Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007867.1 Hibiscus syriacus cultivar Beakdansim tig00110239_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: 3477501
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 3 of 18
Found at i:435576 original size:19 final size:18
Alignment explanation
Indices: 435550--435587 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 18
435540 GGACTTATAA
435550 CTTATTTC-AGATTCATAG
1 CTTATTTCAAG-TTCATAG
435568 CTTATTTTCAAGTTCATAG
1 CTTA-TTTCAAGTTCATAG
435587 C
1 C
435588 CCAATGCATA
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
18 4 0.22
19 12 0.67
20 2 0.11
ACGTcount: A:0.26, C:0.18, G:0.11, T:0.45
Consensus pattern (18 bp):
CTTATTTCAAGTTCATAG
Found at i:443656 original size:20 final size:20
Alignment explanation
Indices: 443624--443722 Score: 101
Period size: 20 Copynumber: 5.0 Consensus size: 20
443614 CAAAGTTTCG
*
443624 AAACTCTTT-CCAAAGTATAA
1 AAACT-TTTACCAAAGTATGA
* * *
443644 AAAGTTTTACCAAAGTACGG
1 AAACTTTTACCAAAGTATGA
* *
443664 ATACTTTTACCAAAGTATGG
1 AAACTTTTACCAAAGTATGA
* * *
443684 AAACTCTTGCCAAAATATGA
1 AAACTTTTACCAAAGTATGA
443704 AAACTTTTACCAAAGTATG
1 AAACTTTTACCAAAGTATG
443723 GATACTCTTG
Statistics
Matches: 63, Mismatches: 15, Indels: 2
0.79 0.19 0.03
Matches are distributed among these distances:
19 3 0.05
20 60 0.95
ACGTcount: A:0.41, C:0.17, G:0.12, T:0.29
Consensus pattern (20 bp):
AAACTTTTACCAAAGTATGA
Found at i:443712 original size:60 final size:60
Alignment explanation
Indices: 443614--443728 Score: 167
Period size: 60 Copynumber: 1.9 Consensus size: 60
443604 GAACGTTTGA
* * * *
443614 CAAAGTTTCGAAACTCTTTCCAAAGTATAAAAAGTTTTACCAAAGTACGGATACTTTTAC
1 CAAAGTATCGAAACTCTTGCCAAAATATAAAAACTTTTACCAAAGTACGGATACTTTTAC
* * *
443674 CAAAGTATGGAAACTCTTGCCAAAATATGAAAACTTTTACCAAAGTATGGATACT
1 CAAAGTATCGAAACTCTTGCCAAAATATAAAAACTTTTACCAAAGTACGGATACT
443729 CTTGCCCTAG
Statistics
Matches: 48, Mismatches: 7, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
60 48 1.00
ACGTcount: A:0.40, C:0.17, G:0.13, T:0.30
Consensus pattern (60 bp):
CAAAGTATCGAAACTCTTGCCAAAATATAAAAACTTTTACCAAAGTACGGATACTTTTAC
Found at i:452256 original size:95 final size:96
Alignment explanation
Indices: 452068--452273 Score: 220
Period size: 95 Copynumber: 2.2 Consensus size: 96
452058 GATATTGTTG
*
452068 GGGTAGTATCGATACCAATGTAAGGGTATCAATACCAAGCAAACATCGAATCTAATTTCGGTATC
1 GGGTAGTATCGATACCAATGTAAGGGTATCAATACCAAGCAAACATCGAACCTAATTTCGGTATC
*** *
452133 GATACCATAAAGAGGTATCAGTACCATAGTA
66 GATACCATAAAGAAACATCAATACCATAGTA
* * * * * *
452164 GGGTATTATCGATACC-ATGGTAAGGGTATCGATATCAGGC-ATCATCGAACCTAATTTTGGTAT
1 GGGTAGTATCGATACCAAT-GTAAGGGTATCAATACCAAGCAAACATCGAACCTAATTTCGGTAT
* * *
452227 CGATACCCA-GAGGAAACATCAATATCATAGTA
65 CGATA-CCATAAAGAAACATCAATACCATAGTA
** *
452259 TTGAAGTATCGATAC
1 GGGTAGTATCGATAC
452274 TTGGGTAGTA
Statistics
Matches: 90, Mismatches: 18, Indels: 5
0.80 0.16 0.04
Matches are distributed among these distances:
95 54 0.60
96 36 0.40
ACGTcount: A:0.35, C:0.17, G:0.20, T:0.27
Consensus pattern (96 bp):
GGGTAGTATCGATACCAATGTAAGGGTATCAATACCAAGCAAACATCGAACCTAATTTCGGTATC
GATACCATAAAGAAACATCAATACCATAGTA
Found at i:452839 original size:79 final size:79
Alignment explanation
Indices: 452708--453016 Score: 476
Period size: 79 Copynumber: 3.9 Consensus size: 79
452698 AATAGAAATA
452708 CATATGGGTGCATTATTGGCATGAAAGGATGCCATAGCTGAAATGTATATGGGTACATTGTCAGC
1 CATATGGGTGCATTATTGGCATGAAAGGATGCCATAGCTGAAATGTATATGGGTACATTGTCAGC
452773 ATAAAAGAATAATG
66 ATAAAAGAATAATG
* * *
452787 CATATAGGTGCAATATTGGCATGAAAGGATGCCATAGCTGAAATGTATATGGGTACATTGTCAGT
1 CATATGGGTGCATTATTGGCATGAAAGGATGCCATAGCTGAAATGTATATGGGTACATTGTCAGC
*
452852 ATAAAATAATAATG
66 ATAAAAGAATAATG
* * * *
452866 TATATGGGTGCATTATTGGTATGAAAGGATGCCATAGCTGAAATGTCTATGGGTTA-ATTGTCAA
1 CATATGGGTGCATTATTGGCATGAAAGGATGCCATAGCTGAAATGTATATGGG-TACATTGTCAG
452930 CATAAAAGAATAATG
65 CATAAAAGAATAATG
* * * * * *
452945 CATATGGGTGCATTATTGACATGAAAGGATACCATCGCTGAAATGCATATGGGTGCATTATCAGC
1 CATATGGGTGCATTATTGGCATGAAAGGATGCCATAGCTGAAATGTATATGGGTACATTGTCAGC
453010 ATAAAAG
66 ATAAAAG
453017 TATATTTTAT
Statistics
Matches: 206, Mismatches: 22, Indels: 4
0.89 0.09 0.02
Matches are distributed among these distances:
78 1 0.00
79 203 0.99
80 2 0.01
ACGTcount: A:0.36, C:0.11, G:0.24, T:0.29
Consensus pattern (79 bp):
CATATGGGTGCATTATTGGCATGAAAGGATGCCATAGCTGAAATGTATATGGGTACATTGTCAGC
ATAAAAGAATAATG
Found at i:457314 original size:16 final size:16
Alignment explanation
Indices: 457293--457326 Score: 68
Period size: 16 Copynumber: 2.1 Consensus size: 16
457283 TTCGTTTCAG
457293 GGCTACCTTTGTCACC
1 GGCTACCTTTGTCACC
457309 GGCTACCTTTGTCACC
1 GGCTACCTTTGTCACC
457325 GG
1 GG
457327 GTAAAAAGGA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.12, C:0.35, G:0.24, T:0.29
Consensus pattern (16 bp):
GGCTACCTTTGTCACC
Found at i:459231 original size:22 final size:23
Alignment explanation
Indices: 459199--459243 Score: 65
Period size: 22 Copynumber: 2.0 Consensus size: 23
459189 CCATAAGGAG
*
459199 GTATCGGTACCATAGT-AGGGTA
1 GTATCGATACCATAGTAAGGGTA
*
459221 GTATCGATACCATGGTAAGGGTA
1 GTATCGATACCATAGTAAGGGTA
459244 TTGATACCAG
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
22 14 0.70
23 6 0.30
ACGTcount: A:0.29, C:0.13, G:0.31, T:0.27
Consensus pattern (23 bp):
GTATCGATACCATAGTAAGGGTA
Found at i:459300 original size:95 final size:96
Alignment explanation
Indices: 459120--459310 Score: 249
Period size: 95 Copynumber: 2.0 Consensus size: 96
459110 GATATTGTTG
* * * *
459120 GGGTAGTATTGATACAATTGTAAGGGTATCGATACCAAGTAAAAATCGAATCTAATTTCGGTATC
1 GGGTAGTATCGATACAATGGTAAGGGTATCGATACCAAGGAAAAATCGAACCTAATTTCGGTATC
* *
459185 AATACCATAAGGAGGTATCGGTACCATAGTA
66 AATACCAGAAGGAAGTATCGGTACCATAGTA
* * * * *
459216 GGGTAGTATCGATACCATGGTAAGGGTATTGATACC-AGGCAACATCGAACCTAATTTTGGTATC
1 GGGTAGTATCGATACAATGGTAAGGGTATCGATACCAAGGAAAAATCGAACCTAATTTCGGTATC
* * *
459280 GATACCCGGAGGAAGTATCGGTACCATAGTA
66 AATACCAGAAGGAAGTATCGGTACCATAGTA
459311 TTGAAGTATC
Statistics
Matches: 81, Mismatches: 14, Indels: 1
0.84 0.15 0.01
Matches are distributed among these distances:
95 49 0.60
96 32 0.40
ACGTcount: A:0.34, C:0.16, G:0.24, T:0.27
Consensus pattern (96 bp):
GGGTAGTATCGATACAATGGTAAGGGTATCGATACCAAGGAAAAATCGAACCTAATTTCGGTATC
AATACCAGAAGGAAGTATCGGTACCATAGTA
Found at i:459891 original size:79 final size:79
Alignment explanation
Indices: 459760--460068 Score: 501
Period size: 79 Copynumber: 3.9 Consensus size: 79
459750 AATAGAAATA
*
459760 CATATGGGTGCATTATTGGCATGAAAGGATGCCATTGCTGAAATGTATATGGGTACATTGTCAGC
1 CATATGGGTGCATTATTGGCATGAAAGGATGCCATAGCTGAAATGTATATGGGTACATTGTCAGC
459825 ATAAAAGAATAATG
66 ATAAAAGAATAATG
** * * *
459839 CATATAAGTACATTATTGGCATGAAAAGATGCCATAGCTTAAATGTATATGGGTACATTGTCAGC
1 CATATGGGTGCATTATTGGCATGAAAGGATGCCATAGCTGAAATGTATATGGGTACATTGTCAGC
459904 ATAAAAGAATAATG
66 ATAAAAGAATAATG
*
459918 CATATGGGTGCATTATTGGCATGAAAGGATGCCATAGTTGAAATGTATATGGGTACATTGTCAGC
1 CATATGGGTGCATTATTGGCATGAAAGGATGCCATAGCTGAAATGTATATGGGTACATTGTCAGC
459983 ATAAAAGAATAATG
66 ATAAAAGAATAATG
* * * * * *
459997 CATATGGGTGCATTATTGGCATGAAAGGATGTCATCGCTGAAATGCATATGGGTGCATTATCAAC
1 CATATGGGTGCATTATTGGCATGAAAGGATGCCATAGCTGAAATGTATATGGGTACATTGTCAGC
460062 ATAAAAG
66 ATAAAAG
460069 TATATTTTAT
Statistics
Matches: 211, Mismatches: 19, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
79 211 1.00
ACGTcount: A:0.36, C:0.12, G:0.24, T:0.29
Consensus pattern (79 bp):
CATATGGGTGCATTATTGGCATGAAAGGATGCCATAGCTGAAATGTATATGGGTACATTGTCAGC
ATAAAAGAATAATG
Found at i:469031 original size:20 final size:20
Alignment explanation
Indices: 468969--469036 Score: 79
Period size: 20 Copynumber: 3.5 Consensus size: 20
468959 CAGCCGAGCA
*
468969 GTATCGATACTATGAGGAAG
1 GTATCAATACTATGAGGAAG
* *
468989 GTATCAATATCGA-AAGG--G
1 GTATCAATA-CTATGAGGAAG
469007 GTATCAATACTATGAGGAAG
1 GTATCAATACTATGAGGAAG
469027 GTATCAATAC
1 GTATCAATAC
469037 CATTGATAAC
Statistics
Matches: 39, Mismatches: 5, Indels: 8
0.75 0.10 0.15
Matches are distributed among these distances:
17 2 0.05
18 13 0.33
20 22 0.56
21 2 0.05
ACGTcount: A:0.38, C:0.12, G:0.25, T:0.25
Consensus pattern (20 bp):
GTATCAATACTATGAGGAAG
Found at i:469569 original size:54 final size:54
Alignment explanation
Indices: 469511--469769 Score: 340
Period size: 54 Copynumber: 4.8 Consensus size: 54
469501 TTTGTATGGG
*
469511 CACTATGTGTGCAACTCACGGAATTCATCATATGTTGATGAACAACCGTTTCGA
1 CACTATGTGTGCAACTCACGGAATTCATCATATGTTGATGAACAACCATTTCGA
* * *
469565 CACTATGTGTGCAACTCACGAAATTCATCATATGTTTGATGAACAATCATTTTGA
1 CACTATGTGTGCAACTCACGGAATTCATCATATG-TTGATGAACAACCATTTCGA
* * * *
469620 CACTATGTATGCAACTCATGGAATTCATCATATGTTGATGAACAACCGTTTCGG
1 CACTATGTGTGCAACTCACGGAATTCATCATATGTTGATGAACAACCATTTCGA
* * * *
469674 CACTATGTGTGCAACTCACGAAATTGATCATATGTTGATGAAAAATCATTTCGGA
1 CACTATGTGTGCAACTCACGGAATTCATCATATGTTGATGAACAACCATTTC-GA
* * * * *
469729 -ACTATGTGTACAACCCACAGAATTCATAATATGTTTATGAA
1 CACTATGTGTGCAACTCACGGAATTCATCATATGTTGATGAA
469770 TGATCGTATA
Statistics
Matches: 177, Mismatches: 26, Indels: 4
0.86 0.13 0.02
Matches are distributed among these distances:
54 128 0.72
55 49 0.28
ACGTcount: A:0.33, C:0.19, G:0.17, T:0.32
Consensus pattern (54 bp):
CACTATGTGTGCAACTCACGGAATTCATCATATGTTGATGAACAACCATTTCGA
Found at i:469598 original size:27 final size:26
Alignment explanation
Indices: 469514--469599 Score: 63
Period size: 27 Copynumber: 3.2 Consensus size: 26
469504 GTATGGGCAC
469514 TATGTGTGCAACTCACGGAATTCATCA
1 TATGTGTGCAACTCAC-GAATTCATCA
* *
469541 TATGTTGATG-AAC-AACCG-TTTCGA-CA
1 TATG-TG-TGCAACTCA-CGAATTC-ATCA
469567 CTATGTGTGCAACTCACGAAATTCATCA
1 -TATGTGTGCAACTCACG-AATTCATCA
469595 TATGT
1 TATGT
469600 TTGATGAACA
Statistics
Matches: 45, Mismatches: 4, Indels: 20
0.65 0.06 0.29
Matches are distributed among these distances:
25 2 0.04
26 12 0.27
27 18 0.40
28 11 0.24
29 2 0.04
ACGTcount: A:0.30, C:0.21, G:0.17, T:0.31
Consensus pattern (26 bp):
TATGTGTGCAACTCACGAATTCATCA
Found at i:469625 original size:109 final size:109
Alignment explanation
Indices: 469511--469769 Score: 396
Period size: 109 Copynumber: 2.4 Consensus size: 109
469501 TTTGTATGGG
469511 CACTATGTGTGCAACTCACGGAATTCATCATATGTTGATGAACAACCGTTTCGACACTATGTGTG
1 CACTATGTGTGCAACTCACGGAATTCATCATATGTTGATGAACAACCGTTTCGACACTATGTGTG
* *
469576 CAACTCACGAAATTCATCATATGTTTGATGAACAATCATTT-TGA
66 CAACTCACGAAATTCATCATATG-TTGATGAAAAATCATTTCGGA
* * *
469620 CACTATGTATGCAACTCATGGAATTCATCATATGTTGATGAACAACCGTTTCGGCACTATGTGTG
1 CACTATGTGTGCAACTCACGGAATTCATCATATGTTGATGAACAACCGTTTCGACACTATGTGTG
*
469685 CAACTCACGAAATTGATCATATGTTGATGAAAAATCATTTCGGA
66 CAACTCACGAAATTCATCATATGTTGATGAAAAATCATTTCGGA
* * * * *
469729 -ACTATGTGTACAACCCACAGAATTCATAATATGTTTATGAA
1 CACTATGTGTGCAACTCACGGAATTCATCATATGTTGATGAA
469770 TGATCGTATA
Statistics
Matches: 136, Mismatches: 13, Indels: 3
0.89 0.09 0.02
Matches are distributed among these distances:
108 50 0.37
109 86 0.63
ACGTcount: A:0.33, C:0.19, G:0.17, T:0.32
Consensus pattern (109 bp):
CACTATGTGTGCAACTCACGGAATTCATCATATGTTGATGAACAACCGTTTCGACACTATGTGTG
CAACTCACGAAATTCATCATATGTTGATGAAAAATCATTTCGGA
Found at i:476901 original size:28 final size:31
Alignment explanation
Indices: 476842--476901 Score: 72
Period size: 31 Copynumber: 2.0 Consensus size: 31
476832 GAACTAATGG
*
476842 AAGGATCTAATTCAAAAAATATTACTACTTT
1 AAGGATCTAATTCAAAAAATATTACTAATTT
* *
476873 AAGGATTTAATT-AAAATAT-TTAC-AATTT
1 AAGGATCTAATTCAAAAAATATTACTAATTT
476901 A
1 A
476902 GTGACCAATT
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
28 5 0.19
29 4 0.15
30 6 0.23
31 11 0.42
ACGTcount: A:0.47, C:0.08, G:0.07, T:0.38
Consensus pattern (31 bp):
AAGGATCTAATTCAAAAAATATTACTAATTT
Found at i:483202 original size:23 final size:23
Alignment explanation
Indices: 483171--483233 Score: 83
Period size: 23 Copynumber: 2.8 Consensus size: 23
483161 AATCATAAGC
483171 TACCA-AAAGGCAGATAAAAACG
1 TACCACAAAGGCAGATAAAAACG
* *
483193 TACTACAAAGGCAGATATAAACG
1 TACCACAAAGGCAGATAAAAACG
* *
483216 TGCCATAAAGGCAGATAA
1 TACCACAAAGGCAGATAA
483234 CATGTCACAA
Statistics
Matches: 34, Mismatches: 6, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
22 4 0.12
23 30 0.88
ACGTcount: A:0.49, C:0.17, G:0.19, T:0.14
Consensus pattern (23 bp):
TACCACAAAGGCAGATAAAAACG
Found at i:484766 original size:31 final size:31
Alignment explanation
Indices: 484731--484808 Score: 129
Period size: 31 Copynumber: 2.5 Consensus size: 31
484721 TTTAAAAAAA
*
484731 TAAGTTTTGGTCATTTACGTTATCGTTTTAT
1 TAAGTTTTGGTCACTTACGTTATCGTTTTAT
* *
484762 TAAGTTTTAGTCACTTACGTTATTGTTTTAT
1 TAAGTTTTGGTCACTTACGTTATCGTTTTAT
484793 TAAGTTTTGGTCACTT
1 TAAGTTTTGGTCACTT
484809 GGACATTGAA
Statistics
Matches: 43, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
31 43 1.00
ACGTcount: A:0.21, C:0.10, G:0.15, T:0.54
Consensus pattern (31 bp):
TAAGTTTTGGTCACTTACGTTATCGTTTTAT
Found at i:485293 original size:17 final size:17
Alignment explanation
Indices: 485268--485307 Score: 53
Period size: 17 Copynumber: 2.4 Consensus size: 17
485258 GTATGTTGTT
*
485268 CATTAAAGCATGCATTG
1 CATTTAAGCATGCATTG
* *
485285 CATTTAAGCATGTATTT
1 CATTTAAGCATGCATTG
485302 CATTTA
1 CATTTA
485308 GGGAAGTAGT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.33, C:0.15, G:0.12, T:0.40
Consensus pattern (17 bp):
CATTTAAGCATGCATTG
Found at i:485334 original size:17 final size:17
Alignment explanation
Indices: 485314--485373 Score: 50
Period size: 17 Copynumber: 3.5 Consensus size: 17
485304 TTTAGGGAAG
485314 TAGTTCATTTATGCATC
1 TAGTTCATTTATGCATC
** *
485331 TAGTT-ATTTAATAAAAC
1 TAGTTCATTT-ATGCATC
* * *
485348 TACTTCATTCATGCATT
1 TAGTTCATTTATGCATC
485365 TAGTTCATT
1 TAGTTCATT
485374 GAATAAAGTT
Statistics
Matches: 31, Mismatches: 10, Indels: 4
0.69 0.22 0.09
Matches are distributed among these distances:
16 4 0.13
17 24 0.77
18 3 0.10
ACGTcount: A:0.30, C:0.15, G:0.08, T:0.47
Consensus pattern (17 bp):
TAGTTCATTTATGCATC
Found at i:485387 original size:18 final size:18
Alignment explanation
Indices: 485364--485409 Score: 74
Period size: 18 Copynumber: 2.6 Consensus size: 18
485354 ATTCATGCAT
485364 TTAGTTCATTGAATAAAG
1 TTAGTTCATTGAATAAAG
*
485382 TTAGTTCATTGAATAATG
1 TTAGTTCATTGAATAAAG
*
485400 TTATTTCATT
1 TTAGTTCATT
485410 AATCAAACTA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
18 26 1.00
ACGTcount: A:0.33, C:0.07, G:0.13, T:0.48
Consensus pattern (18 bp):
TTAGTTCATTGAATAAAG
Found at i:488990 original size:17 final size:17
Alignment explanation
Indices: 488970--489028 Score: 50
Period size: 17 Copynumber: 3.5 Consensus size: 17
488960 TTTAGGGAAG
488970 TAGTTCATTTATGCATC
1 TAGTTCATTTATGCATC
* *
488987 TAGTT-ATTTAAT-AAAC
1 TAGTTCATTT-ATGCATC
* * *
489003 TACTTCATTCATGCATT
1 TAGTTCATTTATGCATC
489020 TAGTTCATT
1 TAGTTCATT
489029 GAATAAAGTT
Statistics
Matches: 31, Mismatches: 8, Indels: 6
0.69 0.18 0.13
Matches are distributed among these distances:
16 12 0.39
17 19 0.61
ACGTcount: A:0.29, C:0.15, G:0.08, T:0.47
Consensus pattern (17 bp):
TAGTTCATTTATGCATC
Found at i:489042 original size:18 final size:18
Alignment explanation
Indices: 489019--489064 Score: 74
Period size: 18 Copynumber: 2.6 Consensus size: 18
489009 ATTCATGCAT
489019 TTAGTTCATTGAATAAAG
1 TTAGTTCATTGAATAAAG
*
489037 TTAGTTCATTGAATAATG
1 TTAGTTCATTGAATAAAG
*
489055 TTATTTCATT
1 TTAGTTCATT
489065 AATCAAACTA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
18 26 1.00
ACGTcount: A:0.33, C:0.07, G:0.13, T:0.48
Consensus pattern (18 bp):
TTAGTTCATTGAATAAAG
Found at i:493771 original size:20 final size:20
Alignment explanation
Indices: 493748--493799 Score: 95
Period size: 20 Copynumber: 2.6 Consensus size: 20
493738 AACTTTAATC
493748 AAAGTTTAGAAATTATTATG
1 AAAGTTTAGAAATTATTATG
493768 AAAGTTTAGAAATTATTATG
1 AAAGTTTAGAAATTATTATG
*
493788 AAAGTTTTGAAA
1 AAAGTTTAGAAA
493800 CTTTGAAACA
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.46, C:0.00, G:0.15, T:0.38
Consensus pattern (20 bp):
AAAGTTTAGAAATTATTATG
Found at i:493954 original size:21 final size:19
Alignment explanation
Indices: 493912--493987 Score: 89
Period size: 20 Copynumber: 3.8 Consensus size: 19
493902 TTTCAGGGTG
* *
493912 CAAAATTTTGAAACTCTTA
1 CAAAAGTTTCAAACTCTTA
493931 CAAAAGTTTCAAAACTCTTTA
1 CAAAAGTTTC-AAACTC-TTA
*
493952 CAAAATTTTTCAAACTCTTA
1 CAAAA-GTTTCAAACTCTTA
493972 CAAAAGTTTCCAAACT
1 CAAAAGTTT-CAAACT
493988 ATGAACAATA
Statistics
Matches: 49, Mismatches: 4, Indels: 7
0.82 0.07 0.12
Matches are distributed among these distances:
19 11 0.22
20 20 0.41
21 14 0.29
22 4 0.08
ACGTcount: A:0.42, C:0.20, G:0.04, T:0.34
Consensus pattern (19 bp):
CAAAAGTTTCAAACTCTTA
Found at i:494067 original size:20 final size:20
Alignment explanation
Indices: 494042--494090 Score: 64
Period size: 20 Copynumber: 2.5 Consensus size: 20
494032 AATGTTTTTG
*
494042 ATATTTTAAA-AGTTTTAAAC
1 ATATTTTAAACA-CTTTAAAC
494062 ATATTTTAAACACTTTAAAC
1 ATATTTTAAACACTTTAAAC
*
494082 ATGTTTTAA
1 ATATTTTAA
494091 TTAACTTAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
20 25 0.96
21 1 0.04
ACGTcount: A:0.43, C:0.08, G:0.04, T:0.45
Consensus pattern (20 bp):
ATATTTTAAACACTTTAAAC
Found at i:494202 original size:31 final size:30
Alignment explanation
Indices: 494167--494224 Score: 82
Period size: 31 Copynumber: 1.9 Consensus size: 30
494157 TTTGATTTAT
494167 TTTTA-AAATATTTGATTAAATCCAAAATCAA
1 TTTTACAAATATTTG-TTAAAT-CAAAATCAA
*
494198 TTTTACAAATATTTGTTATATCAAAAT
1 TTTTACAAATATTTGTTAAATCAAAAT
494225 ATAAGTTCAA
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
30 6 0.24
31 10 0.40
32 9 0.36
ACGTcount: A:0.45, C:0.09, G:0.03, T:0.43
Consensus pattern (30 bp):
TTTTACAAATATTTGTTAAATCAAAATCAA
Found at i:498829 original size:31 final size:31
Alignment explanation
Indices: 498794--498856 Score: 101
Period size: 31 Copynumber: 2.0 Consensus size: 31
498784 CTTCTCTATT
498794 GTTAGAGGTTAG-CCAAATTTTAGAGGAATTA
1 GTTAGA-GTTAGTCCAAATTTTAGAGGAATTA
*
498825 GTTAGAGTTTGTCCAAATTTTAGAGGAATTA
1 GTTAGAGTTAGTCCAAATTTTAGAGGAATTA
498856 G
1 G
498857 CTAAAGTATA
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
30 4 0.13
31 26 0.87
ACGTcount: A:0.33, C:0.06, G:0.25, T:0.35
Consensus pattern (31 bp):
GTTAGAGTTAGTCCAAATTTTAGAGGAATTA
Found at i:504444 original size:47 final size:47
Alignment explanation
Indices: 504382--504473 Score: 148
Period size: 47 Copynumber: 2.0 Consensus size: 47
504372 AATCCATAAT
* * *
504382 TAAAATGCATGAAAGGATGCATTAAGGCATGAAAGGATGTCATAAAC
1 TAAAATGCATGAAAGGATGCATTAAGACATGAAAGAATGCCATAAAC
*
504429 TAAAATGCATGAAAGGATGCATTCAGACATGAAAGAATGCCATAA
1 TAAAATGCATGAAAGGATGCATTAAGACATGAAAGAATGCCATAA
504474 TTTAAATGTA
Statistics
Matches: 41, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
47 41 1.00
ACGTcount: A:0.46, C:0.12, G:0.22, T:0.21
Consensus pattern (47 bp):
TAAAATGCATGAAAGGATGCATTAAGACATGAAAGAATGCCATAAAC
Found at i:513106 original size:78 final size:81
Alignment explanation
Indices: 512955--513160 Score: 253
Period size: 79 Copynumber: 2.6 Consensus size: 81
512945 TTAGCCTTTA
* * * *
512955 ATCTAACTTGCAT-ATTGAC-ACTTTTCTGTCAAATGCACAGCTAGTCCATTATTCTTTTACTCA
1 ATCTAACTGGCATAATTGACAAC-TTTCTGCCAAATGCACAGTTAGGCCATTATTCTTTTACTCA
*
513018 ATGGTATTTAACCATT-
65 ATAGTATTTAACCATTC
*
513034 ATCTAAGTGGCATAATTGACAACTTTCT-CCAAATGCA-AGTTAGGCCATT-TATCTTTTACTCA
1 ATCTAACTGGCATAATTGACAACTTTCTGCCAAATGCACAGTTAGGCCATTAT-TCTTTTACTCA
* *
513096 ATAGTCTTTAACCGTTC
65 ATAGTATTTAACCATTC
* * *
513113 ATCTAACTGGCATAATTGACACCTTTCTGTCAAAAGCACAGTTAGGCC
1 ATCTAACTGGCATAATTGACAACTTTCTGCCAAATGCACAGTTAGGCC
513161 TAAAAGGCAC
Statistics
Matches: 109, Mismatches: 12, Indels: 10
0.83 0.09 0.08
Matches are distributed among these distances:
77 1 0.01
78 34 0.31
79 45 0.41
80 18 0.17
81 11 0.10
ACGTcount: A:0.29, C:0.22, G:0.13, T:0.36
Consensus pattern (81 bp):
ATCTAACTGGCATAATTGACAACTTTCTGCCAAATGCACAGTTAGGCCATTATTCTTTTACTCAA
TAGTATTTAACCATTC
Found at i:513462 original size:54 final size:54
Alignment explanation
Indices: 513380--514115 Score: 844
Period size: 54 Copynumber: 13.6 Consensus size: 54
513370 ATTAAGATGA
* * * **
513380 ACACATTGTGCCTATAC-GATAGTTCATCAACTCATGATGAATTTTGTGGGTTGC
1 ACACATCGTGCCTGTACGGTTA-TTCATCAACTCATGATGAATTCCGTGGGTTGC
* *
513434 ACACATCATGCCTGTACGGTTATTCATCAACTCATGATGAATTTCGTGGGTTGC
1 ACACATCGTGCCTGTACGGTTATTCATCAACTCATGATGAATTCCGTGGGTTGC
* * * * * * *
513488 ATACATCGTTCATGTACGGTTATTCATTAACTCATGATGAATTTCATTGGTTGC
1 ACACATCGTGCCTGTACGGTTATTCATCAACTCATGATGAATTCCGTGGGTTGC
* *
513542 ACACATCGTGCCTGCACGGTTATTCATCAACTCATGATGAATTCTGTGGGTTGC
1 ACACATCGTGCCTGTACGGTTATTCATCAACTCATGATGAATTCCGTGGGTTGC
* * * ** *
513596 ACACATCGTGCTTGTACAGTTATTCATCAACTAATGATGAATTTTGTGGGTTAC
1 ACACATCGTGCCTGTACGGTTATTCATCAACTCATGATGAATTCCGTGGGTTGC
* * * *
513650 ACACATCGTGCCTATAAGATTATTCATCAACTCATGACGAATTCCGTGGGTTGC
1 ACACATCGTGCCTGTACGGTTATTCATCAACTCATGATGAATTCCGTGGGTTGC
* * * *
513704 ACACATCATGCCTCTACGGTTATTCATCAACTCATGAAGAATTTCGTGGGTTGC
1 ACACATCGTGCCTGTACGGTTATTCATCAACTCATGATGAATTCCGTGGGTTGC
* *
513758 ACACATCGTGCCTGTACGGTTATTCATCAACTCATGATTAATTCCGTGGGATGC
1 ACACATCGTGCCTGTACGGTTATTCATCAACTCATGATGAATTCCGTGGGTTGC
* * * *
513812 ACACATCGCGCCTGTAAGGTTATTCATCAACTCATGATGAATTCTGTGGGTTTC
1 ACACATCGTGCCTGTACGGTTATTCATCAACTCATGATGAATTCCGTGGGTTGC
* ** * * *
513866 TCACATCGTGTTTGTATGGTTATTCATCAACTCATGATGCATTCCCTGGGTTGC
1 ACACATCGTGCCTGTACGGTTATTCATCAACTCATGATGAATTCCGTGGGTTGC
* * * * * * *
513920 GCACATCATTCATGTACGGTTATTCATCAACTCAAGATGAATTCCATGGATTTGC
1 ACACATCGTGCCTGTACGGTTATTCATCAACTCATGATGAATTCCGTGG-GTTGC
* ** ** *
513975 ACACATAGTGTATGTACGGTTATTCATCAACTCATGATGAATTTTGTGGATTTGC
1 ACACATCGTGCCTGTACGGTTATTCATCAACTCATGATGAATTCCGTGG-GTTGC
* * * * *
514030 ACACATAGTGCATGTATGGTTATTCATCAACTCATGATGAATTCCGTGGATTTGT
1 ACACATCGTGCCTGTACGGTTATTCATCAACTCATGATGAATTCCGTGG-GTTGC
* * * * *
514085 ACACGTAGTGCCTATACAGTTGTTCATCAAC
1 ACACATCGTGCCTGTACGGTTATTCATCAAC
514116 GTAGGATAAA
Statistics
Matches: 586, Mismatches: 94, Indels: 3
0.86 0.14 0.00
Matches are distributed among these distances:
54 458 0.78
55 128 0.22
ACGTcount: A:0.26, C:0.21, G:0.19, T:0.34
Consensus pattern (54 bp):
ACACATCGTGCCTGTACGGTTATTCATCAACTCATGATGAATTCCGTGGGTTGC
Found at i:514128 original size:55 final size:55
Alignment explanation
Indices: 513380--514207 Score: 381
Period size: 54 Copynumber: 15.3 Consensus size: 55
513370 ATTAAGATGA
* * * ** *
513380 ACACATTGTGCCTATAC-GATAGTTCATCAAC-TCATGATGAATTTTGTGG-GTTGC
1 ACACATAGTGCCTATACGGTTA-TTCATCAACGT-AGGATGAATTCCGTGGATTTGC
* * * *
513434 ACACATCA-TGCCTGTACGGTTATTCATCAAC-TCATGATGAATTTCGTGG-GTTGC
1 ACACAT-AGTGCCTATACGGTTATTCATCAACGT-AGGATGAATTCCGTGGATTTGC
* * * * * * * **
513488 ATACATCGTTCATGTACGGTTATTCATTAAC-TCATGATGAATTTCATTGG--TTGC
1 ACACATAGTGCCTATACGGTTATTCATCAACGT-AGGATGAA-TTCCGTGGATTTGC
* ** * * *
513542 ACACATCGTGCCTGCACGGTTATTCATCAAC-TCATGATGAATTCTGTGG-GTTGC
1 ACACATAGTGCCTATACGGTTATTCATCAACGT-AGGATGAATTCCGTGGATTTGC
* * * * * ** * *
513596 ACACATCGTGCTTGTACAGTTATTCATCAAC-TAATGATGAATTTTGTGG-GTTAC
1 ACACATAGTGCCTATACGGTTATTCATCAACGT-AGGATGAATTCCGTGGATTTGC
* * * * * *
513650 ACACATCGTGCCTATAAGATTATTCATCAAC-TCATGACGAATTCCGTGG-GTTGC
1 ACACATAGTGCCTATACGGTTATTCATCAACGT-AGGATGAATTCCGTGGATTTGC
* * * * *
513704 ACACATCA-TGCCTCTACGGTTATTCATCAAC-TCATGAAGAATTTCGTGG-GTTGC
1 ACACAT-AGTGCCTATACGGTTATTCATCAACGT-AGGATGAATTCCGTGGATTTGC
* * * *
513758 ACACATCGTGCCTGTACGGTTATTCATCAAC-TCATGATTAATTCCGTGGGA--TGC
1 ACACATAGTGCCTATACGGTTATTCATCAACGT-AGGATGAATTCCGT-GGATTTGC
* * * * * * *
513812 ACACATCGCGCCTGTAAGGTTATTCATCAAC-TCATGATGAATTCTGTGGGTTT-C
1 ACACATAGTGCCTATACGGTTATTCATCAACGT-AGGATGAATTCCGTGGATTTGC
* * ** * * * * * *
513866 TCACATCGTGTTTGTATGGTTATTCATCAAC-TCATGATGCATTCCCTGG-GTTGC
1 ACACATAGTGCCTATACGGTTATTCATCAACGT-AGGATGAATTCCGTGGATTTGC
* * * * * *
513920 GCACATCA-TTCATGTACGGTTATTCATCAAC-TCAAGATGAATTCCATGGATTTGC
1 ACACAT-AGTGCCTATACGGTTATTCATCAACGT-AGGATGAATTCCGTGGATTTGC
** * * **
513975 ACACATAGTGTATGTACGGTTATTCATCAAC-TCATGATGAATTTTGTGGATTTGC
1 ACACATAGTGCCTATACGGTTATTCATCAACGT-AGGATGAATTCCGTGGATTTGC
* * * * *
514030 ACACATAGTGCATGTATGGTTATTCATCAAC-TCATGATGAATTCCGTGGATTTGT
1 ACACATAGTGCCTATACGGTTATTCATCAACGT-AGGATGAATTCCGTGGATTTGC
* * * * * **
514085 ACACGTAGTGCCTATACAGTTGTTCATCAACGTAGGATAAATTCTGT-GAAATGC
1 ACACATAGTGCCTATACGGTTATTCATCAACGTAGGATGAATTCCGTGGATTTGC
* * * **
514139 ACACTTAGTG-CTGAAACGGTTATTCATCCACGTAGGATGAATTCCGT-GAAATGC
1 ACACATAGTGCCT-ATACGGTTATTCATCAACGTAGGATGAATTCCGTGGATTTGC
514193 ACA-ATTAGTGCCTAT
1 ACACA-TAGTGCCTAT
514208 TTGGTAATCA
Statistics
Matches: 652, Mismatches: 103, Indels: 38
0.82 0.13 0.05
Matches are distributed among these distances:
53 12 0.02
54 490 0.75
55 149 0.23
56 1 0.00
ACGTcount: A:0.26, C:0.20, G:0.20, T:0.34
Consensus pattern (55 bp):
ACACATAGTGCCTATACGGTTATTCATCAACGTAGGATGAATTCCGTGGATTTGC
Found at i:514688 original size:21 final size:19
Alignment explanation
Indices: 514646--514715 Score: 59
Period size: 21 Copynumber: 3.5 Consensus size: 19
514636 CCCTTTCCAT
* *
514646 GGTATCGATACTACTCATC
1 GGTATCGATACTATTAATC
514665 GGTATCGATACTGATTGAATC
1 GGTATCGATACT-ATT-AATC
* *
514686 GGTATCAATATTTATTCAATC
1 GGTATCGATA-CTATT-AATC
*
514707 AGTATCGAT
1 GGTATCGAT
514716 GCTACTAAGC
Statistics
Matches: 41, Mismatches: 7, Indels: 4
0.79 0.13 0.08
Matches are distributed among these distances:
19 12 0.29
20 2 0.05
21 26 0.63
22 1 0.02
ACGTcount: A:0.30, C:0.17, G:0.17, T:0.36
Consensus pattern (19 bp):
GGTATCGATACTATTAATC
Found at i:517695 original size:81 final size:80
Alignment explanation
Indices: 517604--517845 Score: 270
Period size: 81 Copynumber: 3.0 Consensus size: 80
517594 TATAATTCCT
* * * * ** * * *
517604 TTATTCTTTTACCCAAAGGTATTTAACTTTTAATCTAACTTTCATATTTGACACTTTTATGTCAA
1 TTATTATTTTACTCAACGGTATTTAACATTT-ATCTAACTGGCATAATTGACACATTTCTGTCAA
*
517669 ATGCACAGCTAGTCCA
65 ATGCACAGCTAGGCCA
* *
517685 TTATTATTTTACTCAACGATATTTAACCATTTATCTAACTGGCATAATTGACACATTTCTGCCAA
1 TTATTATTTTACTCAACGGTATTTAA-CATTTATCTAACTGGCATAATTGACACATTTCTGTCAA
*
517750 ATGCACAGTTAGGCCA
65 ATGCACAGCTAGGCCA
* * * *
517766 TT-TATATTTTACTCAACGGTCTTTAACCGTTCATCTAACTGGCATAATTGACACATTTCTGTTA
1 TTAT-TATTTTACTCAACGGTATTTAA-CATTTATCTAACTGGCATAATTGACACATTTCTGTCA
* *
517830 AATACACAGTTAGGCC
64 AATGCACAGCTAGGCC
517846 TTAAAGGCAC
Statistics
Matches: 139, Mismatches: 20, Indels: 4
0.85 0.12 0.02
Matches are distributed among these distances:
80 1 0.01
81 134 0.96
82 4 0.03
ACGTcount: A:0.30, C:0.21, G:0.11, T:0.38
Consensus pattern (80 bp):
TTATTATTTTACTCAACGGTATTTAACATTTATCTAACTGGCATAATTGACACATTTCTGTCAAA
TGCACAGCTAGGCCA
Found at i:518158 original size:54 final size:54
Alignment explanation
Indices: 518069--518614 Score: 531
Period size: 54 Copynumber: 10.4 Consensus size: 54
518059 TGAAAACGTA
* * * *
518069 GTGCCTATACGG-TAGTTCATCAACTCATAATGAATTCTATGGGTTGTGCACATC
1 GTGCCTGTACGGTTA-TTCATCAACTCATGATGAATTCTGTGGGTTGTACACATC
* * *
518123 GTACCTGTACGGTTATTTATCAACTCATGACGAATTCTGTGGG-T-T-----T-
1 GTGCCTGTACGGTTATTCATCAACTCATGATGAATTCTGTGGGTTGTACACATC
* * * *
518169 GTACCTGTACGGTTATTCATCAACTCATGTTGAATTCTTTGGGTTGCACACATC
1 GTGCCTGTACGGTTATTCATCAACTCATGATGAATTCTGTGGGTTGTACACATC
* * *
518223 GTACCTGTACGGTTATTCATCAGCTCATGATGAATTCTAT-GG--GT----ATC
1 GTGCCTGTACGGTTATTCATCAACTCATGATGAATTCTGTGGGTTGTACACATC
* * *
518270 GTGCTTGTACGGTTATTCATCAACTCATGATGAATTTTGTGGGTTGCACACATC
1 GTGCCTGTACGGTTATTCATCAACTCATGATGAATTCTGTGGGTTGTACACATC
* * * * *
518324 GTGCTTGTATGATTATTCATCAACTCGTGAAGAATT-TCGTGGGTTGTACACATC
1 GTGCCTGTACGGTTATTCATCAACTCATGATGAATTCT-GTGGGTTGTACACATC
* *
518378 GTGCCTGTACGGTTAGTCATCAACTCATGATGAATTCCGTGGGTTGTACACATC
1 GTGCCTGTACGGTTATTCATCAACTCATGATGAATTCTGTGGGTTGTACACATC
* *
518432 GTGCTTGTACGGTTATTCATCAACTCATGATGAATTCTGTGGGTT-TCACACATA
1 GTGCCTGTACGGTTATTCATCAACTCATGATGAATTCTGTGGGTTGT-ACACATC
* * * ** * * *
518486 GTGCCTGTACAGTTATTTATCAA-T-ATGATGAATTCCGTAGATTTGCATACATA
1 GTGCCTGTACGGTTATTCATCAACTCATGATGAATTCTGT-GGGTTGTACACATC
* * * *
518539 GTGCATGTACGGTTATTCATCAACTCATGATAAATTCTGTGGATT-TACACACGTA
1 GTGCCTGTACGGTTATTCATCAACTCATGATGAATTCTGTGGGTTGTACACA--TC
* *
518594 GTGCCTGTACAGATATTCATC
1 GTGCCTGTACGGTTATTCATC
518615 CACATAGGAT
Statistics
Matches: 410, Mismatches: 57, Indels: 49
0.79 0.11 0.09
Matches are distributed among these distances:
46 39 0.10
47 40 0.10
48 2 0.00
50 1 0.00
51 1 0.00
52 14 0.03
53 40 0.10
54 239 0.58
55 34 0.08
ACGTcount: A:0.25, C:0.19, G:0.21, T:0.36
Consensus pattern (54 bp):
GTGCCTGTACGGTTATTCATCAACTCATGATGAATTCTGTGGGTTGTACACATC
Found at i:518191 original size:46 final size:46
Alignment explanation
Indices: 518123--518314 Score: 213
Period size: 46 Copynumber: 4.0 Consensus size: 46
518113 TGTGCACATC
* *
518123 GTACCTGTACGGTTATTTATCAACTCATGACGAATTCTGTGGGTTT
1 GTACCTGTACGGTTATTCATCAACTCATGATGAATTCTGTGGGTTT
* *
518169 GTACCTGTACGGTTATTCATCAACTCATGTTGAATTCTTTGGGTTGCACACAT
1 GTACCTGTACGGTTATTCATCAACTCATGATGAATTCTGTGGGTT-------T
* * *
518222 CGTACCTGTACGGTTATTCATCAGCTCATGATGAATTCTATGGGTATC
1 -GTACCTGTACGGTTATTCATCAACTCATGATGAATTCTGTGGGT-TT
* * *
518270 GTGCTTGTACGGTTATTCATCAACTCATGATGAATTTTGTGGGTT
1 GTACCTGTACGGTTATTCATCAACTCATGATGAATTCTGTGGGTT
518315 GCACACATCG
Statistics
Matches: 124, Mismatches: 13, Indels: 18
0.80 0.08 0.12
Matches are distributed among these distances:
46 42 0.34
47 39 0.31
53 1 0.01
54 41 0.33
55 1 0.01
ACGTcount: A:0.22, C:0.18, G:0.21, T:0.39
Consensus pattern (46 bp):
GTACCTGTACGGTTATTCATCAACTCATGATGAATTCTGTGGGTTT
Found at i:524690 original size:27 final size:28
Alignment explanation
Indices: 524636--524701 Score: 107
Period size: 28 Copynumber: 2.4 Consensus size: 28
524626 TCGGGTCTAG
*
524636 TCGGGTCGGGTTTTTTTAAGTGTGATAT
1 TCGGGTCGGGTTTTTTAAAGTGTGATAT
524664 TCGGGTCGGGTTTTTTAAAGTGT-ATAT
1 TCGGGTCGGGTTTTTTAAAGTGTGATAT
*
524691 TCAGGTCGGGT
1 TCGGGTCGGGT
524702 CGGGTTGGGT
Statistics
Matches: 36, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
27 14 0.39
28 22 0.61
ACGTcount: A:0.15, C:0.09, G:0.33, T:0.42
Consensus pattern (28 bp):
TCGGGTCGGGTTTTTTAAAGTGTGATAT
Found at i:525312 original size:17 final size:18
Alignment explanation
Indices: 525287--525333 Score: 69
Period size: 18 Copynumber: 2.7 Consensus size: 18
525277 TATGGAATTG
*
525287 GATTCCAATTCC-TGACA
1 GATTCCAATTCCTTCACA
*
525304 GATTTCAATTCCTTCACA
1 GATTCCAATTCCTTCACA
525322 GATTCCAATTCC
1 GATTCCAATTCC
525334 CTCAGAAACA
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
17 11 0.42
18 15 0.58
ACGTcount: A:0.28, C:0.30, G:0.09, T:0.34
Consensus pattern (18 bp):
GATTCCAATTCCTTCACA
Found at i:527324 original size:20 final size:19
Alignment explanation
Indices: 527280--527331 Score: 72
Period size: 20 Copynumber: 2.7 Consensus size: 19
527270 GGGTTGGGCA
527280 GTCGGGTCGGGT-AGTCAG
1 GTCGGGTCGGGTCAGTCAG
527298 GTCGGGTCGGGTCAGATC-G
1 GTCGGGTCGGGTCAG-TCAG
527317 GATCGGGTCGGGTCA
1 G-TCGGGTCGGGTCA
527332 ATCAACCGGG
Statistics
Matches: 31, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
18 12 0.39
19 4 0.13
20 15 0.48
ACGTcount: A:0.12, C:0.19, G:0.48, T:0.21
Consensus pattern (19 bp):
GTCGGGTCGGGTCAGTCAG
Found at i:541054 original size:38 final size:38
Alignment explanation
Indices: 541003--541078 Score: 125
Period size: 38 Copynumber: 2.0 Consensus size: 38
540993 ATTTGAGAAG
* *
541003 AAATATCCACGCCCTTCTCCCTAAGCAATATGAGCACT
1 AAATAGCCACGCCCTTCTCCCTAAGCAATATGACCACT
*
541041 AAATAGCCACGCCCTTCTCCCTGAGCAATATGACCACT
1 AAATAGCCACGCCCTTCTCCCTAAGCAATATGACCACT
541079 CATTGGTAAC
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
38 35 1.00
ACGTcount: A:0.30, C:0.36, G:0.12, T:0.22
Consensus pattern (38 bp):
AAATAGCCACGCCCTTCTCCCTAAGCAATATGACCACT
Found at i:542828 original size:58 final size:56
Alignment explanation
Indices: 542689--542879 Score: 258
Period size: 57 Copynumber: 3.4 Consensus size: 56
542679 TTTAAGCGAT
* ** *
542689 GATTGAGCACCTCTATGCATCAATCTAGAAACTGGCACCTCTATGCATTAAAGAAAC
1 GATTGAGCACCTCTGTGCATCAATCTTTAAA-TGGCACCTCTGTGCATTAAAGAAAC
*
542746 GATTGAGAACCTCTGTGCATCAATCTTTAAAGTGGCACCTCTGTGCATTAAAGAAAAC
1 GATTGAGCACCTCTGTGCATCAATCTTTAAA-TGGCACCTCTGTGCATTAAAG-AAAC
* * * *
542804 GATTGAGCACCTCTTTGCATCAATCTTTAACA-GACACATATGTGCATTAAAGAAAC
1 GATTGAGCACCTCTGTGCATCAATCTTTAA-ATGGCACCTCTGTGCATTAAAGAAAC
542860 GATTGAGCACCTCTGTGCAT
1 GATTGAGCACCTCTGTGCAT
542880 AAAAGAAACG
Statistics
Matches: 120, Mismatches: 12, Indels: 5
0.88 0.09 0.04
Matches are distributed among these distances:
56 23 0.19
57 64 0.53
58 32 0.27
59 1 0.01
ACGTcount: A:0.33, C:0.23, G:0.17, T:0.27
Consensus pattern (56 bp):
GATTGAGCACCTCTGTGCATCAATCTTTAAATGGCACCTCTGTGCATTAAAGAAAC
Found at i:542848 original size:85 final size:84
Alignment explanation
Indices: 542780--542964 Score: 244
Period size: 85 Copynumber: 2.2 Consensus size: 84
542770 CTTTAAAGTG
* **
542780 GCACCTCTGTGCATTAAAGAAAACGATTGAGCACCTCTTTGCATCAATCTTTAACAGACACATAT
1 GCACCTCTGTGCATAAAAG-AAACGATTGAGCACCTCTGCGCATCAATCTTTAACAGACACATAT
*
542845 GTGCATTAAAGAAACGATTGA
65 GTGCATCAAAGAAACGA-TGA
* * *
542866 GCACCTCTGTGCATAAAAGAAACGATTGAGCACCTCTGCGCATCAATCTTTAAACTGACACCTCT
1 GCACCTCTGTGCATAAAAGAAACGATTGAGCACCTCTGCGCATCAATCTTT-AACAGACACATAT
* * * *
542931 TTTCATAAAAGAAACAATGA
65 GTGCATCAAAGAAACGATGA
542951 GCACCTCTGTGCAT
1 GCACCTCTGTGCAT
542965 CAATCTTTAA
Statistics
Matches: 88, Mismatches: 10, Indels: 3
0.87 0.10 0.03
Matches are distributed among these distances:
85 47 0.53
86 41 0.47
ACGTcount: A:0.35, C:0.24, G:0.16, T:0.26
Consensus pattern (84 bp):
GCACCTCTGTGCATAAAAGAAACGATTGAGCACCTCTGCGCATCAATCTTTAACAGACACATATG
TGCATCAAAGAAACGATGA
Found at i:542998 original size:110 final size:110
Alignment explanation
Indices: 542868--543120 Score: 373
Period size: 110 Copynumber: 2.3 Consensus size: 110
542858 ACGATTGAGC
*
542868 ACCTCTGTGCATAAAAGAAACGATTGAGCACCTCTGCGCATCAATCTTTAAACTGACACCTCTTT
1 ACCTCTGTGCATAAAAGAAACGATTGAGCACCTCTGCGCATCAATCTTTAAACTGACACCTCTGT
*
542933 TCATAAAAGAAACAATGAGCACCTCTGTGCATCAATCTTTAAACTG
66 ACATAAAAG-AACAATGAGCACCTCTGTGCATCAATCTTTAAACTG
* * * *
542979 -CCTCTGTGCATTAAAGAAACGATTGAGCACCTCTGTGCATCAATCTTTAAATTGGCACCTCTGT
1 ACCTCTGTGCATAAAAGAAACGATTGAGCACCTCTGCGCATCAATCTTTAAACTGACACCTCTGT
* * *
543043 ACATTAAAGAAGATTGAGCACCTCTGTGCATCAATCTTTAAACTG
66 ACATAAAAGAACAATGAGCACCTCTGTGCATCAATCTTTAAACTG
* *
543088 ACACCTCTGTACATAAAAGAAACGATTAAGCAC
1 --ACCTCTGTGCATAAAAGAAACGATTGAGCAC
543121 ATTTGTGCAT
Statistics
Matches: 127, Mismatches: 12, Indels: 5
0.88 0.08 0.03
Matches are distributed among these distances:
109 34 0.27
110 66 0.52
112 27 0.21
ACGTcount: A:0.34, C:0.24, G:0.15, T:0.27
Consensus pattern (110 bp):
ACCTCTGTGCATAAAAGAAACGATTGAGCACCTCTGCGCATCAATCTTTAAACTGACACCTCTGT
ACATAAAAGAACAATGAGCACCTCTGTGCATCAATCTTTAAACTG
Found at i:543081 original size:55 final size:57
Alignment explanation
Indices: 542866--543131 Score: 364
Period size: 57 Copynumber: 4.8 Consensus size: 57
542856 AAACGATTGA
* *
542866 GCACCTCTGTGCATAAAAGAAACGATTGAGCACCTCTGCGCATCAATCTTTAAACTG
1 GCACCTCTGTACATAAAAGAAACGATTGAGCACCTCTGTGCATCAATCTTTAAACTG
* * * *
542923 ACACCTCTTTTCATAAAAGAAAC-AATGAGCACCTCTGTGCATCAATCTTTAAACT-
1 GCACCTCTGTACATAAAAGAAACGATTGAGCACCTCTGTGCATCAATCTTTAAACTG
* * *
542978 G--CCTCTGTGCATTAAAGAAACGATTGAGCACCTCTGTGCATCAATCTTTAAATTG
1 GCACCTCTGTACATAAAAGAAACGATTGAGCACCTCTGTGCATCAATCTTTAAACTG
*
543033 GCACCTCTGTACATTAAAG-AA-GATTGAGCACCTCTGTGCATCAATCTTTAAACTG
1 GCACCTCTGTACATAAAAGAAACGATTGAGCACCTCTGTGCATCAATCTTTAAACTG
* * * *
543088 ACACCTCTGTACATAAAAGAAACGATTAAGCACATTTGTGCATC
1 GCACCTCTGTACATAAAAGAAACGATTGAGCACCTCTGTGCATC
543132 TACTTCACCC
Statistics
Matches: 185, Mismatches: 18, Indels: 12
0.86 0.08 0.06
Matches are distributed among these distances:
53 17 0.09
54 30 0.16
55 51 0.28
56 34 0.18
57 53 0.29
ACGTcount: A:0.33, C:0.24, G:0.15, T:0.28
Consensus pattern (57 bp):
GCACCTCTGTACATAAAAGAAACGATTGAGCACCTCTGTGCATCAATCTTTAAACTG
Found at i:559157 original size:60 final size:60
Alignment explanation
Indices: 559088--559255 Score: 187
Period size: 60 Copynumber: 2.8 Consensus size: 60
559078 TTATAATCCT
* * *
559088 CAAACTATGACCCTTATTTTAAATTGGTCCTCAAACTTTTGAACATTCTAATTTCAT-CC
1 CAAACTATGACCCTTATTTTAAATTAGTCCCCAAACTTTTGAACATTCTAAATTCATACC
* * * * *
559147 CTAAACTATGACCCTCAATTTAAATTTGCCCCCTAAACTTTTAAACATTCTAAATTCATACC
1 C-AAACTATGACCCTTATTTTAAATTAGTCCCC-AAACTTTTGAACATTCTAAATTCATACC
* * * * *
559209 CAAACAATGATCC-TCTCTTAAATTAGTCCCCAAACTTTTGAAAATTC
1 CAAACTATGACCCTTATTTTAAATTAGTCCCCAAACTTTTGAACATTC
559256 CAATAACATC
Statistics
Matches: 89, Mismatches: 17, Indels: 6
0.79 0.15 0.05
Matches are distributed among these distances:
59 15 0.17
60 38 0.43
61 33 0.37
62 3 0.03
ACGTcount: A:0.34, C:0.26, G:0.05, T:0.35
Consensus pattern (60 bp):
CAAACTATGACCCTTATTTTAAATTAGTCCCCAAACTTTTGAACATTCTAAATTCATACC
Found at i:566688 original size:28 final size:29
Alignment explanation
Indices: 566638--566693 Score: 80
Period size: 28 Copynumber: 2.0 Consensus size: 29
566628 ATAATTTTTT
566638 ATTTTATTATATTTAATTATTTG-ATTAA
1 ATTTTATTATATTTAATTATTTGTATTAA
*
566666 ATTTTATTGTA-TTAATTATTTTGTATTA
1 ATTTTATTATATTTAATTA-TTTGTATTA
566694 TTTTTTATAG
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
27 7 0.28
28 14 0.56
29 4 0.16
ACGTcount: A:0.32, C:0.00, G:0.05, T:0.62
Consensus pattern (29 bp):
ATTTTATTATATTTAATTATTTGTATTAA
Found at i:567496 original size:143 final size:143
Alignment explanation
Indices: 567234--567503 Score: 441
Period size: 143 Copynumber: 1.9 Consensus size: 143
567224 ATATTTGTTG
567234 AAGTAATGTGTAATGATTTTAACTCGTTAATAGAAAATCCACTTCCTAGTACAATCTCATCAAGT
1 AAGTAATGTGTAATGATTTTAACTCGTTAATAGAAAATCCACTTCCTAGTACAATCTCATCAAGT
* * * *
567299 TCAATGGGGAGATATTCATCAGCAACTTGTTATGATCTCCATCGAGGTGGTTCCACGAACAAGTT
66 TCAATGGGGAGACATTCATCAGCAACTTGTTACGATCTCCACCGAGGTGATTCCACGAACAAGTT
567364 AACAGACCAACTC
131 AACAGACCAACTC
* * * * * *
567377 AAGTAATGTTTAATTATTTTAACTCGTTAATGGGAAATCCACTTCCTGGTACCATCTCATCAAGT
1 AAGTAATGTGTAATGATTTTAACTCGTTAATAGAAAATCCACTTCCTAGTACAATCTCATCAAGT
*
567442 TCAATGGGGAGACATTCATCAGCAACTTGTTACGATCTCTACCGAGGTGATTCCACGAACAA
66 TCAATGGGGAGACATTCATCAGCAACTTGTTACGATCTCCACCGAGGTGATTCCACGAACAA
567504 TCTGCATGGA
Statistics
Matches: 116, Mismatches: 11, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
143 116 1.00
ACGTcount: A:0.32, C:0.21, G:0.17, T:0.30
Consensus pattern (143 bp):
AAGTAATGTGTAATGATTTTAACTCGTTAATAGAAAATCCACTTCCTAGTACAATCTCATCAAGT
TCAATGGGGAGACATTCATCAGCAACTTGTTACGATCTCCACCGAGGTGATTCCACGAACAAGTT
AACAGACCAACTC
Found at i:569289 original size:16 final size:16
Alignment explanation
Indices: 569268--569306 Score: 69
Period size: 16 Copynumber: 2.4 Consensus size: 16
569258 ATTAATGTGT
569268 TACTCAAGTGATGAGC
1 TACTCAAGTGATGAGC
*
569284 TACTCAAGTGATGAGT
1 TACTCAAGTGATGAGC
569300 TACTCAA
1 TACTCAA
569307 TTAAATAAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
16 22 1.00
ACGTcount: A:0.33, C:0.18, G:0.21, T:0.28
Consensus pattern (16 bp):
TACTCAAGTGATGAGC
Found at i:569453 original size:47 final size:47
Alignment explanation
Indices: 569376--569596 Score: 300
Period size: 47 Copynumber: 4.9 Consensus size: 47
569366 TAAAATTCAA
569376 ATAATTAAATAAT-AAAA-A-TAAGAAACAAAATAAATAAAAAGTCC
1 ATAATTAAATAATAAAAACATTAAGAAACAAAATAAATAAAAAGTCC
* * *
569420 ATAATTAAATAATAAAAATATTAAGAAATAAAATAAATAAAAAGTCT
1 ATAATTAAATAATAAAAACATTAAGAAACAAAATAAATAAAAAGTCC
* * *
569467 ATAATTAAATAATAAAAATATTAAGAAACAAAATAAGTAAAAAGTTC
1 ATAATTAAATAATAAAAACATTAAGAAACAAAATAAATAAAAAGTCC
* *
569514 ATAATT--A-AATAAAAACATTAAGAAGCAAAAT-AATAAAAAGTTC
1 ATAATTAAATAATAAAAACATTAAGAAACAAAATAAATAAAAAGTCC
569557 ATAATT--A-AATAAAAACATTAAGAAACAAAATAAATAAAAA
1 ATAATTAAATAATAAAAACATTAAGAAACAAAATAAATAAAAA
569597 TAAGTTTATT
Statistics
Matches: 163, Mismatches: 10, Indels: 8
0.90 0.06 0.04
Matches are distributed among these distances:
43 41 0.25
44 43 0.26
45 5 0.03
46 1 0.01
47 73 0.45
ACGTcount: A:0.67, C:0.05, G:0.05, T:0.24
Consensus pattern (47 bp):
ATAATTAAATAATAAAAACATTAAGAAACAAAATAAATAAAAAGTCC
Found at i:570019 original size:21 final size:21
Alignment explanation
Indices: 569993--570052 Score: 66
Period size: 21 Copynumber: 2.9 Consensus size: 21
569983 ACCCTAGGGT
*
569993 GGTGGCATCTGAAATGGTTAC
1 GGTGGCATCTGAAATGGCTAC
* *
570014 GGTGGCATCAGAAACGGCTAC
1 GGTGGCATCTGAAATGGCTAC
* * *
570035 GATGCCATTTGAAATGGC
1 GGTGGCATCTGAAATGGC
570053 CGTAATGGCA
Statistics
Matches: 31, Mismatches: 8, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
21 31 1.00
ACGTcount: A:0.27, C:0.18, G:0.32, T:0.23
Consensus pattern (21 bp):
GGTGGCATCTGAAATGGCTAC
Found at i:570828 original size:21 final size:22
Alignment explanation
Indices: 570799--570839 Score: 59
Period size: 21 Copynumber: 1.9 Consensus size: 22
570789 TATTTAGTGT
570799 AAAATAAATTCA-TTATATACTC
1 AAAATAAATT-ATTTATATACTC
570821 AAAA-AAATTATTTATATAC
1 AAAATAAATTATTTATATAC
570840 AAACTAATAT
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
20 1 0.06
21 13 0.72
22 4 0.22
ACGTcount: A:0.54, C:0.10, G:0.00, T:0.37
Consensus pattern (22 bp):
AAAATAAATTATTTATATACTC
Found at i:574622 original size:2 final size:2
Alignment explanation
Indices: 574610--574642 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
574600 AGGAGTGTAA
*
574610 AG AG AG GG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
574643 TATCCTACAA
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.52, T:0.00
Consensus pattern (2 bp):
AG
Found at i:581733 original size:30 final size:30
Alignment explanation
Indices: 581697--581756 Score: 120
Period size: 30 Copynumber: 2.0 Consensus size: 30
581687 CTTCCATCTC
581697 TCGGCTCGGGACTGACCAGCTCTAGAAGAG
1 TCGGCTCGGGACTGACCAGCTCTAGAAGAG
581727 TCGGCTCGGGACTGACCAGCTCTAGAAGAG
1 TCGGCTCGGGACTGACCAGCTCTAGAAGAG
581757 ATAATAATAC
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 30 1.00
ACGTcount: A:0.23, C:0.27, G:0.33, T:0.17
Consensus pattern (30 bp):
TCGGCTCGGGACTGACCAGCTCTAGAAGAG
Found at i:584459 original size:3 final size:3
Alignment explanation
Indices: 584446--584484 Score: 69
Period size: 3 Copynumber: 13.0 Consensus size: 3
584436 ACAAAATGTA
*
584446 AAT AGT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
584485 TTAAAACTCG
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 34 1.00
ACGTcount: A:0.64, C:0.00, G:0.03, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:584931 original size:137 final size:137
Alignment explanation
Indices: 584671--585494 Score: 1020
Period size: 137 Copynumber: 6.0 Consensus size: 137
584661 TATTTAAATT
* * * * * * * * * *
584671 TAGAGACAACACGATTCCTACGTGATGAGGAAATCTGGTTATCTAAGGGTAACACTGCTTCTACG
1 TAGAGATAACACGGTTCCTACGCGATGAGGAAGTCTGGCTATCTAAGGATGACGCTACTCCTACG
* **
584736 TGATGAGGAGATATGGTCGGTGGATGACACGGTTCCTATATGATGAGGACGTCTGGCCATCTTTA
66 TGATGAGGAGATCTGGTCGGTGGATGACACGGTTCCTACGTGATGAGGACGTCTGGCCATCTTTA
584801 GGGATAA
131 GGGATAA
* * * * * *
584808 TAAAGATAACATGGTTCCTACACAATGAGGAAGTCTGACTATCTAAGGATGACGCTACTCCTACA
1 TAGAGATAACACGGTTCCTACGCGATGAGGAAGTCTGGCTATCTAAGGATGACGCTACTCCTACG
** * *
584873 TGATGAAAAGATCTGGTCGATGGATGACACAGTTCCTACGTGATGAGGACGTCTGGCCATCTTTA
66 TGATGAGGAGATCTGGTCGGTGGATGACACGGTTCCTACGTGATGAGGACGTCTGGCCATCTTTA
584938 GGGATAA
131 GGGATAA
* * * * * *
584945 TAGAGATAGCATGGTTCTTACGCGATGAGGAAGTCAGGCTATCTAAGGATGATG-TGGCTCCTAC
1 TAGAGATAACACGGTTCCTACGCGATGAGGAAGTCTGGCTATCTAAGGATGACGCT-ACTCCTAC
* * *
585009 GTGATGAGGAGATCTGGTCGGTGGATGACATGGTTCCTACGTGATGAGGATGTCTGACCATCTTT
65 GTGATGAGGAGATCTGGTCGGTGGATGACACGGTTCCTACGTGATGAGGACGTCTGGCCATCTTT
*
585074 AAGGATAA
130 AGGGATAA
* *
585082 TAGAGATAACACGGTTCCTACGCGATGAGGAAGTCTGGCTATCTAATGATGACGCGACTCCTACG
1 TAGAGATAACACGGTTCCTACGCGATGAGGAAGTCTGGCTATCTAAGGATGACGCTACTCCTACG
* * *
585147 TGATGAGGAGATCTGGTCAGTGGATGACACGGTTCCTACATGATGAGGACGTATGGCCATCTTTA
66 TGATGAGGAGATCTGGTCGGTGGATGACACGGTTCCTACGTGATGAGGACGTCTGGCCATCTTTA
*
585212 GTGATAA
131 GGGATAA
* * * * * *
585219 TGGAGATAACACAGTTCCTACGCAATTAGGAAGTCTGGCTATCTAAGGATGACACAACTCCTACG
1 TAGAGATAACACGGTTCCTACGCGATGAGGAAGTCTGGCTATCTAAGGATGACGCTACTCCTACG
* * ** * * * *
585284 TGATGAGGAGATCTGGTTGGTGGATAACATAGTTCCTACGTGATGAGGATGACTAGACATCTTTA
66 TGATGAGGAGATCTGGTCGGTGGATGACACGGTTCCTACGTGATGAGGACGTCTGGCCATCTTTA
585349 GGGATAAA
131 GGGAT-AA
* * * * * * * * *
585357 TGGAGATAATACAGTTCCTATGTGATGAAGAAGTCTGGCTATCTAATGATGATGCTGCTCCTACG
1 TAGAGATAACACGGTTCCTACGCGATGAGGAAGTCTGGCTATCTAAGGATGACGCTACTCCTACG
* * * * *
585422 TGATGAGAAGATCTGGTCGGTGGATAATACGGTTTCTACGTGATGAGGACGTATGGCCATCTTTA
66 TGATGAGGAGATCTGGTCGGTGGATGACACGGTTCCTACGTGATGAGGACGTCTGGCCATCTTTA
585487 GGGATAA
131 GGGATAA
585494 T
1 T
585495 TTGTTTCAAG
Statistics
Matches: 586, Mismatches: 98, Indels: 6
0.85 0.14 0.01
Matches are distributed among these distances:
136 1 0.00
137 470 0.80
138 115 0.20
ACGTcount: A:0.28, C:0.17, G:0.28, T:0.27
Consensus pattern (137 bp):
TAGAGATAACACGGTTCCTACGCGATGAGGAAGTCTGGCTATCTAAGGATGACGCTACTCCTACG
TGATGAGGAGATCTGGTCGGTGGATGACACGGTTCCTACGTGATGAGGACGTCTGGCCATCTTTA
GGGATAA
Found at i:585553 original size:36 final size:36
Alignment explanation
Indices: 585492--585744 Score: 163
Period size: 36 Copynumber: 7.5 Consensus size: 36
585482 CTTTAGGGAT
* *** *
585492 AATTTGTTTCAAGAGAAATTGTCTCAAGCGAGACAA
1 AATTTGTTTCAAGGGAAACAATCTCAAGAGAGACAA
* *
585528 AATTTGTTTCAAGGGAAACAATCTC-----A-ATAT
1 AATTTGTTTCAAGGGAAACAATCTCAAGAGAGACAA
** * *
585558 TTTTATGTTTCAAGAGAAACAGTCTCAAGAGAGACAA
1 AATT-TGTTTCAAGGGAAACAATCTCAAGAGAGACAA
*
585595 AATTTATTTCAAGGGAAACAATCTCAA-AG-G----
1 AATTTGTTTCAAGGGAAACAATCTCAAGAGAGACAA
*
585625 --TTATGTTTCAAGAGGAAACTATCTCAAGAGAGACAA
1 AATT-TGTTTCAAG-GGAAACAATCTCAAGAGAGACAA
585661 AATTTGTTTCAAGGGAAACAATCTCAA-AG-G----
1 AATTTGTTTCAAGGGAAACAATCTCAAGAGAGACAA
* **
585691 --TTATGTTTCAAGAGAAACTGTCTCAAGAGAGACAA
1 AATT-TGTTTCAAGGGAAACAATCTCAAGAGAGACAA
*
585726 AATTTGTTTCAAGAGAAAC
1 AATTTGTTTCAAGGGAAAC
585745 TGTAACACCT
Statistics
Matches: 168, Mismatches: 23, Indels: 52
0.69 0.09 0.21
Matches are distributed among these distances:
28 4 0.02
29 28 0.17
30 19 0.11
31 23 0.14
32 1 0.01
34 2 0.01
35 4 0.02
36 70 0.42
37 15 0.09
38 2 0.01
ACGTcount: A:0.41, C:0.13, G:0.18, T:0.28
Consensus pattern (36 bp):
AATTTGTTTCAAGGGAAACAATCTCAAGAGAGACAA
Found at i:585744 original size:65 final size:65
Alignment explanation
Indices: 585496--585744 Score: 399
Period size: 66 Copynumber: 3.8 Consensus size: 65
585486 AGGGATAATT
* * **
585496 TGTTTCAAGAGAAATTGTCTCAAGCGAGACAAAATTTGTTTCAAGGGAAACAATCTCAATATTTT
1 TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAATTTGTTTCAAGGGAAACAATCTCAA-A-GGT
585561 TA
64 TA
* *
585563 TGTTTCAAGAGAAACAGTCTCAAGAGAGACAAAATTTATTTCAAGGGAAACAATCTCAAAGGTTA
1 TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAATTTGTTTCAAGGGAAACAATCTCAAAGGTTA
*
585628 TGTTTCAAGAGGAAACTATCTCAAGAGAGACAAAATTTGTTTCAAGGGAAACAATCTCAAAGGTT
1 TGTTTCAAGA-GAAACTGTCTCAAGAGAGACAAAATTTGTTTCAAGGGAAACAATCTCAAAGGTT
585693 A
65 A
*
585694 TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAATTTGTTTCAAGAGAAAC
1 TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAATTTGTTTCAAGGGAAAC
585745 TGTAACACCT
Statistics
Matches: 170, Mismatches: 11, Indels: 4
0.92 0.06 0.02
Matches are distributed among these distances:
65 52 0.31
66 63 0.37
67 55 0.32
ACGTcount: A:0.41, C:0.14, G:0.18, T:0.27
Consensus pattern (65 bp):
TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAATTTGTTTCAAGGGAAACAATCTCAAAGGTTA
Found at i:586142 original size:73 final size:73
Alignment explanation
Indices: 586060--586211 Score: 277
Period size: 73 Copynumber: 2.1 Consensus size: 73
586050 AGTAACTTTC
* *
586060 AAAAATACATATAAATTTAATAAAATTCCATTTTGTTTACAAATTTGTTTAACAAAACAAATTAA
1 AAAATTACATATAAATTCAATAAAATTCCATTTTGTTTACAAATTTGTTTAACAAAACAAATTAA
*
586125 ACATTTAT
66 ACATGTAT
586133 AAAATTACATATAAATTCAATAAAATTCCATTTTGTTTACAAATTTGTTTAACAAAACAAATTAA
1 AAAATTACATATAAATTCAATAAAATTCCATTTTGTTTACAAATTTGTTTAACAAAACAAATTAA
586198 ACATGTAT
66 ACATGTAT
586206 AAAATT
1 AAAATT
586212 TCATGCCACT
Statistics
Matches: 76, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
73 76 1.00
ACGTcount: A:0.49, C:0.10, G:0.03, T:0.38
Consensus pattern (73 bp):
AAAATTACATATAAATTCAATAAAATTCCATTTTGTTTACAAATTTGTTTAACAAAACAAATTAA
ACATGTAT
Found at i:586562 original size:47 final size:47
Alignment explanation
Indices: 586494--586664 Score: 228
Period size: 47 Copynumber: 3.8 Consensus size: 47
586484 ATAAAATCTT
* * * *
586494 TTACCATTT--ATCCCATAAGCTCTTAAGTTTATTTTACCAAAATAC
1 TTACCATTTAAATTCCATAAGCTCGTAAGCTTATTTTATCAAAATAC
*
586539 TTACCATTTAAATTCCATAAGCTCGTAAGCTTATTTTATCAACATAC
1 TTACCATTTAAATTCCATAAGCTCGTAAGCTTATTTTATCAAAATAC
*
586586 TTACCATTTAAATTCCATAAGCTCGTAAGCTTATTTTATCAATATAC
1 TTACCATTTAAATTCCATAAGCTCGTAAGCTTATTTTATCAAAATAC
**
586633 TTGTCA-TT--ATT-CATAAGCTCGTAAGCTTATTT
1 TTACCATTTAAATTCCATAAGCTCGTAAGCTTATTT
586665 GCATACTTAC
Statistics
Matches: 116, Mismatches: 8, Indels: 6
0.89 0.06 0.05
Matches are distributed among these distances:
43 21 0.18
44 3 0.03
45 9 0.08
46 2 0.02
47 81 0.70
ACGTcount: A:0.32, C:0.20, G:0.07, T:0.41
Consensus pattern (47 bp):
TTACCATTTAAATTCCATAAGCTCGTAAGCTTATTTTATCAAAATAC
Found at i:586895 original size:61 final size:61
Alignment explanation
Indices: 586779--586895 Score: 171
Period size: 61 Copynumber: 1.9 Consensus size: 61
586769 GCTAAACATG
* * *
586779 CACTAAGCTTACGCCATAGTGCTAATCCGGATATGACACATAAGGTCATGCCCACCACCTA
1 CACTAAGCTTACGCCATAGTGCTAATCCAGACATGACACATAAGGTCATACCCACCACCTA
* * * *
586840 CACTAAGCTTACGCTATAGTGCTAATCCAGACATGATACATTAGGTCATATCCACC
1 CACTAAGCTTACGCCATAGTGCTAATCCAGACATGACACATAAGGTCATACCCACC
586896 TTACCGCACT
Statistics
Matches: 49, Mismatches: 7, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
61 49 1.00
ACGTcount: A:0.32, C:0.29, G:0.15, T:0.24
Consensus pattern (61 bp):
CACTAAGCTTACGCCATAGTGCTAATCCAGACATGACACATAAGGTCATACCCACCACCTA
Found at i:596511 original size:3 final size:3
Alignment explanation
Indices: 596505--596536 Score: 64
Period size: 3 Copynumber: 10.7 Consensus size: 3
596495 GATGATGATG
596505 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
596537 TTAATACCCG
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
ATA
Found at i:597072 original size:235 final size:231
Alignment explanation
Indices: 596630--597169 Score: 647
Period size: 235 Copynumber: 2.3 Consensus size: 231
596620 ACCGACATAG
* * * * * * * *
596630 ACATATAGGAGTGGTTTGAGGGGATATACAACAATAACGATGTTTAAATCACATTCATATTTCCT
1 ACATATAGCACTGGTTTAAGGGGATATATAACAATAATGATGCTTAAATTACATTCATCTTTCCT
** * *
596695 TCCTGACCAATCAAAATTCACCCTAGCAACATCTCAATGGGGGCGGGCATTAACTCAACAAAATC
66 TCCCAACCAATCAAAATTCACCCTAACAACATCTCAAT---GGCGGGAATTAACTCAACAAAATC
* *
596760 CAATACATATAAGACAAGAATTTAAAAGTAATAGTACTTGCAAAAATAAAGCAACAAATCATCAA
128 CAATACATATAAGACAAGAAGTTAAAAGTAATACTACTTGCAAAAATAAAGCAACAAATCATCAA
* * *
596825 CGATAGTAATGAATA-CCAACTTAGACAAAATGAAAAATA
193 CAATAGTAATGAATATCC-ACTTACACAAAAAGAAAAATA
* * * *
596864 ATATATTAGCACTGGTTTAAGGGGATATATAACAATAATAATGCTCAAATTACGTTCATCTTTCC
1 ACATA-TAGCACTGGTTTAAGGGGATATATAACAATAATGATGCTTAAATTACATTCATCTTTCC
* * * *
596929 TTCCCAACCAATCATAATTCACCCTAACAACATCTCAAT-GTGGGAATTAGCTCTACAAAATCCA
65 TTCCCAACCAATCAAAATTCACCCTAACAACATCTCAATGGCGGGAATTAACTCAACAAAATCCA
* *
596993 ATACATGATAAGGCAAG-AGTTAAAATGTAATACTTCTTGCAAAAATAAAGCAACAAATCATCAA
130 ATACAT-ATAAGACAAGAAGTTAAAA-GTAATACTACTTGCAAAAATAAAGCAACAAATCATCAA
*
597057 CAATAGTACTAATGAATATCCACTTACACAAAAAGAAAACTA
193 CAATAG---TAATGAATATCCACTTACACAAAAAGAAAAATA
* * ** * *
597099 ACATATAGTACTAGTTTAA-GGGATATATAACAGGAATGATGCTTTAAATTACATTAATCTTTCA
1 ACATATAGCACTGGTTTAAGGGGATATATAACAATAATGATGC-TTAAATTACATTCATCTTTCC
597163 TTCCCAA
65 TTCCCAA
597170 TTTTCATAAT
Statistics
Matches: 260, Mismatches: 38, Indels: 16
0.83 0.12 0.05
Matches are distributed among these distances:
231 34 0.13
232 50 0.19
233 20 0.08
234 40 0.15
235 114 0.44
236 2 0.01
ACGTcount: A:0.43, C:0.18, G:0.12, T:0.27
Consensus pattern (231 bp):
ACATATAGCACTGGTTTAAGGGGATATATAACAATAATGATGCTTAAATTACATTCATCTTTCCT
TCCCAACCAATCAAAATTCACCCTAACAACATCTCAATGGCGGGAATTAACTCAACAAAATCCAA
TACATATAAGACAAGAAGTTAAAAGTAATACTACTTGCAAAAATAAAGCAACAAATCATCAACAA
TAGTAATGAATATCCACTTACACAAAAAGAAAAATA
Found at i:612992 original size:2 final size:2
Alignment explanation
Indices: 612985--613020 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
612975 CAGAGTGGGG
612985 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
613021 GAATGAGAAA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:624229 original size:2 final size:2
Alignment explanation
Indices: 624224--624301 Score: 156
Period size: 2 Copynumber: 39.0 Consensus size: 2
624214 CCATTGTACC
624224 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
624266 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
624302 CAAATAAATG
Statistics
Matches: 76, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 76 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:630567 original size:36 final size:36
Alignment explanation
Indices: 630509--630606 Score: 92
Period size: 36 Copynumber: 2.7 Consensus size: 36
630499 TCCACAAATT
* * *
630509 TTGAAATTGTTTTTCTT-GAAACAAAATTAATCTCTC
1 TTGAGATTG-TTTTCTTAAAAACAAAATTAATCTCGC
* **
630545 TTGAGATTGTTTTCTTAAAAACAAATTTTGTCTCGC
1 TTGAGATTGTTTTCTTAAAAACAAAATTAATCTCGC
*
630581 TTGAGACAAT-TTTTCTTAAAAACAAA
1 TTGAG--ATTGTTTTCTTAAAAACAAA
630607 TTTCGTCTCA
Statistics
Matches: 52, Mismatches: 7, Indels: 5
0.81 0.11 0.08
Matches are distributed among these distances:
35 7 0.13
36 27 0.52
37 16 0.31
38 2 0.04
ACGTcount: A:0.35, C:0.13, G:0.10, T:0.42
Consensus pattern (36 bp):
TTGAGATTGTTTTCTTAAAAACAAAATTAATCTCGC
Found at i:630604 original size:37 final size:37
Alignment explanation
Indices: 630554--630697 Score: 135
Period size: 37 Copynumber: 4.1 Consensus size: 37
630544 CTTGAGATTG
630554 TTTTCTTAAAAACAAATTTTGTCTCGCTTGAGACAAT
1 TTTTCTTAAAAACAAATTTTGTCTCGCTTGAGACAAT
* *
630591 TTTTCTTAAAAACAAATTTCGTCTCACTTGAGACAAT
1 TTTTCTTAAAAACAAATTTTGTCTCGCTTGAGACAAT
* * * * **
630628 CTTCCTTAAGACACGAA------CAT---TTGAGATTAT
1 TTTTCTTAA-AAACAAATTTTGTC-TCGCTTGAGACAAT
630658 TTTTCTTAAAAACAAATTTTGTCTCGCTTGAGACAAT
1 TTTTCTTAAAAACAAATTTTGTCTCGCTTGAGACAAT
630695 TTT
1 TTT
630698 CCCTCAAAAC
Statistics
Matches: 82, Mismatches: 14, Indels: 22
0.69 0.12 0.19
Matches are distributed among these distances:
29 5 0.06
30 15 0.18
32 1 0.01
33 1 0.01
34 1 0.01
35 1 0.01
37 53 0.65
38 5 0.06
ACGTcount: A:0.33, C:0.17, G:0.10, T:0.40
Consensus pattern (37 bp):
TTTTCTTAAAAACAAATTTTGTCTCGCTTGAGACAAT
Found at i:630717 original size:67 final size:67
Alignment explanation
Indices: 630589--630718 Score: 181
Period size: 67 Copynumber: 1.9 Consensus size: 67
630579 GCTTGAGACA
* * * *
630589 ATTTTTCTTAAAAACAAATTTCGTCTCACTTGAGACAATCTTCCTTAAGACACGAACATTTGAGA
1 ATTTTTCTTAAAAACAAATTTCGTCTCACTTGAGACAATCTTCCTCAAAACACAAAAATTTGAGA
630654 TT
66 TT
* * *
630656 ATTTTTCTTAAAAACAAATTTTGTCTCGCTTGAGACAATTTTCCCTCAAAACA-AAAAATTTGA
1 ATTTTTCTTAAAAACAAATTTCGTCTCACTTGAGACAATCTT-CCTCAAAACACAAAAATTTGA
630719 AAGTTGTTTC
Statistics
Matches: 55, Mismatches: 7, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
67 47 0.85
68 8 0.15
ACGTcount: A:0.36, C:0.18, G:0.09, T:0.36
Consensus pattern (67 bp):
ATTTTTCTTAAAAACAAATTTCGTCTCACTTGAGACAATCTTCCTCAAAACACAAAAATTTGAGA
TT
Found at i:630815 original size:67 final size:66
Alignment explanation
Indices: 630744--631074 Score: 448
Period size: 66 Copynumber: 5.0 Consensus size: 66
630734 AAAAAAATTG
** *
630744 ATAAACCTTTGAGATTGTTTCTCTCGAAACAAATATTTGTCTTTCTTGAGACAGTTTCTCTTTAA
1 ATAAACCTTTGAGATTGTTTCTCTCGAAACAAAT-TTTGTCTCACTTGAGACAGTTTCTCTTGAA
630809 AC
65 AC
* *
630811 ATAAACCTTTGATATTGTTTCTCTCGAAACAAAGTTTTGTCTCACTTAAGACAGTTTCTCTTGAA
1 ATAAACCTTTGAGATTGTTTCTCTCGAAACAAA-TTTTGTCTCACTTGAGACAGTTTCTCTTGAA
*
630876 AA
65 AC
* * * * *
630878 ATAAACCTTTGAGATTATATCTCTTGAAACAAATTTTTTCTCACTTGAGACTGTTTCTCTTGAAA
1 ATAAACCTTTGAGATTGTTTCTCTCGAAACAAATTTTGTCTCACTTGAGACAGTTTCTCTTGAAA
630943 C
66 C
* * ** *
630944 ATAAACCTTTGAGATTGTTTTTCTTGAAACAAATTTCATCTCACTTGAGGCAGTTTCTCTTGAAA
1 ATAAACCTTTGAGATTGTTTCTCTCGAAACAAATTTTGTCTCACTTGAGACAGTTTCTCTTGAAA
631009 C
66 C
* * * *
631010 ATAAACTTTTGAGATTGTTTCCCTC-AACACAAATTTTGTCTCGCTTGAGACAATTTCTCTTGAA
1 ATAAACCTTTGAGATTGTTTCTCTCGAA-ACAAATTTTGTCTCACTTGAGACAGTTTCTCTTGAA
631074 A
65 A
631075 TGAATTATCC
Statistics
Matches: 232, Mismatches: 30, Indels: 5
0.87 0.11 0.02
Matches are distributed among these distances:
65 2 0.01
66 141 0.61
67 88 0.38
68 1 0.00
ACGTcount: A:0.30, C:0.18, G:0.12, T:0.40
Consensus pattern (66 bp):
ATAAACCTTTGAGATTGTTTCTCTCGAAACAAATTTTGTCTCACTTGAGACAGTTTCTCTTGAAA
C
Found at i:630937 original size:36 final size:34
Alignment explanation
Indices: 630897--631010 Score: 94
Period size: 36 Copynumber: 3.4 Consensus size: 34
630887 TGAGATTATA
630897 TCTCTTGAAACAAATTTTTTCTCACTTGAGACTGTT
1 TCTCTTGAAACAAA--TTTTCTCACTTGAGACTGTT
* * *
630933 TCTCTTGAAACATAA---AC-C-TTTGAGATTGTT
1 TCTCTTGAAACA-AATTTTCTCACTTGAGACTGTT
* * *
630963 TTTCTTGAAACAAATTTCATCTCACTTGAGGCAGTT
1 TCTCTTGAAACAAATTT--TCTCACTTGAGACTGTT
630999 TCTCTTGAAACA
1 TCTCTTGAAACA
631011 TAAACTTTTG
Statistics
Matches: 60, Mismatches: 10, Indels: 16
0.70 0.12 0.19
Matches are distributed among these distances:
29 2 0.03
30 21 0.35
31 1 0.02
32 1 0.02
34 1 0.02
35 1 0.02
36 31 0.52
37 2 0.03
ACGTcount: A:0.28, C:0.19, G:0.12, T:0.40
Consensus pattern (34 bp):
TCTCTTGAAACAAATTTTCTCACTTGAGACTGTT
Found at i:631030 original size:30 final size:30
Alignment explanation
Indices: 630922--631030 Score: 85
Period size: 30 Copynumber: 3.4 Consensus size: 30
630912 TTTTTCTCAC
*
630922 TTGAGACTGTTTCTCTTGAAACATAAACCT
1 TTGAGACTGTTTCTCTTGAAACATAAACTT
* * *
630952 TTGAGATTGTTTTTCTTGAAACA-AATTTCATCTCAC
1 TTGAGACTGTTTCTCTTGAAACATAA----A-CT--T
* *
630988 TTGAGGCAGTTTCTCTTGAAACATAAACTT
1 TTGAGACTGTTTCTCTTGAAACATAAACTT
*
631018 TTGAGATTGTTTC
1 TTGAGACTGTTTC
631031 CCTCAACACA
Statistics
Matches: 59, Mismatches: 12, Indels: 16
0.68 0.14 0.18
Matches are distributed among these distances:
29 2 0.03
30 31 0.53
32 2 0.03
33 2 0.03
34 1 0.02
36 19 0.32
37 2 0.03
ACGTcount: A:0.28, C:0.17, G:0.15, T:0.41
Consensus pattern (30 bp):
TTGAGACTGTTTCTCTTGAAACATAAACTT
Found at i:633052 original size:2 final size:2
Alignment explanation
Indices: 633045--633097 Score: 99
Period size: 2 Copynumber: 27.0 Consensus size: 2
633035 GCGTGACATA
633045 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A- AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
633086 AT AT AT AT AT AT
1 AT AT AT AT AT AT
633098 CTTGGTTCTA
Statistics
Matches: 50, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
1 1 0.02
2 49 0.98
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:633207 original size:2 final size:2
Alignment explanation
Indices: 633200--633226 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
633190 TATGTATCAA
633200 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 A
633227 AATCAAATAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:639545 original size:22 final size:21
Alignment explanation
Indices: 639511--639563 Score: 72
Period size: 21 Copynumber: 2.5 Consensus size: 21
639501 ATAATTATTT
*
639511 AAAAA-ATTAAATAAAAATACA
1 AAAAACATTTAATAAAAA-ACA
*
639532 AAAAACATTTAATAAAAAACT
1 AAAAACATTTAATAAAAAACA
639553 AAAAACATTTA
1 AAAAACATTTA
639564 GGTTGAACCG
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
21 18 0.62
22 11 0.38
ACGTcount: A:0.70, C:0.08, G:0.00, T:0.23
Consensus pattern (21 bp):
AAAAACATTTAATAAAAAACA
Found at i:644158 original size:36 final size:36
Alignment explanation
Indices: 644111--644394 Score: 153
Period size: 36 Copynumber: 8.4 Consensus size: 36
644101 AGGGATATTG
*
644111 GTTTCAAGGGAAACCATCTCAAGAGAGACAAAATTT
1 GTTTCAAGAGAAACCATCTCAAGAGAGACAAAATTT
* * * **
644147 GTTTCAAGGGAAACAAACTCAA-AGATG------GGT
1 GTTTCAAGAGAAACCATCTCAAGAGA-GACAAAATTT
** *
644177 GTTTCAAGAGAAACTGTCTCAAGAGAGACAAAATTC
1 GTTTCAAGAGAAACCATCTCAAGAGAGACAAAATTT
* * * **
644213 ATTTCAAGGGAAACAATCTCAA-AGATG------GGT
1 GTTTCAAGAGAAACCATCTCAAGAGA-GACAAAATTT
644243 GTTTCAAGAGAAACTC-TCTCAAGAGAGACAAAATTT
1 GTTTCAAGAGAAAC-CATCTCAAGAGAGACAAAATTT
*** *
644279 GTTTCAAGAGAAAATGTCTCAAGAGAGACAAAATTC
1 GTTTCAAGAGAAACCATCTCAAGAGAGACAAAATTT
* ** * *
644315 GTTTCAAGTGAAATGA-CTC-A-A-AG---ATATGT
1 GTTTCAAGAGAAACCATCTCAAGAGAGACAAAATTT
* *
644344 GTTTCAAGGGAAACCATCTCAAGGGAGACAAAACTTT
1 GTTTCAAGAGAAACCATCTCAAGAGAGACAAAA-TTT
644381 GTTTCAAGAGAAAC
1 GTTTCAAGAGAAAC
644395 AGACTCAAAG
Statistics
Matches: 182, Mismatches: 40, Indels: 51
0.67 0.15 0.19
Matches are distributed among these distances:
29 16 0.09
30 42 0.23
31 7 0.04
32 2 0.01
33 3 0.02
34 1 0.01
35 9 0.05
36 87 0.48
37 15 0.08
ACGTcount: A:0.41, C:0.15, G:0.21, T:0.23
Consensus pattern (36 bp):
GTTTCAAGAGAAACCATCTCAAGAGAGACAAAATTT
Found at i:644287 original size:21 final size:21
Alignment explanation
Indices: 644261--644322 Score: 64
Period size: 21 Copynumber: 3.2 Consensus size: 21
644251 AGAAACTCTC
644261 TCAAGAGAGACAAAATTTGTT
1 TCAAGAGAGACAAAATTTGTT
*
644282 TC-A-AGAG--AAAA--TGTC
1 TCAAGAGAGACAAAATTTGTT
*
644297 TCAAGAGAGACAAAATTCGTT
1 TCAAGAGAGACAAAATTTGTT
644318 TCAAG
1 TCAAG
644323 TGAAATGACT
Statistics
Matches: 32, Mismatches: 3, Indels: 12
0.68 0.06 0.26
Matches are distributed among these distances:
15 5 0.16
16 1 0.03
17 8 0.25
19 8 0.25
20 1 0.03
21 9 0.28
ACGTcount: A:0.44, C:0.13, G:0.19, T:0.24
Consensus pattern (21 bp):
TCAAGAGAGACAAAATTTGTT
Found at i:644288 original size:102 final size:102
Alignment explanation
Indices: 644176--644394 Score: 325
Period size: 102 Copynumber: 2.1 Consensus size: 102
644166 CAAAGATGGG
*
644176 TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAATTCATTTCAAGGGAAACAATCTCAAAGATGG
1 TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAATTCATTTCAAGGGAAACAA-CTCAAAGATAG
644241 GTGTTTCAAGAGAAACTC-TCTCAAGAGAGACAAAA-TT
65 GTGTTTCAAGAGAAAC-CATCTCAAGAGAGACAAAACTT
* * * ** *
644278 TGTTTCAAGAGAAAATGTCTCAAGAGAGACAAAATTCGTTTCAAGTGAAATGACTCAAAGATATG
1 TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAATTCATTTCAAGGGAAACAACTCAAAGATAGG
* *
644343 TGTTTCAAGGGAAACCATCTCAAGGGAGACAAAACTT
66 TGTTTCAAGAGAAACCATCTCAAGAGAGACAAAACTT
644380 TGTTTCAAGAGAAAC
1 TGTTTCAAGAGAAAC
644395 AGACTCAAAG
Statistics
Matches: 105, Mismatches: 10, Indels: 4
0.88 0.08 0.03
Matches are distributed among these distances:
100 1 0.01
101 40 0.38
102 64 0.61
ACGTcount: A:0.41, C:0.15, G:0.20, T:0.24
Consensus pattern (102 bp):
TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAATTCATTTCAAGGGAAACAACTCAAAGATAGG
TGTTTCAAGAGAAACCATCTCAAGAGAGACAAAACTT
Found at i:644300 original size:66 final size:66
Alignment explanation
Indices: 644111--644291 Score: 292
Period size: 66 Copynumber: 2.7 Consensus size: 66
644101 AGGGATATTG
* *
644111 GTTTCAAGGGAAAC-CATCTCAAGAGAGACAAAATTTGTTTCAAGGGAAACAAACTCAAAGATGG
1 GTTTCAAGAGAAACTC-TCTCAAGAGAGACAAAATTTGTTTCAAGGGAAACAATCTCAAAGATGG
644175 GT
65 GT
* **
644177 GTTTCAAGAGAAACTGTCTCAAGAGAGACAAAATTCATTTCAAGGGAAACAATCTCAAAGATGGG
1 GTTTCAAGAGAAACTCTCTCAAGAGAGACAAAATTTGTTTCAAGGGAAACAATCTCAAAGATGGG
644242 T
66 T
*
644243 GTTTCAAGAGAAACTCTCTCAAGAGAGACAAAATTTGTTTCAAGAGAAA
1 GTTTCAAGAGAAACTCTCTCAAGAGAGACAAAATTTGTTTCAAGGGAAA
644292 ATGTCTCAAG
Statistics
Matches: 105, Mismatches: 9, Indels: 2
0.91 0.08 0.02
Matches are distributed among these distances:
66 105 1.00
ACGTcount: A:0.41, C:0.15, G:0.21, T:0.23
Consensus pattern (66 bp):
GTTTCAAGAGAAACTCTCTCAAGAGAGACAAAATTTGTTTCAAGGGAAACAATCTCAAAGATGGG
T
Found at i:645757 original size:23 final size:21
Alignment explanation
Indices: 645714--645761 Score: 69
Period size: 23 Copynumber: 2.2 Consensus size: 21
645704 TTGTTTTTTC
*
645714 TTTTGCTTTTTTTCCCTTTGT
1 TTTTCCTTTTTTTCCCTTTGT
645735 TTTTCCTTTTCTTTGCCCTTTGT
1 TTTTCCTTTT-TTT-CCCTTTGT
645758 TTTT
1 TTTT
645762 TTCTTTGTTT
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
21 9 0.38
22 3 0.12
23 12 0.50
ACGTcount: A:0.00, C:0.21, G:0.08, T:0.71
Consensus pattern (21 bp):
TTTTCCTTTTTTTCCCTTTGT
Found at i:655331 original size:2 final size:2
Alignment explanation
Indices: 655324--655348 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
655314 ATTAACAAAT
655324 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 T
655349 GCGTATTAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:655941 original size:19 final size:18
Alignment explanation
Indices: 655899--655941 Score: 50
Period size: 19 Copynumber: 2.3 Consensus size: 18
655889 AAGGTAAATC
*
655899 TATAAAATAAGGATGAAA
1 TATAAAATAAGGATAAAA
*
655917 TAATAAAATCAGGATCAAAA
1 T-ATAAAATAAGGAT-AAAA
655937 TATAA
1 TATAA
655942 GAACAAATCA
Statistics
Matches: 21, Mismatches: 2, Indels: 3
0.81 0.08 0.12
Matches are distributed among these distances:
18 1 0.05
19 16 0.76
20 4 0.19
ACGTcount: A:0.60, C:0.05, G:0.12, T:0.23
Consensus pattern (18 bp):
TATAAAATAAGGATAAAA
Found at i:658119 original size:18 final size:18
Alignment explanation
Indices: 658098--658140 Score: 86
Period size: 18 Copynumber: 2.4 Consensus size: 18
658088 GAATGTTGTA
658098 CGATCTTCGAGAAAGTCT
1 CGATCTTCGAGAAAGTCT
658116 CGATCTTCGAGAAAGTCT
1 CGATCTTCGAGAAAGTCT
658134 CGATCTT
1 CGATCTT
658141 GTACTCTGAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 25 1.00
ACGTcount: A:0.26, C:0.23, G:0.21, T:0.30
Consensus pattern (18 bp):
CGATCTTCGAGAAAGTCT
Found at i:661606 original size:3 final size:3
Alignment explanation
Indices: 661598--661714 Score: 234
Period size: 3 Copynumber: 39.0 Consensus size: 3
661588 GTGATTTTGT
661598 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
661646 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
661694 ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA
661715 TTTGTAGTCC
Statistics
Matches: 114, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 114 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:661919 original size:23 final size:23
Alignment explanation
Indices: 661893--661938 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 23
661883 GAAAACTATG
*
661893 CAGAGACAAACGTGCCACAAAGA
1 CAGAGACAAACGTACCACAAAGA
* *
661916 CAGAGATAAACGTATCACAAAGA
1 CAGAGACAAACGTACCACAAAGA
661939 GAAAATTATT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.50, C:0.22, G:0.20, T:0.09
Consensus pattern (23 bp):
CAGAGACAAACGTACCACAAAGA
Found at i:663941 original size:64 final size:64
Alignment explanation
Indices: 663781--663941 Score: 175
Period size: 64 Copynumber: 2.5 Consensus size: 64
663771 TTGTTTGAAG
* * ** * *
663781 GTGTATCGATGCACAGGTAGTGCATCGATGCACTCTTTTAAAATAAAAAGATTGAATGCAATTA
1 GTGTATCGATGCACAAGTAGTGCATCGATGCATTCCATTAAAATAAAAACATCGAATGCAATTA
* * * *
663845 GTGCATCGATGCATAAGGCA-TGCATCGATGCATTCCATTAATAAT-AAAACATCGAATGCATTT
1 GTGTATCGATGCACAA-GTAGTGCATCGATGCATTCCATTAA-AATAAAAACATCGAATGCA-AT
663908 TA
63 TA
*
663910 -TGTACCGATGCACAAGTAGTGCATCGATGCAT
1 GTGTATCGATGCACAAGTAGTGCATCGATGCAT
663942 ACCTTCATTA
Statistics
Matches: 79, Mismatches: 14, Indels: 8
0.78 0.14 0.08
Matches are distributed among these distances:
63 2 0.03
64 69 0.87
65 8 0.10
ACGTcount: A:0.34, C:0.17, G:0.20, T:0.29
Consensus pattern (64 bp):
GTGTATCGATGCACAAGTAGTGCATCGATGCATTCCATTAAAATAAAAACATCGAATGCAATTA
Found at i:670813 original size:64 final size:64
Alignment explanation
Indices: 670667--670820 Score: 152
Period size: 64 Copynumber: 2.4 Consensus size: 64
670657 AAAGTGTATT
* * * ** * *
670667 GATGCACAGGTAGTGCATAGATGCACTCTTTTAAAATAAAAAGATCGAATGCAATTAGTGCATC
1 GATGCACAAGTAGTGCATCGATGCATTCCATTAAAATAAAAACATCGAATGCAATTAGTGCACC
* * * *
670731 GATGCATAAGGCA-TGCATCGATGCATTCCATTAATAAT-AAAACATCGAATGCATTTTA-TGTA
1 GATGCACAA-GTAGTGCATCGATGCATTCCATTAA-AATAAAAACATCGAATGCA-ATTAGTGCA
670793 CC
63 CC
*
670795 GATGCACAAGTAGTGCATCTATGCAT
1 GATGCACAAGTAGTGCATCGATGCAT
670821 ACCTTCATTA
Statistics
Matches: 72, Mismatches: 14, Indels: 8
0.77 0.15 0.09
Matches are distributed among these distances:
63 2 0.03
64 62 0.86
65 8 0.11
ACGTcount: A:0.36, C:0.18, G:0.19, T:0.28
Consensus pattern (64 bp):
GATGCACAAGTAGTGCATCGATGCATTCCATTAAAATAAAAACATCGAATGCAATTAGTGCACC
Found at i:680405 original size:36 final size:36
Alignment explanation
Indices: 680353--680460 Score: 126
Period size: 36 Copynumber: 3.0 Consensus size: 36
680343 AACATTCTGC
* *
680353 AGAAGATAGTTATTCTTCTAAATATCTCATGCATCT
1 AGAATATAGTTATTCTTCAAAATATCTCATGCATCT
* * *
680389 ATAATATAGTTATTCTTCAAAATATCTCATGAATTT
1 AGAATATAGTTATTCTTCAAAATATCTCATGCATCT
* ** * *
680425 GGGGTATAGCTATTCTTCGAAATATCTCATGCATCT
1 AGAATATAGTTATTCTTCAAAATATCTCATGCATCT
680461 GAGGCGTTTC
Statistics
Matches: 59, Mismatches: 13, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
36 59 1.00
ACGTcount: A:0.32, C:0.16, G:0.12, T:0.40
Consensus pattern (36 bp):
AGAATATAGTTATTCTTCAAAATATCTCATGCATCT
Found at i:685111 original size:13 final size:13
Alignment explanation
Indices: 685093--685120 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
685083 CAATTTTTCA
685093 ATGCTACTAACAT
1 ATGCTACTAACAT
685106 ATGCTACTAACAT
1 ATGCTACTAACAT
685119 AT
1 AT
685121 TTGTTCATAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.39, C:0.21, G:0.07, T:0.32
Consensus pattern (13 bp):
ATGCTACTAACAT
Found at i:685808 original size:18 final size:18
Alignment explanation
Indices: 685781--685816 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
685771 TTCCAGAATG
*
685781 CAAAATAGGTACCGATAC
1 CAAAAAAGGTACCGATAC
*
685799 CAAAAAAGGTACTGATAC
1 CAAAAAAGGTACCGATAC
685817 TATGTTAAAT
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:0.47, C:0.19, G:0.17, T:0.17
Consensus pattern (18 bp):
CAAAAAAGGTACCGATAC
Found at i:687862 original size:15 final size:16
Alignment explanation
Indices: 687844--687876 Score: 50
Period size: 17 Copynumber: 2.1 Consensus size: 16
687834 GAAGAATAAG
687844 TGAAAAC-ACAATATA
1 TGAAAACAACAATATA
687859 TGAAAACTAACAATATA
1 TGAAAAC-AACAATATA
687876 T
1 T
687877 AAAGGTCCTC
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 7 0.44
17 9 0.56
ACGTcount: A:0.58, C:0.12, G:0.06, T:0.24
Consensus pattern (16 bp):
TGAAAACAACAATATA
Found at i:690033 original size:14 final size:14
Alignment explanation
Indices: 690008--690054 Score: 60
Period size: 14 Copynumber: 3.4 Consensus size: 14
689998 CGTTATAATA
*
690008 ATAATAATATTATT
1 ATAATTATATTATT
*
690022 ATTATTATATTATT
1 ATAATTATATTATT
690036 ATAATTA-ATTATT
1 ATAATTATATTATT
*
690049 ACAATT
1 ATAATT
690055 TTACAAGCCC
Statistics
Matches: 29, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
13 11 0.38
14 18 0.62
ACGTcount: A:0.45, C:0.02, G:0.00, T:0.53
Consensus pattern (14 bp):
ATAATTATATTATT
Found at i:702645 original size:3 final size:3
Alignment explanation
Indices: 702637--702674 Score: 51
Period size: 3 Copynumber: 12.7 Consensus size: 3
702627 TCGTTATAAA
*
702637 TAT TAT TAT TAT TAT TAT TA- TAT TAT AAT TAAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T-AT TAT TA
702675 CAATTTTATA
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
2 2 0.06
3 26 0.84
4 3 0.10
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (3 bp):
TAT
Found at i:702745 original size:25 final size:25
Alignment explanation
Indices: 702698--702746 Score: 64
Period size: 25 Copynumber: 2.0 Consensus size: 25
702688 CTAAATGCAT
* *
702698 ATTAAACCCGAAGGCTCATTTACAC
1 ATTAAACCCGAAGCCTCAATTACAC
702723 ATTAAACCCGAATGCCT-AATTACA
1 ATTAAACCCGAA-GCCTCAATTACA
702747 GCTAAATCCC
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
25 18 0.86
26 3 0.14
ACGTcount: A:0.39, C:0.27, G:0.10, T:0.24
Consensus pattern (25 bp):
ATTAAACCCGAAGCCTCAATTACAC
Found at i:707740 original size:26 final size:26
Alignment explanation
Indices: 707710--707767 Score: 80
Period size: 26 Copynumber: 2.2 Consensus size: 26
707700 GTTTTGTTTT
707710 GTTTTGTTTTAATTTAGCCATTGTTA
1 GTTTTGTTTTAATTTAGCCATTGTTA
* * *
707736 GTTTTTTTTTTATTTAGCTATTGTTA
1 GTTTTGTTTTAATTTAGCCATTGTTA
*
707762 TTTTTG
1 GTTTTG
707768 CATTTTGATA
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
26 27 1.00
ACGTcount: A:0.16, C:0.05, G:0.14, T:0.66
Consensus pattern (26 bp):
GTTTTGTTTTAATTTAGCCATTGTTA
Found at i:707907 original size:25 final size:25
Alignment explanation
Indices: 707878--707933 Score: 67
Period size: 25 Copynumber: 2.2 Consensus size: 25
707868 ATTTTATATT
* *
707878 TATTTTTACTTTTTGTTGTTTTTAC
1 TATTTTTACTATTTGTTGTTTTAAC
** *
707903 TATTTTTGGTATTTGTTGTTTTAAT
1 TATTTTTACTATTTGTTGTTTTAAC
707928 TATTTT
1 TATTTT
707934 AATTAAGTTT
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
25 26 1.00
ACGTcount: A:0.14, C:0.04, G:0.11, T:0.71
Consensus pattern (25 bp):
TATTTTTACTATTTGTTGTTTTAAC
Found at i:709880 original size:29 final size:31
Alignment explanation
Indices: 709843--709900 Score: 93
Period size: 31 Copynumber: 1.9 Consensus size: 31
709833 TGACTAATCA
709843 TTTCAACTAAC-TTGA-TTCTTTTTGTCTTG
1 TTTCAACTAACATTGACTTCTTTTTGTCTTG
*
709872 TTTCTACTAACATTGACTTCTTTTTGTCT
1 TTTCAACTAACATTGACTTCTTTTTGTCT
709901 ATTTTTGTTG
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
29 10 0.38
30 4 0.15
31 12 0.46
ACGTcount: A:0.17, C:0.19, G:0.09, T:0.55
Consensus pattern (31 bp):
TTTCAACTAACATTGACTTCTTTTTGTCTTG
Found at i:713083 original size:20 final size:20
Alignment explanation
Indices: 713041--713096 Score: 69
Period size: 20 Copynumber: 2.9 Consensus size: 20
713031 TATTTTTAGG
* *
713041 AATAGTATTG-TACTATATG
1 AATAGTATTGATACTGTATA
713060 AATAGTATTGATACTGTATA
1 AATAGTATTGATACTGTATA
**
713080 AATAGTACCGATACTGT
1 AATAGTATTGATACTGT
713097 GTGAACAATA
Statistics
Matches: 32, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
19 10 0.31
20 22 0.69
ACGTcount: A:0.38, C:0.09, G:0.16, T:0.38
Consensus pattern (20 bp):
AATAGTATTGATACTGTATA
Found at i:713165 original size:22 final size:22
Alignment explanation
Indices: 713140--713190 Score: 68
Period size: 21 Copynumber: 2.4 Consensus size: 22
713130 AAATTCAAAA
713140 TGCTACAGGGGTATCGATACCC
1 TGCTACAGGGGTATCGATACCC
* *
713162 TGCTACA-GTGTGTCGATACCC
1 TGCTACAGGGGTATCGATACCC
*
713183 TACTACAG
1 TGCTACAG
713191 TAATTTCAGA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
21 18 0.72
22 7 0.28
ACGTcount: A:0.24, C:0.27, G:0.24, T:0.25
Consensus pattern (22 bp):
TGCTACAGGGGTATCGATACCC
Found at i:713742 original size:31 final size:31
Alignment explanation
Indices: 713704--713795 Score: 148
Period size: 31 Copynumber: 3.0 Consensus size: 31
713694 CCCGAAGGAC
*
713704 CAGTCCATATGTTCCGAAGAACATAGGTTAT
1 CAGTCCATATGTTCCGAAGAACATAGGTAAT
*
713735 CAGTCCATATGTTCTGAAGAACATAGGTAAT
1 CAGTCCATATGTTCCGAAGAACATAGGTAAT
* *
713766 CAGTCCATATGTCCCGAAGAACATAAGTAA
1 CAGTCCATATGTTCCGAAGAACATAGGTAA
713796 CCCTCGACTC
Statistics
Matches: 56, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
31 56 1.00
ACGTcount: A:0.36, C:0.20, G:0.18, T:0.26
Consensus pattern (31 bp):
CAGTCCATATGTTCCGAAGAACATAGGTAAT
Found at i:715589 original size:75 final size:76
Alignment explanation
Indices: 715387--715617 Score: 290
Period size: 75 Copynumber: 3.1 Consensus size: 76
715377 GTCTCTCTCA
* ** * * * *
715387 AAAACATACTTCGTCTCGCTTGAGACA-ATTTTACTCGAAATAATATATTCCATTTTAC-TCAAG
1 AAAACATACTTTGTCTCGCTTGAGACAGATTTTACTAAAAACAAGATATTTCATTTCACTTC-AG
715450 ATTGTTTTTCTT
65 ATTGTTTTTCTT
* * * * * *
715462 AAAAAAGACTTTGTCTCGCTTGAGATAGATTTTACTTAAAACAAGACATTTCATTTCACTTCATA
1 AAAACATACTTTGTCTCGCTTGAGACAGATTTTACTAAAAACAAGATATTTCATTTCACTTCAGA
715527 TTGTTTTTCTT
66 TTGTTTTTCTT
*
715538 AAAACATACTTTGTCT-GCTTGAGACAGTTTTTACTAAAAACAAGATATTTCATTTCACTAT-AG
1 AAAACATACTTTGTCTCGCTTGAGACAGATTTTACTAAAAACAAGATATTTCATTTCACT-TCAG
715601 ATTGTTTTTCTT
65 ATTGTTTTTCTT
715613 AAAAC
1 AAAAC
715618 TAGATTTGTC
Statistics
Matches: 134, Mismatches: 19, Indels: 6
0.84 0.12 0.04
Matches are distributed among these distances:
75 80 0.60
76 52 0.39
77 2 0.01
ACGTcount: A:0.32, C:0.16, G:0.10, T:0.41
Consensus pattern (76 bp):
AAAACATACTTTGTCTCGCTTGAGACAGATTTTACTAAAAACAAGATATTTCATTTCACTTCAGA
TTGTTTTTCTT
Found at i:715738 original size:39 final size:39
Alignment explanation
Indices: 715690--715809 Score: 152
Period size: 39 Copynumber: 3.1 Consensus size: 39
715680 TGAAAACCAA
* *
715690 ATTTTATCTCACTTGAGTTAGTTTCACTTGAAACAAAAG
1 ATTTTATCTCACTTGAGATAGTTTCACTCGAAACAAAAG
* * * * *
715729 ATTTTATCTCGCTGGAGATGGTTCCACTCGAAACATAAG
1 ATTTTATCTCACTTGAGATAGTTTCACTCGAAACAAAAG
* *
715768 A-TTTATCTCACTTGAGATAGTTTCGCTCGAAACAAAAA
1 ATTTTATCTCACTTGAGATAGTTTCACTCGAAACAAAAG
715806 ATTT
1 ATTT
715810 AAGAAACTAA
Statistics
Matches: 66, Mismatches: 14, Indels: 2
0.80 0.17 0.02
Matches are distributed among these distances:
38 31 0.47
39 35 0.53
ACGTcount: A:0.33, C:0.17, G:0.15, T:0.35
Consensus pattern (39 bp):
ATTTTATCTCACTTGAGATAGTTTCACTCGAAACAAAAG
Found at i:715785 original size:38 final size:38
Alignment explanation
Indices: 715692--715810 Score: 148
Period size: 38 Copynumber: 3.1 Consensus size: 38
715682 AAAACCAAAT
* *
715692 TTTATCTCACTTGAGTTAGTTTCACTTGAAACAAAAGA
1 TTTATCTCACTTGAGATAGTTTCACTCGAAACAAAAGA
* * * * *
715730 TTTTATCTCGCTGGAGATGGTTCCACTCGAAACATAAGA
1 -TTTATCTCACTTGAGATAGTTTCACTCGAAACAAAAGA
* *
715769 TTTATCTCACTTGAGATAGTTTCGCTCGAAACAAAAAA
1 TTTATCTCACTTGAGATAGTTTCACTCGAAACAAAAGA
715807 TTTA
1 TTTA
715811 AGAAACTAAG
Statistics
Matches: 66, Mismatches: 14, Indels: 1
0.81 0.17 0.01
Matches are distributed among these distances:
38 35 0.53
39 31 0.47
ACGTcount: A:0.33, C:0.18, G:0.15, T:0.34
Consensus pattern (38 bp):
TTTATCTCACTTGAGATAGTTTCACTCGAAACAAAAGA
Found at i:716039 original size:35 final size:36
Alignment explanation
Indices: 715971--716046 Score: 118
Period size: 35 Copynumber: 2.1 Consensus size: 36
715961 AGACAGATCA
* *
715971 TGAGATAGTTTTACCAAGAACAAATTTTTTCTCGCT
1 TGAGATAGTTTTACCAACAACAAATTTTGTCTCGCT
*
716007 TGAGATAGTTTT-CTAACAACAAATTTTGTCTCGCT
1 TGAGATAGTTTTACCAACAACAAATTTTGTCTCGCT
716042 TGAGA
1 TGAGA
716047 CAATTTCTAT
Statistics
Matches: 37, Mismatches: 3, Indels: 1
0.90 0.07 0.02
Matches are distributed among these distances:
35 25 0.68
36 12 0.32
ACGTcount: A:0.30, C:0.16, G:0.16, T:0.38
Consensus pattern (36 bp):
TGAGATAGTTTTACCAACAACAAATTTTGTCTCGCT
Found at i:716080 original size:36 final size:38
Alignment explanation
Indices: 716035--716107 Score: 96
Period size: 36 Copynumber: 2.0 Consensus size: 38
716025 ACAAATTTTG
* *
716035 TCTCGCTTGAGACA-ATTTCTATCAAA-ATAAATTTCA
1 TCTCACTTGAGACATATTTCTATAAAACATAAATTTCA
* *
716071 TCTCACTTGAGACATTTTTCTTTAAAACATAAATTTC
1 TCTCACTTGAGACATATTTCTATAAAACATAAATTTC
716108 GAAGTTGTTT
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
36 13 0.42
37 9 0.29
38 9 0.29
ACGTcount: A:0.34, C:0.19, G:0.07, T:0.40
Consensus pattern (38 bp):
TCTCACTTGAGACATATTTCTATAAAACATAAATTTCA
Found at i:716260 original size:68 final size:65
Alignment explanation
Indices: 716149--716593 Score: 211
Period size: 65 Copynumber: 6.6 Consensus size: 65
716139 TCATTCAGTC
* * * * *
716149 TGTTTCTCTTGAAACAAATTTTATCTCCCTTGAGATAGTTTCTCATGAAACACTAATCTTTGAGA
1 TGTTTCCCTTGAAACAAATTTTATCTCCCTTGAGACAGGTTCTCATGAAACA-TAAACTTTGAAA
*
716214 T
65 A
* *
716215 TGTTTCCCTTGAAACAAAAATTTTGTCTCCCTTGAGACAGGTTCTCTTGAAACATAAACTTTGAA
1 TGTTTCCCTTGAAAC--AAATTTTATCTCCCTTGAGACAGGTTCTCATGAAACATAAACTTTGAA
716280 AA
64 AA
* * * * * * *
716282 TGTTTCCCTTGAAACGAATTTTGTTTCTCTTGTGACA-GTTTTCCTTGAAACA-AATTTTATCTC
1 TGTTTCCCTTGAAACAAATTTTATCTCCCTTGAGACAGGTTCT-CATGAAACATAA----A---C
*
716345 TCTTGAGACA
58 T-TTGA-AAA
* ** * * *
716355 -GTTTCCCTTTAAATGAATTCTGTCTCCCTTGAGACA-GTGTCTCTTGAAACATAAACTTTGAAA
1 TGTTTCCCTTGAAACAAATTTTATCTCCCTTGAGACAGGT-TCTCATGAAACATAAACTTTGAAA
716418 A
65 A
** * * * * * * * * * ***
716419 CATATCCCTTGAAACGAATTTTGTCTCTCTTGAGATAGTTTCCCTTGAAATGAATTTTCTCTCTC
1 TGTTTCCCTTGAAACAAATTTTATCTCCCTTGAGACAGGTTCTCATGAAA--CA---T-AAACT-
*
716484 TTGAGACA
59 TTGA-AAA
* * ** * *
716492 -GTTTCCCTTTAAACAAATTTTGTCTCATTTGAGATA-GTT-TCAAGAGAAACATAAACTTTGAA
1 TGTTTCCCTTGAAACAAATTTTATCTCCCTTGAGACAGGTTCTC-A-TGAAACATAAACTTTGAA
716554 AA
64 AA
* * *
716556 CGTTTCCCTTGAAACAAATTTTGTCTCTCTTGAGACAG
1 TGTTTCCCTTGAAACAAATTTTATCTCCCTTGAGACAG
716594 TTTCCCTTTA
Statistics
Matches: 296, Mismatches: 55, Indels: 56
0.73 0.14 0.14
Matches are distributed among these distances:
64 10 0.03
65 105 0.35
66 19 0.06
67 27 0.09
68 34 0.11
69 1 0.00
70 3 0.01
71 6 0.02
72 83 0.28
73 8 0.03
ACGTcount: A:0.29, C:0.19, G:0.13, T:0.38
Consensus pattern (65 bp):
TGTTTCCCTTGAAACAAATTTTATCTCCCTTGAGACAGGTTCTCATGAAACATAAACTTTGAAAA
Found at i:716332 original size:36 final size:36
Alignment explanation
Indices: 716283--716404 Score: 145
Period size: 36 Copynumber: 3.4 Consensus size: 36
716273 CTTTGAAAAT
* *
716283 GTTTCCCTTGAAACGAATTTTGTTTCTCTTGTGACA
1 GTTTCCCTTGAAACGAATTTTGTCTCTCTTGAGACA
* * *
716319 GTTTTCCTTGAAACAAATTTTATCTCTCTTGAGACA
1 GTTTCCCTTGAAACGAATTTTGTCTCTCTTGAGACA
* * * *
716355 GTTTCCCTTTAAATGAATTCTGTCTCCCTTGAGACA
1 GTTTCCCTTGAAACGAATTTTGTCTCTCTTGAGACA
* *
716391 GTGTCTCTTGAAAC
1 GTTTCCCTTGAAAC
716405 ATAAACTTTG
Statistics
Matches: 70, Mismatches: 16, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
36 70 1.00
ACGTcount: A:0.23, C:0.21, G:0.15, T:0.41
Consensus pattern (36 bp):
GTTTCCCTTGAAACGAATTTTGTCTCTCTTGAGACA
Found at i:716408 original size:137 final size:137
Alignment explanation
Indices: 716233--716662 Score: 601
Period size: 137 Copynumber: 3.1 Consensus size: 137
716223 TTGAAACAAA
*
716233 AATTTTGTCTCCCTTGAGACAG-GTTCTCTTGAAACATAAACTTTGAAAATGTTTCCCTTGAAAC
1 AATTTTGTCTCCCTTGAGACAGTG-TCTCTTGAAACATAAACTTTGAAAACGTTTCCCTTGAAAC
* * * *
716297 GAATTTTGTTTCTCTTGTGACAGTTTTCCTTGAAACAAATTTTATCTCTCTTGAGACAGTTTCCC
65 GAATTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACGAATTTTATCTCTCTTGAGACAGTTTCCC
*
716362 TTTAAATG
130 TTTAAACG
* * *
716370 AATTCTGTCTCCCTTGAGACAGTGTCTCTTGAAACATAAACTTTGAAAACATATCCCTTGAAACG
1 AATTTTGTCTCCCTTGAGACAGTGTCTCTTGAAACATAAACTTTGAAAACGTTTCCCTTGAAACG
* * *
716435 AATTTTGTCTCTCTTGAGATAGTTTCCCTTGAAATGAATTTTCTCTCTCTTGAGACAGTTTCCCT
66 AATTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACGAATTTTATCTCTCTTGAGACAGTTTCCCT
*
716500 TTAAACA
131 TTAAACG
** * * **** *
716507 AATTTTGTCTCATTTGAGATAGTTTCAAGAGAAACATAAACTTTGAAAACGTTTCCCTTGAAACA
1 AATTTTGTCTCCCTTGAGACAGTGTCTCTTGAAACATAAACTTTGAAAACGTTTCCCTTGAAACG
* *
716572 AATTTTGTCTCTCTTGAGACAGTTTCCCTTTAAACGAATTTTATCTCTCTTGAGATAGTTTCCCT
66 AATTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACGAATTTTATCTCTCTTGAGACAGTTTCCCT
*
716637 TGAAACG
131 TTAAACG
* *
716644 AATTTCGTCTCTCTTGAGA
1 AATTTTGTCTCCCTTGAGA
716663 TAGTTTCCCT
Statistics
Matches: 257, Mismatches: 35, Indels: 2
0.87 0.12 0.01
Matches are distributed among these distances:
137 256 1.00
138 1 0.00
ACGTcount: A:0.28, C:0.20, G:0.14, T:0.39
Consensus pattern (137 bp):
AATTTTGTCTCCCTTGAGACAGTGTCTCTTGAAACATAAACTTTGAAAACGTTTCCCTTGAAACG
AATTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACGAATTTTATCTCTCTTGAGACAGTTTCCCT
TTAAACG
Found at i:716474 original size:36 final size:36
Alignment explanation
Indices: 716423--716751 Score: 298
Period size: 36 Copynumber: 9.3 Consensus size: 36
716413 TGAAAACATA
716423 TCCCTTGAAACGAATTTTGTCTCTCTTGAGATAGTT
1 TCCCTTGAAACGAATTTTGTCTCTCTTGAGATAGTT
* * *
716459 TCCCTTGAAATGAATTTTCTCTCTCTTGAGACAGTT
1 TCCCTTGAAACGAATTTTGTCTCTCTTGAGATAGTT
* *
716495 TCCCTTTAAACAAATTTTGTCTCAT-TTGAGATAGTT
1 TCCCTTGAAACGAATTTTGTCTC-TCTTGAGATAGTT
**** *** *
716531 TCAAGAGAAAC--A---T-AAACT-TTGA-AAACGTT
1 TCCCTTGAAACGAATTTTGTCTCTCTTGAGATA-GTT
* *
716560 TCCCTTGAAACAAATTTTGTCTCTCTTGAGACAGTT
1 TCCCTTGAAACGAATTTTGTCTCTCTTGAGATAGTT
* *
716596 TCCCTTTAAACGAATTTTATCTCTCTTGAGATAGTT
1 TCCCTTGAAACGAATTTTGTCTCTCTTGAGATAGTT
*
716632 TCCCTTGAAACGAATTTCGTCTCTCTTGAGATAGTT
1 TCCCTTGAAACGAATTTTGTCTCTCTTGAGATAGTT
* * * *
716668 TCCCTAGAAACAAATTTTGTCTCCCTTGAGACAGTT
1 TCCCTTGAAACGAATTTTGTCTCTCTTGAGATAGTT
** ** * * * *
716704 TATCTAAAAACAAAGTTTTGTCACTCTTGAGACAATT
1 TCCCTTGAAACGAA-TTTTGTCTCTCTTGAGATAGTT
716741 TCCCTTGAAAC
1 TCCCTTGAAAC
716752 AAAAGTCTTT
Statistics
Matches: 235, Mismatches: 47, Indels: 21
0.78 0.16 0.07
Matches are distributed among these distances:
28 2 0.01
29 15 0.06
30 1 0.00
31 2 0.01
34 2 0.01
35 2 0.01
36 182 0.77
37 29 0.12
ACGTcount: A:0.28, C:0.20, G:0.13, T:0.38
Consensus pattern (36 bp):
TCCCTTGAAACGAATTTTGTCTCTCTTGAGATAGTT
Found at i:716506 original size:101 final size:101
Alignment explanation
Indices: 716324--716506 Score: 276
Period size: 101 Copynumber: 1.8 Consensus size: 101
716314 TGACAGTTTT
* *
716324 CCTTGAAACAAATTTTATCTCTCTTGAGACAGTTTCCCTTTAAATGAATTCTGTCTCCCTTGAGA
1 CCTTGAAACAAATTTTATCTCTCTTGAGACAGTTTCCCTTGAAATGAATTCTCTCTCCCTTGAGA
*
716389 CAGTGTCTCTTGAAACATAAACTTTGAAAACATATC
66 CAGTGTCCCTTGAAACATAAACTTTGAAAACATATC
* * * * *
716425 CCTTGAAACGAATTTTGTCTCTCTTGAGATAGTTTCCCTTGAAATGAATTTTCTCTCTCTTGAGA
1 CCTTGAAACAAATTTTATCTCTCTTGAGACAGTTTCCCTTGAAATGAATTCTCTCTCCCTTGAGA
* *
716490 CAGTTTCCCTTTAAACA
66 CAGTGTCCCTTGAAACA
716507 AATTTTGTCT
Statistics
Matches: 72, Mismatches: 10, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
101 72 1.00
ACGTcount: A:0.28, C:0.22, G:0.13, T:0.38
Consensus pattern (101 bp):
CCTTGAAACAAATTTTATCTCTCTTGAGACAGTTTCCCTTGAAATGAATTCTCTCTCCCTTGAGA
CAGTGTCCCTTGAAACATAAACTTTGAAAACATATC
Found at i:716794 original size:173 final size:170
Alignment explanation
Indices: 716283--716817 Score: 433
Period size: 173 Copynumber: 3.1 Consensus size: 170
716273 CTTTGAAAAT
* * * * * *
716283 GTTTCCCTTGAAACGAATTTTGTTTCTCTTGTGACAGTTTTCCTTGAAACAAATTTTATCTCTCT
1 GTTTCCCTTGAAACGAATTTCGTCTCTCTTGAGACAGTTTCCCTTGAAACAAATTTTGTCTCACT
* * ** * * * * * *
716348 TGAGACAGTTTCCCTTTAAATGAATTCTGTCTCCCTTGAGACAGTGTCTCTTGAAACATAAA--C
66 TGAGACAGTTT-TC-TAAAACAAATTATGTCACTCTTGAGACAATTTCCCTTGAAACA-AAAGTC
* * *
716411 TTTGAAAACATATCCCTTGAAACGAATTTTGTCTCTCTTGAGATA
128 TTT-AAGACATTTCCCTTGAAACG-ATTTTATCTCTCTTGAGATA
* * *
716456 GTTTCCCTTGAAATGAATTTTC-TCTCTCTTGAGACAGTTTCCCTTTAAACAAATTTTGTCTCAT
1 GTTTCCCTTGAAACGAA-TTTCGTCTCTCTTGAGACAGTTTCCCTTGAAACAAATTTTGTCTCAC
* * * * ** *
716520 TTGAGATAG-TTTC-AAGAGAAA-CAT-AAACT-TTGA-A-AACGTTTCCCTTGAAACAAATTTT
65 TTGAGACAGTTTTCTAAAACAAATTATGTCACTCTTGAGACAA--TTTCCCTTGAAACAAA---A
* *
716578 GTCTCTCTTGAGACAGTTTCCCTTTAAACGAATTTTATCTCTCTTGAGATA
125 G--TCT-TTAAGACA-TTTCCCTTGAAACG-ATTTTATCTCTCTTGAGATA
* * *
716629 GTTTCCCTTGAAACGAATTTCGTCTCTCTTGAGATAGTTTCCCTAGAAACAAATTTTGTCTCCCT
1 GTTTCCCTTGAAACGAATTTCGTCTCTCTTGAGACAGTTTCCCTTGAAACAAATTTTGTCTCACT
*
716694 TGAGACAGTTTATCTAAAAACAAAGTTTTGTCACTCTTGAGACAATTTCCCTTGAAACAAAAGTC
66 TGAGACAGTTT-TCT-AAAACAAA-TTATGTCACTCTTGAGACAATTTCCCTTGAAACAAAAGTC
* * * * *
716759 TTTAAGTCTATTTCCCTTGAAACGTGTTTTCTCTCTTTTGAGACA
128 TTTAAGAC-ATTTCCCTTGAAACG-ATTTTATCTCTCTTGAGATA
**
716804 GTTTTTCTTGAAAC
1 GTTTCCCTTGAAAC
716818 CATCTTACCC
Statistics
Matches: 284, Mismatches: 54, Indels: 46
0.74 0.14 0.12
Matches are distributed among these distances:
164 1 0.00
165 3 0.01
166 16 0.06
167 1 0.00
168 1 0.00
169 4 0.01
171 1 0.00
172 12 0.04
173 154 0.54
174 5 0.02
175 48 0.17
176 4 0.01
177 6 0.02
178 1 0.00
179 1 0.00
180 3 0.01
181 20 0.07
182 1 0.00
183 2 0.01
ACGTcount: A:0.27, C:0.20, G:0.13, T:0.39
Consensus pattern (170 bp):
GTTTCCCTTGAAACGAATTTCGTCTCTCTTGAGACAGTTTCCCTTGAAACAAATTTTGTCTCACT
TGAGACAGTTTTCTAAAACAAATTATGTCACTCTTGAGACAATTTCCCTTGAAACAAAAGTCTTT
AAGACATTTCCCTTGAAACGATTTTATCTCTCTTGAGATA
Found at i:717030 original size:3 final size:3
Alignment explanation
Indices: 717022--717125 Score: 192
Period size: 3 Copynumber: 34.7 Consensus size: 3
717012 GGTCTAACAA
717022 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
717070 TAT TAT TAT TATT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TA-T TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
717116 TAT TA- TAT TA
1 TAT TAT TAT TA
717126 ATATAAATGT
Statistics
Matches: 99, Mismatches: 0, Indels: 4
0.96 0.00 0.04
Matches are distributed among these distances:
2 2 0.02
3 94 0.95
4 3 0.03
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
TAT
Found at i:718722 original size:30 final size:29
Alignment explanation
Indices: 718655--718722 Score: 79
Period size: 30 Copynumber: 2.4 Consensus size: 29
718645 GGTATTAAGG
718655 CTTTAAG--TTATAGGTTAATCCTTTAAA
1 CTTTAAGATTTATAGGTTAATCCTTTAAA
*
718682 CTTTAAGATTTATAGGTTTAGATCC-TTAAG
1 CTTTAAGATTTATAGG-TTA-ATCCTTTAAA
*
718712 CTTTAGGATTT
1 CTTTAAGATTT
718723 TATATTTAGG
Statistics
Matches: 35, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
27 7 0.20
29 7 0.20
30 17 0.49
31 4 0.11
ACGTcount: A:0.29, C:0.10, G:0.15, T:0.46
Consensus pattern (29 bp):
CTTTAAGATTTATAGGTTAATCCTTTAAA
Found at i:720896 original size:21 final size:21
Alignment explanation
Indices: 720859--720898 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
720849 TGCATCTTTG
720859 CATTAGCATATACACATTGTA
1 CATTAGCATATACACATTGTA
*
720880 CATTA-CATGATATACATTG
1 CATTAGCAT-ATACACATTG
720899 CATCCAAACA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 3 0.18
21 14 0.82
ACGTcount: A:0.38, C:0.17, G:0.10, T:0.35
Consensus pattern (21 bp):
CATTAGCATATACACATTGTA
Found at i:722251 original size:33 final size:33
Alignment explanation
Indices: 722187--722251 Score: 80
Period size: 33 Copynumber: 2.0 Consensus size: 33
722177 AAATATATAG
*
722187 AAAAAAAAAAGAGAAAAGAGAGAAATAAAGAAT
1 AAAAAAAAAAGAGAAAAGAGAAAAATAAAGAAT
*
722220 AAAAAACAAAAGA-AACAGA-AAAAATAGAAGAA
1 AAAAAA-AAAAGAGAAAAGAGAAAAATA-AAGAA
722252 AATAGATAAG
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
32 6 0.21
33 16 0.57
34 6 0.21
ACGTcount: A:0.77, C:0.03, G:0.15, T:0.05
Consensus pattern (33 bp):
AAAAAAAAAAGAGAAAAGAGAAAAATAAAGAAT
Found at i:723486 original size:75 final size:76
Alignment explanation
Indices: 723394--723562 Score: 191
Period size: 76 Copynumber: 2.2 Consensus size: 76
723384 CGCCTCTCTC
* * * * * * * *
723394 AAAAACAGACTTCGTCTCTCTTGAAACAG-TTTTACTCGAAATAATATATTTCGTTTTACTCA-A
1 AAAAA-AGACTTTGTCTCGCTTGAAACAGTTTTTACACAAAACAAGATATTTCATTTCACT-ATA
*
723457 GATTGTTTTTCTT
64 GATTATTTTTCTT
*
723470 AAAAAAGACTTTGTCTCGCTTGAGACAGTTTTTACACAAAACAAGATATTTCATTTCACTATAGA
1 AAAAAAGACTTTGTCTCGCTTGAAACAGTTTTTACACAAAACAAGATATTTCATTTCACTATAGA
723535 TTATTTTTCTT
66 TTATTTTTCTT
*
723546 AAAACTAGA-TTTGTCTC
1 AAAA-AAGACTTTGTCTC
723563 ACAGTTTTTT
Statistics
Matches: 79, Mismatches: 11, Indels: 6
0.82 0.11 0.06
Matches are distributed among these distances:
75 21 0.27
76 55 0.70
77 3 0.04
ACGTcount: A:0.33, C:0.17, G:0.11, T:0.40
Consensus pattern (76 bp):
AAAAAAGACTTTGTCTCGCTTGAAACAGTTTTTACACAAAACAAGATATTTCATTTCACTATAGA
TTATTTTTCTT
Found at i:723619 original size:69 final size:69
Alignment explanation
Indices: 723494--723626 Score: 162
Period size: 69 Copynumber: 1.9 Consensus size: 69
723484 CTCGCTTGAG
** * *
723494 ACAGTTTTTACACAAAACAAGATATTTCATTTCACTATAGATTATTTTTCTTAAAACTAGATTTG
1 ACAGTTTTTACACAAAACAAGATATTTCATTTCACTATAGATTATTTACCTGAAAACCAGATTTG
723559 TCTC
66 TCTC
* * * *
723563 ACAGTTTTTTCCCGAAACAAGA-ATATTCATTTCACTCA-AGATTGTTTACCTGAAAACCAGATT
1 ACAGTTTTTACACAAAACAAGATAT-TTCATTTCACT-ATAGATTATTTACCTGAAAACCAGATT
723626 T
64 T
723627 TATCTCGCTT
Statistics
Matches: 54, Mismatches: 8, Indels: 4
0.82 0.12 0.06
Matches are distributed among these distances:
68 2 0.04
69 51 0.94
70 1 0.02
ACGTcount: A:0.35, C:0.18, G:0.09, T:0.38
Consensus pattern (69 bp):
ACAGTTTTTACACAAAACAAGATATTTCATTTCACTATAGATTATTTACCTGAAAACCAGATTTG
TCTC
Found at i:723666 original size:39 final size:39
Alignment explanation
Indices: 723621--723744 Score: 196
Period size: 39 Copynumber: 3.2 Consensus size: 39
723611 CCTGAAAACC
*
723621 AGATTTTATCTCGCTTGAGATAGTTTCACTTGAAACAAA
1 AGATTTTATCTCGCTTGAGATAGTTTCACTCGAAACAAA
* *
723660 AGATTTTATCTCGCTAGAGATGGTTTCACTCGAAACAAA
1 AGATTTTATCTCGCTTGAGATAGTTTCACTCGAAACAAA
* *
723699 AGA-TTTATCTTGCTTGAGATAGTTTCGCTCGAAACAAA
1 AGATTTTATCTCGCTTGAGATAGTTTCACTCGAAACAAA
723737 AGATTTTA
1 AGATTTTA
723745 AGAAACTAAG
Statistics
Matches: 77, Mismatches: 7, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
38 34 0.44
39 43 0.56
ACGTcount: A:0.33, C:0.15, G:0.17, T:0.35
Consensus pattern (39 bp):
AGATTTTATCTCGCTTGAGATAGTTTCACTCGAAACAAA
Found at i:723718 original size:38 final size:38
Alignment explanation
Indices: 723625--723742 Score: 182
Period size: 38 Copynumber: 3.1 Consensus size: 38
723615 AAAACCAGAT
*
723625 TTTATCTCGCTTGAGATAGTTTCACTTGAAACAAAAGA
1 TTTATCTCGCTTGAGATAGTTTCACTCGAAACAAAAGA
* *
723663 TTTTATCTCGCTAGAGATGGTTTCACTCGAAACAAAAGA
1 -TTTATCTCGCTTGAGATAGTTTCACTCGAAACAAAAGA
* *
723702 TTTATCTTGCTTGAGATAGTTTCGCTCGAAACAAAAGA
1 TTTATCTCGCTTGAGATAGTTTCACTCGAAACAAAAGA
723740 TTT
1 TTT
723743 TAAGAAACTA
Statistics
Matches: 72, Mismatches: 7, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
38 37 0.51
39 35 0.49
ACGTcount: A:0.32, C:0.16, G:0.17, T:0.35
Consensus pattern (38 bp):
TTTATCTCGCTTGAGATAGTTTCACTCGAAACAAAAGA
Found at i:724341 original size:65 final size:66
Alignment explanation
Indices: 724167--724349 Score: 242
Period size: 69 Copynumber: 2.7 Consensus size: 66
724157 CTTTCAGTCT
* * * * *
724167 GTTTCTCTTGAAACAAATTTTGTCTCTCTTGAGAAAGTTTCTCATGAAACACTAATCTTTGAGAT
1 GTTTCCCTTGAAACAAATTTTGTCTCTCTTGAGAAAGTTTCTCTTGAAACACTAAACTTTGAAAA
*
724232 T
66 C
* *
724233 GTTTCCCTTGAAACAAAATTTTTTGTCTCTCTTGAGATAGTTTCTCTTGGAACA-TAAACTTTGA
1 GTTTCCCTTGAAAC-AAA--TTTTGTCTCTCTTGAGAAAGTTTCTCTTGAAACACTAAACTTTGA
724297 AAAC
63 AAAC
* *
724301 GTTTCCCTTGAAACAAATTTTGTCTCTCTTGAGACAGTTTCCCTTGAAA
1 GTTTCCCTTGAAACAAATTTTGTCTCTCTTGAGAAAGTTTCTCTTGAAA
724350 ACATTTTGTC
Statistics
Matches: 103, Mismatches: 11, Indels: 7
0.85 0.09 0.06
Matches are distributed among these distances:
65 29 0.28
66 13 0.13
67 6 0.06
68 24 0.23
69 31 0.30
ACGTcount: A:0.28, C:0.19, G:0.14, T:0.40
Consensus pattern (66 bp):
GTTTCCCTTGAAACAAATTTTGTCTCTCTTGAGAAAGTTTCTCTTGAAACACTAAACTTTGAAAA
C
Found at i:724348 original size:36 final size:36
Alignment explanation
Indices: 724301--724386 Score: 138
Period size: 35 Copynumber: 2.4 Consensus size: 36
724291 CTTTGAAAAC
*
724301 GTTTCCCTTGAAACAAATTTTGTCTCTCTTGAGACA
1 GTTTCCCTTGAAACAAATTTTGTCTCCCTTGAGACA
*
724337 GTTTCCCTTGAAA-ACATTTTGTCTCCCTTGAGACA
1 GTTTCCCTTGAAACAAATTTTGTCTCCCTTGAGACA
*
724372 GTTTCTCTTGAAACA
1 GTTTCCCTTGAAACA
724387 TAAACTTTGA
Statistics
Matches: 46, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
35 32 0.70
36 14 0.30
ACGTcount: A:0.24, C:0.23, G:0.14, T:0.38
Consensus pattern (36 bp):
GTTTCCCTTGAAACAAATTTTGTCTCCCTTGAGACA
Found at i:724375 original size:100 final size:101
Alignment explanation
Indices: 724233--724487 Score: 368
Period size: 100 Copynumber: 2.5 Consensus size: 101
724223 CTTTGAGATT
* * *
724233 GTTTCCCTTGAAACAAAATTTTTTGTCTCTCTTGAGATAGTTTCTCTTGGAACATAAACTTTGAA
1 GTTTCCCTTGAAA-AGAA--TTTTGTCTCTCTTGAGACAGTTTCTCTTGAAACATAAACTTTGAA
* *
724298 AACGTTTCCCTTGAAACAAATTTTGTCTCTCTTGAGACA
63 AACGTTTCCCTTGAAACAAATTTTATCTCTCTTCAGACA
* *
724337 GTTTCCCTTGAAAA-CATTTTGTCTCCCTTGAGACAGTTTCTCTTGAAACATAAACTTTGAAAAC
1 GTTTCCCTTGAAAAGAATTTTGTCTCTCTTGAGACAGTTTCTCTTGAAACATAAACTTTGAAAAC
* *
724401 GTTTCCCTTGAAACGAATTTTATCTCTCTTCAGATA
66 GTTTCCCTTGAAACAAATTTTATCTCTCTTCAGACA
* * *
724437 GTTTCCCTTGAAAAGAATTTTGTCTCTCTTAAGACAATTTCCCTTGAAACA
1 GTTTCCCTTGAAAAGAATTTTGTCTCTCTTGAGACAGTTTCTCTTGAAACA
724488 AATTTTGTCT
Statistics
Matches: 137, Mismatches: 13, Indels: 5
0.88 0.08 0.03
Matches are distributed among these distances:
100 91 0.66
101 31 0.23
102 1 0.01
103 1 0.01
104 13 0.09
ACGTcount: A:0.28, C:0.21, G:0.13, T:0.38
Consensus pattern (101 bp):
GTTTCCCTTGAAAAGAATTTTGTCTCTCTTGAGACAGTTTCTCTTGAAACATAAACTTTGAAAAC
GTTTCCCTTGAAACAAATTTTATCTCTCTTCAGACA
Found at i:724519 original size:36 final size:36
Alignment explanation
Indices: 724403--724696 Score: 178
Period size: 36 Copynumber: 8.4 Consensus size: 36
724393 TTGAAAACGT
* * * * *
724403 TTCCCTTGAAACGAATTTTATCTCTCTTCAGATAGT
1 TTCCCTTGAAACAAATTTTGTCTCTCTTAAGACAGA
724439 TTCCCTTGAAA-AGAATTTTGTCTCTCTTAAGACA-A
1 TTCCCTTGAAACA-AATTTTGTCTCTCTTAAGACAGA
* *
724474 TTTCCCTTGAAACAAATTTTGTCTCCCTTGAGACAGA
1 -TTCCCTTGAAACAAATTTTGTCTCTCTTAAGACAGA
* * * * *
724511 TGCTCTTGAAACATAA-----ACT-T-TGAA-A-ATGT
1 TTCCCTTGAAACA-AATTTTGTCTCTCTTAAGACA-GA
** * * **
724540 TTCCCTTGAAATGAATTTTGTCACTCTTGAGACATT
1 TTCCCTTGAAACAAATTTTGTCTCTCTTAAGACAGA
* *
724576 TTCCCTTGAAACAAATTTTGTCTCTCTTGAGACAGT
1 TTCCCTTGAAACAAATTTTGTCTCTCTTAAGACAGA
* ** * * *
724612 TTGCCTTGAAATGAATTTTGCCTCTCTTGAGACAGT
1 TTCCCTTGAAACAAATTTTGTCTCTCTTAAGACAGA
* * * * * *
724648 TTCCCTTGAAACAAAATTTATCTCCCATGAGACAGT
1 TTCCCTTGAAACAAATTTTGTCTCTCTTAAGACAGA
*
724684 TTCTCTTGAAACA
1 TTCCCTTGAAACA
724697 CAAAATCTTT
Statistics
Matches: 203, Mismatches: 40, Indels: 30
0.74 0.15 0.11
Matches are distributed among these distances:
28 3 0.01
29 11 0.05
30 2 0.01
32 2 0.01
33 1 0.00
34 1 0.00
35 2 0.01
36 176 0.87
37 5 0.02
ACGTcount: A:0.28, C:0.21, G:0.13, T:0.37
Consensus pattern (36 bp):
TTCCCTTGAAACAAATTTTGTCTCTCTTAAGACAGA
Found at i:724546 original size:137 final size:136
Alignment explanation
Indices: 724301--724660 Score: 533
Period size: 137 Copynumber: 2.6 Consensus size: 136
724291 CTTTGAAAAC
*
724301 GTTTCCCTTGAAACAAATTTTGTCTCTCTTGAGACAGTTTCCCTTGAAAACATTTTGTCTCCCTT
1 GTTTCCCTTGAAACAAATTTTGTCTCTCTTGAGACAGTTTCCCTTGAAAAAATTTTGTCTCCCTT
*
724366 GAGACAGTTTCTCTTGAAACATAAACTTTGAAAACGTTTCCCTTGAAACGAATTTTATCTCTCTT
66 GAGACAGTTTCTCTTGAAACATAAACTTTGAAAACGTTTCCCTTGAAACGAATTTTATCACTCTT
*
724431 CAGATA
131 CAGACA
* *
724437 GTTTCCCTTGAAA-AGAATTTTGTCTCTCTTAAGACAATTTCCCTTGAAACAAATTTTGTCTCCC
1 GTTTCCCTTGAAACA-AATTTTGTCTCTCTTGAGACAGTTTCCCTTGAAA-AAATTTTGTCTCCC
* * * * *
724501 TTGAGACAGATGCTCTTGAAACATAAACTTTGAAAATGTTTCCCTTGAAATGAATTTTGTCACTC
64 TTGAGACAGTTTCTCTTGAAACATAAACTTTGAAAACGTTTCCCTTGAAACGAATTTTATCACTC
*
724566 TTGAGACA
129 TTCAGACA
* * * * *
724574 TTTTCCCTTGAAACAAATTTTGTCTCTCTTGAGACAGTTTGCCTTGAAATGAATTTTGCCTCTCT
1 GTTTCCCTTGAAACAAATTTTGTCTCTCTTGAGACAGTTTCCCTTGAAA-AAATTTTGTCTCCCT
*
724639 TGAGACAGTTTCCCTTGAAACA
65 TGAGACAGTTTCTCTTGAAACA
724661 AAATTTATCT
Statistics
Matches: 199, Mismatches: 22, Indels: 5
0.88 0.10 0.02
Matches are distributed among these distances:
135 1 0.01
136 45 0.23
137 152 0.76
138 1 0.01
ACGTcount: A:0.28, C:0.21, G:0.14, T:0.38
Consensus pattern (136 bp):
GTTTCCCTTGAAACAAATTTTGTCTCTCTTGAGACAGTTTCCCTTGAAAAAATTTTGTCTCCCTT
GAGACAGTTTCTCTTGAAACATAAACTTTGAAAACGTTTCCCTTGAAACGAATTTTATCACTCTT
CAGACA
Done.