Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr01 ID=Chr01-JGI_221_v2.0
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: 55868233
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 983842 characters in sequence are not A, C, G, or T
File 173 of 187
Found at i:51775262 original size:29 final size:30
Alignment explanation
Indices: 51775218--51775289 Score: 103
Period size: 29 Copynumber: 2.4 Consensus size: 30
51775208 TATCAAATTG
*
51775218 TGAAAAGGGATAGTGACGACCATC-AA-TAA
1 TGAAAAGGGATAGTGAAGACCATCGAACT-A
*
51775247 TGAAAAGGGATGGTGAAGACCATCGAACTA
1 TGAAAAGGGATAGTGAAGACCATCGAACTA
51775277 TGAAAAGGGATAG
1 TGAAAAGGGATAG
51775290 CTTTGACTAT
Statistics
Matches: 38, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
29 22 0.58
30 15 0.39
31 1 0.03
ACGTcount: A:0.43, C:0.11, G:0.29, T:0.17
Consensus pattern (30 bp):
TGAAAAGGGATAGTGAAGACCATCGAACTA
Found at i:51775391 original size:30 final size:30
Alignment explanation
Indices: 51775352--51775411 Score: 93
Period size: 30 Copynumber: 2.0 Consensus size: 30
51775342 AGGGATGGTG
*
51775352 AAAGGGATAGCTTCAACTATCAAATTATGA
1 AAAGAGATAGCTTCAACTATCAAATTATGA
**
51775382 AAAGAGATAGCTTCTGCTATCAAATTATGA
1 AAAGAGATAGCTTCAACTATCAAATTATGA
51775412 GAAGGGATGG
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
30 27 1.00
ACGTcount: A:0.42, C:0.13, G:0.17, T:0.28
Consensus pattern (30 bp):
AAAGAGATAGCTTCAACTATCAAATTATGA
Found at i:51775400 original size:72 final size:72
Alignment explanation
Indices: 51775280--51775424 Score: 254
Period size: 72 Copynumber: 2.0 Consensus size: 72
51775270 CGAACTATGA
** * *
51775280 AAAGGGATAGCTTTGACTATCGAATTATGAAAAGAGATAGCTTTTGCTATCAAATTATGAGAAGG
1 AAAGGGATAGCTTCAACTATCAAATTATGAAAAGAGATAGCTTCTGCTATCAAATTATGAGAAGG
51775345 GATGGTG
66 GATGGTG
51775352 AAAGGGATAGCTTCAACTATCAAATTATGAAAAGAGATAGCTTCTGCTATCAAATTATGAGAAGG
1 AAAGGGATAGCTTCAACTATCAAATTATGAAAAGAGATAGCTTCTGCTATCAAATTATGAGAAGG
51775417 GATGGTG
66 GATGGTG
51775424 A
1 A
51775425 CGACCATCAA
Statistics
Matches: 69, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
72 69 1.00
ACGTcount: A:0.38, C:0.10, G:0.25, T:0.28
Consensus pattern (72 bp):
AAAGGGATAGCTTCAACTATCAAATTATGAAAAGAGATAGCTTCTGCTATCAAATTATGAGAAGG
GATGGTG
Found at i:51775490 original size:59 final size:59
Alignment explanation
Indices: 51775377--51775491 Score: 137
Period size: 59 Copynumber: 1.9 Consensus size: 59
51775367 ACTATCAAAT
* *
51775377 TATGAAAAGAGATAGCTTCTGCTATCAAATTATGAGAAGGGATGGTGACGACCATCAAC
1 TATGAAAAGAGATAGCTTCTGCTATCAAATTATGAGAAAGGATGGAGACGACCATCAAC
* * *
51775436 TATGAAAAGGGATAGCTTC-GACTATCGAGTTATG-GAAAAGGATGGAGA-GAACCATC
1 TATGAAAAGAGATAGCTTCTG-CTATCAAATTATGAG-AAAGGATGGAGACG-ACCATC
51775492 GTGATTTTAC
Statistics
Matches: 48, Mismatches: 5, Indels: 6
0.81 0.08 0.10
Matches are distributed among these distances:
58 3 0.06
59 45 0.94
ACGTcount: A:0.37, C:0.14, G:0.26, T:0.23
Consensus pattern (59 bp):
TATGAAAAGAGATAGCTTCTGCTATCAAATTATGAGAAAGGATGGAGACGACCATCAAC
Found at i:51784354 original size:29 final size:29
Alignment explanation
Indices: 51784312--51784808 Score: 364
Period size: 29 Copynumber: 17.1 Consensus size: 29
51784302 TATGCTAATA
**
51784312 ATGGTCGAAACCATCCCTTTTCATATTCG
1 ATGGTCGTCACCATCCCTTTTCATATTCG
51784341 ATGGTCGTCACCATCCCTTTTCATAGTT-G
1 ATGGTCGTCACCATCCCTTTTCATA-TTCG
* *** ** * *
51784370 ATAGTCAAAAATATCCTTTTTCATAATCG
1 ATGGTCGTCACCATCCCTTTTCATATTCG
* ** * * *
51784399 ATAGTCGAAACTATCTCTTTTCATAGTCG
1 ATGGTCGTCACCATCCCTTTTCATATTCG
* *
51784428 ATGGCCGTCATCATCCCTTTTCATAGTT-G
1 ATGGTCGTCACCATCCCTTTTCATA-TTCG
*
51784457 ATGGTCGTCACCATCCCTTTCCATATTCG
1 ATGGTCGTCACCATCCCTTTTCATATTCG
* ** *
51784486 ATGGTTGAAACCATCCCTTTTCATTAATCG
1 ATGGTCGTCACCATCCCTTTTCA-TATTCG
*
51784516 ATGGTCGTCATCATCCCTTTTCATAGTT-G
1 ATGGTCGTCACCATCCCTTTTCATA-TTCG
*
51784545 ATGGTCGTCACCATCCCTTTTCATA-GCTG
1 ATGGTCGTCACCATCCCTTTTCATATTC-G
*
51784574 ATGGTCGTCACCATCCTTTTTCATAGTT-G
1 ATGGTCGTCACCATCCCTTTTCATA-TTCG
* *
51784603 ATAGTCGTCACCATCCTTTTTCATAGTT-G
1 ATGGTCGTCACCATCCCTTTTCATA-TTCG
* * ** * *
51784632 ATAGTTGAAACTATCCCTTTTCATAATCG
1 ATGGTCGTCACCATCCCTTTTCATATTCG
* ** * * *
51784661 ATAGTCGAAACTATCACTTTTCATAGTCG
1 ATGGTCGTCACCATCCCTTTTCATATTCG
*
51784690 ATGGTCATCACCATCCCTTTTCATAGTT-G
1 ATGGTCGTCACCATCCCTTTTCATA-TTCG
* *
51784719 ATGGTTGTCACCTTCCCTTTTCATAGTT-G
1 ATGGTCGTCACCATCCCTTTTCATA-TTCG
* ** * *
51784748 -TAGTCGAAACTATCCCTTTTCATAATCG
1 ATGGTCGTCACCATCCCTTTTCATATTCG
* *** *
51784776 ATGGACAAAACCATCCCTTTTCATTTTTCG
1 ATGGTCGTCACCATCCCTTTTCA-TATTCG
51784806 ATG
1 ATG
51784809 ATCATCGATA
Statistics
Matches: 380, Mismatches: 73, Indels: 29
0.79 0.15 0.06
Matches are distributed among these distances:
27 1 0.00
28 23 0.06
29 320 0.84
30 36 0.09
ACGTcount: A:0.23, C:0.25, G:0.14, T:0.38
Consensus pattern (29 bp):
ATGGTCGTCACCATCCCTTTTCATATTCG
Found at i:51784487 original size:87 final size:87
Alignment explanation
Indices: 51784315--51784799 Score: 542
Period size: 87 Copynumber: 5.6 Consensus size: 87
51784305 GCTAATAATG
* * ***
51784315 GTCGAAACCATCCCTTTTCATATTCGATGGTCGTCACCATCCCTTTTCATAGTTGATAGTCAAAA
1 GTCGAAACCATCCCTTTTCATAGTCGATGGTCGTCACCATCCCTTTTCATAGTTGATGGTCGTCA
** *
51784380 ATATCCTTTTTCATAATCGATA
66 CCATCCCTTTTCATAATCGATA
* * * *
51784402 GTCGAAACTATCTCTTTTCATAGTCGATGGCCGTCATCATCCCTTTTCATAGTTGATGGTCGTCA
1 GTCGAAACCATCCCTTTTCATAGTCGATGGTCGTCACCATCCCTTTTCATAGTTGATGGTCGTCA
* * *
51784467 CCATCCCTTTCCATATTCGATG
66 CCATCCCTTTTCATAATCGATA
* * *
51784489 GTTGAAACCATCCCTTTTCATTAATCGATGGTCGTCATCATCCCTTTTCATAGTTGATGGTCGTC
1 GTCGAAACCATCCCTTTTCA-TAGTCGATGGTCGTCACCATCCCTTTTCATAGTTGATGGTCGTC
* *
51784554 ACCATCCCTTTTCAT-AGCTGATG
65 ACCATCCCTTTTCATAATC-GATA
** * * * * * * **
51784577 GTCGTCACCATCCTTTTTCATAGTTGATAGTCGTCACCATCCTTTTTCATAGTTGATAGTTGAAA
1 GTCGAAACCATCCCTTTTCATAGTCGATGGTCGTCACCATCCCTTTTCATAGTTGATGGTCGTCA
*
51784642 CTATCCCTTTTCATAATCGATA
66 CCATCCCTTTTCATAATCGATA
* * * *
51784664 GTCGAAACTATCACTTTTCATAGTCGATGGTCATCACCATCCCTTTTCATAGTTGATGGTTGTCA
1 GTCGAAACCATCCCTTTTCATAGTCGATGGTCGTCACCATCCCTTTTCATAGTTGATGGTCGTCA
* * *
51784729 CCTTCCCTTTTCATAGTTG-TA
66 CCATCCCTTTTCATAATCGATA
* * * ***
51784750 GTCGAAACTATCCCTTTTCATAATCGATGGACAAAACCATCCCTTTTCAT
1 GTCGAAACCATCCCTTTTCATAGTCGATGGTCGTCACCATCCCTTTTCAT
51784800 TTTTCGATGA
Statistics
Matches: 335, Mismatches: 60, Indels: 7
0.83 0.15 0.02
Matches are distributed among these distances:
86 47 0.14
87 210 0.63
88 78 0.23
ACGTcount: A:0.23, C:0.25, G:0.14, T:0.38
Consensus pattern (87 bp):
GTCGAAACCATCCCTTTTCATAGTCGATGGTCGTCACCATCCCTTTTCATAGTTGATGGTCGTCA
CCATCCCTTTTCATAATCGATA
Found at i:51790197 original size:24 final size:23
Alignment explanation
Indices: 51790165--51790211 Score: 67
Period size: 24 Copynumber: 2.0 Consensus size: 23
51790155 TTGTAAAGAA
*
51790165 GAAGAAGAAGATGAAGCTTTTAGT
1 GAAGAAGAAAATGAAG-TTTTAGT
*
51790189 GAAGAAGAAAATGGAGTTTTAGT
1 GAAGAAGAAAATGAAGTTTTAGT
51790212 TAACCATATT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
23 7 0.33
24 14 0.67
ACGTcount: A:0.43, C:0.02, G:0.30, T:0.26
Consensus pattern (23 bp):
GAAGAAGAAAATGAAGTTTTAGT
Found at i:51790397 original size:28 final size:28
Alignment explanation
Indices: 51790359--51790428 Score: 113
Period size: 28 Copynumber: 2.5 Consensus size: 28
51790349 AAAAATAAAA
**
51790359 ATTTACCAAAATATTATAATTTTTTTTT
1 ATTTACCAAAATATTATAAAATTTTTTT
51790387 ATTTACCAAAATATTATAAAATTTTTTT
1 ATTTACCAAAATATTATAAAATTTTTTT
*
51790415 ATTTATCAAAATAT
1 ATTTACCAAAATAT
51790429 ACAAAAAAAT
Statistics
Matches: 39, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
28 39 1.00
ACGTcount: A:0.41, C:0.07, G:0.00, T:0.51
Consensus pattern (28 bp):
ATTTACCAAAATATTATAAAATTTTTTT
Found at i:51790506 original size:27 final size:27
Alignment explanation
Indices: 51790476--51790527 Score: 86
Period size: 27 Copynumber: 1.9 Consensus size: 27
51790466 GGCCAATCAC
*
51790476 ATTGGTGGCACCAAAGGTGCCAAAGAG
1 ATTGGCGGCACCAAAGGTGCCAAAGAG
*
51790503 ATTGGCGGCACCAATGGTGCCAAAG
1 ATTGGCGGCACCAAAGGTGCCAAAG
51790528 GACTAAAATG
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
27 23 1.00
ACGTcount: A:0.31, C:0.21, G:0.33, T:0.15
Consensus pattern (27 bp):
ATTGGCGGCACCAAAGGTGCCAAAGAG
Found at i:51790978 original size:19 final size:19
Alignment explanation
Indices: 51790954--51791002 Score: 64
Period size: 18 Copynumber: 2.6 Consensus size: 19
51790944 TCTAATTAAG
*
51790954 TAATAACTCTATTTTAATT
1 TAATAACTCTATTCTAATT
* *
51790973 TAATAA-ACTATTCTCATT
1 TAATAACTCTATTCTAATT
51790991 TAATAACTCTAT
1 TAATAACTCTAT
51791003 AAAATTAAAT
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
18 15 0.60
19 10 0.40
ACGTcount: A:0.39, C:0.14, G:0.00, T:0.47
Consensus pattern (19 bp):
TAATAACTCTATTCTAATT
Found at i:51791065 original size:37 final size:37
Alignment explanation
Indices: 51791006--51791100 Score: 176
Period size: 37 Copynumber: 2.6 Consensus size: 37
51790996 ACTCTATAAA
51791006 ATTAAATT-AAA-AGAGTTATTAAATGAGAATAGTTT
1 ATTAAATTAAAATAGAGTTATTAAATGAGAATAGTTT
51791041 ATTAAATTAAAATAGAGTTATTAAATGAGAATAGTTT
1 ATTAAATTAAAATAGAGTTATTAAATGAGAATAGTTT
51791078 ATTAAATTAAAATAGAGTTATTA
1 ATTAAATTAAAATAGAGTTATTA
51791101 CTTAATTAGA
Statistics
Matches: 58, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
35 8 0.14
36 3 0.05
37 47 0.81
ACGTcount: A:0.49, C:0.00, G:0.13, T:0.38
Consensus pattern (37 bp):
ATTAAATTAAAATAGAGTTATTAAATGAGAATAGTTT
Found at i:51791105 original size:18 final size:19
Alignment explanation
Indices: 51791006--51791100 Score: 108
Period size: 18 Copynumber: 5.2 Consensus size: 19
51790996 ACTCTATAAA
51791006 ATTAAATT-AAA-AGAGTT
1 ATTAAATTAAAATAGAGTT
* * *
51791023 ATTAAATGAGAATAG-TTT
1 ATTAAATTAAAATAGAGTT
51791041 ATTAAATTAAAATAGAGTT
1 ATTAAATTAAAATAGAGTT
* * *
51791060 ATTAAATGAGAATAG-TTT
1 ATTAAATTAAAATAGAGTT
51791078 ATTAAATTAAAATAGAGTT
1 ATTAAATTAAAATAGAGTT
51791097 ATTA
1 ATTA
51791101 CTTAATTAGA
Statistics
Matches: 62, Mismatches: 12, Indels: 6
0.77 0.15 0.08
Matches are distributed among these distances:
17 7 0.11
18 32 0.52
19 23 0.37
ACGTcount: A:0.49, C:0.00, G:0.13, T:0.38
Consensus pattern (19 bp):
ATTAAATTAAAATAGAGTT
Found at i:51791683 original size:27 final size:27
Alignment explanation
Indices: 51791651--51791702 Score: 77
Period size: 27 Copynumber: 1.9 Consensus size: 27
51791641 CATTTTAGTC
*
51791651 CTTTGGCACCATTGGTGCCGCCAATCT
1 CTTTGGCACCATTAGTGCCGCCAATCT
* *
51791678 CTTTGGCATCTTTAGTGCCGCCAAT
1 CTTTGGCACCATTAGTGCCGCCAAT
51791703 GTGATTGGCC
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
27 22 1.00
ACGTcount: A:0.15, C:0.31, G:0.21, T:0.33
Consensus pattern (27 bp):
CTTTGGCACCATTAGTGCCGCCAATCT
Found at i:51791802 original size:26 final size:28
Alignment explanation
Indices: 51791750--51791817 Score: 113
Period size: 26 Copynumber: 2.5 Consensus size: 28
51791740 GTTTTTTTGT
51791750 ATATTTTGATAAATAAAAAAAAGTTATA
1 ATATTTTGATAAATAAAAAAAAGTTATA
51791778 ATATTTTGATAAAT-AAAAAAA-TTATA
1 ATATTTTGATAAATAAAAAAAAGTTATA
*
51791804 ATATTTTGGTAAAT
1 ATATTTTGATAAAT
51791818 TTTTATTTTT
Statistics
Matches: 39, Mismatches: 1, Indels: 2
0.93 0.02 0.05
Matches are distributed among these distances:
26 18 0.46
27 7 0.18
28 14 0.36
ACGTcount: A:0.53, C:0.00, G:0.07, T:0.40
Consensus pattern (28 bp):
ATATTTTGATAAATAAAAAAAAGTTATA
Found at i:51792110 original size:12 final size:13
Alignment explanation
Indices: 51792081--51792112 Score: 57
Period size: 13 Copynumber: 2.5 Consensus size: 13
51792071 TTTAAGCCGT
51792081 ATTTTAATAATAA
1 ATTTTAATAATAA
51792094 ATTTTAATAAT-A
1 ATTTTAATAATAA
51792106 ATTTTAA
1 ATTTTAA
51792113 ATTTTAAACA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
12 8 0.42
13 11 0.58
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (13 bp):
ATTTTAATAATAA
Found at i:51795620 original size:45 final size:45
Alignment explanation
Indices: 51795521--51795706 Score: 225
Period size: 45 Copynumber: 4.2 Consensus size: 45
51795511 AATAATAACA
* * * * * *
51795521 GATACACGGTGG-ATCAGCACATAGC-ACCACCCTTATAGTCAAC
1 GATACCCGGTGGAATCAGCACACAACAACCACCTTTATAATCAAT
* * * * *
51795564 GATACTCGGTGGAATCAGCAGATAGCAACCACCTTCATAATCAAT
1 GATACCCGGTGGAATCAGCACACAACAACCACCTTTATAATCAAT
51795609 -AGTACCCGGTGGAATCAGCACACAACAACCACCTTTATAATCAAT
1 GA-TACCCGGTGGAATCAGCACACAACAACCACCTTTATAATCAAT
*
51795654 GATACCCGATGGAATCAGCACACAACAACCACCTTTATAATCAAT
1 GATACCCGGTGGAATCAGCACACAACAACCACCTTTATAATCAAT
*
51795699 GGTACCCG
1 GATACCCG
51795707 ATACATGTAG
Statistics
Matches: 126, Mismatches: 13, Indels: 6
0.87 0.09 0.04
Matches are distributed among these distances:
43 11 0.09
44 13 0.10
45 101 0.80
46 1 0.01
ACGTcount: A:0.35, C:0.28, G:0.16, T:0.20
Consensus pattern (45 bp):
GATACCCGGTGGAATCAGCACACAACAACCACCTTTATAATCAAT
Found at i:51801426 original size:3 final size:3
Alignment explanation
Indices: 51801418--51801485 Score: 57
Period size: 3 Copynumber: 22.3 Consensus size: 3
51801408 TAATATTAGT
***
51801418 TTA TTA TTA TTA TTA TTA GCC TT- TTA TTA TTA TTA TATA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T-TA TTA TTA
* * *
51801463 CTC TTA TTA TTA TAGA TTA TTA T
1 TTA TTA TTA TTA T-TA TTA TTA T
51801486 ATTTATCATA
Statistics
Matches: 51, Mismatches: 11, Indels: 6
0.75 0.16 0.09
Matches are distributed among these distances:
2 2 0.04
3 44 0.86
4 5 0.10
ACGTcount: A:0.31, C:0.06, G:0.03, T:0.60
Consensus pattern (3 bp):
TTA
Found at i:51801436 original size:20 final size:20
Alignment explanation
Indices: 51801411--51801485 Score: 66
Period size: 19 Copynumber: 3.7 Consensus size: 20
51801401 ATTTGTTTAA
51801411 TATTAGTTTATTATTATTAT
1 TATTAGTTTATTATTATTAT
51801431 TATTAGCCTTTTATTATTATTAT
1 TATTAG---TTTATTATTATTAT
* *
51801454 ATATTA--TTACTCTTATTAT
1 -TATTAGTTTATTATTATTAT
*
51801473 TA-TAGATTATTAT
1 TATTAGTTTATTAT
51801486 ATTTATCATA
Statistics
Matches: 45, Mismatches: 4, Indels: 13
0.73 0.06 0.21
Matches are distributed among these distances:
17 2 0.04
18 2 0.04
19 16 0.36
20 6 0.13
23 14 0.31
24 5 0.11
ACGTcount: A:0.31, C:0.05, G:0.04, T:0.60
Consensus pattern (20 bp):
TATTAGTTTATTATTATTAT
Found at i:51804797 original size:40 final size:40
Alignment explanation
Indices: 51804744--51804838 Score: 127
Period size: 40 Copynumber: 2.4 Consensus size: 40
51804734 GCGTTTGGAT
51804744 AAAAAACGCCGCTAAAAATCAAGCATTAGCGACACTTTTA
1 AAAAAACGCCGCTAAAAATCAAGCATTAGCGACACTTTTA
* * * * * *
51804784 AAAAAACGCCGCTAAAGATTAAGTATTAGCGGCGCTTTTT
1 AAAAAACGCCGCTAAAAATCAAGCATTAGCGACACTTTTA
*
51804824 TAAAAACGCCGCTAA
1 AAAAAACGCCGCTAA
51804839 TGCTTATTTT
Statistics
Matches: 48, Mismatches: 7, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
40 48 1.00
ACGTcount: A:0.41, C:0.21, G:0.16, T:0.22
Consensus pattern (40 bp):
AAAAAACGCCGCTAAAAATCAAGCATTAGCGACACTTTTA
Found at i:51805115 original size:41 final size:40
Alignment explanation
Indices: 51804918--51805116 Score: 229
Period size: 41 Copynumber: 4.9 Consensus size: 40
51804908 GTTTTCGAGG
*
51804918 CTTTAGTGGCGTTTTTTAAAAAGCGCCGCTAATGCTCAGGGT
1 CTTTAGCGGCG-TTTTTAAAAAGCGCCGCTAATGCTC-GGGT
* * *
51804960 -TTTAGCGGCGTTTTAAAAAAGCGTCGCTAATGATCGGGT
1 CTTTAGCGGCGTTTTTAAAAAGCGCCGCTAATGCTCGGGT
* ** * *
51804999 CTTTAGCGGCATTTTTGGGAAAGCGCCACTAATGATCGGGT
1 CTTTAGCGGCGTTTTT-AAAAAGCGCCGCTAATGCTCGGGT
* *
51805040 CTTTAGCGGCGCTTTCTCAAAAGCGCCGCTAATGCTCGGGT
1 CTTTAGCGGCG-TTTTTAAAAAGCGCCGCTAATGCTCGGGT
* *
51805081 CTTTAGCGGCGTTTTTAATGAAGCGTCGCTAATGCT
1 CTTTAGCGGCGTTTTTAA-AAAGCGCCGCTAATGCT
51805117 TAGGGCAATA
Statistics
Matches: 133, Mismatches: 20, Indels: 9
0.82 0.12 0.06
Matches are distributed among these distances:
39 4 0.03
40 40 0.30
41 85 0.64
42 4 0.03
ACGTcount: A:0.21, C:0.21, G:0.27, T:0.31
Consensus pattern (40 bp):
CTTTAGCGGCGTTTTTAAAAAGCGCCGCTAATGCTCGGGT
Found at i:51808686 original size:16 final size:16
Alignment explanation
Indices: 51808665--51808695 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
51808655 TGTAACCTAT
51808665 CTGATGTTTACAATAA
1 CTGATGTTTACAATAA
51808681 CTGATGTTTACAATA
1 CTGATGTTTACAATA
51808696 GTTAGGGACT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.35, C:0.13, G:0.13, T:0.39
Consensus pattern (16 bp):
CTGATGTTTACAATAA
Found at i:51809978 original size:43 final size:43
Alignment explanation
Indices: 51809871--51810182 Score: 448
Period size: 43 Copynumber: 7.3 Consensus size: 43
51809861 AGATTATGTT
* ** * * *
51809871 TTTAGCGGCGTTTTTGCTAGAAGCGCCGCTAAAGGT-GTGTTC
1 TTTAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGGTCTTGGTC
* ** * *
51809913 TTTAGCGGCGTTTTTGATAAAAGTGCCGCTAAAGGTCATGGTC
1 TTTAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGGTCTTGGTC
* * * *
51809956 TATAGCGGCTTTTGTGGGAAAAGCACCGCTAAAGGTCCTGGTC
1 TTTAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGGTCTTGGTC
*
51809999 TTTAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGGTCCTGGTC
1 TTTAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGGTCTTGGTC
* *
51810042 TTTAGTGGCGTTTGTGTGAAAAGCGCCGCTAAAGGTCTTGGTC
1 TTTAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGGTCTTGGTC
51810085 TTTAGCGGCGTTTGTGGG-AAAGCGCCGCTAAAGGTCTTGGTC
1 TTTAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGGTCTTGGTC
51810127 TTTAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGGTCTTGGTC
1 TTTAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGGTCTTGGTC
51810170 TTTAGCGGCGTTT
1 TTTAGCGGCGTTT
51810183 TTTTCTAAAA
Statistics
Matches: 247, Mismatches: 21, Indels: 3
0.91 0.08 0.01
Matches are distributed among these distances:
42 75 0.30
43 172 0.70
ACGTcount: A:0.19, C:0.19, G:0.32, T:0.30
Consensus pattern (43 bp):
TTTAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGGTCTTGGTC
Found at i:51809985 original size:85 final size:85
Alignment explanation
Indices: 51809871--51810182 Score: 437
Period size: 85 Copynumber: 3.7 Consensus size: 85
51809861 AGATTATGTT
* ** * * * * *
51809871 TTTAGCGGCGTTTTTGCTAGAAGCGCCGCTAAAGGT-GTGTTCTTTAGCGGCGTTTTTGATAAAA
1 TTTAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGGTCTTGGTCTTTAGCGGCGTTTGTG-GAAAA
*
51809935 GTGCCGCTAAAGGTCATGGTC
65 GCGCCGCTAAAGGTCATGGTC
* * * *
51809956 TATAGCGGCTTTTGTGGGAAAAGCACCGCTAAAGGTCCTGGTCTTTAGCGGCGTTTGTGGGAAAA
1 TTTAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGGTCTTGGTCTTTAGCGGCGTTTGT-GGAAAA
*
51810021 GCGCCGCTAAAGGTCCTGGTC
65 GCGCCGCTAAAGGTCATGGTC
* * *
51810042 TTTAGTGGCGTTTGTGTGAAAAGCGCCGCTAAAGGTCTTGGTCTTTAGCGGCGTTTGTGGGAAAG
1 TTTAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGGTCTTGGTCTTTAGCGGCGTTTGTGGAAAAG
*
51810107 CGCCGCTAAAGGTCTTGGTC
66 CGCCGCTAAAGGTCATGGTC
51810127 TTTAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGGTCTTGGTCTTTAGCGGCGTTT
1 TTTAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGGTCTTGGTCTTTAGCGGCGTTT
51810183 TTTTCTAAAA
Statistics
Matches: 202, Mismatches: 23, Indels: 4
0.88 0.10 0.02
Matches are distributed among these distances:
85 108 0.53
86 93 0.46
87 1 0.00
ACGTcount: A:0.19, C:0.19, G:0.32, T:0.30
Consensus pattern (85 bp):
TTTAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGGTCTTGGTCTTTAGCGGCGTTTGTGGAAAAG
CGCCGCTAAAGGTCATGGTC
Found at i:51810128 original size:128 final size:129
Alignment explanation
Indices: 51809871--51810182 Score: 459
Period size: 128 Copynumber: 2.4 Consensus size: 129
51809861 AGATTATGTT
* ** * * * *
51809871 TTTAGCGGCGTTTTTGCTAGAAGCGCCGCTAAAGGT-GTGTTCTTTAGCGGCGTTTTTGATAAAA
1 TTTAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGGTCCTGGTCTTTAGCGGCGTTTGTGATAAAA
* *
51809935 GTGCCGCTAAAGGTCATGGTCTATAGCGGCTTTTGTGGGAAAAGCACCGCTAAAGGTCCTGGTC
66 GCGCCGCTAAAGGTCATGGTCTATAGCGGCGTTTGTGGGAAAAGCACCGCTAAAGGTCCTGGTC
*
51809999 TTTAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGGTCCTGGTCTTTAGTGGCGTTTGTG-TGAAA
1 TTTAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGGTCCTGGTCTTTAGCGGCGTTTGTGAT-AAA
* * * *
51810063 AGCGCCGCTAAAGGTCTTGGTCTTTAGCGGCGTTTGTGGG-AAAGCGCCGCTAAAGGTCTTGGTC
65 AGCGCCGCTAAAGGTCATGGTCTATAGCGGCGTTTGTGGGAAAAGCACCGCTAAAGGTCCTGGTC
*
51810127 TTTAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGGTCTTGGTCTTTAGCGGCGTTT
1 TTTAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGGTCCTGGTCTTTAGCGGCGTTT
51810183 TTTTCTAAAA
Statistics
Matches: 166, Mismatches: 16, Indels: 4
0.89 0.09 0.02
Matches are distributed among these distances:
128 109 0.66
129 57 0.34
ACGTcount: A:0.19, C:0.19, G:0.32, T:0.30
Consensus pattern (129 bp):
TTTAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGGTCCTGGTCTTTAGCGGCGTTTGTGATAAAA
GCGCCGCTAAAGGTCATGGTCTATAGCGGCGTTTGTGGGAAAAGCACCGCTAAAGGTCCTGGTC
Found at i:51818750 original size:39 final size:39
Alignment explanation
Indices: 51818696--51818777 Score: 137
Period size: 39 Copynumber: 2.1 Consensus size: 39
51818686 TAGGCTTGGG
* *
51818696 TCTAGTCTTTTTCATGTTACCTTCAGTAGTTCATAACAT
1 TCTAGTATTTTTCATGTTACCTTCAGCAGTTCATAACAT
*
51818735 TCTAGTATTTTTCATGTTACCTTCAGCAGTTCGTAACAT
1 TCTAGTATTTTTCATGTTACCTTCAGCAGTTCATAACAT
51818774 TCTA
1 TCTA
51818778 AGTAATTGTG
Statistics
Matches: 40, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
39 40 1.00
ACGTcount: A:0.23, C:0.21, G:0.11, T:0.45
Consensus pattern (39 bp):
TCTAGTATTTTTCATGTTACCTTCAGCAGTTCATAACAT
Found at i:51832048 original size:19 final size:20
Alignment explanation
Indices: 51832020--51832058 Score: 62
Period size: 19 Copynumber: 2.0 Consensus size: 20
51832010 TTTAACAATT
*
51832020 GATAATTATTTTATGATAAA
1 GATAATTATTTTATAATAAA
51832040 GATAA-TATTTTATAATAAA
1 GATAATTATTTTATAATAAA
51832059 TAATATCTTA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 13 0.72
20 5 0.28
ACGTcount: A:0.49, C:0.00, G:0.08, T:0.44
Consensus pattern (20 bp):
GATAATTATTTTATAATAAA
Found at i:51832063 original size:17 final size:19
Alignment explanation
Indices: 51832020--51832070 Score: 61
Period size: 17 Copynumber: 2.7 Consensus size: 19
51832010 TTTAACAATT
*
51832020 GATAATTATTTTATGATAAA
1 GATAA-TATTTTATAATAAA
51832040 GATAATATTTTATAAT-AA
1 GATAATATTTTATAATAAA
*
51832058 -ATAATATCTTATA
1 GATAATATTTTATA
51832071 TAGATTTAAT
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
17 12 0.41
18 2 0.07
19 10 0.34
20 5 0.17
ACGTcount: A:0.47, C:0.02, G:0.06, T:0.45
Consensus pattern (19 bp):
GATAATATTTTATAATAAA
Found at i:51832804 original size:21 final size:22
Alignment explanation
Indices: 51832778--51832827 Score: 66
Period size: 22 Copynumber: 2.3 Consensus size: 22
51832768 TTGTTGTTAT
51832778 TAAATAATATT-AATAAAATAA
1 TAAATAATATTCAATAAAATAA
* **
51832799 TAAATAATATTCATTGTAATAA
1 TAAATAATATTCAATAAAATAA
51832821 TAAATAA
1 TAAATAA
51832828 GGCATGATTA
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
21 11 0.44
22 14 0.56
ACGTcount: A:0.60, C:0.02, G:0.02, T:0.36
Consensus pattern (22 bp):
TAAATAATATTCAATAAAATAA
Found at i:51834176 original size:34 final size:34
Alignment explanation
Indices: 51834133--51834273 Score: 192
Period size: 34 Copynumber: 4.1 Consensus size: 34
51834123 TTTAAATTAG
* **
51834133 TGTTGTGCAAATGATGAGTTATTCTACGATTGAA
1 TGTTGTGCAAATGATAAGTTATTCTACGGCTGAA
*
51834167 TGTTGTGCAAATGATAAGTTGTTCTACGGCTGAA
1 TGTTGTGCAAATGATAAGTTATTCTACGGCTGAA
** * * *
51834201 TGTTGTAAAAATGACAAGTTGTTCTATGGCTGAA
1 TGTTGTGCAAATGATAAGTTATTCTACGGCTGAA
*
51834235 TGTTGTGCAAATGATGAGTTATTCTACGGCTGAA
1 TGTTGTGCAAATGATAAGTTATTCTACGGCTGAA
51834269 TGTTG
1 TGTTG
51834274 ATGTATCGTG
Statistics
Matches: 93, Mismatches: 14, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
34 93 1.00
ACGTcount: A:0.28, C:0.10, G:0.26, T:0.37
Consensus pattern (34 bp):
TGTTGTGCAAATGATAAGTTATTCTACGGCTGAA
Found at i:51835359 original size:16 final size:16
Alignment explanation
Indices: 51835338--51835368 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
51835328 TGATAGGCGT
51835338 GGGATGAGAGATGAGA
1 GGGATGAGAGATGAGA
*
51835354 GGGATGAGGGATGAG
1 GGGATGAGAGATGAG
51835369 GGATAAAGTG
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.32, C:0.00, G:0.55, T:0.13
Consensus pattern (16 bp):
GGGATGAGAGATGAGA
Found at i:51839309 original size:20 final size:20
Alignment explanation
Indices: 51839284--51839321 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
51839274 ACCCCCTTTA
51839284 TTAACATAAA-AATTTAAAAT
1 TTAACA-AAATAATTTAAAAT
51839304 TTAACAAAATAATTTAAA
1 TTAACAAAATAATTTAAA
51839322 CTAGAAAAAC
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
19 3 0.18
20 14 0.82
ACGTcount: A:0.61, C:0.05, G:0.00, T:0.34
Consensus pattern (20 bp):
TTAACAAAATAATTTAAAAT
Found at i:51846230 original size:7 final size:7
Alignment explanation
Indices: 51846196--51846230 Score: 61
Period size: 7 Copynumber: 5.0 Consensus size: 7
51846186 TGAGAGATGA
51846196 GAGGGAT
1 GAGGGAT
51846203 GAGGGAT
1 GAGGGAT
51846210 GAGGGAT
1 GAGGGAT
51846217 GAGGGAT
1 GAGGGAT
*
51846224 GAAGGAT
1 GAGGGAT
51846231 AAAGTGAGAA
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
7 27 1.00
ACGTcount: A:0.31, C:0.00, G:0.54, T:0.14
Consensus pattern (7 bp):
GAGGGAT
Found at i:51849894 original size:11 final size:11
Alignment explanation
Indices: 51849873--51849903 Score: 53
Period size: 11 Copynumber: 2.7 Consensus size: 11
51849863 AAAATTATAA
51849873 TAAAAGCAAAAT
1 TAAAAG-AAAAT
51849885 TAAAAGAAAAT
1 TAAAAGAAAAT
51849896 TAAAAGAA
1 TAAAAGAA
51849904 GAAAAACAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
11 13 0.68
12 6 0.32
ACGTcount: A:0.71, C:0.03, G:0.10, T:0.16
Consensus pattern (11 bp):
TAAAAGAAAAT
Found at i:51849894 original size:17 final size:17
Alignment explanation
Indices: 51849861--51849894 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
51849851 GTGGTTAATG
* *
51849861 GCAAAATTATAATAAAA
1 GCAAAATTAAAAGAAAA
51849878 GCAAAATTAAAAGAAAA
1 GCAAAATTAAAAGAAAA
51849895 TTAAAAGAAG
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.68, C:0.06, G:0.09, T:0.18
Consensus pattern (17 bp):
GCAAAATTAAAAGAAAA
Found at i:51850705 original size:40 final size:40
Alignment explanation
Indices: 51850661--51850765 Score: 131
Period size: 40 Copynumber: 2.6 Consensus size: 40
51850651 AATTATTGTA
* *
51850661 TGATTGCACATACGTGCCCTTGTTTGTACTTCAG-TACCCC
1 TGATTGCACATACGTGCCCCTATTTGTACTT-AGATACCCC
* *
51850701 TGATTGCGCATACGTGCCCCTATTTGTACTTTGATACCCC
1 TGATTGCACATACGTGCCCCTATTTGTACTTAGATACCCC
* * *
51850741 TGATTGCACTTTCGTGCCTCTATTT
1 TGATTGCACATACGTGCCCCTATTT
51850766 ATATTTCGGT
Statistics
Matches: 56, Mismatches: 8, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
39 1 0.02
40 55 0.98
ACGTcount: A:0.16, C:0.29, G:0.17, T:0.38
Consensus pattern (40 bp):
TGATTGCACATACGTGCCCCTATTTGTACTTAGATACCCC
Found at i:51855944 original size:17 final size:17
Alignment explanation
Indices: 51855924--51855977 Score: 56
Period size: 17 Copynumber: 3.2 Consensus size: 17
51855914 TGGCTATAAG
51855924 CTTGTGACGGCGATGGA
1 CTTGTGACGGCGATGGA
* * *
51855941 CTTGTGGCAGAGATGGA
1 CTTGTGACGGCGATGGA
*
51855958 CTTG-CAGCGGCGATGGA
1 CTTGTGA-CGGCGATGGA
51855975 CTT
1 CTT
51855978 TCGACGACAA
Statistics
Matches: 29, Mismatches: 7, Indels: 2
0.76 0.18 0.05
Matches are distributed among these distances:
17 29 1.00
ACGTcount: A:0.19, C:0.19, G:0.39, T:0.24
Consensus pattern (17 bp):
CTTGTGACGGCGATGGA
Found at i:51857508 original size:26 final size:26
Alignment explanation
Indices: 51857472--51857524 Score: 106
Period size: 26 Copynumber: 2.0 Consensus size: 26
51857462 GGGTGTCATC
51857472 ATGTTCCAATGCCAAGGAGATCTGGG
1 ATGTTCCAATGCCAAGGAGATCTGGG
51857498 ATGTTCCAATGCCAAGGAGATCTGGG
1 ATGTTCCAATGCCAAGGAGATCTGGG
51857524 A
1 A
51857525 CAATTTGGAT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 27 1.00
ACGTcount: A:0.28, C:0.19, G:0.30, T:0.23
Consensus pattern (26 bp):
ATGTTCCAATGCCAAGGAGATCTGGG
Found at i:51858399 original size:15 final size:15
Alignment explanation
Indices: 51858379--51858408 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
51858369 TGTTAAGAGT
51858379 GTATGGGCCCCTAAA
1 GTATGGGCCCCTAAA
*
51858394 GTATGGGTCCCTAAA
1 GTATGGGCCCCTAAA
51858409 AGACTTAGTG
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.27, C:0.23, G:0.27, T:0.23
Consensus pattern (15 bp):
GTATGGGCCCCTAAA
Found at i:51864760 original size:19 final size:19
Alignment explanation
Indices: 51864738--51864789 Score: 52
Period size: 21 Copynumber: 2.7 Consensus size: 19
51864728 TTTTTATCGT
51864738 TAGAATATTTTTTCAGTTG
1 TAGAATATTTTTTCAGTTG
** *
51864757 TAGAAAATATTTTGGCTGTTG
1 TAG--AATATTTTTTCAGTTG
51864778 TAGAA-ATTTTTT
1 TAGAATATTTTTT
51864790 GTTCTGAAAA
Statistics
Matches: 26, Mismatches: 5, Indels: 5
0.72 0.14 0.14
Matches are distributed among these distances:
18 5 0.19
19 5 0.19
21 16 0.62
ACGTcount: A:0.29, C:0.04, G:0.17, T:0.50
Consensus pattern (19 bp):
TAGAATATTTTTTCAGTTG
Found at i:51864767 original size:21 final size:21
Alignment explanation
Indices: 51864741--51864783 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
51864731 TTATCGTTAG
**
51864741 AATATTTTTTCAGTTGTAGAA
1 AATATTTTGGCAGTTGTAGAA
*
51864762 AATATTTTGGCTGTTGTAGAA
1 AATATTTTGGCAGTTGTAGAA
51864783 A
1 A
51864784 TTTTTTGTTC
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.33, C:0.05, G:0.19, T:0.44
Consensus pattern (21 bp):
AATATTTTGGCAGTTGTAGAA
Found at i:51866726 original size:18 final size:18
Alignment explanation
Indices: 51866702--51866745 Score: 54
Period size: 18 Copynumber: 2.4 Consensus size: 18
51866692 TGTCATTTAT
51866702 TTTCAAAACATTATTC-A
1 TTTCAAAACATTATTCAA
* *
51866719 TTTACAAATCGTTATTCAA
1 TTT-CAAAACATTATTCAA
51866738 TTTCAAAA
1 TTTCAAAA
51866746 TGTTTTCTTA
Statistics
Matches: 22, Mismatches: 3, Indels: 3
0.79 0.11 0.11
Matches are distributed among these distances:
17 3 0.14
18 15 0.68
19 4 0.18
ACGTcount: A:0.41, C:0.16, G:0.02, T:0.41
Consensus pattern (18 bp):
TTTCAAAACATTATTCAA
Found at i:51867658 original size:18 final size:18
Alignment explanation
Indices: 51867618--51867652 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
51867608 CCATGATGTT
51867618 CACCCGTGTGGGCCCACA
1 CACCCGTGTGGGCCCACA
51867636 CACCCGTGT-GGCCCACA
1 CACCCGTGTGGGCCCACA
51867653 TGACCCAAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 8 0.47
18 9 0.53
ACGTcount: A:0.17, C:0.46, G:0.26, T:0.11
Consensus pattern (18 bp):
CACCCGTGTGGGCCCACA
Found at i:51872139 original size:19 final size:21
Alignment explanation
Indices: 51872108--51872157 Score: 61
Period size: 19 Copynumber: 2.5 Consensus size: 21
51872098 ATAATAGGAG
51872108 ATAAA-AAATATGAAAA-ATT
1 ATAAATAAATATGAAAATATT
*
51872127 ATAAATAAA-ATGAAAATTTT
1 ATAAATAAATATGAAAATATT
51872147 ATAATATAAAT
1 ATAA-ATAAAT
51872158 TTTATAAAAT
Statistics
Matches: 26, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
19 12 0.46
20 9 0.35
21 5 0.19
ACGTcount: A:0.64, C:0.00, G:0.04, T:0.32
Consensus pattern (21 bp):
ATAAATAAATATGAAAATATT
Found at i:51876505 original size:51 final size:50
Alignment explanation
Indices: 51876375--51876508 Score: 162
Period size: 50 Copynumber: 2.7 Consensus size: 50
51876365 AAAGTGATGG
* * *
51876375 TCACGTGTGTAGTACTATGTGCAGGCTACTACGTGTACCAGAATGATAGG
1 TCACGTGTGTAGTACTATGTGCAGGCTACTATGCGTACCAGAATGATAGA
* * * * *
51876425 TCGCATGTGTAGTACTATGTGCAGGCTACTATGCGTACCGGACA-GCTTCGA
1 TCACGTGTGTAGTACTATGTGCAGGCTACTATGCGTACCAGA-ATG-ATAGA
*
51876476 TCACGTGTGTAGTACTATGTGTAGGCTACTATG
1 TCACGTGTGTAGTACTATGTGCAGGCTACTATG
51876509 TGAACCGGTA
Statistics
Matches: 71, Mismatches: 11, Indels: 3
0.84 0.13 0.04
Matches are distributed among these distances:
50 38 0.54
51 33 0.46
ACGTcount: A:0.23, C:0.19, G:0.28, T:0.30
Consensus pattern (50 bp):
TCACGTGTGTAGTACTATGTGCAGGCTACTATGCGTACCAGAATGATAGA
Found at i:51876516 original size:51 final size:50
Alignment explanation
Indices: 51876375--51876516 Score: 169
Period size: 51 Copynumber: 2.8 Consensus size: 50
51876365 AAAGTGATGG
* * *
51876375 TCACGTGTGTAGTACTATGTGCAGGCTACTACGTGTACCAGAATGATAGG
1 TCACGTGTGTAGTACTATGTGCAGGCTACTATGTGTACCGGAATGATAGA
* * * * *
51876425 TCGCATGTGTAGTACTATGTGCAGGCTACTATGCGTACCGGACA-GCTTCGA
1 TCACGTGTGTAGTACTATGTGCAGGCTACTATGTGTACCGGA-ATG-ATAGA
* *
51876476 TCACGTGTGTAGTACTATGTGTAGGCTACTATGTGAACCGG
1 TCACGTGTGTAGTACTATGTGCAGGCTACTATGTGTACCGG
51876517 TATCATTAAT
Statistics
Matches: 77, Mismatches: 13, Indels: 3
0.83 0.14 0.03
Matches are distributed among these distances:
50 38 0.49
51 39 0.51
ACGTcount: A:0.23, C:0.20, G:0.28, T:0.29
Consensus pattern (50 bp):
TCACGTGTGTAGTACTATGTGCAGGCTACTATGTGTACCGGAATGATAGA
Found at i:51876604 original size:46 final size:43
Alignment explanation
Indices: 51876512--51876610 Score: 101
Period size: 46 Copynumber: 2.2 Consensus size: 43
51876502 TACTATGTGA
* *
51876512 ACCGGTATCATTAATTATAAGGTGGTTGCTATGTGCTGATCTC
1 ACCGGTATCATTAATTAAAAGGTGGTTGCTATGTGCCGATCTC
* * *
51876555 ACCGGATATCATTGATTACAAAGGGTGGTTGTTCTGTGCCGAATC-C
1 ACCGG-TATCATTAATTA-AAA-GGTGGTTGCTATGTGCCG-ATCTC
51876601 ACCGTGTATC
1 ACCG-GTATC
51876611 TGTTATTATT
Statistics
Matches: 46, Mismatches: 5, Indels: 7
0.79 0.09 0.12
Matches are distributed among these distances:
43 5 0.11
44 11 0.24
45 2 0.04
46 24 0.52
47 4 0.09
ACGTcount: A:0.23, C:0.19, G:0.24, T:0.33
Consensus pattern (43 bp):
ACCGGTATCATTAATTAAAAGGTGGTTGCTATGTGCCGATCTC
Found at i:51876755 original size:16 final size:16
Alignment explanation
Indices: 51876734--51876765 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
51876724 TGATTGAAAG
*
51876734 TGAAAAAGTGAAATTA
1 TGAAAAAGTAAAATTA
51876750 TGAAAAAGTAAAATTA
1 TGAAAAAGTAAAATTA
51876766 GCAACAAAAT
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:0.59, C:0.00, G:0.16, T:0.25
Consensus pattern (16 bp):
TGAAAAAGTAAAATTA
Found at i:51879354 original size:20 final size:19
Alignment explanation
Indices: 51879329--51879396 Score: 68
Period size: 19 Copynumber: 3.5 Consensus size: 19
51879319 ACAAGATACT
51879329 CTTAGAAATTTTGGTATTTG
1 CTTAGAAATTTTGGTA-TTG
*
51879349 CTTAGAAATTTTAGTGCA-TG
1 CTTAGAAATTTT-G-GTATTG
* *
51879369 -TTACAAATTTTGGTATTA
1 CTTAGAAATTTTGGTATTG
51879387 CTTAGAAATT
1 CTTAGAAATT
51879397 CGGTATGATG
Statistics
Matches: 39, Mismatches: 5, Indels: 9
0.74 0.09 0.17
Matches are distributed among these distances:
17 2 0.05
18 2 0.05
19 18 0.46
20 14 0.36
21 1 0.03
22 2 0.05
ACGTcount: A:0.31, C:0.07, G:0.16, T:0.46
Consensus pattern (19 bp):
CTTAGAAATTTTGGTATTG
Found at i:51879953 original size:19 final size:20
Alignment explanation
Indices: 51879929--51879979 Score: 59
Period size: 19 Copynumber: 2.6 Consensus size: 20
51879919 TAAAACGAAG
*
51879929 AACCAAATTAAAATTAATT-
1 AACCAAATTAAAATAAATTA
* *
51879948 AACCAAAATAACATAAATTA
1 AACCAAATTAAAATAAATTA
*
51879968 AACAAAATTAAA
1 AACCAAATTAAA
51879980 GAAAACAAGT
Statistics
Matches: 25, Mismatches: 6, Indels: 1
0.78 0.19 0.03
Matches are distributed among these distances:
19 16 0.64
20 9 0.36
ACGTcount: A:0.65, C:0.12, G:0.00, T:0.24
Consensus pattern (20 bp):
AACCAAATTAAAATAAATTA
Found at i:51881718 original size:35 final size:33
Alignment explanation
Indices: 51881646--51881721 Score: 91
Period size: 35 Copynumber: 2.2 Consensus size: 33
51881636 ATTTGTTTTA
*
51881646 ATTATATAATTAATGATATTTAAATATAATTTGT
1 ATTATATAATTAATGATAATTAAATATAA-TTGT
*
51881680 ATTATATGAATTTATGATAATTAAATTATAA-TGAT
1 ATTATAT-AATTAATGATAATTAAA-TATAATTG-T
51881715 ATTATAT
1 ATTATAT
51881722 TATTCAATAA
Statistics
Matches: 37, Mismatches: 2, Indels: 5
0.84 0.05 0.11
Matches are distributed among these distances:
34 9 0.24
35 23 0.62
36 5 0.14
ACGTcount: A:0.45, C:0.00, G:0.07, T:0.49
Consensus pattern (33 bp):
ATTATATAATTAATGATAATTAAATATAATTGT
Found at i:51882102 original size:11 final size:11
Alignment explanation
Indices: 51882070--51882094 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
51882060 ATTTCGACCC
51882070 AAAAAGGAAAG
1 AAAAAGGAAAG
51882081 AAAAAGGAAAG
1 AAAAAGGAAAG
51882092 AAA
1 AAA
51882095 GAAGAAAGGG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.76, C:0.00, G:0.24, T:0.00
Consensus pattern (11 bp):
AAAAAGGAAAG
Found at i:51882822 original size:39 final size:40
Alignment explanation
Indices: 51882779--51882861 Score: 105
Period size: 40 Copynumber: 2.1 Consensus size: 40
51882769 TTGAGACTGA
* *
51882779 TACTGAACTGAATTATGGA-ATACTGAATATTGTTTTGAG
1 TACTGAACTAAATTATGGAGATACTGAATATTGTTATGAG
* * * *
51882818 TACTGAATTAAATTGTGGAGTTACTGAATATTGTTATGTG
1 TACTGAACTAAATTATGGAGATACTGAATATTGTTATGAG
51882858 TACT
1 TACT
51882862 ACATTGAACT
Statistics
Matches: 37, Mismatches: 6, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
39 16 0.43
40 21 0.57
ACGTcount: A:0.31, C:0.07, G:0.20, T:0.41
Consensus pattern (40 bp):
TACTGAACTAAATTATGGAGATACTGAATATTGTTATGAG
Found at i:51882882 original size:40 final size:40
Alignment explanation
Indices: 51882799--51882885 Score: 106
Period size: 40 Copynumber: 2.2 Consensus size: 40
51882789 AATTATGGAA
* *
51882799 TACTGAATATTGTTTTGAGTACTGAATTAAATTGTGGAGT
1 TACTGAATATTGTTATGAGTACTGAATTAAACTGTGGAGT
* *
51882839 TACTGAATATTGTTATGTGTACT-ACATTGAACTGT-GAGAT
1 TACTGAATATTGTTATGAGTACTGA-ATTAAACTGTGGAG-T
51882879 TACTGAA
1 TACTGAA
51882886 GTAATGAATT
Statistics
Matches: 41, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
39 4 0.10
40 37 0.90
ACGTcount: A:0.31, C:0.08, G:0.21, T:0.40
Consensus pattern (40 bp):
TACTGAATATTGTTATGAGTACTGAATTAAACTGTGGAGT
Found at i:51883155 original size:44 final size:45
Alignment explanation
Indices: 51883090--51883188 Score: 128
Period size: 44 Copynumber: 2.2 Consensus size: 45
51883080 CCGACTACTG
* * *
51883090 TTACTGTTACTGATTCGACACTTTGTGTATCGAATACT-TTACCA
1 TTACTGTTACAGATTCAACACTTTATGTATCGAATACTATTACCA
* * **
51883134 TTACTGTTACAGATTCAACACTTTATGTGTTGAATACTATTACTG
1 TTACTGTTACAGATTCAACACTTTATGTATCGAATACTATTACCA
51883179 TTACTGTTAC
1 TTACTGTTAC
51883189 TTCTACCGTT
Statistics
Matches: 47, Mismatches: 7, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
44 33 0.70
45 14 0.30
ACGTcount: A:0.26, C:0.18, G:0.13, T:0.42
Consensus pattern (45 bp):
TTACTGTTACAGATTCAACACTTTATGTATCGAATACTATTACCA
Found at i:51890379 original size:26 final size:26
Alignment explanation
Indices: 51890347--51890519 Score: 274
Period size: 26 Copynumber: 6.7 Consensus size: 26
51890337 CATCCCAACC
*
51890347 CATAGCTCGTGTGAGCAGGCCTATTT
1 CATAGCTCGTGTGAGCAGGCCCATTT
*
51890373 AATAGCTCGTGTGAGCAGGCCCATTT
1 CATAGCTCGTGTGAGCAGGCCCATTT
51890399 CATAGCTCGTGTGAGCAGGCCCATTT
1 CATAGCTCGTGTGAGCAGGCCCATTT
* *
51890425 AATATCTCGTGTGAGCAGGCCCATTT
1 CATAGCTCGTGTGAGCAGGCCCATTT
51890451 CATAGCTCGTGTGAGCAGGCCCATTT
1 CATAGCTCGTGTGAGCAGGCCCATTT
*
51890477 CATAGCTCGTTTGAGCAGGCCCATTT
1 CATAGCTCGTGTGAGCAGGCCCATTT
* * *
51890503 CACAACTTGTGTGAGCA
1 CATAGCTCGTGTGAGCA
51890520 TATACTGTTA
Statistics
Matches: 135, Mismatches: 12, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
26 135 1.00
ACGTcount: A:0.21, C:0.25, G:0.25, T:0.28
Consensus pattern (26 bp):
CATAGCTCGTGTGAGCAGGCCCATTT
Found at i:51890758 original size:25 final size:25
Alignment explanation
Indices: 51890730--51890780 Score: 68
Period size: 25 Copynumber: 2.0 Consensus size: 25
51890720 AATATATATT
*
51890730 TGATATGTTACAAA-TACATGTTTCA
1 TGATATGCTA-AAATTACATGTTTCA
*
51890755 TGATATGCTAAAATTATATGTTTCA
1 TGATATGCTAAAATTACATGTTTCA
51890780 T
1 T
51890781 TATTGAACTC
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
24 3 0.13
25 20 0.87
ACGTcount: A:0.35, C:0.10, G:0.12, T:0.43
Consensus pattern (25 bp):
TGATATGCTAAAATTACATGTTTCA
Found at i:51891854 original size:18 final size:18
Alignment explanation
Indices: 51891831--51891866 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
51891821 GATTTTTAGG
51891831 TTTCATAAGCTCAATATA
1 TTTCATAAGCTCAATATA
51891849 TTTCATAAGCTCAATATA
1 TTTCATAAGCTCAATATA
51891867 AGGCATGTAT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.39, C:0.17, G:0.06, T:0.39
Consensus pattern (18 bp):
TTTCATAAGCTCAATATA
Found at i:51896553 original size:22 final size:23
Alignment explanation
Indices: 51896508--51896554 Score: 69
Period size: 23 Copynumber: 2.0 Consensus size: 23
51896498 GTACCACGCG
*
51896508 TGTTTCTTTTTGAAGAAAATTTT
1 TGTTCCTTTTTGAAGAAAATTTT
51896531 TGTTCCTTTTATG-AGAAAATTTT
1 TGTTCCTTTT-TGAAGAAAATTTT
51896554 T
1 T
51896555 TGTCTACTTT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 20 0.91
24 2 0.09
ACGTcount: A:0.26, C:0.06, G:0.13, T:0.55
Consensus pattern (23 bp):
TGTTCCTTTTTGAAGAAAATTTT
Found at i:51899889 original size:12 final size:10
Alignment explanation
Indices: 51899854--51899905 Score: 61
Period size: 10 Copynumber: 5.1 Consensus size: 10
51899844 GAATCTGTTG
51899854 AAAA-TAATC
1 AAAATTAATC
51899863 AAAATTAATC
1 AAAATTAATC
51899873 AAAATTAACTAC
1 AAAATTAA-T-C
*
51899885 AAAATTAATT
1 AAAATTAATC
*
51899895 AAAATTCATC
1 AAAATTAATC
51899905 A
1 A
51899906 TGTTCATATT
Statistics
Matches: 37, Mismatches: 3, Indels: 5
0.82 0.07 0.11
Matches are distributed among these distances:
9 4 0.11
10 22 0.59
11 2 0.05
12 9 0.24
ACGTcount: A:0.60, C:0.12, G:0.00, T:0.29
Consensus pattern (10 bp):
AAAATTAATC
Found at i:51901553 original size:2 final size:2
Alignment explanation
Indices: 51901546--51901570 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
51901536 TAAACATAAC
51901546 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
51901571 AACTTTCAAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:51902568 original size:41 final size:41
Alignment explanation
Indices: 51902482--51902637 Score: 163
Period size: 41 Copynumber: 3.8 Consensus size: 41
51902472 GCTTATGAAA
* * * * **
51902482 ATACATCGGCATAAAGCCTTCTA-GCACAAAGCCACATATG
1 ATACACCGGCATGAAGCCTACTAGGCATAAAGCCTGATATG
51902522 ATACACCGGCATGAAGCCTACTAGGCATAAAGCCTGATATG
1 ATACACCGGCATGAAGCCTACTAGGCATAAAGCCTGATATG
* * * *
51902563 GTACACCGGCATGAAGCCTGCTAGGCATAAAGCCTGCTATA
1 ATACACCGGCATGAAGCCTACTAGGCATAAAGCCTGATATG
* * * *
51902604 ACT-CACTGGCATAAAGCCTGCTAGGCATAGAGCC
1 A-TACACCGGCATGAAGCCTACTAGGCATAAAGCC
51902638 CGAATATCAC
Statistics
Matches: 100, Mismatches: 14, Indels: 3
0.85 0.12 0.03
Matches are distributed among these distances:
40 20 0.20
41 79 0.79
42 1 0.01
ACGTcount: A:0.33, C:0.27, G:0.21, T:0.19
Consensus pattern (41 bp):
ATACACCGGCATGAAGCCTACTAGGCATAAAGCCTGATATG
Found at i:51902595 original size:16 final size:16
Alignment explanation
Indices: 51902570--51902601 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
51902560 ATGGTACACC
*
51902570 GGCATGAAGCCTGCTA
1 GGCATAAAGCCTGCTA
51902586 GGCATAAAGCCTGCTA
1 GGCATAAAGCCTGCTA
51902602 TAACTCACTG
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:0.28, C:0.25, G:0.28, T:0.19
Consensus pattern (16 bp):
GGCATAAAGCCTGCTA
Found at i:51910698 original size:41 final size:41
Alignment explanation
Indices: 51910639--51910741 Score: 109
Period size: 41 Copynumber: 2.5 Consensus size: 41
51910629 ACATTGACAT
* * * * *
51910639 AAAGCCTG-TGAGGTATAAAGCTTATTAAAATACATCGGTAT
1 AAAGCCTGCT-AGGCATAAAGCTAAATAAAATACACCGGTAC
* ** *
51910680 AAAGCCTTCTAGGCATAAAGCTAAATATGATACACCGGTGC
1 AAAGCCTGCTAGGCATAAAGCTAAATAAAATACACCGGTAC
51910721 AAAGCCTGCTAGGCATAAAGC
1 AAAGCCTGCTAGGCATAAAGC
51910742 CTGATATGGT
Statistics
Matches: 51, Mismatches: 10, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
41 50 0.98
42 1 0.02
ACGTcount: A:0.38, C:0.18, G:0.20, T:0.23
Consensus pattern (41 bp):
AAAGCCTGCTAGGCATAAAGCTAAATAAAATACACCGGTAC
Found at i:51910749 original size:41 final size:41
Alignment explanation
Indices: 51910680--51910758 Score: 115
Period size: 41 Copynumber: 1.9 Consensus size: 41
51910670 ACATCGGTAT
*
51910680 AAAGCCTTCTAGGCATAAAGCTAAATATGATACACCGGTGC
1 AAAGCCTGCTAGGCATAAAGCTAAATATGATACACCGGTGC
* *
51910721 AAAGCCTGCTAGGCATAAAGCCT-GATATGGTACACCGG
1 AAAGCCTGCTAGGCATAAAG-CTAAATATGATACACCGG
51910759 CATGAAGCCT
Statistics
Matches: 34, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
41 32 0.94
42 2 0.06
ACGTcount: A:0.34, C:0.23, G:0.23, T:0.20
Consensus pattern (41 bp):
AAAGCCTGCTAGGCATAAAGCTAAATATGATACACCGGTGC
Found at i:51910767 original size:41 final size:40
Alignment explanation
Indices: 51910680--51910772 Score: 109
Period size: 41 Copynumber: 2.3 Consensus size: 40
51910670 ACATCGGTAT
*
51910680 AAAGCCTTCTAGGCATAAAGCTAAATATGATACACCGGTG
1 AAAGCCTGCTAGGCATAAAGCTAAATATGATACACCGGTG
* *
51910720 CAAAGCCTGCTAGGCATAAAGCCT-GATATGGTACACCGGCATG
1 -AAAGCCTGCTAGGCATAAAG-CTAAATATGATACACCGG--TG
51910763 -AAGCCTGCTA
1 AAAGCCTGCTA
51910773 TAATTCACCA
Statistics
Matches: 46, Mismatches: 3, Indels: 6
0.84 0.05 0.11
Matches are distributed among these distances:
41 42 0.91
42 2 0.04
43 2 0.04
ACGTcount: A:0.33, C:0.24, G:0.23, T:0.20
Consensus pattern (40 bp):
AAAGCCTGCTAGGCATAAAGCTAAATATGATACACCGGTG
Found at i:51913092 original size:29 final size:27
Alignment explanation
Indices: 51913047--51913102 Score: 69
Period size: 27 Copynumber: 2.0 Consensus size: 27
51913037 TAATATATAA
51913047 TTTATAAATAATATAATTATATATTAAAG
1 TTTATAAATAATATAA-TA-ATATTAAAG
*
51913076 TTTATCAAATTAT-TAATAATATTAAAG
1 TTTAT-AAATAATATAATAATATTAAAG
51913103 ATATTTATTC
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
27 9 0.36
28 2 0.08
29 8 0.32
30 6 0.24
ACGTcount: A:0.50, C:0.02, G:0.04, T:0.45
Consensus pattern (27 bp):
TTTATAAATAATATAATAATATTAAAG
Found at i:51918832 original size:51 final size:50
Alignment explanation
Indices: 51918707--51918900 Score: 214
Period size: 51 Copynumber: 3.8 Consensus size: 50
51918697 TGAAAGTGAT
* *
51918707 GGTCACGTGTGTAGTACTATGTGCCGGCTACTATGTGTACCAGAAT-GAT-A
1 GGTCACATGTGTAGTACTATGTGCAGGCTACTATGTGTACC-GAATAG-TCA
* * * *
51918757 GGTCGCATTTGTAGTAGTATGTGCAGGCTACTATGCGTACCGAATAGCTTCA
1 GGTCACATGTGTAGTACTATGTGCAGGCTACTATGTGTACCGAATAG--TCA
* * * * *
51918809 -ATCACGTGTGTAGTACTATGTGCAGGCTACTACGTGTATCGGATAGTCA
1 GGTCACATGTGTAGTACTATGTGCAGGCTACTATGTGTACCGAATAGTCA
*
51918858 TGGTCACATGTGTAGTACTATGTGCAGGCTACTATGTGAACCG
1 -GGTCACATGTGTAGTACTATGTGCAGGCTACTATGTGTACCG
51918901 GTATCATTAA
Statistics
Matches: 118, Mismatches: 21, Indels: 9
0.80 0.14 0.06
Matches are distributed among these distances:
49 7 0.06
50 36 0.31
51 74 0.63
52 1 0.01
ACGTcount: A:0.24, C:0.19, G:0.27, T:0.30
Consensus pattern (50 bp):
GGTCACATGTGTAGTACTATGTGCAGGCTACTATGTGTACCGAATAGTCA
Found at i:51918895 original size:26 final size:26
Alignment explanation
Indices: 51918815--51918895 Score: 73
Period size: 26 Copynumber: 3.2 Consensus size: 26
51918805 TTCAATCACG
51918815 TGTGTAGTACTATGTGCAGGCTACTA
1 TGTGTAGTACTATGTGCAGGCTACTA
* *
51918841 CGTGTA-T-CGGATAGT-CATGG-TCAC-A
1 TGTGTAGTAC-TAT-GTGCA-GGCT-ACTA
51918866 TGTGTAGTACTATGTGCAGGCTACTA
1 TGTGTAGTACTATGTGCAGGCTACTA
51918892 TGTG
1 TGTG
51918896 AACCGGTATC
Statistics
Matches: 42, Mismatches: 4, Indels: 18
0.66 0.06 0.28
Matches are distributed among these distances:
24 1 0.02
25 18 0.43
26 22 0.52
27 1 0.02
ACGTcount: A:0.22, C:0.16, G:0.28, T:0.33
Consensus pattern (26 bp):
TGTGTAGTACTATGTGCAGGCTACTA
Found at i:51919140 original size:16 final size:16
Alignment explanation
Indices: 51919119--51919150 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
51919109 TGATTGAAAG
*
51919119 TGAAAAAGTGAAATTA
1 TGAAAAAGTAAAATTA
51919135 TGAAAAAGTAAAATTA
1 TGAAAAAGTAAAATTA
51919151 GCAACGAAAC
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:0.59, C:0.00, G:0.16, T:0.25
Consensus pattern (16 bp):
TGAAAAAGTAAAATTA
Found at i:51919949 original size:287 final size:287
Alignment explanation
Indices: 51919433--51920004 Score: 939
Period size: 287 Copynumber: 2.0 Consensus size: 287
51919423 CTTAGAATAT
* *
51919433 TTAATGAGTCTATTTTCAAAAGAAATACACGGAAATATCATCTAAATTCTGTACAATGAGATAAT
1 TTAATGAGTCTATTTTCAAAAGAAATAAACGGAAATATCATCTAAATTCTGTACAATGAAATAAT
* *
51919498 TTATTTTTAGTGAAGAGAGGCCAGAGATGTTGAGCAGTGAAATAGGGGTGACTTTAAAGAATAAA
66 TCATTTTTAGTGAAGAGAGGCCAGAGATGTTGAGCAATGAAATAGGGGTGACTTTAAAGAATAAA
* * * *
51919563 CTGTACTAATTGGATAAGCTAAAAATTCTGAAAATATTATGGTAAGAATATATGTGAGTCTAGTT
131 CAGTACTAATTGGATAAGCCAAAAATTCTAAAAATATTATGGTAAGAAGATATGTGAGTCTAGTT
*
51919628 TCGGAGAAAATTAACGAAACTTAATTTGGAGCTCTGTAGCTCTGGATAAAAATAATTTAGTGACT
196 TCGGAGAAAATTAACGAAACTTAATTTAGAGCTCTGTAGCTCTGGATAAAAATAATTTAGTGACT
51919693 ATAACTCGACTAGACAGCTTGGAATCC
261 ATAACTCGACTAGACAGCTTGGAATCC
** *
51919720 TTAATGAGTCTATTTTCAAATTAAATAAACGGAAATATCATCTGAATTCTGTACAATGAAATAAT
1 TTAATGAGTCTATTTTCAAAAGAAATAAACGGAAATATCATCTAAATTCTGTACAATGAAATAAT
* *
51919785 TCATTTTTAGTGAAGAGAGGTCAGAGATGTTGAGCAATGAAATAGGGGTGACTTTAAAGAATATA
66 TCATTTTTAGTGAAGAGAGGCCAGAGATGTTGAGCAATGAAATAGGGGTGACTTTAAAGAATAAA
* * *
51919850 CAGTACTAATTGGCTAAGCCAAAAATTCTAAAAATTTTATGGTAAGAAGATATGTGAGTGTAGTT
131 CAGTACTAATTGGATAAGCCAAAAATTCTAAAAATATTATGGTAAGAAGATATGTGAGTCTAGTT
* *
51919915 TCGTG-GAAAATTAATGGAACTTAATTTAGAGCTCTGTAGCTCTGGATAAAAATAATTTAGTGAC
196 TCG-GAGAAAATTAACGAAACTTAATTTAGAGCTCTGTAGCTCTGGATAAAAATAATTTAGTGAC
* *
51919979 TGTAACTCGACTAGACAGCTTTGAAT
260 TATAACTCGACTAGACAGCTTGGAAT
51920005 TTAAATATAA
Statistics
Matches: 263, Mismatches: 21, Indels: 2
0.92 0.07 0.01
Matches are distributed among these distances:
287 262 1.00
288 1 0.00
ACGTcount: A:0.38, C:0.11, G:0.20, T:0.31
Consensus pattern (287 bp):
TTAATGAGTCTATTTTCAAAAGAAATAAACGGAAATATCATCTAAATTCTGTACAATGAAATAAT
TCATTTTTAGTGAAGAGAGGCCAGAGATGTTGAGCAATGAAATAGGGGTGACTTTAAAGAATAAA
CAGTACTAATTGGATAAGCCAAAAATTCTAAAAATATTATGGTAAGAAGATATGTGAGTCTAGTT
TCGGAGAAAATTAACGAAACTTAATTTAGAGCTCTGTAGCTCTGGATAAAAATAATTTAGTGACT
ATAACTCGACTAGACAGCTTGGAATCC
Found at i:51925194 original size:51 final size:50
Alignment explanation
Indices: 51925071--51925265 Score: 225
Period size: 51 Copynumber: 3.9 Consensus size: 50
51925061 TGAAAGTGAT
* * *
51925071 GGTCACGTGTGTAGTACTATGTGCCGGCTACTATGTGTACCAGA-ATGAT-A
1 GGTCACATGTGTAGTACTATGTGCAGGCTACTATGTGTACCGGATA-G-TCA
* * *
51925121 GGTCGCATGTGTAGTAGTATGTGCAGGCTACTATGCGTACCGGATAGCTTCA
1 GGTCACATGTGTAGTACTATGTGCAGGCTACTATGTGTACCGGATAG--TCA
* * * *
51925173 -ATCACGTGTGTAGTACTATGTGCAGGCTACTACGTGTATCGGATAGTCA
1 GGTCACATGTGTAGTACTATGTGCAGGCTACTATGTGTACCGGATAGTCA
*
51925222 TGGTCACATGTGTAGTACTATGTGCAGGCTACTATGTGAACCGG
1 -GGTCACATGTGTAGTACTATGTGCAGGCTACTATGTGTACCGG
51925266 TATCATTAAT
Statistics
Matches: 121, Mismatches: 19, Indels: 9
0.81 0.13 0.06
Matches are distributed among these distances:
49 3 0.02
50 39 0.32
51 78 0.64
52 1 0.01
ACGTcount: A:0.23, C:0.18, G:0.29, T:0.30
Consensus pattern (50 bp):
GGTCACATGTGTAGTACTATGTGCAGGCTACTATGTGTACCGGATAGTCA
Found at i:51925259 original size:26 final size:26
Alignment explanation
Indices: 51925179--51925259 Score: 73
Period size: 26 Copynumber: 3.2 Consensus size: 26
51925169 TTCAATCACG
51925179 TGTGTAGTACTATGTGCAGGCTACTA
1 TGTGTAGTACTATGTGCAGGCTACTA
* *
51925205 CGTGTA-T-CGGATAGT-CATGG-TCAC-A
1 TGTGTAGTAC-TAT-GTGCA-GGCT-ACTA
51925230 TGTGTAGTACTATGTGCAGGCTACTA
1 TGTGTAGTACTATGTGCAGGCTACTA
51925256 TGTG
1 TGTG
51925260 AACCGGTATC
Statistics
Matches: 42, Mismatches: 4, Indels: 18
0.66 0.06 0.28
Matches are distributed among these distances:
24 1 0.02
25 18 0.43
26 22 0.52
27 1 0.02
ACGTcount: A:0.22, C:0.16, G:0.28, T:0.33
Consensus pattern (26 bp):
TGTGTAGTACTATGTGCAGGCTACTA
Found at i:51925503 original size:16 final size:16
Alignment explanation
Indices: 51925482--51925513 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
51925472 TGATTGAAAG
*
51925482 TGAAAAAGTGAAATTA
1 TGAAAAAGTAAAATTA
51925498 TGAAAAAGTAAAATTA
1 TGAAAAAGTAAAATTA
51925514 GCAACAAAAT
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:0.59, C:0.00, G:0.16, T:0.25
Consensus pattern (16 bp):
TGAAAAAGTAAAATTA
Found at i:51929800 original size:26 final size:26
Alignment explanation
Indices: 51929760--51929829 Score: 104
Period size: 26 Copynumber: 2.7 Consensus size: 26
51929750 CTTTACAATA
*
51929760 CTGCTCACACAAGCTATGAAATGGGC
1 CTGCTCACACGAGCTATGAAATGGGC
* *
51929786 TTGCTCACACGAGCTATCAAATGGGC
1 CTGCTCACACGAGCTATGAAATGGGC
*
51929812 CTACTCACACGAGCTATG
1 CTGCTCACACGAGCTATG
51929830 GGTCGAAATG
Statistics
Matches: 38, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
26 38 1.00
ACGTcount: A:0.29, C:0.29, G:0.21, T:0.21
Consensus pattern (26 bp):
CTGCTCACACGAGCTATGAAATGGGC
Found at i:51946354 original size:23 final size:23
Alignment explanation
Indices: 51946326--51946372 Score: 60
Period size: 25 Copynumber: 2.0 Consensus size: 23
51946316 TTAATTTGTT
51946326 TTATTAA-ACATATATTAACCTTA
1 TTATTAATAC-TATATTAACCTTA
51946349 TTATTAATTTACTATATTAACCTT
1 TTATTAA--TACTATATTAACCTT
51946373 TACTAATATA
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
23 7 0.33
25 12 0.57
26 2 0.10
ACGTcount: A:0.38, C:0.13, G:0.00, T:0.49
Consensus pattern (23 bp):
TTATTAATACTATATTAACCTTA
Found at i:51946479 original size:22 final size:22
Alignment explanation
Indices: 51946451--51946595 Score: 209
Period size: 22 Copynumber: 6.6 Consensus size: 22
51946441 GGGCTAATTG
*
51946451 AGCTCTCATGTTTCACGTACTA
1 AGCTCTCATGTTTAACGTACTA
51946473 AGCTCTCATGTTTAACGTACTA
1 AGCTCTCATGTTTAACGTACTA
*
51946495 AGCTCTCATGTTTAACGAACTA
1 AGCTCTCATGTTTAACGTACTA
* * **
51946517 AACCCTCATGGCTAACGTACTA
1 AGCTCTCATGTTTAACGTACTA
**
51946539 AGCTCTCATGGCTAACGTACTA
1 AGCTCTCATGTTTAACGTACTA
*
51946561 AGCTCTCATGTTTCACGTACTA
1 AGCTCTCATGTTTAACGTACTA
51946583 AGCTCTCATGTTT
1 AGCTCTCATGTTT
51946596 GAACAATAAA
Statistics
Matches: 111, Mismatches: 12, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 111 1.00
ACGTcount: A:0.26, C:0.26, G:0.14, T:0.33
Consensus pattern (22 bp):
AGCTCTCATGTTTAACGTACTA
Found at i:51953554 original size:23 final size:23
Alignment explanation
Indices: 51953526--51953572 Score: 60
Period size: 25 Copynumber: 2.0 Consensus size: 23
51953516 TTAATTTGTT
51953526 TTATTAA-ACATATATTAACCTTA
1 TTATTAATAC-TATATTAACCTTA
51953549 TTATTAATTTACTATATTAACCTT
1 TTATTAA--TACTATATTAACCTT
51953573 TACTAATATA
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
23 7 0.33
25 12 0.57
26 2 0.10
ACGTcount: A:0.38, C:0.13, G:0.00, T:0.49
Consensus pattern (23 bp):
TTATTAATACTATATTAACCTTA
Found at i:51956993 original size:42 final size:42
Alignment explanation
Indices: 51956873--51957086 Score: 249
Period size: 42 Copynumber: 5.1 Consensus size: 42
51956863 TAATCGTTAC
*
51956873 ACGGTGGAATCAGCACTTAGCAACCATCTTATAATCAATGAT
1 ACGGTGGAATCAGCACTTAGCAACCACCTTATAATCAATGAT
* * *
51956915 ACGG-GGAATCAGCACATAGCAACC-CCTTTCACAATCAAGGAT
1 ACGGTGGAATCAGCACTTAGCAACCACC-TT-ATAATCAATGAT
*
51956957 ACGGTGGAATTAGCACTTAGCAACCACCTTATAATCAATGAT
1 ACGGTGGAATCAGCACTTAGCAACCACCTTATAATCAATGAT
* * * *
51956999 ACAG-GGAATCAGCACATAGCAACC-CCTTTCACAATCAAAGAT
1 ACGGTGGAATCAGCACTTAGCAACCACC-TT-ATAATCAATGAT
* *
51957041 ACAGTGGAATCAGCACTTAGC-ACCAACCTTATAATCAATGTT
1 ACGGTGGAATCAGCACTTAGCAACC-ACCTTATAATCAATGAT
51957083 ACGG
1 ACGG
51957087 GTTCACATAG
Statistics
Matches: 145, Mismatches: 18, Indels: 18
0.80 0.10 0.10
Matches are distributed among these distances:
40 3 0.02
41 41 0.28
42 60 0.41
43 37 0.26
44 4 0.03
ACGTcount: A:0.36, C:0.25, G:0.17, T:0.22
Consensus pattern (42 bp):
ACGGTGGAATCAGCACTTAGCAACCACCTTATAATCAATGAT
Found at i:51957014 original size:84 final size:84
Alignment explanation
Indices: 51956873--51957080 Score: 355
Period size: 84 Copynumber: 2.5 Consensus size: 84
51956863 TAATCGTTAC
* *
51956873 ACGGTGGAATCAGCACTTAGCAACCATCTTATAATCAATGATACGGGGAATCAGCACATAGCAAC
1 ACGGTGGAATCAGCACTTAGCAACCACCTTATAATCAATGATACAGGGAATCAGCACATAGCAAC
*
51956938 CCCTTTCACAATCAAGGAT
66 CCCTTTCACAATCAAAGAT
*
51956957 ACGGTGGAATTAGCACTTAGCAACCACCTTATAATCAATGATACAGGGAATCAGCACATAGCAAC
1 ACGGTGGAATCAGCACTTAGCAACCACCTTATAATCAATGATACAGGGAATCAGCACATAGCAAC
51957022 CCCTTTCACAATCAAAGAT
66 CCCTTTCACAATCAAAGAT
*
51957041 ACAGTGGAATCAGCACTTAGC-ACCAACCTTATAATCAATG
1 ACGGTGGAATCAGCACTTAGCAACC-ACCTTATAATCAATG
51957081 TTACGGGTTC
Statistics
Matches: 117, Mismatches: 6, Indels: 2
0.94 0.05 0.02
Matches are distributed among these distances:
83 3 0.03
84 114 0.97
ACGTcount: A:0.37, C:0.25, G:0.16, T:0.22
Consensus pattern (84 bp):
ACGGTGGAATCAGCACTTAGCAACCACCTTATAATCAATGATACAGGGAATCAGCACATAGCAAC
CCCTTTCACAATCAAAGAT
Found at i:51957170 original size:51 final size:51
Alignment explanation
Indices: 51957094--51957280 Score: 227
Period size: 51 Copynumber: 3.7 Consensus size: 51
51957084 CGGGTTCACA
* *
51957094 TAGTAGCCTACACATAGTACTACACATGTGACCATCA-CTATCCGATACACG
1 TAGTAGCCTGCACATAGTACTACACATGTGACCAT-AGCTATCCGGTACACG
* * * *
51957145 TAGTAGCTTGCACATAGTACTACACATGTGATCGA-AGCTATCCGGTACGCA
1 TAGTAGCCTGCACATAGTACTACACATGTGA-CCATAGCTATCCGGTACACG
* * * * *
51957196 TAGTAGCCTGCACATAGGACTACACATGCGACC-TATCTTTCTGGTACACG
1 TAGTAGCCTGCACATAGTACTACACATGTGACCATAGCTATCCGGTACACG
*
51957246 TAGTAGCCTGCACATAGTACTACACACGTGACCAT
1 TAGTAGCCTGCACATAGTACTACACATGTGACCAT
51957281 CACTTTCACT
Statistics
Matches: 114, Mismatches: 18, Indels: 8
0.81 0.13 0.06
Matches are distributed among these distances:
50 43 0.38
51 69 0.61
52 2 0.02
ACGTcount: A:0.30, C:0.27, G:0.18, T:0.25
Consensus pattern (51 bp):
TAGTAGCCTGCACATAGTACTACACATGTGACCATAGCTATCCGGTACACG
Found at i:51957268 original size:101 final size:101
Alignment explanation
Indices: 51957092--51957276 Score: 273
Period size: 101 Copynumber: 1.8 Consensus size: 101
51957082 TACGGGTTCA
* * *
51957092 CATAGTAGCCTACACATAGTACTACACATGTGACCATCACTATCCGATACACGTAGTAGCTTGCA
1 CATAGTAGCCTACACATAGGACTACACATGCGACCAT-ACTATCCGATACACGTAGTAGCCTGCA
*
51957157 CATAGTACTACACATGTGATCGAAGCTATCCGGTACG
65 CATAGTACTACACACGTGATCGAAGCTATCCGGTACG
* * * *
51957194 CATAGTAGCCTGCACATAGGACTACACATGCGACC-TATCTTTCTGGTACACGTAGTAGCCTGCA
1 CATAGTAGCCTACACATAGGACTACACATGCGACCATA-CTATCCGATACACGTAGTAGCCTGCA
51957258 CATAGTACTACACACGTGA
65 CATAGTACTACACACGTGA
51957277 CCATCACTTT
Statistics
Matches: 74, Mismatches: 8, Indels: 3
0.87 0.09 0.04
Matches are distributed among these distances:
100 1 0.01
101 41 0.55
102 32 0.43
ACGTcount: A:0.30, C:0.27, G:0.18, T:0.24
Consensus pattern (101 bp):
CATAGTAGCCTACACATAGGACTACACATGCGACCATACTATCCGATACACGTAGTAGCCTGCAC
ATAGTACTACACACGTGATCGAAGCTATCCGGTACG
Found at i:51970421 original size:23 final size:23
Alignment explanation
Indices: 51970391--51970436 Score: 92
Period size: 23 Copynumber: 2.0 Consensus size: 23
51970381 TTTTGTCATT
51970391 GTATCATCTATGGTAAAACTAAC
1 GTATCATCTATGGTAAAACTAAC
51970414 GTATCATCTATGGTAAAACTAAC
1 GTATCATCTATGGTAAAACTAAC
51970437 CCAATTTTAG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.39, C:0.17, G:0.13, T:0.30
Consensus pattern (23 bp):
GTATCATCTATGGTAAAACTAAC
Found at i:51973662 original size:25 final size:24
Alignment explanation
Indices: 51973636--51973714 Score: 88
Period size: 25 Copynumber: 3.2 Consensus size: 24
51973626 TGTTCTCGCG
* *
51973636 AGCTGGAAATCGGCAAGCTCATACG
1 AGCT-GAAATCGGTAAGCTCATACA
*
51973661 AGCTGAGAATCGGTATGCTC-TCACA
1 AGCTGA-AATCGGTAAGCTCAT-ACA
*
51973686 AGCTAAAATCGGTAAGCTCATACA
1 AGCTGAAATCGGTAAGCTCATACA
51973710 AGCTG
1 AGCTG
51973715 TGGTGTGTCC
Statistics
Matches: 45, Mismatches: 6, Indels: 7
0.78 0.10 0.12
Matches are distributed among these distances:
24 22 0.49
25 23 0.51
ACGTcount: A:0.33, C:0.23, G:0.24, T:0.20
Consensus pattern (24 bp):
AGCTGAAATCGGTAAGCTCATACA
Found at i:51973699 original size:24 final size:24
Alignment explanation
Indices: 51973642--51973713 Score: 83
Period size: 24 Copynumber: 3.0 Consensus size: 24
51973632 CGCGAGCTGG
* *
51973642 AAATCGGCAAGCTCATACGAGCTGA
1 AAATCGGTAAGCTCATACAAGCT-A
* *
51973667 GAATCGGTATGCTC-TCACAAGCTA
1 AAATCGGTAAGCTCAT-ACAAGCTA
51973691 AAATCGGTAAGCTCATACAAGCT
1 AAATCGGTAAGCTCATACAAGCT
51973714 GTGGTGTGTC
Statistics
Matches: 39, Mismatches: 6, Indels: 5
0.78 0.12 0.10
Matches are distributed among these distances:
24 21 0.54
25 18 0.46
ACGTcount: A:0.35, C:0.24, G:0.21, T:0.21
Consensus pattern (24 bp):
AAATCGGTAAGCTCATACAAGCTA
Found at i:51973714 original size:49 final size:51
Alignment explanation
Indices: 51973604--51973714 Score: 147
Period size: 50 Copynumber: 2.2 Consensus size: 51
51973594 ACATGTATGA
* * * *
51973604 TCATACGAGCT-ATGAATCGGTATGTTCTCGCGAGCTGGAAATCGGCAAGC
1 TCATACGAGCTGATGAATCGGTATGCTCTCACAAGCTGAAAATCGGCAAGC
*
51973654 TCATACGAGCTGA-GAATCGGTATGCTCTCACAAGCT-AAAATCGGTAAGC
1 TCATACGAGCTGATGAATCGGTATGCTCTCACAAGCTGAAAATCGGCAAGC
*
51973703 TCATACAAGCTG
1 TCATACGAGCTG
51973715 TGGTGTGTCC
Statistics
Matches: 54, Mismatches: 6, Indels: 3
0.86 0.10 0.05
Matches are distributed among these distances:
49 22 0.41
50 31 0.57
51 1 0.02
ACGTcount: A:0.30, C:0.23, G:0.24, T:0.23
Consensus pattern (51 bp):
TCATACGAGCTGATGAATCGGTATGCTCTCACAAGCTGAAAATCGGCAAGC
Found at i:51978579 original size:6 final size:6
Alignment explanation
Indices: 51978568--51978614 Score: 58
Period size: 6 Copynumber: 7.8 Consensus size: 6
51978558 ACCGATTTAA
* * * *
51978568 CCACCG CCACCG CCAGCG CCACCG CCACTG CCACTG CCACTG CCACC
1 CCACCG CCACCG CCACCG CCACCG CCACCG CCACCG CCACCG CCACC
51978615 TCACCTTCTC
Statistics
Matches: 37, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
6 37 1.00
ACGTcount: A:0.17, C:0.60, G:0.17, T:0.06
Consensus pattern (6 bp):
CCACCG
Found at i:51981915 original size:16 final size:16
Alignment explanation
Indices: 51981894--51981927 Score: 68
Period size: 16 Copynumber: 2.1 Consensus size: 16
51981884 ATCTAGGCCA
51981894 TAAATTTTCAACACTG
1 TAAATTTTCAACACTG
51981910 TAAATTTTCAACACTG
1 TAAATTTTCAACACTG
51981926 TA
1 TA
51981928 TCATTATCAT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.38, C:0.18, G:0.06, T:0.38
Consensus pattern (16 bp):
TAAATTTTCAACACTG
Found at i:51983243 original size:20 final size:19
Alignment explanation
Indices: 51983218--51983264 Score: 58
Period size: 20 Copynumber: 2.4 Consensus size: 19
51983208 TGAACTTCAA
* *
51983218 AAAATTTAAGAAATTATTAC
1 AAAATTTAAAAAAATA-TAC
51983238 AAAATTCTAAAAAAATATAC
1 AAAATT-TAAAAAAATATAC
51983258 AAAATTT
1 AAAATTT
51983265 CAAATGTACA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
19 1 0.04
20 15 0.62
21 8 0.33
ACGTcount: A:0.60, C:0.06, G:0.02, T:0.32
Consensus pattern (19 bp):
AAAATTTAAAAAAATATAC
Found at i:51983888 original size:18 final size:18
Alignment explanation
Indices: 51983865--51983899 Score: 70
Period size: 18 Copynumber: 1.9 Consensus size: 18
51983855 CAACCGCGAT
51983865 AAACGCGGCCGCGACCGA
1 AAACGCGGCCGCGACCGA
51983883 AAACGCGGCCGCGACCG
1 AAACGCGGCCGCGACCG
51983900 TAATTTAAAT
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:0.26, C:0.40, G:0.34, T:0.00
Consensus pattern (18 bp):
AAACGCGGCCGCGACCGA
Found at i:51989556 original size:28 final size:28
Alignment explanation
Indices: 51989498--51989699 Score: 245
Period size: 27 Copynumber: 7.4 Consensus size: 28
51989488 CATTTTGGTG
* *
51989498 AATCAAGAAA-AAAAATCCTTTGTTGCG-
1 AATCATGAAAGAAAAA-CCTTTGTGGCGA
51989525 AATCATGAAAGAAAAACCTTTGTGGCGA
1 AATCATGAAAGAAAAACCTTTGTGGCGA
* *
51989553 AATCATGAAAGAAAAGCTTTTGTGGCGA
1 AATCATGAAAGAAAAACCTTTGTGGCGA
* **
51989581 AATCATGAAAGAAAAGCCTTTGTGATG-
1 AATCATGAAAGAAAAACCTTTGTGGCGA
* *
51989608 AATCATGAAAGAAAATCTTTTGTGGCG-
1 AATCATGAAAGAAAAACCTTTGTGGCGA
*
51989635 AATCATGAAAGAAAAACCTTTGTGG-AA
1 AATCATGAAAGAAAAACCTTTGTGGCGA
*
51989662 AATCATGAAAGAAAAACCTTTGTGG-AA
1 AATCATGAAAGAAAAACCTTTGTGGCGA
*
51989689 AATTATGAAAG
1 AATCATGAAAG
51989700 GATTGCCTTA
Statistics
Matches: 157, Mismatches: 15, Indels: 6
0.88 0.08 0.03
Matches are distributed among these distances:
27 102 0.65
28 55 0.35
ACGTcount: A:0.44, C:0.11, G:0.20, T:0.25
Consensus pattern (28 bp):
AATCATGAAAGAAAAACCTTTGTGGCGA
Found at i:51989575 original size:55 final size:54
Alignment explanation
Indices: 51989498--51989686 Score: 254
Period size: 55 Copynumber: 3.5 Consensus size: 54
51989488 CATTTTGGTG
* * * *
51989498 AATCAAGAAAAAAAATCCTTTGTTGCGAATCATGAAAGAAAAACCTTTGTGGCGA
1 AATCATGAAAGAAAATCTTTTGTGGCGAATCATGAAAGAAAAACCTTTGTGG-GA
* * *
51989553 AATCATGAAAGAAAAGCTTTTGTGGCGAAATCATGAAAGAAAAGCCTTTGTGATG-
1 AATCATGAAAGAAAATCTTTTGTGGCG-AATCATGAAAGAAAAACCTTTGTG-GGA
*
51989608 AATCATGAAAGAAAATCTTTTGTGGCGAATCATGAAAGAAAAACCTTTGTGGAA
1 AATCATGAAAGAAAATCTTTTGTGGCGAATCATGAAAGAAAAACCTTTGTGGGA
* *
51989662 AATCATGAAAGAAAAACCTTTGTGG
1 AATCATGAAAGAAAATCTTTTGTGG
51989687 AAAATTATGA
Statistics
Matches: 118, Mismatches: 13, Indels: 7
0.86 0.09 0.05
Matches are distributed among these distances:
54 46 0.39
55 48 0.41
56 24 0.20
ACGTcount: A:0.42, C:0.12, G:0.21, T:0.25
Consensus pattern (54 bp):
AATCATGAAAGAAAATCTTTTGTGGCGAATCATGAAAGAAAAACCTTTGTGGGA
Found at i:51991280 original size:50 final size:50
Alignment explanation
Indices: 51991212--51991405 Score: 208
Period size: 50 Copynumber: 3.7 Consensus size: 50
51991202 TTTCCTGTAC
* * **
51991212 TGCCAATGCCATATCCCAGATATGGTCTTACATGGGAGTTCTAATATCGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTAATATCGG
* * * *
51991262 TGCCCATGCCATGTCCCAGACATGGTCTTACAGGGGACCTCTCATCTCGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTAATATCGG
* * * *
51991312 TGCCAACGCCATGTCCCAGACATGATCTTACATGGGACCTCTCATAGTCTCAATGA
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCT-A-A-TATC---GG
*
51991368 TACCAATGCCCATGTCCCAGACATGGTCTTACATGGGA
1 TGCCAATG-CCATGTCCCAGACATGGTCTTACATGGGA
51991406 TCTCATCACC
Statistics
Matches: 120, Mismatches: 17, Indels: 7
0.83 0.12 0.05
Matches are distributed among these distances:
50 80 0.67
52 1 0.01
53 4 0.03
56 7 0.06
57 28 0.23
ACGTcount: A:0.24, C:0.29, G:0.21, T:0.26
Consensus pattern (50 bp):
TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTAATATCGG
Found at i:51993603 original size:26 final size:26
Alignment explanation
Indices: 51993574--51993624 Score: 102
Period size: 26 Copynumber: 2.0 Consensus size: 26
51993564 TTGAATAAAA
51993574 AGGGGTTGCTAAGTGCTGATTCCCCG
1 AGGGGTTGCTAAGTGCTGATTCCCCG
51993600 AGGGGTTGCTAAGTGCTGATTCCCC
1 AGGGGTTGCTAAGTGCTGATTCCCC
51993625 AAATTATTGA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 25 1.00
ACGTcount: A:0.16, C:0.24, G:0.33, T:0.27
Consensus pattern (26 bp):
AGGGGTTGCTAAGTGCTGATTCCCCG
Found at i:51993695 original size:43 final size:43
Alignment explanation
Indices: 51993602--51993793 Score: 146
Period size: 43 Copynumber: 4.5 Consensus size: 43
51993592 ATTCCCCGAG
* * * * *
51993602 GGGTTGCTAAGTGCTGATTCC-CC-AAATTATTGACTCT-AAAG
1 GGGTTGCTAAGTGCTGATCCCACCGTAATT-TTGATTGTGAAAA
* *
51993643 GAGGTTGCTATGTGCTGATCCCACCGTAACTTTGATTGTGAAAA
1 G-GGTTGCTAAGTGCTGATCCCACCGTAATTTTGATTGTGAAAA
* * *
51993687 GGGTTGCTAAGTGCTGATTCC-CCGT-ATTGTTGAATAT--AAA
1 GGGTTGCTAAGTGCTGATCCCACCGTAATT-TTGATTGTGAAAA
* * * * *
51993727 GGTTGTTGCTATGTGCTGATTCTACCGTATTTTTGATTGTGAATA
1 GG--GTTGCTAAGTGCTGATCCCACCGTAATTTTGATTGTGAAAA
51993772 GGGTTGCTAAGTGCTGACTCCC
1 GGGTTGCTAAGTGCTGA-TCCC
51993794 CGTATCACTG
Statistics
Matches: 118, Mismatches: 21, Indels: 21
0.74 0.13 0.13
Matches are distributed among these distances:
40 5 0.04
41 3 0.03
42 45 0.38
43 50 0.42
44 11 0.09
45 4 0.03
ACGTcount: A:0.22, C:0.17, G:0.25, T:0.35
Consensus pattern (43 bp):
GGGTTGCTAAGTGCTGATCCCACCGTAATTTTGATTGTGAAAA
Found at i:51993735 original size:85 final size:85
Alignment explanation
Indices: 51993602--51993921 Score: 313
Period size: 85 Copynumber: 3.8 Consensus size: 85
51993592 ATTCCCCGAG
** * * * *
51993602 GGGTTGCTAAGTGCTGATTCCCCAAATTATTGACTCTAAAGGAGGTTGCTATGTGCTGATCCCAC
1 GGGTTGCTAAGTGCTGATTCCCCGTATTATTGAATATAAAGGTGGTTGCTATGTGCTGATTCCAC
51993667 CGTAACTTTGATTGTGAAAA
66 CGTAACTTTGATTGTGAAAA
* * *
51993687 GGGTTGCTAAGTGCTGATTCCCCGTATTGTTGAATATAAAGGTTGTTGCTATGTGCTGATTCTAC
1 GGGTTGCTAAGTGCTGATTCCCCGTATTATTGAATATAAAGGTGGTTGCTATGTGCTGATTCCAC
** *
51993752 CGTATTTTTGATTGTGAATA
66 CGTAACTTTGATTGTGAAAA
* * * * * *
51993772 GGGTTGCTAAGTGCTGACTCCCCGTATCACTGAATATAAAGGTGGTTACTAAGTTCTGATTCCAC
1 GGGTTGCTAAGTGCTGATTCCCCGTATTATTGAATATAAAGGTGGTTGCTATGTGCTGATTCCAC
* * * * * *
51993837 TG-AATCCTTAACTGGGAAAG
66 CGTAA-CTTTGATTGTGAAAA
* * * * * * * * *
51993857 GGGTTGCTATGTGCTGATT-CCGGTATCACTGAAT-TTATGGTGGTTGTTAAGTGCTGAATCCAC
1 GGGTTGCTAAGTGCTGATTCCCCGTATTATTGAATATAAAGGTGGTTGCTATGTGCTGATTCCAC
51993920 CG
66 CG
51993922 AGTAACGGAT
Statistics
Matches: 194, Mismatches: 40, Indels: 4
0.82 0.17 0.02
Matches are distributed among these distances:
83 24 0.12
84 15 0.08
85 155 0.80
ACGTcount: A:0.23, C:0.17, G:0.25, T:0.34
Consensus pattern (85 bp):
GGGTTGCTAAGTGCTGATTCCCCGTATTATTGAATATAAAGGTGGTTGCTATGTGCTGATTCCAC
CGTAACTTTGATTGTGAAAA
Found at i:51993736 original size:42 final size:40
Alignment explanation
Indices: 51993602--51993834 Score: 162
Period size: 42 Copynumber: 5.5 Consensus size: 40
51993592 ATTCCCCGAG
** * *
51993602 GGGTTGCTAAGTGCTGATTCCCCAAATTATTGACTCTAAA
1 GGGTTGCTAAGTGCTGATTCCCCGTATTATTGAATATAAA
* * * * *
51993642 GGAGGTTGCTATGTGCTGATCCCACCGTAACT-TTGATTGTGAAAA
1 -G-GGTTGCTAAGTGCTGATTCC-CCGT-ATTATTGAATAT--AAA
*
51993687 GGGTTGCTAAGTGCTGATTCCCCGTATTGTTGAATATAAA
1 GGGTTGCTAAGTGCTGATTCCCCGTATTATTGAATATAAA
* * * * *
51993727 GGTTGTTGCTATGTGCTGATTCTACCGTATTTTTGATTGTGAATA
1 GG--GTTGCTAAGTGCTGATTC-CCCGTATTATTGAATAT-AA-A
* * *
51993772 GGGTTGCTAAGTGCTGACTCCCCGTATCACTGAATATAAA
1 GGGTTGCTAAGTGCTGATTCCCCGTATTATTGAATATAAA
* *
51993812 GGTGGTTACTAAGTTCTGATTCC
1 -G-GGTTGCTAAGTGCTGATTCC
51993835 ACTGAATCCT
Statistics
Matches: 151, Mismatches: 28, Indels: 25
0.74 0.14 0.12
Matches are distributed among these distances:
40 6 0.04
41 6 0.04
42 73 0.48
43 55 0.36
44 5 0.03
45 6 0.04
ACGTcount: A:0.24, C:0.17, G:0.24, T:0.35
Consensus pattern (40 bp):
GGGTTGCTAAGTGCTGATTCCCCGTATTATTGAATATAAA
Found at i:52016913 original size:42 final size:42
Alignment explanation
Indices: 52016833--52016914 Score: 103
Period size: 42 Copynumber: 2.0 Consensus size: 42
52016823 CGTTTTCTCT
* * **
52016833 ATGCTATAGTCCAACTATGGTCTTACACATATTTACATATTG
1 ATGCCATAGCCCAACTATGGTCTTACACATATGCACATATTG
*
52016875 ATGCCATAGCCCAGCTATGGTCTTACACAGTA-GCACATAT
1 ATGCCATAGCCCAACTATGGTCTTACACA-TATGCACATAT
52016915 CACACCGATG
Statistics
Matches: 34, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
42 32 0.94
43 2 0.06
ACGTcount: A:0.30, C:0.23, G:0.15, T:0.32
Consensus pattern (42 bp):
ATGCCATAGCCCAACTATGGTCTTACACATATGCACATATTG
Found at i:52019493 original size:85 final size:84
Alignment explanation
Indices: 52019351--52019583 Score: 342
Period size: 85 Copynumber: 2.8 Consensus size: 84
52019341 CCGTTACTCG
*
52019351 GTGGATTCAGCACTTAGCAACCACC-TTAAATTCAGTGATACGGGGAATCAGCACATAGCAACCC
1 GTGGAATCAGCACTTAGCAACCACCTTTAAATTCAGTGATACGGGGAATCAGCACATAGCAACCC
*
52019415 CTTTCACAATCAAAGATAC
66 CTTTCACAATAAAAGATAC
*
52019434 AGTGGAATCAGCACTTAGCAACCACCTTTATATTCAGTGATACGGGGAATCAGCACATAGCAACC
1 -GTGGAATCAGCACTTAGCAACCACCTTTAAATTCAGTGATACGGGGAATCAGCACATAGCAACC
52019499 CCTTTCACAATAAAAGATAC
65 CCTTTCACAATAAAAGATAC
* * * * * * * *
52019519 GATGGAATCAGAACTTAGCAACCACCTTTAGAGTCAATAATTCGGGGAATCAGCACTTAGAAACC
1 G-TGGAATCAGCACTTAGCAACCACCTTTAAATTCAGTGATACGGGGAATCAGCACATAGCAACC
52019584 TCTCAGGGAA
Statistics
Matches: 136, Mismatches: 11, Indels: 3
0.91 0.07 0.02
Matches are distributed among these distances:
84 25 0.18
85 111 0.82
ACGTcount: A:0.36, C:0.24, G:0.18, T:0.22
Consensus pattern (84 bp):
GTGGAATCAGCACTTAGCAACCACCTTTAAATTCAGTGATACGGGGAATCAGCACATAGCAACCC
CTTTCACAATAAAAGATAC
Found at i:52019495 original size:42 final size:42
Alignment explanation
Indices: 52019357--52019583 Score: 228
Period size: 43 Copynumber: 5.4 Consensus size: 42
52019347 CTCGGTGGAT
*
52019357 TCAGCACTTAGCAACCACC-TTA-AATTCAGTGATACGGGGAA
1 TCAGCACTTAGCAACCACCTTTACAA-TCAATGATACGGGGAA
* * *
52019398 TCAGCACATAGCAACC-CCTTTCACAATCAAAGATACAGTGGAA
1 TCAGCACTTAGCAACCACCTTT-ACAATCAATGATAC-GGGGAA
* * *
52019441 TCAGCACTTAGCAACCACCTTTATATTCAGTGATACGGGGAA
1 TCAGCACTTAGCAACCACCTTTACAATCAATGATACGGGGAA
* * * *
52019483 TCAGCACATAGCAACC-CCTTTCACAATAAAAGATACGATGGAA
1 TCAGCACTTAGCAACCACCTTT-ACAATCAATGATACG-GGGAA
* * * * *
52019526 TCAGAACTTAGCAACCACCTTTAGAGTCAATAATTCGGGGAA
1 TCAGCACTTAGCAACCACCTTTACAATCAATGATACGGGGAA
*
52019568 TCAGCACTTAGAAACC
1 TCAGCACTTAGCAACC
52019584 TCTCAGGGAA
Statistics
Matches: 150, Mismatches: 28, Indels: 15
0.78 0.15 0.08
Matches are distributed among these distances:
40 2 0.01
41 22 0.15
42 57 0.38
43 59 0.39
44 10 0.07
ACGTcount: A:0.37, C:0.25, G:0.17, T:0.22
Consensus pattern (42 bp):
TCAGCACTTAGCAACCACCTTTACAATCAATGATACGGGGAA
Found at i:52022207 original size:45 final size:44
Alignment explanation
Indices: 52022143--52022324 Score: 208
Period size: 44 Copynumber: 4.1 Consensus size: 44
52022133 AATAATTACA
* * *
52022143 CGGTGGAATCAGCAGTTAGCAACCACCTTTA-TATTCAAGGTTATC
1 CGGTGGAATCAGCAATTAGCAACCACC-TTACT-TACAAGGATATC
* *
52022188 CGGTGGAATCAGCAATTAGCAACCACCTTACTTACATGGAAATC
1 CGGTGGAATCAGCAATTAGCAACCACCTTACTTACAAGGATATC
* *
52022232 CGATGGAATCAG-AACTTAGCAACCACCTTACTTACATGGATATC
1 CGGTGGAATCAGCAA-TTAGCAACCACCTTACTTACAAGGATATC
* * *
52022276 CGGTGGAATCAGCACTTAGCAACAACCTTTA-TATTCAAGGATATC
1 CGGTGGAATCAGCAATTAGCAACCACC-TTACT-TACAAGGATATC
52022321 CGGT
1 CGGT
52022325 CTAATCCGAG
Statistics
Matches: 120, Mismatches: 12, Indels: 10
0.85 0.08 0.07
Matches are distributed among these distances:
43 2 0.02
44 73 0.61
45 45 0.38
ACGTcount: A:0.32, C:0.24, G:0.19, T:0.26
Consensus pattern (44 bp):
CGGTGGAATCAGCAATTAGCAACCACCTTACTTACAAGGATATC
Found at i:52023657 original size:47 final size:47
Alignment explanation
Indices: 52023588--52023682 Score: 163
Period size: 47 Copynumber: 2.0 Consensus size: 47
52023578 TATAAAGGAC
* *
52023588 AAAAGGATTTTATACATTAAGGGTTAATCAAAGAGAGGTTATGTCGA
1 AAAAGGATTTAATACATGAAGGGTTAATCAAAGAGAGGTTATGTCGA
*
52023635 AAAAGGATTTAATACATGAAGGGTTAATCACAGAGAGGTTATGTCGA
1 AAAAGGATTTAATACATGAAGGGTTAATCAAAGAGAGGTTATGTCGA
52023682 A
1 A
52023683 TCATGACTGC
Statistics
Matches: 45, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
47 45 1.00
ACGTcount: A:0.41, C:0.07, G:0.24, T:0.27
Consensus pattern (47 bp):
AAAAGGATTTAATACATGAAGGGTTAATCAAAGAGAGGTTATGTCGA
Found at i:52035595 original size:40 final size:40
Alignment explanation
Indices: 52035545--52035731 Score: 137
Period size: 40 Copynumber: 4.7 Consensus size: 40
52035535 AGAGCATTCT
* * * *
52035545 TTTCAATAGATTTAGTAGGTATGGCTTGAGAGCTCATACA
1 TTTCAGTAGATTCAGTAGGTATGGCTCGAAAGCTCATACA
* * **
52035585 TTTCAGTAGATTCAATAGGTAAGGCTCGAAAG-TGCATATG
1 TTTCAGTAGATTCAGTAGGTATGGCTCGAAAGCT-CATACA
* * * *
52035625 TTT-AGTAGA-TCTAGTAGGCATGGCTCAAAATCGCATACA
1 TTTCAGTAGATTC-AGTAGGTATGGCTCGAAAGCTCATACA
* ** * * *
52035664 TTTTAGTAGATTCAGTAGGTATCTCTTGAAAGCGCATACG
1 TTTCAGTAGATTCAGTAGGTATGGCTCGAAAGCTCATACA
* * * *
52035704 TATAAGAAGATTCAGTAGGTATCGCTCG
1 TTTCAGTAGATTCAGTAGGTATGGCTCG
52035732 TCCGAGAACA
Statistics
Matches: 114, Mismatches: 28, Indels: 10
0.75 0.18 0.07
Matches are distributed among these distances:
38 2 0.02
39 28 0.25
40 82 0.72
41 2 0.02
ACGTcount: A:0.31, C:0.14, G:0.23, T:0.32
Consensus pattern (40 bp):
TTTCAGTAGATTCAGTAGGTATGGCTCGAAAGCTCATACA
Found at i:52037839 original size:40 final size:40
Alignment explanation
Indices: 52037784--52037867 Score: 116
Period size: 40 Copynumber: 2.1 Consensus size: 40
52037774 AACAAATGCA
*
52037784 GCTATAGATTGAGCATTAGTGGTGCTT-TCTGAAAAACACC
1 GCTATAGATCGAGCATTAGTGGTGCTTCT-TGAAAAACACC
* * *
52037824 GCTATATATCGAGCATTAGTGGTGCTTCTTTAAAAACGCC
1 GCTATAGATCGAGCATTAGTGGTGCTTCTTGAAAAACACC
52037864 GCTA
1 GCTA
52037868 AATCTCATTT
Statistics
Matches: 39, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
40 38 0.97
41 1 0.03
ACGTcount: A:0.29, C:0.19, G:0.21, T:0.31
Consensus pattern (40 bp):
GCTATAGATCGAGCATTAGTGGTGCTTCTTGAAAAACACC
Found at i:52038169 original size:40 final size:39
Alignment explanation
Indices: 52038084--52038174 Score: 101
Period size: 40 Copynumber: 2.3 Consensus size: 39
52038074 GCACTTTAAA
* * *
52038084 AAAAGTGCCGCTAATGCTCGATCTATAGCGACGTTTGGG
1 AAAAGCGCCGCTAATGCTCGATATATAGCGACGTTTGAG
* ** *
52038123 ACAAAGCGCCGCTAATTCTCGATATATAGCGGTGTTTTTAG
1 A-AAAGCGCCGCTAATGCTCGATATATAGCGACG-TTTGAG
52038164 AAAAGCGCCGC
1 AAAAGCGCCGC
52038175 AAAAAAATTA
Statistics
Matches: 43, Mismatches: 7, Indels: 3
0.81 0.13 0.06
Matches are distributed among these distances:
39 1 0.02
40 37 0.86
41 5 0.12
ACGTcount: A:0.27, C:0.22, G:0.25, T:0.25
Consensus pattern (39 bp):
AAAAGCGCCGCTAATGCTCGATATATAGCGACGTTTGAG
Found at i:52038292 original size:155 final size:148
Alignment explanation
Indices: 52037955--52038315 Score: 364
Period size: 155 Copynumber: 2.4 Consensus size: 148
52037945 TAGTGTGCCC
*** * * * * *
52037955 GATCTATAGCGATGCTTGGGACAAAACACCGCTAATTCTTGATATGTAGCGGCATTTTTATAAAA
1 GATCTATAGCGACATTTGGGACAAAGCGCCGCTAATTCTCGATATATAGCGGCATTTTTAGAAAA
* * *
52038020 GCGCCGAAAAAAATTAATCACAATGCCGTTGATTGAGATTTAGTGGCATTAGCGGCACTTTAAAA
66 GCGCCGAAAAAAATTAATCACAACGCCGTTGATTGAGATTCAGTGGCATTAGCGACACTTTAAAA
* *
52038085 AAAGTGCCGCTAATGCTC
131 AAAGCGCCGCTAATGCTA
* **
52038103 GATCTATAGCGACGTTTGGGACAAAGCGCCGCTAATTCTCGATATATAGCGGTGTTTTTAGAAAA
1 GATCTATAGCGACATTTGGGACAAAGCGCCGCTAATTCTCGATATATAGCGGCATTTTTAGAAAA
* **
52038168 GCGCCGCAAAAAAATTAATCACAACGCCGTAGTTTTAGATTGAGCTTCAGTGGCATTAGCGATGC
66 GCGCCG-AAAAAAATTAATCACAACGCC---G--TT-GATTGAGATTCAGTGGCATTAGCGACAC
** * *
52038233 TTTTTAGAAAGCGCGGCTAATGCTA
124 TTTAAAAAAAGCGCCGCTAATGCTA
* * ** * ** * *
52038258 GATCTATAGTGGCATTTTTGATATCGCGCTGCTAA-TCTCAATATATAGCGGCATTTTT
1 GATCTATAGCGACATTTGGGACAAAGCGCCGCTAATTCTCGATATATAGCGGCATTTTT
52038316 TAAAAACCAC
Statistics
Matches: 173, Mismatches: 33, Indels: 8
0.81 0.15 0.04
Matches are distributed among these distances:
148 62 0.36
149 20 0.12
152 1 0.01
154 22 0.13
155 68 0.39
ACGTcount: A:0.30, C:0.18, G:0.22, T:0.30
Consensus pattern (148 bp):
GATCTATAGCGACATTTGGGACAAAGCGCCGCTAATTCTCGATATATAGCGGCATTTTTAGAAAA
GCGCCGAAAAAAATTAATCACAACGCCGTTGATTGAGATTCAGTGGCATTAGCGACACTTTAAAA
AAAGCGCCGCTAATGCTA
Found at i:52038738 original size:7 final size:7
Alignment explanation
Indices: 52038726--52038953 Score: 93
Period size: 7 Copynumber: 32.3 Consensus size: 7
52038716 GTAGTATATA
52038726 TTTAGGG
1 TTTAGGG
52038733 TTTAGGG
1 TTTAGGG
* *
52038740 TGTA-AG
1 TTTAGGG
*
52038746 TTTATGG
1 TTTAGGG
52038753 TTT-GGG
1 TTTAGGG
**
52038759 ATTTAAAG
1 -TTTAGGG
*
52038767 TTTAAGG
1 TTTAGGG
* *
52038774 TTTATGA
1 TTTAGGG
* *
52038781 TTTTGTG
1 TTTAGGG
* *
52038788 TTAAGAG
1 TTTAGGG
*
52038795 TTTAGTG
1 TTTAGGG
* *
52038802 CTTACGG
1 TTTAGGG
52038809 TTTAGGG
1 TTTAGGG
*
52038816 TGT-GGG
1 TTTAGGG
*
52038822 TTTATGG
1 TTTAGGG
*
52038829 TTTAGTG
1 TTTAGGG
*
52038836 TTTAGTG
1 TTTAGGG
52038843 TTTAGGGG
1 TTTA-GGG
*
52038851 TTAAGGG
1 TTTAGGG
* *
52038858 TTAAGAG
1 TTTAGGG
* *
52038865 CTTAGGA
1 TTTAGGG
52038872 TTTAGGG
1 TTTAGGG
*
52038879 GTTATGGG
1 TTTA-GGG
* *
52038887 CTTAGGC
1 TTTAGGG
52038894 TTTAGGG
1 TTTAGGG
52038901 TTTAGGGG
1 TTTA-GGG
* *
52038909 CTTAGAG
1 TTTAGGG
*
52038916 TTTATGG
1 TTTAGGG
*
52038923 CTTAGGG
1 TTTAGGG
*
52038930 TTTAGTG
1 TTTAGGG
*
52038937 TTTAGTG
1 TTTAGGG
52038944 TTTATGGG
1 TTTA-GGG
52038952 TT
1 TT
52038954 AACTGAAAAC
Statistics
Matches: 160, Mismatches: 53, Indels: 15
0.70 0.23 0.07
Matches are distributed among these distances:
6 11 0.07
7 127 0.79
8 22 0.14
ACGTcount: A:0.18, C:0.03, G:0.35, T:0.44
Consensus pattern (7 bp):
TTTAGGG
Found at i:52038859 original size:29 final size:27
Alignment explanation
Indices: 52038827--52038934 Score: 74
Period size: 29 Copynumber: 3.7 Consensus size: 27
52038817 GTGGGTTTAT
52038827 GGTTTAGTGTTTAGTGTTTAGGGGTTAAG
1 GGTTTAG-GTTTAG-GTTTAGGGGTTAAG
* * *
52038856 GGTTAAGAGCTTAGGATTTAGGGGTTATG
1 GGTTTAG-GTTTAGG-TTTAGGGGTTAAG
*
52038885 GGCTTAGGCTTTAGGGTTTAGGGGCTT-AG
1 GGTTTAGG-TTTA-GGTTTAGGGG-TTAAG
* *
52038914 AGTTTATGGCTTAGGGTTTAG
1 GGTTTA-GGTTTA-GGTTTAG
52038935 TGTTTAGTGT
Statistics
Matches: 63, Mismatches: 11, Indels: 10
0.75 0.13 0.12
Matches are distributed among these distances:
28 2 0.03
29 55 0.87
30 6 0.10
ACGTcount: A:0.19, C:0.05, G:0.38, T:0.39
Consensus pattern (27 bp):
GGTTTAGGTTTAGGTTTAGGGGTTAAG
Found at i:52038909 original size:22 final size:22
Alignment explanation
Indices: 52038855--52038913 Score: 73
Period size: 22 Copynumber: 2.7 Consensus size: 22
52038845 TAGGGGTTAA
* *
52038855 GGGTTAAGAGCTTAGGATTTAG
1 GGGTTAGGGGCTTAGGATTTAG
* *
52038877 GGGTTATGGGCTTAGGCTTTAG
1 GGGTTAGGGGCTTAGGATTTAG
*
52038899 GGTTTAGGGGCTTAG
1 GGGTTAGGGGCTTAG
52038914 AGTTTATGGC
Statistics
Matches: 32, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 32 1.00
ACGTcount: A:0.19, C:0.07, G:0.41, T:0.34
Consensus pattern (22 bp):
GGGTTAGGGGCTTAGGATTTAG
Found at i:52038919 original size:22 final size:21
Alignment explanation
Indices: 52038794--52038947 Score: 66
Period size: 22 Copynumber: 7.2 Consensus size: 21
52038784 TGTGTTAAGA
*
52038794 GTTTAGTGCTTACGG-TTTAGG
1 GTTTAGGGCTTA-GGATTTAGG
* * *
52038815 GTGT-GGGTTTATGG-TTTAGT
1 GTTTAGGGCTTA-GGATTTAGG
* * * *
52038835 GTTTAGTGTTTAGGGGTTAAGG
1 GTTTAGGGCTTA-GGATTTAGG
* *
52038857 GTTAAGAGCTTAGGATTTAGG
1 GTTTAGGGCTTAGGATTTAGG
* *
52038878 GGTTATGGGCTTAGGCTTTAGG
1 GTTTA-GGGCTTAGGATTTAGG
*
52038900 GTTTAGGGGCTTA-GAGTTTATG
1 GTTTA-GGGCTTAGGA-TTTAGG
* * *
52038922 GCTTAGGGTTTAGTG-TTTAGT
1 GTTTAGGGCTTAG-GATTTAGG
52038943 GTTTA
1 GTTTA
52038948 TGGGTTAACT
Statistics
Matches: 99, Mismatches: 28, Indels: 12
0.71 0.20 0.09
Matches are distributed among these distances:
20 15 0.15
21 36 0.36
22 47 0.47
23 1 0.01
ACGTcount: A:0.17, C:0.05, G:0.36, T:0.42
Consensus pattern (21 bp):
GTTTAGGGCTTAGGATTTAGG
Found at i:52039494 original size:13 final size:13
Alignment explanation
Indices: 52039476--52039500 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
52039466 CATCCGCTTC
52039476 CTCTATTCACGGG
1 CTCTATTCACGGG
52039489 CTCTATTCACGG
1 CTCTATTCACGG
52039501 TTAGTTTCGC
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:0.16, C:0.32, G:0.20, T:0.32
Consensus pattern (13 bp):
CTCTATTCACGGG
Found at i:52039566 original size:24 final size:24
Alignment explanation
Indices: 52039535--52039582 Score: 96
Period size: 24 Copynumber: 2.0 Consensus size: 24
52039525 TGACTACATT
52039535 TTTGTTTCTATGTTTAATTTTTAA
1 TTTGTTTCTATGTTTAATTTTTAA
52039559 TTTGTTTCTATGTTTAATTTTTAA
1 TTTGTTTCTATGTTTAATTTTTAA
52039583 GCATTACTTT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.21, C:0.04, G:0.08, T:0.67
Consensus pattern (24 bp):
TTTGTTTCTATGTTTAATTTTTAA
Found at i:52041503 original size:9 final size:9
Alignment explanation
Indices: 52041486--52041651 Score: 168
Period size: 9 Copynumber: 18.9 Consensus size: 9
52041476 AAATTAATAT
*
52041486 ATAATTTAC
1 ATAACTTAC
52041495 ATAACTTAC
1 ATAACTTAC
52041504 ATAACTTA-
1 ATAACTTAC
52041512 ATAACTTAC
1 ATAACTTAC
52041521 ATAA--TAC
1 ATAACTTAC
* *
52041528 ATAA-ATAT
1 ATAACTTAC
*
52041536 ATATCATATA-
1 ATAAC-T-TAC
*
52041546 AGAACTTAC
1 ATAACTTAC
52041555 ATAACTTAC
1 ATAACTTAC
*
52041564 ATAATTTA-
1 ATAACTTAC
52041572 ATAACTTAC
1 ATAACTTAC
52041581 ATAACTTA-
1 ATAACTTAC
52041589 ATAACTTAC
1 ATAACTTAC
52041598 ATAACTTAC
1 ATAACTTAC
52041607 ATAACTTATAC
1 ATAAC-T-TAC
*
52041618 ATAATTTA-
1 ATAACTTAC
*
52041626 ATAACTTGC
1 ATAACTTAC
52041635 ATAACTTAC
1 ATAACTTAC
52041644 ATAACTTA
1 ATAACTTA
52041652 ATTATACTTG
Statistics
Matches: 133, Mismatches: 13, Indels: 22
0.79 0.08 0.13
Matches are distributed among these distances:
7 7 0.05
8 36 0.27
9 76 0.57
10 5 0.04
11 9 0.07
ACGTcount: A:0.47, C:0.16, G:0.01, T:0.36
Consensus pattern (9 bp):
ATAACTTAC
Found at i:52041517 original size:17 final size:18
Alignment explanation
Indices: 52041486--52041651 Score: 168
Period size: 17 Copynumber: 9.4 Consensus size: 18
52041476 AAATTAATAT
*
52041486 ATAATTTACATAACTTAC
1 ATAACTTACATAACTTAC
52041504 ATAACTTA-ATAACTTAC
1 ATAACTTACATAACTTAC
* *
52041521 ATAA--TACATAA-ATAT
1 ATAACTTACATAACTTAC
* *
52041536 ATATCATATA-AGAACTTAC
1 ATAAC-T-TACATAACTTAC
*
52041555 ATAACTTACATAATTTA-
1 ATAACTTACATAACTTAC
52041572 ATAACTTACATAACTTA-
1 ATAACTTACATAACTTAC
52041589 ATAACTTACATAACTTAC
1 ATAACTTACATAACTTAC
*
52041607 ATAACTTATACATAATTTA-
1 ATAAC-T-TACATAACTTAC
*
52041626 ATAACTTGCATAACTTAC
1 ATAACTTACATAACTTAC
52041644 ATAACTTA
1 ATAACTTA
52041652 ATTATACTTG
Statistics
Matches: 122, Mismatches: 15, Indels: 22
0.77 0.09 0.14
Matches are distributed among these distances:
15 7 0.06
16 4 0.03
17 57 0.47
18 30 0.25
19 14 0.11
20 10 0.08
ACGTcount: A:0.47, C:0.16, G:0.01, T:0.36
Consensus pattern (18 bp):
ATAACTTACATAACTTAC
Found at i:52041565 original size:43 final size:42
Alignment explanation
Indices: 52041486--52041653 Score: 136
Period size: 43 Copynumber: 4.0 Consensus size: 42
52041476 AAATTAATAT
* *
52041486 ATAATTTACATAACTTACATAACTTA-ATAACTTACATAA-TA
1 ATAAATTACATAACTTA-AGAACTTACATAACTTACATAATTA
* *
52041527 CATAAA-TATATATCATATAAGAACTTACATAACTTACATAATTTA
1 -ATAAATTACATAAC-T-TAAGAACTTACATAACTTACATAA-TTA
* * *
52041572 ATAACTTACATAACTTAATAACTTACATAACTTACATAACT-
1 ATAAATTACATAACTTAAGAACTTACATAACTTACATAATTA
* * *
52041613 -T--A-TACATAATTTAATAACTTGCATAACTTACATAACTTA
1 ATAAATTACATAACTTAAGAACTTACATAACTTACATAA-TTA
52041652 AT
1 AT
52041654 TATACTTGTA
Statistics
Matches: 104, Mismatches: 13, Indels: 20
0.76 0.09 0.15
Matches are distributed among these distances:
37 31 0.30
38 1 0.01
40 2 0.02
41 6 0.06
42 13 0.12
43 38 0.37
44 5 0.05
45 8 0.08
ACGTcount: A:0.47, C:0.15, G:0.01, T:0.36
Consensus pattern (42 bp):
ATAAATTACATAACTTAAGAACTTACATAACTTACATAATTA
Found at i:52041628 original size:37 final size:37
Alignment explanation
Indices: 52041491--52041651 Score: 165
Period size: 37 Copynumber: 4.3 Consensus size: 37
52041481 AATATATAAT
52041491 TTACATAAC-T-TACATAACTTAATAACTTACATAA-
1 TTACATAACTTATACATAACTTAATAACTTACATAAC
* *
52041525 -TACATAAATATATATCATATAAGAACTTACATAACTTACATAAT
1 TTACATAACT-TATA-C--AT---AACTTA-ATAACTTACATAAC
52041569 TTA-ATAAC-T-TACATAACTTAATAACTTACATAAC
1 TTACATAACTTATACATAACTTAATAACTTACATAAC
* *
52041603 TTACATAACTTATACATAATTTAATAACTTGCATAAC
1 TTACATAACTTATACATAACTTAATAACTTACATAAC
52041640 TTACATAACTTA
1 TTACATAACTTA
52041652 ATTATACTTG
Statistics
Matches: 107, Mismatches: 5, Indels: 27
0.77 0.04 0.19
Matches are distributed among these distances:
33 7 0.07
34 16 0.15
35 12 0.11
36 3 0.03
37 36 0.34
38 2 0.02
39 2 0.02
40 1 0.01
41 2 0.02
42 7 0.07
43 13 0.12
44 4 0.04
45 2 0.02
ACGTcount: A:0.47, C:0.16, G:0.01, T:0.36
Consensus pattern (37 bp):
TTACATAACTTATACATAACTTAATAACTTACATAAC
Found at i:52041653 original size:26 final size:26
Alignment explanation
Indices: 52041491--52041651 Score: 154
Period size: 26 Copynumber: 6.1 Consensus size: 26
52041481 AATATATAAT
52041491 TTACATAACTTACATAACTTAATAAC
1 TTACATAACTTACATAACTTAATAAC
* *
52041517 TTACATAA--TACATAA-ATATATATC
1 TTACATAACTTACATAACTTA-ATAAC
* *
52041541 ATATA-AGAACTTACATAACTTACATAAT
1 -T-TACATAACTTACATAACTTA-ATAAC
52041569 TTA-ATAACTTACATAACTTAATAAC
1 TTACATAACTTACATAACTTAATAAC
*
52041594 TTACATAACTTACATAACTTATACATAAT
1 TTACATAACTTACATAAC-T-TA-ATAAC
*
52041623 TTA-ATAACTTGCATAACTTACATAAC
1 TTACATAACTTACATAACTTA-ATAAC
52041649 TTA
1 TTA
52041652 ATTATACTTG
Statistics
Matches: 113, Mismatches: 12, Indels: 20
0.78 0.08 0.14
Matches are distributed among these distances:
23 2 0.02
24 11 0.10
25 11 0.10
26 52 0.46
27 10 0.09
28 20 0.18
29 7 0.06
ACGTcount: A:0.47, C:0.16, G:0.01, T:0.36
Consensus pattern (26 bp):
TTACATAACTTACATAACTTAATAAC
Found at i:52046799 original size:14 final size:15
Alignment explanation
Indices: 52046778--52046820 Score: 54
Period size: 14 Copynumber: 2.9 Consensus size: 15
52046768 TTAGAGTGTA
52046778 TATGAATTTTATATG
1 TATGAATTTTATATG
*
52046793 T-TGAATTTAAT-TG
1 TATGAATTTTATATG
52046806 TATGAATTTTCATAT
1 TATGAATTTT-ATAT
52046821 TTATAGTCGA
Statistics
Matches: 23, Mismatches: 2, Indels: 5
0.77 0.07 0.17
Matches are distributed among these distances:
13 3 0.13
14 16 0.70
15 3 0.13
16 1 0.04
ACGTcount: A:0.33, C:0.02, G:0.12, T:0.53
Consensus pattern (15 bp):
TATGAATTTTATATG
Found at i:52047014 original size:41 final size:40
Alignment explanation
Indices: 52046968--52047116 Score: 147
Period size: 41 Copynumber: 3.6 Consensus size: 40
52046958 GGGCTCTGTC
* *
52046968 CCTAGCAGGCTTTATGCCAGTGAATTATAGCAGGCTTTATG
1 CCTAGCAGGCTTCATGCCAGTGTATTATA-CAGGCTTTATG
** *
52047009 CCTAGCAGGCTTCATGCC-GATGTACCATACCAGGCTTTATA
1 CCTAGCAGGCTTCATGCCAG-TGTATTATA-CAGGCTTTATG
* * * *
52047050 CCTAGCAGGCTTCGTGCCGGTGTATTATATATGGCTTTGTG
1 CCTAGCAGGCTTCATGCCAGTGTATTATACA-GGCTTTATG
* * *
52047091 CCTAGAACGCTTTATGCCAGTGTATT
1 CCTAGCAGGCTTCATGCCAGTGTATT
52047117 TTAATAAGCA
Statistics
Matches: 88, Mismatches: 17, Indels: 6
0.79 0.15 0.05
Matches are distributed among these distances:
40 2 0.02
41 85 0.97
42 1 0.01
ACGTcount: A:0.21, C:0.23, G:0.23, T:0.32
Consensus pattern (40 bp):
CCTAGCAGGCTTCATGCCAGTGTATTATACAGGCTTTATG
Found at i:52047016 original size:16 final size:16
Alignment explanation
Indices: 52046995--52047026 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
52046985 CAGTGAATTA
*
52046995 TAGCAGGCTTTATGCC
1 TAGCAGGCTTCATGCC
52047011 TAGCAGGCTTCATGCC
1 TAGCAGGCTTCATGCC
52047027 GATGTACCAT
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:0.19, C:0.28, G:0.25, T:0.28
Consensus pattern (16 bp):
TAGCAGGCTTCATGCC
Found at i:52055285 original size:43 final size:42
Alignment explanation
Indices: 52055203--52055286 Score: 114
Period size: 43 Copynumber: 2.0 Consensus size: 42
52055193 TATCCTAGAA
* *
52055203 AAAAAAGAATTTAAAAAAGGAGAAGATAATCTTGAGTTGTTG
1 AAAAAAGAATTTAAAAAAGGAGAAGATAAACATGAGTTGTTG
* * *
52055245 AAAAAATAATTTTAAAAGAGGAGAAGATAAACATGGGTTGTT
1 AAAAAAGAA-TTTAAAAAAGGAGAAGATAAACATGAGTTGTT
52055287 CGATTTACCC
Statistics
Matches: 36, Mismatches: 5, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
42 8 0.22
43 28 0.78
ACGTcount: A:0.50, C:0.02, G:0.21, T:0.26
Consensus pattern (42 bp):
AAAAAAGAATTTAAAAAAGGAGAAGATAAACATGAGTTGTTG
Done.