Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr10
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: 48586650
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 2183483 characters in sequence are not A, C, G, or T
File 103 of 145
Found at i:34446310 original size:15 final size:16
Alignment explanation
Indices: 34446290--34446321 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
34446280 TTTAATTGAA
34446290 AGAGAAG-AGAAAAAG
1 AGAGAAGAAGAAAAAG
34446305 AGAGAAGAAGAAAAAG
1 AGAGAAGAAGAAAAAG
34446321 A
1 A
34446322 AAAAAACAGT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 7 0.44
16 9 0.56
ACGTcount: A:0.69, C:0.00, G:0.31, T:0.00
Consensus pattern (16 bp):
AGAGAAGAAGAAAAAG
Found at i:34453099 original size:15 final size:17
Alignment explanation
Indices: 34453060--34453101 Score: 52
Period size: 15 Copynumber: 2.5 Consensus size: 17
34453050 AGTACCCTTA
*
34453060 AATACATAATCAATTTC
1 AATAAATAATCAATTTC
34453077 AGATAAATAAT-AATTT-
1 A-ATAAATAATCAATTTC
34453093 AATAAATAA
1 AATAAATAA
34453102 ATTAGTTTAT
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
15 8 0.35
16 1 0.04
17 6 0.26
18 8 0.35
ACGTcount: A:0.57, C:0.07, G:0.02, T:0.33
Consensus pattern (17 bp):
AATAAATAATCAATTTC
Found at i:34455941 original size:18 final size:18
Alignment explanation
Indices: 34455918--34455952 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
34455908 GTTTTTGGAT
34455918 AAATTTTGTAA-AATTTTG
1 AAATTTT-TAAGAATTTTG
34455936 AAATTTTTAAGAATTTT
1 AAATTTTTAAGAATTTT
34455953 CCCAAAACAT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 3 0.19
18 13 0.81
ACGTcount: A:0.40, C:0.00, G:0.09, T:0.51
Consensus pattern (18 bp):
AAATTTTTAAGAATTTTG
Found at i:34459742 original size:23 final size:21
Alignment explanation
Indices: 34459679--34459746 Score: 66
Period size: 22 Copynumber: 3.1 Consensus size: 21
34459669 AATTCGGTTG
*
34459679 TTATGGATGACGATAATCAAT
1 TTATGCATGACGATAATCAAT
* *
34459700 TTCT-CATGGTCGGATAATCAAT
1 TTATGCAT-GAC-GATAATCAAT
34459722 CCTTATGCATGACGATAATCAAT
1 --TTATGCATGACGATAATCAAT
34459745 TT
1 TT
34459747 GGTTGTTATG
Statistics
Matches: 37, Mismatches: 5, Indels: 10
0.71 0.10 0.19
Matches are distributed among these distances:
20 2 0.05
21 7 0.19
22 10 0.27
23 10 0.27
24 5 0.14
25 3 0.08
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.35
Consensus pattern (21 bp):
TTATGCATGACGATAATCAAT
Found at i:34459905 original size:22 final size:21
Alignment explanation
Indices: 34459880--34459920 Score: 55
Period size: 22 Copynumber: 1.9 Consensus size: 21
34459870 AATATATAAA
* *
34459880 TATAATATTAATATATAAATTG
1 TATAAAATTAAAATA-AAATTG
34459902 TATAAAATTAAAATAAAAT
1 TATAAAATTAAAATAAAAT
34459921 AAAGTAATAA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 4 0.24
22 13 0.76
ACGTcount: A:0.59, C:0.00, G:0.02, T:0.39
Consensus pattern (21 bp):
TATAAAATTAAAATAAAATTG
Found at i:34462600 original size:19 final size:19
Alignment explanation
Indices: 34462576--34462613 Score: 67
Period size: 19 Copynumber: 2.0 Consensus size: 19
34462566 AAAGTTAATA
*
34462576 ACAAATTTGATTACGGTGG
1 ACAAATTTGACTACGGTGG
34462595 ACAAATTTGACTACGGTGG
1 ACAAATTTGACTACGGTGG
34462614 GTGACAATGA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.32, C:0.13, G:0.26, T:0.29
Consensus pattern (19 bp):
ACAAATTTGACTACGGTGG
Found at i:34467266 original size:19 final size:19
Alignment explanation
Indices: 34467243--34467293 Score: 66
Period size: 19 Copynumber: 2.7 Consensus size: 19
34467233 TGCACACACG
* *
34467243 ATTCCACTAATCTCACATA
1 ATTCCACTAATCACACAGA
* *
34467262 GTTCCACTAATCAGACAGA
1 ATTCCACTAATCACACAGA
34467281 ATTCCACTAATCA
1 ATTCCACTAATCA
34467294 AACATCATTA
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
19 27 1.00
ACGTcount: A:0.37, C:0.29, G:0.06, T:0.27
Consensus pattern (19 bp):
ATTCCACTAATCACACAGA
Found at i:34468629 original size:38 final size:38
Alignment explanation
Indices: 34468561--34468677 Score: 153
Period size: 38 Copynumber: 3.1 Consensus size: 38
34468551 AACTTTTAAT
* * * *
34468561 ACACCAGCACTAAGCTTGCTAGGCACAAAGCCCGAATA
1 ACACCGGCACCAAGCCTGCTAGGCACAAAGCCTGAATA
* * * *
34468599 ACACTGGCACCAAGCCTGCTAGTCATAAAGCCTGAACA
1 ACACCGGCACCAAGCCTGCTAGGCACAAAGCCTGAATA
*
34468637 ACACCGGCACCAAGCCTGCTAGGCACAAAGCTTGAATA
1 ACACCGGCACCAAGCCTGCTAGGCACAAAGCCTGAATA
34468675 ACA
1 ACA
34468678 ATATAATTCA
Statistics
Matches: 66, Mismatches: 13, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
38 66 1.00
ACGTcount: A:0.36, C:0.32, G:0.19, T:0.14
Consensus pattern (38 bp):
ACACCGGCACCAAGCCTGCTAGGCACAAAGCCTGAATA
Found at i:34470329 original size:18 final size:18
Alignment explanation
Indices: 34470306--34470366 Score: 63
Period size: 18 Copynumber: 3.3 Consensus size: 18
34470296 TTCATGGTGG
34470306 AAGAAAGAAGAAAATAAA
1 AAGAAAGAAGAAAATAAA
*
34470324 AAGAAAGAAGAGAGATAAA
1 AAGAAAGAAGA-AAATAAA
*
34470343 AA-AAAGGAAGGAAAA-GAA
1 AAGAAA-GAA-GAAAATAAA
34470361 AAGAAA
1 AAGAAA
34470367 TGTAGTTTTT
Statistics
Matches: 36, Mismatches: 3, Indels: 7
0.78 0.07 0.15
Matches are distributed among these distances:
18 18 0.50
19 16 0.44
20 2 0.06
ACGTcount: A:0.74, C:0.00, G:0.23, T:0.03
Consensus pattern (18 bp):
AAGAAAGAAGAAAATAAA
Found at i:34470748 original size:19 final size:21
Alignment explanation
Indices: 34470718--34470761 Score: 65
Period size: 20 Copynumber: 2.2 Consensus size: 21
34470708 TCAAATAATG
34470718 TTTTTTCAATTTTTCGAT-TA
1 TTTTTTCAATTTTTCGATATA
*
34470738 TTTTTTC-ATTTTTTGATATA
1 TTTTTTCAATTTTTCGATATA
34470758 TTTT
1 TTTT
34470762 AAAATTAAAT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
19 9 0.41
20 13 0.59
ACGTcount: A:0.18, C:0.07, G:0.05, T:0.70
Consensus pattern (21 bp):
TTTTTTCAATTTTTCGATATA
Found at i:34471452 original size:12 final size:12
Alignment explanation
Indices: 34471435--34471463 Score: 58
Period size: 12 Copynumber: 2.4 Consensus size: 12
34471425 TAAACTTGAA
34471435 TTATTAATTAAC
1 TTATTAATTAAC
34471447 TTATTAATTAAC
1 TTATTAATTAAC
34471459 TTATT
1 TTATT
34471464 TAGGTCCCAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.38, C:0.07, G:0.00, T:0.55
Consensus pattern (12 bp):
TTATTAATTAAC
Found at i:34476962 original size:21 final size:21
Alignment explanation
Indices: 34476938--34476993 Score: 53
Period size: 20 Copynumber: 2.7 Consensus size: 21
34476928 CTGAACAATT
*
34476938 AAGAAAAAGA-GAAATACAAAA
1 AAGAAAAAGATCAAAT-CAAAA
*
34476959 AAG-AATAGATCAAATCAAAA
1 AAGAAAAAGATCAAATCAAAA
*
34476979 AAGAAATAGAATCAA
1 AAGAAAAAG-ATCAA
34476994 CGATTTGCTC
Statistics
Matches: 30, Mismatches: 2, Indels: 5
0.81 0.05 0.14
Matches are distributed among these distances:
20 13 0.43
21 12 0.40
22 5 0.17
ACGTcount: A:0.70, C:0.07, G:0.12, T:0.11
Consensus pattern (21 bp):
AAGAAAAAGATCAAATCAAAA
Found at i:34476979 original size:20 final size:23
Alignment explanation
Indices: 34476949--34476993 Score: 69
Period size: 21 Copynumber: 2.1 Consensus size: 23
34476939 AGAAAAAGAG
34476949 AAATACAAAAAAG-AATAG-ATC
1 AAATACAAAAAAGAAATAGAATC
34476970 AAAT-CAAAAAAGAAATAGAATC
1 AAATACAAAAAAGAAATAGAATC
34476992 AA
1 AA
34476994 CGATTTGCTC
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
20 8 0.36
21 9 0.41
22 5 0.23
ACGTcount: A:0.69, C:0.09, G:0.09, T:0.13
Consensus pattern (23 bp):
AAATACAAAAAAGAAATAGAATC
Found at i:34479601 original size:35 final size:34
Alignment explanation
Indices: 34479555--34479750 Score: 257
Period size: 35 Copynumber: 5.7 Consensus size: 34
34479545 AAATGATACA
*
34479555 TGAACAGGAGAGATTCCCTGCAACAACATAATGCG
1 TGAACAGGAGAGATTCCCTGCAACAA-ATAATGTG
* * * *
34479590 TGAACAGGAGAGATTCCCTACAAGAAATGATGTA
1 TGAACAGGAGAGATTCCCTGCAACAAATAATGTG
*
34479624 TGAACAGGAGAGTTTCCCTGCAACAAAATAATGTG
1 TGAACAGGAGAGATTCCCTGCAAC-AAATAATGTG
* * *
34479659 TGAACAGGAGAGATTCCCTACAAGAAATGATGTG
1 TGAACAGGAGAGATTCCCTGCAACAAATAATGTG
*
34479693 TGAACAGGAGAGATTCCCTGCAACAAAATAATGCG
1 TGAACAGGAGAGATTCCCTGCAAC-AAATAATGTG
* *
34479728 TGAACAGGAAATATTCCCTGCAA
1 TGAACAGGAGAGATTCCCTGCAA
34479751 GAAAAGACAA
Statistics
Matches: 139, Mismatches: 20, Indels: 4
0.85 0.12 0.02
Matches are distributed among these distances:
34 57 0.41
35 82 0.59
ACGTcount: A:0.39, C:0.18, G:0.23, T:0.20
Consensus pattern (34 bp):
TGAACAGGAGAGATTCCCTGCAACAAATAATGTG
Found at i:34479655 original size:69 final size:69
Alignment explanation
Indices: 34479542--34479754 Score: 345
Period size: 69 Copynumber: 3.1 Consensus size: 69
34479532 CAGGTCCAAA
** *
34479542 AAGAAATGATACATGAACAGGAGAGATTCCCTGCAACAACATAATGCGTGAACAGGAGAGATTCC
1 AAGAAATGATGTATGAACAGGAGAGATTCCCTGCAACAAAATAATGCGTGAACAGGAGAGATTCC
34479607 CTAC
66 CTAC
* *
34479611 AAGAAATGATGTATGAACAGGAGAGTTTCCCTGCAACAAAATAATGTGTGAACAGGAGAGATTCC
1 AAGAAATGATGTATGAACAGGAGAGATTCCCTGCAACAAAATAATGCGTGAACAGGAGAGATTCC
34479676 CTAC
66 CTAC
* * *
34479680 AAGAAATGATGTGTGAACAGGAGAGATTCCCTGCAACAAAATAATGCGTGAACAGGAAATATTCC
1 AAGAAATGATGTATGAACAGGAGAGATTCCCTGCAACAAAATAATGCGTGAACAGGAGAGATTCC
*
34479745 CTGC
66 CTAC
34479749 AAGAAA
1 AAGAAA
34479755 AGACAAGTGA
Statistics
Matches: 133, Mismatches: 11, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
69 133 1.00
ACGTcount: A:0.41, C:0.17, G:0.23, T:0.19
Consensus pattern (69 bp):
AAGAAATGATGTATGAACAGGAGAGATTCCCTGCAACAAAATAATGCGTGAACAGGAGAGATTCC
CTAC
Found at i:34480030 original size:13 final size:13
Alignment explanation
Indices: 34480012--34480050 Score: 51
Period size: 15 Copynumber: 2.8 Consensus size: 13
34480002 AGTTTTCAAA
34480012 TTTTCAAATTAAG
1 TTTTCAAATTAAG
34480025 TTTTCAAAACTTAAG
1 TTTTC-AAA-TTAAG
*
34480040 CTTTCAAATTA
1 TTTTCAAATTA
34480051 CAAATATATC
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
13 8 0.35
14 6 0.26
15 9 0.39
ACGTcount: A:0.38, C:0.13, G:0.05, T:0.44
Consensus pattern (13 bp):
TTTTCAAATTAAG
Found at i:34485942 original size:20 final size:20
Alignment explanation
Indices: 34485917--34485954 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
34485907 GGGAACAATT
*
34485917 TTTCAATCGATTTAAAAATG
1 TTTCAATCGACTTAAAAATG
*
34485937 TTTCAATTGACTTAAAAA
1 TTTCAATCGACTTAAAAA
34485955 ATTTTAAACC
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.42, C:0.11, G:0.08, T:0.39
Consensus pattern (20 bp):
TTTCAATCGACTTAAAAATG
Found at i:34486326 original size:14 final size:15
Alignment explanation
Indices: 34486298--34486328 Score: 55
Period size: 14 Copynumber: 2.1 Consensus size: 15
34486288 TAGGTGTTGA
34486298 CATTAAAATATTAAT
1 CATTAAAATATTAAT
34486313 CATTAAAA-ATTAAT
1 CATTAAAATATTAAT
34486327 CA
1 CA
34486329 ACCAAATACC
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 8 0.50
15 8 0.50
ACGTcount: A:0.55, C:0.10, G:0.00, T:0.35
Consensus pattern (15 bp):
CATTAAAATATTAAT
Found at i:34493704 original size:25 final size:25
Alignment explanation
Indices: 34493651--34493722 Score: 76
Period size: 25 Copynumber: 2.8 Consensus size: 25
34493641 AAGCTCTTTC
* *
34493651 GAGCCATATAACAGGAAG-TTCATGT
1 GAGCCAT-TAACAGGAAGCTCCATGA
34493676 GAGCCATGTAACAGGAAGCTCCA-GA
1 GAGCCAT-TAACAGGAAGCTCCATGA
*
34493701 GAGCCATTAATCGGGAAGCTCC
1 GAGCCATTAA-CAGGAAGCTCC
34493723 TGAAAGAGCC
Statistics
Matches: 41, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
24 3 0.07
25 35 0.85
26 3 0.07
ACGTcount: A:0.33, C:0.22, G:0.26, T:0.18
Consensus pattern (25 bp):
GAGCCATTAACAGGAAGCTCCATGA
Found at i:34493871 original size:25 final size:26
Alignment explanation
Indices: 34493676--34493876 Score: 89
Period size: 25 Copynumber: 7.8 Consensus size: 26
34493666 AAGTTCATGT
* * *
34493676 GAGCCATGTAA-CAGGAAGCTCCAGA
1 GAGCCATATAATCGGGAAGCTCCAAA
34493701 GAGCCAT-TAATCGGGAAGCTCCTGAAA
1 GAGCCATATAATCGGGAAGCTCC--AAA
* * * *
34493728 GAGCC-TTTAATTGGGAAGGTTCAAA
1 GAGCCATATAATCGGGAAGCTCCAAA
* * * * *
34493753 CGAACCA-AT-ATCGGAAAGGTTCAAGT
1 -GAGCCATATAATCGGGAAGCTCCAA-A
** *
34493779 GAGCCA-AT-ATTAGGAAGCTCCAGA
1 GAGCCATATAATCGGGAAGCTCCAAA
*
34493803 GAGCCA-ATTAATCGGGAAGCTCATGAAA
1 GAGCCATA-TAATCGGGAAGCTC--CAAA
* * *
34493831 AAGCC-TTTAATTGGGAAGCTCCAAA
1 GAGCCATATAATCGGGAAGCTCCAAA
*
34493856 GAGCCATAT-ATCGGGACGCTC
1 GAGCCATATAATCGGGAAGCTC
34493877 ATTAGAGTTG
Statistics
Matches: 133, Mismatches: 30, Indels: 26
0.70 0.16 0.14
Matches are distributed among these distances:
24 10 0.08
25 67 0.50
26 18 0.14
27 32 0.24
28 6 0.05
ACGTcount: A:0.35, C:0.20, G:0.25, T:0.19
Consensus pattern (26 bp):
GAGCCATATAATCGGGAAGCTCCAAA
Found at i:34505240 original size:25 final size:24
Alignment explanation
Indices: 34505212--34505269 Score: 71
Period size: 25 Copynumber: 2.3 Consensus size: 24
34505202 ACATAAATGG
*
34505212 GAAGCTCTTTCGAGCCATATAACGA
1 GAAGCTCTGT-GAGCCATATAACGA
* *
34505237 GAAGCTCATGTGAGCCATGTAACGG
1 GAAGCTC-TGTGAGCCATATAACGA
34505262 GAAGCTCT
1 GAAGCTCT
34505270 AGAGAACCGT
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
24 1 0.03
25 26 0.90
26 2 0.07
ACGTcount: A:0.29, C:0.22, G:0.26, T:0.22
Consensus pattern (24 bp):
GAAGCTCTGTGAGCCATATAACGA
Found at i:34505338 original size:25 final size:25
Alignment explanation
Indices: 34505309--34505366 Score: 89
Period size: 25 Copynumber: 2.3 Consensus size: 25
34505299 AGAGCCTTTA
34505309 ATCGGGAAGGTTCAAACGAACCAAT
1 ATCGGGAAGGTTCAAACGAACCAAT
* * *
34505334 ATCGGAAAGGTTCAAGCGAGCCAAT
1 ATCGGGAAGGTTCAAACGAACCAAT
34505359 ATCGGGAA
1 ATCGGGAA
34505367 ACTCATGAAA
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
25 29 1.00
ACGTcount: A:0.38, C:0.19, G:0.28, T:0.16
Consensus pattern (25 bp):
ATCGGGAAGGTTCAAACGAACCAAT
Found at i:34505414 original size:25 final size:27
Alignment explanation
Indices: 34505351--34505424 Score: 75
Period size: 25 Copynumber: 2.9 Consensus size: 27
34505341 AGGTTCAAGC
* *
34505351 GAGCCA-ATATCGGGAAACTCATGAAA
1 GAGCCATATATTGGGAAGCTCATGAAA
*
34505377 GAGCC-TTTAATTGGGAAGCTC-T-AAA
1 GAGCCATAT-ATTGGGAAGCTCATGAAA
*
34505402 GAGCCATATATTGGGACGCTCAT
1 GAGCCATATATTGGGAAGCTCAT
34505425 TAGAGTTGTG
Statistics
Matches: 39, Mismatches: 5, Indels: 8
0.75 0.10 0.15
Matches are distributed among these distances:
25 19 0.49
26 10 0.26
27 10 0.26
ACGTcount: A:0.34, C:0.19, G:0.24, T:0.23
Consensus pattern (27 bp):
GAGCCATATATTGGGAAGCTCATGAAA
Found at i:34511132 original size:33 final size:32
Alignment explanation
Indices: 34511079--34511140 Score: 97
Period size: 33 Copynumber: 1.9 Consensus size: 32
34511069 ATCAACACGC
*
34511079 TTTTATTTTAGCGACCAAATTAACCACTTTTT
1 TTTTATTTTAACGACCAAATTAACCACTTTTT
*
34511111 TTTTTTTTTAACGAACCAAATTAACCACTT
1 TTTTATTTTAACG-ACCAAATTAACCACTT
34511141 AAAATATGAC
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
32 11 0.41
33 16 0.59
ACGTcount: A:0.31, C:0.19, G:0.05, T:0.45
Consensus pattern (32 bp):
TTTTATTTTAACGACCAAATTAACCACTTTTT
Found at i:34511497 original size:24 final size:23
Alignment explanation
Indices: 34511452--34511507 Score: 62
Period size: 24 Copynumber: 2.5 Consensus size: 23
34511442 ATCACATATT
* *
34511452 TTAATAAAATAAGTTATATCAAA
1 TTAATAAAAAAAGTTACATCAAA
*
34511475 TTAATGAAAAAAAGTTACCTC-AA
1 TTAAT-AAAAAAAGTTACATCAAA
34511498 -TAATAAAAAA
1 TTAATAAAAAA
34511508 TATACACTTC
Statistics
Matches: 29, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
21 6 0.21
22 4 0.14
23 7 0.24
24 12 0.41
ACGTcount: A:0.59, C:0.07, G:0.05, T:0.29
Consensus pattern (23 bp):
TTAATAAAAAAAGTTACATCAAA
Found at i:34521085 original size:12 final size:12
Alignment explanation
Indices: 34521068--34521097 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
34521058 CCTCACATGC
34521068 CCATGTGCCAGG
1 CCATGTGCCAGG
*
34521080 CCATGTGCTAGG
1 CCATGTGCCAGG
34521092 CCATGT
1 CCATGT
34521098 AAAAGCCTGA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.17, C:0.30, G:0.30, T:0.23
Consensus pattern (12 bp):
CCATGTGCCAGG
Found at i:34522360 original size:25 final size:25
Alignment explanation
Indices: 34522322--34522414 Score: 80
Period size: 25 Copynumber: 3.7 Consensus size: 25
34522312 TCCTGTACAT
**
34522322 GTATGCTCAGACGAGCTATGAATCG
1 GTATGCTCTCACGAGCTATGAATCG
* * *
34522347 GTATGCTCTCACGAGCTGTAAATTG
1 GTATGCTCTCACGAGCTATGAATCG
* * *
34522372 GTAGGTTCAT-ACGAGCTGTGAATCG
1 GTATGCTC-TCACGAGCTATGAATCG
* *
34522397 GTAAGCTCTCATGAGCTA
1 GTATGCTCTCACGAGCTA
34522415 AAATCAGTAA
Statistics
Matches: 53, Mismatches: 13, Indels: 4
0.76 0.19 0.06
Matches are distributed among these distances:
24 1 0.02
25 51 0.96
26 1 0.02
ACGTcount: A:0.26, C:0.19, G:0.27, T:0.28
Consensus pattern (25 bp):
GTATGCTCTCACGAGCTATGAATCG
Found at i:34526294 original size:17 final size:18
Alignment explanation
Indices: 34526272--34526318 Score: 53
Period size: 17 Copynumber: 2.7 Consensus size: 18
34526262 TTATTTTTAT
34526272 ATATTTTTATATAATTA-
1 ATATTTTTATATAATTAC
* *
34526289 ATATTTTGATA-ATTTAC
1 ATATTTTTATATAATTAC
*
34526306 ATATTTATATATA
1 ATATTTTTATATA
34526319 TCGTAAATGC
Statistics
Matches: 24, Mismatches: 4, Indels: 3
0.77 0.13 0.10
Matches are distributed among these distances:
16 4 0.17
17 19 0.79
18 1 0.04
ACGTcount: A:0.40, C:0.02, G:0.02, T:0.55
Consensus pattern (18 bp):
ATATTTTTATATAATTAC
Found at i:34537962 original size:49 final size:50
Alignment explanation
Indices: 34537894--34537996 Score: 163
Period size: 51 Copynumber: 2.1 Consensus size: 50
34537884 TCTTATAGAG
* * *
34537894 AACATATGGAAAGTGTT-AAACACGTTATATTCTTTCCAAAAAGAATTAT
1 AACATATGGAAAGTATTAAAAAACATTATATTCTTTCCAAAAAGAATTAT
34537943 AACATATGGAAAGTATTAAAAAAACATTATATTCTTTCCAAAAAGAATTAT
1 AACATATGGAAAGTATT-AAAAAACATTATATTCTTTCCAAAAAGAATTAT
34537994 AAC
1 AAC
34537997 TATCATGTTT
Statistics
Matches: 49, Mismatches: 3, Indels: 2
0.91 0.06 0.04
Matches are distributed among these distances:
49 16 0.33
51 33 0.67
ACGTcount: A:0.48, C:0.12, G:0.10, T:0.31
Consensus pattern (50 bp):
AACATATGGAAAGTATTAAAAAACATTATATTCTTTCCAAAAAGAATTAT
Found at i:34540019 original size:17 final size:16
Alignment explanation
Indices: 34539999--34540041 Score: 59
Period size: 18 Copynumber: 2.6 Consensus size: 16
34539989 TTGGGTTGAG
34539999 AAAATAATTTAATTAGAA
1 AAAATAATTTAA-TA-AA
*
34540017 AAATTAATTTAATAAA
1 AAAATAATTTAATAAA
34540033 AAAATAATT
1 AAAATAATT
34540042 AACTAATATT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
16 10 0.43
17 2 0.09
18 11 0.48
ACGTcount: A:0.63, C:0.00, G:0.02, T:0.35
Consensus pattern (16 bp):
AAAATAATTTAATAAA
Found at i:34540026 original size:18 final size:15
Alignment explanation
Indices: 34539999--34540041 Score: 50
Period size: 17 Copynumber: 2.6 Consensus size: 15
34539989 TTGGGTTGAG
34539999 AAAATAATTTAATTAGA
1 AAAATAATTTAA-TA-A
34540016 AAAATTAATTTAATAAA
1 AAAA-TAATTTAAT-AA
34540033 AAAATAATT
1 AAAATAATT
34540042 AACTAATATT
Statistics
Matches: 24, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
16 5 0.21
17 10 0.42
18 9 0.38
ACGTcount: A:0.63, C:0.00, G:0.02, T:0.35
Consensus pattern (15 bp):
AAAATAATTTAATAA
Found at i:34554974 original size:21 final size:22
Alignment explanation
Indices: 34554956--34554998 Score: 63
Period size: 21 Copynumber: 2.0 Consensus size: 22
34554946 GCATTTAATT
34554956 AATT-TTTTAAAAAATTTAAAA
1 AATTATTTTAAAAAATTTAAAA
*
34554977 AATTATTTTTAAAAA-TTAAAA
1 AATTATTTTAAAAAATTTAAAA
34554998 A
1 A
34554999 CTATTAAAAT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
21 11 0.55
22 9 0.45
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (22 bp):
AATTATTTTAAAAAATTTAAAA
Found at i:34555013 original size:19 final size:19
Alignment explanation
Indices: 34554991--34555039 Score: 57
Period size: 19 Copynumber: 2.7 Consensus size: 19
34554981 ATTTTTAAAA
*
34554991 ATTAAAAACTATTAAAATT
1 ATTAAAAAATATTAAAATT
* *
34555010 ATTAAAAAGTA-TAAATTT
1 ATTAAAAAATATTAAAATT
34555028 A-TAAAAAATATT
1 ATTAAAAAATATT
34555040 TTGAATATTT
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
17 8 0.31
18 8 0.31
19 10 0.38
ACGTcount: A:0.59, C:0.02, G:0.02, T:0.37
Consensus pattern (19 bp):
ATTAAAAAATATTAAAATT
Found at i:34555158 original size:121 final size:122
Alignment explanation
Indices: 34555005--34555250 Score: 485
Period size: 121 Copynumber: 2.0 Consensus size: 122
34554995 AAAACTATTA
34555005 AAATTATTAAAAAGTATAAATTTATAAAAAATATTTTGAATATTTTTTAAATTAAAAAAATTAAT
1 AAATTATTAAAAAGTATAAATTTATAAAAAATATTTTGAATATTTTTTAAATTAAAAAAATTAAT
34555070 TAAATGTTAACATGTCATCCACATTAACAAAGTTGTCAAATGTTAATTTTTTCATCC
66 TAAATGTTAACATGTCATCCACATTAACAAAGTTGTCAAATGTTAATTTTTTCATCC
34555127 AAATTATTAAAAA-TATAAATTTATAAAAAATATTTTGAATATTTTTTAAATTAAAAAAATTAAT
1 AAATTATTAAAAAGTATAAATTTATAAAAAATATTTTGAATATTTTTTAAATTAAAAAAATTAAT
34555191 TAAATGTTAACATGTCATCCACATTAACAAAGTTGTCAAATGTTAATTTTTTCATCC
66 TAAATGTTAACATGTCATCCACATTAACAAAGTTGTCAAATGTTAATTTTTTCATCC
34555248 AAA
1 AAA
34555251 ATGATTTGAC
Statistics
Matches: 124, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
121 111 0.90
122 13 0.10
ACGTcount: A:0.47, C:0.08, G:0.05, T:0.40
Consensus pattern (122 bp):
AAATTATTAAAAAGTATAAATTTATAAAAAATATTTTGAATATTTTTTAAATTAAAAAAATTAAT
TAAATGTTAACATGTCATCCACATTAACAAAGTTGTCAAATGTTAATTTTTTCATCC
Found at i:34555299 original size:121 final size:118
Alignment explanation
Indices: 34555053--34555303 Score: 301
Period size: 121 Copynumber: 2.1 Consensus size: 118
34555043 AATATTTTTT
34555053 AAATTAAAAAAATTAATTAAATGTTAACATGTCATCCACATTAACAAAGTTGTCAAATGTTAATT
1 AAATTAAAAAAATTAATTAAATGTTAACATGTCATCCACATTAACAAAGTTGTCAAATGTTAATT
* * * * ******
34555118 TTTTCATCCAAATTATTAAAAATATAAATTTATAAAAAATATTTTGAATATTTTTT
66 TTTTCATCCAAATGATTAAAAATATAAAGTTATAAAAAATA---TAAAAAAAAAGA
34555174 AAATTAAAAAAATTAATTAAATGTTAACATGTCATCCACATTAACAAAGTTGTCAAATGTTAATT
1 AAATTAAAAAAATTAATTAAATGTTAACATGTCATCCACATTAACAAAGTTGTCAAATGTTAATT
*
34555239 TTTTCATCCAAAATGATTTGACAGAAA-ATACAAGTT-TAAAAACTA-AAAAAAAAAGA
66 TTTTCATCC-AAATGA-TT-A-A-AAATATA-AAGTTATAAAAAATATAAAAAAAAAGA
34555295 AAATTAAAA
1 AAATTAAAA
34555304 TGACTTTTTT
Statistics
Matches: 113, Mismatches: 11, Indels: 12
0.83 0.08 0.09
Matches are distributed among these distances:
121 86 0.76
122 5 0.04
123 2 0.02
124 1 0.01
125 12 0.11
126 7 0.06
ACGTcount: A:0.50, C:0.09, G:0.06, T:0.35
Consensus pattern (118 bp):
AAATTAAAAAAATTAATTAAATGTTAACATGTCATCCACATTAACAAAGTTGTCAAATGTTAATT
TTTTCATCCAAATGATTAAAAATATAAAGTTATAAAAAATATAAAAAAAAAGA
Found at i:34557489 original size:23 final size:23
Alignment explanation
Indices: 34557451--34557494 Score: 61
Period size: 23 Copynumber: 1.9 Consensus size: 23
34557441 ATTTTATCAA
*
34557451 ATTTTTGAAACATTTTCATTGAT
1 ATTTTTGAAACATTTTAATTGAT
* *
34557474 ATTTTTGAAGCTTTTTAATTG
1 ATTTTTGAAACATTTTAATTG
34557495 TAATTGGTTT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 18 1.00
ACGTcount: A:0.27, C:0.07, G:0.11, T:0.55
Consensus pattern (23 bp):
ATTTTTGAAACATTTTAATTGAT
Found at i:34562726 original size:325 final size:323
Alignment explanation
Indices: 34562124--34563085 Score: 1358
Period size: 325 Copynumber: 3.0 Consensus size: 323
34562114 TTTTTTAAAA
*
34562124 AATTGGTTAATAAAACAATTCATGGATTACATTAATATACTTTGTATAATTGTCCTCATGTGGTT
1 AATTGGTTAAT-AAACAATTCATGGATTACATTAATATACTTTGTATAATTGACCTCATGTGGTT
*
34562189 TTTGAATGCAAAGAAAAATAGAAAGAAATATTGGCTCATGATCTTTCGTAACTTGATACATCAAA
65 TTTGAATGCAAAGAAAAATAGAAAGAAATATTGGCTCATGATC-TTCGTAATTTGATACATCAAA
** *
34562254 TTAGGCTCTCTGTTACACTTGATGAGCTTATTCTCAATCAATTTAAATGTTTTTATCATGTTTTT
129 TTAGGCTCTCCATTACACTTGATGAGCTTATTCTCAAGCAATTTAAATGTTTTTATCATGTTTTT
* * * *
34562319 AGTTAGTTTTTGTTTTAATAAGTGAATTGGTGTGTTTTAAGCTATTTTTTATACCCGAATTGGCC
194 AGTTAGTTTTTGTTTTAATAAGTGAATTAGTGTGTTTTATG-TAATTTTTATACCTGAATTGGCC
* *
34562384 AAATGCGCCATAGGGAACCTAATGGTTGATTAAGTGTTGTAATGAGTCAATGGATTACAATAACA
258 AAATGCGCCATAGGGAACCTAACGGTTGATTAAGTGTTGTAAGGAGTCAATGGATTACAATAACA
34562449 T
323 T
* * *
34562450 AATTGGTTAATAGAGCAATTCATGGATTACATTAATATAC-TTGTATAATTGACCTCATATAGTT
1 AATTGGTTAATA-AACAATTCATGGATTACATTAATATACTTTGTATAATTGACCTCATGTGGTT
*
34562514 TTTGAATACAAAGAAAAATAG-AAGAAAATATTGGCTCATGATCTGTCGTAATTTGATACATCAA
65 TTTGAATGCAAAGAAAAATAGAAAG-AAATATTGGCTCATGATCT-TCGTAATTTGATACATCAA
*
34562578 ATTAGGCTCTCCATTACACTTGATGAGCTTATTCTCAAGCAATTTAAATGTTTTTATCGTGTTTT
128 ATTAGGCTCTCCATTACACTTGATGAGCTTATTCTCAAGCAATTTAAATGTTTTTATCATGTTTT
* * * * *
34562643 TAGTTGGTTTTTGTTTTAATAAGTGAACTAGTGTGTTTTATGATAATTTTGAAACCTAAATTGGC
193 TAGTTAGTTTTTGTTTTAATAAGTGAATTAGTGTGTTTTATG-TAATTTTTATACCTGAATTGGC
* * * * * ** * * * *
34562708 CAAATACGGCAAAGGGAACTTAACAGTTGATTAAGTACTATAGGGAGTCAATGGATTACATTAAT
257 CAAATGCGCCATAGGGAACCTAACGGTTGATTAAGTGTTGTAAGGAGTCAATGGATTACAATAAC
34562773 AT
322 AT
* * * ** *
34562775 AATTGGTTAATAACACAATTCACGAATTACA-TAATATACTTTGTATAATTGAACAAACGTGGTT
1 AATTGGTTAATAA-ACAATTCATGGATTACATTAATATACTTTGTATAATTGACCTCATGTGGTT
*
34562839 TTTGAATGCAAAGCAAAATAGAAAGAAATATTGGCTCATGATCTTCCGTAATTTGATACATCAAA
65 TTTGAATGCAAAGAAAAATAGAAAGAAATATTGGCTCATGATCTT-CGTAATTTGATACATCAAA
* * * * *
34562904 TTAGGCTCTCCATTACACTTTATGAGCTTATTTTCGAGCAATTTAACTG-TTTTATCATATTTTT
129 TTAGGCTCTCCATTACACTTGATGAGCTTATTCTCAAGCAATTTAAATGTTTTTATCATGTTTTT
* *
34562968 AGTTAGTTTTTATTTTAATAAGTGAATTAGTGTGTTTTATGTTATTCTTTATA-CTCGAATTGGC
194 AGTTAGTTTTTGTTTTAATAAGTGAATTAGTGTGTTTTATGTAATT-TTTATACCT-GAATTGGC
* *
34563032 CAAATGCGCCATACGAAACCTAACGGTTGATTAAGTGTTGTAAGGAGTCAATGG
257 CAAATGCGCCATAGGGAACCTAACGGTTGATTAAGTGTTGTAAGGAGTCAATGG
34563086 TGGCCCGAAC
Statistics
Matches: 559, Mismatches: 68, Indels: 20
0.86 0.11 0.03
Matches are distributed among these distances:
323 6 0.01
324 119 0.21
325 394 0.70
326 40 0.07
ACGTcount: A:0.33, C:0.12, G:0.17, T:0.38
Consensus pattern (323 bp):
AATTGGTTAATAAACAATTCATGGATTACATTAATATACTTTGTATAATTGACCTCATGTGGTTT
TTGAATGCAAAGAAAAATAGAAAGAAATATTGGCTCATGATCTTCGTAATTTGATACATCAAATT
AGGCTCTCCATTACACTTGATGAGCTTATTCTCAAGCAATTTAAATGTTTTTATCATGTTTTTAG
TTAGTTTTTGTTTTAATAAGTGAATTAGTGTGTTTTATGTAATTTTTATACCTGAATTGGCCAAA
TGCGCCATAGGGAACCTAACGGTTGATTAAGTGTTGTAAGGAGTCAATGGATTACAATAACAT
Found at i:34569691 original size:31 final size:32
Alignment explanation
Indices: 34569635--34569694 Score: 104
Period size: 32 Copynumber: 1.9 Consensus size: 32
34569625 AAATTACAAA
*
34569635 AGTAATTGAATCCTAATAAAAACTCTTTAAAG
1 AGTAATTAAATCCTAATAAAAACTCTTTAAAG
34569667 AGTAATTAAATCCTAAT-AAAACTCTTTA
1 AGTAATTAAATCCTAATAAAAACTCTTTA
34569695 CAATTATCTA
Statistics
Matches: 27, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
31 11 0.41
32 16 0.59
ACGTcount: A:0.47, C:0.13, G:0.07, T:0.33
Consensus pattern (32 bp):
AGTAATTAAATCCTAATAAAAACTCTTTAAAG
Found at i:34571764 original size:20 final size:19
Alignment explanation
Indices: 34571739--34571788 Score: 55
Period size: 20 Copynumber: 2.5 Consensus size: 19
34571729 GATCATTAGT
34571739 TTAATTAATTTAAGGTTTAA
1 TTAATTAATTT-AGGTTTAA
* * *
34571759 TTAATTAAATTATGTTTGA
1 TTAATTAATTTAGGTTTAA
34571778 TTAATTTAATT
1 TTAA-TTAATT
34571789 ATATATAATA
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
19 10 0.40
20 15 0.60
ACGTcount: A:0.38, C:0.00, G:0.08, T:0.54
Consensus pattern (19 bp):
TTAATTAATTTAGGTTTAA
Found at i:34571780 original size:19 final size:19
Alignment explanation
Indices: 34571739--34571790 Score: 59
Period size: 19 Copynumber: 2.7 Consensus size: 19
34571729 GATCATTAGT
* *
34571739 TTAATTAATTTAAGGTTTAA
1 TTAATTAAATT-ATGTTTAA
*
34571759 TTAATTAAATTATGTTTGA
1 TTAATTAAATTATGTTTAA
*
34571778 TTAATTTAATTAT
1 TTAATTAAATTAT
34571791 ATATAATATA
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
19 18 0.64
20 10 0.36
ACGTcount: A:0.38, C:0.00, G:0.08, T:0.54
Consensus pattern (19 bp):
TTAATTAAATTATGTTTAA
Found at i:34579604 original size:163 final size:164
Alignment explanation
Indices: 34579323--34579649 Score: 647
Period size: 163 Copynumber: 2.0 Consensus size: 164
34579313 AGGTCATTAA
34579323 ATTACAAAGCAAACAAATAAAAGGATATTAAGTATAGGTATCCATCAAAACAAATATACAATTAT
1 ATTACAAAGCAAACAAATAAAAGGATATTAAGTATAGGTATCCATCAAAACAAATATACAATTAT
34579388 GTTCAATTGAATATGAGTGGTAAAAATATCAATCCTTGGAACAATTTCATCTATATAAAGTACTA
66 GTTCAATTGAATATGAGTGGTAAAAATATCAATCCTTGGAACAATTTCATCTATATAAAGTACTA
34579453 CCTAAATCACATAGGACTTTTCGACTTGTAACAT
131 CCTAAATCACATAGGACTTTTCGACTTGTAACAT
34579487 ATTACAAAGC-AACAAATAAAAGGATATTAAGTATAGGTATCCATCAAAACAAATATACAATTAT
1 ATTACAAAGCAAACAAATAAAAGGATATTAAGTATAGGTATCCATCAAAACAAATATACAATTAT
34579551 GTTCAATTGAATATGAGTGGTAAAAATATCAATCCTTGGAACAATTTCATCTATATAAAGTACTA
66 GTTCAATTGAATATGAGTGGTAAAAATATCAATCCTTGGAACAATTTCATCTATATAAAGTACTA
34579616 CCTAAATCACATAGGACTTTTCGACTTGTAACAT
131 CCTAAATCACATAGGACTTTTCGACTTGTAACAT
34579650 TCTGCGGCTA
Statistics
Matches: 163, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
163 153 0.94
164 10 0.06
ACGTcount: A:0.44, C:0.15, G:0.12, T:0.30
Consensus pattern (164 bp):
ATTACAAAGCAAACAAATAAAAGGATATTAAGTATAGGTATCCATCAAAACAAATATACAATTAT
GTTCAATTGAATATGAGTGGTAAAAATATCAATCCTTGGAACAATTTCATCTATATAAAGTACTA
CCTAAATCACATAGGACTTTTCGACTTGTAACAT
Found at i:34591764 original size:34 final size:34
Alignment explanation
Indices: 34591698--34591765 Score: 118
Period size: 35 Copynumber: 2.0 Consensus size: 34
34591688 ACTTACACAT
34591698 AACATTTACGCATAATAAAACTCAAACAAAAAAA
1 AACATTTACGCATAATAAAACTCAAACAAAAAAA
*
34591732 AACATTATACGCATAATAAACCTCAAACAAAAAA
1 AACATT-TACGCATAATAAAACTCAAACAAAAAA
34591766 TATCAAAGTT
Statistics
Matches: 32, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
34 6 0.19
35 26 0.81
ACGTcount: A:0.60, C:0.19, G:0.03, T:0.18
Consensus pattern (34 bp):
AACATTTACGCATAATAAAACTCAAACAAAAAAA
Found at i:34593622 original size:18 final size:18
Alignment explanation
Indices: 34593599--34593633 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
34593589 TTCTCATAAC
*
34593599 TTATAACTATAAAAAATA
1 TTATAACTAAAAAAAATA
*
34593617 TTATAATTAAAAAAAAT
1 TTATAACTAAAAAAAAT
34593634 GCTAATGTTT
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:0.63, C:0.03, G:0.00, T:0.34
Consensus pattern (18 bp):
TTATAACTAAAAAAAATA
Found at i:34596468 original size:13 final size:13
Alignment explanation
Indices: 34596450--34596487 Score: 60
Period size: 12 Copynumber: 3.0 Consensus size: 13
34596440 TAAGTAAAAA
34596450 GCGAACCCTTTGT
1 GCGAACCCTTTGT
*
34596463 GCGAA-CCTTAGT
1 GCGAACCCTTTGT
34596475 GCGAACCCTTTGT
1 GCGAACCCTTTGT
34596488 ATGTGAAACC
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
12 11 0.50
13 11 0.50
ACGTcount: A:0.18, C:0.29, G:0.24, T:0.29
Consensus pattern (13 bp):
GCGAACCCTTTGT
Found at i:34596927 original size:21 final size:19
Alignment explanation
Indices: 34596879--34596929 Score: 52
Period size: 21 Copynumber: 2.7 Consensus size: 19
34596869 GCCCTAGGTA
34596879 ATATGCAAA-C-ATTGTAT
1 ATATGCAAACCTATTGTAT
* *
34596896 ACATGTAAACCTATTTGTAGT
1 ATATGCAAACCTA-TTGTA-T
34596917 ATATGCAAACCTA
1 ATATGCAAACCTA
34596930 AATGTTTATA
Statistics
Matches: 26, Mismatches: 4, Indels: 4
0.76 0.12 0.12
Matches are distributed among these distances:
17 7 0.27
18 1 0.04
19 1 0.04
20 5 0.19
21 12 0.46
ACGTcount: A:0.39, C:0.16, G:0.12, T:0.33
Consensus pattern (19 bp):
ATATGCAAACCTATTGTAT
Found at i:34597252 original size:34 final size:34
Alignment explanation
Indices: 34597170--34597258 Score: 81
Period size: 34 Copynumber: 2.6 Consensus size: 34
34597160 AACACTATAC
* * * *
34597170 TATGATATGCGAACCCTAGGAATATGCGACCCTG
1 TATGTTATGCGAACCCTAGGTATACGCGACCCTA
* ***
34597204 TATGATT-TGTGAACCCTAGGTATACGCGAGTTTA
1 TATG-TTATGCGAACCCTAGGTATACGCGACCCTA
*
34597238 TATGTTATGCGAACCGTAGGT
1 TATGTTATGCGAACCCTAGGT
34597259 TAGTGTGAGC
Statistics
Matches: 43, Mismatches: 10, Indels: 4
0.75 0.18 0.07
Matches are distributed among these distances:
33 2 0.05
34 40 0.93
35 1 0.02
ACGTcount: A:0.27, C:0.18, G:0.25, T:0.30
Consensus pattern (34 bp):
TATGTTATGCGAACCCTAGGTATACGCGACCCTA
Found at i:34599258 original size:16 final size:16
Alignment explanation
Indices: 34599224--34599261 Score: 51
Period size: 16 Copynumber: 2.4 Consensus size: 16
34599214 TGTTAATAAA
*
34599224 TTTTA-TTTCTTTTAG
1 TTTTATTTTATTTTAG
*
34599239 TTTTATTTTATTTTAT
1 TTTTATTTTATTTTAG
34599255 TTTTATT
1 TTTTATT
34599262 ATTTTTCTTG
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
15 5 0.25
16 15 0.75
ACGTcount: A:0.16, C:0.03, G:0.03, T:0.79
Consensus pattern (16 bp):
TTTTATTTTATTTTAG
Found at i:34608427 original size:123 final size:125
Alignment explanation
Indices: 34608164--34608431 Score: 282
Period size: 123 Copynumber: 2.2 Consensus size: 125
34608154 ATAAAACACA
* *
34608164 CTGATTTAA-AAAATATATAAGTACATAAAGAGATGTGTATACCATAAAATATATTATATATGAA
1 CTGATTTAATAAAA-ATATAAGTACATAAAGAAATGTGTATACCACAAAATATATTATATATGAA
* * * *
34608228 TTTTTTTTACTTTTGATAAATCATAAAACACAGTTCAATAATCCATCAAATTTGGTTTACTC
65 TTATTTTGACTTTTAATAAATCATAAAACACAATTCAATAATCCAT-AAATTTGGTTTACTC
* *
34608290 CTGATTTAAT-AAAATATAAGTACTTGAAGAAATGTGTA-A-CACAAAATATA-TATTATATGAA
1 CTGATTTAATAAAAATATAAGTACATAAAGAAATGTGTATACCACAAAATATATTA-TATATGAA
* * * * *
34608351 TTATTTTGACTTTTAATCAA-CTATAAAACACATTATTTAGTAATTCAT-AA-TTGGTTTATTC
65 TTATTTTGACTTTTAATAAATC-ATAAAACACA--ATTCAATAATCCATAAATTTGGTTTACTC
* **
34608412 CTTATTTTTTAAAAATATAA
1 CTGATTTAATAAAAATATAA
34608432 ACATGTGGAG
Statistics
Matches: 120, Mismatches: 16, Indels: 15
0.79 0.11 0.10
Matches are distributed among these distances:
122 20 0.17
123 55 0.46
124 1 0.01
125 32 0.27
126 12 0.10
ACGTcount: A:0.42, C:0.10, G:0.08, T:0.40
Consensus pattern (125 bp):
CTGATTTAATAAAAATATAAGTACATAAAGAAATGTGTATACCACAAAATATATTATATATGAAT
TATTTTGACTTTTAATAAATCATAAAACACAATTCAATAATCCATAAATTTGGTTTACTC
Found at i:34611694 original size:22 final size:24
Alignment explanation
Indices: 34611644--34611694 Score: 56
Period size: 24 Copynumber: 2.2 Consensus size: 24
34611634 TTGCAATGCT
34611644 TTTATATTTTAATAATTGAGTATTA
1 TTTATATTTTAAT-ATTGAGTATTA
34611669 -TTATATATTTAAT-TTGA-T-TTA
1 TTTATAT-TTTAATATTGAGTATTA
34611690 TTTAT
1 TTTAT
34611695 TTATAAATAA
Statistics
Matches: 24, Mismatches: 0, Indels: 7
0.77 0.00 0.23
Matches are distributed among these distances:
21 3 0.12
22 5 0.21
23 4 0.17
24 6 0.25
25 6 0.25
ACGTcount: A:0.33, C:0.00, G:0.06, T:0.61
Consensus pattern (24 bp):
TTTATATTTTAATATTGAGTATTA
Found at i:34611919 original size:3 final size:3
Alignment explanation
Indices: 34611911--34611942 Score: 64
Period size: 3 Copynumber: 10.7 Consensus size: 3
34611901 NNNNNNNNNN
34611911 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
34611943 AGATATTTGA
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:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:34612297 original size:16 final size:14
Alignment explanation
Indices: 34612262--34612300 Score: 51
Period size: 14 Copynumber: 2.6 Consensus size: 14
34612252 TGACTTGAAT
*
34612262 AATTCGAATAACTC
1 AATTCGATTAACTC
34612276 AATTCGATTAACTC
1 AATTCGATTAACTC
34612290 GAAATTCGATT
1 --AATTCGATT
34612301 TTTTTCGATT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
14 13 0.59
16 9 0.41
ACGTcount: A:0.38, C:0.18, G:0.10, T:0.33
Consensus pattern (14 bp):
AATTCGATTAACTC
Found at i:34617290 original size:9 final size:9
Alignment explanation
Indices: 34617276--34617306 Score: 53
Period size: 9 Copynumber: 3.4 Consensus size: 9
34617266 GTTAAACGAA
34617276 TCGAGTTAT
1 TCGAGTTAT
*
34617285 TCGAGTTAA
1 TCGAGTTAT
34617294 TCGAGTTAT
1 TCGAGTTAT
34617303 TCGA
1 TCGA
34617307 ATCAACTCGA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
9 20 1.00
ACGTcount: A:0.26, C:0.13, G:0.23, T:0.39
Consensus pattern (9 bp):
TCGAGTTAT
Found at i:34622095 original size:85 final size:85
Alignment explanation
Indices: 34621947--34622131 Score: 298
Period size: 85 Copynumber: 2.2 Consensus size: 85
34621937 AACACTCCAC
* * *
34621947 ATACTTGTGTTATTGCAGGTATGTCACAGGATCATCCCAAATTGGATTCTAACCTTATCTCTAAT
1 ATACTTGTGTTGTTGCAGGTATGCCACAGGATCATCCCAAATTGAATTCTAACCTTATCTCTAAT
* *
34622012 ATTGTCTTACGTATGATGAA
66 ATTGTCTTACATATGATAAA
* *
34622032 ATACTTGTGTTGTTGCAGGTATGCCACAGGATCATCCTAAATTGAATTCTAACCTTATTTCTAAT
1 ATACTTGTGTTGTTGCAGGTATGCCACAGGATCATCCCAAATTGAATTCTAACCTTATCTCTAAT
*
34622097 ATTGTCTTACATATGGTAAA
66 ATTGTCTTACATATGATAAA
34622117 ATACTTGTGTTGTTG
1 ATACTTGTGTTGTTG
34622132 TAAAGAAAGG
Statistics
Matches: 92, Mismatches: 8, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
85 92 1.00
ACGTcount: A:0.28, C:0.16, G:0.17, T:0.39
Consensus pattern (85 bp):
ATACTTGTGTTGTTGCAGGTATGCCACAGGATCATCCCAAATTGAATTCTAACCTTATCTCTAAT
ATTGTCTTACATATGATAAA
Found at i:34631232 original size:23 final size:23
Alignment explanation
Indices: 34631202--34631247 Score: 83
Period size: 23 Copynumber: 2.0 Consensus size: 23
34631192 CAAATACGCA
*
34631202 GAAAAACCTAATTTTTAGGCTTT
1 GAAAAACCTAATTTCTAGGCTTT
34631225 GAAAAACCTAATTTCTAGGCTTT
1 GAAAAACCTAATTTCTAGGCTTT
34631248 CTTAGGATTC
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.35, C:0.15, G:0.13, T:0.37
Consensus pattern (23 bp):
GAAAAACCTAATTTCTAGGCTTT
Found at i:34631643 original size:23 final size:23
Alignment explanation
Indices: 34631617--34631664 Score: 87
Period size: 23 Copynumber: 2.1 Consensus size: 23
34631607 ATTCATGTTT
*
34631617 AATGTGCTTTTTTCAGTGGAGAA
1 AATGTGCTTATTTCAGTGGAGAA
34631640 AATGTGCTTATTTCAGTGGAGAA
1 AATGTGCTTATTTCAGTGGAGAA
34631663 AA
1 AA
34631665 AGTCCCTGTT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.31, C:0.08, G:0.25, T:0.35
Consensus pattern (23 bp):
AATGTGCTTATTTCAGTGGAGAA
Found at i:34638463 original size:5 final size:5
Alignment explanation
Indices: 34638453--34638508 Score: 85
Period size: 5 Copynumber: 10.6 Consensus size: 5
34638443 TATCATTGTC
34638453 TTTAT TTTAT TTTAT TTTAT TTTAT TTTATT TTTATT TCTTAT TTTAT
1 TTTAT TTTAT TTTAT TTTAT TTTAT TTTA-T TTTA-T T-TTAT TTTAT
34638501 TTTAT TTT
1 TTTAT TTT
34638509 TTCATTCATT
Statistics
Matches: 49, Mismatches: 0, Indels: 4
0.92 0.00 0.08
Matches are distributed among these distances:
5 36 0.73
6 10 0.20
7 3 0.06
ACGTcount: A:0.18, C:0.02, G:0.00, T:0.80
Consensus pattern (5 bp):
TTTAT
Found at i:34639867 original size:17 final size:17
Alignment explanation
Indices: 34639838--34639870 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
34639828 CTTATGTGAC
34639838 TCGACTCGCTCGACACT
1 TCGACTCGCTCGACACT
34639855 TCGATCTCG-TCGACAC
1 TCGA-CTCGCTCGACAC
34639871 ACCGGAGTAG
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
17 11 0.73
18 4 0.27
ACGTcount: A:0.18, C:0.39, G:0.18, T:0.24
Consensus pattern (17 bp):
TCGACTCGCTCGACACT
Found at i:34650218 original size:15 final size:14
Alignment explanation
Indices: 34650166--34650294 Score: 79
Period size: 14 Copynumber: 9.2 Consensus size: 14
34650156 AAGCTGTGAA
*
34650166 TTTAATTTTTACAT
1 TTTAATTTTTATAT
*
34650180 TTTAATTTGGT-TAT
1 TTTAATTT-TTATAT
34650194 TTTAATTTTTATAT
1 TTTAATTTTTATAT
*
34650208 TTTTATGTTTTATAT
1 TTTAAT-TTTTATAT
* * *
34650223 TTTGAAATTTGAAAT
1 TTT-AATTTTTATAT
* *
34650238 TTGAAATTTTA-AT
1 TTTAATTTTTATAT
34650251 TTTAA-TTTTATA-
1 TTTAATTTTTATAT
* *
34650263 -TTAATTATTAAAT
1 TTTAATTTTTATAT
*
34650276 TATTAAATTTTGATAT
1 T-TT-AATTTTTATAT
34650292 TTT
1 TTT
34650295 CAAAATATCA
Statistics
Matches: 89, Mismatches: 16, Indels: 19
0.72 0.13 0.15
Matches are distributed among these distances:
11 4 0.04
12 10 0.11
13 8 0.09
14 33 0.37
15 24 0.27
16 10 0.11
ACGTcount: A:0.32, C:0.01, G:0.05, T:0.62
Consensus pattern (14 bp):
TTTAATTTTTATAT
Found at i:34651432 original size:8 final size:8
Alignment explanation
Indices: 34651419--34651447 Score: 58
Period size: 8 Copynumber: 3.6 Consensus size: 8
34651409 AGTTTATTGG
34651419 AAAATTAT
1 AAAATTAT
34651427 AAAATTAT
1 AAAATTAT
34651435 AAAATTAT
1 AAAATTAT
34651443 AAAAT
1 AAAAT
34651448 AGTATAATGA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 21 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (8 bp):
AAAATTAT
Found at i:34657326 original size:27 final size:27
Alignment explanation
Indices: 34657288--34657805 Score: 516
Period size: 27 Copynumber: 19.2 Consensus size: 27
34657278 ATTTGTGGGA
* *
34657288 AAAATTACCGAAATACTCTCGAAGGGT
1 AAAATTATCGAAATACCCTCGAAGGGT
*
34657315 AAAATTATCGAAATACCCTTGAAGGGT
1 AAAATTATCGAAATACCCTCGAAGGGT
* *
34657342 AAAATTATCGAAATACCTTCGATGGGT
1 AAAATTATCGAAATACCCTCGAAGGGT
34657369 AAAATTATCGAAATACCCTCGAAGGGT
1 AAAATTATCGAAATACCCTCGAAGGGT
* *
34657396 AAAATTA-CTGAAACACCCTAGAAGGGT
1 AAAATTATC-GAAATACCCTCGAAGGGT
* **
34657423 AAAATTA-CTAAAATACCCTTAAAGGGT
1 AAAATTATC-GAAATACCCTCGAAGGGT
*
34657450 AAAATTATCGAAACA-CCTCTGAAGGGT
1 AAAATTATCGAAATACCCTC-GAAGGGT
* *
34657477 AAAATTATCAAAATACCCTC-AATAGGT
1 AAAATTATCGAAATACCCTCGAA-GGGT
* ** *
34657504 AAAATTA-CTAAAATACCCTTAAAAGGT
1 AAAATTATC-GAAATACCCTCGAAGGGT
* * *
34657531 AAAATTATCGAAATAACCTCAAATGGT
1 AAAATTATCGAAATACCCTCGAAGGGT
*
34657558 AAAATTA-CTGAAATACCCCCGAAGGGT
1 AAAATTATC-GAAATACCCTCGAAGGGT
**
34657585 AAAATTATCGAAATACCCTTAAAGGGT
1 AAAATTATCGAAATACCCTCGAAGGGT
** *
34657612 AAAATTA-CTGAAGCACCC-CTAAAGGGT
1 AAAATTATC-GAAATACCCTC-GAAGGGT
* *
34657639 AAAATTA-CTAAAATTCCCTCGAAGGGT
1 AAAATTATC-GAAATACCCTCGAAGGGT
* * *
34657666 AAAATTATCGAAACACCCCCAAAGGGT
1 AAAATTATCGAAATACCCTCGAAGGGT
* * *
34657693 AAAAATTATCGACATACCCTTGAAGGGA
1 -AAAATTATCGAAATACCCTCGAAGGGT
*
34657721 AAAATTA-CCAAATACCCTCGAAGGGT
1 AAAATTATCGAAATACCCTCGAAGGGT
* *
34657747 AAAATTATTGAAATGCCCTCGAAGGGT
1 AAAATTATCGAAATACCCTCGAAGGGT
* * *
34657774 AAAATTATTGAAATACCCCCGAGGGGT
1 AAAATTATCGAAATACCCTCGAAGGGT
34657801 AAAAT
1 AAAAT
34657806 GACCGTTTAC
Statistics
Matches: 413, Mismatches: 62, Indels: 32
0.81 0.12 0.06
Matches are distributed among these distances:
26 31 0.08
27 350 0.85
28 32 0.08
ACGTcount: A:0.43, C:0.18, G:0.16, T:0.23
Consensus pattern (27 bp):
AAAATTATCGAAATACCCTCGAAGGGT
Found at i:34658061 original size:52 final size:52
Alignment explanation
Indices: 34657999--34658105 Score: 180
Period size: 52 Copynumber: 2.1 Consensus size: 52
34657989 TTTGCCACAA
34657999 ATACTGTTACTGGCAGCTTTGCTGC-TATACTGATACTGGCAGCTCTACTGCG
1 ATACTGTTACTGGCAGCTTTGCTGCGT-TACTGATACTGGCAGCTCTACTGCG
* *
34658051 ATACTGTTACTGGCAGCTTTGCTGCGTTACTGATACTGGCAGCTTTGCTGCG
1 ATACTGTTACTGGCAGCTTTGCTGCGTTACTGATACTGGCAGCTCTACTGCG
34658103 ATA
1 ATA
34658106 TTGGTGTGTT
Statistics
Matches: 52, Mismatches: 2, Indels: 2
0.93 0.04 0.04
Matches are distributed among these distances:
52 51 0.98
53 1 0.02
ACGTcount: A:0.19, C:0.23, G:0.24, T:0.34
Consensus pattern (52 bp):
ATACTGTTACTGGCAGCTTTGCTGCGTTACTGATACTGGCAGCTCTACTGCG
Found at i:34658102 original size:26 final size:26
Alignment explanation
Indices: 34658000--34658102 Score: 145
Period size: 26 Copynumber: 4.0 Consensus size: 26
34657990 TTGCCACAAA
*
34658000 TACTGTTACTGGCAGCTTTGCTGC-T
1 TACTGATACTGGCAGCTTTGCTGCGT
* * *
34658025 ATACTGATACTGGCAGCTCTACTGCGA
1 -TACTGATACTGGCAGCTTTGCTGCGT
*
34658052 TACTGTTACTGGCAGCTTTGCTGCGT
1 TACTGATACTGGCAGCTTTGCTGCGT
34658078 TACTGATACTGGCAGCTTTGCTGCG
1 TACTGATACTGGCAGCTTTGCTGCG
34658103 ATATTGGTGT
Statistics
Matches: 67, Mismatches: 9, Indels: 2
0.86 0.12 0.03
Matches are distributed among these distances:
26 67 1.00
ACGTcount: A:0.17, C:0.24, G:0.25, T:0.34
Consensus pattern (26 bp):
TACTGATACTGGCAGCTTTGCTGCGT
Found at i:34658253 original size:28 final size:29
Alignment explanation
Indices: 34658208--34658284 Score: 95
Period size: 28 Copynumber: 2.7 Consensus size: 29
34658198 ACTGCATTTG
* * *
34658208 TACTGATTACTATTTTGGGCTAAGGCCCA
1 TACTGATTACTGTATTGGGCTAAAGCCCA
34658237 TACT-ATTACTGTATTGGGCTAAAGCCCA
1 TACTGATTACTGTATTGGGCTAAAGCCCA
34658265 TATTCTGA-TACTGTATTGGG
1 TA--CTGATTACTGTATTGGG
34658285 TTATGACCCA
Statistics
Matches: 42, Mismatches: 3, Indels: 5
0.84 0.06 0.10
Matches are distributed among these distances:
28 23 0.55
29 4 0.10
30 14 0.33
31 1 0.02
ACGTcount: A:0.25, C:0.18, G:0.21, T:0.36
Consensus pattern (29 bp):
TACTGATTACTGTATTGGGCTAAAGCCCA
Found at i:34665980 original size:81 final size:80
Alignment explanation
Indices: 34665798--34666182 Score: 483
Period size: 81 Copynumber: 4.8 Consensus size: 80
34665788 GTATAACAGC
* *
34665798 CATTTTACCTTATTGGGGTATTTCGGTCATTTTACCCTATGGGGGTATTTCG-TCATTCTACCTT
1 CATTTTACCCTA-TGGGGTATTTCGGTCATTTTACCCTATGGGGGTATTTCGATCATTTTACCTT
* *
34665862 GT-GGGGTATTTCGGT
65 ATGGGGGTATTTCGAT
*
34665877 CATTTTACCCTATGAGGGTATTTTGGTCATTTTACCCTATGGGGGTATTTCGATCATTTTACCTT
1 CATTTTACCCTATG-GGGTATTTCGGTCATTTTACCCTATGGGGGTATTTCGATCATTTTACCTT
*
34665942 ATGGGGGTATTTCTAT
65 ATGGGGGTATTTCGAT
* ** *
34665958 CATTTTACCTTATAGGGGTATTTTTGTCATTTTACCCTATGAGGGTATTTCGATCATTTTACCTT
1 CATTTTACCCTAT-GGGGTATTTCGGTCATTTTACCCTATGGGGGTATTTCGATCATTTTACCTT
34666023 ATGGGGGTATTTCGAT
65 ATGGGGGTATTTCGAT
* * *
34666039 CATTTTACCCTATGGTGTATTTCGGTCATTCTACCCTATAGGGGTATTTC-AGTCATTTTACCTT
1 CATTTTACCCTATGGGGTATTTCGGTCATTTTACCCTATGGGGGTATTTCGA-TCATTTTACCTT
* *
34666103 ATGAGGGTATTT-TAGT
65 ATGGGGGTATTTCGA-T
* * * * * *
34666119 CATTTTATCCTATGGGGGTATTTCGGTCATTCTACCTTATGAGGGTACTTC-ATTCATTCTACCT
1 CATTTTACCCTAT-GGGGTATTTCGGTCATTTTACCCTATGGGGGTATTTCGA-TCATTTTACCT
34666183 ATTTTTGGGT
Statistics
Matches: 272, Mismatches: 27, Indels: 12
0.87 0.09 0.04
Matches are distributed among these distances:
78 2 0.01
79 49 0.18
80 79 0.29
81 141 0.52
82 1 0.00
ACGTcount: A:0.18, C:0.17, G:0.20, T:0.44
Consensus pattern (80 bp):
CATTTTACCCTATGGGGTATTTCGGTCATTTTACCCTATGGGGGTATTTCGATCATTTTACCTTA
TGGGGGTATTTCGAT
Found at i:34666175 original size:27 final size:27
Alignment explanation
Indices: 34665798--34666182 Score: 369
Period size: 27 Copynumber: 14.4 Consensus size: 27
34665788 GTATAACAGC
*
34665798 CATTTTACCTTATTG-GGGTATTTCGGT
1 CATTTTACCTTA-TGAGGGTATTTCAGT
* *
34665825 CATTTTACCCTATGGGGGTATTTC-GT
1 CATTTTACCTTATGAGGGTATTTCAGT
* * *
34665851 CATTCTACCTTGTG-GGGTATTTCGGT
1 CATTTTACCTTATGAGGGTATTTCAGT
* **
34665877 CATTTTACCCTATGAGGGTATTTTGGT
1 CATTTTACCTTATGAGGGTATTTCAGT
* *
34665904 CATTTTACCCTATGGGGGTATTTC-GAT
1 CATTTTACCTTATGAGGGTATTTCAG-T
*
34665931 CATTTTACCTTATGGGGGTATTTCTA-T
1 CATTTTACCTTATGAGGGTATTTC-AGT
**
34665958 CATTTTACCTTAT-AGGGGTATTTTTGT
1 CATTTTACCTTATGA-GGGTATTTCAGT
*
34665985 CATTTTACCCTATGAGGGTATTTC-GAT
1 CATTTTACCTTATGAGGGTATTTCAG-T
*
34666012 CATTTTACCTTATGGGGGTATTTC-GAT
1 CATTTTACCTTATGAGGGTATTTCAG-T
* * *
34666039 CATTTTACCCTATG-GTGTATTTCGGT
1 CATTTTACCTTATGAGGGTATTTCAGT
* *
34666065 CATTCTACCCTAT-AGGGGTATTTCAGT
1 CATTTTACCTTATGA-GGGTATTTCAGT
*
34666092 CATTTTACCTTATGAGGGTATTTTAGT
1 CATTTTACCTTATGAGGGTATTTCAGT
* *
34666119 CATTTTATCC-TATGGGGGTATTTCGGT
1 CATTTTA-CCTTATGAGGGTATTTCAGT
* * *
34666146 CATTCTACCTTATGAGGGTACTTCATT
1 CATTTTACCTTATGAGGGTATTTCAGT
*
34666173 CATTCTACCT
1 CATTTTACCT
34666183 ATTTTTGGGT
Statistics
Matches: 308, Mismatches: 34, Indels: 32
0.82 0.09 0.09
Matches are distributed among these distances:
25 9 0.03
26 53 0.17
27 242 0.79
28 4 0.01
ACGTcount: A:0.18, C:0.17, G:0.20, T:0.44
Consensus pattern (27 bp):
CATTTTACCTTATGAGGGTATTTCAGT
Found at i:34666176 original size:54 final size:53
Alignment explanation
Indices: 34665798--34666184 Score: 442
Period size: 54 Copynumber: 7.2 Consensus size: 53
34665788 GTATAACAGC
* *
34665798 CATTTTACCTTATTGGGGTATTTCGGTCATTTTACCCTATGGGGGTATTTC-GT
1 CATTTTACC-TATGGGGGTATTTCGGTCATTTTACCCTATGAGGGTATTTCAGT
* **
34665851 CATTCTACCT-TGTGGGGTATTTCGGTCATTTTACCCTATGAGGGTATTTTGGT
1 CATTTTACCTATG-GGGGTATTTCGGTCATTTTACCCTATGAGGGTATTTCAGT
* * *
34665904 CATTTTACCCTATGGGGGTATTTCGATCATTTTACCTTATGGGGGTATTTCTA-T
1 CATTTTA-CCTATGGGGGTATTTCGGTCATTTTACCCTATGAGGGTATTTC-AGT
* **
34665958 CATTTTACCTTATAGGGGTATTTTTGTCATTTTACCCTATGAGGGTATTTC-GAT
1 CATTTTACC-TATGGGGGTATTTCGGTCATTTTACCCTATGAGGGTATTTCAG-T
* * *
34666012 CATTTTACCTTATGGGGGTATTTCGATCATTTTACCCTATG-GTGTATTTCGGT
1 CATTTTACC-TATGGGGGTATTTCGGTCATTTTACCCTATGAGGGTATTTCAGT
* * * * *
34666065 CATTCTACCCTATAGGGGTATTTCAGTCATTTTACCTTATGAGGGTATTTTAGT
1 CATTTTA-CCTATGGGGGTATTTCGGTCATTTTACCCTATGAGGGTATTTCAGT
* * * *
34666119 CATTTTATCCTATGGGGGTATTTCGGTCATTCTACCTTATGAGGGTACTTCATT
1 CATTTTA-CCTATGGGGGTATTTCGGTCATTTTACCCTATGAGGGTATTTCAGT
*
34666173 CATTCTACCTAT
1 CATTTTACCTAT
34666185 TTTTGGGTCT
Statistics
Matches: 285, Mismatches: 38, Indels: 22
0.83 0.11 0.06
Matches are distributed among these distances:
51 1 0.00
52 36 0.13
53 65 0.23
54 181 0.64
55 2 0.01
ACGTcount: A:0.18, C:0.17, G:0.20, T:0.44
Consensus pattern (53 bp):
CATTTTACCTATGGGGGTATTTCGGTCATTTTACCCTATGAGGGTATTTCAGT
Found at i:34673768 original size:16 final size:15
Alignment explanation
Indices: 34673744--34673774 Score: 53
Period size: 16 Copynumber: 2.0 Consensus size: 15
34673734 TTCTATAGAC
34673744 AAAAAAAAAAGAGGA
1 AAAAAAAAAAGAGGA
34673759 AAAAAGAAAAAGAGGA
1 AAAAA-AAAAAGAGGA
34673775 TTTCAGGAAG
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 5 0.33
16 10 0.67
ACGTcount: A:0.77, C:0.00, G:0.23, T:0.00
Consensus pattern (15 bp):
AAAAAAAAAAGAGGA
Found at i:34680460 original size:18 final size:19
Alignment explanation
Indices: 34680437--34680481 Score: 58
Period size: 18 Copynumber: 2.4 Consensus size: 19
34680427 TAGTTTTATA
34680437 ATTTATTTTCATTA-TTGAT
1 ATTTATTTTC-TTATTTGAT
*
34680456 A-TTATTGTCTTATTTGAT
1 ATTTATTTTCTTATTTGAT
34680474 ATTTATTT
1 ATTTATTT
34680482 ATGTGTTCAT
Statistics
Matches: 22, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
17 3 0.14
18 13 0.59
19 6 0.27
ACGTcount: A:0.24, C:0.04, G:0.07, T:0.64
Consensus pattern (19 bp):
ATTTATTTTCTTATTTGAT
Found at i:34714969 original size:13 final size:13
Alignment explanation
Indices: 34714951--34714978 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
34714941 AACAAGGCTC
34714951 CTTTGTTCCTTTG
1 CTTTGTTCCTTTG
34714964 CTTTGTTCCTTTG
1 CTTTGTTCCTTTG
34714977 CT
1 CT
34714979 GATGGCTCTC
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:0.00, C:0.25, G:0.14, T:0.61
Consensus pattern (13 bp):
CTTTGTTCCTTTG
Found at i:34721373 original size:19 final size:17
Alignment explanation
Indices: 34721337--34721375 Score: 51
Period size: 19 Copynumber: 2.2 Consensus size: 17
34721327 TTTTTCTATC
*
34721337 TTTATTTTATTGTTTCT
1 TTTATTTTATTCTTTCT
34721354 TTTATTTTCATTTCTTTCT
1 TTTATTTT-A-TTCTTTCT
34721373 TTT
1 TTT
34721376 GTTTAATTAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
17 8 0.42
18 1 0.05
19 10 0.53
ACGTcount: A:0.10, C:0.10, G:0.03, T:0.77
Consensus pattern (17 bp):
TTTATTTTATTCTTTCT
Found at i:34739257 original size:14 final size:15
Alignment explanation
Indices: 34739236--34739280 Score: 60
Period size: 14 Copynumber: 3.2 Consensus size: 15
34739226 CTAATTTTTT
34739236 TCTC-CTTTTTCTTC
1 TCTCTCTTTTTCTTC
*
34739250 T-TTTCTTTTTCTT-
1 TCTCTCTTTTTCTTC
34739263 TCTCTCTTTTTCTTC
1 TCTCTCTTTTTCTTC
34739278 TCT
1 TCT
34739281 GTTTCGTTCT
Statistics
Matches: 26, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
13 2 0.08
14 21 0.81
15 3 0.12
ACGTcount: A:0.00, C:0.29, G:0.00, T:0.71
Consensus pattern (15 bp):
TCTCTCTTTTTCTTC
Found at i:34739275 original size:25 final size:27
Alignment explanation
Indices: 34739230--34739290 Score: 65
Period size: 25 Copynumber: 2.4 Consensus size: 27
34739220 AAAATCCTAA
* *
34739230 TTTT-TTTCTCCTTTTTCTTCTTTTCT
1 TTTTCTTTCTCCTCTTTCTTCTTCTCT
34739256 TTTTCTTTCT-CTCTTT-TTCTTCTCT
1 TTTTCTTTCTCCTCTTTCTTCTTCTCT
* *
34739281 GTTTCGTTCT
1 TTTTCTTTCT
34739291 ACTTTGTTCT
Statistics
Matches: 30, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
25 16 0.53
26 9 0.30
27 5 0.17
ACGTcount: A:0.00, C:0.25, G:0.03, T:0.72
Consensus pattern (27 bp):
TTTTCTTTCTCCTCTTTCTTCTTCTCT
Found at i:34748262 original size:83 final size:83
Alignment explanation
Indices: 34748159--34748318 Score: 284
Period size: 83 Copynumber: 1.9 Consensus size: 83
34748149 TTAACGGATA
34748159 TATGTTTAACGCATGAACCACTAAAAAACAATAGTATTAGTAAATCATAATATTACTGTATATTA
1 TATGTTTAACGCATGAACCACTAAAAAACAATAGTATTAGTAAATCATAATATTACTGTATATTA
*
34748224 TAAAATTGTATACAATTG
66 TAAAACTGTATACAATTG
* * *
34748242 TATGTTTAACGTATTAACCACTAAAAACCAATAGTATTAGTAAATCATAATATTACTGTATATTA
1 TATGTTTAACGCATGAACCACTAAAAAACAATAGTATTAGTAAATCATAATATTACTGTATATTA
34748307 TAAAACTGTATA
66 TAAAACTGTATA
34748319 TTATAATATT
Statistics
Matches: 73, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
83 73 1.00
ACGTcount: A:0.44, C:0.11, G:0.09, T:0.36
Consensus pattern (83 bp):
TATGTTTAACGCATGAACCACTAAAAAACAATAGTATTAGTAAATCATAATATTACTGTATATTA
TAAAACTGTATACAATTG
Found at i:34748316 original size:15 final size:15
Alignment explanation
Indices: 34748296--34748324 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
34748286 TCATAATATT
34748296 ACTGTATATTATAAA
1 ACTGTATATTATAAA
34748311 ACTGTATATTATAA
1 ACTGTATATTATAA
34748325 TATTATGAAT
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:0.45, C:0.07, G:0.07, T:0.41
Consensus pattern (15 bp):
ACTGTATATTATAAA
Found at i:34751511 original size:45 final size:45
Alignment explanation
Indices: 34751442--34751641 Score: 138
Period size: 45 Copynumber: 4.5 Consensus size: 45
34751432 TACACGGTGG
* * * *
34751442 ATCAGCACACAAC-ACCACCCTTATAGTCAATAGTA-CTCGGTGAA
1 ATCAGCACATAGCAACCACCTTTATAATCAATAGTATC-CGGTGAA
* *
34751486 ATCAGCACATAGCAACCACCTTTATACTCAATGGTA-CCAGGTGAA
1 ATCAGCACATAGCAACCACCTTTATAATCAATAGTATCC-GGTGAA
* * * * * *
34751531 TTCAGGACATAGCAATCA-CTTATATAACCATTGGTATCCGGTGAA
1 ATCAGCACATAGCAACCACCTT-TATAATCAATAGTATCCGGTGAA
* * * * ** * * *
34751576 ATCAACATATAGCGATCACCTTTATTTTCATTAATATCCGGTGGA
1 ATCAGCACATAGCAACCACCTTTATAATCAATAGTATCCGGTGAA
* *
34751621 ATCTGCACATAGCATCCACCT
1 ATCAGCACATAGCAACCACCT
34751642 ATATTTCCAA
Statistics
Matches: 123, Mismatches: 28, Indels: 9
0.77 0.17 0.06
Matches are distributed among these distances:
44 15 0.12
45 103 0.84
46 5 0.04
ACGTcount: A:0.34, C:0.26, G:0.14, T:0.27
Consensus pattern (45 bp):
ATCAGCACATAGCAACCACCTTTATAATCAATAGTATCCGGTGAA
Found at i:34751658 original size:45 final size:45
Alignment explanation
Indices: 34751565--34751660 Score: 104
Period size: 45 Copynumber: 2.1 Consensus size: 45
34751555 TAACCATTGG
* * * *
34751565 TATCCGGTGAAATCAACATATAGCGATCACCTTTATTTTCATTAA
1 TATCCGGTGAAATCAACACATAGCGATCACCTATATTTCCAATAA
* ** *
34751610 TATCCGGTGGAATCTGCACATAGC-ATCCACCTATATTTCCAATGA
1 TATCCGGTGAAATCAACACATAGCGAT-CACCTATATTTCCAATAA
34751655 TATCCG
1 TATCCG
34751661 ATCCATTCCG
Statistics
Matches: 42, Mismatches: 8, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
44 2 0.05
45 40 0.95
ACGTcount: A:0.30, C:0.24, G:0.14, T:0.32
Consensus pattern (45 bp):
TATCCGGTGAAATCAACACATAGCGATCACCTATATTTCCAATAA
Found at i:34756639 original size:14 final size:15
Alignment explanation
Indices: 34756608--34756644 Score: 58
Period size: 14 Copynumber: 2.5 Consensus size: 15
34756598 GAGAACTTGA
34756608 TATAAATAATAGTATG
1 TATAAA-AATAGTATG
34756624 TATAAAAATA-TATG
1 TATAAAAATAGTATG
34756638 TATAAAA
1 TATAAAA
34756645 GTTGAAATAA
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
14 11 0.52
15 4 0.19
16 6 0.29
ACGTcount: A:0.57, C:0.00, G:0.08, T:0.35
Consensus pattern (15 bp):
TATAAAAATAGTATG
Found at i:34757612 original size:17 final size:17
Alignment explanation
Indices: 34757590--34757634 Score: 56
Period size: 17 Copynumber: 2.6 Consensus size: 17
34757580 TTAAGTATAT
34757590 AAAAAAGAAACAAGAAC
1 AAAAAAGAAACAAGAAC
* *
34757607 AAAAAAGATAGAAGAAC
1 AAAAAAGAAACAAGAAC
34757624 AGAAAAA-AAAC
1 A-AAAAAGAAAC
34757635 TTTGAAGAAG
Statistics
Matches: 23, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
17 18 0.78
18 5 0.22
ACGTcount: A:0.76, C:0.09, G:0.13, T:0.02
Consensus pattern (17 bp):
AAAAAAGAAACAAGAAC
Found at i:34758582 original size:44 final size:44
Alignment explanation
Indices: 34758520--34759057 Score: 227
Period size: 44 Copynumber: 11.5 Consensus size: 44
34758510 GATCTACTCT
* *
34758520 ACTGTAA-CTTCAGAGAGATAAGATCCTTTATTTTAATCCGCTCC
1 ACTGTAATC-TCAGGGAGATAAGATCCTTTACTTTAATCCGCTCC
* * * *
34758564 ACTGTAATCTCAGGGAGATAGGAT--TACTAGCTTCAATCTGCTCC
1 ACTGTAATCTCAGGGAGATAAGATCCT-TTA-CTTTAATCCGCTCC
* * * * * *
34758608 GCTGTAATCTCAGGGAGATAAGATTTCTGGCTTCAATCTGATGCGATCTACTC
1 ACTGTAATCTCAGGGAGATAAGA--TC---CTTTACTTTAATCCG--CT-C-C
* *
34758661 TACTGTAA-CTTCAGAGAGATAAGATCCTTTATTTTAATCCGCTCC
1 -ACTGTAATC-TCAGGGAGATAAGATCCTTTACTTTAATCCGCTCC
* * * *
34758706 ACTGTAATCTCAGGGAGATAGGAT--TACTAGCTTCAATCTGCTCC
1 ACTGTAATCTCAGGGAGATAAGATCCT-TTA-CTTTAATCCGCTCC
* * * * * *
34758750 GCTGTAATCTCAGGGAGATAAGATTTCTGGCTTCAATCTGATGCGATCTACTC
1 ACTGTAATCTCAGGGAGATAAGA--TC---CTTTACTTTAATCCG--CT-C-C
* *
34758803 TACTGTAA-CTTCAGAGAGATAAGATCCTTTATTTTAATCCGCTCC
1 -ACTGTAATC-TCAGGGAGATAAGATCCTTTACTTTAATCCGCTCC
* * * *
34758848 ACTGTAATCTCAGGGAGATAGGAT--TACTAGCTTCAATCTGCTCC
1 ACTGTAATCTCAGGGAGATAAGATCCT-TTA-CTTTAATCCGCTCC
* * * * * *
34758892 GCTGTAATCTCAGGGAGATAAGATTTCTGGCTTCAATCTGATGCGATCTACTC
1 ACTGTAATCTCAGGGAGATAAGA--TC---CTTTACTTTAATCCG--CT-C-C
* *
34758945 TACTGTAA-CTTCAGAGAGATAAGATCCTTTATTTTAATCCGCTCC
1 -ACTGTAATC-TCAGGGAGATAAGATCCTTTACTTTAATCCGCTCC
* * * *
34758990 ACTGTAATCTCAGGGAGATAGGAT--TACTAGCTTCAATCTGCTCC
1 ACTGTAATCTCAGGGAGATAAGATCCT-TTA-CTTTAATCCGCTCC
*
34759034 GCTGTAATCTCAGGGAGATAAGAT
1 ACTGTAATCTCAGGGAGATAAGAT
34759058 TTCTGGCTTC
Statistics
Matches: 366, Mismatches: 77, Indels: 102
0.67 0.14 0.19
Matches are distributed among these distances:
42 4 0.01
43 8 0.02
44 209 0.57
45 7 0.02
46 6 0.02
47 6 0.02
49 42 0.11
50 3 0.01
51 9 0.02
52 9 0.02
53 6 0.02
54 57 0.16
ACGTcount: A:0.27, C:0.22, G:0.19, T:0.32
Consensus pattern (44 bp):
ACTGTAATCTCAGGGAGATAAGATCCTTTACTTTAATCCGCTCC
Found at i:34758739 original size:98 final size:93
Alignment explanation
Indices: 34758558--34759057 Score: 288
Period size: 98 Copynumber: 5.3 Consensus size: 93
34758548 TATTTTAATC
* * * * * * *
34758558 CGCTCCACTGTAATCTCAGGGAGATAGGAT--TACTAGCTTCAATCTGCTCCGCTGTAATCTCAG
1 CGCTCCACTGTAATCTCAGAGAGATAAGATCCT-TTA-TTTTAATCCGCTCCACTGTAATCTCAG
* *
34758621 GGAGATAAGATTTCTGGCTTCAATCTGATG
64 GGAGATAAGATTACTAGCTTCAATCTGATG
34758651 CGATCTACTCTACTGTAA-CTTCAGAGAGATAAGATCCTTTATTTTAATCCGCTCCACTGTAATC
1 CG--CT-C-C-ACTGTAATC-TCAGAGAGATAAGATCCTTTATTTTAATCCGCTCCACTGTAATC
*
34758715 TCAGGGAGATAGGATTACTAGCTTCAATC---T-
60 TCAGGGAGATAAGATTACTAGCTTCAATCTGATG
* * * * * * *
34758745 -GCTCCGCTGTAATCTCAGGGAGATAAGATTTCTGGCTTCAATCTGATGCGATCTACTCTACTGT
1 CGCTCCACTGTAATCTCAGAGAGATAAGA--TC---CTTTATTTTAATCCG--CT-C-C-ACTGT
* * * * * *
34758809 AA-CTTCAGAGAGATAAGA-T-C---CTTTATTTTAATC
56 AATC-TCAGGGAGATAAGATTACTAGCTTCAATCTGATG
* * * * * * *
34758842 CGCTCCACTGTAATCTCAGGGAGATAGGAT--TACTAGCTTCAATCTGCTCCGCTGTAATCTCAG
1 CGCTCCACTGTAATCTCAGAGAGATAAGATCCT-TTA-TTTTAATCCGCTCCACTGTAATCTCAG
* *
34758905 GGAGATAAGATTTCTGGCTTCAATCTGATG
64 GGAGATAAGATTACTAGCTTCAATCTGATG
34758935 CGATCTACTCTACTGTAA-CTTCAGAGAGATAAGATCCTTTATTTTAATCCGCTCCACTGTAATC
1 CG--CT-C-C-ACTGTAATC-TCAGAGAGATAAGATCCTTTATTTTAATCCGCTCCACTGTAATC
*
34758999 TCAGGGAGATAGGATTACTAGCTTCAATC---T-
60 TCAGGGAGATAAGATTACTAGCTTCAATCTGATG
* *
34759029 -GCTCCGCTGTAATCTCAGGGAGATAAGAT
1 CGCTCCACTGTAATCTCAGAGAGATAAGAT
34759058 TTCTGGCTTC
Statistics
Matches: 314, Mismatches: 51, Indels: 89
0.69 0.11 0.20
Matches are distributed among these distances:
88 58 0.18
89 7 0.02
90 6 0.02
91 7 0.02
92 1 0.00
93 33 0.11
95 8 0.03
96 6 0.02
97 7 0.02
98 175 0.56
99 4 0.01
100 2 0.01
ACGTcount: A:0.27, C:0.22, G:0.20, T:0.32
Consensus pattern (93 bp):
CGCTCCACTGTAATCTCAGAGAGATAAGATCCTTTATTTTAATCCGCTCCACTGTAATCTCAGGG
AGATAAGATTACTAGCTTCAATCTGATG
Found at i:34758760 original size:142 final size:142
Alignment explanation
Indices: 34758504--34759073 Score: 1140
Period size: 142 Copynumber: 4.0 Consensus size: 142
34758494 AGATAAGACT
34758504 TGATGCGATCTACTCTACTGTAACTTCAGAGAGATAAGATCCTTTATTTTAATCCGCTCCACTGT
1 TGATGCGATCTACTCTACTGTAACTTCAGAGAGATAAGATCCTTTATTTTAATCCGCTCCACTGT
34758569 AATCTCAGGGAGATAGGATTACTAGCTTCAATCTGCTCCGCTGTAATCTCAGGGAGATAAGATTT
66 AATCTCAGGGAGATAGGATTACTAGCTTCAATCTGCTCCGCTGTAATCTCAGGGAGATAAGATTT
34758634 CTGGCTTCAATC
131 CTGGCTTCAATC
34758646 TGATGCGATCTACTCTACTGTAACTTCAGAGAGATAAGATCCTTTATTTTAATCCGCTCCACTGT
1 TGATGCGATCTACTCTACTGTAACTTCAGAGAGATAAGATCCTTTATTTTAATCCGCTCCACTGT
34758711 AATCTCAGGGAGATAGGATTACTAGCTTCAATCTGCTCCGCTGTAATCTCAGGGAGATAAGATTT
66 AATCTCAGGGAGATAGGATTACTAGCTTCAATCTGCTCCGCTGTAATCTCAGGGAGATAAGATTT
34758776 CTGGCTTCAATC
131 CTGGCTTCAATC
34758788 TGATGCGATCTACTCTACTGTAACTTCAGAGAGATAAGATCCTTTATTTTAATCCGCTCCACTGT
1 TGATGCGATCTACTCTACTGTAACTTCAGAGAGATAAGATCCTTTATTTTAATCCGCTCCACTGT
34758853 AATCTCAGGGAGATAGGATTACTAGCTTCAATCTGCTCCGCTGTAATCTCAGGGAGATAAGATTT
66 AATCTCAGGGAGATAGGATTACTAGCTTCAATCTGCTCCGCTGTAATCTCAGGGAGATAAGATTT
34758918 CTGGCTTCAATC
131 CTGGCTTCAATC
34758930 TGATGCGATCTACTCTACTGTAACTTCAGAGAGATAAGATCCTTTATTTTAATCCGCTCCACTGT
1 TGATGCGATCTACTCTACTGTAACTTCAGAGAGATAAGATCCTTTATTTTAATCCGCTCCACTGT
34758995 AATCTCAGGGAGATAGGATTACTAGCTTCAATCTGCTCCGCTGTAATCTCAGGGAGATAAGATTT
66 AATCTCAGGGAGATAGGATTACTAGCTTCAATCTGCTCCGCTGTAATCTCAGGGAGATAAGATTT
34759060 CTGGCTTCAATC
131 CTGGCTTCAATC
34759072 TG
1 TG
34759074 CTCCACTGTT
Statistics
Matches: 428, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
142 428 1.00
ACGTcount: A:0.27, C:0.22, G:0.19, T:0.32
Consensus pattern (142 bp):
TGATGCGATCTACTCTACTGTAACTTCAGAGAGATAAGATCCTTTATTTTAATCCGCTCCACTGT
AATCTCAGGGAGATAGGATTACTAGCTTCAATCTGCTCCGCTGTAATCTCAGGGAGATAAGATTT
CTGGCTTCAATC
Found at i:34759067 original size:44 final size:44
Alignment explanation
Indices: 34758980--34759082 Score: 161
Period size: 44 Copynumber: 2.3 Consensus size: 44
34758970 CCTTTATTTT
* *
34758980 AATCCGCTCCACTGTAATCTCAGGGAGATAGGATTACTAGCTTC
1 AATCTGCTCCACTGTAATCTCAGGGAGATAAGATTACTAGCTTC
* * *
34759024 AATCTGCTCCGCTGTAATCTCAGGGAGATAAGATTTCTGGCTTC
1 AATCTGCTCCACTGTAATCTCAGGGAGATAAGATTACTAGCTTC
34759068 AATCTGCTCCACTGT
1 AATCTGCTCCACTGT
34759083 TGCTTAGGAA
Statistics
Matches: 53, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
44 53 1.00
ACGTcount: A:0.24, C:0.25, G:0.20, T:0.30
Consensus pattern (44 bp):
AATCTGCTCCACTGTAATCTCAGGGAGATAAGATTACTAGCTTC
Found at i:34777460 original size:25 final size:28
Alignment explanation
Indices: 34777426--34777498 Score: 98
Period size: 29 Copynumber: 2.6 Consensus size: 28
34777416 TTTCAAAGGT
*
34777426 TTTAGCAGAAA-G-AAT-CACAAATTAG
1 TTTAGAAGAAACGAAATGCACAAATTAG
34777451 TTTAGAAGAAAACGAAATGCACAAATTAG
1 TTTAGAAG-AAACGAAATGCACAAATTAG
34777480 TTTAGAAGAAAACGAAATG
1 TTTAGAAG-AAACGAAATG
34777499 ACATTAATCC
Statistics
Matches: 43, Mismatches: 1, Indels: 4
0.90 0.02 0.08
Matches are distributed among these distances:
25 7 0.16
26 3 0.07
27 1 0.02
28 3 0.07
29 29 0.67
ACGTcount: A:0.51, C:0.10, G:0.18, T:0.22
Consensus pattern (28 bp):
TTTAGAAGAAACGAAATGCACAAATTAG
Found at i:34777474 original size:29 final size:29
Alignment explanation
Indices: 34777441--34777498 Score: 116
Period size: 29 Copynumber: 2.0 Consensus size: 29
34777431 CAGAAAGAAT
34777441 CACAAATTAGTTTAGAAGAAAACGAAATG
1 CACAAATTAGTTTAGAAGAAAACGAAATG
34777470 CACAAATTAGTTTAGAAGAAAACGAAATG
1 CACAAATTAGTTTAGAAGAAAACGAAATG
34777499 ACATTAATCC
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 29 1.00
ACGTcount: A:0.52, C:0.10, G:0.17, T:0.21
Consensus pattern (29 bp):
CACAAATTAGTTTAGAAGAAAACGAAATG
Found at i:34782875 original size:347 final size:347
Alignment explanation
Indices: 34782240--34782936 Score: 1394
Period size: 347 Copynumber: 2.0 Consensus size: 347
34782230 ACTAGTGAAA
34782240 AAGCAGTCTCTTTTCCTATTGCTATTAACAAATATTGTCATCAACGTTTGTCCTTCAAACGCGAC
1 AAGCAGTCTCTTTTCCTATTGCTATTAACAAATATTGTCATCAACGTTTGTCCTTCAAACGCGAC
34782305 TTTGAGTTCATCTTCTAAGGTTTTTCTTTTCATCTTTTTGTAATTTTACAATTGTTTTTATTGTG
66 TTTGAGTTCATCTTCTAAGGTTTTTCTTTTCATCTTTTTGTAATTTTACAATTGTTTTTATTGTG
34782370 TTTTAAAGTTTATAGTTTAATTTTATTTTATAGCTATTATTTGTTTTTATCTTTTAAGATATTGT
131 TTTTAAAGTTTATAGTTTAATTTTATTTTATAGCTATTATTTGTTTTTATCTTTTAAGATATTGT
34782435 AGTTATGAAGTCAAAAACAATTGATTCGTTTTTTAAAAAGAAAAGTACAAAGACTACACAATCAC
196 AGTTATGAAGTCAAAAACAATTGATTCGTTTTTTAAAAAGAAAAGTACAAAGACTACACAATCAC
34782500 CTTCAGAAGCGTCACAAATTGAGGTACCACCTTCATCGTTTGTTTCTTTAAACTTTGATGCTCGT
261 CTTCAGAAGCGTCACAAATTGAGGTACCACCTTCATCGTTTGTTTCTTTAAACTTTGATGCTCGT
34782565 CCTTCTAAAATTCCTAGAGTTG
326 CCTTCTAAAATTCCTAGAGTTG
34782587 AAGCAGTCTCTTTTCCTATTGCTATTAACAAATATTGTCATCAACGTTTGTCCTTCAAACGCGAC
1 AAGCAGTCTCTTTTCCTATTGCTATTAACAAATATTGTCATCAACGTTTGTCCTTCAAACGCGAC
34782652 TTTGAGTTCATCTTCTAAGGTTTTTCTTTTCATCTTTTTGTAATTTTACAATTGTTTTTATTGTG
66 TTTGAGTTCATCTTCTAAGGTTTTTCTTTTCATCTTTTTGTAATTTTACAATTGTTTTTATTGTG
34782717 TTTTAAAGTTTATAGTTTAATTTTATTTTATAGCTATTATTTGTTTTTATCTTTTAAGATATTGT
131 TTTTAAAGTTTATAGTTTAATTTTATTTTATAGCTATTATTTGTTTTTATCTTTTAAGATATTGT
34782782 AGTTATGAAGTCAAAAACAATTGATTCGTTTTTTAAAAAGAAAAGTACAAAGACTACACAATCAC
196 AGTTATGAAGTCAAAAACAATTGATTCGTTTTTTAAAAAGAAAAGTACAAAGACTACACAATCAC
34782847 CTTCAGAAGCGTCACAAATTGAGGTACCACCTTCATCGTTTGTTTCTTTAAACTTTGATGCTCGT
261 CTTCAGAAGCGTCACAAATTGAGGTACCACCTTCATCGTTTGTTTCTTTAAACTTTGATGCTCGT
34782912 CCTTCTAAAATTCCTAGAGTTG
326 CCTTCTAAAATTCCTAGAGTTG
34782934 AAG
1 AAG
34782937 ATGAGGCACT
Statistics
Matches: 350, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
347 350 1.00
ACGTcount: A:0.28, C:0.15, G:0.13, T:0.43
Consensus pattern (347 bp):
AAGCAGTCTCTTTTCCTATTGCTATTAACAAATATTGTCATCAACGTTTGTCCTTCAAACGCGAC
TTTGAGTTCATCTTCTAAGGTTTTTCTTTTCATCTTTTTGTAATTTTACAATTGTTTTTATTGTG
TTTTAAAGTTTATAGTTTAATTTTATTTTATAGCTATTATTTGTTTTTATCTTTTAAGATATTGT
AGTTATGAAGTCAAAAACAATTGATTCGTTTTTTAAAAAGAAAAGTACAAAGACTACACAATCAC
CTTCAGAAGCGTCACAAATTGAGGTACCACCTTCATCGTTTGTTTCTTTAAACTTTGATGCTCGT
CCTTCTAAAATTCCTAGAGTTG
Found at i:34792253 original size:16 final size:16
Alignment explanation
Indices: 34792232--34792262 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
34792222 TTTCTAGTAT
34792232 TTTATTTACTAGCGTG
1 TTTATTTACTAGCGTG
34792248 TTTATTTACTAGCGT
1 TTTATTTACTAGCGT
34792263 ATTTGCTCTT
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:0.19, C:0.13, G:0.16, T:0.52
Consensus pattern (16 bp):
TTTATTTACTAGCGTG
Found at i:34797898 original size:15 final size:15
Alignment explanation
Indices: 34797874--34797913 Score: 53
Period size: 15 Copynumber: 2.7 Consensus size: 15
34797864 TGAATTTTAT
*
34797874 ATTGAATTGAATTGA
1 ATTGATTTGAATTGA
*
34797889 ATTGATTTGATTTGA
1 ATTGATTTGAATTGA
*
34797904 TTTGATTTGA
1 ATTGATTTGA
34797914 GAAAAATATA
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
15 22 1.00
ACGTcount: A:0.30, C:0.00, G:0.20, T:0.50
Consensus pattern (15 bp):
ATTGATTTGAATTGA
Found at i:34801580 original size:17 final size:17
Alignment explanation
Indices: 34801538--34801581 Score: 70
Period size: 17 Copynumber: 2.6 Consensus size: 17
34801528 AAAGACTGTT
*
34801538 GAACAAAACAAGTTAGC
1 GAACAAAATAAGTTAGC
*
34801555 GAACAAAATACGTTAGC
1 GAACAAAATAAGTTAGC
34801572 GAACAAAATA
1 GAACAAAATA
34801582 TATAAATATA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
17 25 1.00
ACGTcount: A:0.55, C:0.16, G:0.16, T:0.14
Consensus pattern (17 bp):
GAACAAAATAAGTTAGC
Found at i:34801604 original size:16 final size:17
Alignment explanation
Indices: 34801583--34801630 Score: 55
Period size: 16 Copynumber: 2.8 Consensus size: 17
34801573 AACAAAATAT
34801583 ATAAATATATAAATAAA
1 ATAAATATATAAATAAA
*
34801600 A-AAATATTTATATATAAA
1 ATAAATA--TATAAATAAA
34801618 ATAAA-ATATAAAT
1 ATAAATATATAAAT
34801631 TGAATAGTTT
Statistics
Matches: 26, Mismatches: 2, Indels: 7
0.74 0.06 0.20
Matches are distributed among these distances:
16 11 0.42
17 1 0.04
18 11 0.42
19 3 0.12
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (17 bp):
ATAAATATATAAATAAA
Found at i:34801606 original size:22 final size:20
Alignment explanation
Indices: 34801576--34801630 Score: 56
Period size: 22 Copynumber: 2.6 Consensus size: 20
34801566 GTTAGCGAAC
*
34801576 AAAATATATAAATATATAAATA
1 AAAAAATATAAATATAT-AA-A
**
34801598 AAAAAATATTTATATATAAA
1 AAAAAATATAAATATATAAA
*
34801618 ATAAAATATAAAT
1 AAAAAATATAAAT
34801631 TGAATAGTTT
Statistics
Matches: 27, Mismatches: 6, Indels: 2
0.77 0.17 0.06
Matches are distributed among these distances:
20 11 0.41
21 2 0.07
22 14 0.52
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (20 bp):
AAAAAATATAAATATATAAA
Found at i:34801613 original size:20 final size:20
Alignment explanation
Indices: 34801587--34801626 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
34801577 AAATATATAA
34801587 ATATATAAATAAAAAAATATTT
1 ATATAT-AA-AAAAAAATATTT
*
34801609 ATATATAAAATAAAATAT
1 ATATATAAAAAAAAATAT
34801627 AAATTGAATA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 9 0.53
21 2 0.12
22 6 0.35
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (20 bp):
ATATATAAAAAAAAATATTT
Found at i:34802095 original size:20 final size:20
Alignment explanation
Indices: 34802070--34802138 Score: 93
Period size: 20 Copynumber: 3.5 Consensus size: 20
34802060 AGTGGCTATT
* * *
34802070 AAATCAATTTGATAAAAATC
1 AAATCAAATTGATTAGAATC
34802090 AAATCAAATTGATTAGAATC
1 AAATCAAATTGATTAGAATC
*
34802110 AAATAAAATTGATTAGAATC
1 AAATCAAATTGATTAGAATC
*
34802130 AAATAAAAT
1 AAATCAAAT
34802139 AAGGATATAT
Statistics
Matches: 45, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 45 1.00
ACGTcount: A:0.57, C:0.07, G:0.07, T:0.29
Consensus pattern (20 bp):
AAATCAAATTGATTAGAATC
Found at i:34806201 original size:14 final size:14
Alignment explanation
Indices: 34806182--34806235 Score: 58
Period size: 14 Copynumber: 4.0 Consensus size: 14
34806172 ACGTTATCGA
34806182 ATAAATATATAAAT
1 ATAAATATATAAAT
* *
34806196 ATAAATAAACAAAT
1 ATAAATATATAAAT
**
34806210 ATTTATATATAAA-
1 ATAAATATATAAAT
34806223 ATAAA-ATATAAAT
1 ATAAATATATAAAT
34806236 TGGAATAATT
Statistics
Matches: 31, Mismatches: 8, Indels: 3
0.74 0.19 0.07
Matches are distributed among these distances:
12 7 0.23
13 3 0.10
14 21 0.68
ACGTcount: A:0.65, C:0.02, G:0.00, T:0.33
Consensus pattern (14 bp):
ATAAATATATAAAT
Found at i:34806219 original size:22 final size:23
Alignment explanation
Indices: 34806184--34806227 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 23
34806174 GTTATCGAAT
34806184 AAATATATAAATAT-AAATAAAC
1 AAATATATAAATATAAAATAAAC
* *
34806206 AAATATTTATATATAAAATAAA
1 AAATATATAAATATAAAATAAA
34806228 ATATAAATTG
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
22 12 0.63
23 7 0.37
ACGTcount: A:0.66, C:0.02, G:0.00, T:0.32
Consensus pattern (23 bp):
AAATATATAAATATAAAATAAAC
Found at i:34806705 original size:20 final size:20
Alignment explanation
Indices: 34806682--34806722 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 20
34806672 TTAAATCAAT
*
34806682 TTGATTAAAATCAAATTAAA
1 TTGATTAAAATCAAATAAAA
*
34806702 TTGATTAGAATCAAATAAAA
1 TTGATTAAAATCAAATAAAA
34806722 T
1 T
34806723 CAGGATATAT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.54, C:0.05, G:0.07, T:0.34
Consensus pattern (20 bp):
TTGATTAAAATCAAATAAAA
Found at i:34807990 original size:12 final size:14
Alignment explanation
Indices: 34807960--34807991 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
34807950 AATCAAATAA
34807960 AAAAATTAGAATGT
1 AAAAATTAGAATGT
34807974 AAAAATTA-AAT-T
1 AAAAATTAGAATGT
34807986 AAAAAT
1 AAAAAT
34807992 AAAAAATATT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
12 7 0.39
13 3 0.17
14 8 0.44
ACGTcount: A:0.66, C:0.00, G:0.06, T:0.28
Consensus pattern (14 bp):
AAAAATTAGAATGT
Found at i:34808018 original size:12 final size:12
Alignment explanation
Indices: 34808001--34808041 Score: 64
Period size: 12 Copynumber: 3.4 Consensus size: 12
34807991 TAAAAAATAT
*
34808001 TAAAACGAAAAC
1 TAAAACTAAAAC
34808013 TAAAACTAAAAC
1 TAAAACTAAAAC
*
34808025 TAAAACTAAAAA
1 TAAAACTAAAAC
34808037 TAAAA
1 TAAAA
34808042 ATGGCTAAAT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
12 27 1.00
ACGTcount: A:0.71, C:0.12, G:0.02, T:0.15
Consensus pattern (12 bp):
TAAAACTAAAAC
Found at i:34808023 original size:34 final size:34
Alignment explanation
Indices: 34807954--34808029 Score: 82
Period size: 34 Copynumber: 2.2 Consensus size: 34
34807944 TGTAAGAATC
* * * *
34807954 AAATAAAAAAATTAGAATGTAAAAATTAAATTAA
1 AAATAAAAAAATTAAAACGTAAAAATAAAACTAA
*
34807988 AAATAAAAAATATTAAAACG-AAAACTAAAACTAA
1 AAATAAAAAA-ATTAAAACGTAAAAATAAAACTAA
*
34808022 AACTAAAA
1 AAATAAAA
34808030 CTAAAAATAA
Statistics
Matches: 35, Mismatches: 6, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
34 28 0.80
35 7 0.20
ACGTcount: A:0.70, C:0.05, G:0.04, T:0.21
Consensus pattern (34 bp):
AAATAAAAAAATTAAAACGTAAAAATAAAACTAA
Found at i:34808024 original size:18 final size:18
Alignment explanation
Indices: 34808001--34808041 Score: 64
Period size: 18 Copynumber: 2.3 Consensus size: 18
34807991 TAAAAAATAT
*
34808001 TAAAACGAAAACTAAAAC
1 TAAAACGAAAACTAAAAA
*
34808019 TAAAACTAAAACTAAAAA
1 TAAAACGAAAACTAAAAA
34808037 TAAAA
1 TAAAA
34808042 ATGGCTAAAT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.71, C:0.12, G:0.02, T:0.15
Consensus pattern (18 bp):
TAAAACGAAAACTAAAAA
Found at i:34810030 original size:66 final size:66
Alignment explanation
Indices: 34809941--34810161 Score: 406
Period size: 66 Copynumber: 3.3 Consensus size: 66
34809931 TATTTAACTC
*
34809941 TAAATTTAATTATCAAGTCAAAATCGAATTTGAATACTAGTCCAAATTTAAATACAAAATTTGAT
1 TAAATTTAATCA--AAGTCAAAATCGAATTTGAATACTAGTCCAAATTTAAATACAAAATTTGAT
34810006 AAA
64 AAA
34810009 TAAATTTAATCAAAGTCAAAATCGAATTTGAATACTAGTCCAAATTTAAATACAAAATTTGATAA
1 TAAATTTAATCAAAGTCAAAATCGAATTTGAATACTAGTCCAAATTTAAATACAAAATTTGATAA
34810074 A
66 A
34810075 TAAATTTAATCAAAGTCAAAATCGAATTTGAATACTAGTCCAAATTTAAATACAAAATTTGATAA
1 TAAATTTAATCAAAGTCAAAATCGAATTTGAATACTAGTCCAAATTTAAATACAAAATTTGATAA
34810140 A
66 A
*
34810141 TAAATTTAATCAAACTCAAAA
1 TAAATTTAATCAAAGTCAAAA
34810162 GTAAAATATC
Statistics
Matches: 151, Mismatches: 2, Indels: 2
0.97 0.01 0.01
Matches are distributed among these distances:
66 140 0.93
68 11 0.07
ACGTcount: A:0.50, C:0.11, G:0.07, T:0.32
Consensus pattern (66 bp):
TAAATTTAATCAAAGTCAAAATCGAATTTGAATACTAGTCCAAATTTAAATACAAAATTTGATAA
A
Found at i:34818054 original size:24 final size:23
Alignment explanation
Indices: 34818027--34818089 Score: 54
Period size: 25 Copynumber: 2.6 Consensus size: 23
34818017 TAGCTCAAAA
*
34818027 GAGTGTCCCGTTATTAGCTCTCAT
1 GAGT-TCCCGTTATTAGCTCTCAC
* * *
34818051 GAGTATCCTGATATTTGGCTCTCAC
1 GAGT-TCCCGTTA-TTAGCTCTCAC
34818076 GAGCTTCCCGTTAT
1 GAG-TTCCCGTTAT
34818090 ATGGTTCTTG
Statistics
Matches: 30, Mismatches: 7, Indels: 4
0.73 0.17 0.10
Matches are distributed among these distances:
24 11 0.37
25 18 0.60
26 1 0.03
ACGTcount: A:0.17, C:0.25, G:0.21, T:0.37
Consensus pattern (23 bp):
GAGTTCCCGTTATTAGCTCTCAC
Found at i:34818248 original size:25 final size:24
Alignment explanation
Indices: 34818179--34818248 Score: 68
Period size: 24 Copynumber: 2.8 Consensus size: 24
34818169 CACAACTCTT
* * **
34818179 ATGAGCGTCCTGATATTTGGCTCTT
1 ATGAGC-TCCTGTTATATGGCTCAA
* *
34818204 ATGAGCTCCCGTTACATGGCTCAA
1 ATGAGCTCCTGTTATATGGCTCAA
34818228 ATGAGCTTCCTGTTATATGGC
1 ATGAGC-TCCTGTTATATGGC
34818249 ACGAGAGAGA
Statistics
Matches: 36, Mismatches: 8, Indels: 2
0.78 0.17 0.04
Matches are distributed among these distances:
24 18 0.50
25 18 0.50
ACGTcount: A:0.20, C:0.23, G:0.23, T:0.34
Consensus pattern (24 bp):
ATGAGCTCCTGTTATATGGCTCAA
Found at i:34825491 original size:24 final size:24
Alignment explanation
Indices: 34825463--34825543 Score: 83
Period size: 24 Copynumber: 3.3 Consensus size: 24
34825453 CATGTAATGA
*
34825463 GAAGCTCTAGAGAGCCATTAACGG
1 GAAGCTCTAGAGAGCAATTAACGG
* * *
34825487 GAAGCT-TATACGAGCAAATATCGG
1 GAAGCTCTAGA-GAGCAATTAACGG
*
34825511 GAAGCTCTAGAGAGGCAATTAATCGA
1 GAAGCTCTAGAGA-GCAATTAA-CGG
34825537 GAAGCTC
1 GAAGCTC
34825544 CGAAGAGCCA
Statistics
Matches: 45, Mismatches: 8, Indels: 6
0.76 0.14 0.10
Matches are distributed among these distances:
23 3 0.07
24 24 0.53
25 9 0.20
26 9 0.20
ACGTcount: A:0.36, C:0.19, G:0.27, T:0.19
Consensus pattern (24 bp):
GAAGCTCTAGAGAGCAATTAACGG
Found at i:34825654 original size:24 final size:25
Alignment explanation
Indices: 34825627--34825675 Score: 73
Period size: 25 Copynumber: 2.0 Consensus size: 25
34825617 GGATGCTTTG
* *
34825627 AAGAACTAT-TAATGGGAAGCTCGT
1 AAGAACCATATAACGGGAAGCTCGT
34825651 AAGAACCATATAACGGGAAGCTCGT
1 AAGAACCATATAACGGGAAGCTCGT
34825676 GAGAGCCAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
24 8 0.36
25 14 0.64
ACGTcount: A:0.39, C:0.16, G:0.24, T:0.20
Consensus pattern (25 bp):
AAGAACCATATAACGGGAAGCTCGT
Found at i:34864455 original size:27 final size:27
Alignment explanation
Indices: 34864424--34864503 Score: 99
Period size: 27 Copynumber: 3.0 Consensus size: 27
34864414 ATATGTGCAA
* *
34864424 AGGGTAAAATGACTGAAATACCCTCG-
1 AGGGTAAAATGACTAAAATACCCCCGC
* *
34864450 ATGGGTAAAATGGCTAAAATGCCCCCGC
1 A-GGGTAAAATGACTAAAATACCCCCGC
*
34864478 AGGGTAAAATGACCAAAATACCCCCG
1 AGGGTAAAATGACTAAAATACCCCCG
34864504 GAGGATAGAA
Statistics
Matches: 45, Mismatches: 7, Indels: 3
0.82 0.13 0.05
Matches are distributed among these distances:
26 1 0.02
27 43 0.96
28 1 0.02
ACGTcount: A:0.38, C:0.24, G:0.23, T:0.16
Consensus pattern (27 bp):
AGGGTAAAATGACTAAAATACCCCCGC
Found at i:34864565 original size:27 final size:27
Alignment explanation
Indices: 34864530--34864794 Score: 268
Period size: 27 Copynumber: 9.9 Consensus size: 27
34864520 AATACCTCCA
* * **
34864530 TAGGATAAAATAATCGTAATAACCCTG
1 TAGGGTAAAATGATCGTAATGCCCCTG
* *
34864557 TGGGGTAAAATGA-CTGTAATGCCCCTA
1 TAGGGTAAAATGATC-GTAATGCCCCTG
* * *
34864584 TAGGGTAAAATAATCGTAATACCCTTG
1 TAGGGTAAAATGATCGTAATGCCCCTG
* * *
34864611 TAGGATAAAATGACCGTAATGCCCTTG
1 TAGGGTAAAATGATCGTAATGCCCCTG
*
34864638 TAGGGTAAAATGATCGTAATACCCCTG
1 TAGGGTAAAATGATCGTAATGCCCCTG
* *
34864665 TAGGGTAAATTGACCGTAATGCCCCT-
1 TAGGGTAAAATGATCGTAATGCCCCTG
34864691 TAGGGTAAAATGAAT-GTAATGCCCCTG
1 TAGGGTAAAATG-ATCGTAATGCCCCTG
* *
34864718 TAGGGTAAAATGATCGTAATGTCCTTG
1 TAGGGTAAAATGATCGTAATGCCCCTG
* * * * *
34864745 TAAGGTAAAATGACCATAATACCTCTG
1 TAGGGTAAAATGATCGTAATGCCCCTG
*
34864772 TAAGGTAAAATGA-CGGTAATGCC
1 TAGGGTAAAATGATC-GTAATGCC
34864795 TTAGTGGGTA
Statistics
Matches: 197, Mismatches: 35, Indels: 12
0.81 0.14 0.05
Matches are distributed among these distances:
26 26 0.13
27 170 0.86
28 1 0.01
ACGTcount: A:0.35, C:0.17, G:0.22, T:0.27
Consensus pattern (27 bp):
TAGGGTAAAATGATCGTAATGCCCCTG
Found at i:34864620 original size:54 final size:54
Alignment explanation
Indices: 34864529--34864794 Score: 311
Period size: 54 Copynumber: 4.9 Consensus size: 54
34864519 AAATACCTCC
* * * *
34864529 ATAGGATAAAATAATCGTAATAACCCTGTGGGGTAAAATGACTGTAATGCCCCT
1 ATAGGGTAAAATAATCGTAATACCCCTGTAGGGTAAAATGACCGTAATGCCCCT
* * *
34864583 ATAGGGTAAAATAATCGTAATACCCTTGTAGGATAAAATGACCGTAATGCCCTT
1 ATAGGGTAAAATAATCGTAATACCCCTGTAGGGTAAAATGACCGTAATGCCCCT
* * *
34864637 GTAGGGTAAAATGATCGTAATACCCCTGTAGGGTAAATTGACCGTAATGCCCCT
1 ATAGGGTAAAATAATCGTAATACCCCTGTAGGGTAAAATGACCGTAATGCCCCT
* * * *
34864691 -TAGGGTAAAATGAAT-GTAATGCCCCTGTAGGGTAAAATGATCGTAATGTCCTT
1 ATAGGGTAAAAT-AATCGTAATACCCCTGTAGGGTAAAATGACCGTAATGCCCCT
* * * * * * * *
34864744 GTAAGGTAAAATGACCATAATACCTCTGTAAGGTAAAATGACGGTAATGCC
1 ATAGGGTAAAATAATCGTAATACCCCTGTAGGGTAAAATGACCGTAATGCC
34864795 TTAGTGGGTA
Statistics
Matches: 180, Mismatches: 29, Indels: 6
0.84 0.13 0.03
Matches are distributed among these distances:
53 45 0.25
54 135 0.75
ACGTcount: A:0.35, C:0.17, G:0.22, T:0.27
Consensus pattern (54 bp):
ATAGGGTAAAATAATCGTAATACCCCTGTAGGGTAAAATGACCGTAATGCCCCT
Found at i:34864744 original size:107 final size:108
Alignment explanation
Indices: 34864530--34864794 Score: 354
Period size: 107 Copynumber: 2.5 Consensus size: 108
34864520 AATACCTCCA
* * * * *
34864530 TAGGATAAAATAATCGTAATAACCCTGTGGGGTAAAATGACTGTAATGCCCCTATAGGGTAAAAT
1 TAGGGTAAAATGATCGTAATACCCCTGTAGGGTAAAATGACCGTAATGCCCCTATAGGGTAAAAT
*
34864595 AATCGTAATACCCTTGTAGGATAAAATGACCGTAATGCCCTTG
66 AATCGTAATACCCCTGTAGGATAAAATGACCGTAATGCCCTTG
*
34864638 TAGGGTAAAATGATCGTAATACCCCTGTAGGGTAAATTGACCGTAATGCCCCT-TAGGGTAAAAT
1 TAGGGTAAAATGATCGTAATACCCCTGTAGGGTAAAATGACCGTAATGCCCCTATAGGGTAAAAT
* * * *
34864702 GAAT-GTAATGCCCCTGTAGGGTAAAATGATCGTAATGTCCTTG
66 -AATCGTAATACCCCTGTAGGATAAAATGACCGTAATGCCCTTG
* * * * * *
34864745 TAAGGTAAAATGACCATAATACCTCTGTAAGGTAAAATGACGGTAATGCC
1 TAGGGTAAAATGATCGTAATACCCCTGTAGGGTAAAATGACCGTAATGCC
34864795 TTAGTGGGTA
Statistics
Matches: 138, Mismatches: 18, Indels: 3
0.87 0.11 0.02
Matches are distributed among these distances:
107 88 0.64
108 50 0.36
ACGTcount: A:0.35, C:0.17, G:0.22, T:0.27
Consensus pattern (108 bp):
TAGGGTAAAATGATCGTAATACCCCTGTAGGGTAAAATGACCGTAATGCCCCTATAGGGTAAAAT
AATCGTAATACCCCTGTAGGATAAAATGACCGTAATGCCCTTG
Found at i:34864910 original size:24 final size:24
Alignment explanation
Indices: 34864832--34864913 Score: 78
Period size: 24 Copynumber: 3.5 Consensus size: 24
34864822 CTCGAGGTCA
* * * *
34864832 AATGATTGTTTTGTCTGT-AATTA
1 AATGACTGATTTGTCTGTGATTTG
*
34864855 AATGACTGATTTGTTTGTG-TTTGG
1 AATGACTGATTTGTCTGTGATTT-G
* *
34864879 TATAACTGATTTGTCTGTGATTTG
1 AATGACTGATTTGTCTGTGATTTG
34864903 AATGACTGATT
1 AATGACTGATT
34864914 CTGAGCATGG
Statistics
Matches: 46, Mismatches: 10, Indels: 5
0.75 0.16 0.08
Matches are distributed among these distances:
23 17 0.37
24 26 0.57
25 3 0.07
ACGTcount: A:0.23, C:0.06, G:0.22, T:0.49
Consensus pattern (24 bp):
AATGACTGATTTGTCTGTGATTTG
Found at i:34865067 original size:26 final size:26
Alignment explanation
Indices: 34865012--34865067 Score: 76
Period size: 26 Copynumber: 2.2 Consensus size: 26
34865002 ATACTATTAC
* ** *
34865012 TGGCAGCTTTGCTGCGATATTGTTGC
1 TGGCAGCTTTGCTGCGATACTACTGA
34865038 TGGCAGCTTTGCTGCGATACTACTGA
1 TGGCAGCTTTGCTGCGATACTACTGA
34865064 TGGC
1 TGGC
34865068 TTTGTGCCGA
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.14, C:0.21, G:0.30, T:0.34
Consensus pattern (26 bp):
TGGCAGCTTTGCTGCGATACTACTGA
Found at i:34865099 original size:32 final size:32
Alignment explanation
Indices: 34865058--34865278 Score: 185
Period size: 32 Copynumber: 6.9 Consensus size: 32
34865048 GCTGCGATAC
*
34865058 TACTGATGGCTTTGTGCCGATCATATTACCGT
1 TACTGATGGCTTTGTGCCGATCATATTACCAT
* *
34865090 TACTGATGGCTTTGTGCTGATCATAGTACCAT
1 TACTGATGGCTTTGTGCCGATCATATTACCAT
* * ****
34865122 TACTGATGGCTTTGTGCTGATCATGTTATTGC
1 TACTGATGGCTTTGTGCCGATCATATTACCAT
* * *
34865154 TACCGATGGCTGTGTGCCGATCAT-TTCACTAT
1 TACTGATGGCTTTGTGCCGATCATATT-ACCAT
* * * *
34865186 CACTGATGTCTGTGTGCCGATCATGTTACCAT
1 TACTGATGGCTTTGTGCCGATCATATTACCAT
* * * * ***
34865218 TACTAATGGCTGTGT-CCCAGTCATATCACTGC
1 TACTGATGGCTTTGTGCCGA-TCATATTACCAT
* *
34865250 TACTGATGGCTTTGTGCCAATCACATTAC
1 TACTGATGGCTTTGTGCCGATCATATTAC
34865279 TGTGCTTATG
Statistics
Matches: 152, Mismatches: 33, Indels: 8
0.79 0.17 0.04
Matches are distributed among these distances:
31 5 0.03
32 142 0.93
33 5 0.03
ACGTcount: A:0.20, C:0.23, G:0.21, T:0.36
Consensus pattern (32 bp):
TACTGATGGCTTTGTGCCGATCATATTACCAT
Found at i:34865251 original size:96 final size:96
Alignment explanation
Indices: 34865057--34865278 Score: 243
Period size: 96 Copynumber: 2.3 Consensus size: 96
34865047 TGCTGCGATA
* * * *
34865057 CTACTGATGGCTTTGTGCCGATCATATTACCGTTACTGATGGCTTTGTGCTGATCATAGTACCAT
1 CTACTGATGGCTTTGTGCCGATCATATTACCATCACTGATGGCTGTGTGCCGATCATAGTACCAT
* * * * * * *
34865122 TACTGATGGCTTTGTGCTGATCATGTTATTG
66 TACTAATGGCTGTGTCCAGATCATATCACTG
* * * *
34865153 CTACCGATGGCTGTGTGCCGATCAT-TTCACTATCACTGATGTCTGTGTGCCGATCAT-GTTACC
1 CTACTGATGGCTTTGTGCCGATCATATT-ACCATCACTGATGGCTGTGTGCCGATCATAG-TACC
34865216 ATTACTAATGGCTGTGTCCCAG-TCATATCACTG
64 ATTACTAATGGCTGTGT-CCAGATCATATCACTG
* *
34865249 CTACTGATGGCTTTGTGCCAATCACATTAC
1 CTACTGATGGCTTTGTGCCGATCATATTAC
34865279 TGTGCTTATG
Statistics
Matches: 103, Mismatches: 19, Indels: 8
0.79 0.15 0.06
Matches are distributed among these distances:
95 3 0.03
96 96 0.93
97 4 0.04
ACGTcount: A:0.20, C:0.23, G:0.21, T:0.36
Consensus pattern (96 bp):
CTACTGATGGCTTTGTGCCGATCATATTACCATCACTGATGGCTGTGTGCCGATCATAGTACCAT
TACTAATGGCTGTGTCCAGATCATATCACTG
Found at i:34865327 original size:26 final size:26
Alignment explanation
Indices: 34865298--34865350 Score: 79
Period size: 26 Copynumber: 2.0 Consensus size: 26
34865288 GGCTTATAGC
* *
34865298 CATTCTAACTACTGGCAGCTCTGCTG
1 CATTATAACTACTGGCAGCTATGCTG
*
34865324 CATTATTACTACTGGCAGCTATGCTG
1 CATTATAACTACTGGCAGCTATGCTG
34865350 C
1 C
34865351 GATTTTGGTG
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
26 24 1.00
ACGTcount: A:0.21, C:0.28, G:0.19, T:0.32
Consensus pattern (26 bp):
CATTATAACTACTGGCAGCTATGCTG
Found at i:34866570 original size:34 final size:34
Alignment explanation
Indices: 34866527--34866651 Score: 171
Period size: 34 Copynumber: 3.7 Consensus size: 34
34866517 AGGTGGATGG
*
34866527 ATTTGGTGTGCTGGATGGATTAACTCATACGAGC
1 ATTTGGTGTGCTAGATGGATTAACTCATACGAGC
* *
34866561 ATTTGGTGTGCTAGATGGATTAGCTCATATGAGC
1 ATTTGGTGTGCTAGATGGATTAACTCATACGAGC
* * * *
34866595 ATTTGATGTGCTGGATGGATTAGCTCTTACGAGC
1 ATTTGGTGTGCTAGATGGATTAACTCATACGAGC
*
34866629 ATCTGGTGTGCTAGATGG-TTAAC
1 ATTTGGTGTGCTAGATGGATTAAC
34866652 CGTGTACTCG
Statistics
Matches: 80, Mismatches: 11, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
33 4 0.05
34 76 0.95
ACGTcount: A:0.22, C:0.14, G:0.30, T:0.34
Consensus pattern (34 bp):
ATTTGGTGTGCTAGATGGATTAACTCATACGAGC
Found at i:34868547 original size:23 final size:23
Alignment explanation
Indices: 34868521--34868656 Score: 132
Period size: 23 Copynumber: 5.9 Consensus size: 23
34868511 TGCCACAGAA
*
34868521 TATGCCACAAAGGCTTCAAAGAT
1 TATGCCACAAAGGCTTCATAGAT
* * * *
34868544 TATGCCACAAAGGCTCCACAAAG
1 TATGCCACAAAGGCTTCATAGAT
* *
34868567 TGTGCTACAAAGGCTTCATAGAT
1 TATGCCACAAAGGCTTCATAGAT
*
34868590 TATACCACAAAGGCTTCATTA-AT
1 TATGCCACAAAGGCTTCA-TAGAT
** *
34868613 TCCGCCACAAAGGCTTTATAGAAT
1 TATGCCACAAAGGCTTCATAG-AT
*
34868637 GA-GCCACAAAGGCTTCATAG
1 TATGCCACAAAGGCTTCATAG
34868657 GTAACTTTCC
Statistics
Matches: 90, Mismatches: 20, Indels: 6
0.78 0.17 0.05
Matches are distributed among these distances:
22 2 0.02
23 84 0.93
24 4 0.04
ACGTcount: A:0.36, C:0.24, G:0.18, T:0.23
Consensus pattern (23 bp):
TATGCCACAAAGGCTTCATAGAT
Found at i:34876169 original size:39 final size:40
Alignment explanation
Indices: 34876110--34876238 Score: 154
Period size: 40 Copynumber: 3.2 Consensus size: 40
34876100 TACAACACCA
* * * *
34876110 GCACAATGCATGCTAGGCACAAAACCTC-ATAAACACACCG
1 GCACAAAGCCTGCTAGGCACAAAACC-CGATAAATACACTG
* *
34876150 GCACAAA-CCTGCTAGGCACAAACCCCGATAAATACACTA
1 GCACAAAGCCTGCTAGGCACAAAACCCGATAAATACACTG
* * *
34876189 GCATAAAGCCTACTAGGCACAAAGCCCGATAAATACACTG
1 GCACAAAGCCTGCTAGGCACAAAACCCGATAAATACACTG
34876229 GCACAAAGCC
1 GCACAAAGCC
34876239 ACTAACTCGT
Statistics
Matches: 76, Mismatches: 11, Indels: 4
0.84 0.12 0.04
Matches are distributed among these distances:
38 1 0.01
39 31 0.41
40 44 0.58
ACGTcount: A:0.40, C:0.32, G:0.16, T:0.12
Consensus pattern (40 bp):
GCACAAAGCCTGCTAGGCACAAAACCCGATAAATACACTG
Found at i:34880705 original size:4 final size:4
Alignment explanation
Indices: 34880696--34880757 Score: 106
Period size: 4 Copynumber: 15.0 Consensus size: 4
34880686 CTAGTTTCTC
34880696 CTTT CTTT CTTT CTTT CTTT CTTT CTTT CTTT CTTT CTTT CTTTT CTTT
1 CTTT CTTT CTTT CTTT CTTT CTTT CTTT CTTT CTTT CTTT C-TTT CTTT
34880745 CTTT CCTTT CTTT
1 CTTT -CTTT CTTT
34880758 TTCTCCCTGT
Statistics
Matches: 56, Mismatches: 0, Indels: 4
0.93 0.00 0.07
Matches are distributed among these distances:
4 48 0.86
5 8 0.14
ACGTcount: A:0.00, C:0.26, G:0.00, T:0.74
Consensus pattern (4 bp):
CTTT
Found at i:34880824 original size:22 final size:23
Alignment explanation
Indices: 34880787--34880854 Score: 70
Period size: 25 Copynumber: 3.0 Consensus size: 23
34880777 ACTTTTGTTC
34880787 TTTA-TTTATT-TCATTTACTTA-
1 TTTATTTTATTAT-ATTTACTTAT
34880808 TTTATTTTATTATATTTACCTTAT
1 TTTATTTTATTATATTTA-CTTAT
* *
34880832 TATTATATTATTATATATACTTA
1 T-TTATTTTATTATATTTACTTA
34880855 CTTAAATATT
Statistics
Matches: 40, Mismatches: 2, Indels: 7
0.82 0.04 0.14
Matches are distributed among these distances:
21 4 0.10
22 11 0.28
23 5 0.12
24 5 0.12
25 15 0.38
ACGTcount: A:0.29, C:0.07, G:0.00, T:0.63
Consensus pattern (23 bp):
TTTATTTTATTATATTTACTTAT
Found at i:34888654 original size:17 final size:17
Alignment explanation
Indices: 34888634--34888694 Score: 56
Period size: 17 Copynumber: 3.8 Consensus size: 17
34888624 TAGAATTGAG
34888634 TTGAAAAAATAATTTAA
1 TTGAAAAAATAATTTAA
* * *
34888651 TTGAGAAATTAATCTAA
1 TTGAAAAAATAATTTAA
* *
34888668 TT---AATATAAATTAA
1 TTGAAAAAATAATTTAA
34888682 TTGAAAAAATAAT
1 TTGAAAAAATAAT
34888695 ATTTTAGGAA
Statistics
Matches: 32, Mismatches: 9, Indels: 6
0.68 0.19 0.13
Matches are distributed among these distances:
14 10 0.31
17 22 0.69
ACGTcount: A:0.56, C:0.02, G:0.07, T:0.36
Consensus pattern (17 bp):
TTGAAAAAATAATTTAA
Found at i:34900056 original size:19 final size:18
Alignment explanation
Indices: 34900019--34900058 Score: 53
Period size: 19 Copynumber: 2.2 Consensus size: 18
34900009 CGTAAAAATG
*
34900019 AATTTGAAAATGTATTTT
1 AATTTGAAAATGTAATTT
*
34900037 AATTTGATAAATTTAATTT
1 AATTTGA-AAATGTAATTT
34900056 AAT
1 AAT
34900059 CATTATATAG
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
18 7 0.37
19 12 0.63
ACGTcount: A:0.42, C:0.00, G:0.07, T:0.50
Consensus pattern (18 bp):
AATTTGAAAATGTAATTT
Done.