattern (31 bp):
TAAATACACAATCAATAGCGGCGTTTGTCAC
Found at i:25704 original size:43 final size:43
Alignment explanation
Indices: 25493--25706 Score: 266
Period size: 43 Copynumber: 5.0 Consensus size: 43
25483 GCGTTTGTCA
* * * *
25493 CTAAATATACAATCAATAGTGGCGTTTGTAAAGAAAAACACCG
1 CTAAATACACAGTCAATAGCGGCGTTTGTAAAGAAAAACGCCG
* * * *
25536 CTAAATGCACAGTCAATATCGGCATTTGTAAAGAAAAACACCG
1 CTAAATACACAGTCAATAGCGGCGTTTGTAAAGAAAAACGCCG
* * * *
25579 CTAAATACATATTCAATAGCGGCGTTTATAAAGACAAACGCCG
1 CTAAATACACAGTCAATAGCGGCGTTTGTAAAGAAAAACGCCG
* * * * **
25622 CTAAATACACAGTCAATATCGGTGTTTATAAAGACAAACGTTG
1 CTAAATACACAGTCAATAGCGGCGTTTGTAAAGAAAAACGCCG
25665 CTAAATACACAGTCAATAGCGGCGTTTGTAAAGAAAAACGCC
1 CTAAATACACAGTCAATAGCGGCGTTTGTAAAGAAAAACGCC
25707 TCTATATGTC
Statistics
Matches: 145, Mismatches: 26, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
43 145 1.00
ACGTcount: A:0.41, C:0.19, G:0.17, T:0.23
Consensus pattern (43 bp):
CTAAATACACAGTCAATAGCGGCGTTTGTAAAGAAAAACGCCG
Found at i:32981 original size:29 final size:29
Alignment explanation
Indices: 32945--33003 Score: 109
Period size: 29 Copynumber: 2.0 Consensus size: 29
32935 CCTAAATTAA
32945 TTTGATGTCATTACTTACATCAATTTAGT
1 TTTGATGTCATTACTTACATCAATTTAGT
*
32974 TTTGATGTCATTGCTTACATCAATTTAGT
1 TTTGATGTCATTACTTACATCAATTTAGT
33003 T
1 T
33004 AGGTGAGAAA
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
29 29 1.00
ACGTcount: A:0.25, C:0.14, G:0.12, T:0.49
Consensus pattern (29 bp):
TTTGATGTCATTACTTACATCAATTTAGT
Found at i:39848 original size:14 final size:14
Alignment explanation
Indices: 39825--39856 Score: 55
Period size: 14 Copynumber: 2.3 Consensus size: 14
39815 GATTGGATAA
*
39825 TTATTTTAATTTAT
1 TTATTCTAATTTAT
39839 TTATTCTAATTTAT
1 TTATTCTAATTTAT
39853 TTAT
1 TTAT
39857 CTTCCAATAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.28, C:0.03, G:0.00, T:0.69
Consensus pattern (14 bp):
TTATTCTAATTTAT
Found at i:40753 original size:26 final size:28
Alignment explanation
Indices: 40694--40751 Score: 116
Period size: 28 Copynumber: 2.1 Consensus size: 28
40684 GTGGTATCCC
40694 GTGTAGTTTACCCATATATATATATTTG
1 GTGTAGTTTACCCATATATATATATTTG
40722 GTGTAGTTTACCCATATATATATATTTG
1 GTGTAGTTTACCCATATATATATATTTG
40750 GT
1 GT
40752 AGAGCTAAAG
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 30 1.00
ACGTcount: A:0.28, C:0.10, G:0.16, T:0.47
Consensus pattern (28 bp):
GTGTAGTTTACCCATATATATATATTTG
Found at i:41489 original size:20 final size:21
Alignment explanation
Indices: 41464--41503 Score: 64
Period size: 20 Copynumber: 1.9 Consensus size: 21
41454 GATTTTGGGA
41464 TATGATATA-ATATTATTGAT
1 TATGATATACATATTATTGAT
41484 TATGATATATCATATTATTG
1 TATGATATA-CATATTATTG
41504 CAAAATATAG
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 9 0.50
22 9 0.50
ACGTcount: A:0.38, C:0.03, G:0.10, T:0.50
Consensus pattern (21 bp):
TATGATATACATATTATTGAT
Found at i:52636 original size:13 final size:14
Alignment explanation
Indices: 52607--52639 Score: 50
Period size: 13 Copynumber: 2.4 Consensus size: 14
52597 ATATATATAT
*
52607 ATATATATTTCTTC
1 ATATTTATTTCTTC
52621 ATATTTATTT-TTC
1 ATATTTATTTCTTC
52634 ATATTT
1 ATATTT
52640 TTTATATATG
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
13 9 0.50
14 9 0.50
ACGTcount: A:0.27, C:0.09, G:0.00, T:0.64
Consensus pattern (14 bp):
ATATTTATTTCTTC
Found at i:53823 original size:32 final size:32
Alignment explanation
Indices: 53787--53862 Score: 116
Period size: 33 Copynumber: 2.3 Consensus size: 32
53777 CAAAGTTTAA
*
53787 GATAATTGAAATACTTAAATACTTCCAAGTTC
1 GATAATTGAAATACTTAAAAACTTCCAAGTTC
* *
53819 GATAAATTCAAATACTTAAAAATTTCCAAGTTC
1 GAT-AATTGAAATACTTAAAAACTTCCAAGTTC
53852 GATAATTGAAA
1 GATAATTGAAA
53863 CAAAGTTTAC
Statistics
Matches: 39, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
32 10 0.26
33 29 0.74
ACGTcount: A:0.45, C:0.13, G:0.09, T:0.33
Consensus pattern (32 bp):
GATAATTGAAATACTTAAAAACTTCCAAGTTC
Found at i:53876 original size:21 final size:21
Alignment explanation
Indices: 53851--53892 Score: 84
Period size: 21 Copynumber: 2.0 Consensus size: 21
53841 TTTCCAAGTT
53851 CGATAATTGAAACAAAGTTTA
1 CGATAATTGAAACAAAGTTTA
53872 CGATAATTGAAACAAAGTTTA
1 CGATAATTGAAACAAAGTTTA
53893 AAAATAAACT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.48, C:0.10, G:0.14, T:0.29
Consensus pattern (21 bp):
CGATAATTGAAACAAAGTTTA
Found at i:58280 original size:13 final size:14
Alignment explanation
Indices: 58262--58291 Score: 53
Period size: 13 Copynumber: 2.2 Consensus size: 14
58252 AGTTGGACAA
58262 TCTTCATATGCA-G
1 TCTTCATATGCACG
58275 TCTTCATATGCACG
1 TCTTCATATGCACG
58289 TCT
1 TCT
58292 GTAATGGGAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 12 0.75
14 4 0.25
ACGTcount: A:0.20, C:0.27, G:0.13, T:0.40
Consensus pattern (14 bp):
TCTTCATATGCACG
Found at i:60511 original size:30 final size:30
Alignment explanation
Indices: 60425--60540 Score: 87
Period size: 30 Copynumber: 3.9 Consensus size: 30
60415 AATATTTAAA
* * *
60425 ATTACAAGGACCAAAATGGGAAAAACAACAACT
1 ATTA-AAGGACTAAAATAGTAAAAAC-ACAA-T
* * * *
60458 A--AAAGGACCAAATTAGTACAAACATGAAT
1 ATTAAAGGACTAAAATAGTAAAAACA-CAAT
*
60487 -TTAAAGGACTAAAATAGCAAAAACACAAT
1 ATTAAAGGACTAAAATAGTAAAAACACAAT
*
60516 ATTAAAGGGCT-AAATAGTAAAAACA
1 ATTAAAGGACTAAAATAGTAAAAACA
60541 GAAACTAAAA
Statistics
Matches: 67, Mismatches: 12, Indels: 12
0.74 0.13 0.13
Matches are distributed among these distances:
29 18 0.27
30 47 0.70
31 1 0.01
33 1 0.01
ACGTcount: A:0.56, C:0.14, G:0.14, T:0.16
Consensus pattern (30 bp):
ATTAAAGGACTAAAATAGTAAAAACACAAT
Found at i:60551 original size:29 final size:29
Alignment explanation
Indices: 60445--60558 Score: 81
Period size: 30 Copynumber: 3.9 Consensus size: 29
60435 CCAAAATGGG
*
60445 AAAAACA-ACAACTAAAAGGACCAAATTAGT
1 AAAAACAGA-AACTAAAAGGACTAAA-TAGT
* * * *
60475 ACAAACATG-AATTTAAAGGACTAAAATAGC
1 AAAAACA-GAAACTAAAAGGACT-AAATAGT
* * *
60505 AAAAACACAATA-TTAAAGGGCTAAATAGT
1 AAAAACAGAA-ACTAAAAGGACTAAATAGT
*
60534 AAAAACAGAAACTAAAAGGATTAAA
1 AAAAACAGAAACTAAAAGGACTAAA
60559 ACAATAATTA
Statistics
Matches: 65, Mismatches: 13, Indels: 13
0.71 0.14 0.14
Matches are distributed among these distances:
28 1 0.02
29 25 0.38
30 35 0.54
31 4 0.06
ACGTcount: A:0.59, C:0.12, G:0.12, T:0.17
Consensus pattern (29 bp):
AAAAACAGAAACTAAAAGGACTAAATAGT
Found at i:63173 original size:32 final size:31
Alignment explanation
Indices: 63132--63254 Score: 133
Period size: 31 Copynumber: 3.9 Consensus size: 31
63122 AGTTGAAAGT
63132 TTACCTATGTTCTACGGAACATATGGACAGAA
1 TTACCTATGTTCTACGGAACATATGGACA-AA
* *
63164 TTACCTATG-TCTTTCGGGACATATGGACAACA
1 TTACCTATGTTC-TACGGAACATATGGACAA-A
* *
63196 -TACCTATGTTCTAAGGAACATATGGACAAT
1 TTACCTATGTTCTACGGAACATATGGACAAA
* * * *
63226 TTACCTAGGTTCTTCGGGACCTATGGACA
1 TTACCTATGTTCTACGGAACATATGGACA
63255 GTTATCGAGG
Statistics
Matches: 76, Mismatches: 11, Indels: 9
0.79 0.11 0.09
Matches are distributed among these distances:
31 49 0.64
32 27 0.36
ACGTcount: A:0.30, C:0.20, G:0.20, T:0.30
Consensus pattern (31 bp):
TTACCTATGTTCTACGGAACATATGGACAAA
Found at i:63955 original size:12 final size:12
Alignment explanation
Indices: 63938--63978 Score: 64
Period size: 12 Copynumber: 3.4 Consensus size: 12
63928 TTTTCACTGT
63938 TTCATGGTATTG
1 TTCATGGTATTG
63950 TTCATGGTATTG
1 TTCATGGTATTG
* *
63962 TTCACGGTACTG
1 TTCATGGTATTG
63974 TTCAT
1 TTCAT
63979 ATCGTATAAT
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
12 26 1.00
ACGTcount: A:0.17, C:0.15, G:0.22, T:0.46
Consensus pattern (12 bp):
TTCATGGTATTG
Found at i:64563 original size:3 final size:3
Alignment explanation
Indices: 64551--64612 Score: 92
Period size: 3 Copynumber: 20.7 Consensus size: 3
64541 TAATCTAAAG
64551 TAA T-A TAA TAA TAA TAA TAA TAA TAGA TTAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TA-A -TAA TAA TAA TAA TAA TAA
64597 TAA TAA TAA -AA TAA TA
1 TAA TAA TAA TAA TAA TA
64613 TTTTTGGTAG
Statistics
Matches: 55, Mismatches: 0, Indels: 8
0.87 0.00 0.13
Matches are distributed among these distances:
2 4 0.07
3 47 0.85
4 2 0.04
5 2 0.04
ACGTcount: A:0.65, C:0.00, G:0.02, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:64591 original size:26 final size:24
Alignment explanation
Indices: 64551--64612 Score: 92
Period size: 26 Copynumber: 2.6 Consensus size: 24
64541 TAATCTAAAG
64551 TAAT-ATAATAATAATAATAATAA
1 TAATAATAATAATAATAATAATAA
64574 TAGATTAATAATAATAATAATAATAA
1 TA-A-TAATAATAATAATAATAATAA
64600 TAATAA-AATAATA
1 TAATAATAATAATA
64613 TTTTTGGTAG
Statistics
Matches: 36, Mismatches: 0, Indels: 6
0.86 0.00 0.14
Matches are distributed among these distances:
23 9 0.25
24 4 0.11
25 2 0.06
26 21 0.58
ACGTcount: A:0.65, C:0.00, G:0.02, T:0.34
Consensus pattern (24 bp):
TAATAATAATAATAATAATAATAA
Found at i:71415 original size:37 final size:36
Alignment explanation
Indices: 71359--71478 Score: 190
Period size: 35 Copynumber: 3.3 Consensus size: 36
71349 ATCCCATTAT
*
71359 CATTTTTC-AACAAACATTTACCAAACTTTGAAAAAC
1 CATTTTTCAAAGAAACATTTACCAAACTTTG-AAAAC
*
71395 TATTTTTCAAAGAAACATTTACCAAACTTTGAAAAC
1 CATTTTTCAAAGAAACATTTACCAAACTTTGAAAAC
71431 CA-TTTTCAAAGAAACATTTACCAAACTTTGAAAAC
1 CATTTTTCAAAGAAACATTTACCAAACTTTGAAAAC
71466 CATTTTTTCAAAG
1 CA-TTTTTCAAAG
71479 TTGGTTACCA
Statistics
Matches: 78, Mismatches: 3, Indels: 5
0.91 0.03 0.06
Matches are distributed among these distances:
35 35 0.45
36 13 0.17
37 30 0.38
ACGTcount: A:0.43, C:0.19, G:0.05, T:0.33
Consensus pattern (36 bp):
CATTTTTCAAAGAAACATTTACCAAACTTTGAAAAC
Found at i:76034 original size:37 final size:36
Alignment explanation
Indices: 75975--76121 Score: 178
Period size: 35 Copynumber: 4.2 Consensus size: 36
75965 ATCCCATTAT
* *
75975 CATTTTTC-AACAAACATCTACCAAACTTTGAAAAAC
1 CATTTTTCAAAGAAACATTTACCAAACTTTG-AAAAC
* *
76011 TATTTTTCAAAGAAACATTTACCAAAATTTGAAAAC
1 CATTTTTCAAAGAAACATTTACCAAACTTTGAAAAC
76047 CA-TTTTCAAAGAAACATTTACCAAACTTTGAAAAC
1 CATTTTTCAAAGAAACATTTACCAAACTTTGAAAAC
***
76082 CATTTTTTCAAAG-TTGA-TTACCAAAC-TTGAAAAC
1 CA-TTTTTCAAAGAAACATTTACCAAACTTTGAAAAC
76116 CATTTT
1 CATTTT
76122 AATAGTTAAG
Statistics
Matches: 99, Mismatches: 9, Indels: 9
0.85 0.08 0.08
Matches are distributed among these distances:
33 4 0.04
34 10 0.10
35 43 0.43
36 14 0.14
37 28 0.28
ACGTcount: A:0.43, C:0.19, G:0.05, T:0.33
Consensus pattern (36 bp):
CATTTTTCAAAGAAACATTTACCAAACTTTGAAAAC
Found at i:76050 original size:21 final size:21
Alignment explanation
Indices: 76026--76086 Score: 55
Period size: 21 Copynumber: 3.2 Consensus size: 21
76016 TTCAAAGAAA
76026 CATTTACCAAAATTTGAAAAC
1 CATTTACCAAAATTTGAAAAC
*
76047 CATTT-TC-AAA---G-AAA-
1 CATTTACCAAAATTTGAAAAC
*
76061 CATTTACCAAACTTTGAAAAC
1 CATTTACCAAAATTTGAAAAC
76082 CATTT
1 CATTT
76087 TTTCAAAGTT
Statistics
Matches: 30, Mismatches: 3, Indels: 14
0.64 0.06 0.30
Matches are distributed among these distances:
14 5 0.17
15 4 0.13
16 3 0.10
19 4 0.13
20 4 0.13
21 10 0.33
ACGTcount: A:0.44, C:0.20, G:0.05, T:0.31
Consensus pattern (21 bp):
CATTTACCAAAATTTGAAAAC
Found at i:82954 original size:19 final size:18
Alignment explanation
Indices: 82930--82969 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
82920 TTCGGTGGAA
82930 TTTCTTTTGCACCGAAAGT
1 TTTC-TTTGCACCGAAAGT
**
82949 TTTCTTTGCGTCGAAAGT
1 TTTCTTTGCACCGAAAGT
82967 TTT
1 TTT
82970 AAGCCAACTT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
18 15 0.79
19 4 0.21
ACGTcount: A:0.17, C:0.17, G:0.17, T:0.47
Consensus pattern (18 bp):
TTTCTTTGCACCGAAAGT
Found at i:93892 original size:61 final size:61
Alignment explanation
Indices: 93817--93940 Score: 248
Period size: 61 Copynumber: 2.0 Consensus size: 61
93807 GACGGTAGCA
93817 TTTATTCACTTCTTCAAGCTCGACGAACTTAAATTTAAAGTAGGAAAGAACTTATAAAATT
1 TTTATTCACTTCTTCAAGCTCGACGAACTTAAATTTAAAGTAGGAAAGAACTTATAAAATT
93878 TTTATTCACTTCTTCAAGCTCGACGAACTTAAATTTAAAGTAGGAAAGAACTTATAAAATT
1 TTTATTCACTTCTTCAAGCTCGACGAACTTAAATTTAAAGTAGGAAAGAACTTATAAAATT
93939 TT
1 TT
93941 AGAGGACGAA
Statistics
Matches: 63, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
61 63 1.00
ACGTcount: A:0.39, C:0.15, G:0.11, T:0.35
Consensus pattern (61 bp):
TTTATTCACTTCTTCAAGCTCGACGAACTTAAATTTAAAGTAGGAAAGAACTTATAAAATT
Found at i:94891 original size:60 final size:58
Alignment explanation
Indices: 94779--94892 Score: 147
Period size: 60 Copynumber: 1.9 Consensus size: 58
94769 ATGTTTTAAA
* *
94779 TAATTATTTTTTATTTTTAATGTTTTAGATATGGACCAAAAAAAACCCAATAATAAGT
1 TAATTATTGTTTATTTTTAATGTTTTAGATATGGACCAAAAAAAACCAAATAATAAGT
* * * * *
94837 TAATTAATTGTTTACTTTTTAATGTTTTGGGTTTGGACCAAAACATACCAAATAAT
1 TAATT-ATTGTTTA-TTTTTAATGTTTTAGATATGGACCAAAAAAAACCAAATAAT
94893 TTAATTATTT
Statistics
Matches: 47, Mismatches: 7, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
58 5 0.11
59 7 0.15
60 35 0.74
ACGTcount: A:0.38, C:0.10, G:0.11, T:0.42
Consensus pattern (58 bp):
TAATTATTGTTTATTTTTAATGTTTTAGATATGGACCAAAAAAAACCAAATAATAAGT
Found at i:96328 original size:20 final size:20
Alignment explanation
Indices: 96303--96454 Score: 97
Period size: 26 Copynumber: 6.7 Consensus size: 20
96293 TTTAGGTATG
*
96303 GCATCCTTTCTTGCCTTAAT
1 GCATCCTTTCATGCCTTAAT
*
96323 GCATCCTTTCATGCATTTTAGTTAT
1 GCATCCTTTCATGC--CTTA---AT
96348 GACATCCTTTCATGCCTTAAT
1 G-CATCCTTTCATGCCTTAAT
*
96369 GCATCCTTTCATGCATTTTAGTTAT
1 GCATCCTTTCATGC--CTTA---AT
*
96394 GACATCCTTTCATGCATTTTAGTTAT
1 G-CATCCTTTCATGC--CTTA---AT
96420 GGCATCCTTTCATGCCTTAAT
1 -GCATCCTTTCATGCCTTAAT
*
96441 GCATCCGTTCATGC
1 GCATCCTTTCATGC
96455 ATTTTAGTTA
Statistics
Matches: 113, Mismatches: 6, Indels: 26
0.78 0.04 0.18
Matches are distributed among these distances:
20 39 0.35
21 5 0.04
22 6 0.05
24 6 0.05
25 6 0.05
26 50 0.44
27 1 0.01
ACGTcount: A:0.20, C:0.25, G:0.12, T:0.43
Consensus pattern (20 bp):
GCATCCTTTCATGCCTTAAT
Found at i:96402 original size:72 final size:72
Alignment explanation
Indices: 96324--96467 Score: 270
Period size: 72 Copynumber: 2.0 Consensus size: 72
96314 TGCCTTAATG
*
96324 CATCCTTTCATGCATTTTAGTTATGACATCCTTTCATGCCTTAATGCATCCTTTCATGCATTTTA
1 CATCCTTTCATGCATTTTAGTTATGACATCCTTTCATGCCTTAATGCATCCGTTCATGCATTTTA
96389 GTTATGA
66 GTTATGA
*
96396 CATCCTTTCATGCATTTTAGTTATGGCATCCTTTCATGCCTTAATGCATCCGTTCATGCATTTTA
1 CATCCTTTCATGCATTTTAGTTATGACATCCTTTCATGCCTTAATGCATCCGTTCATGCATTTTA
96461 GTTATGA
66 GTTATGA
96468 ATTCGTATTA
Statistics
Matches: 70, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
72 70 1.00
ACGTcount: A:0.22, C:0.22, G:0.12, T:0.44
Consensus pattern (72 bp):
CATCCTTTCATGCATTTTAGTTATGACATCCTTTCATGCCTTAATGCATCCGTTCATGCATTTTA
GTTATGA
Found at i:96405 original size:46 final size:46
Alignment explanation
Indices: 96229--96408 Score: 279
Period size: 46 Copynumber: 3.9 Consensus size: 46
96219 GCCTCTTTTC
* * * * *
96229 ATGCATCCATTCATGCATTTTAGTTATGTCAGCCTTTCTTACCTTA
1 ATGCATCCTTTCATGCATTTTAGTTATGACATCCTTTCATGCCTTA
* * * *
96275 ATGCATCATTTCATGCATTTTAGGTATGGCATCCTTTCTTGCCTTA
1 ATGCATCCTTTCATGCATTTTAGTTATGACATCCTTTCATGCCTTA
96321 ATGCATCCTTTCATGCATTTTAGTTATGACATCCTTTCATGCCTTA
1 ATGCATCCTTTCATGCATTTTAGTTATGACATCCTTTCATGCCTTA
96367 ATGCATCCTTTCATGCATTTTAGTTATGACATCCTTTCATGC
1 ATGCATCCTTTCATGCATTTTAGTTATGACATCCTTTCATGC
96409 ATTTTAGTTA
Statistics
Matches: 124, Mismatches: 10, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
46 124 1.00
ACGTcount: A:0.21, C:0.23, G:0.12, T:0.43
Consensus pattern (46 bp):
ATGCATCCTTTCATGCATTTTAGTTATGACATCCTTTCATGCCTTA
Found at i:97031 original size:95 final size:94
Alignment explanation
Indices: 96888--97066 Score: 243
Period size: 95 Copynumber: 1.9 Consensus size: 94
96878 TACTACCCTG
* * **
96888 GTATCGATACTTCTATGCTATGGTACCGATACCCCCTTTCAGTATCGATACCATTTCT-ATATTC
1 GTATCGATACTACTATACTATAATACCGATACCCCCTTTCAGTATCGATACCATTT-TAATATTC
* *
96952 TGTGTTGCATGGTATCGATACCTTTCTCTCA
65 TG-GATCCATGGTATCGATACCTTTCTCTCA
* * *
96983 GTATCGATACTACTATACTATAATATCGATACTCCTTTTCAGTATCGATACCATTTTAATATTCT
1 GTATCGATACTACTATACTATAATACCGATACCCCCTTTCAGTATCGATACCATTTTAATATTCT
*
97048 GGATCCATGGTATTGATAC
66 GGATCCATGGTATCGATAC
97067 TTCCTCTTGT
Statistics
Matches: 73, Mismatches: 10, Indels: 3
0.85 0.12 0.03
Matches are distributed among these distances:
94 16 0.22
95 57 0.78
ACGTcount: A:0.25, C:0.22, G:0.13, T:0.39
Consensus pattern (94 bp):
GTATCGATACTACTATACTATAATACCGATACCCCCTTTCAGTATCGATACCATTTTAATATTCT
GGATCCATGGTATCGATACCTTTCTCTCA
Found at i:99061 original size:15 final size:15
Alignment explanation
Indices: 99041--99074 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
99031 TAAATATAAA
99041 TATAATATACATTAT-
1 TATAATATA-ATTATG
99056 TATAATATAATTATG
1 TATAATATAATTATG
99071 TATA
1 TATA
99075 TTATTATAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
14 5 0.28
15 13 0.72
ACGTcount: A:0.47, C:0.03, G:0.03, T:0.47
Consensus pattern (15 bp):
TATAATATAATTATG
Found at i:99231 original size:19 final size:19
Alignment explanation
Indices: 99184--99234 Score: 68
Period size: 19 Copynumber: 2.7 Consensus size: 19
99174 TATATTTTAG
99184 TTAAAATAATATTAATATA
1 TTAAAATAATATTAATATA
* *
99203 TTATATTAATATTAA-ATA
1 TTAAAATAATATTAATATA
99221 TATAAAATAATATT
1 T-TAAAATAATATT
99235 GTTTTGAGTA
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
18 4 0.15
19 23 0.85
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (19 bp):
TTAAAATAATATTAATATA
Found at i:99431 original size:24 final size:23
Alignment explanation
Indices: 99387--99440 Score: 108
Period size: 23 Copynumber: 2.3 Consensus size: 23
99377 TCAAACACTA
99387 AAAAAATAAAGAAAATATTTTTC
1 AAAAAATAAAGAAAATATTTTTC
99410 AAAAAATAAAGAAAATATTTTTC
1 AAAAAATAAAGAAAATATTTTTC
99433 AAAAAATA
1 AAAAAATA
99441 TTTTTTGTAA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 31 1.00
ACGTcount: A:0.65, C:0.04, G:0.04, T:0.28
Consensus pattern (23 bp):
AAAAAATAAAGAAAATATTTTTC
Found at i:101357 original size:21 final size:21
Alignment explanation
Indices: 101328--101381 Score: 92
Period size: 21 Copynumber: 2.6 Consensus size: 21
101318 AGTTACCCGT
101328 GACGACCGCAATAGCGTCCGC
1 GACGACCGCAATAGCGTCCGC
101349 GAC-AGCCGCAATAGCGTCCGC
1 GACGA-CCGCAATAGCGTCCGC
101370 GACGACCGCAAT
1 GACGACCGCAAT
101382 CACGGTAAAT
Statistics
Matches: 31, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
20 1 0.03
21 29 0.94
22 1 0.03
ACGTcount: A:0.26, C:0.37, G:0.28, T:0.09
Consensus pattern (21 bp):
GACGACCGCAATAGCGTCCGC
Found at i:102546 original size:2 final size:2
Alignment explanation
Indices: 102539--102609 Score: 142
Period size: 2 Copynumber: 35.5 Consensus size: 2
102529 GTAAGAAAAT
102539 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
102581 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
102610 TGTGATATTC
Statistics
Matches: 69, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 69 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:104122 original size:163 final size:162
Alignment explanation
Indices: 103823--104128 Score: 427
Period size: 163 Copynumber: 1.9 Consensus size: 162
103813 ACTCTAATAT
* *
103823 AAAATCATTCATCGGTTCATATACTTCATTGTGGACTTATCTTGATTTTCTCAGTTTAGACCATT
1 AAAATCATACATCGGTTCATATACTTCATTGTGGACTTATCCTGATTTTCTCAGTTTAGACCATT
* * * * * **
103888 GAAGGTGCTTATAGTGATACTAATGGTTTAGATCTTAATACCCACGATGTGGCTGATATGAATGA
66 AAAGGTGCTTAAAGTGATACTAATGGTTAAGATCTTAATACCCACGATGTGACTGAAACAAATGA
103953 AAATCGACTTTTGTCGAAGTTCGAGAACCACC
131 AAATCGACTTTTGTCGAAGTTCGAGAACCACC
* * **
103985 AAAATC-TACATCTGTTCATGTACTTCATTGTGGACTTATACCTGATTTTCTCAGTTTAGACTTT
1 AAAATCATACATCGGTTCATATACTTCATTGTGGACTTAT-CCTGATTTTCTCAGTTTAGACCAT
* *
104049 TAAAGGATGCTTAAAGTGATACTAATGGCTTAAG-TCTTAATACTCATGATGTGACTGAAACAAA
65 TAAAGG-TGCTTAAAGTGATACTAATGG-TTAAGATCTTAATACCCACGATGTGACTGAAACAAA
*
104113 TGGAAATCGACTTTTG
128 TGAAAATCGACTTTTG
104129 CTGAAAATCG
Statistics
Matches: 125, Mismatches: 16, Indels: 5
0.86 0.11 0.03
Matches are distributed among these distances:
161 30 0.24
162 32 0.26
163 59 0.47
164 4 0.03
ACGTcount: A:0.30, C:0.16, G:0.18, T:0.36
Consensus pattern (162 bp):
AAAATCATACATCGGTTCATATACTTCATTGTGGACTTATCCTGATTTTCTCAGTTTAGACCATT
AAAGGTGCTTAAAGTGATACTAATGGTTAAGATCTTAATACCCACGATGTGACTGAAACAAATGA
AAATCGACTTTTGTCGAAGTTCGAGAACCACC
Found at i:104729 original size:16 final size:14
Alignment explanation
Indices: 104703--104761 Score: 64
Period size: 16 Copynumber: 3.9 Consensus size: 14
104693 GTAACTGATT
*
104703 TTTTGTTTTTTTTC
1 TTTTCTTTTTTTTC
104717 TTATTCATTTTTTTTC
1 TT-TTC-TTTTTTTTC
104733 TTTTGCTTTTTTTTCC
1 TTTT-CTTTTTTTT-C
104749 TTTTTCTTTTTTT
1 -TTTTCTTTTTTT
104762 CCCTCTTTTC
Statistics
Matches: 39, Mismatches: 1, Indels: 8
0.81 0.02 0.17
Matches are distributed among these distances:
14 2 0.05
15 12 0.31
16 21 0.54
17 4 0.10
ACGTcount: A:0.03, C:0.12, G:0.03, T:0.81
Consensus pattern (14 bp):
TTTTCTTTTTTTTC
Found at i:104763 original size:15 final size:15
Alignment explanation
Indices: 104702--104773 Score: 63
Period size: 16 Copynumber: 4.5 Consensus size: 15
104692 TGTAACTGAT
* *
104702 TTTTTGTTTTTTTTC
1 TTTTTCTTTTTTTCC
* *
104717 TTATTCATTTTTTTTC
1 TTTTTC-TTTTTTTCC
*
104733 TTTTGCTTTTTTTTCC
1 TTTTTC-TTTTTTTCC
104749 TTTTTCTTTTTTTCCC
1 TTTTTCTTTTTTT-CC
104765 TCTTTTCTT
1 T-TTTTCTT
104774 CAAGTGTAAT
Statistics
Matches: 47, Mismatches: 7, Indels: 4
0.81 0.12 0.07
Matches are distributed among these distances:
15 11 0.23
16 29 0.62
17 7 0.15
ACGTcount: A:0.03, C:0.17, G:0.03, T:0.78
Consensus pattern (15 bp):
TTTTTCTTTTTTTCC
Found at i:110081 original size:12 final size:12
Alignment explanation
Indices: 110064--110089 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
110054 GAGGAATTTA
110064 AAAATTAAAGGC
1 AAAATTAAAGGC
110076 AAAATTAAAGGC
1 AAAATTAAAGGC
110088 AA
1 AA
110090 TTACCAAGTG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.62, C:0.08, G:0.15, T:0.15
Consensus pattern (12 bp):
AAAATTAAAGGC
Found at i:110462 original size:23 final size:22
Alignment explanation
Indices: 110436--110478 Score: 59
Period size: 23 Copynumber: 1.9 Consensus size: 22
110426 AAGGTACTTT
**
110436 AAGTTAGCGGTTAATAAATTAAC
1 AAGTTAGAAGTTAA-AAATTAAC
110459 AAGTTAGAAGTTAAAAATTA
1 AAGTTAGAAGTTAAAAATTA
110479 GAATTTTACC
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
22 6 0.33
23 12 0.67
ACGTcount: A:0.49, C:0.05, G:0.16, T:0.30
Consensus pattern (22 bp):
AAGTTAGAAGTTAAAAATTAAC
Found at i:111606 original size:54 final size:54
Alignment explanation
Indices: 111547--111723 Score: 275
Period size: 54 Copynumber: 3.3 Consensus size: 54
111537 TTCTCTGGGA
** * *
111547 TGCACACGTAGTGCCAATACAGAAATCCATAAACTTATTATGAATTTATTAAGT
1 TGCACACACAGTGCCAATACAGAAATTCATAAACTTATTATGAATTTCTTAAGT
*
111601 TGCACATACAGTGCCAATAC-GAAAATTCATAAACTTATTATGAATTTCTTAAGT
1 TGCACACACAGTGCCAATACAG-AAATTCATAAACTTATTATGAATTTCTTAAGT
*
111655 TGCACATACAGTGCCAATACAGAAATTCATAAACTTATTATGAATTTCTTAAGT
1 TGCACACACAGTGCCAATACAGAAATTCATAAACTTATTATGAATTTCTTAAGT
*
111709 TGCACACATAGTGCC
1 TGCACACACAGTGCC
111724 CATTTGGAAA
Statistics
Matches: 114, Mismatches: 7, Indels: 4
0.91 0.06 0.03
Matches are distributed among these distances:
53 1 0.01
54 112 0.98
55 1 0.01
ACGTcount: A:0.38, C:0.18, G:0.12, T:0.32
Consensus pattern (54 bp):
TGCACACACAGTGCCAATACAGAAATTCATAAACTTATTATGAATTTCTTAAGT
Found at i:118316 original size:54 final size:54
Alignment explanation
Indices: 117983--118314 Score: 493
Period size: 54 Copynumber: 6.1 Consensus size: 54
117973 TTCTTTGGGG
** * *
117983 TGCACACGTAGTGCTAATACGGAAATTCATAAACTTATTAAGAATTTCTTAAGT
1 TGCACACACAGTGCCAATACGGAAATTCATAAACTTATTATGAATTTCTTAAGT
* **
118037 GGCACACACAGTGCCAATAAAGAAATTCATAAACTTATTATGAATTTCTTAAGT
1 TGCACACACAGTGCCAATACGGAAATTCATAAACTTATTATGAATTTCTTAAGT
** * *
118091 TGCATGCACAGTGCCAATACGGAAATTCATAAACGTATTATGATTTTCTTAAGT
1 TGCACACACAGTGCCAATACGGAAATTCATAAACTTATTATGAATTTCTTAAGT
*
118145 TCCACACACAGTGCCAATACGGAAATTCATAAACTTATTATGAATTTCTTAAGT
1 TGCACACACAGTGCCAATACGGAAATTCATAAACTTATTATGAATTTCTTAAGT
*
118199 TGCACACACAGTGTCAATACGGAAATTCATAAACTTATTATGAATTTCTTAAGT
1 TGCACACACAGTGCCAATACGGAAATTCATAAACTTATTATGAATTTCTTAAGT
* * ** * *
118253 TGCACACATAGTTCCAATACATAAATTTATAAACTTATTATGAATTTCTTAAGA
1 TGCACACACAGTGCCAATACGGAAATTCATAAACTTATTATGAATTTCTTAAGT
118307 TGCACACA
1 TGCACACA
118315 TAATGCTCAT
Statistics
Matches: 250, Mismatches: 28, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
54 250 1.00
ACGTcount: A:0.38, C:0.17, G:0.13, T:0.33
Consensus pattern (54 bp):
TGCACACACAGTGCCAATACGGAAATTCATAAACTTATTATGAATTTCTTAAGT
Found at i:119338 original size:3 final size:3
Alignment explanation
Indices: 119330--119361 Score: 64
Period size: 3 Copynumber: 10.7 Consensus size: 3
119320 GTGAACACGG
119330 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GA
1 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GA
119362 GATGACTTTG
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.66, C:0.00, G:0.34, T:0.00
Consensus pattern (3 bp):
GAA
Found at i:121272 original size:23 final size:23
Alignment explanation
Indices: 121231--121275 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 23
121221 TGTTATATGT
*
121231 GGTCCTTGGGGACATTTCTACGC
1 GGTCCTTGGGGACAATTCTACGC
121254 GGTCCTT-GGGACAAATTCTACG
1 GGTCCTTGGGGAC-AATTCTACG
121276 TGCCCCTAGT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
22 5 0.25
23 15 0.75
ACGTcount: A:0.18, C:0.24, G:0.29, T:0.29
Consensus pattern (23 bp):
GGTCCTTGGGGACAATTCTACGC
Found at i:123947 original size:12 final size:14
Alignment explanation
Indices: 123922--123949 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
123912 CATCATTCGT
123922 GGCCAAATTCTCTC
1 GGCCAAATTCTCTC
123936 GGCCAAATTCTCTC
1 GGCCAAATTCTCTC
123950 CAAGCTTCCA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.21, C:0.36, G:0.14, T:0.29
Consensus pattern (14 bp):
GGCCAAATTCTCTC
Found at i:125294 original size:4 final size:4
Alignment explanation
Indices: 125285--125311 Score: 54
Period size: 4 Copynumber: 6.8 Consensus size: 4
125275 TTAACTTCAT
125285 ATAC ATAC ATAC ATAC ATAC ATAC ATA
1 ATAC ATAC ATAC ATAC ATAC ATAC ATA
125312 ACTTAAGCAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 23 1.00
ACGTcount: A:0.52, C:0.22, G:0.00, T:0.26
Consensus pattern (4 bp):
ATAC
Found at i:126577 original size:2 final size:2
Alignment explanation
Indices: 126565--126598 Score: 61
Period size: 2 Copynumber: 17.5 Consensus size: 2
126555 AGCTCAGATA
126565 AG AG A- AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
126599 AACGAATGGA
Statistics
Matches: 31, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 30 0.97
ACGTcount: A:0.53, C:0.00, G:0.47, T:0.00
Consensus pattern (2 bp):
AG
Found at i:135954 original size:35 final size:35
Alignment explanation
Indices: 135885--135959 Score: 96
Period size: 35 Copynumber: 2.1 Consensus size: 35
135875 TTTATGTCCG
* * *
135885 CAATTAGCATTCATTTTTATTTGAATTATTTGAAT
1 CAATTAACATTCATTATTATTTGAATTATATGAAT
* * *
135920 TAATTAACATTCATTATTCTTTGAATTCTATGAAT
1 CAATTAACATTCATTATTATTTGAATTATATGAAT
135955 CAATT
1 CAATT
135960 TAACTTTATT
Statistics
Matches: 33, Mismatches: 7, Indels: 0
0.82 0.17 0.00
Matches are distributed among these distances:
35 33 1.00
ACGTcount: A:0.33, C:0.11, G:0.07, T:0.49
Consensus pattern (35 bp):
CAATTAACATTCATTATTATTTGAATTATATGAAT
Found at i:141959 original size:14 final size:16
Alignment explanation
Indices: 141940--141977 Score: 62
Period size: 14 Copynumber: 2.5 Consensus size: 16
141930 GTTCTTTGCA
141940 TCATATTCTTTAT-TT
1 TCATATTCTTTATCTT
141955 T-ATATTCTTTATCTT
1 TCATATTCTTTATCTT
141970 TCATATTC
1 TCATATTC
141978 ATATTCCAAT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
14 11 0.52
15 4 0.19
16 6 0.29
ACGTcount: A:0.21, C:0.16, G:0.00, T:0.63
Consensus pattern (16 bp):
TCATATTCTTTATCTT
Found at i:144568 original size:2 final size:2
Alignment explanation
Indices: 144561--144601 Score: 75
Period size: 2 Copynumber: 21.0 Consensus size: 2
144551 ACCTTTTCTA
144561 AT AT AT AT AT AT AT AT AT AT AT -T AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
144602 GTAAAGCTTG
Statistics
Matches: 38, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.03
2 37 0.97
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
AT
Found at i:146556 original size:8 final size:7
Alignment explanation
Indices: 146542--146586 Score: 54
Period size: 7 Copynumber: 6.1 Consensus size: 7
146532 TATTACACTT
146542 AGAAAAA
1 AGAAAAA
146549 ATGAAAAA
1 A-GAAAAA
146557 AGAAAAA
1 AGAAAAA
**
146564 CTAAAAA
1 AGAAAAA
146571 AGAAAAGA
1 AGAAAA-A
146579 AGAAAAA
1 AGAAAAA
146586 A
1 A
146587 AACAAAAATG
Statistics
Matches: 32, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
7 18 0.56
8 14 0.44
ACGTcount: A:0.80, C:0.02, G:0.13, T:0.04
Consensus pattern (7 bp):
AGAAAAA
Found at i:146569 original size:14 final size:15
Alignment explanation
Indices: 146542--146597 Score: 62
Period size: 15 Copynumber: 3.7 Consensus size: 15
146532 TATTACACTT
146542 AGAAAAAATGAAAAA
1 AGAAAAAATGAAAAA
*
146557 AGAAAAACT-AAAAA
1 AGAAAAAATGAAAAA
146571 AGAAAAGAA-GAAAAA
1 AGAAAA-AATGAAAAA
*
146586 AAACAAAAATGA
1 AGA-AAAAATGA
146598 TGAAAAAAGG
Statistics
Matches: 34, Mismatches: 3, Indels: 7
0.77 0.07 0.16
Matches are distributed among these distances:
14 11 0.32
15 18 0.53
16 5 0.15
ACGTcount: A:0.79, C:0.04, G:0.12, T:0.05
Consensus pattern (15 bp):
AGAAAAAATGAAAAA
Found at i:146581 original size:22 final size:22
Alignment explanation
Indices: 146544--146585 Score: 68
Period size: 22 Copynumber: 1.9 Consensus size: 22
146534 TTACACTTAG
146544 AAAAAATGAAAAAAGAAAAACT
1 AAAAAATGAAAAAAGAAAAACT
146566 AAAAAA-GAAAAGAAGAAAAA
1 AAAAAATGAAAA-AAGAAAAA
146586 AAACAAAAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
21 5 0.26
22 14 0.74
ACGTcount: A:0.81, C:0.02, G:0.12, T:0.05
Consensus pattern (22 bp):
AAAAAATGAAAAAAGAAAAACT
Found at i:146593 original size:22 final size:22
Alignment explanation
Indices: 146544--146597 Score: 65
Period size: 22 Copynumber: 2.4 Consensus size: 22
146534 TTACACTTAG
*
146544 AAAAAATGAAAAAAGAAAAACT
1 AAAAAATGAAAAAAGAAAAACA
*
146566 AAAAAA-GAAAAGAAGAAAAAAA
1 AAAAAATGAAAA-AAGAAAAACA
146588 ACAAAAATGA
1 A-AAAAATGA
146598 TGAAAAAAGG
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
21 5 0.19
22 15 0.56
23 5 0.19
24 2 0.07
ACGTcount: A:0.80, C:0.04, G:0.11, T:0.06
Consensus pattern (22 bp):
AAAAAATGAAAAAAGAAAAACA
Found at i:163175 original size:39 final size:40
Alignment explanation
Indices: 163108--163185 Score: 131
Period size: 39 Copynumber: 2.0 Consensus size: 40
163098 GCTCCCTACA
*
163108 TCATTATGTTTTGCAGTTTCTGTCTTTAGATTAGTTAAAT
1 TCATTATGTTTTCCAGTTTCTGTCTTTAGATTAGTTAAAT
*
163148 TCATTATGTTTTCCTG-TTCTGTCTTTAGATTAGTTAAA
1 TCATTATGTTTTCCAGTTTCTGTCTTTAGATTAGTTAAA
163186 CTATTTTTAG
Statistics
Matches: 36, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
39 22 0.61
40 14 0.39
ACGTcount: A:0.22, C:0.12, G:0.14, T:0.53
Consensus pattern (40 bp):
TCATTATGTTTTCCAGTTTCTGTCTTTAGATTAGTTAAAT
Found at i:168516 original size:28 final size:28
Alignment explanation
Indices: 168476--168531 Score: 112
Period size: 28 Copynumber: 2.0 Consensus size: 28
168466 CTTCCAAATC
168476 CCAACGGTGGGAGATGGAGAAGAAGGAA
1 CCAACGGTGGGAGATGGAGAAGAAGGAA
168504 CCAACGGTGGGAGATGGAGAAGAAGGAA
1 CCAACGGTGGGAGATGGAGAAGAAGGAA
168532 GTGAATTGGA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 28 1.00
ACGTcount: A:0.39, C:0.11, G:0.43, T:0.07
Consensus pattern (28 bp):
CCAACGGTGGGAGATGGAGAAGAAGGAA
Found at i:170366 original size:30 final size:29
Alignment explanation
Indices: 170332--170391 Score: 75
Period size: 30 Copynumber: 2.0 Consensus size: 29
170322 AAATGGATTT
* *
170332 AGTTTAATGACCAAATTATAAGATTTTGAA
1 AGTTTAATGACCAAAGTATAA-ACTTTGAA
**
170362 AGTTTGGTGACCAAAGTATAAACTTTGAA
1 AGTTTAATGACCAAAGTATAAACTTTGAA
170391 A
1 A
170392 AGTTCAGGGA
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
29 8 0.31
30 18 0.69
ACGTcount: A:0.42, C:0.08, G:0.17, T:0.33
Consensus pattern (29 bp):
AGTTTAATGACCAAAGTATAAACTTTGAA
Found at i:170394 original size:30 final size:31
Alignment explanation
Indices: 170339--170412 Score: 82
Period size: 30 Copynumber: 2.5 Consensus size: 31
170329 TTTAGTTTAA
* * *
170339 TGACCAAATTATAAGATTTTGAAAGTT-TGG
1 TGACCAAAATATAAGACTTTGAAAGTTCAGG
*
170369 TGACCAAAGTATAA-ACTTTGAAAAGTTCAGG
1 TGACCAAAATATAAGACTTTG-AAAGTTCAGG
170400 -GACCAAAATATAA
1 TGACCAAAATATAA
170413 TTTTAAAAAG
Statistics
Matches: 38, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
29 5 0.13
30 31 0.82
31 2 0.05
ACGTcount: A:0.43, C:0.11, G:0.18, T:0.28
Consensus pattern (31 bp):
TGACCAAAATATAAGACTTTGAAAGTTCAGG
Found at i:171367 original size:30 final size:31
Alignment explanation
Indices: 171324--171395 Score: 101
Period size: 31 Copynumber: 2.4 Consensus size: 31
171314 TCTATTGGCC
* *
171324 TTAGAAAAATTTGGGGACC-ATTATGTAATT
1 TTAGAAAAGTTTGGGGACCAATTAGGTAATT
* *
171354 TTTGAAAAGTTTGGGGACCAATTCGGTAATT
1 TTAGAAAAGTTTGGGGACCAATTAGGTAATT
171385 TTAGAAAAGTT
1 TTAGAAAAGTT
171396 GTAAATGATT
Statistics
Matches: 36, Mismatches: 5, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
30 17 0.47
31 19 0.53
ACGTcount: A:0.35, C:0.07, G:0.22, T:0.36
Consensus pattern (31 bp):
TTAGAAAAGTTTGGGGACCAATTAGGTAATT
Found at i:172710 original size:18 final size:18
Alignment explanation
Indices: 172687--172749 Score: 58
Period size: 18 Copynumber: 3.6 Consensus size: 18
172677 ATATGATAGG
172687 TCCTTCGGGACACAGACA
1 TCCTTCGGGACACAGACA
* * *
172705 TCCTTCGGGATGATAG--G
1 TCCTTCGGGA-CACAGACA
*
172722 TCATTCGGGACACAGACA
1 TCCTTCGGGACACAGACA
*
172740 TCCTTTGGGA
1 TCCTTCGGGA
172750 TGATAGGTCC
Statistics
Matches: 33, Mismatches: 9, Indels: 6
0.69 0.19 0.12
Matches are distributed among these distances:
16 3 0.09
17 9 0.27
18 18 0.55
19 3 0.09
ACGTcount: A:0.24, C:0.25, G:0.27, T:0.24
Consensus pattern (18 bp):
TCCTTCGGGACACAGACA
Found at i:172789 original size:38 final size:35
Alignment explanation
Indices: 172679--172808 Score: 206
Period size: 35 Copynumber: 3.6 Consensus size: 35
172669 TATAAGACAT
172679 ATGATAGGTCCTTCGGGACACAGACATCCTTCGGG
1 ATGATAGGTCCTTCGGGACACAGACATCCTTCGGG
* *
172714 ATGATAGGTCATTCGGGACACAGACATCCTTTGGG
1 ATGATAGGTCCTTCGGGACACAGACATCCTTCGGG
*
172749 ATGATAGGTCCTTCGGGACACAGATGACATCCTTCAGG
1 ATGATAGGTCCTTCGGGACAC--A-GACATCCTTCGGG
172787 ATGATAGGTCCTTCGGGACACA
1 ATGATAGGTCCTTCGGGACACA
172809 TTTTATACGA
Statistics
Matches: 87, Mismatches: 5, Indels: 5
0.90 0.05 0.05
Matches are distributed among these distances:
35 53 0.61
36 1 0.01
37 1 0.01
38 32 0.37
ACGTcount: A:0.25, C:0.23, G:0.28, T:0.24
Consensus pattern (35 bp):
ATGATAGGTCCTTCGGGACACAGACATCCTTCGGG
Found at i:173121 original size:18 final size:18
Alignment explanation
Indices: 173076--173123 Score: 51
Period size: 18 Copynumber: 2.7 Consensus size: 18
173066 AAATGTATTA
**
173076 CATGATAATGATATTGAT
1 CATGATAATGATAGAGAT
** *
173094 GTTGAGAATGATAGAGAT
1 CATGATAATGATAGAGAT
173112 CATGATAATGAT
1 CATGATAATGAT
173124 GTTGATAATG
Statistics
Matches: 22, Mismatches: 8, Indels: 0
0.73 0.27 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.40, C:0.04, G:0.23, T:0.33
Consensus pattern (18 bp):
CATGATAATGATAGAGAT
Found at i:175792 original size:15 final size:18
Alignment explanation
Indices: 175774--175813 Score: 52
Period size: 16 Copynumber: 2.4 Consensus size: 18
175764 AAGAGCTAAA
175774 AAAG-AAAGAA-AA-AAG
1 AAAGAAAAGAAGAAGAAG
175789 AAAGAAAAGAAGAAGAAG
1 AAAGAAAAGAAGAAGAAG
175807 AAA-AAAA
1 AAAGAAAA
175814 AACAAAAACA
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
15 4 0.18
16 6 0.27
17 6 0.27
18 6 0.27
ACGTcount: A:0.80, C:0.00, G:0.20, T:0.00
Consensus pattern (18 bp):
AAAGAAAAGAAGAAGAAG
Found at i:175801 original size:12 final size:11
Alignment explanation
Indices: 175771--175821 Score: 59
Period size: 11 Copynumber: 4.5 Consensus size: 11
175761 CATAAGAGCT
175771 AAAAAAGAAAG
1 AAAAAAGAAAG
175782 AAAAAAGAAAG
1 AAAAAAGAAAG
175793 AAAAGAAGAAGAAG
1 AAAA-AAG-A-AAG
*
175807 AAAAAA-AAAC
1 AAAAAAGAAAG
175817 AAAAA
1 AAAAA
175822 CAAAAAATGA
Statistics
Matches: 36, Mismatches: 1, Indels: 7
0.82 0.02 0.16
Matches are distributed among these distances:
10 7 0.19
11 16 0.44
12 3 0.08
13 3 0.08
14 7 0.19
ACGTcount: A:0.82, C:0.02, G:0.16, T:0.00
Consensus pattern (11 bp):
AAAAAAGAAAG
Found at i:176790 original size:30 final size:30
Alignment explanation
Indices: 176756--176830 Score: 80
Period size: 30 Copynumber: 2.5 Consensus size: 30
176746 AAATGGATTT
* * *
176756 AGTTTAATGTCCAAATTATAAGATTTTG-AA
1 AGTTTAATGACCAAAGTATAA-ACTTTGAAA
*
176786 AGTTTAGTGACCAAAGTATAAACTTTGAAA
1 AGTTTAATGACCAAAGTATAAACTTTGAAA
**
176816 AGTTTAGGGACCAAA
1 AGTTTAATGACCAAA
176831 ATTTAATTTT
Statistics
Matches: 39, Mismatches: 5, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
29 5 0.13
30 34 0.87
ACGTcount: A:0.41, C:0.09, G:0.17, T:0.32
Consensus pattern (30 bp):
AGTTTAATGACCAAAGTATAAACTTTGAAA
Found at i:178059 original size:9 final size:9
Alignment explanation
Indices: 178045--178097 Score: 79
Period size: 9 Copynumber: 5.9 Consensus size: 9
178035 TCCAGTACTG
178045 GAATTTCTT
1 GAATTTCTT
*
178054 GAATTTCTA
1 GAATTTCTT
178063 GAATTTCTT
1 GAATTTCTT
*
178072 GAATTTCTG
1 GAATTTCTT
*
178081 GAATTTCAT
1 GAATTTCTT
178090 GAATTTCT
1 GAATTTCT
178098 GGAAATACTG
Statistics
Matches: 38, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
9 38 1.00
ACGTcount: A:0.26, C:0.11, G:0.13, T:0.49
Consensus pattern (9 bp):
GAATTTCTT
Found at i:178075 original size:27 final size:27
Alignment explanation
Indices: 178045--178113 Score: 86
Period size: 27 Copynumber: 2.6 Consensus size: 27
178035 TCCAGTACTG
*
178045 GAATTTCTTGAATTTCTA-GAATTTCTT
1 GAATTTCTGGAATTTC-ATGAATTTCTT
*
178072 GAATTTCTGGAATTTCATGAATTTCTG
1 GAATTTCTGGAATTTCATGAATTTCTT
* *
178099 GAAATACTGGAATTT
1 GAATTTCTGGAATTT
178114 TTGGTATTTA
Statistics
Matches: 37, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
26 1 0.03
27 36 0.97
ACGTcount: A:0.29, C:0.10, G:0.16, T:0.45
Consensus pattern (27 bp):
GAATTTCTGGAATTTCATGAATTTCTT
Found at i:178098 original size:18 final size:18
Alignment explanation
Indices: 178042--178101 Score: 102
Period size: 18 Copynumber: 3.3 Consensus size: 18
178032 AATTCCAGTA
178042 CTGGAATTTCTTGAATTT
1 CTGGAATTTCTTGAATTT
*
178060 CTAGAATTTCTTGAATTT
1 CTGGAATTTCTTGAATTT
*
178078 CTGGAATTTCATGAATTT
1 CTGGAATTTCTTGAATTT
178096 CTGGAA
1 CTGGAA
178102 ATACTGGAAT
Statistics
Matches: 39, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
18 39 1.00
ACGTcount: A:0.27, C:0.12, G:0.17, T:0.45
Consensus pattern (18 bp):
CTGGAATTTCTTGAATTT
Found at i:178113 original size:18 final size:18
Alignment explanation
Indices: 178071--178105 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
178061 TAGAATTTCT
* *
178071 TGAATTTCTGGAATTTCA
1 TGAATTTCTGGAAATACA
178089 TGAATTTCTGGAAATAC
1 TGAATTTCTGGAAATAC
178106 TGGAATTTTT
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:0.31, C:0.11, G:0.17, T:0.40
Consensus pattern (18 bp):
TGAATTTCTGGAAATACA
Found at i:179192 original size:18 final size:18
Alignment explanation
Indices: 179169--179231 Score: 74
Period size: 18 Copynumber: 3.6 Consensus size: 18
179159 ATATGATAGG
179169 TCCTTCGGGACACATACA
1 TCCTTCGGGACACATACA
** *
179187 TCCTTCGGGA-TGATAGA
1 TCCTTCGGGACACATACA
*
179204 TCCTTTGGGACACATACA
1 TCCTTCGGGACACATACA
*
179222 TCCTTTGGGA
1 TCCTTCGGGA
179232 TGATAGGTCT
Statistics
Matches: 37, Mismatches: 7, Indels: 2
0.80 0.15 0.04
Matches are distributed among these distances:
17 13 0.35
18 24 0.65
ACGTcount: A:0.24, C:0.25, G:0.22, T:0.29
Consensus pattern (18 bp):
TCCTTCGGGACACATACA
Found at i:179208 original size:17 final size:17
Alignment explanation
Indices: 179161--179237 Score: 55
Period size: 18 Copynumber: 4.4 Consensus size: 17
179151 TATAAGACAT
*
179161 ATGATAGGTCCTTCGGG
1 ATGATAGATCCTTCGGG
** *
179178 ACACATACATCCTTCGGG
1 A-TGATAGATCCTTCGGG
*
179196 ATGATAGATCCTTTGGG
1 ATGATAGATCCTTCGGG
** * *
179213 ACACATACATCCTTTGGG
1 A-TGATAGATCCTTCGGG
179231 ATGATAG
1 ATGATAG
179238 GTCTTTCAGG
Statistics
Matches: 44, Mismatches: 14, Indels: 4
0.71 0.23 0.06
Matches are distributed among these distances:
17 17 0.39
18 27 0.61
ACGTcount: A:0.26, C:0.21, G:0.25, T:0.29
Consensus pattern (17 bp):
ATGATAGATCCTTCGGG
Found at i:179291 original size:38 final size:35
Alignment explanation
Indices: 179161--179290 Score: 179
Period size: 35 Copynumber: 3.6 Consensus size: 35
179151 TATAAGACAT
179161 ATGATAGGTCCTTCGGGACACATACATCCTTCGGG
1 ATGATAGGTCCTTCGGGACACATACATCCTTCGGG
* * *
179196 ATGATAGATCCTTTGGGACACATACATCCTTTGGG
1 ATGATAGGTCCTTCGGGACACATACATCCTTCGGG
* * *
179231 ATGATAGGTCTTTCAGGACACAGATGACATCCTTCGGA
1 ATGATAGGTCCTTCGGGACAC--AT-ACATCCTTCGGG
179269 ATGATAGGTCCTTCGGGACACA
1 ATGATAGGTCCTTCGGGACACA
179291 GTTTATACGA
Statistics
Matches: 81, Mismatches: 11, Indels: 5
0.84 0.11 0.05
Matches are distributed among these distances:
35 49 0.60
36 1 0.01
37 2 0.02
38 29 0.36
ACGTcount: A:0.26, C:0.22, G:0.25, T:0.27
Consensus pattern (35 bp):
ATGATAGGTCCTTCGGGACACATACATCCTTCGGG
Found at i:179401 original size:30 final size:30
Alignment explanation
Indices: 179355--179417 Score: 81
Period size: 30 Copynumber: 2.1 Consensus size: 30
179345 CCTTGAGTTC
* *
179355 TCAGTAATGTACATGGGATTATAAAAGATA
1 TCAGTAATGTACATGGGACTACAAAAGATA
* * *
179385 TCAGTATTGTATATGGGCCTACAAAAGATA
1 TCAGTAATGTACATGGGACTACAAAAGATA
179415 TCA
1 TCA
179418 AAAGTATACA
Statistics
Matches: 28, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
30 28 1.00
ACGTcount: A:0.40, C:0.11, G:0.19, T:0.30
Consensus pattern (30 bp):
TCAGTAATGTACATGGGACTACAAAAGATA
Found at i:179601 original size:18 final size:18
Alignment explanation
Indices: 179556--179603 Score: 51
Period size: 18 Copynumber: 2.7 Consensus size: 18
179546 AAATGTATTA
**
179556 CATGATAATGATATTGAT
1 CATGATAATGATAGAGAT
** *
179574 GTTGAGAATGATAGAGAT
1 CATGATAATGATAGAGAT
179592 CATGATAATGAT
1 CATGATAATGAT
179604 GGCATATGTG
Statistics
Matches: 22, Mismatches: 8, Indels: 0
0.73 0.27 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.40, C:0.04, G:0.23, T:0.33
Consensus pattern (18 bp):
CATGATAATGATAGAGAT
Found at i:180583 original size:31 final size:31
Alignment explanation
Indices: 180545--180680 Score: 123
Period size: 30 Copynumber: 4.5 Consensus size: 31
180535 TTCAAGAGTT
* *
180545 AATTGATATTTTATCTAATGTATAAGGGTCA
1 AATTGATATTTTATCTAATGTTTAAAGGTCA
** **
180576 AATTGATATTTTA-CTAACATTTATGGGTCA
1 AATTGATATTTTATCTAATGTTTAAAGGTCA
* * * * **
180606 AATTAATATTTTATTTAAAGTTAAAATATCA
1 AATTGATATTTTATCTAATGTTTAAAGGTCA
* *
180637 AATTGATATTTTATCAAAT-TTTAAAAGTCA
1 AATTGATATTTTATCTAATGTTTAAAGGTCA
*
180667 AATTCATATTTTAT
1 AATTGATATTTTAT
180681 TAAAATTTAG
Statistics
Matches: 83, Mismatches: 21, Indels: 3
0.78 0.20 0.03
Matches are distributed among these distances:
30 46 0.55
31 37 0.45
ACGTcount: A:0.40, C:0.07, G:0.09, T:0.45
Consensus pattern (31 bp):
AATTGATATTTTATCTAATGTTTAAAGGTCA
Found at i:180687 original size:31 final size:32
Alignment explanation
Indices: 180602--180688 Score: 99
Period size: 31 Copynumber: 2.8 Consensus size: 32
180592 ACATTTATGG
* *
180602 GTCAAATTAATATTTTATTTAAA-GTTAAAAT
1 GTCAAATTAATATTTTATTAAAATTTTAAAAT
* * *
180633 ATCAAATTGATATTTTA-TCAAATTTTAAAA-
1 GTCAAATTAATATTTTATTAAAATTTTAAAAT
*
180663 GTCAAATTCATATTTTATTAAAATTT
1 GTCAAATTAATATTTTATTAAAATTT
180689 AGAGTGAAAT
Statistics
Matches: 47, Mismatches: 7, Indels: 4
0.81 0.12 0.07
Matches are distributed among these distances:
30 19 0.40
31 28 0.60
ACGTcount: A:0.44, C:0.06, G:0.05, T:0.46
Consensus pattern (32 bp):
GTCAAATTAATATTTTATTAAAATTTTAAAAT
Found at i:185091 original size:38 final size:36
Alignment explanation
Indices: 184999--185075 Score: 102
Period size: 38 Copynumber: 2.1 Consensus size: 36
184989 TAGCACCAAG
* *
184999 AAGCAATTTATGTATATGAGAGAAACATCAAGAAGTAT
1 AAGCAATATAAGTATATGAGAGAAACATC-A-AAGTAT
*
185037 AAGCAATTTAAGTATATGAGAGAAACATC-AAGTAT
1 AAGCAATATAAGTATATGAGAGAAACATCAAAGTAT
185072 AAGC
1 AAGC
185076 TAACATATCA
Statistics
Matches: 38, Mismatches: 1, Indels: 3
0.90 0.02 0.07
Matches are distributed among these distances:
35 10 0.26
38 28 0.74
ACGTcount: A:0.48, C:0.09, G:0.18, T:0.25
Consensus pattern (36 bp):
AAGCAATATAAGTATATGAGAGAAACATCAAAGTAT
Found at i:185742 original size:20 final size:20
Alignment explanation
Indices: 185717--185755 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
185707 TAAATTAAAT
*
185717 ATTAGATAGGATCAGTTTTA
1 ATTAGATAGAATCAGTTTTA
185737 ATTAGATAGAATCAGTTTT
1 ATTAGATAGAATCAGTTTT
185756 TATTCTATTA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.36, C:0.05, G:0.18, T:0.41
Consensus pattern (20 bp):
ATTAGATAGAATCAGTTTTA
Found at i:185835 original size:53 final size:53
Alignment explanation
Indices: 185710--185866 Score: 239
Period size: 52 Copynumber: 3.0 Consensus size: 53
185700 GAATATCTAA
* * *
185710 ATTAAATATTAGATAGGATCAGTTTTAATTAGATAGAATCAG-TTTTTATTCT
1 ATTAATTATTAGATAAGATCATTTTTAATTAGATAGAATCAGTTTTTTATTCT
* *
185762 ATTAGTTATTAGA-AAGGATCATTTTTAATTAAATAGAATCAGTTTTTTATTCT
1 ATTAATTATTAGATAA-GATCATTTTTAATTAGATAGAATCAGTTTTTTATTCT
185815 ATTAATTATTAGATAAGATCATTTTTAATTAGATAGAATCA-TTTTTTATTCT
1 ATTAATTATTAGATAAGATCATTTTTAATTAGATAGAATCAGTTTTTTATTCT
185867 GTTGTTAATT
Statistics
Matches: 95, Mismatches: 7, Indels: 6
0.88 0.06 0.06
Matches are distributed among these distances:
51 1 0.01
52 46 0.48
53 46 0.48
54 2 0.02
ACGTcount: A:0.36, C:0.06, G:0.11, T:0.47
Consensus pattern (53 bp):
ATTAATTATTAGATAAGATCATTTTTAATTAGATAGAATCAGTTTTTTATTCT
Found at i:185847 original size:20 final size:20
Alignment explanation
Indices: 185822--185860 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 20
185812 TCTATTAATT
185822 ATTAGATA-AGATCATTTTTA
1 ATTAGATAGA-ATCATTTTTA
185842 ATTAGATAGAATCATTTTT
1 ATTAGATAGAATCATTTTT
185861 TATTCTGTTG
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 17 0.94
21 1 0.06
ACGTcount: A:0.38, C:0.05, G:0.10, T:0.46
Consensus pattern (20 bp):
ATTAGATAGAATCATTTTTA
Found at i:187367 original size:20 final size:20
Alignment explanation
Indices: 187342--187432 Score: 72
Period size: 20 Copynumber: 5.0 Consensus size: 20
187332 TAAATTAAAT
*
187342 ATTAGATAGGATCAGTTTTA
1 ATTAGATAGAATCAGTTTTA
*
187362 ATTAGATAGAATCAGTTTTT
1 ATTAGATAGAATCAGTTTTA
* *
187382 ATT--CT---ATTAG--TT-
1 ATTAGATAGAATCAGTTTTA
* *
187394 ATTAGATAGGATCATTTTTA
1 ATTAGATAGAATCAGTTTTA
187414 ATTAGATAGAATCAGTTTT
1 ATTAGATAGAATCAGTTTT
187433 TTATTCTATT
Statistics
Matches: 54, Mismatches: 9, Indels: 16
0.68 0.11 0.20
Matches are distributed among these distances:
12 3 0.06
13 2 0.04
14 1 0.02
15 4 0.07
17 3 0.06
18 1 0.02
19 2 0.04
20 38 0.70
ACGTcount: A:0.34, C:0.05, G:0.15, T:0.45
Consensus pattern (20 bp):
ATTAGATAGAATCAGTTTTA
Found at i:187457 original size:53 final size:53
Alignment explanation
Indices: 187341--187489 Score: 275
Period size: 53 Copynumber: 2.8 Consensus size: 53
187331 CTAAATTAAA
*
187341 TATTAGATAGGATCAGTTTTAATTAGATAGAATCAG-TTTTTATTCTATTAGT
1 TATTAGATAGGATCATTTTTAATTAGATAGAATCAGTTTTTTATTCTATTAGT
187393 TATTAGATAGGATCATTTTTAATTAGATAGAATCAGTTTTTTATTCTATTAGT
1 TATTAGATAGGATCATTTTTAATTAGATAGAATCAGTTTTTTATTCTATTAGT
187446 TATTAGATAGGATCATTTTTAATTAGATAGAATCA-TTTTTTATT
1 TATTAGATAGGATCATTTTTAATTAGATAGAATCAGTTTTTTATT
187490 TTGTTGCTAA
Statistics
Matches: 95, Mismatches: 1, Indels: 2
0.97 0.01 0.02
Matches are distributed among these distances:
52 44 0.46
53 51 0.54
ACGTcount: A:0.33, C:0.05, G:0.13, T:0.48
Consensus pattern (53 bp):
TATTAGATAGGATCATTTTTAATTAGATAGAATCAGTTTTTTATTCTATTAGT
Found at i:187487 original size:21 final size:20
Alignment explanation
Indices: 187447--187485 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
187437 TCTATTAGTT
*
187447 ATTAGATAGGATCATTTTTA
1 ATTAGATAGAATCATTTTTA
187467 ATTAGATAGAATCATTTTT
1 ATTAGATAGAATCATTTTT
187486 TATTTTGTTG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.36, C:0.05, G:0.13, T:0.46
Consensus pattern (20 bp):
ATTAGATAGAATCATTTTTA
Found at i:190874 original size:19 final size:20
Alignment explanation
Indices: 190841--190878 Score: 69
Period size: 19 Copynumber: 1.9 Consensus size: 20
190831 ATCCGAATAA
190841 AAAACTGATTCTATCTAATT
1 AAAACTGATTCTATCTAATT
190861 AAAACTGA-TCTATCTAAT
1 AAAACTGATTCTATCTAAT
190879 ATTTAATTTA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 10 0.56
20 8 0.44
ACGTcount: A:0.42, C:0.16, G:0.05, T:0.37
Consensus pattern (20 bp):
AAAACTGATTCTATCTAATT
Found at i:193379 original size:24 final size:24
Alignment explanation
Indices: 193343--193394 Score: 61
Period size: 24 Copynumber: 2.2 Consensus size: 24
193333 GCAACATTGG
* *
193343 CAGCTGCAGCTGCAGCCT-TTGCAA
1 CAGCAGCACCTGCAG-CTATTGCAA
*
193367 CAGCAGCACCTGCTGCTATTGCAA
1 CAGCAGCACCTGCAGCTATTGCAA
193391 CAGC
1 CAGC
193395 TGCAGAAGTC
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
23 2 0.08
24 22 0.92
ACGTcount: A:0.23, C:0.35, G:0.23, T:0.19
Consensus pattern (24 bp):
CAGCAGCACCTGCAGCTATTGCAA
Found at i:201234 original size:10 final size:10
Alignment explanation
Indices: 201198--201262 Score: 53
Period size: 10 Copynumber: 6.4 Consensus size: 10
201188 CAAATAAATT
*
201198 TGTTT-TTTG
1 TGTTTGTTTA
*
201207 TGTTTGTGT-
1 TGTTTGTTTA
*
201216 TGTTCGTTTA
1 TGTTTGTTTA
201226 TGTTTGTTTA
1 TGTTTGTTTA
201236 TTGTGTTCGTTTA
1 -TGT-TT-GTTTA
*
201249 TGTTCGTTTA
1 TGTTTGTTTA
201259 TGTT
1 TGTT
201263 AGTTCGTTTG
Statistics
Matches: 46, Mismatches: 5, Indels: 9
0.77 0.08 0.15
Matches are distributed among these distances:
9 12 0.26
10 20 0.43
11 4 0.09
12 5 0.11
13 5 0.11
ACGTcount: A:0.06, C:0.05, G:0.23, T:0.66
Consensus pattern (10 bp):
TGTTTGTTTA
Found at i:201269 original size:14 final size:13
Alignment explanation
Indices: 201208--201286 Score: 61
Period size: 10 Copynumber: 6.7 Consensus size: 13
201198 TGTTTTTTGT
*
201208 GTTTGTGTTGTTC
1 GTTTATGTTGTTC
201221 GTTTATG-T-TT-
1 GTTTATGTTGTTC
201231 GTTTAT-TGTGTTC
1 GTTTATGT-TGTTC
201244 GTTTA---TGTTC
1 GTTTATGTTGTTC
201254 GTTTATGTTAGTTC
1 GTTTATGTT-GTTC
201268 G-TT-TG-TGTTC
1 GTTTATGTTGTTC
201278 GTTTATGTT
1 GTTTATGTT
201287 CATTTATTAT
Statistics
Matches: 54, Mismatches: 1, Indels: 22
0.70 0.01 0.29
Matches are distributed among these distances:
10 21 0.39
11 6 0.11
12 7 0.13
13 15 0.28
14 5 0.09
ACGTcount: A:0.08, C:0.06, G:0.24, T:0.62
Consensus pattern (13 bp):
GTTTATGTTGTTC
Found at i:201276 original size:24 final size:23
Alignment explanation
Indices: 201208--201286 Score: 106
Period size: 23 Copynumber: 3.4 Consensus size: 23
201198 TGTTTTTTGT
* *
201208 GTTTGTGTTGTTCGTTTATGTTT
1 GTTTATGTTGTTCGTTTATGTTC
201231 GTTTAT-TGTGTTCGTTTATGTTC
1 GTTTATGT-TGTTCGTTTATGTTC
*
201254 GTTTATGTTAGTTCGTTTGTGTTC
1 GTTTATGTT-GTTCGTTTATGTTC
201278 GTTTATGTT
1 GTTTATGTT
201287 CATTTATTAT
Statistics
Matches: 50, Mismatches: 3, Indels: 5
0.86 0.05 0.09
Matches are distributed among these distances:
22 1 0.02
23 26 0.52
24 23 0.46
ACGTcount: A:0.08, C:0.06, G:0.24, T:0.62
Consensus pattern (23 bp):
GTTTATGTTGTTCGTTTATGTTC
Found at i:201279 original size:34 final size:32
Alignment explanation
Indices: 201201--201293 Score: 116
Period size: 34 Copynumber: 2.8 Consensus size: 32
201191 ATAAATTTGT
* * *
201201 TTTTTGTGTTTGTGT-TGTTCGTTTATGTTTG
1 TTTTTGTGTTCGTTTATGTTCGTTTATGTTAG
201232 TTTATTGTGTTCGTTTATGTTCGTTTATGTTAG
1 TTT-TTGTGTTCGTTTATGTTCGTTTATGTTAG
*
201265 TTCGTTTGTGTTCGTTTATGTTCATTTAT
1 TT--TTTGTGTTCGTTTATGTTCGTTTAT
201294 TATTTAAATG
Statistics
Matches: 54, Mismatches: 4, Indels: 5
0.86 0.06 0.08
Matches are distributed among these distances:
31 3 0.06
32 10 0.19
33 17 0.31
34 23 0.43
35 1 0.02
ACGTcount: A:0.09, C:0.06, G:0.22, T:0.63
Consensus pattern (32 bp):
TTTTTGTGTTCGTTTATGTTCGTTTATGTTAG
Found at i:201379 original size:16 final size:16
Alignment explanation
Indices: 201358--201388 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
201348 AAAAAAAATT
201358 GTTCGTTTATGTTCGC
1 GTTCGTTTATGTTCGC
201374 GTTCGTTTATGTTCG
1 GTTCGTTTATGTTCG
201389 TTTATTTATT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.06, C:0.16, G:0.26, T:0.52
Consensus pattern (16 bp):
GTTCGTTTATGTTCGC
Found at i:202213 original size:20 final size:19
Alignment explanation
Indices: 202171--202213 Score: 52
Period size: 19 Copynumber: 2.3 Consensus size: 19
202161 TTTTTAAAAA
*
202171 ATTATATAAAAATCATAAT
1 ATTATATAAAAATCACAAT
*
202190 -TTATATATAAAATTACAAT
1 ATTATATA-AAAATCACAAT
202209 ATTAT
1 ATTAT
202214 TTTTTTTCTA
Statistics
Matches: 20, Mismatches: 2, Indels: 3
0.80 0.08 0.12
Matches are distributed among these distances:
18 7 0.35
19 9 0.45
20 4 0.20
ACGTcount: A:0.53, C:0.05, G:0.00, T:0.42
Consensus pattern (19 bp):
ATTATATAAAAATCACAAT
Found at i:205996 original size:12 final size:12
Alignment explanation
Indices: 205981--206006 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
205971 TAGAATTCAA
205981 TTCCATATTCTG
1 TTCCATATTCTG
205993 TTCCATATTCTG
1 TTCCATATTCTG
206005 TT
1 TT
206007 TAGTTCGCAG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.15, C:0.23, G:0.08, T:0.54
Consensus pattern (12 bp):
TTCCATATTCTG
Found at i:206239 original size:42 final size:41
Alignment explanation
Indices: 206137--206240 Score: 181
Period size: 41 Copynumber: 2.5 Consensus size: 41
206127 CCCCGAATTC
*
206137 CCGTGTTTGTTTCACGTAATTCATTTTTCGGAAAATGTTTT
1 CCGTGTTTGTTTCACGTAATTCATTTTCCGGAAAATGTTTT
206178 CCGTGTTTGTTTCACGTAATTCATTTTCCGGAAAATGTTTT
1 CCGTGTTTGTTTCACGTAATTCATTTTCCGGAAAATGTTTT
*
206219 CCTGTGTTTATTTCACGTAATT
1 CC-GTGTTTGTTTCACGTAATT
206241 GGTTTTTCGA
Statistics
Matches: 60, Mismatches: 2, Indels: 1
0.95 0.03 0.02
Matches are distributed among these distances:
41 42 0.70
42 18 0.30
ACGTcount: A:0.19, C:0.16, G:0.16, T:0.48
Consensus pattern (41 bp):
CCGTGTTTGTTTCACGTAATTCATTTTCCGGAAAATGTTTT
Found at i:206427 original size:12 final size:13
Alignment explanation
Indices: 206410--206438 Score: 51
Period size: 12 Copynumber: 2.3 Consensus size: 13
206400 CATCAAAATA
206410 TTATTTATT-TAT
1 TTATTTATTATAT
206422 TTATTTATTATAT
1 TTATTTATTATAT
206435 TTAT
1 TTAT
206439 AATAATATAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 9 0.56
13 7 0.44
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (13 bp):
TTATTTATTATAT
Found at i:206454 original size:29 final size:29
Alignment explanation
Indices: 206422--206590 Score: 110
Period size: 29 Copynumber: 5.9 Consensus size: 29
206412 ATTTATTTAT
206422 TTATTTATTATATTTATAATAATATAATA
1 TTATTTATTATATTTATAATAATATAATA
* *
206451 TTATATTTTTA-ATATTAT-ATAAAATAATCA
1 TTAT-TTATTATAT-TTATAATAATATAAT-A
* *
206481 --ATTATATTATAATAAT-ATAATATAAGATA
1 TTATT-TATTATATTTATAATAATAT-A-ATA
*
206510 TTATATTTTTAT-TTTAATAAT-ATATAATA
1 TTAT-TTATTATATTT-ATAATAATATAATA
206539 TT-TTT-TTATATATT-TAATAATGAATAATA
1 TTATTTATTATAT-TTATAATAAT--ATAATA
206568 TTATTTA-TATATTTA-AATAATAT
1 TTATTTATTATATTTATAATAATAT
206591 TTTAATAAAG
Statistics
Matches: 111, Mismatches: 9, Indels: 42
0.69 0.06 0.26
Matches are distributed among these distances:
26 8 0.07
27 8 0.07
28 18 0.16
29 39 0.35
30 22 0.20
31 13 0.12
32 3 0.03
ACGTcount: A:0.46, C:0.01, G:0.01, T:0.53
Consensus pattern (29 bp):
TTATTTATTATATTTATAATAATATAATA
Found at i:206455 original size:22 final size:22
Alignment explanation
Indices: 206427--206469 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 22
206417 TTTATTTATT
206427 TATTATATTTATAATAATATAA
1 TATTATATTTATAATAATATAA
* *
206449 TATTATATTTTTAATATTATA
1 TATTATATTTATAATAATATA
206470 TAAAATAATC
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (22 bp):
TATTATATTTATAATAATATAA
Found at i:206568 original size:19 final size:19
Alignment explanation
Indices: 206546--206598 Score: 54
Period size: 20 Copynumber: 2.7 Consensus size: 19
206536 ATATTTTTTT
*
206546 ATATATTTAATAATGAATA
1 ATATATTTAATAATAAATA
*
206565 ATATTATTTATATATTTAAATA
1 ATA-TATTTA-ATA-ATAAATA
206587 ATAT-TTTAATAA
1 ATATATTTAATAA
206599 AGATATTTAA
Statistics
Matches: 28, Mismatches: 3, Indels: 7
0.74 0.08 0.18
Matches are distributed among these distances:
19 6 0.21
20 10 0.36
21 4 0.14
22 8 0.29
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (19 bp):
ATATATTTAATAATAAATA
Found at i:206619 original size:23 final size:23
Alignment explanation
Indices: 206593--206637 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
206583 AATAATATTT
206593 TAATAAAGATATTTAAAATATAC
1 TAATAAAGATATTTAAAATATAC
* * *
206616 TAATTAATATTTTTAAAATATA
1 TAATAAAGATATTTAAAATATA
206638 ATATAACAAT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.53, C:0.02, G:0.02, T:0.42
Consensus pattern (23 bp):
TAATAAAGATATTTAAAATATAC
Found at i:206707 original size:80 final size:78
Alignment explanation
Indices: 206617--206765 Score: 176
Period size: 80 Copynumber: 1.9 Consensus size: 78
206607 AAAATATACT
* * * *
206617 AATTAATATTTTTA-AAATATAA-TATAACAATATTACTTTAATAAATAATTAATATAATTTATA
1 AATTAATATTTTTATAAATAAAATTATAAAAATAATA-TTTAAT-AATAAATAA-ATAATTT-TA
206680 ATATTTTATTTCACAAA
62 ATATTTTATTTCACAAA
* * * *
206697 AATTATTATTTTTATTATTAAAATTATAAAAATAATATTTAATAATAAATAAATTATTTTAATAT
1 AATTAATATTTTTATAAATAAAATTATAAAAATAATATTTAATAATAAATAAATAATTTTAATAT
206762 TTTA
66 TTTA
206766 AAATAATAAT
Statistics
Matches: 59, Mismatches: 8, Indels: 6
0.81 0.11 0.08
Matches are distributed among these distances:
78 10 0.17
79 6 0.10
80 21 0.36
81 11 0.19
82 11 0.19
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.48
Consensus pattern (78 bp):
AATTAATATTTTTATAAATAAAATTATAAAAATAATATTTAATAATAAATAAATAATTTTAATAT
TTTATTTCACAAA
Found at i:206963 original size:14 final size:14
Alignment explanation
Indices: 206929--206969 Score: 55
Period size: 14 Copynumber: 2.9 Consensus size: 14
206919 AAATGTAATT
*
206929 CATTTTACGGAAAA
1 CATTTTCCGGAAAA
206943 CATTTTCCGGAAAA
1 CATTTTCCGGAAAA
* *
206957 CGTTTTCCAGAAA
1 CATTTTCCGGAAA
206970 CGTAATTCAT
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
14 24 1.00
ACGTcount: A:0.37, C:0.20, G:0.15, T:0.29
Consensus pattern (14 bp):
CATTTTCCGGAAAA
Found at i:207013 original size:15 final size:15
Alignment explanation
Indices: 206971--207016 Score: 67
Period size: 15 Copynumber: 3.1 Consensus size: 15
206961 TTCCAGAAAC
206971 GTAATTCATTTTCCA
1 GTAATTCATTTTCCA
**
206986 G-AATTCAAATTCCA
1 GTAATTCATTTTCCA
207000 GTAATTCATTTTCCA
1 GTAATTCATTTTCCA
207015 GT
1 GT
207017 TTCAGTAATT
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
14 12 0.46
15 14 0.54
ACGTcount: A:0.30, C:0.20, G:0.09, T:0.41
Consensus pattern (15 bp):
GTAATTCATTTTCCA
Found at i:213482 original size:6 final size:6
Alignment explanation
Indices: 213471--213509 Score: 78
Period size: 6 Copynumber: 6.5 Consensus size: 6
213461 AAACGCGTCC
213471 CTTCCT CTTCCT CTTCCT CTTCCT CTTCCT CTTCCT CTT
1 CTTCCT CTTCCT CTTCCT CTTCCT CTTCCT CTTCCT CTT
213510 ATTCCAAACA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 33 1.00
ACGTcount: A:0.00, C:0.49, G:0.00, T:0.51
Consensus pattern (6 bp):
CTTCCT
Found at i:215437 original size:26 final size:25
Alignment explanation
Indices: 215387--215442 Score: 67
Period size: 26 Copynumber: 2.2 Consensus size: 25
215377 CATCACCTTA
* *
215387 AAAATTTTATAAGTTCATCCATTCTT
1 AAAATTTTAGAAGTTCACCCATTC-T
* *
215413 AAAATTTTAGAAGTTCGCCCTTTCT
1 AAAATTTTAGAAGTTCACCCATTCT
215438 AAAAT
1 AAAAT
215443 AAAATTATAC
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
25 6 0.23
26 20 0.77
ACGTcount: A:0.36, C:0.16, G:0.07, T:0.41
Consensus pattern (25 bp):
AAAATTTTAGAAGTTCACCCATTCT
Found at i:216290 original size:44 final size:44
Alignment explanation
Indices: 216227--216326 Score: 164
Period size: 44 Copynumber: 2.3 Consensus size: 44
216217 AAATACGAGT
* **
216227 TTGAGCTTCAATCGAGTTAAGTCTGAAAATATTTTTAGTTCAAG
1 TTGAGCTTCAATCGAGTTAAGCCTGAAAATATTTCGAGTTCAAG
*
216271 TTGAGCTTCAATCGAGTTAAGCCTGAAAATATTTCGAGTTCGAG
1 TTGAGCTTCAATCGAGTTAAGCCTGAAAATATTTCGAGTTCAAG
216315 TTGAGCTTCAAT
1 TTGAGCTTCAAT
216327 TTTTTTATTT
Statistics
Matches: 52, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
44 52 1.00
ACGTcount: A:0.30, C:0.14, G:0.20, T:0.36
Consensus pattern (44 bp):
TTGAGCTTCAATCGAGTTAAGCCTGAAAATATTTCGAGTTCAAG
Found at i:217283 original size:44 final size:44
Alignment explanation
Indices: 217220--217312 Score: 177
Period size: 44 Copynumber: 2.1 Consensus size: 44
217210 AACATGGACC
217220 TTTAACACATTTTCAAACTTTGTTATTTCTTATCTTTTTGGAAT
1 TTTAACACATTTTCAAACTTTGTTATTTCTTATCTTTTTGGAAT
217264 TTTAACACATTTTCAAACTTTGTTATTTCTTATCTTTTTGGAAT
1 TTTAACACATTTTCAAACTTTGTTATTTCTTATCTTTTTGGAAT
*
217308 CTTAA
1 TTTAA
217313 ATTGCTGCCA
Statistics
Matches: 48, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
44 48 1.00
ACGTcount: A:0.26, C:0.14, G:0.06, T:0.54
Consensus pattern (44 bp):
TTTAACACATTTTCAAACTTTGTTATTTCTTATCTTTTTGGAAT
Found at i:222276 original size:17 final size:16
Alignment explanation
Indices: 222256--222288 Score: 57
Period size: 17 Copynumber: 2.0 Consensus size: 16
222246 AAATTCAAGG
222256 ACCTTCAAACTTCAAAA
1 ACCTTCAAAC-TCAAAA
222273 ACCTTCAAACTCAAAA
1 ACCTTCAAACTCAAAA
222289 TGATGACTTC
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 6 0.38
17 10 0.62
ACGTcount: A:0.48, C:0.30, G:0.00, T:0.21
Consensus pattern (16 bp):
ACCTTCAAACTCAAAA
Found at i:239993 original size:7 final size:7
Alignment explanation
Indices: 239981--240015 Score: 70
Period size: 7 Copynumber: 5.0 Consensus size: 7
239971 CGAGAGCAAT
239981 GATTTTA
1 GATTTTA
239988 GATTTTA
1 GATTTTA
239995 GATTTTA
1 GATTTTA
240002 GATTTTA
1 GATTTTA
240009 GATTTTA
1 GATTTTA
240016 AATTAAAGAT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 28 1.00
ACGTcount: A:0.29, C:0.00, G:0.14, T:0.57
Consensus pattern (7 bp):
GATTTTA
Found at i:240025 original size:21 final size:21
Alignment explanation
Indices: 239981--240025 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
239971 CGAGAGCAAT
* **
239981 GATTTTAGATTTTAGATTTTA
1 GATTTTAGATTTTAAATTAAA
240002 GATTTTAGATTTTAAATTAAA
1 GATTTTAGATTTTAAATTAAA
240023 GAT
1 GAT
240026 AGAAGGAAAT
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:0.36, C:0.00, G:0.13, T:0.51
Consensus pattern (21 bp):
GATTTTAGATTTTAAATTAAA
Found at i:241730 original size:17 final size:17
Alignment explanation
Indices: 241708--241757 Score: 54
Period size: 17 Copynumber: 3.1 Consensus size: 17
241698 GTTTCCATTA
241708 TATATTATATATAATAT
1 TATATTATATATAATAT
*
241725 TATA-T-TAT-TACTAT
1 TATATTATATATAATAT
241739 TATATTAT-TATAAATAT
1 TATATTATATAT-AATAT
241756 TA
1 TA
241758 CAAAACTGGG
Statistics
Matches: 27, Mismatches: 2, Indels: 8
0.73 0.05 0.22
Matches are distributed among these distances:
14 9 0.33
15 5 0.19
16 3 0.11
17 10 0.37
ACGTcount: A:0.44, C:0.02, G:0.00, T:0.54
Consensus pattern (17 bp):
TATATTATATATAATAT
Found at i:241739 original size:14 final size:14
Alignment explanation
Indices: 241704--241748 Score: 58
Period size: 14 Copynumber: 3.3 Consensus size: 14
241694 TGACGTTTCC
241704 ATTATATATTATA-T
1 ATTA-ATATTATATT
241718 A-TAATATTATATT
1 ATTAATATTATATT
*
241731 ATTACTATTATATT
1 ATTAATATTATATT
241745 ATTA
1 ATTA
241749 TAAATATTAC
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
12 8 0.29
13 4 0.14
14 16 0.57
ACGTcount: A:0.42, C:0.02, G:0.00, T:0.56
Consensus pattern (14 bp):
ATTAATATTATATT
Found at i:242920 original size:17 final size:18
Alignment explanation
Indices: 242881--242923 Score: 54
Period size: 17 Copynumber: 2.5 Consensus size: 18
242871 ATAGAATTAG
242881 TATTTTA-AATTTACATA
1 TATTTTATAATTTACATA
* *
242898 TTTTTTATAATTTA-ATC
1 TATTTTATAATTTACATA
242915 TATTTTATA
1 TATTTTATA
242924 TTATAATAGG
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
17 16 0.73
18 6 0.27
ACGTcount: A:0.35, C:0.05, G:0.00, T:0.60
Consensus pattern (18 bp):
TATTTTATAATTTACATA
Found at i:250048 original size:89 final size:89
Alignment explanation
Indices: 249863--250037 Score: 233
Period size: 89 Copynumber: 1.9 Consensus size: 89
249853 AAGTGGAAAC
* * *
249863 AAATCAAACCTCGAATCTAATCTTCACAGAGGAGTAGTGAAACAGATTCTTTTCAAGTCAATCCA
1 AAATC-AACCTCGAATCTAATCTTCACAGAAGAGTAGTGAAACAGATTCTTCTCAAATCAATCCA
* *
249928 ATCTTCACGGAAGAGTAGTGGAAGA
65 ACCTTCACGGAAGAGTAATGGAAGA
* * ** * *
249953 AAATCAACCTCGAATCTGATCTTTATGGAAGAGTAGTGAAACAGATTCTTCTCAAATCATTTTCA
1 AAATCAACCTCGAATCTAATCTTCACAGAAGAGTAGTGAAACAGATTCTTCTCAAATCA-ATCCA
250018 ACCTTCACGGAAGAGTAATG
65 ACCTTCACGGAAGAGTAATG
250038 AAGTTAATCA
Statistics
Matches: 73, Mismatches: 11, Indels: 2
0.85 0.13 0.02
Matches are distributed among these distances:
89 47 0.64
90 26 0.36
ACGTcount: A:0.37, C:0.19, G:0.18, T:0.27
Consensus pattern (89 bp):
AAATCAACCTCGAATCTAATCTTCACAGAAGAGTAGTGAAACAGATTCTTCTCAAATCAATCCAA
CCTTCACGGAAGAGTAATGGAAGA
Found at i:250054 original size:36 final size:36
Alignment explanation
Indices: 250016--250291 Score: 381
Period size: 36 Copynumber: 7.7 Consensus size: 36
250006 AAATCATTTT
* ** * *
250016 CAACCTTCACGGAAGAGTAATGAAGTTAATCAAGTT
1 CAACCTTCACGGAAGAGTAGTGAAGTCGATCAAATC
* *
250052 CAACCTTCACGAAAGAGTAGTGAAGTCGATCAAAAC
1 CAACCTTCACGGAAGAGTAGTGAAGTCGATCAAATC
* * *
250088 CAACCTTCACGGAAGAGTAGTGAAGTCAATCAAGTT
1 CAACCTTCACGGAAGAGTAGTGAAGTCGATCAAATC
* *
250124 CAACCTTCACGAAAGAGTAATGAAGTCGATCAAATC
1 CAACCTTCACGGAAGAGTAGTGAAGTCGATCAAATC
* *
250160 CAACCTTCACGGAAGAATAGTGAAGTCGATAAAATC
1 CAACCTTCACGGAAGAGTAGTGAAGTCGATCAAATC
250196 CAACCTTCACGGAAGAGTAGTGAAGTCGATCAAATC
1 CAACCTTCACGGAAGAGTAGTGAAGTCGATCAAATC
* *
250232 CAACCTTCATGAAAGAGTAGTGAAGTCGATCAAATC
1 CAACCTTCACGGAAGAGTAGTGAAGTCGATCAAATC
** *
250268 CAGTCTTCATGGAAGAGTAGTGAA
1 CAACCTTCACGGAAGAGTAGTGAA
250292 ACAGGAACAA
Statistics
Matches: 212, Mismatches: 28, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
36 212 1.00
ACGTcount: A:0.39, C:0.20, G:0.21, T:0.21
Consensus pattern (36 bp):
CAACCTTCACGGAAGAGTAGTGAAGTCGATCAAATC
Found at i:250504 original size:5 final size:5
Alignment explanation
Indices: 250481--250521 Score: 50
Period size: 5 Copynumber: 8.6 Consensus size: 5
250471 GTTTCCATTA
* *
250481 TATAT TATA- TATAA TATAT TATAT TAT-T GATAT TATAT TAT
1 TATAT TATAT TATAT TATAT TATAT TATAT TATAT TATAT TAT
250522 TACAAATATT
Statistics
Matches: 31, Mismatches: 3, Indels: 4
0.82 0.08 0.11
Matches are distributed among these distances:
4 7 0.23
5 24 0.77
ACGTcount: A:0.41, C:0.00, G:0.02, T:0.56
Consensus pattern (5 bp):
TATAT
Found at i:250505 original size:19 final size:19
Alignment explanation
Indices: 250481--250521 Score: 57
Period size: 19 Copynumber: 2.2 Consensus size: 19
250471 GTTTCCATTA
250481 TATATTATAT-ATAATATAT
1 TATATTAT-TGATAATATAT
*
250500 TATATTATTGATATTATAT
1 TATATTATTGATAATATAT
250519 TAT
1 TAT
250522 TACAAATATT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
18 1 0.05
19 19 0.95
ACGTcount: A:0.41, C:0.00, G:0.02, T:0.56
Consensus pattern (19 bp):
TATATTATTGATAATATAT
Done.