Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01002078.1 Hibiscus syriacus cultivar Beakdansim tig00004248_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: 64649
ACGTcount: A:0.32, C:0.19, G:0.17, T:0.32
Found at i:10994 original size:147 final size:147
Alignment explanation
Indices: 10727--11020 Score: 570
Period size: 147 Copynumber: 2.0 Consensus size: 147
10717 ACTGCGAGAC
*
10727 TGTTTCGACCCAATATTAACTGACACAGAGGAGTCAGCTACCCCGGTGTACTCACGATCAAACCT
1 TGTTTCGACCCAATATTAACTGACACAGAGGAGTCACCTACCCCGGTGTACTCACGATCAAACCT
10792 GTGATAGAACTTCTGAACCACATGACCAAATTTTCCACACAGTTGACACTGAGGTCGATTAGAAT
66 GTGATAGAACTTCTGAACCACATGACCAAATTTTCCACACAGTTGACACTGAGGTCGATTAGAAT
10857 TATTAAAACGACCACGG
131 TATTAAAACGACCACGG
*
10874 TGTTTCGACCCATTATTAACTGACACAGAGGAGTCACCTACCCCGGTGTACTCACGATCAAACCT
1 TGTTTCGACCCAATATTAACTGACACAGAGGAGTCACCTACCCCGGTGTACTCACGATCAAACCT
10939 GTGATAGAACTTCTGAACCACATGACCAAATTTTCCACACAGTTGACACTGAGGTCGATTAGAAT
66 GTGATAGAACTTCTGAACCACATGACCAAATTTTCCACACAGTTGACACTGAGGTCGATTAGAAT
11004 TATTAAAACGACCACGG
131 TATTAAAACGACCACGG
11021 CCTCTACCAC
Statistics
Matches: 145, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
147 145 1.00
ACGTcount: A:0.32, C:0.26, G:0.18, T:0.24
Consensus pattern (147 bp):
TGTTTCGACCCAATATTAACTGACACAGAGGAGTCACCTACCCCGGTGTACTCACGATCAAACCT
GTGATAGAACTTCTGAACCACATGACCAAATTTTCCACACAGTTGACACTGAGGTCGATTAGAAT
TATTAAAACGACCACGG
Found at i:16925 original size:24 final size:24
Alignment explanation
Indices: 16897--16945 Score: 98
Period size: 24 Copynumber: 2.0 Consensus size: 24
16887 AGCAGGAAAA
16897 TCAGGCAGTAAAATGTCAAAAATT
1 TCAGGCAGTAAAATGTCAAAAATT
16921 TCAGGCAGTAAAATGTCAAAAATT
1 TCAGGCAGTAAAATGTCAAAAATT
16945 T
1 T
16946 TCGAGTGTTT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.45, C:0.12, G:0.16, T:0.27
Consensus pattern (24 bp):
TCAGGCAGTAAAATGTCAAAAATT
Found at i:19792 original size:12 final size:12
Alignment explanation
Indices: 19762--19792 Score: 53
Period size: 12 Copynumber: 2.6 Consensus size: 12
19752 TATATGGTAT
19762 AATTTTTCAAAG
1 AATTTTTCAAAG
*
19774 AAATTTTCAAAG
1 AATTTTTCAAAG
19786 AATTTTT
1 AATTTTT
19793 ATTATAAGAT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.42, C:0.06, G:0.06, T:0.45
Consensus pattern (12 bp):
AATTTTTCAAAG
Found at i:25210 original size:23 final size:23
Alignment explanation
Indices: 25175--25247 Score: 101
Period size: 23 Copynumber: 3.2 Consensus size: 23
25165 ATACTTTACA
*
25175 ATATAAGCACTACCTATTACATT
1 ATATAAGCGCTACCTATTACATT
* *
25198 ATATAAACGCTACTTATTACATT
1 ATATAAGCGCTACCTATTACATT
* *
25221 ATATAAGCGATACCTATTACATC
1 ATATAAGCGCTACCTATTACATT
25244 ATAT
1 ATAT
25248 TTTTACCTAT
Statistics
Matches: 43, Mismatches: 7, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 43 1.00
ACGTcount: A:0.40, C:0.19, G:0.05, T:0.36
Consensus pattern (23 bp):
ATATAAGCGCTACCTATTACATT
Found at i:25697 original size:21 final size:21
Alignment explanation
Indices: 25660--25729 Score: 97
Period size: 21 Copynumber: 3.3 Consensus size: 21
25650 GATAGATACT
* *
25660 TTACA-TATAAGCACTACCTA
1 TTACATTATAAACGCTACCTA
25680 TTACATTATAAACGCTACCTA
1 TTACATTATAAACGCTACCTA
25701 TTACATTATATAAGCGCTACCTA
1 TTACATTATA-AA-CGCTACCTA
25724 TTACAT
1 TTACAT
25730 CATATTTTTA
Statistics
Matches: 45, Mismatches: 2, Indels: 3
0.90 0.04 0.06
Matches are distributed among these distances:
20 5 0.11
21 23 0.51
22 2 0.04
23 15 0.33
ACGTcount: A:0.37, C:0.23, G:0.06, T:0.34
Consensus pattern (21 bp):
TTACATTATAAACGCTACCTA
Found at i:25718 original size:23 final size:23
Alignment explanation
Indices: 25664--25734 Score: 110
Period size: 23 Copynumber: 3.2 Consensus size: 23
25654 GATACTTTAC
*
25664 ATATAAGCACTACCTATTACATT
1 ATATAAGCGCTACCTATTACATT
25687 ATA-AA-CGCTACCTATTACATT
1 ATATAAGCGCTACCTATTACATT
*
25708 ATATAAGCGCTACCTATTACATC
1 ATATAAGCGCTACCTATTACATT
25731 ATAT
1 ATAT
25735 TTTTACTTAT
Statistics
Matches: 44, Mismatches: 2, Indels: 4
0.88 0.04 0.08
Matches are distributed among these distances:
21 18 0.41
22 4 0.09
23 22 0.50
ACGTcount: A:0.38, C:0.23, G:0.06, T:0.34
Consensus pattern (23 bp):
ATATAAGCGCTACCTATTACATT
Found at i:26186 original size:23 final size:23
Alignment explanation
Indices: 26151--26223 Score: 119
Period size: 23 Copynumber: 3.2 Consensus size: 23
26141 ATACTTTACA
*
26151 ATATAAGCACTACCTATTACATT
1 ATATAAGCGCTACCTATTACATT
*
26174 ATATAAACGCTACCTATTACATT
1 ATATAAGCGCTACCTATTACATT
*
26197 ATATAAGCGCTACCTATTACATC
1 ATATAAGCGCTACCTATTACATT
26220 ATAT
1 ATAT
26224 TTTTACCTAT
Statistics
Matches: 46, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
23 46 1.00
ACGTcount: A:0.38, C:0.22, G:0.05, T:0.34
Consensus pattern (23 bp):
ATATAAGCGCTACCTATTACATT
Found at i:26384 original size:489 final size:489
Alignment explanation
Indices: 24773--26569 Score: 3179
Period size: 489 Copynumber: 3.7 Consensus size: 489
24763 TTATAATATG
* * **
24773 TTGAAAGTGTCTATATTTTTTTATAAAAAATATCGATACTTTTTTTAAAGTTATGTAATTTATGT
1 TTGAAAGTGTCCATA-CTTTTTATAAAAAGGATCGATACTTTTTTTAAAGTTATGTAATTTATGT
* *
24838 TTCAA-TTTTTTAATAGTGTTTCATGTTTTCCACCTACAATATTAATTTAATAATTTTATTTGTA
65 TTCAATTTTTTTAATAGTGTTTCATGTTTTCCACCTACAATATTAATTTAATAATTTCATTTGCA
* *
24902 CAAAAAATTATTTGATTGTTTTTATATTTTATAAAATAATATTTAAAATTTAAATTCAACAATAT
130 CAAAAAATTATTTGATTGTTTTGATATTTTATAAAATAATATTTAAAATTTAAATTTAACAATAT
* * *
24967 TAATCAAAGATAATAATAAATATGTAATATATATGTTTATTGTTTTTAATTTAATGATAATATAT
195 TAACCAAAGATAATAATAAATATGTAATATATATGTTTATTATTTTTAATTTAATAATAATATAT
* ** * *
25032 ACCGTAACATAAAAAATAAATCATTAGATACATATAATTACTAAATTGATATCTTAAAACTCACT
260 ACCGTAACGTAAAAAATAAATCATTAGACGCCTATAATTACTAAATTAATATCTTAAAACTCACT
* * *
25097 CAAAAGATAATCTTAAATTAATGTTTTCCACAATGAAATAAGTATGGACACTTTTATAAAAATGA
325 CAAAAGATAACCTTAAATTAATGTTTTCCACAGTGAAAAAAGTATGGACACTTTTATAAAAATGA
*
25162 TAGATACTTTACAATATAAGCACTACCTATTACATTATATAAACGCTACTTATTACATTATATAA
390 TAGATACTTTACAATATAAGCACTACCTATTACATTATATAAACGCTACCTATTACATTATATAA
*
25227 GCGATACCTATTACATCATATTTTTACCTATTATA
455 GCGCTACCTATTACATCATATTTTTACCTATTATA
* *
25262 TTGAAAGTGTTCATACTTTTTATAAAAATGATCGATACTTTTTTTAAAGTTATGTAATTTATGTT
1 TTGAAAGTGTCCATACTTTTTATAAAAAGGATCGATACTTTTTTTAAAGTTATGTAATTTATGTT
* * *
25327 TCATTTTTTTTTAATAGTGTTTCATGTTTTCCACCTACAATATTAATTTAATAATTTCACTTGTA
66 TCA-ATTTTTTTAATAGTGTTTCATGTTTTCCACCTACAATATTAATTTAATAATTTCATTTGCA
25392 CAAAAAATTATTTGATTGTTTTGATATTTTATAAAATAATATTTAAAATTTAAATTTAACAATAT
130 CAAAAAATTATTTGATTGTTTTGATATTTTATAAAATAATATTTAAAATTTAAATTTAACAATAT
25457 TAACCAAAGATAATAATAAATATGTAATATATATGTTTATTATTTTTAATTTAATAATAATATAT
195 TAACCAAAGATAATAATAAATATGTAATATATATGTTTATTATTTTTAATTTAATAATAATATAT
* * *
25522 ATCGTAACGTAAAAAATAAATCATTAGACGCCTATAATCACTAAATTAATATCTTAAAACTTACT
260 ACCGTAACGTAAAAAATAAATCATTAGACGCCTATAATTACTAAATTAATATCTTAAAACTCACT
*
25587 CAAAAGATAACCTTAAATTAATGTTTTCCACAGTGAAAAAAGTATGGACACTTTTATAAAAAGGA
325 CAAAAGATAACCTTAAATTAATGTTTTCCACAGTGAAAAAAGTATGGACACTTTTATAAAAATGA
25652 TAGATACTTTAC-ATATAAGCACTACCTATTACA-T-TATAAACGCTACCTATTACATTATATAA
390 TAGATACTTTACAATATAAGCACTACCTATTACATTATATAAACGCTACCTATTACATTATATAA
*
25714 GCGCTACCTATTACATCATATTTTTACTTATTATA
455 GCGCTACCTATTACATCATATTTTTACCTATTATA
25749 TTGAAAGTGTCCATACTTTTTATAAAAAGGATCGATACTTTTTTTAAAGTTATGTAATTTATGTT
1 TTGAAAGTGTCCATACTTTTTATAAAAAGGATCGATACTTTTTTTAAAGTTATGTAATTTATGTT
25814 TCAATTTTTTTAATAGTGTTTCATGTTTTCCACCTACAATATTAATTTAATAATTTCATTTGCAC
66 TCAATTTTTTTAATAGTGTTTCATGTTTTCCACCTACAATATTAATTTAATAATTTCATTTGCAC
*
25879 AAAAAATTATTTGATTGTTTTGATATTTTATAAAATAATATTTAGAATTTAAATTTAACAATATT
131 AAAAAATTATTTGATTGTTTTGATATTTTATAAAATAATATTTAAAATTTAAATTTAACAATATT
*
25944 AACTAAAGATAATAATAAATATGTAATATATATGTTTATTATTTTTAATTTAATAATAATATATA
196 AACCAAAGATAATAATAAATATGTAATATATATGTTTATTATTTTTAATTTAATAATAATATATA
* *
26009 TCGTAACGTAAAAAATAAATCATTAGACGCCTATAATTACTACATTAATATCTTAAAACTCACTC
261 CCGTAACGTAAAAAATAAATCATTAGACGCCTATAATTACTAAATTAATATCTTAAAACTCACTC
26074 AAAAGATAACCTTAAATTAATGTTTTCCACAGTGAAAAAAGTATGGACACTTTTATAAAAATGAT
326 AAAAGATAACCTTAAATTAATGTTTTCCACAGTGAAAAAAGTATGGACACTTTTATAAAAATGAT
26139 AGATACTTTACAATATAAGCACTACCTATTACATTATATAAACGCTACCTATTACATTATATAAG
391 AGATACTTTACAATATAAGCACTACCTATTACATTATATAAACGCTACCTATTACATTATATAAG
26204 CGCTACCTATTACATCATATTTTTACCTATTATA
456 CGCTACCTATTACATCATATTTTTACCTATTATA
26238 TTGAAAGTGTCCATACTTTTTATAAAAAGGATCGATACTTTTTTTAAAGTTATGTAATTTATGTT
1 TTGAAAGTGTCCATACTTTTTATAAAAAGGATCGATACTTTTTTTAAAGTTATGTAATTTATGTT
* *
26303 TCAATTCTTTTAATAGTGTTTCATGTTTTCCACCTACAATATTAATTTAATAATTTCATTTACAC
66 TCAATTTTTTTAATAGTGTTTCATGTTTTCCACCTACAATATTAATTTAATAATTTCATTTGCAC
* **
26368 AAAAAATTATTTGATTGTTTTGATATTTTATAAAATATTATTTAGTATTTAAATTTAACAATATT
131 AAAAAATTATTTGATTGTTTTGATATTTTATAAAATAATATTTAAAATTTAAATTTAACAATATT
*
26433 AACCAAAGATAATAATAAATATGTAATATATATGTTTATTATTTTTAATTTAGTAATAATATATA
196 AACCAAAGATAATAATAAATATGTAATATATATGTTTATTATTTTTAATTTAATAATAATATATA
26498 CCGTAACGTAAAAAATAAATCATTAGACGCCTATAATTACTAAATTAATATCTTAAAACTCACTC
261 CCGTAACGTAAAAAATAAATCATTAGACGCCTATAATTACTAAATTAATATCTTAAAACTCACTC
26563 AAAAGAT
326 AAAAGAT
26570 GTACATACCT
Statistics
Matches: 1255, Mismatches: 48, Indels: 10
0.96 0.04 0.01
Matches are distributed among these distances:
486 324 0.26
487 147 0.12
488 52 0.04
489 420 0.33
490 312 0.25
ACGTcount: A:0.40, C:0.11, G:0.07, T:0.42
Consensus pattern (489 bp):
TTGAAAGTGTCCATACTTTTTATAAAAAGGATCGATACTTTTTTTAAAGTTATGTAATTTATGTT
TCAATTTTTTTAATAGTGTTTCATGTTTTCCACCTACAATATTAATTTAATAATTTCATTTGCAC
AAAAAATTATTTGATTGTTTTGATATTTTATAAAATAATATTTAAAATTTAAATTTAACAATATT
AACCAAAGATAATAATAAATATGTAATATATATGTTTATTATTTTTAATTTAATAATAATATATA
CCGTAACGTAAAAAATAAATCATTAGACGCCTATAATTACTAAATTAATATCTTAAAACTCACTC
AAAAGATAACCTTAAATTAATGTTTTCCACAGTGAAAAAAGTATGGACACTTTTATAAAAATGAT
AGATACTTTACAATATAAGCACTACCTATTACATTATATAAACGCTACCTATTACATTATATAAG
CGCTACCTATTACATCATATTTTTACCTATTATA
Found at i:26597 original size:25 final size:25
Alignment explanation
Indices: 26569--26660 Score: 100
Period size: 25 Copynumber: 3.8 Consensus size: 25
26559 ACTCAAAAGA
26569 TGTACATACCTAAATATGTAGTTAT
1 TGTACATACCTAAATATGTAGTTAT
* *
26594 TGTACATACCTAAAT-T-TAATGAT
1 TGTACATACCTAAATATGTAGTTAT
** * * *
26617 AATATATA-CTATATTTGTAGTTAT
1 TGTACATACCTAAATATGTAGTTAT
26641 TGTACATACCTAAATATGTA
1 TGTACATACCTAAATATGTA
26661 CTGCGAATTT
Statistics
Matches: 51, Mismatches: 13, Indels: 6
0.73 0.19 0.09
Matches are distributed among these distances:
22 5 0.10
23 11 0.22
24 11 0.22
25 24 0.47
ACGTcount: A:0.38, C:0.11, G:0.10, T:0.41
Consensus pattern (25 bp):
TGTACATACCTAAATATGTAGTTAT
Found at i:29383 original size:183 final size:183
Alignment explanation
Indices: 29075--30195 Score: 1955
Period size: 183 Copynumber: 6.1 Consensus size: 183
29065 TACTTAAAAT
*
29075 TACCGACACAATATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCTCATAAAACCAGTATA
1 TACCGACACAATATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCTCATAAAACCGGTATA
29140 TTTATACCGGTTATATTACAAAATTATCTATTACATTATAATTCTGGGTTCCGATGTGTAAATGT
66 TTTATACCGGTTATATTACAAAATTATCTATTACATTATAATTCTGGGTTCCGATGTGTAAATGT
* *
29205 CGACACTTTTTGACAAGGTATAGACATATTTTTCTTCCAATCTGGACATAAAG
131 CGACACTTTTTGACAAGGTATCGACACATTTTTCTTCCAATCTGGACATAAAG
*
29258 TACCGACACAATATTAAAAAGTGTCGGTATAGGTTGTAGACCTATTCGCTCATAAAACCGGTATA
1 TACCGACACAATATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCTCATAAAACCGGTATA
* *
29323 TTTATACCGGTTATATTACAAAATTATCTATTACATTATAATTCTTGGTTCCAATGTGTAAATGT
66 TTTATACCGGTTATATTACAAAATTATCTATTACATTATAATTCTGGGTTCCGATGTGTAAATGT
*
29388 CGACACTTTTTGACAAGGTATCGACATATTTTTCTTCCAATCTGGACATAAAG
131 CGACACTTTTTGACAAGGTATCGACACATTTTTCTTCCAATCTGGACATAAAG
29441 TACCGACACAATATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCTCATAAAACCGGTATA
1 TACCGACACAATATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCTCATAAAACCGGTATA
*
29506 TTTATACCGGTTATATTATAAAATTATCTATTACATTATAATTCTGGGTTCCGATGTGTAAATGT
66 TTTATACCGGTTATATTACAAAATTATCTATTACATTATAATTCTGGGTTCCGATGTGTAAATGT
* *
29571 CGACACTTTTTGAAAAGGTATCGACACATTTTTCTTCCAATATGGACATAAAG
131 CGACACTTTTTGACAAGGTATCGACACATTTTTCTTCCAATCTGGACATAAAG
*
29624 TACCGACACAATATTAAAAAGTGTCGGTATAGGTTGTAGACCTATTCGCTCATAAAACCGGTATA
1 TACCGACACAATATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCTCATAAAACCGGTATA
* * *
29689 TTTATACTGGTTATATTACAAAATTATCTATTACATTATAATTCTGGGTTCCGTTGTATAAATGT
66 TTTATACCGGTTATATTACAAAATTATCTATTACATTATAATTCTGGGTTCCGATGTGTAAATGT
29754 CGACACTTTTTGACAAGGTATCGACACATTTTTCTTCCAATCTGGACATAAAG
131 CGACACTTTTTGACAAGGTATCGACACATTTTTCTTCCAATCTGGACATAAAG
*
29807 TACCGACACAATATT--AAAGTGTCGGTATAGGTTGTAGACCTATTCGCTCATAAAACCGGTATA
1 TACCGACACAATATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCTCATAAAACCGGTATA
*
29870 TTTATACTGGTTATATTACAAAATTATCTATTACATTATAATTCTGGGTTCCGATGTGTAAATGT
66 TTTATACCGGTTATATTACAAAATTATCTATTACATTATAATTCTGGGTTCCGATGTGTAAATGT
*
29935 CGACACTTTTTGACAAGGTATCGACACATTTTTCTTACAATCTGGACATAAAG
131 CGACACTTTTTGACAAGGTATCGACACATTTTTCTTCCAATCTGGACATAAAG
* *
29988 TACCAACACAATATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCTCATAAAACCAGTATA
1 TACCGACACAATATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCTCATAAAACCGGTATA
* *
30053 TTTATACCGGTTATATTACAAAATTATCTATTACATTATAATTCTGGGTTCCGATGTTTTTTCAA
66 TTTATACCGGTTATATTACAAAATTATCTATTACATTATAATTCTGGGTTCCGATG---TGTAAA
* *
30118 --TCGACACTTTTTGA-AATGGCATCGACACATTTTTCTTCCATTCTGGACATAAAG
128 TGTCGACACTTTTTGACAA-GGTATCGACACATTTTTCTTCCAATCTGGACATAAAG
*
30172 TACAGACACAATATTAAAAAGTGT
1 TACCGACACAATATTAAAAAGTGT
30196 GAAAACTTTG
Statistics
Matches: 899, Mismatches: 33, Indels: 11
0.95 0.03 0.01
Matches are distributed among these distances:
181 177 0.20
183 648 0.72
184 70 0.08
186 4 0.00
ACGTcount: A:0.33, C:0.17, G:0.15, T:0.35
Consensus pattern (183 bp):
TACCGACACAATATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCTCATAAAACCGGTATA
TTTATACCGGTTATATTACAAAATTATCTATTACATTATAATTCTGGGTTCCGATGTGTAAATGT
CGACACTTTTTGACAAGGTATCGACACATTTTTCTTCCAATCTGGACATAAAG
Found at i:31456 original size:36 final size:36
Alignment explanation
Indices: 31409--31490 Score: 146
Period size: 36 Copynumber: 2.3 Consensus size: 36
31399 GTTTGGATCA
31409 TCATCATCATCATCATCGTCATCTTCATCGTCAGCT
1 TCATCATCATCATCATCGTCATCTTCATCGTCAGCT
*
31445 TCATCGTCATCATCATCGTCATCTTCATCGTCAGCT
1 TCATCATCATCATCATCGTCATCTTCATCGTCAGCT
*
31481 TCATCTTCAT
1 TCATCATCAT
31491 TGACCGCTTG
Statistics
Matches: 44, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
36 44 1.00
ACGTcount: A:0.21, C:0.33, G:0.09, T:0.38
Consensus pattern (36 bp):
TCATCATCATCATCATCGTCATCTTCATCGTCAGCT
Found at i:31482 original size:12 final size:12
Alignment explanation
Indices: 31409--31490 Score: 110
Period size: 12 Copynumber: 6.8 Consensus size: 12
31399 GTTTGGATCA
* *
31409 TCATCATCATCA
1 TCATCGTCATCT
31421 TCATCGTCATCT
1 TCATCGTCATCT
*
31433 TCATCGTCAGCT
1 TCATCGTCATCT
*
31445 TCATCGTCATCA
1 TCATCGTCATCT
31457 TCATCGTCATCT
1 TCATCGTCATCT
*
31469 TCATCGTCAGCT
1 TCATCGTCATCT
*
31481 TCATCTTCAT
1 TCATCGTCAT
31491 TGACCGCTTG
Statistics
Matches: 61, Mismatches: 9, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
12 61 1.00
ACGTcount: A:0.21, C:0.33, G:0.09, T:0.38
Consensus pattern (12 bp):
TCATCGTCATCT
Found at i:31490 original size:6 final size:6
Alignment explanation
Indices: 31409--31477 Score: 75
Period size: 6 Copynumber: 11.5 Consensus size: 6
31399 GTTTGGATCA
* * * * * *
31409 TCATCA TCATCA TCATCG TCATCT TCATCG TCAGCT TCATCG TCATCA
1 TCATCG TCATCG TCATCG TCATCG TCATCG TCATCG TCATCG TCATCG
*
31457 TCATCG TCATCT TCATCG TCA
1 TCATCG TCATCG TCATCG TCA
31478 GCTTCATCTT
Statistics
Matches: 52, Mismatches: 11, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
6 52 1.00
ACGTcount: A:0.22, C:0.33, G:0.09, T:0.36
Consensus pattern (6 bp):
TCATCG
Found at i:31499 original size:18 final size:18
Alignment explanation
Indices: 31427--31490 Score: 67
Period size: 18 Copynumber: 3.6 Consensus size: 18
31417 ATCATCATCG
*
31427 TCATCTTCATCGTCAGCT
1 TCATCTTCATCGACAGCT
* * *
31445 TCATCGTCATC-ATCATCG
1 TCATCTTCATCGA-CAGCT
*
31463 TCATCTTCATCGTCAGCT
1 TCATCTTCATCGACAGCT
31481 TCATCTTCAT
1 TCATCTTCAT
31491 TGACCGCTTG
Statistics
Matches: 36, Mismatches: 8, Indels: 4
0.75 0.17 0.08
Matches are distributed among these distances:
18 36 1.00
ACGTcount: A:0.19, C:0.33, G:0.09, T:0.39
Consensus pattern (18 bp):
TCATCTTCATCGACAGCT
Found at i:33310 original size:200 final size:200
Alignment explanation
Indices: 32986--34148 Score: 2078
Period size: 200 Copynumber: 5.8 Consensus size: 200
32976 AACATTAAAC
* * * * *
32986 AGTGTCGATACA-TATTATATACCAATTATCTCATAAAATCGGTATACTTGTACCGGTTAGATTG
1 AGTGTCGACACATTATT-TAGACCTATTCTCTCATAAAACCGGTATACTTGTACCGGTTAGATTG
* *
33050 AAAAATTACCTATTACATTATACTTATGGGTTTCGATGTTTATGGGATCGACACTTTTTATATAT
65 AAAAATTACATATTACATTATACTTTTGGGTTTCGATGTTTATGGGATCGACACTTTTTATATAT
*
33115 GGATCGACACTTTATGGTTGCAGCCTGTTTGCCATTCATTCTGGACCAAAAATATCGACACAAAC
130 GGATCGACACTTTATGGTTGCACCCTGTTTGCCATTCATTCTGGACCAAAAATATCGACACAAAC
33180 TACAAA
195 TACAAA
33186 AGTGTCGACACATTATTTAGACCTATTCTCTCATAAAACCGGTATACTTGTACCGGTTAGATTGA
1 AGTGTCGACACATTATTTAGACCTATTCTCTCATAAAACCGGTATACTTGTACCGGTTAGATTGA
33251 AAAATTACATATTACATTATACTTTTGGGTTTCGATGTTTATGGGATCGACACTTTTTATATATG
66 AAAATTACATATTACATTATACTTTTGGGTTTCGATGTTTATGGGATCGACACTTTTTATATATG
*
33316 GATCGACACTTTATGGTTGCATCCTGTTTGCCATTCATTCTGGACCAAAAATATCGACACAAACT
131 GATCGACACTTTATGGTTGCACCCTGTTTGCCATTCATTCTGGACCAAAAATATCGACACAAACT
33381 ACAAA
196 ACAAA
* * *
33386 AGTGTCGACACATTATTTAGACCTATTTTTTCATAAAACCGGTATATTTGTACCGGTTAGATTGA
1 AGTGTCGACACATTATTTAGACCTATTCTCTCATAAAACCGGTATACTTGTACCGGTTAGATTGA
33451 AAAATTACATATTACATTATACTTTTGGGTTTCGATGTTTATGGGATCGACACTTTTTATATATG
66 AAAATTACATATTACATTATACTTTTGGGTTTCGATGTTTATGGGATCGACACTTTTTATATATG
*
33516 GATCGACACTTTATGGTTGCACCCTATTTGCCATTCATTCTGGACCAAAAATATCGACACAAACT
131 GATCGACACTTTATGGTTGCACCCTGTTTGCCATTCATTCTGGACCAAAAATATCGACACAAACT
33581 ACAAA
196 ACAAA
*
33586 AGTGTCGACACATTATTTAGACCTATTCTCTCATAAAACCGGTGTACTTGTACCGGTTAGATTGA
1 AGTGTCGACACATTATTTAGACCTATTCTCTCATAAAACCGGTATACTTGTACCGGTTAGATTGA
*
33651 AAAATTACATATTACATTATACTTTTGGTTTTCGATGTTTATGGGATCGACACTTTTTATATATG
66 AAAATTACATATTACATTATACTTTTGGGTTTCGATGTTTATGGGATCGACACTTTTTATATATG
*
33716 GATCGACACTTTATTGTTGCACCCTGTTTGCCATTCATTCTGGACCAAAAATATCGACACAAACT
131 GATCGACACTTTATGGTTGCACCCTGTTTGCCATTCATTCTGGACCAAAAATATCGACACAAACT
33781 ACAAA
196 ACAAA
* *
33786 AGTGTCGACACATTATTTAGACCTATTCTCTCATAAAACTGGTGTACTT-TACCGGTTAGATTGA
1 AGTGTCGACACATTATTTAGACCTATTCTCTCATAAAACCGGTATACTTGTACCGGTTAGATTGA
*
33850 AAAATTACATATTACATTATACTTTTGGTTTTCGATGTTTATGGGATCGACACTTTTTATATATG
66 AAAATTACATATTACATTATACTTTTGGGTTTCGATGTTTATGGGATCGACACTTTTTATATATG
* *
33915 GATCGACACTGTATGGTTGCACCCTGTTTGCCATTCATTCTGGACCAGAAATATCGACACAAACT
131 GATCGACACTTTATGGTTGCACCCTGTTTGCCATTCATTCTGGACCAAAAATATCGACACAAACT
33980 ACAAA
196 ACAAA
* *
33985 AGTGTCGATACATTATTTAGACCTATTCTCTCATAAAACCGGTATACTTGTACCGATTAGATTGA
1 AGTGTCGACACATTATTTAGACCTATTCTCTCATAAAACCGGTATACTTGTACCGGTTAGATTGA
*
34050 AAAATTACCTATTACATTATACTTTTGGGTTTCGATGTTTATGGGATCGACACTTTTTATATATG
66 AAAATTACATATTACATTATACTTTTGGGTTTCGATGTTTATGGGATCGACACTTTTTATATATG
*
34115 GATCGACACTTTATTGTTGCACCCTGTTTGCCAT
131 GATCGACACTTTATGGTTGCACCCTGTTTGCCAT
34149 ATTGTAAATT
Statistics
Matches: 929, Mismatches: 32, Indels: 4
0.96 0.03 0.00
Matches are distributed among these distances:
199 193 0.21
200 732 0.79
201 4 0.00
ACGTcount: A:0.30, C:0.18, G:0.15, T:0.36
Consensus pattern (200 bp):
AGTGTCGACACATTATTTAGACCTATTCTCTCATAAAACCGGTATACTTGTACCGGTTAGATTGA
AAAATTACATATTACATTATACTTTTGGGTTTCGATGTTTATGGGATCGACACTTTTTATATATG
GATCGACACTTTATGGTTGCACCCTGTTTGCCATTCATTCTGGACCAAAAATATCGACACAAACT
ACAAA
Found at i:34285 original size:19 final size:19
Alignment explanation
Indices: 34261--34309 Score: 89
Period size: 19 Copynumber: 2.6 Consensus size: 19
34251 TTATATTGAC
34261 ATACAAAATTATAAATCGT
1 ATACAAAATTATAAATCGT
*
34280 ATACAAAATTATAAATCTT
1 ATACAAAATTATAAATCGT
34299 ATACAAAATTA
1 ATACAAAATTA
34310 ACCCTACATT
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
19 29 1.00
ACGTcount: A:0.55, C:0.10, G:0.02, T:0.33
Consensus pattern (19 bp):
ATACAAAATTATAAATCGT
Found at i:35901 original size:21 final size:21
Alignment explanation
Indices: 35876--35915 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
35866 CCTTCTCATT
35876 TCTTCCATCTCTTCTTCTTCC
1 TCTTCCATCTCTTCTTCTTCC
* *
35897 TCTTCCCTCTTTTCTTCTT
1 TCTTCCATCTCTTCTTCTT
35916 TATATTTTTT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.03, C:0.40, G:0.00, T:0.57
Consensus pattern (21 bp):
TCTTCCATCTCTTCTTCTTCC
Found at i:36138 original size:33 final size:33
Alignment explanation
Indices: 36101--36166 Score: 105
Period size: 33 Copynumber: 2.0 Consensus size: 33
36091 CATCTTAATA
*
36101 TCACCCCTTAACACCCCAACTTCTTTCACCACT
1 TCACCCCTCAACACCCCAACTTCTTTCACCACT
* *
36134 TCACCCCTCAACACCTCTACTTCTTTCACCACT
1 TCACCCCTCAACACCCCAACTTCTTTCACCACT
36167 CCATCTATTT
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.23, C:0.48, G:0.00, T:0.29
Consensus pattern (33 bp):
TCACCCCTCAACACCCCAACTTCTTTCACCACT
Found at i:36225 original size:21 final size:21
Alignment explanation
Indices: 36200--36264 Score: 103
Period size: 21 Copynumber: 3.1 Consensus size: 21
36190 CCCCTTATGC
* *
36200 CTCTCAAGTGTATCTTCGACT
1 CTCTCAAGTTTCTCTTCGACT
36221 CTCTCAAGTTTCTCTTCGACT
1 CTCTCAAGTTTCTCTTCGACT
*
36242 CTATCAAGTTTCTCTTCGACT
1 CTCTCAAGTTTCTCTTCGACT
36263 CT
1 CT
36265 TGATTGTCTT
Statistics
Matches: 41, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
21 41 1.00
ACGTcount: A:0.17, C:0.31, G:0.11, T:0.42
Consensus pattern (21 bp):
CTCTCAAGTTTCTCTTCGACT
Found at i:38504 original size:21 final size:22
Alignment explanation
Indices: 38480--38520 Score: 57
Period size: 21 Copynumber: 1.9 Consensus size: 22
38470 GGTATCATTT
* *
38480 TACCGGTTTTATCAT-TTTTGA
1 TACCGATTTCATCATATTTTGA
38501 TACCGATTTCATCATATTTT
1 TACCGATTTCATCATATTTT
38521 TACCTGTTAT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 13 0.76
22 4 0.24
ACGTcount: A:0.22, C:0.17, G:0.10, T:0.51
Consensus pattern (22 bp):
TACCGATTTCATCATATTTTGA
Found at i:38704 original size:20 final size:19
Alignment explanation
Indices: 38659--38705 Score: 67
Period size: 20 Copynumber: 2.4 Consensus size: 19
38649 TCCGGTAACG
*
38659 TTTTACCGGTTTTATTATT
1 TTTTACCGGTTTTATCATT
38678 TTGTTACCGGTTTTATCATAT
1 TT-TTACCGGTTTTATCAT-T
38699 TTTTACC
1 TTTTACC
38706 TGATATATCG
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
19 2 0.08
20 20 0.80
21 3 0.12
ACGTcount: A:0.17, C:0.15, G:0.11, T:0.57
Consensus pattern (19 bp):
TTTTACCGGTTTTATCATT
Found at i:38749 original size:181 final size:182
Alignment explanation
Indices: 38444--38917 Score: 698
Period size: 182 Copynumber: 2.6 Consensus size: 182
38434 TGTACTTACG
* *
38444 AAAGTATCGACACTTTCAATATATCCGGTATCATTTTACCGGTTTTATCATTTTTGATACCGATT
1 AAAGTATCGACACTTTCAATATATCCGGTAACGTTTTACCGGTTTTATCA-TTTTGATACCGATT
* * * *
38509 TCATCATATTTTTACCTGTTATATCGTTGTGGATCGATATATTTTTTTAAAGTATCGACACATTA
65 TTATCATATTTTTACCTGTTATATCGTTTTGGATCGATACATTTTTTAAAAGTATCGACACATTA
*
38574 TAGGCGCTAAAACTGCTTCTCTTTTAAATTCACAAAGTGTCGATCCTTATA-T
130 TAGGAGCTAAAACTGCTTCTCTTTTAAATTCACAAAGTGTCGATCCTTATATT
* * *
38626 AAAGTATCGACACTTTCAATATATCCGGTAACGTTTTACCGGTTTTATTATTTTGTTACCGGTTT
1 AAAGTATCGACACTTTCAATATATCCGGTAACGTTTTACCGGTTTTATCATTTTGATACCGATTT
* *
38691 TATCATATTTTTACCTGATATATCGTTTTGGATCGATACATTTTTTAAAAGTATCGACACTTTAT
66 TATCATATTTTTACCTGTTATATCGTTTTGGATCGATACATTTTTTAAAAGTATCGACACATTAT
** *
38756 AGGATTTAAAACTGCTTCTCTTTTAAATTCACGAAGTGTCGATCCTTATATT
131 AGGAGCTAAAACTGCTTCTCTTTTAAATTCACAAAGTGTCGATCCTTATATT
* * * * * **
38808 AAAGTACCGACACTTTAAATGTATCCGGTAGCGCTTTACCGGTTTTATCATTTCAATACCGATTT
1 AAAGTATCGACACTTTCAATATATCCGGTAACGTTTTACCGGTTTTATCATTTTGATACCGATTT
* * * *
38873 TTTCATAGTTTTACCAGTTATATCGTTTTGGATCGACACATTTTT
66 TATCATATTTTTACCTGTTATATCGTTTTGGATCGATACATTTTT
38918 AATTTGGATC
Statistics
Matches: 261, Mismatches: 30, Indels: 2
0.89 0.10 0.01
Matches are distributed among these distances:
181 118 0.45
182 143 0.55
ACGTcount: A:0.27, C:0.17, G:0.13, T:0.42
Consensus pattern (182 bp):
AAAGTATCGACACTTTCAATATATCCGGTAACGTTTTACCGGTTTTATCATTTTGATACCGATTT
TATCATATTTTTACCTGTTATATCGTTTTGGATCGATACATTTTTTAAAAGTATCGACACATTAT
AGGAGCTAAAACTGCTTCTCTTTTAAATTCACAAAGTGTCGATCCTTATATT
Found at i:40178 original size:20 final size:21
Alignment explanation
Indices: 40155--40196 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
40145 TTTTAAAAAC
* *
40155 TATGAAAT-GATTTTATTTTT
1 TATGAAATAAATTCTATTTTT
40175 TATGAAATAAATTCTATTTTT
1 TATGAAATAAATTCTATTTTT
40196 T
1 T
40197 TTCATGATGA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
20 8 0.42
21 11 0.58
ACGTcount: A:0.33, C:0.02, G:0.07, T:0.57
Consensus pattern (21 bp):
TATGAAATAAATTCTATTTTT
Found at i:41881 original size:24 final size:24
Alignment explanation
Indices: 41854--41902 Score: 64
Period size: 24 Copynumber: 2.0 Consensus size: 24
41844 CGTTCATTTA
41854 CGTTC-GTGAATGTTCGGTTATGTT
1 CGTTCGGT-AATGTTCGGTTATGTT
* *
41878 CGTTCGGTTATGTTCGTTTATGTT
1 CGTTCGGTAATGTTCGGTTATGTT
41902 C
1 C
41903 ATTCATTTAT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
24 20 0.91
25 2 0.09
ACGTcount: A:0.10, C:0.14, G:0.27, T:0.49
Consensus pattern (24 bp):
CGTTCGGTAATGTTCGGTTATGTT
Found at i:41884 original size:14 final size:14
Alignment explanation
Indices: 41865--41895 Score: 62
Period size: 14 Copynumber: 2.2 Consensus size: 14
41855 GTTCGTGAAT
41865 GTTCGGTTATGTTC
1 GTTCGGTTATGTTC
41879 GTTCGGTTATGTTC
1 GTTCGGTTATGTTC
41893 GTT
1 GTT
41896 TATGTTCATT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.06, C:0.13, G:0.29, T:0.52
Consensus pattern (14 bp):
GTTCGGTTATGTTC
Found at i:41912 original size:24 final size:24
Alignment explanation
Indices: 41863--41915 Score: 70
Period size: 24 Copynumber: 2.2 Consensus size: 24
41853 ACGTTCGTGA
* *
41863 ATGTTCGGTTATGTTCGTTCGGTT
1 ATGTTCGGTTATGTTCATTCAGTT
* *
41887 ATGTTCGTTTATGTTCATTCATTT
1 ATGTTCGGTTATGTTCATTCAGTT
41911 ATGTT
1 ATGTT
41916 TAATTCAATC
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.13, C:0.11, G:0.21, T:0.55
Consensus pattern (24 bp):
ATGTTCGGTTATGTTCATTCAGTT
Found at i:44193 original size:24 final size:24
Alignment explanation
Indices: 44165--44210 Score: 83
Period size: 24 Copynumber: 1.9 Consensus size: 24
44155 AGAGTGTGAA
*
44165 ACATGTTATGTTATCTACTGCTAC
1 ACATGCTATGTTATCTACTGCTAC
44189 ACATGCTATGTTATCTACTGCT
1 ACATGCTATGTTATCTACTGCT
44211 TTAGAGTTCA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.24, C:0.22, G:0.13, T:0.41
Consensus pattern (24 bp):
ACATGCTATGTTATCTACTGCTAC
Found at i:45821 original size:10 final size:10
Alignment explanation
Indices: 45806--45849 Score: 52
Period size: 10 Copynumber: 4.1 Consensus size: 10
45796 GTGTTTGTGT
45806 TGTTCGTTTA
1 TGTTCGTTTA
45816 TGTTCGTTTA
1 TGTTCGTTTA
45826 TTGTGTTCGTTTA
1 ---TGTTCGTTTA
*
45839 TGTTCATTTA
1 TGTTCGTTTA
45849 T
1 T
45850 CATTTAAATG
Statistics
Matches: 30, Mismatches: 1, Indels: 6
0.81 0.03 0.16
Matches are distributed among these distances:
10 20 0.67
13 10 0.33
ACGTcount: A:0.11, C:0.09, G:0.18, T:0.61
Consensus pattern (10 bp):
TGTTCGTTTA
Found at i:45832 original size:23 final size:23
Alignment explanation
Indices: 45806--45849 Score: 79
Period size: 23 Copynumber: 1.9 Consensus size: 23
45796 GTGTTTGTGT
*
45806 TGTTCGTTTATGTTCGTTTATTG
1 TGTTCGTTTATGTTCATTTATTG
45829 TGTTCGTTTATGTTCATTTAT
1 TGTTCGTTTATGTTCATTTAT
45850 CATTTAAATG
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.11, C:0.09, G:0.18, T:0.61
Consensus pattern (23 bp):
TGTTCGTTTATGTTCATTTATTG
Found at i:45937 original size:16 final size:16
Alignment explanation
Indices: 45916--45946 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
45906 AAAAAAATTT
45916 TGTTCGTTTATGTTCG
1 TGTTCGTTTATGTTCG
45932 TGTTCGTTTATGTTC
1 TGTTCGTTTATGTTC
45947 ATTTATTTAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.06, C:0.13, G:0.23, T:0.58
Consensus pattern (16 bp):
TGTTCGTTTATGTTCG
Found at i:48279 original size:31 final size:30
Alignment explanation
Indices: 48243--48310 Score: 100
Period size: 31 Copynumber: 2.2 Consensus size: 30
48233 CAATGAAATC
48243 CCCCAACATTTAATCTATTTACAATATGAT
1 CCCCAACATTTAATCTATTTACAATATGAT
* * *
48273 CTCCCAAAATTTATTCTATTTACAATATGTT
1 C-CCCAACATTTAATCTATTTACAATATGAT
48304 CCCCAAC
1 CCCCAAC
48311 GTAACTTTTA
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
30 6 0.18
31 27 0.82
ACGTcount: A:0.34, C:0.26, G:0.03, T:0.37
Consensus pattern (30 bp):
CCCCAACATTTAATCTATTTACAATATGAT
Found at i:48976 original size:30 final size:30
Alignment explanation
Indices: 48917--48997 Score: 126
Period size: 30 Copynumber: 2.7 Consensus size: 30
48907 AACTTTTAAA
* *
48917 ATTTACAATACAATCCCCTAACTTTTAATCC
1 ATTTACAATATAATCCCC-AACATTTAATCC
*
48948 ATTTACAATATGATCCCCAACATTTAATCC
1 ATTTACAATATAATCCCCAACATTTAATCC
48978 ATTTACAATATAATCCCCAA
1 ATTTACAATATAATCCCCAA
48998 TGTAACTGTT
Statistics
Matches: 46, Mismatches: 4, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
30 30 0.65
31 16 0.35
ACGTcount: A:0.38, C:0.27, G:0.01, T:0.33
Consensus pattern (30 bp):
ATTTACAATATAATCCCCAACATTTAATCC
Found at i:51974 original size:20 final size:19
Alignment explanation
Indices: 51949--52021 Score: 74
Period size: 20 Copynumber: 3.7 Consensus size: 19
51939 GATTTTCCAG
51949 AATCGCAACGCGAATATGAA
1 AATCGCAACGCGAATA-GAA
* *
51969 AATCGCAACGCGAACACATA
1 AATCGCAACGCGAATAGA-A
* * *
51989 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGAAT-AGAA
52009 AATCGCAACGCGA
1 AATCGCAACGCGA
52022 TTTTTAAAGC
Statistics
Matches: 43, Mismatches: 8, Indels: 4
0.78 0.15 0.07
Matches are distributed among these distances:
19 1 0.02
20 42 0.98
ACGTcount: A:0.40, C:0.27, G:0.19, T:0.14
Consensus pattern (19 bp):
AATCGCAACGCGAATAGAA
Found at i:52435 original size:33 final size:33
Alignment explanation
Indices: 52396--52466 Score: 124
Period size: 33 Copynumber: 2.2 Consensus size: 33
52386 TTCACTTAGA
52396 TTTCATTTCGCGTTACGATTCTCTCGTTGCGAT
1 TTTCATTTCGCGTTACGATTCTCTCGTTGCGAT
* *
52429 TTTCATTTCGCGTTGCTATTCTCTCGTTGCGAT
1 TTTCATTTCGCGTTACGATTCTCTCGTTGCGAT
52462 TTTCA
1 TTTCA
52467 AGTTAGTATT
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 36 1.00
ACGTcount: A:0.11, C:0.24, G:0.17, T:0.48
Consensus pattern (33 bp):
TTTCATTTCGCGTTACGATTCTCTCGTTGCGAT
Found at i:52616 original size:20 final size:20
Alignment explanation
Indices: 52546--52618 Score: 92
Period size: 21 Copynumber: 3.5 Consensus size: 20
52536 TGCAGAAGAG
52546 TCGCAACGAGATAAATGAAAA
1 TCGCAACGAGA-AAATGAAAA
* **
52567 TCGCAACGTGAAAATGACTA
1 TCGCAACGAGAAAATGAAAA
*
52587 TCTGCAACGAGAAAAAGAAAA
1 TC-GCAACGAGAAAATGAAAA
52608 TCGCAACGAGA
1 TCGCAACGAGA
52619 GAATCGCAAC
Statistics
Matches: 44, Mismatches: 7, Indels: 3
0.81 0.13 0.06
Matches are distributed among these distances:
20 18 0.41
21 26 0.59
ACGTcount: A:0.48, C:0.18, G:0.21, T:0.14
Consensus pattern (20 bp):
TCGCAACGAGAAAATGAAAA
Found at i:52681 original size:14 final size:14
Alignment explanation
Indices: 52662--52718 Score: 60
Period size: 14 Copynumber: 3.7 Consensus size: 14
52652 TTTTATTTCG
52662 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
*
52676 CGTTGCGATTTTCATTTCG
1 CGTTGCGA--TTC---TCT
52695 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
52709 CGTTGCGATT
1 CGTTGCGATT
52719 TTCATTTCTC
Statistics
Matches: 36, Mismatches: 2, Indels: 10
0.75 0.04 0.21
Matches are distributed among these distances:
14 20 0.56
16 3 0.08
17 3 0.08
19 10 0.28
ACGTcount: A:0.09, C:0.25, G:0.23, T:0.44
Consensus pattern (14 bp):
CGTTGCGATTCTCT
Found at i:52698 original size:33 final size:33
Alignment explanation
Indices: 52646--52767 Score: 156
Period size: 33 Copynumber: 3.5 Consensus size: 33
52636 CAAAATCGCA
52646 TTGCGATTTT-ATTTCGCGTTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
52678 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
*
52711 TTGCGATTTTCATTTCTCTCGTTGCGACAGTCATTCTCTCG
1 TTGCGATTTTCA-TT-TCGCGTT--G-C-G--ATTCTCTCG
52752 TTGCGATTTTCATTTC
1 TTGCGATTTTCATTTC
52768 AACCAAAAGA
Statistics
Matches: 80, Mismatches: 1, Indels: 11
0.87 0.01 0.12
Matches are distributed among these distances:
32 10 0.12
33 34 0.43
34 2 0.03
35 6 0.08
37 1 0.01
38 1 0.01
39 3 0.04
40 2 0.03
41 21 0.26
ACGTcount: A:0.11, C:0.24, G:0.19, T:0.47
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
Found at i:52729 original size:21 final size:21
Alignment explanation
Indices: 52703--52767 Score: 96
Period size: 21 Copynumber: 3.1 Consensus size: 21
52693 CGCGTTGCGA
52703 TTCTCTCGTTGCGATTTTCAT
1 TTCTCTCGTTGCGATTTTCAT
***
52724 TTCTCTCGTTGCGACAGTCA-
1 TTCTCTCGTTGCGATTTTCAT
52744 TTCTCTCGTTGCGATTTTCAT
1 TTCTCTCGTTGCGATTTTCAT
52765 TTC
1 TTC
52768 AACCAAAAGA
Statistics
Matches: 37, Mismatches: 6, Indels: 2
0.82 0.13 0.04
Matches are distributed among these distances:
20 17 0.46
21 20 0.54
ACGTcount: A:0.11, C:0.26, G:0.15, T:0.48
Consensus pattern (21 bp):
TTCTCTCGTTGCGATTTTCAT
Found at i:54594 original size:93 final size:93
Alignment explanation
Indices: 54435--54657 Score: 437
Period size: 93 Copynumber: 2.4 Consensus size: 93
54425 TAGATTGCTT
*
54435 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
54500 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
54528 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
54593 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
54621 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACT
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACT
54658 AATACCCTGA
Statistics
Matches: 129, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
93 129 1.00
ACGTcount: A:0.22, C:0.14, G:0.19, T:0.45
Consensus pattern (93 bp):
AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
TTTGTCTTTGTTTTGTCTTTTGGTTGAA
Found at i:54790 original size:14 final size:14
Alignment explanation
Indices: 54771--54827 Score: 51
Period size: 14 Copynumber: 3.7 Consensus size: 14
54761 ACGAAACTTA
54771 AATCGCAACGAGAG
1 AATCGCAACGAGAG
*
54785 AATCGCAACGCGAAATGAA
1 AATCGCAA--CG--A-GAG
*
54804 AATCGCAACGACAG
1 AATCGCAACGAGAG
54818 AATCGCAACG
1 AATCGCAACG
54828 CGAAACCAAA
Statistics
Matches: 35, Mismatches: 3, Indels: 10
0.73 0.06 0.21
Matches are distributed among these distances:
14 19 0.54
15 1 0.03
16 2 0.06
17 2 0.06
18 1 0.03
19 10 0.29
ACGTcount: A:0.44, C:0.25, G:0.23, T:0.09
Consensus pattern (14 bp):
AATCGCAACGAGAG
Found at i:54791 original size:33 final size:33
Alignment explanation
Indices: 54754--54876 Score: 183
Period size: 33 Copynumber: 3.7 Consensus size: 33
54744 TAGTTTACTT
* ** *
54754 TCGCAACACGAAACTTAAATCGCAACGAGAGAA
1 TCGCAACGCGAAACCAAAATCGCAACGACAGAA
**
54787 TCGCAACGCGAAATGAAAATCGCAACGACAGAA
1 TCGCAACGCGAAACCAAAATCGCAACGACAGAA
*
54820 TCGCAACGCGAAACCAAAATCGCAACGACAAAA
1 TCGCAACGCGAAACCAAAATCGCAACGACAGAA
54853 TCGCAACGCGAAACCAAAATCGCA
1 TCGCAACGCGAAACCAAAATCGCA
54877 TTGCGATTTC
Statistics
Matches: 82, Mismatches: 8, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
33 82 1.00
ACGTcount: A:0.46, C:0.28, G:0.18, T:0.09
Consensus pattern (33 bp):
TCGCAACGCGAAACCAAAATCGCAACGACAGAA
Found at i:54809 original size:19 final size:18
Alignment explanation
Indices: 54785--54876 Score: 65
Period size: 19 Copynumber: 5.4 Consensus size: 18
54775 GCAACGAGAG
54785 AATCGCAACGCGAAATGAA
1 AATCGCAACGCGAAA-GAA
*
54804 AATCGCAA--CGACAG--
1 AATCGCAACGCGAAAGAA
*
54818 AATCGCAACGCGAAACCAA
1 AATCGCAACGCGAAA-GAA
*
54837 AATCGCAA--CG--ACAA
1 AATCGCAACGCGAAAGAA
*
54851 AATCGCAACGCGAAACCAA
1 AATCGCAACGCGAAA-GAA
54870 AATCGCA
1 AATCGCA
54877 TTGCGATTTC
Statistics
Matches: 60, Mismatches: 3, Indels: 20
0.72 0.04 0.24
Matches are distributed among these distances:
14 19 0.32
15 1 0.02
16 7 0.12
17 6 0.10
18 1 0.02
19 26 0.43
ACGTcount: A:0.47, C:0.28, G:0.17, T:0.08
Consensus pattern (18 bp):
AATCGCAACGCGAAAGAA
Found at i:54853 original size:14 final size:14
Alignment explanation
Indices: 54802--54860 Score: 64
Period size: 14 Copynumber: 3.9 Consensus size: 14
54792 ACGCGAAATG
54802 AAAATCGCAACGAC
1 AAAATCGCAACGAC
*
54816 AGAATCGCAACGCGAAACC
1 AAAATCGCAA--CG--A-C
54835 AAAATCGCAACGAC
1 AAAATCGCAACGAC
54849 AAAATCGCAACG
1 AAAATCGCAACG
54861 CGAAACCAAA
Statistics
Matches: 38, Mismatches: 2, Indels: 10
0.76 0.04 0.20
Matches are distributed among these distances:
14 22 0.58
15 1 0.03
16 2 0.05
17 2 0.05
18 1 0.03
19 10 0.26
ACGTcount: A:0.47, C:0.29, G:0.17, T:0.07
Consensus pattern (14 bp):
AAAATCGCAACGAC
Found at i:54931 original size:19 final size:19
Alignment explanation
Indices: 54872--55009 Score: 137
Period size: 19 Copynumber: 7.6 Consensus size: 19
54862 GAAACCAAAA
*
54872 TCGCATTGCGA-TTTCATT
1 TCGCGTTGCGATTTTCATT
*
54890 TCGCGTTGCGA--TTC-TG
1 TCGCGTTGCGATTTTCATT
54906 T--CGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
*
54923 TCGCGTTGCGATTTT-GTT
1 TCGCGTTGCGATTTTCATT
**
54941 TCGCGTTGCGATTTTGGTT
1 TCGCGTTGCGATTTTCATT
* *
54960 TCTCGTTGCGATTCTCATT
1 TCGCGTTGCGATTTTCATT
*
54979 TCGCGTTGCGATTTTAAGTT
1 TCGCGTTGCGATTTTCA-TT
*
54999 TCGTGTTGCGA
1 TCGCGTTGCGA
55010 AAGTAAACTA
Statistics
Matches: 101, Mismatches: 12, Indels: 12
0.81 0.10 0.10
Matches are distributed among these distances:
14 8 0.08
16 5 0.05
17 5 0.05
18 27 0.27
19 44 0.44
20 12 0.12
ACGTcount: A:0.10, C:0.20, G:0.25, T:0.46
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Found at i:54953 original size:51 final size:53
Alignment explanation
Indices: 54872--55009 Score: 163
Period size: 56 Copynumber: 2.5 Consensus size: 53
54862 GAAACCAAAA
* ** *
54872 TCGCATTGCGATTTCATTTCGCGTTGCGATTCT-G-TCGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTGTTTCGCGTTGCGATTCTGGTTCGTTGCGATTCTCATT
*
54923 TCGCGTTGCGATTTTGTTTCGCGTTGCGATTTTGGTTTCTCGTTGCGATTCTCATT
1 TCGCGTTGCGATTTTGTTTCGCGTTGCGATTCTGG--T-TCGTTGCGATTCTCATT
*
54979 TCGCGTTGCGATTTTAAGTTTCGTGTTGCGA
1 TCGCGTTGCGATTTT--GTTTCGCGTTGCGA
55010 AAGTAAACTA
Statistics
Matches: 74, Mismatches: 6, Indels: 7
0.85 0.07 0.08
Matches are distributed among these distances:
51 29 0.39
52 1 0.01
56 31 0.42
58 13 0.18
ACGTcount: A:0.10, C:0.20, G:0.25, T:0.46
Consensus pattern (53 bp):
TCGCGTTGCGATTTTGTTTCGCGTTGCGATTCTGGTTCGTTGCGATTCTCATT
Found at i:54967 original size:37 final size:38
Alignment explanation
Indices: 54872--55009 Score: 137
Period size: 37 Copynumber: 3.8 Consensus size: 38
54862 GAAACCAAAA
* *
54872 TCGCATTGCGA-TTTCATTTCGCGTTGCGA-T-TC-TG
1 TCGCGTTGCGATTTTCATTTCGCGTTGCGATTCTCATT
**
54906 T--CGTTGCGATTTTCATTTCGCGTTGCGATT-TTGTT
1 TCGCGTTGCGATTTTCATTTCGCGTTGCGATTCTCATT
** *
54941 TCGCGTTGCGATTTTGGTTTCTCGTTGCGATTCTCATT
1 TCGCGTTGCGATTTTCATTTCGCGTTGCGATTCTCATT
* *
54979 TCGCGTTGCGATTTTAAGTTTCGTGTTGCGA
1 TCGCGTTGCGATTTTCA-TTTCGCGTTGCGA
55010 AAGTAAACTA
Statistics
Matches: 85, Mismatches: 12, Indels: 9
0.80 0.11 0.08
Matches are distributed among these distances:
32 7 0.08
33 18 0.21
34 3 0.04
35 2 0.02
37 26 0.31
38 18 0.21
39 11 0.13
ACGTcount: A:0.10, C:0.20, G:0.25, T:0.46
Consensus pattern (38 bp):
TCGCGTTGCGATTTTCATTTCGCGTTGCGATTCTCATT
Found at i:56920 original size:14 final size:14
Alignment explanation
Indices: 56901--56932 Score: 55
Period size: 14 Copynumber: 2.3 Consensus size: 14
56891 GTTTAATTGA
56901 TTGTAAAAGATGAT
1 TTGTAAAAGATGAT
*
56915 TTGTAAAAGTTGAT
1 TTGTAAAAGATGAT
56929 TTGT
1 TTGT
56933 GTAATTGATG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.34, C:0.00, G:0.22, T:0.44
Consensus pattern (14 bp):
TTGTAAAAGATGAT
Found at i:57100 original size:20 final size:19
Alignment explanation
Indices: 57023--57110 Score: 114
Period size: 19 Copynumber: 4.8 Consensus size: 19
57013 GCATTATGTT
57023 GAAATGAAAATCGCAATGC
1 GAAATGAAAATCGCAATGC
57042 GAAATGAAAATCGCAA--C
1 GAAATGAAAATCGCAATGC
*
57059 G--A-GAGAATCGCAATGC
1 GAAATGAAAATCGCAATGC
*
57075 GAAATGAAAATCGCAATGTG
1 GAAATGAAAATCGCAATG-C
57095 GAAATGAAAATCGCAA
1 GAAATGAAAATCGCAA
57111 CGAGAGAATC
Statistics
Matches: 60, Mismatches: 3, Indels: 11
0.81 0.04 0.15
Matches are distributed among these distances:
14 10 0.17
15 1 0.02
16 2 0.03
17 2 0.03
18 1 0.02
19 28 0.47
20 16 0.27
ACGTcount: A:0.48, C:0.15, G:0.23, T:0.15
Consensus pattern (19 bp):
GAAATGAAAATCGCAATGC
Found at i:57142 original size:53 final size:52
Alignment explanation
Indices: 57023--57129 Score: 196
Period size: 53 Copynumber: 2.0 Consensus size: 52
57013 GCATTATGTT
57023 GAAATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGC
1 GAAATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGC
*
57075 GAAATGAAAATCGCAATGTGGAAATGAAAATCGCAACGAGAGAATCGCAATGC
1 GAAATGAAAATCGCAATG-CGAAATGAAAATCGCAACGAGAGAATCGCAATGC
57128 GA
1 GA
57130 TTTTCATTTC
Statistics
Matches: 53, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
52 18 0.34
53 35 0.66
ACGTcount: A:0.46, C:0.16, G:0.24, T:0.14
Consensus pattern (52 bp):
GAAATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGC
Found at i:57199 original size:32 final size:33
Alignment explanation
Indices: 57143--57387 Score: 234
Period size: 32 Copynumber: 7.2 Consensus size: 33
57133 TCATTTCGCA
57143 TTGCGATTTTCATTTCCGCATTGCGATTCTCTCG
1 TTGCGATTTTCATTT-CGCATTGCGATTCTCTCG
* *
57177 TTGCGA-TTTCATTTCGCATTGCGATTTCATTTCACA
1 TTGCGATTTTCATTTCGCATTGCGA-TTC---TCTCG
* * * * *
57213 TTGCGATTCTCTCGTTGCG-ATTTC-ATT-TCGCA
1 TTGCGATT-T-TCATTTCGCATTGCGATTCTCTCG
57245 TTGCGATTTTCATTTCGCATTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCATTGCGATTCTCTCG
*
57278 TTGCGA-TTTCATTTCGCATTGC-ATTTTCATTTCG
1 TTGCGATTTTCATTTCGCATTGCGA--TTC-TCTCG
*
57312 CATTGCGATTTTCATTTCCGCATTGCGATT-TCTTG
1 --TTGCGATTTTCATTT-CGCATTGCGATTCTCTCG
*
57347 TTGGGATTTTCATTTCGCATTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCATTGCGATTCTCTCG
57380 TTGCGATT
1 TTGCGATT
57388 GTAATTTCCG
Statistics
Matches: 175, Mismatches: 17, Indels: 39
0.76 0.07 0.17
Matches are distributed among these distances:
30 6 0.03
31 6 0.03
32 53 0.30
33 48 0.27
34 10 0.06
35 3 0.02
36 17 0.10
37 12 0.07
38 13 0.07
39 7 0.04
ACGTcount: A:0.14, C:0.23, G:0.18, T:0.46
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCATTGCGATTCTCTCG
Found at i:57249 original size:102 final size:100
Alignment explanation
Indices: 57125--57387 Score: 377
Period size: 102 Copynumber: 2.6 Consensus size: 100
57115 AGAATCGCAA
57125 TGCGATTTTCATTTCGCATTGCGATTTTCATTTCCGCATTGCGATTCTCTCGTTGCGATTTCATT
1 TGCGA-TTTCATTTCGCATTGCGATTTTCATTT-CGCATTGCGATTCTCTCGTTGCGATTTCATT
57190 TCGCATTGCGA-TTTCATTTCACATTGCGATTCTCTC-GT
64 TCGCATTGC-ATTTTCATTTCACATTGCGATT-T-TCAGT
57228 TGCGATTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATTTCATTTC
1 TGCGATTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATTTCATTTC
* *
57293 GCATTGCATTTTCATTTCGCATTGCGATTTTCATT
66 GCATTGCATTTTCATTTCACATTGCGATTTTCAGT
* * *** *
57328 TCCGCATTGCGATTTCTTGTTGGGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATT
1 TGCG-ATTTC-ATTTCGCATTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATT
57388 GTAATTTCCG
Statistics
Matches: 148, Mismatches: 8, Indels: 9
0.90 0.05 0.05
Matches are distributed among these distances:
99 2 0.01
100 6 0.04
101 63 0.43
102 72 0.49
103 5 0.03
ACGTcount: A:0.14, C:0.23, G:0.17, T:0.46
Consensus pattern (100 bp):
TGCGATTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATTTCATTTC
GCATTGCATTTTCATTTCACATTGCGATTTTCAGT
Found at i:57270 original size:69 final size:69
Alignment explanation
Indices: 57177--57344 Score: 213
Period size: 69 Copynumber: 2.4 Consensus size: 69
57167 GATTCTCTCG
57177 TTGCGA-TTTCATTTCGCATTGCGATTTCATTTCACATTGCGA-TTC-TCTCG-TTGCGA-TTTC
1 TTGCGATTTTCATTTCGCATTGCGATTTC---TCACATTGCGATTTCATCTCGATTGC-ATTTTC
57237 ATTTCGCA
62 ATTTCGCA
* * *
57245 TTGCGATTTTCATTTCGCATTGCGA-TTCTCTCGTTGCGATTTCATTTCGCATTGCATTTTCATT
1 TTGCGATTTTCATTTCGCATTGCGATTTCTCACATTGCGATTTCATCTCG-ATTGCATTTTCATT
57309 TCGCA
65 TCGCA
57314 TTGCGATTTTCATTTCCGCATTGCGATTTCT
1 TTGCGATTTTCATTT-CGCATTGCGATTTCT
57345 TGTTGGGATT
Statistics
Matches: 89, Mismatches: 3, Indels: 13
0.85 0.03 0.12
Matches are distributed among these distances:
65 9 0.10
66 3 0.03
67 4 0.04
68 10 0.11
69 49 0.55
70 10 0.11
71 4 0.04
ACGTcount: A:0.15, C:0.23, G:0.16, T:0.46
Consensus pattern (69 bp):
TTGCGATTTTCATTTCGCATTGCGATTTCTCACATTGCGATTTCATCTCGATTGCATTTTCATTT
CGCA
Found at i:57355 original size:69 final size:70
Alignment explanation
Indices: 57233--57369 Score: 233
Period size: 69 Copynumber: 2.0 Consensus size: 70
57223 CTCGTTGCGA
57233 TTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGA-TTTCATTTCGCAT
1 TTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCAT
57297 TGCAT
66 TGCAT
* *
57302 TTTCATTTCGCATTGCGATTTTCATTTCCGCATTGCGATT-TCTTGTTGGGATTTTCATTTCGCA
1 TTTCATTTCGCATTGCGATTTTCATTT-CGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCA
57366 TTGC
65 TTGC
57370 GATTCTCTCG
Statistics
Matches: 64, Mismatches: 2, Indels: 3
0.93 0.03 0.04
Matches are distributed among these distances:
69 36 0.56
70 28 0.44
ACGTcount: A:0.14, C:0.22, G:0.17, T:0.47
Consensus pattern (70 bp):
TTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCAT
TGCAT
Found at i:60599 original size:20 final size:20
Alignment explanation
Indices: 60571--60753 Score: 150
Period size: 20 Copynumber: 9.6 Consensus size: 20
60561 AAATTTCAGT
* *
60571 GTTGTGATTTACAGATTCTC
1 GTTGCGATTTACGGATTCTC
*
60591 GTTGCGATTTACGGATTATC
1 GTTGCGATTTACGGATTCTC
*
60611 GTTGCGATTTACAGATTCTC
1 GTTGCGATTTACGGATTCTC
*
60631 G-TGCGATTTACGGATTATC
1 GTTGCGATTTACGGATTCTC
* *
60650 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATTCTC
* *
60670 GTTGCGA-TAACGGATACGT-
1 GTTGCGATTTACGGATTC-TC
*
60689 ATTGCGATTTAC-G-----C
1 GTTGCGATTTACGGATTCTC
* * *
60703 GTTGCTATTTACGGATACAC
1 GTTGCGATTTACGGATTCTC
* * *
60723 GTTGCGGTTTACGGATACGC
1 GTTGCGATTTACGGATTCTC
60743 GTTGCGATTTA
1 GTTGCGATTTA
60754 TGTGTTCGCG
Statistics
Matches: 133, Mismatches: 20, Indels: 20
0.77 0.12 0.12
Matches are distributed among these distances:
14 10 0.08
15 1 0.01
19 33 0.25
20 89 0.67
ACGTcount: A:0.21, C:0.17, G:0.26, T:0.36
Consensus pattern (20 bp):
GTTGCGATTTACGGATTCTC
Found at i:60684 original size:39 final size:40
Alignment explanation
Indices: 60571--60677 Score: 171
Period size: 39 Copynumber: 2.7 Consensus size: 40
60561 AAATTTCAGT
*
60571 GTTGTGATTTACAGATTCTCGTTGCGATTTACGGATTATC
1 GTTGCGATTTACAGATTCTCGTTGCGATTTACGGATTATC
60611 GTTGCGATTTACAGATTCTCG-TGCGATTTACGGATTATC
1 GTTGCGATTTACAGATTCTCGTTGCGATTTACGGATTATC
* * *
60650 GTTGCGATTTACGGATACGCGTTGCGAT
1 GTTGCGATTTACAGATTCTCGTTGCGAT
60678 AACGGATACG
Statistics
Matches: 62, Mismatches: 4, Indels: 2
0.91 0.06 0.03
Matches are distributed among these distances:
39 36 0.58
40 26 0.42
ACGTcount: A:0.20, C:0.17, G:0.25, T:0.38
Consensus pattern (40 bp):
GTTGCGATTTACAGATTCTCGTTGCGATTTACGGATTATC
Found at i:60695 original size:59 final size:59
Alignment explanation
Indices: 60576--60701 Score: 148
Period size: 59 Copynumber: 2.1 Consensus size: 59
60566 TCAGTGTTGT
* * * * * *
60576 GATTTACAGATTCTCGTTGCGATTTACGGATTATCGTTGCGATTTACAGATTCTCGTGC
1 GATTTACGGATTATCGTTGCGATTTACGGATTAGCGTTGCGATTAACAGATACTAGTGC
* *
60635 GATTTACGGATTATCGTTGCGATTTACGGA-TACGCGTTGCGA-TAACGGATACGTATTGC
1 GATTTACGGATTATCGTTGCGATTTACGGATTA-GCGTTGCGATTAACAGATAC-TAGTGC
60694 GATTTACG
1 GATTTACG
60702 CGTTGCTATT
Statistics
Matches: 57, Mismatches: 8, Indels: 4
0.83 0.12 0.06
Matches are distributed among these distances:
58 9 0.16
59 48 0.84
ACGTcount: A:0.22, C:0.17, G:0.25, T:0.36
Consensus pattern (59 bp):
GATTTACGGATTATCGTTGCGATTTACGGATTAGCGTTGCGATTAACAGATACTAGTGC
Found at i:60763 original size:20 final size:19
Alignment explanation
Indices: 60740--60790 Score: 59
Period size: 19 Copynumber: 2.6 Consensus size: 19
60730 TTTACGGATA
*
60740 CGCGTTGCGATTT-ATGTGTT
1 CGCGTTGCGATTTCA--TATT
*
60760 CGCGTTGGGATTTCATATT
1 CGCGTTGCGATTTCATATT
60779 CGCGTTGCGATT
1 CGCGTTGCGATT
60791 CTTGAAAATC
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
19 14 0.52
20 12 0.44
21 1 0.04
ACGTcount: A:0.12, C:0.18, G:0.29, T:0.41
Consensus pattern (19 bp):
CGCGTTGCGATTTCATATT
Done.