Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01014141.1 Kokia drynarioides strain JFW-HI SEQ_129174, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 191733
ACGTcount: A:0.33, C:0.17, G:0.16, T:0.34
Warning! 101 characters in sequence are not A, C, G, or T
Found at i:1142 original size:66 final size:66
Alignment explanation
Indices: 1036--1162 Score: 236
Period size: 66 Copynumber: 1.9 Consensus size: 66
1026 TAAGTAACTG
1036 TCAACTAATGGCCTTTTAAGATGAGTGTTTATTTTCAGTGCGATACGTTTAGTTTTTTTTTATAT
1 TCAACTAATGGCCTTTTAAGATGAGTGTTTATTTTCAGTGCGATACGTTTAGTTTTTTTTTATAT
1101 T
66 T
* *
1102 TCAACTAATGGCCTTTTAAGATGGGTGTTTATTTTCAGTGCGGTACGTTTAGTTTTTTTTT
1 TCAACTAATGGCCTTTTAAGATGAGTGTTTATTTTCAGTGCGATACGTTTAGTTTTTTTTT
1163 TTTTTATATC
Statistics
Matches: 59, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
66 59 1.00
ACGTcount: A:0.20, C:0.11, G:0.19, T:0.50
Consensus pattern (66 bp):
TCAACTAATGGCCTTTTAAGATGAGTGTTTATTTTCAGTGCGATACGTTTAGTTTTTTTTTATAT
T
Found at i:5237 original size:20 final size:20
Alignment explanation
Indices: 5214--5251 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
5204 ACATAAAACT
5214 TATTTAATATTAAAATTAAG
1 TATTTAATATTAAAATTAAG
* *
5234 TATTTAATGTTCAAATTA
1 TATTTAATATTAAAATTA
5252 TTTATTAATG
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:0.45, C:0.03, G:0.05, T:0.47
Consensus pattern (20 bp):
TATTTAATATTAAAATTAAG
Found at i:5257 original size:20 final size:20
Alignment explanation
Indices: 5213--5261 Score: 55
Period size: 20 Copynumber: 2.5 Consensus size: 20
5203 TACATAAAAC
*
5213 TTATTTAATATTAAAATTAA
1 TTATTTAATGTTAAAATTAA
* * *
5233 GTATTTAATGTTCAAATTAT
1 TTATTTAATGTTAAAATTAA
5253 TTA-TTAATG
1 TTATTTAATG
5262 CAAGCAATTC
Statistics
Matches: 24, Mismatches: 5, Indels: 1
0.80 0.17 0.03
Matches are distributed among these distances:
19 6 0.25
20 18 0.75
ACGTcount: A:0.41, C:0.02, G:0.06, T:0.51
Consensus pattern (20 bp):
TTATTTAATGTTAAAATTAA
Found at i:6492 original size:5 final size:5
Alignment explanation
Indices: 6479--6517 Score: 60
Period size: 5 Copynumber: 7.6 Consensus size: 5
6469 GAACAAATAT
*
6479 ATTCG ATTCA ATTCA ATTCA ATTCA ATTCA ATTCGA ATT
1 ATTCA ATTCA ATTCA ATTCA ATTCA ATTCA ATTC-A ATT
6518 TCATCATACT
Statistics
Matches: 32, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
5 28 0.88
6 4 0.12
ACGTcount: A:0.36, C:0.18, G:0.05, T:0.41
Consensus pattern (5 bp):
ATTCA
Found at i:13100 original size:108 final size:108
Alignment explanation
Indices: 12906--13109 Score: 311
Period size: 108 Copynumber: 1.9 Consensus size: 108
12896 AAATGAGAAA
*
12906 GGTGCATATTGGTCAATTATTTCTAACCTTCCTCGTGTGAGGATAAATTATGTTGACATCCTCTG
1 GGTGCATATTGGCCAATTATTTCTAACCTTCCTC-TGTGAGGATAAATTATGTTGACATCCTCTG
* *
12971 AACAAGAACAAGCAGATTGCATTTCTAGATGGATATCAATGAAT
65 AACAAGAACAAGCAGACTGCATTCCTAGATGGATATCAATGAAT
** * *
13015 GGTGCATATTGGCCTCTTATTTCTCACCTTCACT-TGTGAGGATAAATTATGTTGACATCTTCTG
1 GGTGCATATTGGCCAATTATTTCTAACCTTC-CTCTGTGAGGATAAATTATGTTGACATCCTCTG
*
13079 AACAAGCACAAGCAGACTGCATTCCTAGATG
65 AACAAGAACAAGCAGACTGCATTCCTAGATG
13110 ATCAGCAAAA
Statistics
Matches: 86, Mismatches: 8, Indels: 3
0.89 0.08 0.03
Matches are distributed among these distances:
108 57 0.66
109 27 0.31
110 2 0.02
ACGTcount: A:0.29, C:0.19, G:0.19, T:0.33
Consensus pattern (108 bp):
GGTGCATATTGGCCAATTATTTCTAACCTTCCTCTGTGAGGATAAATTATGTTGACATCCTCTGA
ACAAGAACAAGCAGACTGCATTCCTAGATGGATATCAATGAAT
Found at i:13374 original size:49 final size:49
Alignment explanation
Indices: 13315--13413 Score: 198
Period size: 49 Copynumber: 2.0 Consensus size: 49
13305 GACACTGTTG
13315 CCCTCTAGAAGAAACAGTTTAATTAATCAACATATTCATGAATAACATT
1 CCCTCTAGAAGAAACAGTTTAATTAATCAACATATTCATGAATAACATT
13364 CCCTCTAGAAGAAACAGTTTAATTAATCAACATATTCATGAATAACATT
1 CCCTCTAGAAGAAACAGTTTAATTAATCAACATATTCATGAATAACATT
13413 C
1 C
13414 TCATAGATTT
Statistics
Matches: 50, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
49 50 1.00
ACGTcount: A:0.42, C:0.19, G:0.08, T:0.30
Consensus pattern (49 bp):
CCCTCTAGAAGAAACAGTTTAATTAATCAACATATTCATGAATAACATT
Found at i:21758 original size:18 final size:18
Alignment explanation
Indices: 21735--21769 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
21725 GACCAATAGA
21735 TCAAAAATAAT-TAAAAAT
1 TCAAAAA-AATCTAAAAAT
21753 TCAAAAAAATCTAAAAA
1 TCAAAAAAATCTAAAAA
21770 AATTTATTAA
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:0.69, C:0.09, G:0.00, T:0.23
Consensus pattern (18 bp):
TCAAAAAAATCTAAAAAT
Found at i:23339 original size:26 final size:25
Alignment explanation
Indices: 23290--23339 Score: 73
Period size: 25 Copynumber: 2.0 Consensus size: 25
23280 AAATTATTAT
* *
23290 TTTAAAAAAATTTAAATTTTTATAA
1 TTTAAAAAAAATTAAATTTATATAA
23315 TTTAAAAAAAATTAAATTATATATA
1 TTTAAAAAAAATTAAATT-TATATA
23340 TATATATATT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
25 17 0.77
26 5 0.23
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (25 bp):
TTTAAAAAAAATTAAATTTATATAA
Found at i:24624 original size:29 final size:29
Alignment explanation
Indices: 24581--24649 Score: 86
Period size: 29 Copynumber: 2.4 Consensus size: 29
24571 TTTTTTTATA
*
24581 AAAATAACTCT-TTTTTTTAATTAATTACG
1 AAAATAA-TCTATTTTTTTAATTAAATACG
* *
24610 TAAATAATCTATTTTTTTGATTAAATACG
1 AAAATAATCTATTTTTTTAATTAAATACG
*
24639 AAAACAATCTA
1 AAAATAATCTA
24650 AAATTTACAG
Statistics
Matches: 34, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
28 3 0.09
29 31 0.91
ACGTcount: A:0.42, C:0.10, G:0.04, T:0.43
Consensus pattern (29 bp):
AAAATAATCTATTTTTTTAATTAAATACG
Found at i:24974 original size:7 final size:7
Alignment explanation
Indices: 24962--24997 Score: 51
Period size: 7 Copynumber: 5.6 Consensus size: 7
24952 TTTTTAAATG
24962 ATTTATT
1 ATTTATT
24969 ATTTATT
1 ATTTATT
24976 ATTTA-T
1 ATTTATT
24982 -TTTATT
1 ATTTATT
24988 ATTTA-T
1 ATTTATT
24994 ATTT
1 ATTT
24998 TTTAAATTTT
Statistics
Matches: 27, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
5 4 0.15
6 7 0.26
7 16 0.59
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (7 bp):
ATTTATT
Found at i:25064 original size:22 final size:21
Alignment explanation
Indices: 25034--25074 Score: 64
Period size: 22 Copynumber: 1.9 Consensus size: 21
25024 TCTAATTCTA
*
25034 ATTTTTTTATTATTATTTATTT
1 ATTTATTTATTATT-TTTATTT
25056 ATTTATTTATTATTTTTAT
1 ATTTATTTATTATTTTTAT
25075 GAATATAAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 5 0.28
22 13 0.72
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (21 bp):
ATTTATTTATTATTTTTATTT
Found at i:25110 original size:47 final size:46
Alignment explanation
Indices: 25041--25135 Score: 147
Period size: 46 Copynumber: 2.0 Consensus size: 46
25031 CTAATTTTTT
25041 TATTATTATTTATTTATTTATTTATTATTTTTATGAATATAAATAAA
1 TATTATTATTTATTTATTTATTTATTA-TTTTATGAATATAAATAAA
* *
25088 TATTAATTTTTTA-TTATTTATTTATTATTTTATGAATATAGATAAA
1 TATT-ATTATTTATTTATTTATTTATTATTTTATGAATATAAATAAA
25134 TA
1 TA
25136 AATAAATCAA
Statistics
Matches: 45, Mismatches: 2, Indels: 3
0.90 0.04 0.06
Matches are distributed among these distances:
46 20 0.44
47 18 0.40
48 7 0.16
ACGTcount: A:0.38, C:0.00, G:0.03, T:0.59
Consensus pattern (46 bp):
TATTATTATTTATTTATTTATTTATTATTTTATGAATATAAATAAA
Found at i:30783 original size:24 final size:24
Alignment explanation
Indices: 30741--30797 Score: 62
Period size: 25 Copynumber: 2.3 Consensus size: 24
30731 GTCAAAAAAA
* * *
30741 TTATTTTTAATATTTTATATTTTAT
1 TTATTTTAAATATTATATA-TATAT
30766 TTATTTTAAATA-TATATATATAT
1 TTATTTTAAATATTATATATATAT
30789 TTATGTTTA
1 TTAT-TTTA
30798 TTTAGAAAGC
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
23 8 0.29
24 9 0.32
25 11 0.39
ACGTcount: A:0.33, C:0.00, G:0.02, T:0.65
Consensus pattern (24 bp):
TTATTTTAAATATTATATATATAT
Found at i:31109 original size:16 final size:16
Alignment explanation
Indices: 31090--31120 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
31080 CAAATAATCC
31090 AACATATATTTTTCTT
1 AACATATATTTTTCTT
*
31106 AACATTTATTTTTCT
1 AACATATATTTTTCT
31121 AATTAACTAA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.29, C:0.13, G:0.00, T:0.58
Consensus pattern (16 bp):
AACATATATTTTTCTT
Found at i:33976 original size:21 final size:22
Alignment explanation
Indices: 33934--33977 Score: 54
Period size: 21 Copynumber: 2.0 Consensus size: 22
33924 CTTCTTCGCA
*
33934 TCGTCGGGACGTGACGATTCTTC
1 TCGTCGGGAC-TGACGACTCTTC
*
33957 TCGTCGGGA-TGACGGCTCTTC
1 TCGTCGGGACTGACGACTCTTC
33978 CTTGTCCCAA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
21 10 0.53
23 9 0.47
ACGTcount: A:0.11, C:0.27, G:0.32, T:0.30
Consensus pattern (22 bp):
TCGTCGGGACTGACGACTCTTC
Found at i:48389 original size:10 final size:9
Alignment explanation
Indices: 48363--48485 Score: 63
Period size: 9 Copynumber: 12.8 Consensus size: 9
48353 TTTTTCTCAC
48363 ATAAAAATT
1 ATAAAAATT
48372 ATAAAAATT
1 ATAAAAATT
*
48381 TTAATAAATT
1 ATAA-AAATT
48391 ATAAAAA-T
1 ATAAAAATT
* ***
48399 ATAACAGCA
1 ATAAAAATT
48408 AT-AAAATAT
1 ATAAAAAT-T
*
48417 ATTTAAAATT
1 A-TAAAAATT
*
48427 TTAAAAATT
1 ATAAAAATT
48436 -TAATAAACCTT
1 ATAA-AAA--TT
48447 ATAAAAATT
1 ATAAAAATT
48456 CATAAAAAAACTT
1 -AT--AAAAA-TT
48469 ATAAAAATTT
1 ATAAAAA-TT
48479 ATAAAAA
1 ATAAAAA
48486 AAGTCATTTA
Statistics
Matches: 89, Mismatches: 12, Indels: 25
0.71 0.10 0.20
Matches are distributed among these distances:
8 11 0.12
9 30 0.34
10 26 0.29
11 10 0.11
12 10 0.11
13 2 0.02
ACGTcount: A:0.61, C:0.05, G:0.01, T:0.33
Consensus pattern (9 bp):
ATAAAAATT
Found at i:48472 original size:22 final size:21
Alignment explanation
Indices: 48428--48487 Score: 77
Period size: 22 Copynumber: 2.8 Consensus size: 21
48418 TTTAAAATTT
* *
48428 TAAAAATT-TAATAAACCTTA
1 TAAAAATTATAAAAAAACTTA
48448 TAAAAATTCATAAAAAAACTTA
1 TAAAAATT-ATAAAAAAACTTA
48470 TAAAAATTTATAAAAAAA
1 TAAAAA-TTATAAAAAAA
48488 GTCATTTAAA
Statistics
Matches: 35, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
20 8 0.23
22 25 0.71
23 2 0.06
ACGTcount: A:0.63, C:0.07, G:0.00, T:0.30
Consensus pattern (21 bp):
TAAAAATTATAAAAAAACTTA
Found at i:48911 original size:81 final size:81
Alignment explanation
Indices: 48776--48946 Score: 265
Period size: 81 Copynumber: 2.1 Consensus size: 81
48766 TAGAAAAAAA
* *
48776 TTTTAAGGGTGGAAGTTAAATTATATTTTTTTATGATAGTAAAAATATAATTTTTAAAAGATTAA
1 TTTTAAGGGTGGAAGTTAAATTATATATTTTTATGATAGTAAAAATATAATTTTTAAAAAATTAA
*
48841 ATAAAAATTTTATTAT
66 ATAAAAATTTTATCAT
* *
48857 TTTTAGAGGGTTGAAGTTAAATTATA-ATTTTTATGATAGTAAAAATGTAATTTTTAAAAAATTA
1 TTTTA-AGGGTGGAAGTTAAATTATATATTTTTATGATAGTAAAAATATAATTTTTAAAAAATTA
*
48921 AATCAAAATTTTATCA-
65 AATAAAAATTTTATCAT
48937 TTTTAAGGGT
1 TTTTAAGGGT
48947 CCAAAATGCA
Statistics
Matches: 83, Mismatches: 6, Indels: 4
0.89 0.06 0.04
Matches are distributed among these distances:
79 5 0.06
80 5 0.06
81 54 0.65
82 19 0.23
ACGTcount: A:0.42, C:0.01, G:0.12, T:0.44
Consensus pattern (81 bp):
TTTTAAGGGTGGAAGTTAAATTATATATTTTTATGATAGTAAAAATATAATTTTTAAAAAATTAA
ATAAAAATTTTATCAT
Found at i:53771 original size:27 final size:29
Alignment explanation
Indices: 53741--53799 Score: 79
Period size: 27 Copynumber: 2.1 Consensus size: 29
53731 TTTTTAATTT
53741 TTTTAA-AAAAATATTTAT-A-TTTTTTTA
1 TTTTAATAAAAAT-TTTATAATTTTTTTTA
*
53768 TTTTAATAATAATTTTATAATTTTTTTTA
1 TTTTAATAAAAATTTTATAATTTTTTTTA
53797 TTT
1 TTT
53800 ATTGAAATTT
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
27 11 0.39
28 6 0.21
29 11 0.39
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (29 bp):
TTTTAATAAAAATTTTATAATTTTTTTTA
Found at i:54666 original size:22 final size:22
Alignment explanation
Indices: 54620--54660 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
54610 ACATTCATCA
*
54620 AAAAAATAGTTAGATATAAAAT
1 AAAAAATAATTAGATATAAAAT
54642 AAAAAATAATTA-ATATAAA
1 AAAAAATAATTAGATATAAA
54661 TTTAAACATG
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 7 0.39
22 11 0.61
ACGTcount: A:0.68, C:0.00, G:0.05, T:0.27
Consensus pattern (22 bp):
AAAAAATAATTAGATATAAAAT
Found at i:55711 original size:15 final size:14
Alignment explanation
Indices: 55691--55720 Score: 51
Period size: 15 Copynumber: 2.1 Consensus size: 14
55681 TCCCTTCTCC
55691 AATAAATTAAATATT
1 AATAAATTAAA-ATT
55706 AATAAATTAAAATT
1 AATAAATTAAAATT
55720 A
1 A
55721 TTACTTTCAA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 4 0.27
15 11 0.73
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (14 bp):
AATAAATTAAAATT
Found at i:56176 original size:16 final size:17
Alignment explanation
Indices: 56151--56189 Score: 53
Period size: 17 Copynumber: 2.4 Consensus size: 17
56141 ATAATCAAAT
*
56151 AAAATAAAAT-TTGTAA
1 AAAATAAAATATGGTAA
*
56167 AAAATTAAATATGGTAA
1 AAAATAAAATATGGTAA
56184 AAAATA
1 AAAATA
56190 TTTAAAAATT
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
16 9 0.47
17 10 0.53
ACGTcount: A:0.64, C:0.00, G:0.08, T:0.28
Consensus pattern (17 bp):
AAAATAAAATATGGTAA
Found at i:56203 original size:20 final size:18
Alignment explanation
Indices: 56151--56208 Score: 57
Period size: 20 Copynumber: 3.2 Consensus size: 18
56141 ATAATCAAAT
*
56151 AAAA-TAAAATTTGT-AA
1 AAAATTAAAAATTGTAAA
* *
56167 AAAATTAAATATGGTAAA
1 AAAATTAAAAATTGTAAA
56185 AAATATTTAAAAATTGTAAA
1 AAA-A-TTAAAAATTGTAAA
56205 AAAA
1 AAAA
56209 AAAAGTAATT
Statistics
Matches: 33, Mismatches: 5, Indels: 5
0.77 0.12 0.12
Matches are distributed among these distances:
16 4 0.12
17 7 0.21
18 5 0.15
19 2 0.06
20 15 0.45
ACGTcount: A:0.64, C:0.00, G:0.07, T:0.29
Consensus pattern (18 bp):
AAAATTAAAAATTGTAAA
Found at i:70667 original size:153 final size:153
Alignment explanation
Indices: 70389--70692 Score: 581
Period size: 153 Copynumber: 2.0 Consensus size: 153
70379 AAGCATGTCC
70389 CTTGATCTGCTTGCTTTCCTAGCCCTCCCACAAGTATCCATCGGGACATTTTGATCCTCTATTTC
1 CTTGATCTGCTTGCTTTCCTAGCCCTCCCACAAGTATCCATCGGGACATTTTGATCCTCTATTTC
70454 TTTTGTCATCTTACTTGGCACCTTACGGACTATGGCTCCTGACACCAACTATCATGACTCAACGA
66 TTTTGTCATCTTACTTGGCACCTTACGGACTATGGCTCCTGACACCAACTATCATGACTCAACGA
70519 ACATGGGCTTTGATACCAACTGT
131 ACATGGGCTTTGATACCAACTGT
*
70542 CTTGATCTGCTTGCTTTCCTAGCCCTCCCACAGGTATCCATCGGGACATTTTGATCCTCTATTTC
1 CTTGATCTGCTTGCTTTCCTAGCCCTCCCACAAGTATCCATCGGGACATTTTGATCCTCTATTTC
* *
70607 TTTTGTCATCTTACTTGGCACCTTACGGATTGTGGCTCCTGACACCAACTATCATGACTCAACGA
66 TTTTGTCATCTTACTTGGCACCTTACGGACTATGGCTCCTGACACCAACTATCATGACTCAACGA
70672 ACATGGGCTTTGATACCAACT
131 ACATGGGCTTTGATACCAACT
70693 TTCATAGGGA
Statistics
Matches: 148, Mismatches: 3, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
153 148 1.00
ACGTcount: A:0.21, C:0.29, G:0.16, T:0.34
Consensus pattern (153 bp):
CTTGATCTGCTTGCTTTCCTAGCCCTCCCACAAGTATCCATCGGGACATTTTGATCCTCTATTTC
TTTTGTCATCTTACTTGGCACCTTACGGACTATGGCTCCTGACACCAACTATCATGACTCAACGA
ACATGGGCTTTGATACCAACTGT
Found at i:97810 original size:16 final size:16
Alignment explanation
Indices: 97789--97821 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
97779 TTTATATATA
97789 TTTTTTAA-ATATTTAT
1 TTTTTTAAGAT-TTTAT
97805 TTTTTTAAGATTTTAT
1 TTTTTTAAGATTTTAT
97821 T
1 T
97822 ATATCTTTAT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 14 0.88
17 2 0.12
ACGTcount: A:0.27, C:0.00, G:0.03, T:0.70
Consensus pattern (16 bp):
TTTTTTAAGATTTTAT
Found at i:106635 original size:2 final size:2
Alignment explanation
Indices: 106628--106659 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
106618 TTTTATAAGA
106628 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
106660 TACGGGTAAA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:109678 original size:29 final size:29
Alignment explanation
Indices: 109635--109908 Score: 205
Period size: 29 Copynumber: 9.2 Consensus size: 29
109625 CTAAACCTTT
* *
109635 CAAAAATTTCTATTTTTACCCCCGAACTTC
1 CAAAAATCTC-ATTTTTACCCCCAAACTTC
* *
109665 CAAAAATCTCATTTTTAACCCCAAAATTTC
1 CAAAAATCTCATTTTT-ACCCCCAAACTTC
* * *
109695 TAAAAAT-TCCATTTTAACCCCCAAACTTT
1 CAAAAATCT-CATTTTTACCCCCAAACTTC
* *
109724 CAAAAATC-CTATTTTTACCTCAAAACTTC
1 CAAAAATCTC-ATTTTTACCCCCAAACTTC
* *
109753 CAAAAAAATCTTATTTTTACCCCTCAAACTTT
1 C--AAAAATCTCATTTTTACCCC-CAAACTTC
* **
109785 CAAAAATCCCATTTTTGA-CCTTAAACTTC
1 CAAAAATCTCATTTTT-ACCCCCAAACTTC
* * *
109814 TAAAAAT-TCCATTTTTACCCTCAAACTTT
1 CAAAAATCT-CATTTTTACCCCCAAACTTC
* * ** *
109843 AAAAAATCACATTTGAACCCCTAAACTTC
1 CAAAAATCTCATTTTTACCCCCAAACTTC
* *
109872 CAAAAATCCCATTTTTATCCCCGAAACTTC
1 CAAAAATCTCATTTTTA-CCCCCAAACTTC
*
109902 TAAAAAT
1 CAAAAAT
109909 TACCATTTTA
Statistics
Matches: 191, Mismatches: 40, Indels: 26
0.74 0.16 0.10
Matches are distributed among these distances:
28 2 0.01
29 101 0.53
30 63 0.33
31 18 0.09
32 7 0.04
ACGTcount: A:0.38, C:0.27, G:0.01, T:0.34
Consensus pattern (29 bp):
CAAAAATCTCATTTTTACCCCCAAACTTC
Found at i:109729 original size:59 final size:58
Alignment explanation
Indices: 109632--109917 Score: 240
Period size: 59 Copynumber: 4.8 Consensus size: 58
109622 TCCCTAAACC
* * *
109632 TTTC-AAAAATTTCTATTTTTACCCCCGAACTTCCAAAAATCTCATTTTTAACCCCAAAA
1 TTTCTAAAAA-TTCCATTTTTACCCCCAAACTTTCAAAAATC-CATTTTTAACCCCAAAA
* *
109691 TTTCTAAAAATTCCATTTTAACCCCCAAACTTTCAAAAATCCTATTTTT-ACCTCAAAA
1 TTTCTAAAAATTCCATTTTTACCCCCAAACTTTCAAAAATCC-ATTTTTAACCCCAAAA
* * * * * **
109749 CTTCCAAAAAAATCTTATTTTTACCCCTCAAACTTTCAAAAATCCCATTTTTGA-CCTTAAA
1 -TTTCTAAAAATTC-CATTTTTACCCC-CAAACTTTCAAAAAT-CCATTTTTAACCCCAAAA
* * * * *
109810 CTTCTAAAAATTCCATTTTTACCCTCAAACTTTAAAAAATCACA-TTTGAACCCCTAAA
1 TTTCTAAAAATTCCATTTTTACCCCCAAACTTTCAAAAATC-CATTTTTAACCCCAAAA
* * * *
109868 CTTCCAAAAATCCCATTTTTATCCCCGAAAC-TTCTAAAAATTACCATTTT
1 TTTCTAAAAATTCCATTTTTA-CCCCCAAACTTTC-AAAAA-T-CCATTTT
109918 ACCCTCGGAT
Statistics
Matches: 185, Mismatches: 28, Indels: 26
0.77 0.12 0.11
Matches are distributed among these distances:
57 5 0.03
58 52 0.28
59 69 0.37
60 27 0.15
61 29 0.16
62 3 0.02
ACGTcount: A:0.37, C:0.27, G:0.01, T:0.35
Consensus pattern (58 bp):
TTTCTAAAAATTCCATTTTTACCCCCAAACTTTCAAAAATCCATTTTTAACCCCAAAA
Found at i:109848 original size:119 final size:120
Alignment explanation
Indices: 109636--109917 Score: 315
Period size: 119 Copynumber: 2.4 Consensus size: 120
109626 TAAACCTTTC
* * * *
109636 AAAAATTTCTATTTTTACCCCCGAACTTCCAAAAATCTCATTTTTAACCCCAAAATTTCTAAAAA
1 AAAAATCTCTATTTTTACCCCCAAACTTCCAAAAATCCCATTTTTAACCCCAAAACTTCTAAAAA
* ** *
109701 TTCCATTTTAACCCCCAAACTTTCAAAAATC-CTATTTTTACCTCAAAACTTCCAA
66 TTCCATTTTAACCCCCAAACTTTAAAAAATCAC-ATTTGAACCCCAAAACTTCCAA
* * **
109756 AAAAATCT-TATTTTTACCCCTCAAACTTTCAAAAATCCCATTTTTGA-CCTTAAACTTCTAAAA
1 AAAAATCTCTATTTTTACCCC-CAAACTTCCAAAAATCCCATTTTTAACCCCAAAACTTCTAAAA
* * *
109819 ATTCCATTTTTACCCTCAAACTTTAAAAAATCACATTTGAACCCCTAAACTTCC--
65 ATTCCATTTTAACCCCCAAACTTTAAAAAATCACATTTGAACCCCAAAACTTCCAA
* * * *
109873 AAAAATC-CCATTTTTATCCCCGAAACTTCTAAAAATTACCATTTT
1 AAAAATCTCTATTTTTA-CCCCCAAACTTCCAAAAA-TCCCATTTT
109918 ACCCTCGGAT
Statistics
Matches: 137, Mismatches: 20, Indels: 12
0.81 0.12 0.07
Matches are distributed among these distances:
117 25 0.18
118 12 0.09
119 70 0.51
120 30 0.22
ACGTcount: A:0.37, C:0.27, G:0.01, T:0.35
Consensus pattern (120 bp):
AAAAATCTCTATTTTTACCCCCAAACTTCCAAAAATCCCATTTTTAACCCCAAAACTTCTAAAAA
TTCCATTTTAACCCCCAAACTTTAAAAAATCACATTTGAACCCCAAAACTTCCAA
Found at i:109933 original size:59 final size:58
Alignment explanation
Indices: 109870--110062 Score: 160
Period size: 58 Copynumber: 3.3 Consensus size: 58
109860 CCCCTAAACT
*
109870 TCCAAAAATCCCATTTTTATCCCCGAAACTTCTAAAAATTACCATTTTACCCTCGGATG
1 TCCAAAAATCCCATTTTTAT-CCCGAAACTTCTCAAAATTACCATTTTACCCTCGGATG
* ** * *
109929 TCCAAAAA-CTCCATTTTCGATCTTGAAAC-TCTCAAAATTACCCTTTTACCCTCGAATG
1 TCCAAAAATC-CCATTTT-TATCCCGAAACTTCTCAAAATTACCATTTTACCCTCGGATG
* * * * * * * * *
109987 TCTAAAGATTCCATTCTTAAACCCG-AACTTTCCCAAAATTACCATTTTGCCC-CGGGTA
1 TCCAAAAATCCCATT-TTTATCCCGAAAC-TTCTCAAAATTACCATTTTACCCTCGGATG
*
110045 TCCAAAAAGTCTCATTTT
1 TCCAAAAA-TCCCATTTT
110063 CAACTCCGAT
Statistics
Matches: 104, Mismatches: 23, Indels: 15
0.73 0.16 0.11
Matches are distributed among these distances:
57 3 0.03
58 52 0.50
59 47 0.45
60 2 0.02
ACGTcount: A:0.31, C:0.28, G:0.08, T:0.33
Consensus pattern (58 bp):
TCCAAAAATCCCATTTTTATCCCGAAACTTCTCAAAATTACCATTTTACCCTCGGATG
Found at i:109944 original size:88 final size:88
Alignment explanation
Indices: 109636--109923 Score: 241
Period size: 88 Copynumber: 3.2 Consensus size: 88
109626 TAAACCTTTC
* * * * * * * * *
109636 AAAAATTTCTATTTTTACCCCCGAACTTCCAAAAATCTCATTTTTAACCCC-AAAATTTCTAAAA
1 AAAAA-TTCCATTTTTACCCTCAAACTTCAAAAAATCACA-TTTGAACCCCTCAAACTTCCAAAA
* * *
109700 ATTCCA-TTTTAACCCCCAAACTT-T
64 ATCCCATTTTTGA-CCCGAAACTTCT
** ** *
109724 CAAAAA-TCCTATTTTTA-CCTCAAAACTTCCAAAAAAATCTTATTTTTACCCCTCAAACTTTCA
1 -AAAAATTCC-ATTTTTACCCTC-AAACTT-C-AAAAAATCACATTTGAACCCCTCAAACTTCCA
**
109787 AAAATCCCATTTTTGACCTTAAACTTCT
61 AAAATCCCATTTTTGACCCGAAACTTCT
*
109815 AAAAATTCCATTTTTACCCTCAAACTTTAAAAAATCACATTTGAACCCCT-AAACTTCCAAAAAT
1 AAAAATTCCATTTTTACCCTCAAACTTCAAAAAATCACATTTGAACCCCTCAAACTTCCAAAAAT
109879 CCCATTTTT-ATCCCCGAAACTTCT
66 CCCATTTTTGA--CCCGAAACTTCT
109903 AAAAATTACCA-TTTTACCCTC
1 AAAAATT-CCATTTTTACCCTC
109924 GGATGTCCAA
Statistics
Matches: 165, Mismatches: 22, Indels: 25
0.78 0.10 0.12
Matches are distributed among these distances:
86 1 0.01
87 27 0.16
88 57 0.35
89 18 0.11
90 49 0.30
91 13 0.08
ACGTcount: A:0.37, C:0.27, G:0.01, T:0.34
Consensus pattern (88 bp):
AAAAATTCCATTTTTACCCTCAAACTTCAAAAAATCACATTTGAACCCCTCAAACTTCCAAAAAT
CCCATTTTTGACCCGAAACTTCT
Found at i:112130 original size:2 final size:2
Alignment explanation
Indices: 112123--112160 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
112113 ATATTAGGTA
112123 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
112161 GTTTTAAAAT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:112356 original size:18 final size:17
Alignment explanation
Indices: 112323--112356 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
112313 ACAATTTTTA
*
112323 TTAAATTATAATTATTT
1 TTAAATTATAAATATTT
112340 TTAAATATATAAATATT
1 TTAAAT-TATAAATATT
112357 ACAAATTCTA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 6 0.40
18 9 0.60
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (17 bp):
TTAAATTATAAATATTT
Found at i:113728 original size:20 final size:20
Alignment explanation
Indices: 113700--113745 Score: 56
Period size: 20 Copynumber: 2.3 Consensus size: 20
113690 AAGTGTGAAT
* *
113700 ATTAAATTTTTATTAAGTAA
1 ATTATATTTTTAGTAAGTAA
* *
113720 ATTATATTTTTAGTCATTAA
1 ATTATATTTTTAGTAAGTAA
113740 ATTATA
1 ATTATA
113746 GATAAATTTT
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.41, C:0.02, G:0.04, T:0.52
Consensus pattern (20 bp):
ATTATATTTTTAGTAAGTAA
Found at i:115054 original size:17 final size:18
Alignment explanation
Indices: 115022--115055 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
115012 AATAATTTTT
115022 AAATTTAAAATATTTATG
1 AAATTTAAAATATTTATG
115040 AAATTTAAAAT-TTTAT
1 AAATTTAAAATATTTAT
115056 ATTTTAGAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 5 0.31
18 11 0.69
ACGTcount: A:0.50, C:0.00, G:0.03, T:0.47
Consensus pattern (18 bp):
AAATTTAAAATATTTATG
Found at i:115084 original size:18 final size:17
Alignment explanation
Indices: 115063--115113 Score: 57
Period size: 18 Copynumber: 2.9 Consensus size: 17
115053 TATATTTTAG
115063 AAAAATATAAAAAATTCT
1 AAAAATATAAAAAATT-T
*
115081 AAAAATATATAAAAAGTT
1 AAAAATATA-AAAAATTT
* *
115099 AAAATTAAAAAAAAT
1 AAAAATATAAAAAAT
115114 AAAACAATAA
Statistics
Matches: 28, Mismatches: 4, Indels: 3
0.80 0.11 0.09
Matches are distributed among these distances:
17 5 0.18
18 17 0.61
19 6 0.21
ACGTcount: A:0.71, C:0.02, G:0.02, T:0.25
Consensus pattern (17 bp):
AAAAATATAAAAAATTT
Found at i:115220 original size:16 final size:16
Alignment explanation
Indices: 115199--115229 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
115189 ATTGAATTTT
115199 TTTCAAATATATATGG
1 TTTCAAATATATATGG
*
115215 TTTCAAATTTATATG
1 TTTCAAATATATATG
115230 TTCTAACATG
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.35, C:0.06, G:0.10, T:0.48
Consensus pattern (16 bp):
TTTCAAATATATATGG
Found at i:117188 original size:18 final size:17
Alignment explanation
Indices: 117149--117198 Score: 64
Period size: 18 Copynumber: 2.9 Consensus size: 17
117139 GTACATAATC
*
117149 ATTTAACAATTTTTTAA
1 ATTTAAAAATTTTTTAA
117166 ATTTAAAAATTTTTATAA
1 ATTTAAAAATTTTT-TAA
* *
117184 TTTTAATAATTTTTT
1 ATTTAAAAATTTTTT
117199 TATCTTTTTA
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
17 14 0.48
18 15 0.52
ACGTcount: A:0.40, C:0.02, G:0.00, T:0.58
Consensus pattern (17 bp):
ATTTAAAAATTTTTTAA
Found at i:124836 original size:13 final size:13
Alignment explanation
Indices: 124818--124849 Score: 55
Period size: 13 Copynumber: 2.4 Consensus size: 13
124808 TAGTTTCCAC
124818 TTGAATTTGAATT
1 TTGAATTTGAATT
124831 TTGAATTTGAATT
1 TTGAATTTGAATT
124844 TATGAA
1 T-TGAA
124850 GAGAAATTGG
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
13 14 0.78
14 4 0.22
ACGTcount: A:0.34, C:0.00, G:0.16, T:0.50
Consensus pattern (13 bp):
TTGAATTTGAATT
Found at i:127299 original size:23 final size:22
Alignment explanation
Indices: 127263--127308 Score: 58
Period size: 22 Copynumber: 2.0 Consensus size: 22
127253 CTCTTTTTCA
*
127263 TTTAGATTTATAATTTATAAAAT
1 TTTAGATTTATAA-TAATAAAAT
127286 TTTAGA-TTAGTAATAATAAAAT
1 TTTAGATTTA-TAATAATAAAAT
127308 T
1 T
127309 ATATTCTGGT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
22 12 0.57
23 9 0.43
ACGTcount: A:0.46, C:0.00, G:0.07, T:0.48
Consensus pattern (22 bp):
TTTAGATTTATAATAATAAAAT
Found at i:133389 original size:84 final size:84
Alignment explanation
Indices: 133285--133450 Score: 278
Period size: 84 Copynumber: 2.0 Consensus size: 84
133275 CCACTACCAC
* **
133285 TAGTTCCACCACTTAAATTCTGTCCACAATCTTGCAACTCATCATTGTCCTTCACATCACCTTCT
1 TAGTTCCACCACTTAAATTCTGTCCACAATCTTGCAACTCACCATCATCCTTCACATCACCTTCT
133350 CTTCTATTCACCACCTCAT
66 CTTCTATTCACCACCTCAT
* *
133369 TAGTTCCACCATTTAGATTCTGTCCACAATCTTGCAACTCACCATCATCCTTCACATCACCTTCT
1 TAGTTCCACCACTTAAATTCTGTCCACAATCTTGCAACTCACCATCATCCTTCACATCACCTTCT
*
133434 CTTTTATTCACCACCTC
66 CTTCTATTCACCACCTC
133451 TTCATTAACC
Statistics
Matches: 76, Mismatches: 6, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
84 76 1.00
ACGTcount: A:0.23, C:0.36, G:0.05, T:0.36
Consensus pattern (84 bp):
TAGTTCCACCACTTAAATTCTGTCCACAATCTTGCAACTCACCATCATCCTTCACATCACCTTCT
CTTCTATTCACCACCTCAT
Found at i:134062 original size:228 final size:219
Alignment explanation
Indices: 133674--134122 Score: 659
Period size: 228 Copynumber: 2.0 Consensus size: 219
133664 CTCTCCTCCA
* * *
133674 CCACCACCAACACTCTTAGACTGTTCGCTGCCTGAATCCCGTGACCATGTTGGCGACCTTGACTT
1 CCACCACCAACACTCTTAGACTGCTCACTGCCCGAATCCCGTGACCATGTTGGCGACCTTGACTT
* *
133739 AGACTTCGACTTGGAGCTTCTCCTCTTCAAATCCTCCTCCCTTGATTCCCCAACAACCCTCCCTG
66 AGACTTCGACTTGGAGCTTCTCCTCCTCAAATCCCCCTCCCTTGATTCCCCAACAACCCTCCCTG
* * *
133804 CCCCCAAAGAATCCCTTGACCGTGTAGGTGAGCTCACATCCCTAACATCCTTCAGATGCACCTTA
131 CCCCCAAAGAATCCCTTGACCGCGTAGGTGAGCTCACATCCCTAAAATCCCTCAGATGCACCTTA
*
133869 CTACTACCTCTAGTC-TCATCAATT
196 CTACTACCTCTA-ACATCATCAATT
*
133893 CCACCACCAACACTCTTAGACTGCTCACTGCCCGAATCTCGTGACCATGTTGGCGACCTTGACAT
1 CCACCACCAACACTCTTAGACTGCTCACTGCCCGAATCCCGTGACCATGTTGGCGACCTTGAC-T
*
133958 AGACGTAGACATT-GCCTTGGAGCTTCTCCTCCTCAAATCTTCCCTCTCCCTTGATTCCCCAACA
65 -----TAGAC-TTCGACTTGGAGCTTCTCCTCCTCAAATC--CCC-CTCCCTTGATTCCCCAACA
*
134022 ACCCTCCCTGGCCCCAAAGAATCCCTTGACCGCGTAGGTGAGCTCACATCCCTAAAATCCCTCAG
121 ACCCTCCCTGCCCCCAAAGAATCCCTTGACCGCGTAGGTGAGCTCACATCCCTAAAATCCCTCAG
* *
134087 TTGCACCTTACTACTCCCTCTAACATCATCAATT
186 ATGCACCTTACTACTACCTCTAACATCATCAATT
134121 CC
1 CC
134123 CAACCTTCGC
Statistics
Matches: 205, Mismatches: 14, Indels: 13
0.88 0.06 0.06
Matches are distributed among these distances:
219 59 0.29
220 1 0.00
225 29 0.14
226 2 0.01
227 3 0.01
228 111 0.54
ACGTcount: A:0.22, C:0.38, G:0.14, T:0.26
Consensus pattern (219 bp):
CCACCACCAACACTCTTAGACTGCTCACTGCCCGAATCCCGTGACCATGTTGGCGACCTTGACTT
AGACTTCGACTTGGAGCTTCTCCTCCTCAAATCCCCCTCCCTTGATTCCCCAACAACCCTCCCTG
CCCCCAAAGAATCCCTTGACCGCGTAGGTGAGCTCACATCCCTAAAATCCCTCAGATGCACCTTA
CTACTACCTCTAACATCATCAATT
Found at i:139740 original size:13 final size:13
Alignment explanation
Indices: 139722--139746 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
139712 TATATATATA
139722 GTTTAAGCAACGC
1 GTTTAAGCAACGC
139735 GTTTAAGCAACG
1 GTTTAAGCAACG
139747 GAGTATAATT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.20, G:0.24, T:0.24
Consensus pattern (13 bp):
GTTTAAGCAACGC
Found at i:141586 original size:2 final size:2
Alignment explanation
Indices: 141581--141613 Score: 59
Period size: 2 Copynumber: 17.0 Consensus size: 2
141571 TTTTACACTA
141581 AT AT AT AT AT AT AT AT AT AT AT AT AT AT -T AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
141614 TCTTACATCG
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 29 0.97
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
AT
Found at i:143153 original size:38 final size:38
Alignment explanation
Indices: 143032--143177 Score: 109
Period size: 38 Copynumber: 3.8 Consensus size: 38
143022 TTTTCTCGTG
* * *
143032 TTTTTTTATACTTTCTCATAATTTTTAGTATTCCCTCGTA-
1 TTTTTTTATATTTTCTCATAATTTTTGGTAAT--CTC-TAT
* * * * *
143072 TTTATTGATA-TTCCTTCATAATTATTGGTGCATCTC-AT
1 TTTTTTTATATTTTC-TCATAATTTTTGGT-AATCTCTAT
*
143110 ATTTTTTATATTTTCTCATAATTTTTGGTAATCTCTAT
1 TTTTTTTATATTTTCTCATAATTTTTGGTAATCTCTAT
* ** *
143148 TTTTTTTGTATTCACTCATAAATTTTGGTA
1 TTTTTTTATATTTTCTCATAATTTTTGGTA
143178 CTCCCTCATA
Statistics
Matches: 83, Mismatches: 18, Indels: 12
0.73 0.16 0.11
Matches are distributed among these distances:
37 6 0.07
38 47 0.57
39 9 0.11
40 20 0.24
41 1 0.01
ACGTcount: A:0.23, C:0.14, G:0.08, T:0.56
Consensus pattern (38 bp):
TTTTTTTATATTTTCTCATAATTTTTGGTAATCTCTAT
Found at i:143173 original size:20 final size:20
Alignment explanation
Indices: 143150--143194 Score: 54
Period size: 20 Copynumber: 2.2 Consensus size: 20
143140 ATCTCTATTT
*
143150 TTTTTGTATTCACTCATAAA
1 TTTTTGTACTCACTCATAAA
* * *
143170 TTTTGGTACTCCCTCATATA
1 TTTTTGTACTCACTCATAAA
143190 TTTTT
1 TTTTT
143195 TATACTTCTT
Statistics
Matches: 20, Mismatches: 5, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.22, C:0.18, G:0.07, T:0.53
Consensus pattern (20 bp):
TTTTTGTACTCACTCATAAA
Found at i:143200 original size:21 final size:21
Alignment explanation
Indices: 143176--143219 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 21
143166 TAAATTTTGG
143176 TACTCCCTCATATATTTTTTA
1 TACTCCCTCATATATTTTTTA
* * *
143197 TACTTCTTCATATTTTTTTTA
1 TACTCCCTCATATATTTTTTA
143218 TA
1 TA
143220 TTTCCTCGTA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.23, C:0.18, G:0.00, T:0.59
Consensus pattern (21 bp):
TACTCCCTCATATATTTTTTA
Found at i:144517 original size:19 final size:19
Alignment explanation
Indices: 144493--144532 Score: 55
Period size: 19 Copynumber: 2.1 Consensus size: 19
144483 TTTAAACTTG
144493 AACAAAAACA-AAATATTAT
1 AACAAAAACAGAAA-ATTAT
*
144512 AACAAATACAGAAAATTAT
1 AACAAAAACAGAAAATTAT
144531 AA
1 AA
144533 AAAGATAGAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
19 16 0.84
20 3 0.16
ACGTcount: A:0.68, C:0.10, G:0.03, T:0.20
Consensus pattern (19 bp):
AACAAAAACAGAAAATTAT
Found at i:146282 original size:40 final size:40
Alignment explanation
Indices: 146206--146283 Score: 95
Period size: 40 Copynumber: 1.9 Consensus size: 40
146196 ATAATGTTGG
* ** * *
146206 TTTTACTAGATTTTTTTATATTTTCTTCTCATCAAACAAA
1 TTTTACTAGATTTTTTTACAAGTTCTCCTCACCAAACAAA
146246 TTTTACTAGA-TTTTTTACAAGTTCTCCTCAACCAAACA
1 TTTTACTAGATTTTTTTACAAGTTCTCCTC-ACCAAACA
146284 CACACACACA
Statistics
Matches: 32, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
39 15 0.47
40 17 0.53
ACGTcount: A:0.31, C:0.19, G:0.04, T:0.46
Consensus pattern (40 bp):
TTTTACTAGATTTTTTTACAAGTTCTCCTCACCAAACAAA
Found at i:148258 original size:18 final size:17
Alignment explanation
Indices: 148231--148266 Score: 54
Period size: 18 Copynumber: 2.1 Consensus size: 17
148221 AACCTTTTTG
*
148231 TTTTATTTTAATTATTT
1 TTTTATTTTAATAATTT
148248 TTTTAATTTTAATAATTT
1 TTTT-ATTTTAATAATTT
148266 T
1 T
148267 GGGAGCGAGA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 4 0.24
18 13 0.76
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (17 bp):
TTTTATTTTAATAATTT
Found at i:164770 original size:54 final size:54
Alignment explanation
Indices: 164704--164813 Score: 184
Period size: 54 Copynumber: 2.0 Consensus size: 54
164694 GTCACTGCCC
* *
164704 CTGATTTTTCCAATGCTGATGATGAGGAAGATGATATTGCTTCAGAAACCGGTT
1 CTGATTTGTCCAATGCTGATGATGAGGAAGATCATATTGCTTCAGAAACCGGTT
* *
164758 CTGATTTGTCCAATGCTGATGATGAGGAAGATCATGTTGCTTCAGAAACTGGTT
1 CTGATTTGTCCAATGCTGATGATGAGGAAGATCATATTGCTTCAGAAACCGGTT
164812 CT
1 CT
164814 TCTAAGGATA
Statistics
Matches: 52, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
54 52 1.00
ACGTcount: A:0.26, C:0.15, G:0.25, T:0.34
Consensus pattern (54 bp):
CTGATTTGTCCAATGCTGATGATGAGGAAGATCATATTGCTTCAGAAACCGGTT
Found at i:165634 original size:75 final size:75
Alignment explanation
Indices: 165507--165655 Score: 244
Period size: 75 Copynumber: 2.0 Consensus size: 75
165497 CAAGTCGCCT
* * * *
165507 CTTGAAGCCCTTTTGTCTGACATGCAAGTAACAGATACTGCTGCTTCCTGCTCTAAGAAAAGTGA
1 CTTGAAGCCCTTTTGTCAGACATGCAAGTAACAGATACTGCTACTTCCTGCTCTAAAAAAAGCGA
165572 TGATGGTTCC
66 TGATGGTTCC
* *
165582 CTTGAAGCCCTTTTGTCAGACATGCAAGTCACAGATACTGCTACTTCTTGCTCTAAAAAAAGCGA
1 CTTGAAGCCCTTTTGTCAGACATGCAAGTAACAGATACTGCTACTTCCTGCTCTAAAAAAAGCGA
165647 TGATGGTTC
66 TGATGGTTC
165656 TCAACCTGGT
Statistics
Matches: 68, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
75 68 1.00
ACGTcount: A:0.27, C:0.23, G:0.20, T:0.30
Consensus pattern (75 bp):
CTTGAAGCCCTTTTGTCAGACATGCAAGTAACAGATACTGCTACTTCCTGCTCTAAAAAAAGCGA
TGATGGTTCC
Found at i:166725 original size:26 final size:26
Alignment explanation
Indices: 166688--166740 Score: 72
Period size: 26 Copynumber: 2.0 Consensus size: 26
166678 TAAAAGAAGT
*
166688 ATTAATTGAAAATTGAAT-AATTTAA
1 ATTAATTGAAAAGTGAATAAATTTAA
*
166713 ATTATATTTAAAAGTGAATAAATTTAA
1 ATTA-ATTGAAAAGTGAATAAATTTAA
166740 A
1 A
166741 AAGAAAACAA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
25 4 0.17
26 12 0.50
27 8 0.33
ACGTcount: A:0.53, C:0.00, G:0.08, T:0.40
Consensus pattern (26 bp):
ATTAATTGAAAAGTGAATAAATTTAA
Found at i:170593 original size:5 final size:5
Alignment explanation
Indices: 170583--170622 Score: 80
Period size: 5 Copynumber: 8.0 Consensus size: 5
170573 TGTCCATTGC
170583 AATGG AATGG AATGG AATGG AATGG AATGG AATGG AATGG
1 AATGG AATGG AATGG AATGG AATGG AATGG AATGG AATGG
170623 GATGCCAGAC
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 35 1.00
ACGTcount: A:0.40, C:0.00, G:0.40, T:0.20
Consensus pattern (5 bp):
AATGG
Found at i:185020 original size:12 final size:12
Alignment explanation
Indices: 185004--185072 Score: 50
Period size: 12 Copynumber: 5.8 Consensus size: 12
184994 AAAAAGTATA
185004 AAAAATAACACC
1 AAAAATAACACC
* * *
185016 CAAAACAACAGC
1 AAAAATAACACC
* *
185028 AAAAATAAAATC
1 AAAAATAACACC
* *
185040 -AAAAGAACAAC
1 AAAAATAACACC
*
185051 AAAAATAACAGC
1 AAAAATAACACC
*
185063 AAAAACAACA
1 AAAAATAACA
185073 TAAAAATAGA
Statistics
Matches: 43, Mismatches: 13, Indels: 2
0.74 0.22 0.03
Matches are distributed among these distances:
11 8 0.19
12 35 0.81
ACGTcount: A:0.70, C:0.20, G:0.04, T:0.06
Consensus pattern (12 bp):
AAAAATAACACC
Found at i:185031 original size:23 final size:24
Alignment explanation
Indices: 185004--185080 Score: 77
Period size: 23 Copynumber: 3.3 Consensus size: 24
184994 AAAAAGTATA
* *
185004 AAAAATAACACCCAAAACAACAGC
1 AAAAATAACAACCAAAACAACAAC
* *
185028 AAAAATAA-AATCAAAAGAACAAC
1 AAAAATAACAACCAAAACAACAAC
* * *
185051 AAAAATAACAGCAAAAACAAC-AT
1 AAAAATAACAACCAAAACAACAAC
185074 AAAAATA
1 AAAAATA
185081 GAAAAAAAAC
Statistics
Matches: 43, Mismatches: 9, Indels: 3
0.78 0.16 0.05
Matches are distributed among these distances:
23 27 0.63
24 16 0.37
ACGTcount: A:0.70, C:0.18, G:0.04, T:0.08
Consensus pattern (24 bp):
AAAAATAACAACCAAAACAACAAC
Found at i:185100 original size:12 final size:12
Alignment explanation
Indices: 185017--185132 Score: 61
Period size: 12 Copynumber: 10.3 Consensus size: 12
185007 AATAACACCC
*
185017 AAAACAACAGCA
1 AAAACAACATCA
* *
185029 AAAATAAAATC-
1 AAAACAACATCA
* *
185040 AAAAGAACAACA
1 AAAACAACATCA
* *
185052 AAAATAACAGCA
1 AAAACAACATCA
185064 AAAACAACAT-A
1 AAAACAACATCA
* *
185075 AAAATAGA-A-AA
1 AAAACA-ACATCA
185086 AAAACAACATC-
1 AAAACAACATCA
185097 AAAAC-A-A-CA
1 AAAACAACATCA
*
185106 AAAGC-ACATCA
1 AAAACAACATCA
*
185117 AAAACAACAACA
1 AAAACAACATCA
185129 AAAA
1 AAAA
185133 AAATAGAAAT
Statistics
Matches: 79, Mismatches: 16, Indels: 18
0.70 0.14 0.16
Matches are distributed among these distances:
8 1 0.01
9 6 0.08
10 3 0.04
11 33 0.42
12 36 0.46
ACGTcount: A:0.72, C:0.18, G:0.04, T:0.06
Consensus pattern (12 bp):
AAAACAACATCA
Found at i:185108 original size:22 final size:22
Alignment explanation
Indices: 185063--185132 Score: 58
Period size: 22 Copynumber: 3.2 Consensus size: 22
185053 AAATAACAGC
* *
185063 AAAAACAACATAAAAATAGA-AA
1 AAAAACAACATCAAAACA-ACAA
185085 AAAAACAACATCAAAACAAC--
1 AAAAACAACATCAAAACAACAA
*
185105 AAAAGC-ACATCAAAAACAACAA
1 AAAAACAACATC-AAAACAACAA
185127 CAAAAA
1 -AAAAA
185133 AAATAGAAAT
Statistics
Matches: 39, Mismatches: 4, Indels: 9
0.75 0.08 0.17
Matches are distributed among these distances:
19 5 0.13
20 13 0.33
21 1 0.03
22 16 0.41
23 4 0.10
ACGTcount: A:0.73, C:0.19, G:0.03, T:0.06
Consensus pattern (22 bp):
AAAAACAACATCAAAACAACAA
Found at i:190577 original size:12 final size:12
Alignment explanation
Indices: 190562--190618 Score: 60
Period size: 12 Copynumber: 4.7 Consensus size: 12
190552 ACAACCAAAA
190562 CAACAAAAATAG
1 CAACAAAAATAG
* *
190574 CAACAAAAAAAA
1 CAACAAAAATAG
**
190586 CAGTAAAAATAG
1 CAACAAAAATAG
190598 CAACAAAAAATAG
1 CAAC-AAAAATAG
*
190611 CATCAAAA
1 CAACAAAA
190619 CAACAACCAA
Statistics
Matches: 35, Mismatches: 9, Indels: 2
0.76 0.20 0.04
Matches are distributed among these distances:
12 24 0.69
13 11 0.31
ACGTcount: A:0.68, C:0.16, G:0.07, T:0.09
Consensus pattern (12 bp):
CAACAAAAATAG
Found at i:190585 original size:24 final size:24
Alignment explanation
Indices: 190558--190607 Score: 82
Period size: 24 Copynumber: 2.1 Consensus size: 24
190548 CCAAACAACC
190558 AAAACAACAAAAATAGCAACAAAA
1 AAAACAACAAAAATAGCAACAAAA
**
190582 AAAACAGTAAAAATAGCAACAAAA
1 AAAACAACAAAAATAGCAACAAAA
190606 AA
1 AA
190608 TAGCATCAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.74, C:0.14, G:0.06, T:0.06
Consensus pattern (24 bp):
AAAACAACAAAAATAGCAACAAAA
Found at i:190606 original size:13 final size:13
Alignment explanation
Indices: 190562--190618 Score: 57
Period size: 13 Copynumber: 4.6 Consensus size: 13
190552 ACAACCAAAA
190562 CAAC-AAAAATAG
1 CAACAAAAAATAG
*
190574 CAACAAAAAA-AA
1 CAACAAAAAATAG
**
190586 C-AGTAAAAATAG
1 CAACAAAAAATAG
190598 CAACAAAAAATAG
1 CAACAAAAAATAG
*
190611 CATCAAAA
1 CAACAAAA
190619 CAACAACCAA
Statistics
Matches: 35, Mismatches: 7, Indels: 5
0.74 0.15 0.11
Matches are distributed among these distances:
11 6 0.17
12 8 0.23
13 21 0.60
ACGTcount: A:0.68, C:0.16, G:0.07, T:0.09
Consensus pattern (13 bp):
CAACAAAAAATAG
Found at i:190653 original size:21 final size:20
Alignment explanation
Indices: 190627--190665 Score: 60
Period size: 21 Copynumber: 1.9 Consensus size: 20
190617 AACAACAACC
190627 AAAATAATAATAAAAAACACA
1 AAAATAATAA-AAAAAACACA
*
190648 AAAATAGTAAAAAAAACA
1 AAAATAATAAAAAAAACA
190666 ACACCAAAAC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 8 0.47
21 9 0.53
ACGTcount: A:0.77, C:0.08, G:0.03, T:0.13
Consensus pattern (20 bp):
AAAATAATAAAAAAAACACA
Found at i:190658 original size:18 final size:18
Alignment explanation
Indices: 190632--190666 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
190622 CAACCAAAAT
*
190632 AATAATAAAAAACACAAA
1 AATAATAAAAAAAACAAA
*
190650 AATAGTAAAAAAAACAA
1 AATAATAAAAAAAACAA
190667 CACCAAAACA
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:0.77, C:0.09, G:0.03, T:0.11
Consensus pattern (18 bp):
AATAATAAAAAAAACAAA
Found at i:190679 original size:23 final size:23
Alignment explanation
Indices: 190615--190684 Score: 83
Period size: 23 Copynumber: 3.1 Consensus size: 23
190605 AAATAGCATC
*
190615 AAAACAACAACCAAAATAATAATAA
1 AAAACAAC-ACCAAAATAGTAA-AA
190640 AAAAC-ACA--AAAATAGTAAAA
1 AAAACAACACCAAAATAGTAAAA
*
190660 AAAACAACACCAAAACAGTAAAA
1 AAAACAACACCAAAATAGTAAAA
190683 AA
1 AA
190685 CAGCACTAGA
Statistics
Matches: 40, Mismatches: 2, Indels: 8
0.80 0.04 0.16
Matches are distributed among these distances:
20 7 0.17
21 12 0.30
23 14 0.35
24 2 0.05
25 5 0.12
ACGTcount: A:0.73, C:0.16, G:0.03, T:0.09
Consensus pattern (23 bp):
AAAACAACACCAAAATAGTAAAA
Done.