Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Gbar_A10
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: 110302803
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.32
Warning! 1825971 characters in sequence are not A, C, G, or T
File 54 of 343
Found at i:17563453 original size:17 final size:17
Alignment explanation
Indices: 17563428--17563466 Score: 60
Period size: 17 Copynumber: 2.3 Consensus size: 17
17563418 TTTATTTTCT
*
17563428 TATTACTTATCTATTTA
1 TATTTCTTATCTATTTA
*
17563445 TATTTCTTATTTATTTA
1 TATTTCTTATCTATTTA
17563462 TATTT
1 TATTT
17563467 TTGTTATTAT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.26, C:0.08, G:0.00, T:0.67
Consensus pattern (17 bp):
TATTTCTTATCTATTTA
Found at i:17563479 original size:17 final size:17
Alignment explanation
Indices: 17563459--17563493 Score: 61
Period size: 17 Copynumber: 2.1 Consensus size: 17
17563449 TCTTATTTAT
*
17563459 TTATATTTTTGTTATTA
1 TTATATTTTTGGTATTA
17563476 TTATATTTTTGGTATTA
1 TTATATTTTTGGTATTA
17563493 T
1 T
17563494 ATCTCTATTT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.23, C:0.00, G:0.09, T:0.69
Consensus pattern (17 bp):
TTATATTTTTGGTATTA
Found at i:17563528 original size:26 final size:26
Alignment explanation
Indices: 17563472--17563529 Score: 68
Period size: 26 Copynumber: 2.3 Consensus size: 26
17563462 TATTTTTGTT
*
17563472 ATTA-TTATATTTTTGGTATTATATC
1 ATTATTTATATTTATGGTATTATATC
17563497 -TCTATTTATATTTAT-GTATTAATATC
1 AT-TATTTATATTTATGGTATT-ATATC
17563523 ATTATTT
1 ATTATTT
17563530 TACTATTGTT
Statistics
Matches: 28, Mismatches: 1, Indels: 7
0.78 0.03 0.19
Matches are distributed among these distances:
24 1 0.04
25 7 0.25
26 19 0.68
27 1 0.04
ACGTcount: A:0.29, C:0.05, G:0.05, T:0.60
Consensus pattern (26 bp):
ATTATTTATATTTATGGTATTATATC
Found at i:17563572 original size:15 final size:15
Alignment explanation
Indices: 17563552--17563581 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
17563542 ATTTTTTCAC
*
17563552 ACTATTATTATCATT
1 ACTATTACTATCATT
17563567 ACTATTACTATCATT
1 ACTATTACTATCATT
17563582 TTTTAATAGT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.33, C:0.17, G:0.00, T:0.50
Consensus pattern (15 bp):
ACTATTACTATCATT
Found at i:17567265 original size:18 final size:19
Alignment explanation
Indices: 17567242--17567277 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
17567232 TCTTTCTAGC
17567242 TTATTTTTATTT-ATTAAA
1 TTATTTTTATTTAATTAAA
*
17567260 TTATTTTTCTTTAATTAA
1 TTATTTTTATTTAATTAA
17567278 TTTTTATTTT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 11 0.69
19 5 0.31
ACGTcount: A:0.31, C:0.03, G:0.00, T:0.67
Consensus pattern (19 bp):
TTATTTTTATTTAATTAAA
Found at i:17567474 original size:23 final size:21
Alignment explanation
Indices: 17567448--17567508 Score: 61
Period size: 21 Copynumber: 2.8 Consensus size: 21
17567438 CCCTGTATAG
17567448 TATGCAAACCATACATGTTTAGT
1 TATGCAAACCATACATG-TTA-T
* *
17567471 TATGTGAAA-CATACTTGTTAT
1 TATG-CAAACCATACATGTTAT
*
17567492 TATGCAAACCCTACATG
1 TATGCAAACCATACATG
17567509 ATAAAATATG
Statistics
Matches: 31, Mismatches: 5, Indels: 6
0.74 0.12 0.14
Matches are distributed among these distances:
20 3 0.10
21 11 0.35
22 3 0.10
23 11 0.35
24 3 0.10
ACGTcount: A:0.34, C:0.18, G:0.13, T:0.34
Consensus pattern (21 bp):
TATGCAAACCATACATGTTAT
Found at i:17574048 original size:43 final size:43
Alignment explanation
Indices: 17573989--17574231 Score: 364
Period size: 43 Copynumber: 5.7 Consensus size: 43
17573979 TTCCGATATA
17573989 TGTAAGACCACGTCTGGGACGTTGGCATCGATATGTGATTATG
1 TGTAAGACCACGTCTGGGACGTTGGCATCGATATGTGATTATG
* *
17574032 TGTAAGACCACATCTGGGACATTGGCATCGATATGTGATTATG
1 TGTAAGACCACGTCTGGGACGTTGGCATCGATATGTGATTATG
*
17574075 TGTAAGACCACGTCTGGGACGTTGGCATTGATATGTGATTATG
1 TGTAAGACCACGTCTGGGACGTTGGCATCGATATGTGATTATG
* * *
17574118 TGTAATACCACGTCTAGGACGTTGGCATCGATATGTGATTACG
1 TGTAAGACCACGTCTGGGACGTTGGCATCGATATGTGATTATG
*
17574161 TGTAAGACC-CTGTCTGGGACAG-TGGCATCGATATGTGATTATA
1 TGTAAGACCAC-GTCTGGGAC-GTTGGCATCGATATGTGATTATG
* **
17574204 TGTAAGACCATGTCTGGGGTGTTGGCAT
1 TGTAAGACCACGTCTGGGACGTTGGCAT
17574232 TGTACGATAT
Statistics
Matches: 180, Mismatches: 16, Indels: 8
0.88 0.08 0.04
Matches are distributed among these distances:
42 2 0.01
43 177 0.98
44 1 0.01
ACGTcount: A:0.24, C:0.16, G:0.29, T:0.31
Consensus pattern (43 bp):
TGTAAGACCACGTCTGGGACGTTGGCATCGATATGTGATTATG
Found at i:17579790 original size:3 final size:3
Alignment explanation
Indices: 17579739--17579778 Score: 80
Period size: 3 Copynumber: 13.3 Consensus size: 3
17579729 AATTTTGTTG
17579739 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
17579779 TAATCTTATT
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 37 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TAT
Found at i:17580315 original size:22 final size:22
Alignment explanation
Indices: 17580273--17580315 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
17580263 TATATATGTT
* * *
17580273 ATAAAAGAAACAAAGATGAAAC
1 ATAAAAGAAAAAAAAAAGAAAC
17580295 ATAAAAGAAAAAAAAAAGAAA
1 ATAAAAGAAAAAAAAAAGAAA
17580316 AGTTACAGAG
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.77, C:0.05, G:0.12, T:0.07
Consensus pattern (22 bp):
ATAAAAGAAAAAAAAAAGAAAC
Found at i:17581982 original size:12 final size:13
Alignment explanation
Indices: 17581958--17581988 Score: 55
Period size: 12 Copynumber: 2.5 Consensus size: 13
17581948 TATGAGAAAG
17581958 TGAAATAATGAAT
1 TGAAATAATGAAT
17581971 TGAAAT-ATGAAT
1 TGAAATAATGAAT
17581983 TGAAAT
1 TGAAAT
17581989 TGAGATATCG
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
12 12 0.67
13 6 0.33
ACGTcount: A:0.52, C:0.00, G:0.16, T:0.32
Consensus pattern (13 bp):
TGAAATAATGAAT
Found at i:17589678 original size:27 final size:26
Alignment explanation
Indices: 17589623--17589698 Score: 91
Period size: 27 Copynumber: 2.9 Consensus size: 26
17589613 TCTCATCCCT
* *
17589623 ATTTTA-CCTCAATAAAATTTTGACT
1 ATTTTACCCCCAATAAAATTTTGACG
17589648 ATTTTACCCCCAATAAAAGTTTTGACG
1 ATTTTACCCCCAATAAAA-TTTTGACG
* * *
17589675 ATTTTACGCCTAGTAAAATTTTGA
1 ATTTTACCCCCAATAAAATTTTGA
17589699 GAAAATATGT
Statistics
Matches: 44, Mismatches: 5, Indels: 3
0.85 0.10 0.06
Matches are distributed among these distances:
25 6 0.14
26 16 0.36
27 22 0.50
ACGTcount: A:0.34, C:0.17, G:0.09, T:0.39
Consensus pattern (26 bp):
ATTTTACCCCCAATAAAATTTTGACG
Found at i:17589859 original size:12 final size:12
Alignment explanation
Indices: 17589842--17589866 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
17589832 TGCAAAAGGA
17589842 TCATTTCCATTT
1 TCATTTCCATTT
17589854 TCATTTCCATTT
1 TCATTTCCATTT
17589866 T
1 T
17589867 TTGGAAACCT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.16, C:0.24, G:0.00, T:0.60
Consensus pattern (12 bp):
TCATTTCCATTT
Found at i:17596527 original size:33 final size:33
Alignment explanation
Indices: 17596490--17596556 Score: 134
Period size: 33 Copynumber: 2.0 Consensus size: 33
17596480 TCCTAAGGTT
17596490 TTTATTTTCTCTTCTCCTTTCTTAGTTTTAGAG
1 TTTATTTTCTCTTCTCCTTTCTTAGTTTTAGAG
17596523 TTTATTTTCTCTTCTCCTTTCTTAGTTTTAGAG
1 TTTATTTTCTCTTCTCCTTTCTTAGTTTTAGAG
17596556 T
1 T
17596557 CAGAACGGTG
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 34 1.00
ACGTcount: A:0.12, C:0.18, G:0.09, T:0.61
Consensus pattern (33 bp):
TTTATTTTCTCTTCTCCTTTCTTAGTTTTAGAG
Found at i:17599409 original size:15 final size:15
Alignment explanation
Indices: 17599391--17599419 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
17599381 ATATTTATAA
17599391 AATTATTATTATTAT
1 AATTATTATTATTAT
17599406 AATTATTATTATTA
1 AATTATTATTATTA
17599420 GATAGGGAAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (15 bp):
AATTATTATTATTAT
Found at i:17610881 original size:11 final size:11
Alignment explanation
Indices: 17610867--17610891 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
17610857 GGAGTAAAGA
17610867 AAATAAGGAAT
1 AAATAAGGAAT
17610878 AAATAAGGAAT
1 AAATAAGGAAT
17610889 AAA
1 AAA
17610892 ATAGAGGAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.68, C:0.00, G:0.16, T:0.16
Consensus pattern (11 bp):
AAATAAGGAAT
Found at i:17615639 original size:30 final size:30
Alignment explanation
Indices: 17615599--17615655 Score: 87
Period size: 30 Copynumber: 1.9 Consensus size: 30
17615589 ACGGCCATGA
* *
17615599 TACACGGGCGTGTGGCTTGCTCGTGTGTCC
1 TACACAGGCGTGTGGCTTGCCCGTGTGTCC
*
17615629 TACACAGGCGTGTGGTTTGCCCGTGTG
1 TACACAGGCGTGTGGCTTGCCCGTGTG
17615656 AAAGTGCCTA
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
30 24 1.00
ACGTcount: A:0.09, C:0.25, G:0.37, T:0.30
Consensus pattern (30 bp):
TACACAGGCGTGTGGCTTGCCCGTGTGTCC
Found at i:17617738 original size:12 final size:12
Alignment explanation
Indices: 17617721--17617745 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
17617711 AGTTTACGAG
17617721 AAATAATTTTAA
1 AAATAATTTTAA
17617733 AAATAATTTTAA
1 AAATAATTTTAA
17617745 A
1 A
17617746 GGGATCACAG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (12 bp):
AAATAATTTTAA
Found at i:17627020 original size:9 final size:9
Alignment explanation
Indices: 17626986--17627016 Score: 55
Period size: 9 Copynumber: 3.6 Consensus size: 9
17626976 TAAAAATATT
17626986 TTTTTATAA
1 TTTTTATAA
17626995 TTTTTATAA
1 TTTTTATAA
17627004 TTTTTA-AA
1 TTTTTATAA
17627012 TTTTT
1 TTTTT
17627017 TAAAAATAAT
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
8 7 0.32
9 15 0.68
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (9 bp):
TTTTTATAA
Found at i:17627028 original size:22 final size:21
Alignment explanation
Indices: 17627000--17627042 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 21
17626990 TATAATTTTT
*
17627000 ATAATTTTTAAATTTTTTAAAA
1 ATAATTTATAAA-TTTTTAAAA
*
17627022 ATAATTTATATATTTTTAAAA
1 ATAATTTATAAATTTTTAAAA
17627043 TTTTAATTTT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
21 9 0.47
22 10 0.53
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (21 bp):
ATAATTTATAAATTTTTAAAA
Found at i:17627047 original size:38 final size:39
Alignment explanation
Indices: 17626988--17627066 Score: 117
Period size: 38 Copynumber: 2.1 Consensus size: 39
17626978 AAAATATTTT
*
17626988 TTTATAATTTTTATAATTTTTAAATTTTTTAAAAA-TAA
1 TTTATAATTTTTATAAATTTTAAATTTTTTAAAAATTAA
*
17627026 TTTATATATTTTTA-AAATTTTAATTTTTTTAAAAATTAA
1 TTTATA-ATTTTTATAAATTTTAAATTTTTTAAAAATTAA
17627065 TT
1 TT
17627067 AATTGCTAAC
Statistics
Matches: 37, Mismatches: 2, Indels: 3
0.88 0.05 0.07
Matches are distributed among these distances:
38 25 0.68
39 12 0.32
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (39 bp):
TTTATAATTTTTATAAATTTTAAATTTTTTAAAAATTAA
Found at i:17627064 original size:16 final size:17
Alignment explanation
Indices: 17627010--17627066 Score: 53
Period size: 17 Copynumber: 3.2 Consensus size: 17
17627000 ATAATTTTTA
*
17627010 AATTTTTTAAAAATAATTT
1 AATTTTTTTAAAAT-A-TT
* *
17627029 ATATATTTTTAAAATTTT
1 A-ATTTTTTTAAAATATT
17627047 AATTTTTTTAAAA-ATT
1 AATTTTTTTAAAATATT
17627063 AATT
1 AATT
17627067 AATTGCTAAC
Statistics
Matches: 32, Mismatches: 5, Indels: 5
0.76 0.12 0.12
Matches are distributed among these distances:
16 6 0.19
17 11 0.34
18 3 0.09
19 1 0.03
20 11 0.34
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (17 bp):
AATTTTTTTAAAATATT
Found at i:17627070 original size:20 final size:20
Alignment explanation
Indices: 17627007--17627070 Score: 64
Period size: 20 Copynumber: 3.3 Consensus size: 20
17626997 TTTATAATTT
*
17627007 TTAAATTTTTTAAAAA-TAA
1 TTAATTTTTTTAAAAATTAA
*
17627026 TTTATATATTTTT-AAAATT--
1 -TTA-ATTTTTTTAAAAATTAA
17627045 TTAATTTTTTTAAAAATTAA
1 TTAATTTTTTTAAAAATTAA
17627065 TTAATT
1 TTAATT
17627071 GCTAACGTGA
Statistics
Matches: 36, Mismatches: 3, Indels: 10
0.73 0.06 0.20
Matches are distributed among these distances:
17 7 0.19
18 9 0.25
20 13 0.36
21 7 0.19
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (20 bp):
TTAATTTTTTTAAAAATTAA
Found at i:17630183 original size:24 final size:24
Alignment explanation
Indices: 17630154--17630240 Score: 138
Period size: 24 Copynumber: 3.6 Consensus size: 24
17630144 CATTCCAATC
17630154 CGCACACATAGTGCCGTACAAATT
1 CGCACACATAGTGCCGTACAAATT
*
17630178 CACACACATAGTGCCGTACAAATT
1 CGCACACATAGTGCCGTACAAATT
* * *
17630202 CGCACACATAGTTCCATTCAAATT
1 CGCACACATAGTGCCGTACAAATT
17630226 CGCACACATAGTGCC
1 CGCACACATAGTGCC
17630241 AAAATCATTT
Statistics
Matches: 57, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 57 1.00
ACGTcount: A:0.33, C:0.31, G:0.14, T:0.22
Consensus pattern (24 bp):
CGCACACATAGTGCCGTACAAATT
Found at i:17630211 original size:72 final size:72
Alignment explanation
Indices: 17630106--17630240 Score: 173
Period size: 72 Copynumber: 1.9 Consensus size: 72
17630096 CATGTTAACC
* ** * *
17630106 CACACACATAATGCCTTAGTAATTCACATACATA-TTGACATTCCAATCCGCACACATAGTGCCG
1 CACACACATAATGCCGTACAAATTCACACACATAGTT-ACATTCAAATCCGCACACATAGTGCCG
17630170 TACAAATT
65 TACAAATT
* * * *
17630178 CACACACATAGTGCCGTACAAATTCGCACACATAGTTCCATTCAAATTCGCACACATAGTGCC
1 CACACACATAATGCCGTACAAATTCACACACATAGTTACATTCAAATCCGCACACATAGTGCC
17630241 AAAATCATTT
Statistics
Matches: 53, Mismatches: 9, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
72 51 0.96
73 2 0.04
ACGTcount: A:0.35, C:0.30, G:0.11, T:0.24
Consensus pattern (72 bp):
CACACACATAATGCCGTACAAATTCACACACATAGTTACATTCAAATCCGCACACATAGTGCCGT
ACAAATT
Found at i:17631437 original size:17 final size:17
Alignment explanation
Indices: 17631415--17631448 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
17631405 CCCCACTTAA
*
17631415 TATATTATAACTTATTT
1 TATATTATAACATATTT
*
17631432 TATATTTTAACATATTT
1 TATATTATAACATATTT
17631449 CCATTATATA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.35, C:0.06, G:0.00, T:0.59
Consensus pattern (17 bp):
TATATTATAACATATTT
Found at i:17635492 original size:30 final size:29
Alignment explanation
Indices: 17635456--17635512 Score: 87
Period size: 29 Copynumber: 1.9 Consensus size: 29
17635446 CACCCTTGAA
* *
17635456 ATATTTACACTATTAGTCCTTCAAATTTTC
1 ATATTTACACT-TTAATCCCTCAAATTTTC
17635486 ATATTTACACTTTAATCCCTCAAATTT
1 ATATTTACACTTTAATCCCTCAAATTT
17635513 GGAGTATTTA
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
29 14 0.56
30 11 0.44
ACGTcount: A:0.32, C:0.21, G:0.02, T:0.46
Consensus pattern (29 bp):
ATATTTACACTTTAATCCCTCAAATTTTC
Found at i:17635521 original size:30 final size:30
Alignment explanation
Indices: 17635456--17635522 Score: 82
Period size: 30 Copynumber: 2.2 Consensus size: 30
17635446 CACCCTTGAA
* * *
17635456 ATATTTACACTATTAGTCCTTCAAATTTTC
1 ATATTTACACTATTAATCCCTCAAATTTGC
*
17635486 ATATTTACACT-TTAATCCCTCAAATTTGG
1 ATATTTACACTATTAATCCCTCAAATTTGC
17635515 AGTATTTA
1 A-TATTTA
17635523 TCTTGGGCCA
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
29 15 0.47
30 17 0.53
ACGTcount: A:0.31, C:0.18, G:0.06, T:0.45
Consensus pattern (30 bp):
ATATTTACACTATTAATCCCTCAAATTTGC
Found at i:17636412 original size:18 final size:18
Alignment explanation
Indices: 17636391--17636450 Score: 59
Period size: 18 Copynumber: 3.2 Consensus size: 18
17636381 ACATCTGAGA
17636391 TTGTTTTTGTACCTGAAC
1 TTGTTTTTGTACCTGAAC
** *
17636409 TTGTAATTGCCACCATGAGA-
1 TTGTTTTTG-TACC-TGA-AC
17636429 TTGTTTTTGTACCTGAAC
1 TTGTTTTTGTACCTGAAC
17636447 TTGT
1 TTGT
17636451 AATTGCCACC
Statistics
Matches: 32, Mismatches: 6, Indels: 8
0.70 0.13 0.17
Matches are distributed among these distances:
17 1 0.03
18 14 0.44
19 6 0.19
20 10 0.31
21 1 0.03
ACGTcount: A:0.20, C:0.17, G:0.18, T:0.45
Consensus pattern (18 bp):
TTGTTTTTGTACCTGAAC
Found at i:17636428 original size:38 final size:38
Alignment explanation
Indices: 17636386--17636462 Score: 154
Period size: 38 Copynumber: 2.0 Consensus size: 38
17636376 AAAGAACATC
17636386 TGAGATTGTTTTTGTACCTGAACTTGTAATTGCCACCA
1 TGAGATTGTTTTTGTACCTGAACTTGTAATTGCCACCA
17636424 TGAGATTGTTTTTGTACCTGAACTTGTAATTGCCACCA
1 TGAGATTGTTTTTGTACCTGAACTTGTAATTGCCACCA
17636462 T
1 T
17636463 TCCTGATCCT
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
38 39 1.00
ACGTcount: A:0.23, C:0.18, G:0.18, T:0.40
Consensus pattern (38 bp):
TGAGATTGTTTTTGTACCTGAACTTGTAATTGCCACCA
Found at i:17647327 original size:22 final size:22
Alignment explanation
Indices: 17647299--17647343 Score: 72
Period size: 22 Copynumber: 2.0 Consensus size: 22
17647289 TTACGCTGAT
* *
17647299 TCATAGAGTTGATTTGTAGGGA
1 TCATAGAATTGATTAGTAGGGA
17647321 TCATAGAATTGATTAGTAGGGA
1 TCATAGAATTGATTAGTAGGGA
17647343 T
1 T
17647344 TTATTTTTAT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.31, C:0.04, G:0.29, T:0.36
Consensus pattern (22 bp):
TCATAGAATTGATTAGTAGGGA
Found at i:17648379 original size:5 final size:5
Alignment explanation
Indices: 17648369--17648395 Score: 54
Period size: 5 Copynumber: 5.4 Consensus size: 5
17648359 TAGATTATTC
17648369 CTTTT CTTTT CTTTT CTTTT CTTTT CT
1 CTTTT CTTTT CTTTT CTTTT CTTTT CT
17648396 GACAAATAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 22 1.00
ACGTcount: A:0.00, C:0.22, G:0.00, T:0.78
Consensus pattern (5 bp):
CTTTT
Found at i:17652035 original size:18 final size:17
Alignment explanation
Indices: 17652012--17652074 Score: 63
Period size: 17 Copynumber: 3.5 Consensus size: 17
17652002 TATTTGTAAC
17652012 ATTATATATATAAATTTT
1 ATTATAT-TATAAATTTT
*
17652030 ATTATATGTTATATATTTTT
1 ATTATA--TTATA-AATTTT
**
17652050 ATTATATTATTTATTTT
1 ATTATATTATAAATTTT
17652067 ATTATATT
1 ATTATATT
17652075 TTATATGTAA
Statistics
Matches: 38, Mismatches: 4, Indels: 7
0.78 0.08 0.14
Matches are distributed among these distances:
17 12 0.32
18 10 0.26
19 4 0.11
20 12 0.32
ACGTcount: A:0.35, C:0.00, G:0.02, T:0.63
Consensus pattern (17 bp):
ATTATATTATAAATTTT
Found at i:17652042 original size:23 final size:20
Alignment explanation
Indices: 17652026--17652080 Score: 71
Period size: 17 Copynumber: 2.9 Consensus size: 20
17652016 TATATATAAA
17652026 TTTTATTATATGTTATATAT
1 TTTTATTATATGTTATATAT
*
17652046 TTTTATTATA--TTATTTA-
1 TTTTATTATATGTTATATAT
*
17652063 TTTTATTATATTTTATAT
1 TTTTATTATATGTTATAT
17652081 GTAAAATATT
Statistics
Matches: 31, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
17 10 0.32
18 6 0.19
19 5 0.16
20 10 0.32
ACGTcount: A:0.29, C:0.00, G:0.02, T:0.69
Consensus pattern (20 bp):
TTTTATTATATGTTATATAT
Found at i:17664431 original size:176 final size:175
Alignment explanation
Indices: 17664198--17664587 Score: 561
Period size: 176 Copynumber: 2.2 Consensus size: 175
17664188 TTTGACGAGA
* * *
17664198 AACAAATCGAAGACATAGCAGATCTGACTTTCAGATGTTTTCACATCAAAACAGATCCAAGATAA
1 AACAAATCGAAGACATAGCAGATTTGACTTTCAGATGTTCTCACACCAAAACAGATCCAAGATAA
* *
17664263 -TAGATCT-AGCATCTCCATTTCGACGGAGAGCAGGTACATAGCAGGTCTAACCTTCAGATG-TT
66 CT-GATCTGA-CATCTCCATTTCGACGGAGAGCAGATACATAGCAGATCTAACCTTCAGATGATT
* *
17664325 TATACTGAAGCAAATCCAAGATGATTTGGGCATTCTTGTGTTTACAAGG
129 T-TACTGAAGCAAATCCAAGATGATTT-GGCATCCTTGTGTTCACAAGG
* *
17664374 AACAAATCGAAGACATAGCAGATTTGACTTTCGGATGTTCTCACACCAAAGCAGATCCAAGATAA
1 AACAAATCGAAGACATAGCAGATTTGACTTTCAGATGTTCTCACACCAAAACAGATCCAAGATAA
*
17664439 CTGATCTGACATCTCCATTTCGACGGAGAGTAGATACATAGCAGATCTAACCTTCAGATGATTTT
66 CTGATCTGACATCTCCATTTCGACGGAGAGCAGATACATAGCAGATCTAACCTTCAGATGATTTT
* *
17664504 ACTGAAGCAGATCTAAGATGATTTGGCATCCTTGTGTTCACAAGG
131 ACTGAAGCAAATCCAAGATGATTTGGCATCCTTGTGTTCACAAGG
* * * * * *
17664549 AGCAAATCAAAGACACAGTAGATTTGGCTTTCAGGTGTT
1 AACAAATCGAAGACATAGCAGATTTGACTTTCAGATGTT
17664588 TACGCTGAAG
Statistics
Matches: 192, Mismatches: 19, Indels: 7
0.88 0.09 0.03
Matches are distributed among these distances:
175 51 0.27
176 136 0.71
177 5 0.03
ACGTcount: A:0.34, C:0.19, G:0.20, T:0.27
Consensus pattern (175 bp):
AACAAATCGAAGACATAGCAGATTTGACTTTCAGATGTTCTCACACCAAAACAGATCCAAGATAA
CTGATCTGACATCTCCATTTCGACGGAGAGCAGATACATAGCAGATCTAACCTTCAGATGATTTT
ACTGAAGCAAATCCAAGATGATTTGGCATCCTTGTGTTCACAAGG
Found at i:17666280 original size:20 final size:21
Alignment explanation
Indices: 17666257--17666297 Score: 66
Period size: 20 Copynumber: 2.0 Consensus size: 21
17666247 ATATATAAAA
17666257 TTTTATTATA-TGTTATATAT
1 TTTTATTATATTGTTATATAT
*
17666277 TTTTATTATATTTTTATATAT
1 TTTTATTATATTGTTATATAT
17666298 AAATATTTTT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 10 0.53
21 9 0.47
ACGTcount: A:0.29, C:0.00, G:0.02, T:0.68
Consensus pattern (21 bp):
TTTTATTATATTGTTATATAT
Found at i:17668828 original size:17 final size:18
Alignment explanation
Indices: 17668796--17668830 Score: 54
Period size: 17 Copynumber: 2.0 Consensus size: 18
17668786 TATAAAATAG
*
17668796 AAATTATATTTTTTATAA
1 AAATTATATATTTTATAA
17668814 AAATTAT-TATTTTATAA
1 AAATTATATATTTTATAA
17668831 TTTAGGTTTT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 9 0.56
18 7 0.44
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (18 bp):
AAATTATATATTTTATAA
Found at i:17673189 original size:12 final size:12
Alignment explanation
Indices: 17673172--17673209 Score: 58
Period size: 12 Copynumber: 3.2 Consensus size: 12
17673162 AAAGATATAT
17673172 AATATATTCCTA
1 AATATATTCCTA
**
17673184 AATATATTTATA
1 AATATATTCCTA
17673196 AATATATTCCTA
1 AATATATTCCTA
17673208 AA
1 AA
17673210 AAATATACAA
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
12 22 1.00
ACGTcount: A:0.47, C:0.11, G:0.00, T:0.42
Consensus pattern (12 bp):
AATATATTCCTA
Found at i:17680588 original size:31 final size:30
Alignment explanation
Indices: 17680545--17680619 Score: 89
Period size: 31 Copynumber: 2.4 Consensus size: 30
17680535 TAAATGACTA
* *
17680545 AAATGAAAGTTGAGTGACAT-CTTTATCATT
1 AAATTAAAGTTGAGTGA-ATAATTTATCATT
*
17680575 GAAATTAAAGTTGAGTGATTAATTTATCATT
1 -AAATTAAAGTTGAGTGAATAATTTATCATT
17680606 AAGATTAAAGTTGA
1 AA-ATTAAAGTTGA
17680620 ATAACTGTTA
Statistics
Matches: 39, Mismatches: 3, Indels: 4
0.85 0.07 0.09
Matches are distributed among these distances:
30 3 0.08
31 36 0.92
ACGTcount: A:0.40, C:0.05, G:0.17, T:0.37
Consensus pattern (30 bp):
AAATTAAAGTTGAGTGAATAATTTATCATT
Found at i:17681956 original size:17 final size:18
Alignment explanation
Indices: 17681925--17681958 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
17681915 AATTTAACTT
17681925 TAATTAAATTATTTAAAA
1 TAATTAAATTATTTAAAA
*
17681943 TAATT-AATTCTTTAAA
1 TAATTAAATTATTTAAA
17681959 TTATAAACAA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 10 0.67
18 5 0.33
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (18 bp):
TAATTAAATTATTTAAAA
Found at i:17684413 original size:16 final size:16
Alignment explanation
Indices: 17684382--17684464 Score: 76
Period size: 16 Copynumber: 5.1 Consensus size: 16
17684372 CTATTTTACA
* *
17684382 AAAATAGTATAAAAAT
1 AAAATATTAAAAAAAT
*
17684398 AAATTATTAAAAAAAT
1 AAAATATTAAAAAAAT
*** *
17684414 ATCTTAATAAAAAAAT
1 AAAATATTAAAAAAAT
*
17684430 AAAATACTAAAAGAAAT
1 AAAATATTAAAA-AAAT
*
17684447 AAAATATGAAAAAAAT
1 AAAATATTAAAAAAAT
17684463 AA
1 AA
17684465 TTTTTTTGGA
Statistics
Matches: 54, Mismatches: 12, Indels: 2
0.79 0.18 0.03
Matches are distributed among these distances:
16 40 0.74
17 14 0.26
ACGTcount: A:0.70, C:0.02, G:0.04, T:0.24
Consensus pattern (16 bp):
AAAATATTAAAAAAAT
Found at i:17684681 original size:151 final size:150
Alignment explanation
Indices: 17684502--17685775 Score: 1821
Period size: 151 Copynumber: 8.4 Consensus size: 150
17684492 GTTTTTTTTT
*
17684502 AAATAATAT-AAAAATAAAATACGAAAATAGTATATTTTAAAAAATAAAATTCAAAAATTTAAAT
1 AAATAATATAAAAAATAAAATACGAAAATAGTATATTTTAAAAAATAAAATTCAAAATTTTAAA-
*
17684566 AATACAAACAAAGGGACAAAATTAGGGTTATTTACTAAATTAATATAAAAAACACTAAAATAATA
65 AATACAAACAAAGGGACAAAATCAGGGTTATTTACTAAATTAATATAAAAAACACTAAAATAATA
*
17684631 CATTTGAAACATTATTTACTA
130 CATTTGAAACATTATGTACTA
* *
17684652 AAATAATATAAAAAATAAAATACGAAAATAGAATA-TTTAAAAAATAAAATCCGAAAATTTTAAA
1 AAATAATATAAAAAATAAAATACGAAAATAGTATATTTTAAAAAATAAAATTC-AAAATTTTAAA
* *
17684716 AATACAAACAAAGGGTCAAAATCAGGGTTATTTATTAAATTAATAT-AAAAACACTAAAATAATA
65 AATACAAACAAAGGGACAAAATCAGGGTTATTTACTAAATTAATATAAAAAACACTAAAATAATA
*
17684780 CATTTCAAACATTATGTACTA
130 CATTTGAAACATTATGTACTA
* * *
17684801 AAATAATATAAAAAATAAAATACGAAAATAATATATTTTAAAAAATAAAATCCGAGAATTTT-AA
1 AAATAATATAAAAAATAAAATACGAAAATAGTATATTTTAAAAAATAAAATTC-AAAATTTTAAA
* * * *
17684865 AATACAAAGAAATGGTCAAAATCAGGGTTATTTACTAAATTAATATAAAAAAACGCTAAAATAAT
65 AATACAAACAAAGGGACAAAATCAGGGTTATTTACTAAATTAATAT-AAAAAACACTAAAATAAT
*
17684930 ACATTTGAAACATTATGTACTC
129 ACATTTGAAACATTATGTACTA
* * * *
17684952 AAATAATATAAAAAATAAAATACAAAAATAATATATTTTTAAAAATAAAATGCGAAAATTTTAAA
1 AAATAATATAAAAAATAAAATACGAAAATAGTATATTTTAAAAAATAAAATTC-AAAATTTTAAA
*
17685017 AATACAAA-AAAGGGGCAAAAATCAGGGTTATTTACTAAATTAATAT-AAAAA-ACTAAAATAAT
65 AATACAAACAAAGGGAC-AAAATCAGGGTTATTTACTAAATTAATATAAAAAACACTAAAATAAT
*
17685079 ATATTTGAAACATTATGTACTA
129 ACATTTGAAACATTATGTACTA
* *
17685101 AAATAATATAAAAAAATAAAAATACGAAAATAGTATATTTTTAAAAATAAAATCTGAAAATTTTA
1 AAATAATAT-AAAAAAT-AAAATACGAAAATAGTATATTTTAAAAAATAAAAT-TCAAAATTTTA
* * * *
17685166 AAAATAAAAACAAAGGGCCAAAATCAAGGTTATTTACTAAATTAATATAAAAAAATACTAAAATA
63 AAAATACAAACAAAGGGACAAAATCAGGGTTATTTACTAAATTAATAT-AAAAAACACTAAAATA
* *
17685231 ATATATTTGAAACATAATGTACTA
127 ATACATTTGAAACATTATGTACTA
*
17685255 AAATAATATAAAAAATAAAATATGAAAATAGTATATATTT-AAAAATAAAATTCAGAAATTTTAA
1 AAATAATATAAAAAATAAAATACGAAAATAGTATAT-TTTAAAAAATAAAATTCA-AAATTTTAA
* * * *
17685319 AAACACAAACAAATGGATAAAATTAGGGTTATTTACTAAATTAATATAAAAAACACTAAAATAAT
64 AAATACAAACAAAGGGACAAAATCAGGGTTATTTACTAAATTAATATAAAAAACACTAAAATAAT
*
17685384 ACATTTAAAACATTATGTACTA
129 ACATTTGAAACATTATGTACTA
* * *
17685406 AAATAATATAAAAAATAAAATACAAAAATATTATATTTT-AAAAATAAAATCTGAAAATTTTAAA
1 AAATAATATAAAAAATAAAATACGAAAATAGTATATTTTAAAAAATAAAAT-TCAAAATTTTAAA
* * * * * *
17685470 AATAAAAAGAAATGGTCAAAATCAGGATTATTTACTAAATTAATATGAAAAAATACTAAAATAAT
65 AATACAAACAAAGGGACAAAATCAGGGTTATTTACTAAATTAATAT-AAAAAACACTAAAATAAT
*
17685535 ACATTTGAAACATTATGTATTA
129 ACATTTGAAACATTATGTACTA
* * * *
17685557 AAATAATATAAAAAATAAAATACGAAAATAGTATATTTTTAAAAATACAATCCGAGAATTTTAAA
1 AAATAATATAAAAAATAAAATACGAAAATAGTATATTTTAAAAAATAAAATTC-AAAATTTTAAA
* * *
17685622 AATACAAACAAAGGGACAAAATTAGGGTTATGTACTAAATTAATAT-AAAAATACTAAAATAATA
65 AATACAAACAAAGGGACAAAATCAGGGTTATTTACTAAATTAATATAAAAAACACTAAAATAATA
17685686 CATTTGAAACATTATGTACTA
130 CATTTGAAACATTATGTACTA
* * *
17685707 AAATAATATAAAAAAATAAAATATGAAAATAGTATATTTTAAAAAATAAGATCCGAAAATTTTAA
1 AAATAATAT-AAAAAATAAAATACGAAAATAGTATATTTTAAAAAATAAAATTC-AAAATTTTAA
17685772 AAAT
64 AAAT
17685776 TTAAAAAATA
Statistics
Matches: 1023, Mismatches: 80, Indels: 41
0.89 0.07 0.04
Matches are distributed among these distances:
149 154 0.15
150 215 0.21
151 414 0.40
152 184 0.18
153 15 0.01
154 41 0.04
ACGTcount: A:0.57, C:0.07, G:0.07, T:0.29
Consensus pattern (150 bp):
AAATAATATAAAAAATAAAATACGAAAATAGTATATTTTAAAAAATAAAATTCAAAATTTTAAAA
ATACAAACAAAGGGACAAAATCAGGGTTATTTACTAAATTAATATAAAAAACACTAAAATAATAC
ATTTGAAACATTATGTACTA
Found at i:17684969 original size:12 final size:13
Alignment explanation
Indices: 17684952--17684986 Score: 54
Period size: 13 Copynumber: 2.8 Consensus size: 13
17684942 TTATGTACTC
17684952 AAATAATATA-AA
1 AAATAATATACAA
*
17684964 AAATAAAATACAA
1 AAATAATATACAA
17684977 AAATAATATA
1 AAATAATATA
17684987 TTTTTAAAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
12 9 0.45
13 11 0.55
ACGTcount: A:0.74, C:0.03, G:0.00, T:0.23
Consensus pattern (13 bp):
AAATAATATACAA
Found at i:17685664 original size:605 final size:602
Alignment explanation
Indices: 17684502--17685775 Score: 2026
Period size: 605 Copynumber: 2.1 Consensus size: 602
17684492 GTTTTTTTTT
* *
17684502 AAATAATAT--AAAAATAAAATACGAAAATAGTATATTTTAAAAAATAAAAT-TCAAAAATTTAA
1 AAATAATATAAAAAAATAAAATACGAAAATAGTATATTTTAAAAAATAAAATCTGAAAATTTTAA
* * *
17684564 ATAATACAAACAAAGGGACAAAATTAGGGTTATTTACTAAATTAATATAAAAAACACTAAAATAA
66 A-AATAAAAACAAAGGGACAAAATCAAGGTTATTTACTAAATTAATATAAAAAACACTAAAATAA
* *
17684629 TACATTTGAAACATTATTTACTAAAATAATATAAAAAATAAAATACGAAAATAGAATATTTAAAA
130 TACATTTGAAACATAATGTACTAAAATAATATAAAAAATAAAATACGAAAATAGAATATTTAAAA
* * * *
17684694 AATAAAATCCGAAAATTTTAAAAATACAAACAAAGGGTCAAAATCAGGGTTATTTATTAAATTAA
195 AATAAAATCAGAAAATTTTAAAAACACAAACAAAGGATCAAAATCAGGGTTATTTACTAAATTAA
*
17684759 TATAAAAACACTAAAATAATACATTTCAAACATTATGTACTAAAATAATATAAAAAATAAAATAC
260 TATAAAAACACTAAAATAATACATTTAAAACATTATGTACTAAAATAATATAAAAAATAAAATAC
* * *
17684824 GAAAATAATATATTTTAAAAAATAAAATCCGAGAATTTTAAAATACAAAGAAATGGTCAAAATCA
325 AAAAATAATATATTTTAAAAAATAAAATCCGAAAATTTTAAAATAAAAAGAAATGGTCAAAATCA
* * *
17684889 GGGTTATTTACTAAATTAATATAAAAAAACGCTAAAATAATACATTTGAAACATTATGTACTCAA
390 GGATTATTTACTAAATTAATATAAAAAAACACTAAAATAATACATTTGAAACATTATGTACTAAA
*
17684954 ATAATATAAAAAATAAAATACAAAAATAATATATTTTTAAAAATAAAATGCGAAAATTTTAAAAA
455 ATAATATAAAAAATAAAATACAAAAATAATATATTTTTAAAAATAAAATCCGAAAATTTTAAAAA
* * *
17685019 TACAAAAAAGGGGCAAAAATCAGGGTTATTTACTAAATTAATATAAAAA-ACTAAAATAATATAT
520 TACAAAAAAGGGACAAAAATCAGGGTTATGTACTAAATTAATATAAAAATACTAAAATAATACAT
17685083 TTGAAACATTATGTACTA
585 TTGAAACATTATGTACTA
*
17685101 AAATAATATAAAAAAATAAAAATACGAAAATAGTATATTTTTAAAAATAAAATCTGAAAATTTTA
1 AAATAATATAAAAAAAT-AAAATACGAAAATAGTATATTTTAAAAAATAAAATCTGAAAATTTTA
* *
17685166 AAAATAAAAACAAAGGGCCAAAATCAAGGTTATTTACTAAATTAATATAAAAAAATACTAAAATA
65 AAAATAAAAACAAAGGGACAAAATCAAGGTTATTTACTAAATTAATAT-AAAAAACACTAAAATA
* *
17685231 ATATATTTGAAACATAATGTACTAAAATAATATAAAAAATAAAATATGAAAATAGTATATATTT-
129 ATACATTTGAAACATAATGTACTAAAATAATATAAAAAATAAAATACGAAAATAG-A-ATATTTA
*
17685295 AAAAATAAAATTCAG-AAATTTTAAAAACACAAACAAATGGAT-AAAATTAGGGTTATTTACTAA
192 AAAAATAAAA-TCAGAAAATTTTAAAAACACAAACAAA-GGATCAAAATCAGGGTTATTTACTAA
17685358 ATTAATATAAAAAACACTAAAATAATACATTTAAAACATTATGTACTAAAATAATATAAAAAATA
255 ATTAATAT-AAAAACACTAAAATAATACATTTAAAACATTATGTACTAAAATAATATAAAAAATA
* *
17685423 AAATACAAAAATATTATATTTT-AAAAATAAAATCTGAAAATTTTAAAAATAAAAAGAAATGGTC
319 AAATACAAAAATAATATATTTTAAAAAATAAAATCCGAAAATTTT-AAAATAAAAAGAAATGGTC
* *
17685487 AAAATCAGGATTATTTACTAAATTAATATGAAAAAATACTAAAATAATACATTTGAAACATTATG
383 AAAATCAGGATTATTTACTAAATTAATATAAAAAAACACTAAAATAATACATTTGAAACATTATG
* * * * *
17685552 TATTAAAATAATATAAAAAATAAAATACGAAAATAGTATATTTTTAAAAATACAATCCGAGAATT
448 TACTAAAATAATATAAAAAATAAAATACAAAAATAATATATTTTTAAAAATAAAATCCGAAAATT
*
17685617 TTAAAAATACAAACAAAGGGAC-AAAATTAGGGTTATGTACTAAATTAATATAAAAATACTAAAA
513 TTAAAAATACAAA-AAAGGGACAAAAATCAGGGTTATGTACTAAATTAATATAAAAATACTAAAA
17685681 TAATACATTTGAAACATTATGTACTA
577 TAATACATTTGAAACATTATGTACTA
* * *
17685707 AAATAATATAAAAAAATAAAATATGAAAATAGTATATTTTAAAAAATAAGATCCGAAAATTTTAA
1 AAATAATATAAAAAAATAAAATACGAAAATAGTATATTTTAAAAAATAAAATCTGAAAATTTTAA
17685772 AAAT
66 AAAT
17685776 TTAAAAAATA
Statistics
Matches: 620, Mismatches: 42, Indels: 20
0.91 0.06 0.03
Matches are distributed among these distances:
599 9 0.01
601 6 0.01
602 76 0.12
603 77 0.12
604 79 0.13
605 317 0.51
606 56 0.09
ACGTcount: A:0.57, C:0.07, G:0.07, T:0.29
Consensus pattern (602 bp):
AAATAATATAAAAAAATAAAATACGAAAATAGTATATTTTAAAAAATAAAATCTGAAAATTTTAA
AAATAAAAACAAAGGGACAAAATCAAGGTTATTTACTAAATTAATATAAAAAACACTAAAATAAT
ACATTTGAAACATAATGTACTAAAATAATATAAAAAATAAAATACGAAAATAGAATATTTAAAAA
ATAAAATCAGAAAATTTTAAAAACACAAACAAAGGATCAAAATCAGGGTTATTTACTAAATTAAT
ATAAAAACACTAAAATAATACATTTAAAACATTATGTACTAAAATAATATAAAAAATAAAATACA
AAAATAATATATTTTAAAAAATAAAATCCGAAAATTTTAAAATAAAAAGAAATGGTCAAAATCAG
GATTATTTACTAAATTAATATAAAAAAACACTAAAATAATACATTTGAAACATTATGTACTAAAA
TAATATAAAAAATAAAATACAAAAATAATATATTTTTAAAAATAAAATCCGAAAATTTTAAAAAT
ACAAAAAAGGGACAAAAATCAGGGTTATGTACTAAATTAATATAAAAATACTAAAATAATACATT
TGAAACATTATGTACTA
Found at i:17689408 original size:46 final size:46
Alignment explanation
Indices: 17689352--17689526 Score: 180
Period size: 46 Copynumber: 3.8 Consensus size: 46
17689342 TGTAACCCGC
* *
17689352 CCATAAGTGAACTCGGACTCAAATCAACAAGCTCGGGCGTTCGCAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCAT
* *
17689398 CCATAGGTGAACTCGGACTCAACTCAACGAGCTCGGATGCCTAGTT-ACAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGG--G-C--GTTCGCAT
* * * *
17689448 CTC-T---TGAACTCGGACTCAACTCAACGAGTTCAGACATTCGCAT
1 C-CATAAGTGAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCAT
*
17689491 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGG
1 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGG
17689527 ATGCCCAAAT
Statistics
Matches: 108, Mismatches: 10, Indels: 22
0.77 0.07 0.16
Matches are distributed among these distances:
42 3 0.03
43 5 0.05
44 1 0.01
46 61 0.56
47 27 0.25
48 1 0.01
49 1 0.01
50 5 0.05
51 4 0.04
ACGTcount: A:0.29, C:0.29, G:0.21, T:0.22
Consensus pattern (46 bp):
CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCAT
Found at i:17689518 original size:93 final size:93
Alignment explanation
Indices: 17689359--17689531 Score: 274
Period size: 93 Copynumber: 1.9 Consensus size: 93
17689349 CGCCCATAAG
* * * *
17689359 TGAACTCGGACTCAAATCAACAAGCTCGGGCGTTCGCATCCATAGGTGAACTCGGACTCAACTCA
1 TGAACTCGGACTCAAATCAACAAGCTCAGACATTCGCATCCATAAGTGAACTCGGACTCAACTCA
17689424 ACGAGCTCGGATGCCTAGTTACATCTCT
66 ACGAGCTCGGATGCCTAGTTACATCTCT
* * *
17689452 TGAACTCGGACTCAACTCAACGAGTTCAGACATTCGCATCCATAAGTGAACTCGGACTCAACTCA
1 TGAACTCGGACTCAAATCAACAAGCTCAGACATTCGCATCCATAAGTGAACTCGGACTCAACTCA
*
17689517 ACGAGTTCGGATGCC
66 ACGAGCTCGGATGCC
17689532 CAAATATCCT
Statistics
Matches: 72, Mismatches: 8, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
93 72 1.00
ACGTcount: A:0.28, C:0.29, G:0.21, T:0.22
Consensus pattern (93 bp):
TGAACTCGGACTCAAATCAACAAGCTCAGACATTCGCATCCATAAGTGAACTCGGACTCAACTCA
ACGAGCTCGGATGCCTAGTTACATCTCT
Found at i:17689546 original size:46 final size:44
Alignment explanation
Indices: 17689404--17689546 Score: 114
Period size: 46 Copynumber: 3.1 Consensus size: 44
17689394 GCATCCATAG
* *
17689404 GTGAACTCGGACTCAACTCAACGAGCTCGGATGCCTAGTTACATCTCT-
1 GTGAACTCGGACTCAACTCAACGAGTTCGGATGCCCA---A-ATC-CTA
* * *
17689452 -TGAACTCGGACTCAACTCAACGAGTTCAGACATTCGC--ATCCATAA
1 GTGAACTCGGACTCAACTCAACGAGTTC-G-GATGCCCAAATCC-T-A
17689497 GTGAACTCGGACTCAACTCAACGAGTTCGGATGCCCAAATATCCTA
1 GTGAACTCGGACTCAACTCAACGAGTTCGGATGCCC-AA-ATCCTA
17689543 GTGA
1 GTGA
17689547 CATGTCACTT
Statistics
Matches: 77, Mismatches: 8, Indels: 22
0.72 0.07 0.21
Matches are distributed among these distances:
42 1 0.01
43 4 0.05
44 4 0.05
45 1 0.01
46 32 0.42
47 27 0.35
48 5 0.06
49 3 0.04
ACGTcount: A:0.29, C:0.28, G:0.20, T:0.23
Consensus pattern (44 bp):
GTGAACTCGGACTCAACTCAACGAGTTCGGATGCCCAAATCCTA
Found at i:17691332 original size:3 final size:3
Alignment explanation
Indices: 17691324--17691359 Score: 54
Period size: 3 Copynumber: 12.0 Consensus size: 3
17691314 CATATATCAA
**
17691324 TAT TAT TAT TAT CCT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
17691360 CATCTTAGTA
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.31, C:0.06, G:0.00, T:0.64
Consensus pattern (3 bp):
TAT
Found at i:17691432 original size:12 final size:13
Alignment explanation
Indices: 17691393--17691436 Score: 63
Period size: 14 Copynumber: 3.3 Consensus size: 13
17691383 ATATGTAATT
17691393 TATATATTATGTA
1 TATATATTATGTA
17691406 TATTATATGTATGTA
1 TA-TATAT-TATGTA
17691421 TATATATT-TGTA
1 TATATATTATGTA
17691433 TATA
1 TATA
17691437 GTACTATTTT
Statistics
Matches: 29, Mismatches: 0, Indels: 5
0.85 0.00 0.15
Matches are distributed among these distances:
12 8 0.28
13 3 0.10
14 10 0.34
15 8 0.28
ACGTcount: A:0.36, C:0.00, G:0.09, T:0.55
Consensus pattern (13 bp):
TATATATTATGTA
Found at i:17691534 original size:31 final size:34
Alignment explanation
Indices: 17691497--17691558 Score: 103
Period size: 32 Copynumber: 1.9 Consensus size: 34
17691487 TTTATATACT
17691497 TCATTA-TTATTTCTAATAT-TAT-TATTATTAG
1 TCATTATTTATTTCTAATATGTATATATTATTAG
17691528 TCATTATTTATTTCTAATATGTATATATTAT
1 TCATTATTTATTTCTAATATGTATATATTAT
17691559 GTAAATGTTT
Statistics
Matches: 28, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
31 6 0.21
32 13 0.46
33 3 0.11
34 6 0.21
ACGTcount: A:0.32, C:0.06, G:0.03, T:0.58
Consensus pattern (34 bp):
TCATTATTTATTTCTAATATGTATATATTATTAG
Found at i:17691680 original size:29 final size:30
Alignment explanation
Indices: 17691630--17691691 Score: 90
Period size: 29 Copynumber: 2.1 Consensus size: 30
17691620 CCATCTTATG
* *
17691630 TATATATTTTTAAATACTATATTGTATATA
1 TATATATTCTTAAATACCATATTGTATATA
*
17691660 TATATATTCTT-AATACCATATTGTCTATA
1 TATATATTCTTAAATACCATATTGTATATA
17691689 TAT
1 TAT
17691692 CATTATTACA
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
29 19 0.66
30 10 0.34
ACGTcount: A:0.37, C:0.08, G:0.03, T:0.52
Consensus pattern (30 bp):
TATATATTCTTAAATACCATATTGTATATA
Found at i:17695904 original size:17 final size:17
Alignment explanation
Indices: 17695884--17695916 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
17695874 CCCAATAAAA
*
17695884 ACAATAAACCAAAATAC
1 ACAAAAAACCAAAATAC
17695901 ACAAAAAACCAAAATA
1 ACAAAAAACCAAAATA
17695917 ATTAAATGTT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.70, C:0.21, G:0.00, T:0.09
Consensus pattern (17 bp):
ACAAAAAACCAAAATAC
Found at i:17697132 original size:29 final size:29
Alignment explanation
Indices: 17697100--17697156 Score: 87
Period size: 29 Copynumber: 2.0 Consensus size: 29
17697090 TTTTAATCCT
* *
17697100 TTTTAAATTTTTTATATATAATTTATTTA
1 TTTTAAATATTTTATATATAATCTATTTA
*
17697129 TTTTAAATATTTTATATATTATCTATTT
1 TTTTAAATATTTTATATATAATCTATTT
17697157 TTACTATAAA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
29 25 1.00
ACGTcount: A:0.33, C:0.02, G:0.00, T:0.65
Consensus pattern (29 bp):
TTTTAAATATTTTATATATAATCTATTTA
Found at i:17697205 original size:12 final size:11
Alignment explanation
Indices: 17697188--17697369 Score: 98
Period size: 12 Copynumber: 16.5 Consensus size: 11
17697178 TATGTAAAAA
17697188 ATTATTGTATAT
1 ATTATT-TATAT
17697200 ATTATTT-T-T
1 ATTATTTATAT
*
17697209 A-T--TTATGT
1 ATTATTTATAT
17697217 ATTATTTATTAT
1 ATTATTTA-TAT
17697229 ATTATTTATAT
1 ATTATTTATAT
17697240 -TATATTATATAT
1 AT-TATT-TATAT
*
17697252 TTTATTTATAT
1 ATTATTTATAT
*
17697263 ATTTTATTATAT
1 ATTAT-TTATAT
17697275 ATTA--TATCAT
1 ATTATTTAT-AT
* *
17697285 TTTATTATACAT
1 ATTATT-TATAT
*
17697297 ATTATTCATTAT
1 ATTATTTA-TAT
*
17697309 ATTATTTTTAT
1 ATTATTTATAT
*
17697320 TTTA-TTATAT
1 ATTATTTATAT
17697330 ATTATATTATAT
1 ATTAT-TTATAT
*
17697342 -TATATTATTATTT
1 AT-TA-T-TTATAT
17697355 ATTATTTAT-T
1 ATTATTTATAT
17697365 ATTAT
1 ATTAT
17697370 GTGTAATTTT
Statistics
Matches: 135, Mismatches: 15, Indels: 42
0.70 0.08 0.22
Matches are distributed among these distances:
6 2 0.01
7 1 0.01
8 3 0.02
9 6 0.04
10 21 0.16
11 31 0.23
12 58 0.43
13 12 0.09
14 1 0.01
ACGTcount: A:0.33, C:0.02, G:0.01, T:0.64
Consensus pattern (11 bp):
ATTATTTATAT
Found at i:17697233 original size:5 final size:5
Alignment explanation
Indices: 17697197--17697369 Score: 104
Period size: 5 Copynumber: 35.6 Consensus size: 5
17697187 AATTATTGTA
*
17697197 TATAT TAT-T TTTAT T-TAT GTATTAT T-TAT TATAT TAT-T TATAT TATAT
1 TATAT TATAT TATAT TATAT -TA-TAT TATAT TATAT TATAT TATAT TATAT
* * *
17697245 TATA- TATTT TAT-T TATA- TATTT TAT-T ATATAT TATAT CAT-T T-TAT
1 TATAT TATAT TATAT TATAT TATAT TATAT -TATAT TATAT TATAT TATAT
* * *
17697290 TATA- CATAT TATTCAT TATAT TAT-T TTTAT TTTATT ATATAT TATAT
1 TATAT TATAT TA-T-AT TATAT TATAT TATAT TATA-T -TATAT TATAT
17697337 TATAT TATAT TATTAT T-TAT TAT-T TATTAT TAT
1 TATAT TATAT TA-TAT TATAT TATAT TA-TAT TAT
17697370 GTGTAATTTT
Statistics
Matches: 136, Mismatches: 9, Indels: 46
0.71 0.05 0.24
Matches are distributed among these distances:
3 1 0.01
4 41 0.30
5 71 0.52
6 13 0.10
7 10 0.07
ACGTcount: A:0.33, C:0.02, G:0.01, T:0.65
Consensus pattern (5 bp):
TATAT
Found at i:17700395 original size:118 final size:118
Alignment explanation
Indices: 17700212--17700448 Score: 465
Period size: 118 Copynumber: 2.0 Consensus size: 118
17700202 GCCATCTCTA
17700212 ACAAAATCTATAACATGCCAAATAAATTTCATAAATATTATCTAATTAACCTAAAACTGGTTTTT
1 ACAAAATCTATAACATGCCAAATAAATTTCATAAATATTATCTAATTAACCTAAAACTGGTTTTT
17700277 TACCCTAATAATATAAAAAATAGAATAAAATACCAAAATAGGTTGTTTGAAAG
66 TACCCTAATAATATAAAAAATAGAATAAAATACCAAAATAGGTTGTTTGAAAG
17700330 ACAAAATCTATAACATGCCAAATAAATTTCATAAATATTATCTAATTAACCTAAAACTGGTTTTT
1 ACAAAATCTATAACATGCCAAATAAATTTCATAAATATTATCTAATTAACCTAAAACTGGTTTTT
*
17700395 TATCCTAATAATATAAAAAATAGAATAAAATACCAAAATAGGTTGTTTGAAAG
66 TACCCTAATAATATAAAAAATAGAATAAAATACCAAAATAGGTTGTTTGAAAG
17700448 A
1 A
17700449 TAAGTACCAT
Statistics
Matches: 118, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
118 118 1.00
ACGTcount: A:0.49, C:0.12, G:0.08, T:0.32
Consensus pattern (118 bp):
ACAAAATCTATAACATGCCAAATAAATTTCATAAATATTATCTAATTAACCTAAAACTGGTTTTT
TACCCTAATAATATAAAAAATAGAATAAAATACCAAAATAGGTTGTTTGAAAG
Found at i:17700723 original size:16 final size:16
Alignment explanation
Indices: 17700702--17700734 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
17700692 ATAGTTTTTT
*
17700702 ACTAACAATAATAATA
1 ACTAACAACAATAATA
17700718 ACTAACAACAATAATA
1 ACTAACAACAATAATA
17700734 A
1 A
17700735 GGGTTTTTAC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.64, C:0.15, G:0.00, T:0.21
Consensus pattern (16 bp):
ACTAACAACAATAATA
Found at i:17700731 original size:39 final size:40
Alignment explanation
Indices: 17700627--17700766 Score: 148
Period size: 41 Copynumber: 3.5 Consensus size: 40
17700617 AATATAAATC
* **
17700627 AACAATAATAATAACTAACAATAAT--TGGGATTTTTTACT
1 AACAATAATAATAACTAACAACAATAATAAG-TTTTTTACT
*
17700666 AAC---AATAATAACCAACAATCCTAATAAT-AGTTTTTTACT
1 AACAATAATAATAACTAACAA--C-AATAATAAGTTTTTTACT
*
17700705 AACAATAATAATAACTAACAACAATAATAAGGGTTTTTACT
1 AACAATAATAATAACTAACAACAATAATAA-GTTTTTTACT
17700746 AACAATAATAATAACTAACAA
1 AACAATAATAATAACTAACAA
17700767 AAAAAATCGA
Statistics
Matches: 86, Mismatches: 5, Indels: 18
0.79 0.05 0.17
Matches are distributed among these distances:
36 14 0.16
39 24 0.28
40 3 0.03
41 31 0.36
42 14 0.16
ACGTcount: A:0.51, C:0.14, G:0.05, T:0.31
Consensus pattern (40 bp):
AACAATAATAATAACTAACAACAATAATAAGTTTTTTACT
Found at i:17703191 original size:6 final size:7
Alignment explanation
Indices: 17703174--17703200 Score: 54
Period size: 7 Copynumber: 3.9 Consensus size: 7
17703164 CGAATAGGTA
17703174 AAAAATT
1 AAAAATT
17703181 AAAAATT
1 AAAAATT
17703188 AAAAATT
1 AAAAATT
17703195 AAAAAT
1 AAAAAT
17703201 CGAAAATAAG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 20 1.00
ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (7 bp):
AAAAATT
Found at i:17703206 original size:14 final size:14
Alignment explanation
Indices: 17703174--17703207 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
17703164 CGAATAGGTA
*
17703174 AAAAATTAAAAATT
1 AAAAATTAAAAATC
17703188 AAAAATTAAAAATC
1 AAAAATTAAAAATC
*
17703202 GAAAAT
1 AAAAAT
17703208 AAGAAAATTC
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.71, C:0.03, G:0.03, T:0.24
Consensus pattern (14 bp):
AAAAATTAAAAATC
Found at i:17703338 original size:17 final size:19
Alignment explanation
Indices: 17703311--17703355 Score: 58
Period size: 17 Copynumber: 2.5 Consensus size: 19
17703301 CTTATTTTAA
*
17703311 AATTTTAATATATATT-TT
1 AATTTTTATATATATTATT
*
17703329 -ATTTTTATATTTATTATT
1 AATTTTTATATATATTATT
17703347 AATTTTTAT
1 AATTTTTAT
17703356 GTTATTTAAT
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
17 13 0.57
18 2 0.09
19 8 0.35
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (19 bp):
AATTTTTATATATATTATT
Found at i:17705080 original size:8 final size:8
Alignment explanation
Indices: 17705067--17705093 Score: 54
Period size: 8 Copynumber: 3.4 Consensus size: 8
17705057 GAAAATATTA
17705067 AAGAATTT
1 AAGAATTT
17705075 AAGAATTT
1 AAGAATTT
17705083 AAGAATTT
1 AAGAATTT
17705091 AAG
1 AAG
17705094 TCATTAATTA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 19 1.00
ACGTcount: A:0.52, C:0.00, G:0.15, T:0.33
Consensus pattern (8 bp):
AAGAATTT
Found at i:17708241 original size:13 final size:14
Alignment explanation
Indices: 17708215--17708246 Score: 57
Period size: 13 Copynumber: 2.4 Consensus size: 14
17708205 ACTAACGACG
17708215 AATTAAACCATTAT
1 AATTAAACCATTAT
17708229 AATTAAA-CATTAT
1 AATTAAACCATTAT
17708242 AATTA
1 AATTA
17708247 TTTATAATAA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
13 11 0.61
14 7 0.39
ACGTcount: A:0.53, C:0.09, G:0.00, T:0.38
Consensus pattern (14 bp):
AATTAAACCATTAT
Found at i:17713211 original size:15 final size:15
Alignment explanation
Indices: 17713193--17713223 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
17713183 ATTTAAAAAC
17713193 TAAGTATTTGTGTTT
1 TAAGTATTTGTGTTT
17713208 TAAGTATTTGTGTTT
1 TAAGTATTTGTGTTT
17713223 T
1 T
17713224 CTTATTCCCT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.19, C:0.00, G:0.19, T:0.61
Consensus pattern (15 bp):
TAAGTATTTGTGTTT
Found at i:17713563 original size:8 final size:9
Alignment explanation
Indices: 17713548--17713587 Score: 64
Period size: 9 Copynumber: 4.6 Consensus size: 9
17713538 AGTTTAAATA
17713548 ATTAAAAAC
1 ATTAAAAAC
17713557 ATTAAAAAC
1 ATTAAAAAC
*
17713566 ATT-AAATC
1 ATTAAAAAC
17713574 ATTAAAAAC
1 ATTAAAAAC
17713583 ATTAA
1 ATTAA
17713588 TTTTCAATTG
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
8 7 0.25
9 21 0.75
ACGTcount: A:0.62, C:0.10, G:0.00, T:0.28
Consensus pattern (9 bp):
ATTAAAAAC
Found at i:17714800 original size:114 final size:113
Alignment explanation
Indices: 17714594--17714800 Score: 244
Period size: 114 Copynumber: 1.8 Consensus size: 113
17714584 CAATCTCCTA
*
17714594 AAAGATATTTGTGGCGTTTCCTTCAAAAACGCCGGTAATTCCAACTTTTTGCGGCGTTTAATAAA
1 AAAGATATTTGTGGCGTTTAC-TCAAAAACGCCGGTAATTCCAACTTTTTGCGGCGTTTAATAAA
*
17714659 ACGCGCCACTAATAAAAAGGATGAAAACAATGACATTTTTCTATCTATTC
65 ACGCGCCACTAATAAAAA-GATCAAAACAATGACATTTTTCTATCTATTC
* * * *
17714709 AAAGATATTTGTGGCGTTTAC-GAATAAACGCTGGTAATT-CATACTTTTTGTGGCATTTTAA-A
1 AAAGATATTTGTGGCGTTTACTCAA-AAACGCCGGTAATTCCA-ACTTTTTGCGGC-GTTTAATA
*
17714771 GAAA-GTGCCACTAATAACAAA-ACTCAAAAC
63 -AAACGCGCCACTAATAA-AAAGA-TCAAAAC
17714801 GACGCCGTCT
Statistics
Matches: 79, Mismatches: 7, Indels: 13
0.80 0.07 0.13
Matches are distributed among these distances:
113 5 0.06
114 43 0.54
115 31 0.39
ACGTcount: A:0.36, C:0.17, G:0.16, T:0.31
Consensus pattern (113 bp):
AAAGATATTTGTGGCGTTTACTCAAAAACGCCGGTAATTCCAACTTTTTGCGGCGTTTAATAAAA
CGCGCCACTAATAAAAAGATCAAAACAATGACATTTTTCTATCTATTC
Found at i:17715155 original size:28 final size:28
Alignment explanation
Indices: 17715123--17715195 Score: 96
Period size: 28 Copynumber: 2.6 Consensus size: 28
17715113 TTAATCAAAA
17715123 CCCTAAACCTTAAA-TCATTAAACTATAT-
1 CCCTAAACCTTAAACTC--TAAACTATATC
17715151 CCCTATAACCTTAAACTCTAAACTATATC
1 CCCTA-AACCTTAAACTCTAAACTATATC
*
17715180 CCCTAAACCCTAAACT
1 CCCTAAACCTTAAACT
17715196 ATATCCCTTA
Statistics
Matches: 41, Mismatches: 1, Indels: 6
0.85 0.02 0.12
Matches are distributed among these distances:
28 25 0.61
29 14 0.34
30 2 0.05
ACGTcount: A:0.40, C:0.32, G:0.00, T:0.29
Consensus pattern (28 bp):
CCCTAAACCTTAAACTCTAAACTATATC
Found at i:17715186 original size:21 final size:21
Alignment explanation
Indices: 17715162--17715214 Score: 79
Period size: 21 Copynumber: 2.5 Consensus size: 21
17715152 CCTATAACCT
*
17715162 TAAACTCTAAACTATATCCCC
1 TAAACCCTAAACTATATCCCC
*
17715183 TAAACCCTAAACTATATCCCT
1 TAAACCCTAAACTATATCCCC
*
17715204 TAAACCATAAA
1 TAAACCCTAAA
17715215 TCACAAAACA
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 29 1.00
ACGTcount: A:0.43, C:0.30, G:0.00, T:0.26
Consensus pattern (21 bp):
TAAACCCTAAACTATATCCCC
Found at i:17715357 original size:28 final size:28
Alignment explanation
Indices: 17715290--17715373 Score: 71
Period size: 28 Copynumber: 3.0 Consensus size: 28
17715280 TAAAGTACCC
*
17715290 TAAACTATATCCCCTAAAACCTAAACCT
1 TAAACTATAACCCCTAAAACCTAAACCT
* * * *
17715318 CAAAATAATAACCCCT-AAGCCTTAACCT
1 TAAACT-ATAACCCCTAAAACCTAAACCT
* **
17715346 TAAACTATTAACCCATAACCCCTAAACC
1 TAAACTA-TAACCCCTAAAACCTAAACC
17715374 CCTAACCAAT
Statistics
Matches: 42, Mismatches: 11, Indels: 5
0.72 0.19 0.09
Matches are distributed among these distances:
27 1 0.02
28 25 0.60
29 16 0.38
ACGTcount: A:0.43, C:0.33, G:0.01, T:0.23
Consensus pattern (28 bp):
TAAACTATAACCCCTAAAACCTAAACCT
Found at i:17715386 original size:29 final size:28
Alignment explanation
Indices: 17715354--17715408 Score: 92
Period size: 29 Copynumber: 1.9 Consensus size: 28
17715344 CTTAAACTAT
17715354 TAACCCATAACCCCTAAACCCCTAACCAA
1 TAACCCATAACCCCTAAACCCC-AACCAA
*
17715383 TAACCCATAACCCTTAAACCCCAACC
1 TAACCCATAACCCCTAAACCCCAACC
17715409 CTTAAAACAT
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
28 4 0.16
29 21 0.84
ACGTcount: A:0.40, C:0.45, G:0.00, T:0.15
Consensus pattern (28 bp):
TAACCCATAACCCCTAAACCCCAACCAA
Found at i:17715419 original size:28 final size:29
Alignment explanation
Indices: 17715359--17715429 Score: 72
Period size: 28 Copynumber: 2.5 Consensus size: 29
17715349 ACTATTAACC
* **
17715359 CATAACCCCTAAACCCCTAACCAATAACC
1 CATAACCCATAAACCCCTAACCAATAAAA
* **
17715388 CATAACCCTTAAACCCC-AACCCTTAAAA
1 CATAACCCATAAACCCCTAACCAATAAAA
*
17715416 CATAAGCCATAAAC
1 CATAACCCATAAAC
17715430 ATAATCCCTA
Statistics
Matches: 35, Mismatches: 7, Indels: 1
0.81 0.16 0.02
Matches are distributed among these distances:
28 19 0.54
29 16 0.46
ACGTcount: A:0.44, C:0.39, G:0.01, T:0.15
Consensus pattern (29 bp):
CATAACCCATAAACCCCTAACCAATAAAA
Found at i:17715431 original size:13 final size:13
Alignment explanation
Indices: 17715413--17715457 Score: 54
Period size: 13 Copynumber: 3.3 Consensus size: 13
17715403 CCAACCCTTA
*
17715413 AAACATAAGCCAT
1 AAACATAATCCAT
*
17715426 AAACATAATCCCT
1 AAACATAATCCAT
17715439 AAACCCATAATCCAT
1 AAA--CATAATCCAT
17715454 AAAC
1 AAAC
17715458 CTATAAATAG
Statistics
Matches: 27, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
13 15 0.56
15 12 0.44
ACGTcount: A:0.51, C:0.29, G:0.02, T:0.18
Consensus pattern (13 bp):
AAACATAATCCAT
Found at i:17715449 original size:15 final size:14
Alignment explanation
Indices: 17715355--17715463 Score: 57
Period size: 15 Copynumber: 7.6 Consensus size: 14
17715345 TTAAACTATT
17715355 AACCCATAACCCCTA
1 AACCCATAA-CCCTA
* *
17715370 AACCCCTAA-CCAA
1 AACCCATAACCCTA
17715383 TAACCCATAACCCTTA
1 -AACCCATAACCC-TA
*
17715399 AACCC-CAACCCTTA
1 AACCCATAACCC-TA
* *
17715413 AA-ACATAAGCCATA
1 AACCCATAA-CCCTA
17715427 AA--CATAATCCCTA
1 AACCCATAA-CCCTA
*
17715440 AACCCATAATCCATA
1 AACCCATAA-CCCTA
*
17715455 AACCTATAA
1 AACCCATAA
17715464 ATAGTAAATC
Statistics
Matches: 75, Mismatches: 12, Indels: 14
0.74 0.12 0.14
Matches are distributed among these distances:
13 15 0.20
14 24 0.32
15 35 0.47
16 1 0.01
ACGTcount: A:0.45, C:0.37, G:0.01, T:0.17
Consensus pattern (14 bp):
AACCCATAACCCTA
Found at i:17723770 original size:14 final size:14
Alignment explanation
Indices: 17723751--17723787 Score: 51
Period size: 12 Copynumber: 2.8 Consensus size: 14
17723741 TCTCAAATTG
*
17723751 CAATTTATCATATT
1 CAATTTATCATAGT
17723765 CAATTTAT--TAGT
1 CAATTTATCATAGT
17723777 CAATTTATCAT
1 CAATTTATCAT
17723788 TTCTTTATGA
Statistics
Matches: 20, Mismatches: 1, Indels: 4
0.80 0.04 0.16
Matches are distributed among these distances:
12 11 0.55
14 9 0.45
ACGTcount: A:0.35, C:0.14, G:0.03, T:0.49
Consensus pattern (14 bp):
CAATTTATCATAGT
Found at i:17726728 original size:17 final size:18
Alignment explanation
Indices: 17726684--17726735 Score: 54
Period size: 17 Copynumber: 2.8 Consensus size: 18
17726674 TACCTCAATT
*
17726684 TTTATAATATCATTAATTAA
1 TTTA-AATAT-ATTTATTAA
17726704 TTTAAATAT-TTTATTATA
1 TTTAAATATATTTATTA-A
17726722 TTT-AATATATTTAT
1 TTTAAATATATTTAT
17726736 ATAAACTTTT
Statistics
Matches: 29, Mismatches: 1, Indels: 6
0.81 0.03 0.17
Matches are distributed among these distances:
17 11 0.38
18 9 0.31
19 5 0.17
20 4 0.14
ACGTcount: A:0.40, C:0.02, G:0.00, T:0.58
Consensus pattern (18 bp):
TTTAAATATATTTATTAA
Found at i:17726734 original size:18 final size:17
Alignment explanation
Indices: 17726688--17726735 Score: 53
Period size: 18 Copynumber: 2.7 Consensus size: 17
17726678 TCAATTTTTA
*
17726688 TAATATCATTAATTAATT
1 TAATAT-ATTTATTAATT
17726706 TAA-ATATTTTATTATATT
1 TAATATA-TTTATTA-ATT
17726724 TAATATATTTAT
1 TAATATATTTAT
17726736 ATAAACTTTT
Statistics
Matches: 26, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
16 1 0.04
17 8 0.31
18 14 0.54
19 3 0.12
ACGTcount: A:0.42, C:0.02, G:0.00, T:0.56
Consensus pattern (17 bp):
TAATATATTTATTAATT
Found at i:17726738 original size:17 final size:18
Alignment explanation
Indices: 17726699--17726733 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
17726689 AATATCATTA
17726699 ATTA-ATTTAAATATTTT
1 ATTATATTTAAATATTTT
17726716 ATTATATTTAATATATTT
1 ATTATATTTAA-ATATTT
17726734 ATATAAACTT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 4 0.25
18 6 0.38
19 6 0.38
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (18 bp):
ATTATATTTAAATATTTT
Found at i:17731039 original size:6 final size:6
Alignment explanation
Indices: 17731028--17731062 Score: 70
Period size: 6 Copynumber: 5.8 Consensus size: 6
17731018 CAACAAGACT
17731028 GGCAAG GGCAAG GGCAAG GGCAAG GGCAAG GGCAA
1 GGCAAG GGCAAG GGCAAG GGCAAG GGCAAG GGCAA
17731063 ATTTGCCGGC
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 29 1.00
ACGTcount: A:0.34, C:0.17, G:0.49, T:0.00
Consensus pattern (6 bp):
GGCAAG
Found at i:17734208 original size:9 final size:9
Alignment explanation
Indices: 17734194--17734236 Score: 50
Period size: 9 Copynumber: 4.6 Consensus size: 9
17734184 TAGTAATTCT
17734194 AAAATATTA
1 AAAATATTA
*
17734203 AAAATAAATA
1 AAAAT-ATTA
*
17734213 TAAATTATTA
1 -AAAATATTA
17734223 AAAATATTA
1 AAAATATTA
17734232 AAAAT
1 AAAAT
17734237 TATATTAAAT
Statistics
Matches: 28, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
9 18 0.64
10 6 0.21
11 4 0.14
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (9 bp):
AAAATATTA
Found at i:17734913 original size:13 final size:13
Alignment explanation
Indices: 17734895--17734922 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
17734885 AGCTTCTTTT
17734895 TATTTTTAATTAA
1 TATTTTTAATTAA
17734908 TATTTTTAATTAA
1 TATTTTTAATTAA
17734921 TA
1 TA
17734923 AATATATTGT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (13 bp):
TATTTTTAATTAA
Found at i:17741840 original size:39 final size:39
Alignment explanation
Indices: 17741797--17741897 Score: 157
Period size: 39 Copynumber: 2.6 Consensus size: 39
17741787 AGCTCTGTGA
*
17741797 GCTTCAGTTATCCTTCGGGCTTCCGTTTAGCACTTATGT
1 GCTTCAGTTAGCCTTCGGGCTTCCGTTTAGCACTTATGT
* *
17741836 GCTTCAGTTAGCTTTCGGGCTTTCGTTTAGCACTTATGT
1 GCTTCAGTTAGCCTTCGGGCTTCCGTTTAGCACTTATGT
* *
17741875 GCTTCAGTTAGACTTCGAGCTTC
1 GCTTCAGTTAGCCTTCGGGCTTC
17741898 AGATCATGAT
Statistics
Matches: 55, Mismatches: 7, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
39 55 1.00
ACGTcount: A:0.14, C:0.24, G:0.22, T:0.41
Consensus pattern (39 bp):
GCTTCAGTTAGCCTTCGGGCTTCCGTTTAGCACTTATGT
Found at i:17749776 original size:39 final size:39
Alignment explanation
Indices: 17749730--17749830 Score: 148
Period size: 39 Copynumber: 2.6 Consensus size: 39
17749720 GCTCTGGTGA
* *
17749730 GCTTCAGTTAGCCTTCGGGCTTCCGTTTAGCACTTATTT
1 GCTTCAGTTAGCCTTCGGGCTTCCGTTAAGCACTTATGT
* * *
17749769 GCTTCAGTTAGCTTTCGAGCTTTCGTTAAGCACTTATGT
1 GCTTCAGTTAGCCTTCGGGCTTCCGTTAAGCACTTATGT
*
17749808 GCTTCAGTTAGACTTCGGGCTTC
1 GCTTCAGTTAGCCTTCGGGCTTC
17749831 AGATCACGAT
Statistics
Matches: 53, Mismatches: 9, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
39 53 1.00
ACGTcount: A:0.15, C:0.24, G:0.22, T:0.40
Consensus pattern (39 bp):
GCTTCAGTTAGCCTTCGGGCTTCCGTTAAGCACTTATGT
Found at i:17749817 original size:21 final size:21
Alignment explanation
Indices: 17749748--17749817 Score: 51
Period size: 21 Copynumber: 3.5 Consensus size: 21
17749738 TAGCCTTCGG
* * *
17749748 GCTTCCGTTTAGCACTTATTT
1 GCTTCAGTTAAGCACTTATGT
*
17749769 GCTTCAGTT-AG--CTT-TCGA
1 GCTTCAGTTAAGCACTTAT-GT
17749787 GCTTTC-GTTAAGCACTTATGT
1 GC-TTCAGTTAAGCACTTATGT
17749808 GCTTCAGTTA
1 GCTTCAGTTA
17749818 GACTTCGGGC
Statistics
Matches: 38, Mismatches: 4, Indels: 14
0.68 0.07 0.25
Matches are distributed among these distances:
17 1 0.03
18 8 0.21
19 5 0.13
20 5 0.13
21 18 0.47
22 1 0.03
ACGTcount: A:0.17, C:0.21, G:0.19, T:0.43
Consensus pattern (21 bp):
GCTTCAGTTAAGCACTTATGT
Found at i:17756821 original size:17 final size:18
Alignment explanation
Indices: 17756791--17756826 Score: 56
Period size: 17 Copynumber: 2.1 Consensus size: 18
17756781 AAATAATGAT
*
17756791 TAAAATACAATTATTTTA
1 TAAAATACAATTATATTA
17756809 TAAAATA-AATTATATTA
1 TAAAATACAATTATATTA
17756826 T
1 T
17756827 TTTGAAGGTA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 10 0.59
18 7 0.41
ACGTcount: A:0.53, C:0.03, G:0.00, T:0.44
Consensus pattern (18 bp):
TAAAATACAATTATATTA
Found at i:17760394 original size:43 final size:43
Alignment explanation
Indices: 17760251--17760394 Score: 120
Period size: 43 Copynumber: 3.4 Consensus size: 43
17760241 TGTGATTTTG
* * * * *
17760251 TGTAAGACCAAGTTTGGGAC-GTTGGC-TCGATTTGTGATTTACG
1 TGTAAGACCATGTCTGGGACAG-TGGCATC-ATATGTGAGTTACA
* * *
17760294 TGTAAGACCATGTCTGGGACA-TCGACATCGTATATGAGTT-CA
1 TGTAAGACCATGTCTGGGACAGT-GGCATCATATGTGAGTTACA
17760336 TGTAAGATCC-TGTCTGGGACAGTGGCATCAATATGTGA-TTACA
1 TGTAAGA-CCATGTCTGGGACAGTGGCATC-ATATGTGAGTTACA
*
17760379 TGTAAGACCACGTCTG
1 TGTAAGACCATGTCTG
17760395 AGACGTTAGT
Statistics
Matches: 81, Mismatches: 12, Indels: 16
0.74 0.11 0.15
Matches are distributed among these distances:
42 29 0.36
43 50 0.62
44 2 0.02
ACGTcount: A:0.26, C:0.17, G:0.26, T:0.31
Consensus pattern (43 bp):
TGTAAGACCATGTCTGGGACAGTGGCATCATATGTGAGTTACA
Found at i:17769069 original size:26 final size:28
Alignment explanation
Indices: 17768977--17769073 Score: 119
Period size: 28 Copynumber: 3.5 Consensus size: 28
17768967 CATGAGATTG
* * *
17768977 GCACTAAGTGTGCGGGTTTAAATTGT-TCA
1 GCACTAAGTGTGCGAGTTT-GATTATAT-A
17769006 GCACTAAGTGTGCGAGTTTGATTATATA
1 GCACTAAGTGTGCGAGTTTGATTATATA
17769034 GCACTAAGTGTGCGAG-TTGATT-TATA
1 GCACTAAGTGTGCGAGTTTGATTATATA
*
17769060 GCACTGAGTGTGCG
1 GCACTAAGTGTGCG
17769074 GACTTAATAT
Statistics
Matches: 63, Mismatches: 4, Indels: 5
0.88 0.06 0.07
Matches are distributed among these distances:
26 17 0.27
27 6 0.10
28 21 0.33
29 19 0.30
ACGTcount: A:0.25, C:0.13, G:0.29, T:0.33
Consensus pattern (28 bp):
GCACTAAGTGTGCGAGTTTGATTATATA
Found at i:17775782 original size:19 final size:20
Alignment explanation
Indices: 17775760--17775799 Score: 55
Period size: 19 Copynumber: 2.0 Consensus size: 20
17775750 AAATAAATTA
*
17775760 AAGAAATGAATTAAA-AAGG
1 AAGAAATGAATAAAATAAGG
*
17775779 AAGAGATGAATAAAATAAGG
1 AAGAAATGAATAAAATAAGG
17775799 A
1 A
17775800 GGGAAGAGGG
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
19 13 0.72
20 5 0.28
ACGTcount: A:0.62, C:0.00, G:0.23, T:0.15
Consensus pattern (20 bp):
AAGAAATGAATAAAATAAGG
Found at i:17777270 original size:27 final size:28
Alignment explanation
Indices: 17777186--17777283 Score: 119
Period size: 27 Copynumber: 3.5 Consensus size: 28
17777176 CATGAGATTG
* * *
17777186 GCACTAAGTGTGCGGGTTTAAATTGT-TCA
1 GCACTAAGTGTGCGAGTTT-GATTATAT-A
17777215 GCACTAAGTGTGCGAGTTTGATTATATA
1 GCACTAAGTGTGCGAGTTTGATTATATA
*
17777243 GCACTAAGTGTGCGAG-TTGATTTTATA
1 GCACTAAGTGTGCGAGTTTGATTATATA
*
17777270 GCACTGAGTGTGCG
1 GCACTAAGTGTGCG
17777284 GACTTAATAT
Statistics
Matches: 63, Mismatches: 5, Indels: 4
0.88 0.07 0.06
Matches are distributed among these distances:
27 23 0.37
28 21 0.33
29 19 0.30
ACGTcount: A:0.24, C:0.13, G:0.29, T:0.34
Consensus pattern (28 bp):
GCACTAAGTGTGCGAGTTTGATTATATA
Found at i:17777296 original size:27 final size:27
Alignment explanation
Indices: 17777214--17777296 Score: 87
Period size: 27 Copynumber: 3.0 Consensus size: 27
17777204 TAAATTGTTC
* *
17777214 AGCACTAAGTGTGCGAGTTTGATTATAT
1 AGCACTAAGTGTGCGA-CTTGAATATAT
* * *
17777242 AGCACTAAGTGTGCGAGTTGATTTTAT
1 AGCACTAAGTGTGCGACTTGAATATAT
*
17777269 AGCACTGAGTGTGCGGACTT-AATATAT
1 AGCACTAAGTGTGC-GACTTGAATATAT
17777296 A
1 A
17777297 TATTTTTGAA
Statistics
Matches: 48, Mismatches: 6, Indels: 3
0.84 0.11 0.05
Matches are distributed among these distances:
27 28 0.58
28 20 0.42
ACGTcount: A:0.29, C:0.12, G:0.25, T:0.34
Consensus pattern (27 bp):
AGCACTAAGTGTGCGACTTGAATATAT
Found at i:17781714 original size:41 final size:41
Alignment explanation
Indices: 17781669--17781969 Score: 408
Period size: 41 Copynumber: 7.4 Consensus size: 41
17781659 CGTTTTACCA
* * * **
17781669 AAAACGCCGCTAAAAA-CGGAGCAATACCGGCATTTTTTGTT
1 AAAACGCCGCTAAAAACCAGAGCATTAGCGGCGCTTTTTG-T
* * * * *
17781710 AAAACGCCGCTAAAAA-TAGAGAAATAGCGGCTCTTTTGGT
1 AAAACGCCGCTAAAAACCAGAGCATTAGCGGCGCTTTTTGT
* * *
17781750 AAAACGCCGCTAAAAACCAGAGCACTAGCAGCGCTTTTGGT
1 AAAACGCCGCTAAAAACCAGAGCATTAGCGGCGCTTTTTGT
17781791 AAAACGCCGCTAAAAACCAGAGCATTAGCGGCGCTTTTTGT
1 AAAACGCCGCTAAAAACCAGAGCATTAGCGGCGCTTTTTGT
*
17781832 AAAACGTCGCTAAAAACCAGAGCATTAGCGGCGCTTTTTGT
1 AAAACGCCGCTAAAAACCAGAGCATTAGCGGCGCTTTTTGT
* *
17781873 AAAACGCCGCTAAAAACCATAGCATTAGCGGTGCTTTTTGT
1 AAAACGCCGCTAAAAACCAGAGCATTAGCGGCGCTTTTTGT
* *
17781914 AAAACGCCGCTAAAAACCAGAGTATTAGCGGCGTTTTTTGT
1 AAAACGCCGCTAAAAACCAGAGCATTAGCGGCGCTTTTTGT
*
17781955 AAAATGCCGCTAAAA
1 AAAACGCCGCTAAAA
17781970 GTCATATAAC
Statistics
Matches: 235, Mismatches: 24, Indels: 2
0.90 0.09 0.01
Matches are distributed among these distances:
40 17 0.07
41 218 0.93
ACGTcount: A:0.34, C:0.22, G:0.21, T:0.23
Consensus pattern (41 bp):
AAAACGCCGCTAAAAACCAGAGCATTAGCGGCGCTTTTTGT
Found at i:17782539 original size:32 final size:32
Alignment explanation
Indices: 17782495--17782556 Score: 88
Period size: 32 Copynumber: 1.9 Consensus size: 32
17782485 GAGTTACTAT
* *
17782495 TTTAAGGTTTAGGGATTATGGTTTAAGTGTGG
1 TTTAAGGGTTAGGGATTAAGGTTTAAGTGTGG
* *
17782527 TTTAAGGGTTAGGGTTTAAGGTTTAGGTGT
1 TTTAAGGGTTAGGGATTAAGGTTTAAGTGT
17782557 TAGGAGTTAG
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
32 26 1.00
ACGTcount: A:0.21, C:0.00, G:0.35, T:0.44
Consensus pattern (32 bp):
TTTAAGGGTTAGGGATTAAGGTTTAAGTGTGG
Found at i:17782544 original size:14 final size:14
Alignment explanation
Indices: 17782525--17782579 Score: 51
Period size: 14 Copynumber: 3.9 Consensus size: 14
17782515 GTTTAAGTGT
17782525 GGTTTAAGGGTTAG
1 GGTTTAAGGGTTAG
*
17782539 GGTTTAAGGTTTA-
1 GGTTTAAGGGTTAG
17782552 GGTGTT-AGGAGTTAG
1 GGT-TTAAGG-GTTAG
* *
17782567 GGGTTAGGGGTTA
1 GGTTTAAGGGTTA
17782580 AGGATTCATG
Statistics
Matches: 33, Mismatches: 4, Indels: 8
0.73 0.09 0.18
Matches are distributed among these distances:
13 6 0.18
14 23 0.70
15 4 0.12
ACGTcount: A:0.20, C:0.00, G:0.44, T:0.36
Consensus pattern (14 bp):
GGTTTAAGGGTTAG
Found at i:17782559 original size:7 final size:7
Alignment explanation
Indices: 17782532--17782579 Score: 51
Period size: 7 Copynumber: 6.9 Consensus size: 7
17782522 TGTGGTTTAA
17782532 GGGTTAG
1 GGGTTAG
* *
17782539 GGTTTAA
1 GGGTTAG
*
17782546 GGTTTAG
1 GGGTTAG
*
17782553 GTGTTAG
1 GGGTTAG
*
17782560 GAGTTAG
1 GGGTTAG
17782567 GGGTTAG
1 GGGTTAG
17782574 GGGTTA
1 GGGTTA
17782580 AGGATTCATG
Statistics
Matches: 34, Mismatches: 7, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
7 34 1.00
ACGTcount: A:0.19, C:0.00, G:0.46, T:0.35
Consensus pattern (7 bp):
GGGTTAG
Found at i:17782765 original size:21 final size:22
Alignment explanation
Indices: 17782730--17782788 Score: 61
Period size: 21 Copynumber: 2.8 Consensus size: 22
17782720 ATTGAGTTAA
* *
17782730 TTAT-ATTTAGAGTTTAGAG-T
1 TTATGATTTAGGGTTTAGAGAC
* *
17782750 TTATGGTTTATGGTTTA-AGAC
1 TTATGATTTAGGGTTTAGAGAC
17782771 TTATGATTTAGGGTTTAG
1 TTATGATTTAGGGTTTAG
17782789 TTTTTAGTGT
Statistics
Matches: 30, Mismatches: 6, Indels: 4
0.75 0.15 0.10
Matches are distributed among these distances:
20 6 0.20
21 24 0.80
ACGTcount: A:0.25, C:0.02, G:0.24, T:0.49
Consensus pattern (22 bp):
TTATGATTTAGGGTTTAGAGAC
Found at i:17783700 original size:16 final size:16
Alignment explanation
Indices: 17783679--17783714 Score: 72
Period size: 16 Copynumber: 2.2 Consensus size: 16
17783669 ATAGCTCCAG
17783679 TTAACGATGGGATTAA
1 TTAACGATGGGATTAA
17783695 TTAACGATGGGATTAA
1 TTAACGATGGGATTAA
17783711 TTAA
1 TTAA
17783715 AGTTGCATAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.39, C:0.06, G:0.22, T:0.33
Consensus pattern (16 bp):
TTAACGATGGGATTAA
Found at i:17786840 original size:19 final size:19
Alignment explanation
Indices: 17786818--17786858 Score: 57
Period size: 19 Copynumber: 2.2 Consensus size: 19
17786808 TTTATTGATA
17786818 TTTTTA-TATTTAATCTAG
1 TTTTTATTATTTAATCTAG
* *
17786836 TTTTTATTATTTATTTTAG
1 TTTTTATTATTTAATCTAG
17786855 TTTT
1 TTTT
17786859 GATTCTAAAT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
18 6 0.30
19 14 0.70
ACGTcount: A:0.22, C:0.02, G:0.05, T:0.71
Consensus pattern (19 bp):
TTTTTATTATTTAATCTAG
Found at i:17787154 original size:43 final size:43
Alignment explanation
Indices: 17787106--17787228 Score: 165
Period size: 43 Copynumber: 2.9 Consensus size: 43
17787096 TTTTTGAATT
* * * * *
17787106 TCATGACCTTTAGCGGCATTTGTGGGAAAAGTGTCGTTAAAGG
1 TCATGATCTTTAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGG
** *
17787149 TCATGATCTTTAGCGATGTTTTTGGGAAAAGCGCCGCTAAAGG
1 TCATGATCTTTAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGG
*
17787192 TCATGATCTTTAGCGGCGTTTGTGCGAAAAGCGCCGC
1 TCATGATCTTTAGCGGCGTTTGTGGGAAAAGCGCCGC
17787229 CTTTTATTTG
Statistics
Matches: 68, Mismatches: 12, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
43 68 1.00
ACGTcount: A:0.24, C:0.18, G:0.29, T:0.29
Consensus pattern (43 bp):
TCATGATCTTTAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGG
Found at i:17793594 original size:56 final size:56
Alignment explanation
Indices: 17793531--17793644 Score: 228
Period size: 56 Copynumber: 2.0 Consensus size: 56
17793521 TTATCCCTTT
17793531 TATTATGATTTTATTTCAATTAAGGTTTTTCATAATTTTTTTAAATTCATTTCACA
1 TATTATGATTTTATTTCAATTAAGGTTTTTCATAATTTTTTTAAATTCATTTCACA
17793587 TATTATGATTTTATTTCAATTAAGGTTTTTCATAATTTTTTTAAATTCATTTCACA
1 TATTATGATTTTATTTCAATTAAGGTTTTTCATAATTTTTTTAAATTCATTTCACA
17793643 TA
1 TA
17793645 CATTTTTTAA
Statistics
Matches: 58, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
56 58 1.00
ACGTcount: A:0.31, C:0.09, G:0.05, T:0.55
Consensus pattern (56 bp):
TATTATGATTTTATTTCAATTAAGGTTTTTCATAATTTTTTTAAATTCATTTCACA
Found at i:17797123 original size:3 final size:3
Alignment explanation
Indices: 17797117--17797161 Score: 51
Period size: 3 Copynumber: 15.7 Consensus size: 3
17797107 TTTAATGAGA
*
17797117 TAT TAT TAAT TAT T-T TAT TAT TAT T-T CAT TAT TAT T-T TAT TAT
1 TAT TAT T-AT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
17797160 TA
1 TA
17797162 ATTAATTAGA
Statistics
Matches: 36, Mismatches: 2, Indels: 8
0.78 0.04 0.17
Matches are distributed among these distances:
2 5 0.14
3 28 0.78
4 3 0.08
ACGTcount: A:0.31, C:0.02, G:0.00, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:17797133 original size:23 final size:20
Alignment explanation
Indices: 17797083--17797124 Score: 61
Period size: 20 Copynumber: 2.2 Consensus size: 20
17797073 ATATTTTATG
*
17797083 ATTA-TTTAATTAGATATAT
1 ATTATTTTAATGAGATATAT
17797102 ATTATTTTAATGAGATAT-T
1 ATTATTTTAATGAGATATAT
17797121 ATTA
1 ATTA
17797125 ATTATTTTAT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
19 9 0.43
20 12 0.57
ACGTcount: A:0.40, C:0.00, G:0.07, T:0.52
Consensus pattern (20 bp):
ATTATTTTAATGAGATATAT
Found at i:17797141 original size:11 final size:11
Alignment explanation
Indices: 17797119--17797161 Score: 68
Period size: 11 Copynumber: 3.8 Consensus size: 11
17797109 TAATGAGATA
17797119 TTATTAATTATT
1 TTATT-ATTATT
17797131 TTATTATTATT
1 TTATTATTATT
*
17797142 TCATTATTATT
1 TTATTATTATT
17797153 TTATTATTA
1 TTATTATTA
17797162 ATTAATTAGA
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
11 24 0.83
12 5 0.17
ACGTcount: A:0.30, C:0.02, G:0.00, T:0.67
Consensus pattern (11 bp):
TTATTATTATT
Found at i:17797169 original size:22 final size:22
Alignment explanation
Indices: 17797125--17797169 Score: 72
Period size: 22 Copynumber: 2.0 Consensus size: 22
17797115 GATATTATTA
* *
17797125 ATTATTTTATTATTATTTCATT
1 ATTATTTTATTATTAATTAATT
17797147 ATTATTTTATTATTAATTAATT
1 ATTATTTTATTATTAATTAATT
17797169 A
1 A
17797170 GATATATATC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.33, C:0.02, G:0.00, T:0.64
Consensus pattern (22 bp):
ATTATTTTATTATTAATTAATT
Found at i:17799267 original size:46 final size:46
Alignment explanation
Indices: 17799215--17799442 Score: 321
Period size: 46 Copynumber: 5.0 Consensus size: 46
17799205 AGTGTGCTCT
* *
17799215 CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGAAAC
1 CTGATATGAAATGAGTAAGACCATGGTTGAAAGATACCATGGCAAC
*
17799261 CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAAC
1 CTGATATGAAATGAGTAAGACCATGGTTGAAAGATACCATGGCAAC
* * *
17799307 GTGATATGAAATGAATAAGACCATGGTTGAAAGATACCATGGCAGC
1 CTGATATGAAATGAGTAAGACCATGGTTGAAAGATACCATGGCAAC
* * *
17799353 GTGACATGAAATGAATAAGACCATGGTTGAAAGATACCATGGCAAC
1 CTGATATGAAATGAGTAAGACCATGGTTGAAAGATACCATGGCAAC
* * * * * *
17799399 ATGACATAAAATGAGTAAGACCATAGTTGAAAGACACTATGGCA
1 CTGATATGAAATGAGTAAGACCATGGTTGAAAGATACCATGGCA
17799443 TCATGTCAAA
Statistics
Matches: 169, Mismatches: 13, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
46 169 1.00
ACGTcount: A:0.40, C:0.14, G:0.24, T:0.22
Consensus pattern (46 bp):
CTGATATGAAATGAGTAAGACCATGGTTGAAAGATACCATGGCAAC
Found at i:17800367 original size:13 final size:13
Alignment explanation
Indices: 17800349--17800380 Score: 55
Period size: 13 Copynumber: 2.5 Consensus size: 13
17800339 ATAACAACAA
17800349 TCAATTCAATTTC
1 TCAATTCAATTTC
17800362 TCAATTCAATTTC
1 TCAATTCAATTTC
*
17800375 TAAATT
1 TCAATT
17800381 ACTTTTCAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.34, C:0.19, G:0.00, T:0.47
Consensus pattern (13 bp):
TCAATTCAATTTC
Found at i:17807562 original size:14 final size:14
Alignment explanation
Indices: 17807543--17807572 Score: 60
Period size: 14 Copynumber: 2.1 Consensus size: 14
17807533 GTATTGATAC
17807543 TTTACCCCTTTAGA
1 TTTACCCCTTTAGA
17807557 TTTACCCCTTTAGA
1 TTTACCCCTTTAGA
17807571 TT
1 TT
17807573 AGGTTGTGAC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.20, C:0.27, G:0.07, T:0.47
Consensus pattern (14 bp):
TTTACCCCTTTAGA
Found at i:17809044 original size:17 final size:17
Alignment explanation
Indices: 17809022--17809054 Score: 66
Period size: 17 Copynumber: 1.9 Consensus size: 17
17809012 GCCCTATTTT
17809022 CAAATTTTATTTTTTGA
1 CAAATTTTATTTTTTGA
17809039 CAAATTTTATTTTTTG
1 CAAATTTTATTTTTTG
17809055 GTGACCAAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.27, C:0.06, G:0.06, T:0.61
Consensus pattern (17 bp):
CAAATTTTATTTTTTGA
Found at i:17809380 original size:108 final size:108
Alignment explanation
Indices: 17809187--17809508 Score: 527
Period size: 108 Copynumber: 3.0 Consensus size: 108
17809177 ACTATCTAAA
* *
17809187 AAAATGCAAAAATTGTCTCCGGTAGTGATTTATGGCCACCATGCTCTGTCATGCCAATCATCAAC
1 AAAATGCAAAAATTGTCTCCGATAGTGA-TTATGACCACCATGCTCTGTCATGCCAATCATCAAC
*
17809252 TCAAGTTCAAGCTTCGTCTATTTAAAGTTCTCATGGTTCTAGGG
65 TCAAGTTCAAGCTTCATCTATTTAAAGTTCTCATGGTTCTAGGG
* * *
17809296 AAAATGCAAAAATTGTCTCTGATAGTGAGTATGACCACCATGCTTTGTCATGCCAATCATCAACT
1 AAAATGCAAAAATTGTCTCCGATAGTGATTATGACCACCATGCTCTGTCATGCCAATCATCAACT
* *
17809361 CAAGTTCAAGCTTCTTCTATTTAAAGTTCTCATTGTTCTAGGG
66 CAAGTTCAAGCTTCATCTATTTAAAGTTCTCATGGTTCTAGGG
* *
17809404 TAAATGTAAAAATTGTCTCCGATAGTGATTATGACCACCATGCTCTGTCATGCCAATCATCAACT
1 AAAATGCAAAAATTGTCTCCGATAGTGATTATGACCACCATGCTCTGTCATGCCAATCATCAACT
* *
17809469 CAAGTTCATGCTTCATCTATTTAAAGTTTTCATGGTTCTA
66 CAAGTTCAAGCTTCATCTATTTAAAGTTCTCATGGTTCTA
17809509 CAACCAATTA
Statistics
Matches: 197, Mismatches: 16, Indels: 1
0.92 0.07 0.00
Matches are distributed among these distances:
108 171 0.87
109 26 0.13
ACGTcount: A:0.29, C:0.21, G:0.16, T:0.34
Consensus pattern (108 bp):
AAAATGCAAAAATTGTCTCCGATAGTGATTATGACCACCATGCTCTGTCATGCCAATCATCAACT
CAAGTTCAAGCTTCATCTATTTAAAGTTCTCATGGTTCTAGGG
Found at i:17815864 original size:33 final size:33
Alignment explanation
Indices: 17815826--17815968 Score: 110
Period size: 33 Copynumber: 4.3 Consensus size: 33
17815816 AATTGACGGA
* * *
17815826 TAAGACCATGGCTGGGCCATGGCAATATAAGTG
1 TAAGACCATAGCTAGGCCATGGCAATACAAGTG
* * **
17815859 TAAGACCATAGCTAAGCTATGGC-AT-CCTGATG
1 TAAGACCATAGCTAGGCCATGGCAATACAAG-TG
* ** ** *
17815891 ATAAGACCATATCTAGGATATGGCACCACGAGTG
1 -TAAGACCATAGCTAGGCCATGGCAATACAAGTG
* * *
17815925 TAAGACCATGGCTGGGCCATGGCAATACACGTG
1 TAAGACCATAGCTAGGCCATGGCAATACAAGTG
17815958 TAAGACCATAG
1 TAAGACCATAG
17815969 TTAGACTATG
Statistics
Matches: 82, Mismatches: 24, Indels: 8
0.72 0.21 0.07
Matches are distributed among these distances:
31 1 0.01
32 4 0.05
33 73 0.89
34 2 0.02
35 2 0.02
ACGTcount: A:0.32, C:0.21, G:0.26, T:0.21
Consensus pattern (33 bp):
TAAGACCATAGCTAGGCCATGGCAATACAAGTG
Found at i:17816094 original size:91 final size:92
Alignment explanation
Indices: 17815986--17816163 Score: 214
Period size: 91 Copynumber: 1.9 Consensus size: 92
17815976 ATGGCATCAT
* * * * ** *
17815986 ACAAAAAATGAGTAAGACCATAGCTGAAAGACGCTATGGCATCACGAT-TCAAATGTGTAAGACC
1 ACAAAAAATGAATAAGACCATAGCTGAAAGACACCATGGCAACACGATAGAAAATGAGTAAGACC
* *
17816050 ATGGTTGAAAGATACAATGGCAATGTG
66 ATAGTTGAAAGACACAATGGCAATGTG
* * * * *
17816077 ACAAGAAATGAATAAGACCATGGTTGAAAGATACCATGGCAACATGATAGAAAATGAGTAAGACC
1 ACAAAAAATGAATAAGACCATAGCTGAAAGACACCATGGCAACACGATAGAAAATGAGTAAGACC
*
17816142 ATAGTTGAAAGACACTATGGCA
66 ATAGTTGAAAGACACAATGGCA
17816164 TCATGTCAAA
Statistics
Matches: 71, Mismatches: 15, Indels: 1
0.82 0.17 0.01
Matches are distributed among these distances:
91 39 0.55
92 32 0.45
ACGTcount: A:0.43, C:0.15, G:0.22, T:0.20
Consensus pattern (92 bp):
ACAAAAAATGAATAAGACCATAGCTGAAAGACACCATGGCAACACGATAGAAAATGAGTAAGACC
ATAGTTGAAAGACACAATGGCAATGTG
Found at i:17816096 original size:46 final size:46
Alignment explanation
Indices: 17816043--17816168 Score: 155
Period size: 46 Copynumber: 2.7 Consensus size: 46
17816033 TTCAAATGTG
**
17816043 TAAGACCATGGTTGAAAGATACAATGGCAATGTGACAAG-AAATGAA
1 TAAGACCATGGTTGAAAGATACAATGGCAACATGA-AAGAAAATGAA
* * *
17816089 TAAGACCATGGTTGAAAGATACCATGGCAACATGATAGAAAATGAG
1 TAAGACCATGGTTGAAAGATACAATGGCAACATGAAAGAAAATGAA
* * * *
17816135 TAAGACCATAGTTGAAAGACACTATGGCATCATG
1 TAAGACCATGGTTGAAAGATACAATGGCAACATG
17816169 TCAAAGATAA
Statistics
Matches: 70, Mismatches: 9, Indels: 2
0.86 0.11 0.02
Matches are distributed among these distances:
45 2 0.03
46 68 0.97
ACGTcount: A:0.43, C:0.13, G:0.23, T:0.21
Consensus pattern (46 bp):
TAAGACCATGGTTGAAAGATACAATGGCAACATGAAAGAAAATGAA
Found at i:17819322 original size:20 final size:18
Alignment explanation
Indices: 17819297--17819333 Score: 56
Period size: 20 Copynumber: 1.9 Consensus size: 18
17819287 AATCACATTA
17819297 ATATTACATATTCCAATTTC
1 ATATTACAT-TT-CAATTTC
17819317 ATATTACATTTCAATTT
1 ATATTACATTTCAATTT
17819334 TCACACTATA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 6 0.35
19 2 0.12
20 9 0.53
ACGTcount: A:0.35, C:0.16, G:0.00, T:0.49
Consensus pattern (18 bp):
ATATTACATTTCAATTTC
Found at i:17819892 original size:7 final size:7
Alignment explanation
Indices: 17819843--17819907 Score: 57
Period size: 7 Copynumber: 9.6 Consensus size: 7
17819833 TTTTAATTAT
17819843 TATAATA
1 TATAATA
17819850 -ATAA-A
1 TATAATA
17819855 TATATATA
1 TATA-ATA
* *
17819863 CATTAATG
1 TA-TAATA
17819871 T-TAATA
1 TATAATA
*
17819877 CAT-ATA
1 TATAATA
17819883 TATAATA
1 TATAATA
17819890 TATAATA
1 TATAATA
17819897 TATAATA
1 TATAATA
17819904 TATA
1 TATA
17819908 CATGCATTTT
Statistics
Matches: 46, Mismatches: 6, Indels: 12
0.72 0.09 0.19
Matches are distributed among these distances:
5 1 0.02
6 16 0.35
7 23 0.50
8 4 0.09
9 2 0.04
ACGTcount: A:0.54, C:0.03, G:0.02, T:0.42
Consensus pattern (7 bp):
TATAATA
Found at i:17820224 original size:9 final size:9
Alignment explanation
Indices: 17820212--17820243 Score: 50
Period size: 9 Copynumber: 3.8 Consensus size: 9
17820202 TCCTTTCTCC
17820212 CTTTCTTTT
1 CTTTCTTTT
17820221 C-TT-TTTT
1 CTTTCTTTT
17820228 CTTTCTTTT
1 CTTTCTTTT
17820237 CTTTCTT
1 CTTTCTT
17820244 AATTTTTCAT
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
7 5 0.24
8 4 0.19
9 12 0.57
ACGTcount: A:0.00, C:0.22, G:0.00, T:0.78
Consensus pattern (9 bp):
CTTTCTTTT
Found at i:17820356 original size:7 final size:7
Alignment explanation
Indices: 17820344--17820374 Score: 62
Period size: 7 Copynumber: 4.4 Consensus size: 7
17820334 GTTAATACAT
17820344 ATATATA
1 ATATATA
17820351 ATATATA
1 ATATATA
17820358 ATATATA
1 ATATATA
17820365 ATATATA
1 ATATATA
17820372 ATA
1 ATA
17820375 CATACATGCA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 24 1.00
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (7 bp):
ATATATA
Found at i:17827466 original size:18 final size:18
Alignment explanation
Indices: 17827443--17827491 Score: 80
Period size: 18 Copynumber: 2.7 Consensus size: 18
17827433 TTTAACAGTC
*
17827443 AATTATTCAGTAATGATA
1 AATTATTCAGTAATAATA
*
17827461 AATTATTCAGTAATAATC
1 AATTATTCAGTAATAATA
17827479 AATTATTCAGTAA
1 AATTATTCAGTAA
17827492 CATTTTTTTA
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 29 1.00
ACGTcount: A:0.45, C:0.08, G:0.08, T:0.39
Consensus pattern (18 bp):
AATTATTCAGTAATAATA
Found at i:17827526 original size:18 final size:18
Alignment explanation
Indices: 17827505--17827549 Score: 54
Period size: 18 Copynumber: 2.5 Consensus size: 18
17827495 TTTTTTACGT
17827505 AGTAGCAGTCAGTTATCC
1 AGTAGCAGTCAGTTATCC
* * *
17827523 AGTAACAATCAGTTATTC
1 AGTAGCAGTCAGTTATCC
*
17827541 ATTAGCAGT
1 AGTAGCAGT
17827550 TAATTATTCA
Statistics
Matches: 21, Mismatches: 6, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.33, C:0.18, G:0.18, T:0.31
Consensus pattern (18 bp):
AGTAGCAGTCAGTTATCC
Found at i:17827741 original size:54 final size:51
Alignment explanation
Indices: 17827676--17827793 Score: 137
Period size: 51 Copynumber: 2.3 Consensus size: 51
17827666 TCGTAACGGT
* *
17827676 AACAGTAACAGTAACAATAGCGGTACACAAAGTACCTCATCGGAACAAATTCGA
1 AACAGTAACAGTAACAATA-AGGT--ACAAAGTACCTCATCGGAACAAATCCGA
* ** * * *
17827730 AACAGTAACAGTAACAGTAAGGTACGGAGTACCTCTTCGGAACGAATCCGG
1 AACAGTAACAGTAACAATAAGGTACAAAGTACCTCATCGGAACAAATCCGA
17827781 AACAGTAACAGTA
1 AACAGTAACAGTA
17827794 GCAGTAAGAC
Statistics
Matches: 56, Mismatches: 8, Indels: 3
0.84 0.12 0.04
Matches are distributed among these distances:
51 35 0.62
53 3 0.05
54 18 0.32
ACGTcount: A:0.42, C:0.21, G:0.20, T:0.17
Consensus pattern (51 bp):
AACAGTAACAGTAACAATAAGGTACAAAGTACCTCATCGGAACAAATCCGA
Found at i:17828814 original size:20 final size:19
Alignment explanation
Indices: 17828780--17828820 Score: 55
Period size: 20 Copynumber: 2.1 Consensus size: 19
17828770 CAAACCCTAA
* *
17828780 TTCTCCCTTTTTCTTTTCT
1 TTCTCCCTCTTTCTTTCCT
17828799 TTCTCCTCTCTTTCTTTCCT
1 TTCTCC-CTCTTTCTTTCCT
17828819 TT
1 TT
17828821 TCGTTTGCCT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
19 6 0.32
20 13 0.68
ACGTcount: A:0.00, C:0.34, G:0.00, T:0.66
Consensus pattern (19 bp):
TTCTCCCTCTTTCTTTCCT
Found at i:17828875 original size:18 final size:18
Alignment explanation
Indices: 17828837--17828875 Score: 53
Period size: 19 Copynumber: 2.2 Consensus size: 18
17828827 GCCTATTCTG
*
17828837 TTTCTTTTCTTTGTTTCA
1 TTTCTTTTCTTTCTTTCA
17828855 TTTCTTTTTCTTTCTTT-A
1 TTTC-TTTTCTTTCTTTCA
17828873 TTT
1 TTT
17828876 ACTATATATA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
18 8 0.42
19 11 0.58
ACGTcount: A:0.05, C:0.15, G:0.03, T:0.77
Consensus pattern (18 bp):
TTTCTTTTCTTTCTTTCA
Found at i:17838451 original size:18 final size:18
Alignment explanation
Indices: 17838410--17838452 Score: 50
Period size: 18 Copynumber: 2.4 Consensus size: 18
17838400 TTCTTAATAA
*
17838410 ATATGTAGTTTATATAGT
1 ATATGTTGTTTATATAGT
* * *
17838428 AAATGTTGTTTATTTATT
1 ATATGTTGTTTATATAGT
17838446 ATATGTT
1 ATATGTT
17838453 TGAATTAACA
Statistics
Matches: 20, Mismatches: 5, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.30, C:0.00, G:0.14, T:0.56
Consensus pattern (18 bp):
ATATGTTGTTTATATAGT
Found at i:17839641 original size:12 final size:12
Alignment explanation
Indices: 17839624--17839648 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
17839614 AATGGTGGAC
17839624 ATGAAGATAAAG
1 ATGAAGATAAAG
17839636 ATGAAGATAAAG
1 ATGAAGATAAAG
17839648 A
1 A
17839649 CGACAGTGGA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.60, C:0.00, G:0.24, T:0.16
Consensus pattern (12 bp):
ATGAAGATAAAG
Done.