Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01000261.1 Hibiscus syriacus cultivar Beakdansim tig00000483_pilon, 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: 228775
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:2379 original size:19 final size:20
Alignment explanation
Indices: 2343--2382 Score: 55
Period size: 19 Copynumber: 2.0 Consensus size: 20
2333 GAATAATAAT
2343 ATAAGTAATGAAAAGAAATA
1 ATAAGTAATGAAAAGAAATA
* *
2363 ATAAG-AATGATATGAAATA
1 ATAAGTAATGAAAAGAAATA
2382 A
1 A
2383 GGAAAGAATA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
19 13 0.72
20 5 0.28
ACGTcount: A:0.62, C:0.00, G:0.15, T:0.23
Consensus pattern (20 bp):
ATAAGTAATGAAAAGAAATA
Found at i:5261 original size:74 final size:74
Alignment explanation
Indices: 5179--5485 Score: 560
Period size: 74 Copynumber: 4.1 Consensus size: 74
5169 TTAAGTATTG
5179 GATAATGCTCATTCAACTAGCATTGTAAATATGCTCAAAATTGTCATTTCTTGATAATGCTCAAT
1 GATAATGCTCATTCAACTAGCATTGTAAATATGCTCAAAATTGTCATTTCTTGATAATGCTCAAT
*
5244 GTTGATAAT
66 TTTGATAAT
*
5253 GATCATGCTCATTCAACTAGCATTGTAAATATGCTCAAAATTGTCATTTCTTGATAATGCTCAAT
1 GATAATGCTCATTCAACTAGCATTGTAAATATGCTCAAAATTGTCATTTCTTGATAATGCTCAAT
5318 TTTGATAAT
66 TTTGATAAT
* *
5327 GATAATGCTCATTCAACTAGCATTTTAAATGTGCTCAAAATTGTCATTTCTTGATAATGCTCAAT
1 GATAATGCTCATTCAACTAGCATTGTAAATATGCTCAAAATTGTCATTTCTTGATAATGCTCAAT
5392 TTTGATAAT
66 TTTGATAAT
*
5401 GATAATGCTCATTCAACTAGCATTGTAAATATGCTCAAAATTGTCATTTCTTCATAATGCTCAAT
1 GATAATGCTCATTCAACTAGCATTGTAAATATGCTCAAAATTGTCATTTCTTGATAATGCTCAAT
5466 TTTGATAAT
66 TTTGATAAT
*
5475 GCTAATGCTCA
1 GATAATGCTCA
5486 AATTAGGTTA
Statistics
Matches: 224, Mismatches: 9, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
74 224 1.00
ACGTcount: A:0.33, C:0.16, G:0.12, T:0.39
Consensus pattern (74 bp):
GATAATGCTCATTCAACTAGCATTGTAAATATGCTCAAAATTGTCATTTCTTGATAATGCTCAAT
TTTGATAAT
Found at i:5913 original size:2 final size:2
Alignment explanation
Indices: 5908--5988 Score: 162
Period size: 2 Copynumber: 40.5 Consensus size: 2
5898 ATAACTAATA
5908 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
5950 AT AT AT AT AT AT AT 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 AT AT AT AT AT AT AT A
5989 ATGAAATCCC
Statistics
Matches: 79, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 79 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:20179 original size:20 final size:20
Alignment explanation
Indices: 20154--20215 Score: 71
Period size: 20 Copynumber: 3.3 Consensus size: 20
20144 AAAATGCTAA
20154 AGTGTACCGATACACCCTGC
1 AGTGTACCGATACACCCTGC
20174 AGTGTATCC-ATACA--CT--
1 AGTGTA-CCGATACACCCTGC
*
20190 AGCGTACCGATACACCCTGC
1 AGTGTACCGATACACCCTGC
20210 AGTGTA
1 AGTGTA
20216 TCCATACTCC
Statistics
Matches: 34, Mismatches: 2, Indels: 12
0.71 0.04 0.25
Matches are distributed among these distances:
15 2 0.06
16 10 0.29
18 4 0.12
20 16 0.47
21 2 0.06
ACGTcount: A:0.27, C:0.31, G:0.19, T:0.23
Consensus pattern (20 bp):
AGTGTACCGATACACCCTGC
Found at i:20303 original size:36 final size:36
Alignment explanation
Indices: 20255--20323 Score: 102
Period size: 36 Copynumber: 1.9 Consensus size: 36
20245 AATGTAATTA
*
20255 GTGTACCGATACACCCTGCAATGTATCCATACATTT
1 GTGTACCAATACACCCTGCAATGTATCCATACATTT
* * *
20291 GTGTACCAATACACTCTGTAGTGTATCCATACA
1 GTGTACCAATACACCCTGCAATGTATCCATACA
20324 CACTGCTTCA
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
36 29 1.00
ACGTcount: A:0.29, C:0.26, G:0.14, T:0.30
Consensus pattern (36 bp):
GTGTACCAATACACCCTGCAATGTATCCATACATTT
Found at i:20736 original size:34 final size:32
Alignment explanation
Indices: 20696--20759 Score: 83
Period size: 34 Copynumber: 1.9 Consensus size: 32
20686 AAAGGGTTTT
20696 GGTTCTAGCTAAGCCAATGTAAAATCTAGGGAAA
1 GGTTCTAGCTAAGCCAATG-AAAA-CTAGGGAAA
* * *
20730 GGTTCTAGTTTAGCCATTGAAAACTAGGGA
1 GGTTCTAGCTAAGCCAATGAAAACTAGGGA
20760 GTTGTAAAGG
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
32 7 0.26
33 4 0.15
34 16 0.59
ACGTcount: A:0.34, C:0.14, G:0.25, T:0.27
Consensus pattern (32 bp):
GGTTCTAGCTAAGCCAATGAAAACTAGGGAAA
Found at i:23096 original size:20 final size:20
Alignment explanation
Indices: 23071--23222 Score: 83
Period size: 20 Copynumber: 8.0 Consensus size: 20
23061 AAATATAATT
23071 AGTGTA-CCGATACACCCTGC
1 AGTGTATCC-ATACACCCTGC
23091 AGTGTATCCATACA--CTG-
1 AGTGTATCCATACACCCTGC
* **
23108 -GTGTA-CCGATACACTCTTT
1 AGTGTATCC-ATACACCCTGC
*
23127 AGTATATCCATACACCCTGC
1 AGTGTATCCATACACCCTGC
*
23147 AGTGTATCCTTACA--CTG-
1 AGTGTATCCATACACCCTGC
** *
23164 -GTGTA-CCAATACACTATGT
1 AGTGTATCC-ATACACCCTGC
* *
23183 AGTATATCCATACACCCTAC
1 AGTGTATCCATACACCCTGC
* * *
23203 AATATATACATACACCCTGC
1 AGTGTATCCATACACCCTGC
23223 TGCAATGGCT
Statistics
Matches: 102, Mismatches: 17, Indels: 26
0.70 0.12 0.18
Matches are distributed among these distances:
15 4 0.04
16 19 0.19
18 10 0.10
20 63 0.62
21 6 0.06
ACGTcount: A:0.30, C:0.29, G:0.13, T:0.28
Consensus pattern (20 bp):
AGTGTATCCATACACCCTGC
Found at i:23119 original size:16 final size:17
Alignment explanation
Indices: 23071--23122 Score: 54
Period size: 16 Copynumber: 2.9 Consensus size: 17
23061 AAATATAATT
23071 AGTGTACCGATACACCCTG
1 AGTGTACCGATACA--CTG
23090 CAGTGTATCC-ATACACTG
1 -AGTGTA-CCGATACACTG
23108 -GTGTACCGATACACT
1 AGTGTACCGATACACT
23123 CTTTAGTATA
Statistics
Matches: 30, Mismatches: 0, Indels: 8
0.79 0.00 0.21
Matches are distributed among these distances:
15 2 0.07
16 12 0.40
18 3 0.10
20 11 0.37
21 2 0.07
ACGTcount: A:0.27, C:0.29, G:0.19, T:0.25
Consensus pattern (17 bp):
AGTGTACCGATACACTG
Found at i:23119 original size:36 final size:36
Alignment explanation
Indices: 23072--23141 Score: 104
Period size: 36 Copynumber: 1.9 Consensus size: 36
23062 AATATAATTA
*
23072 GTGTACCGATACACCCTGCAGTGTATCCATACACTG
1 GTGTACCGATACACCCTGCAGTATATCCATACACTG
* **
23108 GTGTACCGATACACTCTTTAGTATATCCATACAC
1 GTGTACCGATACACCCTGCAGTATATCCATACAC
23142 CCTGCAGTGT
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
36 30 1.00
ACGTcount: A:0.27, C:0.29, G:0.16, T:0.29
Consensus pattern (36 bp):
GTGTACCGATACACCCTGCAGTATATCCATACACTG
Found at i:23217 original size:56 final size:56
Alignment explanation
Indices: 23080--23200 Score: 206
Period size: 56 Copynumber: 2.2 Consensus size: 56
23070 TAGTGTACCG
* * *
23080 ATACACCCTGCAGTGTATCCATACACTGGTGTACCGATACACTCTTTAGTATATCC
1 ATACACCCTGCAGTGTATCCATACACTGGTGTACCAATACACTATGTAGTATATCC
*
23136 ATACACCCTGCAGTGTATCCTTACACTGGTGTACCAATACACTATGTAGTATATCC
1 ATACACCCTGCAGTGTATCCATACACTGGTGTACCAATACACTATGTAGTATATCC
23192 ATACACCCT
1 ATACACCCT
23201 ACAATATATA
Statistics
Matches: 61, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
56 61 1.00
ACGTcount: A:0.28, C:0.29, G:0.13, T:0.30
Consensus pattern (56 bp):
ATACACCCTGCAGTGTATCCATACACTGGTGTACCAATACACTATGTAGTATATCC
Found at i:24505 original size:20 final size:20
Alignment explanation
Indices: 24473--24526 Score: 99
Period size: 20 Copynumber: 2.6 Consensus size: 20
24463 TAGAAAAAGT
24473 ATCCCCAAACGGCTCCAAAAC
1 ATCCCC-AACGGCTCCAAAAC
24494 ATCCCCAACGGCTCCAAAAC
1 ATCCCCAACGGCTCCAAAAC
24514 ATCCCCAACGGCT
1 ATCCCCAACGGCT
24527 AGATACAACT
Statistics
Matches: 33, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
20 27 0.82
21 6 0.18
ACGTcount: A:0.33, C:0.44, G:0.11, T:0.11
Consensus pattern (20 bp):
ATCCCCAACGGCTCCAAAAC
Found at i:24756 original size:34 final size:34
Alignment explanation
Indices: 24713--24779 Score: 98
Period size: 34 Copynumber: 2.0 Consensus size: 34
24703 TGTAAAATGA
* *
24713 AAGGTTCTAGCTGAGCCCTTGAAAAGCTAGGGAT
1 AAGGTTCTAGCTGAGCCCATGAAAAACTAGGGAT
* *
24747 AAGGTTCTAGTTTAGCCCATGAAAAACTAGGGA
1 AAGGTTCTAGCTGAGCCCATGAAAAACTAGGGA
24780 GTTGTAAAGG
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
34 29 1.00
ACGTcount: A:0.33, C:0.16, G:0.27, T:0.24
Consensus pattern (34 bp):
AAGGTTCTAGCTGAGCCCATGAAAAACTAGGGAT
Found at i:59697 original size:25 final size:25
Alignment explanation
Indices: 59659--59708 Score: 91
Period size: 25 Copynumber: 2.0 Consensus size: 25
59649 AAAATTACCA
59659 CTTTGGTCTATAAACTTTTCCCAAG
1 CTTTGGTCTATAAACTTTTCCCAAG
*
59684 CTTTGGTCTCTAAACTTTTCCCAAG
1 CTTTGGTCTATAAACTTTTCCCAAG
59709 TTTACACTTT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.22, C:0.26, G:0.12, T:0.40
Consensus pattern (25 bp):
CTTTGGTCTATAAACTTTTCCCAAG
Found at i:62714 original size:25 final size:25
Alignment explanation
Indices: 62676--62725 Score: 91
Period size: 25 Copynumber: 2.0 Consensus size: 25
62666 AAAATTACCA
62676 CTTTGGTCTATAAACTTTTCCCAAG
1 CTTTGGTCTATAAACTTTTCCCAAG
*
62701 CTTTGGTCTCTAAACTTTTCCCAAG
1 CTTTGGTCTATAAACTTTTCCCAAG
62726 TTTACACTTT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.22, C:0.26, G:0.12, T:0.40
Consensus pattern (25 bp):
CTTTGGTCTATAAACTTTTCCCAAG
Found at i:65734 original size:25 final size:25
Alignment explanation
Indices: 65696--65745 Score: 91
Period size: 25 Copynumber: 2.0 Consensus size: 25
65686 AAAATTACCA
65696 CTTTGGTCTATAAACTTTTCCCAAG
1 CTTTGGTCTATAAACTTTTCCCAAG
*
65721 CTTTGGTCTCTAAACTTTTCCCAAG
1 CTTTGGTCTATAAACTTTTCCCAAG
65746 TTTACACTTT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.22, C:0.26, G:0.12, T:0.40
Consensus pattern (25 bp):
CTTTGGTCTATAAACTTTTCCCAAG
Found at i:68755 original size:25 final size:25
Alignment explanation
Indices: 68717--68766 Score: 91
Period size: 25 Copynumber: 2.0 Consensus size: 25
68707 AAAATTACCA
68717 CTTTGGTCTATAAACTTTTCCCAAG
1 CTTTGGTCTATAAACTTTTCCCAAG
*
68742 CTTTGGTCTCTAAACTTTTCCCAAG
1 CTTTGGTCTATAAACTTTTCCCAAG
68767 TTTACACTTT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.22, C:0.26, G:0.12, T:0.40
Consensus pattern (25 bp):
CTTTGGTCTATAAACTTTTCCCAAG
Found at i:72238 original size:21 final size:21
Alignment explanation
Indices: 72200--72247 Score: 55
Period size: 20 Copynumber: 2.3 Consensus size: 21
72190 CCTTAAAAGG
72200 TAAAAAATGAATAAAATAA-A
1 TAAAAAATGAATAAAATAAGA
**
72220 TAAAAAATTTATAATAATAAGA
1 TAAAAAATGAATAA-AATAAGA
72242 -AAAAAA
1 TAAAAAA
72248 CTAAAATTAA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
20 12 0.50
21 11 0.46
22 1 0.04
ACGTcount: A:0.73, C:0.00, G:0.04, T:0.23
Consensus pattern (21 bp):
TAAAAAATGAATAAAATAAGA
Found at i:73529 original size:37 final size:37
Alignment explanation
Indices: 73478--73576 Score: 114
Period size: 39 Copynumber: 2.6 Consensus size: 37
73468 TAAATAAATA
*
73478 TTTTAAAATC-ATATAATATATAGTTTCAAAAA-T-TAT
1 TTTTAAAAACTATATAATATATA-TTTCAAAAACTGT-T
*
73514 TTTTAAAAACTATATATTATACGTATTTCAAAAACTGTT
1 TTTTAAAAACTATATAATATA--TATTTCAAAAACTGTT
*
73553 TTTTTAAAACTATATAATATATAT
1 TTTTAAAAACTATATAATATATAT
73577 AGATATATAT
Statistics
Matches: 54, Mismatches: 4, Indels: 9
0.81 0.06 0.13
Matches are distributed among these distances:
36 9 0.17
37 12 0.22
38 9 0.17
39 23 0.43
40 1 0.02
ACGTcount: A:0.44, C:0.07, G:0.03, T:0.45
Consensus pattern (37 bp):
TTTTAAAAACTATATAATATATATTTCAAAAACTGTT
Found at i:74474 original size:84 final size:84
Alignment explanation
Indices: 74149--75435 Score: 1005
Period size: 84 Copynumber: 15.6 Consensus size: 84
74139 TGCCTTGGGC
* * * * *
74149 TATGCTGTAAATGATGTACCTTAGAGCTGAGCGTAGTCAAACTCGAAGGTC--T--TTGGCAGAT
1 TATGCTGCAAATGATGTGCCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGGTTGGAAGAT
* * * * *
74210 AGCCCTTCTAGCCTTGAGC
66 AACCCTTCTCGACTTAAGT
* * * * *
74229 TATACCGCAAATGATGTGCCGTT-GAGCTGAGCGTAATCGAACTCAAAGGTCTTT-GTTGGAAGG
1 TATGCTGCAAATGATGTGCC-TTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGGTTGGAAGA
* * *
74292 TAACCCTTCTAGCCTTGAGT
65 TAACCCTTCTCGACTTAAGT
* * * * *
74312 TATGCTGCAAATGATGTGCCCTCGAAGCTGAGTGTAATCGAACTCGAAGGTCTTT-G--GCAA-A
1 TATGCTGCAAATGATGTG-CCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGGTTGGAAGA
* *
74373 TAGCCCTTCTCGACTTAAGC
65 TAACCCTTCTCGACTTAAGT
* * * *
74393 TATGTTGCAAATGATGTGCCTTGGAGTTGAACGTAGTCAAACTCGAAGGTCTTTGGTTGGAAGAT
1 TATGCTGCAAATGATGTGCCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGGTTGGAAGAT
74458 AACCCTTCTCGACTTAAGT
66 AACCCTTCTCGACTTAAGT
* *
74477 TATGCTGCAAATGATATGCCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTTGGGT-GACAG
1 TATGCTGCAAATGATGTGCCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTC-TTTGGTTGGA-AG
* * *
74541 ATAACCCTTCTAGCCTTGAGT
64 ATAACCCTTCTCGACTTAAGT
** * * * * * * * *
74562 TATATTGTAAATGATGTGCCCTCGAAGCTGAGTGTAATCGAACTCG-AGG---GTGTTTGGCAGA
1 TATGCTGCAAATGATGTG-CCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGGTTGGAAGA
* *
74623 TAGCCCTTCTCGACTTAAGC
65 TAACCCTTCTCGACTTAAGT
* * * * *
74643 TATGCTGCAAATGATGTGCCTTGGAGCTGAGCTTAGTCAAACTCGAAGGTATTTTGTTGGTAGAT
1 TATGCTGCAAATGATGTGCCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGGTTGGAAGAT
**
74708 AAATCTTCTCGACTTAAGT
66 AACCCTTCTCGACTTAAGT
* * * * * * *
74727 TATGCTGTAAATGATATGCCTTAGAGTTGAGCATAGTCAAACTCGAAGGTCTTTTGG-TGGCAGA
1 TATGCTGCAAATGATGTGCCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTC-TTTGGTTGGAAGA
* * * *
74791 TAGCCCTTCTAG-CATTGAGC
65 TAACCCTTCTCGAC-TTAAGT
* * ** * * * * * *
74811 TATGTTGTAAATTTTGTGCCCTCGAAGCTGAGTGTAATCGAACTCGAGGGTC--T--TTGGCAGA
1 TATGCTGCAAATGATGTG-CCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGGTTGGAAGA
* * **
74872 TAGCCCTTCTTGACTTAACC
65 TAACCCTTCTCGACTTAAGT
* * * *
74892 TATGCTACAAATGATCTGCCTTGGAGCTGAGCGTAGTCGAACTCGAAGATCTTTGGTTGGCAGAT
1 TATGCTGCAAATGATGTGCCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGGTTGGAAGAT
74957 AACCCTTCTCGACTTAAGT
66 AACCCTTCTCGACTTAAGT
* * * * * *
74976 TATGCTACAAATAATATGCCTTGGAGTTGAGTGTAGTCGAACTCAAAGGTCTTT--TTGTGATAG
1 TATGCTGCAAATGATGTGCCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGGTTG-GA-AG
* * *
75039 ATAACCCTTCTAGCCTTGAGT
64 ATAACCCTTCTCGACTTAAGT
* * * * * * * * *
75060 TATGCTGTAAATGATGTTCCCTCGAAGCTGAGTGTAATCAAACTCGAGGGTCTTT-G--GCAA-A
1 TATGCTGCAAATGATG-TGCCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGGTTGGAAGA
*
75121 TAGCCCTTCTCGACTTAAGT
65 TAACCCTTCTCGACTTAAGT
* * * * * *
75141 TATACTACAAATAATGTGCCTTGGAGCTGAGCATAGTCAAACTCGAAGGTCTTTGG-T-CACAGA
1 TATGCTGCAAATGATGTGCCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGGTTGGA-AGA
* * * *
75204 CAACCCTTCTAGCCTTGAGT
65 TAACCCTTCTCGACTTAAGT
* * * * * * * * *
75224 TATGATGTAAATGATATACCCTCGAAGCTGAGTGTAATCGAACTCGAGGGTCTTTGG-T---AGA
1 TATGCTGCAAATGATGT-GCCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGGTTGGAAGA
* * *
75285 TAGCTCTTC-CTGACTTAAGC
65 TAACCCTTCTC-GACTTAAGT
* *
75305 TATGCTGCAAATGATGTG-C----AGCTGAGCGTAGTTGAACTCGAAGGTATTTGGTTGGAAGAT
1 TATGCTGCAAATGATGTGCCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGGTTGGAAGAT
75365 AACCCTTCTCGACTTAAGT
66 AACCCTTCTCGACTTAAGT
* ** *
75384 TATGTTGCAAATCTTGGTGCCTTTGAGCTGAGCGTAGTCGAACTCGAAGGTC
1 TATGCTGCAAATGAT-GTGCCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTC
75436 ATTTATTGGC
Statistics
Matches: 954, Mismatches: 205, Indels: 91
0.76 0.16 0.07
Matches are distributed among these distances:
75 27 0.03
76 1 0.00
79 31 0.03
80 153 0.16
81 170 0.18
82 13 0.01
83 74 0.08
84 336 0.35
85 126 0.13
86 23 0.02
ACGTcount: A:0.26, C:0.20, G:0.24, T:0.31
Consensus pattern (84 bp):
TATGCTGCAAATGATGTGCCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGGTTGGAAGAT
AACCCTTCTCGACTTAAGT
Found at i:74905 original size:249 final size:249
Alignment explanation
Indices: 74147--75435 Score: 1439
Period size: 249 Copynumber: 5.2 Consensus size: 249
74137 CTTGCCTTGG
** * * *
74147 GCTATGCTGTAAATGATGTACCTTAGAGCTGAGCGTAGTCAAACTCGAAGGTC--T--TTGGCAG
1 GCTATGCTACAAATGATGTGCCTTGGAGCTGAGCGTAGTCAAACTCGAAGGTCTTTGGTTGGAAG
* * * * * * * * *
74208 ATAGCCCTTCTAGCCTTGAGCTATACCGCAAATGATGTGCCGTT-GAGCTGAGCGTAATCGAACT
66 ATAACCCTTCTCGACTTAAGTTATGCTGCAAATGATATGCC-TTGGAGCTGAGCGTAGTCGAACT
* * *
74272 CAAAGGTC-TTTGTTGGA-AGGTAACCCTTCTAGCCTTGAGTTATGCTGCAAATGATGTGCCCTC
130 CAAAGGTCTTTTGGT-GACAGATAACCCTTCTAGCCTTGAGTTATGCTGTAAATGATGTGCCCTC
*
74335 GAAGCTGAGTGTAATCGAACTCGAAGGTCTTTGGCAAATAGCCCTTCTCGACTTAA
194 GAAGCTGAGTGTAATCGAACTCGAGGGTCTTTGGCAAATAGCCCTTCTCGACTTAA
* * * *
74391 GCTATGTTGCAAATGATGTGCCTTGGAGTTGAACGTAGTCAAACTCGAAGGTCTTTGGTTGGAAG
1 GCTATGCTACAAATGATGTGCCTTGGAGCTGAGCGTAGTCAAACTCGAAGGTCTTTGGTTGGAAG
74456 ATAACCCTTCTCGACTTAAGTTATGCTGCAAATGATATGCCTTGGAGCTGAGCGTAGTCGAACTC
66 ATAACCCTTCTCGACTTAAGTTATGCTGCAAATGATATGCCTTGGAGCTGAGCGTAGTCGAACTC
* **
74521 GAAGGTCTTTTGGGTGACAGATAACCCTTCTAGCCTTGAGTTATATTGTAAATGATGTGCCCTCG
131 AAAGGTCTTTT-GGTGACAGATAACCCTTCTAGCCTTGAGTTATGCTGTAAATGATGTGCCCTCG
* *
74586 AAGCTGAGTGTAATCGAACTCGAGGGTGTTTGGCAGATAGCCCTTCTCGACTTAA
195 AAGCTGAGTGTAATCGAACTCGAGGGTCTTTGGCAAATAGCCCTTCTCGACTTAA
* * * * *
74641 GCTATGCTGCAAATGATGTGCCTTGGAGCTGAGCTTAGTCAAACTCGAAGGTATTTTGTTGGTAG
1 GCTATGCTACAAATGATGTGCCTTGGAGCTGAGCGTAGTCAAACTCGAAGGTCTTTGGTTGGAAG
** * * * * *
74706 ATAAATCTTCTCGACTTAAGTTATGCTGTAAATGATATGCCTTAGAGTTGAGCATAGTCAAACTC
66 ATAACCCTTCTCGACTTAAGTTATGCTGCAAATGATATGCCTTGGAGCTGAGCGTAGTCGAACTC
* * * * * * **
74771 GAAGGTCTTTTGGTGGCAGATAGCCCTTCTAGCATTGAGCTATGTTGTAAATTTTGTGCCCTCGA
131 AAAGGTCTTTTGGTGACAGATAACCCTTCTAGCCTTGAGTTATGCTGTAAATGATGTGCCCTCGA
* *
74836 AGCTGAGTGTAATCGAACTCGAGGGTCTTTGGCAGATAGCCCTTCTTGACTTAA
196 AGCTGAGTGTAATCGAACTCGAGGGTCTTTGGCAAATAGCCCTTCTCGACTTAA
* * * * *
74890 CCTATGCTACAAATGATCTGCCTTGGAGCTGAGCGTAGTCGAACTCGAAGATCTTTGGTTGGCAG
1 GCTATGCTACAAATGATGTGCCTTGGAGCTGAGCGTAGTCAAACTCGAAGGTCTTTGGTTGGAAG
* * * *
74955 ATAACCCTTCTCGACTTAAGTTATGCTACAAATAATATGCCTTGGAGTTGAGTGTAGTCGAACTC
66 ATAACCCTTCTCGACTTAAGTTATGCTGCAAATGATATGCCTTGGAGCTGAGCGTAGTCGAACTC
* * *
75020 AAAGGTCTTTTTGTGATAGATAACCCTTCTAGCCTTGAGTTATGCTGTAAATGATGTTCCCTCGA
131 AAAGGTCTTTTGGTGACAGATAACCCTTCTAGCCTTGAGTTATGCTGTAAATGATGTGCCCTCGA
*
75085 AGCTGAGTGTAATCAAACTCGAGGGTCTTTGGCAAATAGCCCTTCTCGACTTAA
196 AGCTGAGTGTAATCGAACTCGAGGGTCTTTGGCAAATAGCCCTTCTCGACTTAA
* * * * *
75139 GTTATACTACAAATAATGTGCCTTGGAGCTGAGCATAGTCAAACTCGAAGGTCTTTGG-T-CACA
1 GCTATGCTACAAATGATGTGCCTTGGAGCTGAGCGTAGTCAAACTCGAAGGTCTTTGGTTGGA-A
* * * * * * * * * * *
75202 GACAACCCTTCTAGCCTTGAGTTATGATGTAAATGATATACCCTCGAAGCTGAGTGTAATCGAAC
65 GATAACCCTTCTCGACTTAAGTTATGCTGCAAATGATAT-GCCTTGGAGCTGAGCGTAGTCGAAC
* * * * * * * *
75267 TCGAGGGTC-TTTGGT---AGATAGCTCTTCCT-GACTTAAGCTATGCTGCAAATGATGTG----
129 TCAAAGGTCTTTTGGTGACAGATAACCCTT-CTAGCCTTGAGTTATGCTGTAAATGATGTGCCCT
* * * * * * *
75323 C--AGCTGAGCGTAGTTGAACTCGAAGGTATTTGGTTGGAAGATAACCCTTCTCGACTTAA
193 CGAAGCTGAGTGTAATCGAACTCGAGGGTCTTT-G--GCAA-ATAGCCCTTCTCGACTTAA
* * * ** * *
75382 GTTATGTTGCAAATCTTGGTGCCTTTGAGCTGAGCGTAGTCGAACTCGAAGGTC
1 GCTATGCTACAAATGAT-GTGCCTTGGAGCTGAGCGTAGTCAAACTCGAAGGTC
75436 ATTTATTGGC
Statistics
Matches: 900, Mismatches: 129, Indels: 32
0.85 0.12 0.03
Matches are distributed among these distances:
239 24 0.03
240 1 0.00
241 1 0.00
242 3 0.00
243 30 0.03
244 80 0.09
245 31 0.03
246 3 0.00
247 2 0.00
248 103 0.11
249 398 0.44
250 224 0.25
ACGTcount: A:0.26, C:0.20, G:0.24, T:0.31
Consensus pattern (249 bp):
GCTATGCTACAAATGATGTGCCTTGGAGCTGAGCGTAGTCAAACTCGAAGGTCTTTGGTTGGAAG
ATAACCCTTCTCGACTTAAGTTATGCTGCAAATGATATGCCTTGGAGCTGAGCGTAGTCGAACTC
AAAGGTCTTTTGGTGACAGATAACCCTTCTAGCCTTGAGTTATGCTGTAAATGATGTGCCCTCGA
AGCTGAGTGTAATCGAACTCGAGGGTCTTTGGCAAATAGCCCTTCTCGACTTAA
Found at i:75258 original size:164 final size:164
Alignment explanation
Indices: 74149--75458 Score: 1003
Period size: 164 Copynumber: 7.9 Consensus size: 164
74139 TGCCTTGGGC
* * * *
74149 TATGCTGTAAATGATGTACCTTAGAGCTGAGCGTAGTCAAACTCGAAGGTCTTT-G-G-CAGATA
1 TATGCTGCAAATGATGTGCCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGGTGACAGATA
* * * * * * *
74211 GCCCTTCTAGCCTTGAGCTAT-ACCGCAAATGATGTGCCGTTG-AGCTGAGCGTAATCGAACTCA
66 ACCCTTCTAGCCTTGAGTTATGA-TGTAAATGATGTGCCCTCGAAGCTGAGCGTAATCGAACTCG
* * * * * *
74274 AAGGTCTTTGTTGGAAGGTAACCCTTCTAGCCTTGAGT
130 AAGGTC--T-TTGGCAGATAGCCCTTCTCGACTTAAGT
* * * * *
74312 TATGCTGCAAATGATGTGCCCTCGAAGCTGAGTGTAATCGAACTCGAAGGTCTTT-G-G-CAAAT
1 TATGCTGCAAATGATGTG-CCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGGTGACAGAT
* * * * * * * * * * * * *
74374 AGCCCTTCTCGACTTAAGCTATGTTGCAAATGATGTG-CCTTGGAGTTGAACGTAGTCAAACTCG
65 AACCCTTCTAGCCTTGAGTTATGATGTAAATGATGTGCCCTCGAAGCTGAGCGTAATCGAACTCG
* *
74438 AAGGTCTTTGGTTGGAAGATAACCCTTCTCGACTTAAGT
130 AAGGTC--T--TTGGCAGATAGCCCTTCTCGACTTAAGT
*
74477 TATGCTGCAAATGATATGCCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTTGGGTGACAGA
1 TATGCTGCAAATGATGTGCCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTC-TTT-GGTGACAGA
*
74542 TAACCCTTCTAGCCTTGAGTTAT-ATTGTAAATGATGTGCCCTCGAAGCTGAGTGTAATCGAACT
64 TAACCCTTCTAGCCTTGAGTTATGA-TGTAAATGATGTGCCCTCGAAGCTGAGCGTAATCGAACT
* * *
74606 CGAGGGTGTTTGGCAGATAGCCCTTCTCGACTTAAGC
128 CGAAGGTCTTTGGCAGATAGCCCTTCTCGACTTAAGT
* * * * **
74643 TATGCTGCAAATGATGTGCCTTGGAGCTGAGCTTAGTCAAACTCGAAGGTATTTTGTTGGTAGAT
1 TATGCTGCAAATGATGTGCCTTGGAGCTGAGCGTAGTCGAACTCGAAGGT-CTTTGGTGACAGAT
** * * * * * * * * * * *
74708 AAATCTTCTCGACTTAAGTTATGCTGTAAATGATATGCCTTAG-AGTTGAGCATAGTCAAACTCG
65 AACCCTTCTAGCCTTGAGTTATGATGTAAATGATGTGCCCTCGAAGCTGAGCGTAATCGAACTCG
* * *
74772 AAGGTCTTTTGGTGGCAGATAGCCCTTCTAG-CATTGAGC
130 AAGGTC--TT--TGGCAGATAGCCCTTCTCGAC-TTAAGT
* * ** * * * * *
74811 TATGTTGTAAATTTTGTGCCCTCGAAGCTGAGTGTAATCGAACTCGAGGGTCTTT-G-G-CAGAT
1 TATGCTGCAAATGATGTG-CCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGGTGACAGAT
* * * * ** * ** * * * *
74873 AGCCCTTCTTGACTTAACCTATGCTACAAATGATCTG-CCTTGGAGCTGAGCGTAGTCGAACTCG
65 AACCCTTCTAGCCTTGAGTTATGATGTAAATGATGTGCCCTCGAAGCTGAGCGTAATCGAACTCG
* *
74937 AAGATCTTTGGTTGGCAGATAACCCTTCTCGACTTAAGT
130 AAGGTC--T--TTGGCAGATAGCCCTTCTCGACTTAAGT
* * * * * * * *
74976 TATGCTACAAATAATATGCCTTGGAGTTGAGTGTAGTCGAACTCAAAGGTCTTTTTGTGATAGAT
1 TATGCTGCAAATGATGTGCCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTC-TTTGGTGACAGAT
* * * *
75041 AACCCTTCTAGCCTTGAGTTATGCTGTAAATGATGTTCCCTCGAAGCTGAGTGTAATCAAACTCG
65 AACCCTTCTAGCCTTGAGTTATGATGTAAATGATGTGCCCTCGAAGCTGAGCGTAATCGAACTCG
* *
75106 AGGGTCTTTGGCAAATAGCCCTTCTCGACTTAAGT
130 AAGGTCTTTGGCAGATAGCCCTTCTCGACTTAAGT
* * * * * * *
75141 TATACTACAAATAATGTGCCTTGGAGCTGAGCATAGTCAAACTCGAAGGTCTTTGGTCACAGACA
1 TATGCTGCAAATGATGTGCCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGGTGACAGATA
* * *
75206 ACCCTTCTAGCCTTGAGTTATGATGTAAATGATATACCCTCGAAGCTGAGTGTAATCGAACTCGA
66 ACCCTTCTAGCCTTGAGTTATGATGTAAATGATGTGCCCTCGAAGCTGAGCGTAATCGAACTCGA
* * * *
75271 GGGTCTTTGGTAGATAGCTCTTC-CTGACTTAAGC
131 AGGTCTTTGGCAGATAGCCCTTCTC-GACTTAAGT
* *
75305 TATGCTGCAAATGATGTG-C----AGCTGAGCGTAGTTGAACTCGAAGGTATTTGGTTGGA-AGA
1 TATGCTGCAAATGATGTGCCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGG-T-GACAGA
* * * * * ** * * *
75364 TAACCCTTCTCGACTTAAGTTATGTTGCAAATCTTGGTGCCTTTG-AGCTGAGCGTAGTCGAACT
64 TAACCCTTCTAGCCTTGAGTTATGATGTAAATGAT-GTGCCCTCGAAGCTGAGCGTAATCGAACT
*
75428 CGAAGGTCATTTATTGGCACATAGCCCTTCT
128 CGAAGGTC---T-TTGGCAGATAGCCCTTCT
75459 TGCCTTGAGC
Statistics
Matches: 926, Mismatches: 184, Indels: 72
0.78 0.16 0.06
Matches are distributed among these distances:
159 28 0.03
160 55 0.06
161 6 0.01
163 23 0.02
164 299 0.32
165 249 0.27
166 80 0.09
167 5 0.01
168 73 0.08
169 84 0.09
170 24 0.03
ACGTcount: A:0.25, C:0.20, G:0.24, T:0.31
Consensus pattern (164 bp):
TATGCTGCAAATGATGTGCCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGGTGACAGATA
ACCCTTCTAGCCTTGAGTTATGATGTAAATGATGTGCCCTCGAAGCTGAGCGTAATCGAACTCGA
AGGTCTTTGGCAGATAGCCCTTCTCGACTTAAGT
Found at i:80077 original size:4 final size:4
Alignment explanation
Indices: 80052--80142 Score: 50
Period size: 4 Copynumber: 23.2 Consensus size: 4
80042 AAAATGTTAG
* **
80052 ATAA ATAA A-AA ATGA ATAAA ATAA ATAA ATAA ATTT AT-A AT-A AT-A
1 ATAA ATAA ATAA ATAA AT-AA ATAA ATAA ATAA ATAA ATAA ATAA ATAA
* * *
80097 AT-A ATAA ACTAAA ATTA A-AA CTAA AGAA ATAA ATAAA ATAA ATAA A
1 ATAA ATAA A-T-AA ATAA ATAA ATAA ATAA ATAA AT-AA ATAA ATAA A
80143 CATGGACATT
Statistics
Matches: 69, Mismatches: 11, Indels: 14
0.73 0.12 0.15
Matches are distributed among these distances:
3 15 0.22
4 42 0.61
5 9 0.13
6 3 0.04
ACGTcount: A:0.70, C:0.02, G:0.02, T:0.25
Consensus pattern (4 bp):
ATAA
Found at i:80078 original size:9 final size:9
Alignment explanation
Indices: 80060--80142 Score: 52
Period size: 9 Copynumber: 9.3 Consensus size: 9
80050 AGATAAATAA
*
80060 AAAATGAAT
1 AAAATAAAT
80069 AAAATAAAT
1 AAAATAAAT
80078 -AAATAAATTT
1 AAAATAAA--T
*
80088 ATAAT-AAT
1 AAAATAAAT
80096 AATAATAAACT
1 AA-AATAAA-T
80107 AAAAT---T
1 AAAATAAAT
80113 AAAACTAAA-
1 AAAA-TAAAT
*
80122 GAAATAAAT
1 AAAATAAAT
80131 AAAATAAAT
1 AAAATAAAT
80140 AAA
1 AAA
80143 CATGGACATT
Statistics
Matches: 58, Mismatches: 5, Indels: 22
0.68 0.06 0.26
Matches are distributed among these distances:
6 5 0.09
7 1 0.02
8 13 0.22
9 25 0.43
10 8 0.14
11 6 0.10
ACGTcount: A:0.70, C:0.02, G:0.02, T:0.25
Consensus pattern (9 bp):
AAAATAAAT
Found at i:86886 original size:20 final size:20
Alignment explanation
Indices: 86861--86916 Score: 96
Period size: 19 Copynumber: 2.9 Consensus size: 20
86851 AATGCTCGGA
86861 GGGAATCGATTCCCCCTAAG
1 GGGAATCGATTCCCCCTAAG
86881 GGGAATCGATT-CCCCTAAG
1 GGGAATCGATTCCCCCTAAG
*
86900 GGGTATCGATTCCCCCT
1 GGGAATCGATTCCCCCT
86917 GTTCAACGGT
Statistics
Matches: 34, Mismatches: 1, Indels: 2
0.92 0.03 0.05
Matches are distributed among these distances:
19 18 0.53
20 16 0.47
ACGTcount: A:0.21, C:0.30, G:0.25, T:0.23
Consensus pattern (20 bp):
GGGAATCGATTCCCCCTAAG
Found at i:95096 original size:43 final size:43
Alignment explanation
Indices: 95023--95180 Score: 235
Period size: 43 Copynumber: 3.7 Consensus size: 43
95013 TGTCAGCTTA
* *
95023 TCCATCACATAAGGAGTTAGATCAGTATCCCTTTACACTTGAT
1 TCCATCACATAAGGAGTTGGATCAGCATCCCTTTACACTTGAT
* *
95066 TCCATCACATAAGGAGTTGGATTAGCATCCCTTTACACTCGAT
1 TCCATCACATAAGGAGTTGGATCAGCATCCCTTTACACTTGAT
* * * *
95109 TCCATCACATAAGGAGTTGGATCAGCATCCTTTTTCGCTTCAT
1 TCCATCACATAAGGAGTTGGATCAGCATCCCTTTACACTTGAT
*
95152 TCCATCACATAAGGAGTTGGATCAACATC
1 TCCATCACATAAGGAGTTGGATCAGCATC
95181 ATATCACTCA
Statistics
Matches: 104, Mismatches: 11, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
43 104 1.00
ACGTcount: A:0.28, C:0.25, G:0.16, T:0.31
Consensus pattern (43 bp):
TCCATCACATAAGGAGTTGGATCAGCATCCCTTTACACTTGAT
Found at i:97371 original size:21 final size:20
Alignment explanation
Indices: 97307--97371 Score: 62
Period size: 21 Copynumber: 3.2 Consensus size: 20
97297 TTATATTATA
*
97307 TTATATAGTACATATGCTA-
1 TTATATAGTATATATGCTAT
*
97326 TTATATAGT-TATATGTTTAT
1 TTATATAGTATATATG-CTAT
*
97346 ATTATATAGTATATATACATAT
1 -TTATATAGTATATATGC-TAT
97368 TTAT
1 TTAT
97372 TACAAAGTGT
Statistics
Matches: 37, Mismatches: 4, Indels: 8
0.76 0.08 0.16
Matches are distributed among these distances:
18 5 0.14
19 11 0.30
21 13 0.35
22 8 0.22
ACGTcount: A:0.37, C:0.05, G:0.08, T:0.51
Consensus pattern (20 bp):
TTATATAGTATATATGCTAT
Found at i:97372 original size:24 final size:24
Alignment explanation
Indices: 97300--97373 Score: 61
Period size: 24 Copynumber: 3.2 Consensus size: 24
97290 AGTCCATTTA
*
97300 TATTATAT--TATATAGTACATATGC
1 TATTATATAGTATATA-TACATAT-T
*
97324 TATTATATAGT-TATAT--GT-TT
1 TATTATATAGTATATATACATATT
97344 ATATTATATAGTATATATACATATT
1 -TATTATATAGTATATATACATATT
97369 TATTA
1 TATTA
97374 CAAAGTGTAT
Statistics
Matches: 40, Mismatches: 3, Indels: 14
0.70 0.05 0.25
Matches are distributed among these distances:
21 12 0.30
22 6 0.15
24 15 0.38
25 6 0.15
26 1 0.03
ACGTcount: A:0.38, C:0.04, G:0.07, T:0.51
Consensus pattern (24 bp):
TATTATATAGTATATATACATATT
Found at i:97443 original size:20 final size:22
Alignment explanation
Indices: 97400--97444 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 22
97390 TATATAATAC
97400 ATATATTATATTAGTATATATT
1 ATATATTATATTAGTATATATT
* *
97422 ATATATTACTATTATTATTTATT
1 ATATATTA-TATTAGTATATATT
97445 TCTTTTGTTT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
22 8 0.40
23 12 0.60
ACGTcount: A:0.38, C:0.02, G:0.02, T:0.58
Consensus pattern (22 bp):
ATATATTATATTAGTATATATT
Found at i:97933 original size:35 final size:35
Alignment explanation
Indices: 97894--97960 Score: 134
Period size: 35 Copynumber: 1.9 Consensus size: 35
97884 TTGTTTGGTC
97894 TCTTTTGTTTTTCTTTTTGACTCAAAAAACCCCTT
1 TCTTTTGTTTTTCTTTTTGACTCAAAAAACCCCTT
97929 TCTTTTGTTTTTCTTTTTGACTCAAAAAACCC
1 TCTTTTGTTTTTCTTTTTGACTCAAAAAACCC
97961 ACGACGAAGG
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
35 32 1.00
ACGTcount: A:0.21, C:0.22, G:0.06, T:0.51
Consensus pattern (35 bp):
TCTTTTGTTTTTCTTTTTGACTCAAAAAACCCCTT
Found at i:105681 original size:22 final size:22
Alignment explanation
Indices: 105602--105682 Score: 74
Period size: 22 Copynumber: 3.6 Consensus size: 22
105592 CTTCATTTCA
*
105602 TTTCATTTCCTTTTGAATTTAAT
1 TTTC-TTTCATTTTGAATTTAAT
* *
105625 TTTCTTTCATTCTGTAA-TTCAT
1 TTTCTTTCATTTTG-AATTTAAT
** * *
105647 TTAATATCCTTTTGAATTTAAT
1 TTTCTTTCATTTTGAATTTAAT
105669 TTTCTTTCATTTTG
1 TTTCTTTCATTTTG
105683 TGTGGGATAT
Statistics
Matches: 43, Mismatches: 13, Indels: 5
0.70 0.21 0.08
Matches are distributed among these distances:
21 2 0.05
22 35 0.81
23 6 0.14
ACGTcount: A:0.21, C:0.14, G:0.05, T:0.60
Consensus pattern (22 bp):
TTTCTTTCATTTTGAATTTAAT
Found at i:106961 original size:95 final size:95
Alignment explanation
Indices: 106832--107042 Score: 305
Period size: 95 Copynumber: 2.2 Consensus size: 95
106822 ATACCAATGA
* ** **
106832 GGTAGTATTGATACCATGGTAAGGGTATTGATACCAGGCAACATCGAATCTAAAATTGGTATCGA
1 GGTAGTATCGATACCATGGTAAGGGTATCAATACCAGAAAACATCGAATCTAAAATTGGTATCGA
106897 TACTGGAAGGGGGTATTGATACCATAGTAT
66 TACTGGAAGGGGGTATTGATACCATAGTAT
** *
106927 GGTAGTATCGATATTATGGTAAGGGTATCAATACCAGAAAACATCGAATCTAAAATTGGTATTGA
1 GGTAGTATCGATACCATGGTAAGGGTATCAATACCAGAAAACATCGAATCTAAAATTGGTATCGA
*
106992 TACTGGAAGGGGGTATTGGTACCATAGTAT
66 TACTGGAAGGGGGTATTGATACCATAGTAT
* * * *
107022 AGAAGTATCGGTACCAGGGTA
1 GGTAGTATCGATACCATGGTA
107043 GTAGTATCGA
Statistics
Matches: 101, Mismatches: 15, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
95 101 1.00
ACGTcount: A:0.34, C:0.12, G:0.27, T:0.28
Consensus pattern (95 bp):
GGTAGTATCGATACCATGGTAAGGGTATCAATACCAGAAAACATCGAATCTAAAATTGGTATCGA
TACTGGAAGGGGGTATTGATACCATAGTAT
Found at i:107540 original size:46 final size:46
Alignment explanation
Indices: 107446--107841 Score: 535
Period size: 46 Copynumber: 8.6 Consensus size: 46
107436 TAAATCGAAT
* ** **
107446 CCATAATTAAAATGCATAAAAAAAATGCATTAAGGCATGAAAATATG
1 CCATAATTAAAATGCAT-GAAAGGATGCATTAAGGCATGAAAGGATG
* *
107493 CCATAATTAAAATGAATGAAAGGATGCATTAAAGCAT-AATAGGATG
1 CCATAATTAAAATGCATGAAAGGATGCATTAAGGCATGAA-AGGATG
* *
107539 CCATAATTAAAATGCATGAAATGATGCATTAATGCATGAAAGGATG
1 CCATAATTAAAATGCATGAAAGGATGCATTAAGGCATGAAAGGATG
* *
107585 CCATAATTAAAATGCATGAAATGATGAATTAAGGCATGAAAGGATG
1 CCATAATTAAAATGCATGAAAGGATGCATTAAGGCATGAAAGGATG
*
107631 TCATAATTAAAATGCATGAAAGGATGCATTAAGGCATGAAAGGATG
1 CCATAATTAAAATGCATGAAAGGATGCATTAAGGCATGAAAGGATG
* *
107677 CCATAATTAAAATGCATGAAAGGATGCATTATGGAATGAAAGGATG
1 CCATAATTAAAATGCATGAAAGGATGCATTAAGGCATGAAAGGATG
* * * * *
107723 TCATAATTAAAATGCATGAAATGATACGTTAAGGCATGAAATGATG
1 CCATAATTAAAATGCATGAAAGGATGCATTAAGGCATGAAAGGATG
* *
107769 CAATAAACTAAAATGCATGAAAGGATGCATTAAGGCATGAAAGGATG
1 CCAT-AATTAAAATGCATGAAAGGATGCATTAAGGCATGAAAGGATG
* *
107816 TCATAATTTAAATGCAT-AAATGGATG
1 CCATAATTAAAATGCATGAAA-GGATG
107842 TGTTAATACG
Statistics
Matches: 309, Mismatches: 36, Indels: 9
0.87 0.10 0.03
Matches are distributed among these distances:
45 5 0.02
46 247 0.80
47 57 0.18
ACGTcount: A:0.46, C:0.09, G:0.20, T:0.25
Consensus pattern (46 bp):
CCATAATTAAAATGCATGAAAGGATGCATTAAGGCATGAAAGGATG
Found at i:108429 original size:13 final size:13
Alignment explanation
Indices: 108413--108437 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
108403 TTGGTATCAG
108413 AGATTGTCAATAA
1 AGATTGTCAATAA
108426 AGATTGTCAATA
1 AGATTGTCAATA
108438 TTACTAGTAT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.44, C:0.08, G:0.16, T:0.32
Consensus pattern (13 bp):
AGATTGTCAATAA
Found at i:115203 original size:42 final size:42
Alignment explanation
Indices: 115113--115223 Score: 125
Period size: 42 Copynumber: 2.6 Consensus size: 42
115103 CGTTTGTGAG
* * *
115113 ACAAACACCGCTAAATAACTACTCTATTGCAGCGTTTTTAGA
1 ACAAACGCCGCTAAATAACTACTCTATTACAGCATTTTTAGA
* * *
115155 ACAAACGTCGCTAAATAACTACTCTATTACGGCATTTGTTTG-
1 ACAAACGCCGCTAAATAACTACTCTATTACAGCATTT-TTAGA
* * *
115197 ATAAACGCCGCTAAATTACTTCTCTAT
1 ACAAACGCCGCTAAATAACTACTCTAT
115224 AGCGTCGTTT
Statistics
Matches: 58, Mismatches: 10, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
42 55 0.95
43 3 0.05
ACGTcount: A:0.33, C:0.23, G:0.12, T:0.32
Consensus pattern (42 bp):
ACAAACGCCGCTAAATAACTACTCTATTACAGCATTTTTAGA
Found at i:116131 original size:19 final size:20
Alignment explanation
Indices: 116097--116136 Score: 64
Period size: 19 Copynumber: 2.0 Consensus size: 20
116087 TATTGTCCAC
116097 ACAGTAACAATATTATTCAT
1 ACAGTAACAATATTATTCAT
*
116117 ACAGT-ACAGTATTATTCAT
1 ACAGTAACAATATTATTCAT
116136 A
1 A
116137 AAAATATTTT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 14 0.74
20 5 0.26
ACGTcount: A:0.42, C:0.15, G:0.07, T:0.35
Consensus pattern (20 bp):
ACAGTAACAATATTATTCAT
Found at i:118377 original size:33 final size:33
Alignment explanation
Indices: 118335--118400 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
118325 TCTTTACAAC
118335 TCCCTAGTTTTT-CAATGGCTAAACTAGAACCAA
1 TCCCTAGTTTTTACAAT-GCTAAACTAGAACCAA
* *
118368 TCCCTAGTTTTTACCATGCTAACCTAGAACCAA
1 TCCCTAGTTTTTACAATGCTAAACTAGAACCAA
118401 AACCCCTTTA
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
33 27 0.90
34 3 0.10
ACGTcount: A:0.32, C:0.27, G:0.11, T:0.30
Consensus pattern (33 bp):
TCCCTAGTTTTTACAATGCTAAACTAGAACCAA
Found at i:118877 original size:19 final size:20
Alignment explanation
Indices: 118838--118882 Score: 65
Period size: 19 Copynumber: 2.3 Consensus size: 20
118828 ATCGGTATTG
*
118838 TTCACACAGTATCAATACTA
1 TTCATACAGTATCAATACTA
*
118858 TTCATACAGTA-CATTACTA
1 TTCATACAGTATCAATACTA
118877 TTCATA
1 TTCATA
118883 AAAAAAATTT
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 13 0.57
20 10 0.43
ACGTcount: A:0.38, C:0.22, G:0.04, T:0.36
Consensus pattern (20 bp):
TTCATACAGTATCAATACTA
Found at i:119181 original size:21 final size:21
Alignment explanation
Indices: 119155--119206 Score: 95
Period size: 21 Copynumber: 2.5 Consensus size: 21
119145 TTAGCTATGA
119155 AGTATCGATATTGATTCAATC
1 AGTATCGATATTGATTCAATC
*
119176 AGTATCGATATTGATTCAATT
1 AGTATCGATATTGATTCAATC
119197 AGTATCGATA
1 AGTATCGATA
119207 CCAACGAGGT
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 30 1.00
ACGTcount: A:0.35, C:0.12, G:0.15, T:0.38
Consensus pattern (21 bp):
AGTATCGATATTGATTCAATC
Found at i:119329 original size:17 final size:18
Alignment explanation
Indices: 119307--119344 Score: 51
Period size: 20 Copynumber: 2.1 Consensus size: 18
119297 GTACCATAGT
119307 ATGGTAA-TATCGATACC
1 ATGGTAAGTATCGATACC
119324 ATGGTAAGGGTATCGATACC
1 ATGGTAA--GTATCGATACC
119344 A
1 A
119345 GGAAACATCG
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
17 7 0.39
20 11 0.61
ACGTcount: A:0.34, C:0.16, G:0.24, T:0.26
Consensus pattern (18 bp):
ATGGTAAGTATCGATACC
Found at i:119340 original size:95 final size:95
Alignment explanation
Indices: 119214--119437 Score: 335
Period size: 95 Copynumber: 2.4 Consensus size: 95
119204 ATACCAACGA
* * *
119214 GGTAGTATCGATACCATGGTAAGGGTATCGATATCAGGCAACATCGAATCTAAAATTGGTATCGA
1 GGTAATATCGATACCATGGTAAGGGTATCGATACCAGGAAACATCGAATCTAAAATTGGTATCGA
*
119279 TACCGGAATGGGGTATCAGTACCATAGTAT
66 TACCGGAAGGGGGTATCAGTACCATAGTAT
119309 GGTAATATCGATACCATGGTAAGGGTATCGATACCAGGAAACATCGAATCTAAAATTGGTATCGA
1 GGTAATATCGATACCATGGTAAGGGTATCGATACCAGGAAACATCGAATCTAAAATTGGTATCGA
*
119374 TACTGGAAGGGGGTATCAGTACCATAGTAT
66 TACCGGAAGGGGGTATCAGTACCATAGTAT
* * * *
119404 AG-AAGTATCGGTACCAGGGT-AGTAGTATCGATAC
1 GGTAA-TATCGATACCATGGTAAG-GGTATCGATAC
119438 TATTAAGCTT
Statistics
Matches: 118, Mismatches: 9, Indels: 4
0.90 0.07 0.03
Matches are distributed among these distances:
94 4 0.03
95 114 0.97
ACGTcount: A:0.33, C:0.15, G:0.26, T:0.25
Consensus pattern (95 bp):
GGTAATATCGATACCATGGTAAGGGTATCGATACCAGGAAACATCGAATCTAAAATTGGTATCGA
TACCGGAAGGGGGTATCAGTACCATAGTAT
Found at i:119891 original size:26 final size:25
Alignment explanation
Indices: 119829--120067 Score: 160
Period size: 26 Copynumber: 10.1 Consensus size: 25
119819 AAATCGAATC
119829 CATAATTAAAATGCATGAAAGGATG
1 CATAATTAAAATGCATGAAAGGATG
* *
119854 C---ATT--AAGGCATGAAAGAATG
1 CATAATTAAAATGCATGAAAGGATG
119874 TCATAATTAAAATGCATGAAAGGATG
1 -CATAATTAAAATGCATGAAAGGATG
* *
119900 CCATAATTAAAATGTATGAAATGATG
1 -CATAATTAAAATGCATGAAAGGATG
* *
119926 C---ATT--AAGGAATGAAAGGGA-G
1 CATAATTAAAATGCATGAAA-GGATG
*
119946 CCATAATTAAAATGCATGAAATGATG
1 -CATAATTAAAATGCATGAAAGGATG
*
119972 C---ATT--AAGGCATGAAAGGATG
1 CATAATTAAAATGCATGAAAGGATG
*
119992 CCATAATTAAAATGCATGAAATGATG
1 -CATAATTAAAATGCATGAAAGGATG
*
120018 C---ATT--AAGGCATGAAAGGATG
1 CATAATTAAAATGCATGAAAGGATG
**
120038 TCATAAACGAAAATGCATGAAAGGATG
1 -CAT-AATTAAAATGCATGAAAGGATG
120065 CAT
1 CAT
120068 TAAGGCATGA
Statistics
Matches: 165, Mismatches: 22, Indels: 53
0.69 0.09 0.22
Matches are distributed among these distances:
20 52 0.32
21 6 0.04
22 12 0.07
24 9 0.05
25 7 0.04
26 64 0.39
27 15 0.09
ACGTcount: A:0.45, C:0.10, G:0.22, T:0.23
Consensus pattern (25 bp):
CATAATTAAAATGCATGAAAGGATG
Found at i:119939 original size:46 final size:46
Alignment explanation
Indices: 119887--120110 Score: 326
Period size: 46 Copynumber: 4.8 Consensus size: 46
119877 TAATTAAAAT
*
119887 GCATGAAAGGATGCCATAATTAAAATGTATGAAATGATGCATTAAG
1 GCATGAAAGGATGCCATAATTAAAATGCATGAAATGATGCATTAAG
*
119933 GAATGAAAGGGA-GCCATAATTAAAATGCATGAAATGATGCATTAAG
1 GCATGAAA-GGATGCCATAATTAAAATGCATGAAATGATGCATTAAG
119979 GCATGAAAGGATGCCATAATTAAAATGCATGAAATGATGCATTAAG
1 GCATGAAAGGATGCCATAATTAAAATGCATGAAATGATGCATTAAG
* ** *
120025 GCATGAAAGGATGTCATAAACGAAAATGCATGAAAGGATGCATTAAG
1 GCATGAAAGGATGCCAT-AATTAAAATGCATGAAATGATGCATTAAG
** *
120072 GCATGAAATAATGCCATAATTTAAATGCAT-AAATAGATG
1 GCATGAAAGGATGCCATAATTAAAATGCATGAAAT-GATG
120111 TGTTAATATG
Statistics
Matches: 160, Mismatches: 14, Indels: 8
0.88 0.08 0.04
Matches are distributed among these distances:
45 6 0.04
46 111 0.69
47 43 0.27
ACGTcount: A:0.45, C:0.10, G:0.22, T:0.24
Consensus pattern (46 bp):
GCATGAAAGGATGCCATAATTAAAATGCATGAAATGATGCATTAAG
Found at i:119951 original size:72 final size:72
Alignment explanation
Indices: 119828--120101 Score: 232
Period size: 72 Copynumber: 3.9 Consensus size: 72
119818 TAAATCGAAT
* *
119828 CCATAATTAAAATGCATGAAAGGATGCATTAAGGCATGAAAGAATGTCATAATTAAAATGCATGA
1 CCATAATTAAAATGCATGAAAGGATGCATTAAGGAATGAAAGAATGCCATAATTAAAATGCATGA
119893 AAGGATG
66 AAGGATG
* * *
119900 CCATAATTAAAATGTATGAAATGATGCATTAAGGAATGAAAGGGA-GCCATAATTAAAATGCATG
1 CCATAATTAAAATGCATGAAAGGATGCATTAAGGAATGAAA-GAATGCCATAATTAAAATGCATG
*
119964 AAATGATG
65 AAAGGATG
* * * * *
119972 -C---ATT--AAGGCATGAAAGGATGCCATAATTAA--AATGCATGAAATG--ATGCATT--AAG
1 CCATAATTAAAATGCATGAAAGGATG-C---ATTAAGGAATGAAAG-AATGCCAT-AATTAAAAT
120025 GCATGAAAGGATG
60 GCATGAAAGGATG
* ** * * *
120038 TCATAAACGAAAATGCATGAAAGGATGCATTAAGGCATGAAATAATGCCATAATTTAAATGCAT
1 CCAT-AATTAAAATGCATGAAAGGATGCATTAAGGAATGAAAGAATGCCATAATTAAAATGCAT
120102 AAATAGATGT
Statistics
Matches: 157, Mismatches: 24, Indels: 41
0.71 0.11 0.18
Matches are distributed among these distances:
66 27 0.17
67 5 0.03
68 12 0.08
69 6 0.04
70 9 0.06
71 9 0.06
72 66 0.42
73 23 0.15
ACGTcount: A:0.45, C:0.10, G:0.21, T:0.24
Consensus pattern (72 bp):
CCATAATTAAAATGCATGAAAGGATGCATTAAGGAATGAAAGAATGCCATAATTAAAATGCATGA
AAGGATG
Found at i:119984 original size:20 final size:20
Alignment explanation
Indices: 119959--120079 Score: 89
Period size: 20 Copynumber: 5.4 Consensus size: 20
119949 TAATTAAAAT
*
119959 GCATGAAATGATGCATTAAG
1 GCATGAAAGGATGCATTAAG
*
119979 GCATGAAAGGATGCCATAATTAAAAT
1 GCATGAAAGGATG-C---ATT--AAG
*
120005 GCATGAAATGATGCATTAAG
1 GCATGAAAGGATGCATTAAG
*
120025 GCATGAAAGGATGTCATAAACG
1 GCATGAAAGGATG-CATTAA-G
120047 AAAATGCATGAAAGGATGCATTAAG
1 -----GCATGAAAGGATGCATTAAG
120072 GCATGAAA
1 GCATGAAA
120080 TAATGCCATA
Statistics
Matches: 81, Mismatches: 7, Indels: 26
0.71 0.06 0.23
Matches are distributed among these distances:
20 34 0.42
21 6 0.07
22 4 0.05
24 3 0.04
25 2 0.02
26 19 0.23
27 13 0.16
ACGTcount: A:0.44, C:0.11, G:0.24, T:0.21
Consensus pattern (20 bp):
GCATGAAAGGATGCATTAAG
Found at i:126739 original size:16 final size:16
Alignment explanation
Indices: 126718--126751 Score: 68
Period size: 16 Copynumber: 2.1 Consensus size: 16
126708 TTGGTCCTTC
126718 TTATTTCTTTTGTTTA
1 TTATTTCTTTTGTTTA
126734 TTATTTCTTTTGTTTA
1 TTATTTCTTTTGTTTA
126750 TT
1 TT
126752 TTACTTATTT
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:0.12, C:0.06, G:0.06, T:0.76
Consensus pattern (16 bp):
TTATTTCTTTTGTTTA
Found at i:133260 original size:21 final size:21
Alignment explanation
Indices: 133236--133286 Score: 75
Period size: 21 Copynumber: 2.4 Consensus size: 21
133226 CAACGGCTCG
133236 CAACACTCAAATCAACCTGAT
1 CAACACTCAAATCAACCTGAT
* *
133257 CAACACTCAAGTCAATCTGAT
1 CAACACTCAAATCAACCTGAT
*
133278 CAGCACTCA
1 CAACACTCA
133287 TAACAGTTAT
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.39, C:0.33, G:0.08, T:0.20
Consensus pattern (21 bp):
CAACACTCAAATCAACCTGAT
Found at i:137337 original size:51 final size:51
Alignment explanation
Indices: 137261--137357 Score: 185
Period size: 51 Copynumber: 1.9 Consensus size: 51
137251 ACCCTCAATG
137261 CTTCCTCATGCTCATCAGATGAACCAGCTCCAACTGGAATTGATCTCGATA
1 CTTCCTCATGCTCATCAGATGAACCAGCTCCAACTGGAATTGATCTCGATA
*
137312 CTTCCTCATGCTCATTAGATGAACCAGCTCCAACTGGAATTGATCT
1 CTTCCTCATGCTCATCAGATGAACCAGCTCCAACTGGAATTGATCT
137358 TTCACTACTA
Statistics
Matches: 45, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
51 45 1.00
ACGTcount: A:0.27, C:0.29, G:0.15, T:0.29
Consensus pattern (51 bp):
CTTCCTCATGCTCATCAGATGAACCAGCTCCAACTGGAATTGATCTCGATA
Found at i:147131 original size:22 final size:22
Alignment explanation
Indices: 147105--147171 Score: 61
Period size: 20 Copynumber: 3.2 Consensus size: 22
147095 ACACTTTTGC
147105 TTTATCATTTCTTTAATGAGTA
1 TTTATCATTTCTTTAATGAGTA
** * * *
147127 TTTAT--TTAATATATTG-G-C
1 TTTATCATTTCTTTAATGAGTA
147145 TTTATCATTTCTTTAATGAGTA
1 TTTATCATTTCTTTAATGAGTA
147167 TTTAT
1 TTTAT
147172 TTAATATATT
Statistics
Matches: 31, Mismatches: 10, Indels: 8
0.63 0.20 0.16
Matches are distributed among these distances:
18 5 0.16
19 1 0.03
20 14 0.45
21 1 0.03
22 10 0.32
ACGTcount: A:0.27, C:0.07, G:0.09, T:0.57
Consensus pattern (22 bp):
TTTATCATTTCTTTAATGAGTA
Found at i:147147 original size:40 final size:40
Alignment explanation
Indices: 147103--147183 Score: 162
Period size: 40 Copynumber: 2.0 Consensus size: 40
147093 ACACACTTTT
147103 GCTTTATCATTTCTTTAATGAGTATTTATTTAATATATTG
1 GCTTTATCATTTCTTTAATGAGTATTTATTTAATATATTG
147143 GCTTTATCATTTCTTTAATGAGTATTTATTTAATATATTG
1 GCTTTATCATTTCTTTAATGAGTATTTATTTAATATATTG
147183 G
1 G
147184 TCATCGACTC
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
40 41 1.00
ACGTcount: A:0.27, C:0.07, G:0.11, T:0.54
Consensus pattern (40 bp):
GCTTTATCATTTCTTTAATGAGTATTTATTTAATATATTG
Found at i:147710 original size:81 final size:81
Alignment explanation
Indices: 147575--147736 Score: 324
Period size: 81 Copynumber: 2.0 Consensus size: 81
147565 CACCACCTTA
147575 ACATAAATGATGGTGGCTAATGGCTATGTTACTTTATTCCAAAACACAGTTATAAGCCAATGGAT
1 ACATAAATGATGGTGGCTAATGGCTATGTTACTTTATTCCAAAACACAGTTATAAGCCAATGGAT
147640 TGGCTTTTTTATTTAT
66 TGGCTTTTTTATTTAT
147656 ACATAAATGATGGTGGCTAATGGCTATGTTACTTTATTCCAAAACACAGTTATAAGCCAATGGAT
1 ACATAAATGATGGTGGCTAATGGCTATGTTACTTTATTCCAAAACACAGTTATAAGCCAATGGAT
147721 TGGCTTTTTTATTTAT
66 TGGCTTTTTTATTTAT
147737 GTGGGATCAT
Statistics
Matches: 81, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
81 81 1.00
ACGTcount: A:0.31, C:0.14, G:0.17, T:0.38
Consensus pattern (81 bp):
ACATAAATGATGGTGGCTAATGGCTATGTTACTTTATTCCAAAACACAGTTATAAGCCAATGGAT
TGGCTTTTTTATTTAT
Found at i:150037 original size:29 final size:29
Alignment explanation
Indices: 149995--150050 Score: 112
Period size: 29 Copynumber: 1.9 Consensus size: 29
149985 TTCACCTAAT
149995 TAAATTGATGTAAGCAATGACATCAAAAC
1 TAAATTGATGTAAGCAATGACATCAAAAC
150024 TAAATTGATGTAAGCAATGACATCAAA
1 TAAATTGATGTAAGCAATGACATCAAA
150051 TTAATTTAGG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 27 1.00
ACGTcount: A:0.48, C:0.12, G:0.14, T:0.25
Consensus pattern (29 bp):
TAAATTGATGTAAGCAATGACATCAAAAC
Found at i:154729 original size:29 final size:29
Alignment explanation
Indices: 154687--154745 Score: 109
Period size: 29 Copynumber: 2.0 Consensus size: 29
154677 ATTTTCACCT
154687 AACTAAATTAATGTAAGCAATGACATCAA
1 AACTAAATTAATGTAAGCAATGACATCAA
*
154716 AACTAAATTGATGTAAGCAATGACATCAA
1 AACTAAATTAATGTAAGCAATGACATCAA
154745 A
1 A
154746 TTAATTTAGG
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
29 29 1.00
ACGTcount: A:0.51, C:0.14, G:0.12, T:0.24
Consensus pattern (29 bp):
AACTAAATTAATGTAAGCAATGACATCAA
Found at i:156210 original size:23 final size:23
Alignment explanation
Indices: 156142--156210 Score: 93
Period size: 23 Copynumber: 3.0 Consensus size: 23
156132 CAACCTTATA
*
156142 TGGCACTTCGGTGCATTTCTACA
1 TGGCACTTCGGTGCATTTCTACG
* * *
156165 CGGCACTACGGTGCAATTCTACG
1 TGGCACTTCGGTGCATTTCTACG
*
156188 TGGCACTTCGGTGCATTTATACG
1 TGGCACTTCGGTGCATTTCTACG
156211 AGCTGTGCTG
Statistics
Matches: 38, Mismatches: 8, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
23 38 1.00
ACGTcount: A:0.19, C:0.26, G:0.25, T:0.30
Consensus pattern (23 bp):
TGGCACTTCGGTGCATTTCTACG
Found at i:159686 original size:20 final size:23
Alignment explanation
Indices: 159629--159686 Score: 68
Period size: 20 Copynumber: 2.6 Consensus size: 23
159619 TCATAAGGAG
159629 TGCATCGATGCACATGTTAAGAGA
1 TGCATCGATGCAC-TGTTAAGAGA
* *
159653 TGCATCAATACACTG-T-AGA-A
1 TGCATCGATGCACTGTTAAGAGA
159673 TGCATCGATGCACT
1 TGCATCGATGCACT
159687 TCAAGGGAAA
Statistics
Matches: 30, Mismatches: 4, Indels: 4
0.79 0.11 0.11
Matches are distributed among these distances:
20 13 0.43
21 3 0.10
22 1 0.03
23 2 0.07
24 11 0.37
ACGTcount: A:0.33, C:0.21, G:0.21, T:0.26
Consensus pattern (23 bp):
TGCATCGATGCACTGTTAAGAGA
Found at i:161149 original size:23 final size:23
Alignment explanation
Indices: 161118--161183 Score: 78
Period size: 23 Copynumber: 2.9 Consensus size: 23
161108 CCTTATATGG
*
161118 CACTTCGGTGTATTTCTACGCGA
1 CACTTCGGTGCATTTCTACGCGA
* * * *
161141 CACTACGGTGCAATTCTACGTGG
1 CACTTCGGTGCATTTCTACGCGA
*
161164 CACTTCGGTGCATTTATACG
1 CACTTCGGTGCATTTCTACG
161184 AGTTGTGCTG
Statistics
Matches: 35, Mismatches: 8, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
23 35 1.00
ACGTcount: A:0.20, C:0.26, G:0.23, T:0.32
Consensus pattern (23 bp):
CACTTCGGTGCATTTCTACGCGA
Found at i:181497 original size:19 final size:18
Alignment explanation
Indices: 181440--181499 Score: 52
Period size: 19 Copynumber: 3.2 Consensus size: 18
181430 TATGCAATAC
181440 CGCAACGAACTTGGAATAAAT
1 CGCAACGAA-TTGG-A-AAAT
**
181461 CGCAACG--TTGGACTAT
1 CGCAACGAATTGGAAAAT
181477 CGCAACGAATTTGGAAAAT
1 CGCAACGAA-TTGGAAAAT
181496 CGCA
1 CGCA
181500 TTGTGATAGT
Statistics
Matches: 32, Mismatches: 4, Indels: 8
0.73 0.09 0.18
Matches are distributed among these distances:
16 9 0.28
17 1 0.03
18 4 0.12
19 11 0.34
21 7 0.22
ACGTcount: A:0.37, C:0.22, G:0.22, T:0.20
Consensus pattern (18 bp):
CGCAACGAATTGGAAAAT
Found at i:181924 original size:12 final size:12
Alignment explanation
Indices: 181909--181950 Score: 57
Period size: 12 Copynumber: 3.4 Consensus size: 12
181899 TAAATAAGAT
*
181909 TTTATATTAATA
1 TTTATATTCATA
181921 TTTATATTCATA
1 TTTATATTCATA
*
181933 TTCATATTCATA
1 TTTATATTCATA
181945 TCTTAT
1 T-TTAT
181951 TTTATTTTGT
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
12 23 0.88
13 3 0.12
ACGTcount: A:0.33, C:0.10, G:0.00, T:0.57
Consensus pattern (12 bp):
TTTATATTCATA
Found at i:182789 original size:51 final size:52
Alignment explanation
Indices: 182726--182840 Score: 169
Period size: 51 Copynumber: 2.2 Consensus size: 52
182716 AATAAAAACA
* *
182726 ATTTATGTTTTTAAGATATATTTTTCGTTTTTTT-TATCATTTTGTATAACC
1 ATTTATGATTTTAAGATATATTTTTCGTTTTTTTCGATCATTTTGTATAACC
* * *
182777 ATTTATGATTTTATGATATGTTTTTCGTTTTTTTCGATCATTTTGTATAATC
1 ATTTATGATTTTAAGATATATTTTTCGTTTTTTTCGATCATTTTGTATAACC
*
182829 ATTTTTGATTTT
1 ATTTATGATTTT
182841 TTTTTATATT
Statistics
Matches: 57, Mismatches: 6, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
51 31 0.54
52 26 0.46
ACGTcount: A:0.22, C:0.07, G:0.10, T:0.62
Consensus pattern (52 bp):
ATTTATGATTTTAAGATATATTTTTCGTTTTTTTCGATCATTTTGTATAACC
Found at i:188570 original size:3 final size:3
Alignment explanation
Indices: 188564--188657 Score: 50
Period size: 3 Copynumber: 30.0 Consensus size: 3
188554 TAATATTATT
* * *
188564 TAA TAA TAT TAT TAA TAA TATA TATA TAA TAA CCTATA TAA TAA TAG
1 TAA TAA TAA TAA TAA TAA TA-A TA-A TAA TAA --TA-A TAA TAA TAA
* * *
188611 TAG TAG T-A TAA TATA TAA TTA T-A TATA TAA TAA T-A TAA TAA TAA
1 TAA TAA TAA TAA TA-A TAA TAA TAA TA-A TAA TAA TAA TAA TAA TAA
188655 TAA
1 TAA
188658 ATAAGACCGA
Statistics
Matches: 77, Mismatches: 5, Indels: 18
0.77 0.05 0.18
Matches are distributed among these distances:
2 5 0.06
3 54 0.70
4 15 0.19
5 2 0.03
6 1 0.01
ACGTcount: A:0.54, C:0.02, G:0.03, T:0.40
Consensus pattern (3 bp):
TAA
Found at i:188635 original size:8 final size:7
Alignment explanation
Indices: 188566--188661 Score: 60
Period size: 6 Copynumber: 13.6 Consensus size: 7
188556 ATATTATTTA
188566 ATAATAT
1 ATAATAT
*
188573 -TATTA-
1 ATAATAT
188578 ATAATAT
1 ATAATAT
188585 AT-ATAT
1 ATAATAT
188591 AATAACCTAT
1 -ATAA--TAT
188601 ATAATAAT
1 ATAAT-AT
*
188609 AGTAGTAGT
1 A-TAATA-T
188618 ATAATAT
1 ATAATAT
188625 ATAAT-T
1 ATAATAT
188631 AT-ATAT
1 ATAATAT
188637 ATAATAAT
1 ATAAT-AT
188645 ATAATA-
1 ATAATAT
*
188651 ATAATAA
1 ATAATAT
188658 ATAA
1 ATAA
188662 GACCGAACGA
Statistics
Matches: 72, Mismatches: 4, Indels: 26
0.71 0.04 0.25
Matches are distributed among these distances:
5 2 0.03
6 24 0.33
7 18 0.25
8 16 0.22
9 9 0.12
10 3 0.04
ACGTcount: A:0.55, C:0.02, G:0.03, T:0.40
Consensus pattern (7 bp):
ATAATAT
Found at i:188638 original size:12 final size:12
Alignment explanation
Indices: 188554--188656 Score: 74
Period size: 12 Copynumber: 8.4 Consensus size: 12
188544 TTGGGATTTG
*
188554 TAATATTATTTAA
1 TAATA-TATATAA
188567 TAATAT-TATTAA
1 TAATATATA-TAA
188579 TAATATATAT-A
1 TAATATATATAA
188590 TAATAACCTATATAA
1 TAAT-A--TATATAA
188605 TAATAGTAGTAGT-A
1 TAATA-TA-TA-TAA
188619 T-A-ATATATAA
1 TAATATATATAA
*
188629 TTATATATATAA
1 TAATATATATAA
188641 TAATATA-ATAA
1 TAATATATATAA
188652 TAATA
1 TAATA
188657 AATAAGACCG
Statistics
Matches: 76, Mismatches: 3, Indels: 24
0.74 0.03 0.23
Matches are distributed among these distances:
9 1 0.01
10 4 0.05
11 18 0.24
12 27 0.36
13 10 0.13
14 10 0.13
15 6 0.08
ACGTcount: A:0.52, C:0.02, G:0.03, T:0.43
Consensus pattern (12 bp):
TAATATATATAA
Found at i:188826 original size:20 final size:20
Alignment explanation
Indices: 188798--188851 Score: 63
Period size: 20 Copynumber: 2.7 Consensus size: 20
188788 AAAAAATCTT
* * * *
188798 ACCCTGAGGTTTTACAGATG
1 ACCCGGAGGATTTACAAATC
*
188818 ACCCGGAGGCTTTACAAATC
1 ACCCGGAGGATTTACAAATC
188838 ACCCGGAGGATTTA
1 ACCCGGAGGATTTA
188852 ATTTTCTAGA
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 29 1.00
ACGTcount: A:0.28, C:0.24, G:0.24, T:0.24
Consensus pattern (20 bp):
ACCCGGAGGATTTACAAATC
Found at i:189011 original size:119 final size:118
Alignment explanation
Indices: 188788--189148 Score: 562
Period size: 119 Copynumber: 3.0 Consensus size: 118
188778 GAAAAACAAT
* *
188788 AAAAAATCTTACCCTGAGGTTTTACAGATGACCCGGAGGCTTTACAAATCACCCGGAGGATTTAA
1 AAAACATCCTACCCTGAGGTTTTACAGATGACCCGGAGGCTTTACAAATCA-CCGGAGGATTTAA
188853 TTTTCTAGAACATTAAATGAGAAACTTTGAAAATCGCTTTCTCATTTTCATGCG
65 TTTTCTAGAACATTAAATGAGAAACTTTGAAAATCGCTTTCTCATTTTCATGCG
188907 AAAACATCCTACCCTGAGGTTTTACAGATGACCCGGAGGCTTTACAAATCACACGGAGGATTTAA
1 AAAACATCCTACCCTGAGGTTTTACAGATGACCCGGAGGCTTTACAAATCAC-CGGAGGATTTAA
* * * * * *
188972 TTTTCTTGAACATTAAATGAGAAACTTTAAAAATTGCTTTCTTATTTTTATG-T
65 TTTTCTAGAACATTAAATGAGAAACTTTGAAAATCGCTTTCTCATTTTCATGCG
* *
189025 AAAACCATCCTACCTTGAGGTTTTACAGATGACCCGGAGGCTTTACAAATCACCTAGAGGATTTA
1 AAAA-CATCCTACCCTGAGGTTTTACAGATGACCCGGAGGCTTTACAAATCACC-GGAGGATTTA
* * *
189090 ATTTTCTAGAACATTAAATAAGAAACTTTGAAAATCACTTTCTCAATTTCATGCG
64 ATTTTCTAGAACATTAAATGAGAAACTTTGAAAATCGCTTTCTCATTTTCATGCG
189145 AAAA
1 AAAA
189149 TCATATGTAA
Statistics
Matches: 219, Mismatches: 19, Indels: 7
0.89 0.08 0.03
Matches are distributed among these distances:
118 6 0.03
119 209 0.95
120 4 0.02
ACGTcount: A:0.34, C:0.19, G:0.15, T:0.32
Consensus pattern (118 bp):
AAAACATCCTACCCTGAGGTTTTACAGATGACCCGGAGGCTTTACAAATCACCGGAGGATTTAAT
TTTCTAGAACATTAAATGAGAAACTTTGAAAATCGCTTTCTCATTTTCATGCG
Found at i:189261 original size:42 final size:42
Alignment explanation
Indices: 189201--189282 Score: 137
Period size: 42 Copynumber: 2.0 Consensus size: 42
189191 AAGGACTTAT
* *
189201 CATCTTGCTCGAAAAACTAACAGATGAACCGAATGATTTAAA
1 CATCATGCTCGAAAAACTAACAGATGAACCGAAGGATTTAAA
*
189243 CATCATGCTCGAAAAACTAACAGATGACCCGAAGGATTTA
1 CATCATGCTCGAAAAACTAACAGATGAACCGAAGGATTTA
189283 TAAATTCATG
Statistics
Matches: 37, Mismatches: 3, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
42 37 1.00
ACGTcount: A:0.41, C:0.21, G:0.16, T:0.22
Consensus pattern (42 bp):
CATCATGCTCGAAAAACTAACAGATGAACCGAAGGATTTAAA
Found at i:201966 original size:3 final size:3
Alignment explanation
Indices: 201960--202070 Score: 99
Period size: 3 Copynumber: 38.0 Consensus size: 3
201950 TAATATTATT
* * *
201960 TAA TAA TAT TAA TAA TAA TTA T-A TATA TAA TAA TAA -CA TATA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TA-A TAA TAA TAA TAA TA-A TAA
* * *
202005 TAA TAG TAG T-A TAA TATA TAA TTA T-A TAA T-A TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TA-A TAA TAA TAA TAA TAA TAA TAA TAA TAA
202048 TAA T-A TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA
202071 ATAAGACCGG
Statistics
Matches: 91, Mismatches: 8, Indels: 18
0.78 0.07 0.15
Matches are distributed among these distances:
2 10 0.11
3 72 0.79
4 9 0.10
ACGTcount: A:0.59, C:0.01, G:0.02, T:0.39
Consensus pattern (3 bp):
TAA
Found at i:201983 original size:15 final size:14
Alignment explanation
Indices: 201949--202074 Score: 99
Period size: 15 Copynumber: 9.3 Consensus size: 14
201939 ATTAGGCTTT
*
201949 ATAAT-ATTATTTA
1 ATAATAATTATATA
201962 ATAAT-ATTA-ATA
1 ATAATAATTATATA
*
201974 ATAATTATATATATA
1 ATAATAAT-TATATA
*
201989 ATAATAACATATATA
1 ATAATAA-TTATATA
*
202004 ATAAT-AGTAGTATA
1 ATAATAATTA-TATA
202018 ATATATAATTATATA
1 ATA-ATAATTATATA
202033 AT-ATAA-TA-ATA
1 ATAATAATTATATA
202044 ATAATAA-TATAATA
1 ATAATAATTAT-ATA
*
202058 ATAATAATAATA-A
1 ATAATAATTATATA
202071 ATAA
1 ATAA
202075 GACCGGACGA
Statistics
Matches: 96, Mismatches: 6, Indels: 22
0.77 0.05 0.18
Matches are distributed among these distances:
11 5 0.05
12 15 0.16
13 22 0.23
14 21 0.22
15 30 0.31
16 3 0.03
ACGTcount: A:0.58, C:0.01, G:0.02, T:0.40
Consensus pattern (14 bp):
ATAATAATTATATA
Found at i:203088 original size:23 final size:23
Alignment explanation
Indices: 203032--203094 Score: 74
Period size: 23 Copynumber: 2.7 Consensus size: 23
203022 AACTCGTATA
203032 AATTATACCGAAGTG-CCACATAG
1 AATTATACCGAA-TGACCACATAG
* *
203055 AAATATTCCGAATGACCACATAG
1 AATTATACCGAATGACCACATAG
* *
203078 TATTATCCCGAATGACC
1 AATTATACCGAATGACC
203095 GCGTATATAT
Statistics
Matches: 34, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
22 2 0.06
23 32 0.94
ACGTcount: A:0.38, C:0.24, G:0.14, T:0.24
Consensus pattern (23 bp):
AATTATACCGAATGACCACATAG
Found at i:203109 original size:23 final size:23
Alignment explanation
Indices: 203083--203148 Score: 80
Period size: 23 Copynumber: 2.9 Consensus size: 23
203073 CATAGTATTA
* *
203083 TCCCGAATGACCGCGTA-TATATG
1 TCCCGAAGGACCGCGTAGAAT-TG
* *
203106 TCCCAAAGGACCACGTAGAATTG
1 TCCCGAAGGACCGCGTAGAATTG
203129 TCCCGAAGGACCGCGTAGAA
1 TCCCGAAGGACCGCGTAGAA
203149 CCCTCGACTC
Statistics
Matches: 36, Mismatches: 6, Indels: 2
0.82 0.14 0.05
Matches are distributed among these distances:
23 34 0.94
24 2 0.06
ACGTcount: A:0.30, C:0.27, G:0.24, T:0.18
Consensus pattern (23 bp):
TCCCGAAGGACCGCGTAGAATTG
Found at i:205079 original size:137 final size:138
Alignment explanation
Indices: 204840--205101 Score: 325
Period size: 137 Copynumber: 1.9 Consensus size: 138
204830 TTCCTTCGCA
* * * * *
204840 TTGAGGAAGTTTGATTGTCTGAGTATGGCACTAATCTTTCGCGTTGAGGAGATCTGGTCGGTGGA
1 TTGAGGAAGTCTGATTGTCTGAGGATGACACTAATCTTTCACATTGAGGAGATCTGGTCGGTGGA
* *
204905 CAACATTGTTTGTTCGCATTGAAGACGTTTATACGTA-TTTGGATAATTTGGAGACAACAAGGTC
66 CAACATTGTTTGTTCGCATTGAAGACGTCTAGACGTATTTTGGATAATTTGGAGACAACAAGGTC
204969 CATTCGTG
131 CATTCGTG
** *
204977 TTGAGGAAGTCTGATTGTCTGAGGATGACACTGCTCCTTT-ACATTGAGGAGATCTGGTCTGTGG
1 TTGAGGAAGTCTGATTGTCTGAGGATGACACTAAT-CTTTCACATTGAGGAGATCTGGTCGGTGG
* * ** * *
205041 GCGACATTGTTCT-TTCGTGTT-AAGGGCGTCTAGCCGTATTTTGGATAATTTGGAGACAACA
65 ACAACATTGTT-TGTTCGCATTGAA-GACGTCTAGACGTATTTTGGATAATTTGGAGACAACA
205102 TGCTTCCTTC
Statistics
Matches: 105, Mismatches: 16, Indels: 7
0.82 0.12 0.05
Matches are distributed among these distances:
136 2 0.02
137 76 0.72
138 27 0.26
ACGTcount: A:0.23, C:0.15, G:0.28, T:0.34
Consensus pattern (138 bp):
TTGAGGAAGTCTGATTGTCTGAGGATGACACTAATCTTTCACATTGAGGAGATCTGGTCGGTGGA
CAACATTGTTTGTTCGCATTGAAGACGTCTAGACGTATTTTGGATAATTTGGAGACAACAAGGTC
CATTCGTG
Found at i:205194 original size:36 final size:36
Alignment explanation
Indices: 205154--205222 Score: 129
Period size: 36 Copynumber: 1.9 Consensus size: 36
205144 AGTGTTCCTA
205154 ATTAAAAAAATCAACACTAAGATAATTAAATAAACT
1 ATTAAAAAAATCAACACTAAGATAATTAAATAAACT
*
205190 ATTAAAAAAATCAACACTAATATAATTAAATAA
1 ATTAAAAAAATCAACACTAAGATAATTAAATAA
205223 TCATAATTTA
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
36 32 1.00
ACGTcount: A:0.62, C:0.10, G:0.01, T:0.26
Consensus pattern (36 bp):
ATTAAAAAAATCAACACTAAGATAATTAAATAAACT
Found at i:205522 original size:6 final size:6
Alignment explanation
Indices: 205511--205545 Score: 61
Period size: 6 Copynumber: 5.8 Consensus size: 6
205501 TTTAGAATTG
*
205511 ATATAA ATATAA ATATTA ATATAA ATATAA ATATA
1 ATATAA ATATAA ATATAA ATATAA ATATAA ATATA
205546 TTATTTTATT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
6 27 1.00
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (6 bp):
ATATAA
Found at i:209582 original size:14 final size:13
Alignment explanation
Indices: 209565--209598 Score: 50
Period size: 14 Copynumber: 2.5 Consensus size: 13
209555 GGGTATATGG
209565 TTTAGGGTTTGTAA
1 TTTAGGGTTT-TAA
209579 TTTAGGGTTTTAA
1 TTTAGGGTTTTAA
*
209592 GTTAGGG
1 TTTAGGG
209599 CAGGGTATAA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
13 9 0.47
14 10 0.53
ACGTcount: A:0.21, C:0.00, G:0.32, T:0.47
Consensus pattern (13 bp):
TTTAGGGTTTTAA
Found at i:209598 original size:13 final size:14
Alignment explanation
Indices: 209566--209598 Score: 50
Period size: 13 Copynumber: 2.4 Consensus size: 14
209556 GGTATATGGT
*
209566 TTAGGGTTTGTAAT
1 TTAGGGTTTGTAAG
209580 TTAGGGTTT-TAAG
1 TTAGGGTTTGTAAG
209593 TTAGGG
1 TTAGGG
209599 CAGGGTATAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
13 9 0.50
14 9 0.50
ACGTcount: A:0.21, C:0.00, G:0.33, T:0.45
Consensus pattern (14 bp):
TTAGGGTTTGTAAG
Found at i:217048 original size:3 final size:3
Alignment explanation
Indices: 217040--217115 Score: 61
Period size: 3 Copynumber: 26.0 Consensus size: 3
217030 TTTTACTTAA
** *
217040 ATT ATT ATT AAA ATT ATT ATT ATT ATT AAAT ATT ATT A-T ATT A-T
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT -ATT ATT ATT ATT ATT ATT
* *
217084 ATAT ATT A-T ATT ATT ATT A-A ATA ATT ATT ATT
1 AT-T ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
217116 TATAAACAGA
Statistics
Matches: 59, Mismatches: 8, Indels: 12
0.75 0.10 0.15
Matches are distributed among these distances:
2 7 0.12
3 47 0.80
4 5 0.08
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (3 bp):
ATT
Found at i:217102 original size:35 final size:36
Alignment explanation
Indices: 217052--217119 Score: 113
Period size: 35 Copynumber: 1.9 Consensus size: 36
217042 TATTATTAAA
217052 ATTATTATTATTATTAAAT-ATTATTATATTATATAT
1 ATTATTATTATTATTAAATAATTATTAT-TTATATAT
217088 ATTA-TATTATTATTAAATAATTATTATTTATA
1 ATTATTATTATTATTAAATAATTATTATTTATA
217120 AACAGACCCA
Statistics
Matches: 31, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
35 19 0.61
36 12 0.39
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (36 bp):
ATTATTATTATTATTAAATAATTATTATTTATATAT
Found at i:217498 original size:13 final size:13
Alignment explanation
Indices: 217479--217513 Score: 52
Period size: 13 Copynumber: 2.6 Consensus size: 13
217469 CCACACCTAA
217479 AAAAAAAGAGAGAC
1 AAAAAAA-AGAGAC
*
217493 AAAAAAAAGAGAG
1 AAAAAAAAGAGAC
217506 AAAAAAAA
1 AAAAAAAA
217514 AGAAAGAAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
13 13 0.65
14 7 0.35
ACGTcount: A:0.80, C:0.03, G:0.17, T:0.00
Consensus pattern (13 bp):
AAAAAAAAGAGAC
Found at i:217521 original size:14 final size:14
Alignment explanation
Indices: 217477--217523 Score: 76
Period size: 14 Copynumber: 3.3 Consensus size: 14
217467 GACCACACCT
217477 AAAAAAAAAGAGAG
1 AAAAAAAAAGAGAG
217491 ACAAAAAAAAGAGAG
1 A-AAAAAAAAGAGAG
*
217506 AAAAAAAAAGAAAG
1 AAAAAAAAAGAGAG
217520 AAAA
1 AAAA
217524 GAACCACAGC
Statistics
Matches: 31, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
14 17 0.55
15 14 0.45
ACGTcount: A:0.81, C:0.02, G:0.17, T:0.00
Consensus pattern (14 bp):
AAAAAAAAAGAGAG
Found at i:218678 original size:20 final size:19
Alignment explanation
Indices: 218653--218694 Score: 57
Period size: 20 Copynumber: 2.2 Consensus size: 19
218643 TTATTTTATA
218653 AATTATATATTAATTGTTTT
1 AATTATATATTAATT-TTTT
* *
218673 AATTATTTATTTATTTTTT
1 AATTATATATTAATTTTTT
218692 AAT
1 AAT
218695 ATCAAAGAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
19 7 0.35
20 13 0.65
ACGTcount: A:0.33, C:0.00, G:0.02, T:0.64
Consensus pattern (19 bp):
AATTATATATTAATTTTTT
Found at i:221317 original size:21 final size:21
Alignment explanation
Indices: 221293--221332 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
221283 CTTTTCATAC
221293 ATGCATTTACATTTTGTATCT
1 ATGCATTTACATTTTGTATCT
*
221314 ATGCATTTTCATTTTGTAT
1 ATGCATTTACATTTTGTAT
221333 TCTTACTTTT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.23, C:0.12, G:0.10, T:0.55
Consensus pattern (21 bp):
ATGCATTTACATTTTGTATCT
Found at i:225700 original size:114 final size:114
Alignment explanation
Indices: 225499--225832 Score: 551
Period size: 114 Copynumber: 2.9 Consensus size: 114
225489 CATGTTCTCG
* *
225499 TAGTAGAAATAAGGAGACCCAATAACATCTTCTGGAAGTATTCTTTGAGTTATCTGATCTGGTTT
1 TAGTAGAAATAAGAAGACCCAATAGCATCTTCTGGAAGTATTCTTTGAGTTATCTGATCTGGTTT
*
225564 GGTATGAACCTCAAAACTAATCATTGGATTTGAAAGATGAATTTGCTCA
66 GGTATGAACCTCAAAACCAATCATTGGATTTGAAAGATGAATTTGCTCA
* *
225613 TAGTAGAAATAAGAAGACCCAATAGTATCTTCTAGAAGTATTCTTTGAGTTATCTGATCTGGTTT
1 TAGTAGAAATAAGAAGACCCAATAGCATCTTCTGGAAGTATTCTTTGAGTTATCTGATCTGGTTT
225678 GGTATGAACCTCAAAACCAATCATTGGATTTGAAAGATGAATTTGCTCA
66 GGTATGAACCTCAAAACCAATCATTGGATTTGAAAGATGAATTTGCTCA
* *
225727 TAGTAGAAATAAGAAGACCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTC
1 TAGTAGAAATAAGAAGACCCAATAGCATCTTCTGGAAGTATTCTTTGAGTTATCTGATCTGGTTT
* * * * * *
225792 GGTAGGAACCCCAGAACCAATCATTAGAATTGAATGATGAA
66 GGTATGAACCTCAAAACCAATCATTGGATTTGAAAGATGAA
225833 CTGCATGATC
Statistics
Matches: 205, Mismatches: 15, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
114 205 1.00
ACGTcount: A:0.34, C:0.15, G:0.20, T:0.32
Consensus pattern (114 bp):
TAGTAGAAATAAGAAGACCCAATAGCATCTTCTGGAAGTATTCTTTGAGTTATCTGATCTGGTTT
GGTATGAACCTCAAAACCAATCATTGGATTTGAAAGATGAATTTGCTCA
Found at i:228131 original size:22 final size:22
Alignment explanation
Indices: 228102--228156 Score: 101
Period size: 22 Copynumber: 2.5 Consensus size: 22
228092 ATCTACACTC
228102 TTCAAAGATGATAGATTCTCTT
1 TTCAAAGATGATAGATTCTCTT
*
228124 TTTAAAGATGATAGATTCTCTT
1 TTCAAAGATGATAGATTCTCTT
228146 TTCAAAGATGA
1 TTCAAAGATGA
228157 AAGCTTTATG
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
22 31 1.00
ACGTcount: A:0.35, C:0.11, G:0.15, T:0.40
Consensus pattern (22 bp):
TTCAAAGATGATAGATTCTCTT
Done.