Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009056.1 Hibiscus syriacus cultivar Beakdansim tig00112471_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: 907955
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 2 of 3
Found at i:340115 original size:20 final size:20
Alignment explanation
Indices: 340090--340221 Score: 179
Period size: 20 Copynumber: 6.8 Consensus size: 20
340080 CTCATTTTCT
340090 GAATCGCGTTGCGATTCTTG
1 GAATCGCGTTGCGATTCTTG
340110 GAATCGCGTTGCGATTCTTG
1 GAATCGCGTTGCGATTCTTG
340130 GAATCGCGTTGCGATTTTCTT-
1 GAATCGCGTTGCGA--TTCTTG
340151 -AATCGCGTTGCGATTCTTG
1 GAATCGCGTTGCGATTCTTG
340170 GAAT--CGTTGCGATT-TT-
1 GAATCGCGTTGCGATTCTTG
340186 -AATCGCGTTGCGATTCTTG
1 GAATCGCGTTGCGATTCTTG
340205 GAAGATCGCGTTGCGAT
1 G-A-ATCGCGTTGCGAT
340222 CTTCTTTTCA
Statistics
Matches: 101, Mismatches: 0, Indels: 20
0.83 0.00 0.17
Matches are distributed among these distances:
15 3 0.03
17 12 0.12
18 17 0.17
20 50 0.50
21 1 0.01
22 18 0.18
ACGTcount: A:0.17, C:0.19, G:0.28, T:0.36
Consensus pattern (20 bp):
GAATCGCGTTGCGATTCTTG
Found at i:340789 original size:35 final size:35
Alignment explanation
Indices: 340743--340809 Score: 134
Period size: 35 Copynumber: 1.9 Consensus size: 35
340733 GAATTTGTTG
340743 GATCTCTTTTTGATTATTCTCAGGAGCCTTTTGCT
1 GATCTCTTTTTGATTATTCTCAGGAGCCTTTTGCT
340778 GATCTCTTTTTGATTATTCTCAGGAGCCTTTT
1 GATCTCTTTTTGATTATTCTCAGGAGCCTTTT
340810 TTTTTTTGAT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
35 32 1.00
ACGTcount: A:0.15, C:0.19, G:0.16, T:0.49
Consensus pattern (35 bp):
GATCTCTTTTTGATTATTCTCAGGAGCCTTTTGCT
Found at i:347662 original size:16 final size:16
Alignment explanation
Indices: 347641--347673 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
347631 CCTAGCAATA
347641 GAATCATAACATGAAG
1 GAATCATAACATGAAG
347657 GAATCATAACATGAAG
1 GAATCATAACATGAAG
347673 G
1 G
347674 GCAAGAAGAG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.48, C:0.12, G:0.21, T:0.18
Consensus pattern (16 bp):
GAATCATAACATGAAG
Found at i:349621 original size:79 final size:80
Alignment explanation
Indices: 349531--349691 Score: 315
Period size: 80 Copynumber: 2.0 Consensus size: 80
349521 TCCCAACAAT
349531 TGTTCCTTGGAAATTGA-CCAATCTGCCCCTTCTAAGATAATTTAATCGCAGCCTCAGCCTTTTA
1 TGTTCCTTGGAAATTGACCCAATCTGCCCCTTCTAAGATAATTTAATCGCAGCCTCAGCCTTTTA
349595 TTCTTCTCACTATCA
66 TTCTTCTCACTATCA
349610 TGTTCCTTGGAAATTGACCCAATCTGCCCCTTCTAAGATAATTTAATCGCAGCCTCAGCCTTTTA
1 TGTTCCTTGGAAATTGACCCAATCTGCCCCTTCTAAGATAATTTAATCGCAGCCTCAGCCTTTTA
349675 TTCTTCTCACTATCA
66 TTCTTCTCACTATCA
349690 TG
1 TG
349692 GCCCACAAAT
Statistics
Matches: 81, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
79 17 0.21
80 64 0.79
ACGTcount: A:0.24, C:0.28, G:0.12, T:0.37
Consensus pattern (80 bp):
TGTTCCTTGGAAATTGACCCAATCTGCCCCTTCTAAGATAATTTAATCGCAGCCTCAGCCTTTTA
TTCTTCTCACTATCA
Found at i:351103 original size:189 final size:189
Alignment explanation
Indices: 350783--351160 Score: 756
Period size: 189 Copynumber: 2.0 Consensus size: 189
350773 AACCAATAAG
350783 ACAGTTCAACTTTCTTATTCAGCCAAGCCTCCATCAAGCTCTCCTCCGAGGAGAAGATTATTATG
1 ACAGTTCAACTTTCTTATTCAGCCAAGCCTCCATCAAGCTCTCCTCCGAGGAGAAGATTATTATG
350848 CAGGAGTTCCACGCATAGCCCCACCTAATTATTTTAACTTGCCCTAGATATTTCTAGTATAATGA
66 CAGGAGTTCCACGCATAGCCCCACCTAATTATTTTAACTTGCCCTAGATATTTCTAGTATAATGA
350913 TAATGATAGTATTTTTTAACATGGGAATTCTAGCCCCAAAAGTTGGGTTGTTACCCTGT
131 TAATGATAGTATTTTTTAACATGGGAATTCTAGCCCCAAAAGTTGGGTTGTTACCCTGT
350972 ACAGTTCAACTTTCTTATTCAGCCAAGCCTCCATCAAGCTCTCCTCCGAGGAGAAGATTATTATG
1 ACAGTTCAACTTTCTTATTCAGCCAAGCCTCCATCAAGCTCTCCTCCGAGGAGAAGATTATTATG
351037 CAGGAGTTCCACGCATAGCCCCACCTAATTATTTTAACTTGCCCTAGATATTTCTAGTATAATGA
66 CAGGAGTTCCACGCATAGCCCCACCTAATTATTTTAACTTGCCCTAGATATTTCTAGTATAATGA
351102 TAATGATAGTATTTTTTAACATGGGAATTCTAGCCCCAAAAGTTGGGTTGTTACCCTGT
131 TAATGATAGTATTTTTTAACATGGGAATTCTAGCCCCAAAAGTTGGGTTGTTACCCTGT
351161 CCAAAAGTTT
Statistics
Matches: 189, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
189 189 1.00
ACGTcount: A:0.28, C:0.23, G:0.16, T:0.33
Consensus pattern (189 bp):
ACAGTTCAACTTTCTTATTCAGCCAAGCCTCCATCAAGCTCTCCTCCGAGGAGAAGATTATTATG
CAGGAGTTCCACGCATAGCCCCACCTAATTATTTTAACTTGCCCTAGATATTTCTAGTATAATGA
TAATGATAGTATTTTTTAACATGGGAATTCTAGCCCCAAAAGTTGGGTTGTTACCCTGT
Found at i:356206 original size:64 final size:63
Alignment explanation
Indices: 356119--356273 Score: 190
Period size: 64 Copynumber: 2.4 Consensus size: 63
356109 TTGAATGTGT
* * ** *
356119 ATCGATGCATTAGTAGTGCATCGATGCACTCTTTTTAAATAA-AAAGATCGAATGCAATTAGTGC
1 ATCGATGCATAAGGAGTGCATCGATGCACTC-CATT-AATAAGAAACATCGAATGCAATTAGTGC
* *
356183 ATCGATGCATAAGGCA-TGCATCGATGCATTCCATTAATAATGAAACATCGAATGCAATTGGTGC
1 ATCGATGCATAAGG-AGTGCATCGATGCACTCCATTAATAA-GAAACATCGAATGCAATTAGTGC
356247 ATCGATGCATAAGGAGTGCATCG-TGCA
1 ATCGATGCATAAGGAGTGCATCGATGCA
356274 TCCCAGCAAT
Statistics
Matches: 80, Mismatches: 7, Indels: 9
0.83 0.07 0.09
Matches are distributed among these distances:
62 5 0.06
63 7 0.09
64 67 0.84
65 1 0.01
ACGTcount: A:0.34, C:0.17, G:0.21, T:0.28
Consensus pattern (63 bp):
ATCGATGCATAAGGAGTGCATCGATGCACTCCATTAATAAGAAACATCGAATGCAATTAGTGC
Found at i:356872 original size:31 final size:31
Alignment explanation
Indices: 356834--356931 Score: 178
Period size: 31 Copynumber: 3.2 Consensus size: 31
356824 AGAGTCGAGG
356834 GTTTACATATGTTTAAAGGCACATATGAACA
1 GTTTACATATGTTTAAAGGCACATATGAACA
* *
356865 GTTTACATATGTTTAAAGGCACTTATGAATA
1 GTTTACATATGTTTAAAGGCACATATGAACA
356896 GTTTACATATGTTTAAAGGCACATATGAACA
1 GTTTACATATGTTTAAAGGCACATATGAACA
356927 GTTTA
1 GTTTA
356932 TATTGTGACC
Statistics
Matches: 63, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
31 63 1.00
ACGTcount: A:0.37, C:0.11, G:0.16, T:0.36
Consensus pattern (31 bp):
GTTTACATATGTTTAAAGGCACATATGAACA
Found at i:367106 original size:38 final size:38
Alignment explanation
Indices: 367063--367139 Score: 154
Period size: 38 Copynumber: 2.0 Consensus size: 38
367053 GTGTTTTGTG
367063 ATGTTGGTATGAAATGGATTTCTTTAGTTCTTTTGATT
1 ATGTTGGTATGAAATGGATTTCTTTAGTTCTTTTGATT
367101 ATGTTGGTATGAAATGGATTTCTTTAGTTCTTTTGATT
1 ATGTTGGTATGAAATGGATTTCTTTAGTTCTTTTGATT
367139 A
1 A
367140 ATGAACTCAG
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
38 39 1.00
ACGTcount: A:0.22, C:0.05, G:0.21, T:0.52
Consensus pattern (38 bp):
ATGTTGGTATGAAATGGATTTCTTTAGTTCTTTTGATT
Found at i:373609 original size:18 final size:17
Alignment explanation
Indices: 373581--373631 Score: 59
Period size: 18 Copynumber: 2.9 Consensus size: 17
373571 AGATTAATAT
373581 ATTTCATATTTAATTTAA
1 ATTT-ATATTTAATTTAA
*
373599 ATTATATATTTAACTTAA
1 ATT-TATATTTAATTTAA
*
373617 ATTTA-ATTAAATTTA
1 ATTTATATTTAATTTA
373632 TATAATACTA
Statistics
Matches: 29, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
16 8 0.28
17 2 0.07
18 18 0.62
19 1 0.03
ACGTcount: A:0.43, C:0.04, G:0.00, T:0.53
Consensus pattern (17 bp):
ATTTATATTTAATTTAA
Found at i:374776 original size:2 final size:2
Alignment explanation
Indices: 374769--374795 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
374759 TGATTACTTT
374769 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
374796 GCAAATGTTA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:382837 original size:2 final size:2
Alignment explanation
Indices: 382824--382875 Score: 95
Period size: 2 Copynumber: 26.0 Consensus size: 2
382814 ATTAAAACCA
*
382824 AT AT AT AC 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
382866 AT AT AT AT AT
1 AT AT AT AT AT
382876 TTGACAAGCG
Statistics
Matches: 48, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
2 48 1.00
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:384654 original size:3 final size:3
Alignment explanation
Indices: 384648--384765 Score: 128
Period size: 3 Copynumber: 39.0 Consensus size: 3
384638 TTTATTTAAA
** * * *
384648 ATT ATT ATT ATT AAA ATT ATT ATT ATT AGT ATT ATT ATT AGT ATT AGT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
* * * * *
384696 ATT ATT ATT ATA ATA ATA ATA ATA ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
*
384744 AAT ATT ATAT ATT ATT ATT ATT
1 ATT ATT AT-T ATT ATT ATT ATT
384766 TAATAAATAA
Statistics
Matches: 100, Mismatches: 14, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
3 97 0.97
4 3 0.03
ACGTcount: A:0.41, C:0.00, G:0.03, T:0.57
Consensus pattern (3 bp):
ATT
Found at i:391325 original size:2 final size:2
Alignment explanation
Indices: 391318--391384 Score: 118
Period size: 2 Copynumber: 34.0 Consensus size: 2
391308 CATTTATCCT
*
391318 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA GA 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
391360 TA TA TA TA -A TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA
391385 GATCCTTTGT
Statistics
Matches: 62, Mismatches: 2, Indels: 2
0.94 0.03 0.03
Matches are distributed among these distances:
1 1 0.02
2 61 0.98
ACGTcount: A:0.51, C:0.00, G:0.01, T:0.48
Consensus pattern (2 bp):
TA
Found at i:394269 original size:91 final size:92
Alignment explanation
Indices: 394003--394246 Score: 400
Period size: 92 Copynumber: 2.7 Consensus size: 92
393993 AGTAGAAATG
* * *
394003 ATGTGCCCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATTTGGTTTGGTATGAACCACA
1 ATGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATATGATTTGGTATGAACCACA
* * *
394068 GAACCAGTTATTGAATTTGGAAGAGGA
66 GAACCAATCATTGAATTTGGAAGAGCA
* *
394095 ATGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGTTTTGGTATGAACCACA
1 ATGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATATGATTTGGTATGAACCACA
394160 GAACCAATCATTGAATTTGGAAGA-CA
66 GAACCAATCATTGAATTTGGAAGAGCA
*
394186 ATGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAATTATCTGATATGATTTGGTATGAAC
1 ATGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATATGATTTGGTATGAAC
394247 TCTAAAATCA
Statistics
Matches: 143, Mismatches: 9, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
91 59 0.41
92 84 0.59
ACGTcount: A:0.26, C:0.15, G:0.23, T:0.36
Consensus pattern (92 bp):
ATGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATATGATTTGGTATGAACCACA
GAACCAATCATTGAATTTGGAAGAGCA
Found at i:397016 original size:22 final size:22
Alignment explanation
Indices: 396987--397044 Score: 98
Period size: 22 Copynumber: 2.6 Consensus size: 22
396977 ATCTACACTC
*
396987 TTCAAAGATGATAGATTCTCTT
1 TTCAAAGATGAAAGATTCTCTT
*
397009 TTTAAAGATGAAAGATTCTCTT
1 TTCAAAGATGAAAGATTCTCTT
397031 TTCAAAGATGAAAG
1 TTCAAAGATGAAAG
397045 CTTTATGGGA
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
22 33 1.00
ACGTcount: A:0.38, C:0.10, G:0.16, T:0.36
Consensus pattern (22 bp):
TTCAAAGATGAAAGATTCTCTT
Found at i:397843 original size:76 final size:76
Alignment explanation
Indices: 397717--398508 Score: 1399
Period size: 76 Copynumber: 10.4 Consensus size: 76
397707 CTATTTCTCA
397717 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
*
397782 ATCCTTCGGGT
66 AGCCTTCGGGT
*
397793 CATCTGTAAGCCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
397858 AGCCTTCGGGT
66 AGCCTTCGGGT
*
397869 CATCTGTAAGTCCTTCAGTGCATGATGTTTTCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
397934 AGCC-TCAGGGT
66 AGCCTTC-GGGT
*
397945 CATCTGTAAGTCCTTCAGTGCATGATGTTTTCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
398010 AGCC-TCAGGGT
66 AGCCTTC-GGGT
*
398021 CATCTGTAAGTCCTTCAGTGCATGATGTTTTCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
398086 AGCCTTCGGGT
66 AGCCTTCGGGT
*
398097 CATCTGTAAGTCCTTCAGTGCATGATATTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
398162 AGCCTTCGGGT
66 AGCCTTCGGGT
*
398173 CATCTGTAAGTCCTTCAGTGCATGATATTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
398238 AGCCTTCGGGT
66 AGCCTTCGGGT
*
398249 CATCTGTAAGCCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
398314 AGCCTTCGGGT
66 AGCCTTCGGGT
*
398325 CATCTGTAAGTCCTTCAGTGCATGATATTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTC-A
*
398390 AAACCTTCGGGT
65 AAGCCTTCGGGT
* *
398402 CATCTGTAAGCCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGTTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTC-A
*
398467 AAACCTTCGGGT
65 AAGCCTTCGGGT
* *
398479 CATCTGTAAGCCCTTCAGTGCCTGATGTTT
1 CATCTGTAAGTCCTTCAGTGCATGATGTTT
398509 TCAACATTTC
Statistics
Matches: 698, Mismatches: 15, Indels: 5
0.97 0.02 0.01
Matches are distributed among these distances:
75 2 0.00
76 579 0.83
77 117 0.17
ACGTcount: A:0.22, C:0.21, G:0.21, T:0.35
Consensus pattern (76 bp):
CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
AGCCTTCGGGT
Found at i:398641 original size:3 final size:3
Alignment explanation
Indices: 398635--398752 Score: 130
Period size: 3 Copynumber: 39.0 Consensus size: 3
398625 TTTTTTTAAA
** * * *
398635 ATT ATT ATT ATT AAA ATT ATT ATT ATT AGT ATT ATT ATT AGT ATT AGT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
* * *
398683 ATT ATT ATT ATT A-T AAT AAT AAT ATT ATT ATT ATT ATTT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT A-TT ATT ATT
*
398728 ATT ATA ATT ATAT ATT ATT ATT ATT
1 ATT ATT ATT AT-T ATT ATT ATT ATT
398753 TAATAAATAA
Statistics
Matches: 99, Mismatches: 13, Indels: 6
0.84 0.11 0.05
Matches are distributed among these distances:
2 2 0.02
3 91 0.92
4 6 0.06
ACGTcount: A:0.39, C:0.00, G:0.03, T:0.58
Consensus pattern (3 bp):
ATT
Found at i:402065 original size:21 final size:21
Alignment explanation
Indices: 402039--402078 Score: 80
Period size: 21 Copynumber: 1.9 Consensus size: 21
402029 GCTTTAAAAG
402039 ATGGGAACGCGCCTCCAGAGT
1 ATGGGAACGCGCCTCCAGAGT
402060 ATGGGAACGCGCCTCCAGA
1 ATGGGAACGCGCCTCCAGA
402079 ATATTATCAG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.25, C:0.30, G:0.33, T:0.12
Consensus pattern (21 bp):
ATGGGAACGCGCCTCCAGAGT
Found at i:402471 original size:58 final size:59
Alignment explanation
Indices: 402375--402495 Score: 208
Period size: 58 Copynumber: 2.1 Consensus size: 59
402365 TTTTTAGATT
* * *
402375 TTAAATGAATGATTATGATTCAATCAGAATCATTAAAATATTATCTTAAAATTCAAATG
1 TTAAATGAATGATTATGAGTAAATCAGAATAATTAAAATATTATCTTAAAATTCAAATG
402434 TTAAATGAATGATTATG-GTAAATCAGAATAATTAAAATATTATCTTAAAATTCAAATG
1 TTAAATGAATGATTATGAGTAAATCAGAATAATTAAAATATTATCTTAAAATTCAAATG
402492 TTAA
1 TTAA
402496 GTGAGTTATC
Statistics
Matches: 59, Mismatches: 3, Indels: 1
0.94 0.05 0.02
Matches are distributed among these distances:
58 42 0.71
59 17 0.29
ACGTcount: A:0.47, C:0.07, G:0.09, T:0.37
Consensus pattern (59 bp):
TTAAATGAATGATTATGAGTAAATCAGAATAATTAAAATATTATCTTAAAATTCAAATG
Found at i:402656 original size:12 final size:12
Alignment explanation
Indices: 402639--402711 Score: 56
Period size: 12 Copynumber: 5.7 Consensus size: 12
402629 TATTTTATCT
*
402639 TTTTAAAATTAC
1 TTTTAAAATTAA
*
402651 TTTTAAACATCAA
1 TTTTAAA-ATTAA
*
402664 TCTTAAATAATTAAA
1 T-TTTAA-AATT-AA
*
402679 TTTTAAAATGTAT
1 TTTTAAAAT-TAA
*
402692 TTTTAAAATTAT
1 TTTTAAAATTAA
402704 TTTTAAAA
1 TTTTAAAA
402712 GTACTTTTTT
Statistics
Matches: 50, Mismatches: 6, Indels: 10
0.76 0.09 0.15
Matches are distributed among these distances:
12 18 0.36
13 17 0.34
14 11 0.22
15 4 0.08
ACGTcount: A:0.45, C:0.05, G:0.01, T:0.48
Consensus pattern (12 bp):
TTTTAAAATTAA
Found at i:402697 original size:13 final size:13
Alignment explanation
Indices: 402679--402720 Score: 61
Period size: 13 Copynumber: 3.3 Consensus size: 13
402669 AATAATTAAA
402679 TTTTAAAATGTAT
1 TTTTAAAATGTAT
402692 TTTTAAAAT-TAT
1 TTTTAAAATGTAT
402704 TTTTAAAA-GTACT
1 TTTTAAAATGTA-T
402717 TTTT
1 TTTT
402721 TTATAGTATC
Statistics
Matches: 27, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
12 13 0.48
13 14 0.52
ACGTcount: A:0.36, C:0.02, G:0.05, T:0.57
Consensus pattern (13 bp):
TTTTAAAATGTAT
Found at i:402719 original size:12 final size:12
Alignment explanation
Indices: 402679--402739 Score: 59
Period size: 12 Copynumber: 4.8 Consensus size: 12
402669 AATAATTAAA
402679 TTTTAAAATGTAT
1 TTTTAAAA-GTAT
*
402692 TTTTAAAATTAT
1 TTTTAAAAGTAT
402704 TTTTAAAAGTACTT
1 TTTTAAAAGTA--T
* *
402718 TTTTTATAGTAT
1 TTTTAAAAGTAT
*
402730 CTTTAAAAGT
1 TTTTAAAAGT
402740 TACTTTTCAA
Statistics
Matches: 39, Mismatches: 7, Indels: 5
0.76 0.14 0.10
Matches are distributed among these distances:
12 21 0.54
13 8 0.21
14 10 0.26
ACGTcount: A:0.36, C:0.03, G:0.07, T:0.54
Consensus pattern (12 bp):
TTTTAAAAGTAT
Found at i:402720 original size:26 final size:26
Alignment explanation
Indices: 402679--402746 Score: 68
Period size: 26 Copynumber: 2.6 Consensus size: 26
402669 AATAATTAAA
*
402679 TTTTAAAATGTA--TTTTTAAAATTAT
1 TTTTAAAA-GTACTTTTTTAAAAGTAT
* *
402704 TTTTAAAAGTACTTTTTTTATAGTAT
1 TTTTAAAAGTACTTTTTTAAAAGTAT
*
402730 CTTTAAAAGTTACTTTT
1 TTTTAAAAG-TACTTTT
402747 CAAAAACAAT
Statistics
Matches: 36, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
24 3 0.08
25 8 0.22
26 18 0.50
27 7 0.19
ACGTcount: A:0.34, C:0.04, G:0.06, T:0.56
Consensus pattern (26 bp):
TTTTAAAAGTACTTTTTTAAAAGTAT
Found at i:402898 original size:2 final size:2
Alignment explanation
Indices: 402893--402929 Score: 56
Period size: 2 Copynumber: 18.5 Consensus size: 2
402883 ATTTTTTGTA
* *
402893 AT AT AT AT AT AT AT AT AT AC AT AC AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
402930 ATTAAGTAAA
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.51, C:0.05, G:0.00, T:0.43
Consensus pattern (2 bp):
AT
Found at i:409382 original size:36 final size:35
Alignment explanation
Indices: 409342--409412 Score: 97
Period size: 36 Copynumber: 2.0 Consensus size: 35
409332 GTAAAGCGTC
* **
409342 TTGAATAGAAATAAGTATATCGATTATGATCCTTTT
1 TTGAATAGAAATAAGCATAGAGATTATGAT-CTTTT
*
409378 TTGAATAGAGATAAGCATAGAGATTATGATCTTTT
1 TTGAATAGAAATAAGCATAGAGATTATGATCTTTT
409413 GATGACTCTC
Statistics
Matches: 31, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
35 5 0.16
36 26 0.84
ACGTcount: A:0.37, C:0.07, G:0.17, T:0.39
Consensus pattern (35 bp):
TTGAATAGAAATAAGCATAGAGATTATGATCTTTT
Found at i:410931 original size:23 final size:24
Alignment explanation
Indices: 410905--410968 Score: 69
Period size: 23 Copynumber: 2.7 Consensus size: 24
410895 TATATTCCAT
*
410905 ATATATATTTTAAAAT-ATAATTA
1 ATATATATTTTAAAATAATAATAA
*
410928 ATATA-AGATTTAAAATAATAATAA
1 ATATATA-TTTTAAAATAATAATAA
*
410952 ATTTAATATTTTAAAAT
1 ATAT-ATATTTTAAAAT
410969 TGAATTCAAT
Statistics
Matches: 33, Mismatches: 4, Indels: 6
0.77 0.09 0.14
Matches are distributed among these distances:
22 1 0.03
23 13 0.39
24 9 0.27
25 9 0.27
26 1 0.03
ACGTcount: A:0.55, C:0.00, G:0.02, T:0.44
Consensus pattern (24 bp):
ATATATATTTTAAAATAATAATAA
Found at i:410938 original size:24 final size:25
Alignment explanation
Indices: 410911--410968 Score: 75
Period size: 24 Copynumber: 2.4 Consensus size: 25
410901 CCATATATAT
*
410911 ATTTTAAAAT-ATAATTAATATAAG
1 ATTTTAAAATAATAATAAATATAAG
* *
410935 A-TTTAAAATAATAATAAATTTAAT
1 ATTTTAAAATAATAATAAATATAAG
410959 ATTTTAAAAT
1 ATTTTAAAAT
410969 TGAATTCAAT
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
23 8 0.28
24 13 0.45
25 8 0.28
ACGTcount: A:0.55, C:0.00, G:0.02, T:0.43
Consensus pattern (25 bp):
ATTTTAAAATAATAATAAATATAAG
Found at i:411058 original size:22 final size:22
Alignment explanation
Indices: 411033--411075 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
411023 TCAAAATATT
411033 ATAATATTAA-ATTAAACTTAAA
1 ATAATA-TAATATTAAACTTAAA
*
411055 ATAATATAATATTAAATTTAA
1 ATAATATAATATTAAACTTAA
411076 TTCAATTTAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
21 3 0.16
22 16 0.84
ACGTcount: A:0.58, C:0.02, G:0.00, T:0.40
Consensus pattern (22 bp):
ATAATATAATATTAAACTTAAA
Found at i:411088 original size:32 final size:32
Alignment explanation
Indices: 411027--411109 Score: 103
Period size: 32 Copynumber: 2.5 Consensus size: 32
411017 CATTTTTCAA
411027 AATATTATAATATTAAATTAAACTTAAAATAATAT
1 AATATTA-AAT-TT-AATTAAACTTAAAATAATAT
* * *
411062 AATATTAAATTTAATTCAATTTAAAATGATAT
1 AATATTAAATTTAATTAAACTTAAAATAATAT
*
411094 AATATTACATTTAATT
1 AATATTAAATTTAATT
411110 TTAAAAAATG
Statistics
Matches: 44, Mismatches: 4, Indels: 3
0.86 0.08 0.06
Matches are distributed among these distances:
32 32 0.73
33 2 0.05
34 3 0.07
35 7 0.16
ACGTcount: A:0.52, C:0.04, G:0.01, T:0.43
Consensus pattern (32 bp):
AATATTAAATTTAATTAAACTTAAAATAATAT
Found at i:411649 original size:14 final size:14
Alignment explanation
Indices: 411630--411677 Score: 62
Period size: 14 Copynumber: 3.4 Consensus size: 14
411620 TAGAGTTACA
411630 ATTTAAGGTTTAAG
1 ATTTAAGGTTTAAG
*
411644 ATTTAA-GTTTTAG
1 ATTTAAGGTTTAAG
411657 AATTTTAAGGTTTAAG
1 -A-TTTAAGGTTTAAG
411673 ATTTA
1 ATTTA
411678 GTGTTCATGG
Statistics
Matches: 29, Mismatches: 2, Indels: 6
0.78 0.05 0.16
Matches are distributed among these distances:
13 6 0.21
14 11 0.38
15 6 0.21
16 6 0.21
ACGTcount: A:0.35, C:0.00, G:0.17, T:0.48
Consensus pattern (14 bp):
ATTTAAGGTTTAAG
Found at i:411710 original size:21 final size:20
Alignment explanation
Indices: 411659--411717 Score: 55
Period size: 21 Copynumber: 2.9 Consensus size: 20
411649 AGTTTTAGAA
*
411659 TTTTAAGGTTTAAGATTTAG
1 TTTTAAGGTTTAAGATTGAG
* * *
411679 TGTTCATGGTTTATGATGTGAG
1 T-TTTAAGGTTTAAGAT-TGAG
*
411701 TTTTAAGGTTTGAGATT
1 TTTTAAGGTTTAAGATT
411718 TTGAGGTTTA
Statistics
Matches: 29, Mismatches: 8, Indels: 4
0.71 0.20 0.10
Matches are distributed among these distances:
20 2 0.07
21 23 0.79
22 4 0.14
ACGTcount: A:0.24, C:0.02, G:0.25, T:0.49
Consensus pattern (20 bp):
TTTTAAGGTTTAAGATTGAG
Found at i:415759 original size:21 final size:22
Alignment explanation
Indices: 415735--415781 Score: 60
Period size: 21 Copynumber: 2.2 Consensus size: 22
415725 GTTTACGTCG
415735 TTGACATGACAATCCACGAT-A
1 TTGACATGACAATCCACGATGA
** *
415756 TTGATGTGACAGTCCACGATGA
1 TTGACATGACAATCCACGATGA
415778 TTGA
1 TTGA
415782 TAATGTAGCA
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
21 17 0.77
22 5 0.23
ACGTcount: A:0.32, C:0.19, G:0.21, T:0.28
Consensus pattern (22 bp):
TTGACATGACAATCCACGATGA
Found at i:418321 original size:19 final size:19
Alignment explanation
Indices: 418297--418335 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
418287 AAACTAGTAT
418297 AACTAAAAGTTATA-AAAAA
1 AACT-AAAGTTATAGAAAAA
*
418316 AACTAAATTTATAGAAAAA
1 AACTAAAGTTATAGAAAAA
418335 A
1 A
418336 TACATAATCC
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
18 8 0.44
19 10 0.56
ACGTcount: A:0.67, C:0.05, G:0.05, T:0.23
Consensus pattern (19 bp):
AACTAAAGTTATAGAAAAA
Found at i:419251 original size:71 final size:71
Alignment explanation
Indices: 419176--419311 Score: 227
Period size: 71 Copynumber: 1.9 Consensus size: 71
419166 AATAATATAA
* * *
419176 TTTTTATATTTATTTAGAGATAGTTGTTATAAAATTGTTCTATACTTTATTATTCAATTAGATTC
1 TTTTTATATTTATTTAGAGATAATTGTTATAAAATTGTACCATACTTTATTATTCAATTAGATTC
419241 ATAATT
66 ATAATT
* *
419247 TTTTTATATTTATTTTGAGATAATTGTTATAATATTGTACCATACTTTATTATTCAATTAGATTC
1 TTTTTATATTTATTTAGAGATAATTGTTATAAAATTGTACCATACTTTATTATTCAATTAGATTC
419312 TTATTTTATC
Statistics
Matches: 60, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
71 60 1.00
ACGTcount: A:0.32, C:0.07, G:0.08, T:0.54
Consensus pattern (71 bp):
TTTTTATATTTATTTAGAGATAATTGTTATAAAATTGTACCATACTTTATTATTCAATTAGATTC
ATAATT
Found at i:420029 original size:61 final size:61
Alignment explanation
Indices: 419902--420029 Score: 138
Period size: 61 Copynumber: 2.1 Consensus size: 61
419892 GACAATTTTT
* * * *
419902 TAAC-TTTTAATAGTCGAATGACTTAACAAAACAACATTCTATAGTCGAAAGACTCTTTTG
1 TAACTTTTTAATAGTCGAAAGACTTAACAAAACAACATCCTAAAGTCGAAAGACTCATTTG
* * *
419962 TAACTTTTTAATAGTC-AAGAGACTTAATAAAACAATATCCTAAAGTC-ATATGAC-CATTTG
1 TAACTTTTTAATAGTCGAA-AGACTTAACAAAACAACATCCTAAAGTCGA-AAGACTCATTTG
420022 TATACTTT
1 TA-ACTTT
420030 ACCCTTTTAT
Statistics
Matches: 57, Mismatches: 7, Indels: 7
0.80 0.10 0.10
Matches are distributed among these distances:
60 14 0.25
61 43 0.75
ACGTcount: A:0.39, C:0.16, G:0.10, T:0.35
Consensus pattern (61 bp):
TAACTTTTTAATAGTCGAAAGACTTAACAAAACAACATCCTAAAGTCGAAAGACTCATTTG
Found at i:420544 original size:13 final size:13
Alignment explanation
Indices: 420524--420563 Score: 55
Period size: 13 Copynumber: 3.0 Consensus size: 13
420514 ATTAGATATT
420524 AGATAAAACAAAAA
1 AGATAAAA-AAAAA
420538 A-ATAAAATAAAAA
1 AGATAAAA-AAAAA
420551 AGATAAAAAAAAA
1 AGATAAAAAAAAA
420564 TATATATATA
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
13 17 0.71
14 7 0.29
ACGTcount: A:0.82, C:0.03, G:0.05, T:0.10
Consensus pattern (13 bp):
AGATAAAAAAAAA
Found at i:420685 original size:43 final size:43
Alignment explanation
Indices: 420596--420685 Score: 110
Period size: 43 Copynumber: 2.1 Consensus size: 43
420586 TAAGAATTGA
* * *
420596 AAAATATTAAATAAATTAAAATAAGAAAAAACATAAAAAAAAT
1 AAAATATTAAATAAATCAAAATAAGAAAAAAAAGAAAAAAAAT
** *
420639 AAAATATTAAATAAATCAAAA-GGGAAAAAAAAGAAAGAAAACT
1 AAAATATTAAATAAATCAAAATAAGAAAAAAAAGAAA-AAAAAT
420682 AAAA
1 AAAA
420686 AAATGTTAAA
Statistics
Matches: 40, Mismatches: 6, Indels: 2
0.83 0.12 0.04
Matches are distributed among these distances:
42 11 0.28
43 29 0.73
ACGTcount: A:0.73, C:0.03, G:0.07, T:0.17
Consensus pattern (43 bp):
AAAATATTAAATAAATCAAAATAAGAAAAAAAAGAAAAAAAAT
Found at i:420955 original size:14 final size:14
Alignment explanation
Indices: 420936--420962 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
420926 ATTGAATCAA
420936 TTGAAAATTCAGAG
1 TTGAAAATTCAGAG
420950 TTGAAAATTCAGA
1 TTGAAAATTCAGA
420963 CAAAATTGAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.44, C:0.07, G:0.19, T:0.30
Consensus pattern (14 bp):
TTGAAAATTCAGAG
Found at i:421644 original size:13 final size:12
Alignment explanation
Indices: 421628--421684 Score: 60
Period size: 13 Copynumber: 4.3 Consensus size: 12
421618 GGAAAAAAAC
421628 AAAAGAAATAAAT
1 AAAA-AAATAAAT
421641 AAAATAAATAAAT
1 AAAA-AAATAAAT
*
421654 AAAAACATAAAAT
1 AAAAAAAT-AAAT
421667 AAATAAAATAAAAT
1 AAA-AAAAT-AAAT
421681 AAAA
1 AAAA
421685 TAAAAAACAA
Statistics
Matches: 39, Mismatches: 3, Indels: 4
0.85 0.07 0.09
Matches are distributed among these distances:
12 3 0.08
13 24 0.62
14 12 0.31
ACGTcount: A:0.79, C:0.02, G:0.02, T:0.18
Consensus pattern (12 bp):
AAAAAAATAAAT
Found at i:421645 original size:5 final size:5
Alignment explanation
Indices: 421633--421689 Score: 66
Period size: 5 Copynumber: 11.6 Consensus size: 5
421623 AAAACAAAAG
*
421633 AAAT- AAATA AAAT- AAATA AATAAA AACATA AAAT- AAATA AAATA AAATA
1 AAATA AAATA AAATA AAATA AA-ATA AA-ATA AAATA AAATA AAATA AAATA
421682 AAATA AAA
1 AAATA AAA
421690 AACAAATATA
Statistics
Matches: 46, Mismatches: 3, Indels: 7
0.82 0.05 0.12
Matches are distributed among these distances:
4 12 0.26
5 26 0.57
6 8 0.17
ACGTcount: A:0.79, C:0.02, G:0.00, T:0.19
Consensus pattern (5 bp):
AAATA
Found at i:421645 original size:9 final size:9
Alignment explanation
Indices: 421633--421688 Score: 67
Period size: 9 Copynumber: 5.8 Consensus size: 9
421623 AAAACAAAAG
421633 AAATAAATA
1 AAATAAATA
421642 AAATAAATAA
1 AAATAAAT-A
*
421652 ATAAAAACATA
1 A-AATAA-ATA
421663 AAATAAATA
1 AAATAAATA
421672 AAATAAAATA
1 AAAT-AAATA
421682 AAATAAA
1 AAATAAA
421689 AAACAAATAT
Statistics
Matches: 41, Mismatches: 2, Indels: 8
0.80 0.04 0.16
Matches are distributed among these distances:
9 18 0.44
10 15 0.37
11 6 0.15
12 2 0.05
ACGTcount: A:0.79, C:0.02, G:0.00, T:0.20
Consensus pattern (9 bp):
AAATAAATA
Found at i:421663 original size:21 final size:19
Alignment explanation
Indices: 421637--421688 Score: 77
Period size: 21 Copynumber: 2.6 Consensus size: 19
421627 CAAAAGAAAT
421637 AAATAAAATAAATAAATAAA
1 AAATAAAATAAATAAA-AAA
*
421657 AACATAAAATAAATAAAATA
1 AA-ATAAAATAAATAAAAAA
421677 AAATAAAATAAA
1 AAATAAAATAAA
421689 AAACAAATAT
Statistics
Matches: 30, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
19 10 0.33
20 6 0.20
21 14 0.47
ACGTcount: A:0.79, C:0.02, G:0.00, T:0.19
Consensus pattern (19 bp):
AAATAAAATAAATAAAAAA
Found at i:421886 original size:34 final size:34
Alignment explanation
Indices: 421696--421886 Score: 247
Period size: 34 Copynumber: 5.4 Consensus size: 34
421686 AAAAAACAAA
* *
421696 TATATATTATATATATTCTAAAATGTTTTCAAAAC
1 TATATAATATATATTTTC-AAAATGTTTTCAAAAC
* * * *
421731 TATATATTATATAATTTAAAAATGTTTTCAAAAAAT
1 TATATAATATATATTTTCAAAATGTTTTC--AAAAC
*
421767 TATATATTATATATATGTTTTCAAAGTGTTTTCAAAAC
1 TATATA--ATATATA--TTTTCAAAATGTTTTCAAAAC
421805 TATATAATATATATTTTCAAAATGTTTTCAAAAC
1 TATATAATATATATTTTCAAAATGTTTTCAAAAC
*
421839 TATATAATATATATTTTCAAAATGTTTTCAAAAT
1 TATATAATATATATTTTCAAAATGTTTTCAAAAC
421873 TATATAATATATAT
1 TATATAATATATAT
421887 ATATATATTC
Statistics
Matches: 139, Mismatches: 11, Indels: 13
0.85 0.07 0.08
Matches are distributed among these distances:
34 78 0.56
35 15 0.11
36 17 0.12
38 16 0.12
40 13 0.09
ACGTcount: A:0.44, C:0.06, G:0.04, T:0.46
Consensus pattern (34 bp):
TATATAATATATATTTTCAAAATGTTTTCAAAAC
Found at i:421938 original size:38 final size:35
Alignment explanation
Indices: 421879--421966 Score: 86
Period size: 36 Copynumber: 2.4 Consensus size: 35
421869 AAATTATATA
*
421879 ATATATATATATATATTCGAAAACCACTTTCTAAAAATT
1 ATATAT-TATAT-TATTCGAAAAACA-TTT-TAAAAATT
* * *
421918 ATATATTATATTTTTCCGAAAAATATTTTCAAAATT
1 ATATATTATATTATT-CGAAAAACATTTTAAAAATT
*
421954 TTATATTATATTA
1 ATATATTATATTA
421967 ATATATATAT
Statistics
Matches: 42, Mismatches: 6, Indels: 5
0.79 0.11 0.09
Matches are distributed among these distances:
36 18 0.43
37 6 0.14
38 12 0.29
39 6 0.14
ACGTcount: A:0.43, C:0.09, G:0.02, T:0.45
Consensus pattern (35 bp):
ATATATTATATTATTCGAAAAACATTTTAAAAATT
Found at i:423520 original size:25 final size:25
Alignment explanation
Indices: 423469--423515 Score: 71
Period size: 25 Copynumber: 2.0 Consensus size: 25
423459 ATTAATAATT
423469 AATTTTATTAATGGTTTTATTTTAA
1 AATTTTATTAATGGTTTTATTTTAA
*
423494 AATTTTATTTAT-G-TTTATTTTA
1 AATTTTATTAATGGTTTTATTTTA
423516 TAAAAAATAT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 9 0.43
24 1 0.05
25 11 0.52
ACGTcount: A:0.30, C:0.00, G:0.06, T:0.64
Consensus pattern (25 bp):
AATTTTATTAATGGTTTTATTTTAA
Found at i:427562 original size:33 final size:34
Alignment explanation
Indices: 427479--427563 Score: 102
Period size: 33 Copynumber: 2.5 Consensus size: 34
427469 TTTGACTCAA
* * *
427479 ATATATTA-AATATTTTAAAATAGTTAAAATATT
1 ATATTTTATAATATTTTAAAAGAGTTAAAATAAT
*
427512 ATATTTTATATAATATTTTAAACGA-TTAAAATAAT
1 ATA-TTT-TATAATATTTTAAAAGAGTTAAAATAAT
427547 ATATTTTATAATATTTT
1 ATATTTTATAATATTTT
427564 TATATTTTTA
Statistics
Matches: 45, Mismatches: 4, Indels: 6
0.82 0.07 0.11
Matches are distributed among these distances:
33 14 0.31
34 5 0.11
35 14 0.31
36 12 0.27
ACGTcount: A:0.47, C:0.01, G:0.02, T:0.49
Consensus pattern (34 bp):
ATATTTTATAATATTTTAAAAGAGTTAAAATAAT
Found at i:428962 original size:39 final size:41
Alignment explanation
Indices: 428885--428962 Score: 106
Period size: 40 Copynumber: 2.0 Consensus size: 41
428875 TCCTGGGGTA
* * *
428885 TTTTTCAATTTTCCTGAAGACGCCATTACAATCGTGGAGTC
1 TTTTTCAATTTGCCTGAAGACACCATTACAATCATGGAGTC
*
428926 TTTTTC-ATTTGCCTGAAGATACCA-TACAATCATGGAG
1 TTTTTCAATTTGCCTGAAGACACCATTACAATCATGGAG
428963 CATTCATATT
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
39 12 0.36
40 15 0.45
41 6 0.18
ACGTcount: A:0.27, C:0.21, G:0.17, T:0.36
Consensus pattern (41 bp):
TTTTTCAATTTGCCTGAAGACACCATTACAATCATGGAGTC
Found at i:432428 original size:65 final size:64
Alignment explanation
Indices: 432349--432516 Score: 255
Period size: 64 Copynumber: 2.6 Consensus size: 64
432339 ATAATTAATT
* *
432349 TTAACTCTCTCGGTCTTATACTTTATATAATTTGTATCTCATAATTAATTTTAACTCTTATAAAA
1 TTAACTCCCTCGGTCTTATAATTTATATAATTTGTATCTCATAATTAA-TTTAACTCTTATAAAA
* * * *
432414 TTAACTCCCGCGGTCTTATAATTTATAGAATTTGTATCTCGTAATTAATTTAACTCTTATAAAT
1 TTAACTCCCTCGGTCTTATAATTTATATAATTTGTATCTCATAATTAATTTAACTCTTATAAAA
* *
432478 TTAACTTCCTCGGTCTTATAATTTATATAATTTATATCT
1 TTAACTCCCTCGGTCTTATAATTTATATAATTTGTATCT
432517 TTTATTGACT
Statistics
Matches: 93, Mismatches: 10, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
64 50 0.54
65 43 0.46
ACGTcount: A:0.31, C:0.15, G:0.07, T:0.47
Consensus pattern (64 bp):
TTAACTCCCTCGGTCTTATAATTTATATAATTTGTATCTCATAATTAATTTAACTCTTATAAAA
Found at i:433706 original size:5 final size:5
Alignment explanation
Indices: 433696--433722 Score: 54
Period size: 5 Copynumber: 5.4 Consensus size: 5
433686 CCCACCCTTA
433696 TATAC TATAC TATAC TATAC TATAC TA
1 TATAC TATAC TATAC TATAC TATAC TA
433723 ACCTGTCACA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 22 1.00
ACGTcount: A:0.41, C:0.19, G:0.00, T:0.41
Consensus pattern (5 bp):
TATAC
Found at i:439006 original size:5 final size:5
Alignment explanation
Indices: 438996--439026 Score: 62
Period size: 5 Copynumber: 6.2 Consensus size: 5
438986 TTAAACTCTT
438996 CACCA CACCA CACCA CACCA CACCA CACCA C
1 CACCA CACCA CACCA CACCA CACCA CACCA C
439027 CAATTTATGC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 26 1.00
ACGTcount: A:0.39, C:0.61, G:0.00, T:0.00
Consensus pattern (5 bp):
CACCA
Found at i:446348 original size:18 final size:18
Alignment explanation
Indices: 446325--446361 Score: 74
Period size: 18 Copynumber: 2.1 Consensus size: 18
446315 TGTTAGGGTT
446325 AGTCTTTTTCTTTGTAGG
1 AGTCTTTTTCTTTGTAGG
446343 AGTCTTTTTCTTTGTAGG
1 AGTCTTTTTCTTTGTAGG
446361 A
1 A
446362 TAGGGCTAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.14, C:0.11, G:0.22, T:0.54
Consensus pattern (18 bp):
AGTCTTTTTCTTTGTAGG
Found at i:451816 original size:17 final size:16
Alignment explanation
Indices: 451773--451817 Score: 56
Period size: 17 Copynumber: 2.8 Consensus size: 16
451763 TTACTTACCC
451773 ATATTAATAAA-AAAA
1 ATATTAATAAATAAAA
* *
451788 ATATAAAAAAATAAAA
1 ATATTAATAAATAAAA
451804 ATTATTAATAAATA
1 A-TATTAATAAATA
451818 TTGATTGTAA
Statistics
Matches: 24, Mismatches: 4, Indels: 2
0.80 0.13 0.07
Matches are distributed among these distances:
15 9 0.38
16 5 0.21
17 10 0.42
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (16 bp):
ATATTAATAAATAAAA
Found at i:460720 original size:23 final size:22
Alignment explanation
Indices: 460681--460732 Score: 59
Period size: 23 Copynumber: 2.3 Consensus size: 22
460671 ATAAACAAAA
* *
460681 ATAACAGTAAAAGAAAATGTGTT
1 ATAA-AGTAAAAGAAAACGTGTC
*
460704 ATAAAGTCAAAGAAAAACGTGTC
1 ATAAAGTAAAAG-AAAACGTGTC
460727 ATAAAG
1 ATAAAG
460733 GTAGAAGGAG
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
22 7 0.28
23 18 0.72
ACGTcount: A:0.54, C:0.08, G:0.17, T:0.21
Consensus pattern (22 bp):
ATAAAGTAAAAGAAAACGTGTC
Found at i:465719 original size:59 final size:59
Alignment explanation
Indices: 465585--465724 Score: 163
Period size: 59 Copynumber: 2.4 Consensus size: 59
465575 AGGACCAACA
* * * * **
465585 TAGAATGAGGTTCATAATTTTGGGATGAAATTGGAATTTTTAAAAGGTCAGAGAACAAAT
1 TAGAATGAGGATCAT-AGTTTGGGATGAAATTGAAATGTCCAAAAGGTCAGAGAACAAAT
** * * *
465645 TAGAATGAAAATCATAGTTTGGGATGAAATTGAAATGTCCAAAAGTTTAGAGATCAAAT
1 TAGAATGAGGATCATAGTTTGGGATGAAATTGAAATGTCCAAAAGGTCAGAGAACAAAT
*
465704 TAGAATGAGGGTCATAGTTTG
1 TAGAATGAGGATCATAGTTTG
465725 AGGAGTATAG
Statistics
Matches: 66, Mismatches: 14, Indels: 1
0.81 0.17 0.01
Matches are distributed among these distances:
59 54 0.82
60 12 0.18
ACGTcount: A:0.40, C:0.06, G:0.24, T:0.31
Consensus pattern (59 bp):
TAGAATGAGGATCATAGTTTGGGATGAAATTGAAATGTCCAAAAGGTCAGAGAACAAAT
Found at i:469353 original size:247 final size:246
Alignment explanation
Indices: 468917--469410 Score: 855
Period size: 247 Copynumber: 2.0 Consensus size: 246
468907 TGCTTTGACC
* *
468917 TATCCGTTTGAAATTGCATGCTTATTTTAATCCGGGGCGGCCTCGACCTCTCTGCTCTGGAGCTT
1 TATCCGTTTGAAATTGCATGCTTATTTTAATCCGGGGCAGCCTCGACCTCTATGCTCTGGAGCTT
*
468982 TAACTTGAGTGAAACTGAATTCATTGAGATTCTTGGTGTTGATTTAGAGAATTTGTTTCGAGCCT
66 TAACTTGAGTGAAACTGAATTCATTGAGAGTCTTGGTGTTGATTTAGAGAATTTGTTTCGAGCCT
469047 ACTTGTTATTGACACCAGGCGAGGCAAGGTGTGGCTATAGAAACTTACATATATAATTGTATATA
131 ACTTGTTATTGACACCAGGCGAGGCAAGGTGTGGCTATAGAAACTTACATATATAATTGTATATA
*
469112 CATGAGTTTTTGTATTTCATGAGAGAGTTTTGGTGTTGATTCAGAGAACTTG
196 CATGAGTTCTTGTA-TTCATGAGAGAGTTTTGGTGTTGATTCAGAGAACTTG
*
469164 TATCCGTTTGATATTGCATGCTTATTTTAATCCGGGGCAGCCTCGACCTCTATGC-CGTGGAGCT
1 TATCCGTTTGAAATTGCATGCTTATTTTAATCCGGGGCAGCCTCGACCTCTATGCTC-TGGAGCT
*
469228 TTAACTTGAGTGAAACTGAATTCATTGAGAGTCTTGGTGTTTATTTAGAGAATTTGTTTCGAGCC
65 TTAACTTGAGTGAAACTGAATTCATTGAGAGTCTTGGTGTTGATTTAGAGAATTTGTTTCGAGCC
* * * * *
469293 TACTTGTTGTTGACTCCAGGCGAGGCAAGGTGTGGCTATTGAAACTTATATGTATAATTGTATAT
130 TACTTGTTATTGACACCAGGCGAGGCAAGGTGTGGCTATAGAAACTTACATATATAATTGTATAT
*
469358 ACATGAGTTCTTGTATTCATGAGAGAGTTTTGGTGTTGATTCAGAGAGCTTG
195 ACATGAGTTCTTGTATTCATGAGAGAGTTTTGGTGTTGATTCAGAGAACTTG
469410 T
1 T
469411 GTCGAGCCTA
Statistics
Matches: 234, Mismatches: 12, Indels: 3
0.94 0.05 0.01
Matches are distributed among these distances:
246 38 0.16
247 196 0.84
ACGTcount: A:0.24, C:0.15, G:0.24, T:0.37
Consensus pattern (246 bp):
TATCCGTTTGAAATTGCATGCTTATTTTAATCCGGGGCAGCCTCGACCTCTATGCTCTGGAGCTT
TAACTTGAGTGAAACTGAATTCATTGAGAGTCTTGGTGTTGATTTAGAGAATTTGTTTCGAGCCT
ACTTGTTATTGACACCAGGCGAGGCAAGGTGTGGCTATAGAAACTTACATATATAATTGTATATA
CATGAGTTCTTGTATTCATGAGAGAGTTTTGGTGTTGATTCAGAGAACTTG
Found at i:470337 original size:15 final size:16
Alignment explanation
Indices: 470309--470338 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
470299 AGAACTGTGA
470309 CAACATATGTTTTTGC
1 CAACATATGTTTTTGC
470325 CAACATA-GTTTTTG
1 CAACATATGTTTTTG
470339 AAATGCACTA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 7 0.50
16 7 0.50
ACGTcount: A:0.27, C:0.17, G:0.13, T:0.43
Consensus pattern (16 bp):
CAACATATGTTTTTGC
Found at i:470977 original size:61 final size:62
Alignment explanation
Indices: 470861--470980 Score: 152
Period size: 62 Copynumber: 2.0 Consensus size: 62
470851 AAAATATTTG
* * * * *
470861 TTCTTTTTAACTTTGAATATTAAAAATAATTATATACTTTTGTATATTTTAAATTAAAATAA
1 TTCTATTTAACTTTGAATAGTAAAAAGAATTATATACTTTTGAATATTTCAAATTAAAATAA
* * * *
470923 TTCTATTTAAGTTTGAATGGTAAAAAGAGTTTTAT-CTTTTGAATATTTCAAATTAAAA
1 TTCTATTTAACTTTGAATAGTAAAAAGAATTATATACTTTTGAATATTTCAAATTAAAA
470981 AATATCGTTA
Statistics
Matches: 49, Mismatches: 9, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
61 21 0.43
62 28 0.57
ACGTcount: A:0.40, C:0.05, G:0.07, T:0.47
Consensus pattern (62 bp):
TTCTATTTAACTTTGAATAGTAAAAAGAATTATATACTTTTGAATATTTCAAATTAAAATAA
Found at i:482237 original size:15 final size:14
Alignment explanation
Indices: 482217--482244 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
482207 TTGTATCAAT
482217 TTAAAAAAATACAA
1 TTAAAAAAATACAA
482231 TTAAAAAAATACAA
1 TTAAAAAAATACAA
482245 AAATAAAGAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.71, C:0.07, G:0.00, T:0.21
Consensus pattern (14 bp):
TTAAAAAAATACAA
Found at i:484684 original size:15 final size:16
Alignment explanation
Indices: 484666--484700 Score: 54
Period size: 15 Copynumber: 2.2 Consensus size: 16
484656 AAAAGTTCAA
484666 AATTCAAAATAT-AAT
1 AATTCAAAATATAAAT
*
484681 AATTCATAATATAAAT
1 AATTCAAAATATAAAT
484697 AATT
1 AATT
484701 ATTATTTTAT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 11 0.61
16 7 0.39
ACGTcount: A:0.57, C:0.06, G:0.00, T:0.37
Consensus pattern (16 bp):
AATTCAAAATATAAAT
Found at i:484768 original size:16 final size:16
Alignment explanation
Indices: 484745--484806 Score: 88
Period size: 16 Copynumber: 3.9 Consensus size: 16
484735 AAATAAAAAC
* *
484745 TAACCGGGTACACGGG
1 TAACCGGGTACCCGAG
*
484761 TTACCGGGTACCCGAG
1 TAACCGGGTACCCGAG
*
484777 TAACTGGGTACCCGAG
1 TAACCGGGTACCCGAG
484793 TAACCGGGTACCCG
1 TAACCGGGTACCCG
484807 GAAAAACTAG
Statistics
Matches: 40, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
16 40 1.00
ACGTcount: A:0.23, C:0.29, G:0.32, T:0.16
Consensus pattern (16 bp):
TAACCGGGTACCCGAG
Found at i:487764 original size:28 final size:29
Alignment explanation
Indices: 487708--487776 Score: 88
Period size: 28 Copynumber: 2.4 Consensus size: 29
487698 ATTAGAAACA
*
487708 TTAAACACATAAAATAATAAAAATAATAAT
1 TTAAACAC-TTAAATAATAAAAATAATAAT
487738 TTAAACACTTAAAT-A-AAAAATATATAAT
1 TTAAACACTTAAATAATAAAAATA-ATAAT
*
487766 TTAAAAACTTA
1 TTAAACACTTA
487777 TTTTTATATT
Statistics
Matches: 36, Mismatches: 2, Indels: 4
0.86 0.05 0.10
Matches are distributed among these distances:
27 7 0.19
28 16 0.44
29 5 0.14
30 8 0.22
ACGTcount: A:0.62, C:0.07, G:0.00, T:0.30
Consensus pattern (29 bp):
TTAAACACTTAAATAATAAAAATAATAAT
Found at i:488080 original size:2 final size:2
Alignment explanation
Indices: 488073--488103 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
488063 TTTTCACAGT
*
488073 TA TA TA TA TA TA TA TA CA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
488104 GCACGCAGCT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.03, G:0.00, T:0.48
Consensus pattern (2 bp):
TA
Found at i:506981 original size:16 final size:18
Alignment explanation
Indices: 506960--506995 Score: 58
Period size: 16 Copynumber: 2.1 Consensus size: 18
506950 GAATTAACCG
506960 AAATTATTA-A-ATATTA
1 AAATTATTATATATATTA
506976 AAATTATTATATATATTA
1 AAATTATTATATATATTA
506994 AA
1 AA
506996 TATATATTTT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
16 9 0.50
17 1 0.06
18 8 0.44
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (18 bp):
AAATTATTATATATATTA
Found at i:510672 original size:21 final size:21
Alignment explanation
Indices: 510632--510673 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
510622 CTTATATAAC
* * *
510632 TTAAGTATTTTTTTTTATTTT
1 TTAAGTATATTTTATAATTTT
510653 TTAAGTATATTTTATAATTTT
1 TTAAGTATATTTTATAATTTT
510674 ATATTCTTAA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.26, C:0.00, G:0.05, T:0.69
Consensus pattern (21 bp):
TTAAGTATATTTTATAATTTT
Found at i:510678 original size:15 final size:16
Alignment explanation
Indices: 510658--510690 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
510648 ATTTTTTAAG
*
510658 TATATT-TTATAATTT
1 TATATTCTTAAAATTT
510673 TATATTCTTAAAATTT
1 TATATTCTTAAAATTT
510689 TA
1 TA
510691 ATATAATTTT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 6 0.38
16 10 0.62
ACGTcount: A:0.36, C:0.03, G:0.00, T:0.61
Consensus pattern (16 bp):
TATATTCTTAAAATTT
Found at i:518008 original size:14 final size:15
Alignment explanation
Indices: 517927--518061 Score: 103
Period size: 15 Copynumber: 8.5 Consensus size: 15
517917 TAATAAGGCT
517927 ATTTATTTTAAAATA
1 ATTTATTTTAAAATA
*
517942 ATTTATTATAAAATA
1 ATTTATTTTAAAATA
* *
517957 AATTATTATAAAATATGGA
1 ATTTATT-TTAAA-AT--A
517976 TTGATTTATTTTAAAATA
1 ---ATTTATTTTAAAATA
517994 ATTTATTTT-AAATA
1 ATTTATTTTAAAATA
** * *
518008 ATTTATTAGTATGGATTG
1 ATTTATT--T-TAAAATA
518026 ATTTATTTTAAAATA
1 ATTTATTTTAAAATA
518041 ATTTATTTT-AAATA
1 ATTTATTTTAAAATA
518055 ATTTATT
1 ATTTATT
518062 AGTATGGATT
Statistics
Matches: 96, Mismatches: 13, Indels: 23
0.73 0.10 0.17
Matches are distributed among these distances:
14 24 0.25
15 41 0.43
16 5 0.05
17 3 0.03
18 10 0.10
19 1 0.01
20 2 0.02
21 4 0.04
22 6 0.06
ACGTcount: A:0.43, C:0.00, G:0.05, T:0.52
Consensus pattern (15 bp):
ATTTATTTTAAAATA
Found at i:518009 original size:94 final size:93
Alignment explanation
Indices: 517904--518087 Score: 241
Period size: 94 Copynumber: 2.0 Consensus size: 93
517894 TATTAAAATA
517904 ATTTTAAATAATTTA-A-TAAGG-CT-ATTTATTTTAAAATAATTTATTATAAAATAAATTATTA
1 ATTTTAAATAATTTATAGTAAGGACTGATTTATTTTAAAATAATTTATT-TAAAAT-AA-T-TTA
517965 TAAAATATGGATTGATTTATTTTAAAATAATTT
62 T-AAATATGGATTGATTTATTTTAAAATAATTT
* * * *
517998 ATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATAATTTATTTTAAATAATTTATTA
1 ATTTTAAATAATTTA-TAGTAAGGACTGATTTATTTTAAAATAATTTATTTAAAATAATTTATAA
*
518063 GTATGGATTGATTTATTTTAAAATA
65 ATATGGATTGATTTATTTTAAAATA
518088 TGAATTGATT
Statistics
Matches: 80, Mismatches: 5, Indels: 10
0.84 0.05 0.11
Matches are distributed among these distances:
94 40 0.50
95 4 0.05
96 2 0.03
97 6 0.08
98 6 0.08
99 22 0.28
ACGTcount: A:0.42, C:0.01, G:0.07, T:0.50
Consensus pattern (93 bp):
ATTTTAAATAATTTATAGTAAGGACTGATTTATTTTAAAATAATTTATTTAAAATAATTTATAAA
TATGGATTGATTTATTTTAAAATAATTT
Found at i:518024 original size:47 final size:47
Alignment explanation
Indices: 517927--518087 Score: 250
Period size: 47 Copynumber: 3.3 Consensus size: 47
517917 TAATAAGGCT
* * *
517927 ATTTATTTTAAAATAATTTATTATAAAATAAATTATTATAAAATATGGATTG
1 ATTTATTTTAAAATAATTTATT-TTAAAT-AA-T-TTAT-TAGTATGGATTG
517979 ATTTATTTTAAAATAATTTATTTTAAATAATTTATTAGTATGGATTG
1 ATTTATTTTAAAATAATTTATTTTAAATAATTTATTAGTATGGATTG
518026 ATTTATTTTAAAATAATTTATTTTAAATAATTTATTAGTATGGATTG
1 ATTTATTTTAAAATAATTTATTTTAAATAATTTATTAGTATGGATTG
518073 ATTTATTTTAAAATA
1 ATTTATTTTAAAATA
518088 TGAATTGATT
Statistics
Matches: 106, Mismatches: 3, Indels: 5
0.93 0.03 0.04
Matches are distributed among these distances:
47 72 0.68
48 4 0.04
49 1 0.01
50 2 0.02
51 5 0.05
52 22 0.21
ACGTcount: A:0.42, C:0.00, G:0.07, T:0.51
Consensus pattern (47 bp):
ATTTATTTTAAAATAATTTATTTTAAATAATTTATTAGTATGGATTG
Found at i:518089 original size:22 final size:22
Alignment explanation
Indices: 518064--518149 Score: 84
Period size: 22 Copynumber: 3.7 Consensus size: 22
518054 AATTTATTAG
*
518064 TATGGATTGATTTATTTTAAAA
1 TATGAATTGATTTATTTTAAAA
** *
518086 TATGAATTGATTTATTATTGTAG
1 TATGAATTGATTTATT-TTAAAA
518109 T-TGTATAGATTGATTTATTTTAAAA
1 TATG---A-ATTGATTTATTTTAAAA
518134 TATGAATTGATTTATT
1 TATGAATTGATTTATT
518150 ATTGTAGTTG
Statistics
Matches: 51, Mismatches: 7, Indels: 12
0.73 0.10 0.17
Matches are distributed among these distances:
22 28 0.55
23 5 0.10
25 5 0.10
26 13 0.25
ACGTcount: A:0.34, C:0.00, G:0.14, T:0.52
Consensus pattern (22 bp):
TATGAATTGATTTATTTTAAAA
Found at i:518097 original size:26 final size:26
Alignment explanation
Indices: 518068--518230 Score: 83
Period size: 26 Copynumber: 6.3 Consensus size: 26
518058 TATTAGTATG
518068 GATTGATTTATTTTAAAATATGAATT
1 GATTGATTTATTTTAAAATATGAATT
* * * * *
518094 GATTTA-TTATTGT--AGT-TGTATA
1 GATTGATTTATTTTAAAATATGAATT
518116 GATTGATTTATTTTAAAATATGAATT
1 GATTGATTTATTTTAAAATATGAATT
* * * * *
518142 GATTTA-TTATTGT--AGT-TGTATA
1 GATTGATTTATTTTAAAATATGAATT
*
518164 GATTGATTTATTTTAAATAATTTATTAGTATAT
1 GATTGATTTATTTT-AA-AA--TA-T-GAAT-T
518197 -ATTGATTTATTTTAAAATATGAATT
1 GATTGATTTATTTTAAAATATGAATT
* *
518222 AATTTATTT
1 GATTGATTT
518231 TAAATAATTT
Statistics
Matches: 100, Mismatches: 21, Indels: 32
0.65 0.14 0.21
Matches are distributed among these distances:
22 18 0.18
23 16 0.16
25 15 0.15
26 24 0.24
27 2 0.02
28 2 0.02
29 1 0.01
30 2 0.02
31 3 0.03
32 17 0.17
ACGTcount: A:0.35, C:0.00, G:0.12, T:0.53
Consensus pattern (26 bp):
GATTGATTTATTTTAAAATATGAATT
Found at i:518134 original size:48 final size:48
Alignment explanation
Indices: 518063--518180 Score: 227
Period size: 48 Copynumber: 2.5 Consensus size: 48
518053 TAATTTATTA
*
518063 GTATGGATTGATTTATTTTAAAATATGAATTGATTTATTATTGTAGTT
1 GTATAGATTGATTTATTTTAAAATATGAATTGATTTATTATTGTAGTT
518111 GTATAGATTGATTTATTTTAAAATATGAATTGATTTATTATTGTAGTT
1 GTATAGATTGATTTATTTTAAAATATGAATTGATTTATTATTGTAGTT
518159 GTATAGATTGATTTATTTTAAA
1 GTATAGATTGATTTATTTTAAA
518181 TAATTTATTA
Statistics
Matches: 69, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
48 69 1.00
ACGTcount: A:0.33, C:0.00, G:0.15, T:0.52
Consensus pattern (48 bp):
GTATAGATTGATTTATTTTAAAATATGAATTGATTTATTATTGTAGTT
Found at i:518167 original size:22 final size:22
Alignment explanation
Indices: 518094--518167 Score: 67
Period size: 22 Copynumber: 3.2 Consensus size: 22
518084 AATATGAATT
518094 GATTTATTATTGTAGTTGTATA
1 GATTTATTATTGTAGTTGTATA
* * * * *
518116 GATTGATTTATTTTAAAATATGAATT
1 GATTTA-TTATTGT--AGT-TGTATA
518142 GATTTATTATTGTAGTTGTATA
1 GATTTATTATTGTAGTTGTATA
518164 GATT
1 GATT
518168 GATTTATTTT
Statistics
Matches: 38, Mismatches: 10, Indels: 8
0.68 0.18 0.14
Matches are distributed among these distances:
22 13 0.34
23 8 0.21
25 8 0.21
26 9 0.24
ACGTcount: A:0.31, C:0.00, G:0.16, T:0.53
Consensus pattern (22 bp):
GATTTATTATTGTAGTTGTATA
Found at i:518294 original size:31 final size:31
Alignment explanation
Indices: 518259--518317 Score: 109
Period size: 31 Copynumber: 1.9 Consensus size: 31
518249 AGTTGTATGG
*
518259 ATTATTTAAATTTCAGTATTGTAAAACTAAA
1 ATTATTTAAATCTCAGTATTGTAAAACTAAA
518290 ATTATTTAAATCTCAGTATTGTAAAACT
1 ATTATTTAAATCTCAGTATTGTAAAACT
518318 CTTTTAAGTT
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
31 27 1.00
ACGTcount: A:0.42, C:0.08, G:0.07, T:0.42
Consensus pattern (31 bp):
ATTATTTAAATCTCAGTATTGTAAAACTAAA
Found at i:522605 original size:27 final size:27
Alignment explanation
Indices: 522567--522620 Score: 83
Period size: 27 Copynumber: 2.0 Consensus size: 27
522557 ATGTTTAATC
522567 TATTGTTAGATT-ATCTTAAATTCAATT
1 TATTGTTAGATTAAT-TTAAATTCAATT
*
522594 TATTGTTCGATTAATTTAAATTCAATT
1 TATTGTTAGATTAATTTAAATTCAATT
522621 ACTACAATGA
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
27 23 0.92
28 2 0.08
ACGTcount: A:0.33, C:0.07, G:0.07, T:0.52
Consensus pattern (27 bp):
TATTGTTAGATTAATTTAAATTCAATT
Found at i:524032 original size:59 final size:58
Alignment explanation
Indices: 523933--524061 Score: 158
Period size: 59 Copynumber: 2.2 Consensus size: 58
523923 ATTTTGTTAC
523933 TTTTAATAGTCGAGAGACTCAATAAAGCAACACCTAATAGTCGGTAAATCATTTTATG-A
1 TTTTAATAGTCGAGAGACTCAATAAAGCAACACCTAATAGTCGGT-AATCA-TTTATGTA
* * *
523992 TTTTTAATAGTTG-GAGACTCAATAAAG-AAGCACTCT-ATAGTTGGTGATCATTTATGTA
1 -TTTTAATAGTCGAGAGACTCAATAAAGCAA-CAC-CTAATAGTCGGTAATCATTTATGTA
524050 TTTTAATAGTCG
1 TTTTAATAGTCG
524062 GATCATTCAG
Statistics
Matches: 62, Mismatches: 4, Indels: 9
0.83 0.05 0.12
Matches are distributed among these distances:
57 17 0.27
58 7 0.11
59 25 0.40
60 13 0.21
ACGTcount: A:0.35, C:0.12, G:0.17, T:0.36
Consensus pattern (58 bp):
TTTTAATAGTCGAGAGACTCAATAAAGCAACACCTAATAGTCGGTAATCATTTATGTA
Found at i:524408 original size:108 final size:108
Alignment explanation
Indices: 524214--524441 Score: 399
Period size: 108 Copynumber: 2.1 Consensus size: 108
524204 GTCTAGTGCC
*
524214 GGCTAGCCATACAACTATTGGTGAACCATGGGTGCTATTGTGAGAAGGTCTTCAAACTCAGAGGA
1 GGCTAGCCATGCAACTATTGGTGAACCATGGGTGCTATTGTGAGAAGGTCTTCAAACTCAGAGGA
524279 GGGTCCCGGAAAGAACGAAATTCAAAAGACAGATTCC-TGCGA
66 GGGTCCCGGAAAGAACGAAATTCAAAAGACAGATTCCATGCGA
524321 GGCTAGCCATGCAACTATTGGTGAACCATGGGTGCTATTGTGGAGAAGGTCTTCAAACTCAGGAG
1 GGCTAGCCATGCAACTATTGGTGAACCATGGGTGCTATTGT-GAGAAGGTCTTCAAACTCA-GAG
524386 GA-GGTCCCGGAAAGAACGAAATTCAAAAGACAGATTCCATGCGA
64 GAGGGTCCCGGAAAGAACGAAATTCAAAAGACAGATTCCATGCGA
524430 -GCTTAGCCATGC
1 GGC-TAGCCATGC
524442 CATCTGCAAC
Statistics
Matches: 116, Mismatches: 1, Indels: 6
0.94 0.01 0.05
Matches are distributed among these distances:
107 40 0.34
108 57 0.49
109 19 0.16
ACGTcount: A:0.32, C:0.20, G:0.28, T:0.21
Consensus pattern (108 bp):
GGCTAGCCATGCAACTATTGGTGAACCATGGGTGCTATTGTGAGAAGGTCTTCAAACTCAGAGGA
GGGTCCCGGAAAGAACGAAATTCAAAAGACAGATTCCATGCGA
Found at i:527125 original size:19 final size:18
Alignment explanation
Indices: 527103--527141 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 18
527093 AGATAAACAA
527103 AAACAACGACAAAAAACGT
1 AAACAAC-ACAAAAAACGT
**
527122 AAACAACAGTAAAAACGT
1 AAACAACACAAAAAACGT
527140 AA
1 AA
527142 GCTGCCAAAA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
18 11 0.61
19 7 0.39
ACGTcount: A:0.64, C:0.18, G:0.10, T:0.08
Consensus pattern (18 bp):
AAACAACACAAAAAACGT
Found at i:528984 original size:2 final size:2
Alignment explanation
Indices: 528977--529005 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
528967 ATAAAATTTA
528977 AT AT 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 AT AT A
529006 AAGAAAACAC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:529916 original size:21 final size:21
Alignment explanation
Indices: 529891--529947 Score: 64
Period size: 21 Copynumber: 2.7 Consensus size: 21
529881 AGCTCGTATA
529891 AATGC-CCGAAGTGC-CATGTAG
1 AATGCACCGAAGTGCGC--GTAG
* *
529912 AATGCATCGTAGTGCGCGTAG
1 AATGCACCGAAGTGCGCGTAG
529933 AATGCACCGAAGTGC
1 AATGCACCGAAGTGC
529948 TATATACGGT
Statistics
Matches: 30, Mismatches: 4, Indels: 4
0.79 0.11 0.11
Matches are distributed among these distances:
21 22 0.73
22 7 0.23
23 1 0.03
ACGTcount: A:0.28, C:0.23, G:0.30, T:0.19
Consensus pattern (21 bp):
AATGCACCGAAGTGCGCGTAG
Found at i:530777 original size:89 final size:87
Alignment explanation
Indices: 530639--530816 Score: 304
Period size: 89 Copynumber: 2.0 Consensus size: 87
530629 TTTCATTCTA
530639 TCCTATACATAGTTTACTATTTATCTTATCTCACTTCCCCTTTCACTCACATAAATCATCTATAT
1 TCCTATACATAGTTTACTATTTATCTTA-CTCACTTCCCCTTTCACTCACATAAATCATCTATAT
530704 ACTAGTTTTATCTATTTATTTAG
65 ACTAGTTTTATCTATTTATTTAG
530727 TCCTATACATAGTTTCTACTTATTTATCTTA-TCACTTCCCCTTTCACTCACATAAATCATCTAT
1 TCCTATACATAG-TT-TAC-TATTTATCTTACTCACTTCCCCTTTCACTCACATAAATCATCTAT
*
530791 ATACTATTTTTATCTATTTATTTAG
63 ATACTAGTTTTATCTATTTATTTAG
530816 T
1 T
530817 TCAATTTTCC
Statistics
Matches: 86, Mismatches: 1, Indels: 5
0.93 0.01 0.05
Matches are distributed among these distances:
88 12 0.14
89 60 0.70
90 3 0.03
91 11 0.13
ACGTcount: A:0.27, C:0.22, G:0.03, T:0.48
Consensus pattern (87 bp):
TCCTATACATAGTTTACTATTTATCTTACTCACTTCCCCTTTCACTCACATAAATCATCTATATA
CTAGTTTTATCTATTTATTTAG
Found at i:532453 original size:2 final size:2
Alignment explanation
Indices: 532446--532505 Score: 120
Period size: 2 Copynumber: 30.0 Consensus size: 2
532436 ATCTTATGTT
532446 CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA
1 CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA
532488 CA CA CA CA CA CA CA CA CA
1 CA CA CA CA CA CA CA CA CA
532506 TATATCAATG
Statistics
Matches: 58, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 58 1.00
ACGTcount: A:0.50, C:0.50, G:0.00, T:0.00
Consensus pattern (2 bp):
CA
Found at i:533572 original size:15 final size:15
Alignment explanation
Indices: 533554--533583 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
533544 AGCTTTCCTT
533554 AAGCTTGTATAACCC
1 AAGCTTGTATAACCC
533569 AAGCTTGTATAACCC
1 AAGCTTGTATAACCC
533584 CCAAAGATTC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.33, C:0.27, G:0.13, T:0.27
Consensus pattern (15 bp):
AAGCTTGTATAACCC
Found at i:540743 original size:36 final size:36
Alignment explanation
Indices: 540702--540773 Score: 117
Period size: 36 Copynumber: 2.0 Consensus size: 36
540692 TTACTTTTGG
*
540702 AAATTACTGGTTTGTGTCTGCCATTTTGTTTTCTGA
1 AAATTACTGGTTTGTGTCTGACATTTTGTTTTCTGA
* *
540738 AAATTAGTGGTTTGTGTCTGACGTTTTGTTTTCTGA
1 AAATTACTGGTTTGTGTCTGACATTTTGTTTTCTGA
540774 TTGCTGCTTT
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
36 33 1.00
ACGTcount: A:0.17, C:0.11, G:0.22, T:0.50
Consensus pattern (36 bp):
AAATTACTGGTTTGTGTCTGACATTTTGTTTTCTGA
Found at i:542891 original size:30 final size:30
Alignment explanation
Indices: 542855--542936 Score: 139
Period size: 30 Copynumber: 2.7 Consensus size: 30
542845 AAAAAAAAAT
542855 AATAGTT-AGTGACTATAATAGAAAGCAAAC
1 AATAGTTGAGTGACTA-AATAGAAAGCAAAC
*
542885 AATAGTTGAGTGACTAAATAGAAAGTAAAC
1 AATAGTTGAGTGACTAAATAGAAAGCAAAC
542915 AATAGTTGAGTGACTAAATAGA
1 AATAGTTGAGTGACTAAATAGA
542937 TAGTTATCCT
Statistics
Matches: 50, Mismatches: 1, Indels: 2
0.94 0.02 0.04
Matches are distributed among these distances:
30 42 0.84
31 8 0.16
ACGTcount: A:0.49, C:0.07, G:0.20, T:0.24
Consensus pattern (30 bp):
AATAGTTGAGTGACTAAATAGAAAGCAAAC
Found at i:554740 original size:205 final size:201
Alignment explanation
Indices: 554334--554740 Score: 737
Period size: 205 Copynumber: 2.0 Consensus size: 201
554324 CCTTTTCCCT
554334 TTCTTAGTTTTCTTGTTACGTGATGTGTATTTAATTCAGTAATCCATAATTTAAAACGAATATTA
1 TTCTTAGTTTTCTTGTTACGTGATGTGTATTTAATTCAGTAATCCATAATTTAAAACGAATATTA
554399 AAGATTAAGATAAAATCAGGATTAACCGAATATTAAAGATAAGCAGCCGCGGCACTATCCCTCAT
66 AAGATTAAGATAAAATCAGGATTAACCGAATATTAAAGATAAGCAGCCGCGGCACTATCCCTCAT
554464 GTTCGTCTCATTGCTGGAGTCGGCCTCCTATTGGTTGGGTGAAGATTAATTCTGATGGCGCTTGT
131 GTTCG-CTCATTGCTGGAGTCGGCCTCCTATTGGTTGGGTGAAGATTAATTCTGATGGCGCTTGT
554529 CACAGGG
195 CACAGGG
554536 TTCTTAGTTTTCTTGTTACGTGATGTGTA-TTAATTCAGTAATCCACTAATTTAAAACGAATATT
1 TTCTTAGTTTTCTTGTTACGTGATGTGTATTTAATTCAGTAATCCA-TAATTTAAAACGAATATT
554600 AAAGATTAAGATAAAAATCAGGATTAACCGAATATTAAAGATAAAGCAGCCGCGGCACTGTATCC
65 AAAGATTAAGAT-AAAATCAGGATTAACCGAATATTAAAGAT-AAGCAGCCGCGGCAC--TATCC
554665 CTCATGTTC-CGTCATTGCTGGAGTCGGCCTCCTATTGGTTGGGTGAAGATTAATTCTGATGGCG
126 CTCATGTTCGC-TCATTGCTGGAGTCGGCCTCCTATTGGTTGGGTGAAGATTAATTCTGATGGCG
554729 CTTGTCACAGGG
190 CTTGTCACAGGG
554741 AGTTGGGTAC
Statistics
Matches: 199, Mismatches: 0, Indels: 9
0.96 0.00 0.04
Matches are distributed among these distances:
201 16 0.08
202 59 0.30
203 29 0.15
204 16 0.08
205 65 0.33
206 14 0.07
ACGTcount: A:0.29, C:0.17, G:0.21, T:0.33
Consensus pattern (201 bp):
TTCTTAGTTTTCTTGTTACGTGATGTGTATTTAATTCAGTAATCCATAATTTAAAACGAATATTA
AAGATTAAGATAAAATCAGGATTAACCGAATATTAAAGATAAGCAGCCGCGGCACTATCCCTCAT
GTTCGCTCATTGCTGGAGTCGGCCTCCTATTGGTTGGGTGAAGATTAATTCTGATGGCGCTTGTC
ACAGGG
Found at i:563408 original size:19 final size:18
Alignment explanation
Indices: 563362--563411 Score: 64
Period size: 18 Copynumber: 2.7 Consensus size: 18
563352 CTATAAAAAG
*
563362 CTACTTTAATAAAGTACT
1 CTACTTTAATTAAGTACT
* *
563380 ATACTTTAATTAAGTTCT
1 CTACTTTAATTAAGTACT
563398 CTACATTTAATTAA
1 CTAC-TTTAATTAA
563412 ATTAGGTTTA
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
18 18 0.67
19 9 0.33
ACGTcount: A:0.38, C:0.14, G:0.04, T:0.44
Consensus pattern (18 bp):
CTACTTTAATTAAGTACT
Found at i:570532 original size:19 final size:17
Alignment explanation
Indices: 570508--570542 Score: 52
Period size: 19 Copynumber: 1.9 Consensus size: 17
570498 GATATACTTG
570508 TAAATATTATTTGTAATTA
1 TAAATATT-TTT-TAATTA
570527 TAAATATTTTTTAATT
1 TAAATATTTTTTAATT
570543 TTAATAAAAC
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 5 0.31
18 3 0.19
19 8 0.50
ACGTcount: A:0.40, C:0.00, G:0.03, T:0.57
Consensus pattern (17 bp):
TAAATATTTTTTAATTA
Found at i:572189 original size:31 final size:32
Alignment explanation
Indices: 572146--572208 Score: 85
Period size: 31 Copynumber: 2.0 Consensus size: 32
572136 TATTTAATTT
* *
572146 TCCCACTCATTTTCTATGGTTGA-TATACTTTG
1 TCCCACTCATTTTC-ATGATTAATTATACTTTG
572178 TCCC-CTCATTTTCATGATTAATTATACTTTG
1 TCCCACTCATTTTCATGATTAATTATACTTTG
572209 CTCCACCTTG
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
30 6 0.21
31 18 0.64
32 4 0.14
ACGTcount: A:0.21, C:0.22, G:0.10, T:0.48
Consensus pattern (32 bp):
TCCCACTCATTTTCATGATTAATTATACTTTG
Found at i:574284 original size:22 final size:22
Alignment explanation
Indices: 574259--574301 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 22
574249 CGATAAAGAC
* *
574259 TCTATTAGATGTCTTTTGAGAT
1 TCTATTAGATATATTTTGAGAT
574281 TCTATTAGATATATTTTGAGA
1 TCTATTAGATATATTTTGAGA
574302 GGAGAATAAT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.28, C:0.07, G:0.16, T:0.49
Consensus pattern (22 bp):
TCTATTAGATATATTTTGAGAT
Found at i:579878 original size:3 final size:3
Alignment explanation
Indices: 579870--579988 Score: 154
Period size: 3 Copynumber: 40.0 Consensus size: 3
579860 TTTTATCCAT
*
579870 TTA TTA TTA TTA ATA TTA TTA TTA TTTA TTA -TA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA -TTA TTA TTA TTA TTA TTA TTA
* * *
579915 TTA ATA TTA TTTA TCA TTA -TA ATA TTA TTA TTA TTA TTA TT- TTA
1 TTA TTA TTA -TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
*
579959 TTA TTA TTA TTA TTA TTA TTA TTA ATA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
579989 AATATAATAT
Statistics
Matches: 102, Mismatches: 9, Indels: 10
0.84 0.07 0.08
Matches are distributed among these distances:
2 6 0.06
3 90 0.88
4 6 0.06
ACGTcount: A:0.36, C:0.01, G:0.00, T:0.63
Consensus pattern (3 bp):
TTA
Found at i:580449 original size:6 final size:6
Alignment explanation
Indices: 580440--580484 Score: 72
Period size: 6 Copynumber: 7.5 Consensus size: 6
580430 AAAAAAAAAA
* *
580440 AGAGAC AGAGAC AGAAAA AGAGAC AGAGAC AGAGAC AGAGAC AGA
1 AGAGAC AGAGAC AGAGAC AGAGAC AGAGAC AGAGAC AGAGAC AGA
580485 CCGGGAAAAA
Statistics
Matches: 35, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
6 35 1.00
ACGTcount: A:0.56, C:0.13, G:0.31, T:0.00
Consensus pattern (6 bp):
AGAGAC
Found at i:580459 original size:18 final size:18
Alignment explanation
Indices: 580436--580484 Score: 80
Period size: 18 Copynumber: 2.7 Consensus size: 18
580426 GAAAAAAAAA
580436 AAAAAGAGACAGAGACAG
1 AAAAAGAGACAGAGACAG
580454 AAAAAGAGACAGAGACAG
1 AAAAAGAGACAGAGACAG
* *
580472 AGACAGAGACAGA
1 AAAAAGAGACAGA
580485 CCGGGAAAAA
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 29 1.00
ACGTcount: A:0.59, C:0.12, G:0.29, T:0.00
Consensus pattern (18 bp):
AAAAAGAGACAGAGACAG
Found at i:581436 original size:16 final size:17
Alignment explanation
Indices: 581404--581437 Score: 61
Period size: 17 Copynumber: 2.1 Consensus size: 17
581394 AATTTAGTCA
581404 TTTATTTTATATGTTTT
1 TTTATTTTATATGTTTT
581421 TTTATTTTAT-TGTTTT
1 TTTATTTTATATGTTTT
581437 T
1 T
581438 AAATATATTG
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 7 0.41
17 10 0.59
ACGTcount: A:0.15, C:0.00, G:0.06, T:0.79
Consensus pattern (17 bp):
TTTATTTTATATGTTTT
Found at i:587123 original size:26 final size:26
Alignment explanation
Indices: 587087--587139 Score: 106
Period size: 26 Copynumber: 2.0 Consensus size: 26
587077 ATCAAGTCAT
587087 CCATTGCCAAATCATGGAGATAAAAA
1 CCATTGCCAAATCATGGAGATAAAAA
587113 CCATTGCCAAATCATGGAGATAAAAA
1 CCATTGCCAAATCATGGAGATAAAAA
587139 C
1 C
587140 GTGAATGCAA
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:0.45, C:0.21, G:0.15, T:0.19
Consensus pattern (26 bp):
CCATTGCCAAATCATGGAGATAAAAA
Found at i:592654 original size:1 final size:1
Alignment explanation
Indices: 592648--592728 Score: 63
Period size: 1 Copynumber: 81.0 Consensus size: 1
592638 TATTATGCTT
* * * * * * * * *
592648 AAAAAAAGAAAAGAAGAAAAAAAAAAAAAAAAAGAAGAAGAAAAAAAAAAAGAAGAAAAAAAATA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
* *
592713 AAATAAAAAGAAAAAA
1 AAAAAAAAAAAAAAAA
592729 GGGTCAAGGT
Statistics
Matches: 58, Mismatches: 22, Indels: 0
0.73 0.28 0.00
Matches are distributed among these distances:
1 58 1.00
ACGTcount: A:0.86, C:0.00, G:0.11, T:0.02
Consensus pattern (1 bp):
A
Found at i:592671 original size:18 final size:17
Alignment explanation
Indices: 592648--592728 Score: 83
Period size: 17 Copynumber: 4.5 Consensus size: 17
592638 TATTATGCTT
*
592648 AAAAAAAGAAAAGAAGAAAA
1 AAAAAAA-AAAA-AAG-AAG
592668 AAAAAAAAAAAAAGAAG
1 AAAAAAAAAAAAAGAAG
592685 AAGAAAAAAAAAAAGAAG
1 AA-AAAAAAAAAAAGAAG
* *
592703 AAAAAAAATAAAATAA-
1 AAAAAAAAAAAAAGAAG
592719 AAAGAAAAAA
1 AAA-AAAAAA
592729 GGGTCAAGGT
Statistics
Matches: 55, Mismatches: 4, Indels: 7
0.83 0.06 0.11
Matches are distributed among these distances:
16 3 0.05
17 21 0.38
18 20 0.36
19 4 0.07
20 7 0.13
ACGTcount: A:0.86, C:0.00, G:0.11, T:0.02
Consensus pattern (17 bp):
AAAAAAAAAAAAAGAAG
Found at i:592672 original size:21 final size:20
Alignment explanation
Indices: 592648--592728 Score: 96
Period size: 20 Copynumber: 4.1 Consensus size: 20
592638 TATTATGCTT
*
592648 AAAAAAAGAAAAGAAG-AAA
1 AAAAAAAAAAAAGAAGAAAA
592667 AAAAAAAAAAAA-AAGAAGAA
1 AAAAAAAAAAAAGAAGAA-AA
*
592687 GAAAAAAAAAAAGAAGAAAA
1 AAAAAAAAAAAAGAAGAAAA
*
592707 AAAATAAAATAAA-AAGAAAA
1 AAAA-AAAAAAAAGAAGAAAA
592727 AA
1 AA
592729 GGGTCAAGGT
Statistics
Matches: 54, Mismatches: 4, Indels: 7
0.83 0.06 0.11
Matches are distributed among these distances:
18 3 0.06
19 12 0.22
20 27 0.50
21 12 0.22
ACGTcount: A:0.86, C:0.00, G:0.11, T:0.02
Consensus pattern (20 bp):
AAAAAAAAAAAAGAAGAAAA
Found at i:594007 original size:52 final size:52
Alignment explanation
Indices: 593860--594115 Score: 464
Period size: 52 Copynumber: 5.0 Consensus size: 52
593850 GAATGTGCTT
593860 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAG-AC
1 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGAAC
593911 ATAGCATCTTCT-GAAGTGTTC-TTGAGTTATCTGATCTGGTTGGACAGAAC
1 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGAAC
*
593961 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATTTGGTTGGACAGAAC
1 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGAAC
*
594013 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATTTGGTTGGACAGAAC
1 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGAAC
*
594065 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGATTGGACAGAA
1 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGAA
594116 TCAAGTATTG
Statistics
Matches: 199, Mismatches: 3, Indels: 5
0.96 0.01 0.02
Matches are distributed among these distances:
49 26 0.13
50 23 0.12
51 21 0.11
52 129 0.65
ACGTcount: A:0.23, C:0.14, G:0.25, T:0.38
Consensus pattern (52 bp):
ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGAAC
Found at i:594226 original size:52 final size:52
Alignment explanation
Indices: 594148--594250 Score: 197
Period size: 52 Copynumber: 2.0 Consensus size: 52
594138 AAATTTGCCA
*
594148 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGAAC
1 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGATTGGACAGAAC
594200 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGATTGGACAGAA
1 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGATTGGACAGAA
594251 TCAAGTATTG
Statistics
Matches: 50, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
52 50 1.00
ACGTcount: A:0.24, C:0.15, G:0.24, T:0.37
Consensus pattern (52 bp):
ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGATTGGACAGAAC
Found at i:594255 original size:135 final size:135
Alignment explanation
Indices: 594013--594586 Score: 1103
Period size: 135 Copynumber: 4.3 Consensus size: 135
594003 TGGACAGAAC
* *
594013 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATTTGGTTGGACAGAACATAGCATCTTCTG
1 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTAATCTGGTTGGACAGAACATAGCATCTTCTG
594078 GAAGTGTTCTTTGAGTTATCTGATCTGATTGGACAGAATCAAGTATTGAACTTAAAAGATAAATT
66 GAAGTGTTCTTTGAGTTATCTGATCTGATTGGACAGAATCAAGTATTGAACTTAAAAGATAAATT
594143 TGCCA
131 TGCCA
*
594148 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGAACATAGCATCTTCTG
1 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTAATCTGGTTGGACAGAACATAGCATCTTCTG
594213 GAAGTGTTCTTTGAGTTATCTGATCTGATTGGACAGAATCAAGTATTGAACTTAAAAGATAAATT
66 GAAGTGTTCTTTGAGTTATCTGATCTGATTGGACAGAATCAAGTATTGAACTTAAAAGATAAATT
594278 TGCCA
131 TGCCA
594283 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTAATCTGGTTGGACAGAACATAGCATCTTCTG
1 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTAATCTGGTTGGACAGAACATAGCATCTTCTG
*
594348 GAAGTGTTCTTTGAGTTATCTGATCTGATTGGACAGAATCAAGTATTGAATTTAAAAGATAAATT
66 GAAGTGTTCTTTGAGTTATCTGATCTGATTGGACAGAATCAAGTATTGAACTTAAAAGATAAATT
594413 TGCCA
131 TGCCA
594418 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTAATCTGGTTGGACAGAACATAGCATCTTCTG
1 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTAATCTGGTTGGACAGAACATAGCATCTTCTG
*
594483 GAAGTGTTCTTTGAGTTATCTGATCTGATTGGACAGAATCAAGTATTGAATTTAAAAGATAAATT
66 GAAGTGTTCTTTGAGTTATCTGATCTGATTGGACAGAATCAAGTATTGAACTTAAAAGATAAATT
594548 TGCCA
131 TGCCA
594553 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCT
1 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCT
594587 TTTACTAGAA
Statistics
Matches: 436, Mismatches: 3, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
135 436 1.00
ACGTcount: A:0.29, C:0.14, G:0.21, T:0.37
Consensus pattern (135 bp):
ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTAATCTGGTTGGACAGAACATAGCATCTTCTG
GAAGTGTTCTTTGAGTTATCTGATCTGATTGGACAGAATCAAGTATTGAACTTAAAAGATAAATT
TGCCA
Found at i:594341 original size:187 final size:184
Alignment explanation
Indices: 593911--594385 Score: 474
Period size: 187 Copynumber: 2.6 Consensus size: 184
593901 TTGGACAGAC
*
593911 ATAGCATCTTCT-GAAGTGTTC-TTGAGTTATCTGATCTGGTTGGACAGAACATAGCATCTTCTG
1 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTAATCTGGTTGGACAGAACATAGCATCTTCTG
*
593974 GAAGTGTTCTTTGAGTTATCTGATTTGGTTGGACAGAACATAGCATCTTCTGGAAGTGTTCTTTG
66 GAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGAACATAGCATCTTCTGGAAGTGTTCTTTG
* * * ** ***
594039 AGTTATCTGATTTGGTTGGACAGAACATAGCATCTTCTGGAAGTGTTCTTTGAG
131 AGTTATCTGATCTGATTGGACAGAACATAGCATCTACTAAAAGTGAAATTTGAG
* * ** * ** *** * *
594093 TTATCTGATCTGAT-TGGACAG-AATCAAGTATTGAACTTA-AAAGAT-AAATTTG-C--CA-AT
1 ATAGC--ATCT--TCTGGA-AGTGTTC---T-TTG-AGTTATCTA-ATCTGGTTGGACAGAACAT
594150 AGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGAACATAGCATCTTCTGGA
55 AGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGAACATAGCATCTTCTGGA
*
594215 AGTGTTCTTTGAGTTATCTGATCTGATTGGACAGAATCA-AGTAT-TGAACTTAAAAGAT-AAAT
120 AGTGTTCTTTGAGTTATCTGATCTGATTGGACAGAA-CATAGCATCT--AC-TAAAAG-TGAAAT
594277 TTGCCA-
180 TTG--AG
594283 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTAATCTGGTTGGACAGAACATAGCATCTTCTG
1 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTAATCTGGTTGGACAGAACATAGCATCTTCTG
*
594348 GAAGTGTTCTTTGAGTTATCTGATCTGATTGGACAGAA
66 GAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGAA
594386 TCAAGTATTG
Statistics
Matches: 229, Mismatches: 36, Indels: 51
0.72 0.11 0.16
Matches are distributed among these distances:
182 9 0.04
183 7 0.03
184 6 0.03
185 1 0.00
186 10 0.04
187 162 0.71
188 8 0.03
189 8 0.03
190 5 0.02
191 7 0.03
192 6 0.03
ACGTcount: A:0.27, C:0.14, G:0.23, T:0.36
Consensus pattern (184 bp):
ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTAATCTGGTTGGACAGAACATAGCATCTTCTG
GAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGAACATAGCATCTTCTGGAAGTGTTCTTTG
AGTTATCTGATCTGATTGGACAGAACATAGCATCTACTAAAAGTGAAATTTGAG
Found at i:594361 original size:52 final size:52
Alignment explanation
Indices: 594283--594385 Score: 188
Period size: 52 Copynumber: 2.0 Consensus size: 52
594273 AAATTTGCCA
*
594283 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTAATCTGGTTGGACAGAAC
1 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTAATCTGATTGGACAGAAC
*
594335 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGATTGGACAGAA
1 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTAATCTGATTGGACAGAA
594386 TCAAGTATTG
Statistics
Matches: 49, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
52 49 1.00
ACGTcount: A:0.25, C:0.15, G:0.23, T:0.37
Consensus pattern (52 bp):
ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTAATCTGATTGGACAGAAC
Found at i:594496 original size:52 final size:52
Alignment explanation
Indices: 594418--594520 Score: 188
Period size: 52 Copynumber: 2.0 Consensus size: 52
594408 AAATTTGCCA
*
594418 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTAATCTGGTTGGACAGAAC
1 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTAATCTGATTGGACAGAAC
*
594470 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGATTGGACAGAA
1 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTAATCTGATTGGACAGAA
594521 TCAAGTATTG
Statistics
Matches: 49, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
52 49 1.00
ACGTcount: A:0.25, C:0.15, G:0.23, T:0.37
Consensus pattern (52 bp):
ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTAATCTGATTGGACAGAAC
Found at i:595457 original size:119 final size:114
Alignment explanation
Indices: 595160--595708 Score: 784
Period size: 119 Copynumber: 4.8 Consensus size: 114
595150 TCAAATCCAC
*
595160 TTGATGGATCATTCTTTTCCAGA-GAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAA
1 TTGATGGATCA-TCATTTCCAGAGGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAA
* * *
595224 GAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGTTTAAATTCATCAT
65 GAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGCTTAAATTCATCAA
* * * *
595274 TTGATGGATTAAC-TTTGCCAG-GTAGAGTTCATAATGAGAAGAACTCGTCATCTGAAGAAGGAA
1 TTGATGGATCATCATTT-CCAGAGGAAAGTTCATAATGAGAAGAA--C-TCATCTGAAGAAGGAA
*
595337 GAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGCTTGAATTCATCAAA
62 GAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGCTTAAATTCATC-AA
*
595391 TTGATGGATCATCATTTCCAGAGGAAGAGTTCATAATAAGAAGAACTCGTCATCTGAAGAAGGAA
1 TTGATGGATCATCATTTCCAGAGGAA-AGTTCATAATGAGAAGAA--C-TCATCTGAAGAAGGAA
*
595456 GAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGTTTAAATTCATCAAA
62 GAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGCTTAAATTCATC-AA
*
595510 CTGATGGATCATCATTTCCAGAGGTAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAA
1 TTGATGGATCATCATTTCCAGAGG-AAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAA
* * *
595575 GAAGTTCATAATGAGAAGAATTTGTTCAAACTTTTGCTTGAATTCATC-A
65 GAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGCTTAAATTCATCAA
* * * *
595624 TTGATGGATCAACATTACCAG-GTAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAA
1 TTGATGGATCATCATTTCCAGAGGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAG
595688 AAGTTCATAATGAGAAGAACT
66 AAGTTCATAATGAGAAGAACT
595709 CATCAAGAGC
Statistics
Matches: 398, Mismatches: 27, Indels: 22
0.89 0.06 0.05
Matches are distributed among these distances:
112 63 0.16
113 25 0.06
114 29 0.07
115 1 0.00
116 127 0.32
117 17 0.04
118 5 0.01
119 129 0.32
120 2 0.01
ACGTcount: A:0.38, C:0.13, G:0.20, T:0.29
Consensus pattern (114 bp):
TTGATGGATCATCATTTCCAGAGGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAG
AAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGCTTAAATTCATCAA
Found at i:595594 original size:235 final size:228
Alignment explanation
Indices: 595160--595708 Score: 829
Period size: 235 Copynumber: 2.4 Consensus size: 228
595150 TCAAATCCAC
*
595160 TTGATGGATCATTCTTTTCCAGA-GAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAA
1 TTGATGGATCA-TCATTTCCAGAGGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAA
* ** *
595224 GAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGTTTAAATTCATCATTTGATGGATTAACTT
65 GAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGTTTAAATTCATCAACTGATGGATCAACTT
*
595289 TGCCAGGTAGAGTTCATAATGAGAAGAACTCGTCATCTGAAGAAGGAAGAAGAAGTTCATAATGA
130 TGCCAGGTAAAGTTCATAATGAGAAGAAC-CGTCATCTGAAGAAGGAAGAAGAAGTTCATAATGA
*
595354 GAAGAACTTGTTCAACCTTTTGCTTGAATTCATCAAA
194 GAAGAACTTGTTCAAACTTTTGCTTGAATTCATC--A
*
595391 TTGATGGATCATCATTTCCAGAGGAAGAGTTCATAATAAGAAGAACTCGTCATCTGAAGAAGGAA
1 TTGATGGATCATCATTTCCAGAGGAA-AGTTCATAATGAGAAGAA--C-TCATCTGAAGAAGGAA
595456 GAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGTTTAAATTCATCAAACTGATGGATCA
62 GAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGTTTAAATTCATC-AACTGATGGATCA
*
595521 TCATTT-CCAGAGGTAAAGTTCATAATGAGAAGAA-C-TCATCTGAAGAAGGAAGAAGAAGTTCA
126 AC-TTTGCC--AGGTAAAGTTCATAATGAGAAGAACCGTCATCTGAAGAAGGAAGAAGAAGTTCA
*
595583 TAATGAGAAGAATTTGTTCAAACTTTTGCTTGAATTCATCA
188 TAATGAGAAGAACTTGTTCAAACTTTTGCTTGAATTCATCA
* * * *
595624 TTGATGGATCAACATTACCAG-GTAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAA
1 TTGATGGATCATCATTTCCAGAGGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAG
595688 AAGTTCATAATGAGAAGAACT
66 AAGTTCATAATGAGAAGAACT
595709 CATCAAGAGC
Statistics
Matches: 294, Mismatches: 15, Indels: 21
0.89 0.05 0.06
Matches are distributed among these distances:
228 40 0.14
229 1 0.00
230 10 0.03
231 31 0.11
232 20 0.07
233 20 0.07
234 1 0.00
235 131 0.45
236 14 0.05
237 3 0.01
238 23 0.08
ACGTcount: A:0.38, C:0.13, G:0.20, T:0.29
Consensus pattern (228 bp):
TTGATGGATCATCATTTCCAGAGGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAG
AAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGTTTAAATTCATCAACTGATGGATCAACTTT
GCCAGGTAAAGTTCATAATGAGAAGAACCGTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGA
AGAACTTGTTCAAACTTTTGCTTGAATTCATCA
Found at i:595962 original size:3 final size:3
Alignment explanation
Indices: 595956--596082 Score: 202
Period size: 3 Copynumber: 42.7 Consensus size: 3
595946 TTTTTATCCA
*
595956 TAT TAT TAT TAT TAA TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
* * * *
596004 TAA TAT TAT TAT TAT CAT TAT TAA TAT TAT TAT TAT TAT TAT TTT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
596052 TAT TAT TAT TAT TAT TAT TAT T-T TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
596083 AATATATTAA
Statistics
Matches: 113, Mismatches: 10, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
2 2 0.02
3 111 0.98
ACGTcount: A:0.35, C:0.01, G:0.00, T:0.65
Consensus pattern (3 bp):
TAT
Found at i:596560 original size:6 final size:6
Alignment explanation
Indices: 596551--596589 Score: 60
Period size: 6 Copynumber: 6.5 Consensus size: 6
596541 AAAAAAAAAA
* *
596551 AGAGAC AGAGAC AGAGAC AGAAAA AGAGAC AGAGAC AGA
1 AGAGAC AGAGAC AGAGAC AGAGAC AGAGAC AGAGAC AGA
596590 ACCGGGAAAA
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
6 29 1.00
ACGTcount: A:0.56, C:0.13, G:0.31, T:0.00
Consensus pattern (6 bp):
AGAGAC
Found at i:600084 original size:4 final size:4
Alignment explanation
Indices: 600075--600114 Score: 80
Period size: 4 Copynumber: 10.0 Consensus size: 4
600065 TGCATGAACG
600075 CCTC CCTC CCTC CCTC CCTC CCTC CCTC CCTC CCTC CCTC
1 CCTC CCTC CCTC CCTC CCTC CCTC CCTC CCTC CCTC CCTC
600115 TCTGCCGCGT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 36 1.00
ACGTcount: A:0.00, C:0.75, G:0.00, T:0.25
Consensus pattern (4 bp):
CCTC
Found at i:603100 original size:20 final size:20
Alignment explanation
Indices: 603075--603187 Score: 118
Period size: 20 Copynumber: 5.6 Consensus size: 20
603065 TAGTTGAAAA
*
603075 TCGCGTTGCGATTTTCTATT
1 TCGCGTTGCGATTTTCCATT
*
603095 TCGCGTTGTGATTTTCCATT
1 TCGCGTTGCGATTTTCCATT
*
603115 TCGCGTTGCAATTTTCCATT
1 TCGCGTTGCGATTTTCCATT
* * ** **
603135 TCACGTTGCGATAGTTGAAAA
1 TCGCGTTGCGAT-TTTCCATT
* *
603156 TCGCGTTGCGGTTTTTCATT
1 TCGCGTTGCGATTTTCCATT
603176 TCGCGTTGCGAT
1 TCGCGTTGCGAT
603188 AGTCTACAAT
Statistics
Matches: 73, Mismatches: 19, Indels: 2
0.78 0.20 0.02
Matches are distributed among these distances:
20 60 0.82
21 13 0.18
ACGTcount: A:0.14, C:0.20, G:0.22, T:0.43
Consensus pattern (20 bp):
TCGCGTTGCGATTTTCCATT
Found at i:603204 original size:41 final size:41
Alignment explanation
Indices: 603059--603214 Score: 156
Period size: 41 Copynumber: 3.8 Consensus size: 41
603049 GCATTTCGAT
* *
603059 TTGCGATAGTTGAAAATCGCGTTGCGATTTTCTATTTCGCG
1 TTGCGATAGTTGAAAATCGCGTTGCGATTTTCCATTTCACG
* * ** ** *
603100 TTGTGAT-TTTCCATTTCGCGTTGCAATTTTCCATTTCACG
1 TTGCGATAGTTGAAAATCGCGTTGCGATTTTCCATTTCACG
* * *
603140 TTGCGATAGTTGAAAATCGCGTTGCGGTTTTTCATTTCGCG
1 TTGCGATAGTTGAAAATCGCGTTGCGATTTTCCATTTCACG
*
603181 TTGCGATAGTCT-ACAAT-GTCGTTGCGATTTTCCA
1 TTGCGATAGT-TGAAAATCG-CGTTGCGATTTTCCA
603215 AATTCGTTGG
Statistics
Matches: 90, Mismatches: 22, Indels: 6
0.76 0.19 0.05
Matches are distributed among these distances:
40 32 0.36
41 57 0.63
42 1 0.01
ACGTcount: A:0.18, C:0.19, G:0.22, T:0.41
Consensus pattern (41 bp):
TTGCGATAGTTGAAAATCGCGTTGCGATTTTCCATTTCACG
Found at i:603223 original size:81 final size:79
Alignment explanation
Indices: 603059--603223 Score: 183
Period size: 81 Copynumber: 2.0 Consensus size: 79
603049 GCATTTCGAT
* * * *
603059 TTGCGATAGTTGAAAATCGCGTTGCGATTTTCTATTTCGCGTTGTGATTTTCCATTTCGCGTTGC
1 TTGCGATAGTTGAAAATCGCGTTGCGATTTTCTATTTCGCGTTGCGATTTACAATGTC-CGTTGC
*
603124 AATTTTCCATTTCACG
65 AATTTTCCAATT-ACG
*
603140 TTGCGATAGTTGAAAATCGCGTTGCGGTTTT-TCATTTCGCGTTGCGATAGTCTACAATGT-CGT
1 TTGCGATAGTTGAAAATCGCGTTGCGATTTTCT-ATTTCGCGTTGCGAT--T-TACAATGTCCGT
*
603203 TGCGATTTTCCAAATT-CG
62 TGCAATTTTCC-AATTACG
603221 TTG
1 TTG
603224 GAAATAAGTG
Statistics
Matches: 72, Mismatches: 7, Indels: 10
0.81 0.08 0.11
Matches are distributed among these distances:
80 1 0.01
81 49 0.68
82 13 0.18
83 4 0.06
84 5 0.07
ACGTcount: A:0.18, C:0.19, G:0.22, T:0.41
Consensus pattern (79 bp):
TTGCGATAGTTGAAAATCGCGTTGCGATTTTCTATTTCGCGTTGCGATTTACAATGTCCGTTGCA
ATTTTCCAATTACG
Found at i:603387 original size:6 final size:6
Alignment explanation
Indices: 603368--603402 Score: 56
Period size: 6 Copynumber: 6.2 Consensus size: 6
603358 TCGTCCCGTC
603368 TCGT-G TCG-GG TCGTGG TCGTGG TCGTGG TCGTGG T
1 TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG T
603403 AATACGTGTC
Statistics
Matches: 28, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
5 7 0.25
6 21 0.75
ACGTcount: A:0.00, C:0.17, G:0.49, T:0.34
Consensus pattern (6 bp):
TCGTGG
Found at i:603589 original size:21 final size:21
Alignment explanation
Indices: 603564--603617 Score: 99
Period size: 21 Copynumber: 2.6 Consensus size: 21
603554 GAACTGGAAA
603564 ATCGCAACGCGATTTTCAACT
1 ATCGCAACGCGATTTTCAACT
*
603585 ATCGCAACGCGATTTTCAATT
1 ATCGCAACGCGATTTTCAACT
603606 ATCGCAACGCGA
1 ATCGCAACGCGA
603618 AATGCAACGC
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 32 1.00
ACGTcount: A:0.30, C:0.28, G:0.17, T:0.26
Consensus pattern (21 bp):
ATCGCAACGCGATTTTCAACT
Found at i:605878 original size:15 final size:17
Alignment explanation
Indices: 605847--605878 Score: 50
Period size: 15 Copynumber: 2.0 Consensus size: 17
605837 ATATATTTTT
605847 ATCTATCTTGCAATTTA
1 ATCTATCTTGCAATTTA
605864 ATCTA-CTTG-AATTTA
1 ATCTATCTTGCAATTTA
605879 TTATATTATG
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
15 6 0.40
16 4 0.27
17 5 0.33
ACGTcount: A:0.31, C:0.16, G:0.06, T:0.47
Consensus pattern (17 bp):
ATCTATCTTGCAATTTA
Found at i:610023 original size:24 final size:24
Alignment explanation
Indices: 609967--610050 Score: 125
Period size: 24 Copynumber: 3.5 Consensus size: 24
609957 AATGCGTCAC
* * *
609967 AAAGACAAAGATAAACGTGCCA-C
1 AAAGACAGAGATAAATGTGCCATA
*
609990 AAAGATAGAGATAAATGTGCCATA
1 AAAGACAGAGATAAATGTGCCATA
610014 AAAGACAGAGATAAATGTGCCATA
1 AAAGACAGAGATAAATGTGCCATA
610038 AAAGACAGAGATA
1 AAAGACAGAGATA
610051 CACGTATCAT
Statistics
Matches: 55, Mismatches: 5, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
23 19 0.35
24 36 0.65
ACGTcount: A:0.52, C:0.13, G:0.20, T:0.14
Consensus pattern (24 bp):
AAAGACAGAGATAAATGTGCCATA
Found at i:610061 original size:24 final size:24
Alignment explanation
Indices: 609967--610063 Score: 97
Period size: 24 Copynumber: 4.1 Consensus size: 24
609957 AATGCGTCAC
* * *
609967 AAAGACAAAGATAAACGTGCCA-C
1 AAAGACAGAGATAAACGTACCATA
* * *
609990 AAAGATAGAGATAAATGTGCCATA
1 AAAGACAGAGATAAACGTACCATA
* *
610014 AAAGACAGAGATAAATGTGCCATA
1 AAAGACAGAGATAAACGTACCATA
* *
610038 AAAGACAGAGATACACGTATCATA
1 AAAGACAGAGATAAACGTACCATA
610062 AA
1 AA
610064 GGCAGAATTA
Statistics
Matches: 64, Mismatches: 9, Indels: 1
0.86 0.12 0.01
Matches are distributed among these distances:
23 19 0.30
24 45 0.70
ACGTcount: A:0.52, C:0.14, G:0.19, T:0.15
Consensus pattern (24 bp):
AAAGACAGAGATAAACGTACCATA
Found at i:610690 original size:20 final size:20
Alignment explanation
Indices: 610653--610691 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
610643 GTATTGTATG
**
610653 AATAGTAACGATGTTGTGTA
1 AATAGTAACGATACTGTGTA
*
610673 AATAGTACCGATACTGTGT
1 AATAGTAACGATACTGTGT
610692 GAACAGTAAT
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.33, C:0.10, G:0.23, T:0.33
Consensus pattern (20 bp):
AATAGTAACGATACTGTGTA
Found at i:611353 original size:31 final size:31
Alignment explanation
Indices: 611303--611394 Score: 121
Period size: 31 Copynumber: 3.0 Consensus size: 31
611293 CCCTAAGGAC
*
611303 CAGTCCATATGTTCTGAAGAACATAGGTAAT
1 CAGTACATATGTTCTGAAGAACATAGGTAAT
* * *
611334 TAGTACATATGTCCCGAAGAACATAGGTAAT
1 CAGTACATATGTTCTGAAGAACATAGGTAAT
* * *
611365 CAGTCCATATTTTCTGAATAACATAGGTAA
1 CAGTACATATGTTCTGAAGAACATAGGTAA
611395 CCCTCGACTC
Statistics
Matches: 51, Mismatches: 10, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
31 51 1.00
ACGTcount: A:0.37, C:0.16, G:0.17, T:0.29
Consensus pattern (31 bp):
CAGTACATATGTTCTGAAGAACATAGGTAAT
Found at i:613717 original size:32 final size:32
Alignment explanation
Indices: 613673--613760 Score: 85
Period size: 32 Copynumber: 2.8 Consensus size: 32
613663 CTAAAAATTA
613673 ATTAACAA-AATTAATATTTTTGATAAAAAAAT
1 ATTAA-AATAATTAATATTTTTGATAAAAAAAT
*** *
613705 ATTATTTTAATTAAT-TTTTT-AT-CAAAAAT
1 ATTAAAATAATTAATATTTTTGATAAAAAAAT
*
613734 ATTAAAATATATTAATATTTATGATAA
1 ATTAAAATA-ATTAATATTTTTGATAA
613761 TTTTTTTAAC
Statistics
Matches: 42, Mismatches: 9, Indels: 9
0.70 0.15 0.15
Matches are distributed among these distances:
29 12 0.29
30 8 0.19
31 9 0.21
32 13 0.31
ACGTcount: A:0.50, C:0.02, G:0.02, T:0.45
Consensus pattern (32 bp):
ATTAAAATAATTAATATTTTTGATAAAAAAAT
Found at i:614807 original size:21 final size:21
Alignment explanation
Indices: 614778--614817 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
614768 TTTTTATTAT
* *
614778 TTTATTAAAAGAATTGGTATG
1 TTTAGTAAAACAATTGGTATG
*
614799 TTTAGTAAAACACTTGGTA
1 TTTAGTAAAACAATTGGTA
614818 CATTTAGACT
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.38, C:0.05, G:0.17, T:0.40
Consensus pattern (21 bp):
TTTAGTAAAACAATTGGTATG
Done.