Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009350.1 Hibiscus syriacus cultivar Beakdansim tig00113145_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: 2139524
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 7 of 9
Found at i:1481599 original size:19 final size:19
Alignment explanation
Indices: 1481575--1481611 Score: 74
Period size: 19 Copynumber: 1.9 Consensus size: 19
1481565 TGCGATACTG
1481575 GAGATCGCGTTGCGATTTA
1 GAGATCGCGTTGCGATTTA
1481594 GAGATCGCGTTGCGATTT
1 GAGATCGCGTTGCGATTT
1481612 TGTAGGTCAT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.19, C:0.16, G:0.32, T:0.32
Consensus pattern (19 bp):
GAGATCGCGTTGCGATTTA
Found at i:1482451 original size:18 final size:18
Alignment explanation
Indices: 1482424--1482476 Score: 63
Period size: 19 Copynumber: 2.9 Consensus size: 18
1482414 TAAATAAAAC
*
1482424 AAAATGAAAATAAAAAGTA
1 AAAATAAAAATAAAAA-TA
*
1482443 AAAGTAAAAATAAAAATA
1 AAAATAAAAATAAAAATA
*
1482461 AAAAT-AACATAAAAAT
1 AAAATAAAAATAAAAAT
1482477 TTATAAAAAT
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
17 10 0.33
18 6 0.20
19 14 0.47
ACGTcount: A:0.75, C:0.02, G:0.06, T:0.17
Consensus pattern (18 bp):
AAAATAAAAATAAAAATA
Found at i:1482472 original size:11 final size:11
Alignment explanation
Indices: 1482415--1482490 Score: 66
Period size: 12 Copynumber: 6.7 Consensus size: 11
1482405 TACTGGCATT
*
1482415 AAATAAAA-CA
1 AAATAAAATAA
1482425 AAATGAAAATAA
1 AAAT-AAAATAA
1482437 AAAGTAAAAGTAA
1 AAA-TAAAA-TAA
1482450 AAATAAAAATAA
1 AAAT-AAAATAA
*
1482462 AAATAACATAA
1 AAATAAAATAA
**
1482473 AAAT-TTATAA
1 AAATAAAATAA
1482483 AAATAAAA
1 AAATAAAA
1482491 AATATCATAA
Statistics
Matches: 54, Mismatches: 6, Indels: 11
0.76 0.08 0.15
Matches are distributed among these distances:
10 12 0.22
11 15 0.28
12 16 0.30
13 11 0.20
ACGTcount: A:0.75, C:0.03, G:0.04, T:0.18
Consensus pattern (11 bp):
AAATAAAATAA
Found at i:1482491 original size:6 final size:6
Alignment explanation
Indices: 1482424--1482476 Score: 63
Period size: 6 Copynumber: 8.8 Consensus size: 6
1482414 TAAATAAAAC
* * *
1482424 AAAATG AAAATA AAAAGTA AAAGTA AAAATA AAAATA AAAAT- AACATA
1 AAAATA AAAATA AAAA-TA AAAATA AAAATA AAAATA AAAATA AAAATA
1482472 AAAAT
1 AAAAT
1482477 TTATAAAAAT
Statistics
Matches: 40, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
5 4 0.10
6 31 0.77
7 5 0.12
ACGTcount: A:0.75, C:0.02, G:0.06, T:0.17
Consensus pattern (6 bp):
AAAATA
Found at i:1482509 original size:27 final size:28
Alignment explanation
Indices: 1482451--1482520 Score: 74
Period size: 27 Copynumber: 2.5 Consensus size: 28
1482441 TAAAAGTAAA
1482451 AATAAAAAT-AAAAATAACATAAAAATTT
1 AATAAAAATAAAAAATAACAT-AAAATTT
* *
1482479 -ATAAAAATAAAAAATATCAT-AATTTT
1 AATAAAAATAAAAAATAACATAAAATTT
1482505 AATAAATACATAAAAA
1 AATAAA-A-ATAAAAA
1482521 GGCTCGTGTT
Statistics
Matches: 36, Mismatches: 2, Indels: 7
0.80 0.04 0.16
Matches are distributed among these distances:
26 5 0.14
27 13 0.36
28 11 0.31
29 7 0.19
ACGTcount: A:0.69, C:0.04, G:0.00, T:0.27
Consensus pattern (28 bp):
AATAAAAATAAAAAATAACATAAAATTT
Found at i:1486372 original size:3 final size:3
Alignment explanation
Indices: 1486366--1486429 Score: 67
Period size: 3 Copynumber: 20.7 Consensus size: 3
1486356 ATAACAGAAA
* * *
1486366 AAT AAT ATT ATT AAT AAT AAT AGT AAT AAT AATT AA- AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA-T AAT AAT AAT AAT
1486411 AAT AATT AATT AAT AAT AA
1 AAT AA-T AA-T AAT AAT AA
1486430 ACAATTAAAA
Statistics
Matches: 54, Mismatches: 4, Indels: 6
0.84 0.06 0.09
Matches are distributed among these distances:
2 2 0.04
3 42 0.78
4 10 0.19
ACGTcount: A:0.61, C:0.00, G:0.02, T:0.38
Consensus pattern (3 bp):
AAT
Found at i:1486417 original size:18 final size:18
Alignment explanation
Indices: 1486364--1486439 Score: 75
Period size: 18 Copynumber: 4.2 Consensus size: 18
1486354 TAATAACAGA
* *
1486364 AAAATAATATTATTAA-T
1 AAAATAATAATAATAATT
*
1486381 AATAATAGTAATAATAATT
1 AA-AATAATAATAATAATT
1486400 AAAATAATAATAATAATT
1 AAAATAATAATAATAATT
* *
1486418 -AATTAATAATAAACAATT
1 AAAATAATAAT-AATAATT
1486436 AAAA
1 AAAA
1486440 AGCTAACAAA
Statistics
Matches: 48, Mismatches: 7, Indels: 6
0.79 0.11 0.10
Matches are distributed among these distances:
17 11 0.23
18 32 0.67
19 5 0.10
ACGTcount: A:0.63, C:0.01, G:0.01, T:0.34
Consensus pattern (18 bp):
AAAATAATAATAATAATT
Found at i:1487404 original size:3 final size:3
Alignment explanation
Indices: 1487398--1487446 Score: 57
Period size: 3 Copynumber: 17.0 Consensus size: 3
1487388 TAGTATTATT
* * *
1487398 TAA TAA TAA TAA -CA TAA TAA T-A TAA TAA TAA TAA TTA TAC TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1487444 TAA
1 TAA
1487447 AAAATGGGGC
Statistics
Matches: 38, Mismatches: 6, Indels: 4
0.79 0.12 0.08
Matches are distributed among these distances:
2 3 0.08
3 35 0.92
ACGTcount: A:0.61, C:0.04, G:0.00, T:0.35
Consensus pattern (3 bp):
TAA
Found at i:1487441 original size:15 final size:14
Alignment explanation
Indices: 1487398--1487446 Score: 55
Period size: 14 Copynumber: 3.4 Consensus size: 14
1487388 TAGTATTATT
*
1487398 TAATAATAATAA-CA
1 TAATAAT-ATAATAA
1487412 TAATAATATAATAA
1 TAATAATATAATAA
*
1487426 TAATAATTATACTAA
1 TAATAA-TATAATAA
1487441 TAATAA
1 TAATAA
1487447 AAAATGGGGC
Statistics
Matches: 31, Mismatches: 2, Indels: 3
0.86 0.06 0.08
Matches are distributed among these distances:
13 4 0.13
14 14 0.45
15 13 0.42
ACGTcount: A:0.61, C:0.04, G:0.00, T:0.35
Consensus pattern (14 bp):
TAATAATATAATAA
Found at i:1488931 original size:14 final size:14
Alignment explanation
Indices: 1488912--1488958 Score: 53
Period size: 14 Copynumber: 3.4 Consensus size: 14
1488902 GAAATGAGTA
1488912 CAAACATAAAGGAC
1 CAAACATAAAGGAC
* *
1488926 CAAACA-ATGAGTA-
1 CAAACATA-AAGGAC
1488939 CAAACATAAAGGAC
1 CAAACATAAAGGAC
1488953 CAAACA
1 CAAACA
1488959 ATGATTAAAC
Statistics
Matches: 26, Mismatches: 4, Indels: 6
0.72 0.11 0.17
Matches are distributed among these distances:
13 10 0.38
14 16 0.62
ACGTcount: A:0.57, C:0.21, G:0.13, T:0.09
Consensus pattern (14 bp):
CAAACATAAAGGAC
Found at i:1488938 original size:27 final size:27
Alignment explanation
Indices: 1488904--1488962 Score: 118
Period size: 27 Copynumber: 2.2 Consensus size: 27
1488894 ACCAAAATGA
1488904 AATGAGTACAAACATAAAGGACCAAAC
1 AATGAGTACAAACATAAAGGACCAAAC
1488931 AATGAGTACAAACATAAAGGACCAAAC
1 AATGAGTACAAACATAAAGGACCAAAC
1488958 AATGA
1 AATGA
1488963 TTAAACCAAA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 32 1.00
ACGTcount: A:0.56, C:0.17, G:0.15, T:0.12
Consensus pattern (27 bp):
AATGAGTACAAACATAAAGGACCAAAC
Found at i:1489377 original size:2 final size:2
Alignment explanation
Indices: 1489370--1489397 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
1489360 TTCGCTCCTC
1489370 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
1489398 TATTCAAAGG
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:1493019 original size:18 final size:18
Alignment explanation
Indices: 1492993--1493028 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
1492983 ATAATTGTAT
*
1492993 TGATTATTTTTAGAGAAA
1 TGATAATTTTTAGAGAAA
1493011 TGATAATTTTTAGAGAAA
1 TGATAATTTTTAGAGAAA
1493029 ACATAATTGT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.42, C:0.00, G:0.17, T:0.42
Consensus pattern (18 bp):
TGATAATTTTTAGAGAAA
Found at i:1493034 original size:18 final size:18
Alignment explanation
Indices: 1492998--1493036 Score: 60
Period size: 18 Copynumber: 2.2 Consensus size: 18
1492988 TGTATTGATT
**
1492998 ATTTTTAGAGAAATGATA
1 ATTTTTAGAGAAAACATA
1493016 ATTTTTAGAGAAAACATA
1 ATTTTTAGAGAAAACATA
1493034 ATT
1 ATT
1493037 GTATTGATAA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.46, C:0.03, G:0.13, T:0.38
Consensus pattern (18 bp):
ATTTTTAGAGAAAACATA
Found at i:1496506 original size:24 final size:24
Alignment explanation
Indices: 1496461--1496506 Score: 74
Period size: 24 Copynumber: 1.9 Consensus size: 24
1496451 GTTTGAGATA
**
1496461 CAACATCAACACCATCTTCCATTT
1 CAACATCAACACCATCAACCATTT
1496485 CAACATCAACACCATCAACCAT
1 CAACATCAACACCATCAACCAT
1496507 CTTTCATCAA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.39, C:0.39, G:0.00, T:0.22
Consensus pattern (24 bp):
CAACATCAACACCATCAACCATTT
Found at i:1501982 original size:24 final size:24
Alignment explanation
Indices: 1501936--1501983 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 24
1501926 GCTTGAGATA
* ***
1501936 CAACATCACCACCATCTTTCATTT
1 CAACATCAACACCATCAACCATTT
1501960 CAACATCAACACCATCAACCATTT
1 CAACATCAACACCATCAACCATTT
1501984 TCCATCAAAG
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.35, C:0.38, G:0.00, T:0.27
Consensus pattern (24 bp):
CAACATCAACACCATCAACCATTT
Found at i:1503844 original size:30 final size:31
Alignment explanation
Indices: 1503805--1503863 Score: 84
Period size: 30 Copynumber: 1.9 Consensus size: 31
1503795 ATTGTCCCGA
*
1503805 ATAACCTATCCAGAGGTCATAAAGAACCTCG
1 ATAACCTATCCAGAGGTCACAAAGAACCTCG
* *
1503836 ATAA-CTATCCATAGGTCCCAAAGAACCT
1 ATAACCTATCCAGAGGTCACAAAGAACCT
1503864 AGTTAAACTG
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
30 21 0.84
31 4 0.16
ACGTcount: A:0.39, C:0.27, G:0.14, T:0.20
Consensus pattern (31 bp):
ATAACCTATCCAGAGGTCACAAAGAACCTCG
Found at i:1503928 original size:31 final size:33
Alignment explanation
Indices: 1503839--1503964 Score: 95
Period size: 31 Copynumber: 4.0 Consensus size: 33
1503829 AACCTCGATA
* * *
1503839 ACTATCCATAGGTCCC-AAAGAACCTAGTTAA-
1 ACTATCCATATGTCCCAAAAGAACATAGGTAAT
* **
1503870 ACTGTCCATATG-CTCC-TTAGAACATAGGT-AT
1 ACTATCCATATGTC-CCAAAAGAACATAGGTAAT
* * *
1503901 ACTGTCTATATGTCTCAAAAGAA-ATAGGTAAT
1 ACTATCCATATGTCCCAAAAGAACATAGGTAAT
* *
1503933 TCTATCCATATGTCCCAAAAG-ACATAAGTAAT
1 ACTATCCATATGTCCCAAAAGAACATAGGTAAT
1503965 TCTGTTCATA
Statistics
Matches: 74, Mismatches: 15, Indels: 11
0.74 0.15 0.11
Matches are distributed among these distances:
30 2 0.03
31 40 0.54
32 32 0.43
ACGTcount: A:0.37, C:0.21, G:0.13, T:0.29
Consensus pattern (33 bp):
ACTATCCATATGTCCCAAAAGAACATAGGTAAT
Found at i:1503946 original size:32 final size:32
Alignment explanation
Indices: 1503908--1503977 Score: 95
Period size: 32 Copynumber: 2.2 Consensus size: 32
1503898 TATACTGTCT
* *
1503908 ATATGTCTCAAAAGAAATAGGTAATTCTATCC
1 ATATGTCCCAAAAGAAATAAGTAATTCTATCC
* * *
1503940 ATATGTCCCAAAAGACATAAGTAATTCTGTTC
1 ATATGTCCCAAAAGAAATAAGTAATTCTATCC
1503972 ATATGT
1 ATATGT
1503978 TCCGTTGAAC
Statistics
Matches: 33, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
32 33 1.00
ACGTcount: A:0.39, C:0.16, G:0.13, T:0.33
Consensus pattern (32 bp):
ATATGTCCCAAAAGAAATAAGTAATTCTATCC
Found at i:1504449 original size:20 final size:20
Alignment explanation
Indices: 1504424--1504471 Score: 87
Period size: 20 Copynumber: 2.4 Consensus size: 20
1504414 CATGTGTACA
1504424 TATATCATGGACACTTAACC
1 TATATCATGGACACTTAACC
1504444 TATATCATGGACACTTAACC
1 TATATCATGGACACTTAACC
*
1504464 TGTATCAT
1 TATATCAT
1504472 ATAAACATGT
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 27 1.00
ACGTcount: A:0.33, C:0.23, G:0.10, T:0.33
Consensus pattern (20 bp):
TATATCATGGACACTTAACC
Found at i:1504871 original size:20 final size:22
Alignment explanation
Indices: 1504836--1504893 Score: 66
Period size: 20 Copynumber: 2.6 Consensus size: 22
1504826 TTCCTTTTGA
* *
1504836 AGTGCATCGGTACATT-TT-AC
1 AGTGCATCGATGCATTCTTAAC
1504856 AGTGCATCGATGCATTCCTTAAC
1 AGTGCATCGATGCATT-CTTAAC
1504879 ATGTGCATCGATGCA
1 A-GTGCATCGATGCA
1504894 CTATCCATAC
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
20 14 0.44
22 2 0.06
23 3 0.09
24 13 0.41
ACGTcount: A:0.26, C:0.22, G:0.21, T:0.31
Consensus pattern (22 bp):
AGTGCATCGATGCATTCTTAAC
Found at i:1517465 original size:627 final size:626
Alignment explanation
Indices: 1516268--1517503 Score: 2355
Period size: 627 Copynumber: 2.0 Consensus size: 626
1516258 TTAATCATTG
1516268 ACATATTAAATTTATTAAAATATAAATAAGTTTATTGATATATATAATTTAATACTACATAACAA
1 ACATATTAAATTTATTAAAATATAAATAAGTTTATTGATATATATAATTTAATACTACATAACAA
*
1516333 GATTATAAAATAATATAGTTGTTTTTTTAGTTTAACTGAATTATTTTGATTATCAAATTTTAAGC
66 GATTATAAAATAATATAGTTGCTTTTTTAGTTTAACTGAATTATTTTGATTATCAAATTTTAAGC
1516398 TGAATGATAGAATATTTAAAAAATGGAACATTTGGGCTAGTGGCTTGGGTGTTTCTCTTCTAACT
131 TGAATGATAGAATATTTAAAAAATGGAACATTTGGGCTAGTGGCTTGGGTGTTTCTCTTCTAACT
1516463 AAATGACCTATATTTAAATCTCCCCAAATGCAAGTTTTCTTTGATTTATTTGAAAATTAAGAAAT
196 AAATGACCTATATTTAAATCTCCCCAAATGCAAGTTTTCTTTGATTTATTTGAAAATTAAGAAAT
1516528 AAAATCAAGAGCGGTTTTTTGAAGCATTAGTGGTTTAGGAATTGTTTAGAATTTGTGTATGGTTT
261 AAAATCAAGAGCGGTTTTTTGAAGCATTAGTGGTTTAGGAATTGTTTAGAATTTGTGTATGGTTT
* **
1516593 AGCCATCGGCCCCGCCTTTGGTTGTGGTTAATCTTAATGTTTTTCCACCCTTAGAGAGGGCATGG
326 AGCCATCGGCCCCGCATTTGGTTGTGGTTAATCTTAACATTTTTCCACCCTTAGAGAGGGCATGG
*
1516658 TTTCACACATTCTCTTGGAGGAGAAACATGCTTCCAAGAAGGGAAGATAGAAGTATTTGGAGGGG
391 TTCCACACATTCTCTTGGAGGAGAAACATGCTTCCAAGAAGGGAAGATAGAAGTATTTGGAGGGG
*
1516723 TTAGTATGTCGTATATTGGTATCGATGGGGTAAATGTTTCTACTGGAAATTGAGCCTAGTATCGT
456 TTAGTATGTCGTATATTGGTATCGATGCGGTAAATGTTTCTACTGGAAATTGAGCCTAGTATCGT
*
1516788 TTTTCTGATGTTGATGAACATTAATCTTTGAATGATTTTTTTTGGGGATGTGGTCCTTCAAATTT
521 TTTTCTGATGATGATGAACATTAATCTTTGAATGATTTTTTTTGGGGATGTGGTCCTTCAAATTT
1516853 TCTAGTTGTGCTCATGATTCCATTAGAGAGGGCATGGTTTC
586 TCTAGTTGTGCTCATGATTCCATTAGAGAGGGCATGGTTTC
1516894 ACATATTAAATTTATTAAAATATAAATAAGTTTATTGATATATATAATTTAATACTACATAACAA
1 ACATATTAAATTTATTAAAATATAAATAAGTTTATTGATATATATAATTTAATACTACATAACAA
1516959 GATTATAAAATAATATAGTTGCTTTTTTAGTTTAACTGAATTATTTTGATTATCAAATTTTAAGC
66 GATTATAAAATAATATAGTTGCTTTTTTAGTTTAACTGAATTATTTTGATTATCAAATTTTAAGC
1517024 TGAATGATAGAATATTTAAAAAATGGAACATTTGGGCTAGTGGCTTGGGTGTTTCTCTTCTAACT
131 TGAATGATAGAATATTTAAAAAATGGAACATTTGGGCTAGTGGCTTGGGTGTTTCTCTTCTAACT
1517089 AAATGACCTATATTTAAATCTCCCCAAATGCAAGTTTTCTTTGATTTATTTGAAAATTAAGAAAT
196 AAATGACCTATATTTAAATCTCCCCAAATGCAAGTTTTCTTTGATTTATTTGAAAATTAAGAAAT
1517154 AAAATCAAGAGCGGTTTTTTTGAAGCATTAGTGGTTTAGGAATTGTTTAGAATTTGTGTATGGTT
261 AAAATCAAGAGCGG-TTTTTTGAAGCATTAGTGGTTTAGGAATTGTTTAGAATTTGTGTATGGTT
*
1517219 TAGCCATCGGCCCCGCATTTGGTTGTGGTTAATCTTAACATTTTTCCACCCTTAGATAGGGCATG
325 TAGCCATCGGCCCCGCATTTGGTTGTGGTTAATCTTAACATTTTTCCACCCTTAGAGAGGGCATG
1517284 GTTCCACACATTCTCTTGGAGGAGAAACATGCTTCCAAGAAGGGAAGATAGAAGTATTTGGAGGG
390 GTTCCACACATTCTCTTGGAGGAGAAACATGCTTCCAAGAAGGGAAGATAGAAGTATTTGGAGGG
* *
1517349 GTTAGTATGTCGTATATTGGTATCGATGCGGTAAATGTTTCTACTGGAAATTGAGCCTAGTTTTG
455 GTTAGTATGTCGTATATTGGTATCGATGCGGTAAATGTTTCTACTGGAAATTGAGCCTAGTATCG
*
1517414 TTTTTCTGATGATGATGAACATTAATCTTTGAATGCTTTTTTTTGGGGATGTGGTCCTTCAAATT
520 TTTTTCTGATGATGATGAACATTAATCTTTGAATGATTTTTTTTGGGGATGTGGTCCTTCAAATT
*
1517479 TTCTAGTTGTGTTCATGATTCCATT
585 TTCTAGTTGTGCTCATGATTCCATT
1517504 GGCTATAATA
Statistics
Matches: 597, Mismatches: 12, Indels: 1
0.98 0.02 0.00
Matches are distributed among these distances:
626 273 0.46
627 324 0.54
ACGTcount: A:0.30, C:0.11, G:0.19, T:0.39
Consensus pattern (626 bp):
ACATATTAAATTTATTAAAATATAAATAAGTTTATTGATATATATAATTTAATACTACATAACAA
GATTATAAAATAATATAGTTGCTTTTTTAGTTTAACTGAATTATTTTGATTATCAAATTTTAAGC
TGAATGATAGAATATTTAAAAAATGGAACATTTGGGCTAGTGGCTTGGGTGTTTCTCTTCTAACT
AAATGACCTATATTTAAATCTCCCCAAATGCAAGTTTTCTTTGATTTATTTGAAAATTAAGAAAT
AAAATCAAGAGCGGTTTTTTGAAGCATTAGTGGTTTAGGAATTGTTTAGAATTTGTGTATGGTTT
AGCCATCGGCCCCGCATTTGGTTGTGGTTAATCTTAACATTTTTCCACCCTTAGAGAGGGCATGG
TTCCACACATTCTCTTGGAGGAGAAACATGCTTCCAAGAAGGGAAGATAGAAGTATTTGGAGGGG
TTAGTATGTCGTATATTGGTATCGATGCGGTAAATGTTTCTACTGGAAATTGAGCCTAGTATCGT
TTTTCTGATGATGATGAACATTAATCTTTGAATGATTTTTTTTGGGGATGTGGTCCTTCAAATTT
TCTAGTTGTGCTCATGATTCCATTAGAGAGGGCATGGTTTC
Found at i:1520243 original size:23 final size:23
Alignment explanation
Indices: 1520211--1520284 Score: 96
Period size: 23 Copynumber: 3.3 Consensus size: 23
1520201 GAGTCGAGGG
*
1520211 TTCTAGGCGGTCCTTCGGGACAT
1 TTCTATGCGGTCCTTCGGGACAT
* *
1520234 TTCTATGCGGTCCTTTGGGGCAT
1 TTCTATGCGGTCCTTCGGGACAT
* *
1520257 TTCTATGTGGTCATTCGGGACA-
1 TTCTATGCGGTCCTTCGGGACAT
1520279 TTCTAT
1 TTCTAT
1520285 ATGGCAATTC
Statistics
Matches: 44, Mismatches: 7, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
22 6 0.14
23 38 0.86
ACGTcount: A:0.14, C:0.22, G:0.27, T:0.38
Consensus pattern (23 bp):
TTCTATGCGGTCCTTCGGGACAT
Found at i:1521024 original size:20 final size:20
Alignment explanation
Indices: 1520979--1521017 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
1520969 TAAGGGTATC
1520979 AGTACTAGAAGAACAATACA
1 AGTACTAGAAGAACAATACA
*
1520999 AGTACTGGAAGAACAATAC
1 AGTACTAGAAGAACAATAC
1521018 CGATACTATA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.51, C:0.15, G:0.18, T:0.15
Consensus pattern (20 bp):
AGTACTAGAAGAACAATACA
Found at i:1525373 original size:45 final size:45
Alignment explanation
Indices: 1525309--1525394 Score: 147
Period size: 45 Copynumber: 1.9 Consensus size: 45
1525299 TCAATTTTGA
1525309 CATTTATGGCATCCTTTCATGCCTGTT-ATGCACTATTATGCATTT
1 CATTTATGGCATCCTTTCATGCCT-TTAATGCACTATTATGCATTT
*
1525354 CATTTATGGCATCCTTTCATGCCTTTAATGCACTGTTATGC
1 CATTTATGGCATCCTTTCATGCCTTTAATGCACTATTATGC
1525395 CTTTTCAATT
Statistics
Matches: 39, Mismatches: 1, Indels: 2
0.93 0.02 0.05
Matches are distributed among these distances:
44 2 0.05
45 37 0.95
ACGTcount: A:0.20, C:0.23, G:0.14, T:0.43
Consensus pattern (45 bp):
CATTTATGGCATCCTTTCATGCCTTTAATGCACTATTATGCATTT
Found at i:1525765 original size:54 final size:54
Alignment explanation
Indices: 1525703--1526319 Score: 402
Period size: 54 Copynumber: 11.5 Consensus size: 54
1525693 ACAGTCGTTT
* * * * *
1525703 ATCAACATATGATGAATTTCGTGAGTTGCACACATAGT-CTCTG-TAGGGTTATTC
1 ATCAACATATGATGAATTCCGTGAATTGAACACATAGTGC-C-GAAACGGTTATTC
* *
1525757 ATCAACATATGATGAATTCCGTGAATTGAACACTTAGTGCCGAAACGGTTGTTC
1 ATCAACATATGATGAATTCCGTGAATTGAACACATAGTGCCGAAACGGTTATTC
* * * ** * * * * *
1525811 ATCAACATATCATGAATTACATGGGTTGCACTCTTAGTGCTGAAACGATTATTC
1 ATCAACATATGATGAATTCCGTGAATTGAACACATAGTGCCGAAACGGTTATTC
* * * * * * *
1525865 ATCCACATAGGATGAATTCTGTGAAATGTACACTTAGTGTCGAAACGGTTATTC
1 ATCAACATATGATGAATTCCGTGAATTGAACACATAGTGCCGAAACGGTTATTC
* * * * * * * * * *
1525919 ATCCACGTAGGATGGATTCTGTGAAAT-ACACACTTAGTGCTGAAATGATTATTC
1 ATCAACATATGATGAATTCCGTGAATTGA-ACACATAGTGCCGAAACGGTTATTC
* * * * * * * * * *
1525973 ATCCACATAGGATGAATTCTGTGAAATGCACACTTAGTGCCGAAATGATTGTTT
1 ATCAACATATGATGAATTCCGTGAATTGAACACATAGTGCCGAAACGGTTATTC
* * * * * * *
1526027 ATCCACATAGGAT-AGATTCTGTGAAATGCACACTTAGTGCCGAGACGGTTATTC
1 ATCAACATATGATGA-ATTCCGTGAATTGAACACATAGTGCCGAAACGGTTATTC
* * ** * * * * * *
1526081 ATCCACATAGGATGAATTATGTGAAATT-CACTCTTAGTGCCAAAACGATTAATC
1 ATCAACATATGATGAATTCCGTG-AATTGAACACATAGTGCCGAAACGGTTATTC
* * * * * *
1526135 ATCCACATAGGATGAATTCCGTGAAATGCACACTTTGTGCCGAAACGGTTATTC
1 ATCAACATATGATGAATTCCGTGAATTGAACACATAGTGCCGAAACGGTTATTC
* * * * * * *
1526189 ATCCACGTAGGATGAATTCCATGAAATGCACAC-TAGTGCCGAAACGATTATTC
1 ATCAACATATGATGAATTCCGTGAATTGAACACATAGTGCCGAAACGGTTATTC
* * * * *
1526242 ATCAATATATGATGAATTCCATGAAATGCACAC-TAGTGCCGAAACGATTATTC
1 ATCAACATATGATGAATTCCGTGAATTGAACACATAGTGCCGAAACGGTTATTC
* * *
1526295 ATCAATATAGGATGAATTCCATGAA
1 ATCAACATATGATGAATTCCGTGAA
1526320 ATGCACACTT
Statistics
Matches: 482, Mismatches: 73, Indels: 17
0.84 0.13 0.03
Matches are distributed among these distances:
53 96 0.20
54 381 0.79
55 5 0.01
ACGTcount: A:0.33, C:0.18, G:0.19, T:0.30
Consensus pattern (54 bp):
ATCAACATATGATGAATTCCGTGAATTGAACACATAGTGCCGAAACGGTTATTC
Found at i:1525867 original size:108 final size:106
Alignment explanation
Indices: 1525751--1526332 Score: 630
Period size: 108 Copynumber: 5.4 Consensus size: 106
1525741 CTCTGTAGGG
* * * * * * *
1525751 TTATTCATCAACATATGATGAATTCCGTGAATTGAACACTTAGTGCCGAAACGGTTGTTCATCAA
1 TTATTCATCCACATAGGATGAATTCCGTGAAATGCACACTTAGTGCCGAAACGATTATTCATCCA
** ** * *
1525816 CATATCATGAATTACATGGGTTGCACTCTTAGTGCTGAAACGA
66 CATAGGATGAATT-C-TGGAATGCACACTTAGTGCCGAAACGA
* * * *
1525859 TTATTCATCCACATAGGATGAATTCTGTGAAATGTACACTTAGTGTCGAAACGGTTATTCATCCA
1 TTATTCATCCACATAGGATGAATTCCGTGAAATGCACACTTAGTGCCGAAACGATTATTCATCCA
* * * * *
1525924 CGTAGGATGGATTCTGTGAAATACACACTTAGTGCTGAAATGA
66 CATAGGATGAATTCTG-G-AATGCACACTTAGTGCCGAAACGA
* * * *
1525967 TTATTCATCCACATAGGATGAATTCTGTGAAATGCACACTTAGTGCCGAAATGATTGTTTATCCA
1 TTATTCATCCACATAGGATGAATTCCGTGAAATGCACACTTAGTGCCGAAACGATTATTCATCCA
* *
1526032 CATAGGAT-AGATTCTGTGAAATGCACACTTAGTGCCGAGACGG
66 CATAGGATGA-ATTCTG-G-AATGCACACTTAGTGCCGAAACGA
** * * * *
1526075 TTATTCATCCACATAGGATGAATTATGTGAAATTCACTCTTAGTGCCAAAACGATTAATCATCCA
1 TTATTCATCCACATAGGATGAATTCCGTGAAATGCACACTTAGTGCCGAAACGATTATTCATCCA
* * *
1526140 CATAGGATGAATTCCGTGAAATGCACACTTTGTGCCGAAACGG
66 CATAGGATGAATT-C-TGGAATGCACACTTAGTGCCGAAACGA
* * *
1526183 TTATTCATCCACGTAGGATGAATTCCATGAAATGCACAC-TAGTGCCGAAACGATTATTCATCAA
1 TTATTCATCCACATAGGATGAATTCCGTGAAATGCACACTTAGTGCCGAAACGATTATTCATCCA
* * *
1526247 TATATGATGAATTCCATGAAATGCACAC-TAGTGCCGAAACGA
66 CATAGGATGAATT-C-TGGAATGCACACTTAGTGCCGAAACGA
* * *
1526289 TTATTCATCAATATAGGATGAATTCCATGAAATGCACACTTAGT
1 TTATTCATCCACATAGGATGAATTCCGTGAAATGCACACTTAGT
1526333 TCCTATTTGG
Statistics
Matches: 409, Mismatches: 58, Indels: 15
0.85 0.12 0.03
Matches are distributed among these distances:
106 50 0.12
107 53 0.13
108 302 0.74
109 2 0.00
110 2 0.00
ACGTcount: A:0.33, C:0.19, G:0.19, T:0.30
Consensus pattern (106 bp):
TTATTCATCCACATAGGATGAATTCCGTGAAATGCACACTTAGTGCCGAAACGATTATTCATCCA
CATAGGATGAATTCTGGAATGCACACTTAGTGCCGAAACGA
Found at i:1525956 original size:162 final size:162
Alignment explanation
Indices: 1525749--1526332 Score: 681
Period size: 162 Copynumber: 3.6 Consensus size: 162
1525739 GTCTCTGTAG
* * * *
1525749 GGTTATTCATCAACATATGATGAATTCCGTGAATTGA-ACACTTAGTGCCGAAACGGTTGTTCAT
1 GGTTATTCATCAACATAGGATGAATTCCGTGAAAT-ACACACTTAGTGCCGAAACGATTATTCAT
** * ** * *
1525813 CAACATATCATGAATTACATGGGTTGCACTCTTAGTGCTGAAACGATTATTCATCCACATAGGAT
65 CAACATAGGATGAATTCCATGGAATGCACACTTAGTGCCGAAACGATTATTCATCCACATAGGAT
* *
1525878 GAATTCTGTGAAATGTACACTTAGTGTCGAAAC
130 GAATTCTGTGAAATGCACACTTAGTGCCGAAAC
* * * * * *
1525911 GGTTATTCATCCACGTAGGATGGATTCTGTGAAATACACACTTAGTGCTGAAATGATTATTCATC
1 GGTTATTCATCAACATAGGATGAATTCCGTGAAATACACACTTAGTGCCGAAACGATTATTCATC
* ** * * * *
1525976 CACATAGGATGAATTCTGTGAAATGCACACTTAGTGCCGAAATGATTGTTTATCCACATAGGAT-
66 AACATAGGATGAATTCCATGGAATGCACACTTAGTGCCGAAACGATTATTCATCCACATAGGATG
*
1526040 AGATTCTGTGAAATGCACACTTAGTGCCGAGAC
131 A-ATTCTGTGAAATGCACACTTAGTGCCGAAAC
* ** * * * *
1526073 GGTTATTCATCCACATAGGATGAATTATGTGAAATTCACTCTTAGTGCCAAAACGATTAATCATC
1 GGTTATTCATCAACATAGGATGAATTCCGTGAAATACACACTTAGTGCCGAAACGATTATTCATC
* * * * * *
1526138 CACATAGGATGAATTCCGTGAAATGCACACTTTGTGCCGAAACGGTTATTCATCCACGTAGGATG
66 AACATAGGATGAATTCCATGGAATGCACACTTAGTGCCGAAACGATTATTCATCCACATAGGATG
**
1526203 AATTCCATGAAATGCACAC-TAGTGCCGAAAC
131 AATTCTGTGAAATGCACACTTAGTGCCGAAAC
* * * * *
1526234 GATTATTCATCAATATATGATGAATTCCATGAAATGCACAC-TAGTGCCGAAACGATTATTCATC
1 GGTTATTCATCAACATAGGATGAATTCCGTGAAATACACACTTAGTGCCGAAACGATTATTCATC
* *
1526298 AATATAGGATGAATTCCATGAAATGCACACTTAGT
66 AACATAGGATGAATTCCATGGAATGCACACTTAGT
1526333 TCCTATTTGG
Statistics
Matches: 358, Mismatches: 61, Indels: 8
0.84 0.14 0.02
Matches are distributed among these distances:
160 52 0.15
161 45 0.13
162 260 0.73
163 1 0.00
ACGTcount: A:0.33, C:0.19, G:0.19, T:0.30
Consensus pattern (162 bp):
GGTTATTCATCAACATAGGATGAATTCCGTGAAATACACACTTAGTGCCGAAACGATTATTCATC
AACATAGGATGAATTCCATGGAATGCACACTTAGTGCCGAAACGATTATTCATCCACATAGGATG
AATTCTGTGAAATGCACACTTAGTGCCGAAAC
Found at i:1526686 original size:22 final size:22
Alignment explanation
Indices: 1526643--1526697 Score: 71
Period size: 22 Copynumber: 2.6 Consensus size: 22
1526633 TGGCTCCTCA
1526643 GTATCGATAC--CCATACCATG
1 GTATCGATACTACCATACCATG
1526663 GTATCGATACTACCATACTC-TG
1 GTATCGATACTACCATAC-CATG
*
1526685 GTAACGATACTAC
1 GTATCGATACTAC
1526698 GCTATGGTAT
Statistics
Matches: 31, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
20 10 0.32
22 20 0.65
23 1 0.03
ACGTcount: A:0.31, C:0.27, G:0.15, T:0.27
Consensus pattern (22 bp):
GTATCGATACTACCATACCATG
Found at i:1526774 original size:20 final size:21
Alignment explanation
Indices: 1526736--1526788 Score: 65
Period size: 20 Copynumber: 2.6 Consensus size: 21
1526726 CTGTTTTGAA
*
1526736 TGGTATCGATAC-CTTCCCTT
1 TGGTATCGATACTCTCCCCTT
1526756 TGGTATCGATACTC-CCCCTT
1 TGGTATCGATACTCTCCCCTT
* *
1526776 CGATATCGATACT
1 TGGTATCGATACT
1526789 TATTGAATTA
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
20 28 0.97
21 1 0.03
ACGTcount: A:0.19, C:0.30, G:0.15, T:0.36
Consensus pattern (21 bp):
TGGTATCGATACTCTCCCCTT
Found at i:1537047 original size:47 final size:45
Alignment explanation
Indices: 1536981--1537090 Score: 141
Period size: 47 Copynumber: 2.4 Consensus size: 45
1536971 TGGTATATGG
* * *
1536981 TTATGGAAT-AATGGCAAGTATATTGATGAAATAAGCTTATGAGC
1 TTATGGAATAAATGGTAAGTATATTGATAAAATAAGCTTACGAGC
* *
1537025 TTATGGAATTTAAATGGTAAGTATTTTGGTAAAATAAGCTTACGAGC
1 TTATGGAA--TAAATGGTAAGTATATTGATAAAATAAGCTTACGAGC
*
1537072 TTATGGGATAAATGGTAAG
1 TTATGGAATAAATGGTAAG
1537091 GGATTTTATA
Statistics
Matches: 57, Mismatches: 6, Indels: 5
0.84 0.09 0.07
Matches are distributed among these distances:
44 8 0.14
45 11 0.19
46 1 0.02
47 37 0.65
ACGTcount: A:0.37, C:0.05, G:0.24, T:0.34
Consensus pattern (45 bp):
TTATGGAATAAATGGTAAGTATATTGATAAAATAAGCTTACGAGC
Found at i:1539685 original size:27 final size:27
Alignment explanation
Indices: 1539623--1539677 Score: 101
Period size: 27 Copynumber: 2.0 Consensus size: 27
1539613 GGCCTAAGAA
*
1539623 AGCCATCTATGCTAACAAGAATTTCAC
1 AGCCATATATGCTAACAAGAATTTCAC
1539650 AGCCATATATGCTAACAAGAATTTCAC
1 AGCCATATATGCTAACAAGAATTTCAC
1539677 A
1 A
1539678 TTGGTATAAT
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
27 27 1.00
ACGTcount: A:0.40, C:0.24, G:0.11, T:0.25
Consensus pattern (27 bp):
AGCCATATATGCTAACAAGAATTTCAC
Found at i:1541866 original size:45 final size:45
Alignment explanation
Indices: 1541782--1541867 Score: 102
Period size: 45 Copynumber: 1.9 Consensus size: 45
1541772 ATCAATTTCA
* *
1541782 CATTTATGGCATCATTTCATGCATGTTATGCACTATTATGCATTT
1 CATTTATGACATCATTTCATGCATGTTATGCACCATTATGCATTT
* * * *
1541827 CATTTATTACATCCTTTCATGCCT-TTAATGCACCGTTATGC
1 CATTTATGACATCATTTCATGCATGTT-ATGCACCATTATGC
1541868 CTTTTCAATT
Statistics
Matches: 34, Mismatches: 6, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
44 2 0.06
45 32 0.94
ACGTcount: A:0.23, C:0.22, G:0.12, T:0.43
Consensus pattern (45 bp):
CATTTATGACATCATTTCATGCATGTTATGCACCATTATGCATTT
Found at i:1542374 original size:54 final size:54
Alignment explanation
Indices: 1542223--1542970 Score: 820
Period size: 54 Copynumber: 13.8 Consensus size: 54
1542213 TGCATGTACA
* * * ** **
1542223 GTTATTCATCAACATATGATGAATTTTGTGAGCTGCACACTTAGTGCCGAAAACG
1 GTTATTCATCCACATAGGATGGATTCAGTGAAATGCACACTTAGTGCCG-AAACG
* * * * * * * * *
1542278 GTTGTTCATCAACATATGATGAATTCCGTGGATTACAAACTTAGTGCCGAAACG
1 GTTATTCATCCACATAGGATGGATTCAGTGAAATGCACACTTAGTGCCGAAACG
* ** * *
1542332 ATTATTCATCCATGTAGGATGTATTCATTGAAATGCACACTTAGTGCCGAAACG
1 GTTATTCATCCACATAGGATGGATTCAGTGAAATGCACACTTAGTGCCGAAACG
* * **
1542386 GTTATTTATCCACATAAGATGGATTCCA-TGAAATGCACACTTAGTGGTGAAACG
1 GTTATTCATCCACATAGGATGGATT-CAGTGAAATGCACACTTAGTGCCGAAACG
* *
1542440 GTTATTCATTCACATAGGATGGATTCTGTGAAATGCACACTTAGTGCCGAAACG
1 GTTATTCATCCACATAGGATGGATTCAGTGAAATGCACACTTAGTGCCGAAACG
* * *
1542494 GTTATTCATCCACATGGGATGAATTCCA-TGAAATGCACACTTAGTGTCGAAACG
1 GTTATTCATCCACATAGGATGGATT-CAGTGAAATGCACACTTAGTGCCGAAACG
* * * * *
1542548 GTTATTCATCCACACAGGATGAATTTAGTGAAATACACACTTAGTGCCTAAACG
1 GTTATTCATCCACATAGGATGGATTCAGTGAAATGCACACTTAGTGCCGAAACG
* * *
1542602 ATTATTCATCCACATAGGATGGATTCCGTGAAATGCACACTTAGTGCTGAAACG
1 GTTATTCATCCACATAGGATGGATTCAGTGAAATGCACACTTAGTGCCGAAACG
* * * * * *
1542656 GTTATTTATCTAGATAGGATGAATTCTA-TGAAATGCACACTTAGTGCTGAAATG
1 GTTATTCATCCACATAGGATGGATTC-AGTGAAATGCACACTTAGTGCCGAAACG
* * * *
1542710 GTTACTCATCCACATAGGATGGATTCCGTGAAATGCACACTTAGTGTCGAAATG
1 GTTATTCATCCACATAGGATGGATTCAGTGAAATGCACACTTAGTGCCGAAACG
* * *
1542764 GTTATTCATCCACATAGGATGGATTCCGTAAAATGTACACTTAGTGCCGAAACG
1 GTTATTCATCCACATAGGATGGATTCAGTGAAATGCACACTTAGTGCCGAAACG
* * * *
1542818 ATTATTCATCCACATTGGATGGATTCCGTGAAATGCACACTTAGTGCTGAAACG
1 GTTATTCATCCACATAGGATGGATTCAGTGAAATGCACACTTAGTGCCGAAACG
* * ** * * * *
1542872 TTTATTCATCCACATAGGATGAATTCCCTGAAATGCATAATTAGTGTCGAAATG
1 GTTATTCATCCACATAGGATGGATTCAGTGAAATGCACACTTAGTGCCGAAACG
* * **
1542926 GTTACTCATCCACATAGGATGAATTCCA-TGAAATATACACTTAGT
1 GTTATTCATCCACATAGGATGGATT-CAGTGAAATGCACACTTAGT
1542971 TCCTATTTGA
Statistics
Matches: 591, Mismatches: 95, Indels: 15
0.84 0.14 0.02
Matches are distributed among these distances:
53 2 0.00
54 544 0.92
55 45 0.08
ACGTcount: A:0.32, C:0.19, G:0.20, T:0.30
Consensus pattern (54 bp):
GTTATTCATCCACATAGGATGGATTCAGTGAAATGCACACTTAGTGCCGAAACG
Found at i:1543323 original size:22 final size:21
Alignment explanation
Indices: 1543293--1543351 Score: 68
Period size: 22 Copynumber: 2.9 Consensus size: 21
1543283 ATCGATACCC
* *
1543293 ATACCATGGTATGGATACTACT
1 ATACTATGGTATCGATACTA-T
1543315 ATACTATGGTATCGATACTAT
1 ATACTATGGTATCGATACTAT
*
1543336 AT--TATGGTATCAATAC
1 ATACTATGGTATCGATAC
1543352 CATTTTTGCA
Statistics
Matches: 34, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
19 13 0.38
21 3 0.09
22 18 0.53
ACGTcount: A:0.34, C:0.15, G:0.15, T:0.36
Consensus pattern (21 bp):
ATACTATGGTATCGATACTAT
Found at i:1543335 original size:19 final size:19
Alignment explanation
Indices: 1543311--1543351 Score: 64
Period size: 19 Copynumber: 2.2 Consensus size: 19
1543301 GTATGGATAC
*
1543311 TACTATACTATGGTATCGA
1 TACTATACTATGGTATCAA
*
1543330 TACTATATTATGGTATCAA
1 TACTATACTATGGTATCAA
1543349 TAC
1 TAC
1543352 CATTTTTGCA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.34, C:0.15, G:0.12, T:0.39
Consensus pattern (19 bp):
TACTATACTATGGTATCAA
Found at i:1547752 original size:11 final size:11
Alignment explanation
Indices: 1547736--1547760 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
1547726 AGTTAGGATG
1547736 AATTTGAAAAT
1 AATTTGAAAAT
1547747 AATTTGAAAAT
1 AATTTGAAAAT
1547758 AAT
1 AAT
1547761 AGTACTTTTG
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:0.56, C:0.00, G:0.08, T:0.36
Consensus pattern (11 bp):
AATTTGAAAAT
Found at i:1548388 original size:53 final size:53
Alignment explanation
Indices: 1548306--1548417 Score: 161
Period size: 53 Copynumber: 2.1 Consensus size: 53
1548296 ACTATTGTAC
* * * **
1548306 TTTCGGCACTATGTGTGCACCCATGGTATTCATAATGAGTTTGTGAATTACCA
1 TTTCGACACTATGTGTGCACCCATAGTATTCATAATGAATTTGCCAATTACCA
* *
1548359 TTTCGACACTATGTGTTCATCCATAGTATTCATAATGAATTTGCCAATTACCA
1 TTTCGACACTATGTGTGCACCCATAGTATTCATAATGAATTTGCCAATTACCA
1548412 TTTCGA
1 TTTCGA
1548418 AACTTAGGTG
Statistics
Matches: 52, Mismatches: 7, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
53 52 1.00
ACGTcount: A:0.27, C:0.20, G:0.16, T:0.38
Consensus pattern (53 bp):
TTTCGACACTATGTGTGCACCCATAGTATTCATAATGAATTTGCCAATTACCA
Found at i:1551229 original size:26 final size:26
Alignment explanation
Indices: 1551172--1551231 Score: 84
Period size: 26 Copynumber: 2.3 Consensus size: 26
1551162 CCAACCGGTC
* *
1551172 AACCCACTCTCCAGGCTTCCAGTAGA
1 AACCCACTCTCCAGGCTGCCAATAGA
*
1551198 AACCCACTCTCCAGGCTGCCAATTGA
1 AACCCACTCTCCAGGCTGCCAATAGA
*
1551224 AGCCCACT
1 AACCCACT
1551232 TACAGGGAGT
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
26 30 1.00
ACGTcount: A:0.27, C:0.40, G:0.15, T:0.18
Consensus pattern (26 bp):
AACCCACTCTCCAGGCTGCCAATAGA
Found at i:1555698 original size:24 final size:25
Alignment explanation
Indices: 1555671--1555735 Score: 68
Period size: 24 Copynumber: 2.7 Consensus size: 25
1555661 ATTAACGGTT
1555671 AACGGTCAACAGCGATCAAT-G-G-TC
1 AACGGTCAACAG-G-TCAATGGTGATC
*
1555695 AACGGTTAAC-GGTCAATGGTGATC
1 AACGGTCAACAGGTCAATGGTGATC
1555719 AACGGTCAACA-GTCAAT
1 AACGGTCAACAGGTCAAT
1555736 AATCAACAGC
Statistics
Matches: 35, Mismatches: 2, Indels: 8
0.78 0.04 0.18
Matches are distributed among these distances:
21 5 0.14
22 2 0.06
23 2 0.06
24 26 0.74
ACGTcount: A:0.34, C:0.22, G:0.25, T:0.20
Consensus pattern (25 bp):
AACGGTCAACAGGTCAATGGTGATC
Found at i:1555700 original size:31 final size:31
Alignment explanation
Indices: 1555655--1555728 Score: 94
Period size: 31 Copynumber: 2.4 Consensus size: 31
1555645 AGTCAACGGG
* *
1555655 TCAACGATTAACGGTTAACGGTCAACAGCGA
1 TCAACGGTCAACGGTTAACGGTCAACAGCGA
* ** *
1555686 TCAATGGTCAACGGTTAACGGTCAATGGTGA
1 TCAACGGTCAACGGTTAACGGTCAACAGCGA
1555717 TCAACGGTCAAC
1 TCAACGGTCAAC
1555729 AGTCAATAAT
Statistics
Matches: 36, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
31 36 1.00
ACGTcount: A:0.32, C:0.22, G:0.24, T:0.22
Consensus pattern (31 bp):
TCAACGGTCAACGGTTAACGGTCAACAGCGA
Found at i:1562972 original size:22 final size:24
Alignment explanation
Indices: 1562929--1562987 Score: 86
Period size: 23 Copynumber: 2.5 Consensus size: 24
1562919 TGAAGATTTA
* *
1562929 TAGAGTTTTGGTGTGAAAAATGGT
1 TAGAGTTTTGGTATGAAAAATGGG
1562953 TAGAG-TTTGGTAT-AAAAATGGG
1 TAGAGTTTTGGTATGAAAAATGGG
1562975 TAGAGTTTTGGTA
1 TAGAGTTTTGGTA
1562988 ATAACAAAAA
Statistics
Matches: 32, Mismatches: 2, Indels: 3
0.86 0.05 0.08
Matches are distributed among these distances:
22 13 0.41
23 14 0.44
24 5 0.16
ACGTcount: A:0.31, C:0.00, G:0.32, T:0.37
Consensus pattern (24 bp):
TAGAGTTTTGGTATGAAAAATGGG
Found at i:1573242 original size:23 final size:23
Alignment explanation
Indices: 1573216--1573287 Score: 101
Period size: 23 Copynumber: 3.1 Consensus size: 23
1573206 TATAAATGAT
1573216 CCGAAGTGCCACGTAGAATTGCA
1 CCGAAGTGCCACGTAGAATTGCA
*
1573239 CCGAAGTGCCACGTAGAATTGCT
1 CCGAAGTGCCACGTAGAATTGCA
* *
1573262 CTGAAGTG-CAGCGTAGAATTTCA
1 CCGAAGTGCCA-CGTAGAATTGCA
1573285 CCG
1 CCG
1573288 TAGTTCCATA
Statistics
Matches: 43, Mismatches: 5, Indels: 2
0.86 0.10 0.04
Matches are distributed among these distances:
22 2 0.05
23 41 0.95
ACGTcount: A:0.28, C:0.25, G:0.26, T:0.21
Consensus pattern (23 bp):
CCGAAGTGCCACGTAGAATTGCA
Found at i:1574618 original size:13 final size:13
Alignment explanation
Indices: 1574600--1574625 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1574590 TCTTCATGGT
1574600 GAAGAAGAAGAAA
1 GAAGAAGAAGAAA
1574613 GAAGAAGAAGAAA
1 GAAGAAGAAGAAA
1574626 AATCTGGAAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.69, C:0.00, G:0.31, T:0.00
Consensus pattern (13 bp):
GAAGAAGAAGAAA
Found at i:1579475 original size:23 final size:23
Alignment explanation
Indices: 1579447--1579530 Score: 123
Period size: 23 Copynumber: 3.7 Consensus size: 23
1579437 CTCGTATAAA
1579447 TGCACCGAAGTGCCACGTAGAAT
1 TGCACCGAAGTGCCACGTAGAAT
*
1579470 TACACCGAAGTGCCACGTAGAAT
1 TGCACCGAAGTGCCACGTAGAAT
* * *
1579493 TGTATCGAAGTGCCGCGTAGAAT
1 TGCACCGAAGTGCCACGTAGAAT
*
1579516 TGCACCGTAGTGCCA
1 TGCACCGAAGTGCCA
1579531 TATAAAATTT
Statistics
Matches: 52, Mismatches: 9, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
23 52 1.00
ACGTcount: A:0.29, C:0.25, G:0.26, T:0.20
Consensus pattern (23 bp):
TGCACCGAAGTGCCACGTAGAAT
Found at i:1580790 original size:13 final size:13
Alignment explanation
Indices: 1580772--1580797 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1580762 TCTTCACGGT
1580772 GAAGAAGAAGAAA
1 GAAGAAGAAGAAA
1580785 GAAGAAGAAGAAA
1 GAAGAAGAAGAAA
1580798 AATCTGGAAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.69, C:0.00, G:0.31, T:0.00
Consensus pattern (13 bp):
GAAGAAGAAGAAA
Found at i:1582311 original size:2 final size:2
Alignment explanation
Indices: 1582304--1582347 Score: 88
Period size: 2 Copynumber: 22.0 Consensus size: 2
1582294 ATACGGGTTA
1582304 AT AT AT AT AT AT AT 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 AT AT AT AT AT AT AT
1582346 AT
1 AT
1582348 GCGCAGTATC
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 42 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1583806 original size:21 final size:20
Alignment explanation
Indices: 1583777--1583818 Score: 50
Period size: 21 Copynumber: 2.0 Consensus size: 20
1583767 CTATTTGTAC
1583777 ATGTGTACAAGCATATGTATAT
1 ATGTGTACAAGCAT-TGT-TAT
*
1583799 ATGT-TACATGCATTGTTAT
1 ATGTGTACAAGCATTGTTAT
1583818 A
1 A
1583819 AATGAGCTAT
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
19 4 0.21
20 3 0.16
21 8 0.42
22 4 0.21
ACGTcount: A:0.33, C:0.10, G:0.17, T:0.40
Consensus pattern (20 bp):
ATGTGTACAAGCATTGTTAT
Found at i:1584134 original size:24 final size:24
Alignment explanation
Indices: 1584107--1584158 Score: 68
Period size: 24 Copynumber: 2.2 Consensus size: 24
1584097 CCTTCGAGAC
* * *
1584107 ATTTCTATGTGGCACTTTGGTGTA
1 ATTTCTACGCGGCACTTTGGTGCA
*
1584131 ATTTCTACGCGGTACTTTGGTGCA
1 ATTTCTACGCGGCACTTTGGTGCA
1584155 ATTT
1 ATTT
1584159 ATAAGAGCTG
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.17, C:0.15, G:0.23, T:0.44
Consensus pattern (24 bp):
ATTTCTACGCGGCACTTTGGTGCA
Found at i:1585112 original size:33 final size:33
Alignment explanation
Indices: 1585037--1585114 Score: 95
Period size: 33 Copynumber: 2.4 Consensus size: 33
1585027 AACTGTGACT
* **
1585037 AAATAAT-TTTGTTACAATTTTTTATTGTGAAA
1 AAATAATATTTGTCACAATTTTTTATAATGAAA
* *
1585069 AAATATTATTTGTCACAATTTTTTATAATGAGA
1 AAATAATATTTGTCACAATTTTTTATAATGAAA
*
1585102 AATTAATATTTGT
1 AAATAATATTTGT
1585115 TATAAATTGT
Statistics
Matches: 38, Mismatches: 7, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
32 6 0.16
33 32 0.84
ACGTcount: A:0.38, C:0.04, G:0.09, T:0.49
Consensus pattern (33 bp):
AAATAATATTTGTCACAATTTTTTATAATGAAA
Found at i:1585171 original size:32 final size:33
Alignment explanation
Indices: 1585058--1585171 Score: 97
Period size: 33 Copynumber: 3.5 Consensus size: 33
1585048 TTACAATTTT
* * * * * *
1585058 TTATTGTGAAAAAATATTATTTGTCACAATTTT
1 TTATTTTGAGAAAATAATATTTGTCATAAATTG
** * *
1585091 TTATAATGAGAAATTAATATTTGTTATAAATTG
1 TTATTTTGAGAAAATAATATTTGTCATAAATTG
**
1585124 TTATTTTGATTAAATAA-ATTTGTCA-AAAGTTG
1 TTATTTTGAGAAAATAATATTTGTCATAAA-TTG
1585156 TTATTTTGAGAAAATA
1 TTATTTTGAGAAAATA
1585172 TCGTGACAAA
Statistics
Matches: 63, Mismatches: 17, Indels: 3
0.76 0.20 0.04
Matches are distributed among these distances:
31 3 0.05
32 24 0.38
33 36 0.57
ACGTcount: A:0.39, C:0.03, G:0.11, T:0.46
Consensus pattern (33 bp):
TTATTTTGAGAAAATAATATTTGTCATAAATTG
Found at i:1585357 original size:198 final size:199
Alignment explanation
Indices: 1585030--1585419 Score: 548
Period size: 198 Copynumber: 2.0 Consensus size: 199
1585020 AACTTTTAAC
* * ** * *
1585030 TGTGACTAAATAATTTTGTTACAATTTTTTATTGTGAAAAAATATTATTTGTCACAATTTTTTAT
1 TGTGACTAAATAAATTTGCTACAATTGATTATTGTGAAAAAATATTATTTGACACAACTTTTTAT
* * *
1585095 AATGAGAAATTAATATTTGTTATAAATTGTTATTTTGATTAAATAAATTTGTCAAAAGTTGTTAT
66 AATGAGAAATTAATATTTGTTATAAATTGTTATTATAACTAAATAAATTTGTCAAAAGTTGTTAT
*
1585160 TTTGAGAAAATATCGTGACAAAATAAATTTAACATAA-ATTTTTATTTTGACTAAATTTAATATG
131 TTTGAGAAAATATCGTGACAAAATAAATTTAACATAATATTTTTATTTTAACTAAATTTAATATG
1585224 TTAT
196 TTAT
* *
1585228 TGTGACTAAATAAATTTGCTATAATTGATTATTGTGAAAAAATATTATTTGACATAACTTTTTAT
1 TGTGACTAAATAAATTTGCTACAATTGATTATTGTGAAAAAATATTATTTGACACAACTTTTTAT
* * ** * * *
1585293 ATTGAGAAATTAATATTTGTTATAATTTGTTATTATAACTATTTAAATTTTTCATAATTTGTTAT
66 AATGAGAAATTAATATTTGTTATAAATTGTTATTATAACTAAATAAATTTGTCAAAAGTTGTTAT
* ** * * *
1585358 TTTGATAAAATATTTTGACTAAATAAATTTGACATAATTTTTTTATTTTAACTAAATTTAAT
131 TTTGAGAAAATATCGTGACAAAATAAATTTAACATAATATTTTTATTTTAACTAAATTTAAT
1585420 TTTTTTGTCT
Statistics
Matches: 166, Mismatches: 25, Indels: 1
0.86 0.13 0.01
Matches are distributed among these distances:
198 144 0.87
199 22 0.13
ACGTcount: A:0.38, C:0.05, G:0.09, T:0.48
Consensus pattern (199 bp):
TGTGACTAAATAAATTTGCTACAATTGATTATTGTGAAAAAATATTATTTGACACAACTTTTTAT
AATGAGAAATTAATATTTGTTATAAATTGTTATTATAACTAAATAAATTTGTCAAAAGTTGTTAT
TTTGAGAAAATATCGTGACAAAATAAATTTAACATAATATTTTTATTTTAACTAAATTTAATATG
TTAT
Found at i:1585448 original size:32 final size:31
Alignment explanation
Indices: 1585412--1585489 Score: 93
Period size: 31 Copynumber: 2.5 Consensus size: 31
1585402 ATTTTAACTA
*
1585412 AATTTAATTTTTTTGTCTATAGAAATTATCAT
1 AATTT-ATTTTTTTGTCTAAAGAAATTATCAT
* * *
1585444 AATTTGTTATTTTGTCTAAATAAATTATCAT
1 AATTTATTTTTTTGTCTAAAGAAATTATCAT
*
1585475 AAATTATCTTTTTTG
1 AATTTAT-TTTTTTG
1585490 CAGGGCATAA
Statistics
Matches: 38, Mismatches: 7, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
31 27 0.71
32 11 0.29
ACGTcount: A:0.33, C:0.06, G:0.06, T:0.54
Consensus pattern (31 bp):
AATTTATTTTTTTGTCTAAAGAAATTATCAT
Found at i:1589818 original size:178 final size:178
Alignment explanation
Indices: 1589595--1590142 Score: 514
Period size: 182 Copynumber: 3.0 Consensus size: 178
1589585 AAAATAGTTA
** * * *
1589595 TGACAATATATACTATCACTATAGTTAAAATTTATAACTACAAATATAATTCGTCACAAAAACGT
1 TGACAATATATTTTATCACTATAATTAAAATATATAACTACAAATATAATTTGTCACAAAAAC-T
* * *
1589660 TAATATCATTATTT-TTGTGGCAATTTTTTTTGTAATGATTATTAACACTTATAGTTACAAAATT
65 TAATATCATTATTTGTTGTGACAATTTTTTTTATAAT-ATTATTAA-ACTTATAGTTACAAAACT
* *
1589724 TGTCACCATATGACTTT-TTTTTGCGCAAAAAAATAGAGGGAAATC-TTTT
128 TGTCACTATATGACTTTATTTTTGCGCAAAAAAATAGAGGGAAATCATTTG
* * * * *
1589773 TGACAATATATTTTATCAGTATAATTAAAATATATAACGACAAATACT-GTTTTTTACTAAAAAC
1 TGACAATATATTTTATCACTATAATTAAAATATATAACTACAAATA-TAATTTGTCAC-AAAAAC
* * * * *
1589837 TTGAATCTCATTATTTGTAGTGACAACTTTTTTTATAATAATAATTATAGCTTATAGTTACAAAA
64 TT-AATATCATTATTTGTTGTGACAATTTTTTTTATAAT-ATTATTA-AACTTATAGTTACAAAA
* * * ** * *
1589902 CATGTCACTATATGATTTTGTTTTTGTACAAAAAAATAG-GAGATAGTCATTTG
126 CTTGTCACTATATGACTTTATTTTTGCGCAAAAAAATAGAGGGA-AATCATTTG
* * * * * * *
1589955 TGACTATACATTTTGTTACTATAATTAAAATATATAATTACAAACAAAATTTGTCACAACAAATC
1 TGACAATATATTTTATCACTATAATTAAAATATATAACTACAAATATAATTTGTCACAA-AAA-C
* * * * * * *
1590020 TAAATTTCATTATTTGTTGTGACAATTTTTTCTATTATAGTTAGTAAAACTTTTAGTTACAAAAG
64 TTAATATCATTATTTGTTGTGACAATTTTTTTTATAATA-TTA-TTAAACTTATAGTTACAAAAC
* * * * *
1590085 TTGTCACTATATGCCTTTAATTTGGCGTAAAAAAATTGGAGGGAAA-CATTTG
127 TTGTCACTATATGACTTTATTTTTGCGCAAAAAAA-TAGAGGGAAATCATTTG
1590137 TGACAA
1 TGACAA
1590143 CAAATCGTAG
Statistics
Matches: 292, Mismatches: 63, Indels: 26
0.77 0.17 0.07
Matches are distributed among these distances:
178 47 0.16
179 19 0.07
180 57 0.20
181 24 0.08
182 135 0.46
183 7 0.02
184 3 0.01
ACGTcount: A:0.38, C:0.11, G:0.11, T:0.40
Consensus pattern (178 bp):
TGACAATATATTTTATCACTATAATTAAAATATATAACTACAAATATAATTTGTCACAAAAACTT
AATATCATTATTTGTTGTGACAATTTTTTTTATAATATTATTAAACTTATAGTTACAAAACTTGT
CACTATATGACTTTATTTTTGCGCAAAAAAATAGAGGGAAATCATTTG
Found at i:1591928 original size:26 final size:25
Alignment explanation
Indices: 1591896--1591955 Score: 77
Period size: 26 Copynumber: 2.4 Consensus size: 25
1591886 TAATAAACCT
1591896 AATAAAAAACA-AATAAAAAAGTAAA
1 AATAAAAAACAGAATAAAAAA-TAAA
*
1591921 AAGTAAAAAATAGAATAAAAAATAAA
1 AA-TAAAAAACAGAATAAAAAATAAA
*
1591947 CATAAAAAA
1 AATAAAAAA
1591956 GGATCTAATT
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
25 9 0.29
26 13 0.42
27 9 0.29
ACGTcount: A:0.78, C:0.03, G:0.05, T:0.13
Consensus pattern (25 bp):
AATAAAAAACAGAATAAAAAATAAA
Found at i:1591941 original size:13 final size:13
Alignment explanation
Indices: 1591908--1591955 Score: 53
Period size: 12 Copynumber: 3.6 Consensus size: 13
1591898 TAAAAAACAA
*
1591908 ATAAAAAAGTAAAA
1 ATAAAAAA-TAAAC
*
1591922 AGTAAAAAATAGA-
1 A-TAAAAAATAAAC
1591935 ATAAAAAATAAAC
1 ATAAAAAATAAAC
1591948 ATAAAAAA
1 ATAAAAAA
1591956 GGATCTAATT
Statistics
Matches: 30, Mismatches: 2, Indels: 5
0.81 0.05 0.14
Matches are distributed among these distances:
12 10 0.33
13 9 0.30
14 4 0.13
15 7 0.23
ACGTcount: A:0.77, C:0.02, G:0.06, T:0.15
Consensus pattern (13 bp):
ATAAAAAATAAAC
Found at i:1593026 original size:2 final size:2
Alignment explanation
Indices: 1592982--1593007 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
1592972 TCTTAACTAA
1592982 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
1593008 TGAAAGTGTT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1594602 original size:3 final size:3
Alignment explanation
Indices: 1594594--1594628 Score: 70
Period size: 3 Copynumber: 11.7 Consensus size: 3
1594584 TATGCATTTA
1594594 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
1594629 AATTTATTAC
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
TAT
Found at i:1602807 original size:26 final size:26
Alignment explanation
Indices: 1602770--1602820 Score: 93
Period size: 26 Copynumber: 2.0 Consensus size: 26
1602760 ATCGAAGTGC
*
1602770 TAATACATATAAGGTCATGCCCACCA
1 TAATACACATAAGGTCATGCCCACCA
1602796 TAATACACATAAGGTCATGCCCACC
1 TAATACACATAAGGTCATGCCCACC
1602821 GTATGCACTT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 24 1.00
ACGTcount: A:0.37, C:0.29, G:0.12, T:0.22
Consensus pattern (26 bp):
TAATACACATAAGGTCATGCCCACCA
Found at i:1610154 original size:13 final size:14
Alignment explanation
Indices: 1610123--1610164 Score: 50
Period size: 14 Copynumber: 3.1 Consensus size: 14
1610113 TAATCCGACA
1610123 TGTTGACTATTGAC
1 TGTTGACTATTGAC
* *
1610137 CGTTGACT-TTGAT
1 TGTTGACTATTGAC
*
1610150 TGTTGACCATTGAC
1 TGTTGACTATTGAC
1610164 T
1 T
1610165 TTTTCAAAGA
Statistics
Matches: 22, Mismatches: 5, Indels: 2
0.76 0.17 0.07
Matches are distributed among these distances:
13 10 0.45
14 12 0.55
ACGTcount: A:0.19, C:0.17, G:0.21, T:0.43
Consensus pattern (14 bp):
TGTTGACTATTGAC
Found at i:1613416 original size:27 final size:27
Alignment explanation
Indices: 1613386--1613446 Score: 86
Period size: 27 Copynumber: 2.3 Consensus size: 27
1613376 AAAATATTAT
* * *
1613386 AATTAAGTGCCCTTGCTCAGTTATCAC
1 AATTAAGTGCCCCTACGCAGTTATCAC
*
1613413 AATTAAGTGCCCCTACGCATTTATCAC
1 AATTAAGTGCCCCTACGCAGTTATCAC
1613440 AATTAAG
1 AATTAAG
1613447 CGCTTTTAAG
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
27 30 1.00
ACGTcount: A:0.31, C:0.25, G:0.13, T:0.31
Consensus pattern (27 bp):
AATTAAGTGCCCCTACGCAGTTATCAC
Found at i:1613463 original size:27 final size:27
Alignment explanation
Indices: 1613406--1613481 Score: 62
Period size: 27 Copynumber: 2.8 Consensus size: 27
1613396 CCTTGCTCAG
* * *
1613406 TTATCACAATTAAGTGCCCCTACGCAT
1 TTATCACAATTAAGCGCCCCTAAGCAA
***
1613433 TTATCACAATTAAGCGCTTTTAAGCAA
1 TTATCACAATTAAGCGCCCCTAAGCAA
* * * *
1613460 TTATTACAGTTAAACACCCCTA
1 TTATCACAATTAAGCGCCCCTA
1613482 CTTTTTTTTA
Statistics
Matches: 36, Mismatches: 13, Indels: 0
0.73 0.27 0.00
Matches are distributed among these distances:
27 36 1.00
ACGTcount: A:0.34, C:0.25, G:0.09, T:0.32
Consensus pattern (27 bp):
TTATCACAATTAAGCGCCCCTAAGCAA
Found at i:1616741 original size:2 final size:2
Alignment explanation
Indices: 1616736--1616782 Score: 71
Period size: 2 Copynumber: 24.5 Consensus size: 2
1616726 TTTACTTTAG
*
1616736 TA TA TA TA TA TA TA T- TA GA T- 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
1616776 TA TA TA T
1 TA TA TA T
1616783 GTGAATTTTC
Statistics
Matches: 41, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
1 2 0.05
2 39 0.95
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.51
Consensus pattern (2 bp):
TA
Found at i:1616850 original size:2 final size:2
Alignment explanation
Indices: 1616845--1616877 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
1616835 ATGTTTTTAT
1616845 TA TA TA 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 TA TA TA T
1616878 TATCATTTCG
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:1620245 original size:18 final size:19
Alignment explanation
Indices: 1620211--1620247 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
1620201 GAAAAAAGAG
*
1620211 AAAAAAGCAAAGTGAAAAT
1 AAAAAAACAAAGTGAAAAT
1620230 AAAAAAACAAAG-GAAAAT
1 AAAAAAACAAAGTGAAAAT
1620248 TGAAGAAAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 6 0.35
19 11 0.65
ACGTcount: A:0.73, C:0.05, G:0.14, T:0.08
Consensus pattern (19 bp):
AAAAAAACAAAGTGAAAAT
Found at i:1620430 original size:69 final size:69
Alignment explanation
Indices: 1620319--1620456 Score: 233
Period size: 69 Copynumber: 2.0 Consensus size: 69
1620309 GATTCAAACT
* *
1620319 ATGAGATTGATCAAGCACAATCATTTTCGAATCACTGAATCACTTCACTCGAAGATCATAGAGCA
1 ATGAGATTGATCAAGCACAATCATTTTCAAATCACTGAATCACTCCACTCGAAGATCATAGAGCA
1620384 TCAA
66 TCAA
*
1620388 ATGAGATTGATCAAGCACAGTCA-TTTCTAAATCACTGAATCACTCCACTCGAAGATCATAGAGC
1 ATGAGATTGATCAAGCACAATCATTTTC-AAATCACTGAATCACTCCACTCGAAGATCATAGAGC
1620452 ATCAA
65 ATCAA
1620457 GAGAGAGACA
Statistics
Matches: 65, Mismatches: 3, Indels: 2
0.93 0.04 0.03
Matches are distributed among these distances:
68 4 0.06
69 61 0.94
ACGTcount: A:0.38, C:0.22, G:0.14, T:0.25
Consensus pattern (69 bp):
ATGAGATTGATCAAGCACAATCATTTTCAAATCACTGAATCACTCCACTCGAAGATCATAGAGCA
TCAA
Found at i:1622051 original size:65 final size:65
Alignment explanation
Indices: 1621940--1622253 Score: 222
Period size: 65 Copynumber: 4.7 Consensus size: 65
1621930 CTTGAGATAG
* * *
1621940 TTTCCCTTGAAACAAAATATTGTCTCCCTTGAGACATTTTCTCTTGAAACATAAA-CACTGAAAA
1 TTTCCCTTGAAAC-AAATTTTGTCT-CCTTGAGACAGTTTCTCTTGAAACAAAAATCACTGAAAA
1622004 CA
64 CA
* * ** ***
1622006 TTTCCCTTGAAACAAATTTTGTCTCTCTTGAAACAGTTTCCCTTGAAA-AAAAATCTTTGAATTT
1 TTTCCCTTGAAACAAATTTTGTCTC-CTTGAGACAGTTTCTCTTGAAACAAAAATCACTGAAAAC
1622070 A
65 A
* * *
1622071 TTTCCCCTGAAACAAATTTTGTCTCCTTTGAGACAGTTTCTCTTGAAACACAAAATC-TTCAAAT
1 TTTCCCTTGAAACAAATTTTGTCTCC-TTGAGACAGTTTCTCTTGAAACA-AAAATCACTGAAA-
**
1622135 TTA
63 ACA
* * ** * **
1622138 TTTCCCTTAAAACAAAATTTTGTTTCCCTTGAGATTGTTT-TCATGAAACAATAGATATCTTTGA
1 TTTCCCTTGAAAC-AAATTTTGTCT-CCTTGAGACAGTTTCTCTTGAAACAA-A-A-ATCACTGA
* *
1622202 GATCA
61 AAACA
* * * * **
1622207 TTTCCCTTGAAACGAATTCTATCTCTTTCGAGACAACTTCTCTTGAA
1 TTTCCCTTGAAACAAATTTTGTCTCCTT-GAGACAGTTTCTCTTGAA
1622254 GCATCATCTG
Statistics
Matches: 199, Mismatches: 35, Indels: 25
0.77 0.14 0.10
Matches are distributed among these distances:
64 6 0.03
65 78 0.39
66 19 0.10
67 33 0.17
68 34 0.17
69 25 0.13
70 4 0.02
ACGTcount: A:0.32, C:0.21, G:0.10, T:0.38
Consensus pattern (65 bp):
TTTCCCTTGAAACAAATTTTGTCTCCTTGAGACAGTTTCTCTTGAAACAAAAATCACTGAAAACA
Found at i:1623054 original size:106 final size:105
Alignment explanation
Indices: 1622801--1623054 Score: 321
Period size: 106 Copynumber: 2.4 Consensus size: 105
1622791 CACGAAAACT
* * * *
1622801 CAAGTTCAACTTCACAAC-AAAGGGACGGCTGGTTGTCAACAAACAACTTCCCAATTTTAGAGCC
1 CAAGCTCAACTTCAC-ACGAAGGGGA-GGCTGATTGTCAACAAACAACTTCCCAATTTCAGAGCC
* * * *
1622865 AATTTCAACTTCACAGCGAAGGATATTGGACTCAAGAGAGCA
64 AAATTCAACTTCACAGCGAAGGATATTGGACCCAAGACAACA
* * * * * *
1622907 CAAGCTCAACTTTACAGCGAAGGGGCGACTGACTGTAAACAAACAACTTCCCAATTTCAGGGCCA
1 CAAGCTCAACTTCACA-CGAAGGGGAGGCTGATTGTCAACAAACAACTTCCCAATTTCAGAGCCA
*
1622972 AATTCAACTTCCCAGCGAAGGATATTGGACCCAAGACAACA
65 AATTCAACTTCACAGCGAAGGATATTGGACCCAAGACAACA
*
1623013 CAAGCTCAACTTCACGACGAAGGGGAGGTTGATTGTCAACAA
1 CAAGCTCAACTTCAC-ACGAAGGGGAGGCTGATTGTCAACAA
1623055 CATTTCCAGA
Statistics
Matches: 124, Mismatches: 21, Indels: 6
0.82 0.14 0.04
Matches are distributed among these distances:
105 1 0.01
106 117 0.94
107 6 0.05
ACGTcount: A:0.35, C:0.25, G:0.20, T:0.20
Consensus pattern (105 bp):
CAAGCTCAACTTCACACGAAGGGGAGGCTGATTGTCAACAAACAACTTCCCAATTTCAGAGCCAA
ATTCAACTTCACAGCGAAGGATATTGGACCCAAGACAACA
Found at i:1624220 original size:22 final size:22
Alignment explanation
Indices: 1624195--1624236 Score: 59
Period size: 22 Copynumber: 1.9 Consensus size: 22
1624185 GTCCCTTACA
1624195 TTTATGT-TTTAATTATTATTAT
1 TTTATGTATTTAATT-TTATTAT
*
1624217 TTTATTTATTTAATTTTATT
1 TTTATGTATTTAATTTTATT
1624237 TATACGCACA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
22 11 0.61
23 7 0.39
ACGTcount: A:0.26, C:0.00, G:0.02, T:0.71
Consensus pattern (22 bp):
TTTATGTATTTAATTTTATTAT
Found at i:1624232 original size:14 final size:15
Alignment explanation
Indices: 1624201--1624239 Score: 53
Period size: 14 Copynumber: 2.7 Consensus size: 15
1624191 TACATTTATG
* *
1624201 TTTTAATTATTATTA
1 TTTTATTTATTATAA
1624216 TTTTATTTATT-TAA
1 TTTTATTTATTATAA
1624230 TTTTATTTAT
1 TTTTATTTAT
1624240 ACGCACATTT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
14 12 0.55
15 10 0.45
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (15 bp):
TTTTATTTATTATAA
Found at i:1624345 original size:2 final size:2
Alignment explanation
Indices: 1624340--1624400 Score: 81
Period size: 2 Copynumber: 31.5 Consensus size: 2
1624330 TTTACTTTAG
* * *
1624340 TA TA TA TA TA TA T- TT TA GA T- TA CA 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
1624380 TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA T
1624401 GTTAATTTTC
Statistics
Matches: 52, Mismatches: 5, Indels: 4
0.85 0.08 0.07
Matches are distributed among these distances:
1 2 0.04
2 50 0.96
ACGTcount: A:0.46, C:0.02, G:0.02, T:0.51
Consensus pattern (2 bp):
TA
Found at i:1624658 original size:22 final size:24
Alignment explanation
Indices: 1624630--1624681 Score: 65
Period size: 22 Copynumber: 2.2 Consensus size: 24
1624620 TTTCACTTGC
1624630 TTTTATGGAC-TTTA-TTTA-TTTA
1 TTTTAT-GACTTTTATTTTATTTTA
*
1624652 TTTTATGTCTTTTATTTTATTTTA
1 TTTTATGACTTTTATTTTATTTTA
1624676 TTTTAT
1 TTTTAT
1624682 TTATTTTTCT
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
21 2 0.08
22 10 0.38
23 4 0.15
24 10 0.38
ACGTcount: A:0.19, C:0.04, G:0.06, T:0.71
Consensus pattern (24 bp):
TTTTATGACTTTTATTTTATTTTA
Found at i:1624689 original size:15 final size:15
Alignment explanation
Indices: 1624640--1624688 Score: 52
Period size: 14 Copynumber: 3.5 Consensus size: 15
1624630 TTTTATGGAC
1624640 TTTA-TTTA-TTTAT
1 TTTATTTTATTTTAT
* *
1624653 TTTA-TGTCTTTTAT
1 TTTATTTTATTTTAT
1624667 TTTATTTTATTTTA-
1 TTTATTTTATTTTAT
1624681 TTTATTTT
1 TTTATTTT
1624689 TCTTTTCTTT
Statistics
Matches: 30, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
13 6 0.20
14 17 0.57
15 7 0.23
ACGTcount: A:0.18, C:0.02, G:0.02, T:0.78
Consensus pattern (15 bp):
TTTATTTTATTTTAT
Found at i:1624694 original size:15 final size:15
Alignment explanation
Indices: 1624644--1624718 Score: 55
Period size: 15 Copynumber: 4.8 Consensus size: 15
1624634 ATGGACTTTA
1624644 TTTATTTATTTTATGTCT
1 TTTATTTA-TTT-T-TCT
*
1624662 TTTATTT-TATTTTAT
1 TTTATTTAT-TTTTCT
1624677 TTTATTTATTTTTCT
1 TTTATTTATTTTTCT
* *
1624692 TTTCTTT-TCTTTTCG
1 TTTATTTAT-TTTTCT
*
1624707 TTTCTTTATTTT
1 TTTATTTATTTT
1624719 ATTTAATTTA
Statistics
Matches: 49, Mismatches: 4, Indels: 11
0.77 0.06 0.17
Matches are distributed among these distances:
14 1 0.02
15 35 0.71
16 4 0.08
17 2 0.04
18 7 0.14
ACGTcount: A:0.12, C:0.08, G:0.03, T:0.77
Consensus pattern (15 bp):
TTTATTTATTTTTCT
Found at i:1624699 original size:10 final size:10
Alignment explanation
Indices: 1624659--1624718 Score: 52
Period size: 10 Copynumber: 6.1 Consensus size: 10
1624649 TTATTTTATG
1624659 TCTTTTATTT
1 TCTTTTATTT
*
1624669 TATTTTATTT
1 TCTTTTATTT
*
1624679 T-ATTTATTTT
1 TCTTTTA-TTT
*
1624689 TCTTTTCTTT
1 TCTTTTATTT
**
1624699 TCTTTTCGTT
1 TCTTTTATTT
1624709 TC-TTTATTT
1 TCTTTTATTT
1624718 T
1 T
1624719 ATTTAATTTA
Statistics
Matches: 41, Mismatches: 7, Indels: 5
0.77 0.13 0.09
Matches are distributed among these distances:
9 10 0.24
10 28 0.68
11 3 0.07
ACGTcount: A:0.10, C:0.10, G:0.02, T:0.78
Consensus pattern (10 bp):
TCTTTTATTT
Found at i:1624720 original size:49 final size:50
Alignment explanation
Indices: 1624662--1624779 Score: 129
Period size: 49 Copynumber: 2.4 Consensus size: 50
1624652 TTTTATGTCT
* *
1624662 TTTATTTTATTTTATTTTATTTATTTTTC-TT-TTCTTTTCTTT-TCGTTTC
1 TTTATTTTATTTTATTTTATTT-GTTATCATTATTCTTTTCTTTGTC-TTTC
* *
1624711 TTTATTTTA-TTTAATTTACTTGTTATCATTATTCTTTTCTTTGTCTTTC
1 TTTATTTTATTTTATTTTATTTGTTATCATTATTCTTTTCTTTGTCTTTC
*
1624760 TTT-TATTAGTTTTATTTTAT
1 TTTATTTTA-TTTTATTTTAT
1624780 CTTCTCTATT
Statistics
Matches: 57, Mismatches: 7, Indels: 9
0.78 0.10 0.12
Matches are distributed among these distances:
47 4 0.07
48 16 0.28
49 27 0.47
50 10 0.18
ACGTcount: A:0.14, C:0.09, G:0.03, T:0.73
Consensus pattern (50 bp):
TTTATTTTATTTTATTTTATTTGTTATCATTATTCTTTTCTTTGTCTTTC
Found at i:1624722 original size:5 final size:5
Alignment explanation
Indices: 1624640--1624688 Score: 52
Period size: 5 Copynumber: 10.6 Consensus size: 5
1624630 TTTTATGGAC
* *
1624640 TTTA- TTTA- TTTAT TTTA- TGTCT TTTAT TTTAT TTTAT TTTA- TTTAT
1 TTTAT TTTAT TTTAT TTTAT TTTAT TTTAT TTTAT TTTAT TTTAT TTTAT
1624686 TTT
1 TTT
1624689 TCTTTTCTTT
Statistics
Matches: 38, Mismatches: 4, Indels: 5
0.81 0.09 0.11
Matches are distributed among these distances:
4 14 0.37
5 24 0.63
ACGTcount: A:0.18, C:0.02, G:0.02, T:0.78
Consensus pattern (5 bp):
TTTAT
Found at i:1626500 original size:21 final size:21
Alignment explanation
Indices: 1626471--1626517 Score: 67
Period size: 21 Copynumber: 2.2 Consensus size: 21
1626461 AATATGTAAA
*
1626471 TCGCATTGCGATTTTCCAAAT
1 TCGCATTGCAATTTTCCAAAT
* *
1626492 TCGCGTTGCAATTTTCGAAAT
1 TCGCATTGCAATTTTCCAAAT
1626513 TCGCA
1 TCGCA
1626518 ATGCGAATCT
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.23, C:0.23, G:0.17, T:0.36
Consensus pattern (21 bp):
TCGCATTGCAATTTTCCAAAT
Found at i:1626556 original size:20 final size:19
Alignment explanation
Indices: 1626509--1626714 Score: 121
Period size: 20 Copynumber: 10.3 Consensus size: 19
1626499 GCAATTTTCG
*
1626509 AAATTCGCAATGCGAA-TC
1 AAATTCGCAACGCGAAGTC
* *
1626527 TATAAATCGCAACACAGAAGTC
1 -A-AATTCGCAACGC-GAAGTC
1626549 AAATTCGCAACGCGATAGTC
1 AAATTCGCAACGCGA-AGTC
* * *
1626569 AAATCCACAACGCGATAGGC
1 AAATTCGCAACGCGA-AGTC
* * *
1626589 AAATTCACAACGTGTTAGTC
1 AAATTCGCAACGCG-AAGTC
*
1626609 AAATTCGCAATGCGATAGTC
1 AAATTCGCAACGCGA-AGTC
1626629 AAATTCGCAACGCGAATTTGT-
1 AAATTCGCAACGCGAA---GTC
*
1626650 AAA-TCGCAACACAGAAGTC
1 AAATTCGCAACGC-GAAGTC
* * *
1626669 AAATTTGCAACGCAATAGCC
1 AAATTCGCAACGCGA-AGTC
* * *
1626689 AAATTCACAACACAAAAGTC
1 AAATTCGCAACGC-GAAGTC
1626709 AAATTC
1 AAATTC
1626715 TGACCTATGC
Statistics
Matches: 147, Mismatches: 26, Indels: 27
0.74 0.13 0.14
Matches are distributed among these distances:
18 2 0.01
19 8 0.05
20 121 0.82
21 12 0.08
22 4 0.03
ACGTcount: A:0.41, C:0.23, G:0.16, T:0.20
Consensus pattern (19 bp):
AAATTCGCAACGCGAAGTC
Found at i:1626657 original size:40 final size:40
Alignment explanation
Indices: 1626509--1626714 Score: 158
Period size: 40 Copynumber: 5.2 Consensus size: 40
1626499 GCAATTTTCG
*
1626509 AAATTCGCAATGCGAATCTA-T-AAATCGCAACACAGAAGTC
1 AAATTCGCAACGCG-AT-TAGTCAAATCGCAACACAGAAGTC
* * *
1626549 AAATTCGCAACGCGA-TAGTCAAATCCACAACGC-GATAGGC
1 AAATTCGCAACGCGATTAGTCAAAT-CGCAACACAGA-AGTC
* * **
1626589 AAATTCACAACGTG-TTAGTCAAATTCGCAATGC-GATAGTC
1 AAATTCGCAACGCGATTAGTCAAA-TCGCAACACAGA-AGTC
*
1626629 AAATTCGCAACGCGAATTTGT-AAATCGCAACACAGAAGTC
1 AAATTCGCAACGCG-ATTAGTCAAATCGCAACACAGAAGTC
* * * * *
1626669 AAATTTGCAACGC-AATAGCCAAATTCACAACACAAAAGTC
1 AAATTCGCAACGCGATTAGTCAAA-TCGCAACACAGAAGTC
1626709 AAATTC
1 AAATTC
1626715 TGACCTATGC
Statistics
Matches: 134, Mismatches: 21, Indels: 22
0.76 0.12 0.12
Matches are distributed among these distances:
37 2 0.01
38 4 0.03
39 10 0.07
40 108 0.81
41 6 0.04
42 4 0.03
ACGTcount: A:0.41, C:0.23, G:0.16, T:0.20
Consensus pattern (40 bp):
AAATTCGCAACGCGATTAGTCAAATCGCAACACAGAAGTC
Found at i:1626669 original size:60 final size:60
Alignment explanation
Indices: 1626509--1626699 Score: 197
Period size: 60 Copynumber: 3.2 Consensus size: 60
1626499 GCAATTTTCG
* * * *
1626509 AAATTCGCAATGCGAATCTATAAATCGCAACACAGAAGTCAAATTCGCAACGCGATAGTC
1 AAATTCACAACGCGAATATGTAAATCGCAACACAGAAGTCAAATTCGCAACGCGATAGTC
* * * * ** * *
1626569 AAATCCACAACGCG-ATAGGCAAATTCACAAC-GTGTTAGTCAAATTCGCAATGCGATAGTC
1 AAATTCACAACGCGAATATGTAAA-TCGCAACACAG-AAGTCAAATTCGCAACGCGATAGTC
* * * * *
1626629 AAATTCGCAACGCGAATTTGTAAATCGCAACACAGAAGTCAAATTTGCAACGCAATAGCC
1 AAATTCACAACGCGAATATGTAAATCGCAACACAGAAGTCAAATTCGCAACGCGATAGTC
1626689 AAATTCACAAC
1 AAATTCACAAC
1626700 ACAAAAGTCA
Statistics
Matches: 101, Mismatches: 26, Indels: 8
0.75 0.19 0.06
Matches are distributed among these distances:
59 6 0.06
60 88 0.87
61 7 0.07
ACGTcount: A:0.40, C:0.24, G:0.16, T:0.20
Consensus pattern (60 bp):
AAATTCACAACGCGAATATGTAAATCGCAACACAGAAGTCAAATTCGCAACGCGATAGTC
Found at i:1627997 original size:65 final size:65
Alignment explanation
Indices: 1627833--1628007 Score: 239
Period size: 65 Copynumber: 2.6 Consensus size: 65
1627823 TCGGGTACAC
1627833 TTTTTTTGCTTGTTTAATTGAATTT-TACATTGAAAGTTGATTTGTTTAATTGATAAGGAAATAA
1 TTTTTTTGCTTGTTTAATTG-ATTTGT--A---AAAGTTGATTTGTTTAATTGATAAGGAAATAA
1627897 GAATTA
60 GAATTA
** *
1627903 -TTTTTTGCTTGTTTAATTGATTTGTAAAAGTTG-TTTGTTTAATTTGATGTGTAAATAAGAATT
1 TTTTTTTGCTTGTTTAATTGATTTGTAAAAGTTGATTTGTTTAA-TTGATAAGGAAATAAGAATT
1627966 A
65 A
1627967 TTTTTTTGCTTGTTTAATTGATTTGTAAAAGTTGATTTGTT
1 TTTTTTTGCTTGTTTAATTGATTTGTAAAAGTTGATTTGTT
1628008 GTTTTAAATT
Statistics
Matches: 98, Mismatches: 3, Indels: 12
0.87 0.03 0.11
Matches are distributed among these distances:
63 9 0.09
64 25 0.26
65 33 0.34
66 6 0.06
67 1 0.01
68 4 0.04
69 20 0.20
ACGTcount: A:0.28, C:0.02, G:0.17, T:0.53
Consensus pattern (65 bp):
TTTTTTTGCTTGTTTAATTGATTTGTAAAAGTTGATTTGTTTAATTGATAAGGAAATAAGAATTA
Found at i:1628490 original size:12 final size:12
Alignment explanation
Indices: 1628474--1628520 Score: 58
Period size: 12 Copynumber: 3.9 Consensus size: 12
1628464 AAGGTGAAGC
*
1628474 CGATTGTGATTG
1 CGATTTTGATTG
* *
1628486 GGATTTTGATTT
1 CGATTTTGATTG
*
1628498 TGATTTTGATTG
1 CGATTTTGATTG
1628510 CGATTTTGATT
1 CGATTTTGATT
1628521 TTGATTTCCT
Statistics
Matches: 29, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
12 29 1.00
ACGTcount: A:0.17, C:0.04, G:0.26, T:0.53
Consensus pattern (12 bp):
CGATTTTGATTG
Found at i:1628496 original size:6 final size:6
Alignment explanation
Indices: 1628487--1628527 Score: 64
Period size: 6 Copynumber: 6.8 Consensus size: 6
1628477 TTGTGATTGG
**
1628487 GATTTT GATTTT GATTTT GATTGC GATTTT GATTTT GATTT
1 GATTTT GATTTT GATTTT GATTTT GATTTT GATTTT GATTT
1628528 CCTTTTGTTT
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
6 31 1.00
ACGTcount: A:0.17, C:0.02, G:0.20, T:0.61
Consensus pattern (6 bp):
GATTTT
Found at i:1628507 original size:24 final size:24
Alignment explanation
Indices: 1628475--1628527 Score: 88
Period size: 24 Copynumber: 2.2 Consensus size: 24
1628465 AGGTGAAGCC
* *
1628475 GATTGTGATTGGGATTTTGATTTT
1 GATTTTGATTGCGATTTTGATTTT
1628499 GATTTTGATTGCGATTTTGATTTT
1 GATTTTGATTGCGATTTTGATTTT
1628523 GATTT
1 GATTT
1628528 CCTTTTGTTT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.17, C:0.02, G:0.25, T:0.57
Consensus pattern (24 bp):
GATTTTGATTGCGATTTTGATTTT
Found at i:1631498 original size:14 final size:15
Alignment explanation
Indices: 1631462--1631499 Score: 51
Period size: 16 Copynumber: 2.5 Consensus size: 15
1631452 AGAAATCATT
1631462 AAAAATTATATAGAA
1 AAAAATTATATAGAA
*
1631477 ATAAAATTATGTA-AA
1 A-AAAATTATATAGAA
1631492 AAAAATTA
1 AAAAATTA
1631500 GAGATGAGGA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
14 7 0.33
15 4 0.19
16 10 0.48
ACGTcount: A:0.66, C:0.00, G:0.05, T:0.29
Consensus pattern (15 bp):
AAAAATTATATAGAA
Found at i:1631716 original size:19 final size:19
Alignment explanation
Indices: 1631657--1631749 Score: 116
Period size: 19 Copynumber: 4.8 Consensus size: 19
1631647 CTAAAACCTA
* *
1631657 TTGCGAAATT-AAATTCATT
1 TTGCGAATTTGAAATTCA-G
* *
1631676 TTGCGAATTCGAAAATCTAG
1 TTGCGAATTTGAAATTC-AG
1631696 TTGCGAATTTGAAATTCAG
1 TTGCGAATTTGAAATTCAG
*
1631715 TTGTGAATTTGAAATTCAG
1 TTGCGAATTTGAAATTCAG
1631734 TTGCGAATTTGAAATT
1 TTGCGAATTTGAAATT
1631750 TCGCGTTACA
Statistics
Matches: 64, Mismatches: 8, Indels: 4
0.84 0.11 0.05
Matches are distributed among these distances:
19 43 0.67
20 20 0.31
21 1 0.02
ACGTcount: A:0.33, C:0.10, G:0.18, T:0.39
Consensus pattern (19 bp):
TTGCGAATTTGAAATTCAG
Found at i:1631741 original size:38 final size:40
Alignment explanation
Indices: 1631636--1631749 Score: 121
Period size: 38 Copynumber: 3.0 Consensus size: 40
1631626 CAAAACATTT
* * * *
1631636 ATGTTGCGAA-ACTAAAACCTA-TTGCGAAATT-AAATTC
1 ATGTTGCGAATTCGAAAATCTAGTTGCGAATTTGAAATTC
*
1631673 ATTTTGCGAATTCGAAAATCTAGTTGCGAATTTGAAATTC
1 ATGTTGCGAATTCGAAAATCTAGTTGCGAATTTGAAATTC
* * *
1631713 A-GTTGTGAATTTGAAATTC-AGTTGCGAATTTGAAATT
1 ATGTTGCGAATTCGAAAATCTAGTTGCGAATTTGAAATT
1631750 TCGCGTTACA
Statistics
Matches: 65, Mismatches: 9, Indels: 5
0.82 0.11 0.06
Matches are distributed among these distances:
37 9 0.14
38 26 0.40
39 23 0.35
40 7 0.11
ACGTcount: A:0.35, C:0.11, G:0.18, T:0.36
Consensus pattern (40 bp):
ATGTTGCGAATTCGAAAATCTAGTTGCGAATTTGAAATTC
Found at i:1631797 original size:20 final size:20
Alignment explanation
Indices: 1631733--1631809 Score: 82
Period size: 20 Copynumber: 3.8 Consensus size: 20
1631723 TTGAAATTCA
*
1631733 GTTGCGAATTTGAAATTTCGC
1 GTTGCGAATTTG-ACTTTCGC
* * * * *
1631754 GTTACAAATTTAACTTTTGT
1 GTTGCGAATTTGACTTTCGC
*
1631774 GTTGCGAATTTGACTATCGC
1 GTTGCGAATTTGACTTTCGC
1631794 GTTGCGAATTTGACTT
1 GTTGCGAATTTGACTT
1631810 CTGTGTTGCG
Statistics
Matches: 43, Mismatches: 13, Indels: 1
0.75 0.23 0.02
Matches are distributed among these distances:
20 34 0.79
21 9 0.21
ACGTcount: A:0.23, C:0.14, G:0.21, T:0.42
Consensus pattern (20 bp):
GTTGCGAATTTGACTTTCGC
Found at i:1631817 original size:20 final size:20
Alignment explanation
Indices: 1631760--1631820 Score: 79
Period size: 20 Copynumber: 3.0 Consensus size: 20
1631750 TCGCGTTACA
* *
1631760 AATTTAACTTTTGTGTTGCG
1 AATTTGACTTCTGTGTTGCG
*
1631780 AATTTGACTATC-GCGTTGCG
1 AATTTGACT-TCTGTGTTGCG
1631800 AATTTGACTTCTGTGTTGCG
1 AATTTGACTTCTGTGTTGCG
1631820 A
1 A
1631821 TTTACAGATT
Statistics
Matches: 35, Mismatches: 4, Indels: 4
0.81 0.09 0.09
Matches are distributed among these distances:
19 2 0.06
20 32 0.91
21 1 0.03
ACGTcount: A:0.20, C:0.15, G:0.23, T:0.43
Consensus pattern (20 bp):
AATTTGACTTCTGTGTTGCG
Found at i:1631834 original size:40 final size:41
Alignment explanation
Indices: 1631733--1631845 Score: 117
Period size: 40 Copynumber: 2.8 Consensus size: 41
1631723 TTGAAATTCA
* * * *
1631733 GTTGCGAATTTGA-AATTTCGCGTTACAAATTTAACTTTTGT
1 GTTGCGAATTTGACGA-TTCGCGTTGCAAATTTGACTTCTGT
* *
1631774 GTTGCGAATTTGACTA-TCGCGTTGCGAATTTGACTTCTGT
1 GTTGCGAATTTGACGATTCGCGTTGCAAATTTGACTTCTGT
*
1631814 GTTGCG-ATTT-ACAGATTCGCGTAGCAAATTTG
1 GTTGCGAATTTGAC-GATTCGCGTTGCAAATTTG
1631846 GAAAATCGCA
Statistics
Matches: 61, Mismatches: 8, Indels: 7
0.80 0.11 0.09
Matches are distributed among these distances:
38 2 0.03
39 5 0.08
40 40 0.66
41 13 0.21
42 1 0.02
ACGTcount: A:0.23, C:0.15, G:0.22, T:0.40
Consensus pattern (41 bp):
GTTGCGAATTTGACGATTCGCGTTGCAAATTTGACTTCTGT
Found at i:1633460 original size:21 final size:19
Alignment explanation
Indices: 1633434--1633483 Score: 55
Period size: 19 Copynumber: 2.5 Consensus size: 19
1633424 TTTTTAAGTT
1633434 ATATTTTTGTCTCGTAAATAA
1 ATATTTTTGT-TCG-AAATAA
* *
1633455 ATATTTTAGTTCGAAATTA
1 ATATTTTTGTTCGAAATAA
*
1633474 AGATTTTTGT
1 ATATTTTTGT
1633484 GGGAATCAGA
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
19 13 0.52
20 3 0.12
21 9 0.36
ACGTcount: A:0.32, C:0.06, G:0.12, T:0.50
Consensus pattern (19 bp):
ATATTTTTGTTCGAAATAA
Found at i:1634918 original size:16 final size:16
Alignment explanation
Indices: 1634897--1634927 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
1634887 AAAGGATTGA
1634897 TTATGGAAATGAATAT
1 TTATGGAAATGAATAT
*
1634913 TTATGGAATTGAATA
1 TTATGGAAATGAATA
1634928 GCAATTTTGG
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:0.42, C:0.00, G:0.19, T:0.39
Consensus pattern (16 bp):
TTATGGAAATGAATAT
Found at i:1641109 original size:21 final size:20
Alignment explanation
Indices: 1641070--1641159 Score: 65
Period size: 21 Copynumber: 4.2 Consensus size: 20
1641060 GTCGAGGGTT
*
1641070 TTATGTGGTCCTTTAGGACAA
1 TTATGTGGT-CTTTGGGACAA
1641091 TTATGTGGTCTTTCGGGACAA
1 TTATGTGGTCTTT-GGGACAA
** *
1641112 AAATGTGGCACTTTGGTG-CAA
1 TTATGTGG-TCTTTGG-GACAA
*
1641133 TCCTATGTGGTCATTCGGGACAA
1 T--TATGTGGTC-TTTGGGACAA
1641156 TTAT
1 TTAT
1641160 ATGGCAATTT
Statistics
Matches: 54, Mismatches: 8, Indels: 14
0.71 0.11 0.18
Matches are distributed among these distances:
20 4 0.07
21 29 0.54
22 7 0.13
23 14 0.26
ACGTcount: A:0.23, C:0.16, G:0.26, T:0.36
Consensus pattern (20 bp):
TTATGTGGTCTTTGGGACAA
Found at i:1641141 original size:44 final size:44
Alignment explanation
Indices: 1641092--1641176 Score: 125
Period size: 44 Copynumber: 1.9 Consensus size: 44
1641082 TTAGGACAAT
* * *
1641092 TATGTGGTCTTTCGGGACAAAAATGTGGCACTTTGGTGCAATCC
1 TATGTGGTCATTCGGGACAAAAATATGGCAATTTGGTGCAATCC
**
1641136 TATGTGGTCATTCGGGACAATTATATGGCAATTTGGTGCAA
1 TATGTGGTCATTCGGGACAAAAATATGGCAATTTGGTGCAA
1641177 ATTACAAGCT
Statistics
Matches: 36, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
44 36 1.00
ACGTcount: A:0.25, C:0.15, G:0.27, T:0.33
Consensus pattern (44 bp):
TATGTGGTCATTCGGGACAAAAATATGGCAATTTGGTGCAATCC
Found at i:1644598 original size:20 final size:20
Alignment explanation
Indices: 1644575--1644632 Score: 64
Period size: 20 Copynumber: 2.9 Consensus size: 20
1644565 TTATGCAAAG
*
1644575 TTTCAAAAAGGATGATCCCT
1 TTTCAAAAGGGATGATCCCT
* *
1644595 TTTC-CAAGGGATTGATCCTT
1 TTTCAAAAGGGA-TGATCCCT
1644615 TTTCAAAAGGGATCGATC
1 TTTCAAAAGGGAT-GATC
1644633 ATTTTTCTTG
Statistics
Matches: 31, Mismatches: 4, Indels: 5
0.77 0.10 0.12
Matches are distributed among these distances:
19 5 0.16
20 16 0.52
21 10 0.32
ACGTcount: A:0.29, C:0.19, G:0.19, T:0.33
Consensus pattern (20 bp):
TTTCAAAAGGGATGATCCCT
Found at i:1644626 original size:21 final size:21
Alignment explanation
Indices: 1644575--1644639 Score: 71
Period size: 21 Copynumber: 3.2 Consensus size: 21
1644565 TTATGCAAAG
* *
1644575 TTTCAAAAAGGA-TGATCCCT
1 TTTCAAAAGGGATTGATCCTT
*
1644595 TTTC-CAAGGGATTGATCCTT
1 TTTCAAAAGGGATTGATCCTT
* *
1644615 TTTCAAAAGGGATCGATCATT
1 TTTCAAAAGGGATTGATCCTT
1644636 TTTC
1 TTTC
1644640 TTGAAAATGT
Statistics
Matches: 37, Mismatches: 6, Indels: 3
0.80 0.13 0.07
Matches are distributed among these distances:
19 5 0.14
20 15 0.41
21 17 0.46
ACGTcount: A:0.28, C:0.18, G:0.17, T:0.37
Consensus pattern (21 bp):
TTTCAAAAGGGATTGATCCTT
Found at i:1654888 original size:5 final size:5
Alignment explanation
Indices: 1654880--1654914 Score: 70
Period size: 5 Copynumber: 7.0 Consensus size: 5
1654870 CTCGTCTCAT
1654880 CTCGG CTCGG CTCGG CTCGG CTCGG CTCGG CTCGG
1 CTCGG CTCGG CTCGG CTCGG CTCGG CTCGG CTCGG
1654915 TTCGTGGTCG
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 30 1.00
ACGTcount: A:0.00, C:0.40, G:0.40, T:0.20
Consensus pattern (5 bp):
CTCGG
Found at i:1655018 original size:6 final size:6
Alignment explanation
Indices: 1654920--1655014 Score: 145
Period size: 6 Copynumber: 15.8 Consensus size: 6
1654910 CTCGGTTCGT
*
1654920 GGTCGA GGTCGA GGTCGA GGTCGA GGTCGA GGTCGA GGTCGT GGTCGA
1 GGTCGA GGTCGA GGTCGA GGTCGA GGTCGA GGTCGA GGTCGA GGTCGA
* * * *
1654968 GGTCGA GGTCGA GGTCGA GGTCGT GGTCGT GGTCGT GGTCGT GGTCG
1 GGTCGA GGTCGA GGTCGA GGTCGA GGTCGA GGTCGA GGTCGA GGTCG
1655015 TGGTAATACG
Statistics
Matches: 86, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
6 86 1.00
ACGTcount: A:0.11, C:0.17, G:0.51, T:0.22
Consensus pattern (6 bp):
GGTCGA
Found at i:1660865 original size:5 final size:5
Alignment explanation
Indices: 1660846--1660889 Score: 61
Period size: 5 Copynumber: 8.8 Consensus size: 5
1660836 GTCTGTCTGT
* * *
1660846 CTCGG CTCGT CTCGG CTCGG CACGG CACGG CTCGG CTCGG CTCG
1 CTCGG CTCGG CTCGG CTCGG CTCGG CTCGG CTCGG CTCGG CTCG
1660890 TGGTCGTGGT
Statistics
Matches: 35, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
5 35 1.00
ACGTcount: A:0.05, C:0.41, G:0.36, T:0.18
Consensus pattern (5 bp):
CTCGG
Found at i:1660898 original size:6 final size:6
Alignment explanation
Indices: 1660887--1660971 Score: 134
Period size: 6 Copynumber: 14.2 Consensus size: 6
1660877 TCGGCTCGGC
* *
1660887 TCGTGG TCGTGG TTGTGG TCATGG TCGTGG TCGTGG TCGTGG TCGTGG
1 TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG
* *
1660935 TCGAGG TCGAGG TCGTGG TCGTGG TCGTGG TCGTGG T
1 TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG T
1660972 AATACGTGTC
Statistics
Matches: 73, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
6 73 1.00
ACGTcount: A:0.04, C:0.15, G:0.48, T:0.33
Consensus pattern (6 bp):
TCGTGG
Found at i:1662644 original size:8 final size:8
Alignment explanation
Indices: 1662611--1662684 Score: 53
Period size: 8 Copynumber: 9.1 Consensus size: 8
1662601 GGGCCTACAA
1662611 AAAATAATT
1 AAAATAA-T
*
1662620 ATAATATAT
1 AAAATA-AT
*
1662629 AAATTAAT
1 AAAATAAT
1662637 AAAATAAT
1 AAAATAAT
1662645 AATAATAAT
1 AA-AATAAT
*
1662654 ATAA-AA-
1 AAAATAAT
*
1662660 ACAATAAT
1 AAAATAAT
*
1662668 AATATAAT
1 AAAATAAT
*
1662676 AATATAAT
1 AAAATAAT
1662684 A
1 A
1662685 TAATGTTTTT
Statistics
Matches: 53, Mismatches: 8, Indels: 9
0.76 0.11 0.13
Matches are distributed among these distances:
6 3 0.06
7 4 0.08
8 28 0.53
9 17 0.32
10 1 0.02
ACGTcount: A:0.66, C:0.01, G:0.00, T:0.32
Consensus pattern (8 bp):
AAAATAAT
Found at i:1662647 original size:3 final size:3
Alignment explanation
Indices: 1662613--1662688 Score: 65
Period size: 3 Copynumber: 27.0 Consensus size: 3
1662603 GCCTACAAAA
* *
1662613 AAT AAT TAT AAT ATAT AA- ATT AAT AA- AAT AAT AAT AAT AAT -AT
1 AAT AAT AAT AAT A-AT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
* *
1662656 AAA AAC AAT AAT AAT -AT AAT AAT -AT AAT -AT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1662689 GTTTTTGTAG
Statistics
Matches: 59, Mismatches: 7, Indels: 14
0.74 0.09 0.17
Matches are distributed among these distances:
2 11 0.19
3 45 0.76
4 3 0.05
ACGTcount: A:0.64, C:0.01, G:0.00, T:0.34
Consensus pattern (3 bp):
AAT
Found at i:1662649 original size:11 final size:11
Alignment explanation
Indices: 1662633--1662688 Score: 53
Period size: 11 Copynumber: 5.1 Consensus size: 11
1662623 ATATATAAAT
1662633 TAATAAAATAA
1 TAATAAAATAA
1662644 TAATAATAAT-A
1 TAATAA-AATAA
*
1662655 TAAAAACAATAA
1 TAATAA-AATAA
*
1662667 TAATATAATAA
1 TAATAAAATAA
*
1662678 T-ATAATATAA
1 TAATAAAATAA
1662688 T
1 T
1662689 GTTTTTGTAG
Statistics
Matches: 37, Mismatches: 6, Indels: 5
0.77 0.12 0.10
Matches are distributed among these distances:
10 8 0.22
11 21 0.57
12 8 0.22
ACGTcount: A:0.66, C:0.02, G:0.00, T:0.32
Consensus pattern (11 bp):
TAATAAAATAA
Found at i:1662677 original size:20 final size:20
Alignment explanation
Indices: 1662633--1662677 Score: 58
Period size: 20 Copynumber: 2.3 Consensus size: 20
1662623 ATATATAAAT
*
1662633 TAAT-AAAATAATAATAATA
1 TAATAAAAACAATAATAATA
1662652 -ATATAAAAACAATAATAATA
1 TA-ATAAAAACAATAATAATA
1662672 TAATAA
1 TAATAA
1662678 TATAATATAA
Statistics
Matches: 22, Mismatches: 1, Indels: 5
0.79 0.04 0.18
Matches are distributed among these distances:
18 1 0.05
19 2 0.09
20 18 0.82
21 1 0.05
ACGTcount: A:0.69, C:0.02, G:0.00, T:0.29
Consensus pattern (20 bp):
TAATAAAAACAATAATAATA
Found at i:1663876 original size:120 final size:121
Alignment explanation
Indices: 1663501--1663957 Score: 659
Period size: 121 Copynumber: 3.8 Consensus size: 121
1663491 GTTAAGGACG
* * *
1663501 ATATACTTCGTCGTGAAGCTG-AATCCTGGATGGCTCATTCGTTGTGAAGTTAAGCTTTGAATTG
1 ATATCCTTCGTCGTGAAGTTGAAATCGTGGATGGCTCATTCGTTGTGAAGTTAAGCTTTGAATTG
* * * *
1663565 AATATCCTTCGTCGTGAAGTTGAAATCCAAGGGTTGCATTACTTCTTGTGGGCACA
66 GATATCTTTCGTCGTGAAATTGAAATCCAAGGGTTGCATTGCTTCTTGTGGGCACA
* * * * * *
1663621 ATATCCTTTGTCGTGAAATTGAAATCGTGGTTGTCTCATTCTTTGTGAAGTTAAGTTTTGAATTG
1 ATATCCTTCGTCGTGAAGTTGAAATCGTGGATGGCTCATTCGTTGTGAAGTTAAGCTTTGAATTG
* *
1663686 GATATTCTTT-GTCGTGAAATTGAAATCCAAGGGTTACATTGCTGCTTGTGGGCACA
66 GATA-TCTTTCGTCGTGAAATTGAAATCCAAGGGTTGCATTGCTTCTTGTGGGCACA
* * * * * *
1663742 ATATCCTTCATCGTGAAGTTAAAATCGTAGATGGCTCCTTCATTGTGAAGTTGAGCTTTGAATTG
1 ATATCCTTCGTCGTGAAGTTGAAATCGTGGATGGCTCATTCGTTGTGAAGTTAAGCTTTGAATTG
* *
1663807 GATATCTTTCGTCGTGAAGTT-AAATCCAAGGGTTGCATTGCTTCTTGTGGGCACG
66 GATATCTTTCGTCGTGAAATTGAAATCCAAGGGTTGCATTGCTTCTTGTGGGCACA
*
1663862 ATATCCTTCGTCGTGAAGTTGAAATCGTGGATGGCTCATTCGTTGTGAAGTTGAGCTTTGAATTG
1 ATATCCTTCGTCGTGAAGTTGAAATCGTGGATGGCTCATTCGTTGTGAAGTTAAGCTTTGAATTG
*
1663927 GATATCTTTCGTCGTGAAATTAAAATCCAAG
66 GATATCTTTCGTCGTGAAATTGAAATCCAAG
1663958 CTTGTGTAAA
Statistics
Matches: 297, Mismatches: 36, Indels: 7
0.87 0.11 0.02
Matches are distributed among these distances:
120 133 0.45
121 160 0.54
122 4 0.01
ACGTcount: A:0.24, C:0.16, G:0.24, T:0.36
Consensus pattern (121 bp):
ATATCCTTCGTCGTGAAGTTGAAATCGTGGATGGCTCATTCGTTGTGAAGTTAAGCTTTGAATTG
GATATCTTTCGTCGTGAAATTGAAATCCAAGGGTTGCATTGCTTCTTGTGGGCACA
Found at i:1664122 original size:127 final size:128
Alignment explanation
Indices: 1663980--1664336 Score: 592
Period size: 127 Copynumber: 2.8 Consensus size: 128
1663970 GCATTGTTTC
* *
1663980 GAGTCCAATATCCTTCACTGTGAAGTTGATATTGACTCTGAATGAAACTGGAAAGTT-TTTGTTG
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGACTCTGAATGAAACTGGAAAGTTGTTTGTTG
*
1664044 AGTCCAATATCCTTCACTGTGAAGTTGAAATTGACTCTGAATGAAACTAGAAAGTTGTTTGTT
66 AGTCCAATATCCTTCGCTGTGAAGTTGAAATTGACTCTGAATGAAACTAGAAAGTTGTTTGTT
1664107 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGACTCTGAATGAAACTGGAAAGTTGTTTGTTG
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGACTCTGAATGAAACTGGAAAGTTGTTTGTTG
* * * * *
1664172 AGTCCAATATCCTTCGTTGTGATGTTAAAATTGACTCTGCATGAAACTTGAAAGTTGTTTGTT
66 AGTCCAATATCCTTCGCTGTGAAGTTGAAATTGACTCTGAATGAAACTAGAAAGTTGTTTGTT
** *
1664235 GAGTTTAATATCCTTCGCTGTG-AGTTGAAATTGACTTTGAATGAAACTGGAAAGTTGTTTGTTG
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGACTCTGAATGAAACTGGAAAGTTGTTTGTTG
*
1664299 AGTCCAATATCCTTCGCTATGAAGTTGAAATTGACTCT
66 AGTCCAATATCCTTCGCTGTGAAGTTGAAATTGACTCT
1664337 AAAAGCTGCA
Statistics
Matches: 214, Mismatches: 15, Indels: 2
0.93 0.06 0.01
Matches are distributed among these distances:
127 130 0.61
128 84 0.39
ACGTcount: A:0.28, C:0.14, G:0.21, T:0.36
Consensus pattern (128 bp):
GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGACTCTGAATGAAACTGGAAAGTTGTTTGTTG
AGTCCAATATCCTTCGCTGTGAAGTTGAAATTGACTCTGAATGAAACTAGAAAGTTGTTTGTT
Found at i:1664134 original size:64 final size:64
Alignment explanation
Indices: 1663980--1664336 Score: 583
Period size: 64 Copynumber: 5.6 Consensus size: 64
1663970 GCATTGTTTC
* *
1663980 GAGTCCAATATCCTTCACTGTGAAGTTGATATTGACTCTGAATGAAACTGGAAAGTT-TTTGTT
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGACTCTGAATGAAACTGGAAAGTTGTTTGTT
* *
1664043 GAGTCCAATATCCTTCACTGTGAAGTTGAAATTGACTCTGAATGAAACTAGAAAGTTGTTTGTT
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGACTCTGAATGAAACTGGAAAGTTGTTTGTT
1664107 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGACTCTGAATGAAACTGGAAAGTTGTTTGTT
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGACTCTGAATGAAACTGGAAAGTTGTTTGTT
* * * * *
1664171 GAGTCCAATATCCTTCGTTGTGATGTTAAAATTGACTCTGCATGAAACTTGAAAGTTGTTTGTT
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGACTCTGAATGAAACTGGAAAGTTGTTTGTT
** *
1664235 GAGTTTAATATCCTTCGCTGTG-AGTTGAAATTGACTTTGAATGAAACTGGAAAGTTGTTTGTT
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGACTCTGAATGAAACTGGAAAGTTGTTTGTT
*
1664298 GAGTCCAATATCCTTCGCTATGAAGTTGAAATTGACTCT
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGACTCT
1664337 AAAAGCTGCA
Statistics
Matches: 271, Mismatches: 21, Indels: 3
0.92 0.07 0.01
Matches are distributed among these distances:
63 110 0.41
64 161 0.59
ACGTcount: A:0.28, C:0.14, G:0.21, T:0.36
Consensus pattern (64 bp):
GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGACTCTGAATGAAACTGGAAAGTTGTTTGTT
Found at i:1664209 original size:191 final size:191
Alignment explanation
Indices: 1663980--1664336 Score: 581
Period size: 191 Copynumber: 1.9 Consensus size: 191
1663970 GCATTGTTTC
* *
1663980 GAGTCCAATATCCTTCACTGTGAAGTTGATATTGACTCTGAATGAAACTGGAAAGTT-TTTGTTG
1 GAGTCCAATATCCTTCACTGTGAAGTTAAAATTGACTCTGAATGAAACTGGAAAGTTGTTTGTTG
1664044 AGTCCAATATCCTTCACTGTGAAGTTGAAATTGACTCTGAATGAAACTAGAAAGTTGTTTGTTGA
66 AGTCCAATATCCTTCACTGTG-AGTTGAAATTGACTCTGAATGAAACTAGAAAGTTGTTTGTTGA
*
1664109 GTCCAATATCCTTCGCTGTGAAGTTGAAATTGACTCTGAATGAAACTGGAAAGTTGTTTGTT
130 GTCCAATATCCTTCGCTATGAAGTTGAAATTGACTCTGAATGAAACTGGAAAGTTGTTTGTT
** * * *
1664171 GAGTCCAATATCCTTCGTTGTGATGTTAAAATTGACTCTGCATGAAACTTGAAAGTTGTTTGTTG
1 GAGTCCAATATCCTTCACTGTGAAGTTAAAATTGACTCTGAATGAAACTGGAAAGTTGTTTGTTG
** * * *
1664236 AGTTTAATATCCTTCGCTGTGAGTTGAAATTGACTTTGAATGAAACTGGAAAGTTGTTTGTTGAG
66 AGTCCAATATCCTTCACTGTGAGTTGAAATTGACTCTGAATGAAACTAGAAAGTTGTTTGTTGAG
1664301 TCCAATATCCTTCGCTATGAAGTTGAAATTGACTCT
131 TCCAATATCCTTCGCTATGAAGTTGAAATTGACTCT
1664337 AAAAGCTGCA
Statistics
Matches: 152, Mismatches: 13, Indels: 2
0.91 0.08 0.01
Matches are distributed among these distances:
191 127 0.84
192 25 0.16
ACGTcount: A:0.28, C:0.14, G:0.21, T:0.36
Consensus pattern (191 bp):
GAGTCCAATATCCTTCACTGTGAAGTTAAAATTGACTCTGAATGAAACTGGAAAGTTGTTTGTTG
AGTCCAATATCCTTCACTGTGAGTTGAAATTGACTCTGAATGAAACTAGAAAGTTGTTTGTTGAG
TCCAATATCCTTCGCTATGAAGTTGAAATTGACTCTGAATGAAACTGGAAAGTTGTTTGTT
Found at i:1667112 original size:21 final size:22
Alignment explanation
Indices: 1667074--1667115 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 22
1667064 GATGTAAATG
* *
1667074 ATAAAAATGAAAATGAAAGAGA
1 ATAAAAACGAAAAGGAAAGAGA
1667096 ATAAAAACG-AAAGGAAAGAG
1 ATAAAAACGAAAAGGAAAGAG
1667116 TTAATGAGGT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 10 0.56
22 8 0.44
ACGTcount: A:0.67, C:0.02, G:0.21, T:0.10
Consensus pattern (22 bp):
ATAAAAACGAAAAGGAAAGAGA
Found at i:1669624 original size:24 final size:24
Alignment explanation
Indices: 1669583--1669676 Score: 75
Period size: 24 Copynumber: 4.0 Consensus size: 24
1669573 AAACGGAGAT
*
1669583 ATCAGAAAT-ATAAAAGAATTCAG
1 ATCAGAAATCATAACAGAATTCAG
* * *
1669606 ATCAGATATCATAACAGAATCCAT
1 ATCAGAAATCATAACAGAATTCAG
* * *
1669630 ATCAGAAATTAGAACAAAATTCAG
1 ATCAGAAATCATAACAGAATTCAG
* * *
1669654 GTCATG-TATCATAACATAATTCA
1 ATCA-GAAATCATAACAGAATTCA
1669677 AGTCGGAAAT
Statistics
Matches: 54, Mismatches: 15, Indels: 3
0.75 0.21 0.04
Matches are distributed among these distances:
23 8 0.15
24 45 0.83
25 1 0.02
ACGTcount: A:0.49, C:0.15, G:0.11, T:0.26
Consensus pattern (24 bp):
ATCAGAAATCATAACAGAATTCAG
Found at i:1673308 original size:3 final size:3
Alignment explanation
Indices: 1673264--1673354 Score: 65
Period size: 3 Copynumber: 33.0 Consensus size: 3
1673254 GCCTGTAAAA
* * *
1673264 AAT AAT TAT AAT ATAT AA- ATT AAT AA- AAT AA- AAT AGT AAT AAT
1 AAT AAT AAT AAT A-AT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
* *
1673307 AAT -AT AAT AAC AAC AAT AAT AAT -AT AAT -AT AAT -AT AAT -AT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1673350 -AT AAT
1 AAT AAT
1673355 GTTTTTGTAG
Statistics
Matches: 70, Mismatches: 8, Indels: 20
0.71 0.08 0.20
Matches are distributed among these distances:
2 17 0.24
3 50 0.71
4 3 0.04
ACGTcount: A:0.63, C:0.02, G:0.01, T:0.34
Consensus pattern (3 bp):
AAT
Found at i:1673354 original size:5 final size:5
Alignment explanation
Indices: 1673265--1673354 Score: 73
Period size: 5 Copynumber: 18.0 Consensus size: 5
1673255 CCTGTAAAAA
* *
1673265 ATAATT ATAAT AT-AT A-AAT -TAAT AAAAT AAAAT AGTAAT AATAAT
1 ATAA-T ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT A-TAAT -ATAAT
*
1673310 ATAAT A-ACA- ACAAT AATAAT ATAAT ATAAT ATAAT ATAAT ATAAT
1 ATAAT ATA-AT ATAAT -ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT
1673355 GTTTTTGTAG
Statistics
Matches: 72, Mismatches: 3, Indels: 19
0.77 0.03 0.20
Matches are distributed among these distances:
4 11 0.15
5 45 0.62
6 15 0.21
7 1 0.01
ACGTcount: A:0.62, C:0.02, G:0.01, T:0.34
Consensus pattern (5 bp):
ATAAT
Found at i:1682150 original size:24 final size:24
Alignment explanation
Indices: 1682118--1682186 Score: 68
Period size: 24 Copynumber: 2.9 Consensus size: 24
1682108 ATAGTTTATC
*
1682118 TGATTTTTGACCTGGATTCTGATA
1 TGATATTTGACCTGGATTCTGATA
* *
1682142 TGATATTTGACCTGAAATT-TTATA
1 TGATATTTGACCTG-GATTCTGATA
* * *
1682166 TGATACTTGACATGGACTCTG
1 TGATATTTGACCTGGATTCTG
1682187 TTTTGTACTT
Statistics
Matches: 35, Mismatches: 8, Indels: 4
0.74 0.17 0.09
Matches are distributed among these distances:
23 2 0.06
24 30 0.86
25 3 0.09
ACGTcount: A:0.26, C:0.13, G:0.19, T:0.42
Consensus pattern (24 bp):
TGATATTTGACCTGGATTCTGATA
Found at i:1686819 original size:78 final size:79
Alignment explanation
Indices: 1686728--1686881 Score: 210
Period size: 78 Copynumber: 2.0 Consensus size: 79
1686718 ATTTCGAATA
*
1686728 AAAATCTTATTTAATTAATTC-AAATTAAATAT-ACATTAAAAGACTTATAAT-ATGAATTACAA
1 AAAATCTTATTTAATT-ATTCTAAATTAAATATCA-ATTAAAAGACTTATAATCA-AAATTA-AA
1686790 -TC-TTTAATGTTTATTT
62 TTCTTTTAATGTTTATTT
* *
1686806 AAAATCTTATTTAATTATTCTGAATTAAATATCAATTAAAAGAGTTATAATCAAAATTAAATTCT
1 AAAATCTTATTTAATTATTCTAAATTAAATATCAATTAAAAGACTTATAATCAAAATTAAATTCT
1686871 TTTAATGTTTA
66 TTTAATGTTTA
1686882 CTTACTATAT
Statistics
Matches: 68, Mismatches: 3, Indels: 9
0.85 0.04 0.11
Matches are distributed among these distances:
77 6 0.09
78 49 0.72
79 13 0.19
ACGTcount: A:0.45, C:0.07, G:0.05, T:0.44
Consensus pattern (79 bp):
AAAATCTTATTTAATTATTCTAAATTAAATATCAATTAAAAGACTTATAATCAAAATTAAATTCT
TTTAATGTTTATTT
Found at i:1688440 original size:63 final size:61
Alignment explanation
Indices: 1688373--1688523 Score: 189
Period size: 59 Copynumber: 2.4 Consensus size: 61
1688363 TTATTTTATT
* *
1688373 ATTATTTTATTTATGAATTAGTTATTTAATTTAATTAGAACTCTTTGTAGGATTTTTAGTTTG
1 ATTATTTTATTTA-GAATTA-TTATTTAATTTAATTAGAACTCTTAGTAGGATTTTTAGTTGG
* *
1688436 ATTATTTTATTTAGAA--ATTATTTATTTTATTTAGAACTCTTAGTAGGATTTTTAGTTGG
1 ATTATTTTATTTAGAATTATTATTTAATTTAATTAGAACTCTTAGTAGGATTTTTAGTTGG
* *
1688495 ATAATTTTATTCAGGAATTAATTACTTTA
1 ATTATTTTATTTA-GAATT-ATTA-TTTA
1688524 TGAGAAATGT
Statistics
Matches: 77, Mismatches: 6, Indels: 9
0.84 0.07 0.10
Matches are distributed among these distances:
59 49 0.64
60 4 0.05
62 3 0.04
63 17 0.22
64 4 0.05
ACGTcount: A:0.30, C:0.04, G:0.12, T:0.54
Consensus pattern (61 bp):
ATTATTTTATTTAGAATTATTATTTAATTTAATTAGAACTCTTAGTAGGATTTTTAGTTGG
Found at i:1690362 original size:17 final size:17
Alignment explanation
Indices: 1690340--1690381 Score: 66
Period size: 17 Copynumber: 2.5 Consensus size: 17
1690330 CTCAGCCTGG
1690340 AATTTTAAGTTAGGATA
1 AATTTTAAGTTAGGATA
* *
1690357 AATTTTATGTTAGGATG
1 AATTTTAAGTTAGGATA
1690374 AATTTTAA
1 AATTTTAA
1690382 ATCACTTTTG
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 22 1.00
ACGTcount: A:0.38, C:0.00, G:0.17, T:0.45
Consensus pattern (17 bp):
AATTTTAAGTTAGGATA
Found at i:1693188 original size:15 final size:15
Alignment explanation
Indices: 1693168--1693197 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
1693158 ATAAATACTG
*
1693168 GTAAAACTAAACTAA
1 GTAAAAATAAACTAA
1693183 GTAAAAATAAACTAA
1 GTAAAAATAAACTAA
1693198 AGTAGTTGTA
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:0.63, C:0.10, G:0.07, T:0.20
Consensus pattern (15 bp):
GTAAAAATAAACTAA
Found at i:1694020 original size:17 final size:17
Alignment explanation
Indices: 1693998--1694052 Score: 56
Period size: 17 Copynumber: 3.2 Consensus size: 17
1693988 AATAACTATA
*
1693998 AAACATATGATAATTGT
1 AAACATCTGATAATTGT
* **
1694015 AAACATCTTATAATTAA
1 AAACATCTGATAATTGT
*
1694032 AAATCATCTGATAACTGT
1 AAA-CATCTGATAATTGT
1694050 AAA
1 AAA
1694053 TATTTAGAAT
Statistics
Matches: 29, Mismatches: 8, Indels: 1
0.76 0.21 0.03
Matches are distributed among these distances:
17 16 0.55
18 13 0.45
ACGTcount: A:0.49, C:0.11, G:0.07, T:0.33
Consensus pattern (17 bp):
AAACATCTGATAATTGT
Found at i:1694053 original size:18 final size:18
Alignment explanation
Indices: 1693989--1694053 Score: 51
Period size: 18 Copynumber: 3.7 Consensus size: 18
1693979 TCTACGTCTA
* *
1693989 ATAACTATAAAACATATG
1 ATAACTATAAATCATCTG
* * *
1694007 ATAATTGTAAA-CATCTT
1 ATAACTATAAATCATCTG
* *
1694024 ATAATTAAAAATCATCTG
1 ATAACTATAAATCATCTG
*
1694042 ATAACTGTAAAT
1 ATAACTATAAAT
1694054 ATTTAGAATT
Statistics
Matches: 36, Mismatches: 10, Indels: 2
0.75 0.21 0.04
Matches are distributed among these distances:
17 13 0.36
18 23 0.64
ACGTcount: A:0.49, C:0.11, G:0.06, T:0.34
Consensus pattern (18 bp):
ATAACTATAAATCATCTG
Done.