Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01014526.1 Corchorus olitorius cultivar O-4 contig14559, 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: 117133
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.33
Found at i:92 original size:34 final size:34
Alignment explanation
Indices: 1--98 Score: 102
Period size: 34 Copynumber: 3.0 Consensus size: 34
1 CTAGACCATGGCGGGTCGCGATCCGCGTCGCGACC
1 CTAGACCATGGCGGGTCGCGATCCGCG-CGCGACC
* * *
36 C--GGCCAT---GGATC-CGGGT-CGCGCGCGACC
1 CTAGACCATGGCGGGTCGC-GATCCGCGCGCGACC
64 CTAGACCATGGCGGGTCGCGATCCGCGCGCGACC
1 CTAGACCATGGCGGGTCGCGATCCGCGCGCGACC
98 C
1 C
99 GCTATTTTTT
Statistics
Matches: 49, Mismatches: 6, Indels: 17
0.68 0.08 0.24
Matches are distributed among these distances:
28 8 0.16
29 5 0.10
30 11 0.22
33 11 0.22
34 13 0.27
35 1 0.02
ACGTcount: A:0.13, C:0.39, G:0.36, T:0.12
Consensus pattern (34 bp):
CTAGACCATGGCGGGTCGCGATCCGCGCGCGACC
Found at i:123 original size:15 final size:17
Alignment explanation
Indices: 103--140 Score: 53
Period size: 18 Copynumber: 2.3 Consensus size: 17
93 CGACCCGCTA
103 TTTTTTC-TG-GGTTTT
1 TTTTTTCGTGCGGTTTT
118 TTTTTTCTGTGCGGTTTT
1 TTTTTTC-GTGCGGTTTT
136 TTTTT
1 TTTTT
141 AATCTTTTTA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
15 7 0.35
17 2 0.10
18 11 0.55
ACGTcount: A:0.00, C:0.08, G:0.18, T:0.74
Consensus pattern (17 bp):
TTTTTTCGTGCGGTTTT
Found at i:7831 original size:616 final size:616
Alignment explanation
Indices: 6658--7853 Score: 2374
Period size: 616 Copynumber: 1.9 Consensus size: 616
6648 TAAAGCCGAA
6658 CTACTTTTCGCAGACGCGAGGGGTATTTTTGGTCATTTGCCACCCAGTTTAGCGCTATTTTGAAA
1 CTACTTTTCGCAGACGCGAGGGGTATTTTTGGTCATTTGCCACCCAGTTTAGCGCTATTTTGAAA
6723 TCCGCGAATTTGATTGGTCGAGAACTATTCAACCGAATTTGAAAAAATTTGAAATCCGTAAAGAT
66 TCCGCGAATTTGATTGGTCGAGAACTATTCAACCGAATTTGAAAAAATTTGAAATCCGTAAAGAT
6788 GATTGGTTAATTATTTTTTGTGGGGTCGCGCAGCGAACAGGATAAAGACAAAAAGTAGAGGTCTC
131 GATTGGTTAATTATTTTTTGTGGGGTCGCGCAGCGAACAGGATAAAGACAAAAAGTAGAGGTCTC
6853 GAAAATCATTGACGAAGACTTGAAACGGTAAAACTTTTTCACTGTGGTAAATATAATTTTATCTG
196 GAAAATCATTGACGAAGACTTGAAACGGTAAAACTTTTTCACTGTGGTAAATATAATTTTATCTG
*
6918 TGGTAAAATTGAATAGTAACTAGGGTAAAGTGCATCAAGTGCATCGGTTTGCTATTTGATGCAAA
261 TGGTAAAATTGAATAGTAACTAGGGTAAAGTGCATCAAGTGCATCAGTTTGCTATTTGATGCAAA
6983 TGATGCAGGAGAGAGAAAGCTGACGTGTCATAATATGGTTGGTTCTTAGGCGCGTGAAGCTCCAC
326 TGATGCAGGAGAGAGAAAGCTGACGTGTCATAATATGGTTGGTTCTTAGGCGCGTGAAGCTCCAC
7048 TCAGAATACCTTTCCAGATGATGAAATCCGGCCTAACTTCTGTTCCGGTGATCAATTTACGACAC
391 TCAGAATACCTTTCCAGATGATGAAATCCGGCCTAACTTCTGTTCCGGTGATCAATTTACGACAC
7113 GCGCGGCGGTGTGTACCCCTGGGAGGGTAGAAACCACTACGCTAGGCAGCCTTAGCTCCGCACGT
456 GCGCGGCGGTGTGTACCCCTGGGAGGGTAGAAACCACTACGCTAGGCAGCCTTAGCTCCGCACGT
7178 AGCTTAACGCCGATCAGAAACCGATCAAGATCCATTGCTGTTTGCACGTACTATTATTACTTTCC
521 AGCTTAACGCCGATCAGAAACCGATCAAGATCCATTGCTGTTTGCACGTACTATTATTACTTTCC
7243 TCCTGATGCCCTTTAGATTCCCATTTTGCCC
586 TCCTGATGCCCTTTAGATTCCCATTTTGCCC
*
7274 CTACTTTTCGCGGACGCGAGGGGTATTTTTGGTCATTTGCCACCCAGTTTAGCGCTATTTTGAAA
1 CTACTTTTCGCAGACGCGAGGGGTATTTTTGGTCATTTGCCACCCAGTTTAGCGCTATTTTGAAA
7339 TCCGCGAATTTGATTGGTCGAGAACTATTCAACCGAATTTGAAAAAATTTGAAATCCGTAAAGAT
66 TCCGCGAATTTGATTGGTCGAGAACTATTCAACCGAATTTGAAAAAATTTGAAATCCGTAAAGAT
7404 GATTGGTTAATTATTTTTTGTGGGGTCGCGCAGCGAACAGGATAAAGACAAAAAGTAGAGGTCTC
131 GATTGGTTAATTATTTTTTGTGGGGTCGCGCAGCGAACAGGATAAAGACAAAAAGTAGAGGTCTC
7469 GAAAATCATTGACGAAGACTTGAAACGGTAAAACTTTTTCACTGTGGTAAATATAATTTTATCTG
196 GAAAATCATTGACGAAGACTTGAAACGGTAAAACTTTTTCACTGTGGTAAATATAATTTTATCTG
7534 TGGTAAAATTGAATAGTAACTAGGGTAAAGTGCATCAAGTGCATCAGTTTGCTATTTGATGCAAA
261 TGGTAAAATTGAATAGTAACTAGGGTAAAGTGCATCAAGTGCATCAGTTTGCTATTTGATGCAAA
7599 TGATGCAGGAGAGAGAAAGCTGACGTGTCATAATATGGTTGGTTCTTAGGCGCGTGAAGCTCCAC
326 TGATGCAGGAGAGAGAAAGCTGACGTGTCATAATATGGTTGGTTCTTAGGCGCGTGAAGCTCCAC
7664 TCAGAATACCTTTCCAGATGATGAAATCCGGCCTAACTTCTGTTCCGGTGATCAATTTACGACAC
391 TCAGAATACCTTTCCAGATGATGAAATCCGGCCTAACTTCTGTTCCGGTGATCAATTTACGACAC
7729 GCGCGGCGGTGTGTACCCCTGGGAGGGTAGAAACCACTACGCTAGGCAGCCTTAGCTCCGCACGT
456 GCGCGGCGGTGTGTACCCCTGGGAGGGTAGAAACCACTACGCTAGGCAGCCTTAGCTCCGCACGT
7794 AGCTTAACGCCGATCAGAAACCGATCAAGATCCATTGCTGTTTGCACGTACTATTATTAC
521 AGCTTAACGCCGATCAGAAACCGATCAAGATCCATTGCTGTTTGCACGTACTATTATTAC
7854 CGTGCAAACA
Statistics
Matches: 578, Mismatches: 2, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
616 578 1.00
ACGTcount: A:0.28, C:0.19, G:0.23, T:0.29
Consensus pattern (616 bp):
CTACTTTTCGCAGACGCGAGGGGTATTTTTGGTCATTTGCCACCCAGTTTAGCGCTATTTTGAAA
TCCGCGAATTTGATTGGTCGAGAACTATTCAACCGAATTTGAAAAAATTTGAAATCCGTAAAGAT
GATTGGTTAATTATTTTTTGTGGGGTCGCGCAGCGAACAGGATAAAGACAAAAAGTAGAGGTCTC
GAAAATCATTGACGAAGACTTGAAACGGTAAAACTTTTTCACTGTGGTAAATATAATTTTATCTG
TGGTAAAATTGAATAGTAACTAGGGTAAAGTGCATCAAGTGCATCAGTTTGCTATTTGATGCAAA
TGATGCAGGAGAGAGAAAGCTGACGTGTCATAATATGGTTGGTTCTTAGGCGCGTGAAGCTCCAC
TCAGAATACCTTTCCAGATGATGAAATCCGGCCTAACTTCTGTTCCGGTGATCAATTTACGACAC
GCGCGGCGGTGTGTACCCCTGGGAGGGTAGAAACCACTACGCTAGGCAGCCTTAGCTCCGCACGT
AGCTTAACGCCGATCAGAAACCGATCAAGATCCATTGCTGTTTGCACGTACTATTATTACTTTCC
TCCTGATGCCCTTTAGATTCCCATTTTGCCC
Found at i:24447 original size:19 final size:19
Alignment explanation
Indices: 24423--24459 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
24413 CTGTTTAGCA
24423 ACTGTACAGATGAGATTAC
1 ACTGTACAGATGAGATTAC
*
24442 ACTGTACAGATTAGATTA
1 ACTGTACAGATGAGATTA
24460 TGTATTGTAC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.38, C:0.14, G:0.19, T:0.30
Consensus pattern (19 bp):
ACTGTACAGATGAGATTAC
Found at i:24970 original size:21 final size:21
Alignment explanation
Indices: 24931--24970 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
24921 CAAATTCTCA
* * *
24931 TTAAAATCTTATAAGCAATGG
1 TTAAAAACTTAAAACCAATGG
24952 TTAAAAACTTAAAACCAAT
1 TTAAAAACTTAAAACCAAT
24971 TATAGAAACA
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.50, C:0.12, G:0.07, T:0.30
Consensus pattern (21 bp):
TTAAAAACTTAAAACCAATGG
Found at i:25943 original size:16 final size:15
Alignment explanation
Indices: 25922--25952 Score: 53
Period size: 16 Copynumber: 2.0 Consensus size: 15
25912 AAAAGGGTCC
25922 TCTTTTTTTTCTTTTT
1 TCTTTTTTTT-TTTTT
25938 TCTTTTTTTTTTTTT
1 TCTTTTTTTTTTTTT
25953 CGGGAACCCT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 5 0.33
16 10 0.67
ACGTcount: A:0.00, C:0.10, G:0.00, T:0.90
Consensus pattern (15 bp):
TCTTTTTTTTTTTTT
Found at i:41499 original size:64 final size:63
Alignment explanation
Indices: 41399--41525 Score: 218
Period size: 64 Copynumber: 2.0 Consensus size: 63
41389 ATGTGTAGCC
** *
41399 AAAAAAAAAGACCCCATTTTACCCTTATCGGGATTAAAATTCGAAATCCTTCATAGAAAATCT
1 AAAAAAAAAGACCCCATTCCACCCTTATAGGGATTAAAATTCGAAATCCTTCATAGAAAATCT
41462 AAAAAGAAAAGACCCCATTCCACCCTTATAGGGATTAAAATTCGAAATCCTTCATAGAAAATCT
1 AAAAA-AAAAGACCCCATTCCACCCTTATAGGGATTAAAATTCGAAATCCTTCATAGAAAATCT
41526 CAATTTTACC
Statistics
Matches: 60, Mismatches: 3, Indels: 1
0.94 0.05 0.02
Matches are distributed among these distances:
63 5 0.08
64 55 0.92
ACGTcount: A:0.43, C:0.21, G:0.10, T:0.25
Consensus pattern (63 bp):
AAAAAAAAAGACCCCATTCCACCCTTATAGGGATTAAAATTCGAAATCCTTCATAGAAAATCT
Found at i:41573 original size:49 final size:50
Alignment explanation
Indices: 41483--41577 Score: 140
Period size: 49 Copynumber: 1.9 Consensus size: 50
41473 ACCCCATTCC
*
41483 ACCCTTATAGGGATTAAAATTCGAAATCCTTCATAGAAAATCTCAATTTT
1 ACCCTTATAGGGATTAAAATTCAAAATCCTTCATAGAAAATCTCAATTTT
* *
41533 ACCCTTATTGGGATT-AGATTCAAAATCTCTT-ATAGAAAATCTCAA
1 ACCCTTATAGGGATTAAAATTCAAAATC-CTTCATAGAAAATCTCAA
41578 GCTCTAACCA
Statistics
Matches: 41, Mismatches: 3, Indels: 3
0.87 0.06 0.06
Matches are distributed among these distances:
49 24 0.59
50 17 0.41
ACGTcount: A:0.38, C:0.18, G:0.11, T:0.34
Consensus pattern (50 bp):
ACCCTTATAGGGATTAAAATTCAAAATCCTTCATAGAAAATCTCAATTTT
Found at i:41775 original size:31 final size:31
Alignment explanation
Indices: 41737--41838 Score: 115
Period size: 31 Copynumber: 3.4 Consensus size: 31
41727 TTAATGTGGC
41737 CAAATAAGGGCCTAACGTTATCGAAAATGCT
1 CAAATAAGGGCCTAACGTTATCGAAAATGCT
* * * *
41768 CAAATAAGGGCCCGATC-TT-T--TAATTGGC-
1 CAAATAAGGG-CCTAACGTTATCGAAAAT-GCT
41796 CAAATAAGGGCCTAACGTTATCGAAAATGCT
1 CAAATAAGGGCCTAACGTTATCGAAAATGCT
41827 CAAATAAGGGCC
1 CAAATAAGGGCC
41839 AGGCGTCAGT
Statistics
Matches: 56, Mismatches: 8, Indels: 14
0.72 0.10 0.18
Matches are distributed among these distances:
27 4 0.07
28 15 0.27
29 3 0.05
30 3 0.05
31 27 0.48
32 4 0.07
ACGTcount: A:0.36, C:0.21, G:0.21, T:0.23
Consensus pattern (31 bp):
CAAATAAGGGCCTAACGTTATCGAAAATGCT
Found at i:41807 original size:28 final size:28
Alignment explanation
Indices: 41708--41807 Score: 87
Period size: 28 Copynumber: 3.4 Consensus size: 28
41698 CCAAAATGCT
*
41708 CAAATAAGAGCCCGATCTTTTAATGTGGC
1 CAAATAAGGGCCCGATCTTTTAAT-TGGC
* * * *
41737 CAAATAAGGG-CCTAACGTTATCGAAAAT-GC
1 CAAATAAGGGCCCGATC-TT-T--TAATTGGC
41767 TCAAATAAGGGCCCGATCTTTTAATTGGC
1 -CAAATAAGGGCCCGATCTTTTAATTGGC
41796 CAAATAAGGGCC
1 CAAATAAGGGCC
41808 TAACGTTATC
Statistics
Matches: 55, Mismatches: 9, Indels: 15
0.70 0.11 0.19
Matches are distributed among these distances:
28 19 0.35
29 13 0.24
30 4 0.07
31 13 0.24
32 6 0.11
ACGTcount: A:0.34, C:0.21, G:0.21, T:0.24
Consensus pattern (28 bp):
CAAATAAGGGCCCGATCTTTTAATTGGC
Found at i:41822 original size:59 final size:60
Alignment explanation
Indices: 41678--41838 Score: 281
Period size: 60 Copynumber: 2.7 Consensus size: 60
41668 CTAATTGCTT
* *
41678 AAATAAGGGCCTAACGTT-TGCCAAAATGCTCAAATAAGAGCCCGATCTTTTAATGTGGCC
1 AAATAAGGGCCTAACGTTAT-CGAAAATGCTCAAATAAGGGCCCGATCTTTTAATGTGGCC
41738 AAATAAGGGCCTAACGTTATCGAAAATGCTCAAATAAGGGCCCGATCTTTTAAT-TGGCC
1 AAATAAGGGCCTAACGTTATCGAAAATGCTCAAATAAGGGCCCGATCTTTTAATGTGGCC
41797 AAATAAGGGCCTAACGTTATCGAAAATGCTCAAATAAGGGCC
1 AAATAAGGGCCTAACGTTATCGAAAATGCTCAAATAAGGGCC
41839 AGGCGTCAGT
Statistics
Matches: 98, Mismatches: 2, Indels: 3
0.95 0.02 0.03
Matches are distributed among these distances:
59 47 0.48
60 50 0.51
61 1 0.01
ACGTcount: A:0.35, C:0.20, G:0.20, T:0.24
Consensus pattern (60 bp):
AAATAAGGGCCTAACGTTATCGAAAATGCTCAAATAAGGGCCCGATCTTTTAATGTGGCC
Found at i:41917 original size:31 final size:31
Alignment explanation
Indices: 41877--42043 Score: 127
Period size: 31 Copynumber: 5.6 Consensus size: 31
41867 TTTTCGACGC
41877 TAGGCCCTTATTTGAGCATTTTGGCAAACGT
1 TAGGCCCTTATTTGAGCATTTTGGCAAACGT
* ** * **
41908 TGGGCCCTTATTTG-GCCAAATT--AAAATAT
1 TAGGCCCTTATTTGAG-CATTTTGGCAAACGT
*
41937 CAGGCCCTTATTTGAGCATTTTGGCAAACGT
1 TAGGCCCTTATTTGAGCATTTTGGCAAACGT
**
41968 TAGGCCCTTATTTG-GCCAAATT---AAA-GAT
1 TAGGCCCTTATTTGAG-CATTTTGGCAAACG-T
* * *
41996 CAAGCCCTTATTTGAGCATTTTGGTAAACGT
1 TAGGCCCTTATTTGAGCATTTTGGCAAACGT
*
42027 TAGGCCC-TAATTGAGCA
1 TAGGCCCTTATTTGAGCA
42044 ATTAGCCAAA
Statistics
Matches: 102, Mismatches: 23, Indels: 23
0.69 0.16 0.16
Matches are distributed among these distances:
27 1 0.01
28 20 0.20
29 21 0.21
30 12 0.12
31 47 0.46
32 1 0.01
ACGTcount: A:0.27, C:0.20, G:0.20, T:0.33
Consensus pattern (31 bp):
TAGGCCCTTATTTGAGCATTTTGGCAAACGT
Found at i:41974 original size:60 final size:59
Alignment explanation
Indices: 41878--42034 Score: 269
Period size: 60 Copynumber: 2.6 Consensus size: 59
41868 TTTCGACGCT
* *
41878 AGGCCCTTATTTGAGCATTTTGGCAAACGTTGGGCCCTTATTTGGCCAAATTAAAATATC
1 AGGCCCTTATTTGAGCATTTTGGCAAACGTTAGGCCCTTATTTGGCCAAATT-AAAGATC
41938 AGGCCCTTATTTGAGCATTTTGGCAAACGTTAGGCCCTTATTTGGCCAAATTAAAGATC
1 AGGCCCTTATTTGAGCATTTTGGCAAACGTTAGGCCCTTATTTGGCCAAATTAAAGATC
* *
41997 AAGCCCTTATTTGAGCATTTTGGTAAACGTTAGGCCCT
1 AGGCCCTTATTTGAGCATTTTGGCAAACGTTAGGCCCT
42035 AATTGAGCAA
Statistics
Matches: 93, Mismatches: 4, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
59 42 0.45
60 51 0.55
ACGTcount: A:0.26, C:0.20, G:0.20, T:0.33
Consensus pattern (59 bp):
AGGCCCTTATTTGAGCATTTTGGCAAACGTTAGGCCCTTATTTGGCCAAATTAAAGATC
Found at i:64722 original size:38 final size:38
Alignment explanation
Indices: 64675--64749 Score: 141
Period size: 38 Copynumber: 2.0 Consensus size: 38
64665 TTGCTAACCA
64675 ATTGACTTGGATGATCTGTCTTGGCTGCACTGCCATTG
1 ATTGACTTGGATGATCTGTCTTGGCTGCACTGCCATTG
*
64713 ATTGACTTGGATGATCTGTTTTGGCTGCACTGCCATT
1 ATTGACTTGGATGATCTGTCTTGGCTGCACTGCCATT
64750 AACAAGGAAC
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
38 36 1.00
ACGTcount: A:0.16, C:0.20, G:0.25, T:0.39
Consensus pattern (38 bp):
ATTGACTTGGATGATCTGTCTTGGCTGCACTGCCATTG
Found at i:70323 original size:73 final size:73
Alignment explanation
Indices: 70238--70381 Score: 252
Period size: 73 Copynumber: 2.0 Consensus size: 73
70228 AGGCCATCAT
*
70238 GATTTTATATCTGCTAATAGCAGGGCAATTCAATTGACTATTATGTTATTACATTAGTGAAATTG
1 GATTTTATATCTGCTAATAGCAGGGCAAGTCAATTGACTATTATGTTATTACATTAGTGAAATTG
70303 ATTATCGA
66 ATTATCGA
* * *
70311 GATTTTATATCTGCTACTAGCAGGGCAAGTCAATTGACTGTTATGTTATTTCATTAGTGAAATTG
1 GATTTTATATCTGCTAATAGCAGGGCAAGTCAATTGACTATTATGTTATTACATTAGTGAAATTG
70376 ATTATC
66 ATTATC
70382 AAATTGACAC
Statistics
Matches: 67, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
73 67 1.00
ACGTcount: A:0.31, C:0.12, G:0.17, T:0.40
Consensus pattern (73 bp):
GATTTTATATCTGCTAATAGCAGGGCAAGTCAATTGACTATTATGTTATTACATTAGTGAAATTG
ATTATCGA
Found at i:72335 original size:40 final size:42
Alignment explanation
Indices: 72280--72363 Score: 127
Period size: 44 Copynumber: 2.0 Consensus size: 42
72270 TTAATATCTC
*
72280 AATTAAATTTCAACTC-A-TACTTATGTTCTACTTTGAATGA
1 AATTAAATTTCAACTCAATTACTTATGTTCCACTTTGAATGA
72320 AATTAAATTTCAACTCATATTTACTTATGTTCCACTTTGAATGA
1 AATTAAATTTCAACTCA-A-TTACTTATGTTCCACTTTGAATGA
72364 TTTTGAGAGA
Statistics
Matches: 39, Mismatches: 1, Indels: 4
0.89 0.02 0.09
Matches are distributed among these distances:
40 16 0.41
42 1 0.03
44 22 0.56
ACGTcount: A:0.35, C:0.15, G:0.07, T:0.43
Consensus pattern (42 bp):
AATTAAATTTCAACTCAATTACTTATGTTCCACTTTGAATGA
Found at i:92838 original size:335 final size:333
Alignment explanation
Indices: 92093--94171 Score: 2847
Period size: 335 Copynumber: 6.2 Consensus size: 333
92083 TTTTGGTCAT
92093 GAGAGTCGTTAAAATATCTATATTCATCTAACCAAATCTCAGCCACATTGGATTTGATGATTAGT
1 GAGAGTCGTTAAAATATCTATATTCATCTAACCAAATCTCAGCCACATTGGATTTGATGATTAGT
* * * *
92158 TTTTATGAGCATCTATATCTTGTTTCGATTTAATCAGAAATTAGTTTAGGAAAAAATTGGAAAAC
66 TTTTATGAGCATCCAAATCTGGTTTCGATTTAATCAGAAATTAATTTAGGAAAAAATTGGAAAAC
* ** *
92223 GATATTAGAAACATTAAACGCCTTTAATGTTTTTTTCGTTGAATTATATATATTTTTTATGAGTA
131 GATATTAGAAACATTAAACGCCTTCAAACTTTTTTGCGTTGAA-T-TATATATTTTTTATGAGTA
* * *
92288 TTTTTGGCCCAAAATTAAGGAAAAATATTTCGGGTCAAATTTTGCAAAATTTTAGTCGAAATCGT
194 -TTTTGGCCAAAAATTAAGGAAAAATATTTCGGGTCAATTTTTGCAAAATTTTAGCCGAAATCGT
* ** * * * * *
92353 GTACTAACCATCACGGTTTTTGGCTAAAAATGC--GTTCCGAGGCACCGACACAGTATTGCATGA
258 GTACTAACCATCACGGTTTTTGGCTAAAAACGCGTGTTTAGGGGCATCGGCTCAGTTTTGCATGA
**
92416 TTTTTGGCGCC
323 TTTTTGGTACC
* * *
92427 GAGAGTCTTTAATATATCTATATTCATCTAACCAAATCTCAGCCACATTGGATTTGAGGATTAGT
1 GAGAGTCGTTAAAATATCTATATTCATCTAACCAAATCTCAGCCACATTGGATTTGATGATTAGT
*
92492 TTTTATGAGCATCCAAATCTTGTTTCGATTTAATCAGAAATTAATTTAGGAAAAAATTGGAAAAA
66 TTTTATGAGCATCCAAATCTGGTTTCGATTTAATCAGAAATTAATTTAGGAAAAAATTGG-AAAA
** * ** * * ** * * *
92557 TAATATTGGAAATGTCAAAAGCCCTTCAAAAATTTTGGCTTTGACTTATATATTTTTTATGAGTA
130 CGATATTAGAAACATTAAACG-CCTTCAAACTTTTTTGCGTTGAATTATATATTTTTTATGAGTA
* * * * * **
92622 TCTTGGCCAAAAATTGAGAAAAAATATTTCGGGTCAATTTTTGTAATATTTTAAACGAAATCGTG
194 TTTTGGCCAAAAATTAAGGAAAAATATTTCGGGTCAATTTTTGCAAAATTTTAGCCGAAATCGTG
* *
92687 TACATTACCATCACGG-TTTTGGCTAAAAAGGCGTGTTTAGGGGCATCGGCTCAGTTTTGCATGA
259 TAC-TAACCATCACGGTTTTTGGCTAAAAACGCGTGTTTAGGGGCATCGGCTCAGTTTTGCATGA
92751 TTTTTGGTACC
323 TTTTTGGTACC
92762 GAGAGTCGTTAAAATATCTATATTCATCTAACCAAATCTCAGCCACATTGGATTTGATGATTAGT
1 GAGAGTCGTTAAAATATCTATATTCATCTAACCAAATCTCAGCCACATTGGATTTGATGATTAGT
*
92827 TTTTATGAGCAT-CAATATCTGGTTTCGATTTAATCAGAAATTAATTTAGGGAAAAATTGGAAAA
66 TTTTATGAGCATCCAA-ATCTGGTTTCGATTTAATCAGAAATTAATTTAGGAAAAAATTGGAAAA
92891 CGATATTAGAAACATTAAACGCCTTCAAACTTTTTTGCGTTGAATTATATATATTTTTTATGAGT
130 CGATATTAGAAACATTAAACGCCTTCAAACTTTTTTGCGTTGAA-T-TATATATTTTTTATGAGT
* * *
92956 ATTTTGGGCAAAAATTGAGGAAAAATATTTCGGGTCAATTTTTGCAATATTTTAGCCGAAATCGT
193 ATTTTGGCCAAAAATTAAGGAAAAATATTTCGGGTCAATTTTTGCAAAATTTTAGCCGAAATCGT
* * * *
93021 GTATTTACCATCACGGTTTTTGGCTAAAAACGCGTGTTTAGGGGCATCGGCTCACTTTTGCATTA
258 GTACTAACCATCACGGTTTTTGGCTAAAAACGCGTGTTTAGGGGCATCGGCTCAGTTTTGCATGA
93086 TTTTTGGTACC
323 TTTTTGGTACC
*
93097 GAGAGTCGTTAAAATATCTATATTCATCTAACCAAATCTCAACCACATTGGATTTGATGATTAGT
1 GAGAGTCGTTAAAATATCTATATTCATCTAACCAAATCTCAGCCACATTGGATTTGATGATTAGT
* * *
93162 TTTTATGAGCATTCATATCTGGTTTCGATTTAATCAGAATTTAATTTAGGAAAAAATTGGAAAAC
66 TTTTATGAGCATCCAAATCTGGTTTCGATTTAATCAGAAATTAATTTAGGAAAAAATTGGAAAAC
93227 GATATTAGAAACATTAAACGCCTTCAAACTTTTTTGCGTTGAATTATATATACTTTTTATGAGTA
131 GATATTAGAAACATTAAACGCCTTCAAACTTTTTTGCGTTGAATTATATAT--TTTTTATGAGTA
* *
93292 TTTTGGCCCAAAATTAAGGAAAAATATTTCGGGTCAAATTTTGCAAAATTTTAGCCGAAATCGTG
194 TTTTGGCCAAAAATTAAGGAAAAATATTTCGGGTCAATTTTTGCAAAATTTTAGCCGAAATCGTG
* * ** * * *
93357 TACTAACCATCACGGTTTTTGACTAAAAATGC--GTTCCGGGGCACCGACACAGTTTTGCATGAT
259 TACTAACCATCACGGTTTTTGGCTAAAAACGCGTGTTTAGGGGCATCGGCTCAGTTTTGCATGAT
**
93420 TTTTGGCGCC
324 TTTTGGTACC
* * * * * *
93430 GAGAGTCTTTAATATATTTATATTCATCTAACCAAATCTCAGCCAGATTGGATTTGAGGATTTGT
1 GAGAGTCGTTAAAATATCTATATTCATCTAACCAAATCTCAGCCACATTGGATTTGATGATTAGT
* * *
93495 TTTTACGAGCATCTAAATCTTGTTTCGATTTAATCAGAAATTAATTTAGGAAAAAATTGGAAAAA
66 TTTTATGAGCATCCAAATCTGGTTTCGATTTAATCAGAAATTAATTTAGGAAAAAATTGG-AAAA
* * * * *
93560 CGATATTAGAAACCTCAAAAGCCCTTCAAACTTTTTGGCTTTGAATTATATA-TTTTTATGAGTA
130 CGATATTAGAAACATTAAACG-CCTTCAAACTTTTTTGCGTTGAATTATATATTTTTTATGAGTA
* * *
93624 TCTTGGCCAAAAATTGAGGAAAAATATTTCGGGTCAATTTTTGAAAAATTTTAGCCGAAATCGTG
194 TTTTGGCCAAAAATTAAGGAAAAATATTTCGGGTCAATTTTTGCAAAATTTTAGCCGAAATCGTG
* * * *
93689 CACTAACCATCACGGTTTTTGGCTAAAAACGCGTGCTTATGGGTATCGGCTCAGTTTTGCATGAT
259 TACTAACCATCACGGTTTTTGGCTAAAAACGCGTGTTTAGGGGCATCGGCTCAGTTTTGCATGAT
*
93754 TTTTAGTACC
324 TTTTGGTACC
* * *
93764 GAGAGTTGTTAAAATTTCTACATTCATCTAACCAAATCTCAGCCACATTGGATTTGATGATTAGT
1 GAGAGTCGTTAAAATATCTATATTCATCTAACCAAATCTCAGCCACATTGGATTTGATGATTAGT
* * *
93829 TTTTATGAGCAT-CAATATATGGTTTCGATTTAATCAGAAATTAATTTAGAAAAAAATTTGAAAA
66 TTTTATGAGCATCCAA-ATCTGGTTTCGATTTAATCAGAAATTAATTTAGGAAAAAATTGGAAAA
*
93893 CGATATTAGAAACATTAAACGTCTTCAAACATTTTTTGCGTTGAATTATATATACTTTTTATGAG
130 CGATATTAGAAACATTAAACGCCTTCAAAC-TTTTTTGCGTTGAATTATATAT--TTTTTATGAG
* * *
93958 TATTTTTTGCCAAAAATTAAGGAAAAACATTTCGGGTCAAGTTTTGCAAAATTTTAGCCGAAATC
192 TA-TTTTGGCCAAAAATTAAGGAAAAATATTTCGGGTCAATTTTTGCAAAATTTTAGCCGAAATC
* * * * * * *
94023 --ATA-T-A-TAT-ACGGGTATCGGCTAAAAACGAGTGTTTAGGGGCATCGGCTCAGTTTTACAT
256 GTGTACTAACCATCACGGTTTTTGGCTAAAAACGCGTGTTTAGGGGCATCGGCTCAGTTTTGCAT
* *
94082 GATTTTTAGTTCC
321 GATTTTTGGTACC
* ** * *
94095 GAGAGTCGTT-AAATATCTATATTCATCAAAATAAATCTTAGCCACATTGGATTTGATGATTAAT
1 GAGAGTCGTTAAAATATCTATATTCATCTAACCAAATCTCAGCCACATTGGATTTGATGATTAGT
*
94159 TTGTATGAGCATC
66 TTTTATGAGCATC
94172 AATATCCGGT
Statistics
Matches: 1547, Mismatches: 175, Indels: 49
0.87 0.10 0.03
Matches are distributed among these distances:
330 58 0.04
331 64 0.04
332 111 0.07
333 287 0.19
334 344 0.22
335 598 0.39
336 29 0.02
337 56 0.04
ACGTcount: A:0.33, C:0.14, G:0.17, T:0.36
Consensus pattern (333 bp):
GAGAGTCGTTAAAATATCTATATTCATCTAACCAAATCTCAGCCACATTGGATTTGATGATTAGT
TTTTATGAGCATCCAAATCTGGTTTCGATTTAATCAGAAATTAATTTAGGAAAAAATTGGAAAAC
GATATTAGAAACATTAAACGCCTTCAAACTTTTTTGCGTTGAATTATATATTTTTTATGAGTATT
TTGGCCAAAAATTAAGGAAAAATATTTCGGGTCAATTTTTGCAAAATTTTAGCCGAAATCGTGTA
CTAACCATCACGGTTTTTGGCTAAAAACGCGTGTTTAGGGGCATCGGCTCAGTTTTGCATGATTT
TTGGTACC
Found at i:93525 original size:668 final size:669
Alignment explanation
Indices: 92093--94171 Score: 2855
Period size: 668 Copynumber: 3.1 Consensus size: 669
92083 TTTTGGTCAT
92093 GAGAGTCGTTAAAATATCTATATTCATCTAACCAAATCTCAGCCACATTGGATTTGATGATTAGT
1 GAGAGTCGTTAAAATATCTATATTCATCTAACCAAATCTCAGCCACATTGGATTTGATGATTAGT
* *
92158 TTTTATGAGCATCTATATCTTGTTTCGATTTAATCAGAAATTAGTTTAGGAAAAAATTGGAAAAC
66 TTTTATGAGCATCTAAATCTTGTTTCGATTTAATCAGAAATTAATTTAGGAAAAAATTGGAAAAC
* ** *
92223 GATATTAGAAACATTAAACGCCTTTAATGTTTTTTTCGTTGAATTATATATATTTTTTATGAGTA
131 GATATTAGAAACATTAAACGCCTTCAAACTTTTTTGCGTTGAATTATATATATTTTTTATGAGTA
* * * *
92288 TTTTTGGCCCAAAATTAAGGAAAAATATTTCGGGTCAAATTTTGCAAAATTTTAGTCGAAATCGT
196 -TTTTGGCCAAAAATTGAGGAAAAATATTTCGGGTCAATTTTTGCAAAATTTTAGCCGAAATCGT
* ** * * * * *
92353 GTACTAACCATCACGGTTTTTGGCTAAAAATGC--GTTCCGAGGCACCGACACAGTATTGCATGA
260 GTACTAACCATCACGGTTTTTGGCTAAAAACGCGTGTTTAGGGGCATCGGCTCAGTTTTGCATGA
** * *
92416 TTTTTGGCGCCGAGAGTCTTTAATATATCTATATTCATCTAACCAAATCTCAGCCACATTGGATT
325 TTTTTGGTACCGAGAGTCGTTAAAATATCTATATTCATCTAACCAAATCTCAGCCACATTGGATT
* * * *
92481 TGAGGATTAGTTTTTATGAGCATCCAAATCTTGTTTCGATTTAATCAGAAATTAATTTAGGAAAA
390 TGATGATTAGTTTTTATGAGCATTCATATCTGGTTTCGATTTAATCAGAAATTAATTTAGGAAAA
** * ** * * ** * * *
92546 AATTGGAAAAATAATATTGGAAATGTCAAAAGCCCTTCAAAAATTTTGGCTTTGACTTATATAT-
455 AATTGG-AAAACGATATTAGAAACATTAAACG-CCTTCAAACTTTTTTGCGTTGAATTATATATA
* * * * * *
92610 -TTTTTATGAGTATCTTGGCCAAAAATTGAGAAAAAATATTTCGGGTCAATTTTTGTAATATTTT
518 CTTTTTATGAGTATTTTGGCCAAAAATTAAGGAAAAATATTTCGGGTCAAATTTTGCAAAATTTT
** * * * * * *
92674 AAACGAAATCGTGTACATTACCATCACGGTTTTGGCTAAAAAGGCGTGTTTAGGGGCATCGGCTC
583 AGCCGAAATCGTGTACATAACCATCACGGTTTTGACTAAAAAGGCG-GTTCAGGGGCACCGACAC
*
92739 AGTTTTGCATGATTTTTGGTACC
647 AGTTTTGCATGATTTTTGGCACC
92762 GAGAGTCGTTAAAATATCTATATTCATCTAACCAAATCTCAGCCACATTGGATTTGATGATTAGT
1 GAGAGTCGTTAAAATATCTATATTCATCTAACCAAATCTCAGCCACATTGGATTTGATGATTAGT
* *
92827 TTTTATGAGCATC-AATATCTGGTTTCGATTTAATCAGAAATTAATTTAGGGAAAAATTGGAAAA
66 TTTTATGAGCATCTAA-ATCTTGTTTCGATTTAATCAGAAATTAATTTAGGAAAAAATTGGAAAA
92891 CGATATTAGAAACATTAAACGCCTTCAAACTTTTTTGCGTTGAATTATATATATTTTTTATGAGT
130 CGATATTAGAAACATTAAACGCCTTCAAACTTTTTTGCGTTGAATTATATATATTTTTTATGAGT
* *
92956 ATTTTGGGCAAAAATTGAGGAAAAATATTTCGGGTCAATTTTTGCAATATTTTAGCCGAAATCGT
195 ATTTTGGCCAAAAATTGAGGAAAAATATTTCGGGTCAATTTTTGCAAAATTTTAGCCGAAATCGT
* * * *
93021 GTATTTACCATCACGGTTTTTGGCTAAAAACGCGTGTTTAGGGGCATCGGCTCACTTTTGCATTA
260 GTACTAACCATCACGGTTTTTGGCTAAAAACGCGTGTTTAGGGGCATCGGCTCAGTTTTGCATGA
*
93086 TTTTTGGTACCGAGAGTCGTTAAAATATCTATATTCATCTAACCAAATCTCAACCACATTGGATT
325 TTTTTGGTACCGAGAGTCGTTAAAATATCTATATTCATCTAACCAAATCTCAGCCACATTGGATT
*
93151 TGATGATTAGTTTTTATGAGCATTCATATCTGGTTTCGATTTAATCAGAATTTAATTTAGGAAAA
390 TGATGATTAGTTTTTATGAGCATTCATATCTGGTTTCGATTTAATCAGAAATTAATTTAGGAAAA
93216 AATTGGAAAACGATATTAGAAACATTAAACGCCTTCAAACTTTTTTGCGTTGAATTATATATACT
455 AATTGGAAAACGATATTAGAAACATTAAACGCCTTCAAACTTTTTTGCGTTGAATTATATATACT
*
93281 TTTTATGAGTATTTTGGCCCAAAATTAAGGAAAAATATTTCGGGTCAAATTTTGCAAAATTTTAG
520 TTTTATGAGTATTTTGGCCAAAAATTAAGGAAAAATATTTCGGGTCAAATTTTGCAAAATTTTAG
* *
93346 CCGAAATCGTGTAC-TAACCATCACGGTTTTTGACTAAAAATGC-GTTCCGGGGCACCGACACAG
585 CCGAAATCGTGTACATAACCATCACGG-TTTTGACTAAAAAGGCGGTTCAGGGGCACCGACACAG
*
93409 TTTTGCATGATTTTTGGCGCC
649 TTTTGCATGATTTTTGGCACC
* * * * * *
93430 GAGAGTCTTTAATATATTTATATTCATCTAACCAAATCTCAGCCAGATTGGATTTGAGGATTTGT
1 GAGAGTCGTTAAAATATCTATATTCATCTAACCAAATCTCAGCCACATTGGATTTGATGATTAGT
*
93495 TTTTACGAGCATCTAAATCTTGTTTCGATTTAATCAGAAATTAATTTAGGAAAAAATTGGAAAAA
66 TTTTATGAGCATCTAAATCTTGTTTCGATTTAATCAGAAATTAATTTAGGAAAAAATTGG-AAAA
* * * * *
93560 CGATATTAGAAACCTCAAAAGCCCTTCAAACTTTTTGGCTTTGAA-T-TATATA-TTTTTATGAG
130 CGATATTAGAAACATTAAACG-CCTTCAAACTTTTTTGCGTTGAATTATATATATTTTTTATGAG
* *
93622 TATCTTGGCCAAAAATTGAGGAAAAATATTTCGGGTCAATTTTTGAAAAATTTTAGCCGAAATCG
194 TATTTTGGCCAAAAATTGAGGAAAAATATTTCGGGTCAATTTTTGCAAAATTTTAGCCGAAATCG
* * * *
93687 TGCACTAACCATCACGGTTTTTGGCTAAAAACGCGTGCTTATGGGTATCGGCTCAGTTTTGCATG
259 TGTACTAACCATCACGGTTTTTGGCTAAAAACGCGTGTTTAGGGGCATCGGCTCAGTTTTGCATG
* * * *
93752 ATTTTTAGTACCGAGAGTTGTTAAAATTTCTACATTCATCTAACCAAATCTCAGCCACATTGGAT
324 ATTTTTGGTACCGAGAGTCGTTAAAATATCTATATTCATCTAACCAAATCTCAGCCACATTGGAT
* *
93817 TTGATGATTAGTTTTTATGAGCA-TCAATATATGGTTTCGATTTAATCAGAAATTAATTTAGAAA
389 TTGATGATTAGTTTTTATGAGCATTC-ATATCTGGTTTCGATTTAATCAGAAATTAATTTAGGAA
* *
93881 AAAATTTGAAAACGATATTAGAAACATTAAACGTCTTCAAACATTTTTTGCGTTGAATTATATAT
453 AAAATTGGAAAACGATATTAGAAACATTAAACGCCTTCAAAC-TTTTTTGCGTTGAATTATATAT
* * *
93946 ACTTTTTATGAGTATTTTTTGCCAAAAATTAAGGAAAAACATTTCGGGTCAAGTTTTGCAAAATT
517 ACTTTTTATGAGTA-TTTTGGCCAAAAATTAAGGAAAAATATTTCGGGTCAAATTTTGCAAAATT
* * * * * * * * * *
94011 TTAGCCGAAATC----ATAT-A-TAT-ACGGGTATCGGCTAAAAACGAGTGTTTAGGGGCATCGG
581 TTAGCCGAAATCGTGTACATAACCATCAC-GGTTTTGACTAAAAAGGCG-GTTCAGGGGCACCGA
* * * **
94069 CTCAGTTTTACATGATTTTTAGTTCC
644 CACAGTTTTGCATGATTTTTGGCACC
* ** * *
94095 GAGAGTCGTT-AAATATCTATATTCATCAAAATAAATCTTAGCCACATTGGATTTGATGATTAAT
1 GAGAGTCGTTAAAATATCTATATTCATCTAACCAAATCTCAGCCACATTGGATTTGATGATTAGT
*
94159 TTGTATGAGCATC
66 TTTTATGAGCATC
94172 AATATCCGGT
Statistics
Matches: 1258, Mismatches: 136, Indels: 37
0.88 0.10 0.03
Matches are distributed among these distances:
663 13 0.01
664 59 0.05
665 43 0.03
666 3 0.00
667 286 0.23
668 304 0.24
669 297 0.24
670 253 0.20
ACGTcount: A:0.33, C:0.14, G:0.17, T:0.36
Consensus pattern (669 bp):
GAGAGTCGTTAAAATATCTATATTCATCTAACCAAATCTCAGCCACATTGGATTTGATGATTAGT
TTTTATGAGCATCTAAATCTTGTTTCGATTTAATCAGAAATTAATTTAGGAAAAAATTGGAAAAC
GATATTAGAAACATTAAACGCCTTCAAACTTTTTTGCGTTGAATTATATATATTTTTTATGAGTA
TTTTGGCCAAAAATTGAGGAAAAATATTTCGGGTCAATTTTTGCAAAATTTTAGCCGAAATCGTG
TACTAACCATCACGGTTTTTGGCTAAAAACGCGTGTTTAGGGGCATCGGCTCAGTTTTGCATGAT
TTTTGGTACCGAGAGTCGTTAAAATATCTATATTCATCTAACCAAATCTCAGCCACATTGGATTT
GATGATTAGTTTTTATGAGCATTCATATCTGGTTTCGATTTAATCAGAAATTAATTTAGGAAAAA
ATTGGAAAACGATATTAGAAACATTAAACGCCTTCAAACTTTTTTGCGTTGAATTATATATACTT
TTTATGAGTATTTTGGCCAAAAATTAAGGAAAAATATTTCGGGTCAAATTTTGCAAAATTTTAGC
CGAAATCGTGTACATAACCATCACGGTTTTGACTAAAAAGGCGGTTCAGGGGCACCGACACAGTT
TTGCATGATTTTTGGCACC
Found at i:95704 original size:20 final size:20
Alignment explanation
Indices: 95644--95943 Score: 214
Period size: 20 Copynumber: 15.1 Consensus size: 20
95634 CATATTAAAC
*
95644 TTCCCAATTGACATTGAACT
1 TTCCCAATTCACATTGAACT
* ** *
95664 TGCCTTGATTCACATTCAACT
1 TTCC-CAATTCACATTGAACT
*
95685 TTCCCAATTGACATTGAACT
1 TTCCCAATTCACATTGAACT
* ** *
95705 TGCCTTGATTCACATTCAACT
1 TTCC-CAATTCACATTGAACT
95726 TT-CCAATTCACATTGAACT
1 TTCCCAATTCACATTGAACT
* ** ** *
95745 TGCCTTATTCACATCCAACA
1 TTCCCAATTCACATTGAACT
95765 TTCCCAATTCACATTGAACT
1 TTCCCAATTCACATTGAACT
* ** * *
95785 TGCCTTATTCACATTCAAAT
1 TTCCCAATTCACATTGAACT
*
95805 TTCCCAAATCACATTGAACT
1 TTCCCAATTCACATTGAACT
* * * *
95825 TGCCTTAA-CCACATTCAACT
1 TTCC-CAATTCACATTGAACT
95845 TT-CCAATTCACATTGAACT
1 TTCCCAATTCACATTGAACT
* * * *
95864 TGCCTTAA-CCACATTCAA-T
1 TTCC-CAATTCACATTGAACT
95883 TTCCCAATTCACATTGAACT
1 TTCCCAATTCACATTGAACT
* ** * *
95903 TGCCTTATCCACATTCAACT
1 TTCCCAATTCACATTGAACT
95923 TTCCCAATTCACATTGAACT
1 TTCCCAATTCACATTGAACT
95943 T
1 T
95944 GCCTTAATTC
Statistics
Matches: 203, Mismatches: 68, Indels: 18
0.70 0.24 0.06
Matches are distributed among these distances:
18 4 0.02
19 38 0.19
20 129 0.64
21 32 0.16
ACGTcount: A:0.29, C:0.29, G:0.06, T:0.35
Consensus pattern (20 bp):
TTCCCAATTCACATTGAACT
Found at i:95867 original size:39 final size:40
Alignment explanation
Indices: 95644--95956 Score: 479
Period size: 40 Copynumber: 7.8 Consensus size: 40
95634 CATATTAAAC
*
95644 TTCCCAATTGACATTGAACTTGCCTTGATTCACATTCAACT
1 TTCCCAATTCACATTGAACTTGCCTT-ATTCACATTCAACT
*
95685 TTCCCAATTGACATTGAACTTGCCTTGATTCACATTCAACT
1 TTCCCAATTCACATTGAACTTGCCTT-ATTCACATTCAACT
* *
95726 TT-CCAATTCACATTGAACTTGCCTTATTCACATCCAACA
1 TTCCCAATTCACATTGAACTTGCCTTATTCACATTCAACT
*
95765 TTCCCAATTCACATTGAACTTGCCTTATTCACATTCAAAT
1 TTCCCAATTCACATTGAACTTGCCTTATTCACATTCAACT
* **
95805 TTCCCAAATCACATTGAACTTGCCTTAACCACATTCAACT
1 TTCCCAATTCACATTGAACTTGCCTTATTCACATTCAACT
**
95845 TT-CCAATTCACATTGAACTTGCCTTAACCACATTCAA-T
1 TTCCCAATTCACATTGAACTTGCCTTATTCACATTCAACT
*
95883 TTCCCAATTCACATTGAACTTGCCTTATCCACATTCAACT
1 TTCCCAATTCACATTGAACTTGCCTTATTCACATTCAACT
95923 TTCCCAATTCACATTGAACTTGCCTTAATTCACA
1 TTCCCAATTCACATTGAACTTGCCTT-ATTCACA
95957 ATGGCCCTCA
Statistics
Matches: 255, Mismatches: 13, Indels: 8
0.92 0.05 0.03
Matches are distributed among these distances:
38 3 0.01
39 82 0.32
40 121 0.47
41 49 0.19
ACGTcount: A:0.29, C:0.29, G:0.06, T:0.35
Consensus pattern (40 bp):
TTCCCAATTCACATTGAACTTGCCTTATTCACATTCAACT
Found at i:96744 original size:43 final size:43
Alignment explanation
Indices: 96680--96786 Score: 171
Period size: 43 Copynumber: 2.5 Consensus size: 43
96670 ACAGCTACAT
*
96680 GAGTGAGAAGAGATGCGATATAACCAAAACAGTCTTGATGC-G
1 GAGTGAGAAGAGATGCGATATAACCAAAACAGTCTTGACGCAG
*
96722 CGAGTGAGAAGAGATGCAATATAACCAAAACAGTCTTGACGCAG
1 -GAGTGAGAAGAGATGCGATATAACCAAAACAGTCTTGACGCAG
*
96766 GAATGAGAAGAGATGCGATAT
1 GAGTGAGAAGAGATGCGATAT
96787 CTATAAAGCC
Statistics
Matches: 59, Mismatches: 4, Indels: 2
0.91 0.06 0.03
Matches are distributed among these distances:
43 58 0.98
44 1 0.02
ACGTcount: A:0.40, C:0.14, G:0.28, T:0.18
Consensus pattern (43 bp):
GAGTGAGAAGAGATGCGATATAACCAAAACAGTCTTGACGCAG
Found at i:99189 original size:33 final size:33
Alignment explanation
Indices: 99147--99209 Score: 99
Period size: 33 Copynumber: 1.9 Consensus size: 33
99137 TAAGTAGCTG
**
99147 TCAAGGTAAAGTTAGTTAAACAGACTAAAAGCA
1 TCAAGGTAAAGTTAGGCAAACAGACTAAAAGCA
*
99180 TCAAGGTAAAGTTAGGCAAACCGACTAAAA
1 TCAAGGTAAAGTTAGGCAAACAGACTAAAA
99210 AACAAGATCA
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
33 27 1.00
ACGTcount: A:0.48, C:0.14, G:0.19, T:0.19
Consensus pattern (33 bp):
TCAAGGTAAAGTTAGGCAAACAGACTAAAAGCA
Found at i:100715 original size:35 final size:35
Alignment explanation
Indices: 100670--100741 Score: 126
Period size: 35 Copynumber: 2.1 Consensus size: 35
100660 GCAGTGTCTA
*
100670 TTTTTTTTTTGGTATCCCATCAGGTATCCAGGGCT
1 TTTTTTTTTTGGTATCCCATCAGGTATCCAGGCCT
*
100705 TTTTTTTTTTGGTATCCTATCAGGTATCCAGGCCT
1 TTTTTTTTTTGGTATCCCATCAGGTATCCAGGCCT
100740 TT
1 TT
100742 GCCCTGACTA
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
35 35 1.00
ACGTcount: A:0.14, C:0.19, G:0.18, T:0.49
Consensus pattern (35 bp):
TTTTTTTTTTGGTATCCCATCAGGTATCCAGGCCT
Found at i:100770 original size:25 final size:25
Alignment explanation
Indices: 100742--100793 Score: 104
Period size: 25 Copynumber: 2.1 Consensus size: 25
100732 CCAGGCCTTT
100742 GCCCTGACTAATCCGGATCCGACCC
1 GCCCTGACTAATCCGGATCCGACCC
100767 GCCCTGACTAATCCGGATCCGACCC
1 GCCCTGACTAATCCGGATCCGACCC
100792 GC
1 GC
100794 GTCGCGCACC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 27 1.00
ACGTcount: A:0.19, C:0.44, G:0.21, T:0.15
Consensus pattern (25 bp):
GCCCTGACTAATCCGGATCCGACCC
Done.