Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01015085.1 Kokia drynarioides strain JFW-HI SEQ_130129, 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: 897486
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.34
Warning! 584 characters in sequence are not A, C, G, or T
File 1 of 3
Found at i:6007 original size:18 final size:17
Alignment explanation
Indices: 5984--6026 Score: 50
Period size: 18 Copynumber: 2.4 Consensus size: 17
5974 GAATAGGTTT
* *
5984 TTAATTAAATAAATTTAA
1 TTAATTAAA-AAAATAAA
6002 TTAATTGAAAAAAATAAA
1 TTAATT-AAAAAAATAAA
6020 TTAATTA
1 TTAATTA
6027 CACCTTGAAC
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
17 1 0.05
18 18 0.82
19 3 0.14
ACGTcount: A:0.58, C:0.00, G:0.02, T:0.40
Consensus pattern (17 bp):
TTAATTAAAAAAATAAA
Found at i:17824 original size:264 final size:265
Alignment explanation
Indices: 17146--17947 Score: 1243
Period size: 266 Copynumber: 3.0 Consensus size: 265
17136 CATCGAAAGA
* *
17146 TTATCCAGCTGGTTCAACAAAGACTTGAGTTCGGGTAAGGATGCCTATTGTCAATTCCTCAAGGT
1 TTATCCAGCTGGTTCAACAAAGACATGAGTTCGGGTAAGGATGCCTATTGTCAACTCCTCAAGGT
* *
17211 GAGTCTGCTTTTGCAACAAACCAATGGGGAAATTTGTCAACCTAGATAGGTCATGGATCTCG-GA
66 GAGTCTGATTTTGCAACAAACCAAT-GGGAAATTTGTCAAGCTAGATAGGTCATGGATCTCGAG-
** * * *
17275 TGAACTAACATCGCGACGACTTAGAAACGAGGCATTGTTCTTTATCCAAATTCGAAGGTTTTCAA
129 TGAACCGATATCGCGACGACTTAGAAACGAGGCATTGTTCCTTGTCCAAATTCGAAGGTTTTCAA
* * * *
17340 GGGTTGGAAATTGTGGCAACTCAATCAACTCAAGACATTTCTTGAACGTCAAGATTCGCAGACAA
194 GGGTTGGAAATTGTGGCAATTCAATCAACTCAAGGCATTTCTTGAACGTCAAGATTAGCAGACGA
17405 GGAAAAT
259 GGAAAAT
*
17412 TTATCCAGCTGGTTTAACAAAGACATGAGTTCGGGTAAGGATGCCTATTGTCAACTCCTCAAGGT
1 TTATCCAGCTGGTTCAACAAAGACATGAGTTCGGGTAAGGATGCCTATTGTCAACTCCTCAAGGT
* * * *
17477 GAGTCTGTTTTTGCAGCAAACGAATGGGAAAATCTGTCAAGCTAGATAGGTCATGGATCTCGAGT
66 GAGTCTGATTTTGCAACAAACCAATGGG-AAATTTGTCAAGCTAGATAGGTCATGGATCTCGAGT
* * * *
17542 GAAACGATATCGCGACGACTTAAAAACGAGGCATTATTCCTTGTCCAAATTCAAAGGTTTTCAAG
130 GAACCGATATCGCGACGACTTAGAAACGAGGCATTGTTCCTTGTCCAAATTCGAAGGTTTTCAAG
* * *
17607 GGTTGAAAATTGTGGCAATTCAATCAACTC-AGGCATTTCTTGAATGTCAAGATTGGCAGACGAG
195 GGTTGGAAATTGTGGCAATTCAATCAACTCAAGGCATTTCTTGAACGTCAAGATTAGCAGACGAG
17671 GAAAAT
260 GAAAAT
* *
17677 TTA-CCTAGCTGGTTCAACAAAGACACGAGTTCGGGTAAGGATG-CTATTGTCAACTCCTCGAGG
1 TTATCC-AGCTGGTTCAACAAAGACATGAGTTCGGGTAAGGATGCCTATTGTCAACTCCTCAAGG
* * *
17740 TGAGTCTGATATTGCAACAAACCAATGGGAATTTTGTTCAAGCTAGATAGGCCATGGATCTCGAG
65 TGAGTCTGATTTTGCAACAAACCAATGGGAAATTTG-TCAAGCTAGATAGGTCATGGATCTCGAG
*
17805 TGAACCGATATCACGACGACTTAGAAACGAGGCATTGTTCCTTGTCCAAATTCGAAGGTTTTCAA
129 TGAACCGATATCGCGACGACTTAGAAACGAGGCATTGTTCCTTGTCCAAATTCGAAGGTTTTCAA
*
17870 GGGTCGGAAATTGTGGCAATTCAATCAACTCAAGGCATTTCTTGAACGTCAAGATTAGCAGACGA
194 GGGTTGGAAATTGTGGCAATTCAATCAACTCAAGGCATTTCTTGAACGTCAAGATTAGCAGACGA
17935 GGAAAAT
259 GGAAAAT
17942 TTATCC
1 TTATCC
17948 TTTTGCTCCC
Statistics
Matches: 488, Mismatches: 42, Indels: 12
0.90 0.08 0.02
Matches are distributed among these distances:
263 5 0.01
264 162 0.33
265 118 0.24
266 202 0.41
267 1 0.00
ACGTcount: A:0.31, C:0.19, G:0.23, T:0.27
Consensus pattern (265 bp):
TTATCCAGCTGGTTCAACAAAGACATGAGTTCGGGTAAGGATGCCTATTGTCAACTCCTCAAGGT
GAGTCTGATTTTGCAACAAACCAATGGGAAATTTGTCAAGCTAGATAGGTCATGGATCTCGAGTG
AACCGATATCGCGACGACTTAGAAACGAGGCATTGTTCCTTGTCCAAATTCGAAGGTTTTCAAGG
GTTGGAAATTGTGGCAATTCAATCAACTCAAGGCATTTCTTGAACGTCAAGATTAGCAGACGAGG
AAAAT
Found at i:21158 original size:59 final size:58
Alignment explanation
Indices: 21095--21214 Score: 136
Period size: 58 Copynumber: 2.1 Consensus size: 58
21085 ATTTGATATT
* *
21095 TAAACCATTTTTA-ACCCAATTTGGTACCT-AGACTTGACAATTTTTCCTAATTTGGTACC
1 TAAA-CATTTTTAGACCCAATGTGGTACATGA-ACTTGAC-ATTTTTCCTAATTTGGTACC
* * * * *
21154 TAAACTTTTTTAGACCTAATGTGGTACATGAACTTGGCATTTTTTCTAATTTGGTATC
1 TAAACATTTTTAGACCCAATGTGGTACATGAACTTGACATTTTTCCTAATTTGGTACC
21212 TAA
1 TAA
21215 GTTTTTTTTT
Statistics
Matches: 52, Mismatches: 7, Indels: 5
0.81 0.11 0.08
Matches are distributed among these distances:
58 28 0.54
59 23 0.44
60 1 0.02
ACGTcount: A:0.28, C:0.17, G:0.12, T:0.42
Consensus pattern (58 bp):
TAAACATTTTTAGACCCAATGTGGTACATGAACTTGACATTTTTCCTAATTTGGTACC
Found at i:21492 original size:31 final size:31
Alignment explanation
Indices: 21438--21496 Score: 84
Period size: 31 Copynumber: 1.9 Consensus size: 31
21428 AATTTTTAAA
*
21438 AAAAAGTGTCAAATTTAGATATTAAATTAGG
1 AAAAAGTGTCAAATTAAGATATTAAATTAGG
*
21469 AAAAAGTGTCAAGTTAA-AGTATTAAATT
1 AAAAAGTGTCAAATTAAGA-TATTAAATT
21497 GAACTAAAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
30 1 0.04
31 24 0.96
ACGTcount: A:0.49, C:0.03, G:0.15, T:0.32
Consensus pattern (31 bp):
AAAAAGTGTCAAATTAAGATATTAAATTAGG
Found at i:26003 original size:141 final size:135
Alignment explanation
Indices: 25627--26042 Score: 421
Period size: 142 Copynumber: 3.0 Consensus size: 135
25617 GCGTGCTTGT
* * * *
25627 GTGTAGCATCGAGAAATGTCTTCCTTTTCTTGAGGGGGGTAGGCTGGTGAGTTTTTGCATGATCC
1 GTGTAGCATCGAGAAATGTCTTCTTTTTCTTGAGGGGGGTAGGCGGGCGAGTTTTTGCGTGATCC
* *
25692 TCGTAAATGATATGGAAATCAGTGTAAATGCTTGATCAAGGATGCTTATTTTTTGTGTC-ATGTG
66 TCATAAATGATACGGAAATC-GTGTAAATGCTTGATCAAGGATG-TT-TTTTTT-TGTCTATGTG
25756 TGTGTGTGC
127 TGTGTGTGC
* *
25765 ----AGCATCGAGAAATGTCTTCTTTTTCTTTGNNNNNNGGGGGGGGTAGGTGGGCGAGTTTTTG
1 GTGTAGCATCGAGAAATGTCTTCTTTTTC-TT-------GAGGGGGGTAGGCGGGCGAGTTTTTG
* ** * **
25826 TGTGGATTGTCATAAATGAAACGGAAATCAAGTAAATGCTTGATCAAGGATGTTTTTTTTTGTCA
58 CGT-GATCCTCATAAATGATACGGAAATCGTGTAAATGCTTGATCAAGGATGTTTTTTTTTGTC-
25891 TATGTGTGTGCATGTATGCGC
121 TATGTGTGTG--TG--T--GC
*
25912 GTGTAGCATCGAGAAATGTCTTCTTTTTCTTGAGGGGGGTA-GCGGGCAAGTTTTTGCGTGATCC
1 GTGTAGCATCGAGAAATGTCTTCTTTTTCTTGAGGGGGGTAGGCGGGCGAGTTTTTGCGTGATCC
* * *
25976 TCATAAATGATACAGAAATCGTGTAAATGCTTGGTCATGGATGTTTATTGTTTTGTCTTATGTGT
66 TCATAAATGATACGGAAATCGTGTAAATGCTTGATCAAGGATGTTT-TT-TTTTGTC-TATGTGT
26041 GT
128 GT
26043 ACAAGGTGCG
Statistics
Matches: 228, Mismatches: 27, Indels: 41
0.77 0.09 0.14
Matches are distributed among these distances:
134 24 0.11
135 2 0.01
139 4 0.02
140 6 0.03
141 54 0.24
142 61 0.27
143 47 0.21
145 1 0.00
147 2 0.01
150 2 0.01
151 25 0.11
ACGTcount: A:0.21, C:0.12, G:0.28, T:0.37
Consensus pattern (135 bp):
GTGTAGCATCGAGAAATGTCTTCTTTTTCTTGAGGGGGGTAGGCGGGCGAGTTTTTGCGTGATCC
TCATAAATGATACGGAAATCGTGTAAATGCTTGATCAAGGATGTTTTTTTTTGTCTATGTGTGTG
TGTGC
Found at i:29338 original size:8 final size:8
Alignment explanation
Indices: 29325--29349 Score: 50
Period size: 8 Copynumber: 3.1 Consensus size: 8
29315 TTTATCAGCT
29325 AATTACAA
1 AATTACAA
29333 AATTACAA
1 AATTACAA
29341 AATTACAA
1 AATTACAA
29349 A
1 A
29350 CTAATCATCT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 17 1.00
ACGTcount: A:0.64, C:0.12, G:0.00, T:0.24
Consensus pattern (8 bp):
AATTACAA
Found at i:36748 original size:21 final size:20
Alignment explanation
Indices: 36714--36752 Score: 51
Period size: 21 Copynumber: 1.9 Consensus size: 20
36704 CAATTCTACT
36714 AAAACAAAACCAGACAATTAA
1 AAAACAAAACCAGA-AATTAA
* *
36735 AAAACATAATCAGAAATT
1 AAAACAAAACCAGAAATT
36753 CATGTTCGTG
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 4 0.25
21 12 0.75
ACGTcount: A:0.64, C:0.15, G:0.05, T:0.15
Consensus pattern (20 bp):
AAAACAAAACCAGAAATTAA
Found at i:39262 original size:8 final size:10
Alignment explanation
Indices: 39227--39264 Score: 58
Period size: 10 Copynumber: 3.8 Consensus size: 10
39217 TTGTCTAAAT
*
39227 TTTCTTTCAC
1 TTTCTCTCAC
39237 TTTCTCTCAC
1 TTTCTCTCAC
*
39247 TTTCTCTCAT
1 TTTCTCTCAC
39257 TTTCTCTC
1 TTTCTCTC
39265 TCTCCTTTTT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
10 26 1.00
ACGTcount: A:0.08, C:0.34, G:0.00, T:0.58
Consensus pattern (10 bp):
TTTCTCTCAC
Found at i:41689 original size:31 final size:31
Alignment explanation
Indices: 41654--41719 Score: 123
Period size: 31 Copynumber: 2.1 Consensus size: 31
41644 TTATTAACTA
*
41654 ATTAAAGCTTGAATTCGATAACTATTTCCGT
1 ATTAAAGCTTGAATTCAATAACTATTTCCGT
41685 ATTAAAGCTTGAATTCAATAACTATTTCCGT
1 ATTAAAGCTTGAATTCAATAACTATTTCCGT
41716 ATTA
1 ATTA
41720 GTCATTGAAC
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 34 1.00
ACGTcount: A:0.35, C:0.15, G:0.11, T:0.39
Consensus pattern (31 bp):
ATTAAAGCTTGAATTCAATAACTATTTCCGT
Found at i:69412 original size:21 final size:21
Alignment explanation
Indices: 69388--69442 Score: 74
Period size: 21 Copynumber: 2.6 Consensus size: 21
69378 TAAAGATAAG
**
69388 ACTTGTATCGGTAGAGGAGTC
1 ACTTGTATCGGTAGAACAGTC
*
69409 ACTTGTATCGGTAGAACTGTC
1 ACTTGTATCGGTAGAACAGTC
*
69430 ACTTGTATTGGTA
1 ACTTGTATCGGTA
69443 CAAATCTGCA
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 30 1.00
ACGTcount: A:0.24, C:0.15, G:0.27, T:0.35
Consensus pattern (21 bp):
ACTTGTATCGGTAGAACAGTC
Found at i:71996 original size:11 final size:11
Alignment explanation
Indices: 71982--72057 Score: 52
Period size: 11 Copynumber: 6.8 Consensus size: 11
71972 GATAATCACT
71982 TTAATATTAAA
1 TTAATATTAAA
71993 TTAATA--AAA
1 TTAATATTAAA
*
72002 -TACTATTAAA
1 TTAATATTAAA
*
72012 ATAAGTATTAAA
1 TTAA-TATTAAA
72024 TTAA-ATTTAATA
1 TTAATA-TTAA-A
72036 TTAAACTATTAAA
1 TT-AA-TATTAAA
*
72049 ATAATATTA
1 TTAATATTA
72058 TTTTTGGAAT
Statistics
Matches: 52, Mismatches: 4, Indels: 18
0.70 0.05 0.24
Matches are distributed among these distances:
8 4 0.08
9 3 0.06
10 4 0.08
11 17 0.33
12 15 0.29
13 4 0.08
14 4 0.08
15 1 0.02
ACGTcount: A:0.55, C:0.03, G:0.01, T:0.41
Consensus pattern (11 bp):
TTAATATTAAA
Found at i:71997 original size:20 final size:18
Alignment explanation
Indices: 71950--72056 Score: 69
Period size: 20 Copynumber: 5.8 Consensus size: 18
71940 CAAGATAAAC
71950 ATTAAATTAA-ATTTAAT
1 ATTAAATTAATATTTAAT
71967 ATTAAGA-TAATCACTTTAAT
1 ATTAA-ATTAAT-A-TTTAAT
** *
71987 ATTAAATTAATAAAATACT
1 ATTAAATTAAT-ATTTAAT
*
72006 ATTAAAATAAGTA-TTAA-
1 ATTAAATTAA-TATTTAAT
*
72023 ATTAAATTTAATATTAAACT
1 ATTAAA-TTAATATTTAA-T
*
72043 ATTAAAATAATATT
1 ATTAAATTAATATT
72057 ATTTTTGGAA
Statistics
Matches: 70, Mismatches: 10, Indels: 18
0.71 0.10 0.18
Matches are distributed among these distances:
17 16 0.23
18 9 0.13
19 22 0.31
20 23 0.33
ACGTcount: A:0.53, C:0.04, G:0.02, T:0.41
Consensus pattern (18 bp):
ATTAAATTAATATTTAAT
Found at i:72044 original size:37 final size:36
Alignment explanation
Indices: 71982--72057 Score: 102
Period size: 37 Copynumber: 2.1 Consensus size: 36
71972 GATAATCACT
71982 TTAATATTAAATTAATAAAATACTATTAAAATAAGTA
1 TTAATATTAAATTAATAAAATACTATTAAAATAA-TA
*
72019 TTAA-ATTAAATTTAATATTAA-ACTATTAAAATAATA
1 TTAATATTAAA-TTAATA-AAATACTATTAAAATAATA
72055 TTA
1 TTA
72058 TTTTTGGAAT
Statistics
Matches: 36, Mismatches: 1, Indels: 5
0.86 0.02 0.12
Matches are distributed among these distances:
36 11 0.31
37 23 0.64
38 2 0.06
ACGTcount: A:0.55, C:0.03, G:0.01, T:0.41
Consensus pattern (36 bp):
TTAATATTAAATTAATAAAATACTATTAAAATAATA
Found at i:72903 original size:36 final size:36
Alignment explanation
Indices: 72856--73122 Score: 345
Period size: 36 Copynumber: 7.4 Consensus size: 36
72846 TTAGCAAAAT
* * * * *
72856 ATATTCACTATCACATGCCATGAAAAACATACTCAC
1 ATATTTACTGTCACATGGCATGAATAACATACCCAC
* * *
72892 ATATTTTCTATCCCATGGCATGAATAACATACCCAC
1 ATATTTACTGTCACATGGCATGAATAACATACCCAC
72928 ATATTTACTGTCACATGGCATGAATAACATACCCAC
1 ATATTTACTGTCACATGGCATGAATAACATACCCAC
* * * *
72964 ATATTTACTATCTCATGGCATGAATAACATACTCAT
1 ATATTTACTGTCACATGGCATGAATAACATACCCAC
* *
73000 ATGTTTACTGTCACATGGAATGAATAACATACCCAC
1 ATATTTACTGTCACATGGCATGAATAACATACCCAC
* *
73036 ATATTTACTGTCTCACGGCATGAATAACATACCCAC
1 ATATTTACTGTCACATGGCATGAATAACATACCCAC
* * * *
73072 ATATTTATTGTCTCATGGCATGAATAACATACTCAT
1 ATATTTACTGTCACATGGCATGAATAACATACCCAC
*
73108 ATATTTACTTTCACA
1 ATATTTACTGTCACA
73123 ATAGTCATCA
Statistics
Matches: 201, Mismatches: 30, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
36 201 1.00
ACGTcount: A:0.36, C:0.24, G:0.09, T:0.31
Consensus pattern (36 bp):
ATATTTACTGTCACATGGCATGAATAACATACCCAC
Found at i:73045 original size:108 final size:108
Alignment explanation
Indices: 72856--73122 Score: 399
Period size: 108 Copynumber: 2.5 Consensus size: 108
72846 TTAGCAAAAT
* * * * * * * *
72856 ATATTCACTATCACATGCCATGAAAAACATACTCACATATTTTCTATCCCATGGCATGAATAACA
1 ATATTTACTATCTCATGGCATGAATAACATACTCATATATTTACTATCACATGGAATGAATAACA
*
72921 TACCCACATATTTACTGTCACATGGCATGAATAACATACCCAC
66 TACCCACATATTTACTGTCACACGGCATGAATAACATACCCAC
* *
72964 ATATTTACTATCTCATGGCATGAATAACATACTCATATGTTTACTGTCACATGGAATGAATAACA
1 ATATTTACTATCTCATGGCATGAATAACATACTCATATATTTACTATCACATGGAATGAATAACA
*
73029 TACCCACATATTTACTGTCTCACGGCATGAATAACATACCCAC
66 TACCCACATATTTACTGTCACACGGCATGAATAACATACCCAC
* * *
73072 ATATTTATTGTCTCATGGCATGAATAACATACTCATATATTTACTTTCACA
1 ATATTTACTATCTCATGGCATGAATAACATACTCATATATTTACTATCACA
73123 ATAGTCATCA
Statistics
Matches: 143, Mismatches: 16, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
108 143 1.00
ACGTcount: A:0.36, C:0.24, G:0.09, T:0.31
Consensus pattern (108 bp):
ATATTTACTATCTCATGGCATGAATAACATACTCATATATTTACTATCACATGGAATGAATAACA
TACCCACATATTTACTGTCACACGGCATGAATAACATACCCAC
Found at i:75076 original size:22 final size:22
Alignment explanation
Indices: 75012--75067 Score: 85
Period size: 22 Copynumber: 2.5 Consensus size: 22
75002 TTGTTGTTTT
*
75012 CTATCTATTTTGCTACAATTTCA
1 CTAT-TATGTTGCTACAATTTCA
75035 CTATTATGTTGCTACAATTTCA
1 CTATTATGTTGCTACAATTTCA
*
75057 CTATTTTGTTG
1 CTATTATGTTG
75068 TTATTATTTG
Statistics
Matches: 31, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
22 27 0.87
23 4 0.13
ACGTcount: A:0.23, C:0.18, G:0.09, T:0.50
Consensus pattern (22 bp):
CTATTATGTTGCTACAATTTCA
Found at i:75139 original size:30 final size:30
Alignment explanation
Indices: 75104--75165 Score: 97
Period size: 30 Copynumber: 2.1 Consensus size: 30
75094 TATTTTATTA
* *
75104 TTAATTTTGTTATTATTTTAGAGACATTTG
1 TTAATTTTGTTACTATTTTAAAGACATTTG
*
75134 TTAATTTTGTTACTATTTTAAAGGCATTTG
1 TTAATTTTGTTACTATTTTAAAGACATTTG
75164 TT
1 TT
75166 TATTAAGTTG
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
30 29 1.00
ACGTcount: A:0.26, C:0.05, G:0.13, T:0.56
Consensus pattern (30 bp):
TTAATTTTGTTACTATTTTAAAGACATTTG
Found at i:76530 original size:68 final size:66
Alignment explanation
Indices: 76450--76636 Score: 197
Period size: 62 Copynumber: 2.8 Consensus size: 66
76440 ATTATTTTAA
* * **
76450 TAAATTTAATTTAATACTTATCTTGGTAGTATTTTATTAATTTAATATTAAAGTGACTATCTTAA
1 TAAATTTAATTTAATATTTATCTT-GTAGTATTATATTAATTTAATATTAAAGTGAAAAT-TTAA
76515 TAT
64 TAT
* * *
76518 TAAATTTAATTTAATATTTATCTTGTA-AATAAATATT-CTATTAAT-TT-AA-T-AAAATTTAA
1 TAAATTTAATTTAATATTTATCTTGTAGTAT-TATATTAAT-TTAATATTAAAGTGAAAATTTAA
76577 TAT
64 TAT
* *
76580 TAAATTTAATCTAATATTTATCTTAATAAGTATTATATTAATTTAATATTAAAGTGA
1 TAAATTTAATTTAATATTTATCTT-GT-AGTATTATATTAATTTAATATTAAAGTGA
76637 TTAAGTTTAA
Statistics
Matches: 97, Mismatches: 12, Indels: 20
0.75 0.09 0.16
Matches are distributed among these distances:
62 30 0.31
63 4 0.04
64 12 0.12
65 7 0.07
66 7 0.07
67 13 0.13
68 24 0.25
ACGTcount: A:0.42, C:0.04, G:0.05, T:0.49
Consensus pattern (66 bp):
TAAATTTAATTTAATATTTATCTTGTAGTATTATATTAATTTAATATTAAAGTGAAAATTTAATA
T
Found at i:89468 original size:25 final size:25
Alignment explanation
Indices: 89434--89484 Score: 93
Period size: 25 Copynumber: 2.0 Consensus size: 25
89424 TAGCTAATGT
89434 ACTTGGTGAGTGTGCAGGAGACCAC
1 ACTTGGTGAGTGTGCAGGAGACCAC
*
89459 ACTTTGTGAGTGTGCAGGAGACCAC
1 ACTTGGTGAGTGTGCAGGAGACCAC
89484 A
1 A
89485 AGAAGTGTAA
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.25, C:0.20, G:0.33, T:0.22
Consensus pattern (25 bp):
ACTTGGTGAGTGTGCAGGAGACCAC
Found at i:96199 original size:228 final size:228
Alignment explanation
Indices: 95794--97131 Score: 1385
Period size: 228 Copynumber: 5.9 Consensus size: 228
95784 AAGATGCAGA
* * * *
95794 GTAGACTCCTTTTGGATGTTATAATCAGCCAATGTCCTG-CCATCTTCAAGCTGCTTGCCAGCAA
1 GTAGACTCCTTTTGGATATTGTAATCAGCCAAGGTGC-GACCATCTTCAAGCTGCTTGCCAGCAA
* * * * * *
95858 ATATGAGCCTTTGCTGGTCTGGTGGGATCCCTTCCTTGTCTTGAATCTTTGCCTTAACATTGTCA
65 AGATAAGCCTCTGCTGATCTGGTGGGATCCCTTCCTTGTCTTGAATCTTTGCCTTCACATTATCA
* * * * * * * * * *
95923 ATGGTGTCTGAACTTTCAACCT-CTAGAGTGATAGTCTTTCCAGTAAGAGTCTTAACAAAGATCT
130 ATGGTATCCGAACTCTCAACCTCCAAG-GTAATTGTCTTTCCAGTGAGAGTTTTGACAAAGATTT
* *
95987 GCATCCCACCACGCAGCCGCAA-CACCAAGTGAAGG
194 GCATCCCACCACGAAGCCG-AAGCACCAAGTGGAGG
* * * * * * * *
96022 GTTGACTCCTTCTGGATATTGTAGTCGGCCAATGTCCTACCATCTTCGAGCTGCTTGCCAGCAAA
1 GTAGACTCCTTTTGGATATTGTAATCAGCCAAGGTGCGACCATCTTCAAGCTGCTTGCCAGCAAA
* * * * * * *
96087 TATGAGCCTTTGCTGGTCTGGGGGGATACCC-TCCTTGTCTTGGATCTTTGCCTTCACATTGTCA
66 GATAAGCCTCTGCTGATCTGGTGGGAT-CCCTTCCTTGTCTTGAATCTTTGCCTTCACATTATCA
* * * * * * * * *
96151 ATGGTATCGGAACTTTCAACCTCCAAAGTGATGGTCTTTCCGGTAAGAGTTTTCACAAAGATCTG
130 ATGGTATCCGAACTCTCAACCTCCAAGGTAATTGTCTTTCCAGTGAGAGTTTTGACAAAGATTTG
* * * * * *
96216 CATACCACCACGAAGGCGGAGAACCAAATGGAGA
195 CATCCCACCACGAAGCCGAAGCACCAAGTGGAGG
* * * * ** * * *
96250 GTAGACTCCTTCTGGATATTATAATC-GGCAAGAGTTCTTCCATCTTCAAGTTGTTTTCCAGCAA
1 GTAGACTCCTTTTGGATATTGTAATCAGCCAAG-GTGCGACCATCTTCAAGCTGCTTGCCAGCAA
* * * * * * * * * *
96314 AAATCAA-TCTTTGTTGGTCTGGTGGGATTCCTTCTTTGTCCTGAATCTTGGCTTTCACATTATC
65 AGAT-AAGCCTCTGCTGATCTGGTGGGATCCCTTCCTTGTCTTGAATCTTTGCCTTCACATTATC
*
96378 AATGGTATCCGAACTCTCGACCTCCAAGGTAATTGTCTTTCCAGTGAGAGTTTTGACAAAGATTT
129 AATGGTATCCGAACTCTCAACCTCCAAGGTAATTGTCTTTCCAGTGAGAGTTTTGACAAAGATTT
* * *
96443 GCATGCCACCACGAAGACGAAGCACCAGGTGGAGG
194 GCATCCCACCACGAAGCCGAAGCACCAAGTGGAGG
* * * * *
96478 GTAGACTCTTTTTGAATGTTGTAATCAGCTAAGGTGCGACCATCTTCAAGCTGCTTTCCAGCAAA
1 GTAGACTCCTTTTGGATATTGTAATCAGCCAAGGTGCGACCATCTTCAAGCTGCTTGCCAGCAAA
* * *
96543 GATAAGCCTCTGCTGATCTGGTGGGATCCCTTCCTTGTCCTGAATCTTGGCTTTCACATTATCAA
66 GATAAGCCTCTGCTGATCTGGTGGGATCCCTTCCTTGTCTTGAATCTTTGCCTTCACATTATCAA
* *
96608 TGGTATCCAAACTCTCGACCTCCAAGGTAATTGTCTTTCCAGTGAGAGTTTTGACAAAGATTTGC
131 TGGTATCCGAACTCTCAACCTCCAAGGTAATTGTCTTTCCAGTGAGAGTTTTGACAAAGATTTGC
* * *
96673 ATTCCACCTCGAAGCCGAAGCACCAGGTGGAGG
196 ATCCCACCACGAAGCCGAAGCACCAAGTGGAGG
* * * * *
96706 GTGGACTCTTTTTGGATATTGTAATCAGCTAAGGTGCGACCATCTTCGAGCTGCTTTCCAGCAAA
1 GTAGACTCCTTTTGGATATTGTAATCAGCCAAGGTGCGACCATCTTCAAGCTGCTTGCCAGCAAA
* *
96771 GATAAGCCTCTGCTGATCTGGTGGGATCCCTTCCTTGTCTTGGATCTTTGCCTTTACATTATCAA
66 GATAAGCCTCTGCTGATCTGGTGGGATCCCTTCCTTGTCTTGAATCTTTGCCTTCACATTATCAA
* * * * * *
96836 TTGTGTCAGAGCTTTCAACCTCCAAGGTAATTGTCTTTCCAGTGAGAGTCTTGACAAAGATTTGC
131 TGGTATCCGAACTCTCAACCTCCAAGGTAATTGTCTTTCCAGTGAGAGTTTTGACAAAGATTTGC
* * * * * *
96901 ATTCCACCTCGGAGTCGAAGAACCAAGTGAAGG
196 ATCCCACCACGAAGCCGAAGCACCAAGTGGAGG
* * * * * * * * * *
96934 GTGGATTCTTTTTGGATGTTGTAGTC-GGCTAGCGTGCGGCCATCCTCAAGTTGCTTGCCAGCAA
1 GTAGACTCCTTTTGGATATTGTAATCAGCCAAG-GTGCGACCATCTTCAAGCTGCTTGCCAGCAA
* * * *
96998 AGATAAGCCTCTGCTGATCCGGTGGGATCCCTTCCTTATCTTGGATCTTAGCCTTCACATTATCA
65 AGATAAGCCTCTGCTGATCTGGTGGGATCCCTTCCTTGTCTTGAATCTTTGCCTTCACATTATCA
* * * * * * * * * *
97063 ATGGTGTCTGAACTCTCCACCTCGAGGGTGATGGTCTTGCCAGTGAGGGTTTTAACAAAGATTTG
130 ATGGTATCCGAACTCTCAACCTCCAAGGTAATTGTCTTTCCAGTGAGAGTTTTGACAAAGATTTG
97128 CATC
195 CATC
97132 TATTGAATCA
Statistics
Matches: 959, Mismatches: 141, Indels: 20
0.86 0.13 0.02
Matches are distributed among these distances:
227 12 0.01
228 937 0.98
229 10 0.01
ACGTcount: A:0.23, C:0.24, G:0.22, T:0.31
Consensus pattern (228 bp):
GTAGACTCCTTTTGGATATTGTAATCAGCCAAGGTGCGACCATCTTCAAGCTGCTTGCCAGCAAA
GATAAGCCTCTGCTGATCTGGTGGGATCCCTTCCTTGTCTTGAATCTTTGCCTTCACATTATCAA
TGGTATCCGAACTCTCAACCTCCAAGGTAATTGTCTTTCCAGTGAGAGTTTTGACAAAGATTTGC
ATCCCACCACGAAGCCGAAGCACCAAGTGGAGG
Found at i:97108 original size:684 final size:684
Alignment explanation
Indices: 95794--97130 Score: 1622
Period size: 684 Copynumber: 2.0 Consensus size: 684
95784 AAGATGCAGA
* *
95794 GTAGACTCCTTTTGGATGTTATAATCAGCCAATGTCCTGCCATCTTCAAGCTGCTTGCCAGCAAA
1 GTAGACTCCTTTTGAATGTTATAATCAGCCAAGGTCCTGCCATCTTCAAGCTGCTTGCCAGCAAA
* * * * * * *
95859 TATGAGCCTTTGCTGGTCTGGTGGGATCCCTTCCTTGTCTTGAATCTTTGCCTTAACATTGTCAA
66 GATAAGCCTCTGCTGATCTGGTGGGATCCCTTCCTTGTCCTGAATCTTGGCCTTAACATTATCAA
* ** * * *
95924 TGGTGTCTGAACTTTCAACCTCTAGAGTGATAGTCTTTCCAGTAAGAGTCTTAACAAAGATCTGC
131 TGGTATCCAAACTCTCAACCTCAAGAGTAATAGTCTTTCCAGTAAGAGTCTTAACAAAGATCTGC
* * * *
95989 ATCCCACCACGCAGCCGCAACACCAAGTGAAGGGTTGACTCCTTCTGGATATTGTAGTCGGCCAA
196 ATCCCACCACGAAGCCGCAACACCAAGTGAAGGGTGGACTCCTTCTGGATATTGTAATCAGCCAA
* * * * * *
96054 TGTCCTACCATCTTCGAGCTGCTTGCCAGCAAATATGAGCCTTTGCTGGTCTGGGGGGATACCCT
261 GGTCCGACCATCTTCGAGCTGCTTGCCAGCAAAGATAAGCCTCTGCTGATCTGGGGGGATACCCT
* * *
96119 CCTTGTCTTGGATCTTTGCCTTCACATTGTCAATGGTATCGGAACTTTCAACCTCCAAAGTGATG
326 CCTTGTCTTGGATCTTTGCCTTCACATTATCAATGGTATCAGAACTTTCAACCTCCAAAGTAATG
* * * *
96184 GTCTTTCCGGTAAGAGTTTTCACAAAGATCTGCATACCACCACGAAGGCGGAGAACCAAATGGAG
391 GTCTTTCCAGTAAGAGTCTTCACAAAGATCTGCATACCACCACGAAGGCGAAGAACCAAATGAAG
* ** * * *
96249 AGTAGACTCCTTCTGGATATTATAATCGGCAAGAGTTCTTCCATCTTCAAGTTGTTTTCCAGCAA
456 AGTAGACTCCTTCTGGATATTATAATCGGCAAGAGTGCGGCCATCCTCAAGTTGCTTGCCAGCAA
* * * * * * * * * *
96314 AAATCAATCTTTGTTGGTCTGGTGGGATTCCTTCTTTGTCCTGAATCTTGGCTTTCACATTATCA
521 AAATCAACCTCTGCTGATCCGGTGGGATCCCTTCCTTATCCTGAATCTTAGCCTTCACATTATCA
* * * *
96379 ATGGTATCCGAACTCTCGACCTCCAAGGTAATTGTCTTTCCAGTGAGAGTTTTGACAAAGATTTG
586 ATGGTATCCGAACTCTCCACCTCCAAGGTAATGGTCTTGCCAGTGAGAGTTTTAACAAAGATTTG
96444 CATGCCACCACGAAGACGAAGCACCAGGTGGAGG
651 CATGCCACCACGAAGACGAAGCACCAGGTGGAGG
* * * * *
96478 GTAGACTCTTTTTGAATGTTGTAATCAGCTAAGGTGC-GACCATCTTCAAGCTGCTTTCCAGCAA
1 GTAGACTCCTTTTGAATGTTATAATCAGCCAAGGTCCTG-CCATCTTCAAGCTGCTTGCCAGCAA
* *
96542 AGATAAGCCTCTGCTGATCTGGTGGGATCCCTTCCTTGTCCTGAATCTTGGCTTTCACATTATCA
65 AGATAAGCCTCTGCTGATCTGGTGGGATCCCTTCCTTGTCCTGAATCTTGGCCTTAACATTATCA
* * * * * *
96607 ATGGTATCCAAACTCTCGACCTCCAAG-GTAATTGTCTTTCCAGTGAGAGTTTTGACAAAGATTT
130 ATGGTATCCAAACTCTCAACCT-CAAGAGTAATAGTCTTTCCAGTAAGAGTCTTAACAAAGATCT
* * * * * *
96671 GCATTCCACCTCGAAGCCG-AAGCACCAGGTGGAGGGTGGACTCTTTTTGGATATTGTAATCAGC
194 GCATCCCACCACGAAGCCGCAA-CACCAAGTGAAGGGTGGACTCCTTCTGGATATTGTAATCAGC
* * * *
96735 TAAGGTGCGACCATCTTCGAGCTGCTTTCCAGCAAAGATAAGCCTCTGCTGATCTGGTGGGAT-C
258 CAAGGTCCGACCATCTTCGAGCTGCTTGCCAGCAAAGATAAGCCTCTGCTGATCTGGGGGGATAC
* * * * *
96799 CCTTCCTTGTCTTGGATCTTTGCCTTTACATTATCAATTGTGTCAGAGCTTTCAACCTCCAAGGT
323 CC-TCCTTGTCTTGGATCTTTGCCTTCACATTATCAATGGTATCAGAACTTTCAACCTCCAAAGT
* * * * * * * * *
96864 AATTGTCTTTCCAGTGAGAGTCTTGACAAAGATTTGCATTCCACCTCGGAGTCGAAGAACCAAGT
387 AATGGTCTTTCCAGTAAGAGTCTTCACAAAGATCTGCATACCACCACGAAGGCGAAGAACCAAAT
* * * * * * * * * *
96929 GAAGGGTGGATTCTTTTTGGATGTTGTAGTCGGCTAGCGTGCGGCCATCCTCAAGTTGCTTGCCA
452 GAAGAGTAGACTCCTTCTGGATATTATAATCGGCAAGAGTGCGGCCATCCTCAAGTTGCTTGCCA
* * *
96994 GCAAAGAT-AAGCCTCTGCTGATCCGGTGGGATCCCTTCCTTATCTTGGATCTTAGCCTTCACAT
517 GCAAAAATCAA-CCTCTGCTGATCCGGTGGGATCCCTTCCTTATCCTGAATCTTAGCCTTCACAT
* * * * * *
97058 TATCAATGGTGTCTGAACTCTCCACCTCGAGGGTGATGGTCTTGCCAGTGAGGGTTTTAACAAAG
581 TATCAATGGTATCCGAACTCTCCACCTCCAAGGTAATGGTCTTGCCAGTGAGAGTTTTAACAAAG
97123 ATTTGCAT
646 ATTTGCAT
97131 CTATTGAATC
Statistics
Matches: 540, Mismatches: 108, Indels: 10
0.82 0.16 0.02
Matches are distributed among these distances:
683 8 0.01
684 529 0.98
685 3 0.01
ACGTcount: A:0.23, C:0.24, G:0.22, T:0.31
Consensus pattern (684 bp):
GTAGACTCCTTTTGAATGTTATAATCAGCCAAGGTCCTGCCATCTTCAAGCTGCTTGCCAGCAAA
GATAAGCCTCTGCTGATCTGGTGGGATCCCTTCCTTGTCCTGAATCTTGGCCTTAACATTATCAA
TGGTATCCAAACTCTCAACCTCAAGAGTAATAGTCTTTCCAGTAAGAGTCTTAACAAAGATCTGC
ATCCCACCACGAAGCCGCAACACCAAGTGAAGGGTGGACTCCTTCTGGATATTGTAATCAGCCAA
GGTCCGACCATCTTCGAGCTGCTTGCCAGCAAAGATAAGCCTCTGCTGATCTGGGGGGATACCCT
CCTTGTCTTGGATCTTTGCCTTCACATTATCAATGGTATCAGAACTTTCAACCTCCAAAGTAATG
GTCTTTCCAGTAAGAGTCTTCACAAAGATCTGCATACCACCACGAAGGCGAAGAACCAAATGAAG
AGTAGACTCCTTCTGGATATTATAATCGGCAAGAGTGCGGCCATCCTCAAGTTGCTTGCCAGCAA
AAATCAACCTCTGCTGATCCGGTGGGATCCCTTCCTTATCCTGAATCTTAGCCTTCACATTATCA
ATGGTATCCGAACTCTCCACCTCCAAGGTAATGGTCTTGCCAGTGAGAGTTTTAACAAAGATTTG
CATGCCACCACGAAGACGAAGCACCAGGTGGAGG
Found at i:98330 original size:29 final size:30
Alignment explanation
Indices: 98270--98336 Score: 82
Period size: 29 Copynumber: 2.3 Consensus size: 30
98260 AAAAGTGGAC
* * *
98270 CTAAATTTTGAAAGCTGAAAAGTAAAATGA
1 CTAAATTTTCAAAACTGAAAAGTAAAAGGA
* *
98300 CTAAATTTTCAAAACT-AAAAGTATAGGGA
1 CTAAATTTTCAAAACTGAAAAGTAAAAGGA
98329 CTAAATTT
1 CTAAATTT
98337 AAAATTTATG
Statistics
Matches: 32, Mismatches: 5, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
29 18 0.56
30 14 0.44
ACGTcount: A:0.48, C:0.09, G:0.13, T:0.30
Consensus pattern (30 bp):
CTAAATTTTCAAAACTGAAAAGTAAAAGGA
Found at i:116063 original size:16 final size:16
Alignment explanation
Indices: 116029--116062 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
116019 AATAAAGAAT
*
116029 AAATTTTAAAACTAAA
1 AAATTTGAAAACTAAA
116045 AAATTTGAAAA-TAAA
1 AAATTTGAAAACTAAA
116060 AAA
1 AAA
116063 AAAAGGGAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 7 0.41
16 10 0.59
ACGTcount: A:0.68, C:0.03, G:0.03, T:0.26
Consensus pattern (16 bp):
AAATTTGAAAACTAAA
Found at i:116943 original size:60 final size:60
Alignment explanation
Indices: 116739--117031 Score: 292
Period size: 59 Copynumber: 4.9 Consensus size: 60
116729 TTAAAAATCC
* ** * * * * *
116739 CATTTTG-ACCCTAAATTTTTTCAAAATTATATTTTAACTCTCATACATTTCCAAAATTA
1 CATTTTGAACCCTAAAATTTCCCAAAATTACATTTTAACCCTTAAACTTTTCCAAAATTA
* ** *
116798 CATTTTGAACCCCAAAATTTTTCAAAATTGCATTTTAACCCTTAAAC-TTTCCAAAATTA
1 CATTTTGAACCCTAAAATTTCCCAAAATTACATTTTAACCCTTAAACTTTTCCAAAATTA
**
116857 CATTTT-AACCCCTAAAATTTTTCAAAATTACATTTTAACCCTTAAACTTTTCCAAAATTA
1 CATTTTGAA-CCCTAAAATTTCCCAAAATTACATTTTAACCCTTAAACTTTTCCAAAATTA
* ** * *
116917 CATTTTG-GCCCTTAAACCTTCCCAAAATCACATTTTAACCC-TAAACTTTTCCAAAATCA
1 CATTTTGAACCC-TAAAATTTCCCAAAATTACATTTTAACCCTTAAACTTTTCCAAAATTA
* * * ** *
116976 TATTTTGATCCC-GAGCTTTCCCAAAATTACATTTTCAACCCCTAAACTTTTCCAAA
1 CATTTTGAACCCTAAAATTTCCCAAAATTACATTTT-AACCCTTAAACTTTTCCAAA
117032 TTTATGTTTT
Statistics
Matches: 204, Mismatches: 22, Indels: 15
0.85 0.09 0.06
Matches are distributed among these distances:
58 21 0.10
59 92 0.45
60 91 0.45
ACGTcount: A:0.35, C:0.24, G:0.03, T:0.38
Consensus pattern (60 bp):
CATTTTGAACCCTAAAATTTCCCAAAATTACATTTTAACCCTTAAACTTTTCCAAAATTA
Found at i:116943 original size:119 final size:118
Alignment explanation
Indices: 116732--117031 Score: 318
Period size: 119 Copynumber: 2.5 Consensus size: 118
116722 ATTTTCTTTA
* * * * * * *
116732 AAAATCCCATTTTGACCCTAAATTTTTTCAAAATTATATTTTAACTCTCATACATTTCCAAAATT
1 AAAATCACATTTTGACCCTAAAATTTTTCAAAATTACATTTTAACCCTTAAACTTTTCCAAAATT
* ** **
116797 ACATTTTGAACCCCAAAATTTTTCAAAATTGCATTTTAACCCTTAAAC-TTTCC
66 ACATTTTGAACCCCAAAACTTCCCAAAATCACATTTTAACCC-TAAACTTTTCC
* *
116850 AAAATTACATTTTAACCCCTAAAATTTTTCAAAATTACATTTTAACCCTTAAACTTTTCCAAAAT
1 AAAATCACATTTTGA-CCCTAAAATTTTTCAAAATTACATTTTAACCCTTAAACTTTTCCAAAAT
* * *
116915 TACATTTTG-GCCCTTAAACCTTCCCAAAATCACATTTTAACCCTAAACTTTTCC
65 TACATTTTGAACCC-CAAAACTTCCCAAAATCACATTTTAACCCTAAACTTTTCC
* * ** ** *
116969 AAAATCATATTTTGATCCC-GAGCTTTCCCAAAATTACATTTTCAACCCCTAAACTTTTCCAAA
1 AAAATCACATTTTGA-CCCTAAAATTTTTCAAAATTACATTTT-AACCCTTAAACTTTTCCAAA
117032 TTTATGTTTT
Statistics
Matches: 151, Mismatches: 27, Indels: 7
0.82 0.15 0.04
Matches are distributed among these distances:
118 38 0.25
119 113 0.75
ACGTcount: A:0.36, C:0.24, G:0.03, T:0.37
Consensus pattern (118 bp):
AAAATCACATTTTGACCCTAAAATTTTTCAAAATTACATTTTAACCCTTAAACTTTTCCAAAATT
ACATTTTGAACCCCAAAACTTCCCAAAATCACATTTTAACCCTAAACTTTTCC
Found at i:117033 original size:30 final size:30
Alignment explanation
Indices: 116739--117031 Score: 274
Period size: 30 Copynumber: 9.9 Consensus size: 30
116729 TTAAAAATCC
* * *
116739 CATTTTGA-CCCTAAATTTTTTCAAAATTA
1 CATTTTAACCCCTAAACTTTTCCAAAATTA
* * * *
116768 TATTTTAA-CTCTCATACATTTCCAAAATTA
1 CATTTTAACCCCT-AAACTTTTCCAAAATTA
* * *
116798 CATTTTGAACCCC-AAAATTTTTCAAAATTG
1 CATTTT-AACCCCTAAACTTTTCCAAAATTA
*
116828 CATTTTAACCCTTAAAC-TTTCCAAAATTA
1 CATTTTAACCCCTAAACTTTTCCAAAATTA
* *
116857 CATTTTAACCCCTAAAATTTTTCAAAATTA
1 CATTTTAACCCCTAAACTTTTCCAAAATTA
*
116887 CATTTTAACCCTTAAACTTTTCCAAAATTA
1 CATTTTAACCCCTAAACTTTTCCAAAATTA
** * * * *
116917 CATTTTGGCCCTTAAACCTTCCCAAAATCA
1 CATTTTAACCCCTAAACTTTTCCAAAATTA
*
116947 CATTTTAA-CCCTAAACTTTTCCAAAATCA
1 CATTTTAACCCCTAAACTTTTCCAAAATTA
* * * * * *
116976 TATTTTGATCCC-GAGCTTTCCCAAAATTA
1 CATTTTAACCCCTAAACTTTTCCAAAATTA
117005 CATTTTCAACCCCTAAACTTTTCCAAA
1 CATTTT-AACCCCTAAACTTTTCCAAA
117032 TTTATGTTTT
Statistics
Matches: 210, Mismatches: 46, Indels: 14
0.78 0.17 0.05
Matches are distributed among these distances:
29 81 0.39
30 115 0.55
31 12 0.06
32 2 0.01
ACGTcount: A:0.35, C:0.24, G:0.03, T:0.38
Consensus pattern (30 bp):
CATTTTAACCCCTAAACTTTTCCAAAATTA
Found at i:126615 original size:3 final size:3
Alignment explanation
Indices: 126607--126639 Score: 66
Period size: 3 Copynumber: 11.0 Consensus size: 3
126597 TTATGATATT
126607 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA
1 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA
126640 AAAAGGGATG
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.67, C:0.00, G:0.33, T:0.00
Consensus pattern (3 bp):
GAA
Found at i:129139 original size:78 final size:78
Alignment explanation
Indices: 129012--129882 Score: 781
Period size: 78 Copynumber: 11.2 Consensus size: 78
129002 GAAGATTCCG
* * ** ** * * **
129012 ATCTCTTACCCCGATCATAGGGCAGATCACAATCATCTGATCTTTTACCCCGAGCCTAGGATAGA
1 ATCTCTTACCCCGAGCCTAGGGCAGATTGCAGCCATCCGATCTTTTACCCCGAGCTTAGGGCAGA
129077 TCACCATCAGCCA
66 TCACCATCAGCCA
* * * * *
129090 ATCTTTTACCCCGAGCCTAGGGTAGATTACAGCCATCCAATCTCTTACCCCGAGCTT-GAGGCAG
1 ATCTCTTACCCCGAGCCTAGGGCAGATTGCAGCCATCCGATCTTTTACCCCGAGCTTAG-GGCAG
*
129154 ATCACCATCAACCA
65 ATCACCATCAGCCA
* * * * * * *
129168 ATCTCTTACGCTGAG-CTTGGCGCAGATTGCAGCTATCCGATCTTTTATCCCGAGCTTGGGGTAG
1 ATCTCTTACCCCGAGCCTAGG-GCAGATTGCAGCCATCCGATCTTTTACCCCGAGCTTAGGGCAG
* *
129232 ATCACCATTAACCA
65 ATCACCATCAGCCA
* * * * * * * *
129246 ATTTGTTACCCCGAG-CTTGTAGCAGATTGTAGCCATCTGATCTTTTACCCCGAGCCTGGGGCAG
1 ATCTCTTACCCCGAGCCTAG-GGCAGATTGCAGCCATCCGATCTTTTACCCCGAGCTTAGGGCAG
*
129310 ATCACCCTCAGCCA
65 ATCACCATCAGCCA
** * * * *
129324 ATCTCTTACATCGAGCCTAGGAC-GTATTGCAGCCATCCTATCTCTT-CCCCAAGCTT-GAGGCA
1 ATCTCTTACCCCGAGCCTAGGGCAG-ATTGCAGCCATCCGATCTTTTACCCCGAGCTTAG-GGCA
129386 GATCACCATCAGCCA
64 GATCACCATCAGCCA
* * * * ** * *
129401 ATTTCTTGCCCTGAGCCTGGGGCAGATTGTGGCCATCCGATCTTTTACCCTGAGCTT-GAGGTAG
1 ATCTCTTACCCCGAGCCTAGGGCAGATTGCAGCCATCCGATCTTTTACCCCGAGCTTAG-GGCAG
**
129465 GCCACCATCAGCCA
65 ATCACCATCAGCCA
** * * * * *
129479 ATCTCAAACCCCGAGCTTAAGGTAGATTGCAGCCATCTGATCTTTTACCCCGAGCCT-GGG-ATG
1 ATCTCTTACCCCGAGCCTAGGGCAGATTGCAGCCATCCGATCTTTTACCCCGAGCTTAGGGCA--
*
129542 GATCACCATTAGCCA
64 GATCACCATCAGCCA
* * * * * * * *
129557 ATCTCTTACCTCGAGCTTGGGGCGGAATGCAGCCATCCTATCTCTTACCCCGAGCTTGGGGCAGA
1 ATCTCTTACCCCGAGCCTAGGGCAGATTGCAGCCATCCGATCTTTTACCCCGAGCTTAGGGCAGA
129622 TCACCATCAGCCA
66 TCACCATCAGCCA
* * * * * * * *
129635 ATCTCTTACCCTGAGCTTGGGGCAGATTGTAGCCATCCAATCTATTACCCCGAGCTTAGGGTAGG
1 ATCTCTTACCCCGAGCCTAGGGCAGATTGCAGCCATCCGATCTTTTACCCCGAGCTTAGGGCAGA
*
129700 TAACCATCAGCCA
66 TCACCATCAGCCA
* ** * * * *
129713 ATCTATTACCTAGAGCCTAGGGCAGATTACAGTCATCCGATCTTTTACCCCGAGCCT-GAGGCGG
1 ATCTCTTACCCCGAGCCTAGGGCAGATTGCAGCCATCCGATCTTTTACCCCGAGCTTAG-GGCAG
129777 ATCACCATCAGCCA
65 ATCACCATCAGCCA
* * ** * * *
129791 ATCTCTTACCCCAAGCCTAGGGCAGATTGCAACCATCTAATCTTTTACCCCAAGCCTAGGGCAAA
1 ATCTCTTACCCCGAGCCTAGGGCAGATTGCAGCCATCCGATCTTTTACCCCGAGCTTAGGGCAGA
129856 TCACCATCAGCCA
66 TCACCATCAGCCA
*
129869 ATCTCTTATCCCGA
1 ATCTCTTACCCCGA
129883 ACTTGAGGCA
Statistics
Matches: 638, Mismatches: 140, Indels: 30
0.79 0.17 0.04
Matches are distributed among these distances:
76 2 0.00
77 68 0.11
78 559 0.88
79 8 0.01
80 1 0.00
ACGTcount: A:0.24, C:0.31, G:0.20, T:0.25
Consensus pattern (78 bp):
ATCTCTTACCCCGAGCCTAGGGCAGATTGCAGCCATCCGATCTTTTACCCCGAGCTTAGGGCAGA
TCACCATCAGCCA
Found at i:129169 original size:39 final size:39
Alignment explanation
Indices: 129012--129892 Score: 325
Period size: 39 Copynumber: 22.6 Consensus size: 39
129002 GAAGATTCCG
* * * * **
129012 ATCTCTTACCCCGATCAT-AGGGCAGATCACAATCATCTG
1 ATCTCTTACCCCGAGCTTGA-GGCAGATCACCATCAGCCA
* * *
129051 ATCTTTTACCCCGAGCCT-AGGATAGATCACCATCAGCCA
1 ATCTCTTACCCCGAGCTTGAGG-CAGATCACCATCAGCCA
* * * * * *
129090 ATCTTTTACCCCGAGCCT-AGGGTAGATTA-CAGCCATCCA
1 ATCTCTTACCCCGAGCTTGA-GGCAGATCACCA-TCAGCCA
*
129129 ATCTCTTACCCCGAGCTTGAGGCAGATCACCATCAACCA
1 ATCTCTTACCCCGAGCTTGAGGCAGATCACCATCAGCCA
* * * * *
129168 ATCTCTTACGCTGAGCTTG-GCGCAGATTGCAGC-T-ATCCG
1 ATCTCTTACCCCGAGCTTGAG-GCAGA-T-CACCATCAGCCA
* * * * * *
129207 ATCTTTTATCCCGAGCTTGGGGTAGATCACCATTAACCA
1 ATCTCTTACCCCGAGCTTGAGGCAGATCACCATCAGCCA
* * * *
129246 ATTTGTTACCCCGAGCTTGTA-GCAGATTGTAGCCATCTG---
1 ATCTCTTACCCCGAGCTTG-AGGCAGA-T-CA-CCATCAGCCA
* * * *
129285 ATCTTTTACCCCGAGCCTGGGGCAGATCACCCTCAGCCA
1 ATCTCTTACCCCGAGCTTGAGGCAGATCACCATCAGCCA
** * *
129324 ATCTCTTACATCGAGCCT-AGG-ACGTATTGCAGCCAT---CCT
1 ATCTCTTACCCCGAGCTTGAGGCA-G-A-T-CA-CCATCAGCCA
*
129363 ATCTCTT-CCCCAAGCTTGAGGCAGATCACCATCAGCCA
1 ATCTCTTACCCCGAGCTTGAGGCAGATCACCATCAGCCA
* * * * * ****** * *
129401 ATTTCTTGCCCTGAGCCTGGGGCAGATTGTGGCCATCCG
1 ATCTCTTACCCCGAGCTTGAGGCAGATCACCATCAGCCA
* * * **
129440 ATCTTTTACCCTGAGCTTGAGGTAGGCCACCATCAGCCA
1 ATCTCTTACCCCGAGCTTGAGGCAGATCACCATCAGCCA
** * * *
129479 ATCTCAAACCCCGAGCTTAAGGTAGATTGCAGCCATCTG---
1 ATCTCTTACCCCGAGCTTGAGGCAGA-T-CA-CCATCAGCCA
* * *
129518 ATCTTTTACCCCGAGCCTG-GG-ATGGATCACCATTAGCCA
1 ATCTCTTACCCCGAGCTTGAGGCA--GATCACCATCAGCCA
* * * *
129557 ATCTCTTACCTCGAGCTTGGGGCGGAATGCAGCCAT---CCT
1 ATCTCTTACCCCGAGCTTGAGGCAG-AT-CA-CCATCAGCCA
*
129596 ATCTCTTACCCCGAGCTTGGGGCAGATCACCATCAGCCA
1 ATCTCTTACCCCGAGCTTGAGGCAGATCACCATCAGCCA
* * *
129635 ATCTCTTACCCTGAGCTTGGGGCAGATTGTAGCCAT---CCA
1 ATCTCTTACCCCGAGCTTGAGGCAGA-T-CA-CCATCAGCCA
* * * *
129674 ATCTATTACCCCGAGCTT-AGGGTAGGTAACCATCAGCCA
1 ATCTCTTACCCCGAGCTTGA-GGCAGATCACCATCAGCCA
* ** * * * *
129713 ATCTATTACCTAGAGCCT-AGGGCAGATTA-CAGTCATCCG
1 ATCTCTTACCCCGAGCTTGA-GGCAGATCACCA-TCAGCCA
* * *
129752 ATCTTTTACCCCGAGCCTGAGGCGGATCACCATCAGCCA
1 ATCTCTTACCCCGAGCTTGAGGCAGATCACCATCAGCCA
* * ** * * * *
129791 ATCTCTTACCCCAAGCCT-AGGGCAGATTGCAACCATCTA
1 ATCTCTTACCCCGAGCTTGA-GGCAGATCACCATCAGCCA
* * * *
129830 ATCTTTTACCCCAAGCCT-AGGGCAAATCACCATCAGCCA
1 ATCTCTTACCCCGAGCTTGA-GGCAGATCACCATCAGCCA
* *
129869 ATCTCTTATCCCGAACTTGAGGCA
1 ATCTCTTACCCCGAGCTTGAGGCA
129893 AATTGTAACC
Statistics
Matches: 630, Mismatches: 154, Indels: 116
0.70 0.17 0.13
Matches are distributed among these distances:
35 4 0.01
36 20 0.03
37 12 0.02
38 35 0.06
39 507 0.80
40 20 0.03
41 11 0.02
42 21 0.03
ACGTcount: A:0.24, C:0.31, G:0.20, T:0.25
Consensus pattern (39 bp):
ATCTCTTACCCCGAGCTTGAGGCAGATCACCATCAGCCA
Found at i:130270 original size:48 final size:48
Alignment explanation
Indices: 130182--130277 Score: 113
Period size: 48 Copynumber: 2.0 Consensus size: 48
130172 TGGACTGAAT
* ** *
130182 TCATCTTTTTGACGAGATACAGAGAAATAAATTAAATCAATGAGGCGA
1 TCATCTTTCTGACGAGATACAGAGAAATAAACCAAATCAATGAAGCGA
* * *
130230 TCATCTTTCTGATGAGATACAGAGAAGA-AGACCAATTCAATGAAGCGA
1 TCATCTTTCTGACGAGATACAGAGAA-ATAAACCAAATCAATGAAGCGA
130278 AGCTCAATAG
Statistics
Matches: 40, Mismatches: 7, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
48 39 0.98
49 1 0.03
ACGTcount: A:0.41, C:0.15, G:0.20, T:0.25
Consensus pattern (48 bp):
TCATCTTTCTGACGAGATACAGAGAAATAAACCAAATCAATGAAGCGA
Found at i:130686 original size:6 final size:6
Alignment explanation
Indices: 130670--130725 Score: 55
Period size: 6 Copynumber: 9.7 Consensus size: 6
130660 TGAACCCAAA
** *
130670 TAAATTT TAAATT TAAATT T--ATT TTTATT TAAATT T-ATTT TAAATT
1 TAAA-TT TAAATT TAAATT TAAATT TAAATT TAAATT TAAATT TAAATT
130716 TAAATT TAAA
1 TAAATT TAAA
130726 AATGGCCCAA
Statistics
Matches: 42, Mismatches: 4, Indels: 7
0.79 0.08 0.13
Matches are distributed among these distances:
4 4 0.10
5 4 0.10
6 30 0.71
7 4 0.10
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (6 bp):
TAAATT
Found at i:130701 original size:16 final size:17
Alignment explanation
Indices: 130673--130723 Score: 86
Period size: 17 Copynumber: 3.1 Consensus size: 17
130663 ACCCAAATAA
130673 ATTTTAAATTTAAATTT
1 ATTTTAAATTTAAATTT
*
130690 ATTTT-TATTTAAATTT
1 ATTTTAAATTTAAATTT
130706 ATTTTAAATTTAAATTT
1 ATTTTAAATTTAAATTT
130723 A
1 A
130724 AAAATGGCCC
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
16 15 0.48
17 16 0.52
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (17 bp):
ATTTTAAATTTAAATTT
Found at i:132338 original size:30 final size:30
Alignment explanation
Indices: 132311--132464 Score: 172
Period size: 30 Copynumber: 5.2 Consensus size: 30
132301 TTAAAAATCC
* *
132311 CATTTTAACCCCCAAACTTTTTCAAAATTA
1 CATTTTAACCCCTAAACTTTTCCAAAATTA
* * *
132341 TATTTTAACCCTTGAACTTTTCCAAAATTA
1 CATTTTAACCCCTAAACTTTTCCAAAATTA
* * *
132371 CATATTAACCCATAAA-TTTATAC-AAATTA
1 CATTTTAACCCCTAAACTTT-TCCAAAATTA
*
132400 CATTTTAACCCTTAAACTTTTCCAAAATTA
1 CATTTTAACCCCTAAACTTTTCCAAAATTA
132430 CATTTTAACCCC-AAA-TTGTTCCAAAATTA
1 CATTTTAACCCCTAAACTT-TTCCAAAATTA
*
132459 CTTTTT
1 CATTTT
132465 TAATTGCTAT
Statistics
Matches: 105, Mismatches: 15, Indels: 9
0.81 0.12 0.07
Matches are distributed among these distances:
28 2 0.02
29 44 0.42
30 59 0.56
ACGTcount: A:0.37, C:0.22, G:0.01, T:0.40
Consensus pattern (30 bp):
CATTTTAACCCCTAAACTTTTCCAAAATTA
Found at i:132457 original size:59 final size:58
Alignment explanation
Indices: 132311--132464 Score: 193
Period size: 59 Copynumber: 2.6 Consensus size: 58
132301 TTAAAAATCC
* * *
132311 CATTTTAACCCCCAAACTTTTTCAAAATTATATTTTAACCCTTGAACTTTTCCAAAATTA
1 CATTTTAA-CCCCAAA-TTTTACAAAATTACATTTTAACCCTTAAACTTTTCCAAAATTA
* *
132371 CATATTAACCCATAAATTTATAC-AAATTACATTTTAACCCTTAAACTTTTCCAAAATTA
1 CATTTTAACCC-CAAATTT-TACAAAATTACATTTTAACCCTTAAACTTTTCCAAAATTA
* *
132430 CATTTTAACCCCAAATTGTTCCAAAATTACTTTTT
1 CATTTTAACCCCAAATT-TTACAAAATTACATTTT
132465 TAATTGCTAT
Statistics
Matches: 81, Mismatches: 9, Indels: 9
0.82 0.09 0.09
Matches are distributed among these distances:
58 7 0.09
59 62 0.77
60 12 0.15
ACGTcount: A:0.37, C:0.22, G:0.01, T:0.40
Consensus pattern (58 bp):
CATTTTAACCCCAAATTTTACAAAATTACATTTTAACCCTTAAACTTTTCCAAAATTA
Found at i:133037 original size:50 final size:50
Alignment explanation
Indices: 132979--133082 Score: 190
Period size: 50 Copynumber: 2.1 Consensus size: 50
132969 TCGATACCAC
**
132979 CTTAAAAATATCGATACCTTTTTTTCAAAATTAGTAAATATAGCTGTAAA
1 CTTAAAAATATCGATACCTTTTTTAAAAAATTAGTAAATATAGCTGTAAA
133029 CTTAAAAATATCGATACCTTTTTTAAAAAATTAGTAAATATAGCTGTAAA
1 CTTAAAAATATCGATACCTTTTTTAAAAAATTAGTAAATATAGCTGTAAA
133079 CTTA
1 CTTA
133083 GTAAAACCCC
Statistics
Matches: 52, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
50 52 1.00
ACGTcount: A:0.43, C:0.12, G:0.08, T:0.38
Consensus pattern (50 bp):
CTTAAAAATATCGATACCTTTTTTAAAAAATTAGTAAATATAGCTGTAAA
Found at i:133893 original size:23 final size:23
Alignment explanation
Indices: 133827--133893 Score: 82
Period size: 23 Copynumber: 2.9 Consensus size: 23
133817 AGTGCTGGGT
*
133827 AACAA-AGAGCACACACAGTGATA
1 AACAATAG-GCACACACAGTGCTA
* *
133850 AACAGTAGGCACACATAGTGCTA
1 AACAATAGGCACACACAGTGCTA
*
133873 AACAATTGGCACACACAGTGC
1 AACAATAGGCACACACAGTGC
133894 AAATCAGTAA
Statistics
Matches: 37, Mismatches: 6, Indels: 2
0.82 0.13 0.04
Matches are distributed among these distances:
23 35 0.95
24 2 0.05
ACGTcount: A:0.43, C:0.24, G:0.19, T:0.13
Consensus pattern (23 bp):
AACAATAGGCACACACAGTGCTA
Found at i:147855 original size:124 final size:124
Alignment explanation
Indices: 147697--147945 Score: 462
Period size: 124 Copynumber: 2.0 Consensus size: 124
147687 ATGCCTTGCT
* *
147697 TACAAGGAAATCAAAACTTGTCTTAAAGAGCCCTTTAGTGAGTATGTCAGCAATATGTTGTTTTG
1 TACAAGGAAATCAAAACTTGTCTTAAAGAACCCTTTAGTGAGTATGTCAACAATATGTTGTTTTG
*
147762 AACGAACAAATGACATGCACACTTGGCCTTCTTCAATCTTTTCCTTGATAAAGTGCCTA
66 AACGAACAAACGACATGCACACTTGGCCTTCTTCAATCTTTTCCTTGATAAAGTGCCTA
*
147821 TACAAGGAAATCAAAACTTGTCTTAAAGAACCCTTTAGTGAGTATGTCAACAATCTGTTGTTTTG
1 TACAAGGAAATCAAAACTTGTCTTAAAGAACCCTTTAGTGAGTATGTCAACAATATGTTGTTTTG
147886 AACGAACAAACGACATGCACACTTGGCCTTCTTCAATCTTTTCCTTGATAAAGTGCCTA
66 AACGAACAAACGACATGCACACTTGGCCTTCTTCAATCTTTTCCTTGATAAAGTGCCTA
147945 T
1 T
147946 CAATCTCAAC
Statistics
Matches: 121, Mismatches: 4, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
124 121 1.00
ACGTcount: A:0.32, C:0.20, G:0.16, T:0.32
Consensus pattern (124 bp):
TACAAGGAAATCAAAACTTGTCTTAAAGAACCCTTTAGTGAGTATGTCAACAATATGTTGTTTTG
AACGAACAAACGACATGCACACTTGGCCTTCTTCAATCTTTTCCTTGATAAAGTGCCTA
Found at i:154512 original size:26 final size:27
Alignment explanation
Indices: 154483--154533 Score: 70
Period size: 26 Copynumber: 1.9 Consensus size: 27
154473 TATCGAAAAT
154483 GAAGAGAAGAAAATA-T-ATGAAAATCG
1 GAAGAGAA-AAAATACTAATGAAAATCG
*
154509 GAAGAGAAAATATACTAATGAAAAT
1 GAAGAGAAAAAATACTAATGAAAAT
154534 TACTTGTATT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
25 5 0.23
26 9 0.41
27 8 0.36
ACGTcount: A:0.59, C:0.04, G:0.20, T:0.18
Consensus pattern (27 bp):
GAAGAGAAAAAATACTAATGAAAATCG
Found at i:157092 original size:166 final size:168
Alignment explanation
Indices: 156811--157142 Score: 533
Period size: 166 Copynumber: 2.0 Consensus size: 168
156801 CCTACATGCC
* *
156811 AACCGCTGTTTCCATCCCAGATTCTAAGAGACAGAGTAGTTAAACTTGGAAAAGGCATGAATTAC
1 AACCACTGTTTCCATCCCAGATTCTAAGAAACAGAGTAGTTAAACTTGGAAAAGGCATGAATTAC
*
156876 TGCTACAGTAAGGAAGGCCTCAATCCAAGTGATGAGAATTCTGCCTTAGTCCACTATATCCAGGT
66 TGCTACAGTAAGGAAGGCCTCAATCCAAGTGATGAGAATTCTGCCTTAGTCCACTATATCCAGAT
* * *
156941 AATTGTGTTTGTCTGGA-GAT-CATAAAATTTTTTGTG
131 AATTATGTTTGTCCGGAGGATGCAAAAAATTTTTTGTG
* * *
156977 AACCACTGTTTCCATTCCAGATTCTAAGAAATAGAGTAGTTAAACTTGGAAAAGGCATGGATTAC
1 AACCACTGTTTCCATCCCAGATTCTAAGAAACAGAGTAGTTAAACTTGGAAAAGGCATGAATTAC
* * *
157042 TGCTACAGTAAGGAAGGCCTTAATCCAAGTGATGAGAATTCTGGCTTAGTCCACTATATCCATAT
66 TGCTACAGTAAGGAAGGCCTCAATCCAAGTGATGAGAATTCTGCCTTAGTCCACTATATCCAGAT
*
157107 AATTATGTTTGTCCGGAGGATGTAAAAAATTTTTTG
131 AATTATGTTTGTCCGGAGGATGCAAAAAATTTTTTG
157143 ACTCTATTTT
Statistics
Matches: 151, Mismatches: 13, Indels: 2
0.91 0.08 0.01
Matches are distributed among these distances:
166 136 0.90
167 3 0.02
168 12 0.08
ACGTcount: A:0.32, C:0.17, G:0.20, T:0.31
Consensus pattern (168 bp):
AACCACTGTTTCCATCCCAGATTCTAAGAAACAGAGTAGTTAAACTTGGAAAAGGCATGAATTAC
TGCTACAGTAAGGAAGGCCTCAATCCAAGTGATGAGAATTCTGCCTTAGTCCACTATATCCAGAT
AATTATGTTTGTCCGGAGGATGCAAAAAATTTTTTGTG
Found at i:160044 original size:82 final size:82
Alignment explanation
Indices: 159907--160140 Score: 371
Period size: 82 Copynumber: 2.9 Consensus size: 82
159897 ATTGGTATTG
* *
159907 GTATTTGTAACACACTCAAGTGCAAAGTATTTTTTATGACATTGAAGTGGAATTATGCTTTCTCT
1 GTATTTGTAACACACTCAAGTGCAGAGTATTTTTGATGACATTGAAGTGGAATTATGCTTTCTCT
*
159972 GTCACCTAAATCTTAAT
66 GTCACCTAAATCTTAAA
* * *
159989 GTATTTGTAACACACTCAAGTGTAGAGTATTTTTGATGACACTGAAGTGGAATTATGTTTTCTCT
1 GTATTTGTAACACACTCAAGTGCAGAGTATTTTTGATGACATTGAAGTGGAATTATGCTTTCTCT
160054 GTCACCTAAATCTTAAA
66 GTCACCTAAATCTTAAA
* * * *
160071 GTATTTGTAACACACTCAACTGCAGAGCATTTTTGATAACATTGAAGTGGGATTATGC-TTCTCT
1 GTATTTGTAACACACTCAAGTGCAGAGTATTTTTGATGACATTGAAGTGGAATTATGCTTTCTCT
160135 GTCACC
66 GTCACC
160141 ATATTGTTTC
Statistics
Matches: 139, Mismatches: 13, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
81 12 0.09
82 127 0.91
ACGTcount: A:0.29, C:0.17, G:0.17, T:0.37
Consensus pattern (82 bp):
GTATTTGTAACACACTCAAGTGCAGAGTATTTTTGATGACATTGAAGTGGAATTATGCTTTCTCT
GTCACCTAAATCTTAAA
Found at i:164437 original size:21 final size:22
Alignment explanation
Indices: 164406--164451 Score: 76
Period size: 21 Copynumber: 2.1 Consensus size: 22
164396 ATTCACATGT
164406 TTTCTTACTCATGATTCTTTTG
1 TTTCTTACTCATGATTCTTTTG
*
164428 TTTC-TACTCATTATTCTTTTG
1 TTTCTTACTCATGATTCTTTTG
164449 TTT
1 TTT
164452 TTGATTTTTC
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
21 19 0.83
22 4 0.17
ACGTcount: A:0.13, C:0.17, G:0.07, T:0.63
Consensus pattern (22 bp):
TTTCTTACTCATGATTCTTTTG
Found at i:168224 original size:21 final size:21
Alignment explanation
Indices: 168185--168224 Score: 64
Period size: 21 Copynumber: 1.9 Consensus size: 21
168175 ACATTTTTCT
168185 TACTCTTTTCTTTTGTGTTTG
1 TACTCTTTTCTTTTGTGTTTG
168206 TACTCATTTTCTTTT-TGTT
1 TACTC-TTTTCTTTTGTGTT
168225 CTTTTCACTT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
21 9 0.50
22 9 0.50
ACGTcount: A:0.07, C:0.15, G:0.10, T:0.68
Consensus pattern (21 bp):
TACTCTTTTCTTTTGTGTTTG
Found at i:171251 original size:10 final size:11
Alignment explanation
Indices: 171238--171282 Score: 51
Period size: 10 Copynumber: 4.3 Consensus size: 11
171228 TTGCTATATA
171238 TTTCTC-TTCT
1 TTTCTCTTTCT
171248 TTTCTCTTT-T
1 TTTCTCTTTCT
*
171258 ATTCTTCTTTCT
1 TTTC-TCTTTCT
171270 TTT-TCTTTCT
1 TTTCTCTTTCT
171280 TTT
1 TTT
171283 TGTGAATTTT
Statistics
Matches: 30, Mismatches: 2, Indels: 6
0.79 0.05 0.16
Matches are distributed among these distances:
10 20 0.67
11 7 0.23
12 3 0.10
ACGTcount: A:0.02, C:0.22, G:0.00, T:0.76
Consensus pattern (11 bp):
TTTCTCTTTCT
Found at i:180168 original size:24 final size:23
Alignment explanation
Indices: 180135--180181 Score: 60
Period size: 22 Copynumber: 2.0 Consensus size: 23
180125 ATCTGCATAC
180135 TAAATAGTTAAAATTGTCAATGTAA
1 TAAATAGTT--AATTGTCAATGTAA
*
180160 TAAA-AGTTAATTGTCAGTGTAA
1 TAAATAGTTAATTGTCAATGTAA
180182 CTGAAAGTAA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
22 13 0.62
24 4 0.19
25 4 0.19
ACGTcount: A:0.45, C:0.04, G:0.15, T:0.36
Consensus pattern (23 bp):
TAAATAGTTAATTGTCAATGTAA
Found at i:180194 original size:23 final size:22
Alignment explanation
Indices: 180145--180194 Score: 64
Period size: 22 Copynumber: 2.2 Consensus size: 22
180135 TAAATAGTTA
180145 AAATTGTCAATGTAATAAAAGT
1 AAATTGTCAATGTAATAAAAGT
* * *
180167 TAATTGTCAGTGTAACTGAAAGT
1 AAATTGTCAATGTAA-TAAAAGT
180190 AAATT
1 AAATT
180195 AAATTGTTGT
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
22 13 0.57
23 10 0.43
ACGTcount: A:0.44, C:0.06, G:0.16, T:0.34
Consensus pattern (22 bp):
AAATTGTCAATGTAATAAAAGT
Found at i:194490 original size:17 final size:17
Alignment explanation
Indices: 194468--194504 Score: 56
Period size: 17 Copynumber: 2.2 Consensus size: 17
194458 TTGTAGTATA
* *
194468 ATTGTCCATGCATTTTT
1 ATTGTCAATGCATTTCT
194485 ATTGTCAATGCATTTCT
1 ATTGTCAATGCATTTCT
194502 ATT
1 ATT
194505 ATTACTGCAT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.22, C:0.16, G:0.11, T:0.51
Consensus pattern (17 bp):
ATTGTCAATGCATTTCT
Found at i:206651 original size:26 final size:26
Alignment explanation
Indices: 206621--206670 Score: 66
Period size: 26 Copynumber: 1.9 Consensus size: 26
206611 AATGTCATTT
*
206621 CTTCATAAAAAT-TCAATCGTTTAAAA
1 CTTCA-AAAAATGTCAATCATTTAAAA
*
206647 CTTCAAAATATGTCAATCATTTAA
1 CTTCAAAAAATGTCAATCATTTAA
206671 GGATCGTAAT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
25 5 0.24
26 16 0.76
ACGTcount: A:0.44, C:0.16, G:0.04, T:0.36
Consensus pattern (26 bp):
CTTCAAAAAATGTCAATCATTTAAAA
Found at i:207771 original size:28 final size:28
Alignment explanation
Indices: 207740--207797 Score: 116
Period size: 28 Copynumber: 2.1 Consensus size: 28
207730 TATTAACTTG
207740 TATAATTTAAATACTAATTATACGAACT
1 TATAATTTAAATACTAATTATACGAACT
207768 TATAATTTAAATACTAATTATACGAACT
1 TATAATTTAAATACTAATTATACGAACT
207796 TA
1 TA
207798 CTCGTCGGAT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 30 1.00
ACGTcount: A:0.47, C:0.10, G:0.03, T:0.40
Consensus pattern (28 bp):
TATAATTTAAATACTAATTATACGAACT
Found at i:208806 original size:13 final size:13
Alignment explanation
Indices: 208788--208813 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
208778 TATGATGTCA
208788 AATGTATCTCAAT
1 AATGTATCTCAAT
208801 AATGTATCTCAAT
1 AATGTATCTCAAT
208814 CGCAATCTCA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.08, T:0.38
Consensus pattern (13 bp):
AATGTATCTCAAT
Found at i:214442 original size:27 final size:27
Alignment explanation
Indices: 214413--214508 Score: 138
Period size: 27 Copynumber: 3.6 Consensus size: 27
214403 GCTTGAGGAG
*
214413 TTATTCTGATTCTGGCTCGAAAGAGCG
1 TTATTCTGATTCTGGCTCGAAAGAGCA
* *
214440 TTATTCTAATTCTGGCTCGAAAAAGCA
1 TTATTCTGATTCTGGCTCGAAAGAGCA
* * *
214467 ATATTCTGATTTTAGCTCGAAAGAGCA
1 TTATTCTGATTCTGGCTCGAAAGAGCA
214494 TTATTCTGATTCTGG
1 TTATTCTGATTCTGG
214509 GCTTGTAAGA
Statistics
Matches: 58, Mismatches: 11, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
27 58 1.00
ACGTcount: A:0.27, C:0.17, G:0.20, T:0.36
Consensus pattern (27 bp):
TTATTCTGATTCTGGCTCGAAAGAGCA
Found at i:214534 original size:24 final size:24
Alignment explanation
Indices: 214502--214595 Score: 93
Period size: 24 Copynumber: 3.9 Consensus size: 24
214492 CATTATTCTG
*
214502 ATTCTGGGCTTGTAAGAGCTAACC
1 ATTCTGGGCTCGTAAGAGCTAACC
*
214526 ATTCTGGGCTCGTGAGAGCTAACC
1 ATTCTGGGCTCGTAAGAGCTAACC
***
214550 -TATCTGGGCTCACGAGAGCTAACC
1 AT-TCTGGGCTCGTAAGAGCTAACC
* *
214574 -TATCTGTGCTCGTATGAGCTAA
1 AT-TCTGGGCTCGTAAGAGCTAA
214596 TTTTGTTCGG
Statistics
Matches: 60, Mismatches: 9, Indels: 2
0.85 0.13 0.03
Matches are distributed among these distances:
23 1 0.02
24 59 0.98
ACGTcount: A:0.23, C:0.23, G:0.26, T:0.28
Consensus pattern (24 bp):
ATTCTGGGCTCGTAAGAGCTAACC
Found at i:221276 original size:26 final size:26
Alignment explanation
Indices: 221247--221297 Score: 77
Period size: 26 Copynumber: 2.0 Consensus size: 26
221237 TAGGGATTTG
221247 TTTTATATTAC-AATGTTAATTTCTTA
1 TTTTATATT-CTAATGTTAATTTCTTA
*
221273 TTTTATATTCTGATGTTAATTTCTT
1 TTTTATATTCTAATGTTAATTTCTT
221298 TTGTCTCATG
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
25 1 0.04
26 22 0.96
ACGTcount: A:0.25, C:0.08, G:0.06, T:0.61
Consensus pattern (26 bp):
TTTTATATTCTAATGTTAATTTCTTA
Found at i:229690 original size:38 final size:38
Alignment explanation
Indices: 229646--229732 Score: 138
Period size: 38 Copynumber: 2.3 Consensus size: 38
229636 AAATTGTGGC
* * *
229646 TGCATCTTTGCACACTTTCCAGCATTGATCTTTAGAAG
1 TGCATCTTTGCACACTTTCCAACATTAATCTTCAGAAG
229684 TGCATCTTTGCACACTTTCCAACATTAATCTTCAGAAG
1 TGCATCTTTGCACACTTTCCAACATTAATCTTCAGAAG
*
229722 TGAATCTTTGC
1 TGCATCTTTGC
229733 GCTGACATTT
Statistics
Matches: 45, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
38 45 1.00
ACGTcount: A:0.25, C:0.24, G:0.14, T:0.37
Consensus pattern (38 bp):
TGCATCTTTGCACACTTTCCAACATTAATCTTCAGAAG
Found at i:230017 original size:18 final size:18
Alignment explanation
Indices: 229990--230031 Score: 59
Period size: 18 Copynumber: 2.4 Consensus size: 18
229980 ATATACTAAG
229990 AAAT-AAAATGCAATGAC
1 AAATAAAAATGCAATGAC
*
230007 AAATAAAAATGTAATGAC
1 AAATAAAAATGCAATGAC
*
230025 AACTAAA
1 AAATAAA
230032 TGAGATGCAT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
17 4 0.18
18 18 0.82
ACGTcount: A:0.62, C:0.10, G:0.10, T:0.19
Consensus pattern (18 bp):
AAATAAAAATGCAATGAC
Found at i:236615 original size:14 final size:15
Alignment explanation
Indices: 236588--236620 Score: 50
Period size: 14 Copynumber: 2.3 Consensus size: 15
236578 AAGAGAAAAT
*
236588 AGAAGAAGAATGAAG
1 AGAAGAAGAATGAAA
236603 AGAAGAA-AATGAAA
1 AGAAGAAGAATGAAA
236617 AGAA
1 AGAA
236621 ATGAAGAAGC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
14 10 0.59
15 7 0.41
ACGTcount: A:0.67, C:0.00, G:0.27, T:0.06
Consensus pattern (15 bp):
AGAAGAAGAATGAAA
Found at i:245741 original size:29 final size:29
Alignment explanation
Indices: 245709--245766 Score: 116
Period size: 29 Copynumber: 2.0 Consensus size: 29
245699 GTTCAAAACC
245709 CTCAATAATTATTTTCTAACCGTGAGGAG
1 CTCAATAATTATTTTCTAACCGTGAGGAG
245738 CTCAATAATTATTTTCTAACCGTGAGGAG
1 CTCAATAATTATTTTCTAACCGTGAGGAG
245767 ATGTGAATAA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 29 1.00
ACGTcount: A:0.31, C:0.17, G:0.17, T:0.34
Consensus pattern (29 bp):
CTCAATAATTATTTTCTAACCGTGAGGAG
Found at i:250119 original size:6 final size:6
Alignment explanation
Indices: 250108--250134 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
250098 AATGTTATAA
250108 TTTCTT TTTCTT TTTCTT TTTCTT TTT
1 TTTCTT TTTCTT TTTCTT TTTCTT TTT
250135 TTGTAATTTC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.00, C:0.15, G:0.00, T:0.85
Consensus pattern (6 bp):
TTTCTT
Found at i:271324 original size:21 final size:20
Alignment explanation
Indices: 271300--271338 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
271290 CTTTCACAAC
271300 AAAATTAAAAAATAATTTTCA
1 AAAATT-AAAAATAATTTTCA
*
271321 AAAATTTAAAATAATTTT
1 AAAATTAAAAATAATTTT
271339 TTAATTTTAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 11 0.65
21 6 0.35
ACGTcount: A:0.59, C:0.03, G:0.00, T:0.38
Consensus pattern (20 bp):
AAAATTAAAAATAATTTTCA
Found at i:271343 original size:28 final size:28
Alignment explanation
Indices: 271312--271365 Score: 76
Period size: 28 Copynumber: 1.9 Consensus size: 28
271302 AATTAAAAAA
271312 TAATTTTCAAAA-ATTTA-AAATAATTTTT
1 TAATTTT-AAAATATTTATAAA-AATTTTT
271340 TAATTTTAAAATATTTATAAAAATTT
1 TAATTTTAAAATATTTATAAAAATTT
271366 CGGAATTTAT
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
27 4 0.17
28 17 0.71
29 3 0.12
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.50
Consensus pattern (28 bp):
TAATTTTAAAATATTTATAAAAATTTTT
Found at i:279561 original size:26 final size:26
Alignment explanation
Indices: 279521--279658 Score: 116
Period size: 26 Copynumber: 5.3 Consensus size: 26
279511 GTTTCAGAGG
*
279521 TTAGCTCTTATGAGCCCAAACAAAAA
1 TTAGCTCTTACGAGCCCAAACAAAAA
* *
279547 TTATCTCTTACGAGCCCAAACAAAAT
1 TTAGCTCTTACGAGCCCAAACAAAAA
* * * *
279573 TTAGCTCTTACGAGCCTAAATAGAAT
1 TTAGCTCTTACGAGCCCAAACAAAAA
* * *** * *
279599 TTAGCTCATACAAGCCTGGACAGAAT
1 TTAGCTCTTACGAGCCCAAACAAAAA
* *
279625 TTAGCTCATATGAGCCCAAAC-AAAA
1 TTAGCTCTTACGAGCCCAAACAAAAA
279650 TTATGCTCT
1 TTA-GCTCT
279659 ATCGAGTCAG
Statistics
Matches: 91, Mismatches: 20, Indels: 2
0.81 0.18 0.02
Matches are distributed among these distances:
25 5 0.05
26 86 0.95
ACGTcount: A:0.37, C:0.23, G:0.13, T:0.27
Consensus pattern (26 bp):
TTAGCTCTTACGAGCCCAAACAAAAA
Found at i:279581 original size:52 final size:52
Alignment explanation
Indices: 279521--279658 Score: 143
Period size: 52 Copynumber: 2.7 Consensus size: 52
279511 GTTTCAGAGG
*
279521 TTAGCTCTTATGAGCCCAAACAAAAATTATCTCTTACGAGCCCAAACAAAAT
1 TTAGCTCTTATGAGCCCAAACAAAAATTATCTCTTACAAGCCCAAACAAAAT
* * * * * * * *** *
279573 TTAGCTCTTACGAGCCTAAATAGAATTTAGCTCATACAAGCCTGGACAGAAT
1 TTAGCTCTTATGAGCCCAAACAAAAATTATCTCTTACAAGCCCAAACAAAAT
*
279625 TTAGCTCATATGAGCCCAAAC-AAAATTATGCTCT
1 TTAGCTCTTATGAGCCCAAACAAAAATTAT-CTCT
279659 ATCGAGTCAG
Statistics
Matches: 65, Mismatches: 20, Indels: 2
0.75 0.23 0.02
Matches are distributed among these distances:
51 5 0.08
52 60 0.92
ACGTcount: A:0.37, C:0.23, G:0.13, T:0.27
Consensus pattern (52 bp):
TTAGCTCTTATGAGCCCAAACAAAAATTATCTCTTACAAGCCCAAACAAAAT
Found at i:283387 original size:19 final size:19
Alignment explanation
Indices: 283363--283415 Score: 79
Period size: 19 Copynumber: 2.8 Consensus size: 19
283353 GTATCAGTAT
283363 CGCTCTTACGAGCCAATAC
1 CGCTCTTACGAGCCAATAC
*
283382 CGCTCTTACGAGCCAATAT
1 CGCTCTTACGAGCCAATAC
* *
283401 CACTCTTTCGAGCCA
1 CGCTCTTACGAGCCA
283416 GTGCAGTAAA
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
19 31 1.00
ACGTcount: A:0.25, C:0.36, G:0.15, T:0.25
Consensus pattern (19 bp):
CGCTCTTACGAGCCAATAC
Found at i:286217 original size:21 final size:21
Alignment explanation
Indices: 286180--286226 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 21
286170 ACCCGACCCG
* *
286180 TTGACTATTAACTGTTGACCA
1 TTGACTATTAACCGTTGACAA
* *
286201 TTGACTATTGACCGTTGGCAA
1 TTGACTATTAACCGTTGACAA
286222 TTGAC
1 TTGAC
286227 CGTTGGCTTT
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.26, C:0.19, G:0.19, T:0.36
Consensus pattern (21 bp):
TTGACTATTAACCGTTGACAA
Found at i:286224 original size:14 final size:14
Alignment explanation
Indices: 286207--286233 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
286197 ACCATTGACT
286207 ATTGACCGTTGGCA
1 ATTGACCGTTGGCA
286221 ATTGACCGTTGGC
1 ATTGACCGTTGGC
286234 TTTTTGGGTT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.19, C:0.22, G:0.30, T:0.30
Consensus pattern (14 bp):
ATTGACCGTTGGCA
Found at i:287293 original size:13 final size:13
Alignment explanation
Indices: 287277--287304 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
287267 TTTTATAGAT
287277 TTATTTTATTTTA
1 TTATTTTATTTTA
287290 TTATTTTATTTTA
1 TTATTTTATTTTA
287303 TT
1 TT
287305 TTGGGTTTTC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.21, C:0.00, G:0.00, T:0.79
Consensus pattern (13 bp):
TTATTTTATTTTA
Found at i:298191 original size:30 final size:28
Alignment explanation
Indices: 298133--298210 Score: 86
Period size: 30 Copynumber: 2.6 Consensus size: 28
298123 TTAATCAAAG
298133 TTCAATTTACTCCCTAAAATTTCTTAAAA
1 TTCAATTTACTCCCT-AAATTTCTTAAAA
298162 TTACAATTTACTCCCTAAATGTTAC-TAAAA
1 TT-CAATTTACTCCCTAAAT-TT-CTTAAAA
* *
298192 TTCTAATTTAGTCCTTAAA
1 TTC-AATTTACTCCCTAAA
298211 ATAAATTTTG
Statistics
Matches: 43, Mismatches: 2, Indels: 7
0.83 0.04 0.13
Matches are distributed among these distances:
29 7 0.16
30 35 0.81
31 1 0.02
ACGTcount: A:0.37, C:0.19, G:0.03, T:0.41
Consensus pattern (28 bp):
TTCAATTTACTCCCTAAATTTCTTAAAA
Found at i:311136 original size:95 final size:95
Alignment explanation
Indices: 310973--311153 Score: 292
Period size: 95 Copynumber: 1.9 Consensus size: 95
310963 AAAATGTACC
*
310973 CCACAAAACTTGAAAAATTCAGCTTATGAAAATTCAAAATGATGTTTAGTCATATTTTTCTGGTA
1 CCACAAAACTTGAAAAATTCAGCTTATGAAAATTCAAAATGATGTGTAGTCATATTTTTCTGGTA
311038 AAAACAGAT-TAATAAATTGGCTCAAAAACT
66 AAAACAGATGT-ATAAATTGGCTCAAAAACT
* * * * *
311068 CCACAAAACTTGAAGAATTCAGCTTATGAAAATTCCAAGTGATGTGTGGTCATCTTTTTCTGGTA
1 CCACAAAACTTGAAAAATTCAGCTTATGAAAATTCAAAATGATGTGTAGTCATATTTTTCTGGTA
311133 AAAACAGATGTATAAATTGGC
66 AAAACAGATGTATAAATTGGC
311154 CCAATAGTTT
Statistics
Matches: 79, Mismatches: 6, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
95 78 0.99
96 1 0.01
ACGTcount: A:0.39, C:0.14, G:0.15, T:0.31
Consensus pattern (95 bp):
CCACAAAACTTGAAAAATTCAGCTTATGAAAATTCAAAATGATGTGTAGTCATATTTTTCTGGTA
AAAACAGATGTATAAATTGGCTCAAAAACT
Found at i:322615 original size:58 final size:58
Alignment explanation
Indices: 322503--322618 Score: 135
Period size: 58 Copynumber: 2.0 Consensus size: 58
322493 GTTAACTGCA
* * * ** * *
322503 TAGACTTAGAAAATTTTCTTGAAAACAATAAGTTAGTATGTAAATCTGCGAGCTATCT
1 TAGACTTAGAAAAATTTCTTAAAAACAAAAACCTAGGATGTAAATCCGCGAGCTATCT
* *
322561 TAGACTTAGAAAAATTTCTTAAAAATAAAAACCTAGGATGTGAATCCGTC-AGCTATCT
1 TAGACTTAGAAAAATTTCTTAAAAACAAAAACCTAGGATGTAAATCCG-CGAGCTATCT
322619 CATATTTGTG
Statistics
Matches: 48, Mismatches: 9, Indels: 2
0.81 0.15 0.03
Matches are distributed among these distances:
58 47 0.98
59 1 0.02
ACGTcount: A:0.40, C:0.14, G:0.15, T:0.32
Consensus pattern (58 bp):
TAGACTTAGAAAAATTTCTTAAAAACAAAAACCTAGGATGTAAATCCGCGAGCTATCT
Found at i:322894 original size:69 final size:68
Alignment explanation
Indices: 322718--322894 Score: 176
Period size: 68 Copynumber: 2.6 Consensus size: 68
322708 TCTTCTCTTA
* * * * * * *
322718 CGAACTTTAAAATGAGAATTAGAGCTTTTCTCTTGCTAACTGTGTTAGAGGTTGTAGCACTTTGC
1 CGAACCTTAAAATGACAATTAGAGCTTTGCTCTCGCTAACCGTGTTAGAGGTTGCAGCACTTCGC
322783 CTG
66 CTG
* *** * * * *
322786 TGAACCTT-AAATGACAGCCAAGAGCTTTGCTTTCACTAACCGTGTTGGAGGTTGCAGCTCTTCG
1 CGAACCTTAAAATGACA-ATTAGAGCTTTGCTCTCGCTAACCGTGTTAGAGGTTGCAGCACTTCG
322850 CCTG
65 CCTG
* *
322854 CGAATCTTAAAATGACAATTGGGAGCTTTGCTCTCGCTAAC
1 CGAACCTTAAAATGACAATT-AGAGCTTTGCTCTCGCTAAC
322895 TTCGTTGTAG
Statistics
Matches: 83, Mismatches: 23, Indels: 5
0.75 0.21 0.05
Matches are distributed among these distances:
67 7 0.08
68 51 0.61
69 25 0.30
ACGTcount: A:0.25, C:0.21, G:0.22, T:0.32
Consensus pattern (68 bp):
CGAACCTTAAAATGACAATTAGAGCTTTGCTCTCGCTAACCGTGTTAGAGGTTGCAGCACTTCGC
CTG
Found at i:327265 original size:62 final size:59
Alignment explanation
Indices: 327155--327271 Score: 153
Period size: 62 Copynumber: 1.9 Consensus size: 59
327145 ATTAGTTTAA
* * * *
327155 TATTAAATTAATATAATATTTATCAAGATAAATATTAGATTAAATTTAATATTAAATCT
1 TATTAAAATAATAGAATATTTATCAAGATAAACATTAAATTAAATTTAATATTAAATCT
* *
327214 TATTAAAATAATAGAATGTTTATCTACTAGATAAACGTTAAATTAAATTTAATATTAA
1 TATTAAAATAATAGAATATTTATC-A--AGATAAACATTAAATTAAATTTAATATTAA
327272 GATAATCACT
Statistics
Matches: 49, Mismatches: 6, Indels: 3
0.84 0.10 0.05
Matches are distributed among these distances:
59 21 0.43
60 1 0.02
62 27 0.55
ACGTcount: A:0.49, C:0.04, G:0.05, T:0.42
Consensus pattern (59 bp):
TATTAAAATAATAGAATATTTATCAAGATAAACATTAAATTAAATTTAATATTAAATCT
Found at i:327296 original size:11 final size:11
Alignment explanation
Indices: 327282--327357 Score: 52
Period size: 11 Copynumber: 6.8 Consensus size: 11
327272 GATAATCACT
327282 TTAATATTAAA
1 TTAATATTAAA
327293 TTAATA--AAA
1 TTAATATTAAA
*
327302 -TACTATTAAA
1 TTAATATTAAA
*
327312 ATAAGTATTAAA
1 TTAA-TATTAAA
327324 TTAA-ATTTAACA
1 TTAATA-TTAA-A
327336 TTAAACTATTAAA
1 TT-AA-TATTAAA
*
327349 ATAATATTA
1 TTAATATTA
327358 TTTTTGAAAT
Statistics
Matches: 52, Mismatches: 4, Indels: 18
0.70 0.05 0.24
Matches are distributed among these distances:
8 4 0.08
9 3 0.06
10 4 0.08
11 17 0.33
12 15 0.29
13 4 0.08
14 4 0.08
15 1 0.02
ACGTcount: A:0.55, C:0.04, G:0.01, T:0.39
Consensus pattern (11 bp):
TTAATATTAAA
Found at i:349598 original size:151 final size:151
Alignment explanation
Indices: 349421--349760 Score: 445
Period size: 153 Copynumber: 2.2 Consensus size: 151
349411 TATGTTTTTT
349421 AGAAAAGTTTAAATTTTTAAACAAAGTTTTGATTTCTTTTAACTATTTCAAAATAAAAGTTTAGA
1 AGAAAAGTTTAAATTTTTAAACAAAGTTTTGATTT-TTTTAACTATTTCAAAATAAAAGTTTAGA
** ***** * **
349486 -TTTTAAGTAAAAT-AGTGATTTTTTTTTTTTTTAA-AAAGAAAGTTTATATTT-TTAAAAATAA
65 TTTTTAAGT-AAATGAGTGA-TTTTCATTAAAAAAACAAAGAAAGTTTAGATTTCAAAAAAATAA
* *
349547 AAATCAGTTTTTTAGTTATTTTAA
128 AAATCAGGTTTTTAGTGATTTTAA
* * * *
349571 AGAAAATGTTTAAAATTTTAAATAAAGTTTTGATTTTTTTAATTATTTCGAAATAAAAGTTTAGA
1 AGAAAA-GTTTAAATTTTTAAACAAAGTTTTGATTTTTTTAACTATTTCAAAATAAAAGTTTAGA
349636 TTTTTAAGTAAATGAGTGATTTTCATTAAAAAAACGAAAGAAAGTTTAGATTTCAAAAAAATAAA
65 TTTTTAAGTAAATGAGTGATTTTCATTAAAAAAAC-AAAGAAAGTTTAGATTTCAAAAAAATAAA
*
349701 AATCTGGTTTTTAGTGATTTTAA
129 AATCAGGTTTTTAGTGATTTTAA
349724 AGAAAAAGTTTAAATTTTTAAACAAAGTTTTGATTTT
1 AG-AAAAGTTTAAATTTTTAAACAAAGTTTTGATTTT
349761 GAAGTAAATT
Statistics
Matches: 164, Mismatches: 19, Indels: 11
0.85 0.10 0.06
Matches are distributed among these distances:
150 45 0.27
151 40 0.24
152 16 0.10
153 59 0.36
154 4 0.02
ACGTcount: A:0.42, C:0.03, G:0.11, T:0.44
Consensus pattern (151 bp):
AGAAAAGTTTAAATTTTTAAACAAAGTTTTGATTTTTTTAACTATTTCAAAATAAAAGTTTAGAT
TTTTAAGTAAATGAGTGATTTTCATTAAAAAAACAAAGAAAGTTTAGATTTCAAAAAAATAAAAA
TCAGGTTTTTAGTGATTTTAA
Found at i:349633 original size:51 final size:51
Alignment explanation
Indices: 349423--349647 Score: 167
Period size: 51 Copynumber: 4.5 Consensus size: 51
349413 TGTTTTTTAG
* * * *
349423 AAAAGTTTAAATTTTTAAACAAAGTTTTGATTTCTTTTAACTATTTCAAAAT
1 AAAAGTTTAAATTTTTAAATAAAGTATTGATTT-TTTTAATTATTTCTAAAT
* * * * * *
349475 AAAAGTTTAGA-TTTTAAGTAAAATAGTGATTTTTTT--TT-TTTTTAAAA
1 AAAAGTTTAAATTTTTAAATAAAGTATTGATTTTTTTAATTATTTCTAAAT
* * * * * *
349522 AGAAAGTTTATATTTTTAAAAATAAA--AATCAGTTTTTTAGTTATTT-TAAAG
1 A-AAAGTTTAAATTTTT--AAATAAAGTATTGATTTTTTTAATTATTTCTAAAT
* * *
349573 AAAATGTTTAAAATTTTAAATAAAGTTTTGATTTTTTTAATTATTTCGAAAT
1 AAAA-GTTTAAATTTTTAAATAAAGTATTGATTTTTTTAATTATTTCTAAAT
* *
349625 AAAAGTTTAGATTTTTAAGTAAA
1 AAAAGTTTAAATTTTTAAATAAA
349648 TGAGTGATTT
Statistics
Matches: 134, Mismatches: 28, Indels: 23
0.72 0.15 0.12
Matches are distributed among these distances:
47 7 0.05
48 10 0.07
49 20 0.15
50 7 0.05
51 70 0.52
52 20 0.15
ACGTcount: A:0.41, C:0.03, G:0.09, T:0.47
Consensus pattern (51 bp):
AAAAGTTTAAATTTTTAAATAAAGTATTGATTTTTTTAATTATTTCTAAAT
Found at i:350591 original size:22 final size:22
Alignment explanation
Indices: 350519--350583 Score: 85
Period size: 27 Copynumber: 2.7 Consensus size: 22
350509 GATTTTAAAC
350519 TAATTTTAAATATCATATAGGA
1 TAATTTTAAATATCATATAGGA
350541 TAATTAATATGTAAATATCATATAGGA
1 TAA-T--T-T-TAAATATCATATAGGA
350568 TAATTTTAAATATCAT
1 TAATTTTAAATATCAT
350584 CTAAGATATA
Statistics
Matches: 38, Mismatches: 0, Indels: 10
0.79 0.00 0.21
Matches are distributed among these distances:
22 13 0.34
23 2 0.05
24 1 0.03
25 1 0.03
26 2 0.05
27 19 0.50
ACGTcount: A:0.46, C:0.05, G:0.08, T:0.42
Consensus pattern (22 bp):
TAATTTTAAATATCATATAGGA
Found at i:360549 original size:36 final size:36
Alignment explanation
Indices: 360500--360637 Score: 174
Period size: 36 Copynumber: 3.9 Consensus size: 36
360490 TGGTAACAGG
*
360500 CATGACCTTTGGGTCAATAGGTAGTAAAACGAGCAT
1 CATGACCTCTGGGTCAATAGGTAGTAAAACGAGCAT
*
360536 CATGACCTCTGGGTCAATAAGG-AGTAAAACAAGCAT
1 CATGACCTCTGGGTCAAT-AGGTAGTAAAACGAGCAT
* *
360572 CATGACCTCTAGGTCAAT-GGT-GTAAAATGAGCAT
1 CATGACCTCTGGGTCAATAGGTAGTAAAACGAGCAT
* * * *
360606 AATGACCTTTGGGTCAACAGGGAGTAAAACGA
1 CATGACCTCTGGGTCAATAGGTAGTAAAACGA
360638 ATATCGATCG
Statistics
Matches: 87, Mismatches: 11, Indels: 8
0.82 0.10 0.08
Matches are distributed among these distances:
34 27 0.31
35 2 0.02
36 55 0.63
37 3 0.03
ACGTcount: A:0.36, C:0.17, G:0.25, T:0.22
Consensus pattern (36 bp):
CATGACCTCTGGGTCAATAGGTAGTAAAACGAGCAT
Found at i:360619 original size:70 final size:72
Alignment explanation
Indices: 360500--360635 Score: 195
Period size: 70 Copynumber: 1.9 Consensus size: 72
360490 TGGTAACAGG
* * * *
360500 CATGACCTTTGGGTCAATAGGTAGTAAAACGAGCATCATGACCTCTGGGTCAATAAGGAGTAAAA
1 CATGACCTCTAGGTCAATAGGTAGTAAAACGAGCATAATGACCTCTGGGTCAACAAGGAGTAAAA
360565 CAAGCAT
66 CAAGCAT
* * *
360572 CATGACCTCTAGGTCAAT-GGT-GTAAAATGAGCATAATGACCTTTGGGTCAACAGGGAGTAAAA
1 CATGACCTCTAGGTCAATAGGTAGTAAAACGAGCATAATGACCTCTGGGTCAACAAGGAGTAAAA
360635 C
66 C
360636 GAATATCGAT
Statistics
Matches: 57, Mismatches: 7, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
70 38 0.67
71 3 0.05
72 16 0.28
ACGTcount: A:0.35, C:0.18, G:0.24, T:0.23
Consensus pattern (72 bp):
CATGACCTCTAGGTCAATAGGTAGTAAAACGAGCATAATGACCTCTGGGTCAACAAGGAGTAAAA
CAAGCAT
Found at i:363500 original size:11 final size:12
Alignment explanation
Indices: 363470--363502 Score: 59
Period size: 12 Copynumber: 2.8 Consensus size: 12
363460 TGTGTTCTCC
363470 CAAATTCCTCTA
1 CAAATTCCTCTA
363482 CAAATTCCTCTA
1 CAAATTCCTCTA
363494 C-AATTCCTC
1 CAAATTCCTC
363503 ATTAAGGGAT
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
11 8 0.38
12 13 0.62
ACGTcount: A:0.30, C:0.36, G:0.00, T:0.33
Consensus pattern (12 bp):
CAAATTCCTCTA
Found at i:383112 original size:19 final size:19
Alignment explanation
Indices: 383081--383119 Score: 53
Period size: 18 Copynumber: 2.1 Consensus size: 19
383071 TTAAATTCTA
383081 ATTTAACCCAAAA-TATTT
1 ATTTAACCCAAAATTATTT
*
383099 ATTTTACCCAAAAATTATTT
1 ATTTAACCC-AAAATTATTT
383119 A
1 A
383120 AAATCATAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
18 8 0.44
19 4 0.22
20 6 0.33
ACGTcount: A:0.44, C:0.15, G:0.00, T:0.41
Consensus pattern (19 bp):
ATTTAACCCAAAATTATTT
Found at i:384694 original size:30 final size:30
Alignment explanation
Indices: 384660--384722 Score: 126
Period size: 30 Copynumber: 2.1 Consensus size: 30
384650 AATTTAATAA
384660 TATAAGAAAAAATTTCATTTATTACATATG
1 TATAAGAAAAAATTTCATTTATTACATATG
384690 TATAAGAAAAAATTTCATTTATTACATATG
1 TATAAGAAAAAATTTCATTTATTACATATG
384720 TAT
1 TAT
384723 TATAACTGTT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 33 1.00
ACGTcount: A:0.46, C:0.06, G:0.06, T:0.41
Consensus pattern (30 bp):
TATAAGAAAAAATTTCATTTATTACATATG
Found at i:406784 original size:21 final size:18
Alignment explanation
Indices: 406741--406781 Score: 64
Period size: 18 Copynumber: 2.3 Consensus size: 18
406731 TTCCACAGGA
406741 TCTTCCTTAGGATTTTTT
1 TCTTCCTTAGGATTTTTT
* *
406759 TCTTCCTTAGGATCTTCT
1 TCTTCCTTAGGATTTTTT
406777 TCTTC
1 TCTTC
406782 TTCTTCTTCA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.10, C:0.24, G:0.10, T:0.56
Consensus pattern (18 bp):
TCTTCCTTAGGATTTTTT
Found at i:407698 original size:8 final size:7
Alignment explanation
Indices: 407684--407734 Score: 50
Period size: 7 Copynumber: 6.7 Consensus size: 7
407674 AATTTAAAAT
407684 AAATTAA
1 AAATTAA
407691 AAAGTTAA
1 AAA-TTAA
407699 TAAATTAAA
1 -AAATT-AA
407708 TAAATTAA
1 -AAATTAA
407716 AAATTAGA
1 AAATTA-A
407724 AAA-TAA
1 AAATTAA
407730 AAATT
1 AAATT
407735 TCTTACCACC
Statistics
Matches: 39, Mismatches: 0, Indels: 10
0.80 0.00 0.20
Matches are distributed among these distances:
6 4 0.10
7 12 0.31
8 12 0.31
9 11 0.28
ACGTcount: A:0.67, C:0.00, G:0.04, T:0.29
Consensus pattern (7 bp):
AAATTAA
Found at i:407702 original size:16 final size:16
Alignment explanation
Indices: 407681--407727 Score: 60
Period size: 16 Copynumber: 2.9 Consensus size: 16
407671 AACAATTTAA
*
407681 AATAAATTAAAAAGTT
1 AATAAATTAAAAAATT
407697 AATAAATTAAATAAATT
1 AATAAATTAAA-AAATT
*
407714 AA-AAATTAGAAAAT
1 AATAAATTAAAAAAT
407728 AAAAATTTCT
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
15 4 0.14
16 18 0.64
17 6 0.21
ACGTcount: A:0.66, C:0.00, G:0.04, T:0.30
Consensus pattern (16 bp):
AATAAATTAAAAAATT
Found at i:407711 original size:9 final size:9
Alignment explanation
Indices: 407680--407716 Score: 51
Period size: 9 Copynumber: 4.3 Consensus size: 9
407670 TAACAATTTA
407680 AAATAAATT
1 AAATAAATT
*
407689 AAA-AAGTT
1 AAATAAATT
407697 -AATAAATT
1 AAATAAATT
407705 AAATAAATT
1 AAATAAATT
407714 AAA
1 AAA
407717 AATTAGAAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
7 2 0.08
8 8 0.33
9 14 0.58
ACGTcount: A:0.68, C:0.00, G:0.03, T:0.30
Consensus pattern (9 bp):
AAATAAATT
Found at i:407733 original size:25 final size:25
Alignment explanation
Indices: 407678--407731 Score: 76
Period size: 25 Copynumber: 2.2 Consensus size: 25
407668 ATTAACAATT
407678 TAAAATAAATTAAAAAGTTAATAAA
1 TAAAATAAATTAAAAAGTTAATAAA
*
407703 TTAAATAAATTAAAAA-TTAGA-AAA
1 TAAAATAAATTAAAAAGTTA-ATAAA
407727 TAAAA
1 TAAAA
407732 ATTTCTTACC
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
24 10 0.38
25 16 0.62
ACGTcount: A:0.69, C:0.00, G:0.04, T:0.28
Consensus pattern (25 bp):
TAAAATAAATTAAAAAGTTAATAAA
Found at i:408507 original size:29 final size:29
Alignment explanation
Indices: 408452--408510 Score: 75
Period size: 29 Copynumber: 2.0 Consensus size: 29
408442 TTGTTTTGGA
*
408452 AATATTTACAAAAAAAGACAACTAATTTT
1 AATATTTACAAAAAAAGACAACAAATTTT
**
408481 AATATTTACAAAATTA-ACAACCAAATTTT
1 AATATTTACAAAAAAAGACAA-CAAATTTT
408510 A
1 A
408511 CAAAGAATTC
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
28 4 0.15
29 22 0.85
ACGTcount: A:0.54, C:0.12, G:0.02, T:0.32
Consensus pattern (29 bp):
AATATTTACAAAAAAAGACAACAAATTTT
Found at i:414749 original size:16 final size:16
Alignment explanation
Indices: 414728--414761 Score: 68
Period size: 16 Copynumber: 2.1 Consensus size: 16
414718 ATCACAAGGG
414728 TAATGCAATAATAACT
1 TAATGCAATAATAACT
414744 TAATGCAATAATAACT
1 TAATGCAATAATAACT
414760 TA
1 TA
414762 GGCATGATAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.50, C:0.12, G:0.06, T:0.32
Consensus pattern (16 bp):
TAATGCAATAATAACT
Found at i:414914 original size:12 final size:12
Alignment explanation
Indices: 414899--414924 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
414889 AATTAAAGAA
414899 ATAATAGCATTC
1 ATAATAGCATTC
414911 ATAATAGCATTC
1 ATAATAGCATTC
414923 AT
1 AT
414925 CATGATAACA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.42, C:0.15, G:0.08, T:0.35
Consensus pattern (12 bp):
ATAATAGCATTC
Found at i:416591 original size:9 final size:9
Alignment explanation
Indices: 416578--416696 Score: 71
Period size: 9 Copynumber: 12.7 Consensus size: 9
416568 TTTTTTACGA
*
416578 ATTTTATAT
1 ATTTTTTAT
*
416587 TTTTTTTAT
1 ATTTTTTAT
416596 ATTTTTTAT
1 ATTTTTTAT
*
416605 AATTTTCTTACG
1 -ATTTT-TTA-T
*
416617 ATTTTATTAA
1 ATTTT-TTAT
*
416627 ATTTTATA-
1 ATTTTTTAT
*
416635 ATTTTTTCT
1 ATTTTTTAT
*
416644 ATATTTCTAT
1 AT-TTTTTAT
*
416654 A-TATTTAT
1 ATTTTTTAT
*
416662 ATTTTTTTAC
1 A-TTTTTTAT
*
416672 AATTTTTAT
1 ATTTTTTAT
416681 AATTTTTTAT
1 -ATTTTTTAT
416691 ATTTTT
1 ATTTTT
416697 AATAAAATTT
Statistics
Matches: 84, Mismatches: 18, Indels: 16
0.71 0.15 0.14
Matches are distributed among these distances:
8 12 0.14
9 31 0.37
10 30 0.36
11 11 0.13
ACGTcount: A:0.27, C:0.04, G:0.01, T:0.68
Consensus pattern (9 bp):
ATTTTTTAT
Found at i:416592 original size:10 final size:10
Alignment explanation
Indices: 416579--416696 Score: 54
Period size: 10 Copynumber: 12.2 Consensus size: 10
416569 TTTTTACGAA
416579 TTTTATATTT
1 TTTTATATTT
416589 TTTT-TATATT
1 TTTTATAT-TT
416599 TTTTATAATTT
1 TTTTAT-ATTT
* *
416610 TCTTACGATTT
1 TTTTA-TATTT
* *
416621 TATTA-AATT
1 TTTTATATTT
*
416630 TTATA-ATTT
1 TTTTATATTT
416639 TTTCTATA--T
1 TTT-TATATTT
*
416648 TTCTATA--T
1 TTTTATATTT
*
416656 ATTTATATTT
1 TTTTATATTT
* *
416666 TTTTACA-AT
1 TTTTATATTT
*
416675 TTTTATAATT
1 TTTTATATTT
416685 TTTTATATTT
1 TTTTATATTT
416695 TT
1 TT
416697 AATAAAATTT
Statistics
Matches: 82, Mismatches: 17, Indels: 18
0.70 0.15 0.15
Matches are distributed among these distances:
8 10 0.12
9 24 0.29
10 30 0.37
11 16 0.20
12 2 0.02
ACGTcount: A:0.26, C:0.04, G:0.01, T:0.69
Consensus pattern (10 bp):
TTTTATATTT
Found at i:416621 original size:29 final size:28
Alignment explanation
Indices: 416589--416696 Score: 89
Period size: 28 Copynumber: 3.8 Consensus size: 28
416579 TTTTATATTT
*
416589 TTTTTATATTTTTTATAATTTTCTTACGA
1 TTTTTATATTTTTTATAATTTT-TTACAA
**
416618 -TTTTATTAAATTTTATAATTTTTT-CTATA
1 TTTTTA-TATTTTTTATAATTTTTTAC-A-A
* * *
416647 TTTCTATA-TATTTATATTTTTTTACAA
1 TTTTTATATTTTTTATAATTTTTTACAA
416674 TTTTTATAATTTTTTAT-ATTTTT
1 TTTTTAT-ATTTTTTATAATTTTT
416697 AATAAAATTT
Statistics
Matches: 62, Mismatches: 10, Indels: 15
0.71 0.11 0.17
Matches are distributed among these distances:
27 8 0.13
28 26 0.42
29 24 0.39
30 4 0.06
ACGTcount: A:0.27, C:0.05, G:0.01, T:0.68
Consensus pattern (28 bp):
TTTTTATATTTTTTATAATTTTTTACAA
Found at i:417163 original size:24 final size:24
Alignment explanation
Indices: 417136--417215 Score: 74
Period size: 24 Copynumber: 3.2 Consensus size: 24
417126 ACTATTTTTA
417136 TTAATTACTCTCTTACTTTTACTT
1 TTAATTACTCTCTTACTTTTACTT
** * *
417160 TTAATTTTTATAATTTACTATTT--TT
1 TTAATTACTCT--CTTACT-TTTACTT
417185 ATTAATTACTCTCTTACTTTTACTT
1 -TTAATTACTCTCTTACTTTTACTT
417210 TTAATT
1 TTAATT
417216 TTTCTTTTTC
Statistics
Matches: 42, Mismatches: 8, Indels: 12
0.68 0.13 0.19
Matches are distributed among these distances:
23 3 0.07
24 19 0.45
25 4 0.10
26 13 0.31
27 3 0.07
ACGTcount: A:0.25, C:0.14, G:0.00, T:0.61
Consensus pattern (24 bp):
TTAATTACTCTCTTACTTTTACTT
Found at i:417213 original size:50 final size:50
Alignment explanation
Indices: 417117--417218 Score: 204
Period size: 50 Copynumber: 2.0 Consensus size: 50
417107 TTATTTTCCA
417117 TTATAATTTACTATTTTTATTAATTACTCTCTTACTTTTACTTTTAATTT
1 TTATAATTTACTATTTTTATTAATTACTCTCTTACTTTTACTTTTAATTT
417167 TTATAATTTACTATTTTTATTAATTACTCTCTTACTTTTACTTTTAATTT
1 TTATAATTTACTATTTTTATTAATTACTCTCTTACTTTTACTTTTAATTT
417217 TT
1 TT
417219 CTTTTTCCTT
Statistics
Matches: 52, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
50 52 1.00
ACGTcount: A:0.25, C:0.12, G:0.00, T:0.63
Consensus pattern (50 bp):
TTATAATTTACTATTTTTATTAATTACTCTCTTACTTTTACTTTTAATTT
Found at i:419507 original size:27 final size:27
Alignment explanation
Indices: 419458--419570 Score: 129
Period size: 27 Copynumber: 4.2 Consensus size: 27
419448 GCCCGAGTCT
* * *
419458 TATCATCCGGG-TGGTCAAGCCATGGA
1 TATCATACGGGTTGGTCAGGCCATGAA
419484 TATCATACGGGTTGGTCAGGCCATGAA
1 TATCATACGGGTTGGTCAGGCCATGAA
* * * *
419511 TATTATACAGGTTGGTCAGGCCAAGTA
1 TATCATACGGGTTGGTCAGGCCATGAA
* * *
419538 TATCATACGGGTTGGTTAGGGCACGAA
1 TATCATACGGGTTGGTCAGGCCATGAA
419565 TATCAT
1 TATCAT
419571 TCGGAGTTTT
Statistics
Matches: 73, Mismatches: 13, Indels: 1
0.84 0.15 0.01
Matches are distributed among these distances:
26 10 0.14
27 63 0.86
ACGTcount: A:0.27, C:0.18, G:0.28, T:0.27
Consensus pattern (27 bp):
TATCATACGGGTTGGTCAGGCCATGAA
Found at i:419960 original size:16 final size:16
Alignment explanation
Indices: 419939--419999 Score: 53
Period size: 16 Copynumber: 4.2 Consensus size: 16
419929 AGTTTATGTT
*
419939 TGTATTTAATTCATTA
1 TGTATTTAATTAATTA
*
419955 TGTATTTCATTAATTA
1 TGTATTTAATTAATTA
*
419971 TG--TTT-A-T-GTT-
1 TGTATTTAATTAATTA
419981 TGTATTTAATTAATTA
1 TGTATTTAATTAATTA
419997 TGT
1 TGT
420000 TTAAGGTTTA
Statistics
Matches: 35, Mismatches: 4, Indels: 12
0.69 0.08 0.24
Matches are distributed among these distances:
10 2 0.06
11 2 0.06
12 4 0.11
13 2 0.06
14 4 0.11
15 2 0.06
16 19 0.54
ACGTcount: A:0.28, C:0.03, G:0.10, T:0.59
Consensus pattern (16 bp):
TGTATTTAATTAATTA
Found at i:419979 original size:22 final size:23
Alignment explanation
Indices: 419955--420002 Score: 60
Period size: 26 Copynumber: 2.0 Consensus size: 23
419945 TAATTCATTA
*
419955 TGTATTTCATTAATTATGTTTATGTT
1 TGTATTTAATTAATTATGTTTA---T
419981 TGTATTTAATTAATTATGTTTA
1 TGTATTTAATTAATTATGTTTA
420003 AGGTTTAAGG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
26 21 1.00
ACGTcount: A:0.27, C:0.02, G:0.10, T:0.60
Consensus pattern (23 bp):
TGTATTTAATTAATTATGTTTAT
Found at i:421465 original size:27 final size:27
Alignment explanation
Indices: 421434--421498 Score: 78
Period size: 27 Copynumber: 2.4 Consensus size: 27
421424 AAGCACTGGT
* *
421434 GTGCCGCCTATCTGTAT-GGCACCATTG
1 GTGCCGCCTATCAG-ATGGGCACCATTA
* *
421461 GTGCCGCCTACCAGATGGGCATCATTA
1 GTGCCGCCTATCAGATGGGCACCATTA
421488 GTGCCGCCTAT
1 GTGCCGCCTAT
421499 TTGACAGGCA
Statistics
Matches: 32, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
26 2 0.06
27 30 0.94
ACGTcount: A:0.17, C:0.31, G:0.26, T:0.26
Consensus pattern (27 bp):
GTGCCGCCTATCAGATGGGCACCATTA
Found at i:421855 original size:27 final size:27
Alignment explanation
Indices: 421825--421883 Score: 66
Period size: 27 Copynumber: 2.2 Consensus size: 27
421815 AAAAATCTAT
*
421825 TAAACTAAACTTTATAAT-AATTAAAAA
1 TAAACT-AACTTTAAAATAAATTAAAAA
* *
421852 TAAAATAATTTTAAAATAAATTAAAAA
1 TAAACTAACTTTAAAATAAATTAAAAA
*
421879 CAAAC
1 TAAAC
421884 AACAACAAAA
Statistics
Matches: 26, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
26 9 0.35
27 17 0.65
ACGTcount: A:0.63, C:0.07, G:0.00, T:0.31
Consensus pattern (27 bp):
TAAACTAACTTTAAAATAAATTAAAAA
Found at i:421998 original size:129 final size:127
Alignment explanation
Indices: 421855--422096 Score: 371
Period size: 128 Copynumber: 1.9 Consensus size: 127
421845 TTAAAAATAA
421855 AATAATTTTAAAATAAATTAAAAACAAACAACAACAAAATTTACCTATCTTTTAAC-TTTTTTTC
1 AATAATTTTAAAATAAATTAAAAAC-AACAAC-A-AAAA-TTACCTATCTTTTAACTTTTTTTTC
*
421919 CCCTTTAATCTACTCTACTAAAC-AAAAAAATTATAACAAATTATAAACATTAAACTAAATTTTA
62 CCCTTTAATCTACTCTACTAAACAAAAAAAATTATAACAAATCATAAACATTAAACTAAATTTTA
421983 T
127 T
* * **
421984 AATAATTTTAAAATAAATTAAAAACAACAACAAAAATTACCTCTCTTTTAGCTTTTTTTTTTTCC
1 AATAATTTTAAAATAAATTAAAAACAACAACAAAAATTACCTATCTTTTAAC-TTTTTTTTCCCC
*
422049 TTTAATCTATTCTACTAAACAAAAAAAATTATAACAAATCATAAACAT
65 TTTAATCTACTCTACTAAACAAAAAAAATTATAACAAATCATAAACAT
422097 GCCTATATAT
Statistics
Matches: 104, Mismatches: 6, Indels: 7
0.89 0.05 0.06
Matches are distributed among these distances:
125 14 0.13
126 4 0.04
127 29 0.28
128 32 0.31
129 25 0.24
ACGTcount: A:0.48, C:0.15, G:0.00, T:0.36
Consensus pattern (127 bp):
AATAATTTTAAAATAAATTAAAAACAACAACAAAAATTACCTATCTTTTAACTTTTTTTTCCCCT
TTAATCTACTCTACTAAACAAAAAAAATTATAACAAATCATAAACATTAAACTAAATTTTAT
Found at i:430634 original size:70 final size:70
Alignment explanation
Indices: 430550--430725 Score: 298
Period size: 70 Copynumber: 2.5 Consensus size: 70
430540 AGCATATATA
*
430550 AAAGAACTCCTTACTTTGGTTCATGTTTTGGAAATTAACCAGGACTTAACTCAATTATTCCACAT
1 AAAGAACTCCTTACTTTGGTTCGTGTTTTGGAAATTAACCAGGACTTAACTCAATTATTCCACAT
430615 TTTAT
66 TTTAT
* * * * *
430620 AAAGAACTCATTACTTTGGTTCGTGTTTTTGAAATTAACTAGGACTTAACTCAATTATTCCCCGT
1 AAAGAACTCCTTACTTTGGTTCGTGTTTTGGAAATTAACCAGGACTTAACTCAATTATTCCACAT
430685 TTTAT
66 TTTAT
430690 AAAGAACTCCTTACTTTGGTTCGTGTTTTGGAAATT
1 AAAGAACTCCTTACTTTGGTTCGTGTTTTGGAAATT
430726 TGACAACATT
Statistics
Matches: 98, Mismatches: 8, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
70 98 1.00
ACGTcount: A:0.29, C:0.17, G:0.14, T:0.40
Consensus pattern (70 bp):
AAAGAACTCCTTACTTTGGTTCGTGTTTTGGAAATTAACCAGGACTTAACTCAATTATTCCACAT
TTTAT
Found at i:431320 original size:19 final size:18
Alignment explanation
Indices: 431287--431322 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
431277 TAACGTATAT
*
431287 TTAATTGATTCAATAAAC
1 TTAATTGATTAAATAAAC
431305 TTAATTAGATTAAATAAA
1 TTAATT-GATTAAATAAA
431323 AAAGGAAAGT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 6 0.38
19 10 0.62
ACGTcount: A:0.50, C:0.06, G:0.06, T:0.39
Consensus pattern (18 bp):
TTAATTGATTAAATAAAC
Found at i:437371 original size:2 final size:2
Alignment explanation
Indices: 437360--437403 Score: 72
Period size: 2 Copynumber: 22.5 Consensus size: 2
437350 TAATAGTAAT
*
437360 CA CA -A CA CA CA CA CA CA CA CA CA CA CA TA CA CA CA CA CA CA
1 CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA
437401 CA C
1 CA C
437404 CCATATATAT
Statistics
Matches: 39, Mismatches: 2, Indels: 2
0.91 0.05 0.05
Matches are distributed among these distances:
1 1 0.03
2 38 0.97
ACGTcount: A:0.50, C:0.48, G:0.00, T:0.02
Consensus pattern (2 bp):
CA
Found at i:439270 original size:56 final size:57
Alignment explanation
Indices: 439209--439320 Score: 172
Period size: 56 Copynumber: 2.0 Consensus size: 57
439199 GAGAAAATAG
** *
439209 AAAATATCATTAAATAATAATTATTTAATAGAAAGGATAAA-TATTATTTTTAATTT
1 AAAATATCATTAAATAATAACCATTTAATAGAAAGGATAAATTACTATTTTTAATTT
* *
439265 AAAATATCATTAAATAGTAACCATTTGATAGAAAGGATAAATTACTATTTTTAATT
1 AAAATATCATTAAATAATAACCATTTAATAGAAAGGATAAATTACTATTTTTAATT
439321 CAATTAATAT
Statistics
Matches: 50, Mismatches: 5, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
56 37 0.74
57 13 0.26
ACGTcount: A:0.48, C:0.04, G:0.07, T:0.40
Consensus pattern (57 bp):
AAAATATCATTAAATAATAACCATTTAATAGAAAGGATAAATTACTATTTTTAATTT
Found at i:439973 original size:14 final size:15
Alignment explanation
Indices: 439943--439975 Score: 50
Period size: 14 Copynumber: 2.3 Consensus size: 15
439933 AATTGTGTAT
439943 AATTTTATTAAATCA
1 AATTTTATTAAATCA
*
439958 AATTTTA-TATATCA
1 AATTTTATTAAATCA
439972 AATT
1 AATT
439976 GCATATTAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
14 10 0.59
15 7 0.41
ACGTcount: A:0.45, C:0.06, G:0.00, T:0.48
Consensus pattern (15 bp):
AATTTTATTAAATCA
Found at i:440384 original size:29 final size:28
Alignment explanation
Indices: 440311--440384 Score: 69
Period size: 29 Copynumber: 2.5 Consensus size: 28
440301 TGGATTAATT
* *
440311 TTTTAAATTGATTTCTAAATTTTAAAATA
1 TTTT-AATTGATTTTTAAATTTAAAAATA
**
440340 TTTTAATTGGGCTTTTAAA-TTAAAATATGA
1 TTTTAATT-GATTTTTAAATTTAAAA-AT-A
440370 TTTTAATTGATTTTT
1 TTTTAATTGATTTTT
440385 TTTTTAATTT
Statistics
Matches: 36, Mismatches: 6, Indels: 6
0.75 0.12 0.12
Matches are distributed among these distances:
28 9 0.25
29 18 0.50
30 9 0.25
ACGTcount: A:0.35, C:0.03, G:0.08, T:0.54
Consensus pattern (28 bp):
TTTTAATTGATTTTTAAATTTAAAAATA
Found at i:442777 original size:11 final size:11
Alignment explanation
Indices: 442755--442796 Score: 57
Period size: 11 Copynumber: 3.8 Consensus size: 11
442745 AAATGACAGC
*
442755 AAAACAAAAAG
1 AAAACAACAAG
* *
442766 AAAATAGCAAG
1 AAAACAACAAG
442777 AAAACAACAAG
1 AAAACAACAAG
442788 AAAACAACA
1 AAAACAACA
442797 TTATTTTTTT
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
11 26 1.00
ACGTcount: A:0.74, C:0.14, G:0.10, T:0.02
Consensus pattern (11 bp):
AAAACAACAAG
Found at i:443933 original size:18 final size:16
Alignment explanation
Indices: 443901--443936 Score: 54
Period size: 16 Copynumber: 2.1 Consensus size: 16
443891 TTGGGATGAG
443901 AATAAATTTTTAATTA
1 AATAAATTTTTAATTA
443917 AATAAATTTAATTAATTA
1 AATAAATTT--TTAATTA
443935 AA
1 AA
443937 AATTTAAAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
16 9 0.50
18 9 0.50
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (16 bp):
AATAAATTTTTAATTA
Found at i:445539 original size:23 final size:25
Alignment explanation
Indices: 445513--445571 Score: 58
Period size: 23 Copynumber: 2.6 Consensus size: 25
445503 AGTTTAAGTT
445513 AATTAAGGATTAAA-GA-TTAATTA
1 AATTAAGGATTAAATGACTTAATTA
* *
445536 AATT--TGATTAAATTACTTAATTA
1 AATTAAGGATTAAATGACTTAATTA
445559 AATTAA--ATTAAAT
1 AATTAAGGATTAAAT
445572 TAAACTTACT
Statistics
Matches: 30, Mismatches: 2, Indels: 8
0.75 0.05 0.20
Matches are distributed among these distances:
21 7 0.23
22 1 0.03
23 22 0.73
ACGTcount: A:0.51, C:0.02, G:0.07, T:0.41
Consensus pattern (25 bp):
AATTAAGGATTAAATGACTTAATTA
Found at i:445572 original size:23 final size:23
Alignment explanation
Indices: 445529--445573 Score: 72
Period size: 23 Copynumber: 2.0 Consensus size: 23
445519 GGATTAAAGA
**
445529 TTAATTAAATTTGATTAAATTAC
1 TTAATTAAATTAAATTAAATTAC
445552 TTAATTAAATTAAATTAAATTA
1 TTAATTAAATTAAATTAAATTA
445574 AACTTACTGT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.49, C:0.02, G:0.02, T:0.47
Consensus pattern (23 bp):
TTAATTAAATTAAATTAAATTAC
Found at i:455086 original size:14 final size:16
Alignment explanation
Indices: 455055--455086 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
455045 GTTAGTTGCA
455055 TGCATTTCTTTTTCAT
1 TGCATTTCTTTTTCAT
455071 TGCATTT-TTTTT-AT
1 TGCATTTCTTTTTCAT
455085 TG
1 TG
455087 TTCTTGCATT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
14 4 0.25
15 5 0.31
16 7 0.44
ACGTcount: A:0.12, C:0.12, G:0.09, T:0.66
Consensus pattern (16 bp):
TGCATTTCTTTTTCAT
Found at i:457023 original size:14 final size:14
Alignment explanation
Indices: 457004--457031 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
456994 CTTAAGGCAA
457004 GGAGGAATTCTAGC
1 GGAGGAATTCTAGC
457018 GGAGGAATTCTAGC
1 GGAGGAATTCTAGC
457032 CACTTGTTCT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.29, C:0.14, G:0.36, T:0.21
Consensus pattern (14 bp):
GGAGGAATTCTAGC
Found at i:458991 original size:20 final size:20
Alignment explanation
Indices: 458942--458994 Score: 63
Period size: 20 Copynumber: 2.6 Consensus size: 20
458932 GTCTTTAAGA
* * *
458942 TATCAGTAGAATTGTAGTTG
1 TATCGGTAGAAGTGTAGTTC
458962 TATCGGTAGAAGTGTAGTTC
1 TATCGGTAGAAGTGTAGTTC
458982 TA-CGGATAGAAGT
1 TATCGG-TAGAAGT
458995 CTCACTAGAG
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
19 3 0.10
20 26 0.90
ACGTcount: A:0.30, C:0.08, G:0.28, T:0.34
Consensus pattern (20 bp):
TATCGGTAGAAGTGTAGTTC
Found at i:462052 original size:20 final size:20
Alignment explanation
Indices: 461999--462052 Score: 63
Period size: 20 Copynumber: 2.7 Consensus size: 20
461989 AGTCTTCAAG
*
461999 GTATCGGTAGAACTGTAGTT
1 GTATCGGTAGAAGTGTAGTT
**
462019 GTATCAATAGAAGTGTAGTT
1 GTATCGGTAGAAGTGTAGTT
* *
462039 TTATCGGTATAAGT
1 GTATCGGTAGAAGT
462053 CTCACTGGAG
Statistics
Matches: 27, Mismatches: 7, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
20 27 1.00
ACGTcount: A:0.30, C:0.07, G:0.26, T:0.37
Consensus pattern (20 bp):
GTATCGGTAGAAGTGTAGTT
Found at i:463435 original size:31 final size:31
Alignment explanation
Indices: 463394--463452 Score: 100
Period size: 31 Copynumber: 1.9 Consensus size: 31
463384 TAATGAAGAT
*
463394 TAACCTAAATAGAAACGATCTAAAACATAAG
1 TAACCAAAATAGAAACGATCTAAAACATAAG
*
463425 TAACCAAAATAGAAATGATCTAAAACAT
1 TAACCAAAATAGAAACGATCTAAAACAT
463453 TTGTGATTAA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
31 26 1.00
ACGTcount: A:0.56, C:0.15, G:0.08, T:0.20
Consensus pattern (31 bp):
TAACCAAAATAGAAACGATCTAAAACATAAG
Found at i:463697 original size:2 final size:2
Alignment explanation
Indices: 463690--463714 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
463680 TTCAAAAATA
463690 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
463715 CTAAAATTGA
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:464111 original size:14 final size:14
Alignment explanation
Indices: 464079--464118 Score: 55
Period size: 14 Copynumber: 2.9 Consensus size: 14
464069 TAAAAATTAT
*
464079 AAAAATTAT-AAAC
1 AAAAGTTATAAAAC
*
464092 AAAAGTTATAAAAG
1 AAAAGTTATAAAAC
464106 AAAAGTTATAAAA
1 AAAAGTTATAAAA
464119 ATTTTAAATT
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
13 8 0.33
14 16 0.67
ACGTcount: A:0.68, C:0.03, G:0.07, T:0.23
Consensus pattern (14 bp):
AAAAGTTATAAAAC
Found at i:465285 original size:23 final size:23
Alignment explanation
Indices: 465253--465300 Score: 62
Period size: 24 Copynumber: 2.1 Consensus size: 23
465243 TAAAAAAGCA
465253 TTTTTAAAATAAT-ATAATTTAT
1 TTTTTAAAATAATAATAATTTAT
* *
465275 TTTTGTAAAATGATAATATTTTAT
1 TTTT-TAAAATAATAATAATTTAT
465299 TT
1 TT
465301 ATTATTTAAT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
22 4 0.18
23 8 0.36
24 10 0.45
ACGTcount: A:0.40, C:0.00, G:0.04, T:0.56
Consensus pattern (23 bp):
TTTTTAAAATAATAATAATTTAT
Found at i:465852 original size:23 final size:22
Alignment explanation
Indices: 465786--465852 Score: 64
Period size: 23 Copynumber: 3.0 Consensus size: 22
465776 GTTCAAATCT
*
465786 AATTTTATCTAAAAAAT-TTATTA
1 AATTTT-TC-AAAAAATATAATTA
* * *
465809 GATTTTTCAAAAAAAAAAATTA
1 AATTTTTCAAAAAATATAATTA
465831 AATTCTTTCAAAAAATATAATT
1 AATT-TTTCAAAAAATATAATT
465853 TATTTTAATT
Statistics
Matches: 35, Mismatches: 7, Indels: 4
0.76 0.15 0.09
Matches are distributed among these distances:
21 6 0.17
22 9 0.26
23 20 0.57
ACGTcount: A:0.52, C:0.06, G:0.01, T:0.40
Consensus pattern (22 bp):
AATTTTTCAAAAAATATAATTA
Found at i:467065 original size:17 final size:17
Alignment explanation
Indices: 467035--467069 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
467025 TTCAAAATTC
467035 TCATTAAACTTAAAACT
1 TCATTAAACTTAAAACT
467052 TCATCTAAAC-TAAAACT
1 TCAT-TAAACTTAAAACT
467069 T
1 T
467070 AAGATCAAAT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 12 0.71
18 5 0.29
ACGTcount: A:0.46, C:0.20, G:0.00, T:0.34
Consensus pattern (17 bp):
TCATTAAACTTAAAACT
Found at i:471019 original size:28 final size:27
Alignment explanation
Indices: 470961--471021 Score: 70
Period size: 28 Copynumber: 2.2 Consensus size: 27
470951 AGGATTGTCT
* * *
470961 TTGTGGCAAACTAAAAAGGGACTGCCT
1 TTGTGGAAAACTAAAAAGGGACCGCCC
470988 TTGTGGAAAACTCAAAAA-GGATCCGCCC
1 TTGTGGAAAACT-AAAAAGGGA-CCGCCC
471016 TTGTGG
1 TTGTGG
471022 CATACGTAGG
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
27 14 0.48
28 15 0.52
ACGTcount: A:0.31, C:0.20, G:0.26, T:0.23
Consensus pattern (27 bp):
TTGTGGAAAACTAAAAAGGGACCGCCC
Found at i:473181 original size:10 final size:10
Alignment explanation
Indices: 473160--473202 Score: 61
Period size: 10 Copynumber: 4.3 Consensus size: 10
473150 AATTGAATTG
473160 ATTTTTAT-A
1 ATTTTTATAA
473169 ATTTTTATAA
1 ATTTTTATAA
*
473179 ATTTTTACAA
1 ATTTTTATAA
473189 ATTTTTTATAA
1 A-TTTTTATAA
473200 ATT
1 ATT
473203 ATTTGATTTA
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
9 8 0.27
10 13 0.43
11 9 0.30
ACGTcount: A:0.37, C:0.02, G:0.00, T:0.60
Consensus pattern (10 bp):
ATTTTTATAA
Done.