Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008270.1 Hibiscus syriacus cultivar Beakdansim tig00110927_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: 726180
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 5 of 5
Found at i:567038 original size:157 final size:156
Alignment explanation
Indices: 566736--567049 Score: 553
Period size: 157 Copynumber: 2.0 Consensus size: 156
566726 TTCTCTCGGT
566736 CCTACAATGTCAAACAACCAGTTTTAATGATGATTTATAATTTGTTAAAATTATTTTTGAAAAAA
1 CCTACAATGTCAAACAACCAGTTTTAATGATGATTTATAATTTGTTAAAATTATTTTTGAAAAAA
566801 TACATCATACATGTCCTTTTTGTGAACTCCAAAATCTTGCATCTTCCCTTGGTATCTAAGCATTC
66 TACATCATACATGTCCTTTTTGTGAACTCCAAAATCTTGCATCTTCCCTTGGTATCTAAGCATTC
566866 AGGTGGGACTGTTTGTAGCTTCTCTTC
131 AGGTGGGAC-GTTTGTAGCTTCTCTTC
566893 CCTACAATGTCAAACAACCAGTTTTAATGATGATTTATAATTTGTTAAAATTA-TTTTG-AAAAA
1 CCTACAATGTCAAACAACCAGTTTTAATGATGATTTATAATTTGTTAAAATTATTTTTGAAAAAA
*
566956 TACATCATACATGTCCTTTTTGTGAACTCCAAAATCTGACTGCATCTTCCTTTGGTATCTAAGCA
66 TACATCATACATGTCCTTTTTGTGAACTCCAAAATCT---TGCATCTTCCCTTGGTATCTAAGCA
567021 TTCCAGGTGGGAC-TTTGTAGCTTCTCTTC
128 TT-CAGGTGGGACGTTTGTAGCTTCTCTTC
567050 AAGGCTCAGA
Statistics
Matches: 152, Mismatches: 1, Indels: 8
0.94 0.01 0.05
Matches are distributed among these distances:
155 42 0.28
156 5 0.03
157 69 0.45
158 26 0.17
159 10 0.07
ACGTcount: A:0.29, C:0.19, G:0.13, T:0.39
Consensus pattern (156 bp):
CCTACAATGTCAAACAACCAGTTTTAATGATGATTTATAATTTGTTAAAATTATTTTTGAAAAAA
TACATCATACATGTCCTTTTTGTGAACTCCAAAATCTTGCATCTTCCCTTGGTATCTAAGCATTC
AGGTGGGACGTTTGTAGCTTCTCTTC
Found at i:567548 original size:17 final size:18
Alignment explanation
Indices: 567523--567557 Score: 54
Period size: 17 Copynumber: 2.0 Consensus size: 18
567513 CCTCGGCATG
567523 ATATCTGTAATAA-ACAA
1 ATATCTGTAATAAGACAA
*
567540 ATATTTGTAATAAGACAA
1 ATATCTGTAATAAGACAA
567558 CTAATTACTT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 12 0.75
18 4 0.25
ACGTcount: A:0.51, C:0.09, G:0.09, T:0.31
Consensus pattern (18 bp):
ATATCTGTAATAAGACAA
Found at i:575768 original size:41 final size:41
Alignment explanation
Indices: 575697--575852 Score: 179
Period size: 41 Copynumber: 3.8 Consensus size: 41
575687 TTCGAAAACC
*
575697 CTATTGCGGTATTTTTGTTACAAACGCCGCTAAATTACCACT
1 CTATTGCGGCATTTTT-TTACAAACGCCGCTAAATTACCACT
*
575739 CTATTGCGACATTTTTTTACAAACGCCGCTAAATTACCACT
1 CTATTGCGGCATTTTTTTACAAACGCCGCTAAATTACCACT
* *** *
575780 CTATTGCGGCGTTTGGGCTA-AAACACCGCTAAATTACCACT
1 CTATTGCGGCATTT-TTTTACAAACGCCGCTAAATTACCACT
** * *
575821 CTATTGCGGTGTTTTTACTATAAACGCCGCTA
1 CTATTGCGGCATTTTT-TTACAAACGCCGCTA
575853 TTGATTAACC
Statistics
Matches: 99, Mismatches: 12, Indels: 6
0.85 0.10 0.05
Matches are distributed among these distances:
41 73 0.74
42 26 0.26
ACGTcount: A:0.26, C:0.25, G:0.15, T:0.33
Consensus pattern (41 bp):
CTATTGCGGCATTTTTTTACAAACGCCGCTAAATTACCACT
Found at i:579966 original size:14 final size:15
Alignment explanation
Indices: 579943--579986 Score: 58
Period size: 14 Copynumber: 3.1 Consensus size: 15
579933 TACGTTTCTG
*
579943 TTTA-TATGCAGAGA
1 TTTATTATGCAGGGA
579957 TTT-TTATGCAGGGA
1 TTTATTATGCAGGGA
579971 TTTATT-TGCAGGGA
1 TTTATTATGCAGGGA
579985 TT
1 TT
579987 ACTTCACATT
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
14 25 0.93
15 2 0.07
ACGTcount: A:0.25, C:0.07, G:0.25, T:0.43
Consensus pattern (15 bp):
TTTATTATGCAGGGA
Found at i:582656 original size:21 final size:22
Alignment explanation
Indices: 582632--582674 Score: 61
Period size: 21 Copynumber: 2.0 Consensus size: 22
582622 TAAGAATAAC
* *
582632 ATATTATAATTAT-TTATTAAA
1 ATATTAAAATTATAATATTAAA
582653 ATATTAAAATTATAATATTAAA
1 ATATTAAAATTATAATATTAAA
582675 CTAAGAATAT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
21 12 0.63
22 7 0.37
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (22 bp):
ATATTAAAATTATAATATTAAA
Found at i:582664 original size:27 final size:27
Alignment explanation
Indices: 582570--582668 Score: 71
Period size: 31 Copynumber: 3.6 Consensus size: 27
582560 TATTATATTG
*
582570 TATTAAAA-TAAAATTA-TTA-TAAAA
1 TATTAAAATTATAATTATTTATTAAAA
*
582594 T-TATAAATTATATTAATTATTTATTAAATAA
1 TAT-TAAAAT-TA-TAATTATTTATT-AA-AA
* *
582625 GAATAACATATTATAATTATTTATTAAAA
1 TATTAA-A-ATTATAATTATTTATTAAAA
582654 TATTAAAATTATAAT
1 TATTAAAATTATAAT
582669 ATTAAACTAA
Statistics
Matches: 57, Mismatches: 7, Indels: 19
0.69 0.08 0.23
Matches are distributed among these distances:
23 1 0.02
24 5 0.09
26 2 0.04
27 13 0.23
28 4 0.07
29 7 0.12
30 4 0.07
31 17 0.30
32 3 0.05
33 1 0.02
ACGTcount: A:0.54, C:0.01, G:0.01, T:0.44
Consensus pattern (27 bp):
TATTAAAATTATAATTATTTATTAAAA
Found at i:582727 original size:23 final size:24
Alignment explanation
Indices: 582684--582728 Score: 58
Period size: 23 Copynumber: 1.9 Consensus size: 24
582674 ACTAAGAATA
*
582684 TTATATTTTATGTATTCAATAACG
1 TTATATTTTATGAATTCAATAACG
582708 TTAT-TTTTATGAAATT-AATAA
1 TTATATTTTATG-AATTCAATAA
582729 ATAATACTGA
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
23 12 0.63
24 7 0.37
ACGTcount: A:0.38, C:0.04, G:0.07, T:0.51
Consensus pattern (24 bp):
TTATATTTTATGAATTCAATAACG
Found at i:589038 original size:15 final size:18
Alignment explanation
Indices: 589001--589040 Score: 52
Period size: 15 Copynumber: 2.4 Consensus size: 18
588991 CCTCCTTCAT
589001 CTTCTTCTCTCCATTTTC
1 CTTCTTCTCTCCATTTTC
589019 C-TCTT-TCT-CA-TTTC
1 CTTCTTCTCTCCATTTTC
589033 CTTCTTCT
1 CTTCTTCT
589041 TCTTCCTCCT
Statistics
Matches: 20, Mismatches: 0, Indels: 6
0.77 0.00 0.23
Matches are distributed among these distances:
14 5 0.25
15 6 0.30
16 4 0.20
17 4 0.20
18 1 0.05
ACGTcount: A:0.05, C:0.38, G:0.00, T:0.57
Consensus pattern (18 bp):
CTTCTTCTCTCCATTTTC
Found at i:594482 original size:113 final size:113
Alignment explanation
Indices: 594319--594551 Score: 448
Period size: 113 Copynumber: 2.1 Consensus size: 113
594309 CAATACTCGA
*
594319 GTTCGACTTGGCTAGTTTAACAAACGACGTTATTTGGTTTAATTTTTTTTTTAAAAACAAATTTC
1 GTTCAACTTGGCTAGTTTAACAAACGACGTTATTTGGTTTAATTTTTTTTTTAAAAACAAATTTC
*
594384 TTGGTTTTTCTCGGTTTTTTCCGGTTTTCAGCCGGCCCGGTTCGAACG
66 CTGGTTTTTCTCGGTTTTTTCCGGTTTTCAGCCGGCCCGGTTCGAACG
594432 GTTCAACTTGGCTAGTTTAACAAACGACGTTATTTGGTTTAATTTTTTTTTTAAAAACAAATTTC
1 GTTCAACTTGGCTAGTTTAACAAACGACGTTATTTGGTTTAATTTTTTTTTTAAAAACAAATTTC
594497 CTGGTTTTTCTCGGTTTTTTCCGGTTTTCAGCCGGCCCGGTTCGAACG
66 CTGGTTTTTCTCGGTTTTTTCCGGTTTTCAGCCGGCCCGGTTCGAACG
594545 GTTCAAC
1 GTTCAAC
594552 GGTTCTGGCC
Statistics
Matches: 118, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
113 118 1.00
ACGTcount: A:0.20, C:0.18, G:0.19, T:0.42
Consensus pattern (113 bp):
GTTCAACTTGGCTAGTTTAACAAACGACGTTATTTGGTTTAATTTTTTTTTTAAAAACAAATTTC
CTGGTTTTTCTCGGTTTTTTCCGGTTTTCAGCCGGCCCGGTTCGAACG
Found at i:596637 original size:45 final size:45
Alignment explanation
Indices: 596559--596645 Score: 120
Period size: 45 Copynumber: 1.9 Consensus size: 45
596549 CTAGCTTGGT
* *
596559 GAGGTGCCAATGTTGTGTGACCCAGACCTAGCCTGAGGTAATGGA
1 GAGGTACCAATGTTGTGTGACCCAGACCCAGCCTGAGGTAATGGA
* * * *
596604 GAGGTACCGATGTTGTGTGTCTCGGACCCAGCCTGAGGTAAT
1 GAGGTACCAATGTTGTGTGACCCAGACCCAGCCTGAGGTAAT
596646 AGGGAGATAT
Statistics
Matches: 36, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
45 36 1.00
ACGTcount: A:0.22, C:0.21, G:0.33, T:0.24
Consensus pattern (45 bp):
GAGGTACCAATGTTGTGTGACCCAGACCCAGCCTGAGGTAATGGA
Found at i:596661 original size:45 final size:45
Alignment explanation
Indices: 596568--596664 Score: 115
Period size: 45 Copynumber: 2.2 Consensus size: 45
596558 TGAGGTGCCA
* *
596568 ATGTTGTGTGACCCAGACCTAGCCTGAGGTAATGGAGAGGTACCG
1 ATGTTGTGTGACCCAGACCCAGCCTGAGGTAATGGAGAGATACCG
* * * **
596613 ATGTTGTGTGTCTCGGACCCAGCCTGAGGTAATAGG-GAGATATTG
1 ATGTTGTGTGACCCAGACCCAGCCTGAGGTAAT-GGAGAGATACCG
596658 ATGTTGT
1 ATGTTGT
596665 AGTTTCCTTA
Statistics
Matches: 44, Mismatches: 7, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
45 42 0.95
46 2 0.05
ACGTcount: A:0.23, C:0.16, G:0.33, T:0.28
Consensus pattern (45 bp):
ATGTTGTGTGACCCAGACCCAGCCTGAGGTAATGGAGAGATACCG
Found at i:609652 original size:28 final size:29
Alignment explanation
Indices: 609621--609682 Score: 83
Period size: 28 Copynumber: 2.2 Consensus size: 29
609611 AGGATGTGGG
609621 ATTCCCATGTTTAGTTGGCCG-AGAATCT-
1 ATTCCCATGTTTAGTTGGCCGTA-AATCTA
* *
609649 ATTCCTATGTTTGGTTGGCCGTAAATCTA
1 ATTCCCATGTTTAGTTGGCCGTAAATCTA
609678 ATTCC
1 ATTCC
609683 TGATAATGTT
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
28 24 0.80
29 6 0.20
ACGTcount: A:0.21, C:0.21, G:0.19, T:0.39
Consensus pattern (29 bp):
ATTCCCATGTTTAGTTGGCCGTAAATCTA
Found at i:610209 original size:18 final size:19
Alignment explanation
Indices: 610186--610230 Score: 65
Period size: 18 Copynumber: 2.4 Consensus size: 19
610176 ACATTTTCAG
610186 TAATCTTTTATT-CACAGA
1 TAATCTTTTATTCCACAGA
*
610204 TAATCTTTTATTCCCACTGA
1 TAATCTTTTATT-CCACAGA
610224 TAATCTT
1 TAATCTT
610231 ACATTCTGTG
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
18 12 0.50
20 12 0.50
ACGTcount: A:0.29, C:0.20, G:0.04, T:0.47
Consensus pattern (19 bp):
TAATCTTTTATTCCACAGA
Found at i:611868 original size:6 final size:6
Alignment explanation
Indices: 611857--611889 Score: 66
Period size: 6 Copynumber: 5.5 Consensus size: 6
611847 TGATTGTCTT
611857 CTTTCA CTTTCA CTTTCA CTTTCA CTTTCA CTT
1 CTTTCA CTTTCA CTTTCA CTTTCA CTTTCA CTT
611890 CGCTTCTTCA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 27 1.00
ACGTcount: A:0.15, C:0.33, G:0.00, T:0.52
Consensus pattern (6 bp):
CTTTCA
Found at i:614109 original size:3 final size:3
Alignment explanation
Indices: 614101--614148 Score: 62
Period size: 3 Copynumber: 15.7 Consensus size: 3
614091 ATTTATTTAT
*
614101 ATA ATA ATA ATA ATA ATA TATA TTA ATA ATA ATA ATA A-A ATTA ATA
1 ATA ATA ATA ATA ATA ATA -ATA ATA ATA ATA ATA ATA ATA A-TA ATA
614147 AT
1 AT
614149 TTTAATTTTA
Statistics
Matches: 40, Mismatches: 2, Indels: 6
0.83 0.04 0.12
Matches are distributed among these distances:
2 2 0.05
3 33 0.82
4 5 0.12
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (3 bp):
ATA
Found at i:614120 original size:19 final size:19
Alignment explanation
Indices: 614098--614137 Score: 71
Period size: 19 Copynumber: 2.1 Consensus size: 19
614088 GTAATTTATT
614098 TATATAATAATAATAATAA
1 TATATAATAATAATAATAA
*
614117 TATATATTAATAATAATAA
1 TATATAATAATAATAATAA
614136 TA
1 TA
614138 AAATTAATAA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (19 bp):
TATATAATAATAATAATAA
Found at i:615180 original size:76 final size:76
Alignment explanation
Indices: 614287--615153 Score: 1556
Period size: 76 Copynumber: 11.4 Consensus size: 76
614277 GAAATGTTGA
* * * * * *
614287 AAACATCATGCACTAAAGGGCTTACAGATGATCCTAAGGTTTTGAAAACATCAAAACGCTCCCAA
1 AAACATCATGCACTGAAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGA
614352 AGGCTTTTTTGG
66 AGGC-TTTTTGG
* ** **
614364 AAACATCATGCACTGCAGGACTTACAGATGACCCTAAGATTTTGAAAACATCAAAAAAAATCCCG
1 AAACATCATGCACTGAAGGACTTACAGATGACCCTAAGGCTTTGAAAACATC-AAAAAGCTCCCG
614429 AAGGCTTTTTGG
65 AAGGCTTTTTGG
614441 AAACATCATGCACTGAAGGACTTACA-ATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGA
1 AAACATCATGCACTGAAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGA
614505 AGGCTTTTTGG
66 AGGCTTTTTGG
* *
614516 AAACATTATGCACTGAAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGATCCCGA
1 AAACATCATGCACTGAAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGA
614581 AGGCTTTTTGG
66 AGGCTTTTTGG
*
614592 AAACATCATGCACTGAAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGATCCCGA
1 AAACATCATGCACTGAAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGA
614657 AGGCTTTTTGG
66 AGGCTTTTTGG
*
614668 AAACATCATGCGCTGAAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGA
1 AAACATCATGCACTGAAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGA
614733 AGGCTTTTTGG
66 AGGCTTTTTGG
614744 AAACATCATGCACTGAAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGA
1 AAACATCATGCACTGAAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGA
614809 AGGCTTTTTGG
66 AGGCTTTTTGG
614820 AAACATCATGCACTGAAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGA
1 AAACATCATGCACTGAAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGA
614885 AGGCTTTTTGG
66 AGGCTTTTTGG
*
614896 AAACATCATGCACTGAAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGATCCCGA
1 AAACATCATGCACTGAAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGA
614961 AGGCTTTTTGG
66 AGGCTTTTTGG
614972 AAACATCATGCACTGAAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGA
1 AAACATCATGCACTGAAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGA
615037 AGGCTTTTTGG
66 AGGCTTTTTGG
615048 AAACATCATGCACTGAAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGA
1 AAACATCATGCACTGAAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGA
615113 AGGCTTTTTGG
66 AGGCTTTTTGG
*
615124 AAACATCATGCACTGAAGGACTTATAGATG
1 AAACATCATGCACTGAAGGACTTACAGATG
615154 TGGGAAATAG
Statistics
Matches: 765, Mismatches: 23, Indels: 5
0.96 0.03 0.01
Matches are distributed among these distances:
75 47 0.06
76 626 0.82
77 79 0.10
78 13 0.02
ACGTcount: A:0.36, C:0.21, G:0.19, T:0.23
Consensus pattern (76 bp):
AAACATCATGCACTGAAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGA
AGGCTTTTTGG
Found at i:615430 original size:164 final size:168
Alignment explanation
Indices: 615156--615483 Score: 529
Period size: 168 Copynumber: 2.0 Consensus size: 168
615146 TATAGATGTG
* *
615156 GGAAATAGTTTATTAAGTAAAAAAAACTAAGGAAATTGTTTTCTTACTTTTCAACAATTTCATTT
1 GGAAATAGTTTACTAAGTAAAAAAAACTAAGGAAAATGTTTTCTTACTTTTCAACAATTTCATTT
** * *
615221 TTAGAAAAGATTGAATGAGAAACTATGGAAATCGTTTTCTCATTA-TTTTTCAAAATAACATGTT
66 TTAGAAAAGATAAAATGAGAAACTATGAAAATCATTTTCTCATTATTTTTTCAAAATAACATGTT
615285 GATTGGGTAACATGCCCCAATCTCAAGATAAGGTTGTT
131 GATTGGGTAACATGCCCCAATCTCAAGATAAGGTTGTT
615323 GGAAATAGTTTACTAAGT-AAAAAAACTAA-GAAAATGTTTTCTTACTTTTCAACAATTTCA-TT
1 GGAAATAGTTTACTAAGTAAAAAAAACTAAGGAAAATGTTTTCTTACTTTTCAACAATTTCATTT
**
615385 TTAGAAAAGATAAAATGAGAAACTATGAAAATCATTTTCTCATTATGTTTTTTTTGAAATAACAT
66 TTAGAAAAGATAAAATGAGAAACTATGAAAATCATTTTCTCATTA---TTTTTTCAAAATAACAT
615450 GTTGATTGGGTAACATGCCCCAATCTCAAGATAA
128 GTTGATTGGGTAACATGCCCCAATCTCAAGATAA
615484 TGCTCGTTCT
Statistics
Matches: 149, Mismatches: 8, Indels: 7
0.91 0.05 0.04
Matches are distributed among these distances:
164 43 0.29
165 30 0.20
166 11 0.07
167 17 0.11
168 48 0.32
ACGTcount: A:0.39, C:0.12, G:0.14, T:0.36
Consensus pattern (168 bp):
GGAAATAGTTTACTAAGTAAAAAAAACTAAGGAAAATGTTTTCTTACTTTTCAACAATTTCATTT
TTAGAAAAGATAAAATGAGAAACTATGAAAATCATTTTCTCATTATTTTTTCAAAATAACATGTT
GATTGGGTAACATGCCCCAATCTCAAGATAAGGTTGTT
Found at i:616022 original size:22 final size:22
Alignment explanation
Indices: 615997--616051 Score: 92
Period size: 22 Copynumber: 2.5 Consensus size: 22
615987 CATAAAGCTT
615997 TCATCTTTGAAAAGAGAATCTA
1 TCATCTTTGAAAAGAGAATCTA
* *
616019 TCATCTTTAAAAAGCGAATCTA
1 TCATCTTTGAAAAGAGAATCTA
616041 TCATCTTTGAA
1 TCATCTTTGAA
616052 GAGTGTAGAT
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 30 1.00
ACGTcount: A:0.38, C:0.16, G:0.11, T:0.35
Consensus pattern (22 bp):
TCATCTTTGAAAAGAGAATCTA
Found at i:618850 original size:115 final size:114
Alignment explanation
Indices: 618543--618883 Score: 556
Period size: 114 Copynumber: 3.0 Consensus size: 114
618533 GATCATGCAG
* * * * * *
618543 TTCATCTTTCAATTCCAATGATCGGTTCTGGGGTTCCTACCGAATCAGATCAGATAACTCAAAGA
1 TTCATCTTTCAAATCCAATGATTGGTTTTGGGGTTCATACCAAACCAGATCAGATAACTCAAAGA
*
618608 ACACTTCCAGAAGATGCTATTGGGTCTCCTTATTTCTACTATGAGCAAA
66 ACACTTCCAGAAGATGCTATTGGGTCTTCTTATTTCTACTATGAGCAAA
*
618657 TTCATCTTTCAAATCCAATTATTGGTTTTGGGGTTCATACCAAACCAGATCAGATAACTCAAAGA
1 TTCATCTTTCAAATCCAATGATTGGTTTTGGGGTTCATACCAAACCAGATCAGATAACTCAAAGA
* * * * *
618722 ACACTTCCAGAAGATTCTATTGAGTCTTCGTATTTTTAATATGAGCAAA
66 ACACTTCCAGAAGATGCTATTGGGTCTTCTTATTTCTACTATGAGCAAA
618771 TTCATCTTTCAAATCCAATGATTGGTTTTTGGGGTTCATACCAAACCAGATCAGATAACTCAAAG
1 TTCATCTTTCAAATCCAATGATTGG-TTTTGGGGTTCATACCAAACCAGATCAGATAACTCAAAG
618836 AACACTTCCAGAAGATGCTATTGGGTCTTCTTATTTCTACTATGAGCA
65 AACACTTCCAGAAGATGCTATTGGGTCTTCTTATTTCTACTATGAGCA
618884 CATGGCACTT
Statistics
Matches: 207, Mismatches: 19, Indels: 1
0.91 0.08 0.00
Matches are distributed among these distances:
114 125 0.60
115 82 0.40
ACGTcount: A:0.31, C:0.21, G:0.16, T:0.33
Consensus pattern (114 bp):
TTCATCTTTCAAATCCAATGATTGGTTTTGGGGTTCATACCAAACCAGATCAGATAACTCAAAGA
ACACTTCCAGAAGATGCTATTGGGTCTTCTTATTTCTACTATGAGCAAA
Found at i:621144 original size:15 final size:14
Alignment explanation
Indices: 621124--621164 Score: 55
Period size: 15 Copynumber: 2.8 Consensus size: 14
621114 CTTGATTCAA
621124 TTTTTTTCTTTTCCT
1 TTTTTTTCTTTT-CT
*
621139 TTTTTTTCTTTTTT
1 TTTTTTTCTTTTCT
621153 TTTTCTTTCTTT
1 TTTT-TTTCTTT
621165 GCTGGATGAG
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
14 5 0.21
15 19 0.79
ACGTcount: A:0.00, C:0.15, G:0.00, T:0.85
Consensus pattern (14 bp):
TTTTTTTCTTTTCT
Found at i:626072 original size:16 final size:16
Alignment explanation
Indices: 626051--626098 Score: 60
Period size: 16 Copynumber: 2.9 Consensus size: 16
626041 ATTCTTGAAT
626051 ATAATAAAAAAAAATA
1 ATAATAAAAAAAAATA
* *
626067 ATAATATATAAAAATA
1 ATAATAAAAAAAAATA
*
626083 ATAAGTAATAAAAAAT
1 ATAA-TAAAAAAAAAT
626099 TTGAAAGAAA
Statistics
Matches: 26, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
16 18 0.69
17 8 0.31
ACGTcount: A:0.73, C:0.00, G:0.02, T:0.25
Consensus pattern (16 bp):
ATAATAAAAAAAAATA
Found at i:628333 original size:3 final size:3
Alignment explanation
Indices: 628325--628369 Score: 56
Period size: 3 Copynumber: 14.7 Consensus size: 3
628315 ATTTATTTAT
*
628325 ATA ATA ATA ATA ATA TATA TTA ATA ATA ATA ATA A-A ATTA ATA AT
1 ATA ATA ATA ATA ATA -ATA ATA ATA ATA ATA ATA ATA A-TA ATA AT
628370 TTTAATTTTA
Statistics
Matches: 37, Mismatches: 2, Indels: 6
0.82 0.04 0.13
Matches are distributed among these distances:
2 2 0.05
3 30 0.81
4 5 0.14
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (3 bp):
ATA
Found at i:633302 original size:21 final size:21
Alignment explanation
Indices: 633278--633324 Score: 85
Period size: 21 Copynumber: 2.2 Consensus size: 21
633268 AGGATTCATG
*
633278 GTTTATGATATGAGGTTTAAA
1 GTTTATGATATGAGATTTAAA
633299 GTTTATGATATGAGATTTAAA
1 GTTTATGATATGAGATTTAAA
633320 GTTTA
1 GTTTA
633325 AGGTCGAGGT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.34, C:0.00, G:0.21, T:0.45
Consensus pattern (21 bp):
GTTTATGATATGAGATTTAAA
Found at i:634699 original size:225 final size:224
Alignment explanation
Indices: 634295--634736 Score: 746
Period size: 225 Copynumber: 2.0 Consensus size: 224
634285 GTAAATTATC
* * *
634295 TATCCTTTTTATAAAAGTATCCATACTTATTTCACTGTGAAAATATATTTATTATTATCTTTAGT
1 TATCATTTTTATAAAAGTATCCATACTTATTTCACTGTGAAAACATATTTATTATTATATTTAGT
**
634360 TAATATTGTTAAATTTAAAATCTAAATAATATTTATAAAATATCAAAACAATCAAATAATTTTTT
66 TAATATTGTTAAATTTAAAATCTAAATAATATTTATAAAATATCAAAACAATCAAATAAAATTTT
634425 GTGTAAATGAAATTATTAAATTAATATGTAGGTGGAAACATGAAACACTATTAAA-AAATTGAAA
131 GTGTAAATGAAATTATTAAATTAATATGTAGGTGGAAACATGAAACACTATTAAATAAATTGAAA
634489 CATAAATTACATAACTTTCAAAAAAGTATA
196 CATAAATTACATAACTTT-AAAAAAGTATA
* *
634519 TATCATTTTTATAAAAGTGTCCATACTTATTTCACTGTTGAAAACATATTTATTATTATATTTGG
1 TATCATTTTTATAAAAGTATCCATACTTATTTCACTG-TGAAAACATATTTATTATTATATTTAG
*
634584 TTAATATTGTTAAATTTAAATTCTAAATAATATTTTATAAAATATC-AAACAATCAAATAAAATT
65 TTAATATTGTTAAATTTAAAATCTAAATAATA-TTTATAAAATATCAAAACAATCAAATAAAATT
*
634648 TTGTGTAAATTAAATTATTAAATTAATATTGTAGGTGGAAACATG-AACACTATTAAATAAATTG
129 TTGTGTAAATGAAATTATTAAATTAATA-TGTAGGTGGAAACATGAAACACTATTAAATAAATTG
634712 AAACATAAATTACATAACTTTAAAA
193 AAACATAAATTACATAACTTTAAAA
634737 GCAGTTTTAA
Statistics
Matches: 205, Mismatches: 9, Indels: 7
0.93 0.04 0.03
Matches are distributed among these distances:
224 35 0.17
225 114 0.56
226 56 0.27
ACGTcount: A:0.45, C:0.08, G:0.07, T:0.40
Consensus pattern (224 bp):
TATCATTTTTATAAAAGTATCCATACTTATTTCACTGTGAAAACATATTTATTATTATATTTAGT
TAATATTGTTAAATTTAAAATCTAAATAATATTTATAAAATATCAAAACAATCAAATAAAATTTT
GTGTAAATGAAATTATTAAATTAATATGTAGGTGGAAACATGAAACACTATTAAATAAATTGAAA
CATAAATTACATAACTTTAAAAAAGTATA
Found at i:634831 original size:20 final size:20
Alignment explanation
Indices: 634806--634844 Score: 78
Period size: 20 Copynumber: 1.9 Consensus size: 20
634796 ATACCAGGTA
634806 AAAATGATAAAACCGGTAAC
1 AAAATGATAAAACCGGTAAC
634826 AAAATGATAAAACCGGTAA
1 AAAATGATAAAACCGGTAA
634845 ATTTAAAAGT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.56, C:0.13, G:0.15, T:0.15
Consensus pattern (20 bp):
AAAATGATAAAACCGGTAAC
Found at i:635010 original size:17 final size:18
Alignment explanation
Indices: 634964--635012 Score: 82
Period size: 19 Copynumber: 2.7 Consensus size: 18
634954 CGAGATAACA
634964 GGTAAAAATGATAAAACC
1 GGTAAAAATGATAAAACC
634982 GGTAATAAATGATAAAACC
1 GGTAA-AAATGATAAAACC
635001 GGT-AAAATGATA
1 GGTAAAAATGATA
635013 CCGATATATT
Statistics
Matches: 30, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
17 8 0.27
18 6 0.20
19 16 0.53
ACGTcount: A:0.53, C:0.08, G:0.18, T:0.20
Consensus pattern (18 bp):
GGTAAAAATGATAAAACC
Found at i:639740 original size:21 final size:21
Alignment explanation
Indices: 639716--639776 Score: 55
Period size: 21 Copynumber: 3.2 Consensus size: 21
639706 CAAACTTTAC
639716 CAAACTTTGAAAAACATTTTT
1 CAAACTTTGAAAAACATTTTT
*
639737 CAAA----G--AAACA-TTTA
1 CAAACTTTGAAAAACATTTTT
639751 CTAAACTTTGAAAAACATTTTT
1 C-AAACTTTGAAAAACATTTTT
639773 CAAA
1 CAAA
639777 GTTGGTTGCC
Statistics
Matches: 30, Mismatches: 2, Indels: 16
0.62 0.04 0.33
Matches are distributed among these distances:
14 4 0.13
15 8 0.27
17 1 0.03
19 1 0.03
21 12 0.40
22 4 0.13
ACGTcount: A:0.48, C:0.15, G:0.05, T:0.33
Consensus pattern (21 bp):
CAAACTTTGAAAAACATTTTT
Found at i:639758 original size:36 final size:35
Alignment explanation
Indices: 639707--639777 Score: 124
Period size: 36 Copynumber: 2.0 Consensus size: 35
639697 AACATCTATC
639707 AAACTTTACCAAACTTTGAAAAACATTTTTCAAAG
1 AAACTTTACCAAACTTTGAAAAACATTTTTCAAAG
*
639742 AAACATTTACTAAACTTTGAAAAACATTTTTCAAAG
1 AAAC-TTTACCAAACTTTGAAAAACATTTTTCAAAG
639778 TTGGTTGCCA
Statistics
Matches: 34, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
35 4 0.12
36 30 0.88
ACGTcount: A:0.46, C:0.15, G:0.06, T:0.32
Consensus pattern (35 bp):
AAACTTTACCAAACTTTGAAAAACATTTTTCAAAG
Found at i:643783 original size:16 final size:16
Alignment explanation
Indices: 643739--643783 Score: 81
Period size: 16 Copynumber: 2.8 Consensus size: 16
643729 GACGATAAAT
*
643739 TTCACTATTCACAAAA
1 TTCACTATTCACGAAA
643755 TTCACTATTCACGAAA
1 TTCACTATTCACGAAA
643771 TTCACTATTCACG
1 TTCACTATTCACG
643784 TGAATATTAA
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
16 28 1.00
ACGTcount: A:0.36, C:0.27, G:0.04, T:0.33
Consensus pattern (16 bp):
TTCACTATTCACGAAA
Found at i:652480 original size:200 final size:201
Alignment explanation
Indices: 651276--652610 Score: 2231
Period size: 201 Copynumber: 6.7 Consensus size: 201
651266 TATTTAAATT
* * * *
651276 AGTATCGACACAAAATTAAAAAAGTATCGATACATGTTGTAGACATATTCTCTCATAAAACTGGT
1 AGTATCGACACAAAATTAAACAAGTGTCGATACATGTTGTAGACCTATTCTCTCATAAAACCGGT
* * * * *
651341 ATATTTACACCTGTTACATTGTAAATTTACCTATTACATTATACTTGTGGGTTTCA-ATGTTTCT
66 ATATTTATACCGGTTACATTGTAAATTTACCTATTACATTATACTTAT-GGATGCATATGTTTCT
*
651405 GGGATCGACACTTTTTGAAAATGTATCGACACTTTATGCGTTCACCC-TTTTGGCATCCATTGTG
130 GGGATCGACACTTTTTGAAAATGTATCGACACTTTATGCGTTCACCCTTTTTGGCATCCATTCTG
651469 GACCAAA
195 GACCAAA
* * **
651476 AGTATCGACACAAAATTAAACAAGTGTCGATACATATTGTTGACCTATTCTCTCATAAAATTGGT
1 AGTATCGACACAAAATTAAACAAGTGTCGATACATGTTGTAGACCTATTCTCTCATAAAACCGGT
* * *
651541 ATAGTTATACCGGTTACATTGTAAATTTACCTA-TATATTA-ACTTATGGATGCATATGTTTATG
66 ATATTTATACCGGTTACATTGTAAATTTACCTATTACATTATACTTATGGATGCATATGTTTCTG
* * * *
651604 GGATAGACACTTTTTGAAAATGTATCGACACTTTATACGTTCATCCTTTTTGGCATCCATTGTGG
131 GGATCGACACTTTTTGAAAATGTATCGACACTTTATGCGTTCACCCTTTTTGGCATCCATTCTGG
651669 ACCAAA
196 ACCAAA
* *
651675 ACTA-CGAC-CAAAATTAAACAAGTATCGATACATGTTGTAGACCTATTCTCTCATAAAACCGGT
1 AGTATCGACACAAAATTAAACAAGTGTCGATACATGTTGTAGACCTATTCTCTCATAAAACCGGT
*
651738 ATATTTATACCGGTTACATTGTAAATTTACCTATTTCATTATACTTATGGATGCATATGTTTCTG
66 ATATTTATACCGGTTACATTGTAAATTTACCTATTACATTATACTTATGGATGCATATGTTTCTG
651803 GGATCGACACTTTTTGAAAATGTATCGACACTTTATGCGTTCACCCTTTTTGGCATCCATTCTGG
131 GGATCGACACTTTTTGAAAATGTATCGACACTTTATGCGTTCACCCTTTTTGGCATCCATTCTGG
651868 ACCAAA
196 ACCAAA
* *
651874 AGTATCGACACAAAATTAAACAAGTGTCGATACACGTTGTAGATCTATTCTCTCATAAAACCGGT
1 AGTATCGACACAAAATTAAACAAGTGTCGATACATGTTGTAGACCTATTCTCTCATAAAACCGGT
651939 ATATTTATACCGGTTACATTGTAAATTTACCTATTACATTATACTTATGGATGCATATGTTTCTG
66 ATATTTATACCGGTTACATTGTAAATTTACCTATTACATTATACTTATGGATGCATATGTTTCTG
* *
652004 GGATCGACGCTTTTTGAAAATGTATCGACACTTTATGCGTTCACCCTTTTTGGCATCCATTGTGG
131 GGATCGACACTTTTTGAAAATGTATCGACACTTTATGCGTTCACCCTTTTTGGCATCCATTCTGG
652069 ACCAAA
196 ACCAAA
* * *
652075 AGTATCAACACAAAATTAAACAAGTGTCGATACATGTTGTAAACCTATTCTCTCATAAAACCGAT
1 AGTATCGACACAAAATTAAACAAGTGTCGATACATGTTGTAGACCTATTCTCTCATAAAACCGGT
652140 AT-TTTATACCGGTTACATTGTAAATTTACCTATTACATTATACTTATGGATGCATATGTTTCTG
66 ATATTTATACCGGTTACATTGTAAATTTACCTATTACATTATACTTATGGATGCATATGTTTCTG
*
652204 TGATCGACACTTTTTG-AAATGTATCGACACTTTATGCGTTCACCCTTTTTGGCATCCATTCTGG
131 GGATCGACACTTTTTGAAAATGTATCGACACTTTATGCGTTCACCCTTTTTGGCATCCATTCTGG
652268 ACCAAA
196 ACCAAA
*
652274 AGTATCGACACAAAATTAAACAAGTGTCGATACATGTTGTAGACCTATTCTCT-ATAAAACCAGT
1 AGTATCGACACAAAATTAAACAAGTGTCGATACATGTTGTAGACCTATTCTCTCATAAAACCGGT
* **
652338 ATATTTATATCGGTTACATTGTAAA-TTACCTATTACATTATACTTATGGATGTGTATGTTTCTG
66 ATATTTATACCGGTTACATTGTAAATTTACCTATTACATTATACTTATGGATGCATATGTTTCTG
*
652402 TGATCGACACTTTTTTGAAAATGTATCGACACTTTATGCGTTCACCCTTTTTGGCATCCATTCTG
131 GGATCGACAC-TTTTTGAAAATGTATCGACACTTTATGCGTTCACCCTTTTTGGCATCCATTCTG
*
652467 GACTAAA
195 GACCAAA
*
652474 AGTATCGACACAAAATTAAACAAGTGTCGATACATGTTGTAGACCTATTCTCTCATAAAACCAGT
1 AGTATCGACACAAAATTAAACAAGTGTCGATACATGTTGTAGACCTATTCTCTCATAAAACCGGT
652539 ATATTTATACCGGTTACATTGTAAATTTACCTATTACATTATACTTATGGATGCATATGTTTCTG
66 ATATTTATACCGGTTACATTGTAAATTTACCTATTACATTATACTTATGGATGCATATGTTTCTG
652604 GGATCGA
131 GGATCGA
652611 TAAATTTTAC
Statistics
Matches: 1066, Mismatches: 58, Indels: 20
0.93 0.05 0.02
Matches are distributed among these distances:
197 87 0.08
198 123 0.12
199 256 0.24
200 275 0.26
201 282 0.26
202 43 0.04
ACGTcount: A:0.31, C:0.18, G:0.15, T:0.36
Consensus pattern (201 bp):
AGTATCGACACAAAATTAAACAAGTGTCGATACATGTTGTAGACCTATTCTCTCATAAAACCGGT
ATATTTATACCGGTTACATTGTAAATTTACCTATTACATTATACTTATGGATGCATATGTTTCTG
GGATCGACACTTTTTGAAAATGTATCGACACTTTATGCGTTCACCCTTTTTGGCATCCATTCTGG
ACCAAA
Found at i:652689 original size:200 final size:199
Alignment explanation
Indices: 651276--652610 Score: 2123
Period size: 200 Copynumber: 6.7 Consensus size: 199
651266 TATTTAAATT
* * * **
651276 AGTATCGACACAAAATTAAAAAAGTATCGATACATGTTGTAGACATATTCTCTCATAAAACTGGT
1 AGTATCGACACAAAATTAAACAAGTGTCGATACATGTTGTAGACCTATTCTCTCATAAAACCAGT
* * * * *
651341 ATATTTACACCTGTTACATTGTAAATTTACCTATTACATTATACTTGTGGGTTTCA-ATGTTTCT
66 ATATTTATACCGGTTACATTGTAAATTTACCTATTACATTATACTTAT-GGATGCATATGTTTCT
* *
651405 GGGATCGACACTTTTTGAAAATGTATCGACACTTTATGCGTTCACCCTTTTGGCATCCATTGTGG
130 GGGATCGACACTTTTTGAAAATGTATCGACACTTTATGCGTTCACCTTTTTGGCATCCATTCTGG
651470 ACCAAA
195 A-CAAA
* * ***
651476 AGTATCGACACAAAATTAAACAAGTGTCGATACATATTGTTGACCTATTCTCTCATAAAATTGGT
1 AGTATCGACACAAAATTAAACAAGTGTCGATACATGTTGTAGACCTATTCTCTCATAAAACCAGT
* * *
651541 ATAGTTATACCGGTTACATTGTAAATTTACCTA-TATATTA-ACTTATGGATGCATATGTTTATG
66 ATATTTATACCGGTTACATTGTAAATTTACCTATTACATTATACTTATGGATGCATATGTTTCTG
* * *
651604 GGATAGACACTTTTTGAAAATGTATCGACACTTTATACGTTCATCCTTTTTGGCATCCATTGTGG
131 GGATCGACACTTTTTGAAAATGTATCGACACTTTATGCGTTCA-CCTTTTTGGCATCCATTCTGG
651669 ACCAAA
195 A-CAAA
* * *
651675 ACTA-CGAC-CAAAATTAAACAAGTATCGATACATGTTGTAGACCTATTCTCTCATAAAACCGGT
1 AGTATCGACACAAAATTAAACAAGTGTCGATACATGTTGTAGACCTATTCTCTCATAAAACCAGT
*
651738 ATATTTATACCGGTTACATTGTAAATTTACCTATTTCATTATACTTATGGATGCATATGTTTCTG
66 ATATTTATACCGGTTACATTGTAAATTTACCTATTACATTATACTTATGGATGCATATGTTTCTG
651803 GGATCGACACTTTTTGAAAATGTATCGACACTTTATGCGTTCACCCTTTTTGGCATCCATTCTGG
131 GGATCGACACTTTTTGAAAATGTATCGACACTTTATGCGTTCA-CCTTTTTGGCATCCATTCTGG
651868 ACCAAA
195 A-CAAA
* * *
651874 AGTATCGACACAAAATTAAACAAGTGTCGATACACGTTGTAGATCTATTCTCTCATAAAACCGGT
1 AGTATCGACACAAAATTAAACAAGTGTCGATACATGTTGTAGACCTATTCTCTCATAAAACCAGT
651939 ATATTTATACCGGTTACATTGTAAATTTACCTATTACATTATACTTATGGATGCATATGTTTCTG
66 ATATTTATACCGGTTACATTGTAAATTTACCTATTACATTATACTTATGGATGCATATGTTTCTG
* *
652004 GGATCGACGCTTTTTGAAAATGTATCGACACTTTATGCGTTCACCCTTTTTGGCATCCATTGTGG
131 GGATCGACACTTTTTGAAAATGTATCGACACTTTATGCGTTCA-CCTTTTTGGCATCCATTCTGG
652069 ACCAAA
195 A-CAAA
* *
652075 AGTATCAACACAAAATTAAACAAGTGTCGATACATGTTGTAAACCTATTCTCTCATAAAACC-G-
1 AGTATCGACACAAAATTAAACAAGTGTCGATACATGTTGTAGACCTATTCTCTCATAAAACCAGT
652138 ATATTTTATACCGGTTACATTGTAAATTTACCTATTACATTATACTTATGGATGCATATGTTTCT
66 ATA-TTTATACCGGTTACATTGTAAATTTACCTATTACATTATACTTATGGATGCATATGTTTCT
*
652203 GTGATCGACACTTTTTG-AAATGTATCGACACTTTATGCGTTCACCCTTTTTGGCATCCATTCTG
130 GGGATCGACACTTTTTGAAAATGTATCGACACTTTATGCGTTCA-CCTTTTTGGCATCCATTCTG
652267 GACCAAA
194 GA-CAAA
652274 AGTATCGACACAAAATTAAACAAGTGTCGATACATGTTGTAGACCTATTCTCT-ATAAAACCAGT
1 AGTATCGACACAAAATTAAACAAGTGTCGATACATGTTGTAGACCTATTCTCTCATAAAACCAGT
* **
652338 ATATTTATATCGGTTACATTGTAAA-TTACCTATTACATTATACTTATGGATGTGTATGTTTCTG
66 ATATTTATACCGGTTACATTGTAAATTTACCTATTACATTATACTTATGGATGCATATGTTTCTG
*
652402 TGATCGACACTTTTTTGAAAATGTATCGACACTTTATGCGTTCACCCTTTTTGGCATCCATTCTG
131 GGATCGACAC-TTTTTGAAAATGTATCGACACTTTATGCGTTCA-CCTTTTTGGCATCCATTCTG
652467 GACTAAA
194 GAC-AAA
652474 AGTATCGACACAAAATTAAACAAGTGTCGATACATGTTGTAGACCTATTCTCTCATAAAACCAGT
1 AGTATCGACACAAAATTAAACAAGTGTCGATACATGTTGTAGACCTATTCTCTCATAAAACCAGT
652539 ATATTTATACCGGTTACATTGTAAATTTACCTATTACATTATACTTATGGATGCATATGTTTCTG
66 ATATTTATACCGGTTACATTGTAAATTTACCTATTACATTATACTTATGGATGCATATGTTTCTG
652604 GGATCGA
131 GGATCGA
652611 TAAATTTTAC
Statistics
Matches: 1067, Mismatches: 54, Indels: 26
0.93 0.05 0.02
Matches are distributed among these distances:
197 87 0.08
198 118 0.11
199 263 0.25
200 278 0.26
201 278 0.26
202 43 0.04
ACGTcount: A:0.31, C:0.18, G:0.15, T:0.36
Consensus pattern (199 bp):
AGTATCGACACAAAATTAAACAAGTGTCGATACATGTTGTAGACCTATTCTCTCATAAAACCAGT
ATATTTATACCGGTTACATTGTAAATTTACCTATTACATTATACTTATGGATGCATATGTTTCTG
GGATCGACACTTTTTGAAAATGTATCGACACTTTATGCGTTCACCTTTTTGGCATCCATTCTGGA
CAAA
Found at i:654512 original size:16 final size:17
Alignment explanation
Indices: 654491--654529 Score: 53
Period size: 18 Copynumber: 2.3 Consensus size: 17
654481 TCCTCCTCCC
*
654491 TTTTTTC-TTCTTCATA
1 TTTTTTCATTCATCATA
654507 TTTTTTCAGTTCATCATA
1 TTTTTTCA-TTCATCATA
654525 TTTTT
1 TTTTT
654530 GATCTACATA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
16 7 0.35
18 13 0.65
ACGTcount: A:0.15, C:0.15, G:0.03, T:0.67
Consensus pattern (17 bp):
TTTTTTCATTCATCATA
Found at i:654811 original size:21 final size:21
Alignment explanation
Indices: 654798--654850 Score: 106
Period size: 21 Copynumber: 2.5 Consensus size: 21
654788 CTCAAGAGTA
654798 TCTTCGACTCTCTCAAGTTTC
1 TCTTCGACTCTCTCAAGTTTC
654819 TCTTCGACTCTCTCAAGTTTC
1 TCTTCGACTCTCTCAAGTTTC
654840 TCTTCGACTCT
1 TCTTCGACTCT
654851 TGATTGTCTT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 32 1.00
ACGTcount: A:0.13, C:0.34, G:0.09, T:0.43
Consensus pattern (21 bp):
TCTTCGACTCTCTCAAGTTTC
Found at i:657127 original size:20 final size:19
Alignment explanation
Indices: 657082--657127 Score: 56
Period size: 20 Copynumber: 2.3 Consensus size: 19
657072 CCGGTAGCTC
*
657082 TTTACCGGTTTTATCATTT
1 TTTATCGGTTTTATCATTT
*
657101 TGATATCGGTTTTATCATATT
1 T-TTATCGGTTTTATCAT-TT
657122 TTTATC
1 TTTATC
657128 TGTTATATCG
Statistics
Matches: 22, Mismatches: 3, Indels: 3
0.79 0.11 0.11
Matches are distributed among these distances:
19 1 0.05
20 18 0.82
21 3 0.14
ACGTcount: A:0.20, C:0.13, G:0.11, T:0.57
Consensus pattern (19 bp):
TTTATCGGTTTTATCATTT
Found at i:658426 original size:2 final size:2
Alignment explanation
Indices: 658419--658447 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
658409 TATGCATAAC
658419 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
658448 GTTTGTATTC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:661743 original size:6 final size:6
Alignment explanation
Indices: 661732--662498 Score: 1467
Period size: 6 Copynumber: 128.7 Consensus size: 6
661722 AAAAATGAAT
661732 ATAAAC ATAAAC ATAAAC ATAAAC ATAAAC ATAAAC ATAAAC ATAAAC
1 ATAAAC ATAAAC ATAAAC ATAAAC ATAAAC ATAAAC ATAAAC ATAAAC
661780 ATAAAC ATAAAC ATAAAC ATAAAC ATAAAC ATAAAC ATAAAC ATAAAC
1 ATAAAC ATAAAC ATAAAC ATAAAC ATAAAC ATAAAC ATAAAC ATAAAC
661828 ATAAAC ATAAAC ATAAAC ATAAAC ATAAAC ATAAAC ATAAAC ATAAAC
1 ATAAAC ATAAAC ATAAAC ATAAAC ATAAAC ATAAAC ATAAAC ATAAAC
661876 ATAAAC ATAAAC ATAAAC ATAAAC ATAAACAC ATAAAC ATAAAC ATAAAC
1 ATAAAC ATAAAC ATAAAC ATAAAC AT-AA-AC ATAAAC ATAAAC ATAAAC
661926 ATAAAC AT-AAC ATAAAC ATAAAC ATAAAC ATAAAC ATAAAC ATAAAC
1 ATAAAC ATAAAC ATAAAC ATAAAC ATAAAC ATAAAC ATAAAC ATAAAC
661973 ATAAAC ATAAAC ATAAAC ATAAAC ATAAAC ATAAAC ATAAAC ATAAAC
1 ATAAAC ATAAAC ATAAAC ATAAAC ATAAAC ATAAAC ATAAAC ATAAAC
662021 ATAAAC ATAAAC ATAAAC ATAAAC ATAAAC ATAAAC ATAAAC ATAAAC
1 ATAAAC ATAAAC ATAAAC ATAAAC ATAAAC ATAAAC ATAAAC ATAAAC
662069 ATAAAC ATAAAC ATAAAC ATAAAC AT-AAC ATAAAC ATAAAC ATAAAC
1 ATAAAC ATAAAC ATAAAC ATAAAC ATAAAC ATAAAC ATAAAC ATAAAC
662116 ATAAAC ATAAAC ATAAAC ATAAAC ATAAAC ATAAAC ATAAAC ATAAAC
1 ATAAAC ATAAAC ATAAAC ATAAAC ATAAAC ATAAAC ATAAAC ATAAAC
662164 ATAAAC ATAAAC ATAAAC ATAAAC ATAAAC ATAAAC ATAAAC ATAAAC
1 ATAAAC ATAAAC ATAAAC ATAAAC ATAAAC ATAAAC ATAAAC ATAAAC
662212 AT-AAC ATAAAC ATAAAC ATAAAC ATAAAC ATAAAC AT--AC ATAAAC
1 ATAAAC ATAAAC ATAAAC ATAAAC ATAAAC ATAAAC ATAAAC ATAAAC
662257 ATAAAC ATAAAC ATAAAC ATAAAC ATAAAC ATAAAC ATAAAC ATAAAC
1 ATAAAC ATAAAC ATAAAC ATAAAC ATAAAC ATAAAC ATAAAC ATAAAC
662305 ATAAAC ATAAAC ATAAAC AT-AAC ATAAAC ATAAAC ATAAAC ATAAAC
1 ATAAAC ATAAAC ATAAAC ATAAAC ATAAAC ATAAAC ATAAAC ATAAAC
662352 ATAAAC AT-AAC ATAAAC ATAAAC ATAAAC ATAAAC ATAAAC ATAAAC
1 ATAAAC ATAAAC ATAAAC ATAAAC ATAAAC ATAAAC ATAAAC ATAAAC
662399 ATAAAC ATAAAC ATAAAC ATAAAC ATAAAC ATAAAC ATAAAC ATAAAC
1 ATAAAC ATAAAC ATAAAC ATAAAC ATAAAC ATAAAC ATAAAC ATAAAC
662447 ATAAAC ATAAAC ATAAAC ATAAAC ATAAAC ATAAAC ATAAAC ATAAAC
1 ATAAAC ATAAAC ATAAAC ATAAAC ATAAAC ATAAAC ATAAAC ATAAAC
662495 ATAA
1 ATAA
662499 GTATAAGGGT
Statistics
Matches: 752, Mismatches: 0, Indels: 18
0.98 0.00 0.02
Matches are distributed among these distances:
4 4 0.01
5 25 0.03
6 715 0.95
7 4 0.01
8 4 0.01
ACGTcount: A:0.66, C:0.17, G:0.00, T:0.17
Consensus pattern (6 bp):
ATAAAC
Found at i:664174 original size:31 final size:32
Alignment explanation
Indices: 664134--664194 Score: 81
Period size: 32 Copynumber: 1.9 Consensus size: 32
664124 TTTAAACTAA
664134 AATACCTAAAAC-AAAATAAAATA-TAAAAAT
1 AATACCTAAAACTAAAATAAAATACTAAAAAT
* *
664164 AATATCCTAAAACTTAATTAAAATACTAAAA
1 AATA-CCTAAAACTAAAATAAAATACTAAAA
664195 CCTATTTAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
30 4 0.15
31 8 0.31
32 9 0.35
33 5 0.19
ACGTcount: A:0.64, C:0.11, G:0.00, T:0.25
Consensus pattern (32 bp):
AATACCTAAAACTAAAATAAAATACTAAAAAT
Found at i:664194 original size:19 final size:19
Alignment explanation
Indices: 664170--664271 Score: 54
Period size: 19 Copynumber: 5.4 Consensus size: 19
664160 AAATAATATC
664170 CTAAAACTTAATTAAAATA
1 CTAAAACTTAATTAAAATA
* *
664189 CTAAAACCT-ATT-TAA-A
1 CTAAAACTTAATTAAAATA
* * *
664205 CTAAATACCTAAAATAAAAGA
1 CTAAA-A-CTTAATTAAAATA
*
664226 -TAAAA-TATAA-AAATAATA
1 CTAAAACT-TAATTAA-AATA
664244 TCCTAAAACTTAATTAAAATA
1 --CTAAAACTTAATTAAAATA
664265 CTAAAAC
1 CTAAAAC
664272 CTATTTAAAC
Statistics
Matches: 61, Mismatches: 10, Indels: 24
0.64 0.11 0.25
Matches are distributed among these distances:
16 6 0.10
17 6 0.10
18 9 0.15
19 18 0.30
20 6 0.10
21 13 0.21
22 3 0.05
ACGTcount: A:0.59, C:0.13, G:0.01, T:0.27
Consensus pattern (19 bp):
CTAAAACTTAATTAAAATA
Found at i:664232 original size:44 final size:43
Alignment explanation
Indices: 664182--664308 Score: 116
Period size: 44 Copynumber: 3.2 Consensus size: 43
664172 AAAACTTAAT
664182 TAAAATACTAAAACCTATTTAAACTAAATACCTAAAATAAAAGA
1 TAAAATACTAAAACCTATTTAAACTAAATACCTAAAAT-AAAGA
* *
664226 TAAAATA-TAAAA---A--T-AA-T--AT-CCTAAAACTTAA-T
1 TAAAATACTAAAACCTATTTAAACTAAATACCTAAAA-TAAAGA
*
664258 TAAAATACTAAAACCTATTTAAACTAAAATACCTAAAACAAAGA
1 TAAAATACTAAAACCTATTTAAACT-AAATACCTAAAATAAAGA
664302 TAAAATA
1 TAAAATA
664309 TAATATTTAA
Statistics
Matches: 64, Mismatches: 5, Indels: 28
0.66 0.05 0.29
Matches are distributed among these distances:
32 7 0.11
33 14 0.22
34 3 0.05
36 2 0.03
37 2 0.03
38 2 0.03
39 2 0.03
40 2 0.03
43 9 0.14
44 21 0.33
ACGTcount: A:0.60, C:0.13, G:0.02, T:0.26
Consensus pattern (43 bp):
TAAAATACTAAAACCTATTTAAACTAAATACCTAAAATAAAGA
Found at i:664242 original size:76 final size:76
Alignment explanation
Indices: 664116--664311 Score: 353
Period size: 76 Copynumber: 2.6 Consensus size: 76
664106 AATTAACACT
664116 TAAAA-CTATTTAAACTAAAATACCTAAAACAAA-ATAAAATATAAAAATAATATCCTAAAACTT
1 TAAAACCTATTTAAACTAAAATACCTAAAACAAAGATAAAATATAAAAATAATATCCTAAAACTT
664179 AATTAAAATAC
66 AATTAAAATAC
*
664190 TAAAACCTATTTAAACT-AAATACCTAAAATAAAAGATAAAATATAAAAATAATATCCTAAAACT
1 TAAAACCTATTTAAACTAAAATACCTAAAA-CAAAGATAAAATATAAAAATAATATCCTAAAACT
664254 TAATTAAAATAC
65 TAATTAAAATAC
664266 TAAAACCTATTTAAACTAAAATACCTAAAACAAAGATAAAATATAA
1 TAAAACCTATTTAAACTAAAATACCTAAAACAAAGATAAAATATAA
664312 TATTTAAAAT
Statistics
Matches: 116, Mismatches: 2, Indels: 6
0.94 0.02 0.05
Matches are distributed among these distances:
74 17 0.15
75 14 0.12
76 73 0.63
77 12 0.10
ACGTcount: A:0.60, C:0.12, G:0.01, T:0.27
Consensus pattern (76 bp):
TAAAACCTATTTAAACTAAAATACCTAAAACAAAGATAAAATATAAAAATAATATCCTAAAACTT
AATTAAAATAC
Found at i:666117 original size:16 final size:16
Alignment explanation
Indices: 666096--666127 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
666086 ACCAAATCTA
*
666096 TTTTTTTTCTGCACTG
1 TTTTTTTTCCGCACTG
666112 TTTTTTTTCCGCACTG
1 TTTTTTTTCCGCACTG
666128 CATTGTTCAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.06, C:0.22, G:0.12, T:0.59
Consensus pattern (16 bp):
TTTTTTTTCCGCACTG
Found at i:666296 original size:5 final size:5
Alignment explanation
Indices: 666286--666387 Score: 57
Period size: 5 Copynumber: 19.8 Consensus size: 5
666276 TGTTTAGAGA
* * * *
666286 AAAAT AAAAT -AAAT TAATT AAAAT AAAAT -AAAT AGAAT GAAAAT AAAGTTT
1 AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT -AAAAT AAA--AT
** * *
666337 GCTAA- AAAAT ACAGT AAAAAT AAAACT AAAAT AAAAT AAAAT AAAAT
1 -AAAAT AAAAT AAAAT AAA-AT AAAA-T AAAAT AAAAT AAAAT AAAAT
666384 AAAA
1 AAAA
666388 AATAGAACGA
Statistics
Matches: 73, Mismatches: 15, Indels: 18
0.69 0.14 0.17
Matches are distributed among these distances:
4 10 0.14
5 48 0.66
6 13 0.18
7 1 0.01
8 1 0.01
ACGTcount: A:0.70, C:0.03, G:0.05, T:0.23
Consensus pattern (5 bp):
AAAAT
Found at i:666310 original size:19 final size:20
Alignment explanation
Indices: 666286--666332 Score: 69
Period size: 19 Copynumber: 2.4 Consensus size: 20
666276 TGTTTAGAGA
* *
666286 AAAATAAAATAAAT-TAATT
1 AAAATAAAATAAATAGAATG
666305 AAAATAAAATAAATAGAATG
1 AAAATAAAATAAATAGAATG
666325 AAAATAAA
1 AAAATAAA
666333 GTTTGCTAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
19 14 0.56
20 11 0.44
ACGTcount: A:0.72, C:0.00, G:0.04, T:0.23
Consensus pattern (20 bp):
AAAATAAAATAAATAGAATG
Found at i:666383 original size:15 final size:16
Alignment explanation
Indices: 666353--666387 Score: 63
Period size: 15 Copynumber: 2.2 Consensus size: 16
666343 AAATACAGTA
666353 AAAATAAAACTAAAAT
1 AAAATAAAACTAAAAT
666369 AAAATAAAA-TAAAAT
1 AAAATAAAACTAAAAT
666384 AAAA
1 AAAA
666388 AATAGAACGA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
15 10 0.53
16 9 0.47
ACGTcount: A:0.80, C:0.03, G:0.00, T:0.17
Consensus pattern (16 bp):
AAAATAAAACTAAAAT
Found at i:666388 original size:11 final size:11
Alignment explanation
Indices: 666341--666388 Score: 55
Period size: 11 Copynumber: 4.5 Consensus size: 11
666331 AAGTTTGCTA
* *
666341 AAAAATACAGT
1 AAAAATAAAAT
666352 AAAAATAAAACT
1 AAAAATAAAA-T
666364 -AAAATAAAAT
1 AAAAATAAAAT
666374 -AAAATAAAAT
1 AAAAATAAAAT
666384 AAAAA
1 AAAAA
666389 ATAGAACGAA
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
10 11 0.33
11 21 0.64
12 1 0.03
ACGTcount: A:0.77, C:0.04, G:0.02, T:0.17
Consensus pattern (11 bp):
AAAAATAAAAT
Found at i:671864 original size:19 final size:19
Alignment explanation
Indices: 671827--671865 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 19
671817 ATTCCAGATG
* * *
671827 AAATTAAAAAGATAGAATA
1 AAATAAAAAAGAGAAAATA
671846 AAATAAAAAAGAGAAAATA
1 AAATAAAAAAGAGAAAATA
671865 A
1 A
671866 TAAAATAATA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.74, C:0.00, G:0.10, T:0.15
Consensus pattern (19 bp):
AAATAAAAAAGAGAAAATA
Found at i:671970 original size:17 final size:17
Alignment explanation
Indices: 671945--671978 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
671935 AATGAGATAA
*
671945 AAATTAAATAAACAAAT
1 AAATAAAATAAACAAAT
*
671962 AAATAAAATAAATAAAT
1 AAATAAAATAAACAAAT
671979 TGAGATAAAG
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.74, C:0.03, G:0.00, T:0.24
Consensus pattern (17 bp):
AAATAAAATAAACAAAT
Found at i:672683 original size:76 final size:76
Alignment explanation
Indices: 672585--672793 Score: 368
Period size: 76 Copynumber: 2.8 Consensus size: 76
672575 TTTTAAATCC
* *
672585 TAATTAAAACACTTAAAA-CTATTTAAACTAAAATACCTAAAACAAAGATAAAATATAAAAGTAA
1 TAATTAAAATAC-TAAAACCTATTTAAACTAAAATACCTAAAACAAAGATAAAATATAAAAATAA
672649 TATCTTAAAACT
65 TATCTTAAAACT
672661 TAATTAAAATACTAAAACCTATTTAAACTAAAATACCTAAAACAAAGATAAAATATAAAAATAAT
1 TAATTAAAATACTAAAACCTATTTAAACTAAAATACCTAAAACAAAGATAAAATATAAAAATAAT
672726 ATCTTAAAACT
66 ATCTTAAAACT
*
672737 TAATTAAAATACTAAAACCTATTTAAACTAAAATATCTAAAA-AAAGATAAAATATAA
1 TAATTAAAATACTAAAACCTATTTAAACTAAAATACCTAAAACAAAGATAAAATATAA
672794 TATTTAAAAT
Statistics
Matches: 129, Mismatches: 3, Indels: 3
0.96 0.02 0.02
Matches are distributed among these distances:
75 20 0.16
76 109 0.84
ACGTcount: A:0.59, C:0.11, G:0.02, T:0.28
Consensus pattern (76 bp):
TAATTAAAATACTAAAACCTATTTAAACTAAAATACCTAAAACAAAGATAAAATATAAAAATAAT
ATCTTAAAACT
Found at i:674914 original size:22 final size:22
Alignment explanation
Indices: 674895--674973 Score: 74
Period size: 22 Copynumber: 3.6 Consensus size: 22
674885 TCGTAATTTT
674895 CACCGAAGTGCCACATAA-TTG
1 CACCGAAGTGCCACATAAGTTG
*
674916 TC-TCGAAG-GACCACATAAGTTG
1 -CACCGAAGTG-CCACATAAGTTG
* * *
674938 CATCAAAGTGCCACATAGGGTTG
1 CACCGAAGTGCCACATA-AGTTG
674961 CACCGAAGTGCCA
1 CACCGAAGTGCCA
674974 TATATTTGTC
Statistics
Matches: 47, Mismatches: 5, Indels: 9
0.77 0.08 0.15
Matches are distributed among these distances:
20 1 0.02
21 14 0.30
22 16 0.34
23 16 0.34
ACGTcount: A:0.32, C:0.27, G:0.23, T:0.19
Consensus pattern (22 bp):
CACCGAAGTGCCACATAAGTTG
Found at i:674923 original size:21 final size:22
Alignment explanation
Indices: 674898--674973 Score: 77
Period size: 23 Copynumber: 3.5 Consensus size: 22
674888 TAATTTTCAC
674898 CGAAGTGCCACATAA-TTGTC-T
1 CGAAGTGCCACATAAGTTG-CAT
674919 CGAAG-GACCACATAAGTTGCAT
1 CGAAGTG-CCACATAAGTTGCAT
* * *
674941 CAAAGTGCCACATAGGGTTGCAC
1 CGAAGTGCCACATA-AGTTGCAT
674964 CGAAGTGCCA
1 CGAAGTGCCA
674974 TATATTTGTC
Statistics
Matches: 46, Mismatches: 4, Indels: 8
0.79 0.07 0.14
Matches are distributed among these distances:
20 1 0.02
21 14 0.30
22 15 0.33
23 16 0.35
ACGTcount: A:0.32, C:0.25, G:0.24, T:0.20
Consensus pattern (22 bp):
CGAAGTGCCACATAAGTTGCAT
Found at i:675179 original size:21 final size:21
Alignment explanation
Indices: 675150--675199 Score: 66
Period size: 21 Copynumber: 2.4 Consensus size: 21
675140 ATAGAGTATA
* *
675150 TTCACATTCAC-TGATTCGAAG
1 TTCATATTCACATG-TTCAAAG
675171 TTCATATTCACATGTTCAAAG
1 TTCATATTCACATGTTCAAAG
675192 TTCATATT
1 TTCATATT
675200 TTCATAACAC
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
21 24 0.92
22 2 0.08
ACGTcount: A:0.30, C:0.20, G:0.10, T:0.40
Consensus pattern (21 bp):
TTCATATTCACATGTTCAAAG
Found at i:679025 original size:20 final size:20
Alignment explanation
Indices: 679000--679039 Score: 80
Period size: 20 Copynumber: 2.0 Consensus size: 20
678990 AATATATATG
679000 AATTTGAATTGGATGAGTTA
1 AATTTGAATTGGATGAGTTA
679020 AATTTGAATTGGATGAGTTA
1 AATTTGAATTGGATGAGTTA
679040 GAGGATACAT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.35, C:0.00, G:0.25, T:0.40
Consensus pattern (20 bp):
AATTTGAATTGGATGAGTTA
Found at i:680358 original size:18 final size:22
Alignment explanation
Indices: 680300--680349 Score: 100
Period size: 22 Copynumber: 2.3 Consensus size: 22
680290 CTACCTTAGC
680300 ATCCACACTAAGGATTTATCAA
1 ATCCACACTAAGGATTTATCAA
680322 ATCCACACTAAGGATTTATCAA
1 ATCCACACTAAGGATTTATCAA
680344 ATCCAC
1 ATCCAC
680350 TAGATTTATT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 28 1.00
ACGTcount: A:0.40, C:0.26, G:0.08, T:0.26
Consensus pattern (22 bp):
ATCCACACTAAGGATTTATCAA
Found at i:681547 original size:45 final size:43
Alignment explanation
Indices: 681480--681563 Score: 114
Period size: 43 Copynumber: 1.9 Consensus size: 43
681470 AAATATTTTT
* * *
681480 GATATTAATATTTTTGGTAAAAAATTAATACTTTAAGTAACGCCC
1 GATATTAATA-TTTTAG-AAAAAAATAATACTTTAAATAACGCCC
*
681525 GATATTAATATTTTAGAAAAAAATAATATTTTAAATAAC
1 GATATTAATATTTTAGAAAAAAATAATACTTTAAATAAC
681564 ATTCTACAAA
Statistics
Matches: 35, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
43 20 0.57
44 5 0.14
45 10 0.29
ACGTcount: A:0.46, C:0.07, G:0.08, T:0.38
Consensus pattern (43 bp):
GATATTAATATTTTAGAAAAAAATAATACTTTAAATAACGCCC
Found at i:688287 original size:20 final size:20
Alignment explanation
Indices: 688264--688337 Score: 78
Period size: 20 Copynumber: 3.7 Consensus size: 20
688254 AAATATGTAA
* *
688264 ATCGCAATGCGATTATAACT
1 ATCGCAACGCGATTATGACT
* *
688284 ATCGCAACGAGATTCTGACT
1 ATCGCAACGCGATTATGACT
*
688304 GTCGCAACGCGA-TACTGACT
1 ATCGCAACGCGATTA-TGACT
*
688324 ATCGCAATGCGATT
1 ATCGCAACGCGATT
688338 TTCAAAGCGC
Statistics
Matches: 43, Mismatches: 9, Indels: 3
0.78 0.16 0.05
Matches are distributed among these distances:
19 1 0.02
20 41 0.95
21 1 0.02
ACGTcount: A:0.30, C:0.24, G:0.20, T:0.26
Consensus pattern (20 bp):
ATCGCAACGCGATTATGACT
Found at i:688538 original size:22 final size:22
Alignment explanation
Indices: 688513--688555 Score: 86
Period size: 22 Copynumber: 2.0 Consensus size: 22
688503 GGCGACATCC
688513 GTCCCCATCTCCGACGAAATCA
1 GTCCCCATCTCCGACGAAATCA
688535 GTCCCCATCTCCGACGAAATC
1 GTCCCCATCTCCGACGAAATC
688556 CGTCTATCTC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.26, C:0.42, G:0.14, T:0.19
Consensus pattern (22 bp):
GTCCCCATCTCCGACGAAATCA
Found at i:688963 original size:19 final size:19
Alignment explanation
Indices: 688941--689041 Score: 79
Period size: 20 Copynumber: 5.5 Consensus size: 19
688931 AGAATCGCAA
688941 TGCGATTTT-AGTTTCGCGT
1 TGCGATTTTCA-TTTCGCGT
688960 TGCGATTTTCATTTCGCGT
1 TGCGATTTTCATTTCGCGT
*
688979 TGCGA--TTC---TCGCAT
1 TGCGATTTTCATTTCGCGT
** *
688993 TGCGATAGTCATTTTCGTGT
1 TGCGATTTTCA-TTTCGCGT
* *
689013 TGCGATTTTCATTTTTGTGT
1 TGCGATTTTCA-TTTCGCGT
689033 TGCGATTTT
1 TGCGATTTT
689042 AAGTTTCAGA
Statistics
Matches: 68, Mismatches: 7, Indels: 13
0.77 0.08 0.15
Matches are distributed among these distances:
14 10 0.15
16 2 0.03
17 3 0.04
19 22 0.32
20 31 0.46
ACGTcount: A:0.12, C:0.17, G:0.23, T:0.49
Consensus pattern (19 bp):
TGCGATTTTCATTTCGCGT
Found at i:689005 original size:33 final size:34
Alignment explanation
Indices: 688954--689019 Score: 89
Period size: 33 Copynumber: 2.0 Consensus size: 34
688944 GATTTTAGTT
* **
688954 TCGCGTTGCGATTTTCA-TTTCGCGTTGCGATTC
1 TCGCATTGCGATAGTCATTTTCGCGTTGCGATTC
*
688987 TCGCATTGCGATAGTCATTTTCGTGTTGCGATT
1 TCGCATTGCGATAGTCATTTTCGCGTTGCGATT
689020 TTCATTTTTG
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
33 14 0.50
34 14 0.50
ACGTcount: A:0.12, C:0.21, G:0.24, T:0.42
Consensus pattern (34 bp):
TCGCATTGCGATAGTCATTTTCGCGTTGCGATTC
Found at i:690746 original size:18 final size:18
Alignment explanation
Indices: 690723--690772 Score: 100
Period size: 18 Copynumber: 2.8 Consensus size: 18
690713 TTTACTCGTA
690723 ATTTCACTTAGATTAACC
1 ATTTCACTTAGATTAACC
690741 ATTTCACTTAGATTAACC
1 ATTTCACTTAGATTAACC
690759 ATTTCACTTAGATT
1 ATTTCACTTAGATT
690773 GCTTAGTAAA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 32 1.00
ACGTcount: A:0.32, C:0.20, G:0.06, T:0.42
Consensus pattern (18 bp):
ATTTCACTTAGATTAACC
Found at i:691044 original size:20 final size:20
Alignment explanation
Indices: 690990--691045 Score: 94
Period size: 20 Copynumber: 2.8 Consensus size: 20
690980 GCGATTCTCT
**
690990 CGTTGCGATAGTCAAATTCG
1 CGTTGCGATAGTCATTTTCG
691010 CGTTGCGATAGTCATTTTCG
1 CGTTGCGATAGTCATTTTCG
691030 CGTTGCGATAGTCATT
1 CGTTGCGATAGTCATT
691046 CGTGTTGTGA
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 34 1.00
ACGTcount: A:0.20, C:0.20, G:0.25, T:0.36
Consensus pattern (20 bp):
CGTTGCGATAGTCATTTTCG
Found at i:691052 original size:18 final size:18
Alignment explanation
Indices: 690990--691052 Score: 81
Period size: 20 Copynumber: 3.3 Consensus size: 18
690980 GCGATTCTCT
690990 CGTTGCGATAGTCAAATTCG
1 CGTTGCGATAGTC--ATTCG
691010 CGTTGCGATAGTCATTTTCG
1 CGTTGCGATAGTCA--TTCG
691030 CGTTGCGATAGTCATTCG
1 CGTTGCGATAGTCATTCG
*
691048 TGTTG
1 CGTTG
691053 TGATTTTAAG
Statistics
Matches: 40, Mismatches: 1, Indels: 6
0.85 0.02 0.13
Matches are distributed among these distances:
18 9 0.22
20 31 0.77
ACGTcount: A:0.17, C:0.19, G:0.27, T:0.37
Consensus pattern (18 bp):
CGTTGCGATAGTCATTCG
Found at i:691607 original size:18 final size:18
Alignment explanation
Indices: 691548--691607 Score: 75
Period size: 18 Copynumber: 3.2 Consensus size: 18
691538 CTCACCTGTC
691548 ATCGTTCAAGAGGCCTCCCCT
1 ATCGTTCAAGAGG---CCCCT
* *
691569 ATAGTTTAAGAGGCCCCT
1 ATCGTTCAAGAGGCCCCT
691587 ATCGTTCAAGAGGCCCCT
1 ATCGTTCAAGAGGCCCCT
691605 ATC
1 ATC
691608 ATCCTTCAAG
Statistics
Matches: 35, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
18 24 0.69
21 11 0.31
ACGTcount: A:0.23, C:0.32, G:0.20, T:0.25
Consensus pattern (18 bp):
ATCGTTCAAGAGGCCCCT
Found at i:691617 original size:21 final size:20
Alignment explanation
Indices: 691576--691667 Score: 64
Period size: 21 Copynumber: 4.5 Consensus size: 20
691566 CCTATAGTTT
*
691576 AAGAGGCCCC-T-ATCGTTC
1 AAGAGGCCCCTTCATCCTTC
691594 AAGAGGCCCCTATCATCCTTC
1 AAGAGGCCCCT-TCATCCTTC
* *
691615 AAGAGTCCCCTCCCA-CCATTC
1 AAGAGGCCCCT-TCATCC-TTC
* * *
691636 AAGAGGCCACTGTCATCGTTG
1 AAGAGGCCCCT-TCATCCTTC
*
691657 AAGAGGTCCCT
1 AAGAGGCCCCT
691668 CCCAACATTC
Statistics
Matches: 57, Mismatches: 12, Indels: 7
0.75 0.16 0.09
Matches are distributed among these distances:
18 10 0.18
20 3 0.05
21 43 0.75
22 1 0.02
ACGTcount: A:0.24, C:0.35, G:0.20, T:0.22
Consensus pattern (20 bp):
AAGAGGCCCCTTCATCCTTC
Found at i:691642 original size:42 final size:42
Alignment explanation
Indices: 691591--691682 Score: 114
Period size: 42 Copynumber: 2.2 Consensus size: 42
691581 GCCCCTATCG
* *
691591 TTCAAGAGGCCCCTATCATCCTTCAAGA-GTCCCCTCCCACCA
1 TTCAAGAGGCCACTATCATCCTTCAAGAGGT-CCCTCCCAACA
* * *
691633 TTCAAGAGGCCACTGTCATCGTTGAAGAGGTCCCTCCCAACA
1 TTCAAGAGGCCACTATCATCCTTCAAGAGGTCCCTCCCAACA
*
691675 TTCTAGAG
1 TTCAAGAG
691683 CCCGATTCAC
Statistics
Matches: 43, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
42 41 0.95
43 2 0.05
ACGTcount: A:0.25, C:0.35, G:0.17, T:0.23
Consensus pattern (42 bp):
TTCAAGAGGCCACTATCATCCTTCAAGAGGTCCCTCCCAACA
Found at i:693079 original size:14 final size:14
Alignment explanation
Indices: 693060--693121 Score: 70
Period size: 14 Copynumber: 4.3 Consensus size: 14
693050 TTGCTTGTTT
693060 AATTGATTTGTAAA
1 AATTGATTTGTAAA
693074 AATTGATTTGTAAA
1 AATTGATTTGTAAA
* *
693088 AGTTGATTTGTTTAA
1 AATTGATTTG-TAAA
* *
693103 TATTGATGTGTAAA
1 AATTGATTTGTAAA
693117 TAATT
1 -AATT
693122 CTTATTTGTG
Statistics
Matches: 39, Mismatches: 7, Indels: 3
0.80 0.14 0.06
Matches are distributed among these distances:
14 26 0.67
15 13 0.33
ACGTcount: A:0.37, C:0.00, G:0.16, T:0.47
Consensus pattern (14 bp):
AATTGATTTGTAAA
Found at i:693093 original size:28 final size:29
Alignment explanation
Indices: 693062--693116 Score: 76
Period size: 29 Copynumber: 1.9 Consensus size: 29
693052 GCTTGTTTAA
*
693062 TTGATTTG-TAAAAATTGATTTGTAAAAG
1 TTGATTTGTTAAAAATTGATGTGTAAAAG
* *
693090 TTGATTTGTTTAATATTGATGTGTAAA
1 TTGATTTGTTAAAAATTGATGTGTAAA
693117 TAATTCTTAT
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
28 8 0.35
29 15 0.65
ACGTcount: A:0.35, C:0.00, G:0.18, T:0.47
Consensus pattern (29 bp):
TTGATTTGTTAAAAATTGATGTGTAAAAG
Found at i:693245 original size:20 final size:20
Alignment explanation
Indices: 693220--693271 Score: 63
Period size: 20 Copynumber: 2.6 Consensus size: 20
693210 AGGTACACTT
693220 TCGCAACGCTAAA-CTCAAAA
1 TCGCAACGCTAAAGC-CAAAA
* *
693240 TCGCAATGCGAAAGCCAAAA
1 TCGCAACGCTAAAGCCAAAA
693260 TCGCAACG-TAAA
1 TCGCAACGCTAAA
693272 AGTCAATTCG
Statistics
Matches: 27, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
19 3 0.11
20 23 0.85
21 1 0.04
ACGTcount: A:0.44, C:0.27, G:0.15, T:0.13
Consensus pattern (20 bp):
TCGCAACGCTAAAGCCAAAA
Found at i:693341 original size:20 final size:20
Alignment explanation
Indices: 693316--693466 Score: 134
Period size: 20 Copynumber: 7.8 Consensus size: 20
693306 GCCATTTTCT
* * *
693316 CGTTGCGATAGTCGAATACC
1 CGTTGCGATAGTCAAATTCA
*
693336 CGTTGCGATAATCAAATTCA
1 CGTTGCGATAGTCAAATTCA
*
693356 CATTGCGATAGTCAAATTCA
1 CGTTGCGATAGTCAAATTCA
*
693376 CGTTGCGATAGTCAAATTCG
1 CGTTGCGATAGTCAAATTCA
* *
693396 CGTTGCGAT--T---TTTGA
1 CGTTGCGATAGTCAAATTCA
* * *
693411 -GTTGCGATAATCAAATCCG
1 CGTTGCGATAGTCAAATTCA
*
693430 CGTTGCGATAGTCAAATTCG
1 CGTTGCGATAGTCAAATTCA
* *
693450 CATTGCGATATTCAAAT
1 CGTTGCGATAGTCAAAT
693467 GAATGTGTAA
Statistics
Matches: 106, Mismatches: 19, Indels: 12
0.77 0.14 0.09
Matches are distributed among these distances:
14 8 0.08
15 2 0.02
16 1 0.01
18 1 0.01
19 1 0.01
20 93 0.88
ACGTcount: A:0.28, C:0.20, G:0.21, T:0.31
Consensus pattern (20 bp):
CGTTGCGATAGTCAAATTCA
Found at i:693380 original size:40 final size:40
Alignment explanation
Indices: 693316--693466 Score: 152
Period size: 40 Copynumber: 3.9 Consensus size: 40
693306 GCCATTTTCT
* * * *
693316 CGTTGCGATAGTCGAATACCCGTTGCGATAATCAAATTCA
1 CGTTGCGATAGTCAAATTCACGTTGCGATAATCAAATTCG
* *
693356 CATTGCGATAGTCAAATTCACGTTGCGATAGTCAAATTCG
1 CGTTGCGATAGTCAAATTCACGTTGCGATAATCAAATTCG
* * *
693396 CGTTGCGAT--T---TTTGA-GTTGCGATAATCAAATCCG
1 CGTTGCGATAGTCAAATTCACGTTGCGATAATCAAATTCG
* * *
693430 CGTTGCGATAGTCAAATTCGCATTGCGATATTCAAAT
1 CGTTGCGATAGTCAAATTCACGTTGCGATAATCAAAT
693467 GAATGTGTAA
Statistics
Matches: 89, Mismatches: 16, Indels: 12
0.76 0.14 0.10
Matches are distributed among these distances:
34 26 0.29
35 3 0.03
36 1 0.01
38 1 0.01
39 2 0.02
40 56 0.63
ACGTcount: A:0.28, C:0.20, G:0.21, T:0.31
Consensus pattern (40 bp):
CGTTGCGATAGTCAAATTCACGTTGCGATAATCAAATTCG
Found at i:693415 original size:94 final size:94
Alignment explanation
Indices: 693284--693466 Score: 244
Period size: 94 Copynumber: 1.9 Consensus size: 94
693274 TCAATTCGCA
* * * * *
693284 TTGCGATAGTCTAATACGCTTTGCCATTTTCTCGTTGCGATAGTCGAATACC-CGTTGCGATAAT
1 TTGCGATAGTCAAATACGCGTTGCCATTTTCTAGTTGCGATAATCAAAT-CCGCGTTGCGATAAT
693348 CAAATTCACATTGCGATAGTCAAATTCACG
65 CAAATTCACATTGCGATAGTCAAATTCACG
* * *
693378 TTGCGATAGTCAAATTCGCGTTGCGATTTT-TGAGTTGCGATAATCAAATCCGCGTTGCGATAGT
1 TTGCGATAGTCAAATACGCGTTGCCATTTTCT-AGTTGCGATAATCAAATCCGCGTTGCGATAAT
* *
693442 CAAATTCGCATTGCGATATTCAAAT
65 CAAATTCACATTGCGATAGTCAAAT
693467 GAATGTGTAA
Statistics
Matches: 77, Mismatches: 10, Indels: 4
0.85 0.11 0.04
Matches are distributed among these distances:
93 3 0.04
94 74 0.96
ACGTcount: A:0.27, C:0.20, G:0.20, T:0.33
Consensus pattern (94 bp):
TTGCGATAGTCAAATACGCGTTGCCATTTTCTAGTTGCGATAATCAAATCCGCGTTGCGATAATC
AAATTCACATTGCGATAGTCAAATTCACG
Found at i:693658 original size:18 final size:18
Alignment explanation
Indices: 693632--693672 Score: 64
Period size: 18 Copynumber: 2.3 Consensus size: 18
693622 AGGTGAAGCC
*
693632 GATTGTGATTGGGATTTT
1 GATTGTGATTGCGATTTT
*
693650 GATTTTGATTGCGATTTT
1 GATTGTGATTGCGATTTT
693668 GATTG
1 GATTG
693673 CCTTTTTCTT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.17, C:0.02, G:0.29, T:0.51
Consensus pattern (18 bp):
GATTGTGATTGCGATTTT
Found at i:695725 original size:14 final size:14
Alignment explanation
Indices: 695706--695742 Score: 56
Period size: 14 Copynumber: 2.6 Consensus size: 14
695696 TCCCGTGGCA
695706 TTTTCTTCGGGGAC
1 TTTTCTTCGGGGAC
*
695720 TTTTCTTCGGGGAT
1 TTTTCTTCGGGGAC
695734 TTCTTCTTC
1 TT-TTCTTC
695743 TTCTTTTTCT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
14 15 0.71
15 6 0.29
ACGTcount: A:0.05, C:0.22, G:0.22, T:0.51
Consensus pattern (14 bp):
TTTTCTTCGGGGAC
Found at i:695971 original size:24 final size:24
Alignment explanation
Indices: 695944--695990 Score: 76
Period size: 24 Copynumber: 2.0 Consensus size: 24
695934 CAAAATCCGA
*
695944 GTATTGACCAAGATCAAAGTTCGG
1 GTATTGACAAAGATCAAAGTTCGG
*
695968 GTATTGACAAAGATCAAATTTCG
1 GTATTGACAAAGATCAAAGTTCG
695991 AATACCGACT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.36, C:0.15, G:0.21, T:0.28
Consensus pattern (24 bp):
GTATTGACAAAGATCAAAGTTCGG
Found at i:696855 original size:20 final size:20
Alignment explanation
Indices: 696809--696899 Score: 87
Period size: 20 Copynumber: 4.5 Consensus size: 20
696799 AAATTCAGTG
* * *
696809 TTGCGACAGTCAGAATCGGA
1 TTGCGATAGTCATAATCGCA
696829 TTGCGATAGTCATAATCGCA
1 TTGCGATAGTCATAATCGCA
* *
696849 TTGCGAT-TTACATATTCGCA
1 TTGCGATAGT-CATAATCGCA
* *
696869 TTGCGAT-TTACATATTCGCA
1 TTGCGATAGT-CATAATCGCA
696889 TTGCGATAGTC
1 TTGCGATAGTC
696900 GGAAAATCGC
Statistics
Matches: 63, Mismatches: 6, Indels: 4
0.86 0.08 0.05
Matches are distributed among these distances:
19 1 0.02
20 61 0.97
21 1 0.02
ACGTcount: A:0.26, C:0.20, G:0.21, T:0.33
Consensus pattern (20 bp):
TTGCGATAGTCATAATCGCA
Found at i:699358 original size:22 final size:22
Alignment explanation
Indices: 699328--699369 Score: 75
Period size: 22 Copynumber: 1.9 Consensus size: 22
699318 TGTGAAATTA
699328 GTCCCGAAGGACCTATGTAAAT
1 GTCCCGAAGGACCTATGTAAAT
*
699350 GTCCTGAAGGACCTATGTAA
1 GTCCCGAAGGACCTATGTAA
699370 CCCTCGACTC
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.31, C:0.21, G:0.24, T:0.24
Consensus pattern (22 bp):
GTCCCGAAGGACCTATGTAAAT
Found at i:707599 original size:63 final size:64
Alignment explanation
Indices: 707532--707655 Score: 189
Period size: 63 Copynumber: 1.9 Consensus size: 64
707522 TCAGATTTGA
*
707532 GCAAAAATTCCAGAATTCAAAAAGGGTACCGATA-CCCCCAGGGGTATCC-ATACCCCCTGAAAG
1 GCAAAAATTCCAGAATACAAAAAGGGTACCGATACCCCCCAGGGGTA-CCGATACCCCCTGAAAG
* *
707595 GCAAAAATTCCAGAATACAAAGAGGGTATCGATATCCCCCCAGGGGTACCGATACCCCCTG
1 GCAAAAATTCCAGAATACAAAAAGGGTACCGATA-CCCCCCAGGGGTACCGATACCCCCTG
707656 TAGGGGTACC
Statistics
Matches: 55, Mismatches: 3, Indels: 4
0.89 0.05 0.06
Matches are distributed among these distances:
63 31 0.56
64 2 0.04
65 22 0.40
ACGTcount: A:0.35, C:0.29, G:0.20, T:0.16
Consensus pattern (64 bp):
GCAAAAATTCCAGAATACAAAAAGGGTACCGATACCCCCCAGGGGTACCGATACCCCCTGAAAG
Found at i:708810 original size:17 final size:17
Alignment explanation
Indices: 708788--708820 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
708778 TTTTTTAAGA
*
708788 TTAAAACTTAATTTGAT
1 TTAAAAATTAATTTGAT
708805 TTAAAAATTAATTTGA
1 TTAAAAATTAATTTGA
708821 AAGATTAAAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.45, C:0.03, G:0.06, T:0.45
Consensus pattern (17 bp):
TTAAAAATTAATTTGAT
Found at i:710122 original size:19 final size:20
Alignment explanation
Indices: 710087--710124 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
710077 CAAAATTTCA
710087 TTTTGATTTTCAAAATCAAC
1 TTTTGATTTTCAAAATCAAC
*
710107 TTTTGCTTTT-AAAATCAA
1 TTTTGATTTTCAAAATCAA
710125 ATTATCTTTA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 8 0.47
20 9 0.53
ACGTcount: A:0.34, C:0.13, G:0.05, T:0.47
Consensus pattern (20 bp):
TTTTGATTTTCAAAATCAAC
Found at i:715223 original size:18 final size:18
Alignment explanation
Indices: 715188--715245 Score: 62
Period size: 21 Copynumber: 3.1 Consensus size: 18
715178 CAACAATTGG
* *
715188 TAACAATAGGTATATTTT
1 TAACAATTGATATATTTT
*
715206 TAACAATTGATATCTTTTTGT
1 TAACAATTGATA--TATTT-T
715227 TAACAATTGATATATTTT
1 TAACAATTGATATATTTT
715245 T
1 T
715246 CATTAAACAT
Statistics
Matches: 33, Mismatches: 4, Indels: 6
0.77 0.09 0.14
Matches are distributed among these distances:
18 12 0.36
19 4 0.12
20 4 0.12
21 13 0.39
ACGTcount: A:0.34, C:0.07, G:0.09, T:0.50
Consensus pattern (18 bp):
TAACAATTGATATATTTT
Found at i:715231 original size:21 final size:21
Alignment explanation
Indices: 715205--715245 Score: 73
Period size: 21 Copynumber: 2.0 Consensus size: 21
715195 AGGTATATTT
*
715205 TTAACAATTGATATCTTTTTG
1 TTAACAATTGATATATTTTTG
715226 TTAACAATTGATATATTTTT
1 TTAACAATTGATATATTTTT
715246 CATTAAACAT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.32, C:0.07, G:0.07, T:0.54
Consensus pattern (21 bp):
TTAACAATTGATATATTTTTG
Found at i:715254 original size:23 final size:21
Alignment explanation
Indices: 715205--715251 Score: 67
Period size: 21 Copynumber: 2.2 Consensus size: 21
715195 AGGTATATTT
* *
715205 TTAACAATTGATATCTTTTTG
1 TTAACAATTGATATATTTTTA
715226 TTAACAATTGATATATTTTTCA
1 TTAACAATTGATATATTTTT-A
715248 TTAA
1 TTAA
715252 ACATTTATTA
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
21 19 0.83
22 4 0.17
ACGTcount: A:0.34, C:0.09, G:0.06, T:0.51
Consensus pattern (21 bp):
TTAACAATTGATATATTTTTA
Found at i:715526 original size:22 final size:20
Alignment explanation
Indices: 715463--715537 Score: 100
Period size: 19 Copynumber: 3.8 Consensus size: 20
715453 AATGCAAAGA
*
715463 GGGTACCGATA-CCCCTCAT
1 GGGTACCGATACCCCCTCAG
715482 GGGTACCGATACCCCC-CAG
1 GGGTACCGATACCCCCTCAG
715501 GGGTACCGATACCCCCCTGCAG
1 GGGTACCGATA-CCCCCT-CAG
*
715523 GGGTACCCATACCCC
1 GGGTACCGATACCCC
715538 TTGGCTATAA
Statistics
Matches: 50, Mismatches: 2, Indels: 6
0.86 0.03 0.10
Matches are distributed among these distances:
19 24 0.48
20 9 0.18
21 4 0.08
22 13 0.26
ACGTcount: A:0.20, C:0.41, G:0.24, T:0.15
Consensus pattern (20 bp):
GGGTACCGATACCCCCTCAG
Found at i:718154 original size:12 final size:12
Alignment explanation
Indices: 718134--718165 Score: 55
Period size: 12 Copynumber: 2.7 Consensus size: 12
718124 CGCCTTTCAA
*
718134 CCTACTCTTCCT
1 CCTAATCTTCCT
718146 CCTAATCTTCCT
1 CCTAATCTTCCT
718158 CCTAATCT
1 CCTAATCT
718166 CTACATTGCT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.16, C:0.44, G:0.00, T:0.41
Consensus pattern (12 bp):
CCTAATCTTCCT
Found at i:720806 original size:54 final size:55
Alignment explanation
Indices: 720742--720867 Score: 200
Period size: 55 Copynumber: 2.3 Consensus size: 55
720732 CCACCCCAAA
* *
720742 AGGGTACCGATACCCC-ATGTAAGATTTAGCTCCGAGAAATTACAGATTGCTCGG
1 AGGGTACCGATACCCCAATGTAAGATTTAGCTCCGAGAAATAACAAATTGCTCGG
*
720796 AGGGTACCGATACCCCAATGTAAGATTTGGCTCCGAGAAATAACAAATTGCTCGG
1 AGGGTACCGATACCCCAATGTAAGATTTAGCTCCGAGAAATAACAAATTGCTCGG
*
720851 AGGGTATCGATAGCCCC
1 AGGGTACCGATA-CCCC
720868 TAGGAGGTAC
Statistics
Matches: 66, Mismatches: 4, Indels: 2
0.92 0.06 0.03
Matches are distributed among these distances:
54 16 0.24
55 46 0.70
56 4 0.06
ACGTcount: A:0.30, C:0.23, G:0.25, T:0.22
Consensus pattern (55 bp):
AGGGTACCGATACCCCAATGTAAGATTTAGCTCCGAGAAATAACAAATTGCTCGG
Found at i:722315 original size:19 final size:20
Alignment explanation
Indices: 722283--722320 Score: 51
Period size: 19 Copynumber: 1.9 Consensus size: 20
722273 AACAAAGAGA
* *
722283 AAAATCAAATCAAATCAAAT
1 AAAATCAAAACAAAACAAAT
722303 AAAA-CAAAACAAAACAAA
1 AAAATCAAAACAAAACAAA
722321 ACTTGGGAGA
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
19 12 0.75
20 4 0.25
ACGTcount: A:0.74, C:0.16, G:0.00, T:0.11
Consensus pattern (20 bp):
AAAATCAAAACAAAACAAAT
Found at i:724183 original size:23 final size:23
Alignment explanation
Indices: 724157--724202 Score: 83
Period size: 23 Copynumber: 2.0 Consensus size: 23
724147 ATTGACATTG
*
724157 AATCAAAGCTTCATTTCTTTGAT
1 AATCAAAGCTTCATTCCTTTGAT
724180 AATCAAAGCTTCATTCCTTTGAT
1 AATCAAAGCTTCATTCCTTTGAT
724203 TTTTTGTTTT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.30, C:0.20, G:0.09, T:0.41
Consensus pattern (23 bp):
AATCAAAGCTTCATTCCTTTGAT
Done.