Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008040.1 Hibiscus syriacus cultivar Beakdansim tig00110527_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: 437554
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.33
File 2 of 2
Found at i:300822 original size:24 final size:24
Alignment explanation
Indices: 300795--300845 Score: 102
Period size: 24 Copynumber: 2.1 Consensus size: 24
300785 ACTACCGGAA
300795 AGTAAGATTAAATGATGTTCCAAC
1 AGTAAGATTAAATGATGTTCCAAC
300819 AGTAAGATTAAATGATGTTCCAAC
1 AGTAAGATTAAATGATGTTCCAAC
300843 AGT
1 AGT
300846 TAAAGTGTTT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.41, C:0.12, G:0.18, T:0.29
Consensus pattern (24 bp):
AGTAAGATTAAATGATGTTCCAAC
Found at i:305079 original size:49 final size:49
Alignment explanation
Indices: 304999--305471 Score: 596
Period size: 49 Copynumber: 9.6 Consensus size: 49
304989 AACTACTCTA
* * *
304999 TAATACAAGTTAAATGCATAATGGTGCATTTTTGGAAGAAATGTGCCAC
1 TAATGCAAGTTAAATGCATAATGGTGCATTTTTGGCAGAAAGGTGCCAC
*
305048 TAATGCAAGTTAAATGCATAATGGTGTATTTTTGGCAGAAAGGTGCCAC
1 TAATGCAAGTTAAATGCATAATGGTGCATTTTTGGCAGAAAGGTGCCAC
* *
305097 TAATGCAAGTTAAATTCATAATGGTACATTTTTGGCAGAAAGGTGCCAC
1 TAATGCAAGTTAAATGCATAATGGTGCATTTTTGGCAGAAAGGTGCCAC
* * *
305146 TAATGCAAGTTAAATGCATAATGGTGCATTTTGTTTTGCAGAAATGTACCAC
1 TAATGCAAGTTAAATGCATAATGGTGCA--TT-TTTGGCAGAAAGGTGCCAC
* ** * * *
305198 TAATGCAAGTTAAATGCATATTGGTGCATTTTTTACAGAAATGTGCTAG
1 TAATGCAAGTTAAATGCATAATGGTGCATTTTTGGCAGAAAGGTGCCAC
* * * *
305247 TAAGGCAAATTAAATGCATAATAGTGCGTTTTTGGCAGAAAGGTGCCAC
1 TAATGCAAGTTAAATGCATAATGGTGCATTTTTGGCAGAAAGGTGCCAC
* *
305296 TGATGCAAGTTAAATGCATAATGGTGCATTTTT-GCATAAAGGTGCCAC
1 TAATGCAAGTTAAATGCATAATGGTGCATTTTTGGCAGAAAGGTGCCAC
* * * * *
305344 TAATGAAAATTAAATGTATAATGGTGCCTTTTTGGCATAAAGGTGCCAC
1 TAATGCAAGTTAAATGCATAATGGTGCATTTTTGGCAGAAAGGTGCCAC
*
305393 TAATG-AGAGTTAAATGCATAACT-GTGCA-TTTTGGCAGAAAGGTGCCTC
1 TAATGCA-AGTTAAATGCATAA-TGGTGCATTTTTGGCAGAAAGGTGCCAC
* *
305441 TAATG-ATAGTTAAATGTATAACGGTGCATTT
1 TAATGCA-AGTTAAATGCATAATGGTGCATTT
305472 CGGCATAAAA
Statistics
Matches: 370, Mismatches: 46, Indels: 16
0.86 0.11 0.04
Matches are distributed among these distances:
48 85 0.23
49 237 0.64
50 3 0.01
51 2 0.01
52 43 0.12
ACGTcount: A:0.34, C:0.13, G:0.22, T:0.32
Consensus pattern (49 bp):
TAATGCAAGTTAAATGCATAATGGTGCATTTTTGGCAGAAAGGTGCCAC
Found at i:305279 original size:150 final size:145
Alignment explanation
Indices: 304999--305471 Score: 592
Period size: 150 Copynumber: 3.2 Consensus size: 145
304989 AACTACTCTA
* * *
304999 TAATACAAGTTAAATGCATAATGGTGCATTTTTGGAAGAAATGTGCCACTAATGCAAGTTAAATG
1 TAATGCAAGTTAAATGCATAATGGTGCATTTTTTGCAGAAATGTGCCACTAATGCAAGTTAAATG
* * *
305064 CATAATGGTGTATTTTTGGCAGAAAGGTGCCACTAATGCAAGTTAAATTCATAATGGTACATTTT
66 CATAATGGTGCATTTTTGGCAGAAAGGTGCCACTAATGCAAGTTAAATGCATAAT-GTGC-TTTT
305129 TGGCAGAAAGGTGCCAC
129 TGGCAGAAAGGTGCCAC
*
305146 TAATGCAAGTTAAATGCATAATGGTGCATTTTGTTTTGCAGAAATGTACCACTAATGCAAGTTAA
1 TAATGCAAGTTAAATGCATAATGGTGCA--TT-TTTTGCAGAAATGTGCCACTAATGCAAGTTAA
* ** * * * * *
305211 ATGCATATTGGTGCATTTTTTACAGAAATGTGCTAGTAAGGCAAATTAAATGCATAATAGTGCGT
63 ATGCATAATGGTGCATTTTTGGCAGAAAGGTGCCACTAATGCAAGTTAAATGCATAAT-GTGC-T
305276 TTTTGGCAGAAAGGTGCCAC
126 TTTTGGCAGAAAGGTGCCAC
* * * * *
305296 TGATGCAAGTTAAATGCATAATGGTGCA-TTTTTGCATAAAGGTGCCACTAATGAAAATTAAATG
1 TAATGCAAGTTAAATGCATAATGGTGCATTTTTTGCAGAAATGTGCCACTAATGCAAGTTAAATG
* * * *
305360 TATAATGGTGCCTTTTTGGCATAAAGGTGCCACTAATG-AGAGTTAAATGCATAACTGTGCATTT
66 CATAATGGTGCATTTTTGGCAGAAAGGTGCCACTAATGCA-AGTTAAATGCATAA-TGTGCTTTT
*
305424 TGGCAGAAAGGTGCCTC
129 TGGCAGAAAGGTGCCAC
* *
305441 TAATG-ATAGTTAAATGTATAACGGTGCATTT
1 TAATGCA-AGTTAAATGCATAATGGTGCATTT
305472 CGGCATAAAA
Statistics
Matches: 280, Mismatches: 39, Indels: 15
0.84 0.12 0.04
Matches are distributed among these distances:
144 1 0.00
145 43 0.15
146 77 0.28
147 29 0.10
149 2 0.01
150 128 0.46
ACGTcount: A:0.34, C:0.13, G:0.22, T:0.32
Consensus pattern (145 bp):
TAATGCAAGTTAAATGCATAATGGTGCATTTTTTGCAGAAATGTGCCACTAATGCAAGTTAAATG
CATAATGGTGCATTTTTGGCAGAAAGGTGCCACTAATGCAAGTTAAATGCATAATGTGCTTTTTG
GCAGAAAGGTGCCAC
Found at i:306818 original size:29 final size:31
Alignment explanation
Indices: 306769--306845 Score: 81
Period size: 29 Copynumber: 2.6 Consensus size: 31
306759 CCCGAATTTT
* * *
306769 AGTT-AGTGACCAAAATGTAAA-TTTTG-AA
1 AGTTAAGTGACCAAAGTATAAACTTTAGAAA
306797 AGTTAAGTGACCAAAGTATAAACTTTAGAAA
1 AGTTAAGTGACCAAAGTATAAACTTTAGAAA
*
306828 AGTTTAAG-GACTAAAGTA
1 AG-TTAAGTGACCAAAGTA
306846 CAATTTTAAA
Statistics
Matches: 41, Mismatches: 4, Indels: 5
0.82 0.08 0.10
Matches are distributed among these distances:
28 4 0.10
29 15 0.37
30 4 0.10
31 13 0.32
32 5 0.12
ACGTcount: A:0.45, C:0.08, G:0.18, T:0.29
Consensus pattern (31 bp):
AGTTAAGTGACCAAAGTATAAACTTTAGAAA
Found at i:310231 original size:130 final size:129
Alignment explanation
Indices: 309936--310308 Score: 387
Period size: 130 Copynumber: 2.9 Consensus size: 129
309926 GTGAGATTCA
* * * * * *
309936 AGATTTGATCTCCCCTAAAGAGTAGTGGAGCAAATCTACCTCAATTCAATCTTTCCTGAAGATTA
1 AGATTTGATCT-TCCTAAAGAGTAGTGGAGAAAATCTACCTCGATTCAATCTTT-TTAAAGAGTA
*
310001 GTGAAGTGAATC-AAGATTTTCAGATCTAATCTT-TCTAAAGAGCAGTGAAGCAAATCCATTCTT
64 GTGAAGTGAATCAAAG-TTTTCAGATCTAATCTTCCCTAAAGAGCAGTGAAGCAAATCCATTCTT
310064 CC
128 CC
* * * ** *
310066 AGGTTTGATATTCCCTGAAGAGCGGTGGAGAAAATCTATCTCGATTCAATCTTTATTAAAGAGTA
1 AGATTTGATCTT-CCTAAAGAGTAGTGGAGAAAATCTACCTCGATTCAATCTTT-TTAAAGAGTA
* * **
310131 GTGAAGTGAATCAAAGTTTTCAGATCTAATCTTCCCTAAAGAGTAGT-AGAGTAGGTCTCATTC-
64 GTGAAGTGAATCAAAGTTTTCAGATCTAATCTTCCCTAAAGAGCAGTGA-AGCAAATC-CATTCT
310194 TCC
127 TCC
* * * * * ** *
310197 ATATTTGATCTTCCTAAAAAGTAGTGAAGGAAATCGACCTCGAACCTATCTTTTGTAAAGAGTAG
1 AGATTTGATCTTCCTAAAGAGTAGTGGAGAAAATCTACCTCGATTCAATCTTTT-TAAAGAGTAG
* *
310262 TGAAGTGAATCAAAGTTTTCAGATCCAAT-TACCCTAAAGATGCAGTG
65 TGAAGTGAATCAAAGTTTTCAGATCTAATCTTCCCTAAAGA-GCAGTG
310309 GGGAAGATTA
Statistics
Matches: 200, Mismatches: 35, Indels: 15
0.80 0.14 0.06
Matches are distributed among these distances:
129 11 0.05
130 153 0.76
131 31 0.16
132 5 0.03
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.31
Consensus pattern (129 bp):
AGATTTGATCTTCCTAAAGAGTAGTGGAGAAAATCTACCTCGATTCAATCTTTTTAAAGAGTAGT
GAAGTGAATCAAAGTTTTCAGATCTAATCTTCCCTAAAGAGCAGTGAAGCAAATCCATTCTTCC
Found at i:316769 original size:12 final size:12
Alignment explanation
Indices: 316752--316781 Score: 60
Period size: 12 Copynumber: 2.5 Consensus size: 12
316742 TCTGATGAAT
316752 GGCGGCCGACGA
1 GGCGGCCGACGA
316764 GGCGGCCGACGA
1 GGCGGCCGACGA
316776 GGCGGC
1 GGCGGC
316782 GCACAGCCAG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.13, C:0.33, G:0.53, T:0.00
Consensus pattern (12 bp):
GGCGGCCGACGA
Found at i:317216 original size:18 final size:17
Alignment explanation
Indices: 317179--317214 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
317169 TTTGATCCAA
*
317179 TATTTTTATTTATTTATT
1 TATTTTT-TTTATTCATT
317197 TATTTTTTTTATTCATT
1 TATTTTTTTTATTCATT
317214 T
1 T
317215 TACTTTCTTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 10 0.59
18 7 0.41
ACGTcount: A:0.19, C:0.03, G:0.00, T:0.78
Consensus pattern (17 bp):
TATTTTTTTTATTCATT
Found at i:318958 original size:20 final size:19
Alignment explanation
Indices: 318933--318984 Score: 77
Period size: 20 Copynumber: 2.6 Consensus size: 19
318923 TGATTCAATC
318933 AGTATCGATACCGAAGGGGA
1 AGTATCGATACCGAA-GGGA
*
318953 AGTATCGATACTGAAGGGA
1 AGTATCGATACCGAAGGGA
318972 AGGTATCGATACC
1 A-GTATCGATACC
318985 ATTCAAAACA
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
19 5 0.17
20 24 0.83
ACGTcount: A:0.35, C:0.15, G:0.31, T:0.19
Consensus pattern (19 bp):
AGTATCGATACCGAAGGGA
Found at i:319444 original size:55 final size:55
Alignment explanation
Indices: 319378--319811 Score: 600
Period size: 55 Copynumber: 7.9 Consensus size: 55
319368 TACCAAATAG
* *
319378 GCACTATGTGTGCAAATCCATAGAATTCATCATGAGTTGATTAATAACCGTACAT
1 GCACTATGTGTGCAAATCCACAGAATTCATCATGAGTTGATGAATAACCGTACAT
**
319433 GCACTATGTGTGCAAATCCACAGAATTCATCATGAGTTGATGAATAACATTACA-
1 GCACTATGTGTGCAAATCCACAGAATTCATCATGAGTTGATGAATAACCGTACAT
* * * * * *
319487 GACACTATGTGTGCAAATCCACAAAATTCATCATGAGCTCATGGATAATCGTACAA
1 G-CACTATGTGTGCAAATCCACAGAATTCATCATGAGTTGATGAATAACCGTACAT
* * * *
319543 GCACTATATGTGCAAATCCACGGAATTCGTCATGAGTTGATGAATAACCATACAT
1 GCACTATGTGTGCAAATCCACAGAATTCATCATGAGTTGATGAATAACCGTACAT
* * *
319598 GCACTATGTATGCAAATCCACAGAATTCATCATGAGTTGATGAATAATCGTACTT
1 GCACTATGTGTGCAAATCCACAGAATTCATCATGAGTTGATGAATAACCGTACAT
* *
319653 GCATTATGTGTGCAAATCTACAGAATTCATCATGAGTTGATGAATAACCGTACAT
1 GCACTATGTGTGCAAATCCACAGAATTCATCATGAGTTGATGAATAACCGTACAT
* * * *
319708 GCACTATGTATGCAAATCCACAAAATTCATCATGAGTTGATGAAGAACCGTACAG
1 GCACTATGTGTGCAAATCCACAGAATTCATCATGAGTTGATGAATAACCGTACAT
* * * *
319763 GCACTATGTGTACAAATCCACGGAATTCATCACGAATTGATGAACTAAC
1 GCACTATGTGTGCAAATCCACAGAATTCATCATGAGTTGATGAA-TAAC
319812 GTATAGGTAC
Statistics
Matches: 330, Mismatches: 46, Indels: 5
0.87 0.12 0.01
Matches are distributed among these distances:
54 1 0.00
55 325 0.98
56 4 0.01
ACGTcount: A:0.36, C:0.19, G:0.17, T:0.28
Consensus pattern (55 bp):
GCACTATGTGTGCAAATCCACAGAATTCATCATGAGTTGATGAATAACCGTACAT
Found at i:320153 original size:21 final size:21
Alignment explanation
Indices: 320083--320156 Score: 60
Period size: 21 Copynumber: 3.4 Consensus size: 21
320073 TGCATAACGT
*
320083 TGTATAAAAGGCATAAAAGGA
1 TGTATAAAAGGCATGAAAGGA
* * **
320104 TGCCATAAATGAAATGTATAATGG-
1 TG-TATAAAAGGCATG-A-AA-GGA
320128 TGTATAAAAGGCATGAAAGGA
1 TGTATAAAAGGCATGAAAGGA
320149 TGTATAAA
1 TGTATAAA
320157 TGAAATTAAT
Statistics
Matches: 39, Mismatches: 9, Indels: 10
0.67 0.16 0.17
Matches are distributed among these distances:
20 2 0.05
21 12 0.31
22 9 0.23
23 10 0.26
24 4 0.10
25 2 0.05
ACGTcount: A:0.47, C:0.05, G:0.23, T:0.24
Consensus pattern (21 bp):
TGTATAAAAGGCATGAAAGGA
Found at i:322284 original size:23 final size:26
Alignment explanation
Indices: 322241--322290 Score: 70
Period size: 23 Copynumber: 2.0 Consensus size: 26
322231 ATTATGAGAA
*
322241 AAAATAATTTATATATATTTATAAAT
1 AAAATAATTTATATATATTTAGAAAT
322267 AAAAT-ATTTAT-T-TATTTAGAAAT
1 AAAATAATTTATATATATTTAGAAAT
322290 A
1 A
322291 TCAGAAAAGG
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
23 11 0.48
24 1 0.04
25 6 0.26
26 5 0.22
ACGTcount: A:0.52, C:0.00, G:0.02, T:0.46
Consensus pattern (26 bp):
AAAATAATTTATATATATTTAGAAAT
Found at i:323533 original size:21 final size:20
Alignment explanation
Indices: 323493--323563 Score: 60
Period size: 18 Copynumber: 3.7 Consensus size: 20
323483 TCGTTCTCTG
* * *
323493 TTTTTGCTGTTTTTTTTTTT
1 TTTTTGCTGGTTGTTGTTTT
323513 ATTTTTGCTGGTTGTTG--TT
1 -TTTTTGCTGGTTGTTGTTTT
*
323532 TTGTTGCTGGTTGTTG--TT
1 TTTTTGCTGGTTGTTGTTTT
*
323550 TTGTTGCTGGTTGT
1 TTTTTGCTGGTTGT
323564 CCTGCTTTTT
Statistics
Matches: 46, Mismatches: 4, Indels: 3
0.87 0.08 0.06
Matches are distributed among these distances:
18 31 0.67
19 2 0.04
21 13 0.28
ACGTcount: A:0.01, C:0.06, G:0.25, T:0.68
Consensus pattern (20 bp):
TTTTTGCTGGTTGTTGTTTT
Found at i:323540 original size:18 final size:18
Alignment explanation
Indices: 323517--323563 Score: 94
Period size: 18 Copynumber: 2.6 Consensus size: 18
323507 TTTTTTATTT
323517 TTGCTGGTTGTTGTTTTG
1 TTGCTGGTTGTTGTTTTG
323535 TTGCTGGTTGTTGTTTTG
1 TTGCTGGTTGTTGTTTTG
323553 TTGCTGGTTGT
1 TTGCTGGTTGT
323564 CCTGCTTTTT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 29 1.00
ACGTcount: A:0.00, C:0.06, G:0.34, T:0.60
Consensus pattern (18 bp):
TTGCTGGTTGTTGTTTTG
Found at i:324054 original size:3 final size:3
Alignment explanation
Indices: 324048--324107 Score: 59
Period size: 3 Copynumber: 20.0 Consensus size: 3
324038 TATTATTTTT
* * * *
324048 TAA TAA TAA TAA TAA T-A TATG TAA TAG TTA TAA TAA TAA TAA TTA
1 TAA TAA TAA TAA TAA TAA TA-A TAA TAA TAA TAA TAA TAA TAA TAA
*
324093 TAG TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA
324108 AAATGGGTAA
Statistics
Matches: 45, Mismatches: 10, Indels: 4
0.76 0.17 0.07
Matches are distributed among these distances:
2 2 0.04
3 41 0.91
4 2 0.04
ACGTcount: A:0.57, C:0.00, G:0.05, T:0.38
Consensus pattern (3 bp):
TAA
Found at i:324467 original size:124 final size:122
Alignment explanation
Indices: 324247--324531 Score: 369
Period size: 124 Copynumber: 2.3 Consensus size: 122
324237 GTTGAATAAA
* *
324247 TTCTTCTCTTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTGCTGGGGATGATGTTGACCTA
1 TTCTT-TCTTT-TTCAGATGAGTTCTTCTCATTATGAACTTTCTGCTGGGGATGATGCTAACCTA
* *
324312 TTTCCTTCTGTGATAGAGTCATTCAAAAGGTTGAATAAGCTCTTCTCATTATGAACTTC
64 TTTCCTTCTGTGATAGAATCATGCAAAAGGTTGAATAAGCTCTTCTCATTATGAACTTC
* *
324371 TTCTTTCTTTTTCAGATGAGTTCTTCTCATTATGAACTTTCT-CTGGAAAGGTTGATGCTAATCT
1 TTCTTTCTTTTTCAGATGAGTTCTTCTCATTATGAACTTTCTGCTGG---GGATGATGCTAACCT
* * * * *
324435 ATTTGCTTCTGTGATAGAATTATGCAAAAGGTTGAATAAGCTCTTCTTATTGTGAACTTT
63 ATTTCCTTCTGTGATAGAATCATGCAAAAGGTTGAATAAGCTCTTCTCATTATGAACTTC
***
324495 TTC-TTC-TTCAGATGATGAGTTCTTCTCATTATGAACT
1 TTCTTTCTTTTTCA-GATGAGTTCTTCTCATTATGAACT
324532 CTACATGGCA
Statistics
Matches: 143, Mismatches: 14, Indels: 9
0.86 0.08 0.05
Matches are distributed among these distances:
121 4 0.03
122 35 0.24
123 32 0.22
124 72 0.50
ACGTcount: A:0.23, C:0.17, G:0.16, T:0.44
Consensus pattern (122 bp):
TTCTTTCTTTTTCAGATGAGTTCTTCTCATTATGAACTTTCTGCTGGGGATGATGCTAACCTATT
TCCTTCTGTGATAGAATCATGCAAAAGGTTGAATAAGCTCTTCTCATTATGAACTTC
Found at i:324656 original size:113 final size:113
Alignment explanation
Indices: 324508--325239 Score: 1078
Period size: 113 Copynumber: 6.5 Consensus size: 113
324498 TTCTTCAGAT
* * *** * *
324508 GATGAGTTCTTCTCATTATGAACTCTAC-ATGGCAATGTTAATCCATCAAATGATGAATTTAAAC
1 GATGAGTTCTTCTCATTATGAACT-TACTCTGGAAAAACTGATCCATCAAATGATGAATTCAAAC
324572 AAAAGGTTGAACAAATTCTTCTCATTATGAATTTCTTCTTCCTTCTTCA
65 AAAAGGTTGAACAAATTCTTCTCATTATGAATTTCTTCTTCCTTCTTCA
* * ***
324621 GATGAGTTCTTCTCTTTATGAACTATAC-CTGGCAATGTTGATCCATCAAATGATGAATTCAAAC
1 GATGAGTTCTTCTCATTATGAACT-TACTCTGGAAAAACTGATCCATCAAATGATGAATTCAAAC
324685 AAAAGGTTGAACAAATTCTTCTCATTATGAATTTCTTCTTCCTTCTTCA
65 AAAAGGTTGAACAAATTCTTCTCATTATGAATTTCTTCTTCCTTCTTCA
* *
324734 GATGAGTTCTTCTTATTATGAACTTTCTCTGGAAAAACTGATCCATCAAATGATGAATTCAAACA
1 GATGAGTTCTTCTCATTATGAACTTACTCTGGAAAAACTGATCCATCAAATGATGAATTCAAACA
*
324799 AAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCA
66 AAAGGTTGAACAAATTCTTCTCATTATGAATTTCTTCTTCCTTCTTCA
* *
324847 GATGAGTTCTTCTCATTATGAACTTTCTCTGAAAAAACTGATCCATCAAATGATGAATTCAAACA
1 GATGAGTTCTTCTCATTATGAACTTACTCTGGAAAAACTGATCCATCAAATGATGAATTCAAACA
324912 AAAGGTTGAACAAATTCTTCTCATTATGAATTTCTTCTTCCTTCTTCA
66 AAAGGTTGAACAAATTCTTCTCATTATGAATTTCTTCTTCCTTCTTCA
* * * ** *
324960 GATGAGTTCTTCTCATTATGATCTTTCTCTGGAAAAACTGATCCATCAAATGATGGATTTGAGCA
1 GATGAGTTCTTCTCATTATGAACTTACTCTGGAAAAACTGATCCATCAAATGATGAATTCAAACA
* * **
325025 AAAAGTTGAACAAATTCTTCTCATTATAAATTTCTTCTT-CTTC-AGA
66 AAAGGTTGAACAAATTCTTCTCATTATGAATTTCTTCTTCCTTCTTCA
* * ***
325071 TGACGAGTTCTTCTCATTATGAACTCTAC-CTGGCAATGTTGATCCATCAAATGATGAATTCAAA
1 -GATGAGTTCTTCTCATTATGAACT-TACTCTGGAAAAACTGATCCATCAAATGATGAATTCAAA
*
325135 CAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCA
64 CAAAAGGTTGAACAAATTCTTCTCATTATGAATTTCTTCTTCCTTCTTCA
* *
325185 GATGAGTTCTTCTCATTATGAACTTTCTCTGGAAAAACTGATCCATCAAGTGATG
1 GATGAGTTCTTCTCATTATGAACTTACTCTGGAAAAACTGATCCATCAAATGATG
325240 GATTTGAGCT
Statistics
Matches: 564, Mismatches: 49, Indels: 12
0.90 0.08 0.02
Matches are distributed among these distances:
111 1 0.00
112 95 0.17
113 467 0.83
114 1 0.00
ACGTcount: A:0.31, C:0.19, G:0.12, T:0.37
Consensus pattern (113 bp):
GATGAGTTCTTCTCATTATGAACTTACTCTGGAAAAACTGATCCATCAAATGATGAATTCAAACA
AAAGGTTGAACAAATTCTTCTCATTATGAATTTCTTCTTCCTTCTTCA
Found at i:326194 original size:93 final size:93
Alignment explanation
Indices: 326035--326324 Score: 501
Period size: 93 Copynumber: 3.1 Consensus size: 93
326025 CTTATTTCTA
* * *
326035 CTATGATCACATTCATCTTTCAAATTCAATGATTGG-TTCTGTGGTTTCATACCAAACCAGATCA
1 CTATGAGCACATTCATCTTTCAAATTCAATGATTGGTTTTTG-GGGTTCATACCAAACCAGATCA
326099 GATAACTCAAAGAACACTTCCAGAAGATG
65 GATAACTCAAAGAACACTTCCAGAAGATG
*
326128 CTATGAGCACATTCATCTTCCAAATTCAATGATTGGTTTTTGGGGTTCATACCAAACCAGATCAG
1 CTATGAGCACATTCATCTTTCAAATTCAATGATTGGTTTTTGGGGTTCATACCAAACCAGATCAG
326193 ATAACTCAAAGAACACTTCCAGAAGATG
66 ATAACTCAAAGAACACTTCCAGAAGATG
*
326221 CTATGAGCACATTCATCTTTCAAATTCAATGATTGGTTTTTGGGGTTCATATCAAACCAGATCAG
1 CTATGAGCACATTCATCTTTCAAATTCAATGATTGGTTTTTGGGGTTCATACCAAACCAGATCAG
*
326286 ATAATTCAAAGAACACTTCCAGAAGATG
66 ATAACTCAAAGAACACTTCCAGAAGATG
*
326314 CTATAAGCACA
1 CTATGAGCACA
326325 CGGCACTTGT
Statistics
Matches: 188, Mismatches: 8, Indels: 2
0.95 0.04 0.01
Matches are distributed among these distances:
93 184 0.98
94 4 0.02
ACGTcount: A:0.35, C:0.21, G:0.15, T:0.29
Consensus pattern (93 bp):
CTATGAGCACATTCATCTTTCAAATTCAATGATTGGTTTTTGGGGTTCATACCAAACCAGATCAG
ATAACTCAAAGAACACTTCCAGAAGATG
Found at i:327342 original size:15 final size:17
Alignment explanation
Indices: 327317--327357 Score: 59
Period size: 15 Copynumber: 2.5 Consensus size: 17
327307 CCTTGACCCC
*
327317 CTTTTTTTTTTC-TTTT
1 CTTTCTTTTTTCTTTTT
327333 C-TTCTTTTTTCTTTTT
1 CTTTCTTTTTTCTTTTT
327349 CTTTCTTTT
1 CTTTCTTTT
327358 CTTCAAGCAT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
15 9 0.41
16 6 0.27
17 7 0.32
ACGTcount: A:0.00, C:0.17, G:0.00, T:0.83
Consensus pattern (17 bp):
CTTTCTTTTTTCTTTTT
Found at i:338524 original size:28 final size:25
Alignment explanation
Indices: 338493--338544 Score: 59
Period size: 28 Copynumber: 2.0 Consensus size: 25
338483 ATTTCAAAAT
338493 TATAATTATGAGAAAAAAATAATTTATA
1 TATAATTAT-A-AAAAAAAT-ATTTATA
* *
338521 TATATTTATAAATAAAATATTTAT
1 TATAATTATAAAAAAAATATTTAT
338545 TTATTTAGAA
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
25 6 0.27
26 7 0.32
27 1 0.05
28 8 0.36
ACGTcount: A:0.54, C:0.00, G:0.04, T:0.42
Consensus pattern (25 bp):
TATAATTATAAAAAAAATATTTATA
Found at i:338551 original size:23 final size:26
Alignment explanation
Indices: 338503--338557 Score: 73
Period size: 23 Copynumber: 2.3 Consensus size: 26
338493 TATAATTATG
338503 AGAAA-AAAATAATTTATATATATTT
1 AGAAATAAAATAATTTATATATATTT
*
338528 ATAAATAAAAT-ATTTAT-T-TATTT
1 AGAAATAAAATAATTTATATATATTT
338551 AGAAATA
1 AGAAATA
338558 TCAGAAAAGG
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
23 11 0.41
24 1 0.04
25 10 0.37
26 5 0.19
ACGTcount: A:0.55, C:0.00, G:0.04, T:0.42
Consensus pattern (26 bp):
AGAAATAAAATAATTTATATATATTT
Found at i:339771 original size:21 final size:21
Alignment explanation
Indices: 339746--339791 Score: 74
Period size: 21 Copynumber: 2.2 Consensus size: 21
339736 TTTCGTTCTC
* *
339746 TGTTTTTGCTGGTTTTTTTTT
1 TGTTTTTGCTGGTTGTTGTTT
339767 TGTTTTTGCTGGTTGTTGTTT
1 TGTTTTTGCTGGTTGTTGTTT
339788 TGTT
1 TGTT
339792 GCTGGTTGTC
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.00, C:0.04, G:0.24, T:0.72
Consensus pattern (21 bp):
TGTTTTTGCTGGTTGTTGTTT
Found at i:340293 original size:3 final size:3
Alignment explanation
Indices: 340287--340361 Score: 89
Period size: 3 Copynumber: 25.0 Consensus size: 3
340277 TATTATTTTT
* * *
340287 TAA TAA TAA TAA TAA T-A TATA TAA TAG TTA TAA TAA TAA TAA TTA
1 TAA TAA TAA TAA TAA TAA TA-A TAA TAA TAA TAA TAA TAA TAA TAA
* *
340332 TAA TAA TAA TAA TTA TAG TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
340362 AAATGGGTAA
Statistics
Matches: 60, Mismatches: 10, Indels: 4
0.81 0.14 0.05
Matches are distributed among these distances:
2 2 0.03
3 55 0.92
4 3 0.05
ACGTcount: A:0.59, C:0.00, G:0.03, T:0.39
Consensus pattern (3 bp):
TAA
Found at i:344892 original size:22 final size:22
Alignment explanation
Indices: 344864--344936 Score: 92
Period size: 22 Copynumber: 3.3 Consensus size: 22
344854 GTCGGATAGT
*
344864 TAAAGTTTCTTAGCACTAATAC
1 TAAAGTTCCTTAGCACTAATAC
**
344886 TAAAGTTCCTTAGCACTGGTAC
1 TAAAGTTCCTTAGCACTAATAC
* *
344908 TAAAGTGCCTTGGCACTGAATAC
1 TAAAGTTCCTTAGCACT-AATAC
344931 TAAAGT
1 TAAAGT
344937 GTTTTAGCAC
Statistics
Matches: 43, Mismatches: 7, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
22 34 0.79
23 9 0.21
ACGTcount: A:0.33, C:0.19, G:0.16, T:0.32
Consensus pattern (22 bp):
TAAAGTTCCTTAGCACTAATAC
Found at i:344935 original size:23 final size:23
Alignment explanation
Indices: 344872--344971 Score: 100
Period size: 22 Copynumber: 4.5 Consensus size: 23
344862 GTTAAAGTTT
*
344872 CTTAGCACT-AATACTAAAGTTC
1 CTTAGCACTGAATACTAAAGTGC
*
344894 CTTAGCACTG-GTACTAAAGTGC
1 CTTAGCACTGAATACTAAAGTGC
* *
344916 CTTGGCACTGAATACTAAAGTGT
1 CTTAGCACTGAATACTAAAGTGC
* *
344939 TTTAGCACTG-ATA-TGGAAGTGC
1 CTTAGCACTGAATACT-AAAGTGC
*
344961 ATTAGCACTGA
1 CTTAGCACTGA
344972 TCAAAGTATA
Statistics
Matches: 64, Mismatches: 10, Indels: 7
0.79 0.12 0.09
Matches are distributed among these distances:
21 1 0.02
22 45 0.70
23 18 0.28
ACGTcount: A:0.31, C:0.19, G:0.20, T:0.30
Consensus pattern (23 bp):
CTTAGCACTGAATACTAAAGTGC
Found at i:344959 original size:45 final size:45
Alignment explanation
Indices: 344873--344971 Score: 114
Period size: 45 Copynumber: 2.2 Consensus size: 45
344863 TTAAAGTTTC
* *
344873 TTAGCACT-AATACTAAAGTTCCTTAGCACTGGTACTAAAGTGCC
1 TTAGCACTGAATACTAAAGTTCCTTAGCACTGATACTAAAGTGCA
* * *
344917 TTGGCACTGAATACTAAAGTGT-TTTAGCACTGATA-TGGAAGTGCA
1 TTAGCACTGAATACTAAAGT-TCCTTAGCACTGATACT-AAAGTGCA
344962 TTAGCACTGA
1 TTAGCACTGA
344972 TCAAAGTATA
Statistics
Matches: 46, Mismatches: 6, Indels: 5
0.81 0.11 0.09
Matches are distributed among these distances:
44 8 0.17
45 37 0.80
46 1 0.02
ACGTcount: A:0.31, C:0.18, G:0.20, T:0.30
Consensus pattern (45 bp):
TTAGCACTGAATACTAAAGTTCCTTAGCACTGATACTAAAGTGCA
Found at i:364781 original size:69 final size:64
Alignment explanation
Indices: 364699--364842 Score: 164
Period size: 64 Copynumber: 2.2 Consensus size: 64
364689 TCTTTTAATG
*
364699 CTTTTAATAGCCTATTTTCATTTCCTATT-TAATGATCTTTATGGGTTTGATAAAAGTTCCCTGA
1 CTTTTAATGGCCTA-TTTCATTTCCTATTGT--T-A--TTTATGGGTTTGATAAAAGTTCCCTGA
364763 GAACC
60 GAACC
* * * * **
364768 CTTTTAATGGCCTATTTCGTTTTCTGTTGTTATTTATGTGTTTGATAAAAGTTCCCTGAGAATT
1 CTTTTAATGGCCTATTTCATTTCCTATTGTTATTTATGGGTTTGATAAAAGTTCCCTGAGAACC
364832 CTTTTAATGGC
1 CTTTTAATGGC
364843 TTACAGCTTG
Statistics
Matches: 67, Mismatches: 7, Indels: 7
0.83 0.09 0.09
Matches are distributed among these distances:
64 40 0.60
66 1 0.01
67 1 0.01
68 11 0.16
69 14 0.21
ACGTcount: A:0.23, C:0.15, G:0.15, T:0.47
Consensus pattern (64 bp):
CTTTTAATGGCCTATTTCATTTCCTATTGTTATTTATGGGTTTGATAAAAGTTCCCTGAGAACC
Found at i:392525 original size:22 final size:22
Alignment explanation
Indices: 392497--392542 Score: 65
Period size: 22 Copynumber: 2.1 Consensus size: 22
392487 TTTTTCGGTT
392497 AAAGTCAACGGTCATAACAGTC
1 AAAGTCAACGGTCATAACAGTC
* * *
392519 AAAGTCAATGGTCTTACCAGTC
1 AAAGTCAACGGTCATAACAGTC
392541 AA
1 AA
392543 CGGTAAACTT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.39, C:0.22, G:0.17, T:0.22
Consensus pattern (22 bp):
AAAGTCAACGGTCATAACAGTC
Found at i:396800 original size:59 final size:59
Alignment explanation
Indices: 396704--397056 Score: 476
Period size: 59 Copynumber: 6.0 Consensus size: 59
396694 TTACCAAATT
* * * * *
396704 GCACTATGTGAGCTAAAATGTTATGAAATTCAGACTAAGTGTATTAATTTCCGTATGGG
1 GCACTTTGTGTGCTAAAATGTTAAGAAATTCATACTAAGTGTATGAATTTCCGTATGGG
* *
396763 GCACTTTGTGTGCTAAAATGTTAAGAAATTCATACTAAGTGTATCAAATTT-CGTATTGG
1 GCACTTTGTGTGCTAAAATGTTAAGAAATTCATACTAAGTGTAT-GAATTTCCGTATGGG
** * * *
396822 GCACTAGGTCTGCTAAAATATAAAGAAATTCATACTAAGTGTATGAATTTCCGTATGGG
1 GCACTTTGTGTGCTAAAATGTTAAGAAATTCATACTAAGTGTATGAATTTCCGTATGGG
** *
396881 GCACTTTGTGTGCTAAAATGTTAAGAAATTCATACTAAGCATATGAATTTCCGTATTGG
1 GCACTTTGTGTGCTAAAATGTTAAGAAATTCATACTAAGTGTATGAATTTCCGTATGGG
* * *
396940 GCACTTTATGTGCTAAAATGTTTAGAAATTCATACTAAGTGTATGAATTTCCGTATTGG
1 GCACTTTGTGTGCTAAAATGTTAAGAAATTCATACTAAGTGTATGAATTTCCGTATGGG
* * * * *
396999 GCACTTTATGTG-TAAAAAGATAAGAAACTCATACTAAGTGTATGAATTTCCATATGGG
1 GCACTTTGTGTGCTAAAATGTTAAGAAATTCATACTAAGTGTATGAATTTCCGTATGGG
397057 AAATTTATGT
Statistics
Matches: 261, Mismatches: 31, Indels: 5
0.88 0.10 0.02
Matches are distributed among these distances:
58 45 0.17
59 211 0.81
60 5 0.02
ACGTcount: A:0.33, C:0.12, G:0.20, T:0.35
Consensus pattern (59 bp):
GCACTTTGTGTGCTAAAATGTTAAGAAATTCATACTAAGTGTATGAATTTCCGTATGGG
Found at i:397424 original size:29 final size:29
Alignment explanation
Indices: 397382--397442 Score: 88
Period size: 29 Copynumber: 2.1 Consensus size: 29
397372 TATTCCAGTT
397382 AGATGAACATTTAAAAATTGTTAAGTAAA
1 AGATGAACATTTAAAAATTGTTAAGTAAA
* *
397411 AGATGAACGA-TTAAACATTGTTGAGTAAA
1 AGATGAAC-ATTTAAAAATTGTTAAGTAAA
397440 AGA
1 AGA
397443 ATAATGGACT
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
29 28 0.97
30 1 0.03
ACGTcount: A:0.49, C:0.05, G:0.18, T:0.28
Consensus pattern (29 bp):
AGATGAACATTTAAAAATTGTTAAGTAAA
Found at i:397593 original size:2 final size:2
Alignment explanation
Indices: 397586--397646 Score: 122
Period size: 2 Copynumber: 30.5 Consensus size: 2
397576 AGAAGGGATG
397586 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
397628 AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT A
397647 ATGTACAATA
Statistics
Matches: 59, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 59 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:401501 original size:12 final size:12
Alignment explanation
Indices: 401480--401520 Score: 57
Period size: 12 Copynumber: 3.4 Consensus size: 12
401470 TCGATTTGAA
401480 TTCTGTTCTGAT
1 TTCTGTTCTGAT
*
401492 TTCT-TATCTGAA
1 TTCTGT-TCTGAT
401504 TTCTGTTCTGAT
1 TTCTGTTCTGAT
401516 TTCTG
1 TTCTG
401521 GTATGTATTC
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
11 1 0.04
12 23 0.92
13 1 0.04
ACGTcount: A:0.12, C:0.17, G:0.15, T:0.56
Consensus pattern (12 bp):
TTCTGTTCTGAT
Found at i:401571 original size:24 final size:24
Alignment explanation
Indices: 401468--401572 Score: 113
Period size: 24 Copynumber: 4.4 Consensus size: 24
401458 TTTATCCGAT
* *
401468 TTTC-GATTTGAATTCTGTTCTGA
1 TTTCTGATATGAATTCTATTCTGA
* * *
401491 TTTCTTATCTGAATTCTGTTCTGA
1 TTTCTGATATGAATTCTATTCTGA
* * *
401515 TTTCTGGTATGTATTCTATTTTGA
1 TTTCTGATATGAATTCTATTCTGA
* *
401539 TATCTGATATGAATTCTATTTTGA
1 TTTCTGATATGAATTCTATTCTGA
401563 TTTCTGATAT
1 TTTCTGATAT
401573 CTCCGTTTAC
Statistics
Matches: 69, Mismatches: 12, Indels: 1
0.84 0.15 0.01
Matches are distributed among these distances:
23 4 0.06
24 65 0.94
ACGTcount: A:0.20, C:0.11, G:0.14, T:0.54
Consensus pattern (24 bp):
TTTCTGATATGAATTCTATTCTGA
Found at i:405532 original size:22 final size:22
Alignment explanation
Indices: 405492--405537 Score: 58
Period size: 22 Copynumber: 2.1 Consensus size: 22
405482 TTTTTTTGTT
* *
405492 AAAGTCAACTGTCAGACCGGTC
1 AAAGTCAACGGTCAGACCGATC
405514 AAAGTCAACGGTCTA-ACCGATC
1 AAAGTCAACGGTC-AGACCGATC
405536 AA
1 AA
405538 CGGTCAACTT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
22 20 0.95
23 1 0.05
ACGTcount: A:0.37, C:0.26, G:0.20, T:0.17
Consensus pattern (22 bp):
AAAGTCAACGGTCAGACCGATC
Found at i:406613 original size:25 final size:25
Alignment explanation
Indices: 406580--406630 Score: 77
Period size: 25 Copynumber: 2.0 Consensus size: 25
406570 TACCCACATG
406580 ATATCTACTTGGACATGATTT-AAT
1 ATATCTACTTGGACATGATTTCAAT
*
406604 ATATCCTACTTGGACATGCTTTCAAT
1 ATAT-CTACTTGGACATGATTTCAAT
406630 A
1 A
406631 GAAAAAAATC
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
24 4 0.17
25 16 0.67
26 4 0.17
ACGTcount: A:0.31, C:0.18, G:0.12, T:0.39
Consensus pattern (25 bp):
ATATCTACTTGGACATGATTTCAAT
Found at i:409796 original size:20 final size:20
Alignment explanation
Indices: 409733--409796 Score: 51
Period size: 20 Copynumber: 3.2 Consensus size: 20
409723 CTATAAAGAA
**
409733 AATAAAAAATAGCATTTA-AT
1 AATAAAAAATAG-AAATACAT
* *
409753 AATTAAAAATAGAAATACAA
1 AATAAAAAATAGAAATACAT
*
409773 AATAAAAATATAGTAA-ACAT
1 AATAAAAA-ATAGAAATACAT
409793 AATA
1 AATA
409797 TATACATTGC
Statistics
Matches: 35, Mismatches: 7, Indels: 4
0.76 0.15 0.09
Matches are distributed among these distances:
19 3 0.09
20 26 0.74
21 6 0.17
ACGTcount: A:0.66, C:0.05, G:0.05, T:0.25
Consensus pattern (20 bp):
AATAAAAAATAGAAATACAT
Found at i:411236 original size:20 final size:20
Alignment explanation
Indices: 411187--411242 Score: 60
Period size: 20 Copynumber: 2.8 Consensus size: 20
411177 GATTTAACTA
*
411187 AGTAGTATCAATACTGATTG
1 AGTAGTATCAATACCGATTG
*
411207 AATCAGTATCAATACCGA-TG
1 AGT-AGTATCAATACCGATTG
*
411227 AGGTAGTATCGATACC
1 A-GTAGTATCAATACC
411243 ATGGTAATGG
Statistics
Matches: 30, Mismatches: 4, Indels: 4
0.79 0.11 0.11
Matches are distributed among these distances:
20 16 0.53
21 14 0.47
ACGTcount: A:0.36, C:0.16, G:0.20, T:0.29
Consensus pattern (20 bp):
AGTAGTATCAATACCGATTG
Found at i:414554 original size:20 final size:20
Alignment explanation
Indices: 414529--414656 Score: 238
Period size: 20 Copynumber: 6.4 Consensus size: 20
414519 ATTCTATCAA
414529 TATCGATATCGATGAGGTAG
1 TATCGATATCGATGAGGTAG
414549 TATCGATATCGATGAGGTAG
1 TATCGATATCGATGAGGTAG
414569 TATCGATATCGATGAGGTAG
1 TATCGATATCGATGAGGTAG
*
414589 TATCGATATCGATTAGGTAG
1 TATCGATATCGATGAGGTAG
*
414609 TATCGATATCGATGAGGTAA
1 TATCGATATCGATGAGGTAG
414629 TATCGATATCGATGAGGTAG
1 TATCGATATCGATGAGGTAG
414649 TATCGATA
1 TATCGATA
414657 CCATGGTAAA
Statistics
Matches: 104, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 104 1.00
ACGTcount: A:0.31, C:0.10, G:0.27, T:0.31
Consensus pattern (20 bp):
TATCGATATCGATGAGGTAG
Found at i:415167 original size:59 final size:59
Alignment explanation
Indices: 415094--415385 Score: 399
Period size: 59 Copynumber: 5.0 Consensus size: 59
415084 ATTACCAAAT
* * *
415094 GGCACTATGTGTGCTAAAATGTTAAGAATTTCATACTAAGTGTATGAATTTCCGTATTG
1 GGCACTTTGTGTGCTAAAATGTTAAGAAATTCATACTAAGTGTATGAATTTCCATATTG
** * *
415153 GGCACTAGGTGTGCTGAAATATTAAGAAATTCATACTAAGTGTATGAATTTCCAT-TTG
1 GGCACTTTGTGTGCTAAAATGTTAAGAAATTCATACTAAGTGTATGAATTTCCATATTG
* * *
415211 TGACACTTTGTGTGCTAAAATGTTAAGAAATTCATACTAAGTGTATGATTTTCCGTATTG
1 -GGCACTTTGTGTGCTAAAATGTTAAGAAATTCATACTAAGTGTATGAATTTCCATATTG
* *
415271 GGCACTTTGTGTGCTAAAATGTTAACAAATTCATACTAAGTGTATGAATTTTCATATTG
1 GGCACTTTGTGTGCTAAAATGTTAAGAAATTCATACTAAGTGTATGAATTTCCATATTG
* * * * * *
415330 GGCACTTTATGTAC-AAAAAGATAAGAAACTCATACTATGTGTATGAATTTCCATAT
1 GGCACTTTGTGTGCTAAAATGTTAAGAAATTCATACTAAGTGTATGAATTTCCATAT
415386 GGGAAATATA
Statistics
Matches: 206, Mismatches: 25, Indels: 5
0.87 0.11 0.02
Matches are distributed among these distances:
58 39 0.19
59 164 0.80
60 3 0.01
ACGTcount: A:0.33, C:0.12, G:0.18, T:0.37
Consensus pattern (59 bp):
GGCACTTTGTGTGCTAAAATGTTAAGAAATTCATACTAAGTGTATGAATTTCCATATTG
Found at i:415748 original size:29 final size:29
Alignment explanation
Indices: 415715--415775 Score: 88
Period size: 29 Copynumber: 2.1 Consensus size: 29
415705 TATGCCAGTT
415715 AGATGAACGGTTAAAAACTGTT-ATGTAAA
1 AGATGAACGGTTAAAAACTGTTGA-GTAAA
* *
415744 AGATGAACGGTTAAACATTGTTGAGTAAA
1 AGATGAACGGTTAAAAACTGTTGAGTAAA
415773 AGA
1 AGA
415776 ATAATTGACT
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
29 28 0.97
30 1 0.03
ACGTcount: A:0.44, C:0.07, G:0.23, T:0.26
Consensus pattern (29 bp):
AGATGAACGGTTAAAAACTGTTGAGTAAA
Found at i:416711 original size:18 final size:19
Alignment explanation
Indices: 416663--416711 Score: 59
Period size: 18 Copynumber: 2.7 Consensus size: 19
416653 ACATACATAG
416663 TATATTT-TAAAAGTAATA
1 TATATTTATAAAAGTAATA
*
416681 TGTATGTTA-AAAA-TAATA
1 TATAT-TTATAAAAGTAATA
416699 TATATTTATAAAA
1 TATATTTATAAAA
416712 AAAAATAATT
Statistics
Matches: 26, Mismatches: 2, Indels: 6
0.76 0.06 0.18
Matches are distributed among these distances:
17 3 0.12
18 17 0.65
19 6 0.23
ACGTcount: A:0.51, C:0.00, G:0.06, T:0.43
Consensus pattern (19 bp):
TATATTTATAAAAGTAATA
Found at i:417429 original size:59 final size:58
Alignment explanation
Indices: 417354--417477 Score: 153
Period size: 57 Copynumber: 2.1 Consensus size: 58
417344 TGATTTTTCG
* * *
417354 AAAGATTAATTTTTTATATATTGTAAAAAAATGTGCCCACTAAACCCTAAATT-GTTTAA
1 AAAGATTAA-ATTTT-TATATTCTAAAAAAATATGCCCACTAAACCCTAAATTAGTTTAA
* * * *
417413 AAAGGTTAAATTTTTATATTCTCAAAAAATATGCCCATTAAACCCTAAATTATTTTAA
1 AAAGATTAAATTTTTATATTCTAAAAAAATATGCCCACTAAACCCTAAATTAGTTTAA
417471 AAA-ATTA
1 AAAGATTA
417478 TATTAATCTG
Statistics
Matches: 56, Mismatches: 8, Indels: 4
0.82 0.12 0.06
Matches are distributed among these distances:
57 36 0.64
58 12 0.21
59 8 0.14
ACGTcount: A:0.44, C:0.12, G:0.06, T:0.37
Consensus pattern (58 bp):
AAAGATTAAATTTTTATATTCTAAAAAAATATGCCCACTAAACCCTAAATTAGTTTAA
Found at i:419800 original size:38 final size:38
Alignment explanation
Indices: 419749--419827 Score: 140
Period size: 38 Copynumber: 2.1 Consensus size: 38
419739 GAATGAAAAT
*
419749 GAGATTTAGGTGATGAAATCAAGCTTGAAACAAAGTTG
1 GAGATTTAGGTGATGAAATCAAACTTGAAACAAAGTTG
*
419787 GAGATTTAGGTGATGAAATCAAATTTGAAACAAAGTTG
1 GAGATTTAGGTGATGAAATCAAACTTGAAACAAAGTTG
419825 GAG
1 GAG
419828 TGTAATACCC
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
38 39 1.00
ACGTcount: A:0.41, C:0.06, G:0.27, T:0.27
Consensus pattern (38 bp):
GAGATTTAGGTGATGAAATCAAACTTGAAACAAAGTTG
Found at i:426656 original size:20 final size:20
Alignment explanation
Indices: 426631--426704 Score: 60
Period size: 20 Copynumber: 3.5 Consensus size: 20
426621 AAATGAAATC
426631 CATGAAAAGATGCATTAAGG
1 CATGAAAAGATGCATTAAGG
* *
426651 CATGAAATGATGCCATAAATGAAATG
1 CATGAAAAGATG-CAT---T--AAGG
*
426677 CATGAAAGGATGCATTAAGG
1 CATGAAAAGATGCATTAAGG
426697 CAT-AAAAG
1 CATGAAAAG
426705 TGTGCCATAA
Statistics
Matches: 43, Mismatches: 5, Indels: 13
0.70 0.08 0.21
Matches are distributed among these distances:
19 4 0.09
20 17 0.40
21 3 0.07
22 1 0.02
24 1 0.02
25 3 0.07
26 14 0.33
ACGTcount: A:0.46, C:0.11, G:0.23, T:0.20
Consensus pattern (20 bp):
CATGAAAAGATGCATTAAGG
Found at i:426670 original size:46 final size:46
Alignment explanation
Indices: 426617--426859 Score: 389
Period size: 46 Copynumber: 5.3 Consensus size: 46
426607 TAAAACGAAT
* *
426617 CCATAAATGAAATCCATGAAAAGATGCATTAAGGCATGAAATGATG
1 CCATAAATGAAATGCATGAAAGGATGCATTAAGGCATGAAATGATG
*
426663 CCATAAATGAAATGCATGAAAGGATGCATTAAGGCATAAAAGTG-TG
1 CCATAAATGAAATGCATGAAAGGATGCATTAAGGCATGAAA-TGATG
* *
426709 CCATAAATGAAATGCATGAGAGGATGCATTAAGGCATGAAATAATG
1 CCATAAATGAAATGCATGAAAGGATGCATTAAGGCATGAAATGATG
* * *
426755 CCATAAATAAAATGCATGAAAGGATGCATTAAGGCATGAAAGGATT
1 CCATAAATGAAATGCATGAAAGGATGCATTAAGGCATGAAATGATG
*
426801 CCATAAATGAAATGCATGAAAGGATGCATTAAGGCATGAAAGGATG
1 CCATAAATGAAATGCATGAAAGGATGCATTAAGGCATGAAATGATG
426847 CCATAAATGAAAT
1 CCATAAATGAAAT
426860 AGAAGAATGC
Statistics
Matches: 182, Mismatches: 13, Indels: 4
0.91 0.07 0.02
Matches are distributed among these distances:
45 1 0.01
46 179 0.98
47 2 0.01
ACGTcount: A:0.45, C:0.12, G:0.22, T:0.21
Consensus pattern (46 bp):
CCATAAATGAAATGCATGAAAGGATGCATTAAGGCATGAAATGATG
Found at i:426682 original size:26 final size:26
Alignment explanation
Indices: 426650--426727 Score: 71
Period size: 26 Copynumber: 3.2 Consensus size: 26
426640 ATGCATTAAG
426650 GCATGAAATGATGCCATAAATGAAAT
1 GCATGAAATGATGCCATAAATGAAAT
* *
426676 GCATGAAAGGATG-CAT---T--AAG
1 GCATGAAATGATGCCATAAATGAAAT
*
426696 GCATAAAAGTG-TGCCATAAATGAAAT
1 GCATGAAA-TGATGCCATAAATGAAAT
426722 GCATGA
1 GCATGA
426728 GAGGATGCAT
Statistics
Matches: 39, Mismatches: 6, Indels: 14
0.66 0.10 0.24
Matches are distributed among these distances:
20 11 0.28
21 4 0.10
22 1 0.03
24 1 0.03
25 3 0.08
26 19 0.49
ACGTcount: A:0.44, C:0.12, G:0.23, T:0.22
Consensus pattern (26 bp):
GCATGAAATGATGCCATAAATGAAAT
Found at i:426747 original size:20 final size:20
Alignment explanation
Indices: 426722--426847 Score: 90
Period size: 20 Copynumber: 5.7 Consensus size: 20
426712 TAAATGAAAT
*
426722 GCATGAGAGGATGCATTAAG
1 GCATGAAAGGATGCATTAAG
** *
426742 GCATGAAATAATGCCATAAATAAAAT
1 GCATGAAAGGATG-CAT---T--AAG
426768 GCATGAAAGGATGCATTAAG
1 GCATGAAAGGATGCATTAAG
* *
426788 GCATGAAAGGATTCCATAAATGAAAT
1 GCATGAAAGGA-TGCAT---T--AAG
426814 GCATGAAAGGATGCATTAAG
1 GCATGAAAGGATGCATTAAG
426834 GCATGAAAGGATGC
1 GCATGAAAGGATGC
426848 CATAAATGAA
Statistics
Matches: 83, Mismatches: 11, Indels: 24
0.70 0.09 0.20
Matches are distributed among these distances:
20 39 0.47
21 7 0.08
22 2 0.02
24 2 0.02
25 7 0.08
26 26 0.31
ACGTcount: A:0.43, C:0.11, G:0.25, T:0.21
Consensus pattern (20 bp):
GCATGAAAGGATGCATTAAG
Found at i:426886 original size:2 final size:2
Alignment explanation
Indices: 426879--426907 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
426869 CCATAAATGA
426879 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
426908 ACAGTGCATA
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:428636 original size:2 final size:2
Alignment explanation
Indices: 428629--428673 Score: 90
Period size: 2 Copynumber: 22.5 Consensus size: 2
428619 CCATAAATGA
428629 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
428671 AT A
1 AT A
428674 ACAGTGCATA
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 43 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:429217 original size:619 final size:620
Alignment explanation
Indices: 428036--430234 Score: 3271
Period size: 619 Copynumber: 3.6 Consensus size: 620
428026 CCATAAATGA
*
428036 ATATATATATATATATATAACAGTGCATAATTGGCATGAAAAGATGCCACAAAT-AAAAATACAT
1 ATATATATATATATATATAACAGTGCATAATTGGCATGAAAGGATGCCACAAATGAAAAA-ACAT
* *
428100 AACGATATATTAATGTTGTATAAAGTGCCACTCATGATAATTATAAAAGATAAAGGATTAATTGG
65 AACGATATATTAATGGTGTATAAGGTGCCACTCATGATAATTATAAAAGATAAAGGATTAATTGG
* * * *
428165 TACTTTGGTACAATACATGTGCATTACTTTCTAATTTAATGTACATAGGACAAATAAAGAGTAAT
130 CACTTTGGTGCAATACATGTGCATTACTTTCTAATTTAACGTACATAGGACAAATAAAGAATAAT
* *
428230 TGGGAATAATATATGGAAGGATAGGTAGGCTGGACCTATTAAGAATAAATTCGATAAGTGTATAA
195 TGGGAATAATATATGGAAGGATAGGTAGGCTGGACCTACTAAGAATAAATTCGATGAGTGTATAA
428295 AAGAAACTTGGTTGAACTGAGAAGGATTTATTTGATCCTTATGGAATATGCGATTTAATTCGTCA
260 AAGAAACTTGGTTGAACTGAGAAGGATTTATTTGATCCTTATGGAATATGCGATTTAATTCGTCA
428360 TTTAATAGTCACGAGATAG-GTATGTATAAA-TTCAGTTTCTTTATAATATTATGTCTCACTAAG
325 TTTAATAGTCACGAGAT-GCGTATGTATAAATTTCAGTTTCTTTATAATATTATGTCTCACTAAG
* * * * *
428423 TAAATACTAAGCGTGCGTTGATTTCACGTGTAGGTAAAAGCAAAGATTAGTTGGATACGGGGTGC
389 TAAATACTTAGCGTGTGTTGATTTCACGTGTAGGTAAAAGAAAAGATTAGTTTGATACCGGGTGC
* *
428488 ATAAACTAGTCGTGCAAGTTGGATATGGGGTGCAAGTTGGAT-AAATGACTAATTGCTTACTC-A
454 ATAAACTAGTTGTGCAAGTTGGATACGGGGTGCAAGTTGGATGAAA-GACTAATTGCTTACTCGA
* *
428551 TTCTAATTGATATGAAAGGATGCCATAAATGAAAATGTATGACCACACATAATTGGCATGAAAGA
518 -GCTAATTGATATGAAAGGATGCCATAAATGAAAATGTATAACCACACATAATTGGCATGAAAGA
428616 ATGCCATAAATGAATATATATATATATATATATATATAT
582 ATGCCATAAATGAATATATATATATATATATATATATAT
428655 ATATATATATATATATATAACAGTGCATAATTGGCATGAAAGGATGCCACAAATGAAAAAACATA
1 ATATATATATATATATATAACAGTGCATAATTGGCATGAAAGGATGCCACAAATGAAAAAACATA
428720 ACGATATATTAATGGTGTATAAGGTGCCACTCATGATAATTATAAAAGATAAAGGATTAATTGGC
66 ACGATATATTAATGGTGTATAAGGTGCCACTCATGATAATTATAAAAGATAAAGGATTAATTGGC
*
428785 ACTTTGGTGCAATACATGTGCATTACTTTCTCATTTAACGTACATAGGACAAATAAAGAATAATT
131 ACTTTGGTGCAATACATGTGCATTACTTTCTAATTTAACGTACATAGGACAAATAAAGAATAATT
* * * * * * *
428850 GGGAAGAATATGTGGAAGGATAAGTAGGTTGGTCCTATTAAGAATAAATTTGATGAGTG-ATTAA
196 GGGAATAATATATGGAAGGATAGGTAGGCTGGACCTACTAAGAATAAATTCGATGAGTGTA-TAA
* *
428914 AAGAAACTTGGTTGAACTTAGAAGGATTTATTTGATCCTTATGGAATATGCGATTTAATT-GTTA
260 AAGAAACTTGGTTGAACTGAGAAGGATTTATTTGATCCTTATGGAATATGCGATTTAATTCGTCA
* *
428978 TTAAATAGTCAGGAGATGCGTATGTATAAATTTCAGTTTCTTTATAATATTATGTCTCACTAAGT
325 TTTAATAGTCACGAGATGCGTATGTATAAATTTCAGTTTCTTTATAATATTATGTCTCACTAAGT
* * *
429043 AAATACTTAGCATGTGTTGATTTCACATGTAGGTAAAAGAAAAGATTAGTTTGTTACCGGGTGCA
390 AAATACTTAGCGTGTGTTGATTTCACGTGTAGGTAAAAGAAAAGATTAGTTTGATACCGGGTGCA
*
429108 TAAACTAGTTGTGCAAGTTGGATACGGGGTGCAAGATGGATGAAAGACTAATTGCTTACTCGAGC
455 TAAACTAGTTGTGCAAGTTGGATACGGGGTGCAAGTTGGATGAAAGACTAATTGCTTACTCGAGC
* *
429173 TAATTGATATGAAAGGATGCCATAAATGAAAATGTATAACCACACATAATTGGTATGGAAGAATG
520 TAATTGATATGAAAGGATGCCATAAATGAAAATGTATAACCACACATAATTGGCATGAAAGAATG
429238 CCATAAATG-A-A-A-ATATATATA-A-ATATATA-
585 CCATAAATGAATATATATATATATATATATATATAT
* * * * *
429267 ACA-ATACATA-AT-T-T-CCA-TG-A-AA-T----T------ATGCCACAAATCAAAATACATA
1 ATATATATATATATATATAACAGTGCATAATTGGCATGAAAGGATGCCACAAATGAAAAAACATA
* * *
429313 ACAATATATTAATGGTGTATAAGGTGTCACTCATGATAATTATAAAAGATAAAGGATTAATTTGC
66 ACGATATATTAATGGTGTATAAGGTGCCACTCATGATAATTATAAAAGATAAAGGATTAATTGGC
429378 ACTTTGGTGCAATACATGTGCATTACTTTCTAATTTAACGTACATAGGACAAATAAAGAATAATT
131 ACTTTGGTGCAATACATGTGCATTACTTTCTAATTTAACGTACATAGGACAAATAAAGAATAATT
* * * * *
429443 TGGAATAATATATGGAGGGATAGGTAGG-TAGGAACTACTAAGAATAAATCCGATTAGTGTATAA
196 GGGAATAATATATGGAAGGATAGGTAGGCT-GGACCTACTAAGAATAAATTCGATGAGTGTATAA
* * * *
429507 AAGAAACTTGGTTGAACTGAAAATGATTTATTTGATCCTTATGGAATATGCTATTTAATTCGTAA
260 AAGAAACTTGGTTGAACTGAGAAGGATTTATTTGATCCTTATGGAATATGCGATTTAATTCGTCA
* * * *
429572 TTTAATAGTCACGAGATACATATGTATTATTTTCAGTTTCTTTATAATATTATGTCTCACTAAGT
325 TTTAATAGTCACGAGATGCGTATGTATAAATTTCAGTTTCTTTATAATATTATGTCTCACTAAGT
* * *
429637 AAATACTTAGCGTGTGTTGATTTCACGTATATGTAAAAGAAAAGACTAGTTTGATACCGGGTGCA
390 AAATACTTAGCGTGTGTTGATTTCACGTGTAGGTAAAAGAAAAGATTAGTTTGATACCGGGTGCA
* * ** * *
429702 TAAACTAGTTGTGCAAGTTGGCTACGAGGTGCAAGTTTTATGAATGACTAATTGCTTACTCGTGC
455 TAAACTAGTTGTGCAAGTTGGATACGGGGTGCAAGTTGGATGAAAGACTAATTGCTTACTCGAGC
*
429767 TAATTGATATGAAAGGATGCCATAAATGAAAATGTATAACCACACATAATTGGCATGTAAGAATG
520 TAATTGATATGAAAGGATGCCATAAATGAAAATGTATAACCACACATAATTGGCATGAAAGAATG
429832 CCATAAATGAATATATATATATATATATATATATATATATATATAT
585 CCATAAATG---------A-ATATATATATATATATATATATATAT
* * * *
429878 ATATATATATATATATATAACAGTGCATAATTGGTATGAAGGGATGCCAAAAATGAAAATACATA
1 ATATATATATATATATATAACAGTGCATAATTGGCATGAAAGGATGCCACAAATGAAAAAACATA
* *
429943 ACGATATATTAATGGTGTGTAAGGTGCCACTCATGATAATTATAAAAGATAAAGGATTAATTGGT
66 ACGATATATTAATGGTGTATAAGGTGCCACTCATGATAATTATAAAAGATAAAGGATTAATTGGC
* * *
430008 ACTTTGGTGCAATACATGTGCATTACTTTCTCATTAAACGTACATAGGAAAAATAAAGAATAATT
131 ACTTTGGTGCAATACATGTGCATTACTTTCTAATTTAACGTACATAGGACAAATAAAGAATAATT
* *
430073 GGGAAAAATACATGGAAGGATAGGTAGGCTGGACCTACTAAGAATAAATTCGATGAGTGTATAAA
196 GGGAATAATATATGGAAGGATAGGTAGGCTGGACCTACTAAGAATAAATTCGATGAGTGTATAAA
* *
430138 AGAAACTTGGTTGAATTGAGAAGGATTTATTTGATCCTTATGGAATATGTGATTTAATTCGTCAT
261 AGAAACTTGGTTGAACTGAGAAGGATTTATTTGATCCTTATGGAATATGCGATTTAATTCGTCAT
*
430203 TTAATAGTCTA-GAGATGCTTATGTATAAATTT
326 TTAATAGTC-ACGAGATGCGTATGTATAAATTT
430235 AAGTGAAGAA
Statistics
Matches: 1423, Mismatches: 110, Indels: 83
0.88 0.07 0.05
Matches are distributed among these distances:
592 1 0.00
593 251 0.18
594 252 0.18
599 1 0.00
603 1 0.00
604 2 0.00
605 2 0.00
606 3 0.00
607 3 0.00
608 10 0.01
609 2 0.00
610 9 0.01
611 8 0.01
612 8 0.01
613 9 0.01
614 2 0.00
615 10 0.01
616 3 0.00
617 4 0.00
618 32 0.02
619 514 0.36
620 10 0.01
624 1 0.00
630 283 0.20
631 2 0.00
ACGTcount: A:0.39, C:0.10, G:0.19, T:0.33
Consensus pattern (620 bp):
ATATATATATATATATATAACAGTGCATAATTGGCATGAAAGGATGCCACAAATGAAAAAACATA
ACGATATATTAATGGTGTATAAGGTGCCACTCATGATAATTATAAAAGATAAAGGATTAATTGGC
ACTTTGGTGCAATACATGTGCATTACTTTCTAATTTAACGTACATAGGACAAATAAAGAATAATT
GGGAATAATATATGGAAGGATAGGTAGGCTGGACCTACTAAGAATAAATTCGATGAGTGTATAAA
AGAAACTTGGTTGAACTGAGAAGGATTTATTTGATCCTTATGGAATATGCGATTTAATTCGTCAT
TTAATAGTCACGAGATGCGTATGTATAAATTTCAGTTTCTTTATAATATTATGTCTCACTAAGTA
AATACTTAGCGTGTGTTGATTTCACGTGTAGGTAAAAGAAAAGATTAGTTTGATACCGGGTGCAT
AAACTAGTTGTGCAAGTTGGATACGGGGTGCAAGTTGGATGAAAGACTAATTGCTTACTCGAGCT
AATTGATATGAAAGGATGCCATAAATGAAAATGTATAACCACACATAATTGGCATGAAAGAATGC
CATAAATGAATATATATATATATATATATATATAT
Found at i:429849 original size:2 final size:2
Alignment explanation
Indices: 429842--429896 Score: 110
Period size: 2 Copynumber: 27.5 Consensus size: 2
429832 CCATAAATGA
429842 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
429884 AT AT AT AT AT AT A
1 AT AT AT AT AT AT A
429897 ACAGTGCATA
Statistics
Matches: 53, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 53 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:430764 original size:2 final size:2
Alignment explanation
Indices: 430757--430799 Score: 86
Period size: 2 Copynumber: 21.5 Consensus size: 2
430747 ATGTCAAAAT
430757 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
430799 T
1 T
430800 TTTCTGGCTA
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:433097 original size:46 final size:50
Alignment explanation
Indices: 433044--433245 Score: 166
Period size: 46 Copynumber: 4.3 Consensus size: 50
433034 TAAAACGAAT
* *
433044 CCATAAATGAACTGCATGAAATGATG-CAT-T-AAGT-CATGAAAGGATG
1 CCATAAATGAAATGCATGAAATGATGCCATATGAAATACATGAAAGGATG
433090 CCATAAATGAAATGCAT-AAA-GAATGCCATAAATGAAATACATGAAAGGATG
1 CCATAAATGAAATGCATGAAATG-ATGCCAT--ATGAAATACATGAAAGGATG
* * * *
433141 -CAT---T--AAGGCATGAAAGGATGTCATAAATGAAATGCATGAAAGGATG
1 CCATAAATGAAATGCATGAAATGATGCCAT--ATGAAATACATGAAAGGATG
* **
433187 CCATAAATGAAATGCATGGAATGATG-CAT-T--AAGGCATGAAAGGATG
1 CCATAAATGAAATGCATGAAATGATGCCATATGAAATACATGAAAGGATG
433233 CCATAAATGAAAT
1 CCATAAATGAAAT
433246 TAACGAATAA
Statistics
Matches: 132, Mismatches: 9, Indels: 30
0.77 0.05 0.18
Matches are distributed among these distances:
44 1 0.01
45 12 0.09
46 77 0.58
47 5 0.04
48 1 0.01
49 1 0.01
50 7 0.05
51 15 0.11
52 13 0.10
ACGTcount: A:0.45, C:0.11, G:0.22, T:0.22
Consensus pattern (50 bp):
CCATAAATGAAATGCATGAAATGATGCCATATGAAATACATGAAAGGATG
Found at i:433109 original size:13 final size:14
Alignment explanation
Indices: 433087--433127 Score: 61
Period size: 12 Copynumber: 3.1 Consensus size: 14
433077 TCATGAAAGG
433087 ATGCCATAAATGAA
1 ATGCCATAAATGAA
433101 ATG-CATAAA-G-A
1 ATGCCATAAATGAA
433112 ATGCCATAAATGAA
1 ATGCCATAAATGAA
433126 AT
1 AT
433128 ACATGAAAGG
Statistics
Matches: 24, Mismatches: 0, Indels: 6
0.80 0.00 0.20
Matches are distributed among these distances:
11 4 0.17
12 7 0.29
13 7 0.29
14 6 0.25
ACGTcount: A:0.51, C:0.12, G:0.15, T:0.22
Consensus pattern (14 bp):
ATGCCATAAATGAA
Found at i:433179 original size:26 final size:26
Alignment explanation
Indices: 433078--433245 Score: 182
Period size: 26 Copynumber: 7.0 Consensus size: 26
433068 TGCATTAAGT
433078 CATGAAAGGATGCCATAAATGAAATG
1 CATGAAAGGATGCCATAAATGAAATG
* *
433104 CAT-AAAGAATGCCATAAATGAAATA
1 CATGAAAGGATGCCATAAATGAAATG
*
433129 CATGAAAGGATG-CAT---T--AAGG
1 CATGAAAGGATGCCATAAATGAAATG
*
433149 CATGAAAGGATGTCATAAATGAAATG
1 CATGAAAGGATGCCATAAATGAAATG
433175 CATGAAAGGATGCCATAAATGAAATG
1 CATGAAAGGATGCCATAAATGAAATG
* * *
433201 CATGGAATGATG-CAT---T--AAGG
1 CATGAAAGGATGCCATAAATGAAATG
433221 CATGAAAGGATGCCATAAATGAAAT
1 CATGAAAGGATGCCATAAATGAAAT
433246 TAACGAATAA
Statistics
Matches: 116, Mismatches: 13, Indels: 26
0.75 0.08 0.17
Matches are distributed among these distances:
20 27 0.23
21 6 0.05
22 2 0.02
24 2 0.02
25 29 0.25
26 50 0.43
ACGTcount: A:0.46, C:0.11, G:0.23, T:0.21
Consensus pattern (26 bp):
CATGAAAGGATGCCATAAATGAAATG
Found at i:433220 original size:72 final size:71
Alignment explanation
Indices: 433040--433245 Score: 333
Period size: 72 Copynumber: 2.9 Consensus size: 71
433030 ACTCTAAAAC
* *
433040 GAAT-CCATAAATGAACTGCATGAAATGATGCATTAAGTCATGAAAGGATGCCATAAATGAAATG
1 GAATGCCATAAATGAAATGCATGAAATGATGCATTAAGGCATGAAAGGATGCCATAAATGAAATG
433104 CATAAA
66 CATAAA
* * *
433110 GAATGCCATAAATGAAATACATGAAAGGATGCATTAAGGCATGAAAGGATGTCATAAATGAAATG
1 GAATGCCATAAATGAAATGCATGAAATGATGCATTAAGGCATGAAAGGATGCCATAAATGAAATG
433175 CATGAAA
66 CAT-AAA
* *
433182 GGATGCCATAAATGAAATGCATGGAATGATGCATTAAGGCATGAAAGGATGCCATAAATGAAAT
1 GAATGCCATAAATGAAATGCATGAAATGATGCATTAAGGCATGAAAGGATGCCATAAATGAAAT
433246 TAACGAATAA
Statistics
Matches: 124, Mismatches: 10, Indels: 2
0.91 0.07 0.01
Matches are distributed among these distances:
70 4 0.03
71 58 0.47
72 62 0.50
ACGTcount: A:0.45, C:0.11, G:0.22, T:0.22
Consensus pattern (71 bp):
GAATGCCATAAATGAAATGCATGAAATGATGCATTAAGGCATGAAAGGATGCCATAAATGAAATG
CATAAA
Found at i:434898 original size:600 final size:599
Alignment explanation
Indices: 433765--436344 Score: 3831
Period size: 598 Copynumber: 4.3 Consensus size: 599
433755 ATGCCAATAA
* * *
433765 TGCAAGTTGGATGAATGACTAATTTCTTACTCGTGTTAATTGATATGAAAGGATGCCATAAATGA
1 TGCAAGTTGGATGAATGACTAATTGCTTACTCGTGCTAATTGATATGAAAGGATGTCATAAATGA
* * * *
433830 AAATGTATAACCACACATATTTGGTATGGAAGAATGCCACAAATGAATATATATATATATATA-A
66 AAATGTATAACCACACATAATTGGTATGGAAGAATGCCATAAATAAATATATATATAAATATATA
* *
433894 ACAATGTATAATTGGC-----ATGAAAGGATACCACAAATGAAAATACATAACGATATATTAATG
131 ACAATGCATAATTGGCATGAAATGAAAGGATGCCACAAATGAAAATACATAACGATATATTAATG
433954 GTGCATAAGGTGTCACTCATGATAATTATAAAAGATAAAGGATTAATTGGCACTTTGGTGCAATA
196 GTGCATAAGGTGTCACTCATGATAATTATAAAAGATAAAGGATTAATTGGCACTTTGGTGCAATA
* * *
434019 CATCTGCATTACTTTCTCATTTAACGTACAAAGGACAAATAAAGAATAATCGGTAAGAATATATG
261 CATGTGCATTACTTTCTCATTTAACGTACATAGGACAAATAAAGAATAATCGGGAAGAATATATG
* * * *
434084 GAATGATAGGTAGGCTGGACCTACTAAGAATAAATTCGATGAGTGAACAAAAGAAACTTGGTTGA
326 GAAGGATAGGTAGGTTGGACCTACTAAGAATAAATTCGATGAGTGTATAAAAGAAACTTGGTTGA
* *
434149 ACTGAGAAGGATTTATTTGATCCTTATGGAATATGCGATTTAATTCGTCATTTAATAGTCAGGAG
391 ACTGAGAAGGATTTATTTGATCCTTATGGAATATACGATTTAATTCGTCATTTAATAGTCAAGAG
** *
434214 ATGTGTATGTATAAATTTCAGTTTCTTTATAATATTATGTCTCACTAAGTAAATACTTAGCGTAT
456 ATACGTATGTATAAATTTCAGTTTCTTTATAATATTATGTCTCACTAAGTAAATACTTAGCGTGT
* * * **
434279 GTTGATTTCAGGTGTAGGT-AAAGGAAAGGATTAGTTTGATACCGGGTGCATAAACTAGTTTTGC
521 GTTGATTTCACGTGTAGGTAAAAGCAAA-GATTAGTTGGATACCGGGTGCATAAACTAGTCGTGC
434343 AAGTTGGATACGGGG
585 AAGTTGGATACGGGG
**
434358 TGCAAGTTTTATGAATGACTAATTGCTTACTCGTGCTAATTGATATGAAAGGATGTCATAAATGA
1 TGCAAGTTGGATGAATGACTAATTGCTTACTCGTGCTAATTGATATGAAAGGATGTCATAAATGA
* * * * *
434423 AAATGTATAACCACACATTATTGGAATGAAATAATGCCATAAATAAATATATATATAAACATATA
66 AAATGTATAACCACACATAATTGGTATGGAAGAATGCCATAAATAAATATATATATAAATATATA
* * *
434488 ACAGTGCATAATTGGCATGAAAATGAAAGGATGCCACAAATCAAAATACATAAAGATATATTAAT
131 ACAATGCATAATTGGCATG-AAATGAAAGGATGCCACAAATGAAAATACATAACGATATATTAAT
* * *
434553 GGTGCATATGGTGTCACTCATGATAATAATAAAATATAAAGGATTAATTGGCACTTTGGTGCAAT
195 GGTGCATAAGGTGTCACTCATGATAATTATAAAAGATAAAGGATTAATTGGCACTTTGGTGCAAT
* * * *
434618 ACATGTGCATTACTTTCTCATTTAATGTACATATGACAAATAATGAATAATTGGGAAGAATATAT
260 ACATGTGCATTACTTTCTCATTTAACGTACATAGGACAAATAAAGAATAATCGGGAAGAATATAT
* *
434683 GGAAGGATAGGTAGGTTGGTCCTACTAAGAATAAATTCAATGAGTGTATAAAAGAAACTTGGTTG
325 GGAAGGATAGGTAGGTTGGACCTACTAAGAATAAATTCGATGAGTGTATAAAAGAAACTTGGTTG
** *
434748 AACTGAGAAGGATTTATTTGATCCTTATGGAATATGTGATTTAATTCGTCATTTAATAGTTAAGA
390 AACTGAGAAGGATTTATTTGATCCTTATGGAATATACGATTTAATTCGTCATTTAATAGTCAAGA
** *
434813 GATGTGTATGTATAAATTTCAGTTTCTTTATCATATTATGTCTCACTAAGTAAATACTTAGCGTG
455 GATACGTATGTATAAATTTCAGTTTCTTTATAATATTATGTCTCACTAAGTAAATACTTAGCGTG
* *
434878 TGTTGATTTCACGTGTAGGTAAAAGCAAAGATTAGTTTGATACCGGGTGCATAAACTAGTTGTGC
520 TGTTGATTTCACGTGTAGGTAAAAGCAAAGATTAGTTGGATACCGGGTGCATAAACTAGTCGTGC
434943 AAGTTGGATACGGGG
585 AAGTTGGATACGGGG
* ** *
434958 TACAAGTTTTATGAATGACTAATTGCTTACTCGTGCTAATTGATATGAAAGGATGCCATAAATGA
1 TGCAAGTTGGATGAATGACTAATTGCTTACTCGTGCTAATTGATATGAAAGGATGTCATAAATGA
*
435023 AAATGTATAACCACACATAATTGATATGGAAGAATGCCATAAAT-AA-ATATATATAAATATATA
66 AAATGTATAACCACACATAATTGGTATGGAAGAATGCCATAAATAAATATATATATAAATATATA
* * * * *
435086 ACAGTGCATAATTGGGATGAAAATGAAAGGATGCCACAAGTCACAATACATAACGATATATTAAT
131 ACAATGCATAATTGGCATG-AAATGAAAGGATGCCACAAATGAAAATACATAACGATATATTAAT
*
435151 GGTGCATAAGGTGTCACTCATGATAATTATAAAAGATAAAGGATTAATTGTCACTTTGGTGCAAT
195 GGTGCATAAGGTGTCACTCATGATAATTATAAAAGATAAAGGATTAATTGGCACTTTGGTGCAAT
* * * **
435216 ACATATGCATTACTTTATCATTTAACGTACATAGGACAAATAAAGAATAATCGAGAATTATATAT
260 ACATGTGCATTACTTTCTCATTTAACGTACATAGGACAAATAAAGAATAATCGGGAAGAATATAT
* * *
435281 GGAAGGATAGGTAGGTTGGACCTACTAAGAACAAATTCGATGAGTGTATAAAAGATACTTGGTTA
325 GGAAGGATAGGTAGGTTGGACCTACTAAGAATAAATTCGATGAGTGTATAAAAGAAACTTGGTTG
* *
435346 AACTGATAAGGATTTATTTGATCCTTATGGAATATACGATTTAATTCGTCATTTAATAGTCATGA
390 AACTGAGAAGGATTTATTTGATCCTTATGGAATATACGATTTAATTCGTCATTTAATAGTCAAGA
435411 GATACGTATGTATAAATTTCAGTTTCTTTATAATATTATGTCTCACTAAGTAAATACTTAGCGTG
455 GATACGTATGTATAAATTTCAGTTTCTTTATAATATTATGTCTCACTAAGTAAATACTTAGCGTG
* * *
435476 TGTTGATTTTACGTGTAGGTAAAAGGAAAGATTAGTTGGATACCGGGTGCATAAATTAGTCGTGC
520 TGTTGATTTCACGTGTAGGTAAAAGCAAAGATTAGTTGGATACCGGGTGCATAAACTAGTCGTGC
*
435541 AAGTTGGATACGAGG
585 AAGTTGGATACGGGG
* * *
435556 TGCAAGTTGGATAAAGGACTAATTGCTTACTCGTGCTGATTGATATGAAAGGATGTCATAAATGA
1 TGCAAGTTGGATGAATGACTAATTGCTTACTCGTGCTAATTGATATGAAAGGATGTCATAAATGA
* *
435621 AAATGTATAACCACACATAATTGGTATGGAAGAATGCCACAAA-AGA-ATATATATAAATATATA
66 AAATGTATAACCACACATAATTGGTATGGAAGAATGCCATAAATAAATATATATATAAATATATA
* * * *
435684 ACAATGCATAATTGGCATGAAAT-----TATGCCTCAAATGAATATACATAATGATATATTAATG
131 ACAATGCATAATTGGCATGAAATGAAAGGATGCCACAAATGAAAATACATAACGATATATTAATG
* *
435744 GTGTATAAGGAT-CCACTCATGATAATTATAAAAGATAAAGGATTAATTGGCACTTTGGTGCAAT
196 GTGCATAAGG-TGTCACTCATGATAATTATAAAAGATAAAGGATTAATTGGCACTTTGGTGCAAT
* * * * * *
435808 ACATGTGCATTGCTTTCTTATTTAATGTACATAGGACAAATAAAGAATTATTGGGAATAATATAT
260 ACATGTGCATTACTTTCTCATTTAACGTACATAGGACAAATAAAGAATAATCGGGAAGAATATAT
* * *
435873 GGAAGGATAGGTAGGTTGGACCT-CGAAAGAATAAATTTGATGAGTGTATAAAAGAAACTTAGTT
325 GGAAGGATAGGTAGGTTGGACCTAC-TAAGAATAAATTCGATGAGTGTATAAAAGAAACTTGGTT
* *
435937 GAACTGAGAAGGATTTATTTGATCCTCATGGAATATACGATTTAATTCGTCATTTAATAGTCACG
389 GAACTGAGAAGGATTTATTTGATCCTTATGGAATATACGATTTAATTCGTCATTTAATAGTCAAG
* * * *
436002 AGATACATATTTATAAATTTCAGTTTCTTTATAATATTATGTCTCACTAAGTAAAAAATTAGCGT
454 AGATACGTATGTATAAATTTCAGTTTCTTTATAATATTATGTCTCACTAAGTAAATACTTAGCGT
* *
436067 GTGTTGATTTCACGTATAGGTAAAAGCAAAGATTAGTTGGATTA-GGGGTGCATAAACTAGTCGT
519 GTGTTGATTTCACGTGTAGGTAAAAGCAAAGATTAGTTGGA-TACCGGGTGCATAAACTAGTCGT
*
436131 GTAAGTTGGATACGGGG
583 GCAAGTTGGATACGGGG
* * * * *
436148 TGCAAGCTGGATAAAGGACTAATTGCTTACTCGTGCTAATTAATATGAAAGGATCTCATAAATGA
1 TGCAAGTTGGATGAATGACTAATTGCTTACTCGTGCTAATTGATATGAAAGGATGTCATAAATGA
* * * *
436213 AAATGTATAACCACGCATAATTGGTAGGGAAGAATACTATAAATGAATATATATATATAATAATA
66 AAATGTATAACCACACATAATTGGTATGGAAGAATGCCATAAAT-AA-ATATATATAT-A-AATA
* * *
436278 TATAACAATGCATAATTGGC-----ATGAAAGGATGCCTCAAATGAAAATACATAATGATATGTT
127 TATAACAATGCATAATTGGCATGAAATGAAAGGATGCCACAAATGAAAATACATAACGATATATT
436338 AATGGTG
192 AATGGTG
436345 TCTCACTAAG
Statistics
Matches: 1813, Mismatches: 151, Indels: 41
0.90 0.08 0.02
Matches are distributed among these distances:
591 1 0.00
592 494 0.27
593 119 0.07
594 16 0.01
595 1 0.00
596 8 0.00
597 5 0.00
598 645 0.36
599 2 0.00
600 515 0.28
601 7 0.00
ACGTcount: A:0.38, C:0.11, G:0.19, T:0.32
Consensus pattern (599 bp):
TGCAAGTTGGATGAATGACTAATTGCTTACTCGTGCTAATTGATATGAAAGGATGTCATAAATGA
AAATGTATAACCACACATAATTGGTATGGAAGAATGCCATAAATAAATATATATATAAATATATA
ACAATGCATAATTGGCATGAAATGAAAGGATGCCACAAATGAAAATACATAACGATATATTAATG
GTGCATAAGGTGTCACTCATGATAATTATAAAAGATAAAGGATTAATTGGCACTTTGGTGCAATA
CATGTGCATTACTTTCTCATTTAACGTACATAGGACAAATAAAGAATAATCGGGAAGAATATATG
GAAGGATAGGTAGGTTGGACCTACTAAGAATAAATTCGATGAGTGTATAAAAGAAACTTGGTTGA
ACTGAGAAGGATTTATTTGATCCTTATGGAATATACGATTTAATTCGTCATTTAATAGTCAAGAG
ATACGTATGTATAAATTTCAGTTTCTTTATAATATTATGTCTCACTAAGTAAATACTTAGCGTGT
GTTGATTTCACGTGTAGGTAAAAGCAAAGATTAGTTGGATACCGGGTGCATAAACTAGTCGTGCA
AGTTGGATACGGGG
Done.