Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008015.1 Hibiscus syriacus cultivar Beakdansim tig00110481_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: 961110
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 3 of 4
Found at i:448636 original size:21 final size:21
Alignment explanation
Indices: 448612--448653 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
448602 ATATATTATT
448612 AATTTATAATAATAA-AAAATA
1 AATTTATAATAA-AACAAAATA
*
448633 AATTTATTATAAAACAAAATA
1 AATTTATAATAAAACAAAATA
448654 TGTGTCTGCT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
20 2 0.11
21 17 0.89
ACGTcount: A:0.64, C:0.02, G:0.00, T:0.33
Consensus pattern (21 bp):
AATTTATAATAAAACAAAATA
Found at i:448975 original size:47 final size:48
Alignment explanation
Indices: 448921--449012 Score: 168
Period size: 49 Copynumber: 1.9 Consensus size: 48
448911 GTTGGGTGCT
448921 TAATTTAGCCCTAAT-AGTTATCTTGAAAACTGAAATATAATACTATG
1 TAATTTAGCCCTAATAAGTTATCTTGAAAACTGAAATATAATACTATG
448968 TAATTTAGCCCTAATAAAGTTATCTTGAAAACTGAAATATAATAC
1 TAATTTAGCCCTAAT-AAGTTATCTTGAAAACTGAAATATAATAC
449013 ATCAAATGGA
Statistics
Matches: 43, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
47 15 0.35
49 28 0.65
ACGTcount: A:0.42, C:0.13, G:0.10, T:0.35
Consensus pattern (48 bp):
TAATTTAGCCCTAATAAGTTATCTTGAAAACTGAAATATAATACTATG
Found at i:450381 original size:17 final size:17
Alignment explanation
Indices: 450320--450384 Score: 51
Period size: 17 Copynumber: 3.5 Consensus size: 17
450310 TTGTCTCTAT
*
450320 TATTAAAAATTCAAAATA
1 TATTTAAAATT-AAAATA
*
450338 TATTT-AATTTAAATTTATA
1 TATTTAAAATTAAA---ATA
450357 TTATTTTAAAATTAAAATA
1 -TA-TTTAAAATTAAAATA
450376 TATTTAAAA
1 TATTTAAAA
450385 ATATCGGAAA
Statistics
Matches: 38, Mismatches: 3, Indels: 13
0.70 0.06 0.24
Matches are distributed among these distances:
16 3 0.08
17 11 0.29
18 6 0.16
19 6 0.16
20 2 0.05
21 3 0.08
22 7 0.18
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.46
Consensus pattern (17 bp):
TATTTAAAATTAAAATA
Found at i:450584 original size:15 final size:17
Alignment explanation
Indices: 450564--450595 Score: 50
Period size: 15 Copynumber: 2.0 Consensus size: 17
450554 GAAAATAAAT
450564 AAAAAT-TAT-TATTTA
1 AAAAATATATATATTTA
450579 AAAAATATATATATTTA
1 AAAAATATATATATTTA
450596 TATGACTAAG
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
15 6 0.40
16 3 0.20
17 6 0.40
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (17 bp):
AAAAATATATATATTTA
Found at i:451210 original size:13 final size:13
Alignment explanation
Indices: 451192--451220 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
451182 CCACCGTACT
451192 CCGCCGCCGGCCA
1 CCGCCGCCGGCCA
451205 CCGCCGCCGGCCA
1 CCGCCGCCGGCCA
451218 CCG
1 CCG
451221 TAACGGTGGT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.07, C:0.62, G:0.31, T:0.00
Consensus pattern (13 bp):
CCGCCGCCGGCCA
Found at i:451936 original size:3 final size:3
Alignment explanation
Indices: 451928--452024 Score: 131
Period size: 3 Copynumber: 31.7 Consensus size: 3
451918 TTATTTATTA
*
451928 AAT AAT AAT ATAT AAT ATT AAT AAT AAT AAAT AAT AAT AAT AAT AAT
1 AAT AAT AAT A-AT AAT AAT AAT AAT AAT -AAT AAT AAT AAT AAT AAT
* * **
451975 AAT TAT AAT AAT AAT AAT AAT ACT AAT AAT AAT AAT TTT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
452023 AA
1 AA
452025 CTTTAAATAA
Statistics
Matches: 82, Mismatches: 10, Indels: 4
0.85 0.10 0.04
Matches are distributed among these distances:
3 76 0.93
4 6 0.07
ACGTcount: A:0.62, C:0.01, G:0.00, T:0.37
Consensus pattern (3 bp):
AAT
Found at i:452396 original size:76 final size:76
Alignment explanation
Indices: 452157--453026 Score: 1645
Period size: 76 Copynumber: 11.5 Consensus size: 76
452147 GATGGAAATG
* *
452157 TTTGAAAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGTTTTTGAAAACATCAAAAAGC
1 TTTGGAAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGG-CTTTGAAAACATCAAAAAGC
452222 TCCCGAAGGCTT
65 TCCCGAAGGCTT
452234 TTTGGAAACATCATGCACTGAAGGGCTTACAGATGA-CCGAAGGCTTTGAAAACATCAAAAAGCT
1 TTTGGAAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCT
452298 CCCGAAGGCTT
66 CCCGAAGGCTT
452309 TTTGGAAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCT
1 TTTGGAAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCT
452374 CCCGAAGGCTT
66 CCCGAAGGCTT
*
452385 TTTGGAAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGACTTTGAAAACATCAAAAAGCT
1 TTTGGAAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCT
452450 CCCGAAGGCTT
66 CCCGAAGGCTT
*
452461 TTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCT
1 TTTGGAAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCT
452526 CCCGAAGGCTT
66 CCCGAAGGCTT
452537 TTTGGAAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGCTTTGAAAACATC-AAAAGCT
1 TTTGGAAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCT
452601 CCCGAAGGCTT
66 CCCGAAGGCTT
* *
452612 TTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGACTTTGAAAACATCAAAAAGCT
1 TTTGGAAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCT
452677 CCCGAAGGCTT
66 CCCGAAGGCTT
452688 TTTGGAAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCT
1 TTTGGAAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCT
452753 CCCGAAGGCTT
66 CCCGAAGGCTT
452764 TTTGGAAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCT
1 TTTGGAAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCT
452829 CCCGAAGGCTT
66 CCCGAAGGCTT
*
452840 TTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCT
1 TTTGGAAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCT
452905 CCCGAAGGCTT
66 CCCGAAGGCTT
*
452916 TTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCT
1 TTTGGAAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCT
452981 CCCGAAGGCTT
66 CCCGAAGGCTT
452992 TTTGGAAACATCATGCACTGAAGGGCTTACAGATG
1 TTTGGAAACATCATGCACTGAAGGGCTTACAGATG
453027 TGGGAAATAG
Statistics
Matches: 779, Mismatches: 12, Indels: 5
0.98 0.02 0.01
Matches are distributed among these distances:
75 140 0.18
76 604 0.78
77 35 0.04
ACGTcount: A:0.35, C:0.22, G:0.22, T:0.21
Consensus pattern (76 bp):
TTTGGAAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCT
CCCGAAGGCTT
Found at i:452710 original size:303 final size:304
Alignment explanation
Indices: 452157--453026 Score: 1654
Period size: 303 Copynumber: 2.9 Consensus size: 304
452147 GATGGAAATG
* *
452157 TTTGAAAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGTTTTTGAAAACATCAAAAAGC
1 TTTGGAAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGG-CTTTGAAAACATCAAAAAGC
452222 TCCCGAAGGCTTTTTGGAAACATCATGCACTGAAGGGCTTACAGATGA-CCGAAGGCTTTGAAAA
65 TCCCGAAGGCTTTTTGGAAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGCTTTGAAAA
*
452286 CATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGAAGGGCTTACAGATGACCCGAA
130 CATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAA
452351 GGCTTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGAAGGGCTTACA
195 GGCTTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGAAGGGCTTACA
452416 GATGACCCGAAGACTTTGAAAACATCAAAAAGCTCCCGAAGGCTT
260 GATGACCCGAAGACTTTGAAAACATCAAAAAGCTCCCGAAGGCTT
*
452461 TTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCT
1 TTTGGAAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCT
452526 CCCGAAGGCTTTTTGGAAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGCTTTGAAAAC
66 CCCGAAGGCTTTTTGGAAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGCTTTGAAAAC
452591 ATC-AAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAG
131 ATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAG
*
452655 ACTTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGAAGGGCTTACAG
196 GCTTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGAAGGGCTTACAG
*
452720 ATGACCCGAAGGCTTTGAAAACATCAAAAAGCTCCCGAAGGCTT
261 ATGACCCGAAGACTTTGAAAACATCAAAAAGCTCCCGAAGGCTT
452764 TTTGGAAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCT
1 TTTGGAAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCT
*
452829 CCCGAAGGCTTTTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAAC
66 CCCGAAGGCTTTTTGGAAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGCTTTGAAAAC
452894 ATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAG
131 ATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAG
452959 GCTTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGAAGGGCTTACAG
196 GCTTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGAAGGGCTTACAG
453024 ATG
261 ATG
453027 TGGGAAATAG
Statistics
Matches: 555, Mismatches: 9, Indels: 4
0.98 0.02 0.01
Matches are distributed among these distances:
303 365 0.66
304 190 0.34
ACGTcount: A:0.35, C:0.22, G:0.22, T:0.21
Consensus pattern (304 bp):
TTTGGAAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCT
CCCGAAGGCTTTTTGGAAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGCTTTGAAAAC
ATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAG
GCTTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGAAGGGCTTACAG
ATGACCCGAAGACTTTGAAAACATCAAAAAGCTCCCGAAGGCTT
Found at i:453298 original size:161 final size:163
Alignment explanation
Indices: 453029--453348 Score: 493
Period size: 162 Copynumber: 2.0 Consensus size: 163
453019 TACAGATGTG
* * * * *
453029 GGAAATAGTTTACTAAGTAAGAAACTATGGAAATTGTTTTCTTACTATTCAACAATTTTATTTTC
1 GGAAATAGTTTAATAAGTAAGAAACTAAGAAAATCGTTTTCTTACTATTCAACAATTTCATTTT-
**
453094 AGAAAAGATTGAATGAGAAACTATGGAAATCGTTTTCTCATTA-TTTTTCAAGATAACATGTTGA
65 A-AAAAGATAAAATGAGAAACTATGGAAATCGTTTTCTCATTAGTTTTTCAA-ATAACATGTTGA
*
453158 TTGGGTAACATGCCCCAATCTCCAGATAAGGTTGTT
128 TTGGGTAACATGCCCCAATCTCAAGATAAGGTTGTT
*
453194 GGAAATAGTTTAATAAGTAA-AAACTAAGAAAATCGTTTTCTTACTTTTCAACAATTTCATTTT-
1 GGAAATAGTTTAATAAGTAAGAAACTAAGAAAATCGTTTTCTTACTATTCAACAATTTCATTTTA
*
453257 AAAAGATAAAATGAGAAACTATGGAAATCGTTTTCTCATTATGTTTTTGAAATAACATGTTGATT
66 AAAAGATAAAATGAGAAACTATGGAAATCGTTTTCTCATTA-GTTTTTCAAATAACATGTTGATT
453322 GGGTAACATGCCCCAATCTCAAGATAA
130 GGGTAACATGCCCCAATCTCAAGATAA
453349 TACTCATTCT
Statistics
Matches: 143, Mismatches: 10, Indels: 7
0.89 0.06 0.04
Matches are distributed among these distances:
161 39 0.27
162 40 0.28
163 7 0.05
164 38 0.27
165 19 0.13
ACGTcount: A:0.37, C:0.12, G:0.15, T:0.36
Consensus pattern (163 bp):
GGAAATAGTTTAATAAGTAAGAAACTAAGAAAATCGTTTTCTTACTATTCAACAATTTCATTTTA
AAAAGATAAAATGAGAAACTATGGAAATCGTTTTCTCATTAGTTTTTCAAATAACATGTTGATTG
GGTAACATGCCCCAATCTCAAGATAAGGTTGTT
Found at i:456651 original size:162 final size:161
Alignment explanation
Indices: 456389--456744 Score: 578
Period size: 162 Copynumber: 2.2 Consensus size: 161
456379 ATTTCTACTA
456389 TGAGCAAATTCATCTTCCAAATTCAATGATTGGTTCTGCCAAACCAGATAACTCAAAGAACACTT
1 TGAGCAAATTCATCTTCCAAATTCAATGATTGGTTCTGCCAAACCAGATAACTCAAAGAACACTT
456454 CCAGAAGATGCTATTAACAAATTCATCTTCCAAATTCAATGATTGGTTCTG-CC-A-A-ATCAGA
66 CCAGAAGATGCTATTAACAAATTCATCTTCCAAATTCAATGATTGGTTCTGTCCAACAGATCAGA
456515 TAACTCAAAGAACACTTCCAGAAGATGCTAT
131 TAACTCAAAGAACACTTCCAGAAGATGCTAT
456546 TGAGCAAATTCATCTTCCAAATTCAATGATTGGTTCTGCCAAACCAGATCAGATAACTCAAAGAA
1 TGAGCAAATTCATCTTCCAAATTCAATGATTGGTTCTGCCAAA-C----CAGATAACTCAAAGAA
* *
456611 CACTTCCAGAAGATGCTATTGACAAATTCATCTTCCAAATTTAATGATTGGTTCTGTCCAACCAG
61 CACTTCCAGAAGATGCTATTAACAAATTCATCTTCCAAATTCAATGATTGGTTCTGTCCAA-CAG
*
456676 ATCATATAACTCAAAGAACACTTCCAGAAGATGCTAT
125 ATCAGATAACTCAAAGAACACTTCCAGAAGATGCTAT
* *
456713 T-AACAAATTCATATTCCAAATTCAATGATTGG
1 TGAGCAAATTCATCTTCCAAATTCAATGATTGG
456745 ACTAAGATAT
Statistics
Matches: 184, Mismatches: 5, Indels: 11
0.92 0.03 0.05
Matches are distributed among these distances:
157 43 0.23
158 1 0.01
162 70 0.38
163 2 0.01
164 1 0.01
166 30 0.16
167 37 0.20
ACGTcount: A:0.37, C:0.22, G:0.13, T:0.28
Consensus pattern (161 bp):
TGAGCAAATTCATCTTCCAAATTCAATGATTGGTTCTGCCAAACCAGATAACTCAAAGAACACTT
CCAGAAGATGCTATTAACAAATTCATCTTCCAAATTCAATGATTGGTTCTGTCCAACAGATCAGA
TAACTCAAAGAACACTTCCAGAAGATGCTAT
Found at i:456676 original size:83 final size:78
Alignment explanation
Indices: 456393--456744 Score: 551
Period size: 83 Copynumber: 4.4 Consensus size: 78
456383 CTACTATGAG
*
456393 CAAATTCATCTTCCAAATTCAATGATTGGTTCTGCCAAACCAGATAACTCAAAGAACACTTCCAG
1 CAAATTCATCTTCCAAATTCAATGATTGGTTCTGCCAAATCAGATAACTCAAAGAACACTTCCAG
456458 AAGATGCTATTAA
66 AAGATGCTATTAA
456471 CAAATTCATCTTCCAAATTCAATGATTGGTTCTGCCAAATCAGATAACTCAAAGAACACTTCCAG
1 CAAATTCATCTTCCAAATTCAATGATTGGTTCTGCCAAATCAGATAACTCAAAGAACACTTCCAG
*
456536 AAGATGCTATTGAG
66 AAGATGCTATT-AA
456550 CAAATTCATCTTCCAAATTCAATGATTGGTTCTGCCAAACCAGATCAGATAACTCAAAGAACACT
1 CAAATTCATCTTCCAAATTCAATGATTGGTTCTGCC--A--A-ATCAGATAACTCAAAGAACACT
*
456615 TCCAGAAGATGCTATTGA
61 TCCAGAAGATGCTATTAA
* *
456633 CAAATTCATCTTCCAAATTTAATGATTGGTTCTGTCCAACCAGATCATATAACTCAAAGAACACT
1 CAAATTCATCTTCCAAATTCAATGATTGGTTCTG-CC-A--A-ATCAGATAACTCAAAGAACACT
456698 TCCAGAAGATGCTATTAA
61 TCCAGAAGATGCTATTAA
*
456716 CAAATTCATATTCCAAATTCAATGATTGG
1 CAAATTCATCTTCCAAATTCAATGATTGG
456745 ACTAAGATAT
Statistics
Matches: 258, Mismatches: 9, Indels: 9
0.93 0.03 0.03
Matches are distributed among these distances:
78 75 0.29
79 37 0.14
81 1 0.00
83 105 0.41
84 40 0.16
ACGTcount: A:0.38, C:0.22, G:0.12, T:0.28
Consensus pattern (78 bp):
CAAATTCATCTTCCAAATTCAATGATTGGTTCTGCCAAATCAGATAACTCAAAGAACACTTCCAG
AAGATGCTATTAA
Found at i:463696 original size:16 final size:15
Alignment explanation
Indices: 463660--463700 Score: 50
Period size: 14 Copynumber: 2.8 Consensus size: 15
463650 TTAATACCTG
*
463660 AATAA-AAAAATATT
1 AATAATAAAAATATA
463674 AAT-ATAAAAATAATA
1 AATAATAAAAAT-ATA
463689 AATAATAAAAAT
1 AATAATAAAAAT
463701 TTGAAAGAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
13 1 0.04
14 9 0.39
15 5 0.22
16 8 0.35
ACGTcount: A:0.73, C:0.00, G:0.00, T:0.27
Consensus pattern (15 bp):
AATAATAAAAATATA
Found at i:464180 original size:17 final size:17
Alignment explanation
Indices: 464119--464183 Score: 51
Period size: 17 Copynumber: 3.5 Consensus size: 17
464109 TTGTCTCTAT
*
464119 TATTAAAAATTCAAAATA
1 TATTTAAAATT-AAAATA
*
464137 TATTT-AATTTAAATTTATA
1 TATTTAAAATTAAA---ATA
464156 GTATTTTAAAATTAAAATA
1 -TA-TTTAAAATTAAAATA
464175 TATTTAAAA
1 TATTTAAAA
464184 ATATCGGAAA
Statistics
Matches: 38, Mismatches: 3, Indels: 13
0.70 0.06 0.24
Matches are distributed among these distances:
16 3 0.08
17 11 0.29
18 6 0.16
19 6 0.16
20 2 0.05
21 3 0.08
22 7 0.18
ACGTcount: A:0.52, C:0.02, G:0.02, T:0.45
Consensus pattern (17 bp):
TATTTAAAATTAAAATA
Found at i:464397 original size:19 final size:18
Alignment explanation
Indices: 464359--464397 Score: 53
Period size: 18 Copynumber: 2.1 Consensus size: 18
464349 ATATCGAAAA
464359 TAAATAAAAATTATTATT
1 TAAATAAAAATTATTATT
464377 TAAA-AAAAATATATATATT
1 TAAATAAAAAT-TAT-TATT
464396 TA
1 TA
464398 TATGACTAAG
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
17 6 0.32
18 7 0.37
19 6 0.32
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (18 bp):
TAAATAAAAATTATTATT
Found at i:465014 original size:13 final size:13
Alignment explanation
Indices: 464996--465024 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
464986 CCACCGTACT
464996 CCGCCGCCGGCCA
1 CCGCCGCCGGCCA
465009 CCGCCGCCGGCCA
1 CCGCCGCCGGCCA
465022 CCG
1 CCG
465025 TAACGGTGGT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.07, C:0.62, G:0.31, T:0.00
Consensus pattern (13 bp):
CCGCCGCCGGCCA
Found at i:465742 original size:3 final size:3
Alignment explanation
Indices: 465734--465827 Score: 134
Period size: 3 Copynumber: 30.7 Consensus size: 3
465724 TTATTTATTA
*
465734 AAT AAT AAT ATAT AAT ATT AAT AAT AAT AAAT AAT AAT AAT AAT AAT
1 AAT AAT AAT A-AT AAT AAT AAT AAT AAT -AAT AAT AAT AAT AAT AAT
* **
465781 AAT TAT AAT AAT AAT AAT AAT AAT AAT AAT AAT TTT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
465828 CTTTAAATAA
Statistics
Matches: 81, Mismatches: 8, Indels: 4
0.87 0.09 0.04
Matches are distributed among these distances:
3 75 0.93
4 6 0.07
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (3 bp):
AAT
Found at i:471169 original size:31 final size:32
Alignment explanation
Indices: 471134--471197 Score: 85
Period size: 32 Copynumber: 2.0 Consensus size: 32
471124 GTCGGTGGTG
471134 ATTTTACTATTA-ATTTAATATAAAAATATAT
1 ATTTTACTATTATATTTAATATAAAAATATAT
* * * *
471165 ATTTTACTCTTATTTTTATTTTAAAAATATAT
1 ATTTTACTATTATATTTAATATAAAAATATAT
471197 A
1 A
471198 ATATTTTAAT
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
31 11 0.39
32 17 0.61
ACGTcount: A:0.42, C:0.05, G:0.00, T:0.53
Consensus pattern (32 bp):
ATTTTACTATTATATTTAATATAAAAATATAT
Found at i:471240 original size:29 final size:29
Alignment explanation
Indices: 471205--471521 Score: 140
Period size: 29 Copynumber: 10.3 Consensus size: 29
471195 ATAATATTTT
*
471205 AATATATTTTTAAAAGTTAAGATAATAATAA
1 AATATATTTTT--AAGTTAAGATAAAAATAA
* *
471236 AATATATTTTTAATTTAAAATAAAAATAA
1 AATATATTTTTAAGTTAAGATAAAAATAA
* *
471265 AATATATTTTTAAGTAAAGATAAGAAAAAAAA
1 AATATATTTTTAAGTTAAGAT---AAAAATAA
* * * *
471297 TATTATATATTTTTTAATTTAAAATAAGAGTAA
1 -A--ATATA-TTTTTAAGTTAAGATAAAAATAA
* * * *
471330 AATATTTTATATTAAATTAATAATAAAAATTTA
1 AATATATT-T-TTAAGTTAA-GATAAAAA-TAA
* *
471363 AATATA-TTTCAAGTTAAGATATTTAAA-AA
1 AATATATTTTTAAGTTAAGATA--AAAATAA
* * *
471392 AA-ATATTTTTAAGTGATGATAAAGATAAA
1 AATATATTTTTAAGTTAAGATAAAAAT-AA
* *
471421 ATATATAATTTTTACA-TTAAAATAAAAACAA
1 A-ATAT-ATTTTTA-AGTTAAGATAAAAATAA
* * * * * *
471452 CATATATTTAATAAATTATGACAGAAATAA
1 AATATATTT-TTAAGTTAAGATAAAAATAA
* *
471482 AA-ATATTTAATAAGTTAAAATAAAAATAA
1 AATATATTT-TTAAGTTAAGATAAAAATAA
*
471511 AGAGATATTTT
1 A-ATATATTTT
471522 AAAATTTAAG
Statistics
Matches: 214, Mismatches: 48, Indels: 49
0.69 0.15 0.16
Matches are distributed among these distances:
27 2 0.01
28 3 0.01
29 84 0.39
30 31 0.14
31 33 0.15
32 30 0.14
33 14 0.07
35 5 0.02
36 12 0.06
ACGTcount: A:0.55, C:0.02, G:0.06, T:0.38
Consensus pattern (29 bp):
AATATATTTTTAAGTTAAGATAAAAATAA
Found at i:471393 original size:97 final size:96
Alignment explanation
Indices: 471206--471398 Score: 212
Period size: 94 Copynumber: 2.0 Consensus size: 96
471196 TAATATTTTA
* * *
471206 ATATATTTTTAAAAGTTAAGATAATAATAAAATATATTTTTAATTTAAAATAAAAATAAAATATA
1 ATATATTTTTAAAAGTTAAAATAAGAATAAAATATATTTTTAAATTAAAATAAAAATAAAATATA
*
471271 TTTTTAAGTAAAGATAAG-AAAAAAAATATT
66 TTTTCAAGTAAAGATAAGAAAAAAAAATATT
* * * * *
471301 ATATATTTTT-TAATTTAAAATAAGAGTAAAATATTTTATATTAAATTAATAATAAAAATTTAAA
1 ATATATTTTTAAAAGTTAAAATAAGAATAAAATATATT-T-TTAAATTAA-AATAAAAA-TAAAA
* ***
471365 TATA-TTTCAAGTTAAGATATTTAAAAAAAATATT
62 TATATTTTCAAGTAAAGATAAGAAAAAAAAATATT
471399 TTTAAGTGAT
Statistics
Matches: 81, Mismatches: 12, Indels: 7
0.81 0.12 0.07
Matches are distributed among these distances:
94 21 0.26
95 11 0.14
96 8 0.10
97 21 0.26
98 20 0.25
ACGTcount: A:0.54, C:0.01, G:0.05, T:0.40
Consensus pattern (96 bp):
ATATATTTTTAAAAGTTAAAATAAGAATAAAATATATTTTTAAATTAAAATAAAAATAAAATATA
TTTTCAAGTAAAGATAAGAAAAAAAAATATT
Found at i:471750 original size:16 final size:17
Alignment explanation
Indices: 471725--471757 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
471715 TGGTAGAAAT
*
471725 AAATATATT-AAATTAA
1 AAATAAATTAAAATTAA
471741 AAATAAATTAAAATTAA
1 AAATAAATTAAAATTAA
471758 TTTAGTCTTC
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 8 0.53
17 7 0.47
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (17 bp):
AAATAAATTAAAATTAA
Found at i:484199 original size:39 final size:39
Alignment explanation
Indices: 484156--484230 Score: 141
Period size: 39 Copynumber: 1.9 Consensus size: 39
484146 GGTTGTCCTC
484156 TAACATAGGATATGCATAGAGCAACTTTAGAACCGTGGT
1 TAACATAGGATATGCATAGAGCAACTTTAGAACCGTGGT
*
484195 TAACATAGGATATTCATAGAGCAACTTTAGAACCGT
1 TAACATAGGATATGCATAGAGCAACTTTAGAACCGT
484231 TGTTGACCTC
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
39 35 1.00
ACGTcount: A:0.37, C:0.16, G:0.20, T:0.27
Consensus pattern (39 bp):
TAACATAGGATATGCATAGAGCAACTTTAGAACCGTGGT
Found at i:486989 original size:23 final size:23
Alignment explanation
Indices: 486959--487023 Score: 130
Period size: 23 Copynumber: 2.8 Consensus size: 23
486949 GTATCATCAT
486959 GACTGTATGTCTGAAGATATAAC
1 GACTGTATGTCTGAAGATATAAC
486982 GACTGTATGTCTGAAGATATAAC
1 GACTGTATGTCTGAAGATATAAC
487005 GACTGTATGTCTGAAGATA
1 GACTGTATGTCTGAAGATA
487024 GAAGGCTGTA
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 42 1.00
ACGTcount: A:0.34, C:0.12, G:0.23, T:0.31
Consensus pattern (23 bp):
GACTGTATGTCTGAAGATATAAC
Found at i:490704 original size:17 final size:18
Alignment explanation
Indices: 490661--490706 Score: 58
Period size: 19 Copynumber: 2.6 Consensus size: 18
490651 TTTATATATT
490661 TATAATTATATTCTTAAG
1 TATAATTATATTCTTAAG
* *
490679 TAGTAATTATATTTTTCA-
1 TA-TAATTATATTCTTAAG
490697 TATAATTATA
1 TATAATTATA
490707 ATATAGTGTC
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
17 8 0.32
18 4 0.16
19 13 0.52
ACGTcount: A:0.39, C:0.04, G:0.04, T:0.52
Consensus pattern (18 bp):
TATAATTATATTCTTAAG
Found at i:494770 original size:6 final size:6
Alignment explanation
Indices: 494759--494783 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
494749 GACACGTATT
494759 ACCACG ACCACG ACCACG ACCACG A
1 ACCACG ACCACG ACCACG ACCACG A
494784 GACGGCGGCA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.36, C:0.48, G:0.16, T:0.00
Consensus pattern (6 bp):
ACCACG
Found at i:495413 original size:22 final size:22
Alignment explanation
Indices: 495385--495436 Score: 104
Period size: 22 Copynumber: 2.4 Consensus size: 22
495375 ATTTGGAAAT
495385 TCGCAACGACAACTGTAGACTA
1 TCGCAACGACAACTGTAGACTA
495407 TCGCAACGACAACTGTAGACTA
1 TCGCAACGACAACTGTAGACTA
495429 TCGCAACG
1 TCGCAACG
495437 CGAAATGAAA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 30 1.00
ACGTcount: A:0.35, C:0.29, G:0.19, T:0.17
Consensus pattern (22 bp):
TCGCAACGACAACTGTAGACTA
Found at i:495456 original size:20 final size:20
Alignment explanation
Indices: 495428--495500 Score: 83
Period size: 20 Copynumber: 3.6 Consensus size: 20
495418 ACTGTAGACT
495428 ATCGCAACGCGAAATGAAAA
1 ATCGCAACGCGAAATGAAAA
* ** * **
495448 ATCGTAACGCGATTTTCAACT
1 ATCGCAACGCGA-AATGAAAA
495469 ATCGCAACGCGAAATGAAAA
1 ATCGCAACGCGAAATGAAAA
495489 ATCGCAACGCGA
1 ATCGCAACGCGA
495501 TTTTCAACTA
Statistics
Matches: 40, Mismatches: 12, Indels: 2
0.74 0.22 0.04
Matches are distributed among these distances:
20 26 0.65
21 14 0.35
ACGTcount: A:0.41, C:0.23, G:0.19, T:0.16
Consensus pattern (20 bp):
ATCGCAACGCGAAATGAAAA
Found at i:495473 original size:41 final size:41
Alignment explanation
Indices: 495425--495525 Score: 184
Period size: 41 Copynumber: 2.5 Consensus size: 41
495415 ACAACTGTAG
*
495425 ACTATCGCAACGCGAAATGAAAAATCGTAACGCGATTTTCA
1 ACTATCGCAACGCGAAATGAAAAATCGCAACGCGATTTTCA
495466 ACTATCGCAACGCGAAATGAAAAATCGCAACGCGATTTTCA
1 ACTATCGCAACGCGAAATGAAAAATCGCAACGCGATTTTCA
*
495507 ACTATCGCAACACGAAATG
1 ACTATCGCAACGCGAAATG
495526 CAACGCGAAT
Statistics
Matches: 58, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
41 58 1.00
ACGTcount: A:0.40, C:0.24, G:0.17, T:0.20
Consensus pattern (41 bp):
ACTATCGCAACGCGAAATGAAAAATCGCAACGCGATTTTCA
Found at i:495529 original size:21 final size:21
Alignment explanation
Indices: 495403--495529 Score: 89
Period size: 21 Copynumber: 6.1 Consensus size: 21
495393 ACAACTGTAG
* *
495403 ACTATCGCAACGAC-AACTGTA
1 ACTATCGCAACG-CGAAATGCA
495424 GACTATCGCAACGCGAAATG-A
1 -ACTATCGCAACGCGAAATGCA
** * ** *
495445 AAAATCGTAACGCGATTTTCA
1 ACTATCGCAACGCGAAATGCA
495466 ACTATCGCAACGCGAAATG-A
1 ACTATCGCAACGCGAAATGCA
** ** *
495486 AAAATCGCAACGCGATTTTCA
1 ACTATCGCAACGCGAAATGCA
*
495507 ACTATCGCAACACGAAATGCA
1 ACTATCGCAACGCGAAATGCA
495528 AC
1 AC
495530 GCGAATTTGC
Statistics
Matches: 78, Mismatches: 24, Indels: 7
0.72 0.22 0.06
Matches are distributed among these distances:
20 28 0.36
21 34 0.44
22 16 0.21
ACGTcount: A:0.39, C:0.25, G:0.17, T:0.19
Consensus pattern (21 bp):
ACTATCGCAACGCGAAATGCA
Found at i:509440 original size:36 final size:36
Alignment explanation
Indices: 509400--509470 Score: 124
Period size: 36 Copynumber: 2.0 Consensus size: 36
509390 ATAAGATTTC
509400 AATACCGATATTTTACAGATATAATTATTAGAACTT
1 AATACCGATATTTTACAGATATAATTATTAGAACTT
* *
509436 AATACCGATATTTTACAGATGTAATTATTCGAACT
1 AATACCGATATTTTACAGATATAATTATTAGAACT
509471 CAAGATCTTT
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
36 33 1.00
ACGTcount: A:0.39, C:0.13, G:0.10, T:0.38
Consensus pattern (36 bp):
AATACCGATATTTTACAGATATAATTATTAGAACTT
Found at i:509502 original size:40 final size:40
Alignment explanation
Indices: 509449--509557 Score: 146
Period size: 40 Copynumber: 2.7 Consensus size: 40
509439 ACCGATATTT
*
509449 TACAGATGTAATTATTCGAACTCAAGATCTTTAGACATCA
1 TACAGATGCAATTATTCGAACTCAAGATCTTTAGACATCA
* * * *
509489 TGCGGATGCAATTATTCGAACTAAAGATCTTTAGACATCC
1 TACAGATGCAATTATTCGAACTCAAGATCTTTAGACATCA
* * *
509529 TATAGATACATTTATTCGAACTCAAGATC
1 TACAGATGCAATTATTCGAACTCAAGATC
509558 GATATCCTAT
Statistics
Matches: 58, Mismatches: 11, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
40 58 1.00
ACGTcount: A:0.36, C:0.18, G:0.14, T:0.32
Consensus pattern (40 bp):
TACAGATGCAATTATTCGAACTCAAGATCTTTAGACATCA
Found at i:515586 original size:23 final size:23
Alignment explanation
Indices: 515560--515625 Score: 80
Period size: 23 Copynumber: 2.9 Consensus size: 23
515550 CATTTAAATT
* *
515560 TAAATTTAAAATTATTAAAAAAA
1 TAAATATAAAAATATTAAAAAAA
*
515583 TAAATATAAAAATATTTAAAAAA
1 TAAATATAAAAATATTAAAAAAA
*
515606 TAATTACTAAAAATA-TAAAA
1 TAAATA-TAAAAATATTAAAA
515626 TTTAGGAAAA
Statistics
Matches: 37, Mismatches: 5, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
23 29 0.78
24 8 0.22
ACGTcount: A:0.67, C:0.02, G:0.00, T:0.32
Consensus pattern (23 bp):
TAAATATAAAAATATTAAAAAAA
Found at i:516040 original size:22 final size:23
Alignment explanation
Indices: 515988--516040 Score: 63
Period size: 22 Copynumber: 2.3 Consensus size: 23
515978 TTATAAAATA
* *
515988 TATATTTAAAAACTATTTAATTT
1 TATATTTTAAAACTATATAATTT
* *
516011 TATTTTTTAAAA-TATATATTTT
1 TATATTTTAAAACTATATAATTT
516033 TATATTTT
1 TATATTTT
516041 TATCAATAAT
Statistics
Matches: 25, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
22 15 0.60
23 10 0.40
ACGTcount: A:0.38, C:0.02, G:0.00, T:0.60
Consensus pattern (23 bp):
TATATTTTAAAACTATATAATTT
Found at i:516048 original size:24 final size:23
Alignment explanation
Indices: 516008--516059 Score: 61
Period size: 25 Copynumber: 2.2 Consensus size: 23
515998 AACTATTTAA
*
516008 TTTTATTTTTTAAAAT-ATATAT
1 TTTTATTTTTTAAAATAATAAAT
*
516030 TTTTATATTTTTATCAATAATAAAT
1 TTTTAT-TTTTTA-AAATAATAAAT
516055 TTTTA
1 TTTTA
516060 AAAATAATAA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
22 6 0.24
23 6 0.24
24 3 0.12
25 10 0.40
ACGTcount: A:0.37, C:0.02, G:0.00, T:0.62
Consensus pattern (23 bp):
TTTTATTTTTTAAAATAATAAAT
Found at i:520893 original size:13 final size:13
Alignment explanation
Indices: 520877--520907 Score: 62
Period size: 13 Copynumber: 2.4 Consensus size: 13
520867 ATGAAACCCT
520877 AACAACTAAACCA
1 AACAACTAAACCA
520890 AACAACTAAACCA
1 AACAACTAAACCA
520903 AACAA
1 AACAA
520908 ATTCCCCCCT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.65, C:0.29, G:0.00, T:0.06
Consensus pattern (13 bp):
AACAACTAAACCA
Found at i:523208 original size:2 final size:2
Alignment explanation
Indices: 523203--523253 Score: 102
Period size: 2 Copynumber: 25.5 Consensus size: 2
523193 TTCTAACTTT
523203 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
523245 TA TA TA TA T
1 TA TA TA TA T
523254 CATTATTTTT
Statistics
Matches: 49, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 49 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:524822 original size:24 final size:23
Alignment explanation
Indices: 524786--524830 Score: 54
Period size: 24 Copynumber: 1.9 Consensus size: 23
524776 ATTCTAATGA
*
524786 AAATATAAATATATTATTTTATTG
1 AAATATAAATATA-AATTTTATTG
* *
524810 AAATATGATTATAAATTTTAT
1 AAATATAAATATAAATTTTAT
524831 ATGTAAAAAT
Statistics
Matches: 18, Mismatches: 3, Indels: 1
0.82 0.14 0.05
Matches are distributed among these distances:
23 7 0.39
24 11 0.61
ACGTcount: A:0.47, C:0.00, G:0.04, T:0.49
Consensus pattern (23 bp):
AAATATAAATATAAATTTTATTG
Found at i:533467 original size:2 final size:2
Alignment explanation
Indices: 533462--533503 Score: 84
Period size: 2 Copynumber: 21.0 Consensus size: 2
533452 TCCCGTGTTA
533462 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
533504 GTTACCAAAA
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:541223 original size:56 final size:56
Alignment explanation
Indices: 541137--541252 Score: 196
Period size: 56 Copynumber: 2.1 Consensus size: 56
541127 ATATATACTT
* * *
541137 AATTTGACTCATATTCAATTCAATCCGAATTGACCCGAAGATTCAAAGTTGACACA
1 AATTTGACTCATACTCAACTCAATCCGAATTGACCCGAAGATCCAAAGTTGACACA
*
541193 AATTTGACTCATACTCAACTCAATCCGAATTGACCCGAAGATCCAAAGTTGACTCA
1 AATTTGACTCATACTCAACTCAATCCGAATTGACCCGAAGATCCAAAGTTGACACA
541249 AATT
1 AATT
541253 GAAAATAATT
Statistics
Matches: 56, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
56 56 1.00
ACGTcount: A:0.37, C:0.23, G:0.12, T:0.28
Consensus pattern (56 bp):
AATTTGACTCATACTCAACTCAATCCGAATTGACCCGAAGATCCAAAGTTGACACA
Found at i:541313 original size:31 final size:31
Alignment explanation
Indices: 541269--541340 Score: 76
Period size: 31 Copynumber: 2.3 Consensus size: 31
541259 AATTGATCAT
*
541269 ATATTGA-CTCGACCAAAAAATCAATCGATCTG
1 ATATTGATC-CGACC-AAAAATCAACCGATCTG
** *
541301 AT-TTGATCCGACCCGAAATCAACCGATTTG
1 ATATTGATCCGACCAAAAATCAACCGATCTG
541331 ATATTGATCC
1 ATATTGATCC
541341 AAATCGAAAA
Statistics
Matches: 34, Mismatches: 4, Indels: 5
0.79 0.09 0.12
Matches are distributed among these distances:
30 15 0.44
31 16 0.47
32 3 0.09
ACGTcount: A:0.35, C:0.24, G:0.14, T:0.28
Consensus pattern (31 bp):
ATATTGATCCGACCAAAAATCAACCGATCTG
Found at i:541599 original size:17 final size:18
Alignment explanation
Indices: 541577--541615 Score: 55
Period size: 17 Copynumber: 2.2 Consensus size: 18
541567 TGATCAATAC
541577 TATTGCTAAT-GTT-TTGT
1 TATTGCT-ATGGTTATTGT
541594 TATTGCTATGGTTATTGT
1 TATTGCTATGGTTATTGT
541612 TATT
1 TATT
541616 CTTATTGCAT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
16 2 0.10
17 10 0.50
18 8 0.40
ACGTcount: A:0.18, C:0.05, G:0.18, T:0.59
Consensus pattern (18 bp):
TATTGCTATGGTTATTGT
Found at i:541638 original size:23 final size:24
Alignment explanation
Indices: 541583--541638 Score: 62
Period size: 23 Copynumber: 2.4 Consensus size: 24
541573 ATACTATTGC
* *
541583 TAATGTT-TTGTTATTGCTATGGT
1 TAATGTTATTCTTATTGCTATGAT
* *
541606 TATTGTTATTCTTATTGC-ATTAT
1 TAATGTTATTCTTATTGCTATGAT
541629 TAATGTTATT
1 TAATGTTATT
541639 GTTGATGCCA
Statistics
Matches: 27, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
23 18 0.67
24 9 0.33
ACGTcount: A:0.21, C:0.05, G:0.14, T:0.59
Consensus pattern (24 bp):
TAATGTTATTCTTATTGCTATGAT
Found at i:544418 original size:24 final size:23
Alignment explanation
Indices: 544391--544437 Score: 67
Period size: 24 Copynumber: 2.0 Consensus size: 23
544381 ATAGAGATTT
* *
544391 TTATTTTTATATTATTAAAATATA
1 TTATTTTAATAAT-TTAAAATATA
544415 TTATTTTAATAATTTAAAATATA
1 TTATTTTAATAATTTAAAATATA
544438 ATAAATATTT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
23 10 0.48
24 11 0.52
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (23 bp):
TTATTTTAATAATTTAAAATATA
Found at i:544487 original size:41 final size:41
Alignment explanation
Indices: 544408--544489 Score: 105
Period size: 42 Copynumber: 2.0 Consensus size: 41
544398 TATATTATTA
544408 AAATATATTATTTTAATAATTTAAAATATAATAAATATTTAT
1 AAATATATTATTTTAATAATTTAAAATATAAT-AATATTTAT
* *
544450 AAATAT-TTTTTTTAATTATTTTAAAATATTAAT-ATATTTA
1 AAATATATTATTTTAA-TAATTTAAAATA-TAATAATATTTA
544490 GATCGGGTCA
Statistics
Matches: 36, Mismatches: 2, Indels: 5
0.84 0.05 0.12
Matches are distributed among these distances:
41 15 0.42
42 17 0.47
43 4 0.11
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (41 bp):
AAATATATTATTTTAATAATTTAAAATATAATAATATTTAT
Found at i:544905 original size:22 final size:22
Alignment explanation
Indices: 544880--544925 Score: 56
Period size: 22 Copynumber: 2.1 Consensus size: 22
544870 TTATATAAAC
544880 ATCGAACACTAATTTTGTCATT
1 ATCGAACACTAATTTTGTCATT
* ***
544902 ATCGGATGTTAATTTTGTCATT
1 ATCGAACACTAATTTTGTCATT
544924 AT
1 AT
544926 GGGTTTTTGA
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.28, C:0.13, G:0.13, T:0.46
Consensus pattern (22 bp):
ATCGAACACTAATTTTGTCATT
Found at i:556010 original size:137 final size:137
Alignment explanation
Indices: 555842--556094 Score: 393
Period size: 137 Copynumber: 1.8 Consensus size: 137
555832 AATCATACAC
* *
555842 AGACGGCAAGTGAGGGATTGCACGAGTCTCTTGATAAAAGAAAGAGAGAGAAACAGGAAATGGAG
1 AGACAGCAAGTGAGGGATTGCACGAGTCTCTTGAGAAAAGAAAGAGAGAGAAACAGG-AATGGAG
*
555907 CAGTAAAATGTTTGAAACAAAATAT-AACATTACAATTAGTGAATAAGGACATGGACGGTCAATC
65 CAGTAAAATGTTTGAAACAAAATATAAACATTACAATTAGAGAATAAGGACATGGACGGTCAATC
555971 ATAAAATG
130 ATAAAATG
* * * *
555979 AGACAGCAATTGAGGG-TGTGCATGAGTCTCTTGAGGAAAGAAAGAGAGGGAAACAGGAATGGAG
1 AGACAGCAAGTGAGGGAT-TGCACGAGTCTCTTGAGAAAAGAAAGAGAGAGAAACAGGAATGGAG
* *
556043 TAGTAAAATGTTTGAAATAAAATATAAACATTACAATTAGAGAATAAGGACA
65 CAGTAAAATGTTTGAAACAAAATATAAACATTACAATTAGAGAATAAGGACA
556095 CTCCCAAATC
Statistics
Matches: 105, Mismatches: 9, Indels: 4
0.89 0.08 0.03
Matches are distributed among these distances:
136 31 0.30
137 74 0.70
ACGTcount: A:0.45, C:0.09, G:0.26, T:0.20
Consensus pattern (137 bp):
AGACAGCAAGTGAGGGATTGCACGAGTCTCTTGAGAAAAGAAAGAGAGAGAAACAGGAATGGAGC
AGTAAAATGTTTGAAACAAAATATAAACATTACAATTAGAGAATAAGGACATGGACGGTCAATCA
TAAAATG
Found at i:560994 original size:36 final size:32
Alignment explanation
Indices: 560947--561026 Score: 88
Period size: 34 Copynumber: 2.4 Consensus size: 32
560937 TGTTTATGAG
* *
560947 GGAATTGGAATCTGTGAAGGAATTGAAATCTGTGAA
1 GGAATTAGAATCTGT--AGGAATTGAAATATGT--A
*
560983 GGAATTAGAATCTGTAGGAATTGGAATATGTA
1 GGAATTAGAATCTGTAGGAATTGAAATATGTA
*
561015 GGAATTTGAATC
1 GGAATTAGAATC
561027 CAATTCCATA
Statistics
Matches: 40, Mismatches: 4, Indels: 4
0.83 0.08 0.08
Matches are distributed among these distances:
32 12 0.30
34 14 0.35
36 14 0.35
ACGTcount: A:0.36, C:0.05, G:0.29, T:0.30
Consensus pattern (32 bp):
GGAATTAGAATCTGTAGGAATTGAAATATGTA
Found at i:561003 original size:16 final size:17
Alignment explanation
Indices: 560947--561026 Score: 92
Period size: 18 Copynumber: 4.7 Consensus size: 17
560937 TGTTTATGAG
560947 GGAATTGGAATCTGTGAA
1 GGAATTGGAATCTGT-AA
*
560965 GGAATTGAAATCTGTGAA
1 GGAATTGGAATCTGT-AA
*
560983 GGAATTAGAATCTGT-A
1 GGAATTGGAATCTGTAA
*
560999 GGAATTGGAATATGT-A
1 GGAATTGGAATCTGTAA
*
561015 GGAATTTGAATC
1 GGAATTGGAATC
561027 CAATTCCATA
Statistics
Matches: 55, Mismatches: 7, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
16 25 0.45
18 30 0.55
ACGTcount: A:0.36, C:0.05, G:0.29, T:0.30
Consensus pattern (17 bp):
GGAATTGGAATCTGTAA
Found at i:561790 original size:9 final size:9
Alignment explanation
Indices: 561776--561845 Score: 59
Period size: 9 Copynumber: 7.3 Consensus size: 9
561766 GCTGCTGGAA
561776 ACCGGTTTG
1 ACCGGTTTG
*
561785 ACCGGTTTTCA
1 ACCGG-TTT-G
*
561796 ACCGGTTCG
1 ACCGGTTTG
561805 AACCGGTTTG
1 -ACCGGTTTG
*
561815 ACCGGTCTG
1 ACCGGTTTG
*
561824 AATCGGTTTG
1 -ACCGGTTTG
*
561834 ACCGGTCTG
1 ACCGGTTTG
561843 ACC
1 ACC
561846 CGACCCGACC
Statistics
Matches: 48, Mismatches: 9, Indels: 8
0.74 0.14 0.12
Matches are distributed among these distances:
9 23 0.48
10 20 0.42
11 5 0.10
ACGTcount: A:0.16, C:0.27, G:0.29, T:0.29
Consensus pattern (9 bp):
ACCGGTTTG
Found at i:561800 original size:20 final size:21
Alignment explanation
Indices: 561775--561813 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 21
561765 GGCTGCTGGA
*
561775 AACCGGTTTG-ACCGGTTTTC
1 AACCGGTTCGAACCGGTTTTC
561795 AACCGGTTCGAACCGGTTT
1 AACCGGTTCGAACCGGTTT
561814 GACCGGTCTG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 9 0.53
21 8 0.47
ACGTcount: A:0.18, C:0.26, G:0.26, T:0.31
Consensus pattern (21 bp):
AACCGGTTCGAACCGGTTTTC
Found at i:561820 original size:19 final size:20
Alignment explanation
Indices: 561796--561843 Score: 66
Period size: 19 Copynumber: 2.5 Consensus size: 20
561786 CCGGTTTTCA
561796 ACCGGTTC-GAACCGGTTTG
1 ACCGGTTCTGAACCGGTTTG
*
561815 ACCGG-TCTGAATCGGTTTG
1 ACCGGTTCTGAACCGGTTTG
561834 ACCGG-TCTGA
1 ACCGGTTCTGA
561844 CCCGACCCGA
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
18 2 0.07
19 25 0.93
ACGTcount: A:0.17, C:0.25, G:0.31, T:0.27
Consensus pattern (20 bp):
ACCGGTTCTGAACCGGTTTG
Found at i:561852 original size:5 final size:5
Alignment explanation
Indices: 561842--561899 Score: 62
Period size: 5 Copynumber: 10.8 Consensus size: 5
561832 TGACCGGTCT
* *
561842 GACCC GACCC GACCGTT GACCC GACCC GACCC GACCATT GACCC GACCC
1 GACCC GACCC GACC--C GACCC GACCC GACCC GACC--C GACCC GACCC
561891 GACCC GACC
1 GACCC GACC
561900 GTTGACCGTT
Statistics
Matches: 45, Mismatches: 4, Indels: 8
0.79 0.07 0.14
Matches are distributed among these distances:
5 37 0.82
7 8 0.18
ACGTcount: A:0.21, C:0.52, G:0.21, T:0.07
Consensus pattern (5 bp):
GACCC
Found at i:561868 original size:22 final size:22
Alignment explanation
Indices: 561842--561906 Score: 121
Period size: 22 Copynumber: 3.0 Consensus size: 22
561832 TGACCGGTCT
561842 GACCCGACCCGACCGTTGACCC
1 GACCCGACCCGACCGTTGACCC
*
561864 GACCCGACCCGACCATTGACCC
1 GACCCGACCCGACCGTTGACCC
561886 GACCCGACCCGACCGTTGACC
1 GACCCGACCCGACCGTTGACC
561907 GTTGACCGTT
Statistics
Matches: 41, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 41 1.00
ACGTcount: A:0.20, C:0.49, G:0.22, T:0.09
Consensus pattern (22 bp):
GACCCGACCCGACCGTTGACCC
Found at i:562857 original size:63 final size:63
Alignment explanation
Indices: 562789--562912 Score: 155
Period size: 63 Copynumber: 2.0 Consensus size: 63
562779 CTAATGTGAC
* * *
562789 TCTTAGGTAGG-CTCTGCGGCCCTGAGATC-ATTCTCGGGTAGGCCCTGC-GGCCCTAAGATGTG
1 TCTTAGGTAGGCCTC-ACGGCCCCGAAATCTA-TCTCGGGTAGGCCCT-CAGGCCCTAAGATGTG
562851 T
63 T
* *
562852 TCTTAGGTAGGCCTCACGGCCCCGAAATCTATCTTGGGTAGGCTCTCAGGCCCTAAGATGT
1 TCTTAGGTAGGCCTCACGGCCCCGAAATCTATCTCGGGTAGGCCCTCAGGCCCTAAGATGT
562913 TCCCTTAGGG
Statistics
Matches: 53, Mismatches: 5, Indels: 6
0.83 0.08 0.09
Matches are distributed among these distances:
62 1 0.02
63 48 0.91
64 4 0.08
ACGTcount: A:0.17, C:0.27, G:0.29, T:0.27
Consensus pattern (63 bp):
TCTTAGGTAGGCCTCACGGCCCCGAAATCTATCTCGGGTAGGCCCTCAGGCCCTAAGATGTGT
Found at i:562872 original size:32 final size:32
Alignment explanation
Indices: 562789--562912 Score: 80
Period size: 31 Copynumber: 4.0 Consensus size: 32
562779 CTAATGTGAC
* * *
562789 TCTTAGGTAGGCTCT-GCGGCCCTGAGAT-CA
1 TCTTAGGTAGGCTCTCACGGCCCTAAGATGTA
** * * *
562819 TTCTCGGGTAGGCCCT-GCGGCCCTAAGATGTGT
1 -TCTTAGGTAGGCTCTCACGGCCCTAAGATGT-A
* *
562852 TCTTAGGTAGGC-CTCACGGCCCCGAA-ATCTA
1 TCTTAGGTAGGCTCTCACGG-CCCTAAGATGTA
*
562883 TCTTGGGTAGGCTCTCA-GGCCCTAAGATGT
1 TCTTAGGTAGGCTCTCACGGCCCTAAGATGT
562913 TCCCTTAGGG
Statistics
Matches: 72, Mismatches: 15, Indels: 12
0.73 0.15 0.12
Matches are distributed among these distances:
30 5 0.07
31 42 0.58
32 20 0.28
33 5 0.07
ACGTcount: A:0.17, C:0.27, G:0.29, T:0.27
Consensus pattern (32 bp):
TCTTAGGTAGGCTCTCACGGCCCTAAGATGTA
Found at i:563721 original size:21 final size:21
Alignment explanation
Indices: 563695--563739 Score: 72
Period size: 21 Copynumber: 2.1 Consensus size: 21
563685 GATTTCTGGG
*
563695 CAAGGGGAATCGGTACCCATT
1 CAAGGGGAATCGATACCCATT
*
563716 CAAGGGGAATCGATACCCCTT
1 CAAGGGGAATCGATACCCATT
563737 CAA
1 CAA
563740 ACGAACAAGA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.31, C:0.27, G:0.24, T:0.18
Consensus pattern (21 bp):
CAAGGGGAATCGATACCCATT
Found at i:565496 original size:23 final size:22
Alignment explanation
Indices: 565437--565503 Score: 116
Period size: 22 Copynumber: 3.0 Consensus size: 22
565427 AATGGACATC
*
565437 ATTCTACGGGCACTACGGTGCA
1 ATTCTACGGGCACTTCGGTGCA
565459 ATTCTACGGGCACTTCGGTGCA
1 ATTCTACGGGCACTTCGGTGCA
565481 ATTCTACGGGGCACTTCGGTGCA
1 ATTCTAC-GGGCACTTCGGTGCA
565504 TTTATACGAG
Statistics
Matches: 43, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
22 28 0.65
23 15 0.35
ACGTcount: A:0.19, C:0.27, G:0.28, T:0.25
Consensus pattern (22 bp):
ATTCTACGGGCACTTCGGTGCA
Found at i:572239 original size:20 final size:20
Alignment explanation
Indices: 572214--572271 Score: 82
Period size: 20 Copynumber: 2.9 Consensus size: 20
572204 GGCTGCTGGA
572214 AACCGGTTTGACCGATTTTC
1 AACCGGTTTGACCGATTTTC
*
572234 AACCGGTTTGACCG-GTTTC
1 AACCGGTTTGACCGATTTTC
*
572253 AACCGGTTCGAACCGATTT
1 AACCGGTTTG-ACCGATTT
572272 GACCGGTCTG
Statistics
Matches: 33, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
19 13 0.39
20 18 0.55
21 2 0.06
ACGTcount: A:0.21, C:0.26, G:0.22, T:0.31
Consensus pattern (20 bp):
AACCGGTTTGACCGATTTTC
Found at i:572276 original size:19 final size:19
Alignment explanation
Indices: 572269--572320 Score: 104
Period size: 19 Copynumber: 2.7 Consensus size: 19
572259 TTCGAACCGA
572269 TTTGACCGGTCTGAATCGG
1 TTTGACCGGTCTGAATCGG
572288 TTTGACCGGTCTGAATCGG
1 TTTGACCGGTCTGAATCGG
572307 TTTGACCGGTCTGA
1 TTTGACCGGTCTGA
572321 CCCGACCCGA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 33 1.00
ACGTcount: A:0.15, C:0.21, G:0.31, T:0.33
Consensus pattern (19 bp):
TTTGACCGGTCTGAATCGG
Found at i:572288 original size:29 final size:29
Alignment explanation
Indices: 572234--572289 Score: 76
Period size: 29 Copynumber: 1.9 Consensus size: 29
572224 ACCGATTTTC
* *
572234 AACCGGTTTGACCGGTTTCAACCGGTTCG
1 AACCGATTTGACCGGTCTCAACCGGTTCG
* *
572263 AACCGATTTGACCGGTCTGAATCGGTT
1 AACCGATTTGACCGGTCTCAACCGGTT
572290 TGACCGGTCT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
29 23 1.00
ACGTcount: A:0.20, C:0.25, G:0.27, T:0.29
Consensus pattern (29 bp):
AACCGATTTGACCGGTCTCAACCGGTTCG
Found at i:572329 original size:5 final size:5
Alignment explanation
Indices: 572319--572359 Score: 55
Period size: 5 Copynumber: 7.8 Consensus size: 5
572309 TGACCGGTCT
*
572319 GACCC GACCC GACCGTT GACCC GACCC GACCC GACCC GACC
1 GACCC GACCC GACC--C GACCC GACCC GACCC GACCC GACC
572360 GTTGACCGTT
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
5 28 0.88
7 4 0.12
ACGTcount: A:0.20, C:0.54, G:0.22, T:0.05
Consensus pattern (5 bp):
GACCC
Found at i:572368 original size:7 final size:7
Alignment explanation
Indices: 572356--572386 Score: 62
Period size: 7 Copynumber: 4.4 Consensus size: 7
572346 GACCCGACCC
572356 GACCGTT
1 GACCGTT
572363 GACCGTT
1 GACCGTT
572370 GACCGTT
1 GACCGTT
572377 GACCGTT
1 GACCGTT
572384 GAC
1 GAC
572387 TTTCTTTGAC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 24 1.00
ACGTcount: A:0.16, C:0.29, G:0.29, T:0.26
Consensus pattern (7 bp):
GACCGTT
Found at i:573324 original size:63 final size:63
Alignment explanation
Indices: 573256--573379 Score: 155
Period size: 63 Copynumber: 2.0 Consensus size: 63
573246 CTAATGTGAC
* * *
573256 TCTTAGGTAGG-CTCTGCGGCCCTGAGATC-ATTCTCGGGTAGGCCCTGC-GGCCCTAAGATGTG
1 TCTTAGGTAGGCCTC-ACGGCCCCGAAATCTA-TCTCGGGTAGGCCCT-CAGGCCCTAAGATGTG
573318 T
63 T
* *
573319 TCTTAGGTAGGCCTCACGGCCCCGAAATCTATCTTGGGTAGGCTCTCAGGCCCTAAGATGT
1 TCTTAGGTAGGCCTCACGGCCCCGAAATCTATCTCGGGTAGGCCCTCAGGCCCTAAGATGT
573380 TCCCTTAGGG
Statistics
Matches: 53, Mismatches: 5, Indels: 6
0.83 0.08 0.09
Matches are distributed among these distances:
62 1 0.02
63 48 0.91
64 4 0.08
ACGTcount: A:0.17, C:0.27, G:0.29, T:0.27
Consensus pattern (63 bp):
TCTTAGGTAGGCCTCACGGCCCCGAAATCTATCTCGGGTAGGCCCTCAGGCCCTAAGATGTGT
Found at i:573339 original size:32 final size:32
Alignment explanation
Indices: 573256--573379 Score: 80
Period size: 31 Copynumber: 4.0 Consensus size: 32
573246 CTAATGTGAC
* * *
573256 TCTTAGGTAGGCTCT-GCGGCCCTGAGAT-CA
1 TCTTAGGTAGGCTCTCACGGCCCTAAGATGTA
** * * *
573286 TTCTCGGGTAGGCCCT-GCGGCCCTAAGATGTGT
1 -TCTTAGGTAGGCTCTCACGGCCCTAAGATGT-A
* *
573319 TCTTAGGTAGGC-CTCACGGCCCCGAA-ATCTA
1 TCTTAGGTAGGCTCTCACGG-CCCTAAGATGTA
*
573350 TCTTGGGTAGGCTCTCA-GGCCCTAAGATGT
1 TCTTAGGTAGGCTCTCACGGCCCTAAGATGT
573380 TCCCTTAGGG
Statistics
Matches: 72, Mismatches: 15, Indels: 12
0.73 0.15 0.12
Matches are distributed among these distances:
30 5 0.07
31 42 0.58
32 20 0.28
33 5 0.07
ACGTcount: A:0.17, C:0.27, G:0.29, T:0.27
Consensus pattern (32 bp):
TCTTAGGTAGGCTCTCACGGCCCTAAGATGTA
Found at i:576753 original size:6 final size:6
Alignment explanation
Indices: 576742--576787 Score: 92
Period size: 6 Copynumber: 7.7 Consensus size: 6
576732 TAAAAGAAGT
576742 GGAAAG GGAAAG GGAAAG GGAAAG GGAAAG GGAAAG GGAAAG GGAA
1 GGAAAG GGAAAG GGAAAG GGAAAG GGAAAG GGAAAG GGAAAG GGAA
576788 CCTTCAAGCT
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 40 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (6 bp):
GGAAAG
Found at i:578471 original size:121 final size:123
Alignment explanation
Indices: 578279--578524 Score: 478
Period size: 122 Copynumber: 2.0 Consensus size: 123
578269 TTGGCGAAAA
578279 TTGGGACTGAATTGAAAGATTTTAAAACTTGGAGCTTGTTTTAAAGTTAAAGAAAATTCAGGGAC
1 TTGGGACTGAATTGAAAGATTTTAAAACTTGGAGCTTGTTTTAAAGTTAAAGAAAATTCAGGGAC
578344 CAAGCCCTGAATTT-ACCTTGGAGTGTCGGCAGTCAATTGTTATATGCGTGATTTCTG
66 CAAGCCCTGAATTTAACCTTGGAGTGTCGGCAGTCAATTGTTATATGCGTGATTTCTG
578401 TTGGGACTGAATTGAAAGA-TTTAAAACTTGGAGCTTGTTTTAAAGTTAAAGAAAATTCAGGGAC
1 TTGGGACTGAATTGAAAGATTTTAAAACTTGGAGCTTGTTTTAAAGTTAAAGAAAATTCAGGGAC
578465 CAAGCCCTGAATTTAACCTTGGAGTGTCGGCAGTCAATTGTTATATGCGTGATTTCTG
66 CAAGCCCTGAATTTAACCTTGGAGTGTCGGCAGTCAATTGTTATATGCGTGATTTCTG
578523 TT
1 TT
578525 TTGAAAAACA
Statistics
Matches: 123, Mismatches: 0, Indels: 2
0.98 0.00 0.02
Matches are distributed among these distances:
121 59 0.48
122 64 0.52
ACGTcount: A:0.30, C:0.13, G:0.24, T:0.34
Consensus pattern (123 bp):
TTGGGACTGAATTGAAAGATTTTAAAACTTGGAGCTTGTTTTAAAGTTAAAGAAAATTCAGGGAC
CAAGCCCTGAATTTAACCTTGGAGTGTCGGCAGTCAATTGTTATATGCGTGATTTCTG
Found at i:579114 original size:17 final size:17
Alignment explanation
Indices: 579092--579147 Score: 103
Period size: 17 Copynumber: 3.3 Consensus size: 17
579082 TGGACCGGTC
579092 TGACCCGACCCGACCGT
1 TGACCCGACCCGACCGT
579109 TGACCCGACCCGACCGT
1 TGACCCGACCCGACCGT
*
579126 TGACCCGACCCCACCGT
1 TGACCCGACCCGACCGT
579143 TGACC
1 TGACC
579148 GTTGACCGCT
Statistics
Matches: 38, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
17 38 1.00
ACGTcount: A:0.18, C:0.48, G:0.21, T:0.12
Consensus pattern (17 bp):
TGACCCGACCCGACCGT
Found at i:579148 original size:7 final size:7
Alignment explanation
Indices: 579138--579180 Score: 77
Period size: 7 Copynumber: 6.1 Consensus size: 7
579128 ACCCGACCCC
579138 ACCGTTG
1 ACCGTTG
579145 ACCGTTG
1 ACCGTTG
*
579152 ACCGCTG
1 ACCGTTG
579159 ACCGTTG
1 ACCGTTG
579166 ACCGTTG
1 ACCGTTG
579173 ACCGTTG
1 ACCGTTG
579180 A
1 A
579181 TTTTTTTTGA
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
7 34 1.00
ACGTcount: A:0.16, C:0.30, G:0.28, T:0.26
Consensus pattern (7 bp):
ACCGTTG
Found at i:585710 original size:10 final size:9
Alignment explanation
Indices: 585675--585773 Score: 90
Period size: 10 Copynumber: 10.3 Consensus size: 9
585665 GCTGCTGGAA
*
585675 ACCGGTTTA
1 ACCGGTTTG
*
585684 ACCGGTTTTCA
1 ACCGG-TTT-G
585695 ACCGGTTCTG
1 ACCGGTT-TG
585705 ACCGGTTTG
1 ACCGGTTTG
*
585714 ACCGGTTTCA
1 ACCGGTTT-G
*
585724 ACCGGTTCG
1 ACCGGTTTG
585733 AACCGGTTTG
1 -ACCGGTTTG
*
585743 ACCGGTCTG
1 ACCGGTTTG
585752 AACCGGTTTG
1 -ACCGGTTTG
*
585762 ACCGGTCTG
1 ACCGGTTTG
585771 ACC
1 ACC
585774 CGACCCGACC
Statistics
Matches: 76, Mismatches: 8, Indels: 12
0.79 0.08 0.12
Matches are distributed among these distances:
9 34 0.45
10 35 0.46
11 7 0.09
ACGTcount: A:0.16, C:0.28, G:0.27, T:0.28
Consensus pattern (9 bp):
ACCGGTTTG
Found at i:585719 original size:19 final size:19
Alignment explanation
Indices: 585676--585773 Score: 87
Period size: 19 Copynumber: 5.1 Consensus size: 19
585666 CTGCTGGAAA
* * *
585676 CCGGTTTAACCGGTTTTCAA
1 CCGGTTTGACCGGTTCT-GA
585696 CCGGTTCTGACCGGTT-TGA
1 CCGGTT-TGACCGGTTCTGA
*
585715 CCGGTTTCAACCGGTTC-GAA
1 CCGGTTT-GACCGGTTCTG-A
585735 CCGGTTTGACCGG-TCTGAA
1 CCGGTTTGACCGGTTCTG-A
585754 CCGGTTTGACCGG-TCTGA
1 CCGGTTTGACCGGTTCTGA
585772 CC
1 CC
585774 CGACCCGACC
Statistics
Matches: 69, Mismatches: 4, Indels: 12
0.81 0.05 0.14
Matches are distributed among these distances:
18 6 0.09
19 40 0.58
20 15 0.22
21 8 0.12
ACGTcount: A:0.15, C:0.29, G:0.28, T:0.29
Consensus pattern (19 bp):
CCGGTTTGACCGGTTCTGA
Found at i:585737 original size:29 final size:28
Alignment explanation
Indices: 585675--585773 Score: 126
Period size: 29 Copynumber: 3.4 Consensus size: 28
585665 GCTGCTGGAA
*
585675 ACCGGTTTAACCGGTTTTCAACCGGTTCTG
1 ACCGGTTTGACCGG-TTTCAACCGGTTC-G
585705 ACCGGTTTGACCGGTTTCAACCGGTTCG
1 ACCGGTTTGACCGGTTTCAACCGGTTCG
* * *
585733 AACCGGTTTGACCGGTCTGAACCGGTTTG
1 -ACCGGTTTGACCGGTTTCAACCGGTTCG
*
585762 ACCGGTCTGACC
1 ACCGGTTTGACC
585774 CGACCCGACC
Statistics
Matches: 63, Mismatches: 5, Indels: 4
0.88 0.07 0.06
Matches are distributed among these distances:
28 12 0.19
29 38 0.60
30 13 0.21
ACGTcount: A:0.16, C:0.28, G:0.27, T:0.28
Consensus pattern (28 bp):
ACCGGTTTGACCGGTTTCAACCGGTTCG
Found at i:585791 original size:17 final size:17
Alignment explanation
Indices: 585769--585807 Score: 78
Period size: 17 Copynumber: 2.3 Consensus size: 17
585759 TTGACCGGTC
585769 TGACCCGACCCGACCGT
1 TGACCCGACCCGACCGT
585786 TGACCCGACCCGACCGT
1 TGACCCGACCCGACCGT
585803 TGACC
1 TGACC
585808 GTTGACCGTT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 22 1.00
ACGTcount: A:0.18, C:0.46, G:0.23, T:0.13
Consensus pattern (17 bp):
TGACCCGACCCGACCGT
Found at i:585807 original size:7 final size:7
Alignment explanation
Indices: 585797--585826 Score: 60
Period size: 7 Copynumber: 4.3 Consensus size: 7
585787 GACCCGACCC
585797 GACCGTT
1 GACCGTT
585804 GACCGTT
1 GACCGTT
585811 GACCGTT
1 GACCGTT
585818 GACCGTT
1 GACCGTT
585825 GA
1 GA
585827 TTTTCTTTGA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 23 1.00
ACGTcount: A:0.17, C:0.27, G:0.30, T:0.27
Consensus pattern (7 bp):
GACCGTT
Found at i:588943 original size:18 final size:18
Alignment explanation
Indices: 588920--588960 Score: 55
Period size: 18 Copynumber: 2.3 Consensus size: 18
588910 ACCGGTCACA
* *
588920 ACCCGACCCGTTTACCCG
1 ACCCGACCCATTGACCCG
*
588938 ACCCGACCTATTGACCCG
1 ACCCGACCCATTGACCCG
588956 ACCCG
1 ACCCG
588961 TTGACCCGTT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.20, C:0.49, G:0.17, T:0.15
Consensus pattern (18 bp):
ACCCGACCCATTGACCCG
Found at i:588978 original size:15 final size:17
Alignment explanation
Indices: 588958--588991 Score: 54
Period size: 15 Copynumber: 2.1 Consensus size: 17
588948 TTGACCCGAC
588958 CCGTTGACC-C-GTTGA
1 CCGTTGACCACTGTTGA
588973 CCGTTGACCACTGTTGA
1 CCGTTGACCACTGTTGA
588990 CC
1 CC
588992 AAAACTTTGA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 9 0.53
16 1 0.06
17 7 0.41
ACGTcount: A:0.15, C:0.35, G:0.24, T:0.26
Consensus pattern (17 bp):
CCGTTGACCACTGTTGA
Found at i:590308 original size:18 final size:18
Alignment explanation
Indices: 590282--590317 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
590272 TCAAAATGAC
*
590282 TGAAGTAAATGATAAGAT
1 TGAAGTAAATAATAAGAT
*
590300 TGAATTAAATAATAAGAT
1 TGAAGTAAATAATAAGAT
590318 CGGATGGCAG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.53, C:0.00, G:0.17, T:0.31
Consensus pattern (18 bp):
TGAAGTAAATAATAAGAT
Found at i:591452 original size:12 final size:12
Alignment explanation
Indices: 591414--591505 Score: 57
Period size: 12 Copynumber: 7.8 Consensus size: 12
591404 ATTTCCGAAT
591414 TGAATTCTGTTC
1 TGAATTCTGTTC
*
591426 TG-ATAC-GTTACC
1 TGAATTCTGTT--C
591438 TGAATTCTGTTC
1 TGAATTCTGTTC
* *
591450 TG-ATTCTGATA
1 TGAATTCTGTTC
*
591461 TGGATTCTGTTC
1 TGAATTCTGTTC
* *
591473 TG-ATATCTGATA
1 TGAAT-TCTGTTC
*
591485 TGAATTCTGTTT
1 TGAATTCTGTTC
*
591497 TGATTTCTG
1 TGAATTCTG
591506 ATATCTCCGT
Statistics
Matches: 62, Mismatches: 11, Indels: 14
0.71 0.13 0.16
Matches are distributed among these distances:
10 3 0.05
11 14 0.23
12 37 0.60
13 5 0.08
14 3 0.05
ACGTcount: A:0.20, C:0.14, G:0.18, T:0.48
Consensus pattern (12 bp):
TGAATTCTGTTC
Found at i:591468 original size:47 final size:48
Alignment explanation
Indices: 591417--591509 Score: 129
Period size: 47 Copynumber: 2.0 Consensus size: 48
591407 TCCGAATTGA
*
591417 ATTCTGTTCTGATA-C-GTTACCTGAATTCTGTTCTGA-TTCTGATATGG
1 ATTCTGTTCTGATATCTGATA--TGAATTCTGTTCTGATTTCTGATATGG
*
591464 ATTCTGTTCTGATATCTGATATGAATTCTGTTTTGATTTCTGATAT
1 ATTCTGTTCTGATATCTGATATGAATTCTGTTCTGATTTCTGATAT
591510 CTCCGTTTAA
Statistics
Matches: 41, Mismatches: 2, Indels: 5
0.85 0.04 0.10
Matches are distributed among these distances:
47 28 0.68
48 10 0.24
49 3 0.07
ACGTcount: A:0.20, C:0.14, G:0.17, T:0.48
Consensus pattern (48 bp):
ATTCTGTTCTGATATCTGATATGAATTCTGTTCTGATTTCTGATATGG
Found at i:591486 original size:24 final size:23
Alignment explanation
Indices: 591414--591509 Score: 113
Period size: 24 Copynumber: 4.0 Consensus size: 23
591404 ATTTCCGAAT
* *
591414 TGAATTCTGTTCTGATAC-GTTA
1 TGAATTCTGTTCTGATTCTGATA
591436 CCTGAATTCTGTTCTGATTCTGATA
1 --TGAATTCTGTTCTGATTCTGATA
*
591461 TGGATTCTGTTCTGATATCTGATA
1 TGAATTCTGTTCTGAT-TCTGATA
*
591485 TGAATTCTGTTTTGATTTCTGATA
1 TGAATTCTGTTCTGA-TTCTGATA
591509 T
1 T
591510 CTCCGTTTAA
Statistics
Matches: 64, Mismatches: 5, Indels: 6
0.85 0.07 0.08
Matches are distributed among these distances:
23 15 0.23
24 45 0.70
25 4 0.06
ACGTcount: A:0.21, C:0.14, G:0.18, T:0.48
Consensus pattern (23 bp):
TGAATTCTGTTCTGATTCTGATA
Found at i:593425 original size:15 final size:15
Alignment explanation
Indices: 593405--593433 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
593395 GATCTCAGGA
593405 ACATGAACGTGTGCC
1 ACATGAACGTGTGCC
593420 ACATGAACGTGTGC
1 ACATGAACGTGTGC
593434 AACGAAAAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.28, C:0.24, G:0.28, T:0.21
Consensus pattern (15 bp):
ACATGAACGTGTGCC
Found at i:599714 original size:17 final size:18
Alignment explanation
Indices: 599681--599714 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
599671 AATTATTAAA
*
599681 GGTTATAATATTGATCCG
1 GGTTATAATAATGATCCG
599699 GGTTATAA-AATGATCC
1 GGTTATAATAATGATCC
599715 TCAAAATATA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 7 0.47
18 8 0.53
ACGTcount: A:0.32, C:0.12, G:0.21, T:0.35
Consensus pattern (18 bp):
GGTTATAATAATGATCCG
Found at i:601155 original size:24 final size:24
Alignment explanation
Indices: 601128--601174 Score: 94
Period size: 24 Copynumber: 2.0 Consensus size: 24
601118 TCCGTGCTTC
601128 CCATGCTTCCCGTGCTTGAATTTT
1 CCATGCTTCCCGTGCTTGAATTTT
601152 CCATGCTTCCCGTGCTTGAATTT
1 CCATGCTTCCCGTGCTTGAATTT
601175 CCCACCACCA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.13, C:0.30, G:0.17, T:0.40
Consensus pattern (24 bp):
CCATGCTTCCCGTGCTTGAATTTT
Found at i:601193 original size:12 final size:11
Alignment explanation
Indices: 601176--601228 Score: 51
Period size: 9 Copynumber: 5.0 Consensus size: 11
601166 CTTGAATTTC
601176 CCACCACCATA
1 CCACCACCATA
601187 --ACCACCATGA
1 CCACCACCAT-A
601197 CCACCACCATA
1 CCACCACCATA
*
601208 --AGCACCATGA
1 CCACCACCAT-A
601218 CCACCACCATA
1 CCACCACCATA
601229 AGCACCGTGA
Statistics
Matches: 34, Mismatches: 2, Indels: 12
0.71 0.04 0.25
Matches are distributed among these distances:
9 15 0.44
10 2 0.06
11 2 0.06
12 15 0.44
ACGTcount: A:0.38, C:0.47, G:0.06, T:0.09
Consensus pattern (11 bp):
CCACCACCATA
Found at i:601201 original size:18 final size:19
Alignment explanation
Indices: 601177--601255 Score: 88
Period size: 21 Copynumber: 4.0 Consensus size: 19
601167 TTGAATTTCC
*
601177 CACCACCATAACCACCATG
1 CACCACCATAAGCACCATG
601196 ACCACCACCATAAGCACCATG
1 --CACCACCATAAGCACCATG
*
601217 ACCACCACCATAAGCACCGTG
1 --CACCACCATAAGCACCATG
*
601238 -ACCACCGTAAGCACCATG
1 CACCACCATAAGCACCATG
601256 AGAACCGTGA
Statistics
Matches: 54, Mismatches: 4, Indels: 3
0.89 0.07 0.05
Matches are distributed among these distances:
18 16 0.30
21 38 0.70
ACGTcount: A:0.35, C:0.43, G:0.11, T:0.10
Consensus pattern (19 bp):
CACCACCATAAGCACCATG
Found at i:601202 original size:21 final size:21
Alignment explanation
Indices: 601176--601243 Score: 118
Period size: 21 Copynumber: 3.2 Consensus size: 21
601166 CTTGAATTTC
*
601176 CCACCACCATAACCACCATGA
1 CCACCACCATAAGCACCATGA
601197 CCACCACCATAAGCACCATGA
1 CCACCACCATAAGCACCATGA
*
601218 CCACCACCATAAGCACCGTGA
1 CCACCACCATAAGCACCATGA
601239 CCACC
1 CCACC
601244 GTAAGCACCA
Statistics
Matches: 45, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 45 1.00
ACGTcount: A:0.35, C:0.47, G:0.09, T:0.09
Consensus pattern (21 bp):
CCACCACCATAAGCACCATGA
Found at i:601262 original size:18 final size:18
Alignment explanation
Indices: 601206--601263 Score: 53
Period size: 18 Copynumber: 3.1 Consensus size: 18
601196 ACCACCACCA
*
601206 TAAGCACCATGACCACCACCA
1 TAAGCACCATGA-CA--ACCG
* *
601227 TAAGCACCGTGACCACCG
1 TAAGCACCATGACAACCG
*
601245 TAAGCACCATGAGAACCG
1 TAAGCACCATGACAACCG
601263 T
1 T
601264 GAGCCACGTG
Statistics
Matches: 31, Mismatches: 6, Indels: 3
0.77 0.15 0.08
Matches are distributed among these distances:
18 19 0.61
20 1 0.03
21 11 0.35
ACGTcount: A:0.34, C:0.36, G:0.17, T:0.12
Consensus pattern (18 bp):
TAAGCACCATGACAACCG
Found at i:601516 original size:36 final size:34
Alignment explanation
Indices: 601470--601573 Score: 147
Period size: 33 Copynumber: 3.0 Consensus size: 34
601460 GCCGGGATAA
* * *
601470 CCAGCGGGTGGATAGCCCTGAGGGGGGTATCCTC
1 CCAGCAGGTGGATAGCCCTGAGGGGGATACCCTC
*
601504 CAGCAGCAGGTGGATAGCCTTGAGGGGGATACCCT-
1 C--CAGCAGGTGGATAGCCCTGAGGGGGATACCCTC
601539 CCAGCAGGTGGATAGCCCTGAGGGGGATACCCTC
1 CCAGCAGGTGGATAGCCCTGAGGGGGATACCCTC
601573 C
1 C
601574 TCCACGACCA
Statistics
Matches: 62, Mismatches: 5, Indels: 6
0.85 0.07 0.08
Matches are distributed among these distances:
33 31 0.50
34 2 0.03
35 1 0.02
36 28 0.45
ACGTcount: A:0.19, C:0.27, G:0.38, T:0.16
Consensus pattern (34 bp):
CCAGCAGGTGGATAGCCCTGAGGGGGATACCCTC
Found at i:601576 original size:36 final size:35
Alignment explanation
Indices: 601470--601577 Score: 139
Period size: 36 Copynumber: 3.1 Consensus size: 35
601460 GCCGGGATAA
* * *
601470 CCAGCGGGTGGATAGCCCTGAGGGGGGTATCCTCCA
1 CCAGCAGGTGGATAGCCCTGAGGGGGATA-CCTCCT
* *
601506 GCAGCAGGTGGATAGCCTTGAGGGGGATA-C-CCT
1 CCAGCAGGTGGATAGCCCTGAGGGGGATACCTCCT
601539 CCAGCAGGTGGATAGCCCTGAGGGGGATACCCTCCT
1 CCAGCAGGTGGATAGCCCTGAGGGGGATA-CCTCCT
601575 CCA
1 CCA
601578 CGACCATGAG
Statistics
Matches: 62, Mismatches: 7, Indels: 6
0.83 0.09 0.08
Matches are distributed among these distances:
33 29 0.47
34 1 0.02
35 1 0.02
36 31 0.50
ACGTcount: A:0.19, C:0.28, G:0.36, T:0.17
Consensus pattern (35 bp):
CCAGCAGGTGGATAGCCCTGAGGGGGATACCTCCT
Found at i:606551 original size:23 final size:23
Alignment explanation
Indices: 606508--606552 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
606498 TTTAAGAAAA
* *
606508 AATAAGATTTTTTTTATAAATAT
1 AATAAGATTTTTTTAAAAAATAT
*
606531 AATAATATTTTTTTAAAAAATA
1 AATAAGATTTTTTTAAAAAATA
606553 AATTTTAAAA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (23 bp):
AATAAGATTTTTTTAAAAAATAT
Found at i:607687 original size:14 final size:15
Alignment explanation
Indices: 607668--607697 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
607658 TACATTCTCT
607668 ATCTTA-TTTTACTC
1 ATCTTATTTTTACTC
607682 ATCTTATTTTTACTC
1 ATCTTATTTTTACTC
607697 A
1 A
607698 CCGTAATTTT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 6 0.40
15 9 0.60
ACGTcount: A:0.23, C:0.20, G:0.00, T:0.57
Consensus pattern (15 bp):
ATCTTATTTTTACTC
Found at i:608057 original size:13 final size:13
Alignment explanation
Indices: 608039--608063 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
608029 ATCTTACCAC
608039 TTTATATTTTTAT
1 TTTATATTTTTAT
608052 TTTATATTTTTA
1 TTTATATTTTTA
608064 ATTATTTTAT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (13 bp):
TTTATATTTTTAT
Found at i:611047 original size:187 final size:188
Alignment explanation
Indices: 610732--611106 Score: 743
Period size: 187 Copynumber: 2.0 Consensus size: 188
610722 GTAAATAAGA
610732 AAAACAAAAATGGGGATAACAGTTAACATGAAGTTACTTGGATGTTATGAGCTCAAATTTCCTGT
1 AAAACAAAAATGGGGATAACAGTTAACATGAAGTTACTTGGATGTTATGAGCTCAAATTTCCTGT
610797 CAAGGAGCCTGCAATAGGAAAAACCATTCACCTCCATACTCATCAAATATATCCTCGGCAACTAT
66 CAAGGAGCCTGCAATAGGAAAAACCATTCACCTCCATACTCATCAAATATATCCTCGGCAACTAT
610862 TTG-TGATTGGGATCATCCAGTCGAAATCCACCACGAGGAGGACTCAAACCTGGTTTT
131 TTGTTGATTGGGATCATCCAGTCGAAATCCACCACGAGGAGGACTCAAACCTGGTTTT
610919 AAAACAAAAATGGGGATAACAGTTAACATGAAGTTACTTGGATGTTATGAGCTCAAATTTCCTGT
1 AAAACAAAAATGGGGATAACAGTTAACATGAAGTTACTTGGATGTTATGAGCTCAAATTTCCTGT
610984 CAAGGAGCCTGCAATAGGAAAAACCATTCACCTCCATACTCATCAAATATATCCTCGGCAACTAT
66 CAAGGAGCCTGCAATAGGAAAAACCATTCACCTCCATACTCATCAAATATATCCTCGGCAACTAT
611049 TTGTTGATTGGGATCATCCAGTCGAAATCCACCACGAGGAGGACTCAAACCTGGTTTT
131 TTGTTGATTGGGATCATCCAGTCGAAATCCACCACGAGGAGGACTCAAACCTGGTTTT
611107 TGCTTCAGCT
Statistics
Matches: 187, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
187 133 0.71
188 54 0.29
ACGTcount: A:0.34, C:0.21, G:0.19, T:0.26
Consensus pattern (188 bp):
AAAACAAAAATGGGGATAACAGTTAACATGAAGTTACTTGGATGTTATGAGCTCAAATTTCCTGT
CAAGGAGCCTGCAATAGGAAAAACCATTCACCTCCATACTCATCAAATATATCCTCGGCAACTAT
TTGTTGATTGGGATCATCCAGTCGAAATCCACCACGAGGAGGACTCAAACCTGGTTTT
Found at i:620127 original size:158 final size:157
Alignment explanation
Indices: 619812--620129 Score: 602
Period size: 158 Copynumber: 2.0 Consensus size: 157
619802 ATTTAATTAT
619812 GTGAATGACCGTATATTAGATCTATTTATTCGTAATGCTAAATTAGAGATACCGAGTCGTGTCTG
1 GTGAATGACCGTATATTAGATCTATTTATTCGTAATGCTAAATTAGAGATACCGAGTCGTGTCTG
619877 GCCGAATTCAGCTAAGGCTGAATTCAATTACATAGTGAAATATGAATGGTACGAACCTTGAATCC
66 GCCGAATTCAGCTAAGGCTGAATTCAATTACATAGTGAAATATGAATGGTACGAACCTTGAATCC
619942 AACTTTATTTCTGCACTGATTGAGAGAG
131 AACTTTATTTCTGCACTGATT-AGAGAG
619970 GTGAATGACCGTATATTAGATCTATTTATTCGTAATGCTAAATTAGAGATACCGAGTCGTGTCTG
1 GTGAATGACCGTATATTAGATCTATTTATTCGTAATGCTAAATTAGAGATACCGAGTCGTGTCTG
620035 GCCGAATTCAGCTAAGGCTGAATTCAATTACATAGTGAAATATGAATGGTACTGTAACCTTGAAT
66 GCCGAATTCAGCTAAGGCTGAATTCAATTACATAGTGAAATATGAATGGTAC-G-AACCTTGAAT
620100 CCAACTTTATTTCTGCACTGATT-GAGAG
129 CCAACTTTATTTCTGCACTGATTAGAGAG
620128 GT
1 GT
620130 CGAGACTAGA
Statistics
Matches: 158, Mismatches: 0, Indels: 4
0.98 0.00 0.02
Matches are distributed among these distances:
158 124 0.78
159 1 0.01
160 33 0.21
ACGTcount: A:0.31, C:0.16, G:0.21, T:0.32
Consensus pattern (157 bp):
GTGAATGACCGTATATTAGATCTATTTATTCGTAATGCTAAATTAGAGATACCGAGTCGTGTCTG
GCCGAATTCAGCTAAGGCTGAATTCAATTACATAGTGAAATATGAATGGTACGAACCTTGAATCC
AACTTTATTTCTGCACTGATTAGAGAG
Found at i:621473 original size:21 final size:21
Alignment explanation
Indices: 621444--621489 Score: 56
Period size: 21 Copynumber: 2.2 Consensus size: 21
621434 TTATATTCTC
* *
621444 CAGTAATTTCAGATGTCACCG
1 CAGTAATTTCAAATGGCACCG
* *
621465 CAGTCATTTTAAATGGCACCG
1 CAGTAATTTCAAATGGCACCG
621486 CAGT
1 CAGT
621490 TGTTTTTAAT
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.28, C:0.24, G:0.20, T:0.28
Consensus pattern (21 bp):
CAGTAATTTCAAATGGCACCG
Found at i:621495 original size:21 final size:21
Alignment explanation
Indices: 621460--621526 Score: 71
Period size: 21 Copynumber: 3.2 Consensus size: 21
621450 TTTCAGATGT
*
621460 CACCGCAGTCATTTTAAATGG
1 CACCGCAGTCATTTTAAATGC
** *
621481 CACCGCAGTTGTTTTTAATGC
1 CACCGCAGTCATTTTAAATGC
* * *
621502 CACCGAAGCCATTTTAGATGC
1 CACCGCAGTCATTTTAAATGC
621523 CACC
1 CACC
621527 ATCGCAGAGT
Statistics
Matches: 36, Mismatches: 10, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
21 36 1.00
ACGTcount: A:0.25, C:0.28, G:0.18, T:0.28
Consensus pattern (21 bp):
CACCGCAGTCATTTTAAATGC
Found at i:622011 original size:46 final size:46
Alignment explanation
Indices: 621917--622048 Score: 207
Period size: 46 Copynumber: 2.9 Consensus size: 46
621907 GATAGACTTG
* *
621917 TTTTTATTTATTTTGTCTCTTAA--TTTT-TTATTTAATTATGGGC
1 TTTTTATTTATTTTGTTTCTTAATGTTTTATTATTTAATTATGGAC
*
621960 TTTTTATTTATTTTATTTCTTAATGTTTTATTATTTAATTATGGAC
1 TTTTTATTTATTTTGTTTCTTAATGTTTTATTATTTAATTATGGAC
622006 TTTTTATTTATTTTGTTTCTTAATGTTTTTATTATTTAATTAT
1 TTTTTATTTATTTTGTTTCTTAATG-TTTTATTATTTAATTAT
622049 ATGAATTATA
Statistics
Matches: 81, Mismatches: 4, Indels: 4
0.91 0.04 0.04
Matches are distributed among these distances:
43 21 0.26
45 4 0.05
46 39 0.48
47 17 0.21
ACGTcount: A:0.21, C:0.05, G:0.07, T:0.67
Consensus pattern (46 bp):
TTTTTATTTATTTTGTTTCTTAATGTTTTATTATTTAATTATGGAC
Found at i:624660 original size:35 final size:35
Alignment explanation
Indices: 624606--624718 Score: 163
Period size: 35 Copynumber: 3.2 Consensus size: 35
624596 AAGTTTGTAT
*
624606 CGATTCATGTCGAACGGAAGGAAGCATCGCACTTC
1 CGATTCAAGTCGAACGGAAGGAAGCATCGCACTTC
* *
624641 CGTTTCAAGTCGAATGGAAGGAAGCATCGCACTTC
1 CGATTCAAGTCGAACGGAAGGAAGCATCGCACTTC
* * * *
624676 CAATTCAAGTCGAACAGAAGGAGGCATCGCACTTT
1 CGATTCAAGTCGAACGGAAGGAAGCATCGCACTTC
624711 CGATTCAA
1 CGATTCAA
624719 CTAGAACAGA
Statistics
Matches: 68, Mismatches: 10, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
35 68 1.00
ACGTcount: A:0.31, C:0.24, G:0.24, T:0.21
Consensus pattern (35 bp):
CGATTCAAGTCGAACGGAAGGAAGCATCGCACTTC
Found at i:632693 original size:26 final size:26
Alignment explanation
Indices: 632655--632704 Score: 64
Period size: 26 Copynumber: 1.9 Consensus size: 26
632645 CGCGTTTATT
* * * *
632655 TTCGCAACGCGAATTTTATTTTCGAA
1 TTCGAAACACGAATATTAATTTCGAA
632681 TTCGAAACACGAATATTAATTTCG
1 TTCGAAACACGAATATTAATTTCG
632705 CAACACAAAT
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
26 20 1.00
ACGTcount: A:0.32, C:0.18, G:0.14, T:0.36
Consensus pattern (26 bp):
TTCGAAACACGAATATTAATTTCGAA
Found at i:632823 original size:22 final size:22
Alignment explanation
Indices: 632798--632848 Score: 66
Period size: 22 Copynumber: 2.3 Consensus size: 22
632788 TCACTCTCTA
*
632798 CGACGACATCCGTCCCCATCTC
1 CGACGACATCCGTCCCCATATC
* *
632820 CGACAACATCTGTCCCCATATC
1 CGACGACATCCGTCCCCATATC
*
632842 CAACGAC
1 CGACGAC
632849 CCCCTCCATC
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.25, C:0.45, G:0.12, T:0.18
Consensus pattern (22 bp):
CGACGACATCCGTCCCCATATC
Found at i:633234 original size:20 final size:20
Alignment explanation
Indices: 633211--633253 Score: 77
Period size: 20 Copynumber: 2.1 Consensus size: 20
633201 AATCGTAACT
633211 CGAAAATGAAATTCGCAACG
1 CGAAAATGAAATTCGCAACG
*
633231 CGAAAATGAAATTCGCAATG
1 CGAAAATGAAATTCGCAACG
633251 CGA
1 CGA
633254 TTTTAGTTTT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.44, C:0.19, G:0.21, T:0.16
Consensus pattern (20 bp):
CGAAAATGAAATTCGCAACG
Found at i:633294 original size:20 final size:20
Alignment explanation
Indices: 633265--633331 Score: 89
Period size: 20 Copynumber: 3.4 Consensus size: 20
633255 TTTAGTTTTC
*
633265 GTTGCGAATTTCATTTTCGA
1 GTTGCGAATTTAATTTTCGA
* * *
633285 GTTGCAAATTTTATTTTCGT
1 GTTGCGAATTTAATTTTCGA
*
633305 GTTGCGAATTTAAGTTTCGA
1 GTTGCGAATTTAATTTTCGA
633325 GTTGCGA
1 GTTGCGA
633332 TTTTCATGTT
Statistics
Matches: 40, Mismatches: 7, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 40 1.00
ACGTcount: A:0.21, C:0.12, G:0.22, T:0.45
Consensus pattern (20 bp):
GTTGCGAATTTAATTTTCGA
Found at i:633311 original size:40 final size:39
Alignment explanation
Indices: 633253--633329 Score: 111
Period size: 40 Copynumber: 1.9 Consensus size: 39
633243 TCGCAATGCG
* *
633253 ATTTTAGTTTTCGTTGCGAATTTCATTTTCGAGTTGCAA
1 ATTTTAGTTTTCGTTGCGAATTTAAGTTTCGAGTTGCAA
633292 ATTTTA-TTTTCGTGTTGCGAATTTAAGTTTCGAGTTGC
1 ATTTTAGTTTTC--GTTGCGAATTTAAGTTTCGAGTTGC
633330 GATTTTCATG
Statistics
Matches: 34, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
38 5 0.15
39 6 0.18
40 23 0.68
ACGTcount: A:0.19, C:0.12, G:0.19, T:0.49
Consensus pattern (39 bp):
ATTTTAGTTTTCGTTGCGAATTTAAGTTTCGAGTTGCAA
Found at i:635072 original size:21 final size:21
Alignment explanation
Indices: 635048--635092 Score: 72
Period size: 21 Copynumber: 2.1 Consensus size: 21
635038 GTTAGGGTAG
*
635048 TTACGTGATGAGGTCAGTGCT
1 TTACGTAATGAGGTCAGTGCT
*
635069 TTACGTAATGAGGTCGGTGCT
1 TTACGTAATGAGGTCAGTGCT
635090 TTA
1 TTA
635093 TTTGACGACA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.20, C:0.13, G:0.31, T:0.36
Consensus pattern (21 bp):
TTACGTAATGAGGTCAGTGCT
Found at i:635159 original size:21 final size:21
Alignment explanation
Indices: 635116--635215 Score: 71
Period size: 21 Copynumber: 4.8 Consensus size: 21
635106 GTGCATGGAA
* *
635116 TGATGAGGTAG-GGTCTTTGCG
1 TGATGAGGTAGTTG-CTTTACG
* *
635137 TGGTGAGGTAGTTGTTTTACG
1 TGATGAGGTAGTTGCTTTACG
** *
635158 TGATGA-CAATGGTGCTTTACG
1 TGATGAGGTA-GTTGCTTTACG
*
635179 TGGTGAGGTA-TATGCTTTACG
1 TGATGAGGTAGT-TGCTTTACG
*
635200 TGATGAGGTAGCTGCT
1 TGATGAGGTAGTTGCT
635216 CTGCGTGAGA
Statistics
Matches: 59, Mismatches: 15, Indels: 10
0.70 0.18 0.12
Matches are distributed among these distances:
20 1 0.02
21 56 0.95
22 2 0.03
ACGTcount: A:0.18, C:0.10, G:0.36, T:0.36
Consensus pattern (21 bp):
TGATGAGGTAGTTGCTTTACG
Found at i:635162 original size:42 final size:43
Alignment explanation
Indices: 635116--635210 Score: 115
Period size: 42 Copynumber: 2.3 Consensus size: 43
635106 GTGCATGGAA
* *
635116 TGATGAGGTAGGGT-CTTTGCGTGGTGAGGTAGT-TGTTTTACG
1 TGATGAGGTAGGGTGCTTTACGTGGTGAGGTA-TATGCTTTACG
** *
635158 TGATGA-CAATGGTGCTTTACGTGGTGAGGTATATGCTTTACG
1 TGATGAGGTAGGGTGCTTTACGTGGTGAGGTATATGCTTTACG
635200 TGATGAGGTAG
1 TGATGAGGTAG
635211 CTGCTCTGCG
Statistics
Matches: 42, Mismatches: 8, Indels: 5
0.76 0.15 0.09
Matches are distributed among these distances:
41 5 0.12
42 36 0.86
43 1 0.02
ACGTcount: A:0.19, C:0.08, G:0.37, T:0.36
Consensus pattern (43 bp):
TGATGAGGTAGGGTGCTTTACGTGGTGAGGTATATGCTTTACG
Found at i:635565 original size:21 final size:21
Alignment explanation
Indices: 635539--635589 Score: 66
Period size: 21 Copynumber: 2.4 Consensus size: 21
635529 ATTCACCTGT
* *
635539 CATCGTTCAAAAGGCCCCTCC
1 CATCGTTCAAAAGACCCCTCA
*
635560 CATCGTTCAAGAGACCCCTCA
1 CATCGTTCAAAAGACCCCTCA
*
635581 TATCGTTCA
1 CATCGTTCA
635590 GGATCCATTT
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.25, C:0.37, G:0.14, T:0.24
Consensus pattern (21 bp):
CATCGTTCAAAAGACCCCTCA
Found at i:636747 original size:20 final size:20
Alignment explanation
Indices: 636719--636821 Score: 107
Period size: 20 Copynumber: 5.2 Consensus size: 20
636709 CGATTTTTGT
*
636719 GTTATGAATTTTATTTTCGC
1 GTTACGAATTTTATTTTCGC
* * *
636739 TTTACGAATATGATTTTCGC
1 GTTACGAATTTTATTTTCGC
* * *
636759 GTTGCAAATTTGATTTTCGC
1 GTTACGAATTTTATTTTCGC
* *
636779 GTTACAAATTTTATTTTCGA
1 GTTACGAATTTTATTTTCGC
* *
636799 GTTAAGAATTTTATTTTCAC
1 GTTACGAATTTTATTTTCGC
636819 GTT
1 GTT
636822 GCGTATTTGA
Statistics
Matches: 68, Mismatches: 15, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
20 68 1.00
ACGTcount: A:0.24, C:0.12, G:0.15, T:0.50
Consensus pattern (20 bp):
GTTACGAATTTTATTTTCGC
Found at i:636847 original size:60 final size:60
Alignment explanation
Indices: 636725--636849 Score: 135
Period size: 60 Copynumber: 2.1 Consensus size: 60
636715 TTGTGTTATG
** * * * *
636725 AATTTTATTTTCGCTTTACGAATATGATTTTCGCGTTGCAAATTTGATTTTCGCGTTACA
1 AATTTTATTTTCGAGTTAAGAATATGATTTTCACGTTGCAAATTTGATATTCGAGTTACA
* * ** *
636785 AATTTTATTTTCGAGTTAAGAATTTTATTTTCACGTTGCGTATTTGAATATT-GAGTTGCA
1 AATTTTATTTTCGAGTTAAGAATATGATTTTCACGTTGCAAATTTG-ATATTCGAGTTACA
636845 AATTT
1 AATTT
636850 GAGTTGCAAA
Statistics
Matches: 53, Mismatches: 11, Indels: 2
0.80 0.17 0.03
Matches are distributed among these distances:
60 49 0.92
61 4 0.08
ACGTcount: A:0.26, C:0.11, G:0.15, T:0.48
Consensus pattern (60 bp):
AATTTTATTTTCGAGTTAAGAATATGATTTTCACGTTGCAAATTTGATATTCGAGTTACA
Found at i:636883 original size:13 final size:13
Alignment explanation
Indices: 636830--636886 Score: 87
Period size: 13 Copynumber: 4.3 Consensus size: 13
636820 TTGCGTATTT
636830 GAATATTGAGTTGC
1 GAAT-TTGAGTTGC
*
636844 AAATTTGAGTTGC
1 GAATTTGAGTTGC
*
636857 AAATTTGAGTTGC
1 GAATTTGAGTTGC
636870 GAATTTGAGTTGC
1 GAATTTGAGTTGC
636883 GAAT
1 GAAT
636887 CAGAGAAGTT
Statistics
Matches: 41, Mismatches: 2, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
13 38 0.93
14 3 0.07
ACGTcount: A:0.30, C:0.07, G:0.26, T:0.37
Consensus pattern (13 bp):
GAATTTGAGTTGC
Found at i:637001 original size:66 final size:66
Alignment explanation
Indices: 636924--637056 Score: 266
Period size: 66 Copynumber: 2.0 Consensus size: 66
636914 TTCTAGTTTC
636924 AATTCAAGGCAAACACCTTCAAAAAGATAACAGACAACAATCTAATAAGTGATAACAATTGAACA
1 AATTCAAGGCAAACACCTTCAAAAAGATAACAGACAACAATCTAATAAGTGATAACAATTGAACA
636989 A
66 A
636990 AATTCAAGGCAAACACCTTCAAAAAGATAACAGACAACAATCTAATAAGTGATAACAATTGAACA
1 AATTCAAGGCAAACACCTTCAAAAAGATAACAGACAACAATCTAATAAGTGATAACAATTGAACA
637055 A
66 A
637056 A
1 A
637057 TCATAGCAAT
Statistics
Matches: 67, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
66 67 1.00
ACGTcount: A:0.53, C:0.18, G:0.11, T:0.18
Consensus pattern (66 bp):
AATTCAAGGCAAACACCTTCAAAAAGATAACAGACAACAATCTAATAAGTGATAACAATTGAACA
A
Found at i:639525 original size:24 final size:24
Alignment explanation
Indices: 639498--639546 Score: 80
Period size: 24 Copynumber: 2.0 Consensus size: 24
639488 TCAAAATCCA
*
639498 AGTATTGACCAATATCAAAGTTCG
1 AGTATTGACCAAGATCAAAGTTCG
*
639522 AGTATTGACCAAGATCAAATTTCG
1 AGTATTGACCAAGATCAAAGTTCG
639546 A
1 A
639547 ATACTGACTA
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.39, C:0.16, G:0.16, T:0.29
Consensus pattern (24 bp):
AGTATTGACCAAGATCAAAGTTCG
Found at i:639554 original size:24 final size:24
Alignment explanation
Indices: 639503--639554 Score: 68
Period size: 24 Copynumber: 2.2 Consensus size: 24
639493 ATCCAAGTAT
* * *
639503 TGACCAATATCAAAGTTCGAGTAT
1 TGACCAAGATCAAAGTTCGAATAC
*
639527 TGACCAAGATCAAATTTCGAATAC
1 TGACCAAGATCAAAGTTCGAATAC
639551 TGAC
1 TGAC
639555 TAGTACTCAC
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.38, C:0.19, G:0.15, T:0.27
Consensus pattern (24 bp):
TGACCAAGATCAAAGTTCGAATAC
Found at i:640537 original size:20 final size:20
Alignment explanation
Indices: 640454--640581 Score: 72
Period size: 20 Copynumber: 6.5 Consensus size: 20
640444 CAAAACATTT
* *
640454 GTGTTGCGAAAATAAAAGT-
1 GTGTTGCGAAAACAAAATTC
*
640473 -TGTTGC-AAAATTAAAATTC
1 GTGTTGCGAAAA-CAAAATTC
** *
640492 GTGTTGCGAATTCGGAAA-TC
1 GTGTTGCGAAAAC-AAAATTC
*
640512 GAGTTGCGAAAACAAAATTC
1 GTGTTGCGAAAACAAAATTC
640532 GTGTTGCGAATTAA-AAAA-TC
1 GTGTTGCGAA--AACAAAATTC
* * *
640552 ATGTTGCGAAAAGGAAACTT-
1 GTGTTGCGAAAA-CAAAATTC
640572 GTGTTGCGAA
1 GTGTTGCGAA
640582 TTTAAAAACC
Statistics
Matches: 85, Mismatches: 13, Indels: 21
0.71 0.11 0.18
Matches are distributed among these distances:
17 4 0.05
18 14 0.16
19 3 0.04
20 52 0.61
21 10 0.12
22 2 0.02
ACGTcount: A:0.38, C:0.11, G:0.23, T:0.28
Consensus pattern (20 bp):
GTGTTGCGAAAACAAAATTC
Found at i:640645 original size:40 final size:40
Alignment explanation
Indices: 640486--640645 Score: 155
Period size: 40 Copynumber: 4.0 Consensus size: 40
640476 TGCAAAATTA
**
640486 AAATTCGTGTTGCGAATTCGGAAATCGAGTTGCGAAAACA-
1 AAATTCGTGTTGCGAATTCAAAAATCGAGTTGCGAAAA-AG
* *
640526 AAATTCGTGTTGCGAATTAAAAAATC-ATGTTGCGAAAAGG
1 AAATTCGTGTTGCGAATTCAAAAATCGA-GTTGCGAAAAAG
* * ** *
640566 AAACTT-GTGTTGCGAATTTAAAAACCGCTTTGCTAAAAAG
1 AAA-TTCGTGTTGCGAATTCAAAAATCGAGTTGCGAAAAAG
** * *
640606 AAATTCGCCTTGCGAATTCAGAAATCGAGTTGCTAAAAAG
1 AAATTCGTGTTGCGAATTCAAAAATCGAGTTGCGAAAAAG
640646 GAAACTGCGT
Statistics
Matches: 98, Mismatches: 17, Indels: 10
0.78 0.14 0.08
Matches are distributed among these distances:
39 3 0.03
40 93 0.95
41 2 0.02
ACGTcount: A:0.38, C:0.14, G:0.21, T:0.27
Consensus pattern (40 bp):
AAATTCGTGTTGCGAATTCAAAAATCGAGTTGCGAAAAAG
Found at i:642963 original size:31 final size:31
Alignment explanation
Indices: 642928--642987 Score: 77
Period size: 32 Copynumber: 1.9 Consensus size: 31
642918 AGCCGATCAT
*
642928 TTTAA-AGGTAAATTGGGGCAAAAAGTAATAG
1 TTTAAGAGGTAAATTGGGACAAAAA-TAATAG
* *
642959 TTTAAGGGGTCAATTGGGACAAAAATAAT
1 TTTAAGAGGTAAATTGGGACAAAAATAAT
642988 TCAAGATCCA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
31 9 0.36
32 16 0.64
ACGTcount: A:0.43, C:0.05, G:0.25, T:0.27
Consensus pattern (31 bp):
TTTAAGAGGTAAATTGGGACAAAAATAATAG
Found at i:643316 original size:2 final size:2
Alignment explanation
Indices: 643309--643339 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
643299 TATTTAAAAT
643309 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
643340 TAGATTTTAA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:647091 original size:17 final size:18
Alignment explanation
Indices: 647071--647111 Score: 57
Period size: 18 Copynumber: 2.3 Consensus size: 18
647061 GAATTATATT
647071 AGTAAAATA-TTAAATAA
1 AGTAAAATACTTAAATAA
*
647088 AGTAAAATACTTGAATAA
1 AGTAAAATACTTAAATAA
*
647106 ATTAAA
1 AGTAAA
647112 TGTATAATAT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
17 9 0.43
18 12 0.57
ACGTcount: A:0.61, C:0.02, G:0.07, T:0.29
Consensus pattern (18 bp):
AGTAAAATACTTAAATAA
Found at i:651939 original size:2 final size:2
Alignment explanation
Indices: 651932--651969 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
651922 TTACGACAGT
651932 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
651970 CCAAGCTCTG
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:654005 original size:25 final size:24
Alignment explanation
Indices: 653968--654038 Score: 79
Period size: 24 Copynumber: 2.9 Consensus size: 24
653958 GATAAAATAA
* * *
653968 TTTTATTTCTTAAATTAATGTGCT
1 TTTTTTTTATTAAATTAATGTGAT
* *
653992 CTTTTTTTTATTAAATTAATATAAT
1 -TTTTTTTTATTAAATTAATGTGAT
*
654017 TATTTTTTATTAAATTAATGTG
1 TTTTTTTTATTAAATTAATGTG
654039 TAGCTTACAC
Statistics
Matches: 38, Mismatches: 8, Indels: 1
0.81 0.17 0.02
Matches are distributed among these distances:
24 19 0.50
25 19 0.50
ACGTcount: A:0.31, C:0.04, G:0.06, T:0.59
Consensus pattern (24 bp):
TTTTTTTTATTAAATTAATGTGAT
Found at i:663319 original size:11 final size:11
Alignment explanation
Indices: 663303--663345 Score: 50
Period size: 11 Copynumber: 3.5 Consensus size: 11
663293 GAGACTTTAC
663303 CCGCCCCGCAT
1 CCGCCCCGCAT
663314 CCGCCCCGCAT
1 CCGCCCCGCAT
663325 CCACCCGCCCCGCAT
1 ----CCGCCCCGCAT
663340 CCGCCC
1 CCGCCC
663346 GCCCCACATC
Statistics
Matches: 28, Mismatches: 0, Indels: 8
0.78 0.00 0.22
Matches are distributed among these distances:
11 17 0.61
15 11 0.39
ACGTcount: A:0.09, C:0.67, G:0.16, T:0.07
Consensus pattern (11 bp):
CCGCCCCGCAT
Found at i:663334 original size:15 final size:15
Alignment explanation
Indices: 663314--663361 Score: 78
Period size: 15 Copynumber: 3.2 Consensus size: 15
663304 CGCCCCGCAT
*
663314 CCGCCCCGCATCCAC
1 CCGCCCCGCATCCGC
663329 CCGCCCCGCATCCGC
1 CCGCCCCGCATCCGC
*
663344 CCGCCCCACATCCGC
1 CCGCCCCGCATCCGC
663359 CCG
1 CCG
663362 TCCAAATAAA
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 31 1.00
ACGTcount: A:0.10, C:0.67, G:0.17, T:0.06
Consensus pattern (15 bp):
CCGCCCCGCATCCGC
Done.