Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01000063.1 Hibiscus syriacus cultivar Beakdansim tig00000103_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: 63270
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.32
Found at i:3562 original size:18 final size:18
Alignment explanation
Indices: 3539--3573 Score: 70
Period size: 18 Copynumber: 1.9 Consensus size: 18
3529 TTAGAAAGTT
3539 AAAATTAAATTAGTAGTA
1 AAAATTAAATTAGTAGTA
3557 AAAATTAAATTAGTAGT
1 AAAATTAAATTAGTAGT
3574 TAAAGTTTAC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.54, C:0.00, G:0.11, T:0.34
Consensus pattern (18 bp):
AAAATTAAATTAGTAGTA
Found at i:4721 original size:37 final size:37
Alignment explanation
Indices: 4645--4721 Score: 102
Period size: 37 Copynumber: 2.1 Consensus size: 37
4635 TTTTTATATT
*
4645 TTTAATTTTGTAAAAAAAATTATATAAATATTATGAA
1 TTTAATTTTGTAAAAAAAATTATATAAATATTATCAA
* * *
4682 TTTAATTTTTTAAAGAAAA-TATATAAATATTTTACAA
1 TTTAATTTTGTAAAAAAAATTATATAAATATTAT-CAA
4719 TTT
1 TTT
4722 GTAATATTAT
Statistics
Matches: 35, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
36 13 0.37
37 22 0.63
ACGTcount: A:0.48, C:0.01, G:0.04, T:0.47
Consensus pattern (37 bp):
TTTAATTTTGTAAAAAAAATTATATAAATATTATCAA
Found at i:4845 original size:582 final size:581
Alignment explanation
Indices: 3742--4904 Score: 2161
Period size: 582 Copynumber: 2.0 Consensus size: 581
3732 ATTCCCATGT
*
3742 TTGGTTGGTCGGAAATCTCATTCTCGGTAATGTTTTATTACCAATAGTAGATTTTTTGGGGTATA
1 TTGGTTGGTCGGAAATCTCATTCCCGGTAATGTTTTATTACCAATAGTAGATTTTTTGGGGTATA
*
3807 TTACCGGGAATGTTATTACCTCCCTTCCCTTAGGTATTGTAACATTACCGGCGTTTTAGACTAAA
66 TTACCGGGAATGTTATTACCTCCCTTCCCTTAGGTATTGTAACATTACCGGCATTTTAGACTAAA
* *
3872 ATACTCTTAAATTTTTATTTTTTTTCAAAAATATCATTATTTTGTCATTAAATAATAAAAATTCT
131 ATACCCTTAAATTTTTATTTTTTTTCAAAAATATCATTATTCTGTCATTAAATAATAAAAATTCT
*
3937 ACGAAAGTTAAATTACAAATTTATCTTTAAATTATTTTAGATTTACAAAAAAAATCTATAATTAA
196 ACGAAAGTTAAATTACAAATTTATCCTTAAATTATTTTAGATTTACAAAAAAAATCTATAATTAA
**
4002 AATTTTATATGAAGTTCAGGGGTTAAAATTTTTTTTACCCTTTCATTAAACTTTTTTTATATTTT
261 AATTTTATATGAAGTTCAGGGGTTAAAAAATTTTTTACCCTTTCATTAAACTTTTTTTATATTTT
4067 TAATTTTGTAAAAAAAAATTATATAAATATTATGAATTTAATTTTTTAAAGAAAATATAATATTT
326 TAATTTTGTAAAAAAAAATTATATAAATATTATGAATTTAATTTTTTAAAGAAAATATAATATTT
4132 TACAATTTGTAATATTATACAAATATATAATAAGGGCAATTTGGTCAAATATACATTCCAATTAT
391 TACAATTTGTAATATTATACAAATATATAATAAGGGCAATTTGGTCAAATATACATTCCAATTAT
*
4197 CTTTTATTCCTTTAACCAAATACGATAATCTTACATTCCTGCTAAACCAACCAAACACAAAATAC
456 CTTTTATTCCTTTAACCAAACACGATAATCTTACATTCCTGCTAAACCAACCAAACACAAAATAC
*
4262 AATATTACCAGTAATCCTATTTCCTGGTAATCTTTTATTCCCACTAGTAATCTTACATTCC
521 AATATTACCAGTAATCATATTTCCTGGTAATCTTTTATTCCCACTAGTAATCTTACATTCC
4323 TTGGTTGGTCGGAAATCTCATTCCCGGTAATGTTTTATTACCAATAGTAGATTTTTTGGGGTATA
1 TTGGTTGGTCGGAAATCTCATTCCCGGTAATGTTTTATTACCAATAGTAGATTTTTTGGGGTATA
* *
4388 TTACCGGGAATGTTATTACCTCCCTTCCCTTAGGTATTGTAACATTACCGGTATTTTGGACTAAA
66 TTACCGGGAATGTTATTACCTCCCTTCCCTTAGGTATTGTAACATTACCGGCATTTTAGACTAAA
4453 ATACCCTTAAATTTTTATTTTTTTTTCAAAAATATCATTATTCTGTCATTAAATAATAAAAATTC
131 ATACCCTTAAATTTTTA-TTTTTTTTCAAAAATATCATTATTCTGTCATTAAATAATAAAAATTC
*
4518 TACGAAAGTTAAATTACAATTTTATCCTTAAATTATTTTAGATTTACAAAAAAAATCTATAATTA
195 TACGAAAGTTAAATTACAAATTTATCCTTAAATTATTTTAGATTTACAAAAAAAATCTATAATTA
4583 AAATTTTATATGAAGTTCAGGGGTTAAAAAATTTTTTACCC-TTCATT-AACTTTTTTTATATTT
260 AAATTTTATATGAAGTTCAGGGGTTAAAAAATTTTTTACCCTTTCATTAAACTTTTTTTATATTT
4646 TTAATTTTGT-AAAAAAAATTATATAAATATTATGAATTTAATTTTTTAAAGAAAATATATAAAT
325 TTAATTTTGTAAAAAAAAATTATATAAATATTATGAATTTAATTTTTTAAAG-AAA-ATAT-AAT
4710 ATTTTACAATTTGTAATATTATACAAATATATAATAAGGGCAATTTGGTCAAATATACATTCCAA
387 ATTTTACAATTTGTAATATTATACAAATATATAATAAGGGCAATTTGGTCAAATATACATTCCAA
4775 TTATCTTTTATTCCTTTAACCAAACACGATAATCTTACATTCCTGCTAAACCAACCAAACACAAA
452 TTATCTTTTATTCCTTTAACCAAACACGATAATCTTACATTCCTGCTAAACCAACCAAACACAAA
4840 ATACAATATTACCAGTAATCATATTTCCTGGTAATCTTTTATTCCCACTAGTAATCTTACATTCC
517 ATACAATATTACCAGTAATCATATTTCCTGGTAATCTTTTATTCCCACTAGTAATCTTACATTCC
4905 GTGAACCAAA
Statistics
Matches: 566, Mismatches: 12, Indels: 7
0.97 0.02 0.01
Matches are distributed among these distances:
579 41 0.07
580 29 0.05
581 152 0.27
582 344 0.61
ACGTcount: A:0.36, C:0.14, G:0.09, T:0.41
Consensus pattern (581 bp):
TTGGTTGGTCGGAAATCTCATTCCCGGTAATGTTTTATTACCAATAGTAGATTTTTTGGGGTATA
TTACCGGGAATGTTATTACCTCCCTTCCCTTAGGTATTGTAACATTACCGGCATTTTAGACTAAA
ATACCCTTAAATTTTTATTTTTTTTCAAAAATATCATTATTCTGTCATTAAATAATAAAAATTCT
ACGAAAGTTAAATTACAAATTTATCCTTAAATTATTTTAGATTTACAAAAAAAATCTATAATTAA
AATTTTATATGAAGTTCAGGGGTTAAAAAATTTTTTACCCTTTCATTAAACTTTTTTTATATTTT
TAATTTTGTAAAAAAAAATTATATAAATATTATGAATTTAATTTTTTAAAGAAAATATAATATTT
TACAATTTGTAATATTATACAAATATATAATAAGGGCAATTTGGTCAAATATACATTCCAATTAT
CTTTTATTCCTTTAACCAAACACGATAATCTTACATTCCTGCTAAACCAACCAAACACAAAATAC
AATATTACCAGTAATCATATTTCCTGGTAATCTTTTATTCCCACTAGTAATCTTACATTCC
Found at i:12611 original size:24 final size:26
Alignment explanation
Indices: 12578--12627 Score: 68
Period size: 25 Copynumber: 2.0 Consensus size: 26
12568 ACTCATCGGA
*
12578 AGCATTAAAAAA-ATCGATTTATTTG
1 AGCATTAAAAAATATCAATTTATTTG
*
12603 AGCA-TAAAAAATATCAATTTTTTTG
1 AGCATTAAAAAATATCAATTTATTTG
12628 GATTTGTCAA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
24 7 0.32
25 15 0.68
ACGTcount: A:0.44, C:0.08, G:0.10, T:0.38
Consensus pattern (26 bp):
AGCATTAAAAAATATCAATTTATTTG
Found at i:12796 original size:20 final size:20
Alignment explanation
Indices: 12773--13079 Score: 192
Period size: 20 Copynumber: 15.3 Consensus size: 20
12763 AATCTGTAAA
12773 TCGCAACAAAGAAGTCAAAT
1 TCGCAACAAAGAAGTCAAAT
**
12793 TCGCAAC-GCGATAGTCAAAT
1 TCGCAACAAAGA-AGTCAAAT
*
12813 TCGCAATACAA-AAGTCAAAT
1 TCGCAACA-AAGAAGTCAAAT
* * *
12833 TCACAAC-GAGATAGTCAGAT
1 TCGCAACAAAGA-AGTCAAAT
*
12853 TCGCAAC-GAGAATTTGT-AAA-
1 TCGCAACAAAGAA---GTCAAAT
* *
12873 TCGCAACACAGTAGTCAAAT
1 TCGCAACAAAGAAGTCAAAT
*
12893 TCGCAAC-ACGATAGTCAAAT
1 TCGCAACAAAGA-AGTCAAAT
*
12913 TCACAACACAA-AAGTCAAAT
1 TCGCAACA-AAGAAGTCAAAT
12933 TCGCAACACAA-AAGTCAAAT
1 TCGCAACA-AAGAAGTCAAAT
**
12953 TCGCAAC-GCGATAGTCAAAT
1 TCGCAACAAAGA-AGTCAAAT
* *
12973 TCGCAACACATAAGTCAAAT
1 TCGCAACAAAGAAGTCAAAT
** *
12993 TCGCAAC-GCGATAGCCAAAT
1 TCGCAACAAAGA-AGTCAAAT
13013 TCGCAACACAA-AAGTCAAAT
1 TCGCAACA-AAGAAGTCAAAT
** *
13033 TCGCAAC-GCGATAGCCAAAT
1 TCGCAACAAAGA-AGTCAAAT
*
13053 TCGCAACACAA-AAATCAAAT
1 TCGCAACA-AAGAAGTCAAAT
13073 TCGCAAC
1 TCGCAAC
13080 GCGAAACACA
Statistics
Matches: 225, Mismatches: 38, Indels: 48
0.72 0.12 0.15
Matches are distributed among these distances:
18 3 0.01
19 11 0.05
20 198 0.88
21 10 0.04
22 3 0.01
ACGTcount: A:0.43, C:0.24, G:0.14, T:0.18
Consensus pattern (20 bp):
TCGCAACAAAGAAGTCAAAT
Found at i:12798 original size:40 final size:40
Alignment explanation
Indices: 12749--13083 Score: 403
Period size: 40 Copynumber: 8.4 Consensus size: 40
12739 GCGATTTTCT
*
12749 AAATTCGCAACGCGAATCTGT-AAA-TCGCAACA-AAGAAGTC
1 AAATTCGCAACGCG-AT-AGTCAAATTCGCAACACAA-AAGTC
*
12789 AAATTCGCAACGCGATAGTCAAATTCGCAATACAAAAGTC
1 AAATTCGCAACGCGATAGTCAAATTCGCAACACAAAAGTC
* * * * **
12829 AAATTCACAACGAGATAGTCAGATTCGCAACGAGAATTTGT-
1 AAATTCGCAACGCGATAGTCAAATTCGCAAC-ACAA-AAGTC
* * *
12870 AAA-TCGCAACAC-AGTAGTCAAATTCGCAACACGATAGTC
1 AAATTCGCAACGCGA-TAGTCAAATTCGCAACACAAAAGTC
* * * *
12909 AAATTCACAACACAAAAGTCAAATTCGCAACACAAAAGTC
1 AAATTCGCAACGCGATAGTCAAATTCGCAACACAAAAGTC
*
12949 AAATTCGCAACGCGATAGTCAAATTCGCAACACATAAGTC
1 AAATTCGCAACGCGATAGTCAAATTCGCAACACAAAAGTC
*
12989 AAATTCGCAACGCGATAGCCAAATTCGCAACACAAAAGTC
1 AAATTCGCAACGCGATAGTCAAATTCGCAACACAAAAGTC
* *
13029 AAATTCGCAACGCGATAGCCAAATTCGCAACACAAAAATC
1 AAATTCGCAACGCGATAGTCAAATTCGCAACACAAAAGTC
13069 AAATTCGCAACGCGA
1 AAATTCGCAACGCGA
13084 AACACAATAT
Statistics
Matches: 258, Mismatches: 28, Indels: 18
0.85 0.09 0.06
Matches are distributed among these distances:
38 5 0.02
39 11 0.04
40 231 0.90
41 9 0.03
42 2 0.01
ACGTcount: A:0.43, C:0.24, G:0.15, T:0.18
Consensus pattern (40 bp):
AAATTCGCAACGCGATAGTCAAATTCGCAACACAAAAGTC
Found at i:12849 original size:60 final size:61
Alignment explanation
Indices: 12785--13080 Score: 336
Period size: 60 Copynumber: 4.9 Consensus size: 61
12775 GCAACAAAGA
* *
12785 AGTCAAATTCGCAACGCGATAGTCAAATTCGCAATACAAAAGTCAAATTCACAACGA-GAT
1 AGTCAAATTCGCAACGCGATAGTCAAATTCGCAACACAAAAGTCAAATTCGCAACGACGAT
* * * **
12845 AGTCAGATTCGCAACGAGAATTTGT-AAA-TCGCAACACAGTAGTCAAATTCGCAAC-ACGAT
1 AGTCAAATTCGCAACGCG-A-TAGTCAAATTCGCAACACAAAAGTCAAATTCGCAACGACGAT
* * * *
12905 AGTCAAATTCACAACACAAAAGTCAAATTCGCAACACAAAAGTCAAATTCGCAACG-CGAT
1 AGTCAAATTCGCAACGCGATAGTCAAATTCGCAACACAAAAGTCAAATTCGCAACGACGAT
* * * * * * *
12965 AGTCAAATTCGCAACAC-ATAAGTCAAATTCGCAACGCGATAGCCAAATTCGCAAC-ACAAA
1 AGTCAAATTCGCAACGCGAT-AGTCAAATTCGCAACACAAAAGTCAAATTCGCAACGACGAT
* *
13025 AGTCAAATTCGCAACGCGATAGCCAAATTCGCAACACAAAAATCAAATTCGCAACG
1 AGTCAAATTCGCAACGCGATAGTCAAATTCGCAACACAAAAGTCAAATTCGCAACG
13081 CGAAACACAA
Statistics
Matches: 195, Mismatches: 31, Indels: 19
0.80 0.13 0.08
Matches are distributed among these distances:
58 2 0.01
59 6 0.03
60 178 0.91
61 6 0.03
62 3 0.02
ACGTcount: A:0.43, C:0.24, G:0.15, T:0.18
Consensus pattern (61 bp):
AGTCAAATTCGCAACGCGATAGTCAAATTCGCAACACAAAAGTCAAATTCGCAACGACGAT
Found at i:12873 original size:100 final size:100
Alignment explanation
Indices: 12749--13059 Score: 430
Period size: 100 Copynumber: 3.1 Consensus size: 100
12739 GCGATTTTCT
* *
12749 AAATTCGCAACGCGAATCTGTAAATCGCAACAAAGAAGTCAAATTCGCAACGCGATAGTCAAATT
1 AAATTCGCAACGCGAATTTGTAAATCGCAACACAGAAGTCAAATTCGCAACGCGATAGTCAAATT
* *
12814 CGCAATACAAAAGTCAAATTCACAACGAGATAGTC
66 CGCAACACAAAAGTCAAATTCGCAACGAGATAGTC
* * * *
12849 AGATTCGCAACGAGAATTTGTAAATCGCAACACAGTAGTCAAATTCGCAACACGATAGTCAAATT
1 AAATTCGCAACGCGAATTTGTAAATCGCAACACAGAAGTCAAATTCGCAACGCGATAGTCAAATT
* * *
12914 CACAACACAAAAGTCAAATTCGCAAC-ACAAAAGTC
66 CGCAACACAAAAGTCAAATTCGCAACGA-GATAGTC
* * *
12949 AAATTCGCAACGCG-A-TAGTCAAATTCGCAACACATAAGTCAAATTCGCAACGCGATAGCCAAA
1 AAATTCGCAACGCGAATTTGT-AAA-TCGCAACACAGAAGTCAAATTCGCAACGCGATAGTCAAA
* *
13012 TTCGCAACACAAAAGTCAAATTCGCAACGCGATAGCC
64 TTCGCAACACAAAAGTCAAATTCGCAACGAGATAGTC
13049 AAATTCGCAAC
1 AAATTCGCAAC
13060 ACAAAAATCA
Statistics
Matches: 184, Mismatches: 23, Indels: 8
0.86 0.11 0.04
Matches are distributed among these distances:
98 3 0.02
99 5 0.03
100 176 0.96
ACGTcount: A:0.42, C:0.24, G:0.15, T:0.18
Consensus pattern (100 bp):
AAATTCGCAACGCGAATTTGTAAATCGCAACACAGAAGTCAAATTCGCAACGCGATAGTCAAATT
CGCAACACAAAAGTCAAATTCGCAACGAGATAGTC
Found at i:13220 original size:22 final size:22
Alignment explanation
Indices: 13195--13245 Score: 75
Period size: 22 Copynumber: 2.3 Consensus size: 22
13185 CTACGGCGAC
*
13195 ATCCGTCCCCATCTCCGACGAA
1 ATCCGTCCCAATCTCCGACGAA
* *
13217 ATCCGTCCCAATCTCTGGCGAA
1 ATCCGTCCCAATCTCCGACGAA
13239 ATCCGTC
1 ATCCGTC
13246 TATCTCCATC
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 26 1.00
ACGTcount: A:0.22, C:0.41, G:0.16, T:0.22
Consensus pattern (22 bp):
ATCCGTCCCAATCTCCGACGAA
Found at i:14130 original size:18 final size:18
Alignment explanation
Indices: 14107--14143 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
14097 CGAAATTTAT
14107 ATTGAAATTCAAACTCAA
1 ATTGAAATTCAAACTCAA
* *
14125 ATTGAAATTTAAATTCAA
1 ATTGAAATTCAAACTCAA
14143 A
1 A
14144 CTCCAATTAC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.51, C:0.11, G:0.05, T:0.32
Consensus pattern (18 bp):
ATTGAAATTCAAACTCAA
Found at i:17713 original size:19 final size:18
Alignment explanation
Indices: 17670--17716 Score: 58
Period size: 18 Copynumber: 2.6 Consensus size: 18
17660 CAAAACATTT
17670 GTGTTGCGAAACTAAAAC
1 GTGTTGCGAAACTAAAAC
* * *
17688 CTGTTGCGAAATTAAATTC
1 GTGTTGCGAAACTAAA-AC
17707 GTGTTGCGAA
1 GTGTTGCGAA
17717 TTCGAAAATA
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
18 14 0.58
19 10 0.42
ACGTcount: A:0.32, C:0.15, G:0.23, T:0.30
Consensus pattern (18 bp):
GTGTTGCGAAACTAAAAC
Found at i:17750 original size:19 final size:19
Alignment explanation
Indices: 17690--17765 Score: 75
Period size: 19 Copynumber: 3.9 Consensus size: 19
17680 ACTAAAACCT
* *
17690 GTTGCGAAATT-AAATTCGT
1 GTTGCGAATTTGAAATTC-A
*
17709 GTTGCGAATTCGAAAATAT-A
1 GTTGCGAATTTG-AAAT-TCA
17729 GTTGCGAATTTGAAATTCA
1 GTTGCGAATTTGAAATTCA
*
17748 GTTGTGAATTTGAAATTC
1 GTTGCGAATTTGAAATTC
17766 CGCGTTGTGA
Statistics
Matches: 48, Mismatches: 5, Indels: 8
0.79 0.08 0.13
Matches are distributed among these distances:
18 1 0.02
19 31 0.65
20 11 0.23
21 4 0.08
22 1 0.02
ACGTcount: A:0.33, C:0.09, G:0.21, T:0.37
Consensus pattern (19 bp):
GTTGCGAATTTGAAATTCA
Found at i:17774 original size:21 final size:19
Alignment explanation
Indices: 17728--17781 Score: 72
Period size: 19 Copynumber: 2.7 Consensus size: 19
17718 TCGAAAATAT
*
17728 AGTTGCGAATTTGAAATTC
1 AGTTGTGAATTTGAAATTC
17747 AGTTGTGAATTTGAAATTCC
1 AGTTGTGAATTTGAAATT-C
*
17767 GCGTTGTGAATTTGA
1 -AGTTGTGAATTTGA
17782 CTATCGCGTT
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
19 17 0.55
20 1 0.03
21 13 0.42
ACGTcount: A:0.28, C:0.09, G:0.24, T:0.39
Consensus pattern (19 bp):
AGTTGTGAATTTGAAATTC
Found at i:17791 original size:20 final size:22
Alignment explanation
Indices: 17748--17803 Score: 73
Period size: 20 Copynumber: 2.7 Consensus size: 22
17738 TTGAAATTCA
*
17748 GTTGTGAATTTGA-AATTCCGC
1 GTTGTGAATTTGACTATTCCGC
17769 GTTGTGAATTTGACTA-T-CGC
1 GTTGTGAATTTGACTATTCCGC
*
17789 GTTGCGAATTTGACT
1 GTTGTGAATTTGACT
17804 TCTGTGTTGC
Statistics
Matches: 32, Mismatches: 2, Indels: 3
0.86 0.05 0.08
Matches are distributed among these distances:
20 17 0.53
21 14 0.44
22 1 0.03
ACGTcount: A:0.21, C:0.14, G:0.25, T:0.39
Consensus pattern (22 bp):
GTTGTGAATTTGACTATTCCGC
Found at i:17876 original size:20 final size:19
Alignment explanation
Indices: 17823--17876 Score: 54
Period size: 20 Copynumber: 2.7 Consensus size: 19
17813 CGATTTACAA
17823 ATTCGCGTTGCGAAATTGG
1 ATTCGCGTTGCGAAATTGG
** * *
17842 AAACTGGGTTACGAAATTGG
1 ATTC-GCGTTGCGAAATTGG
17862 AGTTCGCGTTGCGAA
1 A-TTCGCGTTGCGAA
17877 TTTGTTGGTC
Statistics
Matches: 25, Mismatches: 8, Indels: 3
0.69 0.22 0.08
Matches are distributed among these distances:
19 2 0.08
20 22 0.88
21 1 0.04
ACGTcount: A:0.26, C:0.15, G:0.31, T:0.28
Consensus pattern (19 bp):
ATTCGCGTTGCGAAATTGG
Found at i:20500 original size:33 final size:32
Alignment explanation
Indices: 20463--20546 Score: 116
Period size: 33 Copynumber: 2.6 Consensus size: 32
20453 TTAATTTGTG
20463 CAATAAAATAAAATGTTAGTA-AGTTAGTAAGAA
1 CAATAAAATAAAA-GTTAGTATA-TTAGTAAGAA
* *
20496 CAATAAAAAAAAAGTTAGTATATTAGTATGAA
1 CAATAAAATAAAAGTTAGTATATTAGTAAGAA
20528 CAAATAAAATAAAAGTTAG
1 C-AATAAAATAAAAGTTAG
20547 GGGGTGTTTT
Statistics
Matches: 46, Mismatches: 3, Indels: 4
0.87 0.06 0.08
Matches are distributed among these distances:
32 17 0.37
33 29 0.63
ACGTcount: A:0.57, C:0.04, G:0.13, T:0.26
Consensus pattern (32 bp):
CAATAAAATAAAAGTTAGTATATTAGTAAGAA
Found at i:20694 original size:28 final size:27
Alignment explanation
Indices: 20663--20729 Score: 84
Period size: 25 Copynumber: 2.5 Consensus size: 27
20653 TAGTTTATGC
*
20663 AATAAAAAATGTTAGTAAGAACAATAAA
1 AATAAAAAA-GTTAGTAAGAACAACAAA
* *
20691 AAT--AAAAGTTAGTATGAATAACAAA
1 AATAAAAAAGTTAGTAAGAACAACAAA
20716 AATAAAAAAGTTAG
1 AATAAAAAAGTTAG
20730 AATGTTATTA
Statistics
Matches: 34, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
25 18 0.53
26 4 0.12
27 9 0.26
28 3 0.09
ACGTcount: A:0.63, C:0.03, G:0.12, T:0.22
Consensus pattern (27 bp):
AATAAAAAAGTTAGTAAGAACAACAAA
Found at i:23023 original size:13 final size:13
Alignment explanation
Indices: 23005--23029 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
22995 ACAAACTCGC
23005 ATATGAAGACTGG
1 ATATGAAGACTGG
23018 ATATGAAGACTG
1 ATATGAAGACTG
23030 TTCAACTATG
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:0.40, C:0.08, G:0.28, T:0.24
Consensus pattern (13 bp):
ATATGAAGACTGG
Found at i:24532 original size:122 final size:122
Alignment explanation
Indices: 24339--24606 Score: 349
Period size: 122 Copynumber: 2.2 Consensus size: 122
24329 GTTGAGGACT
* * *
24339 TCGGGTCAATATGGATATAACTTGGTGTTGAAGATGAAATTGCTCATCCATGTTGAAGAGATCTG
1 TCGGGTCAATATGGAGATAATTTGATGTTGAAGATGAAATTGCTCATCCATGTTGAAGAGATCTG
* ** *
24404 GCCGCTTTTAGATAAATTGTTTGCTGAAAATGACGTTGTTCCTTCTCATTGAGGAAA
66 GCCGCTTTTAGATAAATTGTTTACTGAAAATGAAATTGTTCCTTCTCATTAAGGAAA
* * * *
24461 TTGGGTCAATTTGGAGATAATTTTATGTTGAAGATG-ACTCTGCTCATCCATGTTGAAGAGATCT
1 TCGGGTCAATATGGAGATAATTTGATGTTGAAGATGAAAT-TGCTCATCCATGTTGAAGAGATCT
* * * * * *
24525 GGTCGCTTTTAGATAAATTTTTTATTGAATATGAAATTGTTCCTTCTCGTTAAGGAAG
65 GGCCGCTTTTAGATAAATTGTTTACTGAAAATGAAATTGTTCCTTCTCATTAAGGAAA
* *
24583 TCGAGTCAATCTGGAGATAATTTG
1 TCGGGTCAATATGGAGATAATTTG
24607 GAGACAACAC
Statistics
Matches: 124, Mismatches: 21, Indels: 2
0.84 0.14 0.01
Matches are distributed among these distances:
121 2 0.02
122 122 0.98
ACGTcount: A:0.28, C:0.13, G:0.23, T:0.37
Consensus pattern (122 bp):
TCGGGTCAATATGGAGATAATTTGATGTTGAAGATGAAATTGCTCATCCATGTTGAAGAGATCTG
GCCGCTTTTAGATAAATTGTTTACTGAAAATGAAATTGTTCCTTCTCATTAAGGAAA
Found at i:24553 original size:61 final size:60
Alignment explanation
Indices: 24364--24558 Score: 164
Period size: 61 Copynumber: 3.2 Consensus size: 60
24354 TATAACTTGG
* * *
24364 TGTTGAAGATGAAATTGCTCATCCATGTTGAAGAGATCTGGCCGCTTTTAGATAAATTGTT
1 TGTTGAAGATG-ACTTGCTCATCCATGTTGAAGAGATCTGGTCGCTTTTAGATAAATTTTT
* * * * * * ** * *
24425 TGCTGAAAATGACGTTGTTCCTTCTCA--TTGAGGAAAT-TGGGTCAATTTGGAGAT-AATTTTA
1 TGTTGAAGATGAC-TTGCT-CATC-CATGTTGAAGAGATCT-GGTCGCTTT-TAGATAAATTTTT
24486 TGTTGAAGATGACTCTGCTCATCCATGTTGAAGAGATCTGGTCGCTTTTAGATAAATTTTT
1 TGTTGAAGATGACT-TGCTCATCCATGTTGAAGAGATCTGGTCGCTTTTAGATAAATTTTT
* *
24547 TATTGAATATGA
1 TGTTGAAGATGA
24559 AATTGTTCCT
Statistics
Matches: 99, Mismatches: 25, Indels: 20
0.69 0.17 0.14
Matches are distributed among these distances:
59 2 0.02
60 10 0.10
61 77 0.78
62 8 0.08
63 2 0.02
ACGTcount: A:0.28, C:0.12, G:0.22, T:0.38
Consensus pattern (60 bp):
TGTTGAAGATGACTTGCTCATCCATGTTGAAGAGATCTGGTCGCTTTTAGATAAATTTTT
Found at i:24942 original size:342 final size:342
Alignment explanation
Indices: 24309--25017 Score: 888
Period size: 342 Copynumber: 2.1 Consensus size: 342
24299 GATGATTCAG
* * * * *
24309 AGATGACACTGCTCTTTCATGTTGAGGACTTCGGGTCAATATGGATATAACTTGGTGTTGAAGAT
1 AGATGACACTGCTCATTCACGTTGAGGACGTCGGGTCAATATGGAGATAACTTGGTGTTGAAGAC
* *
24374 GAAATTGCTCATCCATGTTGAAGAGATCTGGCCGCTTTTAGATAAATTGTTTGCTGAAAATGACG
66 GAAATTGCTCATCCATGTTGAAGAGATCTGGCCGCTTTCAGATAAATTGTTTGCTGAAAATGAAG
* * * * * * *
24439 TTGTTCCTTCTCATTGAGGAAATTGGGTCAATTTGGAGATAATTTTATGTTGAAGATGACTCTGC
131 TCGTTCCTTCTCATTAAGGAAATTAGGTCAATTTAGAGATAATTTGATGTTGAAAATGACACTGC
* ** * * * * *
24504 TCATCCATGTTGAAGAGATCTGGTCGCTTTTAGATAAATTTTTTATTGAATATGAAATTGTTCCT
196 TCATCCATGTTGAAGAGATATGACCGCTTTTAGATAAATTGTTTATTGAAGATGAAACTATTCAT
* * ** *
24569 TCTCGTTAAGGAAGTCGAGTCAATCTGGAGATAATTTGGAGACAACACGGTTCCTTCGCGTTAAA
261 TCTCGTTAAGGAAATCGAGTCAATATGGAGATAATTCAGAGACAACACGGTTCATTCGCGTTAAA
24634 GAAGTCTGATTGTCT-A
326 GAAGTCTGATTGTCTGA
* *
24650 AGGATGACATTGCTCATTCACGTTGAGGAGGTCGGGTCAATATGGAGATAA-TTAGGTGTTGAAG
1 A-GATGACACTGCTCATTCACGTTGAGGACGTCGGGTCAATATGGAGATAACTT-GGTGTTGAAG
* * * * *
24714 ACG-ACTCTGCTCATCCGTGTTGAAGAGATCTGGTCGCTTTCAGATAAATTGTTTGTTGAATATG
64 ACGAAAT-TGCTCATCCATGTTGAAGAGATCTGGCCGCTTTCAGATAAATTGTTTGCTGAAAATG
* * * * *
24778 AAGTCGTTCCTTCTCGTTAAGG-ACTTCAGGTTAATTTAGATATAATTTGGTGTTGAAAATGACA
128 AAGTCGTTCCTTCTCATTAAGGAAATT-AGGTCAATTTAGAGATAATTTGATGTTGAAAATGACA
* *
24842 CTGCTCATCCATGTTGAAGAGATATGACCGCTTTTAGATAAATTGTTTGTTGAAGATGACACTAT
192 CTGCTCATCCATGTTGAAGAGATATGACCGCTTTTAGATAAATTGTTTATTGAAGATGAAACTAT
* * *
24907 TCATTCTCGTTGAGGAAATCTG-GTCAATATGGAGATAATTCAGAGACAACACGGTTTATTCGTG
257 TCATTCTCGTTAAGGAAATC-GAGTCAATATGGAGATAATTCAGAGACAACACGGTTCATTCGCG
* *
24971 TTGAGGAAGTCTGATTGTCTGA
321 TTAAAGAAGTCTGATTGTCTGA
* * * *
24993 AGATGATACTGTTCTTTCGCGTTGA
1 AGATGACACTGCTCATTCACGTTGA
25018 AGAGATATGG
Statistics
Matches: 311, Mismatches: 51, Indels: 11
0.83 0.14 0.03
Matches are distributed among these distances:
341 8 0.03
342 300 0.96
343 3 0.01
ACGTcount: A:0.27, C:0.14, G:0.24, T:0.35
Consensus pattern (342 bp):
AGATGACACTGCTCATTCACGTTGAGGACGTCGGGTCAATATGGAGATAACTTGGTGTTGAAGAC
GAAATTGCTCATCCATGTTGAAGAGATCTGGCCGCTTTCAGATAAATTGTTTGCTGAAAATGAAG
TCGTTCCTTCTCATTAAGGAAATTAGGTCAATTTAGAGATAATTTGATGTTGAAAATGACACTGC
TCATCCATGTTGAAGAGATATGACCGCTTTTAGATAAATTGTTTATTGAAGATGAAACTATTCAT
TCTCGTTAAGGAAATCGAGTCAATATGGAGATAATTCAGAGACAACACGGTTCATTCGCGTTAAA
GAAGTCTGATTGTCTGA
Found at i:24945 original size:122 final size:122
Alignment explanation
Indices: 24663--24946 Score: 327
Period size: 122 Copynumber: 2.3 Consensus size: 122
24653 ATGACATTGC
* ** * * *
24663 TCATTCACGTTGAGGAGGTCGGGTCAATATGGAGATAATTAGGTGTTGAAGACGACTCTGCTCAT
1 TCATTCTCGTTGAGGAAATCAGGTCAATATGGAGATAATTAGGTGTTGAAAACGACACTGCTCAT
* * ** * * *
24728 CCGTGTTGAAGAGATCTGGTCGCTTTCAGATAAATTGTTTGTTGAATATGAAGTCGT
66 CCATGTTGAAGAGATATGACCGCTTTCAGATAAATTGTTTGTTGAAGATGAACTCAT
* * ** * * * * * *
24785 TCCTTCTCGTTAAGGACTTCAGGTTAATTTAGATATAATTTGGTGTTGAAAATGACACTGCTCAT
1 TCATTCTCGTTGAGGAAATCAGGTCAATATGGAGATAATTAGGTGTTGAAAACGACACTGCTCAT
*
24850 CCATGTTGAAGAGATATGACCGCTTTTAGATAAATTGTTTGTTGAAGATGACACT-AT
66 CCATGTTGAAGAGATATGACCGCTTTCAGATAAATTGTTTGTTGAAGATGA-ACTCAT
*
24907 TCATTCTCGTTGAGGAAATCTGGTCAATATGGAGATAATT
1 TCATTCTCGTTGAGGAAATCAGGTCAATATGGAGATAATT
24947 CAGAGACAAC
Statistics
Matches: 130, Mismatches: 31, Indels: 2
0.80 0.19 0.01
Matches are distributed among these distances:
122 128 0.98
123 2 0.02
ACGTcount: A:0.28, C:0.14, G:0.24, T:0.35
Consensus pattern (122 bp):
TCATTCTCGTTGAGGAAATCAGGTCAATATGGAGATAATTAGGTGTTGAAAACGACACTGCTCAT
CCATGTTGAAGAGATATGACCGCTTTCAGATAAATTGTTTGTTGAAGATGAACTCAT
Found at i:25194 original size:139 final size:139
Alignment explanation
Indices: 24940--25503 Score: 553
Period size: 139 Copynumber: 4.1 Consensus size: 139
24930 TCAATATGGA
** ** * * * * *
24940 GATAATTCAGAGACAACACGGTTTATTCGTGT-TGAGGAAGTCTGATTGTCTGAAGATGATACTG
1 GATAATTTGGAGACAACACGGTTCCTACGT-TATGAGGAAGTCTGGTTGTCTAAAGATGACACTA
* * * * * * * * *
25004 TTCTTTCGCGTTGAA-GAGATATGGTCGGTGAACGAAATTGTTCCTATGTGATAAGGATGTCTAG
65 CTCCTTCGCGTT-AAGGAGATCTGGTCGATGGACGACATTGTTCCTACGTGATGAGGACGTCTAG
*
25068 TTGTATTTAGG
129 TCGTATTTAGG
* **
25079 GATAATTTGGAGACAACACGGTTCCTACGTTATGAGGAAGTCTGGTTGTCTAAAGATGACATTGT
1 GATAATTTGGAGACAACACGGTTCCTACGTTATGAGGAAGTCTGGTTGTCTAAAGATGACACTAC
* * *
25144 TCCTTCGTGTTAAGGAGATCTTGTCGATGGACGACATTGTTCCTACGTGATGAGGACGTCTA-AC
66 TCCTTCGCGTTAAGGAGATCTGGTCGATGGACGACATTGTTCCTACGTGATGAGGACGTCTAGTC
* * *
25208 TTCCTTTAGA
131 GT-ATTTAGG
* * * **
25218 AATAATTTGGAGACAACACGGTTCCTA-ATTGATGAGGAAGTCTGGTTGTCTAAGGATGACGTTA
1 GATAATTTGGAGACAACACGGTTCCTACGTT-ATGAGGAAGTCTGGTTGTCTAAAGATGACACTA
* * * * *
25282 CTCCTTCGCGTTGAGGAGATCTGGTCGATTGATGACATTGTTCCTACGTGATGAGGACATCTAGC
65 CTCCTTCGCGTTAAGGAGATCTGGTCGATGGACGACATTGTTCCTACGTGATGAGGACGTCTAGT
25347 CGTATTTAGG
130 CGTATTTAGG
* * ** * * *
25357 GATAATTTGGAGACAACACAGTTTCTACGTGGTGAGGAAGTCTGGTTGTCTAAGGGTGACGCTAC
1 GATAATTTGGAGACAACACGGTTCCTACGTTATGAGGAAGTCTGGTTGTCTAAAGATGACACTAC
* * * * * * * * * *
25422 TCCTTCGTGTTGAGGATACCTGGTCAATGGACGACATTATTCTTTCGTGTTGAGGAAGTCTAGTC
66 TCCTTCGCGTTAAGGAGATCTGGTCGATGGACGACATTGTTCCTACGTGATGAGGACGTCTAGTC
25487 GT-TTTAGG
131 GTATTTAGG
25495 AGATAATTT
1 -GATAATTT
25504 TTCTTTAGAA
Statistics
Matches: 357, Mismatches: 61, Indels: 14
0.83 0.14 0.03
Matches are distributed among these distances:
138 12 0.03
139 342 0.96
140 3 0.01
ACGTcount: A:0.25, C:0.15, G:0.27, T:0.33
Consensus pattern (139 bp):
GATAATTTGGAGACAACACGGTTCCTACGTTATGAGGAAGTCTGGTTGTCTAAAGATGACACTAC
TCCTTCGCGTTAAGGAGATCTGGTCGATGGACGACATTGTTCCTACGTGATGAGGACGTCTAGTC
GTATTTAGG
Found at i:25503 original size:278 final size:277
Alignment explanation
Indices: 24937--25503 Score: 637
Period size: 278 Copynumber: 2.0 Consensus size: 277
24927 TGGTCAATAT
* * *
24937 GGAGATAATTCAGAGACAACACGGTTTATTCGTGTTGAGGAAGTCTGATTGTCTGAAGATGATAC
1 GGAGATAATTTAGAGACAACACGGTTTAATC-TGATGAGGAAGTCTGATTGTCTGAAGATGA-AC
* **
25002 TGTTCTTTCGCGTTGAAGAGATATGGTCGGTGAACGAAATTGTTCCTATGTGATAAGGATGTCTA
64 TGTTCTTTCGCGTTGAAGAGATATGGTCGGTGAACGAAATTGTTCCTACGTGATAAGGACATCTA
** * *
25067 GTTGTATTTAGGGATAATTTGGAGACAACACGGTTCCTACGTTATGAGGAAGTCTGGTTGTCTAA
129 GCCGTATTTAGGGATAATTTGGAGACAACACAGTTCCTACGTGATGAGGAAGTCTGGTTGTCTAA
* ** * * * *
25132 AGATGACATTGTTCCTTCGTGTTAAGGAGATCTTGTCGATGGACGACATTGTTCCTACGTGATGA
194 AGATGACACTACTCCTTCGTGTTAAGGAGACCTGGTCAATGGACGACATTATTCCTACGTGATGA
* *
25197 GGACGTCTAACTTCCTTTA
259 GGAAGTCTAACGTCCTTTA
* * *
25216 -GAAATAATTTGGAGACAACACGGTTCCTAAT-TGATGAGGAAGTCTGGTTGTCT-AAGGATG-A
1 GGAGATAATTTAGAGACAACACGGTT--TAATCTGATGAGGAAGTCTGATTGTCTGAA-GATGAA
* * * * * *
25277 C-GTTACTCCTTCGCGTTGAGGAGATCTGGTCGATTG-ATGACATTGTTCCTACGTGATGAGGAC
63 CTGTT-CT--TTCGCGTTGAAGAGATATGGTCG-GTGAACGAAATTGTTCCTACGTGATAAGGAC
* *
25340 ATCTAGCCGTATTTAGGGATAATTTGGAGACAACACAGTTTCTACGTGGTGAGGAAGTCTGGTTG
124 ATCTAGCCGTATTTAGGGATAATTTGGAGACAACACAGTTCCTACGTGATGAGGAAGTCTGGTTG
* * * * * * *
25405 TCTAAGGGTGACGCTACTCCTTCGTGTTGAGGATACCTGGTCAATGGACGACATTATTCTTTCGT
189 TCTAAAGATGACACTACTCCTTCGTGTTAAGGAGACCTGGTCAATGGACGACATTATTCCTACGT
* *
25470 GTTGAGGAAGTCT-A-GTCGTTTTA
254 GATGAGGAAGTCTAACGTC-CTTTA
25493 GGAGATAATTT
1 GGAGATAATTT
25504 TTCTTTAGAA
Statistics
Matches: 239, Mismatches: 40, Indels: 19
0.80 0.13 0.06
Matches are distributed among these distances:
275 3 0.01
276 6 0.03
277 7 0.03
278 218 0.91
279 2 0.01
280 3 0.01
ACGTcount: A:0.25, C:0.15, G:0.27, T:0.33
Consensus pattern (277 bp):
GGAGATAATTTAGAGACAACACGGTTTAATCTGATGAGGAAGTCTGATTGTCTGAAGATGAACTG
TTCTTTCGCGTTGAAGAGATATGGTCGGTGAACGAAATTGTTCCTACGTGATAAGGACATCTAGC
CGTATTTAGGGATAATTTGGAGACAACACAGTTCCTACGTGATGAGGAAGTCTGGTTGTCTAAAG
ATGACACTACTCCTTCGTGTTAAGGAGACCTGGTCAATGGACGACATTATTCCTACGTGATGAGG
AAGTCTAACGTCCTTTA
Found at i:27673 original size:24 final size:24
Alignment explanation
Indices: 27619--27681 Score: 74
Period size: 25 Copynumber: 2.6 Consensus size: 24
27609 TTTTATTTTC
27619 AAAATTTTGAAAAATATCAATTAA
1 AAAATTTTGAAAAATATCAATTAA
* * *
27643 AAGAATTTTGAAAAATGTTTAA-TCA
1 AA-AATTTTGAAAAAT-ATCAATTAA
27668 AAAATTTTGAAAAA
1 AAAATTTTGAAAAA
27682 AATATTGCCC
Statistics
Matches: 34, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
24 14 0.41
25 17 0.50
26 3 0.09
ACGTcount: A:0.56, C:0.03, G:0.08, T:0.33
Consensus pattern (24 bp):
AAAATTTTGAAAAATATCAATTAA
Found at i:28569 original size:16 final size:16
Alignment explanation
Indices: 28548--28620 Score: 80
Period size: 16 Copynumber: 4.7 Consensus size: 16
28538 TATTGTCTTT
* *
28548 TTTTTTTCTCTATTTC
1 TTTTTTTCTTTGTTTC
28564 TTTTTTTTCTTTGTTTC
1 -TTTTTTTCTTTGTTTC
*
28581 TTTGTTTCTTTGTTTC
1 TTTTTTTCTTTGTTTC
*
28597 TTTTTTT-TAT-TTTC
1 TTTTTTTCTTTGTTTC
28611 -TTTTTTCTTT
1 TTTTTTTCTTT
28621 TTGCTTTGAT
Statistics
Matches: 49, Mismatches: 6, Indels: 5
0.82 0.10 0.08
Matches are distributed among these distances:
13 6 0.12
14 6 0.12
15 2 0.04
16 21 0.43
17 14 0.29
ACGTcount: A:0.03, C:0.12, G:0.04, T:0.81
Consensus pattern (16 bp):
TTTTTTTCTTTGTTTC
Found at i:28569 original size:17 final size:17
Alignment explanation
Indices: 28547--28604 Score: 82
Period size: 17 Copynumber: 3.5 Consensus size: 17
28537 TTATTGTCTT
* *
28547 TTTTTTTTCTCTATTTC
1 TTTTTTTTCTTTGTTTC
28564 TTTTTTTTCTTTGTTTC
1 TTTTTTTTCTTTGTTTC
*
28581 -TTTGTTTCTTTGTTTC
1 TTTTTTTTCTTTGTTTC
28597 TTTTTTTT
1 TTTTTTTT
28605 ATTTTCTTTT
Statistics
Matches: 36, Mismatches: 4, Indels: 2
0.86 0.10 0.05
Matches are distributed among these distances:
16 15 0.42
17 21 0.58
ACGTcount: A:0.02, C:0.12, G:0.05, T:0.81
Consensus pattern (17 bp):
TTTTTTTTCTTTGTTTC
Found at i:28580 original size:8 final size:7
Alignment explanation
Indices: 28543--28627 Score: 77
Period size: 7 Copynumber: 11.7 Consensus size: 7
28533 TTGTTTATTG
28543 TCTTTTT
1 TCTTTTT
*
28550 T-TTTTC
1 TCTTTTT
28556 TCTATTTCT
1 TCT-TTT-T
28565 T-TTTTT
1 TCTTTTT
28571 TCTTTGTT
1 TCTTT-TT
28579 TCTTTGTT
1 TCTTT-TT
28587 TCTTTGTT
1 TCTTT-TT
28595 TCTTTTT
1 TCTTTTT
28602 T-TTATTT
1 TCTT-TTT
28609 TCTTTTT
1 TCTTTTT
28616 TCTTTTT
1 TCTTTTT
*
28623 GCTTT
1 TCTTT
28628 GATTTGATCT
Statistics
Matches: 68, Mismatches: 3, Indels: 14
0.80 0.04 0.16
Matches are distributed among these distances:
6 9 0.13
7 29 0.43
8 29 0.43
9 1 0.01
ACGTcount: A:0.02, C:0.13, G:0.05, T:0.80
Consensus pattern (7 bp):
TCTTTTT
Found at i:34963 original size:24 final size:24
Alignment explanation
Indices: 34936--34982 Score: 67
Period size: 24 Copynumber: 2.0 Consensus size: 24
34926 AATTATGTAC
** *
34936 AAAATAAATTAAAAAATTAAAATA
1 AAAATAAAGGAAAAAAATAAAATA
34960 AAAATAAAGGAAAAAAATAAAAT
1 AAAATAAAGGAAAAAAATAAAAT
34983 TATTATTTAT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.77, C:0.00, G:0.04, T:0.19
Consensus pattern (24 bp):
AAAATAAAGGAAAAAAATAAAATA
Found at i:45964 original size:35 final size:34
Alignment explanation
Indices: 45903--45984 Score: 96
Period size: 35 Copynumber: 2.4 Consensus size: 34
45893 TTAGTTTTTG
*
45903 CAAT-AAAATAAAATATTAGTAAGTTAGTAAGAA
1 CAATAAAAATAAAAAATTAGTAAGTTAGTAAGAA
* *
45936 CAATAAAAATAAAAAAGTTAGTACGTTAGTATGAA
1 CAATAAAAATAAAAAA-TTAGTAAGTTAGTAAGAA
*
45971 TAA-ATAAAATAAAA
1 CAATA-AAAATAAAA
45985 GTTTGGGTTT
Statistics
Matches: 42, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
33 4 0.10
34 11 0.26
35 27 0.64
ACGTcount: A:0.60, C:0.04, G:0.11, T:0.26
Consensus pattern (34 bp):
CAATAAAAATAAAAAATTAGTAAGTTAGTAAGAA
Found at i:55436 original size:11 final size:11
Alignment explanation
Indices: 55420--55449 Score: 53
Period size: 10 Copynumber: 2.8 Consensus size: 11
55410 ATTTTTATTT
55420 AATAAAAAACA
1 AATAAAAAACA
55431 AAT-AAAAACA
1 AATAAAAAACA
55441 AATAAAAAA
1 AATAAAAAA
55450 ATATTATTTA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
10 10 0.56
11 8 0.44
ACGTcount: A:0.83, C:0.07, G:0.00, T:0.10
Consensus pattern (11 bp):
AATAAAAAACA
Found at i:56671 original size:39 final size:39
Alignment explanation
Indices: 56611--56686 Score: 116
Period size: 39 Copynumber: 1.9 Consensus size: 39
56601 CCTGGCAGTG
* *
56611 CTGGAAGCTGTTGCAACTGATGCGTGGAGGGGCTGCTCA
1 CTGGAAGCTGCTGCAAATGATGCGTGGAGGGGCTGCTCA
* *
56650 CTGGAAGCTGCTGGAAATGATGTGTGGAGGGGCTGCT
1 CTGGAAGCTGCTGCAAATGATGCGTGGAGGGGCTGCT
56687 GGATGGAGGG
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
39 33 1.00
ACGTcount: A:0.18, C:0.17, G:0.41, T:0.24
Consensus pattern (39 bp):
CTGGAAGCTGCTGCAAATGATGCGTGGAGGGGCTGCTCA
Found at i:57519 original size:73 final size:73
Alignment explanation
Indices: 57395--57712 Score: 456
Period size: 73 Copynumber: 4.3 Consensus size: 73
57385 GAGGTCTTAT
* * * * *
57395 CATCTTGCACTGTAGGGCTTATAGATGACCCTGAGGCTTTAAGATCAAAAAGCTCCCGAAGGTTT
1 CATCATGCACTGTAGGTCTTACAGATGACCCTGAGGCTTTAAAATCAAAAAGCTCCCGAAGGCTT
57460 TTTGAAAA
66 TTTGAAAA
* * * *
57468 CATCATGCACTATAGGTCTTACAGATGACCCTGAGGCTATAAAATCAAAAAGCTTCTGAAGGCTT
1 CATCATGCACTGTAGGTCTTACAGATGACCCTGAGGCTTTAAAATCAAAAAGCTCCCGAAGGCTT
*
57533 TTTGATAA
66 TTTGAAAA
*
57541 CATCATGCACTGTAGGTCTTACAGATGACCCTGAGGCTTTAAGATCAAAAAGCTCCCGAAGGCTT
1 CATCATGCACTGTAGGTCTTACAGATGACCCTGAGGCTTTAAAATCAAAAAGCTCCCGAAGGCTT
57606 TTTGAAAA
66 TTTGAAAA
* *
57614 CATCATGCACTGTAGGTCTTACAGATGACCCTGAGGGTTTTGAAAACATCAAAAAGCTCCCAAAG
1 CATCATGCACTGTAGGTCTTACAGATGACCCTGA-GGCTTT--AAA-ATCAAAAAGCTCCCGAAG
57679 GCTTTTTGAAAA
62 GCTTTTTGAAAA
* * *
57691 CATCCTGCACTGCAGGGCTTAC
1 CATCATGCACTGTAGGTCTTAC
57713 GAATGTTGGA
Statistics
Matches: 219, Mismatches: 22, Indels: 4
0.89 0.09 0.02
Matches are distributed among these distances:
73 164 0.75
74 5 0.02
76 2 0.01
77 48 0.22
ACGTcount: A:0.31, C:0.21, G:0.20, T:0.27
Consensus pattern (73 bp):
CATCATGCACTGTAGGTCTTACAGATGACCCTGAGGCTTTAAAATCAAAAAGCTCCCGAAGGCTT
TTTGAAAA
Found at i:58435 original size:22 final size:22
Alignment explanation
Indices: 58384--58441 Score: 80
Period size: 22 Copynumber: 2.6 Consensus size: 22
58374 GATAAAGCTT
* *
58384 TCATCTTCGAAAAGAGAATATA
1 TCATCTTTGAAGAGAGAATATA
* *
58406 TCATCTTTGAAGATAGAATCTA
1 TCATCTTTGAAGAGAGAATATA
58428 TCATCTTTGAAGAG
1 TCATCTTTGAAGAG
58442 TGTAGATGTA
Statistics
Matches: 31, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 31 1.00
ACGTcount: A:0.38, C:0.14, G:0.16, T:0.33
Consensus pattern (22 bp):
TCATCTTTGAAGAGAGAATATA
Done.