Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007926.1 Hibiscus syriacus cultivar Beakdansim tig00110332_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: 10075380
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 12 of 42
Found at i:2510589 original size:3 final size:3
Alignment explanation
Indices: 2510581--2510614 Score: 50
Period size: 3 Copynumber: 11.3 Consensus size: 3
2510571 CATAAAATGG
* *
2510581 ATA ATA ATA ACA ATG ATA ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
2510615 AGCAAAAGAC
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.65, C:0.03, G:0.03, T:0.29
Consensus pattern (3 bp):
ATA
Found at i:2520449 original size:12 final size:12
Alignment explanation
Indices: 2520432--2520458 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
2520422 TTTATTCAAC
2520432 AAATGCCGCTAA
1 AAATGCCGCTAA
2520444 AAATGCCGCTAA
1 AAATGCCGCTAA
2520456 AAA
1 AAA
2520459 CCCAAGTGAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.48, C:0.22, G:0.15, T:0.15
Consensus pattern (12 bp):
AAATGCCGCTAA
Found at i:2523554 original size:59 final size:61
Alignment explanation
Indices: 2523482--2523637 Score: 173
Period size: 59 Copynumber: 2.6 Consensus size: 61
2523472 TCAAATGATC
* * * *
2523482 ATTTTATAACTTTTAATAGTCGATGGACTCAACAAATGAATATC-CTATTA-TC-GG-GGGTT
1 ATTTTGTAACTTTTAATAGTCGATGGACTCAACAAATCAATA-CACT-CTAGTCAGGAGAGTT
*
2523541 ATTTTGTAACTTTTAATAGTC-ATGGAACTCAACAAAACAATACACTCTAGTCAGGAGAGTT
1 ATTTTGTAACTTTTAATAGTCGATGG-ACTCAACAAATCAATACACTCTAGTCAGGAGAGTT
*
2523602 ATTTTGTAACTTTTAATAGTTGAAT--ACTCAACAAAT
1 ATTTTGTAACTTTTAATAGTCG-ATGGACTCAACAAAT
2523638 TAATGTCATA
Statistics
Matches: 83, Mismatches: 7, Indels: 13
0.81 0.07 0.13
Matches are distributed among these distances:
58 7 0.08
59 38 0.46
60 12 0.14
61 24 0.29
63 2 0.02
ACGTcount: A:0.36, C:0.14, G:0.14, T:0.36
Consensus pattern (61 bp):
ATTTTGTAACTTTTAATAGTCGATGGACTCAACAAATCAATACACTCTAGTCAGGAGAGTT
Found at i:2530561 original size:27 final size:27
Alignment explanation
Indices: 2530531--2530610 Score: 105
Period size: 27 Copynumber: 3.1 Consensus size: 27
2530521 TAATGGCTCT
*
2530531 GAATGTATTTCTGTGCTGAATAATTCA
1 GAATGTATTTCTGTGCTGAATTATTCA
*
2530558 GAATGTACTTCTGTGCTGAATTATTCA
1 GAATGTATTTCTGTGCTGAATTATTCA
2530585 GAACTG--TTT-T-TGCTGAATTATTCA
1 GAA-TGTATTTCTGTGCTGAATTATTCA
2530609 GA
1 GA
2530611 GCGTTTTGCT
Statistics
Matches: 49, Mismatches: 3, Indels: 5
0.86 0.05 0.09
Matches are distributed among these distances:
24 16 0.33
25 1 0.02
26 2 0.04
27 28 0.57
28 2 0.04
ACGTcount: A:0.28, C:0.12, G:0.19, T:0.41
Consensus pattern (27 bp):
GAATGTATTTCTGTGCTGAATTATTCA
Found at i:2530620 original size:22 final size:24
Alignment explanation
Indices: 2530544--2530624 Score: 87
Period size: 24 Copynumber: 3.3 Consensus size: 24
2530534 TGTATTTCTG
*
2530544 TGCTGAATAATTCAGAA-TGTACTTCT
1 TGCTGAATTATTCAGAACTGT--TT-T
2530570 GTGCTGAATTATTCAGAACTGTTTT
1 -TGCTGAATTATTCAGAACTGTTTT
*
2530595 TGCTGAATTATTCAGAGC-G-TTT
1 TGCTGAATTATTCAGAACTGTTTT
2530617 TGCTGAAT
1 TGCTGAAT
2530625 CAGTCATCAT
Statistics
Matches: 51, Mismatches: 2, Indels: 7
0.85 0.03 0.12
Matches are distributed among these distances:
22 11 0.22
23 1 0.02
24 17 0.33
25 1 0.02
26 2 0.04
27 16 0.31
28 3 0.06
ACGTcount: A:0.26, C:0.14, G:0.20, T:0.41
Consensus pattern (24 bp):
TGCTGAATTATTCAGAACTGTTTT
Found at i:2533006 original size:15 final size:15
Alignment explanation
Indices: 2532986--2533014 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
2532976 TCGATTGTCA
2532986 ACCGAAAATGTTACG
1 ACCGAAAATGTTACG
2533001 ACCGAAAATGTTAC
1 ACCGAAAATGTTAC
2533015 AAAAAAAAGT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.41, C:0.21, G:0.17, T:0.21
Consensus pattern (15 bp):
ACCGAAAATGTTACG
Found at i:2533503 original size:63 final size:63
Alignment explanation
Indices: 2533404--2533528 Score: 223
Period size: 63 Copynumber: 2.0 Consensus size: 63
2533394 GTTGTCCCTT
*
2533404 GTTCCCATATGTAATGGGGTAAGGGGAGGTAAGATAGTAGGCTGCCCCCAACACTAGGTTGAG
1 GTTCCCATATGTAATGGGGTAAGGGGAGGTAAGATAGTAGACTGCCCCCAACACTAGGTTGAG
* *
2533467 GTTCCCATATGTAATGGGGTAAGGGGAGGTAAGATAGTAGATTGTCCCCAACACTAGGTTGA
1 GTTCCCATATGTAATGGGGTAAGGGGAGGTAAGATAGTAGACTGCCCCCAACACTAGGTTGA
2533529 AAGCAGCTTC
Statistics
Matches: 59, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
63 59 1.00
ACGTcount: A:0.28, C:0.16, G:0.32, T:0.24
Consensus pattern (63 bp):
GTTCCCATATGTAATGGGGTAAGGGGAGGTAAGATAGTAGACTGCCCCCAACACTAGGTTGAG
Found at i:2534346 original size:22 final size:21
Alignment explanation
Indices: 2534319--2534363 Score: 54
Period size: 22 Copynumber: 2.1 Consensus size: 21
2534309 GTTTTGTGAT
2534319 TTTAATACTAATAATTATTAAA
1 TTTAATACTAATAATTA-TAAA
* * *
2534341 TTTAATTCTCATATTTATAAA
1 TTTAATACTAATAATTATAAA
2534362 TT
1 TT
2534364 CTACAAATAT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
21 6 0.30
22 14 0.70
ACGTcount: A:0.42, C:0.07, G:0.00, T:0.51
Consensus pattern (21 bp):
TTTAATACTAATAATTATAAA
Found at i:2544029 original size:15 final size:15
Alignment explanation
Indices: 2544009--2544039 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
2543999 TCTTTCTCTT
2544009 ACAAATAAAATGATA
1 ACAAATAAAATGATA
2544024 ACAAATAAAATGATA
1 ACAAATAAAATGATA
2544039 A
1 A
2544040 AAAAAGAGAG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.68, C:0.06, G:0.06, T:0.19
Consensus pattern (15 bp):
ACAAATAAAATGATA
Found at i:2544078 original size:23 final size:23
Alignment explanation
Indices: 2544052--2544111 Score: 57
Period size: 23 Copynumber: 2.6 Consensus size: 23
2544042 AAAGAGAGTC
2544052 TAAACATTAAACGAATATGTTCG
1 TAAACATTAAACGAATATGTTCG
* * **
2544075 TAAACGTAAAATAAATATGTTCG
1 TAAACATTAAACGAATATGTTCG
** *
2544098 CGAGCATTAAACGA
1 TAAACATTAAACGA
2544112 CGAGCACAAA
Statistics
Matches: 26, Mismatches: 11, Indels: 0
0.70 0.30 0.00
Matches are distributed among these distances:
23 26 1.00
ACGTcount: A:0.45, C:0.13, G:0.15, T:0.27
Consensus pattern (23 bp):
TAAACATTAAACGAATATGTTCG
Found at i:2545996 original size:225 final size:227
Alignment explanation
Indices: 2545579--2546051 Score: 580
Period size: 225 Copynumber: 2.1 Consensus size: 227
2545569 TAGTTTTATT
* *
2545579 AAATAAAAAATAATTAACTAACATGATTTGATTCAAGTGGTAAGCAGTTTGATATCGCTTAAATA
1 AAATAAAAAATAATTAACTAACATGAGTTGATTCAAGTGGTAAACAGTTTGATATCGCTTAAATA
** ** * * * *
2545644 TTTTTTTAGTGGTAAAAGAATTGTTGTTATTTCTTAAGATCTTGTGTTCGAACATCAGAAATACC
66 --TAATTAGTAATAAAAGAA-T-TTGTTATTTCTTAAGATCTTGTGTTAGAACATAAAAAACACC
* * * * **
2545709 AAGAATACGAACGGTCAATATGAATCAAATAAGTATCAAAGGTATTGAATTATCGGTGATTGTAT
127 AAGAATACAAACGGTCAATAAGAATCAAATAAATATCAAAGATATTGAATTATCAATGATTGTAT
**
2545774 GTGACTATCAAAAATAAAAGAATTGGTCTAAAGATCC
192 GTGACTATC-AAAATAAAAGAATTGGTCTAAAGAGAC
* *
2545811 AAATAAAAAATAATTAACTAACAT-AGGTTGATTCAAGTTGTAAACAGTTTGATATCGCTTAAGT
1 AAATAAAAAATAATTAACTAACATGA-GTTGATTCAAGTGGTAAACAGTTTGATATCGCTTAAAT
* *
2545875 A-AATT-GTAATAAAAGAA-TTGTTA-TTCTTTAAGGTCTTGTGTTAGAACATAAAAAACATCTA
65 ATAATTAGTAATAAAAGAATTTGTTATTTC-TTAAGATCTTGTGTTAGAACATAAAAAACA-CCA
* * * *
2545936 A-AATATAAACGTTGAATAAGAATCAAATAAATATCAAAGATATTGAATTATTAATGATTGTATG
128 AGAATACAAACGGTCAATAAGAATCAAATAAATATCAAAGATATTGAATTATCAATGATTGTATG
* *
2546000 TGACTATCAAAATAAAAGAATTGGTCTAAGGGGAC
193 TGACTATCAAAATAAAAGAATTGGTCTAAAGAGAC
2546035 AAATAAAAAATAATTAA
1 AAATAAAAAATAATTAA
2546052 TAAATGTTAG
Statistics
Matches: 210, Mismatches: 28, Indels: 14
0.83 0.11 0.06
Matches are distributed among these distances:
224 43 0.20
225 92 0.44
226 3 0.01
228 10 0.05
229 2 0.01
231 1 0.00
232 59 0.28
ACGTcount: A:0.44, C:0.09, G:0.15, T:0.32
Consensus pattern (227 bp):
AAATAAAAAATAATTAACTAACATGAGTTGATTCAAGTGGTAAACAGTTTGATATCGCTTAAATA
TAATTAGTAATAAAAGAATTTGTTATTTCTTAAGATCTTGTGTTAGAACATAAAAAACACCAAGA
ATACAAACGGTCAATAAGAATCAAATAAATATCAAAGATATTGAATTATCAATGATTGTATGTGA
CTATCAAAATAAAAGAATTGGTCTAAAGAGAC
Found at i:2553850 original size:16 final size:16
Alignment explanation
Indices: 2553829--2553868 Score: 55
Period size: 16 Copynumber: 2.5 Consensus size: 16
2553819 CAGACCTTTA
2553829 ACTTTGACC-AGAGTTG
1 ACTTTGACCAAG-GTTG
2553845 ACTTTGACCAAGGTTG
1 ACTTTGACCAAGGTTG
*
2553861 GCTTTGAC
1 ACTTTGAC
2553869 AAAAAAGTTA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
16 20 0.91
17 2 0.09
ACGTcount: A:0.23, C:0.20, G:0.25, T:0.33
Consensus pattern (16 bp):
ACTTTGACCAAGGTTG
Found at i:2556952 original size:90 final size:90
Alignment explanation
Indices: 2556839--2557193 Score: 678
Period size: 90 Copynumber: 4.0 Consensus size: 90
2556829 CAATAATTAT
2556839 TGATCATAC--GTAGTTTGCTCTCTATCATTTGCTTCTAAAACATTAGAGTATGTTAATAGGTAT
1 TGATCATACGAGTAGTTTGCTCTCTATCATTTGCTTCTAAAACATTAGAGTATGTTAATAGGTAT
2556902 CAATTTAGTGTAGACAAAGCTTAAA
66 CAATTTAGTGTAGACAAAGCTTAAA
2556927 TGATCATACGAGTAGTTTGCTCTCTATCATTTGCTTCTAAAACATTAGAGTATGTTAATAGGTAT
1 TGATCATACGAGTAGTTTGCTCTCTATCATTTGCTTCTAAAACATTAGAGTATGTTAATAGGTAT
2556992 CAATTTAGTGTAGACAAAGCTTAAA
66 CAATTTAGTGTAGACAAAGCTTAAA
2557017 TGATCATACGAGTAGTTTGCTCTCTATCATTTGCTTCTAAAACATTAGAGTATGTTAATAGGTAT
1 TGATCATACGAGTAGTTTGCTCTCTATCATTTGCTTCTAAAACATTAGAGTATGTTAATAGGTAT
2557082 CAATTTAGTGTAGACAAAGCTTAAA
66 CAATTTAGTGTAGACAAAGCTTAAA
*
2557107 TGATCATACGAGTAGTTTGCTCTCTATCATTTGCTTCTAAAACATTTGAGTATGTTAATAGGTAT
1 TGATCATACGAGTAGTTTGCTCTCTATCATTTGCTTCTAAAACATTAGAGTATGTTAATAGGTAT
*
2557172 CAATTTAGTGTAGGCAAAGCTT
66 CAATTTAGTGTAGACAAAGCTT
2557194 CGTCAATTTT
Statistics
Matches: 263, Mismatches: 2, Indels: 2
0.99 0.01 0.01
Matches are distributed among these distances:
88 9 0.03
90 254 0.97
ACGTcount: A:0.32, C:0.14, G:0.17, T:0.37
Consensus pattern (90 bp):
TGATCATACGAGTAGTTTGCTCTCTATCATTTGCTTCTAAAACATTAGAGTATGTTAATAGGTAT
CAATTTAGTGTAGACAAAGCTTAAA
Found at i:2562731 original size:17 final size:17
Alignment explanation
Indices: 2562709--2562758 Score: 55
Period size: 17 Copynumber: 2.9 Consensus size: 17
2562699 GTCTCCCAAC
*
2562709 CCGGATGTTACGGGTAT
1 CCGGATATTACGGGTAT
*
2562726 CCGGATATTACGGATAT
1 CCGGATATTACGGGTAT
* * *
2562743 CCAGATTTTACAGGTA
1 CCGGATATTACGGGTA
2562759 CCCGATTTTT
Statistics
Matches: 27, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
17 27 1.00
ACGTcount: A:0.26, C:0.18, G:0.26, T:0.30
Consensus pattern (17 bp):
CCGGATATTACGGGTAT
Found at i:2564469 original size:15 final size:16
Alignment explanation
Indices: 2564446--2564475 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
2564436 TATTTATATC
2564446 TATTATATTTATTTTT
1 TATTATATTTATTTTT
2564462 TATT-TATTTATTTT
1 TATTATATTTATTTT
2564476 AAGATAAGTA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 10 0.71
16 4 0.29
ACGTcount: A:0.23, C:0.00, G:0.00, T:0.77
Consensus pattern (16 bp):
TATTATATTTATTTTT
Found at i:2567147 original size:38 final size:37
Alignment explanation
Indices: 2567060--2567162 Score: 95
Period size: 39 Copynumber: 2.7 Consensus size: 37
2567050 GTTTACTTTC
* *
2567060 TTATTTT--TTTTTCAGAACAAATCAAAGTTATACCTT
1 TTATTTTACTTTTTCAGAACAAA-CAAAGTTAGACATT
*
2567096 TTTTTTTACTTTTTCAGAACAACACAAAGTTGGAGA-ATT
1 TTATTTTACTTTTTCAGAACAA-ACAAAGTT--AGACATT
* *
2567135 TTATTTTATTTTTTAAGAACAAAACAAA
1 TTATTTTACTTTTTCAGAAC-AAACAAA
2567163 CTTTTGTTTT
Statistics
Matches: 55, Mismatches: 6, Indels: 9
0.79 0.09 0.13
Matches are distributed among these distances:
36 6 0.11
38 20 0.36
39 25 0.45
40 4 0.07
ACGTcount: A:0.37, C:0.12, G:0.08, T:0.44
Consensus pattern (37 bp):
TTATTTTACTTTTTCAGAACAAACAAAGTTAGACATT
Found at i:2574548 original size:21 final size:20
Alignment explanation
Indices: 2574523--2574582 Score: 68
Period size: 21 Copynumber: 3.0 Consensus size: 20
2574513 TCAACTCAGT
2574523 TTCCAAATTCGCAACGCGAA
1 TTCCAAATTCGCAACGCGAA
*
2574543 TATCCAGATTCGCAACGC-AA
1 T-TCCAAATTCGCAACGCGAA
**
2574563 TTGTAAGATTCGCAACGCGA
1 TTCCAA-ATTCGCAACGCGA
2574583 TTTTGAAAAA
Statistics
Matches: 33, Mismatches: 4, Indels: 5
0.79 0.10 0.12
Matches are distributed among these distances:
19 2 0.06
20 15 0.45
21 16 0.48
ACGTcount: A:0.33, C:0.27, G:0.18, T:0.22
Consensus pattern (20 bp):
TTCCAAATTCGCAACGCGAA
Found at i:2574661 original size:44 final size:41
Alignment explanation
Indices: 2574584--2574665 Score: 110
Period size: 44 Copynumber: 1.9 Consensus size: 41
2574574 GCAACGCGAT
* *
2574584 TTTGAAAAATGTGTTGCGATAGTTAAAATGTGTTGCGAGAG
1 TTTGAAAAATGTGTTGCGATAGTGAAAAAGTGTTGCGAGAG
*
2574625 TTTGAAAAACGTGTTGTTGTGATAGTGAAAAAGTGTTGCGA
1 TTTGAAAAA--TG-TGTTGCGATAGTGAAAAAGTGTTGCGA
2574666 TAGTGAAAAA
Statistics
Matches: 35, Mismatches: 3, Indels: 3
0.85 0.07 0.07
Matches are distributed among these distances:
41 9 0.26
43 2 0.06
44 24 0.69
ACGTcount: A:0.32, C:0.05, G:0.29, T:0.34
Consensus pattern (41 bp):
TTTGAAAAATGTGTTGCGATAGTGAAAAAGTGTTGCGAGAG
Found at i:2574675 original size:19 final size:20
Alignment explanation
Indices: 2574586--2574676 Score: 96
Period size: 19 Copynumber: 4.4 Consensus size: 20
2574576 AACGCGATTT
2574586 TGAAAAATGTGTTGCGATAG
1 TGAAAAATGTGTTGCGATAG
* *
2574606 T-TAAAATGTGTTGCGAGAG
1 TGAAAAATGTGTTGCGATAG
*
2574625 TTTGAAAAACGTGTTGTTGTGATAG
1 --TGAAAAA--TG-TGTTGCGATAG
2574650 TGAAAAA-GTGTTGCGATAG
1 TGAAAAATGTGTTGCGATAG
2574669 TGAAAAAT
1 TGAAAAAT
2574677 CTAAAATAAG
Statistics
Matches: 58, Mismatches: 6, Indels: 14
0.74 0.08 0.18
Matches are distributed among these distances:
19 33 0.57
20 2 0.03
21 1 0.02
22 4 0.07
23 7 0.12
24 2 0.03
25 9 0.16
ACGTcount: A:0.35, C:0.04, G:0.29, T:0.32
Consensus pattern (20 bp):
TGAAAAATGTGTTGCGATAG
Found at i:2574970 original size:6 final size:6
Alignment explanation
Indices: 2574959--2574988 Score: 51
Period size: 6 Copynumber: 5.0 Consensus size: 6
2574949 TCGCCGCCGC
*
2574959 CGTGGT CATGGT CGTGGT CGTGGT CGTGGT
1 CGTGGT CGTGGT CGTGGT CGTGGT CGTGGT
2574989 AATACGTGTC
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
6 22 1.00
ACGTcount: A:0.03, C:0.17, G:0.47, T:0.33
Consensus pattern (6 bp):
CGTGGT
Found at i:2576363 original size:41 final size:41
Alignment explanation
Indices: 2576318--2576398 Score: 99
Period size: 41 Copynumber: 2.0 Consensus size: 41
2576308 CATATGTTGT
* * *
2576318 TACAGACTTCTAATTTAGTGGTGTTTCCAAACAAACGCCGC
1 TACAGACTACTAATTTAGTAGTATTTCCAAACAAACGCCGC
** **
2576359 TACAGACTACTTCTTTAGTAGTATTTTTAAACAAACGCCG
1 TACAGACTACTAATTTAGTAGTATTTCCAAACAAACGCCG
2576399 TAATAAGATG
Statistics
Matches: 33, Mismatches: 7, Indels: 0
0.82 0.17 0.00
Matches are distributed among these distances:
41 33 1.00
ACGTcount: A:0.31, C:0.22, G:0.15, T:0.32
Consensus pattern (41 bp):
TACAGACTACTAATTTAGTAGTATTTCCAAACAAACGCCGC
Found at i:2576621 original size:20 final size:20
Alignment explanation
Indices: 2576598--2576645 Score: 96
Period size: 20 Copynumber: 2.4 Consensus size: 20
2576588 TTTTGCTGCT
2576598 TCTTCGTCAATCTCACTCCC
1 TCTTCGTCAATCTCACTCCC
2576618 TCTTCGTCAATCTCACTCCC
1 TCTTCGTCAATCTCACTCCC
2576638 TCTTCGTC
1 TCTTCGTC
2576646 GATTCTGCTG
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 28 1.00
ACGTcount: A:0.12, C:0.44, G:0.06, T:0.38
Consensus pattern (20 bp):
TCTTCGTCAATCTCACTCCC
Found at i:2576641 original size:60 final size:60
Alignment explanation
Indices: 2576557--2576682 Score: 171
Period size: 60 Copynumber: 2.1 Consensus size: 60
2576547 CATCTGCCGT
* * *
2576557 CTCTTCGCCGATCTAACGCCCTCTTCATCGATTTTGCTGCTTCTTCGTCAATCTCACTCC
1 CTCTTCGCCAATCTAACGCCCTCTTCATCGATTCTGCTGCTTCTTCGCCAATCTCACTCC
* * * * * *
2576617 CTCTTCGTCAATCTCACTCCCTCTTCGTCGATTCTGCTGCTTCTTCGCCGATCTTACTCC
1 CTCTTCGCCAATCTAACGCCCTCTTCATCGATTCTGCTGCTTCTTCGCCAATCTCACTCC
2576677 CTCTTC
1 CTCTTC
2576683 TCTGAATCTG
Statistics
Matches: 57, Mismatches: 9, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
60 57 1.00
ACGTcount: A:0.11, C:0.40, G:0.11, T:0.38
Consensus pattern (60 bp):
CTCTTCGCCAATCTAACGCCCTCTTCATCGATTCTGCTGCTTCTTCGCCAATCTCACTCC
Found at i:2576662 original size:40 final size:40
Alignment explanation
Indices: 2576618--2576699 Score: 103
Period size: 40 Copynumber: 2.0 Consensus size: 40
2576608 TCTCACTCCC
* *
2576618 TCTTCGTCAATCTCACTCCCTCTTCGTC-GATTCTGCTGCT
1 TCTTCGCCAATCTCACTCCCTCTTC-TCTGAATCTGCTGCT
* * *
2576658 TCTTCGCCGATCTTACTCCCTCTTCTCTGAATCTGTTGCT
1 TCTTCGCCAATCTCACTCCCTCTTCTCTGAATCTGCTGCT
2576698 TC
1 TC
2576700 GCAAGTTTTG
Statistics
Matches: 36, Mismatches: 5, Indels: 2
0.84 0.12 0.05
Matches are distributed among these distances:
39 2 0.06
40 34 0.94
ACGTcount: A:0.10, C:0.37, G:0.12, T:0.41
Consensus pattern (40 bp):
TCTTCGCCAATCTCACTCCCTCTTCTCTGAATCTGCTGCT
Found at i:2576681 original size:20 final size:20
Alignment explanation
Indices: 2576557--2576682 Score: 92
Period size: 20 Copynumber: 6.3 Consensus size: 20
2576547 CATCTGCCGT
* * *
2576557 CTCTTCGCCGATCTAACGCC
1 CTCTTCGTCGATCTTACTCC
* * * *
2576577 CTCTTCATCGATTTTGCTGC
1 CTCTTCGTCGATCTTACTCC
* * *
2576597 TTCTTCGTCAATCTCACTCC
1 CTCTTCGTCGATCTTACTCC
* *
2576617 CTCTTCGTCAATCTCACTCC
1 CTCTTCGTCGATCTTACTCC
* *
2576637 CTCTTCGTCGAT-TCTGCTGC
1 CTCTTCGTCGATCT-TACTCC
* *
2576657 TTCTTCGCCGATCTTACTCC
1 CTCTTCGTCGATCTTACTCC
2576677 CTCTTC
1 CTCTTC
2576683 TCTGAATCTG
Statistics
Matches: 80, Mismatches: 24, Indels: 4
0.74 0.22 0.04
Matches are distributed among these distances:
19 1 0.01
20 78 0.98
21 1 0.01
ACGTcount: A:0.11, C:0.40, G:0.11, T:0.38
Consensus pattern (20 bp):
CTCTTCGTCGATCTTACTCC
Found at i:2583874 original size:3 final size:3
Alignment explanation
Indices: 2583866--2583923 Score: 66
Period size: 3 Copynumber: 19.7 Consensus size: 3
2583856 ACTTGTAATT
* * *
2583866 TAA TAA TAA GAA TAA TAA -AA TAA TAG TAA TAA TAA TTA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
2583913 TAGA TAA -AA TA
1 TA-A TAA TAA TA
2583924 TTAAACAAAA
Statistics
Matches: 46, Mismatches: 6, Indels: 6
0.79 0.10 0.10
Matches are distributed among these distances:
2 4 0.09
3 39 0.85
4 3 0.07
ACGTcount: A:0.64, C:0.00, G:0.05, T:0.31
Consensus pattern (3 bp):
TAA
Found at i:2583881 original size:9 final size:8
Alignment explanation
Indices: 2583867--2583938 Score: 54
Period size: 9 Copynumber: 8.2 Consensus size: 8
2583857 CTTGTAATTT
2583867 AATAATAA
1 AATAATAA
2583875 GAATAATAA
1 -AATAATAA
*
2583884 AATAATAGT
1 AATAATA-A
2583893 AATAATAA
1 AATAATAA
*
2583901 TTATAATAA
1 -AATAATAA
2583910 TAATAGATAA
1 -AATA-ATAA
*
2583920 AATATTAA
1 AATAATAA
*
2583928 ACAAAATAA
1 A-ATAATAA
2583937 AA
1 AA
2583939 AAGACCCGGA
Statistics
Matches: 52, Mismatches: 7, Indels: 9
0.76 0.10 0.13
Matches are distributed among these distances:
8 12 0.23
9 36 0.69
10 4 0.08
ACGTcount: A:0.67, C:0.01, G:0.04, T:0.28
Consensus pattern (8 bp):
AATAATAA
Found at i:2584321 original size:40 final size:42
Alignment explanation
Indices: 2584225--2584335 Score: 138
Period size: 40 Copynumber: 2.7 Consensus size: 42
2584215 AAGGGCGATA
* *
2584225 ACACGGTTCCTACGTGATGAGGACGACTAGTTATCTAGGGTTG
1 ACACGGTTCCTACGTGATGAGGACGACTAG-TATCAAGGGATG
* * *
2584268 ACACGGCTCCTACGCGATGAGGA-GATCT-G-GTCAAGGGATG
1 ACACGGTTCCTACGTGATGAGGACGA-CTAGTATCAAGGGATG
2584308 ACACGGTTCCTACGTGATGAGGACGACT
1 ACACGGTTCCTACGTGATGAGGACGACT
2584336 GGCCATCTCT
Statistics
Matches: 59, Mismatches: 7, Indels: 7
0.81 0.10 0.10
Matches are distributed among these distances:
40 31 0.53
41 2 0.03
42 3 0.05
43 23 0.39
ACGTcount: A:0.24, C:0.22, G:0.32, T:0.23
Consensus pattern (42 bp):
ACACGGTTCCTACGTGATGAGGACGACTAGTATCAAGGGATG
Found at i:2584713 original size:35 final size:35
Alignment explanation
Indices: 2584672--2584768 Score: 99
Period size: 36 Copynumber: 2.7 Consensus size: 35
2584662 GACAAAATTC
***
2584672 GTTTCAAGAGAAACGATCTCAAAGAT-GTTTGTTTT
1 GTTTCAAGAGAAACGA-CTCAAAGATGGTAAATTTT
*
2584707 GTTTCAAGGGAAACAGACTCAAAGATGGTAAATTTT
1 GTTTCAAGAGAAAC-GACTCAAAGATGGTAAATTTT
*
2584743 GTTTCCAA-AGAAACAAACTCAAAGAT
1 GTTT-CAAGAGAAAC-GACTCAAAGAT
2584769 TTTTTCCAAA
Statistics
Matches: 53, Mismatches: 6, Indels: 5
0.83 0.09 0.08
Matches are distributed among these distances:
35 22 0.42
36 28 0.53
37 3 0.06
ACGTcount: A:0.39, C:0.13, G:0.19, T:0.29
Consensus pattern (35 bp):
GTTTCAAGAGAAACGACTCAAAGATGGTAAATTTT
Found at i:2584899 original size:19 final size:19
Alignment explanation
Indices: 2584853--2584901 Score: 89
Period size: 19 Copynumber: 2.6 Consensus size: 19
2584843 AAGAGAAAAT
*
2584853 GTTTCAAGAGACAAAATTC
1 GTTTCAAGGGACAAAATTC
2584872 GTTTCAAGGGACAAAATTC
1 GTTTCAAGGGACAAAATTC
2584891 GTTTCAAGGGA
1 GTTTCAAGGGA
2584902 AACGACTCAA
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:0.37, C:0.14, G:0.22, T:0.27
Consensus pattern (19 bp):
GTTTCAAGGGACAAAATTC
Found at i:2585307 original size:27 final size:28
Alignment explanation
Indices: 2585259--2585442 Score: 103
Period size: 28 Copynumber: 6.2 Consensus size: 28
2585249 TTTTTTTTTA
*
2585259 AGAAATAGACTCAAAGATGATTTTGTT-AAG
1 AGAAACAGACTC-AA-A-GATTTTGTTCAAG
*
2585289 AGAAACAAACTCAAAGATTTT-TCTCAA-
1 AGAAACAGACTCAAAGATTTTGT-TCAAG
2585316 A-ATAACAGACTCGAAA-A-TTTGTTTCAAG
1 AGA-AACAGACTC-AAAGATTTTG-TTCAAG
* *
2585344 AGAAACAGACTCAAAGATTTTTTTCAAA
1 AGAAACAGACTCAAAGATTTTGTTCAAG
** *
2585372 AGAAATTGTCTCAAGAGACAAAATTTTGTTTCCAA-
1 AGAAACAGACTCAA-AG-----ATTTTG-TT-CAAG
2585407 AGAAACAGACTCAAAGATTTTTGTTTCAAG
1 AGAAACAGACTCAAAGA-TTTTG-TTCAAG
2585437 AGAAAC
1 AGAAAC
2585443 TGTCTCACAA
Statistics
Matches: 122, Mismatches: 12, Indels: 40
0.70 0.07 0.23
Matches are distributed among these distances:
26 5 0.04
27 24 0.20
28 34 0.28
29 12 0.10
30 24 0.20
34 7 0.06
35 13 0.11
36 3 0.02
ACGTcount: A:0.44, C:0.14, G:0.14, T:0.28
Consensus pattern (28 bp):
AGAAACAGACTCAAAGATTTTGTTCAAG
Found at i:2585310 original size:28 final size:27
Alignment explanation
Indices: 2585259--2585376 Score: 107
Period size: 28 Copynumber: 4.2 Consensus size: 27
2585249 TTTTTTTTTA
* *
2585259 AGAAATAGACTCAAAGATGATTTTGTTAAG
1 AGAAACAGACTCAAAGAT--TTTT-TCAAG
*
2585289 AGAAACAAACTCAAAGATTTTTCTCAA-
1 AGAAACAGACTCAAAGATTTTT-TCAAG
2585316 A-ATAACAGACTCGAAA-ATTTGTTTCAAG
1 AGA-AACAGACTC-AAAGATTT-TTTCAAG
*
2585344 AGAAACAGACTCAAAGATTTTTTTCAAA
1 AGAAACAGACTCAAAGA-TTTTTTCAAG
2585372 AGAAA
1 AGAAA
2585377 TTGTCTCAAG
Statistics
Matches: 75, Mismatches: 6, Indels: 16
0.77 0.06 0.16
Matches are distributed among these distances:
26 1 0.01
27 20 0.27
28 34 0.45
29 4 0.05
30 16 0.21
ACGTcount: A:0.47, C:0.13, G:0.14, T:0.27
Consensus pattern (27 bp):
AGAAACAGACTCAAAGATTTTTTCAAG
Found at i:2585414 original size:63 final size:65
Alignment explanation
Indices: 2585329--2585491 Score: 199
Period size: 63 Copynumber: 2.5 Consensus size: 65
2585319 AACAGACTCG
*
2585329 AAAATTTGTTTCAAGAGAAACAGACTCAAAGA-TTTT-TTTCAAAAGAAATTGTCT-CAAGAGAC
1 AAAATTTGTTTCAAGAGAAACAGACTCAAAGATTTTTGTTTCAAAAGAAACTGTCTACAAGAGAC
*
2585391 AAAATTTTGTTTCCAA-AGAAACAGACTCAAAGATTTTTGTTTCAAGAGAAACTGTCTCACAAGA
1 AAAA-TTTGTTT-CAAGAGAAACAGACTCAAAGATTTTTGTTTCAAAAGAAACTGTCT-ACAAGA
2585455 GAC
63 GAC
* * * * * *
2585458 AAAAATCGTTTTAAGAGAAAAATATTCAAAGATT
1 AAAATTTGTTTCAAGAGAAACAGACTCAAAGATT
2585492 ATCGATTTTA
Statistics
Matches: 86, Mismatches: 8, Indels: 10
0.83 0.08 0.10
Matches are distributed among these distances:
62 4 0.05
63 24 0.28
64 7 0.08
65 18 0.21
66 21 0.24
67 12 0.14
ACGTcount: A:0.44, C:0.13, G:0.14, T:0.29
Consensus pattern (65 bp):
AAAATTTGTTTCAAGAGAAACAGACTCAAAGATTTTTGTTTCAAAAGAAACTGTCTACAAGAGAC
Found at i:2585686 original size:95 final size:97
Alignment explanation
Indices: 2585579--2585796 Score: 230
Period size: 105 Copynumber: 2.2 Consensus size: 97
2585569 AAGGGGAAAC
* *
2585579 TGTCTCACGCGAGACGAATCAGCTTTG-AA-AATCTCAAGTGATATTAATTTTGTTTCAAGT-AC
1 TGTCTCAAGCGAGACGAATCAGCTTTGAAACAATCTCAAGTGAGATTAATTTTGTTTCAAGTGA-
*
2585641 AACAAATT-TAAATTTGTATCTCAGAGAA-AAAAA
65 AACAAATTCAAAATTTGTATCTCA-A-AAGAAAAA
** *
2585674 TGTCTCAAGCGAGACGAAATTTGTTTTGAAATAAACAACAATCTCAAGTGAGATTAATTTTGTTT
1 TGTCTCAAGCGAGACG-AATCAGCTTTG------A-AACAATCTCAAGTGAGATTAATTTTGTTT
*
2585739 CAAGTGAAGCAAATTCAAAATTTGTATCTCAAAAGAAAAA
58 CAAGTGAAACAAATTCAAAATTTGTATCTCAAAAGAAAAA
*
2585779 TGTCTAAAGCGAGACGAA
1 TGTCTCAAGCGAGACGAA
2585797 ATTTGTTTTA
Statistics
Matches: 102, Mismatches: 8, Indels: 17
0.80 0.06 0.13
Matches are distributed among these distances:
95 15 0.15
96 8 0.08
104 6 0.06
105 58 0.57
106 15 0.15
ACGTcount: A:0.40, C:0.14, G:0.16, T:0.30
Consensus pattern (97 bp):
TGTCTCAAGCGAGACGAATCAGCTTTGAAACAATCTCAAGTGAGATTAATTTTGTTTCAAGTGAA
ACAAATTCAAAATTTGTATCTCAAAAGAAAAA
Found at i:2585790 original size:105 final size:105
Alignment explanation
Indices: 2585608--2585810 Score: 313
Period size: 105 Copynumber: 1.9 Consensus size: 105
2585598 CAGCTTTGAA
* *
2585608 AATCTCAAGTGATATTAATTTTGTTTCAAGTACAACAAATTTAAATTTGTATCTCAGAGAAAAAA
1 AATCTCAAGTGAGATTAATTTTGTTTCAAGTACAACAAATTAAAATTTGTATCTCAGAGAAAAAA
* *
2585673 ATGTCTCAAGCGAGACGAAATTTGTTTTGAAATAAACAAC
66 ATGTCTAAAGCGAGACGAAATTTGTTTTAAAATAAACAAC
*
2585713 AATCTCAAGTGAGATTAATTTTGTTTCAAGTGA-AGCAAATTCAAAATTTGTATCTCA-A-AAGA
1 AATCTCAAGTGAGATTAATTTTGTTTCAAGT-ACAACAAATT-AAAATTTGTATCTCAGAGAA-A
2585775 AAAATGTCTAAAGCGAGACGAAATTTGTTTTAAAAT
63 AAAATGTCTAAAGCGAGACGAAATTTGTTTTAAAAT
2585811 TCTCAAAAAT
Statistics
Matches: 90, Mismatches: 5, Indels: 6
0.89 0.05 0.06
Matches are distributed among these distances:
104 2 0.02
105 73 0.81
106 15 0.17
ACGTcount: A:0.42, C:0.11, G:0.14, T:0.33
Consensus pattern (105 bp):
AATCTCAAGTGAGATTAATTTTGTTTCAAGTACAACAAATTAAAATTTGTATCTCAGAGAAAAAA
ATGTCTAAAGCGAGACGAAATTTGTTTTAAAATAAACAAC
Found at i:2585909 original size:36 final size:36
Alignment explanation
Indices: 2585825--2585933 Score: 119
Period size: 38 Copynumber: 2.9 Consensus size: 36
2585815 AAAAATTTTG
* *
2585825 GAAAAATGTCTCAAGCGAGACATAATTTGTTTTAAA
1 GAAAAATGTCTCAAGCGAGACAAAATTTGTTTTTAA
* *
2585861 GAGAAAGTTGTCTCAAGCAAGACAAAATTTGTTTTTAA
1 GA-AAA-ATGTCTCAAGCGAGACAAAATTTGTTTTTAA
* * * *
2585899 GAAAACTGTCTCTAGCGAGACGACACTTTGTTTTT
1 GAAAAATGTCTCAAGCGAGAC-AAAATTTGTTTTT
2585934 TTTTAAGAAA
Statistics
Matches: 61, Mismatches: 9, Indels: 5
0.81 0.12 0.07
Matches are distributed among these distances:
36 15 0.25
37 17 0.28
38 29 0.48
ACGTcount: A:0.36, C:0.14, G:0.18, T:0.32
Consensus pattern (36 bp):
GAAAAATGTCTCAAGCGAGACAAAATTTGTTTTTAA
Found at i:2588195 original size:26 final size:26
Alignment explanation
Indices: 2588117--2588198 Score: 86
Period size: 26 Copynumber: 3.4 Consensus size: 26
2588107 TTTCAAGGTG
2588117 GAAAGAATGTTTCAAGGTCTCAAAGA
1 GAAAGAATGTTTCAAGGTCTCAAAGA
**
2588143 GAGGGAATGTTTCAAGG--TC---GA
1 GAAAGAATGTTTCAAGGTCTCAAAGA
*
2588164 -AAAGAATATTTCAAGGTCTCAAAGA
1 GAAAGAATGTTTCAAGGTCTCAAAGA
*
2588189 GATAGAATGT
1 GAAAGAATGT
2588199 CAAAAATTGG
Statistics
Matches: 43, Mismatches: 7, Indels: 12
0.69 0.11 0.19
Matches are distributed among these distances:
20 13 0.30
21 2 0.05
22 2 0.05
24 2 0.05
25 2 0.05
26 22 0.51
ACGTcount: A:0.40, C:0.10, G:0.26, T:0.24
Consensus pattern (26 bp):
GAAAGAATGTTTCAAGGTCTCAAAGA
Found at i:2588197 original size:46 final size:45
Alignment explanation
Indices: 2588105--2588198 Score: 143
Period size: 46 Copynumber: 2.1 Consensus size: 45
2588095 ATAAATACAG
* * *
2588105 TGTTTCAAGGTGGAAAGAATGTTTCAAGGTCTCAAAGAGAGGGAA
1 TGTTTCAAGGTGAAAAGAATATTTCAAGGTCTCAAAGAGAGAGAA
*
2588150 TGTTTCAAGGTCGAAAAGAATATTTCAAGGTCTCAAAGAGATAGAA
1 TGTTTCAAGGT-GAAAAGAATATTTCAAGGTCTCAAAGAGAGAGAA
2588196 TGT
1 TGT
2588199 CAAAAATTGG
Statistics
Matches: 44, Mismatches: 4, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
45 11 0.25
46 33 0.75
ACGTcount: A:0.37, C:0.10, G:0.27, T:0.27
Consensus pattern (45 bp):
TGTTTCAAGGTGAAAAGAATATTTCAAGGTCTCAAAGAGAGAGAA
Found at i:2589654 original size:31 final size:32
Alignment explanation
Indices: 2589598--2589659 Score: 117
Period size: 32 Copynumber: 2.0 Consensus size: 32
2589588 TGACAAAATG
2589598 ACACAAACAAAAGAGAAGAAATAAGTTAGTAT
1 ACACAAACAAAAGAGAAGAAATAAGTTAGTAT
2589630 ACACAAACAAAAGAGAA-AAATAAGTTAGTA
1 ACACAAACAAAAGAGAAGAAATAAGTTAGTA
2589660 CATGTAAAAT
Statistics
Matches: 30, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
31 13 0.43
32 17 0.57
ACGTcount: A:0.61, C:0.10, G:0.15, T:0.15
Consensus pattern (32 bp):
ACACAAACAAAAGAGAAGAAATAAGTTAGTAT
Found at i:2591386 original size:16 final size:16
Alignment explanation
Indices: 2591365--2591396 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
2591355 GCATAAATGA
2591365 ATATATATACATACAT
1 ATATATATACATACAT
*
2591381 ATATATATATATACAT
1 ATATATATACATACAT
2591397 GCATATGTTG
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.50, C:0.09, G:0.00, T:0.41
Consensus pattern (16 bp):
ATATATATACATACAT
Found at i:2591390 original size:20 final size:20
Alignment explanation
Indices: 2591365--2591402 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
2591355 GCATAAATGA
2591365 ATATATATACATACATATAT
1 ATATATATACATACATATAT
*
2591385 ATATATATACATGCATAT
1 ATATATATACATACATAT
2591403 GTTGATACAT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.47, C:0.11, G:0.03, T:0.39
Consensus pattern (20 bp):
ATATATATACATACATATAT
Found at i:2593423 original size:3 final size:3
Alignment explanation
Indices: 2593415--2593472 Score: 66
Period size: 3 Copynumber: 19.7 Consensus size: 3
2593405 ACTTGTAATT
* * *
2593415 TAA TAA TAA GAA TAA TAA -AA TAA TAG TAA TAA TAA TTA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
2593462 TAGA TAA -AA TA
1 TA-A TAA TAA TA
2593473 TAAACAAAAT
Statistics
Matches: 46, Mismatches: 6, Indels: 6
0.79 0.10 0.10
Matches are distributed among these distances:
2 4 0.09
3 39 0.85
4 3 0.07
ACGTcount: A:0.64, C:0.00, G:0.05, T:0.31
Consensus pattern (3 bp):
TAA
Found at i:2593430 original size:9 final size:8
Alignment explanation
Indices: 2593416--2593486 Score: 54
Period size: 9 Copynumber: 8.2 Consensus size: 8
2593406 CTTGTAATTT
2593416 AATAATAA
1 AATAATAA
2593424 GAATAATAA
1 -AATAATAA
*
2593433 AATAATAGT
1 AATAATA-A
2593442 AATAATAA
1 AATAATAA
*
2593450 TTATAATAA
1 -AATAATAA
2593459 TAATAGATAA
1 -AATA-ATAA
2593469 AAT-ATAA
1 AATAATAA
*
2593476 ACAAAATAA
1 A-ATAATAA
2593485 AA
1 AA
2593487 AAGACCCGGA
Statistics
Matches: 52, Mismatches: 5, Indels: 11
0.76 0.07 0.16
Matches are distributed among these distances:
7 5 0.10
8 9 0.17
9 34 0.65
10 4 0.08
ACGTcount: A:0.68, C:0.01, G:0.04, T:0.27
Consensus pattern (8 bp):
AATAATAA
Found at i:2594057 original size:20 final size:20
Alignment explanation
Indices: 2594028--2594101 Score: 121
Period size: 20 Copynumber: 3.7 Consensus size: 20
2594018 TTATTCCCTA
*
2594028 GTAATCTTACATTCTCACTG
1 GTAATCTTACATTCCCACTG
*
2594048 GTAGTCTTACATTCCCACTG
1 GTAATCTTACATTCCCACTG
2594068 GTAATCTTACATTCCCACTG
1 GTAATCTTACATTCCCACTG
*
2594088 GTAATCTTATATTC
1 GTAATCTTACATTC
2594102 TGTGAACCAA
Statistics
Matches: 50, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
20 50 1.00
ACGTcount: A:0.24, C:0.26, G:0.11, T:0.39
Consensus pattern (20 bp):
GTAATCTTACATTCCCACTG
Found at i:2596044 original size:114 final size:115
Alignment explanation
Indices: 2595836--2596045 Score: 244
Period size: 114 Copynumber: 1.8 Consensus size: 115
2595826 GAGTGAAAGA
* * * * *
2595836 TTGAATAAGTTCTTCTCATTATGAATTTCTTTTTTCTTATTGGATGAGTTATTCTCATTATAAAC
1 TTGAACAAGTTCTTCTCATTATGAAATTCTTGTTCCTTATCGGATGAGTTATTCTCATTATAAAC
* *** *
2595901 TCTTCATTGGAAATACTGACCCACTTCCTTTTGCGATGGACGAGCCAAGG
66 TCTCCAGCAGAAATACTGACCCACCTCCTTTTGCGATGGACGAGCCAAGG
* * *
2595951 TTGAACAAGTTCTTCTCATTA-GAAATT-TTGTTCCTTAATCGGATGAGTTCTTCTCGTTATGAA
1 TTGAACAAGTTCTTCTCATTATGAAATTCTTGTTCCTT-ATCGGATGAGTTATTCTCATTATAAA
* ** *
2596014 CTCTCCAGCAGAAGTGTTGATCCACCTCCTTT
65 CTCTCCAGCAGAAATACTGACCCACCTCCTTT
2596046 ATGATGGAAT
Statistics
Matches: 77, Mismatches: 17, Indels: 3
0.79 0.18 0.03
Matches are distributed among these distances:
113 7 0.09
114 50 0.65
115 20 0.26
ACGTcount: A:0.24, C:0.20, G:0.16, T:0.40
Consensus pattern (115 bp):
TTGAACAAGTTCTTCTCATTATGAAATTCTTGTTCCTTATCGGATGAGTTATTCTCATTATAAAC
TCTCCAGCAGAAATACTGACCCACCTCCTTTTGCGATGGACGAGCCAAGG
Found at i:2597191 original size:68 final size:68
Alignment explanation
Indices: 2597109--2597240 Score: 185
Period size: 68 Copynumber: 1.9 Consensus size: 68
2597099 ATGAAATTTA
*
2597109 TTTTAAGAAAAACAATTTCAAAATGTGT-TTTCAAGAAAAAACTATCTCAAACGAGATAAAACTT
1 TTTTAAGAAAAACAATCTCAAAATGTGTATTTCAAG-AAAAACTATCTCAAACGAGATAAAACTT
2597173 TTTG
65 TTTG
** * * * *
2597177 TTTTAAGCGAAACAATCTCAATATTTGTATTTCAAGAGAAACTATCTCAATCGAGATAAAACTT
1 TTTTAAGAAAAACAATCTCAAAATGTGTATTTCAAGAAAAACTATCTCAAACGAGATAAAACTT
2597241 ATTTCTTAAA
Statistics
Matches: 56, Mismatches: 7, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
68 49 0.88
69 7 0.12
ACGTcount: A:0.43, C:0.14, G:0.11, T:0.33
Consensus pattern (68 bp):
TTTTAAGAAAAACAATCTCAAAATGTGTATTTCAAGAAAAACTATCTCAAACGAGATAAAACTTT
TTG
Found at i:2597203 original size:27 final size:29
Alignment explanation
Indices: 2597173--2597227 Score: 78
Period size: 29 Copynumber: 2.0 Consensus size: 29
2597163 GATAAAACTT
*
2597173 TTTGT-TTT-AAGCGAAACAATCTCAATA
1 TTTGTATTTCAAGAGAAACAATCTCAATA
*
2597200 TTTGTATTTCAAGAGAAACTATCTCAAT
1 TTTGTATTTCAAGAGAAACAATCTCAAT
2597228 CGAGATAAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
27 5 0.21
28 3 0.12
29 16 0.67
ACGTcount: A:0.36, C:0.15, G:0.11, T:0.38
Consensus pattern (29 bp):
TTTGTATTTCAAGAGAAACAATCTCAATA
Found at i:2612471 original size:56 final size:56
Alignment explanation
Indices: 2612385--2612501 Score: 189
Period size: 56 Copynumber: 2.1 Consensus size: 56
2612375 AAATGTTTAT
* * *
2612385 TACATGTCATGTCCACTGTTAGGACTAATAGACCAGAGAGAACATATCAATTTTCA
1 TACATGTCATGTCAACTGTTAGGACTAATAGACAAGAGACAACATATCAATTTTCA
*
2612441 TACATGTCATGTCAACTGTTAGGACTAATAGACAAGAGACCACATATCAATTTTCA
1 TACATGTCATGTCAACTGTTAGGACTAATAGACAAGAGACAACATATCAATTTTCA
*
2612497 AACAT
1 TACAT
2612502 ACAACTTAAT
Statistics
Matches: 56, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
56 56 1.00
ACGTcount: A:0.38, C:0.20, G:0.15, T:0.28
Consensus pattern (56 bp):
TACATGTCATGTCAACTGTTAGGACTAATAGACAAGAGACAACATATCAATTTTCA
Found at i:2616697 original size:15 final size:15
Alignment explanation
Indices: 2616677--2616709 Score: 66
Period size: 15 Copynumber: 2.2 Consensus size: 15
2616667 TCATACTGTT
2616677 GACACACACATTAAA
1 GACACACACATTAAA
2616692 GACACACACATTAAA
1 GACACACACATTAAA
2616707 GAC
1 GAC
2616710 TCGCTATAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.52, C:0.27, G:0.09, T:0.12
Consensus pattern (15 bp):
GACACACACATTAAA
Found at i:2620457 original size:22 final size:22
Alignment explanation
Indices: 2620389--2620468 Score: 76
Period size: 23 Copynumber: 3.7 Consensus size: 22
2620379 AGAACCCCAG
*
2620389 GGGGGTATCGATTCCCC-T--A
1 GGGGGAATCGATTCCCCTTCAA
* * *
2620408 GGGGGAATCGGTTTCCATTCAAA
1 GGGGGAATCGATTCCCCTTC-AA
*
2620431 TGGGGAATCGATTCCCCTTCAA
1 GGGGGAATCGATTCCCCTTCAA
*
2620453 GGGGGTATCGATTCCC
1 GGGGGAATCGATTCCC
2620469 TATGCCCTAT
Statistics
Matches: 47, Mismatches: 10, Indels: 5
0.76 0.16 0.08
Matches are distributed among these distances:
19 13 0.28
20 1 0.02
22 16 0.34
23 17 0.36
ACGTcount: A:0.20, C:0.24, G:0.30, T:0.26
Consensus pattern (22 bp):
GGGGGAATCGATTCCCCTTCAA
Found at i:2629025 original size:81 final size:82
Alignment explanation
Indices: 2628940--2629089 Score: 230
Period size: 82 Copynumber: 1.8 Consensus size: 82
2628930 TACTCACTGT
* *
2628940 ACTTACAGATTGAATCA-TTTGCTCACTCCTTATTTTCTCTCTAACGTATGGATGATGTGACATT
1 ACTTACAGATTGAATCATTTTACTCACTCCTTATTTTCTCTCTAACGTATGGATGACGTGACATT
2629004 TTTTAATTATTTTTTTA
66 TTTTAATTATTTTTTTA
* * * * *
2629021 ACTTACATATTGAATCATTTTACTTACTCTTTGTTTTCTCTCTAACGTATGGATGACGTGGCATT
1 ACTTACAGATTGAATCATTTTACTCACTCCTTATTTTCTCTCTAACGTATGGATGACGTGACATT
2629086 TTTT
66 TTTT
2629090 TTTAATTATT
Statistics
Matches: 61, Mismatches: 7, Indels: 1
0.88 0.10 0.01
Matches are distributed among these distances:
81 16 0.26
82 45 0.74
ACGTcount: A:0.23, C:0.17, G:0.12, T:0.48
Consensus pattern (82 bp):
ACTTACAGATTGAATCATTTTACTCACTCCTTATTTTCTCTCTAACGTATGGATGACGTGACATT
TTTTAATTATTTTTTTA
Found at i:2631750 original size:17 final size:17
Alignment explanation
Indices: 2631728--2631762 Score: 61
Period size: 17 Copynumber: 2.1 Consensus size: 17
2631718 TTCACGTTGG
*
2631728 AGAAGAGAAGAAGATGA
1 AGAAGAGAAGAAAATGA
2631745 AGAAGAGAAGAAAATGA
1 AGAAGAGAAGAAAATGA
2631762 A
1 A
2631763 TTGTTTGGAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.63, C:0.00, G:0.31, T:0.06
Consensus pattern (17 bp):
AGAAGAGAAGAAAATGA
Found at i:2652864 original size:58 final size:60
Alignment explanation
Indices: 2652778--2652955 Score: 204
Period size: 65 Copynumber: 2.9 Consensus size: 60
2652768 ATGTAGTTTC
* * * *
2652778 CATGAACAATCAAA-CTCTCATTCTGTCGAAATTTGACTAGGTGGTTTGGATGGTG-A-T
1 CATGAACAATCAAAGCTCTCATTCAGTCGAAATTCGACTAGGTGGCTTGGTTGGTGTATT
2652835 CATGAACAATCAAAGCTCTCATTCAGTCGAAATTCGA-TCAGGTGGCTTGGTTGGTGAAGTATTT
1 CATGAACAATCAAAGCTCTCATTCAGTCGAAATTCGACT-AGGTGGCTTGGTTGGT---GTA---
2652899 TT
59 TT
* *
2652901 CATGAACAATC-AAGCTCTCATTCGGTCGAAATTCGACCAGGTGGCTTGGTTGGTG
1 CATGAACAATCAAAGCTCTCATTCAGTCGAAATTCGACTAGGTGGCTTGGTTGGTG
2652956 GCATGCCATT
Statistics
Matches: 104, Mismatches: 6, Indels: 17
0.82 0.05 0.13
Matches are distributed among these distances:
57 15 0.14
58 34 0.33
61 1 0.01
62 2 0.02
65 40 0.38
66 12 0.12
ACGTcount: A:0.26, C:0.18, G:0.24, T:0.31
Consensus pattern (60 bp):
CATGAACAATCAAAGCTCTCATTCAGTCGAAATTCGACTAGGTGGCTTGGTTGGTGTATT
Found at i:2652955 original size:123 final size:123
Alignment explanation
Indices: 2652729--2652955 Score: 319
Period size: 123 Copynumber: 1.8 Consensus size: 123
2652719 TTTTCATGAA
* * *
2652729 CTCATTCTGTAGAAATTCGACCAGGTGATTTGGTTGCTGATGTAGTTTCCATGAACAATCAAACT
1 CTCATTCAGTAGAAATTCGACCAGGTGACTTGGTTGCTGAAGTAGTTTCCATGAACAATCAAACT
* * * *
2652794 CTCATTCTGTCGAAATTTGACTAGGTGGTTTGGATGGTGATCATGAACAATCAAAGCT
66 CTCATTCGGTCGAAATTCGACCAGGTGGCTTGGATGGTGATCATGAACAATCAAAGCT
* * * * * * *
2652852 CTCATTCAGTCGAAATTCGATCAGGTGGCTTGGTTGGTGAAGTATTTTTCATGAACAATCAAGCT
1 CTCATTCAGTAGAAATTCGACCAGGTGACTTGGTTGCTGAAGTAGTTTCCATGAACAATCAAACT
*
2652917 CTCATTCGGTCGAAATTCGACCAGGTGGCTTGGTTGGTG
66 CTCATTCGGTCGAAATTCGACCAGGTGGCTTGGATGGTG
2652956 GCATGCCATT
Statistics
Matches: 89, Mismatches: 15, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
123 89 1.00
ACGTcount: A:0.25, C:0.18, G:0.24, T:0.33
Consensus pattern (123 bp):
CTCATTCAGTAGAAATTCGACCAGGTGACTTGGTTGCTGAAGTAGTTTCCATGAACAATCAAACT
CTCATTCGGTCGAAATTCGACCAGGTGGCTTGGATGGTGATCATGAACAATCAAAGCT
Found at i:2658233 original size:34 final size:33
Alignment explanation
Indices: 2658168--2658233 Score: 89
Period size: 34 Copynumber: 2.0 Consensus size: 33
2658158 CAGAAATTAG
**
2658168 AAAAATATATATTACCATTAAATCCTATCAAAA
1 AAAAATATATATTACCATTAAATAATATCAAAA
2658201 AAAATATATATATTACCATTAAA-AATATTCAAA
1 AAAA-ATATATATTACCATTAAATAATA-TCAAA
2658234 TTCAAGCAGG
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
33 6 0.21
34 23 0.79
ACGTcount: A:0.56, C:0.12, G:0.00, T:0.32
Consensus pattern (33 bp):
AAAAATATATATTACCATTAAATAATATCAAAA
Found at i:2663964 original size:29 final size:29
Alignment explanation
Indices: 2663911--2663968 Score: 75
Period size: 29 Copynumber: 2.0 Consensus size: 29
2663901 CCCTAAAACT
*
2663911 ATTTTATTTTATTTTATTTAGATTTAGCC
1 ATTTAATTTTATTTTATTTAGATTTAGCC
2663940 ATTTAATTTTGATTTGT-TTTA-ATTTAGCC
1 ATTTAATTTT-ATTT-TATTTAGATTTAGCC
2663969 CCTTTTTATG
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
29 17 0.65
30 8 0.31
31 1 0.04
ACGTcount: A:0.24, C:0.07, G:0.09, T:0.60
Consensus pattern (29 bp):
ATTTAATTTTATTTTATTTAGATTTAGCC
Found at i:2671770 original size:21 final size:21
Alignment explanation
Indices: 2671744--2671787 Score: 70
Period size: 21 Copynumber: 2.1 Consensus size: 21
2671734 AGAGTTGGAC
2671744 GGTTATAATAAAGATAAAGAT
1 GGTTATAATAAAGATAAAGAT
* *
2671765 GGTTATAATCATGATAAAGAT
1 GGTTATAATAAAGATAAAGAT
2671786 GG
1 GG
2671788 ATACAACAGT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.45, C:0.02, G:0.23, T:0.30
Consensus pattern (21 bp):
GGTTATAATAAAGATAAAGAT
Found at i:2672352 original size:2 final size:2
Alignment explanation
Indices: 2672345--2672413 Score: 138
Period size: 2 Copynumber: 34.5 Consensus size: 2
2672335 TAACATCTAT
2672345 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
2672387 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
2672414 TCACACACAC
Statistics
Matches: 67, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 67 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:2676777 original size:63 final size:62
Alignment explanation
Indices: 2676656--2676779 Score: 151
Period size: 62 Copynumber: 2.0 Consensus size: 62
2676646 AACCTCGAAA
* * ** *
2676656 ACTGTCCATAGGTCCCGAAGAACCTAGGTAAATTGTCCATATGTTCCTTAGAACATAGGTAT
1 ACTGTCCATAGGTCCCGAAGAACATAGGTAAATTGTCCATATGTCCCGAAAAACATAGGTAT
* * *
2676718 ACTGTTCATATGTCCCGAA-AGACATAGGTAATTTTGTCCATATGTCCCGAAAAACATAGGTA
1 ACTGTCCATAGGTCCCGAAGA-ACATAGGTAA-ATTGTCCATATGTCCCGAAAAACATAGGTA
2676780 ATTCTCGACT
Statistics
Matches: 52, Mismatches: 8, Indels: 3
0.83 0.13 0.05
Matches are distributed among these distances:
61 1 0.02
62 26 0.50
63 25 0.48
ACGTcount: A:0.32, C:0.20, G:0.19, T:0.29
Consensus pattern (62 bp):
ACTGTCCATAGGTCCCGAAGAACATAGGTAAATTGTCCATATGTCCCGAAAAACATAGGTAT
Found at i:2676782 original size:32 final size:32
Alignment explanation
Indices: 2676658--2676781 Score: 135
Period size: 31 Copynumber: 3.9 Consensus size: 32
2676648 CCTCGAAAAC
* * *
2676658 TGTCCATAGGTCCCGAAGAACCTAGGTAA-AT
1 TGTCCATATGTCCCGAAAAACATAGGTAATAT
* ** * *
2676689 TGTCCATATGTTCCTTAGAACATAGGT-ATAC
1 TGTCCATATGTCCCGAAAAACATAGGTAATAT
* * *
2676720 TGTTCATATGTCCCGAAAGACATAGGTAATTT
1 TGTCCATATGTCCCGAAAAACATAGGTAATAT
2676752 TGTCCATATGTCCCGAAAAACATAGGTAAT
1 TGTCCATATGTCCCGAAAAACATAGGTAAT
2676782 TCTCGACTCT
Statistics
Matches: 75, Mismatches: 16, Indels: 3
0.80 0.17 0.03
Matches are distributed among these distances:
30 1 0.01
31 44 0.59
32 30 0.40
ACGTcount: A:0.32, C:0.19, G:0.19, T:0.30
Consensus pattern (32 bp):
TGTCCATATGTCCCGAAAAACATAGGTAATAT
Found at i:2676990 original size:23 final size:25
Alignment explanation
Indices: 2676943--2676993 Score: 72
Period size: 23 Copynumber: 2.1 Consensus size: 25
2676933 ATATGTATGT
2676943 ATAAACATCTATACTTCTATATCAC
1 ATAAACATCTATACTTCTATATCAC
2676968 ATAAAC-TC-ATATCTTCT-TATCAC
1 ATAAACATCTATA-CTTCTATATCAC
2676991 ATA
1 ATA
2676994 CCTTCTTATT
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
23 12 0.48
24 7 0.28
25 6 0.24
ACGTcount: A:0.39, C:0.24, G:0.00, T:0.37
Consensus pattern (25 bp):
ATAAACATCTATACTTCTATATCAC
Found at i:2679605 original size:23 final size:23
Alignment explanation
Indices: 2679575--2679618 Score: 79
Period size: 23 Copynumber: 1.9 Consensus size: 23
2679565 ACGGGTTATG
*
2679575 TATCGATATAGTCATATTGAGCA
1 TATCGATACAGTCATATTGAGCA
2679598 TATCGATACAGTCATATTGAG
1 TATCGATACAGTCATATTGAG
2679619 GTACCGATAC
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:0.34, C:0.14, G:0.18, T:0.34
Consensus pattern (23 bp):
TATCGATACAGTCATATTGAGCA
Found at i:2679629 original size:22 final size:23
Alignment explanation
Indices: 2679578--2679629 Score: 70
Period size: 23 Copynumber: 2.3 Consensus size: 23
2679568 GGTTATGTAT
* *
2679578 CGATATAGTCATATTGAGCATAT
1 CGATACAGTCATATTGAGCATAC
*
2679601 CGATACAGTCATATTGAG-GTAC
1 CGATACAGTCATATTGAGCATAC
2679623 CGATACA
1 CGATACA
2679630 ACAACTTCAT
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
22 9 0.35
23 17 0.65
ACGTcount: A:0.35, C:0.17, G:0.19, T:0.29
Consensus pattern (23 bp):
CGATACAGTCATATTGAGCATAC
Found at i:2681502 original size:17 final size:17
Alignment explanation
Indices: 2681480--2681518 Score: 69
Period size: 17 Copynumber: 2.3 Consensus size: 17
2681470 ACAATTATGG
2681480 TATCAGTACACAACCAA
1 TATCAGTACACAACCAA
*
2681497 TATCAGTACACAACCAG
1 TATCAGTACACAACCAA
2681514 TATCA
1 TATCA
2681519 TACTCGGATG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 21 1.00
ACGTcount: A:0.44, C:0.28, G:0.08, T:0.21
Consensus pattern (17 bp):
TATCAGTACACAACCAA
Found at i:2683435 original size:32 final size:32
Alignment explanation
Indices: 2683394--2683489 Score: 192
Period size: 32 Copynumber: 3.0 Consensus size: 32
2683384 TATAGATTTT
2683394 CTAGCTTTCATTCAATAATTAAAAACAAATAA
1 CTAGCTTTCATTCAATAATTAAAAACAAATAA
2683426 CTAGCTTTCATTCAATAATTAAAAACAAATAA
1 CTAGCTTTCATTCAATAATTAAAAACAAATAA
2683458 CTAGCTTTCATTCAATAATTAAAAACAAATAA
1 CTAGCTTTCATTCAATAATTAAAAACAAATAA
2683490 GGGGGAGAAG
Statistics
Matches: 64, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 64 1.00
ACGTcount: A:0.50, C:0.16, G:0.03, T:0.31
Consensus pattern (32 bp):
CTAGCTTTCATTCAATAATTAAAAACAAATAA
Found at i:2684855 original size:25 final size:25
Alignment explanation
Indices: 2684822--2684871 Score: 73
Period size: 25 Copynumber: 2.0 Consensus size: 25
2684812 GTACCATACG
*
2684822 ACTTACTCTCTTCTACAGCTTGTTC
1 ACTTACTCTCTGCTACAGCTTGTTC
* *
2684847 ACTTGCTCTCTGCTATAGCTTGTTC
1 ACTTACTCTCTGCTACAGCTTGTTC
2684872 TTTCTTCGAT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
25 22 1.00
ACGTcount: A:0.14, C:0.30, G:0.12, T:0.44
Consensus pattern (25 bp):
ACTTACTCTCTGCTACAGCTTGTTC
Found at i:2685685 original size:191 final size:191
Alignment explanation
Indices: 2685372--2685725 Score: 557
Period size: 191 Copynumber: 1.9 Consensus size: 191
2685362 ATACATTGTG
* * *
2685372 ACTTCATAACATAATTAGACACTTAATTTATTTCATATTTTATGATAATAATATACATTATAAAT
1 ACTTCATAACATAATTAGACACTTAATTTATGTCATATTTAATGATAACAATATACATTATAAAT
* *
2685437 ATGTGCTCATAATTATGGATTTTAATCTAACAATCTTCCACTTGAGTAACATATGTTTCTTGATA
66 ATGTGCCCATAATTATGGATTTTAATCCAACAATCTTCCACTTGAGTAACATATGTTTCTTGATA
2685502 AATATATAACCTTATGAGCTCAAAATTTGTTATATTTCCATGACACTTCTAATACCTTACA
131 AATATATAACCTTATGAGCTCAAAATTTGTTATATTTCCATGACACTTCTAATACCTTACA
* * * *
2685563 ACTTTATAACATAATTGGTCACTTAATTTATGTCATATTTAATTATAACAATATACATTATAAAT
1 ACTTCATAACATAATTAGACACTTAATTTATGTCATATTTAATGATAACAATATACATTATAAAT
* * *
2685628 ATGTTCCCATAATTATGGATTTTAATCCAACAATC-TCTCACTTGGGTAACGTATGTTTCTTGAT
66 ATGTGCCCATAATTATGGATTTTAATCCAACAATCTTC-CACTTGAGTAACATATGTTTCTTGAT
* **
2685692 AAATGTATAGTCTTATGAGCTCAAAATTTGTTAT
130 AAATATATAACCTTATGAGCTCAAAATTTGTTAT
2685726 CATGTAATAT
Statistics
Matches: 147, Mismatches: 15, Indels: 2
0.90 0.09 0.01
Matches are distributed among these distances:
190 2 0.01
191 145 0.99
ACGTcount: A:0.36, C:0.14, G:0.09, T:0.41
Consensus pattern (191 bp):
ACTTCATAACATAATTAGACACTTAATTTATGTCATATTTAATGATAACAATATACATTATAAAT
ATGTGCCCATAATTATGGATTTTAATCCAACAATCTTCCACTTGAGTAACATATGTTTCTTGATA
AATATATAACCTTATGAGCTCAAAATTTGTTATATTTCCATGACACTTCTAATACCTTACA
Found at i:2688920 original size:2 final size:2
Alignment explanation
Indices: 2688909--2688943 Score: 54
Period size: 2 Copynumber: 18.0 Consensus size: 2
2688899 GAAAAACTGA
*
2688909 AT AT -T AT AT AT AT AT AA AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
2688944 TGCATTAGCA
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
1 1 0.03
2 29 0.97
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:2689245 original size:20 final size:20
Alignment explanation
Indices: 2689224--2689329 Score: 106
Period size: 20 Copynumber: 5.2 Consensus size: 20
2689214 ATCGCACAAT
*
2689224 GCGATACTGACTATCGCAAT
1 GCGATACTGACTATCGCAAC
* *
2689244 GCGATACTTACTATCGCAAT
1 GCGATACTGACTATCGCAAC
* *
2689264 GCGATAAT-ACAAAATCGCAAC
1 GCGATACTGAC--TATCGCAAC
* *
2689285 GAGATACTGACTTTCGCAAC
1 GCGATACTGACTATCGCAAC
* *
2689305 GCGATTCTGACTTTCGCAAC
1 GCGATACTGACTATCGCAAC
2689325 GCGAT
1 GCGAT
2689330 TTACATAGCG
Statistics
Matches: 73, Mismatches: 10, Indels: 6
0.82 0.11 0.07
Matches are distributed among these distances:
19 2 0.03
20 56 0.77
21 13 0.18
22 2 0.03
ACGTcount: A:0.31, C:0.25, G:0.19, T:0.25
Consensus pattern (20 bp):
GCGATACTGACTATCGCAAC
Found at i:2689908 original size:19 final size:19
Alignment explanation
Indices: 2689848--2689928 Score: 73
Period size: 19 Copynumber: 4.5 Consensus size: 19
2689838 TTCGAGAATG
2689848 AAAATCGCAACGCGGAAATA
1 AAAATCGCAACGC-GAAATA
** *
2689868 ACTATCGCAA--CGAGAT-
1 AAAATCGCAACGCGAAATA
2689884 --AATCGCAACGCGAAATA
1 AAAATCGCAACGCGAAATA
**
2689901 AAAATCGCAACGCGAAACC
1 AAAATCGCAACGCGAAATA
2689920 AAAATCGCA
1 AAAATCGCA
2689929 TTGCGATTTT
Statistics
Matches: 49, Mismatches: 7, Indels: 11
0.73 0.10 0.16
Matches are distributed among these distances:
14 7 0.14
16 5 0.10
17 4 0.08
18 1 0.02
19 24 0.49
20 8 0.16
ACGTcount: A:0.47, C:0.25, G:0.17, T:0.11
Consensus pattern (19 bp):
AAAATCGCAACGCGAAATA
Found at i:2689998 original size:39 final size:38
Alignment explanation
Indices: 2689924--2690055 Score: 139
Period size: 39 Copynumber: 3.6 Consensus size: 38
2689914 GAAACCAAAA
* *
2689924 TCGCATTGCGATTTTCATTTCGCGTTGCGATTTTCATT
1 TCGCGTTGCAATTTTCATTTCGCGTTGCGATTTTCATT
*
2689962 TCGCGTTGCAATTTTTATTTCGCGGTTGCGATTTTCATT
1 TCGCGTTGCAATTTTCATTTCGC-GTTGCGATTTTCATT
* * **
2690001 TCGCGTTGCGA--TTC---TCTCGTTGCGATAGTCATT
1 TCGCGTTGCAATTTTCATTTCGCGTTGCGATTTTCATT
*
2690034 TCCGCGTTGCGATTTTCATTTC
1 T-CGCGTTGCAATTTTCATTTC
2690056 AACCAAAAGA
Statistics
Matches: 79, Mismatches: 8, Indels: 13
0.79 0.08 0.13
Matches are distributed among these distances:
33 14 0.18
34 13 0.16
36 3 0.04
37 2 0.03
38 20 0.25
39 27 0.34
ACGTcount: A:0.12, C:0.22, G:0.20, T:0.45
Consensus pattern (38 bp):
TCGCGTTGCAATTTTCATTTCGCGTTGCGATTTTCATT
Found at i:2690052 original size:20 final size:19
Alignment explanation
Indices: 2689924--2690055 Score: 157
Period size: 19 Copynumber: 7.1 Consensus size: 19
2689914 GAAACCAAAA
*
2689924 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
2689943 TCGCGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
* *
2689962 TCGCGTTGCAATTTTTATT
1 TCGCGTTGCGATTTTCATT
2689981 TCGCGGTTGCGATTTTCATT
1 TCGC-GTTGCGATTTTCATT
2690001 TCGCGTTGCGA--TTC---
1 TCGCGTTGCGATTTTCATT
* **
2690015 TCTCGTTGCGATAGTCATT
1 TCGCGTTGCGATTTTCATT
2690034 TCCGCGTTGCGATTTTCATT
1 T-CGCGTTGCGATTTTCATT
2690054 TC
1 TC
2690056 AACCAAAAGA
Statistics
Matches: 96, Mismatches: 10, Indels: 14
0.80 0.08 0.12
Matches are distributed among these distances:
14 10 0.10
16 2 0.02
17 3 0.03
19 48 0.50
20 33 0.34
ACGTcount: A:0.12, C:0.22, G:0.20, T:0.45
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Found at i:2692117 original size:42 final size:42
Alignment explanation
Indices: 2692057--2692179 Score: 108
Period size: 42 Copynumber: 2.9 Consensus size: 42
2692047 GCCCGACTCG
* * *
2692057 CCTATCATCTCTCAAGAGTCCACTCCTATCGTTGAAGAGGCC
1 CCTATCATCTCTCAAGAGTCCACTCCCACCGTTCAAGAGGCC
* *
2692099 CCTATCAT-TCCTCGAGAGTCCCCTCCCACCGTTCAAGAGGCC
1 CCTATCATCT-CTCAAGAGTCCACTCCCACCGTTCAAGAGGCC
* * * * *
2692141 ACTGTCATCGT-TGAAGAGGTCC-CTCCTACCATTCAAGAG
1 CCTATCATC-TCTCAAGA-GTCCACTCCCACCGTTCAAGAG
2692180 CCCGATTCAC
Statistics
Matches: 66, Mismatches: 11, Indels: 8
0.78 0.13 0.09
Matches are distributed among these distances:
41 1 0.02
42 60 0.91
43 4 0.06
44 1 0.02
ACGTcount: A:0.23, C:0.35, G:0.18, T:0.24
Consensus pattern (42 bp):
CCTATCATCTCTCAAGAGTCCACTCCCACCGTTCAAGAGGCC
Found at i:2693431 original size:20 final size:20
Alignment explanation
Indices: 2693406--2693463 Score: 98
Period size: 20 Copynumber: 2.9 Consensus size: 20
2693396 AATCATTTGA
2693406 CTATCGCAACGCGAAAATGG
1 CTATCGCAACGCGAAAATGG
2693426 CTATCGCAACGCGAAAATGG
1 CTATCGCAACGCGAAAATGG
* *
2693446 TTATCGCAACGAGAAAAT
1 CTATCGCAACGCGAAAAT
2693464 CGCAATGCGA
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 36 1.00
ACGTcount: A:0.38, C:0.22, G:0.22, T:0.17
Consensus pattern (20 bp):
CTATCGCAACGCGAAAATGG
Found at i:2693633 original size:14 final size:14
Alignment explanation
Indices: 2693614--2693650 Score: 56
Period size: 14 Copynumber: 2.6 Consensus size: 14
2693604 CATCAATTAA
2693614 ACAAATCAACATTT
1 ACAAATCAACATTT
* *
2693628 ACAAATCATCTTTT
1 ACAAATCAACATTT
2693642 ACAAATCAA
1 ACAAATCAA
2693651 TTAAACAATC
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.49, C:0.22, G:0.00, T:0.30
Consensus pattern (14 bp):
ACAAATCAACATTT
Found at i:2695544 original size:19 final size:19
Alignment explanation
Indices: 2695520--2695593 Score: 67
Period size: 19 Copynumber: 3.8 Consensus size: 19
2695510 GAAACTTAAA
2695520 ATCGCAACGCAAAATGACT
1 ATCGCAACGCAAAATGACT
* * *
2695539 ATCGCAATGCGGAAATGGCT
1 ATCGCAACGC-AAAATGACT
* * **
2695559 ATCGCAATGCGAAATGAAA
1 ATCGCAACGCAAAATGACT
2695578 ATCGCAACGACAAAAT
1 ATCGCAACG-CAAAAT
2695594 CGCAACGCGA
Statistics
Matches: 45, Mismatches: 8, Indels: 3
0.80 0.14 0.05
Matches are distributed among these distances:
19 23 0.51
20 22 0.49
ACGTcount: A:0.42, C:0.22, G:0.20, T:0.16
Consensus pattern (19 bp):
ATCGCAACGCAAAATGACT
Found at i:2695560 original size:20 final size:19
Alignment explanation
Indices: 2695520--2695575 Score: 76
Period size: 20 Copynumber: 2.9 Consensus size: 19
2695510 GAAACTTAAA
* *
2695520 ATCGCAACGCAAAATGACT
1 ATCGCAATGCGAAATGACT
*
2695539 ATCGCAATGCGGAAATGGCT
1 ATCGCAATGC-GAAATGACT
2695559 ATCGCAATGCGAAATGA
1 ATCGCAATGCGAAATGA
2695576 AAATCGCAAC
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
19 15 0.47
20 17 0.53
ACGTcount: A:0.38, C:0.21, G:0.23, T:0.18
Consensus pattern (19 bp):
ATCGCAATGCGAAATGACT
Found at i:2695653 original size:14 final size:14
Alignment explanation
Indices: 2695634--2695691 Score: 71
Period size: 14 Copynumber: 3.9 Consensus size: 14
2695624 TTTCATTTCG
2695634 CGTTGCGATTTTGT
1 CGTTGCGATTTTGT
*
2695648 CGTTGCGATTTCATTT
1 CGTTGCGATTT--TGT
2695664 CGCATTGCGATTTTGT
1 CG--TTGCGATTTTGT
2695680 CGTTGCGATTTT
1 CGTTGCGATTTT
2695692 TATTTCGCAT
Statistics
Matches: 38, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
14 21 0.55
16 8 0.21
18 9 0.24
ACGTcount: A:0.10, C:0.17, G:0.24, T:0.48
Consensus pattern (14 bp):
CGTTGCGATTTTGT
Found at i:2695702 original size:33 final size:33
Alignment explanation
Indices: 2695617--2695707 Score: 157
Period size: 32 Copynumber: 2.8 Consensus size: 33
2695607 ACAAATCGCA
*
2695617 TTGCGATTTTCATTTCGCGTTGCGATTTTGTCG
1 TTGCGATTTTCATTTCGCATTGCGATTTTGTCG
2695650 TTGCGA-TTTCATTTCGCATTGCGATTTTGTCG
1 TTGCGATTTTCATTTCGCATTGCGATTTTGTCG
*
2695682 TTGCGATTTTTATTTCGCATTGCGAT
1 TTGCGATTTTCATTTCGCATTGCGAT
2695708 AGCCATTTCC
Statistics
Matches: 55, Mismatches: 2, Indels: 2
0.93 0.03 0.03
Matches are distributed among these distances:
32 31 0.56
33 24 0.44
ACGTcount: A:0.12, C:0.18, G:0.22, T:0.48
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCATTGCGATTTTGTCG
Found at i:2695715 original size:19 final size:20
Alignment explanation
Indices: 2695693--2695735 Score: 61
Period size: 20 Copynumber: 2.2 Consensus size: 20
2695683 TGCGATTTTT
2695693 ATTT-CGCATTGCGATAGCC
1 ATTTCCGCATTGCGATAGCC
* *
2695712 ATTTCCGCGTTGCGATAGTC
1 ATTTCCGCATTGCGATAGCC
2695732 ATTT
1 ATTT
2695736 TCGTGTTGCG
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 4 0.19
20 17 0.81
ACGTcount: A:0.19, C:0.23, G:0.21, T:0.37
Consensus pattern (20 bp):
ATTTCCGCATTGCGATAGCC
Found at i:2695726 original size:20 final size:20
Alignment explanation
Indices: 2695701--2695746 Score: 65
Period size: 20 Copynumber: 2.3 Consensus size: 20
2695691 TTATTTCGCA
2695701 TTGCGATAGCCATTTCCGCG
1 TTGCGATAGCCATTTCCGCG
* * *
2695721 TTGCGATAGTCATTTTCGTG
1 TTGCGATAGCCATTTCCGCG
2695741 TTGCGA
1 TTGCGA
2695747 AAGTAAACTA
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.15, C:0.22, G:0.26, T:0.37
Consensus pattern (20 bp):
TTGCGATAGCCATTTCCGCG
Found at i:2696254 original size:18 final size:18
Alignment explanation
Indices: 2696228--2696272 Score: 72
Period size: 18 Copynumber: 2.5 Consensus size: 18
2696218 GTCGATCAGA
*
2696228 TGATGGCTCTGGGTGAGG
1 TGATGGCTCTGGGCGAGG
*
2696246 TGATAGCTCTGGGCGAGG
1 TGATGGCTCTGGGCGAGG
2696264 TGATGGCTC
1 TGATGGCTC
2696273 CCGAAGTGGA
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.13, C:0.16, G:0.44, T:0.27
Consensus pattern (18 bp):
TGATGGCTCTGGGCGAGG
Found at i:2697617 original size:20 final size:20
Alignment explanation
Indices: 2697592--2697629 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
2697582 AATAGTTTCT
2697592 GAAAATGAAAATCGCAACAC
1 GAAAATGAAAATCGCAACAC
**
2697612 GAAAATGACTATCGCAAC
1 GAAAATGAAAATCGCAAC
2697630 GAGAGAATCG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.50, C:0.21, G:0.16, T:0.13
Consensus pattern (20 bp):
GAAAATGAAAATCGCAACAC
Found at i:2697920 original size:22 final size:22
Alignment explanation
Indices: 2697893--2697936 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
2697883 GATGGAGATA
2697893 GACGGATTTCGCCGGAGATGGG
1 GACGGATTTCGCCGGAGATGGG
*
2697915 GACGGATTTCGTCGGAGATGGG
1 GACGGATTTCGCCGGAGATGGG
2697937 TGAGAGAGTG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.18, C:0.16, G:0.45, T:0.20
Consensus pattern (22 bp):
GACGGATTTCGCCGGAGATGGG
Found at i:2698149 original size:20 final size:20
Alignment explanation
Indices: 2698124--2698217 Score: 89
Period size: 20 Copynumber: 4.7 Consensus size: 20
2698114 GATTATGTAT
2698124 TATCGCGTTGCGAAAGTCAG
1 TATCGCGTTGCGAAAGTCAG
*
2698144 TATCGCGTTGCGAAAGTAAG
1 TATCGCGTTGCGAAAGTCAG
* *** * *
2698164 TATCTCGTTGCGATTTTTTAT
1 TATCGCGTTGCGA-AAGTCAG
* *
2698185 TATCGCATTGCGATAGTCAG
1 TATCGCGTTGCGAAAGTCAG
*
2698205 TATCGCATTGCGA
1 TATCGCGTTGCGA
2698218 TTTTCCCAAT
Statistics
Matches: 60, Mismatches: 13, Indels: 2
0.80 0.17 0.03
Matches are distributed among these distances:
20 47 0.78
21 13 0.22
ACGTcount: A:0.23, C:0.18, G:0.24, T:0.34
Consensus pattern (20 bp):
TATCGCGTTGCGAAAGTCAG
Found at i:2698218 original size:20 final size:20
Alignment explanation
Indices: 2698104--2698218 Score: 88
Period size: 20 Copynumber: 5.7 Consensus size: 20
2698094 CGCTTTGAAA
*
2698104 ATCGCATTGCGATTATGT-ATT
1 ATCGCATTGCGA-TA-GTCAGT
* *
2698125 ATCGCGTTGCGAAAGTCAGT
1 ATCGCATTGCGATAGTCAGT
* * *
2698145 ATCGCGTTGCGAAAGTAAGT
1 ATCGCATTGCGATAGTCAGT
* * ** * *
2698165 ATCTCGTTGCGATTTTTTATT
1 ATCGCATTGCGA-TAGTCAGT
2698186 ATCGCATTGCGATAGTCAGT
1 ATCGCATTGCGATAGTCAGT
2698206 ATCGCATTGCGAT
1 ATCGCATTGCGAT
2698219 TTTCCCAATT
Statistics
Matches: 76, Mismatches: 16, Indels: 5
0.78 0.16 0.05
Matches are distributed among these distances:
19 2 0.03
20 50 0.66
21 24 0.32
ACGTcount: A:0.23, C:0.17, G:0.23, T:0.36
Consensus pattern (20 bp):
ATCGCATTGCGATAGTCAGT
Found at i:2698236 original size:21 final size:21
Alignment explanation
Indices: 2698207--2698299 Score: 100
Period size: 20 Copynumber: 4.5 Consensus size: 21
2698197 ATAGTCAGTA
2698207 TCGCATTGCGATTTTCCCAAT
1 TCGCATTGCGATTTTCCCAAT
* * **
2698228 TCGCGTTGCGA-TTTACTTAT
1 TCGCATTGCGATTTTCCCAAT
2698248 TCGCATTGCGATTTTCCCAAT
1 TCGCATTGCGATTTTCCCAAT
* * **
2698269 TCGCGTTGCGA-TTTACTTAT
1 TCGCATTGCGATTTTCCCAAT
2698289 TCGCATTGCGA
1 TCGCATTGCGA
2698300 ATTGGGAAAA
Statistics
Matches: 58, Mismatches: 13, Indels: 3
0.78 0.18 0.04
Matches are distributed among these distances:
20 32 0.55
21 26 0.45
ACGTcount: A:0.17, C:0.25, G:0.18, T:0.40
Consensus pattern (21 bp):
TCGCATTGCGATTTTCCCAAT
Found at i:2698237 original size:41 final size:41
Alignment explanation
Indices: 2698146--2698280 Score: 139
Period size: 41 Copynumber: 3.3 Consensus size: 41
2698136 AAAGTCAGTA
* * * ** *
2698146 TCGCGTTGCGAAAGTAAGTATCTCGTTGCGATTTT-TTATT
1 TCGCGTTGCGATAGTAAGTATCGCATTGCGATTTTCCCAAT
* *
2698186 ATCGCATTGCGATAGTCAGTATCGCATTGCGATTTTCCCAAT
1 -TCGCGTTGCGATAGTAAGTATCGCATTGCGATTTTCCCAAT
* **
2698228 TCGCGTTGCGAT-TTACTTATTCGCATTGCGATTTTCCCAAT
1 TCGCGTTGCGATAGTAAGTA-TCGCATTGCGATTTTCCCAAT
2698269 TCGCGTTGCGAT
1 TCGCGTTGCGAT
2698281 TTACTTATTC
Statistics
Matches: 79, Mismatches: 13, Indels: 4
0.82 0.14 0.04
Matches are distributed among these distances:
40 3 0.04
41 74 0.94
42 2 0.03
ACGTcount: A:0.19, C:0.21, G:0.21, T:0.39
Consensus pattern (41 bp):
TCGCGTTGCGATAGTAAGTATCGCATTGCGATTTTCCCAAT
Found at i:2698281 original size:41 final size:41
Alignment explanation
Indices: 2698207--2698299 Score: 186
Period size: 41 Copynumber: 2.3 Consensus size: 41
2698197 ATAGTCAGTA
2698207 TCGCATTGCGATTTTCCCAATTCGCGTTGCGATTTACTTAT
1 TCGCATTGCGATTTTCCCAATTCGCGTTGCGATTTACTTAT
2698248 TCGCATTGCGATTTTCCCAATTCGCGTTGCGATTTACTTAT
1 TCGCATTGCGATTTTCCCAATTCGCGTTGCGATTTACTTAT
2698289 TCGCATTGCGA
1 TCGCATTGCGA
2698300 ATTGGGAAAA
Statistics
Matches: 52, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
41 52 1.00
ACGTcount: A:0.17, C:0.25, G:0.18, T:0.40
Consensus pattern (41 bp):
TCGCATTGCGATTTTCCCAATTCGCGTTGCGATTTACTTAT
Found at i:2699413 original size:2 final size:2
Alignment explanation
Indices: 2699406--2699433 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
2699396 TGTTAATGCA
2699406 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
2699434 TAACAATAAT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2700954 original size:20 final size:20
Alignment explanation
Indices: 2700931--2700972 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
2700921 ACAAAAAAAA
2700931 GAAAATAAAGTAAAA-GAAAT
1 GAAAATAAAG-AAAATGAAAT
*
2700951 GAAAATTAAGAAAATGAAAT
1 GAAAATAAAGAAAATGAAAT
2700971 GA
1 GA
2700973 TTCTGAATAT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
19 4 0.20
20 16 0.80
ACGTcount: A:0.67, C:0.00, G:0.17, T:0.17
Consensus pattern (20 bp):
GAAAATAAAGAAAATGAAAT
Found at i:2710878 original size:14 final size:14
Alignment explanation
Indices: 2710859--2710886 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
2710849 TTCATCCAAA
2710859 ACTCTACCTTATCT
1 ACTCTACCTTATCT
2710873 ACTCTACCTTATCT
1 ACTCTACCTTATCT
2710887 CATCATTTTC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.21, C:0.36, G:0.00, T:0.43
Consensus pattern (14 bp):
ACTCTACCTTATCT
Found at i:2719783 original size:5 final size:5
Alignment explanation
Indices: 2719773--2719856 Score: 87
Period size: 5 Copynumber: 16.8 Consensus size: 5
2719763 TCTTATTCCC
* * * * *
2719773 CCCAA CCCAA CCCAG CCCAG CCCAC CCCAG CCCAC CCCAG CCCAC CCCAG
1 CCCAG CCCAG CCCAG CCCAG CCCAG CCCAG CCCAG CCCAG CCCAG CCCAG
* * * *
2719823 CCCAG CCCAG CCCAC CCCAC CCCAA CCCAC CCCA
1 CCCAG CCCAG CCCAG CCCAG CCCAG CCCAG CCCA
2719857 AAGGAGGAGA
Statistics
Matches: 69, Mismatches: 10, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
5 69 1.00
ACGTcount: A:0.24, C:0.68, G:0.08, T:0.00
Consensus pattern (5 bp):
CCCAG
Found at i:2719857 original size:10 final size:10
Alignment explanation
Indices: 2719773--2719856 Score: 105
Period size: 10 Copynumber: 8.4 Consensus size: 10
2719763 TCTTATTCCC
* *
2719773 CCCAACCCAA
1 CCCACCCCAG
*
2719783 CCCAGCCCAG
1 CCCACCCCAG
2719793 CCCACCCCAG
1 CCCACCCCAG
2719803 CCCACCCCAG
1 CCCACCCCAG
2719813 CCCACCCCAG
1 CCCACCCCAG
*
2719823 CCCAGCCCAG
1 CCCACCCCAG
*
2719833 CCCACCCCAC
1 CCCACCCCAG
* *
2719843 CCCAACCCAC
1 CCCACCCCAG
2719853 CCCA
1 CCCA
2719857 AAGGAGGAGA
Statistics
Matches: 67, Mismatches: 7, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
10 67 1.00
ACGTcount: A:0.24, C:0.68, G:0.08, T:0.00
Consensus pattern (10 bp):
CCCACCCCAG
Found at i:2720237 original size:16 final size:16
Alignment explanation
Indices: 2720204--2720255 Score: 52
Period size: 17 Copynumber: 3.2 Consensus size: 16
2720194 ATTTGCTAAC
*
2720204 TGATATCAATAAAT-TT
1 TGAT-TCAATAATTGTT
2720220 TGATTCAATAATTGTT
1 TGATTCAATAATTGTT
**
2720236 TGAATTGTATAATTGTT
1 TG-ATTCAATAATTGTT
2720253 TGA
1 TGA
2720256 ACTATATAGT
Statistics
Matches: 31, Mismatches: 3, Indels: 4
0.82 0.08 0.11
Matches are distributed among these distances:
15 8 0.26
16 9 0.29
17 14 0.45
ACGTcount: A:0.35, C:0.04, G:0.13, T:0.48
Consensus pattern (16 bp):
TGATTCAATAATTGTT
Found at i:2720249 original size:17 final size:17
Alignment explanation
Indices: 2720227--2720272 Score: 65
Period size: 17 Copynumber: 2.7 Consensus size: 17
2720217 TTTTGATTCA
* *
2720227 ATAATTGTTTGAATTGT
1 ATAATTGTTTGAACTAT
2720244 ATAATTGTTTGAACTAT
1 ATAATTGTTTGAACTAT
*
2720261 ATAGTTGTTTGA
1 ATAATTGTTTGA
2720273 GAGTGTGAGA
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
17 26 1.00
ACGTcount: A:0.30, C:0.02, G:0.17, T:0.50
Consensus pattern (17 bp):
ATAATTGTTTGAACTAT
Found at i:2720988 original size:17 final size:17
Alignment explanation
Indices: 2720966--2721001 Score: 72
Period size: 17 Copynumber: 2.1 Consensus size: 17
2720956 GGCCCCTTAA
2720966 TTCGTGCAACTACCTAG
1 TTCGTGCAACTACCTAG
2720983 TTCGTGCAACTACCTAG
1 TTCGTGCAACTACCTAG
2721000 TT
1 TT
2721002 TATATTTCCA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.22, C:0.28, G:0.17, T:0.33
Consensus pattern (17 bp):
TTCGTGCAACTACCTAG
Found at i:2721385 original size:196 final size:198
Alignment explanation
Indices: 2721014--2721390 Score: 528
Period size: 196 Copynumber: 1.9 Consensus size: 198
2721004 TATTTCCAAT
*
2721014 ATAACCTTAAAAGTTTAAATTTTCAGCTTTTGTTATGAAATATTAAATTTTAAGTAAAATTATAT
1 ATAACCTTAAAAGTTTAAATTTTCAGCTTTTGTTATGAAATAATAAATTTTAAGTAAAATTATAT
*
2721079 TGTTATCATCAATTATTTAATTTTTATTAGATTTTAAATTAATATACATACATATATATAATTAT
66 TGTTATCATCAATTATTTAATTTTAATTAGATTTTAAATTAATATACATACA-ATATATAATTAT
* *
2721144 GTAGTACTTACTTTTATTAATATTCAAATTGATTGTTAAATATAAGCTGATAGAAAATTAATTTT
130 ATAGTAATTACTTTTATTAATATTCAAATTGATTGTTAAATATAAGCTGATAGAAAATTAATTTT
2721209 CAGC
195 CAGC
* * **
2721213 ATAACCTTAAAAG-TTAAA-TTTCAGTTTTTGTTATGATAA-AATAATTTTTAAGTGGAATTATA
1 ATAACCTTAAAAGTTTAAATTTTCAGCTTTTGTTATGA-AATAATAAATTTTAAGTAAAATTATA
* * * ** **
2721275 TTTTTTATCCTCAATTATTTAATTTTAATTAGTTTTTAGTTTAATATGTATAC-ATATATAATTA
65 -TTGTTATCATCAATTATTTAATTTTAATTAGATTTTAAATTAATATACATACAATATATAATTA
* * * *
2721339 TATATTAATTATTTTTATTAATATTCAAATTGATTGTTAGATATAAGTTGAT
129 TATAGTAATTACTTTTATTAATATTCAAATTGATTGTTAAATATAAGCTGAT
2721391 GGAACTTTAA
Statistics
Matches: 157, Mismatches: 19, Indels: 7
0.86 0.10 0.04
Matches are distributed among these distances:
196 57 0.36
197 36 0.23
198 51 0.32
199 13 0.08
ACGTcount: A:0.38, C:0.06, G:0.08, T:0.48
Consensus pattern (198 bp):
ATAACCTTAAAAGTTTAAATTTTCAGCTTTTGTTATGAAATAATAAATTTTAAGTAAAATTATAT
TGTTATCATCAATTATTTAATTTTAATTAGATTTTAAATTAATATACATACAATATATAATTATA
TAGTAATTACTTTTATTAATATTCAAATTGATTGTTAAATATAAGCTGATAGAAAATTAATTTTC
AGC
Found at i:2722061 original size:25 final size:25
Alignment explanation
Indices: 2722008--2722055 Score: 78
Period size: 25 Copynumber: 1.9 Consensus size: 25
2721998 TTTTCAAAAT
2722008 ATATAAAATTAAATCAAAATTATAA
1 ATATAAAATTAAATCAAAATTATAA
* *
2722033 ATATATAATTAAATTAAAATTAT
1 ATATAAAATTAAATCAAAATTAT
2722056 GCATATGATT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
25 21 1.00
ACGTcount: A:0.60, C:0.02, G:0.00, T:0.38
Consensus pattern (25 bp):
ATATAAAATTAAATCAAAATTATAA
Found at i:2733675 original size:52 final size:52
Alignment explanation
Indices: 2733619--2733723 Score: 201
Period size: 52 Copynumber: 2.0 Consensus size: 52
2733609 AACATAACTT
*
2733619 TTGACGTGGTATTTTTACTTTTATTTTTCAATGATGATGTGTCATTATCTTA
1 TTGACGTGGTATTTTTACTTTTATTTTTCAATGATGATGTGTCATTATATTA
2733671 TTGACGTGGTATTTTTACTTTTATTTTTCAATGATGATGTGTCATTATATTA
1 TTGACGTGGTATTTTTACTTTTATTTTTCAATGATGATGTGTCATTATATTA
2733723 T
1 T
2733724 AATGACACAT
Statistics
Matches: 52, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
52 52 1.00
ACGTcount: A:0.22, C:0.09, G:0.15, T:0.54
Consensus pattern (52 bp):
TTGACGTGGTATTTTTACTTTTATTTTTCAATGATGATGTGTCATTATATTA
Found at i:2737331 original size:106 final size:106
Alignment explanation
Indices: 2737139--2737613 Score: 711
Period size: 106 Copynumber: 4.5 Consensus size: 106
2737129 GTATTGCTCC
* * ** * *
2737139 GAGTCTAATATCCTCCGCCGTGAAGTTGAAATTGTCTCT-AGAACTGGGAAAATTGTTTGTTGAC
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGA-AATTGGG-AAATTGTTTGTTGAC
*
2737203 AGTCAGCCGCCCCTTCGCTGTGAAGTTGAGCTTGTGATGTCTT
64 AGTCAGCCGCCCCTTCGCTGTGAAGTTGAGCTTGTGCTGTCTT
* * * *
2737246 AAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGAGACATTGTTTGTTGACAG
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTGTTGACAG
2737311 TCAGCCGCCCCTTCGCTGTGAAGTTGAGCTTGTGCTGTCTT
66 TCAGCCGCCCCTTCGCTGTGAAGTTGAGCTTGTGCTGTCTT
*
2737352 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTATTTGTTGACAG
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTGTTGACAG
* * *
2737417 TAAGCCACCCCTTCGCTATGAAGTTGAGCTTGTGCTGTCTT
66 TCAGCCGCCCCTTCGCTGTGAAGTTGAGCTTGTGCTGTCTT
2737458 GAG-CCTAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTGTTGACA
1 GAGTCC-AATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTGTTGACA
* ** * * *
2737522 ATCAGTTGCCCTTTCGCTGTGAAGTTAAGCTTGTGCTGTCAT
65 GTCAGCCGCCCCTTCGCTGTGAAGTTGAGCTTGTGCTGTCTT
*
2737564 GAGTCCAATATCATTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAA
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAA
2737614 GCCCCTTCGT
Statistics
Matches: 337, Mismatches: 28, Indels: 7
0.91 0.08 0.02
Matches are distributed among these distances:
105 2 0.01
106 293 0.87
107 41 0.12
108 1 0.00
ACGTcount: A:0.23, C:0.18, G:0.25, T:0.34
Consensus pattern (106 bp):
GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTGTTGACAG
TCAGCCGCCCCTTCGCTGTGAAGTTGAGCTTGTGCTGTCTT
Found at i:2739357 original size:106 final size:106
Alignment explanation
Indices: 2739165--2739639 Score: 700
Period size: 106 Copynumber: 4.5 Consensus size: 106
2739155 GTATTGCTCC
* * ** * *
2739165 GAGTCTAATATCCTCCGCCGTGAAGTTGAAATTGTCTCT-AGAACTGGGAAAATTGTTTGTTGAC
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGA-AATTGGG-AAATTGTTTGTTGAC
* *
2739229 AGTCAGCCGCCCCTTCGCTGTGAAGTTGAGCTTGTGATTTCTT
64 AGTCAGCCGCCCCTTCGCTGTGAAGTTGAGCTTGTGCTGTCTT
* * * *
2739272 AAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGAGACATTGTTTGTTGACAG
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTGTTGACAG
2739337 TCAGCCGCCCCTTCGCTGTGAAGTTGAGCTTGTGCTGTCTT
66 TCAGCCGCCCCTTCGCTGTGAAGTTGAGCTTGTGCTGTCTT
* *
2739378 GAGTCCAATATCCTTCGTTGTTAAGTTGAAATTGGCTCTGAAATTGGGAAATTATTTGTTGACAG
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTGTTGACAG
* * * *
2739443 TAAGCCACCCCTTCGCTATGAAATTGAGCTTGTGCTGTCTT
66 TCAGCCGCCCCTTCGCTGTGAAGTTGAGCTTGTGCTGTCTT
* * *
2739484 GAGTCTAATATCCTTCGTTGTGATGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTGTTGACAA
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTGTTGACAG
* * *
2739549 TCAGCCGCCCTTTCGCTGTGAAGTTAAGCTTGTGCTGTCAT
66 TCAGCCGCCCCTTCGCTGTGAAGTTGAGCTTGTGCTGTCTT
*
2739590 GAGTCCAATATCATTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAA
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAA
2739640 GCCCCTTCGT
Statistics
Matches: 332, Mismatches: 35, Indels: 3
0.90 0.09 0.01
Matches are distributed among these distances:
106 292 0.88
107 39 0.12
108 1 0.00
ACGTcount: A:0.23, C:0.18, G:0.24, T:0.35
Consensus pattern (106 bp):
GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTGTTGACAG
TCAGCCGCCCCTTCGCTGTGAAGTTGAGCTTGTGCTGTCTT
Found at i:2741381 original size:106 final size:106
Alignment explanation
Indices: 2741189--2741663 Score: 709
Period size: 106 Copynumber: 4.5 Consensus size: 106
2741179 GTATTGCTCC
* * ** * *
2741189 GAGTCTAATATCCTCCGCCGTGAAGTTGAAATTGTCTCT-AGAACTGGGAAAATTGTTTGTTGAC
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGA-AATTGGG-AAATTGTTTGTTGAC
*
2741253 AGTCAGCCGCCCCTTCGCTGTGAAGTTGAGCTTGTGATGTCTT
64 AGTCAGCCGCCCCTTCGCTGTGAAGTTGAGCTTGTGCTGTCTT
* * * *
2741296 AAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGAGACATTGTTTGTTGACAG
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTGTTGACAG
*
2741361 TCAGCCGCCCCTTCGCTGTGAAGTTGAGCTTGTGCTATCTT
66 TCAGCCGCCCCTTCGCTGTGAAGTTGAGCTTGTGCTGTCTT
* *
2741402 GAGTCCTATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTATTTGTTGACAG
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTGTTGACAG
* *
2741467 TAAGCCGCCCCTTCGCTATGAAGTTGAGCTTGTGCTGTCTT
66 TCAGCCGCCCCTTCGCTGTGAAGTTGAGCTTGTGCTGTCTT
* *
2741508 GAGTCTAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTGTTGACAA
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTGTTGACAG
* * * *
2741573 TCAGCTGCCCTTTCGCTGTGAAGTTAAGCTTGTGCTGTCAT
66 TCAGCCGCCCCTTCGCTGTGAAGTTGAGCTTGTGCTGTCTT
* *
2741614 GAGTCCAATATCATTCATTGTGAAGTTGAAATTGGCTCTGAAATTGGGAA
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAA
2741664 GCCCCTTCGT
Statistics
Matches: 335, Mismatches: 32, Indels: 3
0.91 0.09 0.01
Matches are distributed among these distances:
106 295 0.88
107 39 0.12
108 1 0.00
ACGTcount: A:0.23, C:0.18, G:0.24, T:0.35
Consensus pattern (106 bp):
GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTGTTGACAG
TCAGCCGCCCCTTCGCTGTGAAGTTGAGCTTGTGCTGTCTT
Found at i:2747513 original size:34 final size:36
Alignment explanation
Indices: 2747442--2747522 Score: 85
Period size: 34 Copynumber: 2.3 Consensus size: 36
2747432 AGAGAAACTA
*
2747442 TCTCAAGAGAGACAAAACTTAGTTCTAAAAGAAATTG
1 TCTCAAGGGAGACAAAACTTAGTTC-AAAAGAAATTG
* * *
2747479 TCTCAAGGGAGACGAAA-TTTGTTC-AAAGATATTG
1 TCTCAAGGGAGACAAAACTTAGTTCAAAAGAAATTG
* *
2747513 TTTTAAGGGA
1 TCTCAAGGGA
2747523 AACTGTCTCA
Statistics
Matches: 38, Mismatches: 6, Indels: 3
0.81 0.13 0.06
Matches are distributed among these distances:
34 17 0.45
36 6 0.16
37 15 0.39
ACGTcount: A:0.40, C:0.11, G:0.21, T:0.28
Consensus pattern (36 bp):
TCTCAAGGGAGACAAAACTTAGTTCAAAAGAAATTG
Found at i:2748223 original size:106 final size:106
Alignment explanation
Indices: 2748027--2748496 Score: 674
Period size: 106 Copynumber: 4.4 Consensus size: 106
2748017 GTATTACTCC
* * ** * * * * *
2748027 GAGTCTAATATCCTCCGCCGTGAAGTTGAAATTGTCTCTGGAACTGGAAAAATTGTTTGTTGAAA
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCT-GAAATTGAGAAATTGTTTGTTGATA
* * * *
2748092 GTCAGCTGCCCCTTCGCTGTCAAGTTGTGCTTGTGATGTCTT
65 GTCAGCCGCCCCTTCGCTGTGAAGTTGAGCTTGTGCTGTCTT
* * * *
2748134 AAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGAGACATTGTTTGTTGAGAG
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAATTGTTTGTTGATAG
* * *
2748199 TCATCCGCCTCTTCGCTGTAAAGTTGAGCTTGTGCTGTCTT
66 TCAGCCGCCCCTTCGCTGTGAAGTTGAGCTTGTGCTGTCTT
* *
2748240 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGACTCTGAAATTGGGAAATTGTTTGTTGATAG
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAATTGTTTGTTGATAG
*
2748305 TCAGCCGCCCCTTCGCTGTGAAGTTGAGCTTGTGTTGTCTT
66 TCAGCCGCCCCTTCGCTGTGAAGTTGAGCTTGTGCTGTCTT
2748346 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATT-AGGAAATTGTTTGTTGATA
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGA-GAAATTGTTTGTTGATA
2748410 GTCAGCCG-CCCTTCGCTGTGAAGTTGAGCTTGTGCTGTCTT
65 GTCAGCCGCCCCTTCGCTGTGAAGTTGAGCTTGTGCTGTCTT
* * *
2748451 GAGTCCAATATCATTCGTTGTAAAGTTGAAATTGGATCTGAAATTG
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTG
2748497 GGAAGCCCCT
Statistics
Matches: 329, Mismatches: 32, Indels: 5
0.90 0.09 0.01
Matches are distributed among these distances:
105 74 0.22
106 221 0.67
107 34 0.10
ACGTcount: A:0.22, C:0.17, G:0.24, T:0.36
Consensus pattern (106 bp):
GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAATTGTTTGTTGATAG
TCAGCCGCCCCTTCGCTGTGAAGTTGAGCTTGTGCTGTCTT
Found at i:2753756 original size:3 final size:3
Alignment explanation
Indices: 2753745--2753784 Score: 53
Period size: 3 Copynumber: 12.3 Consensus size: 3
2753735 AAATGAAAAA
2753745 AAT ATAT AAT AAT AAT AAT AAT AAT AAAT AAAT AAT AAT A
1 AAT A-AT AAT AAT AAT AAT AAT AAT -AAT -AAT AAT AAT A
2753785 TAAAACCCGG
Statistics
Matches: 35, Mismatches: 0, Indels: 4
0.90 0.00 0.10
Matches are distributed among these distances:
3 25 0.71
4 10 0.29
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:2754936 original size:18 final size:19
Alignment explanation
Indices: 2754908--2754943 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
2754898 GAACCTAGAC
*
2754908 ATTTAAAACAATTAAGAAA
1 ATTTAAAACAAATAAGAAA
2754927 ATTT-AAACAAATAAGAA
1 ATTTAAAACAAATAAGAA
2754944 TGTTTTAGAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 12 0.75
19 4 0.25
ACGTcount: A:0.64, C:0.06, G:0.06, T:0.25
Consensus pattern (19 bp):
ATTTAAAACAAATAAGAAA
Found at i:2756364 original size:53 final size:53
Alignment explanation
Indices: 2756284--2756508 Score: 317
Period size: 53 Copynumber: 4.2 Consensus size: 53
2756274 CCTCTTCTTT
* * * *
2756284 GAACAATCTTC-GACTAGCGGGTTCGCTCCCTCTTACTTTAGGGAGTAAAACTC
1 GAACAATCTTCTGCCTA-CGGGTTCGCTCCCTCTTGCTTCAGGGAGTAGAACTC
* *
2756337 GAACACTCTTTTGCCTACGGGTTCGCTCCCTCTTGCTTCAGGGAGTAGAACTC
1 GAACAATCTTCTGCCTACGGGTTCGCTCCCTCTTGCTTCAGGGAGTAGAACTC
* *
2756390 GAATAATCTTCTGCCTACGGGTTTGCTCCCTCTTGCTTCAGGGAGTAGAACTC
1 GAACAATCTTCTGCCTACGGGTTCGCTCCCTCTTGCTTCAGGGAGTAGAACTC
* * * * *
2756443 GAATAATCTTCTGCCTACGGGTTCGTTGCCTCTTGCTTTAGAGAGTAGAACTC
1 GAACAATCTTCTGCCTACGGGTTCGCTCCCTCTTGCTTCAGGGAGTAGAACTC
2756496 GAACAATCTTCTG
1 GAACAATCTTCTG
2756509 GTGTGATTCT
Statistics
Matches: 155, Mismatches: 16, Indels: 2
0.90 0.09 0.01
Matches are distributed among these distances:
53 151 0.97
54 4 0.03
ACGTcount: A:0.21, C:0.26, G:0.22, T:0.31
Consensus pattern (53 bp):
GAACAATCTTCTGCCTACGGGTTCGCTCCCTCTTGCTTCAGGGAGTAGAACTC
Found at i:2756596 original size:42 final size:42
Alignment explanation
Indices: 2756547--2756812 Score: 231
Period size: 42 Copynumber: 6.4 Consensus size: 42
2756537 GAAGGCTTAA
* *
2756547 GATGGCCCGAAGGACTTAATCACCATGCTCGAAAGGCTTACT
1 GATGGCCCGAAGGACTTAATCATCATGCTCGAAAGACTTACT
* *
2756589 GATGGCCCGAAGGACTTCATCATCATGCTTGAAAGACTTACT
1 GATGGCCCGAAGGACTTAATCATCATGCTCGAAAGACTTACT
** * * * * *
2756631 GATGG---GATTG-CTTCA-CTACTC-TTC-CGTGAAGGCTTACA
1 GATGGCCCGAAGGACTTAATC-A-TCATGCTCG-AAAGACTTACT
* ** * * *
2756669 AATTACCCGAATGATTTAATCATCATGCTCAAAAGACTTACT
1 GATGGCCCGAAGGACTTAATCATCATGCTCGAAAGACTTACT
* * * *
2756711 GATGGCCCGAAGGATTTAAGCATCATGCTTGAAAGACTTATT
1 GATGGCCCGAAGGACTTAATCATCATGCTCGAAAGACTTACT
* * *
2756753 GATGGCCCGAAGGATTTAAGCATCATGCTCGAAAGACTTATT
1 GATGGCCCGAAGGACTTAATCATCATGCTCGAAAGACTTACT
*
2756795 GATGGCCCAAAGGACTTA
1 GATGGCCCGAAGGACTTA
2756813 CTAAGTGAGA
Statistics
Matches: 181, Mismatches: 33, Indels: 20
0.77 0.14 0.09
Matches are distributed among these distances:
37 2 0.01
38 18 0.10
39 5 0.03
41 6 0.03
42 148 0.82
43 2 0.01
ACGTcount: A:0.30, C:0.22, G:0.21, T:0.27
Consensus pattern (42 bp):
GATGGCCCGAAGGACTTAATCATCATGCTCGAAAGACTTACT
Found at i:2756736 original size:122 final size:121
Alignment explanation
Indices: 2756520--2756757 Score: 341
Period size: 122 Copynumber: 2.0 Consensus size: 121
2756510 TGTGATTCTC
** * * * *
2756520 CTTCACTACTCTTTTGTGAAGGCTTAAGATGGCCCGAAGGACTTAATCACCATGCTCGAAAGGCT
1 CTTCACTACTCTTCCGTGAAGGCTTAAAATGACCCGAAGGACTTAATCACCATGCTCAAAAGACT
* *
2756585 TACTGATGGCCCGAAGGACTTCATCATCATGCTTGAAAGACTTACTGATGGGATTG
66 TACTGATGGCCCGAAGGACTTAAGCATCATGCTTGAAAGACTTACTGATGGGATTG
* * * *
2756641 CTTCACTACTCTTCCGTGAAGGCTTACAAATTACCCGAATGATTTAATCATCATGCTCAAAAGAC
1 CTTCACTACTCTTCCGTGAAGGCTTA-AAATGACCCGAAGGACTTAATCACCATGCTCAAAAGAC
* *
2756706 TTACTGATGGCCCGAAGGATTTAAGCATCATGCTTGAAAGACTTATTGATGG
65 TTACTGATGGCCCGAAGGACTTAAGCATCATGCTTGAAAGACTTACTGATGG
2756758 CCCGAAGGAT
Statistics
Matches: 102, Mismatches: 14, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
121 24 0.24
122 78 0.76
ACGTcount: A:0.29, C:0.22, G:0.21, T:0.29
Consensus pattern (121 bp):
CTTCACTACTCTTCCGTGAAGGCTTAAAATGACCCGAAGGACTTAATCACCATGCTCAAAAGACT
TACTGATGGCCCGAAGGACTTAAGCATCATGCTTGAAAGACTTACTGATGGGATTG
Found at i:2765581 original size:53 final size:53
Alignment explanation
Indices: 2765499--2765670 Score: 265
Period size: 53 Copynumber: 3.2 Consensus size: 53
2765489 CCTCTTATTT
* *
2765499 AAACAATCTTC-GACTAGCGGGTTCACTCCCTCTTGCTTCAGGGAGTAGAACTC
1 AAACAATCTTCTGCCTA-CGGGTTCGCTCCCTCTTGCTTCAGGGAGTAGAACTC
*
2765552 AAACAGTCTTCTGCCTACGGGTTCGCTCCCTCTTGCTTCAGGGAGTAGAACTC
1 AAACAATCTTCTGCCTACGGGTTCGCTCCCTCTTGCTTCAGGGAGTAGAACTC
* * *
2765605 GAATAATCTTCTGCCTACGGGTTCGCTCCCTCTTGCTTTAGGGAGTAGAACTC
1 AAACAATCTTCTGCCTACGGGTTCGCTCCCTCTTGCTTCAGGGAGTAGAACTC
*
2765658 GAACAATCTTCTG
1 AAACAATCTTCTG
2765671 GTGTGATTCT
Statistics
Matches: 110, Mismatches: 8, Indels: 2
0.92 0.07 0.02
Matches are distributed among these distances:
53 106 0.96
54 4 0.04
ACGTcount: A:0.22, C:0.28, G:0.22, T:0.29
Consensus pattern (53 bp):
AAACAATCTTCTGCCTACGGGTTCGCTCCCTCTTGCTTCAGGGAGTAGAACTC
Found at i:2765727 original size:36 final size:36
Alignment explanation
Indices: 2765680--2765748 Score: 111
Period size: 36 Copynumber: 1.9 Consensus size: 36
2765670 GGTGTGATTC
* **
2765680 TGCTTCACTACTCTTCTGTGAAGGTTTAAGATGTTT
1 TGCTTCACTACTCTTCCGTGAAGGCATAAGATGTTT
2765716 TGCTTCACTACTCTTCCGTGAAGGCATAAGATG
1 TGCTTCACTACTCTTCCGTGAAGGCATAAGATG
2765749 GCCCGGGAGA
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
36 30 1.00
ACGTcount: A:0.22, C:0.20, G:0.20, T:0.38
Consensus pattern (36 bp):
TGCTTCACTACTCTTCCGTGAAGGCATAAGATGTTT
Found at i:2765885 original size:36 final size:36
Alignment explanation
Indices: 2765834--2765904 Score: 106
Period size: 36 Copynumber: 2.0 Consensus size: 36
2765824 TACTGATGAC
2765834 TTGCTTCACTACTCTTCCGTGAACACTTAAGATGGT
1 TTGCTTCACTACTCTTCCGTGAACACTTAAGATGGT
* * **
2765870 TTGCTTCACTTCTCTTTCGTGAAGGCTTAAGATGG
1 TTGCTTCACTACTCTTCCGTGAACACTTAAGATGG
2765905 CCCGAAGGAC
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
36 31 1.00
ACGTcount: A:0.20, C:0.23, G:0.20, T:0.38
Consensus pattern (36 bp):
TTGCTTCACTACTCTTCCGTGAACACTTAAGATGGT
Found at i:2765904 original size:155 final size:156
Alignment explanation
Indices: 2765680--2765987 Score: 401
Period size: 155 Copynumber: 2.0 Consensus size: 156
2765670 GGTGTGATTC
* *** *
2765680 TGCTTCACTACTCTTCTGTGAAGGTTTAAGATGTTTTGCTTCACTACTCTTCCGTGAAGGCATAA
1 TGCTTCACTACTCTTCCGTGAACACTTAAGATGGTTTGCTTCACTACTCTTCCGTGAAGGCATAA
* * * * *
2765745 GATGGCCCG-GGAGACTT-ATCATCTTGCTC-GAAAGTCTTA-TAGATGACCCGTATGA-TTTAA
66 GATGGCCCGAAG-GACTTAATCATCATGCTCAG-AAGGCTTACT-GATGACCCGAAGGACTTT-A
* *
2765805 TCATCATGCTCGGAAGGCTTACTGATGACT
127 TCATCATGCTCGAAAGACTTACTGATGACT
* * *
2765835 TGCTTCACTACTCTTCCGTGAACACTTAAGATGGTTTGCTTCACTTCTCTTTCGTGAAGGCTTAA
1 TGCTTCACTACTCTTCCGTGAACACTTAAGATGGTTTGCTTCACTACTCTTCCGTGAAGGCATAA
*
2765900 GATGGCCCGAAGGACTTAATCATCATGCTCAGAAGGCTTACTGATGGCCCGAAGGACTTTATCAT
66 GATGGCCCGAAGGACTTAATCATCATGCTCAGAAGGCTTACTGATGACCCGAAGGACTTTATCAT
2765965 CATGCTCGAAAGACTTACTGATG
131 CATGCTCGAAAGACTTACTGATG
2765988 GTACTTACTA
Statistics
Matches: 132, Mismatches: 16, Indels: 9
0.84 0.10 0.06
Matches are distributed among these distances:
155 71 0.54
156 56 0.42
157 5 0.04
ACGTcount: A:0.24, C:0.22, G:0.21, T:0.32
Consensus pattern (156 bp):
TGCTTCACTACTCTTCCGTGAACACTTAAGATGGTTTGCTTCACTACTCTTCCGTGAAGGCATAA
GATGGCCCGAAGGACTTAATCATCATGCTCAGAAGGCTTACTGATGACCCGAAGGACTTTATCAT
CATGCTCGAAAGACTTACTGATGACT
Found at i:2765950 original size:42 final size:41
Alignment explanation
Indices: 2765890--2765988 Score: 146
Period size: 42 Copynumber: 2.4 Consensus size: 41
2765880 TCTCTTTCGT
*
2765890 GAAGGCTTA-AGATGGCCCGAAGGACTTAATCATCATGCTC
1 GAAGGCTTACTGATGGCCCGAAGGACTTAATCATCATGCTC
*
2765930 AGAAGGCTTACTGATGGCCCGAAGGACTTTATCATCATGCTC
1 -GAAGGCTTACTGATGGCCCGAAGGACTTAATCATCATGCTC
*
2765972 GAAAGACTTACTGATGG
1 G-AAGGCTTACTGATGG
2765989 TACTTACTAA
Statistics
Matches: 53, Mismatches: 3, Indels: 3
0.90 0.05 0.05
Matches are distributed among these distances:
41 10 0.19
42 43 0.81
ACGTcount: A:0.29, C:0.21, G:0.25, T:0.24
Consensus pattern (41 bp):
GAAGGCTTACTGATGGCCCGAAGGACTTAATCATCATGCTC
Found at i:2766086 original size:42 final size:42
Alignment explanation
Indices: 2766040--2766132 Score: 141
Period size: 42 Copynumber: 2.2 Consensus size: 42
2766030 TTACAAATTA
**
2766040 CCCGAAGGATTTAATTATCATGCTCGAAAGACTTACTGATGG
1 CCCGAAGGATTTAAGAATCATGCTCGAAAGACTTACTGATGG
* *
2766082 CCCGAAAGATTTAAGAATCATGCTCGAAAGACTTATTGATGG
1 CCCGAAGGATTTAAGAATCATGCTCGAAAGACTTACTGATGG
*
2766124 CTCGAAGGA
1 CCCGAAGGA
2766133 CTTACTAAGT
Statistics
Matches: 45, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
42 45 1.00
ACGTcount: A:0.33, C:0.18, G:0.23, T:0.26
Consensus pattern (42 bp):
CCCGAAGGATTTAAGAATCATGCTCGAAAGACTTACTGATGG
Found at i:2766111 original size:135 final size:134
Alignment explanation
Indices: 2765870--2766123 Score: 352
Period size: 135 Copynumber: 1.9 Consensus size: 134
2765860 TTAAGATGGT
* * *
2765870 TTGCTTCACTTCTCTTTCGTGAAGGCTTAAGATGGCCCGAAGGACTTAATCATCATGCTCAGAAG
1 TTGCTTCACTACTCTTTCGTGAAGGCTTAAAATGACCCGAAGGACTTAATCATCATGCTCAGAAG
* * **
2765935 GCTTACTGATGGCCCGAAGGACTTTATCATCATGCTCGAAAGACTTACTGATGGTACTTACTAAT
66 ACTTACTGATGGCCCGAAAGACTTTAGAATCATGCTCGAAAGACTTACTGATGGTACTTACTAAT
2766000 GGGA
131 GGGA
* * *
2766004 TTGCTTCACTACTC-TTCTGTGAAGGCTTACAAATTACCCGAAGGATTTAATTATCATGCTC-GA
1 TTGCTTCACTACTCTTTC-GTGAAGGCTTA-AAATGACCCGAAGGACTTAATCATCATGCTCAG-
*
2766067 AAGACTTACTGATGGCCCGAAAGA-TTTAAGAATCATGCTCGAAAGACTTATTGATGG
63 AAGACTTACTGATGGCCCGAAAGACTTT-AGAATCATGCTCGAAAGACTTACTGATGG
2766124 CTCGAAGGAC
Statistics
Matches: 105, Mismatches: 11, Indels: 7
0.85 0.09 0.06
Matches are distributed among these distances:
133 3 0.03
134 28 0.27
135 74 0.70
ACGTcount: A:0.28, C:0.20, G:0.21, T:0.30
Consensus pattern (134 bp):
TTGCTTCACTACTCTTTCGTGAAGGCTTAAAATGACCCGAAGGACTTAATCATCATGCTCAGAAG
ACTTACTGATGGCCCGAAAGACTTTAGAATCATGCTCGAAAGACTTACTGATGGTACTTACTAAT
GGGA
Found at i:2766128 original size:20 final size:19
Alignment explanation
Indices: 2766061--2766136 Score: 62
Period size: 20 Copynumber: 3.7 Consensus size: 19
2766051 TAATTATCAT
2766061 GCTCGAAAGACTTACTGATG
1 GCTCGAAAGACTTA-TGATG
* * * *
2766081 GCCCGAAAGATTTAAGAATCAT
1 GCTCGAAAGACTTATG-AT--G
2766103 GCTCGAAAGACTTATTGATG
1 GCTCGAAAGACTTA-TGATG
*
2766123 GCTCGAAGGACTTA
1 GCTCGAAAGACTTA
2766137 CTAAGTGAGA
Statistics
Matches: 43, Mismatches: 9, Indels: 8
0.72 0.15 0.13
Matches are distributed among these distances:
19 1 0.02
20 27 0.63
22 14 0.33
23 1 0.02
ACGTcount: A:0.33, C:0.18, G:0.24, T:0.25
Consensus pattern (19 bp):
GCTCGAAAGACTTATGATG
Found at i:2766303 original size:41 final size:41
Alignment explanation
Indices: 2766237--2766352 Score: 126
Period size: 42 Copynumber: 2.8 Consensus size: 41
2766227 AAACATCCTA
* * *
2766237 CTCG-AAGGTCTTACGGATGACCCGAATGACTTATCATCTTG
1 CTCGAAAGG-CTTACAGATGACCCGAAGGACTTATCATCATG
** *
2766278 CTTTAAAGGCTTACAGATGACCCGAAGGATTTCATCATCATG
1 CTCGAAAGGCTTACAGATGACCCGAAGGACTT-ATCATCATG
* * *
2766320 CTCGAAAGACTTACTGATGGCCCGAAGGACTTA
1 CTCGAAAGGCTTACAGATGACCCGAAGGACTTA
2766353 AATTGTTTAC
Statistics
Matches: 61, Mismatches: 12, Indels: 4
0.79 0.16 0.05
Matches are distributed among these distances:
41 23 0.38
42 38 0.62
ACGTcount: A:0.28, C:0.23, G:0.22, T:0.27
Consensus pattern (41 bp):
CTCGAAAGGCTTACAGATGACCCGAAGGACTTATCATCATG
Found at i:2772338 original size:6 final size:6
Alignment explanation
Indices: 2772329--2772358 Score: 51
Period size: 6 Copynumber: 5.0 Consensus size: 6
2772319 TGCTAATAAG
*
2772329 AATGCA AATGCA AATGCA AATGAA AATGCA
1 AATGCA AATGCA AATGCA AATGCA AATGCA
2772359 CACGGTGTTA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
6 22 1.00
ACGTcount: A:0.53, C:0.13, G:0.17, T:0.17
Consensus pattern (6 bp):
AATGCA
Done.