Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01009478.1 Kokia drynarioides strain JFW-HI SEQ_124186, 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: 181484
ACGTcount: A:0.33, C:0.18, G:0.15, T:0.34
Found at i:3973 original size:36 final size:35
Alignment explanation
Indices: 3900--3985 Score: 102
Period size: 36 Copynumber: 2.4 Consensus size: 35
3890 GCTAAAATGA
*
3900 CATTATGCTCTAACCGAGACATAAACAATCACTTAG
1 CATTATGCTCTAACCAAGACATAAACAATCAC-TAG
* *
3936 CATTAAGCTCTAACCAAGACATAAGCAAATTCA-TAG
1 CATTATGCTCTAACCAAGACATAAAC-AA-TCACTAG
*
3972 CAATATGCTCTAAC
1 CATTATGCTCTAAC
3986 TGGGACGTAG
Statistics
Matches: 43, Mismatches: 5, Indels: 4
0.83 0.10 0.08
Matches are distributed among these distances:
36 38 0.88
37 2 0.05
38 3 0.07
ACGTcount: A:0.41, C:0.24, G:0.10, T:0.24
Consensus pattern (35 bp):
CATTATGCTCTAACCAAGACATAAACAATCACTAG
Found at i:4086 original size:72 final size:72
Alignment explanation
Indices: 3994--4182 Score: 234
Period size: 72 Copynumber: 2.6 Consensus size: 72
3984 ACTGGGACGT
* * * * * *
3994 AGACGTATGCAACTTCATAATAATACGCTCTAACCGAGATGTATGCAACATCTTTGCTATACGTT
1 AGACGTATGCAACATCATAATAATACGCTCTAACCGAGACGTATGCAACATCATAGCAATACGCT
* *
4059 TTTACCG
66 ATAACCG
* * *
4066 AGATGTATGCAACATCATAATAATATGCTCTAATCGAGACGTATGCAACATCATAGCAATACGCT
1 AGACGTATGCAACATCATAATAATACGCTCTAACCGAGACGTATGCAACATCATAGCAATACGCT
4131 ATAACCG
66 ATAACCG
* * * * *
4138 AGACATATGTAACATCATAGTAACACGCTCTAACCAAGACGTATG
1 AGACGTATGCAACATCATAATAATACGCTCTAACCGAGACGTATG
4183 TAACTTTATA
Statistics
Matches: 98, Mismatches: 19, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
72 98 1.00
ACGTcount: A:0.36, C:0.22, G:0.15, T:0.27
Consensus pattern (72 bp):
AGACGTATGCAACATCATAATAATACGCTCTAACCGAGACGTATGCAACATCATAGCAATACGCT
ATAACCG
Found at i:4186 original size:36 final size:36
Alignment explanation
Indices: 3994--4182 Score: 200
Period size: 36 Copynumber: 5.2 Consensus size: 36
3984 ACTGGGACGT
* *
3994 AGACGTATGCAACTTCATAATAATACGCTCTAACCG
1 AGACGTATGCAACATCATAGTAATACGCTCTAACCG
* * * * * *
4030 AGATGTATGCAACATCTTTGCT-ATACGTTTTTACCG
1 AGACGTATGCAACATCATAG-TAATACGCTCTAACCG
* * * *
4066 AGATGTATGCAACATCATAATAATATGCTCTAATCG
1 AGACGTATGCAACATCATAGTAATACGCTCTAACCG
* *
4102 AGACGTATGCAACATCATAGCAATACGCTATAACCG
1 AGACGTATGCAACATCATAGTAATACGCTCTAACCG
* * * *
4138 AGACATATGTAACATCATAGTAACACGCTCTAACCA
1 AGACGTATGCAACATCATAGTAATACGCTCTAACCG
4174 AGACGTATG
1 AGACGTATG
4183 TAACTTTATA
Statistics
Matches: 122, Mismatches: 29, Indels: 4
0.79 0.19 0.03
Matches are distributed among these distances:
35 1 0.01
36 120 0.98
37 1 0.01
ACGTcount: A:0.36, C:0.22, G:0.15, T:0.27
Consensus pattern (36 bp):
AGACGTATGCAACATCATAGTAATACGCTCTAACCG
Found at i:10313 original size:51 final size:51
Alignment explanation
Indices: 10237--10335 Score: 189
Period size: 51 Copynumber: 1.9 Consensus size: 51
10227 GATTATACAT
10237 AGAATTCATTAAAAAATAGGTCACACGGTTGTGCCCCAAACTGTGTGCTAG
1 AGAATTCATTAAAAAATAGGTCACACGGTTGTGCCCCAAACTGTGTGCTAG
*
10288 AGAATTCATTAAAAAATGGGTCACACGGTTGTGCCCCAAACTGTGTGC
1 AGAATTCATTAAAAAATAGGTCACACGGTTGTGCCCCAAACTGTGTGC
10336 CAGACCTTGT
Statistics
Matches: 47, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
51 47 1.00
ACGTcount: A:0.32, C:0.20, G:0.22, T:0.25
Consensus pattern (51 bp):
AGAATTCATTAAAAAATAGGTCACACGGTTGTGCCCCAAACTGTGTGCTAG
Found at i:14676 original size:43 final size:43
Alignment explanation
Indices: 14580--14667 Score: 169
Period size: 43 Copynumber: 2.1 Consensus size: 43
14570 CAGATAAGTA
14580 AATGCAAAAAATTAAGCATAAGATAAAATACGAAATATGATAG
1 AATGCAAAAAATTAAGCATAAGATAAAATACGAAATATGATAG
14623 AATGCAAAAAATTAAGCATAAGATAAAATACGAAATAT-ATAG
1 AATGCAAAAAATTAAGCATAAGATAAAATACGAAATATGATAG
14665 AAT
1 AAT
14668 CATGAAAAAA
Statistics
Matches: 45, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
42 7 0.16
43 38 0.84
ACGTcount: A:0.59, C:0.07, G:0.12, T:0.22
Consensus pattern (43 bp):
AATGCAAAAAATTAAGCATAAGATAAAATACGAAATATGATAG
Found at i:14801 original size:29 final size:29
Alignment explanation
Indices: 14761--15134 Score: 317
Period size: 29 Copynumber: 12.8 Consensus size: 29
14751 ATTCGAGTTT
* * *
14761 AAAATGCAATTTTGGACAAGTTTAGGGTT
1 AAAATGTAATTTTGGAGAAGTTTAGGGTC
* *
14790 AAAATGTAATTTTGG-GAAGGTTAGGGTTA
1 AAAATGTAATTTTGGAGAAGTTTAGGG-TC
* * * *
14819 AAAATGTAATTTTGTAAAATTTTATGGTC
1 AAAATGTAATTTTGGAGAAGTTTAGGGTC
* * * * * *
14848 AAAATGTGATTTTAGAAAAGTTCAAGGTT
1 AAAATGTAATTTTGGAGAAGTTTAGGGTC
* * *
14877 AAAATGTAATTTTTGAGAAGTTTGGGGTT
1 AAAATGTAATTTTGGAGAAGTTTAGGGTC
* *
14906 AAAATGTAATTTTGGAGAAGTTCAATGGTC
1 AAAATGTAATTTTGGAGAAGTT-TAGGGTC
* ** *
14936 AAAACGTAATTTTAAAGAAGTTT-GAGGTT
1 AAAATGTAATTTTGGAGAAGTTTAG-GGTC
* *
14965 AAAATGTAATTTTTGAGAAGTTCGAGGGTC
1 AAAATGTAATTTTGGAGAAGTT-TAGGGTC
* *
14995 AAAATGTAATTTTAGAGAAG-TTCGAGGTC
1 AAAATGTAATTTTGGAGAAGTTTAG-GGTC
* *
15024 AAAATGTGATTTTAGGA-AAGTTTAAGGTC
1 AAAATGTAATTTT-GGAGAAGTTTAGGGTC
* * *
15053 AAAATATAATTTTGGAGAGGTTCGAGGGTC
1 AAAATGTAATTTTGGAGAAGTT-TAGGGTC
* *
15083 AAAATGTTATTTTGGAGAAGTTCAGGGTC
1 AAAATGTAATTTTGGAGAAGTTTAGGGTC
*
15112 AAAATGTGATTTTGG-GAAAGTTT
1 AAAATGTAATTTTGGAG-AAGTTT
15135 GTGGACTACC
Statistics
Matches: 276, Mismatches: 57, Indels: 24
0.77 0.16 0.07
Matches are distributed among these distances:
28 14 0.05
29 182 0.66
30 79 0.29
31 1 0.00
ACGTcount: A:0.36, C:0.04, G:0.25, T:0.35
Consensus pattern (29 bp):
AAAATGTAATTTTGGAGAAGTTTAGGGTC
Found at i:14824 original size:58 final size:58
Alignment explanation
Indices: 14759--15134 Score: 262
Period size: 59 Copynumber: 6.4 Consensus size: 58
14749 AGATTCGAGT
* * *
14759 TTAAAATGCAATTTTGGACAAGTTTAGGGTTAAAATGTAATTTTGGGAAGGTT-AGGG
1 TTAAAATGTAATTTTGGAAAAGTTTAGGGTTAAAATGTAATTTTGGGAAGGTTCAAGG
* * * * * * * *
14816 TTAAAAATGTAATTTTGTAAAATTTTATGGTCAAAATGTGATTTTAGAAAAGTTCAAGG
1 TT-AAAATGTAATTTTGGAAAAGTTTAGGGTTAAAATGTAATTTTGGGAAGGTTCAAGG
* * *
14875 TTAAAATGTAATTTTTGAGAAGTTTGGGGTTAAAATGTAATTTTGGAGAA-GTTCAATGG
1 TTAAAATGTAATTTTGGAAAAGTTTAGGGTTAAAATGTAATTTTGG-GAAGGTTCAA-GG
* * * * *
14934 TCAAAACGTAATTTT-AAAGAAGTTT-GAGGTTAAAATGTAATTTTTGAGAA-GTTCGAGGG
1 TTAAAATGTAATTTTGGAA-AAGTTTAG-GGTTAAAATGTAA-TTTTGGGAAGGTTC-AAGG
* * * * * * * * *
14993 TCAAAATGTAATTTTAGAGAAG-TTCGAGGTCAAAATGTGATTTTAGGAAAGTTTAAGG
1 TTAAAATGTAATTTTGGAAAAGTTTAG-GGTTAAAATGTAATTTTGGGAAGGTTCAAGG
* * * * * * * *
15051 TCAAAATATAATTTTGGAGAGGTTCGAGGGTCAAAATGTTATTTTGGAGAA-GTTCAGGG
1 TTAAAATGTAATTTTGGAAAAGTT-TAGGGTTAAAATGTAATTTTGG-GAAGGTTCAAGG
* * *
15110 TCAAAATGTGATTTTGGGAAAGTTT
1 TTAAAATGTAATTTTGGAAAAGTTT
15135 GTGGACTACC
Statistics
Matches: 254, Mismatches: 51, Indels: 27
0.77 0.15 0.08
Matches are distributed among these distances:
57 2 0.01
58 115 0.45
59 126 0.50
60 11 0.04
ACGTcount: A:0.36, C:0.04, G:0.24, T:0.36
Consensus pattern (58 bp):
TTAAAATGTAATTTTGGAAAAGTTTAGGGTTAAAATGTAATTTTGGGAAGGTTCAAGG
Found at i:14957 original size:88 final size:88
Alignment explanation
Indices: 14778--15124 Score: 402
Period size: 88 Copynumber: 4.0 Consensus size: 88
14768 AATTTTGGAC
* * * * * *
14778 AAGTTTAGGGTTAAAATGTAA-TTTTGGGAAGGTT--AGGGTTAAAAATGTAATTTTGTAAAATT
1 AAGTTTAAGGTTAAAATGTAATTTTTGAGAA-GTTCGAGGG-TCAAAATGTAATTTTGGAGAAGT
*
14840 TTATGGTCAAAATGTGATTTTAGAA-
64 TCATGGTCAAAATGTGATTTTA-AAG
* * *
14865 AAGTTCAAGGTTAAAATGTAATTTTTGAGAAGTTTG-GGGTTAAAATGTAATTTTGGAGAAGTTC
1 AAGTTTAAGGTTAAAATGTAATTTTTGAGAAGTTCGAGGGTCAAAATGTAATTTTGGAGAAGTTC
* *
14929 AATGGTCAAAACGTAATTTTAAAG
66 -ATGGTCAAAATGTGATTTTAAAG
* *
14953 AAGTTTGAGGTTAAAATGTAATTTTTGAGAAGTTCGAGGGTCAAAATGTAATTTTAGAGAAGTTC
1 AAGTTTAAGGTTAAAATGTAATTTTTGAGAAGTTCGAGGGTCAAAATGTAATTTTGGAGAAGTTC
*
15018 GA-GGTCAAAATGTGATTTT-AGG
66 -ATGGTCAAAATGTGATTTTAAAG
* * * * *
15040 AAAGTTTAAGGTCAAAATATAATTTTGGAGAGGTTCGAGGGTCAAAATGTTATTTTGGAGAAGTT
1 -AAGTTTAAGGTTAAAATGTAATTTTTGAGAAGTTCGAGGGTCAAAATGTAATTTTGGAGAAGTT
*
15105 CAGGGTCAAAATGTGATTTT
65 CATGGTCAAAATGTGATTTT
15125 GGGAAAGTTT
Statistics
Matches: 226, Mismatches: 26, Indels: 15
0.85 0.10 0.06
Matches are distributed among these distances:
87 47 0.21
88 152 0.67
89 27 0.12
ACGTcount: A:0.36, C:0.04, G:0.24, T:0.36
Consensus pattern (88 bp):
AAGTTTAAGGTTAAAATGTAATTTTTGAGAAGTTCGAGGGTCAAAATGTAATTTTGGAGAAGTTC
ATGGTCAAAATGTGATTTTAAAG
Found at i:15126 original size:59 final size:58
Alignment explanation
Indices: 14844--15124 Score: 321
Period size: 59 Copynumber: 4.8 Consensus size: 58
14834 AAAATTTTAT
* * * * * * *
14844 GGTCAAAATGTGATTTTAGAAAAGTTCAAGGTTAAAATGTAATTTTTGAGAAGTTTGG
1 GGTCAAAATGTAATTTTGGAGAAGTTCAAGGTCAAAATGTAATTTTAGAGAAGTTCGA
* * * *
14902 GGTTAAAATGTAATTTTGGAGAAGTTCAATGGTCAAAACGTAATTTTAAAGAAGTTTGA
1 GGTCAAAATGTAATTTTGGAGAAGTTCAA-GGTCAAAATGTAATTTTAGAGAAGTTCGA
* * *
14961 GGTTAAAATGTAATTTTTGAGAAGTTCGAGGGTCAAAATGTAATTTTAGAGAAGTTCGA
1 GGTCAAAATGTAATTTTGGAGAAGTTC-AAGGTCAAAATGTAATTTTAGAGAAGTTCGA
* * * * *
15020 GGTCAAAATGTGATTTTAGGA-AAGTTTAAGGTCAAAATATAATTTTGGAGAGGTTCGA
1 GGTCAAAATGTAATTTT-GGAGAAGTTCAAGGTCAAAATGTAATTTTAGAGAAGTTCGA
* * *
15078 GGGTCAAAATGTTATTTTGGAGAAGTTCAGGGTCAAAATGTGATTTT
1 -GGTCAAAATGTAATTTTGGAGAAGTTCAAGGTCAAAATGTAATTTT
15125 GGGAAAGTTT
Statistics
Matches: 191, Mismatches: 27, Indels: 9
0.84 0.12 0.04
Matches are distributed among these distances:
58 55 0.29
59 133 0.70
60 3 0.02
ACGTcount: A:0.36, C:0.05, G:0.25, T:0.35
Consensus pattern (58 bp):
GGTCAAAATGTAATTTTGGAGAAGTTCAAGGTCAAAATGTAATTTTAGAGAAGTTCGA
Found at i:15544 original size:36 final size:36
Alignment explanation
Indices: 15495--15584 Score: 126
Period size: 36 Copynumber: 2.5 Consensus size: 36
15485 TCAACATAAA
*
15495 CCAAAACGACGTCGTTTTGGGAGATTTAAGTCATTC
1 CCAAAACGACGTCGTTTTGAGAGATTTAAGTCATTC
* *
15531 CCAAAACGGCGTCGTTTTGAGTGATTTAAGTCATTC
1 CCAAAACGACGTCGTTTTGAGAGATTTAAGTCATTC
* **
15567 CTAAAATTACGTCGTTTT
1 CCAAAACGACGTCGTTTT
15585 AGGACCCTAT
Statistics
Matches: 47, Mismatches: 7, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
36 47 1.00
ACGTcount: A:0.27, C:0.19, G:0.20, T:0.34
Consensus pattern (36 bp):
CCAAAACGACGTCGTTTTGAGAGATTTAAGTCATTC
Found at i:23554 original size:36 final size:36
Alignment explanation
Indices: 23359--23561 Score: 219
Period size: 36 Copynumber: 5.6 Consensus size: 36
23349 CACTTAGCAT
* * * *
23359 TACGCTCTAACCGATACGTAAGCAAATTCATAGAAA
1 TACGCTCTAATCGAGACGTATGCAACTTCATAGAAA
* * **
23395 TACGCTCTAATCAAGATGTATGCAACTTCATATTAA
1 TACGCTCTAATCGAGACGTATGCAACTTCATAGAAA
* * * *
23431 TACGCTTTAATCAAGACGTATGCAACATCATAGTAA
1 TACGCTCTAATCGAGACGTATGCAACTTCATAGAAA
* * * *
23467 TACGCTTTAATCGAGACGTATACAACATCATAGCAA
1 TACGCTCTAATCGAGACGTATGCAACTTCATAGAAA
*
23503 TACGCTTTAATCGAGACGTATGCAACTTCATATG-AA
1 TACGCTCTAATCGAGACGTATGCAACTTCATA-GAAA
* *
23539 TACGCTCTAACCGAGACATATGC
1 TACGCTCTAATCGAGACGTATGC
23562 TTCCTTTGAA
Statistics
Matches: 146, Mismatches: 20, Indels: 2
0.87 0.12 0.01
Matches are distributed among these distances:
36 145 0.99
37 1 0.01
ACGTcount: A:0.37, C:0.22, G:0.14, T:0.27
Consensus pattern (36 bp):
TACGCTCTAATCGAGACGTATGCAACTTCATAGAAA
Found at i:25088 original size:12 final size:12
Alignment explanation
Indices: 25071--25103 Score: 57
Period size: 12 Copynumber: 2.8 Consensus size: 12
25061 AAAATGTTTG
25071 AATAAGAATTCA
1 AATAAGAATTCA
*
25083 AATAAGAATTTA
1 AATAAGAATTCA
25095 AATAAGAAT
1 AATAAGAAT
25104 ATATTTGAGG
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.61, C:0.03, G:0.09, T:0.27
Consensus pattern (12 bp):
AATAAGAATTCA
Found at i:25165 original size:3 final size:3
Alignment explanation
Indices: 25157--25186 Score: 60
Period size: 3 Copynumber: 10.0 Consensus size: 3
25147 TTTTATTGTT
25157 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
25187 ATGGGAAGGT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:25228 original size:25 final size:26
Alignment explanation
Indices: 25199--25248 Score: 84
Period size: 26 Copynumber: 2.0 Consensus size: 26
25189 GGGAAGGTTT
*
25199 TATTTG-GGTAATTTAAATAAGAATA
1 TATTTGAGGAAATTTAAATAAGAATA
25224 TATTTGAGGAAATTTAAATAAGAAT
1 TATTTGAGGAAATTTAAATAAGAAT
25249 TTTATATAAT
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
25 6 0.26
26 17 0.74
ACGTcount: A:0.46, C:0.00, G:0.16, T:0.38
Consensus pattern (26 bp):
TATTTGAGGAAATTTAAATAAGAATA
Found at i:38225 original size:158 final size:158
Alignment explanation
Indices: 37937--38250 Score: 470
Period size: 158 Copynumber: 2.0 Consensus size: 158
37927 ATTTCAGGAT
37937 TTACAGGTTATATGGGTGCTAGTCTTACATATCCTACAGATGGTTGAGATCCGACATTTGTTGCG
1 TTACAGGTTATATGGGTGCTAGTCTTACATATCCTACAGATGGTTGAGATCCGACATTTGTTGCG
* * * * *
38002 GATTCTCCACAGCTCGTGTGAGTAGCATAGTGTAACTTTACATCTTGACCCATAGCTCGTGTGAG
66 AATTCTCCACAGCTCGTGTGAGCAGCATAGTGTAACTTTACATCTCGACCCACAACTCGTGTGAG
*
38067 CAAACCCACTTCACAGCTCGTGTGAGCA
131 CAAACCCACTTCACAGCTCATGTGAGCA
* * *
38095 TTACAGGTTATATGGGTG-TTGATCTTAGATGTCCTATC-GATGGTTGAGATCCGACATTTGTTG
1 TTACAGGTTATATGGGTGCTAG-TCTTACATATCCTA-CAGATGGTTGAGATCCGACATTTGTTG
* * *
38158 CGAATTCTCCATAGCTCGTGTGAGCAGCATTGTGTAGCTTTACATCTCGACCCACAACTCGTGTG
64 CGAATTCTCCACAGCTCGTGTGAGCAGCATAGTGTAACTTTACATCTCGACCCACAACTCGTGTG
* *
38223 AGCAAGCCCATTTCACAGCTCATGTGAG
129 AGCAAACCCACTTCACAGCTCATGTGAG
38251 TAATACATGT
Statistics
Matches: 140, Mismatches: 14, Indels: 4
0.89 0.09 0.03
Matches are distributed among these distances:
157 2 0.01
158 137 0.98
159 1 0.01
ACGTcount: A:0.23, C:0.22, G:0.23, T:0.31
Consensus pattern (158 bp):
TTACAGGTTATATGGGTGCTAGTCTTACATATCCTACAGATGGTTGAGATCCGACATTTGTTGCG
AATTCTCCACAGCTCGTGTGAGCAGCATAGTGTAACTTTACATCTCGACCCACAACTCGTGTGAG
CAAACCCACTTCACAGCTCATGTGAGCA
Found at i:39708 original size:16 final size:15
Alignment explanation
Indices: 39687--39716 Score: 51
Period size: 16 Copynumber: 1.9 Consensus size: 15
39677 ATTGTGTAAA
39687 ATTAATTAATATAATT
1 ATTAATTAAT-TAATT
39703 ATTAATTAATTAAT
1 ATTAATTAATTAAT
39717 ATTTTGAGAA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 4 0.29
16 10 0.71
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (15 bp):
ATTAATTAATTAATT
Found at i:46107 original size:23 final size:22
Alignment explanation
Indices: 46077--46123 Score: 60
Period size: 23 Copynumber: 2.1 Consensus size: 22
46067 ATTTAATGTC
*
46077 TTTA-TTTTTTAATATTAAAGTT
1 TTTATTTTTTTAAT-TTAAAATT
46099 TTTATTTTTTTTAATTTAAAATT
1 TTTA-TTTTTTTAATTTAAAATT
46122 TT
1 TT
46124 AGTTTCATTC
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
22 4 0.18
23 9 0.41
24 9 0.41
ACGTcount: A:0.30, C:0.00, G:0.02, T:0.68
Consensus pattern (22 bp):
TTTATTTTTTTAATTTAAAATT
Found at i:52316 original size:13 final size:13
Alignment explanation
Indices: 52298--52328 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
52288 TCAAACAACA
52298 TAATTATATTTAG
1 TAATTATATTTAG
*
52311 TAATTATATTTAT
1 TAATTATATTTAG
52324 TAATT
1 TAATT
52329 TACTGAACAG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.39, C:0.00, G:0.03, T:0.58
Consensus pattern (13 bp):
TAATTATATTTAG
Found at i:52754 original size:23 final size:21
Alignment explanation
Indices: 52726--52788 Score: 63
Period size: 23 Copynumber: 2.9 Consensus size: 21
52716 GTGTATTTAT
52726 AATATTTCACATATAAACATAA
1 AATATTTCACATATAAA-ATAA
* * * *
52748 CAATATTTGAAATAATTAATTAA
1 -AATATTTCACAT-ATAAAATAA
52771 AATATTTCACATATAAAA
1 AATATTTCACATATAAAA
52789 ATTTTTGAAA
Statistics
Matches: 31, Mismatches: 8, Indels: 4
0.72 0.19 0.09
Matches are distributed among these distances:
21 4 0.13
22 10 0.32
23 13 0.42
24 4 0.13
ACGTcount: A:0.54, C:0.10, G:0.02, T:0.35
Consensus pattern (21 bp):
AATATTTCACATATAAAATAA
Found at i:53441 original size:28 final size:29
Alignment explanation
Indices: 53382--53441 Score: 70
Period size: 28 Copynumber: 2.1 Consensus size: 29
53372 ACTTTCACAT
*
53382 ATTTTTTCCAAAATCGACTTATTTCCTTA
1 ATTTTTTCCAAAATCGACTTATTTCATTA
**
53411 ATTTTTTTTAAAAT-GACTTATTT-ATTCA
1 ATTTTTTCCAAAATCGACTTATTTCATT-A
53439 ATT
1 ATT
53442 AACAAAAAAA
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
27 2 0.07
28 13 0.48
29 12 0.44
ACGTcount: A:0.30, C:0.13, G:0.03, T:0.53
Consensus pattern (29 bp):
ATTTTTTCCAAAATCGACTTATTTCATTA
Found at i:53821 original size:29 final size:32
Alignment explanation
Indices: 53788--53850 Score: 78
Period size: 33 Copynumber: 2.0 Consensus size: 32
53778 AATTACAACT
53788 GTAAACATCAA-T-T-AAAATAAAGTATAGTG
1 GTAAACATCAACTATCAAAATAAAGTATAGTG
**
53817 GTAAATTTCAACTTATCAAAATAAAGTATAGTG
1 GTAAACATCAAC-TATCAAAATAAAGTATAGTG
53850 G
1 G
53851 CAAATATGTC
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
29 9 0.32
31 1 0.04
32 1 0.04
33 17 0.61
ACGTcount: A:0.48, C:0.08, G:0.14, T:0.30
Consensus pattern (32 bp):
GTAAACATCAACTATCAAAATAAAGTATAGTG
Found at i:55817 original size:79 final size:78
Alignment explanation
Indices: 55685--55847 Score: 263
Period size: 79 Copynumber: 2.1 Consensus size: 78
55675 TAGAAATTGA
*
55685 ATTTCTGTTTCCAAACAGAAATAAATTAAAATAATTCTGTTTTAGGATTTATTCCTACCGTTCAA
1 ATTTCTGTTTCCAAACAGAAATAAATTAAAATAATTCTGTTTGAGGATTTATTCCTACCGTTCAA
55750 CAGAATTCATTCG
66 CAGAATTCATTCG
* * *
55763 AGTTTCTGTTTCCAAACAGAAATAAATTAAAGTAATTTTGTTTGAGGATTTATTCCTATCGTTCA
1 A-TTTCTGTTTCCAAACAGAAATAAATTAAAATAATTCTGTTTGAGGATTTATTCCTACCGTTCA
* *
55828 ATAGAATTTATTCG
65 ACAGAATTCATTCG
55842 ATTTCT
1 ATTTCT
55848 ATTGCTAACA
Statistics
Matches: 78, Mismatches: 6, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
78 6 0.08
79 72 0.92
ACGTcount: A:0.33, C:0.14, G:0.12, T:0.41
Consensus pattern (78 bp):
ATTTCTGTTTCCAAACAGAAATAAATTAAAATAATTCTGTTTGAGGATTTATTCCTACCGTTCAA
CAGAATTCATTCG
Found at i:59508 original size:170 final size:170
Alignment explanation
Indices: 59226--59567 Score: 524
Period size: 170 Copynumber: 2.0 Consensus size: 170
59216 GCACAACAAT
* * *
59226 AGCATAGTCTGATCCTTATCGTTAATATGAACCTTAACGTTATTTAAATCATTTAAAAGATGATT
1 AGCATAGTCTGATCCTTATCATCAATATGAACCTCAACGTTATTTAAATCATTTAAAAGATGATT
* * * * *
59291 GAATTGATTGATGTGATCTTTAAGAAGCTCATATTTGTTAATGCGAAACATAAATAGACGTTGTT
66 GAACTGACTGATATGATCTTTAAGAAGCTCACATTCGTTAATGCGAAACATAAATAGACGTTGTT
*
59356 TCAACACTAAACGGTTAGCTAGAGACTTAGTCGCATAAAG
131 TCAACACTAAACGGTTAGCCAGAGACTTAGTCGCATAAAG
* *
59396 AGCATAGTTTGATCCTTATCATCAATCTGAACCTCAACGTTATTTAAATCATTTAAAAGA-GTAT
1 AGCATAGTCTGATCCTTATCATCAATATGAACCTCAACGTTATTTAAATCATTTAAAAGATG-AT
*
59460 TGAACTGACTGATATGATCTTTAAGAAGCTCACATTCGTTAATGCGAAACGTAAATAGACGTTGT
65 TGAACTGACTGATATGATCTTTAAGAAGCTCACATTCGTTAATGCGAAACATAAATAGACGTTGT
* * * *
59525 TTCAATATTAAATGGTTAGCCAGAGACTTAGTCGGATAAAG
130 TTCAACACTAAACGGTTAGCCAGAGACTTAGTCGCATAAAG
59566 AG
1 AG
59568 TTTCAAACTT
Statistics
Matches: 155, Mismatches: 16, Indels: 2
0.90 0.09 0.01
Matches are distributed among these distances:
169 1 0.01
170 154 0.99
ACGTcount: A:0.35, C:0.14, G:0.17, T:0.33
Consensus pattern (170 bp):
AGCATAGTCTGATCCTTATCATCAATATGAACCTCAACGTTATTTAAATCATTTAAAAGATGATT
GAACTGACTGATATGATCTTTAAGAAGCTCACATTCGTTAATGCGAAACATAAATAGACGTTGTT
TCAACACTAAACGGTTAGCCAGAGACTTAGTCGCATAAAG
Found at i:66197 original size:21 final size:21
Alignment explanation
Indices: 66149--66201 Score: 79
Period size: 21 Copynumber: 2.5 Consensus size: 21
66139 TGTGACCCTA
* *
66149 CACATGACCATGTGGCTACCC
1 CACATGCCCGTGTGGCTACCC
66170 CACATGCCCGTGTGGCTACCC
1 CACATGCCCGTGTGGCTACCC
*
66191 TACATGCCCGT
1 CACATGCCCGT
66202 ATCCCAAATT
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 29 1.00
ACGTcount: A:0.19, C:0.40, G:0.21, T:0.21
Consensus pattern (21 bp):
CACATGCCCGTGTGGCTACCC
Found at i:73077 original size:17 final size:17
Alignment explanation
Indices: 73055--73094 Score: 62
Period size: 17 Copynumber: 2.4 Consensus size: 17
73045 TCTCCACCTT
* *
73055 AACAAGAATTCTCTACG
1 AACAAGAACTCTCAACG
73072 AACAAGAACTCTCAACG
1 AACAAGAACTCTCAACG
73089 AACAAG
1 AACAAG
73095 TTCTTCACCT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
17 21 1.00
ACGTcount: A:0.47, C:0.25, G:0.12, T:0.15
Consensus pattern (17 bp):
AACAAGAACTCTCAACG
Found at i:76572 original size:75 final size:74
Alignment explanation
Indices: 76493--76748 Score: 314
Period size: 75 Copynumber: 3.4 Consensus size: 74
76483 ACATTTGACA
76493 TCGTCGGTTATCCGACTAGCGCTGGGCGCAACCTTTGTCAGTTTATTTGACTAGTGTTGTGCACA
1 TCGTCGGTTATCCGACTAGCGCTGGGCGCAACCTTTGTCAGTTTATTTGACTAGTGTTG-GCACA
76558 TTTCTTATAT
65 TTTCTTATAT
* * * * * *
76568 TCGTCGATTATCCGACTAGCGCTGGGCACAACCTTTTTTAGTTTATTTGAGTAGTGTTAGGAACA
1 TCGTCGGTTATCCGACTAGCGCTGGGCGCAACCTTTGTCAGTTTATTTGACTAGTGTT-GGCACA
*
76633 CTTCTTATAT
65 TTTCTTATAT
* * * * * * * * *
76643 TCGTTGGTTATCCAACTAGTGTTGGGTGCAACCTTTGTCAGTTTATCTAACTAGTGCTGGGCATA
1 TCGTCGGTTATCCGACTAGCGCTGGGCGCAACCTTTGTCAGTTTATTTGACTAGTG-TTGGCACA
76708 TTTCTTATAT
65 TTTCTTATAT
** *
76718 TTTTCGGTTATCCGACTAGCGTTGGGCGCAA
1 TCGTCGGTTATCCGACTAGCGCTGGGCGCAA
76749 AAGCTTAATA
Statistics
Matches: 150, Mismatches: 29, Indels: 4
0.82 0.16 0.02
Matches are distributed among these distances:
75 148 0.99
76 2 0.01
ACGTcount: A:0.20, C:0.20, G:0.22, T:0.39
Consensus pattern (74 bp):
TCGTCGGTTATCCGACTAGCGCTGGGCGCAACCTTTGTCAGTTTATTTGACTAGTGTTGGCACAT
TTCTTATAT
Found at i:85838 original size:17 final size:17
Alignment explanation
Indices: 85811--85853 Score: 70
Period size: 17 Copynumber: 2.5 Consensus size: 17
85801 TCAAAAGATA
85811 AAAAGTCATTGAAATGTT
1 AAAA-TCATTGAAATGTT
85829 AAAATCATTGAAATGTT
1 AAAATCATTGAAATGTT
85846 AAAA-CATT
1 AAAATCATT
85854 TTCCTTTACA
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
16 4 0.16
17 17 0.68
18 4 0.16
ACGTcount: A:0.49, C:0.07, G:0.12, T:0.33
Consensus pattern (17 bp):
AAAATCATTGAAATGTT
Found at i:87216 original size:25 final size:25
Alignment explanation
Indices: 87135--87219 Score: 71
Period size: 25 Copynumber: 3.4 Consensus size: 25
87125 GACTATTTTA
* * * * *
87135 CAGAGAGTTCACTATAAAGGCCTTA
1 CAGAGAATTCACCAAAAAGGCTTTC
**
87160 CAGAGAATTTGCCAAAAAGGCTTTC
1 CAGAGAATTCACCAAAAAGGCTTTC
* * *
87185 CAAAGAATTCACCACAAAGGCTTTT
1 CAGAGAATTCACCAAAAAGGCTTTC
*
87210 TAGAGAATTC
1 CAGAGAATTC
87220 GTGTTTATTG
Statistics
Matches: 46, Mismatches: 14, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
25 46 1.00
ACGTcount: A:0.38, C:0.20, G:0.18, T:0.25
Consensus pattern (25 bp):
CAGAGAATTCACCAAAAAGGCTTTC
Found at i:87973 original size:3 final size:3
Alignment explanation
Indices: 87965--87994 Score: 60
Period size: 3 Copynumber: 10.0 Consensus size: 3
87955 CGATCTTAAC
87965 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA
1 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA
87995 TGGTAGGTAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.67, C:0.00, G:0.33, T:0.00
Consensus pattern (3 bp):
GAA
Found at i:92018 original size:7 final size:7
Alignment explanation
Indices: 92006--92049 Score: 63
Period size: 7 Copynumber: 6.4 Consensus size: 7
91996 GAAAAAAGTT
92006 AACGATC
1 AACGATC
92013 AACGATC
1 AACGATC
*
92020 AAAG-TC
1 AACGATC
*
92026 AACAATC
1 AACGATC
92033 AACGATC
1 AACGATC
92040 AACGATC
1 AACGATC
92047 AAC
1 AAC
92050 AGTCAATGGT
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
6 4 0.12
7 28 0.88
ACGTcount: A:0.48, C:0.27, G:0.11, T:0.14
Consensus pattern (7 bp):
AACGATC
Found at i:92033 original size:20 final size:20
Alignment explanation
Indices: 92000--92055 Score: 67
Period size: 20 Copynumber: 2.8 Consensus size: 20
91990 ATTTTCGAAA
* *
92000 AAAGTTAACGATCAACGATC
1 AAAGTCAACAATCAACGATC
92020 AAAGTCAACAATCAACGATC
1 AAAGTCAACAATCAACGATC
* *
92040 AACGATCAACAGTCAA
1 AAAG-TCAACAATCAA
92056 TGGTCAACGG
Statistics
Matches: 31, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
20 21 0.68
21 10 0.32
ACGTcount: A:0.48, C:0.23, G:0.12, T:0.16
Consensus pattern (20 bp):
AAAGTCAACAATCAACGATC
Found at i:92055 original size:14 final size:14
Alignment explanation
Indices: 92011--92055 Score: 58
Period size: 14 Copynumber: 3.3 Consensus size: 14
92001 AAGTTAACGA
92011 TCAACGATCAA-AG
1 TCAACGATCAACAG
*
92024 TCAACAATCAAC-G
1 TCAACGATCAACAG
92037 ATCAACGATCAACAG
1 -TCAACGATCAACAG
92052 TCAA
1 TCAA
92056 TGGTCAACGG
Statistics
Matches: 27, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
13 11 0.41
14 15 0.56
15 1 0.04
ACGTcount: A:0.47, C:0.27, G:0.11, T:0.16
Consensus pattern (14 bp):
TCAACGATCAACAG
Found at i:92062 original size:21 final size:21
Alignment explanation
Indices: 92010--92064 Score: 67
Period size: 21 Copynumber: 2.7 Consensus size: 21
92000 AAAGTTAACG
*
92010 ATCAACGATCAAAG-TCAACA
1 ATCAACGATCAACGATCAACA
92030 ATCAACGATCAACGATCAACA
1 ATCAACGATCAACGATCAACA
* * *
92051 GTCAATGGTCAACG
1 ATCAACGATCAACG
92065 GTTGATCAAT
Statistics
Matches: 30, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
20 13 0.43
21 17 0.57
ACGTcount: A:0.44, C:0.25, G:0.15, T:0.16
Consensus pattern (21 bp):
ATCAACGATCAACGATCAACA
Found at i:99198 original size:22 final size:22
Alignment explanation
Indices: 99144--99198 Score: 58
Period size: 22 Copynumber: 2.5 Consensus size: 22
99134 TTGAACGGTT
* *
99144 AACGGTCAGTCAACGATCGATT
1 AACGGTCGGTCAACGATCGATC
* *
99166 AA-TGACTGGTCAACGATCGATC
1 AACGGTC-GGTCAACGATCGATC
99188 AACGGTCGGTC
1 AACGGTCGGTC
99199 CACAATTTGA
Statistics
Matches: 25, Mismatches: 6, Indels: 4
0.71 0.17 0.11
Matches are distributed among these distances:
21 2 0.08
22 21 0.84
23 2 0.08
ACGTcount: A:0.29, C:0.24, G:0.25, T:0.22
Consensus pattern (22 bp):
AACGGTCGGTCAACGATCGATC
Found at i:101269 original size:17 final size:18
Alignment explanation
Indices: 101232--101270 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
101222 GGTATGAGTT
*
101232 TTTTTAATAAATTAATCA
1 TTTTTAATAAATAAATCA
*
101250 TTTTTAATAAA-AAATTA
1 TTTTTAATAAATAAATCA
101267 TTTT
1 TTTT
101271 GTTGTTTTGG
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
17 8 0.42
18 11 0.58
ACGTcount: A:0.44, C:0.03, G:0.00, T:0.54
Consensus pattern (18 bp):
TTTTTAATAAATAAATCA
Found at i:101353 original size:12 final size:12
Alignment explanation
Indices: 101336--101414 Score: 53
Period size: 12 Copynumber: 6.9 Consensus size: 12
101326 TTTTTTACTG
*
101336 TTTTGGTTGTT-
1 TTTTTGTTGTTA
* *
101347 TTTTTGGTGTTG
1 TTTTTGTTGTTA
*
101359 TTTTTGATGTTA
1 TTTTTGTTGTTA
101371 TTTTTGTTGTT-
1 TTTTTGTTGTTA
*
101382 TTTAATGTTG---
1 TTT-TTGTTGTTA
101392 -TTTTGATTGTTA
1 TTTTTG-TTGTTA
101404 TTTTTGTTGTT
1 TTTTTGTTGTT
101415 TAGATGATAT
Statistics
Matches: 54, Mismatches: 7, Indels: 13
0.73 0.09 0.18
Matches are distributed among these distances:
8 2 0.04
9 5 0.09
11 12 0.22
12 30 0.56
13 5 0.09
ACGTcount: A:0.08, C:0.00, G:0.22, T:0.71
Consensus pattern (12 bp):
TTTTTGTTGTTA
Found at i:101357 original size:20 final size:20
Alignment explanation
Indices: 101282--101351 Score: 106
Period size: 20 Copynumber: 3.5 Consensus size: 20
101272 TTGTTTTGGC
101282 GTTGTTTTTTTACTGTTTTG
1 GTTGTTTTTTTACTGTTTTG
*
101302 GTTTTTTTTTTACTGTTTT-
1 GTTGTTTTTTTACTGTTTTG
* *
101321 GATGCTTTTTTACTGTTTTG
1 GTTGTTTTTTTACTGTTTTG
101341 GTTGTTTTTTT
1 GTTGTTTTTTT
101352 GGTGTTGTTT
Statistics
Matches: 43, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
19 16 0.37
20 27 0.63
ACGTcount: A:0.06, C:0.06, G:0.17, T:0.71
Consensus pattern (20 bp):
GTTGTTTTTTTACTGTTTTG
Found at i:101374 original size:24 final size:23
Alignment explanation
Indices: 101334--101381 Score: 60
Period size: 23 Copynumber: 2.0 Consensus size: 23
101324 GCTTTTTTAC
*
101334 TGTTTTGGTTGTTTTTTTGGTGT
1 TGTTTTGGATGTTTTTTTGGTGT
* *
101357 TGTTTTTGATGTTATTTTTGTTGT
1 TGTTTTGGATGTT-TTTTTGGTGT
101381 T
1 T
101382 TTTAATGTTG
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
23 11 0.52
24 10 0.48
ACGTcount: A:0.04, C:0.00, G:0.25, T:0.71
Consensus pattern (23 bp):
TGTTTTGGATGTTTTTTTGGTGT
Found at i:101380 original size:21 final size:21
Alignment explanation
Indices: 101354--101395 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
101344 GTTTTTTTGG
*
101354 TGTTGTTTTTGATGTTATTTT
1 TGTTGTTTTTAATGTTATTTT
*
101375 TGTTGTTTTTAATGTTGTTTT
1 TGTTGTTTTTAATGTTATTTT
101396 GATTGTTATT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.10, C:0.00, G:0.19, T:0.71
Consensus pattern (21 bp):
TGTTGTTTTTAATGTTATTTT
Found at i:101401 original size:21 final size:19
Alignment explanation
Indices: 101354--101415 Score: 61
Period size: 21 Copynumber: 3.0 Consensus size: 19
101344 GTTTTTTTGG
*
101354 TGTTGTTTTTGATGTTATTTT
1 TGTTGTTTTT-ATGTT-GTTT
101375 TGTTGTTTTTAATGTTGTTT
1 TGTTGTTTTT-ATGTTGTTT
*
101395 TGATTGTTATTTTTGTTGTTT
1 TG-TTGTT-TTTATGTTGTTT
101416 AGATGATATT
Statistics
Matches: 36, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
20 5 0.14
21 28 0.78
22 3 0.08
ACGTcount: A:0.10, C:0.00, G:0.19, T:0.71
Consensus pattern (19 bp):
TGTTGTTTTTATGTTGTTT
Found at i:101429 original size:21 final size:21
Alignment explanation
Indices: 101387--101428 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
101377 TTGTTTTTAA
* *
101387 TGTTGTTTTGATTGTTATTTT
1 TGTTGTTTAGATTGATATTTT
101408 TGTTGTTTAGA-TGATATTTT
1 TGTTGTTTAGATTGATATTTT
101428 T
1 T
101429 TTATGCGTTT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
20 9 0.47
21 10 0.53
ACGTcount: A:0.14, C:0.00, G:0.19, T:0.67
Consensus pattern (21 bp):
TGTTGTTTAGATTGATATTTT
Found at i:101615 original size:21 final size:21
Alignment explanation
Indices: 101573--101616 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
101563 ATTTATTTAT
* *
101573 TTTTTAATGTTTGTTTTAATA
1 TTTTTAATGTGTGTTTGAATA
101594 TTTTTAA-GTGTGTTTGATATA
1 TTTTTAATGTGTGTTTGA-ATA
101615 TT
1 TT
101617 ATATATTTTA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
20 8 0.40
21 12 0.60
ACGTcount: A:0.23, C:0.00, G:0.14, T:0.64
Consensus pattern (21 bp):
TTTTTAATGTGTGTTTGAATA
Found at i:112754 original size:23 final size:23
Alignment explanation
Indices: 112728--112775 Score: 96
Period size: 23 Copynumber: 2.1 Consensus size: 23
112718 AAAACTCAAA
112728 TAGTTTCACTCTAATTTAAATCT
1 TAGTTTCACTCTAATTTAAATCT
112751 TAGTTTCACTCTAATTTAAATCT
1 TAGTTTCACTCTAATTTAAATCT
112774 TA
1 TA
112776 CTCCCTATTT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 25 1.00
ACGTcount: A:0.31, C:0.17, G:0.04, T:0.48
Consensus pattern (23 bp):
TAGTTTCACTCTAATTTAAATCT
Found at i:115705 original size:21 final size:22
Alignment explanation
Indices: 115672--115747 Score: 57
Period size: 21 Copynumber: 3.3 Consensus size: 22
115662 ATGATAATGA
*
115672 ATTTAAATATTAAGATAAATAAT
1 ATTTATAT-TTAAGATAAATAAT
115695 ATTTAT-TTTAATGATAATTAAATAAT
1 ATTTATATTTAA-G---A-TAAATAAT
* *
115721 ATTTATATTTATGAT-AATATT
1 ATTTATATTTAAGATAAATAAT
115742 ATTTAT
1 ATTTAT
115748 CTTTGTGATA
Statistics
Matches: 44, Mismatches: 3, Indels: 14
0.72 0.05 0.23
Matches are distributed among these distances:
21 15 0.34
22 3 0.07
23 6 0.14
25 1 0.02
26 15 0.34
27 4 0.09
ACGTcount: A:0.46, C:0.00, G:0.04, T:0.50
Consensus pattern (22 bp):
ATTTATATTTAAGATAAATAAT
Found at i:115717 original size:26 final size:26
Alignment explanation
Indices: 115687--115738 Score: 88
Period size: 26 Copynumber: 2.0 Consensus size: 26
115677 AATATTAAGA
115687 TAAATAATATTTAT-TTTAATGATAAT
1 TAAATAATATTTATATTT-ATGATAAT
115713 TAAATAATATTTATATTTATGATAAT
1 TAAATAATATTTATATTTATGATAAT
115739 ATTATTTATC
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
26 22 0.88
27 3 0.12
ACGTcount: A:0.46, C:0.00, G:0.04, T:0.50
Consensus pattern (26 bp):
TAAATAATATTTATATTTATGATAAT
Found at i:115756 original size:21 final size:21
Alignment explanation
Indices: 115715--115757 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
115705 ATGATAATTA
115715 AATAATATTTATATTTATGAT
1 AATAATATTTATATTTATGAT
* * *
115736 AATATTATTTATCTTTGTGAT
1 AATAATATTTATATTTATGAT
115757 A
1 A
115758 TTTTATATAT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.37, C:0.02, G:0.07, T:0.53
Consensus pattern (21 bp):
AATAATATTTATATTTATGAT
Found at i:116495 original size:16 final size:17
Alignment explanation
Indices: 116474--116508 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
116464 AAATATAATT
116474 TTTAGTAT-GAATATTA
1 TTTAGTATGGAATATTA
*
116490 TTTAGTATGGATTATTA
1 TTTAGTATGGAATATTA
116507 TT
1 TT
116509 AATTAAATGT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 8 0.47
17 9 0.53
ACGTcount: A:0.31, C:0.00, G:0.14, T:0.54
Consensus pattern (17 bp):
TTTAGTATGGAATATTA
Found at i:121490 original size:27 final size:27
Alignment explanation
Indices: 121451--121507 Score: 69
Period size: 27 Copynumber: 2.1 Consensus size: 27
121441 AATTCTACTG
* *
121451 AATTTCTCGATTTATTAATATACAATA
1 AATTTATCGATTTATCAATATACAATA
* * *
121478 AATTTATCTATTTATCATTATACAGTA
1 AATTTATCGATTTATCAATATACAATA
121505 AAT
1 AAT
121508 AAAAAAATTA
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
27 25 1.00
ACGTcount: A:0.40, C:0.11, G:0.04, T:0.46
Consensus pattern (27 bp):
AATTTATCGATTTATCAATATACAATA
Found at i:126215 original size:20 final size:21
Alignment explanation
Indices: 126179--126229 Score: 54
Period size: 20 Copynumber: 2.5 Consensus size: 21
126169 ATTGGTATGG
*
126179 TTTATATTAAATATAAATA-GA
1 TTTA-ATTAAATATAAAAATGA
126200 TTTAATTAAGAT-TAAAAATGA
1 TTTAATTAA-ATATAAAAATGA
126221 -TTAATTAAA
1 TTTAATTAAA
126230 GCTTAATGAT
Statistics
Matches: 27, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
19 1 0.04
20 18 0.67
21 8 0.30
ACGTcount: A:0.53, C:0.00, G:0.06, T:0.41
Consensus pattern (21 bp):
TTTAATTAAATATAAAAATGA
Found at i:138105 original size:7 final size:7
Alignment explanation
Indices: 138093--138124 Score: 64
Period size: 7 Copynumber: 4.6 Consensus size: 7
138083 CAAATCATCC
138093 CTCAACA
1 CTCAACA
138100 CTCAACA
1 CTCAACA
138107 CTCAACA
1 CTCAACA
138114 CTCAACA
1 CTCAACA
138121 CTCA
1 CTCA
138125 TCCTTCTTTC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 25 1.00
ACGTcount: A:0.41, C:0.44, G:0.00, T:0.16
Consensus pattern (7 bp):
CTCAACA
Found at i:152853 original size:21 final size:21
Alignment explanation
Indices: 152827--152867 Score: 82
Period size: 21 Copynumber: 2.0 Consensus size: 21
152817 CATTTGTAAA
152827 TAAATAAATAATTAGAACTTG
1 TAAATAAATAATTAGAACTTG
152848 TAAATAAATAATTAGAACTT
1 TAAATAAATAATTAGAACTT
152868 ATTTTTCTTA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.54, C:0.05, G:0.07, T:0.34
Consensus pattern (21 bp):
TAAATAAATAATTAGAACTTG
Found at i:163876 original size:29 final size:29
Alignment explanation
Indices: 163844--163986 Score: 80
Period size: 29 Copynumber: 4.9 Consensus size: 29
163834 AAAATCAAAC
*
163844 TTTTGGAAAATTTGAGGGCTAAATGGTAA
1 TTTTGGAAAATTTGAGGGCAAAATGGTAA
*** * *
163873 TTTTTGG-ATGCTCGAGGG-AGAAATAGTAA
1 -TTTTGGAAAATTTGAGGGCA-AAATGGTAA
163902 TTTTGGAAAAGTTT-AGGGTCAAAATGGTAA
1 TTTTGGAAAA-TTTGAGGG-CAAAATGGTAA
** * * *
163932 TTTTTGG-ATGTTCGAGAGTAAAATGGTAA
1 -TTTTGGAAAATTTGAGGGCAAAATGGTAA
*
163961 TTTTTGGAAAGTTT-AGGGTCAAAATG
1 -TTTTGGAAAATTTGAGGG-CAAAATG
163987 TATTTTTTTT
Statistics
Matches: 84, Mismatches: 20, Indels: 18
0.69 0.16 0.15
Matches are distributed among these distances:
28 6 0.07
29 42 0.50
30 29 0.35
31 7 0.08
ACGTcount: A:0.33, C:0.04, G:0.28, T:0.35
Consensus pattern (29 bp):
TTTTGGAAAATTTGAGGGCAAAATGGTAA
Found at i:163938 original size:59 final size:56
Alignment explanation
Indices: 163844--164053 Score: 196
Period size: 59 Copynumber: 3.6 Consensus size: 56
163834 AAAATCAAAC
*
163844 TTTTGGAAAA-TTTGAGGG-CTAAATGGTAATTTTTGGATGCTCGAGGGAGAAATAGTAA
1 TTTTGGAAAAGTTT-AGGGTCAAAAT-GTAATTTTTGGATGCTCGAGGGA-AAAT-GTAA
* *
163902 TTTTGGAAAAGTTTAGGGTCAAAATGGTAATTTTTGGATGTTCGAGAGTAAAATGGTAA
1 TTTTGGAAAAGTTTAGGGTCAAAAT-GTAATTTTTGGATGCTCGAG-GGAAAAT-GTAA
* * *
163961 TTTTTGG-AAAGTTTAGGGTCAAAATGTATTTTTTTTGAAGCTC-AGGGTTAAAATGTAA
1 -TTTTGGAAAAGTTTAGGGTCAAAATGTA-ATTTTTGGATGCTCGAGGG--AAAATGTAA
* *
164019 TTTT-TAGAAAGTTTAGAGGTTAAAATGTAATTTTT
1 TTTTGGA-AAAGTTTAG-GGTCAAAATGTAATTTTT
164054 AAGAAGTTTA
Statistics
Matches: 130, Mismatches: 12, Indels: 20
0.80 0.07 0.12
Matches are distributed among these distances:
57 5 0.04
58 37 0.28
59 80 0.62
60 8 0.06
ACGTcount: A:0.33, C:0.04, G:0.25, T:0.39
Consensus pattern (56 bp):
TTTTGGAAAAGTTTAGGGTCAAAATGTAATTTTTGGATGCTCGAGGGAAAATGTAA
Found at i:163995 original size:30 final size:29
Alignment explanation
Indices: 163893--164093 Score: 187
Period size: 30 Copynumber: 6.8 Consensus size: 29
163883 CTCGAGGGAG
*
163893 AAATAGTAA-TTTTGGAAAAGTTTAGGGTCA
1 AAAT-GTAATTTTTGG-AAAGTTTAGGGTTA
* * *
163923 AAATGGTAATTTTTGG-ATGTTCGAGAG-TA
1 AAAT-GTAATTTTTGGAAAGTT-TAGGGTTA
*
163952 AAATGGTAATTTTTGGAAAGTTTAGGGTCA
1 AAAT-GTAATTTTTGGAAAGTTTAGGGTTA
* * * *
163982 AAATGTATTTTTTTTG-AAGCTCAGGGTTA
1 AAATGTA-ATTTTTGGAAAGTTTAGGGTTA
*
164011 AAATGTAATTTTTAGAAAGTTTAGAGGTTA
1 AAATGTAATTTTTGGAAAGTTTAG-GGTTA
*
164041 AAATGTAATTTTT-AAGAAGTTTAGGGGTTA
1 AAATGTAATTTTTGGA-AAGTTTA-GGGTTA
164071 AAATGTAATTTTTGGAAAGTTTA
1 AAATGTAATTTTTGGAAAGTTTA
164094 ACTTCAAAAT
Statistics
Matches: 141, Mismatches: 20, Indels: 20
0.78 0.11 0.11
Matches are distributed among these distances:
28 6 0.04
29 51 0.36
30 76 0.54
31 8 0.06
ACGTcount: A:0.35, C:0.02, G:0.23, T:0.39
Consensus pattern (29 bp):
AAATGTAATTTTTGGAAAGTTTAGGGTTA
Found at i:164081 original size:60 final size:58
Alignment explanation
Indices: 163893--164093 Score: 219
Period size: 59 Copynumber: 3.4 Consensus size: 58
163883 CTCGAGGGAG
* * * *
163893 AAATAGTAA-TTTTGGAAAAGTTTAGGGTCAAAATGGTAATTTTT-GGATGTTCGAGAG-TA
1 AAAT-GTAATTTTTGG-AAAGTTTAGGGTCAAAAT-GTAATTTTTAAGAAGCTC-AGGGTTA
* **
163952 AAATGGTAATTTTTGGAAAGTTTAGGGTCAAAATGTATTTTTTTTGAAGCTCAGGGTTA
1 AAAT-GTAATTTTTGGAAAGTTTAGGGTCAAAATGTAATTTTTAAGAAGCTCAGGGTTA
* * * *
164011 AAATGTAATTTTTAGAAAGTTTAGAGGTTAAAATGTAATTTTTAAGAAGTTTAGGGGTTA
1 AAATGTAATTTTTGGAAAGTTTAG-GGTCAAAATGTAATTTTTAAGAAGCTCA-GGGTTA
164071 AAATGTAATTTTTGGAAAGTTTA
1 AAATGTAATTTTTGGAAAGTTTA
164094 ACTTCAAAAT
Statistics
Matches: 123, Mismatches: 14, Indels: 9
0.84 0.10 0.06
Matches are distributed among these distances:
58 30 0.24
59 59 0.48
60 34 0.28
ACGTcount: A:0.35, C:0.02, G:0.23, T:0.39
Consensus pattern (58 bp):
AAATGTAATTTTTGGAAAGTTTAGGGTCAAAATGTAATTTTTAAGAAGCTCAGGGTTA
Found at i:164667 original size:6 final size:6
Alignment explanation
Indices: 164656--164719 Score: 60
Period size: 6 Copynumber: 11.0 Consensus size: 6
164646 TTTTATGAAT
** * *
164656 TTTAAA TTTAAA AGTAAA ATTAAA CTT-AA TTTAAA TTTAAA TTTAAA
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA
**
164703 -ACAAA TTTAAA TTTAAA
1 TTTAAA TTTAAA TTTAAA
164720 ATAAATGTAA
Statistics
Matches: 47, Mismatches: 9, Indels: 4
0.78 0.15 0.07
Matches are distributed among these distances:
5 7 0.15
6 40 0.85
ACGTcount: A:0.55, C:0.03, G:0.02, T:0.41
Consensus pattern (6 bp):
TTTAAA
Found at i:164695 original size:17 final size:17
Alignment explanation
Indices: 164656--164747 Score: 94
Period size: 17 Copynumber: 5.4 Consensus size: 17
164646 TTTTATGAAT
*
164656 TTTAAATTTAAAAGTAAA
1 TTTAAACTTAAAA-TAAA
* **
164674 ATTAAACTTAATTTAAA
1 TTTAAACTTAAAATAAA
* *
164691 TTTAAATTTAAAACAAA
1 TTTAAACTTAAAATAAA
*
164708 TTTAAATTTAAAATAAA
1 TTTAAACTTAAAATAAA
* *
164725 TGTAATCTTAAAATAAA
1 TTTAAACTTAAAATAAA
164742 TTTAAA
1 TTTAAA
164748 AAAGGTATAG
Statistics
Matches: 59, Mismatches: 15, Indels: 1
0.79 0.20 0.01
Matches are distributed among these distances:
17 50 0.85
18 9 0.15
ACGTcount: A:0.55, C:0.03, G:0.02, T:0.39
Consensus pattern (17 bp):
TTTAAACTTAAAATAAA
Found at i:164696 original size:23 final size:23
Alignment explanation
Indices: 164659--164721 Score: 74
Period size: 23 Copynumber: 2.7 Consensus size: 23
164649 TATGAATTTT
**
164659 AAATTTAAAAGTAAAATT-AAAC
1 AAATTTAAATTTAAAATTAAAAC
* *
164681 TTAATTTAAATTTAAATTTAAAAC
1 -AAATTTAAATTTAAAATTAAAAC
164705 AAATTTAAATTTAAAAT
1 AAATTTAAATTTAAAAT
164722 AAATGTAATC
Statistics
Matches: 33, Mismatches: 6, Indels: 2
0.80 0.15 0.05
Matches are distributed among these distances:
23 29 0.88
24 4 0.12
ACGTcount: A:0.57, C:0.03, G:0.02, T:0.38
Consensus pattern (23 bp):
AAATTTAAATTTAAAATTAAAAC
Found at i:165720 original size:208 final size:207
Alignment explanation
Indices: 165306--168610 Score: 3563
Period size: 208 Copynumber: 15.9 Consensus size: 207
165296 TTTCAATTAG
* * * * * * * * *
165306 CTTCTCTATATCTCATTAGGAAGACGAATTTGGTCCACTTCGCAGTATCTCATCAGGAAGCTGAT
1 CTTCTCT-GATCTCATCAGGAAGACGGATCTGGTTCACTTCTCTGTATCTCATCAGGAAGGT-AA
*** * * * * *
165371 CATTTTATTACTTTGACCATGCTTTTCAGTATCTCATCAGGAAGCTAGGGTTCGAAG-TTTCACT
64 CCGCTTATTGCTTCGACC-TGCTTCTCAGTATCTCATCAGGAAGCTGGGGTTCGAAGATTT-GCT
* * * * * * * * *
165435 TACATCGAGCTTTGGCTTCATTAATTTGGTCTACTTCTTAGTATCTCATCAGGAAGATGACTGCA
127 CACTTTGAGC-CTGGTTTCATTGATTTGGTCTACTTCTCAGTATCTCATCAAGAAGATGACCGCA
*
165500 TCACTTGTTTTGATTCA
191 TCACTTGTTTTGATCCA
* *
165517 CTTCTCTGAGTCTCATTAGGAAGACGGATCTGGTTGACTTCTCTGTATCTCATCAGGAAGGTAAC
1 CTTCTCTGA-TCTCATCAGGAAGACGGATCTGGTTCACTTCTCTGTATCTCATCAGGAAGGTAAC
* *
165582 CGCCTATTGCTTCGACCTGCTTCTCAGTATCTCATCAGGAAGCTGGAGTTCGAAGATTTGCTCAC
65 CGCTTATTGCTTCGACCTGCTTCTCAGTATCTCATCAGGAAGCTGGGGTTCGAAGATTTGCTCAC
** * * *
165647 TTTGAGTTTGGTTTCATTGATTTGATCTACTTCTAAGTATCTCATCAGGAAGATGACCGCATCAC
130 TTTGAGCCTGGTTTCATTGATTTGGTCTACTTCTCAGTATCTCATCAAGAAGATGACCGCATCAC
165712 TTGTTTTGATCCA
195 TTGTTTTGATCCA
* * *
165725 CTTCTCT-ATGTCTTATCAAGAAGACGGATCTAGTTCACTTCTCT-TATCTCATCAGGAAGGTAA
1 CTTCTCTGA--TCTCATCAGGAAGACGGATCTGGTTCACTTCTCTGTATCTCATCAGGAAGGTAA
* * *
165788 CCGCTTTATTGCTTCGACCTGCTTCTCAGTATCTCATCAGGACGCTGAGGTTCAAAGATTTGCTC
64 CCGC-TTATTGCTTCGACCTGCTTCTCAGTATCTCATCAGGAAGCTGGGGTTCGAAGATTTGCTC
* * * * * *
165853 ACTTTGAGCTTGGTTTCATTTATTTGGTCTACTTCTCAATATCTTATCAGGAAGATGAACGCATC
128 ACTTTGAGCCTGGTTTCATTGATTTGGTCTACTTCTCAGTATCTCATCAAGAAGATGACCGCATC
* *
165918 ACTTTTTTTTATCCA
193 ACTTGTTTTGATCCA
* * * * * ** * * *
165933 CTTCTTTGTGTCTCATCAGGAAGATGGATCTGGTCCACTTTTCTACATATCATCAGGAAGTTGAC
1 CTTCTCTG-ATCTCATCAGGAAGACGGATCTGGTTCACTTCTCTGTATCTCATCAGGAAGGTAAC
*** * * * * *
165998 TATTTTATTGCTTAGAACTGCTTCTTAGTATCTCATAAGGAAGCTGGGGTTCGAAGATTAGCTCA
65 -CGCTTATTGCTTCGACCTGCTTCTCAGTATCTCATCAGGAAGCTGGGGTTCGAAGATTTGCTCA
* * * * * *
166063 CTTTGAGCCTAGTTTCATTGATTTGGTCGACTTCTCAATATCTCATCAGGAAGATGACCACCTCA
129 CTTTGAGCCTGGTTTCATTGATTTGGTCTACTTCTCAGTATCTCATCAAGAAGATGACCGCATCA
166128 -TTGTTTTGATCCA
194 CTTGTTTTGATCCA
* * * * *
166141 CTTTTCTGTACCTCATTAGGAAGACGGATTTGGTTCACTTCTCTATATCTCATCAGGAAGGTAAC
1 CTTCTCTG-ATCTCATCAGGAAGACGGATCTGGTTCACTTCTCTGTATCTCATCAGGAAGGTAAC
* * *
166206 CACTTTATTGCTTCGACCTGCTTCTCAGTATCAT-ATAAGGAAGCTGGGCTTCGAAGATTTGCTC
65 CGC-TTATTGCTTCGACCTGCTTCTCAGTATC-TCATCAGGAAGCTGGGGTTCGAAGATTTGCTC
* * *
166270 ACTTTGAGCCTAGTTTCATTGATTTGGTCTACTTCTCAGTATCTCATCAAGAAGATGATCGCTTC
128 ACTTTGAGCCTGGTTTCATTGATTTGGTCTACTTCTCAGTATCTCATCAAGAAGATGACCGCATC
*
166335 -GTTGTTTTGATCCA
193 ACTTGTTTTGATCCA
* * * * * * ** * *
166349 CTTCTCCGTATCTCATCAAGAAGACGGATCTGGTCCACTTTTCTGCATCTCATTAAAAAGCTGAC
1 CTTCTCTG-ATCTCATCAGGAAGACGGATCTGGTTCACTTCTCTGTATCTCATCAGGAAGGTAAC
** * * * *
166414 CATTTTATTGCATCGACTTGCTTC-CTAGTATTTCATCAGGAAGTTGGGGTTCGAAGATTTGCTC
65 C-GCTTATTGCTTCGACCTGCTTCTC-AGTATCTCATCAGGAAGCTGGGGTTCGAAGATTTGCTC
* * * *
166478 ACTTTGAGTCTGGTTTCGTTGGTTTGGTCTACTTCTCAGTATCTCATCAAGAAGATGACTGTC-T
128 ACTTTGAGCCTGGTTTCATTGATTTGGTCTACTTCTCAGTATCTCATCAAGAAGATGACCG-CAT
166542 CA-TTGTTTTGATCCA
192 CACTTGTTTTGATCCA
*
166557 CTTCTCTGTATCTCATCAGGAAGACGGATCTGGTTCACTTCTCTATATCTCATCAGGAAGGTAAC
1 CTTCTCTG-ATCTCATCAGGAAGACGGATCTGGTTCACTTCTCTGTATCTCATCAGGAAGGTAAC
* * * *
166622 CGCTTTATTGCTTCGACCTGCTTCTCAGTATCTCATAAGGAAACTAGGGTTCGAAGATTTGTTCA
65 CGC-TTATTGCTTCGACCTGCTTCTCAGTATCTCATCAGGAAGCTGGGGTTCGAAGATTTGCTCA
* * * * * * *
166687 CTTTGAGCTTGGTTTCATTGATTTGGTCTGCTTTTCAGTATCTCATTAGGGAA-ATGATCGCCTC
129 CTTTGAGCCTGGTTTCATTGATTTGGTCTACTTCTCAGTATCTCATCA-AGAAGATGACCGCATC
* *
166751 -GTTATTTTGATCCA
193 ACTTGTTTTGATCCA
* * * ** * * *
166765 CTTCTCTATATCTCATTAAGAAGACAAATCTGATTCACATCTCTGTATCTCATCAAGAAGGTAAC
1 CTTCTCT-GATCTCATCAGGAAGACGGATCTGGTTCACTTCTCTGTATCTCATCAGGAAGGTAAC
** * * * **
166830 CGCTTTATTGCTTAAACCTGATTCTCAATATCTCATAAGGAAAAT-GGGTTCGAAGATTTGCTCA
65 CGC-TTATTGCTTCGACCTGCTTCTCAGTATCTCATCAGGAAGCTGGGGTTCGAAGATTTGCTCA
* * * *
166894 CTTTAAGCCTGGTTTCATTTATTTGGTCTACTTCTCAATATCTAATCAAGAAGATGACCGCATCA
129 CTTTGAGCCTGGTTTCATTGATTTGGTCTACTTCTCAGTATCTCATCAAGAAGATGACCGCATCA
* *
166959 CTTATTTTGATCAA
194 CTTGTTTTGATCCA
* * * * * ** * *
166973 CTTCTCTGTGTCTCATCAGGAAGACAGATCGGGTCCA-TTTTCTACATCTCATCAGGAAGCTGAC
1 CTTCTCTG-ATCTCATCAGGAAGACGGATCTGGTTCACTTCTCTGTATCTCATCAGGAAGGTAAC
** * * * *
167037 CATTTTATTGCTTCGACCTGCTTCTTAGTATTTCATCAGGAAGTTGGGCTTCGAAGATTTGCTCA
65 C-GCTTATTGCTTCGACCTGCTTCTCAGTATCTCATCAGGAAGCTGGGGTTCGAAGATTTGCTCA
* * * * * * * *
167102 CTTTGTGCCTAGTTTCGTTGATTTGGTCTACTTCTAAGTATCTCATCAGGAACATGATCGCCTCA
129 CTTTGAGCCTGGTTTCATTGATTTGGTCTACTTCTCAGTATCTCATCAAGAAGATGACCGCATCA
*
167167 -TTATTTTGATCCA
194 CTTGTTTTGATCCA
* * * *
167180 CTTCTCTGTATCTCATCATGAAGACGGATCTGGTTCACTTCTATTTATCTCATCAAGAAGGTAAC
1 CTTCTCTG-ATCTCATCAGGAAGACGGATCTGGTTCACTTCTCTGTATCTCATCAGGAAGGTAAC
* * * *
167245 TGCTTCATTACTTCGACCTGCTTCTCAGTATCTCATAAGGAAGCTGAGGTTCGAAGATTTGCTCA
65 CGCTT-ATTGCTTCGACCTGCTTCTCAGTATCTCATCAGGAAGCTGGGGTTCGAAGATTTGCTCA
* ** *
167310 CTTTGAGCCTAGTTTCATTGATTTGGTCTACTTCTCAGTATCTCATCAAGAAGATGATAGCCTC-
129 CTTTGAGCCTGGTTTCATTGATTTGGTCTACTTCTCAGTATCTCATCAAGAAGATGACCGCATCA
*
167374 GTTGTTTTGATCCA
194 CTTGTTTTGATCCA
* * *
167388 CTTCTCT-ATTCTCATCAGGAAGACGGATCTGGTTCACTTCTTTGTATCTTATCAGAAAGGTAAC
1 CTTCTCTGA-TCTCATCAGGAAGACGGATCTGGTTCACTTCTCTGTATCTCATCAGGAAGGTAAC
* * * * * *
167452 CACTTTATTGCTTGGACTTACTTCTCAGTATTTCATCAGGAAGCTGGGGTTCGAAGATTTGCTTA
65 CGC-TTATTGCTTCGACCTGCTTCTCAGTATCTCATCAGGAAGCTGGGGTTCGAAGATTTGCTCA
* * *
167517 CTTTGAGTCTGGTTTCATTTATTTGGTCTACTTCTCAGTATCTCATCAGGAAGATGACCGCATCA
129 CTTTGAGCCTGGTTTCATTGATTTGGTCTACTTCTCAGTATCTCATCAAGAAGATGACCGCATCA
167582 CTTGTTTTGATCCA
194 CTTGTTTTGATCCA
* * * * * *
167596 CTTCTCT-ATGTCTCATCAGGAAGACGGATCTGGTCCACTTTTTTGCATCTCATC-GAGAAGCTG
1 CTTCTCTGA--TCTCATCAGGAAGACGGATCTGGTTCACTTCTCTGTATCTCATCAG-GAAGGTA
** * * *
167659 ACCATTTTATTACTTCGACCTGCTTCTCAGTATCTCATCAGGAAGATGGGGTTCAAAGATTTGCT
63 ACC-GCTTATTGCTTCGACCTGCTTCTCAGTATCTCATCAGGAAGCTGGGGTTCGAAGATTTGCT
* * * * * *
167724 CAC-TTGAGCATGGTTTCGTTAATTTGATCTACTTCTCAGTATCTCATCAAGAAGATGACCACCT
127 CACTTTGAGCCTGGTTTCATTGATTTGGTCTACTTCTCAGTATCTCATCAAGAAGATGACCGCAT
*
167788 C-GTTGTTTTGATCCA
192 CACTTGTTTTGATCCA
* *
167803 CTTCTCTGTATCTCATCAGGAAGACAGATCTGGTTCACTTCTCTGTATCTCATCAAGAAGGTAAC
1 CTTCTCTG-ATCTCATCAGGAAGACGGATCTGGTTCACTTCTCTGTATCTCATCAGGAAGGTAAC
* * * * *
167868 TGTTTTATTGCTTCAACCTGCTTCTCAATATCTCATAAGGAAGCTGGGGTTCGAAGATTTGCTCA
65 CG-CTTATTGCTTCGACCTGCTTCTCAGTATCTCATCAGGAAGCTGGGGTTCGAAGATTTGCTCA
* * * *
167933 CTTTGAGCCTTGTTTCATTGATTTGGTCTACTTCTCAGTATCTCATCAAGAAGATGATCGCCTCT
129 CTTTGAGCCTGGTTTCATTGATTTGGTCTACTTCTCAGTATCTCATCAAGAAGATGACCGCATCA
167998 C-TGTTTTGATCCA
194 CTTGTTTTGATCCA
* * *
168011 CTTCTTTGTATCTCATCAGGAAGACGGATCTGGTACACTTCTTTGTATCTCATCAGGAAGGTAAC
1 CTTCTCTG-ATCTCATCAGGAAGACGGATCTGGTTCACTTCTCTGTATCTCATCAGGAAGGTAAC
* * * *
168076 CACTTTATTACTTCGACCTGCTTCTCAGTATCTTATCAGGAAGCTGGGGTTCGAAGATTTGCTTA
65 CGC-TTATTGCTTCGACCTGCTTCTCAGTATCTCATCAGGAAGCTGGGGTTCGAAGATTTGCTCA
* * * * * *
168141 CTTTGTG-TTCGGTTTCATTTATTTGGCCTACTTCTCTGTATCTCATCAAGAAGATGACTGCATC
129 CTTTGAGCCT-GGTTTCATTGATTTGGTCTACTTCTCAGTATCTCATCAAGAAGATGACCGCATC
168205 ACTTGTTTTGATCCA
193 ACTTGTTTTGATCCA
* * * * * * * *
168220 CTTCTCT-ATGTCTCATCAAGAGGACGGATCTGGTCCAATT-TCATGCATCTCATCAAGAAGCTG
1 CTTCTCTGA--TCTCATCAGGAAGACGGATCTGGTTCACTTCTC-TGTATCTCATCAGGAAGGTA
** * * *
168283 ACCATTTTGTTTCTTCGA-CTAGCTTCTCAGTATCTCATCAGTAAGCTGGGGTTCGAAGATTTGC
63 ACC-GCTTATTGCTTCGACCT-GCTTCTCAGTATCTCATCAGGAAGCTGGGGTTCGAAGATTTGC
* * * *
168347 TCACTTTGAGCCTGGTTTCGTTGATTTGGTCTACTTCTAAGTATCTCATCAGGAAGATGATCGCA
126 TCACTTTGAGCCTGGTTTCATTGATTTGGTCTACTTCTCAGTATCTCATCAAGAAGATGACCGCA
* * * *
168412 TC-GTTATTTTGGTCTA
191 TCACTTGTTTTGATCCA
* * * * *
168428 CTACTCTGTATCAT-ATCAGGAAGATGGATCCGGTTCACTTCTTTGTATCTCATCAAG-AGTGTA
1 CTTCTCTG-ATC-TCATCAGGAAGACGGATCTGGTTCACTTCTCTGTATCTCATCAGGAAG-GTA
* * * * **
168491 ACCGCTTTATTGCTTTGACCTGCTTCTTAGTATCTCATAAGGAAACT-AAGTTCGAAGATTTGCT
63 ACCGC-TTATTGCTTCGACCTGCTTCTCAGTATCTCATCAGGAAGCTGGGGTTCGAAGATTTGCT
* * * * *
168555 CACTTTGAGTCTAGTTTCATTGATTTGGTCTAGTTATCAATATCTCATCAAGAAGA
127 CACTTTGAGCCTGGTTTCATTGATTTGGTCTACTTCTCAGTATCTCATCAAGAAGA
168611 CGGATCTGGT
Statistics
Matches: 2610, Mismatches: 426, Indels: 120
0.83 0.13 0.04
Matches are distributed among these distances:
206 4 0.00
207 541 0.21
208 1545 0.59
209 449 0.17
210 19 0.01
211 52 0.02
ACGTcount: A:0.23, C:0.22, G:0.18, T:0.37
Consensus pattern (207 bp):
CTTCTCTGATCTCATCAGGAAGACGGATCTGGTTCACTTCTCTGTATCTCATCAGGAAGGTAACC
GCTTATTGCTTCGACCTGCTTCTCAGTATCTCATCAGGAAGCTGGGGTTCGAAGATTTGCTCACT
TTGAGCCTGGTTTCATTGATTTGGTCTACTTCTCAGTATCTCATCAAGAAGATGACCGCATCACT
TGTTTTGATCCA
Found at i:166707 original size:624 final size:622
Alignment explanation
Indices: 165306--168610 Score: 4113
Period size: 624 Copynumber: 5.3 Consensus size: 622
165296 TTTCAATTAG
* * * * * * * * *
165306 CTTCTCTATATCTCATTAGGAAGACGAATTTGGTCCACTTCGC-AGTATCTCATCAGGAAGCTGA
1 CTTCTCTGTATCTCATCAGGAAGACGGATCTGGTTCACTTCTCTA-TATCTCATCAAGAAGGTAA
* ** * * * * *
165370 TCATTTTATTACTTTGACCATGCTTTTCAGTATCTCATCAGGAAGCTAGGGTTCGAAG-TTTCAC
65 CCGCTTTATTGCTTCGACC-TGCTTCTCAGTATCTCATAAGGAAGCTAGGGTTCGAAGATTT-GC
* * * * * * * * *
165434 TTACATCGAGCTTTGGCTTCATTAATTTGGTCTACTTCTTAGTATCTCATCAGGAAGATGACTGC
128 TCACTTTGAGC-TTAGTTTCATTGATTTGGTCTACTTCTCAGTATCTCATCAAGAAGATGACCGC
* * *
165499 ATCACTTGTTTTGATTCACTTCTCTG-AGTCTCATTAGGAAGACGGATCTGGTTGACTTCTCTGT
192 CTCA-TTGTTTTGATCCACTTCTCTGTA-TCTCATTAGGAAGACGGATCTGGTTCACTTCTCTGT
* *
165563 ATCTCATCAGGAAGGTAACCGC-CTATTGCTTCGACCTGCTTCTCAGTATCTCATCAGGAAGCTG
255 ATCTCATCAGGAAGGTAACCACTTTATTGCTTCGACCTGCTTCTCAGTATCTCATCAGGAAGCTG
** * * *
165627 GAGTTCGAAGATTTGCTCACTTTGAGTTTGGTTTCATTGATTTGATCTACTTCTAAGTATCTCAT
320 G-GTTCGAAGATTTGCTCACTTTGAGCCTGGTTTCATTTATTTGGTCTACTTCTCAGTATCTCAT
* * *
165692 CAGGAAGATGACCGCATCACTTGTTTTGATCCACTTCTCTATGTCTTATCAAGAAGACGGATCTA
384 CAAGAAGATGACCGCATCACTTGTTTTGATCCACTTCTCTATGTCTCATCAAGAAGACGGATCTG
* * * * * * **
165757 GTTCACTTCTCT-TATCTCATCAGGAAGGTAACCGCTTTATTGCTTCGACCTGCTTCTCAGTATC
449 GTCCACTTTTCTGCATCTCATCAAGAAGCTGACCATTTTATTGCTTCGACCTGCTTCTCAGTATC
* * * * *
165821 TCATCAGGACGCTGAGGTTCAAAGATTTGCTCACTTTGAGCTTGGTTTCATTTATTTGGTCTACT
514 TCATCAGGAAGCTGGGGTTCGAAGATTTGCTCACTTTGAGC-TGGTTTCGTTGATTTGGTCTACT
* * * *
165886 TCTCAATATCTTATCAGGAAGATGAAC-GCATCACTTTTTTTTATCCA
578 TCTCAGTATCTCATCAGGAAGATG-ACTGC-TCA-TTATTTTGATCCA
* * * * * * * * * *
165933 CTTCTTTGTGTCTCATCAGGAAGATGGATCTGGTCCACTTTTCTACATATCATCAGGAAGTTGAC
1 CTTCTCTGTATCTCATCAGGAAGACGGATCTGGTTCACTTCTCTATATCTCATCAAGAAGGTAAC
*** * * * * *
165998 TATTTTATTGCTTAGAACTGCTTCTTAGTATCTCATAAGGAAGCTGGGGTTCGAAGATTAGCTCA
66 CGCTTTATTGCTTCGACCTGCTTCTCAGTATCTCATAAGGAAGCTAGGGTTCGAAGATTTGCTCA
* * * * *
166063 CTTTGAGCCTAGTTTCATTGATTTGGTCGACTTCTCAATATCTCATCAGGAAGATGACCACCTCA
131 CTTTGAGCTTAGTTTCATTGATTTGGTCTACTTCTCAGTATCTCATCAAGAAGATGACCGCCTCA
* * * *
166128 TTGTTTTGATCCACTTTTCTGTACCTCATTAGGAAGACGGATTTGGTTCACTTCTCTATATCTCA
196 TTGTTTTGATCCACTTCTCTGTATCTCATTAGGAAGACGGATCTGGTTCACTTCTCTGTATCTCA
*
166193 TCAGGAAGGTAACCACTTTATTGCTTCGACCTGCTTCTCAGTATCAT-ATAAGGAAGCTGGGCTT
261 TCAGGAAGGTAACCACTTTATTGCTTCGACCTGCTTCTCAGTATC-TCATCAGGAAGCTGGG-TT
* *
166257 CGAAGATTTGCTCACTTTGAGCCTAGTTTCATTGATTTGGTCTACTTCTCAGTATCTCATCAAGA
324 CGAAGATTTGCTCACTTTGAGCCTGGTTTCATTTATTTGGTCTACTTCTCAGTATCTCATCAAGA
* * * ** *
166322 AGATGATCGCTTC-GTTGTTTTGATCCACTTCTCCGTATCTCATCAAGAAGACGGATCTGGTCCA
389 AGATGACCGCATCACTTGTTTTGATCCACTTCTCTATGTCTCATCAAGAAGACGGATCTGGTCCA
* * * * *
166386 CTTTTCTGCATCTCATTAAAAAGCTGACCATTTTATTGCATCGACTTGCTTC-CTAGTATTTCAT
454 CTTTTCTGCATCTCATCAAGAAGCTGACCATTTTATTGCTTCGACCTGCTTCTC-AGTATCTCAT
* *
166450 CAGGAAGTTGGGGTTCGAAGATTTGCTCACTTTGAGTCTGGTTTCGTTGGTTTGGTCTACTTCTC
518 CAGGAAGCTGGGGTTCGAAGATTTGCTCACTTTGAG-CTGGTTTCGTTGATTTGGTCTACTTCTC
* *
166515 AGTATCTCATCAAGAAGATGACTGTCTCATTGTTTTGATCCA
582 AGTATCTCATCAGGAAGATGACTG-CTCATTATTTTGATCCA
*
166557 CTTCTCTGTATCTCATCAGGAAGACGGATCTGGTTCACTTCTCTATATCTCATCAGGAAGGTAAC
1 CTTCTCTGTATCTCATCAGGAAGACGGATCTGGTTCACTTCTCTATATCTCATCAAGAAGGTAAC
* *
166622 CGCTTTATTGCTTCGACCTGCTTCTCAGTATCTCATAAGGAAACTAGGGTTCGAAGATTTGTTCA
66 CGCTTTATTGCTTCGACCTGCTTCTCAGTATCTCATAAGGAAGCTAGGGTTCGAAGATTTGCTCA
* * * * * *
166687 CTTTGAGCTTGGTTTCATTGATTTGGTCTGCTTTTCAGTATCTCATTAGGGAA-ATGATCGCCTC
131 CTTTGAGCTTAGTTTCATTGATTTGGTCTACTTCTCAGTATCTCATCA-AGAAGATGACCGCCTC
* * * * ** * *
166751 GTTATTTTGATCCACTTCTCTATATCTCATTAAGAAGACAAATCTGATTCACATCTCTGTATCTC
195 ATTGTTTTGATCCACTTCTCTGTATCTCATTAGGAAGACGGATCTGGTTCACTTCTCTGTATCTC
* * ** * * * **
166816 ATCAAGAAGGTAACCGCTTTATTGCTTAAACCTGATTCTCAATATCTCATAAGGAAAATGGGTTC
260 ATCAGGAAGGTAACCACTTTATTGCTTCGACCTGCTTCTCAGTATCTCATCAGGAAGCTGGGTTC
* * *
166881 GAAGATTTGCTCACTTTAAGCCTGGTTTCATTTATTTGGTCTACTTCTCAATATCTAATCAAGAA
325 GAAGATTTGCTCACTTTGAGCCTGGTTTCATTTATTTGGTCTACTTCTCAGTATCTCATCAAGAA
* * * * * *
166946 GATGACCGCATCACTTATTTTGATCAACTTCTCTGTGTCTCATCAGGAAGACAGATCGGGTCCA-
390 GATGACCGCATCACTTGTTTTGATCCACTTCTCTATGTCTCATCAAGAAGACGGATCTGGTCCAC
* * * *
167010 TTTTCTACATCTCATCAGGAAGCTGACCATTTTATTGCTTCGACCTGCTTCTTAGTATTTCATCA
455 TTTTCTGCATCTCATCAAGAAGCTGACCATTTTATTGCTTCGACCTGCTTCTCAGTATCTCATCA
* * * * *
167075 GGAAGTTGGGCTTCGAAGATTTGCTCACTTTGTGCCTAGTTTCGTTGATTTGGTCTACTTCTAAG
520 GGAAGCTGGGGTTCGAAGATTTGCTCACTTTGAG-CTGGTTTCGTTGATTTGGTCTACTTCTCAG
*
167140 TATCTCATCAGGAACATGA-TCGCCTCATTATTTTGATCCA
584 TATCTCATCAGGAAGATGACT-G-CTCATTATTTTGATCCA
* * *
167180 CTTCTCTGTATCTCATCATGAAGACGGATCTGGTTCACTTCTATTTATCTCATCAAGAAGGTAAC
1 CTTCTCTGTATCTCATCAGGAAGACGGATCTGGTTCACTTCTCTATATCTCATCAAGAAGGTAAC
* * *
167245 TGCTTCATTACTTCGACCTGCTTCTCAGTATCTCATAAGGAAGCT-GAGGTTCGAAGATTTGCTC
66 CGCTTTATTGCTTCGACCTGCTTCTCAGTATCTCATAAGGAAGCTAG-GGTTCGAAGATTTGCTC
* **
167309 ACTTTGAGCCTAGTTTCATTGATTTGGTCTACTTCTCAGTATCTCATCAAGAAGATGATAGCCTC
130 ACTTTGAGCTTAGTTTCATTGATTTGGTCTACTTCTCAGTATCTCATCAAGAAGATGACCGCCTC
* * * * *
167374 GTTGTTTTGATCCACTTCTCTAT-TCTCATCAGGAAGACGGATCTGGTTCACTTCTTTGTATCTT
195 ATTGTTTTGATCCACTTCTCTGTATCTCATTAGGAAGACGGATCTGGTTCACTTCTCTGTATCTC
* * * * *
167438 ATCAGAAAGGTAACCACTTTATTGCTTGGACTTACTTCTCAGTATTTCATCAGGAAGCTGGGGTT
260 ATCAGGAAGGTAACCACTTTATTGCTTCGACCTGCTTCTCAGTATCTCATCAGGAAGCT-GGGTT
* * *
167503 CGAAGATTTGCTTACTTTGAGTCTGGTTTCATTTATTTGGTCTACTTCTCAGTATCTCATCAGGA
324 CGAAGATTTGCTCACTTTGAGCCTGGTTTCATTTATTTGGTCTACTTCTCAGTATCTCATCAAGA
*
167568 AGATGACCGCATCACTTGTTTTGATCCACTTCTCTATGTCTCATCAGGAAGACGGATCTGGTCCA
389 AGATGACCGCATCACTTGTTTTGATCCACTTCTCTATGTCTCATCAAGAAGACGGATCTGGTCCA
* * *
167633 CTTTTTTGCATCTCATCGAGAAGCTGACCATTTTATTACTTCGACCTGCTTCTCAGTATCTCATC
454 CTTTTCTGCATCTCATCAAGAAGCTGACCATTTTATTGCTTCGACCTGCTTCTCAGTATCTCATC
* * * *
167698 AGGAAGATGGGGTTCAAAGATTTGCTCAC-TTGAGCATGGTTTCGTTAATTTGATCTACTTCTCA
519 AGGAAGCTGGGGTTCGAAGATTTGCTCACTTTGAGC-TGGTTTCGTTGATTTGGTCTACTTCTCA
* ** * *
167762 GTATCTCATCAAGAAGATGACCACCTCGTTGTTTTGATCCA
583 GTATCTCATCAGGAAGATGA-CTGCTCATTATTTTGATCCA
* *
167803 CTTCTCTGTATCTCATCAGGAAGACAGATCTGGTTCACTTCTCTGTATCTCATCAAGAAGGTAAC
1 CTTCTCTGTATCTCATCAGGAAGACGGATCTGGTTCACTTCTCTATATCTCATCAAGAAGGTAAC
* * * * *
167868 TGTTTTATTGCTTCAACCTGCTTCTCAATATCTCATAAGGAAGCTGGGGTTCGAAGATTTGCTCA
66 CGCTTTATTGCTTCGACCTGCTTCTCAGTATCTCATAAGGAAGCTAGGGTTCGAAGATTTGCTCA
*
167933 CTTTGAGCCTT-GTTTCATTGATTTGGTCTACTTCTCAGTATCTCATCAAGAAGATGATCGCCTC
131 CTTTGAG-CTTAGTTTCATTGATTTGGTCTACTTCTCAGTATCTCATCAAGAAGATGACCGCCTC
* * * *
167997 -TCTGTTTTGATCCACTTCTTTGTATCTCATCAGGAAGACGGATCTGGTACACTTCTTTGTATCT
195 AT-TGTTTTGATCCACTTCTCTGTATCTCATTAGGAAGACGGATCTGGTTCACTTCTCTGTATCT
* *
168061 CATCAGGAAGGTAACCACTTTATTACTTCGACCTGCTTCTCAGTATCTTATCAGGAAGCTGGGGT
259 CATCAGGAAGGTAACCACTTTATTGCTTCGACCTGCTTCTCAGTATCTCATCAGGAAGCT-GGGT
* * * * *
168126 TCGAAGATTTGCTTACTTTGTG-TTCGGTTTCATTTATTTGGCCTACTTCTCTGTATCTCATCAA
323 TCGAAGATTTGCTCACTTTGAGCCT-GGTTTCATTTATTTGGTCTACTTCTCAGTATCTCATCAA
* *
168190 GAAGATGACTGCATCACTTGTTTTGATCCACTTCTCTATGTCTCATCAAGAGGACGGATCTGGTC
387 GAAGATGACCGCATCACTTGTTTTGATCCACTTCTCTATGTCTCATCAAGAAGACGGATCTGGTC
* * *
168255 CA-ATTTCATGCATCTCATCAAGAAGCTGACCATTTTGTTTCTTCGA-CTAGCTTCTCAGTATCT
452 CACTTTTC-TGCATCTCATCAAGAAGCTGACCATTTTATTGCTTCGACCT-GCTTCTCAGTATCT
*
168318 CATCAGTAAGCTGGGGTTCGAAGATTTGCTCACTTTGAGCCTGGTTTCGTTGATTTGGTCTACTT
515 CATCAGGAAGCTGGGGTTCGAAGATTTGCTCACTTTGAG-CTGGTTTCGTTGATTTGGTCTACTT
* * * *
168383 CTAAGTATCTCATCAGGAAGATGA-TCGCATCGTTATTTTGGTCTA
579 CTCAGTATCTCATCAGGAAGATGACT-GC-TCATTATTTTGATCCA
* * * * *
168428 CTACTCTGTATCAT-ATCAGGAAGATGGATCCGGTTCACTTCTTTGTATCTCATCAAG-AGTGTA
1 CTTCTCTGTATC-TCATCAGGAAGACGGATCTGGTTCACTTCTCTATATCTCATCAAGAAG-GTA
* * * *
168491 ACCGCTTTATTGCTTTGACCTGCTTCTTAGTATCTCATAAGGAAACTA-AGTTCGAAGATTTGCT
64 ACCGCTTTATTGCTTCGACCTGCTTCTCAGTATCTCATAAGGAAGCTAGGGTTCGAAGATTTGCT
* * *
168555 CACTTTGAG-TCTAGTTTCATTGATTTGGTCTAGTTATCAATATCTCATCAAGAAGA
129 CACTTTGAGCT-TAGTTTCATTGATTTGGTCTACTTCTCAGTATCTCATCAAGAAGA
168611 CGGATCTGGT
Statistics
Matches: 2342, Mismatches: 298, Indels: 79
0.86 0.11 0.03
Matches are distributed among these distances:
622 87 0.04
623 807 0.34
624 895 0.38
625 438 0.19
626 48 0.02
627 66 0.03
628 1 0.00
ACGTcount: A:0.23, C:0.22, G:0.18, T:0.37
Consensus pattern (622 bp):
CTTCTCTGTATCTCATCAGGAAGACGGATCTGGTTCACTTCTCTATATCTCATCAAGAAGGTAAC
CGCTTTATTGCTTCGACCTGCTTCTCAGTATCTCATAAGGAAGCTAGGGTTCGAAGATTTGCTCA
CTTTGAGCTTAGTTTCATTGATTTGGTCTACTTCTCAGTATCTCATCAAGAAGATGACCGCCTCA
TTGTTTTGATCCACTTCTCTGTATCTCATTAGGAAGACGGATCTGGTTCACTTCTCTGTATCTCA
TCAGGAAGGTAACCACTTTATTGCTTCGACCTGCTTCTCAGTATCTCATCAGGAAGCTGGGTTCG
AAGATTTGCTCACTTTGAGCCTGGTTTCATTTATTTGGTCTACTTCTCAGTATCTCATCAAGAAG
ATGACCGCATCACTTGTTTTGATCCACTTCTCTATGTCTCATCAAGAAGACGGATCTGGTCCACT
TTTCTGCATCTCATCAAGAAGCTGACCATTTTATTGCTTCGACCTGCTTCTCAGTATCTCATCAG
GAAGCTGGGGTTCGAAGATTTGCTCACTTTGAGCTGGTTTCGTTGATTTGGTCTACTTCTCAGTA
TCTCATCAGGAAGATGACTGCTCATTATTTTGATCCA
Found at i:168634 original size:159 final size:160
Alignment explanation
Indices: 168442--168770 Score: 491
Period size: 159 Copynumber: 2.1 Consensus size: 160
168432 TCTGTATCAT
* *
168442 ATCAGGAAGATGGATCCGGTTCACTTCTTTGTATCTCATCAAG-AGTGTAACCGCTTTATTGCTT
1 ATCAGGAAGACGGATCCGGTTCACTTCTCTGTATCTCATCAAGAAG-GTAACCGCTTTATTGCTT
* * *
168506 TGACCTGCTTCTTAGTATCTCATAAGGAAACTA-AGTTCGAAGATTTGCTCACTTTGAGTCTAGT
65 CGACCTACTTCTTAGTATCTCATAAGGAAACTAGAGTTCGAAGATTTGCTCACTTTGAGCCTAGT
*
168570 TTCATTGATTTGGTCTAGTTATCAATATCTC
130 TTCATTGAGTTGGTCTAGTTATCAATATCTC
* * *
168601 ATCAAGAAGACGGATCTGGTTCACTTCTCTGTATCTCATCAGGAAGGTAACCGCTTTATTGCTTC
1 ATCAGGAAGACGGATCCGGTTCACTTCTCTGTATCTCATCAAGAAGGTAACCGCTTTATTGCTTC
* * * *
168666 GACCTACTTCTTAGTATCTCATAAGGAAGCTAGGGTTCGAAGATTTTCTCACTTTGAGCCTGGTT
66 GACCTACTTCTTAGTATCTCATAAGGAAACTAGAGTTCGAAGATTTGCTCACTTTGAGCCTAGTT
* * *
168731 TCATTGAGTTGGTCTATTTCTCAGTATCTC
131 TCATTGAGTTGGTCTAGTTATCAATATCTC
168761 ATCAGGAAGA
1 ATCAGGAAGA
168771 TGATCACCTC
Statistics
Matches: 151, Mismatches: 17, Indels: 3
0.88 0.10 0.02
Matches are distributed among these distances:
159 86 0.57
160 65 0.43
ACGTcount: A:0.24, C:0.20, G:0.19, T:0.36
Consensus pattern (160 bp):
ATCAGGAAGACGGATCCGGTTCACTTCTCTGTATCTCATCAAGAAGGTAACCGCTTTATTGCTTC
GACCTACTTCTTAGTATCTCATAAGGAAACTAGAGTTCGAAGATTTGCTCACTTTGAGCCTAGTT
TCATTGAGTTGGTCTAGTTATCAATATCTC
Found at i:168962 original size:208 final size:207
Alignment explanation
Indices: 168595--173849 Score: 4993
Period size: 208 Copynumber: 25.3 Consensus size: 207
168585 TAGTTATCAA
* *
168595 TATCTCATCAAGAAGACGGATCTGGTTCACTTCTCTGTATCTCATCAGGAAGGTAACCGCTTTAT
1 TATCTCATCAGGAAGACGGATCTGGTTCACTTCTCTGTATCTCATCAGGAAGGTGACCGCTTTAT
* * * * *
168660 TGCTTCGACCTACTTCTTAGTATCTCATAAGGAAGCTAGGGTTCGAAGATTTTCTCACTTTGAGC
66 TGCTTCGACCTGCTTCTCAGTATCTCATCAGGAAGCTGGGGTTCGAAG-TTTGCTCACTTTGAGC
* * * * * * *
168725 CTGGTTTCATTGAGTTGGTCTATTTCTCAGTATCTCATCAGGAAGATGATCACCTCGTTTTTTTG
130 TTGGTTTCATTGATTTGGTCTACTTCTCAGTATCTCATCAGGAAGATGACCGCCTCCTTGTTTTG
*
168790 ATCCACTTCTATG
195 ATCCACTTCTCTG
** ** *
168803 TATCTCATCAGGAAGACGGATCTGGTTCACTTCTCTACATCTCATCAAAAAGGTAACCGCTTTAT
1 TATCTCATCAGGAAGACGGATCTGGTTCACTTCTCTGTATCTCATCAGGAAGGTGACCGCTTTAT
** * * * * *
168868 TTTTTTGACTTGCTTCTCAGTATCTCATCAGAAAGTTGGGGTTTGAAGTTTCGCTCACTTTGAGC
66 TGCTTCGACCTGCTTCTCAGTATCTCATCAGGAAGCTGGGGTTCGAAGTTT-GCTCACTTTGAGC
* * *
168933 TTGGTTTCATTGATTTGATCTACTTCTCAGTATCTCATCAAGAAGATGACCGCCTCGTTGTTTTG
130 TTGGTTTCATTGATTTGGTCTACTTCTCAGTATCTCATCAGGAAGATGACCGCCTCCTTGTTTTG
*
168998 ATCCACTTCTTTG
195 ATCCACTTCTCTG
* ** * * * * **
169011 TATCTCATAATAAAGTCGGATCTGGTTTACTTCTCTATATCTCATGAGGAAGACGACCGCTTTAT
1 TATCTCATCAGGAAGACGGATCTGGTTCACTTCTCTGTATCTCATCAGGAAGGTGACCGCTTTAT
* * * * * * *
169076 TGCTTC-ATCCTGCTTCTTAGTATCTCATTAGAAAGCTAGGGTTCGAAGTTTCACTCGCATTGAG
66 TGCTTCGA-CCTGCTTCTCAGTATCTCATCAGGAAGCTGGGGTTCGAAGTTT-GCTCACTTTGAG
* * * * * *
169140 CTTTGGTCTCATTGATTTGGTCTAATTCTTAGTATCGCATTAGGAAGATGACCGCATCACTTGTT
129 C-TTGGTTTCATTGATTTGGTCTACTTCTCAGTATCTCATCAGGAAGATGACCGCCTC-CTTGTT
*** * *
169205 CCAATTCGCTTCTCTG
192 TTGATCCACTTCTCTG
* * * * * * * * * * **
169221 TATTTCATCAAGAAGACGAATTTGGTCCACTTCTCTATATATCACCAAGAAGCTGACCATTTTAT
1 TATCTCATCAGGAAGACGGATCTGGTTCACTTCTCTGTATCTCATCAGGAAGGTGACCGCTTTAT
* * * * * *
169286 TGCTTCGACCTGCTTCTCAGTATCTCATAAGGAAGTTGAGGTTCGAAGTTT-CACCCTCATTAAG
66 TGCTTCGACCTGCTTCTCAGTATCTCATCAGGAAGCTGGGGTTCGAAGTTTGCTCACT--TTGAG
* * * * * * ** *
169350 -TT-TTTTACATTGAGTTGGTATACTTCTCTGTATCACATCAAGAAGATGACTACCTAACTTGTT
129 CTTGGTTT-CATTGATTTGGTCTACTTCTCAGTATCTCATCAGGAAGATGACCGCCT-CCTTGTT
** * *
169413 TCAATTCGCTTCTCTG
192 TTGATCCACTTCTCTG
* * * * * * * *
169429 TATCTTATTAGGAAGATGAATTTGGTTTACTTCTCT-TCATCTCATCAGGAAGATGATCGCTTTA
1 TATCTCATCAGGAAGACGGATCTGGTTCACTTCTCTGT-ATCTCATCAGGAAGGTGACCGCTTTA
* * * * * * * *
169493 TTGCTTTGACCTGCTTCTCAGTATCTTATCAAGAAGTTGAGGTTCGAAGTTTCACTCGCGTTGAG
65 TTGCTTCGACCTGCTTCTCAGTATCTCATCAGGAAGCTGGGGTTCGAAGTTT-GCTCACTTTGAG
* * * *
169558 CTTTGGTTTCATTGATTTGGTCTACTTCTCAATATCTCATCTGGAAGATGA-CACATCACTTGTT
129 C-TTGGTTTCATTGATTTGGTCTACTTCTCAGTATCTCATCAGGAAGATGACCGCCTC-CTTGTT
** *
169622 TCAATCCGCTTCTCTG
192 TTGATCCACTTCTCTG
* * * * * * * **
169638 TATCTCATCAGAAAGACGAATTTGG-TCTACTTTTCTGAATGTCATCAGGAAGCTGACCATTTTA
1 TATCTCATCAGGAAGACGGATCTGGTTC-ACTTCTCTGTATCTCATCAGGAAGGTGACCGCTTTA
* * ** *
169702 TTCCTTCGACCTGCTTCTCAGTATTTCATCAGGAAGCTAAGGTTCCAAGATTTGCTCACTTTGAG
65 TTGCTTCGACCTGCTTCTCAGTATCTCATCAGGAAGCTGGGGTTCGAAG-TTTGCTCACTTTGAG
* * * * * *
169767 -TCTGGTTTCGTTGATTTGGTCTACTTCTCAATATCTCATCAGAAAGATAACCGCCTCGTTATTT
129 CT-TGGTTTCATTGATTTGGTCTACTTCTCAGTATCTCATCAGGAAGATGACCGCCTCCTTGTTT
*
169831 TGATCCACTTCTCTA
193 TGATCCACTTCTCTG
* * * *
169846 TATCTCATCAAGAAGACGGATCTAGTTCACTTTTCTGTATCTCATCAGGAAGGTAACCGCTTTAT
1 TATCTCATCAGGAAGACGGATCTGGTTCACTTCTCTGTATCTCATCAGGAAGGTGACCGCTTTAT
* * *
169911 TGTTTCGACCTGCTTCTCAGTATCTCATAAGGAAGTTGGGGTTCGAAGATTTGCTCACTTTGAGC
66 TGCTTCGACCTGCTTCTCAGTATCTCATCAGGAAGCTGGGGTTCGAAG-TTTGCTCACTTTGAGC
* * * * * *
169976 CTGGTTTCATTAATTTGGTCTACTTCTCAGTTTCTCATCAGGAAGATGATCGCCTCATTATTTTG
130 TTGGTTTCATTGATTTGGTCTACTTCTCAGTATCTCATCAGGAAGATGACCGCCTCCTTGTTTTG
*
170041 ATCCACTTCTCTT
195 ATCCACTTCTCTG
* * * *
170054 TATCTCATCAAGAAGATGGATCTGGTTCACTTCTCTGTATCTCATCAGGAAGGTAACTGCTTTAT
1 TATCTCATCAGGAAGACGGATCTGGTTCACTTCTCTGTATCTCATCAGGAAGGTGACCGCTTTAT
170119 TGCTTCGACCTGCTTCTCAGTATCTCATCAGGAAGCTGGGGTTCGAAGGTTTGCTCACTTTGAGC
66 TGCTTCGACCTGCTTCTCAGTATCTCATCAGGAAGCTGGGGTTCGAA-GTTTGCTCACTTTGAGC
* * * * *
170184 CTGGTTTCATTTATTTGGTCTACTTCTCAGTATCTCTTCAAGAAGATGACCGCATCACTTGTTTT
130 TTGGTTTCATTGATTTGGTCTACTTCTCAGTATCTCATCAGGAAGATGACCGCCTC-CTTGTTTT
*
170249 GATTCACTTCTCTG
194 GATCCACTTCTCTG
* * * * * * * * * **
170263 TGTCTCATTAGGAAGACAGATCGGGTCCACTTTTTTGTATCTCATTAGGAAGCTGACCATTTTAT
1 TATCTCATCAGGAAGACGGATCTGGTTCACTTCTCTGTATCTCATCAGGAAGGTGACCGCTTTAT
*
170328 TGCTTCGACCTGCTTCTCAGTATCTCATCACGG-AGCTGGGGTTTGAAGATTTGCTCACTTTGAG
66 TGCTTCGACCTGCTTCTCAGTATCTCATCA-GGAAGCTGGGGTTCGAAG-TTTGCTCACTTTGAG
* ** ** * * * *
170392 CCTGGTTTTGTTGATTTGGTCTACTTCAGAGTATCTCATCA-AAAGAATGACCACCTCGTTATTT
129 CTTGGTTTCATTGATTTGGTCTACTTCTCAGTATCTCATCAGGAAG-ATGACCGCCTCCTTGTTT
170456 TGATCCACTTCTCTG
193 TGATCCACTTCTCTG
* * * *
170471 TATCTCATCATGAAGACGGATCTGGTTCACTTCTCTATATCTCATCATGAA---GA-CG---GA-
1 TATCTCATCAGGAAGACGGATCTGGTTCACTTCTCTGTATCTCATCAGGAAGGTGACCGCTTTAT
* * * * * * * *
170528 T-C-T-GGCCTACTTTTGAGTATCTCATCAGGAAGCTGAGGTTCGAAGTTTCACTCGCATTGAGC
66 TGCTTCGACCTGCTTCTCAGTATCTCATCAGGAAGCTGGGGTTCGAAGTTT-GCTCACTTTGAGC
* * * * **
170590 TTTGGTCTT-ATTGATTTGGTTTAATTCTTAGTATCGCATCAGGAAGATGACCGTATCACTTGTT
130 -TTGGT-TTCATTGATTTGGTCTACTTCTCAGTATCTCATCAGGAAGATGACCGCCTC-CTTGTT
** *
170654 TCAATCTACTTCTCTG
192 TTGATCCACTTCTCTG
* * * * * * * * * **
170670 TATTTCATTAGAAAGACGAATTTGGTCCACTTCTCTGTATCTCCTTAGGAAGCTGACCATTTTAT
1 TATCTCATCAGGAAGACGGATCTGGTTCACTTCTCTGTATCTCATCAGGAAGGTGACCGCTTTAT
* * * * * * *
170735 TGCTTCAACCTGCTTCTCAGTATCTCATAAGGAAGTTGAGGTTCGAAGTTTCGCTCGCATTGAGT
66 TGCTTCGACCTGCTTCTCAGTATCTCATCAGGAAGCTGGGGTTCGAAGTTT-GCTCACTTTGAGC
* * * * ** * *
170800 TTTGTTCCATTGAGTTGGTATACTTCTTTGTATCTCATCAGGAAGATGACCACCTCACTTGTTTC
130 TTGGTTTCATTGATTTGGTCTACTTCTCAGTATCTCATCAGGAAGATGACCGCCTC-CTTGTTTT
* * *
170865 AATTCGCTTCTCTG
194 GATCCACTTCTCTG
* * * * * * * *
170879 TATCTCATTAGGAAGATGAATTTGGTTCACTTCTCTATATCTCATCAGAAAGATGACCGTTTTAT
1 TATCTCATCAGGAAGACGGATCTGGTTCACTTCTCTGTATCTCATCAGGAAGGTGACCGCTTTAT
* * ** *
170944 TGCTTCGACCTGCTTCTCAGTGTCTCATCAGGAAGCTGGGGTTCGAAGTTTCACTTGCATTGAGC
66 TGCTTCGACCTGCTTCTCAGTATCTCATCAGGAAGCTGGGGTTCGAAGTTT-GCTCACTTTGAGC
* * *
171009 TTTGGTTTCATTGATTTGGTCTACTTCTCAGTATCTCATTAGGAAGATGAGCGCATCACTTGTTT
130 -TTGGTTTCATTGATTTGGTCTACTTCTCAGTATCTCATCAGGAAGATGACCGCCTC-CTTGTTT
*
171074 CT-ATCCGCTTCTCTG
193 -TGATCCACTTCTCTG
* * * * ** * * * **
171089 TATCTTATTAGGAAGACGAATTTGGCCCTCTTCTTTGTATCTCATCAGGAAGCTGACCATTTTAT
1 TATCTCATCAGGAAGACGGATCTGGTTCACTTCTCTGTATCTCATCAGGAAGGTGACCGCTTTAT
* * * *
171154 TGCTTCGACCTACTTCTCAGTATTTCATCAGGAAGCTGGGCTTCGAAGATTTTCTCACTTTGAG-
66 TGCTTCGACCTGCTTCTCAGTATCTCATCAGGAAGCTGGGGTTCGAAG-TTTGCTCACTTTGAGC
* * *
171218 TCTGGTTTCGTTGATTTGGTCTACTTCTCAGTATCTCATCAGGAAGATGACCGCCTCATTATTTT
130 T-TGGTTTCATTGATTTGGTCTACTTCTCAGTATCTCATCAGGAAGATGACCGCCTCCTTGTTTT
171283 GATCCACTTCTCTG
194 GATCCACTTCTCTG
* * *
171297 TATCTCATCAAGAAGACGGATCTGGTTCACTTCTCTGTATCTCATCAGAAAGGTAACCGCTTTAT
1 TATCTCATCAGGAAGACGGATCTGGTTCACTTCTCTGTATCTCATCAGGAAGGTGACCGCTTTAT
* * *
171362 TGCTTCGACTTGCTTTTCAGTATCTCATAAGGAAGCTGGGGTTCGAAGATTTGCTCACTTTGAGC
66 TGCTTCGACCTGCTTCTCAGTATCTCATCAGGAAGCTGGGGTTCGAAG-TTTGCTCACTTTGAGC
* * * * *
171427 CTGGTTTCATTAATTTGGTCTACTTCTCAGTATCTCATCGGGAAGATGATCGCCTCGTTGTTTTG
130 TTGGTTTCATTGATTTGGTCTACTTCTCAGTATCTCATCAGGAAGATGACCGCCTCCTTGTTTTG
171492 ATCCACTTCTCTG
195 ATCCACTTCTCTG
* * * *
171505 TATCTCATCAAGAAGATGGATCTAGTTCACTTCTCTGTATCTCATCAGGAAGGTAACCGCTTTAT
1 TATCTCATCAGGAAGACGGATCTGGTTCACTTCTCTGTATCTCATCAGGAAGGTGACCGCTTTAT
*
171570 TGCTTCGACCTGCTTCTTAGTATCTCATCAGGAAGCTGGGGTTCGAAGATTTGCTCACTTTGAG-
66 TGCTTCGACCTGCTTCTCAGTATCTCATCAGGAAGCTGGGGTTCGAAG-TTTGCTCACTTTGAGC
* * * * *
171634 TCTGGTTTCATTTATTTGGTCTACTTCTCAGTATCTCTTCAAGAAGATGATCGCATCACTTGTTT
130 T-TGGTTTCATTGATTTGGTCTACTTCTCAGTATCTCATCAGGAAGATGACCGCCTC-CTTGTTT
171699 TGATCCACTTCTCTG
193 TGATCCACTTCTCTG
* * * * * * * * * **
171714 TGTCTCATCAGGAAGAAGAATCGGGTCCACTTTTCTGCATATCATCAGGAAGCTGACCATTTTAT
1 TATCTCATCAGGAAGACGGATCTGGTTCACTTCTCTGTATCTCATCAGGAAGGTGACCGCTTTAT
* * * * * *
171779 TGTTTCAACCTGCTTCTCAATATCTCATCAAGAAGTTGGGGTTTGAAGATTTGCTCACTTTGAGC
66 TGCTTCGACCTGCTTCTCAGTATCTCATCAGGAAGCTGGGGTTCGAAG-TTTGCTCACTTTGAGC
* * * ** *
171844 CTGGTTTCGTTGATTTGGTCTACTGCAAAGTATCTCATCAGGAAGATGACCGCCTCGTTGTTTTG
130 TTGGTTTCATTGATTTGGTCTACTTCTCAGTATCTCATCAGGAAGATGACCGCCTCCTTGTTTTG
171909 ATCCACTTCTCTG
195 ATCCACTTCTCTG
* * * *
171922 TATCTCTTCATGAAGACGGATCTGGTTCACTTCTCTGTATCTCATCATGAA---GA-CG---GA-
1 TATCTCATCAGGAAGACGGATCTGGTTCACTTCTCTGTATCTCATCAGGAAGGTGACCGCTTTAT
** * * * * *
171979 T-C-T-GGTCTACTTCTCAGTATCTCATCAGGAAGCTGGTGTTCGAAGTTTCACTCGCATTGAGC
66 TGCTTCGACCTGCTTCTCAGTATCTCATCAGGAAGCTGGGGTTCGAAGTTT-GCTCACTTTGAGC
* * * * * * * *
172041 TTTGGTCTCATTGATTTGGACTAATTCTTAGTATCGCATCAAGAAGATGACTGCAC-CACTTATT
130 -TTGGTTTCATTGATTTGGTCTACTTCTCAGTATCTCATCAGGAAGATGACCGC-CTC-CTTGTT
** * *
172105 TCAATTCGCTTCTCTG
192 TTGATCCACTTCTCTG
* * * * * * **
172121 TAT-TCCATCAGGAAGACGAATTTGGTCCACATATCTGTATCTCATCAGGAAGCTGACCATTTTA
1 TATCT-CATCAGGAAGACGGATCTGGTTCACTTCTCTGTATCTCATCAGGAAGGTGACCGCTTTA
* * * * *
172185 TTGCTTCGACCTGCTTCTCAATATCTTATAAGGAAGCTGAGGTTCGAAGTTTCGCCTGCA--TTA
65 TTGCTTCGACCTGCTTCTCAGTATCTCATCAGGAAGCTGGGGTTCGAAGTTT-G-CT-CACTTTG
* * * * * * * * *
172248 AGTTTTGTTCCATTAAGTTGGTATACTTCTCTGTATCTCATTAGGAAGATGACGGCCTCACTTGT
127 AGCTTGGTTTCATTGATTTGGTCTACTTCTCAGTATCTCATCAGGAAGATGACCGCCTC-CTTGT
** * *
172313 TTCAATTCGCTTCTCTG
191 TTTGATCCACTTCTCTG
* * * * * * *
172330 TATCTCATTAGGAAGATGAATTTGGTTCACTTTTCTGTATCTCATCAAGAAGATGACCGCTTTAT
1 TATCTCATCAGGAAGACGGATCTGGTTCACTTCTCTGTATCTCATCAGGAAGGTGACCGCTTTAT
* * * * * * * *
172395 TGCTTCGACCTGCTTCTCAATTTCTCATTAGGAAGCTGGAGTTCGAGGTTTCACTCGCGTTGAGC
66 TGCTTCGACCTGCTTCTCAGTATCTCATCAGGAAGCTGGGGTTCGAAGTTT-GCTCACTTTGAGC
* ** *
172460 TTTGGTTTCATTGATTTGGTCTACTTCTCAGTATCTCATCAGGAAGAGGACTACATCACTTGTTT
130 -TTGGTTTCATTGATTTGGTCTACTTCTCAGTATCTCATCAGGAAGATGACCGCCTC-CTTGTTT
** * *
172525 CAATCCGCTTCTCTA
193 TGATCCACTTCTCTG
* * * * * * **
172540 TATCTCATCAGGAAGACGAATTTGGTTCACTTCTCTGTATCTCATCAAGAAGCTAATCATTTTAT
1 TATCTCATCAGGAAGACGGATCTGGTTCACTTCTCTGTATCTCATCAGGAAGGTGACCGCTTTAT
* * * *
172605 TGCTTCGACCTGCTGCTCAGTATTTCATCAGGAAGCTGGGGATCCAAGATTTGCTCACTTTGAGC
66 TGCTTCGACCTGCTTCTCAGTATCTCATCAGGAAGCTGGGGTTCGAAG-TTTGCTCACTTTGAGC
* * * ** *
172670 CTGGTTT-AGTTGATTTGGTCTACTTCTCAGTATCTCATTAGGAAGATGACTGTTTCGTTGTTTT
130 TTGGTTTCA-TTGATTTGGTCTACTTCTCAGTATCTCATCAGGAAGATGACCGCCTCCTTGTTTT
*
172734 GATCCACTTTTCTG
194 GATCCACTTCTCTG
* * *
172748 TATCTCATCAAGAAGACGGATCTGGTTCACTTCTCTGTATCTCATCAGGAAGGTAACCACTTTAT
1 TATCTCATCAGGAAGACGGATCTGGTTCACTTCTCTGTATCTCATCAGGAAGGTGACCGCTTTAT
*
172813 TGCTTCGACCTGCTTCTCAGTATCTCATAAGGAAGCTGGGGTTCGAAGATTTGCTCACTTTGAGC
66 TGCTTCGACCTGCTTCTCAGTATCTCATCAGGAAGCTGGGGTTCGAAG-TTTGCTCACTTTGAGC
* ** * * *
172878 CTGGTTTCATTGATTTGGTCTACTTCTTGGTATCTCATCAAGAAGATGATCGCCTCATTGTTTTG
130 TTGGTTTCATTGATTTGGTCTACTTCTCAGTATCTCATCAGGAAGATGACCGCCTCCTTGTTTTG
* *
172943 ATCCACATCTTTG
195 ATCCACTTCTCTG
* * * * *
172956 TATCTCATCAAGAAGATGGATCTGGTTCACTTCTCTGTATCTCATCAGGAAGATAACCGCTTCAT
1 TATCTCATCAGGAAGACGGATCTGGTTCACTTCTCTGTATCTCATCAGGAAGGTGACCGCTTTAT
* *
173021 TGCTTCGACCTGCTTCTCAGTATCTCATCAGGAAGCTGGGGTTCGAAGATTTGCTTACTTTAAGC
66 TGCTTCGACCTGCTTCTCAGTATCTCATCAGGAAGCTGGGGTTCGAAG-TTTGCTCACTTTGAGC
** * * * * * * *
173086 CAGGTTTTATTGATTTGGACTACTTCTTAGTATCTCATCAGGGAGATGATCGCCTCGTTATTTTG
130 TTGGTTTCATTGATTTGGTCTACTTCTCAGTATCTCATCAGGAAGATGACCGCCTCCTTGTTTTG
*
173151 ATCCACTTCTCTA
195 ATCCACTTCTCTG
* * * * * * **
173164 TATCTCATCAAGAAGACGGATCTGATTCACTTCTCTGCATCTCATTAAGAAGGTAACTACTTTAT
1 TATCTCATCAGGAAGACGGATCTGGTTCACTTCTCTGTATCTCATCAGGAAGGTGACCGCTTTAT
* * * **
173229 TGCTTCGACCTACTGCTCAGCATCTCATCAGGAAGCTAAGGTTCGAAGATTTGCTCACTTTGAGC
66 TGCTTCGACCTGCTTCTCAGTATCTCATCAGGAAGCTGGGGTTCGAAG-TTTGCTCACTTTGAGC
* * * * * *
173294 CTAGTTTCGTTGATTTGGTCTACTTCTGAGTATCTCATCAGGAAGATGACCGCCTCGTTATTTTG
130 TTGGTTTCATTGATTTGGTCTACTTCTCAGTATCTCATCAGGAAGATGACCGCCTCCTTGTTTTG
173359 ATCCACTTCTCTG
195 ATCCACTTCTCTG
* * * * *
173372 TATCTCATCATGAAGACAGATCTGGTTCACTTTTCTGTATCTCATCATGAA---GA-CG---GA-
1 TATCTCATCAGGAAGACGGATCTGGTTCACTTCTCTGTATCTCATCAGGAAGGTGACCGCTTTAT
* * * * * *
173429 T-CTT-G-TCTACTTCTCAGTATCTCATCAGGAAGCTAGGGTTCGAAGTTTCACTCGCATTGAGC
66 TGCTTCGACCTGCTTCTCAGTATCTCATCAGGAAGCTGGGGTTCGAAGTTT-GCTCACTTTGAGC
* * * * * ** *
173491 TTTGATCTCATTGATTTGGTTTAATTCTTAGTATCTCATCAGGAAGATGTTCGCATCACTTGTTT
130 -TTGGTTTCATTGATTTGGTCTACTTCTCAGTATCTCATCAGGAAGATGACCGCCTC-CTTGTTT
** ****
173556 CAATTTGTTTCTCTG
193 TGATCCACTTCTCTG
* * * * * * **
173571 TATCTCATC-GAGAAGATGAATTTGGTCCACTTCTCTATATCTCATCAGGAAGCTGACCATTTTA
1 TATCTCATCAG-GAAGACGGATCTGGTTCACTTCTCTGTATCTCATCAGGAAGGTGACCGCTTTA
* * * * * *
173635 TTGCTTCGACCTGCTTCTCAATATCTCATTAAGAAGCTGGGGTTCGAAGATTCGCTCGCATTGAG
65 TTGCTTCGACCTGCTTCTCAGTATCTCATCAGGAAGCTGGGGTTCGAAG-TTTGCTCACTTTGAG
* * * * * * ** *
173700 CTTTGTTCCATTGAGTTGGTATACTTCTCTGTATCTCATCAAGAAGATGGTCACCTCACTTGTTT
129 CTTGGTTTCATTGATTTGGTCTACTTCTCAGTATCTCATCAGGAAGATGACCGCCTC-CTTGTTT
** *
173765 CAATCCGCTTCTCTG
193 TGATCCACTTCTCTG
* * * * * * * * **
173780 TATCTTATCAAGAAGACGAATTTGGTCCAGTTCT-TAGTATCTCATCAGGAAGCTTACCATTTTA
1 TATCTCATCAGGAAGACGGATCTGGTTCACTTCTCT-GTATCTCATCAGGAAGGTGACCGCTTTA
173844 TTGCTT
65 TTGCTT
173850 TGGATAACTG
Statistics
Matches: 4207, Mismatches: 741, Indels: 197
0.82 0.14 0.04
Matches are distributed among these distances:
196 11 0.00
197 132 0.03
198 130 0.03
199 179 0.04
200 3 0.00
201 3 0.00
202 6 0.00
203 3 0.00
204 2 0.00
205 5 0.00
206 3 0.00
207 13 0.00
208 1971 0.47
209 1092 0.26
210 639 0.15
211 14 0.00
212 1 0.00
ACGTcount: A:0.22, C:0.22, G:0.19, T:0.37
Consensus pattern (207 bp):
TATCTCATCAGGAAGACGGATCTGGTTCACTTCTCTGTATCTCATCAGGAAGGTGACCGCTTTAT
TGCTTCGACCTGCTTCTCAGTATCTCATCAGGAAGCTGGGGTTCGAAGTTTGCTCACTTTGAGCT
TGGTTTCATTGATTTGGTCTACTTCTCAGTATCTCATCAGGAAGATGACCGCCTCCTTGTTTTGA
TCCACTTCTCTG
Found at i:170512 original size:37 final size:37
Alignment explanation
Indices: 170461--170532 Score: 135
Period size: 37 Copynumber: 1.9 Consensus size: 37
170451 TATTTTGATC
*
170461 CACTTCTCTGTATCTCATCATGAAGACGGATCTGGTT
1 CACTTCTCTATATCTCATCATGAAGACGGATCTGGTT
170498 CACTTCTCTATATCTCATCATGAAGACGGATCTGG
1 CACTTCTCTATATCTCATCATGAAGACGGATCTGG
170533 CCTACTTTTG
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
37 34 1.00
ACGTcount: A:0.24, C:0.25, G:0.18, T:0.33
Consensus pattern (37 bp):
CACTTCTCTATATCTCATCATGAAGACGGATCTGGTT
Found at i:170549 original size:37 final size:38
Alignment explanation
Indices: 170461--170559 Score: 127
Period size: 37 Copynumber: 2.7 Consensus size: 38
170451 TATTTTGATC
*
170461 CACTTCTCT-GTATCTCATCATGAAGACGGATCTGGTT
1 CACTTCTCTAGTATCTCATCATGAAGACGGATCTGGCT
170498 CACTTCTCTA-TATCTCATCATGAAGACGGATCTGGC-
1 CACTTCTCTAGTATCTCATCATGAAGACGGATCTGGCT
*
170534 CTACTT-T-TGAGTATCTCATCAGGAAG
1 C-ACTTCTCT-AGTATCTCATCATGAAG
170560 CTGAGGTTCG
Statistics
Matches: 56, Mismatches: 2, Indels: 8
0.85 0.03 0.12
Matches are distributed among these distances:
35 1 0.02
36 3 0.05
37 52 0.93
ACGTcount: A:0.24, C:0.24, G:0.18, T:0.33
Consensus pattern (38 bp):
CACTTCTCTAGTATCTCATCATGAAGACGGATCTGGCT
Found at i:171962 original size:37 final size:36
Alignment explanation
Indices: 171912--172010 Score: 153
Period size: 37 Copynumber: 2.7 Consensus size: 36
171902 TGTTTTGATC
*
171912 CACTTCTCTGTATCTCTTCATGAAGACGGATCTGGTT
1 CACTTCTCTGTATCTCATCATGAAGACGGATCTGG-T
171949 CACTTCTCTGTATCTCATCATGAAGACGGATCTGGT
1 CACTTCTCTGTATCTCATCATGAAGACGGATCTGGT
* *
171985 CTACTTCTCAGTATCTCATCAGGAAG
1 C-ACTTCTCTGTATCTCATCATGAAG
172011 CTGGTGTTCG
Statistics
Matches: 58, Mismatches: 3, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
36 2 0.03
37 56 0.97
ACGTcount: A:0.22, C:0.25, G:0.18, T:0.34
Consensus pattern (36 bp):
CACTTCTCTGTATCTCATCATGAAGACGGATCTGGT
Found at i:173412 original size:37 final size:36
Alignment explanation
Indices: 173362--173460 Score: 135
Period size: 37 Copynumber: 2.7 Consensus size: 36
173352 TATTTTGATC
173362 CACTTCTCTGTATCTCATCATGAAGACAGATCTGGTT
1 CACTTCTCTGTATCTCATCATGAAGACAGATCTGG-T
* * *
173399 CACTTTTCTGTATCTCATCATGAAGACGGATCTTGT
1 CACTTCTCTGTATCTCATCATGAAGACAGATCTGGT
* *
173435 CTACTTCTCAGTATCTCATCAGGAAG
1 C-ACTTCTCTGTATCTCATCATGAAG
173461 CTAGGGTTCG
Statistics
Matches: 55, Mismatches: 6, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
36 2 0.04
37 53 0.96
ACGTcount: A:0.24, C:0.24, G:0.16, T:0.35
Consensus pattern (36 bp):
CACTTCTCTGTATCTCATCATGAAGACAGATCTGGT
Found at i:174005 original size:78 final size:77
Alignment explanation
Indices: 173857--174008 Score: 180
Period size: 78 Copynumber: 2.0 Consensus size: 77
173847 CTTTGGATAA
* * * * *
173857 CTGCAATCTGCCCCATGATCGGGTAAGAGATTGGATGGTTGTGATCTACCCTATGGTCAGGGTAA
1 CTGCAATCTGCCCCAAGATCGGGTAAGAGATTGGATGATGGTGATCTACCCCATGGTCAGGGCAA
173922 AAGATCGAATGG
66 AAGATCGAATGG
* * * * *
173934 CTGCAATTTGCCCCAAGCTCGGGGTAAGAGATTGGCTGATGGTGATCTGCCCCA-GGCTCGGGGC
1 CTGCAATCTGCCCCAAGATC-GGGTAAGAGATTGGATGATGGTGATCTACCCCATGG-TCAGGGC
*
173998 AAGAGATCGAA
64 AAAAGATCGAA
174009 ATCTTCATTC
Statistics
Matches: 62, Mismatches: 11, Indels: 3
0.82 0.14 0.04
Matches are distributed among these distances:
77 19 0.31
78 43 0.69
ACGTcount: A:0.24, C:0.21, G:0.32, T:0.23
Consensus pattern (77 bp):
CTGCAATCTGCCCCAAGATCGGGTAAGAGATTGGATGATGGTGATCTACCCCATGGTCAGGGCAA
AAGATCGAATGG
Found at i:175397 original size:35 final size:33
Alignment explanation
Indices: 175357--175472 Score: 92
Period size: 35 Copynumber: 3.3 Consensus size: 33
175347 ACCTTTCCTT
*
175357 TTCTTTTTCTCCTTTTTCTATTTTCTTTTTCTTTC
1 TTCTTTTT-TCCTTTTTCT-TTTTCTTTTTCTTTA
* *
175392 TTCTTTTTTCCTTTCCTT-TGTTTCTTTCTTTTTTA
1 TTCTTTTTTCCTTT--TTCTTTTTCTTT-TTCTTTA
*
175427 TTCTTTTTTTCTCTCTTTTCTTTCTCTTTTT-TTTA
1 TTC-TTTTTTC-CT-TTTTCTTTTTCTTTTTCTTTA
*
175462 TTTATTTTTTC
1 -TTCTTTTTTC
175473 TTCATTGAAT
Statistics
Matches: 67, Mismatches: 6, Indels: 16
0.75 0.07 0.18
Matches are distributed among these distances:
34 13 0.19
35 28 0.42
36 15 0.22
37 9 0.13
38 2 0.03
ACGTcount: A:0.03, C:0.20, G:0.01, T:0.76
Consensus pattern (33 bp):
TTCTTTTTTCCTTTTTCTTTTTCTTTTTCTTTA
Found at i:175436 original size:11 final size:10
Alignment explanation
Indices: 175369--175474 Score: 61
Period size: 11 Copynumber: 9.8 Consensus size: 10
175359 CTTTTTCTCC
175369 TTTTTCTATTT
1 TTTTTCT-TTT
* *
175380 TCTTT-TTCT
1 TTTTTCTTTT
*
175389 TTCTTCTTTT
1 TTTTTCTTTT
175399 TTCCTTTCCTTTGT
1 TT--TTT-CTTT-T
175413 TTCTTTCTTTT
1 TT-TTTCTTTT
*
175424 TTATTCTTTT
1 TTTTTCTTTT
*
175434 TTTCTCTCTTT
1 TTTTTCT-TTT
*
175445 TCTTTCTCTTT
1 TTTTTCT-TTT
*
175456 TTTTTATTTAT
1 TTTTTCTTT-T
175467 TTTTTCTT
1 TTTTTCTT
175475 CATTGAATCC
Statistics
Matches: 74, Mismatches: 14, Indels: 14
0.73 0.14 0.14
Matches are distributed among these distances:
9 5 0.07
10 20 0.27
11 32 0.43
12 6 0.08
13 8 0.11
14 3 0.04
ACGTcount: A:0.04, C:0.18, G:0.01, T:0.77
Consensus pattern (10 bp):
TTTTTCTTTT
Found at i:175437 original size:22 final size:23
Alignment explanation
Indices: 175360--175459 Score: 73
Period size: 22 Copynumber: 4.2 Consensus size: 23
175350 TTTCCTTTTC
*
175360 TTTTTCTC-CTTTTTCTATTTTCTTT
1 TTTTTCTCTC-TTTTCT-TTCTC-TT
*
175385 TTCTTTCTTCTTTTTTCCTTTC-CTT
1 TT-TTTC-TCTCTTTT-CTTTCTCTT
* *
175410 TGTTTCTTTCTTTT-TTAT-TCTT
1 TTTTTCTCTCTTTTCTT-TCTCTT
175432 TTTTTCTCTCTTTTCTTTCTCTT
1 TTTTTCTCTCTTTTCTTTCTCTT
175455 TTTTT
1 TTTTT
175460 TATTTATTTT
Statistics
Matches: 60, Mismatches: 7, Indels: 18
0.71 0.08 0.21
Matches are distributed among these distances:
21 2 0.03
22 17 0.28
23 17 0.28
24 4 0.07
25 5 0.08
26 5 0.08
27 8 0.13
28 2 0.03
ACGTcount: A:0.02, C:0.21, G:0.01, T:0.76
Consensus pattern (23 bp):
TTTTTCTCTCTTTTCTTTCTCTT
Found at i:175450 original size:13 final size:13
Alignment explanation
Indices: 175354--175457 Score: 53
Period size: 12 Copynumber: 8.4 Consensus size: 13
175344 TCGACCTTTC
*
175354 CTTTTCTTTTTCT
1 CTTTTCTTTCTCT
*
175367 CCTTTTTCTATTTTCT
1 -C-TTTTCT-TTCTCT
175383 -TTTTCTTTCT-T
1 CTTTTCTTTCTCT
* *
175394 CTTTT-TTCCTTT
1 CTTTTCTTTCTCT
* * *
175406 CCTTTGTTTCTTT
1 CTTTTCTTTCTCT
*
175419 C-TTT-TTTAT-T
1 CTTTTCTTTCTCT
175429 CTTTT-TTTCTCT
1 CTTTTCTTTCTCT
175441 CTTTTCTTTCTCT
1 CTTTTCTTTCTCT
175454 -TTTT
1 CTTTT
175458 TTTATTTATT
Statistics
Matches: 76, Mismatches: 6, Indels: 18
0.76 0.06 0.18
Matches are distributed among these distances:
10 2 0.03
11 16 0.21
12 25 0.33
13 20 0.26
14 1 0.01
15 6 0.08
16 6 0.08
ACGTcount: A:0.02, C:0.22, G:0.01, T:0.75
Consensus pattern (13 bp):
CTTTTCTTTCTCT
Found at i:175458 original size:13 final size:13
Alignment explanation
Indices: 175349--175458 Score: 66
Period size: 13 Copynumber: 8.0 Consensus size: 13
175339 TCACCTCGAC
175349 CTTTC-CTTTTCTT
1 CTTTCTCTTTT-TT
*
175362 -TTTCTCCTTTTT
1 CTTTCTCTTTTTT
*
175374 CTATTTTC-TTTTT
1 CT-TTCTCTTTTTT
175387 CTTTCTTCTTTTTT
1 CTTTC-TCTTTTTT
175401 CCTTTC-CTTTGTTT
1 -CTTTCTCTTT-TTT
*
175415 CTTTCTTTTTTATT
1 CTTTCTCTTTT-TT
*
175429 CTTTTTTTCTCTCTTTT
1 C----TTTCTCTTTTTT
175446 CTTTCTCTTTTTT
1 CTTTCTCTTTTTT
175459 TTATTTATTT
Statistics
Matches: 77, Mismatches: 7, Indels: 26
0.70 0.06 0.24
Matches are distributed among these distances:
12 8 0.10
13 35 0.45
14 18 0.23
15 5 0.06
17 3 0.04
18 8 0.10
ACGTcount: A:0.02, C:0.23, G:0.01, T:0.75
Consensus pattern (13 bp):
CTTTCTCTTTTTT
Found at i:180820 original size:30 final size:30
Alignment explanation
Indices: 180705--180847 Score: 152
Period size: 29 Copynumber: 4.9 Consensus size: 30
180695 GGAAAATTTA
***
180705 AGGGCAAAATGGTAATTTTTGGATTCTT-G
1 AGGGCAAAATGGTAATTTTTGGAAAGTTCG
* * *
180734 -GGGGAAAATGGTAATTTTT-GTATGTTCG
1 AGGGCAAAATGGTAATTTTTGGAAAGTTCG
** *
180762 AGGGCAAAATTATGATTTTTGG-AAGTTCG
1 AGGGCAAAATGGTAATTTTTGGAAAGTTCG
180791 AGGGCAAAATGGTAATTTTTGGAAAGTTCG
1 AGGGCAAAATGGTAATTTTTGGAAAGTTCG
* *
180821 AGGTCAAAAT-GTAATTTTTAGAAAGTT
1 AGGGCAAAATGGTAATTTTTGGAAAGTT
180848 TAGGGGTTAA
Statistics
Matches: 96, Mismatches: 14, Indels: 8
0.81 0.12 0.07
Matches are distributed among these distances:
27 4 0.04
28 19 0.20
29 56 0.58
30 17 0.18
ACGTcount: A:0.31, C:0.06, G:0.27, T:0.36
Consensus pattern (30 bp):
AGGGCAAAATGGTAATTTTTGGAAAGTTCG
Found at i:180844 original size:29 final size:28
Alignment explanation
Indices: 180738--180927 Score: 127
Period size: 29 Copynumber: 6.5 Consensus size: 28
180728 TTCTTGGGGG
* * *
180738 AAAATGGTAATTTTTGTATGTTCGAGGGC
1 AAAAT-GTAATTTTTGAAAGTTCGAGGTC
* *
180767 AAAAT-TATGATTTTTGGAAGTTCGAGGGC
1 AAAATGTA--ATTTTTGAAAGTTCGAGGTC
180796 AAAATGGTAATTTTTGGAAAGTTCGAGGTC
1 AAAAT-GTAATTTTT-GAAAGTTCGAGGTC
* * *
180826 AAAATGTAATTTTTAGAAAGTTTAGGGGTT
1 AAAATGTAATTTTT-GAAAG-TTCGAGGTC
* * *
180856 AAAAAGTAATTTTTGAGAAGTT-TAGGGTT
1 AAAATGTAATTTTTGA-AAGTTCGA-GGTC
*
180885 AAAATGT-ATTTTTGGAAAGTT-TAGGGTC
1 AAAATGTAATTTTT-GAAAGTTCGA-GGTC
* *
180913 AAAACGTGATTTTTG
1 AAAATGTAATTTTTG
180928 GATAGTTCAG
Statistics
Matches: 137, Mismatches: 14, Indels: 21
0.80 0.08 0.12
Matches are distributed among these distances:
27 2 0.01
28 24 0.18
29 70 0.51
30 39 0.28
31 2 0.01
ACGTcount: A:0.33, C:0.04, G:0.25, T:0.37
Consensus pattern (28 bp):
AAAATGTAATTTTTGAAAGTTCGAGGTC
Found at i:180934 original size:29 final size:29
Alignment explanation
Indices: 180776--180939 Score: 158
Period size: 29 Copynumber: 5.7 Consensus size: 29
180766 CAAAATTATG
*
180776 ATTTTTGG-AAGTTCGAGGG-CAAAATGGTA
1 ATTTTTGGAAAGTT-TAGGGTCAAAAT-GTA
*
180805 ATTTTTGGAAAG-TTCGAGGTCAAAATGTA
1 ATTTTTGGAAAGTTTAG-GGTCAAAATGTA
* * *
180834 ATTTTTAGAAAGTTTAGGGGTTAAAAAGTA
1 ATTTTTGGAAAGTTTA-GGGTCAAAATGTA
*
180864 ATTTTT-GAGAAGTTTAGGGTTAAAATGT-
1 ATTTTTGGA-AAGTTTAGGGTCAAAATGTA
* *
180892 ATTTTTGGAAAGTTTAGGGTCAAAACGTG
1 ATTTTTGGAAAGTTTAGGGTCAAAATGTA
* *
180921 ATTTTTGGATAGTTCAGGG
1 ATTTTTGGAAAGTTTAGGG
180940 ACCTTCTAGG
Statistics
Matches: 116, Mismatches: 11, Indels: 16
0.81 0.08 0.11
Matches are distributed among these distances:
28 24 0.21
29 57 0.49
30 34 0.29
31 1 0.01
ACGTcount: A:0.32, C:0.04, G:0.27, T:0.37
Consensus pattern (29 bp):
ATTTTTGGAAAGTTTAGGGTCAAAATGTA
Done.