Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01013752.1 Kokia drynarioides strain JFW-HI SEQ_128780, 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: 286890
ACGTcount: A:0.34, C:0.15, G:0.16, T:0.35
Warning! 165 characters in sequence are not A, C, G, or T
Found at i:4069 original size:4 final size:4
Alignment explanation
Indices: 4062--4142 Score: 53
Period size: 4 Copynumber: 20.0 Consensus size: 4
4052 TTATCTTTTT
* * *
4062 TTTC TTTC TCCTTC TTTCC CTTC TTCTC CTTC -TTC CTTC -TTC T-TC
1 TTTC TTTC T--TTC TTT-C TTTC TT-TC TTTC TTTC TTTC TTTC TTTC
*
4107 TTTC TTTC TTTC TTTC TCTTT TTTC TTTC TTT- TTTC
1 TTTC TTTC TTTC TTTC T-TTC TTTC TTTC TTTC TTTC
4143 CTTCAATTTT
Statistics
Matches: 63, Mismatches: 5, Indels: 18
0.73 0.06 0.21
Matches are distributed among these distances:
3 12 0.19
4 38 0.60
5 9 0.14
6 4 0.06
ACGTcount: A:0.00, C:0.32, G:0.00, T:0.68
Consensus pattern (4 bp):
TTTC
Found at i:4119 original size:25 final size:24
Alignment explanation
Indices: 4055--4138 Score: 72
Period size: 21 Copynumber: 3.7 Consensus size: 24
4045 AAACACATTA
4055 TCTT-TTT-TTTCTTTCTCCTTCT
1 TCTTCTTTCTTTCTTTCTCCTTCT
* * *
4077 T-TCCCTTCTTCTCCTTCTTCCTTCT
1 TCTTCTTTCTT-TCTTTC-TCCTTCT
4102 TCTTCTTTCTTTCTTTCT--TTC-
1 TCTTCTTTCTTTCTTTCTCCTTCT
*
4123 TCTTTTTTCTTTCTTT
1 TCTTCTTTCTTTCTTT
4139 TTTCCTTCAA
Statistics
Matches: 50, Mismatches: 7, Indels: 11
0.74 0.10 0.16
Matches are distributed among these distances:
21 16 0.32
22 6 0.12
23 2 0.04
24 6 0.12
25 13 0.26
26 7 0.14
ACGTcount: A:0.00, C:0.31, G:0.00, T:0.69
Consensus pattern (24 bp):
TCTTCTTTCTTTCTTTCTCCTTCT
Found at i:4137 original size:35 final size:31
Alignment explanation
Indices: 4059--4137 Score: 77
Period size: 31 Copynumber: 2.4 Consensus size: 31
4049 ACATTATCTT
*
4059 TTTTTTCTTTCTCCTTCTTTCCCTTCTTCTC
1 TTTTTTCTTTCTTCTTCTTTCCCTTCTTCTC
* * * *
4090 CTTCTTCCTTCTTCTTCTTTCTTTCTTTCTTTCTC
1 TTTTTTCTTTCTTCTTCTTTC---CCTTC-TTCTC
4125 TTTTTTCTTTCTT
1 TTTTTTCTTTCTT
4138 TTTTCCTTCA
Statistics
Matches: 36, Mismatches: 8, Indels: 4
0.75 0.17 0.08
Matches are distributed among these distances:
31 17 0.47
34 4 0.11
35 15 0.42
ACGTcount: A:0.00, C:0.32, G:0.00, T:0.68
Consensus pattern (31 bp):
TTTTTTCTTTCTTCTTCTTTCCCTTCTTCTC
Found at i:4799 original size:18 final size:18
Alignment explanation
Indices: 4763--4817 Score: 58
Period size: 18 Copynumber: 3.1 Consensus size: 18
4753 TGTATATCAC
* *
4763 ATTAACAAATTATTT-AA
1 ATTAAAAAAATATTTAAA
* *
4780 ATTCATAAAATATTTAAA
1 ATTAAAAAAATATTTAAA
*
4798 ATTAAAAAAATATTAAAA
1 ATTAAAAAAATATTTAAA
4816 AT
1 AT
4818 ATTCATAATT
Statistics
Matches: 31, Mismatches: 6, Indels: 1
0.82 0.16 0.03
Matches are distributed among these distances:
17 12 0.39
18 19 0.61
ACGTcount: A:0.60, C:0.04, G:0.00, T:0.36
Consensus pattern (18 bp):
ATTAAAAAAATATTTAAA
Found at i:4808 original size:27 final size:27
Alignment explanation
Indices: 4778--4834 Score: 71
Period size: 27 Copynumber: 2.1 Consensus size: 27
4768 CAAATTATTT
*
4778 AAAT-TCATAAAATATTTAAAATTAAAA
1 AAATATCA-AAAATATTCAAAATTAAAA
* *
4805 AAATATTAAAAATATTCATAATTAAAA
1 AAATATCAAAAATATTCAAAATTAAAA
4832 AAA
1 AAA
4835 CAAAAAGTAC
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
27 24 0.92
28 2 0.08
ACGTcount: A:0.65, C:0.04, G:0.00, T:0.32
Consensus pattern (27 bp):
AAATATCAAAAATATTCAAAATTAAAA
Found at i:12969 original size:85 final size:84
Alignment explanation
Indices: 12788--13118 Score: 441
Period size: 85 Copynumber: 3.9 Consensus size: 84
12778 TATATGTATG
* * * ** * *
12788 TATAGGGATAGTCTTCTCTGGCTCATATAGGA-GAAAGGAATACGATTTATTGAAACCTAAACTG
1 TATAGGGATAGTCTACTCCGGTTTGTATAGGAGGAATGGAATACGATTTATTGAAACCTAAAATG
* *
12852 TTCTTTTGGAAATTACATA
66 TTCTTTTGGAAATCATATA
* * *
12871 TATAGGGATAGTCTACTCCGGTTTGTATAGGAGGAACGAAATATGATTTATTGAAACCTAAAATG
1 TATAGGGATAGTCTACTCCGGTTTGTATAGGAGGAATGGAATACGATTTATTGAAACCTAAAATG
12936 TTCTTTTTGGAAATCATATA
66 TTC-TTTTGGAAATCATATA
* *
12956 TATAGGGATAGTCTTCTCTGGTTTGTATAGGAGGAATGGAATACGATTTATTGAAACCTAAAATG
1 TATAGGGATAGTCTACTCCGGTTTGTATAGGAGGAATGGAATACGATTTATTGAAACCTAAAATG
13021 TTCTTTTGGAAATTC-TATA
66 TTCTTTTGGAAA-TCATATA
* * * * * *
13040 TATAGGGGATATTCTACTACAGTTTGTATTGGAGGAGTGGAATATGATTTATTGAAACCTAAAAT
1 TATA-GGGATAGTCTACTCCGGTTTGTATAGGAGGAATGGAATACGATTTATTGAAACCTAAAAT
13105 GTTCTTTTGGAAAT
65 GTTCTTTTGGAAAT
13119 TGTGTATATA
Statistics
Matches: 220, Mismatches: 24, Indels: 7
0.88 0.10 0.03
Matches are distributed among these distances:
83 27 0.12
84 49 0.22
85 144 0.65
ACGTcount: A:0.33, C:0.10, G:0.21, T:0.36
Consensus pattern (84 bp):
TATAGGGATAGTCTACTCCGGTTTGTATAGGAGGAATGGAATACGATTTATTGAAACCTAAAATG
TTCTTTTGGAAATCATATA
Found at i:13115 original size:169 final size:168
Alignment explanation
Indices: 12788--13118 Score: 513
Period size: 169 Copynumber: 2.0 Consensus size: 168
12778 TATATGTATG
*
12788 TATAGGGATAGTCTTCTCTGGCTCATATAGGAGAAAGGAATACGATTTATTGAAACCTAAACTGT
1 TATAGGGATAGTCTTCTCTGGCTCATATAGGAGAAAGGAATACGATTTATTGAAACCTAAAATGT
* *
12853 TCTTTTGGAAATTACATATATAGGGATAGTCTACTCCGGTTTGTATAGGAGGAACGAAATATGAT
66 TCTTTTGGAAATTACATATATAGGGATAGTCTACTACAGTTTGTATAGGAGGAACGAAATATGAT
12918 TTATTGAAACCTAAAATGTTCTTTTTGGAAATCATATA
131 TTATTGAAACCTAAAATGTTCTTTTTGGAAATCATATA
* ** *
12956 TATAGGGATAGTCTTCTCTGGTTTGTATAGGAGGAATGGAATACGATTTATTGAAACCTAAAATG
1 TATAGGGATAGTCTTCTCTGGCTCATATAGGA-GAAAGGAATACGATTTATTGAAACCTAAAATG
* * ** *
13021 TTCTTTTGGAAATT-CTATATATAGGGGATATTCTACTACAGTTTGTATTGGAGGAGTGGAATAT
65 TTCTTTTGGAAATTAC-ATATATA-GGGATAGTCTACTACAGTTTGTATAGGAGGAACGAAATAT
13085 GATTTATTGAAACCTAAAATGTTC-TTTTGGAAAT
128 GATTTATTGAAACCTAAAATGTTCTTTTTGGAAAT
13119 TGTGTATATA
Statistics
Matches: 148, Mismatches: 12, Indels: 5
0.90 0.07 0.03
Matches are distributed among these distances:
168 30 0.20
169 61 0.41
170 57 0.39
ACGTcount: A:0.33, C:0.10, G:0.21, T:0.36
Consensus pattern (168 bp):
TATAGGGATAGTCTTCTCTGGCTCATATAGGAGAAAGGAATACGATTTATTGAAACCTAAAATGT
TCTTTTGGAAATTACATATATAGGGATAGTCTACTACAGTTTGTATAGGAGGAACGAAATATGAT
TTATTGAAACCTAAAATGTTCTTTTTGGAAATCATATA
Found at i:27956 original size:18 final size:18
Alignment explanation
Indices: 27917--27964 Score: 60
Period size: 18 Copynumber: 2.7 Consensus size: 18
27907 ATGAGGGAAA
* *
27917 ACATATACATATACATAT
1 ACATATACATATACACAC
*
27935 ACATATACATATATACAC
1 ACATATACATATACACAC
*
27953 ACATATATATAT
1 ACATATACATAT
27965 TTACTATATA
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
18 26 1.00
ACGTcount: A:0.50, C:0.17, G:0.00, T:0.33
Consensus pattern (18 bp):
ACATATACATATACACAC
Found at i:27964 original size:6 final size:6
Alignment explanation
Indices: 27917--27947 Score: 62
Period size: 6 Copynumber: 5.2 Consensus size: 6
27907 ATGAGGGAAA
27917 ACATAT ACATAT ACATAT ACATAT ACATAT A
1 ACATAT ACATAT ACATAT ACATAT ACATAT A
27948 TACACACATA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 25 1.00
ACGTcount: A:0.52, C:0.16, G:0.00, T:0.32
Consensus pattern (6 bp):
ACATAT
Found at i:29375 original size:142 final size:143
Alignment explanation
Indices: 29094--29385 Score: 376
Period size: 142 Copynumber: 2.0 Consensus size: 143
29084 CCAAAACTCA
* *
29094 TTCCACACACCTCTTCTTCATCTCATCTTCTTCCCTTTTGATTCCAATATCTTTAGTCACAAATT
1 TTCCACACACCTCTTCTTCATCTCAACTTCTTCCCTTTTAATTCCAATATCTTTAGTCACAAATT
* * * * *
29159 TGTCTCAAAGCTTGAATCTTTGAAACTCATTAACCCCAAAAAACTTAACAGGAAGAAGATATTGG
66 TATCTCAAA---TG-A-CTTTGAAACCCATTAACCCAAAAAAACTTAACAGGAAGAAAACATTGG
29224 AATCAAAGATATTGAATC
126 AATCAAAGATATTGAATC
* * *
29242 TTCCACACATCTCTCTTCTTCATCTTTAACTTCTTCCC-TTTAATTCCAATATCTTTTGTTACAA
1 TTCCACACA-C-CTCTTCTTCATC-TCAACTTCTTCCCTTTTAATTCCAATATCTTTAGTCACAA
* *
29306 ATTTATCTCAAA-G-C-TTGAAACCCATTAACCCAAAAAAATTTAACGGGAAGAAAACATTGGAA
63 ATTTATCTCAAATGACTTTGAAACCCATTAACCCAAAAAAACTTAACAGGAAGAAAACATTGGAA
29368 TCAAAGATATTGAATC
128 TCAAAGATATTGAATC
29384 TT
1 TT
29386 TGGTTAACGG
Statistics
Matches: 129, Mismatches: 12, Indels: 12
0.84 0.08 0.08
Matches are distributed among these distances:
142 60 0.47
143 1 0.01
146 1 0.01
148 9 0.07
149 1 0.01
150 46 0.36
151 11 0.09
ACGTcount: A:0.34, C:0.23, G:0.09, T:0.35
Consensus pattern (143 bp):
TTCCACACACCTCTTCTTCATCTCAACTTCTTCCCTTTTAATTCCAATATCTTTAGTCACAAATT
TATCTCAAATGACTTTGAAACCCATTAACCCAAAAAAACTTAACAGGAAGAAAACATTGGAATCA
AAGATATTGAATC
Found at i:30025 original size:21 final size:23
Alignment explanation
Indices: 29981--30025 Score: 58
Period size: 23 Copynumber: 2.0 Consensus size: 23
29971 TTCTTTAATT
*
29981 TTTTATATTTAGTTCTTATTTTC
1 TTTTATATTTAGGTCTTATTTTC
*
30004 TTTTATATTTTGGT-TT-TTTTC
1 TTTTATATTTAGGTCTTATTTTC
30025 T
1 T
30026 AATTTTTATT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
21 6 0.30
22 2 0.10
23 12 0.60
ACGTcount: A:0.13, C:0.07, G:0.07, T:0.73
Consensus pattern (23 bp):
TTTTATATTTAGGTCTTATTTTC
Found at i:33662 original size:21 final size:21
Alignment explanation
Indices: 33612--33665 Score: 65
Period size: 21 Copynumber: 2.6 Consensus size: 21
33602 ATTAATTTAA
33612 CAAAAAA-TAAATCACCAATT
1 CAAAAAATTAAATCACCAATT
*** *
33632 CAATTGATTAAATCACTAATT
1 CAAAAAATTAAATCACCAATT
33653 CAAAAAATTAAAT
1 CAAAAAATTAAAT
33666 AAACATAACC
Statistics
Matches: 26, Mismatches: 7, Indels: 1
0.76 0.21 0.03
Matches are distributed among these distances:
20 4 0.15
21 22 0.85
ACGTcount: A:0.56, C:0.15, G:0.02, T:0.28
Consensus pattern (21 bp):
CAAAAAATTAAATCACCAATT
Found at i:39535 original size:59 final size:59
Alignment explanation
Indices: 39443--39560 Score: 236
Period size: 59 Copynumber: 2.0 Consensus size: 59
39433 GGAACCTTGA
39443 GTATCCAGTTTCCTGTCCTACCATACGTAAAATGTCATATATGGATTATTTTCTTGATT
1 GTATCCAGTTTCCTGTCCTACCATACGTAAAATGTCATATATGGATTATTTTCTTGATT
39502 GTATCCAGTTTCCTGTCCTACCATACGTAAAATGTCATATATGGATTATTTTCTTGATT
1 GTATCCAGTTTCCTGTCCTACCATACGTAAAATGTCATATATGGATTATTTTCTTGATT
39561 ATTCTGAATT
Statistics
Matches: 59, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
59 59 1.00
ACGTcount: A:0.25, C:0.19, G:0.14, T:0.42
Consensus pattern (59 bp):
GTATCCAGTTTCCTGTCCTACCATACGTAAAATGTCATATATGGATTATTTTCTTGATT
Found at i:39623 original size:16 final size:15
Alignment explanation
Indices: 39599--39642 Score: 56
Period size: 13 Copynumber: 3.0 Consensus size: 15
39589 GATACTACTC
39599 AAATTTATTGTGATTT
1 AAATTTATTGTG-TTT
*
39615 AATTTTATT-T-TTT
1 AAATTTATTGTGTTT
39628 AAATTTATTGTGTTT
1 AAATTTATTGTGTTT
39643 TATATTGAAT
Statistics
Matches: 24, Mismatches: 2, Indels: 5
0.77 0.06 0.16
Matches are distributed among these distances:
13 11 0.46
14 1 0.04
15 4 0.17
16 8 0.33
ACGTcount: A:0.27, C:0.00, G:0.09, T:0.64
Consensus pattern (15 bp):
AAATTTATTGTGTTT
Found at i:41098 original size:27 final size:27
Alignment explanation
Indices: 41060--41113 Score: 108
Period size: 27 Copynumber: 2.0 Consensus size: 27
41050 AAAAAAACTC
41060 ATAAAAAAGGTACAAATGCTATTGGGA
1 ATAAAAAAGGTACAAATGCTATTGGGA
41087 ATAAAAAAGGTACAAATGCTATTGGGA
1 ATAAAAAAGGTACAAATGCTATTGGGA
41114 TTTTGATTTC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 27 1.00
ACGTcount: A:0.48, C:0.07, G:0.22, T:0.22
Consensus pattern (27 bp):
ATAAAAAAGGTACAAATGCTATTGGGA
Found at i:42169 original size:126 final size:126
Alignment explanation
Indices: 41911--42211 Score: 352
Period size: 126 Copynumber: 2.4 Consensus size: 126
41901 GATTGAACTG
* * *
41911 ATTGGTTGATTTTTAACTATATTATGATTATGATTGTTGTTATTGCGTTATTATTACTCTTGTTT
1 ATTGGTTAATTTTTAACTATATTATGATTATGATTGTTGTTATTGTGTTATTATTACTATTGTTT
* * * *
41976 GACGCCTACTGCTTAATTTAAGCATTAGGGTTTAATTCTCAGCTTAACTATTATCCAATTC
66 GACGCCTACTACTTAATTTAAGCATTAAGGTTTAATTCTCAGCTTAACTATTATCAAAATC
* * ** *
42037 AATGGTTAATTTTTAACTACAACATGATTATGATTGTTGTTATTGTGTTATT-TTAGTATTGTTT
1 ATTGGTTAATTTTTAACTATATTATGATTATGATTGTTGTTATTGTGTTATTATTACTATTGTTT
* * * * ** * *
42101 GATGCGTACTACTTAGTTTCAGGGTTTAAGGTTTAATTCTCAGTTTAACTATTATTAAAATC
66 GACGCCTACTACTTAATTT-AAGCATTAAGGTTTAATTCTCAGCTTAACTATTATCAAAATC
* * * * * *
42163 TTTGGTTAATGTTTAGCTTTATTATGATTGTGATTGTTGCTATTGTGTT
1 ATTGGTTAATTTTTAACTATATTATGATTATGATTGTTGTTATTGTGTT
42212 GTTACTGATG
Statistics
Matches: 144, Mismatches: 30, Indels: 2
0.82 0.17 0.01
Matches are distributed among these distances:
125 25 0.17
126 119 0.83
ACGTcount: A:0.25, C:0.10, G:0.16, T:0.49
Consensus pattern (126 bp):
ATTGGTTAATTTTTAACTATATTATGATTATGATTGTTGTTATTGTGTTATTATTACTATTGTTT
GACGCCTACTACTTAATTTAAGCATTAAGGTTTAATTCTCAGCTTAACTATTATCAAAATC
Found at i:45128 original size:23 final size:24
Alignment explanation
Indices: 45102--45159 Score: 84
Period size: 23 Copynumber: 2.5 Consensus size: 24
45092 TAATATTCAT
**
45102 GAACATGTTCATTTAAC-TTAATC
1 GAACATGTTCATCGAACATTAATC
45125 GAACATGTTCA-CGAACATTAATC
1 GAACATGTTCATCGAACATTAATC
45148 GAACATGTTCAT
1 GAACATGTTCAT
45160 GAGCATATAA
Statistics
Matches: 31, Mismatches: 2, Indels: 3
0.86 0.06 0.08
Matches are distributed among these distances:
22 3 0.10
23 28 0.90
ACGTcount: A:0.36, C:0.19, G:0.12, T:0.33
Consensus pattern (24 bp):
GAACATGTTCATCGAACATTAATC
Found at i:45318 original size:23 final size:24
Alignment explanation
Indices: 45288--45332 Score: 74
Period size: 23 Copynumber: 1.9 Consensus size: 24
45278 ATCATTAATA
*
45288 AATAAACGAG-CTATAAATGAGTT
1 AATAAACGAGCCAATAAATGAGTT
45311 AATAAACGAGCCAATAAATGAG
1 AATAAACGAGCCAATAAATGAG
45333 CTTGTTCGCG
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
23 10 0.50
24 10 0.50
ACGTcount: A:0.51, C:0.11, G:0.18, T:0.20
Consensus pattern (24 bp):
AATAAACGAGCCAATAAATGAGTT
Found at i:64299 original size:2 final size:2
Alignment explanation
Indices: 64292--64316 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
64282 AATAATAATA
64292 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
64317 CACATCACTA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:67867 original size:16 final size:16
Alignment explanation
Indices: 67846--67876 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
67836 TGTTTTTCAA
*
67846 AATTTTTTAATTATAT
1 AATTTTGTAATTATAT
67862 AATTTTGTAATTATA
1 AATTTTGTAATTATA
67877 CATACTCAAT
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:0.39, C:0.00, G:0.03, T:0.58
Consensus pattern (16 bp):
AATTTTGTAATTATAT
Found at i:68016 original size:33 final size:33
Alignment explanation
Indices: 67974--68037 Score: 119
Period size: 33 Copynumber: 1.9 Consensus size: 33
67964 TATATTATAT
67974 TTATTAGTGCATCAAATACGAGCTAATAATTCA
1 TTATTAGTGCATCAAATACGAGCTAATAATTCA
*
68007 TTATTAGTGCATCAAATACGAGCTCATAATT
1 TTATTAGTGCATCAAATACGAGCTAATAATT
68038 TAAAAAAAAA
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.38, C:0.16, G:0.12, T:0.34
Consensus pattern (33 bp):
TTATTAGTGCATCAAATACGAGCTAATAATTCA
Found at i:68153 original size:4 final size:4
Alignment explanation
Indices: 68144--68170 Score: 54
Period size: 4 Copynumber: 6.8 Consensus size: 4
68134 ATAAAATAAT
68144 AAAG AAAG AAAG AAAG AAAG AAAG AAA
1 AAAG AAAG AAAG AAAG AAAG AAAG AAA
68171 AAGGGAAAGC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 23 1.00
ACGTcount: A:0.78, C:0.00, G:0.22, T:0.00
Consensus pattern (4 bp):
AAAG
Found at i:74087 original size:32 final size:32
Alignment explanation
Indices: 74059--74132 Score: 89
Period size: 31 Copynumber: 2.3 Consensus size: 32
74049 GATTAATGAG
*
74059 ATTTTCGAAAAATATTAAAAAAGCTTAATTAAA
1 ATTTTC-AAAAACATTAAAAAAGCTTAATTAAA
*
74092 ATTTTCAAAAACATT-AAAAAG-TGTAATGAAA
1 ATTTTCAAAAACATTAAAAAAGCT-TAATTAAA
*
74123 GTTTTCAAAA
1 ATTTTCAAAA
74133 TTTTGGGAGA
Statistics
Matches: 37, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
30 1 0.03
31 22 0.59
32 8 0.22
33 6 0.16
ACGTcount: A:0.53, C:0.07, G:0.08, T:0.32
Consensus pattern (32 bp):
ATTTTCAAAAACATTAAAAAAGCTTAATTAAA
Found at i:75262 original size:2 final size:2
Alignment explanation
Indices: 75257--75284 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
75247 ATATATATAT
75257 AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG
75285 GGGCTTCAAG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:76360 original size:12 final size:12
Alignment explanation
Indices: 76343--76378 Score: 54
Period size: 12 Copynumber: 2.9 Consensus size: 12
76333 CGAATCTGAC
76343 AAAAAAATGAAG
1 AAAAAAATGAAG
*
76355 AAAAAAAAGAAG
1 AAAAAAATGAAG
76367 AAGAAAAATGAA
1 AA-AAAAATGAA
76379 CAAATGATTA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
12 13 0.62
13 8 0.38
ACGTcount: A:0.78, C:0.00, G:0.17, T:0.06
Consensus pattern (12 bp):
AAAAAAATGAAG
Found at i:77941 original size:60 final size:59
Alignment explanation
Indices: 77755--77941 Score: 141
Period size: 60 Copynumber: 3.2 Consensus size: 59
77745 CAATTTTTAG
* * * *
77755 GTACCTAATTGGACCAAAATAAACTTTGGGTACCAACTT-AAGCCTTAAAGCCAAGTTCAA
1 GTACCTAATT-GACCAAAATAAACCTTAGGTACCAAATTGAA-CCATAAAGCCAAGTTCAA
* ** * * ** * *
77815 GTACCTAATCG--GGAAA-AAACCTTAGGTACCGACA-TGAACCATGAAGTTAAGTTTAG
1 GTACCTAATTGACCAAAATAAACCTTAGGTACC-AAATTGAACCATAAAGCCAAGTTCAA
* * * * *
77871 GTATCAAATTGAACTAAAATAAACGTTAGGTACCAAATTGAACCATAAAACCAAGTTCAA
1 GTACCTAATTG-ACCAAAATAAACCTTAGGTACCAAATTGAACCATAAAGCCAAGTTCAA
77931 GTACCTAATTG
1 GTACCTAATTG
77942 GGAAAAATCT
Statistics
Matches: 92, Mismatches: 28, Indels: 14
0.69 0.21 0.10
Matches are distributed among these distances:
56 33 0.36
57 6 0.07
59 6 0.07
60 47 0.51
ACGTcount: A:0.41, C:0.19, G:0.16, T:0.25
Consensus pattern (59 bp):
GTACCTAATTGACCAAAATAAACCTTAGGTACCAAATTGAACCATAAAGCCAAGTTCAA
Found at i:87022 original size:13 final size:13
Alignment explanation
Indices: 86987--87015 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
86977 TTGCGCCTTA
86987 ATCCAAATTGACT
1 ATCCAAATTGACT
87000 ATCCAAATTGACT
1 ATCCAAATTGACT
87013 ATC
1 ATC
87016 ACCATTGTGT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.38, C:0.24, G:0.07, T:0.31
Consensus pattern (13 bp):
ATCCAAATTGACT
Found at i:94103 original size:22 final size:20
Alignment explanation
Indices: 94057--94103 Score: 58
Period size: 22 Copynumber: 2.2 Consensus size: 20
94047 ATGTATCAAT
94057 TTAATTATTATTTTATAAAA
1 TTAATTATTATTTTATAAAA
* *
94077 ATAATTAATTTTTTTAATAAAA
1 TTAATT-ATTATTTT-ATAAAA
94099 TTAAT
1 TTAAT
94104 ATTTATTATT
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
20 5 0.23
21 7 0.32
22 10 0.45
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (20 bp):
TTAATTATTATTTTATAAAA
Found at i:94107 original size:20 final size:20
Alignment explanation
Indices: 94057--94107 Score: 59
Period size: 20 Copynumber: 2.5 Consensus size: 20
94047 ATGTATCAAT
*
94057 TTAATTATTATTTTATAAAA
1 TTAATTATTTTTTTATAAAA
*
94077 ATAATTAATTTTTTTAATAAAA
1 TTAATT-ATTTTTTT-ATAAAA
94099 TTAA-TATTT
1 TTAATTATTT
94108 ATTATTTAAA
Statistics
Matches: 26, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
20 9 0.35
21 8 0.31
22 9 0.35
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (20 bp):
TTAATTATTTTTTTATAAAA
Found at i:100901 original size:29 final size:30
Alignment explanation
Indices: 100864--100926 Score: 92
Period size: 29 Copynumber: 2.1 Consensus size: 30
100854 AAGGACTTGG
*
100864 TCAATTTAGTCCCTCTACTATT-AAATGAA
1 TCAATTTAGTCCCTCTACTATTAAAAAGAA
* *
100893 TCAATTTAGTCCTTGTACTATTAAAAAGAA
1 TCAATTTAGTCCCTCTACTATTAAAAAGAA
100923 TCAA
1 TCAA
100927 ACAAGGCCAA
Statistics
Matches: 30, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
29 20 0.67
30 10 0.33
ACGTcount: A:0.38, C:0.17, G:0.08, T:0.37
Consensus pattern (30 bp):
TCAATTTAGTCCCTCTACTATTAAAAAGAA
Found at i:117931 original size:60 final size:56
Alignment explanation
Indices: 117855--118075 Score: 142
Period size: 60 Copynumber: 3.8 Consensus size: 56
117845 AAACGAAGTC
* *
117855 AAAAATGCG-ATTTTTGGATGCCTGAAGGTAAAATGGTAATTTTCAAAAAGTTCAAGGTCT
1 AAAAATG-GAATTTTTGGATG-CTGAAGGTAAAATGGTAATTTT-AAAAAGCTCAAGG--G
* * *** *
117915 AAAAATGGAATTTTTGGAAATTC-GAGGGTAAAATGGTAATTTTTGGAAGCTCGAGGG
1 AAAAATGGAATTTTTGG--ATGCTGAAGGTAAAATGGTAATTTTAAAAAGCTCAAGGG
* * * * * * *
117972 AAAAATGGAATTTTTGGAAGTTCAAGGTAAAATGGTAATTTT-GAAAGTTTAGGGG
1 AAAAATGGAATTTTTGGATGCTGAAGGTAAAATGGTAATTTTAAAAAGCTCAAGGG
* * * * *
118027 TAAAAATGTAATTTTTTGTAAAGTTCAAGGGTAAAATGGTAATTTTAAA
1 -AAAAATGGAA-TTTTTG-GATGCTGAA-GGTAAAATGGTAATTTTAAA
118076 GTTTAGGGGT
Statistics
Matches: 131, Mismatches: 21, Indels: 18
0.77 0.12 0.11
Matches are distributed among these distances:
55 9 0.07
56 27 0.21
57 23 0.18
58 8 0.06
59 26 0.20
60 35 0.27
61 1 0.01
62 2 0.02
ACGTcount: A:0.38, C:0.05, G:0.24, T:0.33
Consensus pattern (56 bp):
AAAAATGGAATTTTTGGATGCTGAAGGTAAAATGGTAATTTTAAAAAGCTCAAGGG
Found at i:118063 original size:30 final size:28
Alignment explanation
Indices: 117881--118419 Score: 249
Period size: 29 Copynumber: 18.6 Consensus size: 28
117871 GATGCCTGAA
**
117881 GGTAAAATGGTAATTTTCAAAAAGTTCAAG
1 GGTAAAAT-GTAATTTT-TGAAAGTTCAAG
* * *
117911 GTCTAAAAATGGAATTTTTGGAAA-TTCGAG
1 G-GT-AAAATGTAATTTTT-GAAAGTTCAAG
* * *
117941 GGTAAAATGGTAATTTTTGGAAGCTCGAG
1 GGTAAAAT-GTAATTTTTGAAAGTTCAAG
* * *
117970 GGAAAAATGGAATTTTTGGAAGTTCAA-
1 GGTAAAATGTAATTTTTGAAAGTTCAAG
* *
117997 GGTAAAATGGTAA-TTTTGAAAGTTTAGG
1 GGTAAAAT-GTAATTTTTGAAAGTTCAAG
118025 GGTAAAAATGTAATTTTTTGTAAAGTTCAAG
1 GGT-AAAATGTAA-TTTTTG-AAAGTTCAAG
* *
118056 GGTAAAATGGTAA-TTTT-AAAGTTTAGG
1 GGTAAAAT-GTAATTTTTGAAAGTTCAAG
* *
118083 GGTAAAAATGTAATTTTGTG-AAGTTTAGG
1 GGT-AAAATGTAATTTT-TGAAAGTTCAAG
* **
118112 GGTAAAATGGTAATTTTGGAAAGTTCGGG
1 GGTAAAAT-GTAATTTTTGAAAGTTCAAG
* *
118141 GGTCAAAATGGAATTTTTTGAAA-TT-TAG
1 GGT-AAAATGTAA-TTTTTGAAAGTTCAAG
* *
118169 GAT-AAATCGTAATTTTTGAAAAGTT-TAG
1 GGTAAAAT-GTAATTTTTG-AAAGTTCAAG
* * *
118197 GGTCAAGAATGAAATTTCTAGAAA-TTCGAG
1 GGT-AA-AATGTAATTT-TTGAAAGTTCAAG
* **
118227 GGT-AAATGTAATTTTTGGAAGTTCGGG
1 GGTAAAATGTAATTTTTGAAAGTTCAAG
* * * * *
118254 GGAAAAATGGGATTTTTTGGAAGTTCGAG
1 GGTAAAAT-GTAATTTTTGAAAGTTCAAG
* * * * ***
118283 GGCAAAAATATAATTTATGGAAGTTTGGG
1 GG-TAAAATGTAATTTTTGAAAGTTCAAG
* * **
118312 GGTAAAAATGTAGTTTTTGTGAAGTTTGAG
1 GGT-AAAATGTAATTTTTG-AAAGTTCAAG
* * * *
118342 GGTAAAAATGTATTTTTTGTGAAGTTTAGG
1 GGT-AAAATGTAATTTTTG-AAAGTTCAAG
*
118372 GGTTAAAATGTAATTTTTAGAAAGTTCAGG
1 GG-TAAAATGTAATTTTT-GAAAGTTCAAG
*
118402 GGTCAAAATAT-ATTTTTG
1 GGT-AAAATGTAATTTTTG
118420 GACATTTCAG
Statistics
Matches: 411, Mismatches: 61, Indels: 76
0.75 0.11 0.14
Matches are distributed among these distances:
26 14 0.03
27 55 0.13
28 64 0.16
29 122 0.30
30 118 0.29
31 33 0.08
32 5 0.01
ACGTcount: A:0.35, C:0.04, G:0.26, T:0.35
Consensus pattern (28 bp):
GGTAAAATGTAATTTTTGAAAGTTCAAG
Found at i:118079 original size:58 final size:58
Alignment explanation
Indices: 117881--118410 Score: 358
Period size: 58 Copynumber: 9.1 Consensus size: 58
117871 GATGCCTGAA
* * ** * *
117881 GGTAAAATGGTAATTTTCAAAAAGTTCAAGGTCTAAAAATGGAATTTTTGGAAA-TTCGAG
1 GGTAAAATGGTAATTTT--GAAAGTT-TAGGGGTAAAAATGGAATTTTTTGAAAGTTCAAG
* * * *
117941 GGTAAAATGGTAATTTTTGGAAG-CTCGAGGG-AAAAATGGAA-TTTTTGGAAGTTCAA-
1 GGTAAAATGGTAA-TTTTGAAAGTTTAG-GGGTAAAAATGGAATTTTTTGAAAGTTCAAG
*
117997 GGTAAAATGGTAATTTTGAAAGTTTAGGGGTAAAAATGTAATTTTTTGTAAAGTTCAAG
1 GGTAAAATGGTAATTTTGAAAGTTTAGGGGTAAAAATGGAATTTTTTG-AAAGTTCAAG
* * * *
118056 GGTAAAATGGTAATTTT-AAAGTTTAGGGGTAAAAATGTAATTTTGTG-AAGTTTAGG
1 GGTAAAATGGTAATTTTGAAAGTTTAGGGGTAAAAATGGAATTTTTTGAAAGTTCAAG
** * *
118112 GGTAAAATGGTAATTTTGGAAAGTTCGGGGGTCAAAATGGAATTTTTTGAAA-TT-TAG
1 GGTAAAATGGTAATTTT-GAAAGTTTAGGGGTAAAAATGGAATTTTTTGAAAGTTCAAG
* * * * * * *
118169 GAT-AAATCGTAATTTTTGAAAAGTTTA-GGGTCAAGAATGAAATTTCTAGAAA-TTCGAG
1 GGTAAAATGGTAA-TTTTG-AAAGTTTAGGGGT-AAAAATGGAATTTTTTGAAAGTTCAAG
* * * * * *
118227 GGT-AAAT-GTAATTTTTGGAAG-TTCGGGGGAAAAATGGGATTTTTTGGAAGTTCGAG
1 GGTAAAATGGTAA-TTTTGAAAGTTTAGGGGTAAAAATGGAATTTTTTGAAAGTTCAAG
* * * * * * **
118283 GGCAAAAAT-ATAATTTATGGAAGTTTGGGGGTAAAAATGTAGTTTTTGTG-AAGTTTGAG
1 GG-TAAAATGGTAATTT-TGAAAGTTTAGGGGTAAAAATGGAATTTTT-TGAAAGTTCAAG
* * * * * *
118342 GGTAAAAAT-GTATTTTTTGTGAAGTTTAGGGGTTAAAATGTAATTTTTAGAAAGTTCAGG
1 GGT-AAAATGGTA-ATTTTG-AAAGTTTAGGGGTAAAAATGGAATTTTTTGAAAGTTCAAG
118402 GGTCAAAAT
1 GGT-AAAAT
118411 ATATTTTTGG
Statistics
Matches: 380, Mismatches: 64, Indels: 52
0.77 0.13 0.10
Matches are distributed among these distances:
55 27 0.07
56 82 0.22
57 64 0.17
58 86 0.23
59 60 0.16
60 57 0.15
61 4 0.01
ACGTcount: A:0.35, C:0.04, G:0.26, T:0.35
Consensus pattern (58 bp):
GGTAAAATGGTAATTTTGAAAGTTTAGGGGTAAAAATGGAATTTTTTGAAAGTTCAAG
Found at i:118192 original size:115 final size:116
Alignment explanation
Indices: 117881--118348 Score: 371
Period size: 115 Copynumber: 4.1 Consensus size: 116
117871 GATGCCTGAA
** * ** * *
117881 GGTAAAATGGTAATTTTCAAAAAGTTCAAGGTCTAAAAATGGAATTTTTGGAAATTCGAGGGTAA
1 GGTAAAATGGTAATTTT-GGAAAGTTC-GGGGGTAAAAATGGAATTTTTTGAAATTCGAGGATAA
* * * * *
117946 AATGGTAATTTTTGGAAG-CTCGAGGG-AAAAATGGAATTTTTGGAAGTTCA-A-
64 AATGGTAATTTTTGAAAGTTTAG-GGGTAAAAATGTAATTTTT-GAAGTTTAGAG
** * * *
117997 GGTAAAATGGTAATTTT-GAAAGTTTAGGGGTAAAAATGTAATTTTTTGTAAAGTTCAAGGGTAA
1 GGTAAAATGGTAATTTTGGAAAGTTCGGGGGTAAAAATGGAATTTTTTG-AAA-TTCGAGGATAA
118061 AATGGTAA-TTTT-AAAGTTTAGGGGTAAAAATGTAATTTTGTGAAGTTTAG-G
64 AATGGTAATTTTTGAAAGTTTAGGGGTAAAAATGTAATTTT-TGAAGTTTAGAG
* *
118112 GGTAAAATGGTAATTTTGGAAAGTTCGGGGGTCAAAATGGAATTTTTTGAAATT-TAGGAT-AAA
1 GGTAAAATGGTAATTTTGGAAAGTTCGGGGGTAAAAATGGAATTTTTTGAAATTCGAGGATAAAA
* * * * * *
118175 TCGTAATTTTTGAAAAGTTTA-GGGTCAAGAATGAAATTTCTAGAA-ATTCGAG
66 TGGTAATTTTTG-AAAGTTTAGGGGT-AAAAATGTAATTT-TTGAAGTTTAGAG
* *
118227 GGT-AAAT-GTAATTTTTGG-AAGTTCGGGGG-AAAAATGGGATTTTTTGGAAGTTCGAGGGCA-
1 GGTAAAATGGTAA-TTTTGGAAAGTTCGGGGGTAAAAATGGAATTTTTT-GAAATTCGA-GG-AT
* * * * *
118287 AAAAT-ATAATTTATGGAAGTTTGGGGGTAAAAATGTAGTTTTTGTGAAGTTT-GAG
62 AAAATGGTAATTTTTGAAAGTTTAGGGGTAAAAATGTA-ATTTT-TGAAGTTTAGAG
118342 GGTAAAA
1 GGTAAAA
118349 ATGTATTTTT
Statistics
Matches: 290, Mismatches: 37, Indels: 50
0.77 0.10 0.13
Matches are distributed among these distances:
112 22 0.08
113 53 0.18
114 69 0.24
115 91 0.31
116 55 0.19
ACGTcount: A:0.36, C:0.04, G:0.26, T:0.34
Consensus pattern (116 bp):
GGTAAAATGGTAATTTTGGAAAGTTCGGGGGTAAAAATGGAATTTTTTGAAATTCGAGGATAAAA
TGGTAATTTTTGAAAGTTTAGGGGTAAAAATGTAATTTTTGAAGTTTAGAG
Found at i:118274 original size:29 final size:29
Alignment explanation
Indices: 118230--118418 Score: 143
Period size: 30 Copynumber: 6.4 Consensus size: 29
118220 ATTCGAGGGT
*
118230 AAATGTAATTTTTGGAAGTTCG-GGGGAA
1 AAATGTATTTTTTGGAAGTTCGAGGGGAA
* *
118258 AAATGGGATTTTTTGGAAGTTCGAGGGCAA
1 AAAT-GTATTTTTTGGAAGTTCGAGGGGAA
* * * *
118288 AAATATAATTTATGGAAGTTTG-GGGGTAA
1 AAATGTATTTTTTGGAAGTTCGAGGGG-AA
* * *
118317 AAATGTAGTTTTTGTGAAGTTTGAGGGTAA
1 AAATGTATTTTTTG-GAAGTTCGAGGGGAA
* *
118347 AAATGTATTTTTTGTGAAGTT-TAGGGGTTA
1 AAATGTATTTTTTG-GAAGTTCGAGGGG-AA
* * *
118377 AAATGTAATTTTTAGAAAGTTC-AGGGGTCA
1 AAATGT-ATTTTTTGGAAGTTCGAGGGG-AA
*
118407 AAATATATTTTT
1 AAATGTATTTTT
118419 GGACATTTCA
Statistics
Matches: 132, Mismatches: 21, Indels: 15
0.79 0.12 0.09
Matches are distributed among these distances:
28 7 0.05
29 52 0.39
30 63 0.48
31 10 0.08
ACGTcount: A:0.33, C:0.03, G:0.27, T:0.38
Consensus pattern (29 bp):
AAATGTATTTTTTGGAAGTTCGAGGGGAA
Found at i:120979 original size:14 final size:14
Alignment explanation
Indices: 120938--120985 Score: 53
Period size: 14 Copynumber: 3.4 Consensus size: 14
120928 AACGATCAAA
*
120938 GTCAACTATCAACG
1 GTCAACTGTCAACG
*
120952 GTCAA-TAGTTAACG
1 GTCAACT-GTCAACG
120966 GTCAACTGTCAACG
1 GTCAACTGTCAACG
*
120980 ATCAAC
1 GTCAAC
120986 GGTCGGTCAA
Statistics
Matches: 28, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
13 1 0.04
14 26 0.93
15 1 0.04
ACGTcount: A:0.35, C:0.25, G:0.17, T:0.23
Consensus pattern (14 bp):
GTCAACTGTCAACG
Found at i:122472 original size:11 final size:11
Alignment explanation
Indices: 122458--122510 Score: 52
Period size: 11 Copynumber: 4.7 Consensus size: 11
122448 AATTAATTTT
122458 AATTTAAAATA
1 AATTTAAAATA
*
122469 AATTTAAACTCA
1 AATTTAAAAT-A
* * **
122481 AAATGAATTTA
1 AATTTAAAATA
122492 AATTTAAAATA
1 AATTTAAAATA
122503 AATTTAAA
1 AATTTAAA
122511 CTTAAAATAA
Statistics
Matches: 32, Mismatches: 9, Indels: 2
0.74 0.21 0.05
Matches are distributed among these distances:
11 25 0.78
12 7 0.22
ACGTcount: A:0.58, C:0.04, G:0.02, T:0.36
Consensus pattern (11 bp):
AATTTAAAATA
Found at i:122483 original size:17 final size:17
Alignment explanation
Indices: 122461--122534 Score: 103
Period size: 17 Copynumber: 4.4 Consensus size: 17
122451 TAATTTTAAT
122461 TTAAAATAAATTTAAAC
1 TTAAAATAAATTTAAAC
* * *
122478 TCAAAATGAATTTAAAT
1 TTAAAATAAATTTAAAC
122495 TTAAAATAAATTTAAAC
1 TTAAAATAAATTTAAAC
* *
122512 TTAAAATAAATTAAAAT
1 TTAAAATAAATTTAAAC
122529 TTAAAA
1 TTAAAA
122535 ATTTGGACTC
Statistics
Matches: 49, Mismatches: 8, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
17 49 1.00
ACGTcount: A:0.59, C:0.04, G:0.01, T:0.35
Consensus pattern (17 bp):
TTAAAATAAATTTAAAC
Found at i:122496 original size:34 final size:34
Alignment explanation
Indices: 122452--122534 Score: 130
Period size: 34 Copynumber: 2.4 Consensus size: 34
122442 CTTTTTAATT
* *
122452 AATTTTAATTTAAAATAAATTTAAACTCAAAATG
1 AATTTAAATTTAAAATAAATTTAAACTCAAAATA
*
122486 AATTTAAATTTAAAATAAATTTAAACTTAAAATA
1 AATTTAAATTTAAAATAAATTTAAACTCAAAATA
*
122520 AATTAAAATTTAAAA
1 AATTTAAATTTAAAA
122535 ATTTGGACTC
Statistics
Matches: 45, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
34 45 1.00
ACGTcount: A:0.58, C:0.04, G:0.01, T:0.37
Consensus pattern (34 bp):
AATTTAAATTTAAAATAAATTTAAACTCAAAATA
Found at i:124914 original size:18 final size:18
Alignment explanation
Indices: 124891--124926 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
124881 GATAATTTTT
124891 AGTGAAGAAAGGTCGAAA
1 AGTGAAGAAAGGTCGAAA
124909 AGTGAAGAAAGGTCGAAA
1 AGTGAAGAAAGGTCGAAA
124927 CTGTCAAGCA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.50, C:0.06, G:0.33, T:0.11
Consensus pattern (18 bp):
AGTGAAGAAAGGTCGAAA
Found at i:125329 original size:24 final size:26
Alignment explanation
Indices: 125302--125349 Score: 66
Period size: 24 Copynumber: 1.9 Consensus size: 26
125292 AGAGAAATGT
125302 AAATG-TGATATATGA-A-ATTATGAG
1 AAATGATGA-ATATGAGAGATTATGAG
125326 AAATGATGAATATGAGAGATTATG
1 AAATGATGAATATGAGAGATTATG
125350 CCCATGTAGA
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
24 11 0.52
25 4 0.19
26 6 0.29
ACGTcount: A:0.46, C:0.00, G:0.23, T:0.31
Consensus pattern (26 bp):
AAATGATGAATATGAGAGATTATGAG
Found at i:125451 original size:23 final size:22
Alignment explanation
Indices: 125412--125584 Score: 84
Period size: 23 Copynumber: 7.5 Consensus size: 22
125402 AAGCTAGCAC
*
125412 GCTTACTG-TTCAACACTGTGTGT
1 GCTTACTGTTTC-GCACT-TGTGT
125435 GCTTACTGTTTCGCACTTCGTGT
1 GCTTACTGTTTCGCACTT-GTGT
* *
125458 GTTTACTGTTTCGCACCTCGTGT
1 GCTTACTGTTTCGCA-CTTGTGT
* * ** *
125481 GCCTATTGATTT-GCGTTATGTGC
1 GCTTACTG-TTTCGCACT-TGTGT
* * *
125504 GCCTATTGATT-GCACTGTGTGT
1 GCTTACTGTTTCGCACT-TGTGT
* *
125526 GCCTACTGGATT-GCACTGTGTGT
1 GCTTACT-GTTTCGCACT-TGTGT
125549 GCTTACTGTTTCCCCAGCACTTGTGT
1 GCTTACTGTTT---C-GCACTTGTGT
125575 GCTTACTGTT
1 GCTTACTGTT
125585 AAGTACTTCG
Statistics
Matches: 121, Mismatches: 18, Indels: 19
0.77 0.11 0.12
Matches are distributed among these distances:
22 20 0.17
23 73 0.60
24 8 0.07
26 15 0.12
27 5 0.04
ACGTcount: A:0.12, C:0.23, G:0.24, T:0.41
Consensus pattern (22 bp):
GCTTACTGTTTCGCACTTGTGT
Found at i:128351 original size:3 final size:3
Alignment explanation
Indices: 128343--128367 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
128333 AATGTTGCCT
128343 TTC TTC TTC TTC TTC TTC TTC TTC T
1 TTC TTC TTC TTC TTC TTC TTC TTC T
128368 GTTTTCCCCT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.00, C:0.32, G:0.00, T:0.68
Consensus pattern (3 bp):
TTC
Found at i:128964 original size:11 final size:11
Alignment explanation
Indices: 128948--128974 Score: 54
Period size: 11 Copynumber: 2.5 Consensus size: 11
128938 ACGTCCATTA
128948 TAATCTAGGTT
1 TAATCTAGGTT
128959 TAATCTAGGTT
1 TAATCTAGGTT
128970 TAATC
1 TAATC
128975 GATTTTCATG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 16 1.00
ACGTcount: A:0.30, C:0.11, G:0.15, T:0.44
Consensus pattern (11 bp):
TAATCTAGGTT
Found at i:138030 original size:29 final size:27
Alignment explanation
Indices: 137997--138063 Score: 71
Period size: 30 Copynumber: 2.3 Consensus size: 27
137987 TTCGTCATTC
137997 TATTAAAAAATAAGTAAATTAATTTTTT
1 TATTAAAAAA-AAGTAAATTAATTTTTT
* *
138025 ATATTAAATCAAAGAGTAAATTGATTTTTT
1 -TATTAAA--AAAAAGTAAATTAATTTTTT
*
138055 TGTTAAAAA
1 TATTAAAAA
138064 TTTCATTCAA
Statistics
Matches: 33, Mismatches: 3, Indels: 6
0.79 0.07 0.14
Matches are distributed among these distances:
27 2 0.06
29 13 0.39
30 15 0.45
31 3 0.09
ACGTcount: A:0.48, C:0.01, G:0.07, T:0.43
Consensus pattern (27 bp):
TATTAAAAAAAAGTAAATTAATTTTTT
Found at i:148754 original size:15 final size:14
Alignment explanation
Indices: 148713--148754 Score: 50
Period size: 14 Copynumber: 3.0 Consensus size: 14
148703 GATGTGAAAG
*
148713 AATTTTTTATATTC
1 AATTTTTTATATTT
*
148727 AATATTTT-TATTT
1 AATTTTTTATATTT
148740 ACATTTTTTATATTT
1 A-ATTTTTTATATTT
148755 CACACGTGTA
Statistics
Matches: 23, Mismatches: 3, Indels: 3
0.79 0.10 0.10
Matches are distributed among these distances:
13 5 0.22
14 13 0.57
15 5 0.22
ACGTcount: A:0.29, C:0.05, G:0.00, T:0.67
Consensus pattern (14 bp):
AATTTTTTATATTT
Found at i:161448 original size:27 final size:28
Alignment explanation
Indices: 161418--161490 Score: 71
Period size: 28 Copynumber: 2.6 Consensus size: 28
161408 TTATTAATAG
161418 TTTATGAAAATTGCATC-AAATCAAAAT
1 TTTATGAAAATTGCATCAAAATCAAAAT
*
161445 TTTATGTATAAAATG-A-CAAAATCAAAAT
1 TTTATG-A-AAATTGCATCAAAATCAAAAT
*
161473 TTATATATAAAATTGCAT
1 TT-TAT-GAAAATTGCAT
161491 ATTAAACCGA
Statistics
Matches: 36, Mismatches: 3, Indels: 11
0.72 0.06 0.22
Matches are distributed among these distances:
27 7 0.19
28 19 0.53
29 10 0.28
ACGTcount: A:0.49, C:0.08, G:0.07, T:0.36
Consensus pattern (28 bp):
TTTATGAAAATTGCATCAAAATCAAAAT
Found at i:167315 original size:48 final size:48
Alignment explanation
Indices: 167244--167363 Score: 181
Period size: 48 Copynumber: 2.5 Consensus size: 48
167234 GATGGAGGAC
* *
167244 TAGTTGGCGGCGGAGCTGCTGCGGTTGGTGG-TG-GTGTAGAAGGAGTGT
1 TAGTTGGCGGCGGAGTTGCTGCGGTTGGTGGCTGCGTG--GAAGGAGTGG
167292 TAGTTGGCGGCGGAGTTGCTGCGGTTGGTGGCTGCGTGGAAGGAGTGG
1 TAGTTGGCGGCGGAGTTGCTGCGGTTGGTGGCTGCGTGGAAGGAGTGG
*
167340 TAGTTGGCGGCGGAGTTGCAGCGG
1 TAGTTGGCGGCGGAGTTGCTGCGG
167364 ATGGCGGCGA
Statistics
Matches: 67, Mismatches: 3, Indels: 4
0.91 0.04 0.05
Matches are distributed among these distances:
48 62 0.93
49 2 0.03
50 3 0.04
ACGTcount: A:0.12, C:0.12, G:0.51, T:0.25
Consensus pattern (48 bp):
TAGTTGGCGGCGGAGTTGCTGCGGTTGGTGGCTGCGTGGAAGGAGTGG
Found at i:167382 original size:48 final size:47
Alignment explanation
Indices: 167244--167384 Score: 167
Period size: 48 Copynumber: 2.9 Consensus size: 47
167234 GATGGAGGAC
* * * *
167244 TAGTTGGCGGCGGAGCTGCTGCGGTTGGTGGTGGTGTAGAAGGAGTGT
1 TAGTTGGCGGCGGAGTTGCTGCGGTTGGTGG-CGTGGAGAAGGAGTGG
*
167292 TAGTTGGCGGCGGAGTTGCTGCGGTTGGTGGC-TGCGTGGAAGGAGTGG
1 TAGTTGGCGGCGGAGTTGCTGCGGTTGGTGGCGTG-G-AGAAGGAGTGG
* * *
167340 TAGTTGGCGGCGGAGTTGCAGCGGATGGCGGCGATGGAGAAGGAG
1 TAGTTGGCGGCGGAGTTGCTGCGGTTGGTGGCG-TGGAGAAGGAG
167385 GACTACTCGG
Statistics
Matches: 80, Mismatches: 9, Indels: 8
0.82 0.09 0.08
Matches are distributed among these distances:
46 2 0.03
48 75 0.94
49 1 0.01
50 2 0.03
ACGTcount: A:0.14, C:0.12, G:0.51, T:0.23
Consensus pattern (47 bp):
TAGTTGGCGGCGGAGTTGCTGCGGTTGGTGGCGTGGAGAAGGAGTGG
Found at i:174733 original size:2 final size:2
Alignment explanation
Indices: 174726--174757 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
174716 TAGATTCATG
174726 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
174758 GCGCTCGTGT
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:183885 original size:6 final size:6
Alignment explanation
Indices: 183874--183898 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
183864 CTATTCGACG
183874 CGCACA CGCACA CGCACA CGCACA C
1 CGCACA CGCACA CGCACA CGCACA C
183899 CCGCATAATA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.32, C:0.52, G:0.16, T:0.00
Consensus pattern (6 bp):
CGCACA
Found at i:189860 original size:36 final size:36
Alignment explanation
Indices: 189820--189892 Score: 146
Period size: 36 Copynumber: 2.0 Consensus size: 36
189810 AAGAGGTGGT
189820 GCAGACATAGTTTGATTTGAAAGATGGTGGCAGAAG
1 GCAGACATAGTTTGATTTGAAAGATGGTGGCAGAAG
189856 GCAGACATAGTTTGATTTGAAAGATGGTGGCAGAAG
1 GCAGACATAGTTTGATTTGAAAGATGGTGGCAGAAG
189892 G
1 G
189893 TGGTGCAGTA
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
36 37 1.00
ACGTcount: A:0.33, C:0.08, G:0.34, T:0.25
Consensus pattern (36 bp):
GCAGACATAGTTTGATTTGAAAGATGGTGGCAGAAG
Found at i:192256 original size:12 final size:13
Alignment explanation
Indices: 192241--192271 Score: 55
Period size: 12 Copynumber: 2.5 Consensus size: 13
192231 AAGAAAATTG
192241 AAGAAAAAA-AGA
1 AAGAAAAAAGAGA
192253 AAGAAAAAAGAGA
1 AAGAAAAAAGAGA
192266 AAGAAA
1 AAGAAA
192272 GAAGGAAGAA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
12 9 0.50
13 9 0.50
ACGTcount: A:0.81, C:0.00, G:0.19, T:0.00
Consensus pattern (13 bp):
AAGAAAAAAGAGA
Found at i:192280 original size:7 final size:7
Alignment explanation
Indices: 192270--192297 Score: 56
Period size: 7 Copynumber: 4.0 Consensus size: 7
192260 AAGAGAAAGA
192270 AAGAAGG
1 AAGAAGG
192277 AAGAAGG
1 AAGAAGG
192284 AAGAAGG
1 AAGAAGG
192291 AAGAAGG
1 AAGAAGG
192298 GGAAGAAAGA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 21 1.00
ACGTcount: A:0.57, C:0.00, G:0.43, T:0.00
Consensus pattern (7 bp):
AAGAAGG
Found at i:192280 original size:17 final size:16
Alignment explanation
Indices: 192248--192322 Score: 55
Period size: 17 Copynumber: 4.6 Consensus size: 16
192238 TTGAAGAAAA
*
192248 AAAGAAAGAAAAAAGAG
1 AAAGAAAG-AAGAAGAG
192265 AAAGAAAGAAGGAAGAAG
1 AAAGAAAGAA-GAAG-AG
* * *
192283 GAAGAAGGAAGAAGGG
1 AAAGAAAGAAGAAGAG
*
192299 GAAGAAAGAA-AAGA-
1 AAAGAAAGAAGAAGAG
*
192313 AAAAAAAGAA
1 AAAGAAAGAA
192323 TAATGTGTTT
Statistics
Matches: 48, Mismatches: 8, Indels: 7
0.76 0.13 0.11
Matches are distributed among these distances:
14 8 0.17
15 3 0.06
16 12 0.25
17 15 0.31
18 10 0.21
ACGTcount: A:0.69, C:0.00, G:0.31, T:0.00
Consensus pattern (16 bp):
AAAGAAAGAAGAAGAG
Found at i:192700 original size:20 final size:21
Alignment explanation
Indices: 192659--192701 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 21
192649 TAATTTACTT
192659 TAATTTAATTTTGCTAGTTAG
1 TAATTTAATTTTGCTAGTTAG
* *
192680 TAATTTTATTTTG-TTGTTAG
1 TAATTTAATTTTGCTAGTTAG
192700 TA
1 TA
192702 GTAGTAAGTA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
20 8 0.40
21 12 0.60
ACGTcount: A:0.26, C:0.02, G:0.14, T:0.58
Consensus pattern (21 bp):
TAATTTAATTTTGCTAGTTAG
Found at i:193215 original size:16 final size:16
Alignment explanation
Indices: 193170--193219 Score: 52
Period size: 16 Copynumber: 3.2 Consensus size: 16
193160 TAAATCTAGC
*
193170 TAATTAATTACCAAAA
1 TAATTAATTATCAAAA
*
193186 T-A-TAA-TATAAAAAA
1 TAATTAATTAT-CAAAA
193200 TAATTAATTATCAAAA
1 TAATTAATTATCAAAA
193216 TAAT
1 TAAT
193220 ATCCTCATCA
Statistics
Matches: 27, Mismatches: 3, Indels: 8
0.71 0.08 0.21
Matches are distributed among these distances:
13 2 0.07
14 8 0.30
15 2 0.07
16 12 0.44
17 3 0.11
ACGTcount: A:0.60, C:0.06, G:0.00, T:0.34
Consensus pattern (16 bp):
TAATTAATTATCAAAA
Found at i:194591 original size:43 final size:43
Alignment explanation
Indices: 194509--194593 Score: 109
Period size: 43 Copynumber: 2.0 Consensus size: 43
194499 ATTAACATGT
* * *
194509 TAAATTATATTACTTGACTCGTGTTAATATGGTTGCATGTTAC
1 TAAATTATATTACTTGACTCGTATTAATATGCTTACATGTTAC
* *
194552 TAAATTATATTACTTTACTCTTATTAATAT-CTTCACATGTTA
1 TAAATTATATTACTTGACTCGTATTAATATGCTT-ACATGTTA
194594 TTAATTGTGC
Statistics
Matches: 36, Mismatches: 5, Indels: 2
0.84 0.12 0.05
Matches are distributed among these distances:
42 2 0.06
43 34 0.94
ACGTcount: A:0.31, C:0.13, G:0.09, T:0.47
Consensus pattern (43 bp):
TAAATTATATTACTTGACTCGTATTAATATGCTTACATGTTAC
Found at i:195225 original size:45 final size:45
Alignment explanation
Indices: 195161--195297 Score: 175
Period size: 45 Copynumber: 3.0 Consensus size: 45
195151 GCATAGCTCA
195161 TCAAGCCAAGGATATCAGCCTCAATTTGACGAGCCACCGCAATAC
1 TCAAGCCAAGGATATCAGCCTCAATTTGACGAGCCACCGCAATAC
* *
195206 TCAAGCCAAGGATATCAGCCTTAATTTGACGAGCCAACGCAATAC
1 TCAAGCCAAGGATATCAGCCTCAATTTGACGAGCCACCGCAATAC
** * * * ** * *
195251 TCAAGGGAAGGATATTAGGCTGAGGTTGACGAGCCACCACGATAC
1 TCAAGCCAAGGATATCAGCCTCAATTTGACGAGCCACCGCAATAC
195296 TC
1 TC
195298 TATTCTTCTC
Statistics
Matches: 80, Mismatches: 12, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
45 80 1.00
ACGTcount: A:0.33, C:0.26, G:0.22, T:0.19
Consensus pattern (45 bp):
TCAAGCCAAGGATATCAGCCTCAATTTGACGAGCCACCGCAATAC
Found at i:195334 original size:21 final size:21
Alignment explanation
Indices: 195292--195330 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
195282 AGCCACCACG
*
195292 ATACTCTATTCTTCTCGGGCA
1 ATACTCTACTCTTCTCGGGCA
195313 ATACTCTACTCTT-TCGGG
1 ATACTCTACTCTTCTCGGG
195331 GCAAATGGAC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 5 0.29
21 12 0.71
ACGTcount: A:0.18, C:0.28, G:0.15, T:0.38
Consensus pattern (21 bp):
ATACTCTACTCTTCTCGGGCA
Found at i:195608 original size:28 final size:27
Alignment explanation
Indices: 195563--195629 Score: 71
Period size: 28 Copynumber: 2.4 Consensus size: 27
195553 CATTAAACCC
* *
195563 TAAAACCTAAATTATAAACCCTAAACT
1 TAAAACCTAAATCATAAACACTAAACT
* *
195590 TAAAACCTTAAATCGTAAACACTAGACT
1 TAAAACC-TAAATCATAAACACTAAACT
*
195618 TGAAACTCTAAA
1 TAAAAC-CTAAA
195630 CTGTAAACAC
Statistics
Matches: 33, Mismatches: 5, Indels: 3
0.80 0.12 0.07
Matches are distributed among these distances:
27 7 0.21
28 25 0.76
29 1 0.03
ACGTcount: A:0.49, C:0.21, G:0.04, T:0.25
Consensus pattern (27 bp):
TAAAACCTAAATCATAAACACTAAACT
Found at i:198952 original size:17 final size:18
Alignment explanation
Indices: 198932--198965 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
198922 AATAAACATC
*
198932 AATTGGGTTT-AAATTTT
1 AATTGGATTTGAAATTTT
198949 AATTGGATTTGAAATTT
1 AATTGGATTTGAAATTT
198966 GGGTTTAGGG
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 9 0.60
18 6 0.40
ACGTcount: A:0.32, C:0.00, G:0.18, T:0.50
Consensus pattern (18 bp):
AATTGGATTTGAAATTTT
Found at i:199438 original size:14 final size:15
Alignment explanation
Indices: 199414--199445 Score: 57
Period size: 14 Copynumber: 2.2 Consensus size: 15
199404 TAAAGTACGA
199414 ACTACATATATTATC
1 ACTACATATATTATC
199429 ACTA-ATATATTATC
1 ACTACATATATTATC
199443 ACT
1 ACT
199446 CATTAGTAGT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 13 0.76
15 4 0.24
ACGTcount: A:0.41, C:0.19, G:0.00, T:0.41
Consensus pattern (15 bp):
ACTACATATATTATC
Found at i:206123 original size:32 final size:31
Alignment explanation
Indices: 206086--206152 Score: 80
Period size: 31 Copynumber: 2.1 Consensus size: 31
206076 AACATCCTAG
**
206086 TGACTTAAATAAGAAACTTTTGAATAGTTAAA
1 TGACTTAAATAA-AAACTTTCAAATAGTTAAA
* * *
206118 TGACTTTAATGAAAACTTTCAAATAGTTCAA
1 TGACTTAAATAAAAACTTTCAAATAGTTAAA
206149 TGAC
1 TGAC
206153 CATTTTGTAA
Statistics
Matches: 30, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
31 20 0.67
32 10 0.33
ACGTcount: A:0.43, C:0.10, G:0.12, T:0.34
Consensus pattern (31 bp):
TGACTTAAATAAAAACTTTCAAATAGTTAAA
Found at i:207300 original size:96 final size:96
Alignment explanation
Indices: 207176--207374 Score: 285
Period size: 96 Copynumber: 2.1 Consensus size: 96
207166 TTAAATGATT
* * *
207176 AAATTTATATATTTGGAGATAAAATGATGACTTGAATTGAGCGAATTTAA-AGGAA-TTTTATTT
1 AAATTGATATATTTGGAGATAAAATGATGACTTGAATTGAACGAATTTAATA--AAGTTTCATTT
*
207239 ATGTAAAAAGGAAATTTAACATCTTTCTTAACG
64 ATGTAAAAAGGAAACTTAACATCTTTCTTAACG
* *
207272 AAATTGATATATTTGGAGATAAGATGATGACTTGAATTGAACGAATTTAATAAAGTTTCATTTGT
1 AAATTGATATATTTGGAGATAAAATGATGACTTGAATTGAACGAATTTAATAAAGTTTCATTTAT
* *
207337 GTAAAAAGGAAACTTGACATCTTTCTTGACG
66 GTAAAAAGGAAACTTAACATCTTTCTTAACG
*
207368 AAGTTGA
1 AAATTGA
207375 AGGACGAGCT
Statistics
Matches: 92, Mismatches: 9, Indels: 4
0.88 0.09 0.04
Matches are distributed among these distances:
95 2 0.02
96 89 0.97
97 1 0.01
ACGTcount: A:0.39, C:0.07, G:0.18, T:0.36
Consensus pattern (96 bp):
AAATTGATATATTTGGAGATAAAATGATGACTTGAATTGAACGAATTTAATAAAGTTTCATTTAT
GTAAAAAGGAAACTTAACATCTTTCTTAACG
Found at i:210080 original size:149 final size:149
Alignment explanation
Indices: 209853--210596 Score: 1204
Period size: 149 Copynumber: 5.0 Consensus size: 149
209843 TCTCACAGCC
* * * * *
209853 ACAGGTATCCCTTGTGTTTGATCTTTACTTGCCTAATTGCCTCTTCGCATTGGAGCTCTTCTGAT
1 ACAGGTATCCCTCGTGTTTGATCTTTACTTGCCTGATTGCCTCTTCACACTGGAACTCTTCTGAT
* *
209918 CTCTGTAACTGTTCTCTAGGACCGATTTAAAAAATACGGGTCTTTCCATGTCAATGGTGATGATA
66 CTCTGTAATTGTTCTCTAGGACCGACTTAAAAAATACGGGTCTTTCCATGTCAATGGTGATGATA
*
209983 ATAAATCAAATTATGGAAA
131 ATAAATCAAATGATGGAAA
* * *
210002 ACAGGTATCCCTCATGTTTGATCTTTACTTGCCTGATTGCATCTTCACACTGAAACTCTTCTGAT
1 ACAGGTATCCCTCGTGTTTGATCTTTACTTGCCTGATTGCCTCTTCACACTGGAACTCTTCTGAT
210067 CTCTGTAATTGTTCTCTAGGACCGACTTAAAAAATACGGGTCTTTCCATGTCAATGGTGATGATA
66 CTCTGTAATTGTTCTCTAGGACCGACTTAAAAAATACGGGTCTTTCCATGTCAATGGTGATGATA
210132 ATAAATCAAATGATGGAAA
131 ATAAATCAAATGATGGAAA
* * * * *
210151 ACAGGTATCACTCGTGTTTGATCTTTACTTGCCTGTTTACCTCTTCACACTGAAACTCTTCTAAT
1 ACAGGTATCCCTCGTGTTTGATCTTTACTTGCCTGATTGCCTCTTCACACTGGAACTCTTCTGAT
210216 CTCTGTAATTGTTCTCTAGGACCGACTTAAAAAATACGGGTCTTTCCATGTCAATGGTGATGATA
66 CTCTGTAATTGTTCTCTAGGACCGACTTAAAAAATACGGGTCTTTCCATGTCAATGGTGATGATA
210281 ATAAATCAAAT-AGTGGAAA
131 ATAAATCAAATGA-TGGAAA
*
210300 ACAGGTATCCCTCGTGTTTGATCTTTACTTGTCTGATTGCCTCTTCACACTGGAACTCTTCTGAT
1 ACAGGTATCCCTCGTGTTTGATCTTTACTTGCCTGATTGCCTCTTCACACTGGAACTCTTCTGAT
*
210365 CTCTGTAATTGTTCTCTAGGACCGACTTAAAAAATATGGGTCTTTCCATGTCAATGGTGATGATA
66 CTCTGTAATTGTTCTCTAGGACCGACTTAAAAAATACGGGTCTTTCCATGTCAATGGTGATGATA
210430 ATAAATCAAATGATGGAAA
131 ATAAATCAAATGATGGAAA
* ** *
210449 ACAGGTATCCCTCATGTTTGCA-CTTTACTTGCCTGATTATCTCTTCACACTGGAACTCTTCTAA
1 ACAGGTATCCCTCGTGTTTG-ATCTTTACTTGCCTGATTGCCTCTTCACACTGGAACTCTTCTGA
* * * * *
210513 TCTCTGTAAGTATTCTCTAGGGCCGACCTAAGAAATACGGGTCTTTCCATGTCAATGGTGATGAT
65 TCTCTGTAATTGTTCTCTAGGACCGACTTAAAAAATACGGGTCTTTCCATGTCAATGGTGATGAT
*
210578 AATAAATCAAACGATGGAA
130 AATAAATCAAATGATGGAA
210597 CAAGTGCTGA
Statistics
Matches: 556, Mismatches: 36, Indels: 6
0.93 0.06 0.01
Matches are distributed among these distances:
148 1 0.00
149 553 0.99
150 2 0.00
ACGTcount: A:0.28, C:0.20, G:0.17, T:0.35
Consensus pattern (149 bp):
ACAGGTATCCCTCGTGTTTGATCTTTACTTGCCTGATTGCCTCTTCACACTGGAACTCTTCTGAT
CTCTGTAATTGTTCTCTAGGACCGACTTAAAAAATACGGGTCTTTCCATGTCAATGGTGATGATA
ATAAATCAAATGATGGAAA
Found at i:215999 original size:10 final size:10
Alignment explanation
Indices: 215984--216008 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
215974 GAACTAACCC
215984 AATTCTAAAT
1 AATTCTAAAT
215994 AATTCTAAAT
1 AATTCTAAAT
216004 AATTC
1 AATTC
216009 AAGCCTTAGG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.48, C:0.12, G:0.00, T:0.40
Consensus pattern (10 bp):
AATTCTAAAT
Found at i:216782 original size:2 final size:2
Alignment explanation
Indices: 216775--216810 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
216765 GTATGTATGC
216775 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
216811 CAGATTGCAG
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:218494 original size:5 final size:5
Alignment explanation
Indices: 218486--218512 Score: 54
Period size: 5 Copynumber: 5.4 Consensus size: 5
218476 ATCAAAACAA
218486 AAGAG AAGAG AAGAG AAGAG AAGAG AA
1 AAGAG AAGAG AAGAG AAGAG AAGAG AA
218513 AAGGGAAGGA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 22 1.00
ACGTcount: A:0.63, C:0.00, G:0.37, T:0.00
Consensus pattern (5 bp):
AAGAG
Found at i:234540 original size:4 final size:4
Alignment explanation
Indices: 234531--234561 Score: 62
Period size: 4 Copynumber: 7.8 Consensus size: 4
234521 GTGTTTGTGT
234531 CATA CATA CATA CATA CATA CATA CATA CAT
1 CATA CATA CATA CATA CATA CATA CATA CAT
234562 GGTCCAAAGA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 27 1.00
ACGTcount: A:0.48, C:0.26, G:0.00, T:0.26
Consensus pattern (4 bp):
CATA
Found at i:242100 original size:13 final size:13
Alignment explanation
Indices: 242082--242106 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
242072 ACGTTCTTGA
242082 TAATATTATTATC
1 TAATATTATTATC
242095 TAATATTATTAT
1 TAATATTATTAT
242107 TATCTAATAA
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:0.40, C:0.04, G:0.00, T:0.56
Consensus pattern (13 bp):
TAATATTATTATC
Found at i:242106 original size:16 final size:16
Alignment explanation
Indices: 242085--242115 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
242075 TTCTTGATAA
242085 TATTATTATCTAATAT
1 TATTATTATCTAATAT
242101 TATTATTATCTAATA
1 TATTATTATCTAATA
242116 ATACGTTCTT
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:0.39, C:0.06, G:0.00, T:0.55
Consensus pattern (16 bp):
TATTATTATCTAATAT
Found at i:242225 original size:3 final size:3
Alignment explanation
Indices: 242217--242252 Score: 54
Period size: 3 Copynumber: 11.7 Consensus size: 3
242207 ACCTTTCGAT
*
242217 TTA TTA TTA TTA TCTA ATA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA T-TA TTA TTA TTA TTA TTA TTA TT
242253 CATTTAATAC
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
3 28 0.93
4 2 0.07
ACGTcount: A:0.33, C:0.03, G:0.00, T:0.64
Consensus pattern (3 bp):
TTA
Found at i:244323 original size:29 final size:30
Alignment explanation
Indices: 244286--244359 Score: 87
Period size: 30 Copynumber: 2.5 Consensus size: 30
244276 AAATTTTAAA
* * *
244286 TTAATAATGATAAAATTAT-ATTTTATTCT
1 TTAAAAATGATAAAATTATGATTTAATCCT
* *
244315 TTCAAAATGATAAAATTTTGATTTAATCCT
1 TTAAAAATGATAAAATTATGATTTAATCCT
*
244345 TTAAAAATTATAAAA
1 TTAAAAATGATAAAA
244360 AATATAGATC
Statistics
Matches: 37, Mismatches: 7, Indels: 1
0.82 0.16 0.02
Matches are distributed among these distances:
29 16 0.43
30 21 0.57
ACGTcount: A:0.46, C:0.05, G:0.04, T:0.45
Consensus pattern (30 bp):
TTAAAAATGATAAAATTATGATTTAATCCT
Found at i:260672 original size:93 final size:92
Alignment explanation
Indices: 260513--260698 Score: 327
Period size: 93 Copynumber: 2.0 Consensus size: 92
260503 ATACTTGGTT
*
260513 TAAAACATTTCACCACTCGTACAGATGTAGTTAGTGTAATACAAGCAATTTTCCAGAATAGAAAC
1 TAAAACATTTCACCACTCGTACAGATGTAGTTAGTGTAATACAAGCAATTTTCCACAATAGAAAC
260578 GAGGTTTGTATATACACGCATGCATACA
66 GAGGTTTGTAT-TACACGCATGCATACA
* *
260606 TAAAACATTTCACCACTCGTACAGATGTAGTTCGTGTAATACAAGCAATTTTCCACTATAGAAAC
1 TAAAACATTTCACCACTCGTACAGATGTAGTTAGTGTAATACAAGCAATTTTCCACAATAGAAAC
*
260671 GAGGTTTGTATTACATGCATGCATACA
66 GAGGTTTGTATTACACGCATGCATACA
260698 T
1 T
260699 TACTTACATA
Statistics
Matches: 89, Mismatches: 4, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
92 16 0.18
93 73 0.82
ACGTcount: A:0.36, C:0.19, G:0.16, T:0.30
Consensus pattern (92 bp):
TAAAACATTTCACCACTCGTACAGATGTAGTTAGTGTAATACAAGCAATTTTCCACAATAGAAAC
GAGGTTTGTATTACACGCATGCATACA
Found at i:260836 original size:113 final size:112
Alignment explanation
Indices: 260599--260804 Score: 304
Period size: 113 Copynumber: 1.8 Consensus size: 112
260589 ATACACGCAT
*
260599 GCATACATAAAACATTTCACCACTCGTACAGATGTAGTTCGTGTAATACAAGCAATTTTCCACTA
1 GCATACATAAAACATTTCACCACTCGTACAGATGTAGTTCGTGTAATACAAGCAATTTTCCACCA
* ** * * * * *
260664 TAGAAACGAGGTTTGTATTACATGCATGCATACATTACTTACATACAT
66 CAGAAACGAGGCCTGTAATACATACAT-CATACATTACTGACAAACAA
*
260712 GCATACATAAAACATTTCACCACTCGTACAGATTTAGTTCGTGTAATACAAGCAATTTTCCACCA
1 GCATACATAAAACATTTCACCACTCGTACAGATGTAGTTCGTGTAATACAAGCAATTTTCCACCA
260777 CAGAAACGAGGCCTGTACATACATACAT
66 CAGAAACGAGGCCTGTA-ATACATACAT
260805 ATAATTTGAT
Statistics
Matches: 85, Mismatches: 7, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
113 77 0.91
114 8 0.09
ACGTcount: A:0.36, C:0.22, G:0.13, T:0.29
Consensus pattern (112 bp):
GCATACATAAAACATTTCACCACTCGTACAGATGTAGTTCGTGTAATACAAGCAATTTTCCACCA
CAGAAACGAGGCCTGTAATACATACATCATACATTACTGACAAACAA
Found at i:261894 original size:132 final size:133
Alignment explanation
Indices: 261670--262052 Score: 486
Period size: 132 Copynumber: 2.9 Consensus size: 133
261660 GTGTTAGTTG
* * * * ** **
261670 CCCAAAGCCGACAAACCCCTCAACATGTCCAATATTGTCCCCAATCAAGCTAAGGTTTTATCTCC
1 CCCAAAGCCAACGAACCCCTCAACATGTCCAGTATTGTCCCCGATCGGGCCGAGGTTTTATCTCC
* *
261735 CGACTTAATCGGGAGCCCGAGTACATGAGGCTACCTAAAGAAGCGACAAG-TTTAGAAGTGTCAT
66 CGACTTAGTCGAGAGCCCGAGTACATGAGGCTACCTAAAGAAGCGACAAGATTTAGAAGTGTCAT
261799 CTA
131 CTA
* * ** *
261802 CCCAGAGCCGACGTGCCCCTCAACATGTCCAGTATTGTCCTCGATCGGGCCGAGGTTTTATCTCC
1 CCCAAAGCCAACGAACCCCTCAACATGTCCAGTATTGTCCCCGATCGGGCCGAGGTTTTATCTCC
* * *
261867 CGACTTAGTCGAGAGCCGGAGTACATGAGGCTACGC-GAAGAAGCGA-TAGATTTAGAAGTGTCA
66 CGACTTAGTCGAGAGCCCGAGTACATGAGGCTAC-CTAAAGAAGCGACAAGATTTAGAAGTGTCA
261930 TCTA
130 TCTA
** * * *
261934 CCCAAAGCCAACGAACCCCTCAACACATTCAGTATTGTCCCCGATTGGGCCGAGATTTTATCTCC
1 CCCAAAGCCAACGAACCCCTCAACATGTCCAGTATTGTCCCCGATCGGGCCGAGGTTTTATCTCC
* * * *
261999 CAACTTAGTCGAGAGCCTGAATACATGAGGCTACCTAAAGAAGTGAC-AGATTTA
66 CGACTTAGTCGAGAGCCCGAGTACATGAGGCTACCTAAAGAAGCGACAAGATTTA
262053 CTGGGTAAGA
Statistics
Matches: 216, Mismatches: 31, Indels: 8
0.85 0.12 0.03
Matches are distributed among these distances:
131 3 0.01
132 212 0.98
133 1 0.00
ACGTcount: A:0.29, C:0.27, G:0.21, T:0.22
Consensus pattern (133 bp):
CCCAAAGCCAACGAACCCCTCAACATGTCCAGTATTGTCCCCGATCGGGCCGAGGTTTTATCTCC
CGACTTAGTCGAGAGCCCGAGTACATGAGGCTACCTAAAGAAGCGACAAGATTTAGAAGTGTCAT
CTA
Found at i:269195 original size:62 final size:59
Alignment explanation
Indices: 269085--269252 Score: 185
Period size: 59 Copynumber: 2.8 Consensus size: 59
269075 TAATAACTTT
* * * *
269085 AGGTATCAAATTGAATCTAAAAAAGCCTTAGGTACCAAATTAGGAAAAAAAATACCAAGTTC
1 AGGTACCAAATTGAGTCCAAAAAAG-TTTAGGTACCAAATTAGG--AAAAAATACCAAGTTC
* * *
269147 AGGTACCAAATTGGGTCCAAAAAAGTTTAGGTACCAGATTAGGAAAAAATATCAAGTTC
1 AGGTACCAAATTGAGTCCAAAAAAGTTTAGGTACCAAATTAGGAAAAAATACCAAGTTC
* * ** * *
269206 AGGTACTAAATTGAGT-CAAAAAAATTTAAATATCAAATTAAGAAAAA
1 AGGTACCAAATTGAGTCCAAAAAAGTTTAGGTACCAAATTAGGAAAAA
269253 TTGTCAAGTT
Statistics
Matches: 91, Mismatches: 15, Indels: 4
0.83 0.14 0.04
Matches are distributed among these distances:
58 25 0.27
59 29 0.32
61 16 0.18
62 21 0.23
ACGTcount: A:0.49, C:0.12, G:0.15, T:0.24
Consensus pattern (59 bp):
AGGTACCAAATTGAGTCCAAAAAAGTTTAGGTACCAAATTAGGAAAAAATACCAAGTTC
Found at i:269218 original size:59 final size:58
Alignment explanation
Indices: 269092--269274 Score: 186
Period size: 58 Copynumber: 3.1 Consensus size: 58
269082 TTTAGGTATC
* * * *
269092 AAATTGAATCTAAAAAAGCCTTAGGTACCAAATTAGGAAAAAAAATACCAAGTTCAGGTACC
1 AAATTGAGTC-AAAAAAG-TTTAGGTACCAAATTAGG--AAAAAATATCAAGTTCAGGTACT
* *
269154 AAATTGGGTCCAAAAAAGTTTAGGTACCAGATTAGGAAAAAATATCAAGTTCAGGTACT
1 AAATTGAGT-CAAAAAAGTTTAGGTACCAAATTAGGAAAAAATATCAAGTTCAGGTACT
* ** * * * * * *
269213 AAATTGAGTCAAAAAAATTTAAATATCAAATTAAGAAAAATTGTCAAGTTCAAGTATT
1 AAATTGAGTCAAAAAAGTTTAGGTACCAAATTAGGAAAAAATATCAAGTTCAGGTACT
269271 AAAT
1 AAAT
269275 ATTATATTAA
Statistics
Matches: 103, Mismatches: 17, Indels: 6
0.82 0.13 0.05
Matches are distributed among these distances:
58 43 0.42
59 29 0.28
61 16 0.16
62 14 0.14
63 1 0.01
ACGTcount: A:0.48, C:0.11, G:0.15, T:0.26
Consensus pattern (58 bp):
AAATTGAGTCAAAAAAGTTTAGGTACCAAATTAGGAAAAAATATCAAGTTCAGGTACT
Found at i:273197 original size:19 final size:20
Alignment explanation
Indices: 273170--273214 Score: 56
Period size: 20 Copynumber: 2.2 Consensus size: 20
273160 AATAACAATA
273170 TTATGATATGATAA-TAAATT
1 TTAT-ATATGATAATTAAATT
**
273190 TTATATATTCTAATTAAATT
1 TTATATATGATAATTAAATT
273210 TTATA
1 TTATA
273215 AATAATTAAT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
19 7 0.32
20 15 0.68
ACGTcount: A:0.42, C:0.02, G:0.04, T:0.51
Consensus pattern (20 bp):
TTATATATGATAATTAAATT
Found at i:273468 original size:13 final size:13
Alignment explanation
Indices: 273452--273476 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
273442 CTTAAATCAA
273452 AATTTTCAAAAGT
1 AATTTTCAAAAGT
273465 AATTTTCAAAAG
1 AATTTTCAAAAG
273477 CACTTTTTCA
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:0.48, C:0.08, G:0.08, T:0.36
Consensus pattern (13 bp):
AATTTTCAAAAGT
Found at i:277284 original size:21 final size:21
Alignment explanation
Indices: 277201--277294 Score: 64
Period size: 21 Copynumber: 4.4 Consensus size: 21
277191 ATCTTCAATA
*
277201 AAATTTAAGTCAATTTAAATTC
1 AAATTTTAGTCAA-TTAAATTC
* *
277223 GAATTTTGAGT-ATTTTAAATTC
1 AAATTTT-AGTCA-ATTAAATTC
* * * *
277245 AAGTTTCAATCAATCAAATTC
1 AAATTTTAGTCAATTAAATTC
* *
277266 AAATTTTAGTTAATTAAATTG
1 AAATTTTAGTCAATTAAATTC
*
277287 GAATTTTA
1 AAATTTTA
277295 AATGTAATTA
Statistics
Matches: 53, Mismatches: 16, Indels: 7
0.70 0.21 0.09
Matches are distributed among these distances:
21 31 0.58
22 19 0.36
23 3 0.06
ACGTcount: A:0.40, C:0.07, G:0.09, T:0.44
Consensus pattern (21 bp):
AAATTTTAGTCAATTAAATTC
Found at i:278541 original size:31 final size:28
Alignment explanation
Indices: 278506--278565 Score: 75
Period size: 29 Copynumber: 2.0 Consensus size: 28
278496 AAATTGTATG
278506 AAATCAAAAATTATATATAATATCACATATT
1 AAATC-AAAATT-TATATAATAT-ACATATT
* *
278537 AAATCAAAATTTATCTAATATATATATT
1 AAATCAAAATTTATATAATATACATATT
278565 A
1 A
278566 TCACCATATG
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
28 7 0.26
29 9 0.33
30 6 0.22
31 5 0.19
ACGTcount: A:0.53, C:0.08, G:0.00, T:0.38
Consensus pattern (28 bp):
AAATCAAAATTTATATAATATACATATT
Found at i:279491 original size:19 final size:21
Alignment explanation
Indices: 279467--279510 Score: 65
Period size: 22 Copynumber: 2.1 Consensus size: 21
279457 TTTTTACTGT
279467 ATTATAT-AAATATT-TAAAA
1 ATTATATAAAATATTATAAAA
279486 ATTATATAAAAATATTATAAAA
1 ATTATAT-AAAATATTATAAAA
279508 ATT
1 ATT
279511 TAATATGGGC
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
19 7 0.32
21 7 0.32
22 8 0.36
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (21 bp):
ATTATATAAAATATTATAAAA
Found at i:279498 original size:21 final size:22
Alignment explanation
Indices: 279469--279510 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 22
279459 TTTACTGTAT
*
279469 TATATAAATATT-TAAAAATTA
1 TATAAAAATATTATAAAAATTA
279490 TATAAAAATATTATAAAAATT
1 TATAAAAATATTATAAAAATT
279511 TAATATGGGC
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 11 0.58
22 8 0.42
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (22 bp):
TATAAAAATATTATAAAAATTA
Done.