Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold2640
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: 56948
ACGTcount: A:0.30, C:0.20, G:0.19, T:0.32
Found at i:8625 original size:105 final size:104
Alignment explanation
Indices: 8497--8841 Score: 272
Period size: 105 Copynumber: 3.3 Consensus size: 104
8487 CCGATGAAAT
* * *
8497 AACGAGGTTGGAGTATCCTCGATTGTGAAAAATTGGTATTTTTGGAAATAAAATCGGAATTGGAG
1 AACGGGGTTGGAGTATCCCCGATTGTGAAAAATTGGTATTTTTGGAAATAAAATCGGAGTTGGAG
*
8562 TATCCCCGATTAAAGGAGAAATTGGTGTTGTGAAAATAA
66 TATCCCCGATTAAAGGAGAAATTGGTGTTCTGAAAATAA
* * * * * *
8601 AACCGGGGTTGGAGTATCCCCGATTATGAAAAATCGATA-TTTTGAAAATAAAGTCGGGGTTGGA
1 AA-CGGGGTTGGAGTATCCCCGATTGTGAAAAATTGGTATTTTTGGAAATAAAATCGGAGTTGGA
* * * * * ** *
8665 GTATCCCCTCAGAAATAACGG-G--GTTGGAGTATCCCCGATGAT-T
65 GTAT-CCC-C-G-ATTAAAGGAGAAATTGGTGT-T--CTGAAAATAA
* *
8708 AACGGGGTTGGAGTGTCCCCGATTGTGAAGAAATTGGTGTTTTTTTTGGAAATAAAATCGGAGTT
1 AACGGGGTTGGAGTATCCCCGATTGTGAA-AAATT-G-G-TATTTTTGGAAATAAAATCGGAGTT
* ** * *
8773 GGAGTATCCCCGATTATA-GA-AAATTAATGTTTTGAAAGTAA
62 GGAGTATCCCCGATTAAAGGAGAAATTGGTGTTCTGAAAATAA
* * *
8814 AATCGGAGTTGGAATATCCTCGATTGTG
1 AA-CGGGGTTGGAGTATCCCCGATTGTG
8842 GAGAATTGAG
Statistics
Matches: 180, Mismatches: 43, Indels: 33
0.70 0.17 0.13
Matches are distributed among these distances:
104 27 0.15
105 43 0.24
106 30 0.17
107 33 0.18
108 16 0.09
109 1 0.01
110 4 0.02
111 26 0.14
ACGTcount: A:0.32, C:0.12, G:0.27, T:0.30
Consensus pattern (104 bp):
AACGGGGTTGGAGTATCCCCGATTGTGAAAAATTGGTATTTTTGGAAATAAAATCGGAGTTGGAG
TATCCCCGATTAAAGGAGAAATTGGTGTTCTGAAAATAA
Found at i:8662 original size:51 final size:51
Alignment explanation
Indices: 8502--8672 Score: 198
Period size: 51 Copynumber: 3.3 Consensus size: 51
8492 GAAATAACGA
* * *
8502 GGTTGGAGTATCCTCGATTGTGAAAAATTGGTATTTTTGGAAATAAAATCGG
1 GGTTGGAGTATCCCCGATTATGAAAAATTGGTA-TTTTGAAAATAAAATCGG
** * * * * *
8554 AATTGGAGTATCCCCGATTAAAGGAGAAATTGGTGTTGTGAAAATAAAACCGG
1 GGTTGGAGTATCCCCGATT--ATGAAAAATTGGTATTTTGAAAATAAAATCGG
* * *
8607 GGTTGGAGTATCCCCGATTATGAAAAATCGATATTTTGAAAATAAAGTCGG
1 GGTTGGAGTATCCCCGATTATGAAAAATTGGTATTTTGAAAATAAAATCGG
8658 GGTTGGAGTATCCCC
1 GGTTGGAGTATCCCC
8673 TCAGAAATAA
Statistics
Matches: 97, Mismatches: 20, Indels: 5
0.80 0.16 0.04
Matches are distributed among these distances:
51 39 0.40
52 16 0.16
53 32 0.33
54 10 0.10
ACGTcount: A:0.33, C:0.12, G:0.26, T:0.29
Consensus pattern (51 bp):
GGTTGGAGTATCCCCGATTATGAAAAATTGGTATTTTGAAAATAAAATCGG
Found at i:8718 original size:27 final size:28
Alignment explanation
Indices: 8655--8730 Score: 102
Period size: 27 Copynumber: 2.8 Consensus size: 28
8645 AAAATAAAGT
*
8655 CGGGGTTGGAGTATCCCCTCA-GAAATAA
1 CGGGGTTGGAGTATCCCC-GATGAAATAA
*
8683 CGGGGTTGGAGTATCCCCGATG-ATTAA
1 CGGGGTTGGAGTATCCCCGATGAAATAA
*
8710 CGGGGTTGGAGTGTCCCCGAT
1 CGGGGTTGGAGTATCCCCGAT
8731 TGTGAAGAAA
Statistics
Matches: 44, Mismatches: 3, Indels: 3
0.88 0.06 0.06
Matches are distributed among these distances:
27 25 0.57
28 19 0.43
ACGTcount: A:0.21, C:0.21, G:0.34, T:0.24
Consensus pattern (28 bp):
CGGGGTTGGAGTATCCCCGATGAAATAA
Found at i:11210 original size:13 final size:13
Alignment explanation
Indices: 11192--11216 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
11182 CAAAGATCCA
11192 TGTATCGATACAT
1 TGTATCGATACAT
11205 TGTATCGATACA
1 TGTATCGATACA
11217 CAGAAAAATG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:11214 original size:33 final size:33
Alignment explanation
Indices: 11172--11238 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
11162 AATTTCCAAA
***
11172 TGTATCGATACAAAGATCCATGTATCGATACAT
1 TGTATCGATACAAAGAAAAATGTATCGATACAT
*
11205 TGTATCGATACACAGAAAAATGTATCGATACAT
1 TGTATCGATACAAAGAAAAATGTATCGATACAT
11238 T
1 T
11239 TCCTTGGCAG
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.39, C:0.16, G:0.15, T:0.30
Consensus pattern (33 bp):
TGTATCGATACAAAGAAAAATGTATCGATACAT
Found at i:11280 original size:19 final size:18
Alignment explanation
Indices: 11256--11323 Score: 83
Period size: 19 Copynumber: 3.9 Consensus size: 18
11246 CAGTAGCTAA
11256 TTATGTATCGATACAATAC
1 TTATGTATCGATACAA-AC
11275 TTATGTATCGATAC--A-
1 TTATGTATCGATACAAAC
11290 -T-TGTATCGATACAAAAC
1 TTATGTATCGATAC-AAAC
11307 TTATGTATCGATACAAA
1 TTATGTATCGATACAAA
11324 TCGTTGAATT
Statistics
Matches: 43, Mismatches: 0, Indels: 13
0.77 0.00 0.23
Matches are distributed among these distances:
13 11 0.26
14 1 0.02
16 2 0.05
18 4 0.09
19 25 0.58
ACGTcount: A:0.38, C:0.15, G:0.12, T:0.35
Consensus pattern (18 bp):
TTATGTATCGATACAAAC
Found at i:11296 original size:13 final size:13
Alignment explanation
Indices: 11278--11302 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
11268 ACAATACTTA
11278 TGTATCGATACAT
1 TGTATCGATACAT
11291 TGTATCGATACA
1 TGTATCGATACA
11303 AAACTTATGT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:11300 original size:32 final size:32
Alignment explanation
Indices: 11259--11321 Score: 117
Period size: 32 Copynumber: 2.0 Consensus size: 32
11249 TAGCTAATTA
*
11259 TGTATCGATACAATACTTATGTATCGATACAT
1 TGTATCGATACAAAACTTATGTATCGATACAT
11291 TGTATCGATACAAAACTTATGTATCGATACA
1 TGTATCGATACAAAACTTATGTATCGATACA
11322 AATCGTTGAA
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 30 1.00
ACGTcount: A:0.37, C:0.16, G:0.13, T:0.35
Consensus pattern (32 bp):
TGTATCGATACAAAACTTATGTATCGATACAT
Found at i:11403 original size:20 final size:20
Alignment explanation
Indices: 11359--11434 Score: 107
Period size: 21 Copynumber: 3.7 Consensus size: 20
11349 GTTGGGACCC
***
11359 TGTATCGATACATTTGTAGAA
1 TGTATCGATACATTCACA-AA
11380 TGTATCGATACATTCACAAA
1 TGTATCGATACATTCACAAA
11400 TGTATCGATACATTCTACAAA
1 TGTATCGATACATTC-ACAAA
11421 TGTATCGATACATT
1 TGTATCGATACATT
11435 TGGAATTTTT
Statistics
Matches: 51, Mismatches: 3, Indels: 2
0.91 0.05 0.04
Matches are distributed among these distances:
20 17 0.33
21 34 0.67
ACGTcount: A:0.36, C:0.16, G:0.13, T:0.36
Consensus pattern (20 bp):
TGTATCGATACATTCACAAA
Found at i:11640 original size:20 final size:20
Alignment explanation
Indices: 11615--11689 Score: 89
Period size: 20 Copynumber: 3.8 Consensus size: 20
11605 AGGTGTCTAC
11615 ATGTATCGATACATTTTTTA
1 ATGTATCGATACATTTTTTA
* * *
11635 ATGTATCGATACATGTATGA
1 ATGTATCGATACATTTTTTA
* *
11655 ATGTCTCGATACATTCTTCT-
1 ATGTATCGATACATT-TTTTA
11675 ATGTATCGATACATT
1 ATGTATCGATACATT
11690 CTGTCTTTTT
Statistics
Matches: 45, Mismatches: 9, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
20 44 0.98
21 1 0.02
ACGTcount: A:0.29, C:0.15, G:0.13, T:0.43
Consensus pattern (20 bp):
ATGTATCGATACATTTTTTA
Found at i:18842 original size:115 final size:113
Alignment explanation
Indices: 18567--18883 Score: 316
Period size: 115 Copynumber: 2.8 Consensus size: 113
18557 AAGTAAAATC
* * * * * *
18567 ATAAATTATTTAATTTGAGATTATATCTTATAAAAATATATATTAAATAAAAAAAAATCTT-ATA
1 ATAAATTATTTAATTTAAGGTTA-ATCTTATAAAAATATATATTAGAT-AAAATAAGT-TTCATG
* * *
18631 TGCTTA-TTAA-TAAGTTATTTAGACATATTTTATTTAATTATCTTGGATT
63 TACTTATTTAATTAATTTATTTAGACATATTTTATTTAATTATCTTAGATT
* * * *
18680 ATAAATGATTTAATTTAAAGTTAAATTTTATAAAAAAAATATATTAGATAAAATAAGTTTCATGT
1 ATAAATTATTTAATTTAAGGTT-AATCTTAT-AAAAATATATATTAGATAAAATAAGTTTCATGT
*** * *
18745 ACTTATTTAATTAATTTATTTAGGTTTATTTTGTTTAATTATATTTAGATT
64 ACTTATTTAATTAATTTATTTAGACATATTTTATTTAATTAT-CTTAGATT
* * * *
18796 ATAAATTATTTAATTTAAGGTCAAGTCTTATAAAAATATATGTTAGATAAAATAGGTCTCATGTA
1 ATAAATTATTTAATTTAAGGTTAA-TCTTATAAAAATATATATTAGATAAAATAAGTTTCATGTA
* *
18861 TTTATTTAGATCTATTTTATTTA
65 CTTATTTA-AT-TAATTTATTTA
18884 ATTGTATTGG
Statistics
Matches: 167, Mismatches: 28, Indels: 14
0.80 0.13 0.07
Matches are distributed among these distances:
112 2 0.01
113 38 0.23
114 20 0.12
115 65 0.39
116 32 0.19
117 10 0.06
ACGTcount: A:0.41, C:0.04, G:0.08, T:0.47
Consensus pattern (113 bp):
ATAAATTATTTAATTTAAGGTTAATCTTATAAAAATATATATTAGATAAAATAAGTTTCATGTAC
TTATTTAATTAATTTATTTAGACATATTTTATTTAATTATCTTAGATT
Found at i:18920 original size:101 final size:102
Alignment explanation
Indices: 18758--18950 Score: 280
Period size: 101 Copynumber: 1.9 Consensus size: 102
18748 TATTTAATTA
* * * * * **
18758 ATTTATTTAGGTTTATTTTGTTTAATTATATTTAGATTATAAATTATTTAATTTAAGGTCAAGTC
1 ATTTATTTAGATCTATTTTATTTAATTATATTTAGATCATAAATTATTGAATTTAAGGTCAAACC
**
18823 TTATAAAAATATATGTTAGATAAAATAGGTCTCATGT
66 TTATAAAAATATAAATTAGATAAAATAGGTCTCATGT
* *
18860 ATTTATTTAGATCTATTTTATTTAATTGTA-TTGGATCATAAATTATTGAATTTAAGGTCAAACC
1 ATTTATTTAGATCTATTTTATTTAATTATATTTAGATCATAAATTATTGAATTTAAGGTCAAACC
18924 TTATAAAAATATAAATTAGATAAAATA
66 TTATAAAAATATAAATTAGATAAAATA
18951 AGGGCCATTT
Statistics
Matches: 80, Mismatches: 11, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
101 54 0.68
102 26 0.32
ACGTcount: A:0.39, C:0.05, G:0.10, T:0.46
Consensus pattern (102 bp):
ATTTATTTAGATCTATTTTATTTAATTATATTTAGATCATAAATTATTGAATTTAAGGTCAAACC
TTATAAAAATATAAATTAGATAAAATAGGTCTCATGT
Found at i:18968 original size:101 final size:101
Alignment explanation
Indices: 18761--18981 Score: 259
Period size: 101 Copynumber: 2.2 Consensus size: 101
18751 TTAATTAATT
* * * * **
18761 TATTTAGGTTTATTTTGTTTAATTATATTTAGATTATAAATTATTTAATTTAAGGTCAAGTCTTA
1 TATTTA-GATTATTTTATTTAATTATATTTAGATCATAAATTATTGAATTTAAGGTCAAACCTTA
** * **
18826 TAAAAATATATGTTAGATAAAATAGGTCTCATGTATT
65 TAAAAATATAAATTAGATAAAATAGGGCTCATGTACA
* *
18863 TATTTAGATCTATTTTATTTAATTGTA-TTGGATCATAAATTATTGAATTTAAGGTCAAACCTTA
1 TATTTAGAT-TATTTTATTTAATTATATTTAGATCATAAATTATTGAATTTAAGGTCAAACCTTA
*
18927 TAAAAATATAAATTAGATAAAATAAGGGC-CATTTACA
65 TAAAAATATAAATTAGATAAAAT-AGGGCTCATGTACA
*
18964 TATTTA-ATTAATTTATTT
1 TATTTAGATTATTTTATTT
18982 GAGACCTATT
Statistics
Matches: 102, Mismatches: 15, Indels: 7
0.82 0.12 0.06
Matches are distributed among these distances:
99 9 0.09
100 2 0.02
101 66 0.65
102 25 0.25
ACGTcount: A:0.38, C:0.05, G:0.10, T:0.46
Consensus pattern (101 bp):
TATTTAGATTATTTTATTTAATTATATTTAGATCATAAATTATTGAATTTAAGGTCAAACCTTAT
AAAAATATAAATTAGATAAAATAGGGCTCATGTACA
Found at i:19016 original size:24 final size:25
Alignment explanation
Indices: 18966--19016 Score: 61
Period size: 25 Copynumber: 2.1 Consensus size: 25
18956 CATTTACATA
*
18966 TTTAATTAATTTATTTGAGACCTAT
1 TTTAATTAATTTATTTGAGACCAAT
*
18991 TTTATTTAA-TTATGTTGAG-CCAAT
1 TTTAATTAATTTAT-TTGAGACCAAT
19015 TT
1 TT
19017 GTAAATATTT
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
24 10 0.43
25 13 0.57
ACGTcount: A:0.29, C:0.08, G:0.10, T:0.53
Consensus pattern (25 bp):
TTTAATTAATTTATTTGAGACCAAT
Found at i:25840 original size:16 final size:15
Alignment explanation
Indices: 25814--25844 Score: 53
Period size: 16 Copynumber: 2.0 Consensus size: 15
25804 GAAAAAGAAA
25814 ATTTTTTATTATTTT
1 ATTTTTTATTATTTT
25829 ATTTTCTTATTATTTT
1 ATTTT-TTATTATTTT
25845 TAATTTTAAT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 5 0.33
16 10 0.67
ACGTcount: A:0.19, C:0.03, G:0.00, T:0.77
Consensus pattern (15 bp):
ATTTTTTATTATTTT
Found at i:27170 original size:107 final size:107
Alignment explanation
Indices: 26984--27293 Score: 268
Period size: 107 Copynumber: 2.9 Consensus size: 107
26974 TTGCTATTCG
* * * * **
26984 TGCTTGTTGGAGCTGCTGTCATTGCTGTCGTGGAAGCTGTTGCTTGTTGGAGCTGCTGGTTTCAA
1 TGCTTGTTGGAGCTGCTGTCGTTGCTCTCGTGGAAGCTGTTGCTTGTTCGAGCTACAAGTTTCAA
* * * * * *
27049 GTGTTTTGTGGAGCTATTGTTCATGCTTGTTGTGGGAGCCGT
66 GTGCTTTATGGAGCTACTGTTCATGCTTGTTGCGGAAGCCGC
* *
27091 TGCTTGTTGGAGCTGCTGTCGTTGCTACT-TTGGAAGCTGCTT-CTTGTTCGAGTTACAAGTTTC
1 TGCTTGTTGGAGCTGCTGTCGTTGCT-CTCGTGGAAGCTG-TTGCTTGTTCGAGCTACAAGTTTC
* * * *
27154 AGGTGCTTTATGGAGCTGCTGTTCGTGCTTGTTGCGGAAGCTGC
64 AAGTGCTTTATGGAGCTACTGTTCATGCTTGTTGCGGAAGCCGC
* * * * * * * * *
27198 AGCTTGTTGGAGCTGCTATCG-TACTGC-CGTGGAAGTTATTGCTTGTTGGAGCTGCTAGTTTCG
1 TGCTTGTTGGAGCTGCTGTCGTTGCT-CTCGTGGAAGCTGTTGCTTGTTCGAGCTACAAGTTTCA
* * * * * *
27261 GGTACTTTCTGGAGCTGCTGTTCGTACTTGTTG
65 AGTGCTTTATGGAGCTACTGTTCATGCTTGTTG
27294 GAGCTTTTGA
Statistics
Matches: 166, Mismatches: 33, Indels: 9
0.80 0.16 0.04
Matches are distributed among these distances:
105 2 0.01
106 58 0.35
107 103 0.62
108 3 0.02
ACGTcount: A:0.12, C:0.17, G:0.32, T:0.39
Consensus pattern (107 bp):
TGCTTGTTGGAGCTGCTGTCGTTGCTCTCGTGGAAGCTGTTGCTTGTTCGAGCTACAAGTTTCAA
GTGCTTTATGGAGCTACTGTTCATGCTTGTTGCGGAAGCCGC
Found at i:27287 original size:22 final size:25
Alignment explanation
Indices: 27239--27298 Score: 74
Period size: 22 Copynumber: 2.5 Consensus size: 25
27229 GAAGTTATTG
27239 CTTGTTGGAGCTGCTAGTTTCGGGTA
1 CTTGTTGGAGCTGCTAGTTTC-GGTA
27265 CTT-TCTGGAGCTGCT-G-TTC-GTA
1 CTTGT-TGGAGCTGCTAGTTTCGGTA
27287 CTTGTTGGAGCT
1 CTTGTTGGAGCT
27299 TTTGATCGCT
Statistics
Matches: 32, Mismatches: 0, Indels: 8
0.80 0.00 0.20
Matches are distributed among these distances:
22 13 0.41
23 1 0.03
24 3 0.09
25 2 0.06
26 13 0.41
ACGTcount: A:0.10, C:0.18, G:0.32, T:0.40
Consensus pattern (25 bp):
CTTGTTGGAGCTGCTAGTTTCGGTA
Found at i:28551 original size:43 final size:43
Alignment explanation
Indices: 28495--29087 Score: 562
Period size: 43 Copynumber: 14.0 Consensus size: 43
28485 AGGCAGTATT
* *
28495 CAGGGTCAAAGCCGATAGGCAGACTGAGGGATA-AAGAAGTCTC
1 CAGGGTCAAAGCCGACAGGCAGACTGAGGGATAGGA-AAGTCTC
* *
28538 CAGGGTCAAAGCCGACAAGCAGACTAAGGGATAGGAAAGTCTC
1 CAGGGTCAAAGCCGACAGGCAGACTGAGGGATAGGAAAGTCTC
* * * *
28581 TAGGGTCAAAGTCGACAGGCAGACTAAGGGATAAGAAAGTCTC
1 CAGGGTCAAAGCCGACAGGCAGACTGAGGGATAGGAAAGTCTC
* * * *
28624 CAGGGTCAAAACCGATAGGCAGACTAAGGGA-AGAAAAGTCTC
1 CAGGGTCAAAGCCGACAGGCAGACTGAGGGATAGGAAAGTCTC
* * *
28666 CAAGGTCAAAACCGACAGGCAGACTGAGGGAAAGGAAAGTCTC
1 CAGGGTCAAAGCCGACAGGCAGACTGAGGGATAGGAAAGTCTC
* * * * * * *
28709 CAGGATCAAAACCAAC-GACAAATTAAGGGA-AGGAAAGTCTC
1 CAGGGTCAAAGCCGACAGGCAGACTGAGGGATAGGAAAGTCTC
* * ** *
28750 CAAGGTC--A----ACAGGCAGATTGAGGGA-AAAAAAGTTTC
1 CAGGGTCAAAGCCGACAGGCAGACTGAGGGATAGGAAAGTCTC
* * *
28786 CAAGGTTAAAGCCGACTGGCAGACTGAGGGATAGGAAAGTCTC
1 CAGGGTCAAAGCCGACAGGCAGACTGAGGGATAGGAAAGTCTC
* * * *
28829 TAGGGTCAAAGCTGATAGGCAGACTGAGGGATAAGAAAGTCTC
1 CAGGGTCAAAGCCGACAGGCAGACTGAGGGATAGGAAAGTCTC
* ** *
28872 CAAGGTCAAAGTTGACAGGCAGATTGAGGGATAGGAAAGTCTC
1 CAGGGTCAAAGCCGACAGGCAGACTGAGGGATAGGAAAGTCTC
* * * *
28915 CAAGGTCAAAGGCGACAGGCAGAATGAAGGATAGGAAAGTCTC
1 CAGGGTCAAAGCCGACAGGCAGACTGAGGGATAGGAAAGTCTC
* * * * * * *
28958 TAGGGTCAAAGCCGATAAGCAAACTAAAGGATAGGAAAGTCTA
1 CAGGGTCAAAGCCGACAGGCAGACTGAGGGATAGGAAAGTCTC
* * * * *
29001 TAGGGTCAAAGCCAACAGGCAGACTAAAGGATAGGAAAGTCTT
1 CAGGGTCAAAGCCGACAGGCAGACTGAGGGATAGGAAAGTCTC
* * * * *
29044 CAAGGTTAAAGCCGACAGGCATACTTAGGGATAGG-GAGTCTC
1 CAGGGTCAAAGCCGACAGGCAGACTGAGGGATAGGAAAGTCTC
29086 CA
1 CA
29088 AAAGTTTAAT
Statistics
Matches: 461, Mismatches: 79, Indels: 21
0.82 0.14 0.04
Matches are distributed among these distances:
35 2 0.00
36 25 0.05
38 1 0.00
39 1 0.00
41 16 0.03
42 69 0.15
43 346 0.75
44 1 0.00
ACGTcount: A:0.38, C:0.17, G:0.30, T:0.15
Consensus pattern (43 bp):
CAGGGTCAAAGCCGACAGGCAGACTGAGGGATAGGAAAGTCTC
Found at i:36502 original size:52 final size:52
Alignment explanation
Indices: 36424--36551 Score: 224
Period size: 52 Copynumber: 2.5 Consensus size: 52
36414 CGAAATATGA
*
36424 AAATTTGCCTGCATGTATCGATACA-TTTAATAGTGTATCGATACATCTGGGC
1 AAATTTGCCTGCATGTATCGATACATTTTAA-AATGTATCGATACATCTGGGC
36476 AAATTTGCCTGCATGTATCGATACATTTTAAAATGTATCGATACATCTGGGC
1 AAATTTGCCTGCATGTATCGATACATTTTAAAATGTATCGATACATCTGGGC
36528 AAA-TTGCCTGCATGTATCGATACA
1 AAATTTGCCTGCATGTATCGATACA
36552 AAGATCAGTG
Statistics
Matches: 74, Mismatches: 1, Indels: 3
0.95 0.01 0.04
Matches are distributed among these distances:
51 21 0.28
52 48 0.65
53 5 0.07
ACGTcount: A:0.30, C:0.18, G:0.18, T:0.34
Consensus pattern (52 bp):
AAATTTGCCTGCATGTATCGATACATTTTAAAATGTATCGATACATCTGGGC
Found at i:36578 original size:13 final size:13
Alignment explanation
Indices: 36560--36584 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
36550 CAAAGATCAG
36560 TGTATCGATACAA
1 TGTATCGATACAA
36573 TGTATCGATACA
1 TGTATCGATACA
36585 TTTGAGTAAT
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:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:36662 original size:33 final size:33
Alignment explanation
Indices: 36625--36691 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
36615 AGTAGCTTAA
36625 ATTGTATCGATACAAAAAAATATGTATCGATAC
1 ATTGTATCGATACAAAAAAATATGTATCGATAC
* ***
36658 ATTGTATCGATACAACATTTTATGTATCGATAC
1 ATTGTATCGATACAAAAAAATATGTATCGATAC
36691 A
1 A
36692 GATCGTTGAA
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.40, C:0.13, G:0.12, T:0.34
Consensus pattern (33 bp):
ATTGTATCGATACAAAAAAATATGTATCGATAC
Found at i:36665 original size:13 final size:13
Alignment explanation
Indices: 36647--36671 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
36637 CAAAAAAATA
36647 TGTATCGATACAT
1 TGTATCGATACAT
36660 TGTATCGATACA
1 TGTATCGATACA
36672 ACATTTTATG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:41604 original size:31 final size:31
Alignment explanation
Indices: 41559--41900 Score: 286
Period size: 31 Copynumber: 11.0 Consensus size: 31
41549 TCTTCAAATC
* * *
41559 TCTTTTC-CCAAAGTCCATGTCTCAGTGGCA
1 TCTTTTCTTCAAAGTCCACGACTCAGTGGCA
* **
41589 TCTTTTCTTCAAAGTCCACAACTTTGTGGCAA
1 TCTTTTCTTCAAAGTCCACGACTCAGTGGC-A
*
41621 T-TTCTTC-TCAAAGTCCACGACTTAGTGGCA
1 TCTT-TTCTTCAAAGTCCACGACTCAGTGGCA
41651 TCTTTTCTTCAAAGTCCACGACTCAGTGGCAA
1 TCTTTTCTTCAAAGTCCACGACTCAGTGGC-A
** *
41683 TCCCTTC-TCAAAGTCCACAACTCAGTGGCA
1 TCTTTTCTTCAAAGTCCACGACTCAGTGGCA
* *
41713 TCTCTTT-TCCCAAAGTCCACGACTTAGTGGCA
1 TCT-TTTCT-TCAAAGTCCACGACTCAGTGGCA
* * *
41745 TCTTTTTTTCAAAATCCACGACTTAGTGGCAA
1 TCTTTTCTTCAAAGTCCACGACTCAGTGGC-A
* *
41777 TCCTTTCTTCAAAGTCCACGACTCAATGGCA
1 TCTTTTCTTCAAAGTCCACGACTCAGTGGCA
* * * *
41808 TCTCTTC-TCAAAATCCACAACTTAGTGGCA
1 TCTTTTCTTCAAAGTCCACGACTCAGTGGCA
* * *
41838 TCTCTTT-TCTCAAAGTCTACAACTTAGTGGCAA
1 TCT-TTTCT-TCAAAGTCCACGACTCAGTGGC-A
* * * * *
41871 TCTCTTC-ACAAAGCCCACAACTCCGTGGCA
1 TCTTTTCTTCAAAGTCCACGACTCAGTGGCA
41901 CCCTTTTAAG
Statistics
Matches: 257, Mismatches: 39, Indels: 32
0.78 0.12 0.10
Matches are distributed among these distances:
30 38 0.15
31 132 0.51
32 83 0.32
33 4 0.02
ACGTcount: A:0.25, C:0.30, G:0.14, T:0.31
Consensus pattern (31 bp):
TCTTTTCTTCAAAGTCCACGACTCAGTGGCA
Found at i:41664 original size:62 final size:62
Alignment explanation
Indices: 41567--41888 Score: 355
Period size: 62 Copynumber: 5.2 Consensus size: 62
41557 TCTCTTTTCC
* * * * * *
41567 CAAAGTCCATGTCTCAGTGGCATCTTTTCTTCAAAGTCCACAACTTTGTGGCAATTTCTTCT
1 CAAAGTCCACGACTTAGTGGCATCTTTTCTTCAAAGTCCACGACTTAGTGGCAATCTCTTCT
* *
41629 CAAAGTCCACGACTTAGTGGCATCTTTTCTTCAAAGTCCACGACTCAGTGGCAATCCCTTCT
1 CAAAGTCCACGACTTAGTGGCATCTTTTCTTCAAAGTCCACGACTTAGTGGCAATCTCTTCT
* * * * *
41691 CAAAGTCCACAACTCAGTGGCATCTCTTT-TCCCAAAGTCCACGACTTAGTGGC-ATCTTTTTTT
1 CAAAGTCCACGACTTAGTGGCATCT-TTTCT-TCAAAGTCCACGACTTAGTGGCAATC-TCTTCT
* * * *
41754 CAAAATCCACGACTTAGTGGCAATCCTTTCTTCAAAGTCCACGACTCAATGGC-ATCTCTTCT
1 CAAAGTCCACGACTTAGTGGC-ATCTTTTCTTCAAAGTCCACGACTTAGTGGCAATCTCTTCT
* * * * *
41816 CAAAATCCACAACTTAGTGGCATCTCTTT-TCTCAAAGTCTACAACTTAGTGGCAATCTCTTCA
1 CAAAGTCCACGACTTAGTGGCATCT-TTTCT-TCAAAGTCCACGACTTAGTGGCAATCTCTTCT
*
41879 CAAAGCCCAC
1 CAAAGTCCAC
41889 AACTCCGTGG
Statistics
Matches: 219, Mismatches: 33, Indels: 15
0.82 0.12 0.06
Matches are distributed among these distances:
61 4 0.02
62 126 0.58
63 85 0.39
64 4 0.02
ACGTcount: A:0.26, C:0.29, G:0.14, T:0.31
Consensus pattern (62 bp):
CAAAGTCCACGACTTAGTGGCATCTTTTCTTCAAAGTCCACGACTTAGTGGCAATCTCTTCT
Found at i:41900 original size:125 final size:126
Alignment explanation
Indices: 41579--41888 Score: 432
Period size: 125 Copynumber: 2.5 Consensus size: 126
41569 AAGTCCATGT
* *
41579 CTCAGTGGCA--TCTTTTCTTCAAAGTCCACAACTTTGTGGCAATTTCTTCTCAAAGTCCACGAC
1 CTCAGTGGCATCTCTTTTC-TCAAAGTCCACAACTTAGTGGCAATCTCTTCTCAAAGTCCACGAC
* * *
41642 TTAGTGGC-ATCTTTTCTTCAAAGTCCACGACTCAGTGGCAATCCCTTCTCAAAGTCCACAA
65 TTAGTGGCAATCCTTTCTTCAAAGTCCACGACTCAATGGCAATCCCTTCTCAAAATCCACAA
* * * * *
41703 CTCAGTGGCATCTCTTTTCCCAAAGTCCACGACTTAGTGGC-ATCTTTTTTTCAAAATCCACGAC
1 CTCAGTGGCATCTCTTTTCTCAAAGTCCACAACTTAGTGGCAATC-TCTTCTCAAAGTCCACGAC
*
41767 TTAGTGGCAATCCTTTCTTCAAAGTCCACGACTCAATGGC-ATCTCTTCTCAAAATCCACAA
65 TTAGTGGCAATCCTTTCTTCAAAGTCCACGACTCAATGGCAATCCCTTCTCAAAATCCACAA
* * * *
41828 CTTAGTGGCATCTCTTTTCTCAAAGTCTACAACTTAGTGGCAATCTCTTCACAAAGCCCAC
1 CTCAGTGGCATCTCTTTTCTCAAAGTCCACAACTTAGTGGCAATCTCTTCTCAAAGTCCAC
41889 AACTCCGTGG
Statistics
Matches: 161, Mismatches: 20, Indels: 9
0.85 0.11 0.05
Matches are distributed among these distances:
124 12 0.07
125 110 0.68
126 39 0.24
ACGTcount: A:0.26, C:0.29, G:0.14, T:0.31
Consensus pattern (126 bp):
CTCAGTGGCATCTCTTTTCTCAAAGTCCACAACTTAGTGGCAATCTCTTCTCAAAGTCCACGACT
TAGTGGCAATCCTTTCTTCAAAGTCCACGACTCAATGGCAATCCCTTCTCAAAATCCACAA
Found at i:41924 original size:27 final size:27
Alignment explanation
Indices: 41885--42025 Score: 120
Period size: 27 Copynumber: 4.9 Consensus size: 27
41875 TTCACAAAGC
41885 CCACAACTCCGTGGCACCCTTTTAAGT
1 CCACAACTCCGTGGCACCCTTTTAAGT
* *
41912 TCACAACTCCGTGGCACCTTTTTCTTTTTAAGGC
1 CCACAACTCCGTGGCACC-----C-TTTTAA-GT
* **
41946 CCACAACTTCGTGGCACTTTTTTTTTAAGT
1 CCACAACTCCGTGGCAC---CCTTTTAAGT
* **
41976 CCACAACTCTGTGTTACCCTTTTAAGT
1 CCACAACTCCGTGGCACCCTTTTAAGT
42003 CCACAACTCCGTGGCACCCTTTT
1 CCACAACTCCGTGGCACCCTTTT
42026 CCCTTTTAAG
Statistics
Matches: 88, Mismatches: 16, Indels: 20
0.71 0.13 0.16
Matches are distributed among these distances:
27 45 0.51
30 14 0.16
31 6 0.07
32 1 0.01
33 6 0.07
34 16 0.18
ACGTcount: A:0.20, C:0.32, G:0.13, T:0.35
Consensus pattern (27 bp):
CCACAACTCCGTGGCACCCTTTTAAGT
Found at i:41953 original size:34 final size:33
Alignment explanation
Indices: 41902--42835 Score: 727
Period size: 34 Copynumber: 28.9 Consensus size: 33
41892 TCCGTGGCAC
*
41902 CCTTTTAAGTTCACAACTCCGTGGCACCTTTTT
1 CCTTTTAAGTCCACAACTCCGTGGCACCTTTTT
* * *
41935 CTTTTTAAGGCCCACAACTTCGTGGCA-CTTTTT
1 CCTTTTAA-GTCCACAACTCCGTGGCACCTTTTT
* **
41968 --TTTTAAGTCCACAACTCTGT-G-----TTAC
1 CCTTTTAAGTCCACAACTCCGTGGCACCTTTTT
*
41993 CCTTTTAAGTCCACAACTCCGTGGCACCCTTTTC
1 CCTTTTAAGTCCACAACTCCGTGGCA-CCTTTTT
* * *
42027 CCTTTTAAGTCGACATCTCCATGGCATCCCTTTTT
1 CCTTTTAAGTCCACAACTCCGTGGCA--CCTTTTT
** * *
42062 -CTTGAAAGTCCATAACTCTGTGGCA-C-----
1 CCTTTTAAGTCCACAACTCCGTGGCACCTTTTT
* *
42088 CCTTTTAAGTCCACAACTCTC-TAGCACATTTTT
1 CCTTTTAAGTCCACAACTC-CGTGGCACCTTTTT
* *
42121 CCCTTTAAAGCCCACAACTCCGTGGCATTCC-TTTT
1 -CCTTTTAAGTCCACAACTCCGTGGCA--CCTTTTT
* *
42156 CCTTTTAAGTCCACGACTCTGTGGCACTCTTTTT
1 CCTTTTAAGTCCACAACTCCGTGGCAC-CTTTTT
*
42190 CCTTTTAAGTCCACAACTTCGTGGCACCTTTTT
1 CCTTTTAAGTCCACAACTCCGTGGCACCTTTTT
* * *
42223 CTTTTTAAAG-CGCATAACTCTGTGGCA-CTTTTT
1 CCTTTT-AAGTC-CACAACTCCGTGGCACCTTTTT
42256 --TTTTAAGTCCACAACTCCGTGGCA-C-----
1 CCTTTTAAGTCCACAACTCCGTGGCACCTTTTT
* *
42281 CGTTTTAAGTCCAAAACTCCGTGGCACCTTTTT
1 CCTTTTAAGTCCACAACTCCGTGGCACCTTTTT
* *
42314 CCCTTTTAAG-CCGACACCTCCATGGCATCCCTTTTT
1 -CCTTTTAAGTCC-ACAACTCCGTGGCA--CCTTTTT
** * *
42350 -CTTGAAAGTCCACAACTCTGTGGTACCTTTTT
1 CCTTTTAAGTCCACAACTCCGTGGCACCTTTTT
* * *
42382 CCCTTTAAAGCCCATAACTCCGTGGCACTCTTTTT
1 -CCTTTTAAGTCCACAACTCCGTGGCAC-CTTTTT
* *
42417 CTTTTTAAGTCCACGACTCCGTGGCACTCTTTTT
1 CCTTTTAAGTCCACAACTCCGTGGCAC-CTTTTT
* * * *
42451 CCTTTTAAATCCATAACTCTGTGGTA-C-----
1 CCTTTTAAGTCCACAACTCCGTGGCACCTTTTT
* *
42478 CCTTTTAAGTCCACAACTCCATGGCATCTTTTT
1 CCTTTTAAGTCCACAACTCCGTGGCACCTTTTT
* *
42511 CCTTTTAAGTCCACAACTTCGTGGCACCTTGTT
1 CCTTTTAAGTCCACAACTCCGTGGCACCTTTTT
42544 CCTTTTAAGTCCACAACTCCGTGGCACC-TTTT
1 CCTTTTAAGTCCACAACTCCGTGGCACCTTTTT
* * * * *
42576 CTTTTTAAGTCCACGACTCTGTAGCACCCTTTT
1 CCTTTTAAGTCCACAACTCCGTGGCACCTTTTT
* *
42609 CCTTTTTAAG-CCGACACCTCTGTGGCATCCTTTTTT
1 CC-TTTTAAGTCC-ACAACTCCGTGGCA-CC-TTTTT
*
42645 CCTTTTAAGTCTACAACTCCGTGGCA-C-----
1 CCTTTTAAGTCCACAACTCCGTGGCACCTTTTT
* *
42672 CCTTTTAAGTCCACAACTCTGTGGCATCTTTTT
1 CCTTTTAAGTCCACAACTCCGTGGCACCTTTTT
* *
42705 CCTTTTAAGTCCACGACTCTGTGGCACC-TTTT
1 CCTTTTAAGTCCACAACTCCGTGGCACCTTTTT
* * * *
42737 CTTTTTAAGTCCACGACTCTGTGGCACCCTTTTC
1 CCTTTTAAGTCCACAACTCCGTGGCA-CCTTTTT
* * *
42771 CCTTTTAAGCCCACACCTCCATGGCATCCCTTTTT
1 CCTTTTAAGTCCACAACTCCGTGGCA--CCTTTTT
*
42806 CC-TATAAGTCCACAACTCCGTGGCACCTTT
1 CCTTTTAAGTCCACAACTCCGTGGCACCTTT
42836 AAGTCCAATA
Statistics
Matches: 724, Mismatches: 112, Indels: 131
0.75 0.12 0.14
Matches are distributed among these distances:
25 2 0.00
27 106 0.15
28 4 0.01
29 1 0.00
30 28 0.04
31 12 0.02
32 70 0.10
33 127 0.18
34 310 0.43
35 49 0.07
36 15 0.02
ACGTcount: A:0.19, C:0.31, G:0.13, T:0.37
Consensus pattern (33 bp):
CCTTTTAAGTCCACAACTCCGTGGCACCTTTTT
Found at i:42120 original size:27 final size:27
Alignment explanation
Indices: 42067--42120 Score: 63
Period size: 27 Copynumber: 2.0 Consensus size: 27
42057 TTTTTCTTGA
* * * *
42067 AAGTCCATAACTCTGTGGCACCCTTTT
1 AAGTCCACAACTCTCTAGCACACTTTT
*
42094 AAGTCCACAACTCTCTAGCACATTTTT
1 AAGTCCACAACTCTCTAGCACACTTTT
42121 CCCTTTAAAG
Statistics
Matches: 22, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
27 22 1.00
ACGTcount: A:0.26, C:0.30, G:0.11, T:0.33
Consensus pattern (27 bp):
AAGTCCACAACTCTCTAGCACACTTTT
Found at i:42257 original size:288 final size:282
Alignment explanation
Indices: 41902--42831 Score: 1009
Period size: 288 Copynumber: 3.2 Consensus size: 282
41892 TCCGTGGCAC
* *
41902 CCTTTTAAGTTCACAACTCCGTGGCACCTTTTTCTTTTTAAGGCCCACAACTTCGTGGCACTTTT
1 CCTTTTAAGTCCACAACTCCGTGGCACCTTTTTCTTTTTAAAG-CCACAACTTCGTGGCACTTTT
* **
41967 TTTTTAAGTCCACAACTCTGTGTTACCCTTTTAAGTCCACAACTCCGTGGCACCCTTTTCCCTTT
65 TTTTTAAGTCCACAACTCCGTGGCACCCTTTTAAGTCCACAACTCCGTGGCACCCTTTTCCCTTT
* * *
42032 TAAGTCGACATCTCCATGGCATCCCTTTTTCTTGAAAGTCCATAACTCTGTGGCACCCTTTTAAG
130 TAAGCCGACACCTCCATGGCATCCCTTTTTCTTGAAAGTCCACAACTCTGTGGCACCCTTTTAAG
* * * *
42097 TCCACAACTCTCTAGCACATTTTTCCCTTTAAAGCCCACAACTCCGTGGCATTCCTTTTCCTTTT
195 TCCACAACTCTCTGGCAC-TTTTT-CCTTTTAAGTCCACGACTCCGTGGCA-TCCTTTTCCTTTT
42162 AAGTCCACGACTCTGTGGCACTCTTTTT
257 AAGTCCACGACTCTGTGGCAC-C-TTTT
* *
42190 CCTTTTAAGTCCACAACTTCGTGGCACCTTTTTCTTTTTAAAGCGCATAAC-TCTGTGGCACTTT
1 CCTTTTAAGTCCACAACTCCGTGGCACCTTTTTCTTTTTAAAGC-CACAACTTC-GTGGCACTTT
* * *
42254 TTTTTTAAGTCCACAACTCCGTGGCACCGTTTTAAGTCCAAAACTCCGTGGCACCTTTTTCCCTT
64 TTTTTTAAGTCCACAACTCCGTGGCACCCTTTTAAGTCCACAACTCCGTGGCACCCTTTTCCCTT
*
42319 TTAAGCCGACACCTCCATGGCATCCCTTTTTCTTGAAAGTCCACAACTCTGTGGTACCTTTTTCC
129 TTAAGCCGACACCTCCATGGCATCCCTTTTTCTTGAAAGTCCACAACTCTGTGG---C----ACC
* * * * *
42384 CTTTAAAGCCCATAACTC-CGTGGCACTCTTTTTCTTTTTAAGTCCACGACTCCGTGGCACTCTT
187 CTTTTAAGTCCACAACTCTC-TGGCA--CTTTTTCCTTTTAAGTCCACGACTCCGTGGCA-TCCT
* ** *
42448 TTTCCTTTTAAATCCATAACTCTGTGGTA-C----
248 TTTCCTTTTAAGTCCACGACTCTGTGGCACCTTTT
* * *
42478 CCTTTTAAGTCCACAACTCCATGGCATCTTTTTCCTTTT-AAGTCCACAACTTCGTGGCACCTTG
1 CCTTTTAAGTCCACAACTCCGTGGCACCTTTTTCTTTTTAAAG-CCACAACTTCGTGGCA-CTT-
* * * *
42542 TTCCTTTTAAGTCCACAACTCCGTGGCACCTTTTCTTTTTAAGTCCACGACTCTGTAGCACCCTT
63 TT-TTTTTAAGTCCACAACTCCGTGGCACC----C-TTTTAAGTCCACAACTCCGTGGCACCCTT
* ** * ** * *
42607 TTCCTTTTTAAGCCGACACCTCTGTGGCATCCTTTTTTCCTTTTAAGTCTACAACTCCGTGGCAC
122 TTCCCTTTTAAGCCGACACCTCCATGGCATCCCTTTTT-CTTGAAAGTCCACAACTCTGTGGCAC
* *
42672 CCTTTTAAGTCCACAACTCTGTGGCATCTTTTTCCTTTTAAGTCCACGACTCTGTGGCA-CCTTT
186 CCTTTTAAGTCCACAACTCTCTGGCA-CTTTTTCCTTTTAAGTCCACGACTCCGTGGCATCCTTT
*
42736 TCTTTTTAAGTCCACGACTCTGTGGCACCCTTTT
250 TCCTTTTAAGTCCACGACTCTGTGGCA-CCTTTT
* * * * * *
42770 CCCTTTTAAGCCCACACCTCCATGGCATCCCTTTTTC-CTAT-AAGTCCACAACTCCGTGGCAC
1 -CCTTTTAAGTCCACAACTCCGTGGCA--CCTTTTTCTTTTTAAAG-CCACAACTTCGTGGCAC
42832 CTTTAAGTCC
Statistics
Matches: 542, Mismatches: 67, Indels: 61
0.81 0.10 0.09
Matches are distributed among these distances:
286 26 0.05
287 17 0.03
288 238 0.44
289 24 0.04
290 26 0.05
291 1 0.00
293 27 0.05
294 22 0.04
295 136 0.25
296 24 0.04
297 1 0.00
ACGTcount: A:0.19, C:0.31, G:0.13, T:0.37
Consensus pattern (282 bp):
CCTTTTAAGTCCACAACTCCGTGGCACCTTTTTCTTTTTAAAGCCACAACTTCGTGGCACTTTTT
TTTTAAGTCCACAACTCCGTGGCACCCTTTTAAGTCCACAACTCCGTGGCACCCTTTTCCCTTTT
AAGCCGACACCTCCATGGCATCCCTTTTTCTTGAAAGTCCACAACTCTGTGGCACCCTTTTAAGT
CCACAACTCTCTGGCACTTTTTCCTTTTAAGTCCACGACTCCGTGGCATCCTTTTCCTTTTAAGT
CCACGACTCTGTGGCACCTTTT
Found at i:42298 original size:27 final size:27
Alignment explanation
Indices: 42256--42313 Score: 98
Period size: 27 Copynumber: 2.1 Consensus size: 27
42246 GGCACTTTTT
*
42256 TTTTAAGTCCACAACTCCGTGGCACCG
1 TTTTAAGTCCAAAACTCCGTGGCACCG
*
42283 TTTTAAGTCCAAAACTCCGTGGCACCT
1 TTTTAAGTCCAAAACTCCGTGGCACCG
42310 TTTT
1 TTTT
42314 CCCTTTTAAG
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
27 29 1.00
ACGTcount: A:0.22, C:0.29, G:0.16, T:0.33
Consensus pattern (27 bp):
TTTTAAGTCCAAAACTCCGTGGCACCG
Found at i:42367 original size:227 final size:223
Alignment explanation
Indices: 42125--42830 Score: 674
Period size: 227 Copynumber: 3.1 Consensus size: 223
42115 ATTTTTCCCT
* *
42125 TTAAAGCCCACAACTCCGTGGCATTCCTTTTCCTTTTAAGTCCACGACTCTGTGGCACTCTTTTT
1 TTAAAGTCCACAACTCCGTGGCATACCTTTTCCTTTTAAG-CCAC-ACTCTGTGGCACTCTTTTT
*
42190 CCTTTTAAGTCCACAACTTCGTGGCACCTTTTTCTTTTTAAAGCGCATAACTCTGTGGCACTTTT
64 CCTTTTAAGTCCACAACTCCGTGGCACCTTTTTC-TTTTAAAGC-CATAACTCTGTGGCACTTTT
* *
42255 TTTTTAAGTCCACAACTCCGTGGCA-C-CGTTTTAAGTCCAAAACTCCGTGGCACCTTTTTCCCT
127 TTTTTAAGTCCACAACTCCGTGGCACCTCCTTTTAAGTCCACAACTCCGTGGCACCTTTTTCCCT
42318 TTTAAGCCGACACCTCCATGGCATCCCTTTTTC
192 TTTAAGCC-ACACCTCCATGGCATCCCTTTTTC
* * * *
42351 TTGAAAGTCCACAACTCTGTGG--TACCTTTTTCCCTTTAAAGCCCATAACTCCGTGGCACTCTT
1 TT-AAAGTCCACAACTCCGTGGCATACC-TTTT-CCTTTTAAG-CCA-CACTCTGTGGCACTCTT
* * * *
42414 TTTCTTTTTAAGTCCACGACTCCGTGGCACTCTTTTTCCTTTTAAATCCATAACTCTGTGGTAC-
61 TTTCCTTTTAAGTCCACAACTCCGTGGCAC-CTTTTT-CTTTTAAAGCCATAACTCTGTGGCACT
** * * *
42478 --CCTTTTAAGTCCACAACTCCATGGCATCTTTTTCCTTTTAAGTCCACAACTTCGTGGCACCTT
124 TTTTTTTTAAGTCCACAACTCCGTGGCA-C---CTCCTTTTAAGTCCACAACTCCGTGGCACCTT
* * * *
42541 GTT-CCTTTTAAGTCCACAACTCCGTGGCA--CCTTTTCTT
185 TTTCCCTTTTAAG-CCACACCTCCATGGCATCCCTTTT-TC
* * * * *
42579 TTTAAGTCCACGACTCTGTAGCA-CCCTTTTCCTTTTTAAGCCGACACCTCTGTGGCA-TCCTTT
1 TTAAAGTCCACAACTCCGTGGCATACCTTTTCC-TTTTAAGCC-ACA-CTCTGTGGCACT-C-TT
* *
42642 TTTCCTTTTAAGTCTACAACTCCGTGGCACC-----CTTTT-AAGTCCACAACTCTGTGGCATCT
61 TTTCCTTTTAAGTCCACAACTCCGTGGCACCTTTTTCTTTTAAAG-CCATAACTCTGTGGCA-CT
* * * * * *
42701 TTTTCCTTTTAAGTCCACGACTCTGTGGCACCTTTTCTTTTTAAGTCCACGACTCTGTGGCACCC
124 TTTT--TTTTAAGTCCACAACTCCGTGGCACC---TCCTTTTAAGTCCACAACTCCGTGGCACCT
42766 TTTTCCCTTTTAAGCCCACACCTCCATGGCATCCCTTTTTC
184 TTTTCCCTTTTAAG-CCACACCTCCATGGCATCCCTTTTTC
*
42807 CTATAAGTCCACAACTCCGTGGCA
1 TTA-AAGTCCACAACTCCGTGGCA
42831 CCTTTAAGTC
Statistics
Matches: 388, Mismatches: 57, Indels: 67
0.76 0.11 0.13
Matches are distributed among these distances:
220 2 0.01
221 19 0.05
222 1 0.00
224 23 0.06
225 3 0.01
226 41 0.11
227 173 0.45
228 50 0.13
229 45 0.12
230 31 0.08
ACGTcount: A:0.19, C:0.31, G:0.13, T:0.37
Consensus pattern (223 bp):
TTAAAGTCCACAACTCCGTGGCATACCTTTTCCTTTTAAGCCACACTCTGTGGCACTCTTTTTCC
TTTTAAGTCCACAACTCCGTGGCACCTTTTTCTTTTAAAGCCATAACTCTGTGGCACTTTTTTTT
TAAGTCCACAACTCCGTGGCACCTCCTTTTAAGTCCACAACTCCGTGGCACCTTTTTCCCTTTTA
AGCCACACCTCCATGGCATCCCTTTTTC
Found at i:42687 original size:27 final size:27
Alignment explanation
Indices: 42645--42769 Score: 115
Period size: 27 Copynumber: 4.2 Consensus size: 27
42635 ATCCTTTTTT
* *
42645 CCTTTTAAGTCTACAACTCCGTGGCAC
1 CCTTTTAAGTCCACAACTCTGTGGCAC
42672 CCTTTTAAGTCCACAACTCTGTGGCATC
1 CCTTTTAAGTCCACAACTCTGTGGCA-C
*
42700 TTTTTCCTTTTAAGTCCACGACTCTGTGGCAC
1 -----CCTTTTAAGTCCACAACTCTGTGGCAC
*
42732 CTTTTCTTTTTAAGTCCACGACTCTGTGGCAC
1 C----C-TTTTAAGTCCACAACTCTGTGGCAC
42764 CCTTTT
1 CCTTTT
42770 CCCTTTTAAG
Statistics
Matches: 84, Mismatches: 3, Indels: 22
0.77 0.03 0.20
Matches are distributed among these distances:
27 29 0.35
28 2 0.02
31 1 0.01
32 27 0.32
33 25 0.30
ACGTcount: A:0.18, C:0.30, G:0.14, T:0.38
Consensus pattern (27 bp):
CCTTTTAAGTCCACAACTCTGTGGCAC
Found at i:42913 original size:51 final size:48
Alignment explanation
Indices: 42832--43616 Score: 448
Period size: 49 Copynumber: 16.8 Consensus size: 48
42822 TCCGTGGCAC
42832 CTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTT-T
1 CTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTGT
* * *
42879 ACCATCTTGAGTCCAATATCGCTGGCCTAGAATCAACATATTGGCACCTTGT
1 --C-T-TTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTGT
* * *
42931 CTTTAAGACCAATATTGCTGGCCTTGAATCAGCACATTGG---C--G-
1 CTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTGT
**
42973 C---AAACCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTGT
1 CTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTGT
* * * * * * *
43018 CTCTAAGACCAATGTCGCTGACCTTAAATCAACACATTGGCA------
1 CTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTGT
* *
43060 ---TAAGCCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTAT
1 CTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTGT
* * * *
43105 CTCTAAGACCAATGTCGCTGGCCTTGAATCAGCACATTGGCA------
1 CTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTGT
* * *
43147 ---TAAGCCCAATATCACTGGCCTTGAATCAGCATATTGGCACCTTGC
1 CTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTGT
* * *
43192 CTTTAAGACCAATGTCGCTGGCCTTGGATCAGCATATTGGCA------
1 CTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTGT
* **
43234 ---TAAGCCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTCCAT
1 CTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCT-TGT
* * * * * * *
43280 CTTTAAGACCGATGTCGTTGGCCTTGAATTAGCACATTGGCA-CTGTAACCAT
1 CTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCT-T----GT
* * * * * * *
43332 CTTTAAGTCCAATGTTGCCGACCTTGAATCAGCACATTGGCATCTTCAT
1 CTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTT-GT
** * ** *
43381 CTTTAAGTCCGGTATCGCTAGCCTTGAATCAGCATATTGGCATGTTTAT
1 CTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCA-CCTTGT
** * * * * *
43430 CTTTAAAACCAATGTCGTTGGCCTTGAATCAGCACATTGGCATCTTCAT
1 CTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTT-GT
* * * * *
43479 ATTTAAGTCCAAAATCACTGGCCTTAAATCAGCATATTGGCATCTT-T
1 CTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTGT
* * ** *
43526 AACATTCCTAAG-CCTAATGTCACTGGCCTTGTCTCAGCATATTGGCA--TTCTT
1 --C-TT--TAAGTCC-AATATCGCTGGCCTTGAATCAGCATATTGGCACCTT-GT
* * ** *
43578 CTTCAAGTCGAACGTCGCTGGCCATGAATCAGCATATTG
1 CTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTG
43617 TCATTCTTCG
Statistics
Matches: 583, Mismatches: 97, Indels: 114
0.73 0.12 0.14
Matches are distributed among these distances:
39 136 0.23
42 2 0.00
43 1 0.00
44 1 0.00
45 2 0.00
47 28 0.05
48 139 0.24
49 149 0.26
50 9 0.02
51 43 0.07
52 71 0.12
53 2 0.00
ACGTcount: A:0.26, C:0.26, G:0.18, T:0.30
Consensus pattern (48 bp):
CTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTGT
Found at i:42993 original size:39 final size:39
Alignment explanation
Indices: 42939--43273 Score: 215
Period size: 39 Copynumber: 7.9 Consensus size: 39
42929 GTCTTTAAGA
* * *
42939 CCAATATTGCTGGCCTTGAATCAGCACATTGGCGCAAAC
1 CCAATATCGCTGGCCTTGAATCAGCATATTGGCACAAAC
42978 CCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTGTCTCTAAGA-
1 CCAATATCGCTGGCCTTGAATCAGCATATTGGCA--------C-AA-AC
* * * * * * *
43026 CCAATGTCGCTGACCTTAAATCAACACATTGGCATAAGC
1 CCAATATCGCTGGCCTTGAATCAGCATATTGGCACAAAC
*
43065 CCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTATCTCTAAGA
1 CCAATATCGCTGGCCTTGAATCAGCATATTGGCA-C--A-----AA-C
* * * *
43113 CCAATGTCGCTGGCCTTGAATCAGCACATTGGCATAAGC
1 CCAATATCGCTGGCCTTGAATCAGCATATTGGCACAAAC
*
43152 CCAATATCACTGGCCTTGAATCAGCATATTGGCACCTTGCCTTTAAGA-
1 CCAATATCGCTGGCCTTGAATCAGCATATTGGCA------C---AA-AC
* * * *
43200 CCAATGTCGCTGGCCTTGGATCAGCATATTGGCATAAGC
1 CCAATATCGCTGGCCTTGAATCAGCATATTGGCACAAAC
43239 CCAATATCGCTGGCCTTGAATCAGCATATTGGCAC
1 CCAATATCGCTGGCCTTGAATCAGCATATTGGCAC
43274 CTCCATCTTT
Statistics
Matches: 229, Mismatches: 36, Indels: 62
0.70 0.11 0.19
Matches are distributed among these distances:
39 127 0.55
40 1 0.00
42 1 0.00
45 1 0.00
47 2 0.01
48 96 0.42
49 1 0.00
ACGTcount: A:0.27, C:0.27, G:0.19, T:0.26
Consensus pattern (39 bp):
CCAATATCGCTGGCCTTGAATCAGCATATTGGCACAAAC
Found at i:43048 original size:87 final size:87
Alignment explanation
Indices: 42891--43321 Score: 655
Period size: 87 Copynumber: 4.9 Consensus size: 87
42881 CATCTTGAGT
* * * *
42891 CCAATATCGCTGGCCTAGAATCAACATATTGGCACCTTGTCTTTAAGACCAATATTGCTGGCCTT
1 CCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTGTCTTTAAGACCAATGTCGCTGGCCTT
** *
42956 GAATCAGCACATTGGCGCAAAC
66 GAATCAGCACATTGGCATAAGC
* *
42978 CCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTGTCTCTAAGACCAATGTCGCTGACCTT
1 CCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTGTCTTTAAGACCAATGTCGCTGGCCTT
* *
43043 AAATCAACACATTGGCATAAGC
66 GAATCAGCACATTGGCATAAGC
* *
43065 CCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTATCTCTAAGACCAATGTCGCTGGCCTT
1 CCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTGTCTTTAAGACCAATGTCGCTGGCCTT
43130 GAATCAGCACATTGGCATAAGC
66 GAATCAGCACATTGGCATAAGC
* *
43152 CCAATATCACTGGCCTTGAATCAGCATATTGGCACCTTGCCTTTAAGACCAATGTCGCTGGCCTT
1 CCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTGTCTTTAAGACCAATGTCGCTGGCCTT
* *
43217 GGATCAGCATATTGGCATAAGC
66 GAATCAGCACATTGGCATAAGC
** * *
43239 CCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTCCATCTTTAAGACCGATGTCGTTGGCCT
1 CCAATATCGCTGGCCTTGAATCAGCATATTGGCACCT-TGTCTTTAAGACCAATGTCGCTGGCCT
*
43304 TGAATTAGCACATTGGCA
65 TGAATCAGCACATTGGCA
43322 CTGTAACCAT
Statistics
Matches: 313, Mismatches: 30, Indels: 1
0.91 0.09 0.00
Matches are distributed among these distances:
87 276 0.88
88 37 0.12
ACGTcount: A:0.27, C:0.27, G:0.19, T:0.27
Consensus pattern (87 bp):
CCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTGTCTTTAAGACCAATGTCGCTGGCCTT
GAATCAGCACATTGGCATAAGC
Found at i:43468 original size:98 final size:98
Alignment explanation
Indices: 43239--43616 Score: 334
Period size: 101 Copynumber: 3.8 Consensus size: 98
43229 TGGCATAAGC
* * * * * * *
43239 CCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTCCATCTTTAAGACCGATGTCGTTGGCCT
1 CCAATGTCGCTGGCCTTGAATCAGCACATTGGCATCTTCATCTTTAAGTCCGATATCGCTGGCCT
* * ** **
43304 TGAATTAGCACATTGGCACTGTAACCATCTTTAAGT
66 TGAATCAGCATATTGGCA-TGT--TTATCTTTAAAA
* * * * *
43340 CCAATGTTGCCGACCTTGAATCAGCACATTGGCATCTTCATCTTTAAGTCCGGTATCGCTAGCCT
1 CCAATGTCGCTGGCCTTGAATCAGCACATTGGCATCTTCATCTTTAAGTCCGATATCGCTGGCCT
43405 TGAATCAGCATATTGGCATGTTTATCTTTAAAA
66 TGAATCAGCATATTGGCATGTTTATCTTTAAAA
* * * * *
43438 CCAATGTCGTTGGCCTTGAATCAGCACATTGGCATCTTCATATTTAAGTCCAAAATCACTGGCCT
1 CCAATGTCGCTGGCCTTGAATCAGCACATTGGCATCTTCATCTTTAAGTCCGATATCGCTGGCCT
* * * *
43503 TAAATCAGCATATTGGCATCTTTAACATTCCT-AAG
66 TGAATCAGCATATTGGCATGTTTATC-TT--TAAAA
* ** * * *
43538 CCTAATGTCACTGGCCTTGTCTCAGCATATTGGCA--TTCTTCTTCAAGT-CGA-ACGTCGCTGG
1 CC-AATGTCGCTGGCCTTGAATCAGCACATTGGCATCTTCATCTTTAAGTCCGATA--TCGCTGG
*
43599 CCATGAATCAGCATATTG
63 CCTTGAATCAGCATATTG
43617 TCATTCTTCG
Statistics
Matches: 227, Mismatches: 44, Indels: 14
0.80 0.15 0.05
Matches are distributed among these distances:
97 1 0.00
98 88 0.39
99 34 0.15
100 7 0.03
101 97 0.43
ACGTcount: A:0.25, C:0.25, G:0.18, T:0.32
Consensus pattern (98 bp):
CCAATGTCGCTGGCCTTGAATCAGCACATTGGCATCTTCATCTTTAAGTCCGATATCGCTGGCCT
TGAATCAGCATATTGGCATGTTTATCTTTAAAA
Found at i:43555 original size:150 final size:147
Alignment explanation
Indices: 43234--43573 Score: 360
Period size: 150 Copynumber: 2.3 Consensus size: 147
43224 CATATTGGCA
* * *
43234 TAAGCCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTCCATCTTTAAGACCGATGTCGTT
1 TAAG-CCAATATCGCTGGCCTTGAATCAGCATATTGGCATCTCCATCTTTAAAACCAATGTCGTT
* * ** ** *
43299 GGCCTTGAATTAGCACATTGGCACTGTAACCATCTTTAAGTCCAATGTTGCCGACCTTGAATCAG
65 GGCCTTGAATCAGCACATTGGCACTGT-A-CATATTTAAGTCCAAAATCACCGACCTTAAATCAG
*
43364 CACATTGGCATCTTCATCTT
128 CACATTGGCATCTTCAACTT
** * * **
43384 TAAGTCCGGTATCGCTAGCCTTGAATCAGCATATTGGCATGTTTATCTTTAAAACCAATGTCGTT
1 TAAG-CCAATATCGCTGGCCTTGAATCAGCATATTGGCATCTCCATCTTTAAAACCAATGTCGTT
* *
43449 GGCCTTGAATCAGCACATTGGCATCT-T-CATATTTAAGTCCAAAATCACTGGCCTTAAATCAGC
65 GGCCTTGAATCAGCACATTGGCA-CTGTACATATTTAAGTCCAAAATCACCGACCTTAAATCAGC
* *
43512 ATATTGGCATCTTTAACATT
129 ACATTGGCATCTTCAAC-TT
* * **
43532 CCTAAGCCTAATGTCACTGGCCTTGTCTCAGCATATTGGCAT
1 --TAAGCC-AATATCGCTGGCCTTGAATCAGCATATTGGCAT
43574 TCTTCTTCAA
Statistics
Matches: 156, Mismatches: 29, Indels: 10
0.80 0.15 0.05
Matches are distributed among these distances:
147 42 0.27
148 2 0.01
149 2 0.01
150 108 0.69
151 2 0.01
ACGTcount: A:0.26, C:0.25, G:0.17, T:0.32
Consensus pattern (147 bp):
TAAGCCAATATCGCTGGCCTTGAATCAGCATATTGGCATCTCCATCTTTAAAACCAATGTCGTTG
GCCTTGAATCAGCACATTGGCACTGTACATATTTAAGTCCAAAATCACCGACCTTAAATCAGCAC
ATTGGCATCTTCAACTT
Found at i:49594 original size:52 final size:51
Alignment explanation
Indices: 49509--49632 Score: 205
Period size: 52 Copynumber: 2.4 Consensus size: 51
49499 ATATGAAAAG
* *
49509 TTGCTTGCATGTATCGATACATTTAATAGTGTATCGATACATCTGGGCAAA
1 TTGCCTGCATGTATCGATACATTTAATAATGTATCGATACATCTGGGCAAA
49560 TTTGCCTGCATGTATCGATACATTTTAA-AATGTATCGATACATCTGGGCAAA
1 -TTGCCTGCATGTATCGATACA-TTTAATAATGTATCGATACATCTGGGCAAA
49612 TTGCCTGCATGTATCGATACA
1 TTGCCTGCATGTATCGATACA
49633 AAGATCAGTG
Statistics
Matches: 69, Mismatches: 2, Indels: 3
0.93 0.03 0.04
Matches are distributed among these distances:
51 21 0.30
52 43 0.62
53 5 0.07
ACGTcount: A:0.29, C:0.18, G:0.19, T:0.35
Consensus pattern (51 bp):
TTGCCTGCATGTATCGATACATTTAATAATGTATCGATACATCTGGGCAAA
Found at i:49645 original size:51 final size:50
Alignment explanation
Indices: 49509--49652 Score: 177
Period size: 52 Copynumber: 2.8 Consensus size: 50
49499 ATATGAAAAG
* *
49509 TTGCTTGCATGTATCGATACATTTAATAGTGTATCGATACATCTGGGCAAAT
1 TTGCCTGCATGTATCGATACA--AAATAGTGTATCGATACATCTGGGCAAAT
49561 TTGCCTGCATGTATCGATACATTTTAAA-A-TGTATCGATACATCTGGGCAAA-
1 TTGCCTGCATGTATCGATACA----AAATAGTGTATCGATACATCTGGGCAAAT
49612 TTGCCTGCATGTATCGATACAAAGATCAGTGTATCGATACA
1 TTGCCTGCATGTATCGATACAAA-AT-AGTGTATCGATACA
49653 ATGTATCGAT
Statistics
Matches: 84, Mismatches: 2, Indels: 13
0.85 0.02 0.13
Matches are distributed among these distances:
47 2 0.02
48 1 0.01
50 1 0.01
51 33 0.39
52 42 0.50
53 1 0.01
54 4 0.05
ACGTcount: A:0.31, C:0.17, G:0.19, T:0.33
Consensus pattern (50 bp):
TTGCCTGCATGTATCGATACAAAATAGTGTATCGATACATCTGGGCAAAT
Found at i:49659 original size:13 final size:13
Alignment explanation
Indices: 49641--49665 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
49631 CAAAGATCAG
49641 TGTATCGATACAA
1 TGTATCGATACAA
49654 TGTATCGATACA
1 TGTATCGATACA
49666 TGTGAGTAAT
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:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:49747 original size:33 final size:33
Alignment explanation
Indices: 49705--49774 Score: 104
Period size: 33 Copynumber: 2.1 Consensus size: 33
49695 GGCAGTAGCT
49705 TACATTGTATCGATACAAAAAAATATGTATCGA
1 TACATTGTATCGATACAAAAAAATATGTATCGA
* ***
49738 TACATTGTATCGATACAACATTTTATGTATCGA
1 TACATTGTATCGATACAAAAAAATATGTATCGA
49771 TACA
1 TACA
49775 AATCGTTGAA
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
33 33 1.00
ACGTcount: A:0.40, C:0.14, G:0.11, T:0.34
Consensus pattern (33 bp):
TACATTGTATCGATACAAAAAAATATGTATCGA
Found at i:49748 original size:13 final size:13
Alignment explanation
Indices: 49730--49754 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
49720 CAAAAAAATA
49730 TGTATCGATACAT
1 TGTATCGATACAT
49743 TGTATCGATACA
1 TGTATCGATACA
49755 ACATTTTATG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:50527 original size:12 final size:12
Alignment explanation
Indices: 50510--50534 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
50500 AGAGTGTTTG
50510 AAAAAAAAAATT
1 AAAAAAAAAATT
50522 AAAAAAAAAATT
1 AAAAAAAAAATT
50534 A
1 A
50535 TCCAAATGTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.84, C:0.00, G:0.00, T:0.16
Consensus pattern (12 bp):
AAAAAAAAAATT
Found at i:50565 original size:21 final size:21
Alignment explanation
Indices: 50539--50595 Score: 105
Period size: 21 Copynumber: 2.7 Consensus size: 21
50529 AAATTATCCA
50539 AATGTATCGATACATTTGTAG
1 AATGTATCGATACATTTGTAG
*
50560 AATGTATCGATACATTTGTGG
1 AATGTATCGATACATTTGTAG
50581 AATGTATCGATACAT
1 AATGTATCGATACAT
50596 CCTACAAATG
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 35 1.00
ACGTcount: A:0.33, C:0.11, G:0.19, T:0.37
Consensus pattern (21 bp):
AATGTATCGATACATTTGTAG
Found at i:50675 original size:19 final size:19
Alignment explanation
Indices: 50651--50718 Score: 85
Period size: 19 Copynumber: 3.9 Consensus size: 19
50641 AATTCAACAA
50651 TTTGTATCGATACATAAGT
1 TTTGTATCGATACATAAGT
50670 TTTGTATCGATAC--AA--
1 TTTGTATCGATACATAAGT
50685 --TGTATCGATACATAAGT
1 TTTGTATCGATACATAAGT
*
50702 ATTGTATCGATACATAA
1 TTTGTATCGATACATAA
50719 TTAGCTACTG
Statistics
Matches: 43, Mismatches: 0, Indels: 12
0.78 0.00 0.22
Matches are distributed among these distances:
13 11 0.26
15 2 0.05
17 2 0.05
19 28 0.65
ACGTcount: A:0.35, C:0.12, G:0.15, T:0.38
Consensus pattern (19 bp):
TTTGTATCGATACATAAGT
Found at i:50690 original size:13 final size:13
Alignment explanation
Indices: 50672--50696 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
50662 ACATAAGTTT
50672 TGTATCGATACAA
1 TGTATCGATACAA
50685 TGTATCGATACA
1 TGTATCGATACA
50697 TAAGTATTGT
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:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:50694 original size:32 final size:32
Alignment explanation
Indices: 50653--50715 Score: 117
Period size: 32 Copynumber: 2.0 Consensus size: 32
50643 TTCAACAATT
*
50653 TGTATCGATACATAAGTTTTGTATCGATACAA
1 TGTATCGATACATAAGTATTGTATCGATACAA
50685 TGTATCGATACATAAGTATTGTATCGATACA
1 TGTATCGATACATAAGTATTGTATCGATACA
50716 TAATTAGCTA
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 30 1.00
ACGTcount: A:0.35, C:0.13, G:0.16, T:0.37
Consensus pattern (32 bp):
TGTATCGATACATAAGTATTGTATCGATACAA
Found at i:50776 original size:13 final size:13
Alignment explanation
Indices: 50758--50783 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
50748 CATTTTTCTG
50758 TGTATCGATACAT
1 TGTATCGATACAT
50771 TGTATCGATACAT
1 TGTATCGATACAT
50784 GGATCTTTGT
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:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:50780 original size:33 final size:33
Alignment explanation
Indices: 50738--50804 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
50728 GCCAAGGAAA
***
50738 TGTATCGATACATTTTTCTGTGTATCGATACAT
1 TGTATCGATACATGGATCTGTGTATCGATACAT
*
50771 TGTATCGATACATGGATCTTTGTATCGATACAT
1 TGTATCGATACATGGATCTGTGTATCGATACAT
50804 T
1 T
50805 TGGAAATTTT
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.25, C:0.15, G:0.16, T:0.43
Consensus pattern (33 bp):
TGTATCGATACATGGATCTGTGTATCGATACAT
Found at i:53273 original size:27 final size:28
Alignment explanation
Indices: 53243--53318 Score: 109
Period size: 27 Copynumber: 2.8 Consensus size: 28
53233 TTTCTTCACA
53243 ATCGGGGATACTCCAACCCCGTTA-ATC
1 ATCGGGGATACTCCAACCCCGTTATATC
*
53270 ATCGGGGATACTCCAACCCCGTTATTTC
1 ATCGGGGATACTCCAACCCCGTTATATC
***
53298 CGAGGGGATACTCCAACCCCG
1 ATCGGGGATACTCCAACCCCG
53319 GTTTTATCGC
Statistics
Matches: 44, Mismatches: 4, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
27 24 0.55
28 20 0.45
ACGTcount: A:0.24, C:0.34, G:0.21, T:0.21
Consensus pattern (28 bp):
ATCGGGGATACTCCAACCCCGTTATATC
Found at i:53386 original size:52 final size:52
Alignment explanation
Indices: 53301--53468 Score: 166
Period size: 52 Copynumber: 3.2 Consensus size: 52
53291 TTATTTCCGA
* *
53301 GGGGATACTCCAACCCCGGTTTTA--TCGCTAAAACACTAATTTTTCCACAATC
1 GGGGATACTCCAA-CCCGGTTTTATTTC-CAAAAACACCAATTTTTCCACAATC
* * **
53353 GGGGATACTCCAATCCCGGTTTTATTTTC-AAAACGCCAA-TTTTCCTTTAATC
1 GGGGATACTCCAA-CCCGGTTTTATTTCCAAAAACACCAATTTTTCC-ACAATC
* * *
53405 GGGGATACTCCAACTCTGATTTTATTTCCAAAAATACCAATTTTT-CACAATC
1 GGGGATACTCCAAC-CCGGTTTTATTTCCAAAAACACCAATTTTTCCACAATC
*
53457 GAGGATACTCCA
1 GGGGATACTCCA
53469 CCTCGTTATT
Statistics
Matches: 96, Mismatches: 14, Indels: 12
0.79 0.11 0.10
Matches are distributed among these distances:
51 7 0.07
52 74 0.77
53 10 0.10
54 5 0.05
ACGTcount: A:0.29, C:0.26, G:0.13, T:0.32
Consensus pattern (52 bp):
GGGGATACTCCAACCCGGTTTTATTTCCAAAAACACCAATTTTTCCACAATC
Found at i:53489 original size:27 final size:27
Alignment explanation
Indices: 53454--53523 Score: 77
Period size: 28 Copynumber: 2.6 Consensus size: 27
53444 ATTTTTCACA
* * *
53454 ATCGAGGATACTCCACCTCGTTATTTC
1 ATCGGGGATACTCCACCCCGTTACTTC
53481 ATCGGGGATACTCCAACCCCGTTACTTC
1 ATCGGGGATACTCC-ACCCCGTTACTTC
***
53509 CGAGGGGATACTCCA
1 ATCGGGGATACTCCA
53524 ATCCCGATTT
Statistics
Matches: 36, Mismatches: 6, Indels: 2
0.82 0.14 0.05
Matches are distributed among these distances:
27 14 0.39
28 22 0.61
ACGTcount: A:0.23, C:0.31, G:0.20, T:0.26
Consensus pattern (27 bp):
ATCGGGGATACTCCACCCCGTTACTTC
Found at i:53503 original size:211 final size:212
Alignment explanation
Indices: 53132--53534 Score: 616
Period size: 211 Copynumber: 1.9 Consensus size: 212
53122 TTCTCAATTC
* *
53132 TCCACAATCGGGGATATTCCAACTCCGATTTTATTTTCAAAACACTAATTTTCTATAATCGGGAA
1 TCCACAATCGGGGATACTCCAACTCCGATTTTATTTTCAAAACACCAATTTTCTATAATCGGGAA
* * *
53197 TACTCTAACTCCGATTTTATTTCCAAAAAATGCCAATTTCTTCACAATCGGGGATACTCCAACCC
66 TACTCCAACTCCGATTTTATTTCCAAAAAATACCAATTTCTTCACAATCGAGGATACTCCAACCC
* *
53262 CGTTAATCATCGGGGATACTCCAACCCCGTTATTTCCGAGGGGATACTCCAACCCCGGTTTTATC
131 CGTTAATCATCGGGGATACTCCAACCCCGTTACTTCCGAGGGGATACTCCAACCCCGATTTTATC
53327 GCTAAAACACTAATTTT
196 GCTAAAACACTAATTTT
* * *
53344 TCCACAATCGGGGATACTCCAA-TCCCGGTTTTATTTTCAAAACGCCAATTTTCCTTTAATCGGG
1 TCCACAATCGGGGATACTCCAACT-CCGATTTTATTTTCAAAACACCAATTTT-CTATAATCGGG
* *
53408 GATACTCCAACTCTGATTTTATTTCC-AAAAATACCAATTT-TTCACAATCGAGGATACTCC-AC
64 AATACTCCAACTCCGATTTTATTTCCAAAAAATACCAATTTCTTCACAATCGAGGATACTCCAAC
* * *
53470 CTCGTTATTTCATCGGGGATACTCCAACCCCGTTACTTCCGAGGGGATACTCCAATCCCGATTTT
129 CCCGTTA-ATCATCGGGGATACTCCAACCCCGTTACTTCCGAGGGGATACTCCAACCCCGATTTT
53535 TTTTTTCTTC
Statistics
Matches: 173, Mismatches: 15, Indels: 7
0.89 0.08 0.04
Matches are distributed among these distances:
210 8 0.05
211 73 0.42
212 59 0.34
213 33 0.19
ACGTcount: A:0.28, C:0.27, G:0.14, T:0.32
Consensus pattern (212 bp):
TCCACAATCGGGGATACTCCAACTCCGATTTTATTTTCAAAACACCAATTTTCTATAATCGGGAA
TACTCCAACTCCGATTTTATTTCCAAAAAATACCAATTTCTTCACAATCGAGGATACTCCAACCC
CGTTAATCATCGGGGATACTCCAACCCCGTTACTTCCGAGGGGATACTCCAACCCCGATTTTATC
GCTAAAACACTAATTTT
Done.