Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr06 132263754
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: 132263754
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Warning! 372 characters in sequence are not A, C, G, or T
File 213 of 433
Found at i:66338539 original size:30 final size:30
Alignment explanation
Indices: 66338437--66338539 Score: 93
Period size: 30 Copynumber: 3.5 Consensus size: 30
66338427 TGAGTTTAAA
*
66338437 CTAAA-ATGAGCTAAGCTTTAGCTCGTGAG
1 CTAAATATGAGCTAAGGTTTAGCTCGTGAG
* * * * * * * *
66338466 CTAAAGATAAGCTGAGGCTAAACTCCTAAG
1 CTAAATATGAGCTAAGGTTTAGCTCGTGAG
66338496 CTAAAGT-TGAGCTAAGGTTTAGCTCGTGAG
1 CTAAA-TATGAGCTAAGGTTTAGCTCGTGAG
*
66338526 CTGAATATGAGCTA
1 CTAAATATGAGCTA
66338540 GGAGTGAGTT
Statistics
Matches: 54, Mismatches: 17, Indels: 5
0.71 0.22 0.07
Matches are distributed among these distances:
29 6 0.11
30 48 0.89
ACGTcount: A:0.33, C:0.17, G:0.24, T:0.26
Consensus pattern (30 bp):
CTAAATATGAGCTAAGGTTTAGCTCGTGAG
Found at i:66345028 original size:10 final size:10
Alignment explanation
Indices: 66345013--66345039 Score: 54
Period size: 10 Copynumber: 2.7 Consensus size: 10
66345003 TAAGTTGAAG
66345013 TTGAGCTGAT
1 TTGAGCTGAT
66345023 TTGAGCTGAT
1 TTGAGCTGAT
66345033 TTGAGCT
1 TTGAGCT
66345040 TGAAGGAGTA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 17 1.00
ACGTcount: A:0.19, C:0.11, G:0.30, T:0.41
Consensus pattern (10 bp):
TTGAGCTGAT
Found at i:66354012 original size:24 final size:23
Alignment explanation
Indices: 66353969--66354013 Score: 56
Period size: 24 Copynumber: 1.9 Consensus size: 23
66353959 TACATCAGTG
66353969 AAAGATTTATTGATTAGAAGCGT
1 AAAGATTTATTGATTAGAAGCGT
*
66353992 AAAGAGTTTCTTGAATT-GAAGC
1 AAAGA-TTTATTG-ATTAGAAGC
66354014 AGGGGAGCAT
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
23 5 0.26
24 11 0.58
25 3 0.16
ACGTcount: A:0.38, C:0.07, G:0.22, T:0.33
Consensus pattern (23 bp):
AAAGATTTATTGATTAGAAGCGT
Found at i:66358932 original size:29 final size:28
Alignment explanation
Indices: 66358900--66359002 Score: 116
Period size: 29 Copynumber: 3.6 Consensus size: 28
66358890 GGGACGAGAT
* *
66358900 TGGCACTGAGTGTGCGAGCTTGTAATGTA
1 TGGCACTAAGTGTGCGAGCTTG-AATATA
* *
66358929 TGGCACTAAGTGTGCGAGTTTGGACTATA
1 TGGCACTAAGTGTGCGAGCTT-GAATATA
* * *
66358958 TGGCACTATGTGTGCGGGCTTGAATCACA
1 TGGCACTAAGTGTGCGAGCTTGAAT-ATA
66358987 TGGCACTAAGTGTGCG
1 TGGCACTAAGTGTGCG
66359003 TGATTGAGTA
Statistics
Matches: 62, Mismatches: 10, Indels: 4
0.82 0.13 0.05
Matches are distributed among these distances:
28 3 0.05
29 58 0.94
30 1 0.02
ACGTcount: A:0.21, C:0.17, G:0.33, T:0.29
Consensus pattern (28 bp):
TGGCACTAAGTGTGCGAGCTTGAATATA
Found at i:66368023 original size:30 final size:30
Alignment explanation
Indices: 66367950--66368032 Score: 82
Period size: 30 Copynumber: 2.8 Consensus size: 30
66367940 AGCTCACGAT
*
66367950 CTAAACCTTAGCTCAACTTCAGCTTAGGAG
1 CTAAACCTTAGCTCAACTTTAGCTTAGGAG
* *
66367980 -TATAATCTCAGCTCAACTTTAGCTTAAGG-G
1 CTA-AACCTTAGCTCAACTTTAGCTT-AGGAG
* *
66368010 CTAAAGCTTAGCTC-ATTTTAGCT
1 CTAAACCTTAGCTCAACTTTAGCT
66368033 CAAACCCGAT
Statistics
Matches: 44, Mismatches: 6, Indels: 7
0.77 0.11 0.12
Matches are distributed among these distances:
29 10 0.23
30 29 0.66
31 5 0.11
ACGTcount: A:0.29, C:0.23, G:0.16, T:0.33
Consensus pattern (30 bp):
CTAAACCTTAGCTCAACTTTAGCTTAGGAG
Found at i:66370106 original size:20 final size:20
Alignment explanation
Indices: 66370081--66370147 Score: 55
Period size: 20 Copynumber: 3.3 Consensus size: 20
66370071 AACTCAAGTT
66370081 AGCTCAGAGTACTCTACACC
1 AGCTCAGAGTACTCTACACC
*** * * *
66370101 AGCTCATCTTCAGCTCAAGA-T
1 AGCTCAGAGT-A-CTCTACACC
66370122 AGCTCAGAGTACTCTACACC
1 AGCTCAGAGTACTCTACACC
66370142 AGCTCA
1 AGCTCA
66370148 TGTCAGCTCC
Statistics
Matches: 32, Mismatches: 12, Indels: 6
0.64 0.24 0.12
Matches are distributed among these distances:
19 5 0.16
20 14 0.44
21 8 0.25
22 5 0.16
ACGTcount: A:0.30, C:0.33, G:0.15, T:0.22
Consensus pattern (20 bp):
AGCTCAGAGTACTCTACACC
Found at i:66370106 original size:41 final size:41
Alignment explanation
Indices: 66370059--66370148 Score: 162
Period size: 41 Copynumber: 2.2 Consensus size: 41
66370049 AGTGTATATG
*
66370059 CAGCTCATCTTCAACTCAAGTTAGCTCAGAGTACTCTACAC
1 CAGCTCATCTTCAACTCAAGATAGCTCAGAGTACTCTACAC
*
66370100 CAGCTCATCTTCAGCTCAAGATAGCTCAGAGTACTCTACAC
1 CAGCTCATCTTCAACTCAAGATAGCTCAGAGTACTCTACAC
66370141 CAGCTCAT
1 CAGCTCAT
66370149 GTCAGCTCCC
Statistics
Matches: 47, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
41 47 1.00
ACGTcount: A:0.29, C:0.32, G:0.13, T:0.26
Consensus pattern (41 bp):
CAGCTCATCTTCAACTCAAGATAGCTCAGAGTACTCTACAC
Found at i:66371003 original size:13 final size:13
Alignment explanation
Indices: 66370985--66371009 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
66370975 GTATTGATCA
66370985 TGTGTTCACACCT
1 TGTGTTCACACCT
66370998 TGTGTTCACACC
1 TGTGTTCACACC
66371010 ATGATGACCA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.16, C:0.32, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTGTTCACACCT
Found at i:66374015 original size:23 final size:23
Alignment explanation
Indices: 66373987--66374034 Score: 96
Period size: 23 Copynumber: 2.1 Consensus size: 23
66373977 ACTCACGAGC
66373987 TAAACCTTAGCTCAACTTCAGCT
1 TAAACCTTAGCTCAACTTCAGCT
66374010 TAAACCTTAGCTCAACTTCAGCT
1 TAAACCTTAGCTCAACTTCAGCT
66374033 TA
1 TA
66374035 GGAGTTTAGC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 25 1.00
ACGTcount: A:0.31, C:0.29, G:0.08, T:0.31
Consensus pattern (23 bp):
TAAACCTTAGCTCAACTTCAGCT
Found at i:66375621 original size:30 final size:30
Alignment explanation
Indices: 66375587--66375683 Score: 97
Period size: 30 Copynumber: 3.2 Consensus size: 30
66375577 TAAACTAAAA
*
66375587 TGAGCTAAGATTTAGCTCGTGAGCTAAAGT
1 TGAGCTAAGGTTTAGCTCGTGAGCTAAAGT
* * * * * * *
66375617 TGAGCTGAGGCTAAACTCCTAAGCTGAAGT
1 TGAGCTAAGGTTTAGCTCGTGAGCTAAAGT
*
66375647 TGAGCTAAGGTTTAGCTCGTGAGTTGAAAG-
1 TGAGCTAAGGTTTAGCTCGTGAGCT-AAAGT
66375677 TGAGCTA
1 TGAGCTA
66375684 GGAGTGAGCT
Statistics
Matches: 50, Mismatches: 16, Indels: 2
0.74 0.24 0.03
Matches are distributed among these distances:
30 47 0.94
31 3 0.06
ACGTcount: A:0.29, C:0.14, G:0.29, T:0.28
Consensus pattern (30 bp):
TGAGCTAAGGTTTAGCTCGTGAGCTAAAGT
Found at i:66378569 original size:10 final size:11
Alignment explanation
Indices: 66378554--66378610 Score: 64
Period size: 11 Copynumber: 5.4 Consensus size: 11
66378544 TATACAAGTT
*
66378554 AAAAAAATAAA
1 AAAAAAATCAA
*
66378565 AAAAAAATCGA
1 AAAAAAATCAA
* *
66378576 AAAAAATTC-G
1 AAAAAAATCAA
66378586 AAAAAAAT-AA
1 AAAAAAATCAA
66378596 AAAAAAATCAA
1 AAAAAAATCAA
66378607 AAAA
1 AAAA
66378611 TAAAAAGAAG
Statistics
Matches: 38, Mismatches: 6, Indels: 4
0.79 0.12 0.08
Matches are distributed among these distances:
10 15 0.39
11 23 0.61
ACGTcount: A:0.81, C:0.05, G:0.04, T:0.11
Consensus pattern (11 bp):
AAAAAAATCAA
Found at i:66392036 original size:19 final size:19
Alignment explanation
Indices: 66392012--66392051 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
66392002 AGCTCCCATG
66392012 TAGCTCCACACCAGCTCAT
1 TAGCTCCACACCAGCTCAT
***
66392031 TAGCTCGGGACCAGCTCAT
1 TAGCTCCACACCAGCTCAT
66392050 TA
1 TA
66392052 TCAGCTCACA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.25, C:0.35, G:0.17, T:0.23
Consensus pattern (19 bp):
TAGCTCCACACCAGCTCAT
Found at i:66395530 original size:13 final size:13
Alignment explanation
Indices: 66395501--66395540 Score: 53
Period size: 14 Copynumber: 2.9 Consensus size: 13
66395491 AACTGACCAA
*
66395501 TTTGTTCATATCCC
1 TTTGTTCCTA-CCC
66395515 TTTGTTCCTACCC
1 TTTGTTCCTACCC
66395528 TTTCGTTCCTACC
1 TTT-GTTCCTACC
66395541 ATTCCGTTCG
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
13 6 0.25
14 18 0.75
ACGTcount: A:0.10, C:0.35, G:0.07, T:0.47
Consensus pattern (13 bp):
TTTGTTCCTACCC
Found at i:66396384 original size:30 final size:30
Alignment explanation
Indices: 66396350--66396446 Score: 88
Period size: 30 Copynumber: 3.2 Consensus size: 30
66396340 AGCTCACTCC
*
66396350 TAGCTCACTTTCAACTCACGAGCTAAACCT
1 TAGCTCACTTTCAGCTCACGAGCTAAACCT
* * * * * * *
66396380 TAGCTCAATTTCAGCTTAGGAGTTTAGCTT
1 TAGCTCACTTTCAGCTCACGAGCTAAACCT
* *
66396410 TAGCTCAACTTT-AGCTCACAAGCTAAAGCT
1 TAGCTC-ACTTTCAGCTCACGAGCTAAACCT
66396440 TAGCTCA
1 TAGCTCA
66396447 TTTTAGTTTA
Statistics
Matches: 49, Mismatches: 17, Indels: 3
0.71 0.25 0.04
Matches are distributed among these distances:
29 1 0.02
30 44 0.90
31 4 0.08
ACGTcount: A:0.29, C:0.26, G:0.14, T:0.31
Consensus pattern (30 bp):
TAGCTCACTTTCAGCTCACGAGCTAAACCT
Found at i:66398267 original size:13 final size:13
Alignment explanation
Indices: 66398249--66398276 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
66398239 ACATATTATA
66398249 AATATTTTGTGTT
1 AATATTTTGTGTT
66398262 AATATTTTGTGTT
1 AATATTTTGTGTT
66398275 AA
1 AA
66398277 AAATAATAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.29, C:0.00, G:0.14, T:0.57
Consensus pattern (13 bp):
AATATTTTGTGTT
Found at i:66399796 original size:39 final size:40
Alignment explanation
Indices: 66399678--66399840 Score: 233
Period size: 40 Copynumber: 4.1 Consensus size: 40
66399668 ACTAAGATCT
* *
66399678 GAAGGCATTTGTGCTAGTGACTATATCTGGGCTAAGTCTC
1 GAAGGCATTTGTGCTAGTGACTATATCCGGGCTAAGTCCC
*
66399718 GAAGGCATTTGTGCTAGTTACTATATCCGGGCTAAGTCCC
1 GAAGGCATTTGTGCTAGTGACTATATCCGGGCTAAGTCCC
* *
66399758 GAAGGCATTTGGGCTAGTGATTA-ATCCGGGCTAAGTCCC
1 GAAGGCATTTGTGCTAGTGACTATATCCGGGCTAAGTCCC
* *
66399797 GAAGGCATTTGTGCGAGTTG-CTATATCC-GGCTAAATCCC
1 GAAGGCATTTGTGCTAG-TGACTATATCCGGGCTAAGTCCC
66399836 GAAGG
1 GAAGG
66399841 TACTTGGGTT
Statistics
Matches: 111, Mismatches: 10, Indels: 5
0.88 0.08 0.04
Matches are distributed among these distances:
39 48 0.43
40 63 0.57
ACGTcount: A:0.23, C:0.20, G:0.28, T:0.28
Consensus pattern (40 bp):
GAAGGCATTTGTGCTAGTGACTATATCCGGGCTAAGTCCC
Found at i:66399809 original size:79 final size:79
Alignment explanation
Indices: 66399678--66399840 Score: 247
Period size: 79 Copynumber: 2.1 Consensus size: 79
66399668 ACTAAGATCT
* * * *
66399678 GAAGGCATTTGTGCTAGTGACTATATCTGGGCTAAGTCTCGAAGGCATTTGTGCTAGTTACTATA
1 GAAGGCATTTGGGCTAGTGACTATATCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATA
*
66399743 TCCGGGCTAAGTCCC
66 TCC-GGCTAAATCCC
* *
66399758 GAAGGCATTTGGGCTAGTGATTA-ATCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTGCTATA
1 GAAGGCATTTGGGCTAGTGACTATATCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATA
66399822 TCCGGCTAAATCCC
66 TCCGGCTAAATCCC
66399836 GAAGG
1 GAAGG
66399841 TACTTGGGTT
Statistics
Matches: 76, Mismatches: 7, Indels: 2
0.89 0.08 0.02
Matches are distributed among these distances:
78 15 0.20
79 40 0.53
80 21 0.28
ACGTcount: A:0.23, C:0.20, G:0.28, T:0.28
Consensus pattern (79 bp):
GAAGGCATTTGGGCTAGTGACTATATCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATA
TCCGGCTAAATCCC
Found at i:66409276 original size:30 final size:30
Alignment explanation
Indices: 66409196--66409285 Score: 78
Period size: 30 Copynumber: 3.0 Consensus size: 30
66409186 CACTTTCAAC
* *
66409196 TCACGAGCTAAACCTTAGCTCAACTTCAGCT
1 TCACGAGCTAAAGCTTAGCTCAACTTTAG-T
* ** *
66409227 T-AGGAG-TTTAGCCTCAGCTCAACTTTAGT
1 TCACGAGCTAAAG-CTTAGCTCAACTTTAGT
*
66409256 TCACGAGCTAAAGCTTAGCTC-ATTTTAGT
1 TCACGAGCTAAAGCTTAGCTCAACTTTAGT
66409285 T
1 T
66409286 TAAACTCGGT
Statistics
Matches: 45, Mismatches: 11, Indels: 8
0.70 0.17 0.12
Matches are distributed among these distances:
29 12 0.27
30 29 0.64
31 4 0.09
ACGTcount: A:0.27, C:0.24, G:0.17, T:0.32
Consensus pattern (30 bp):
TCACGAGCTAAAGCTTAGCTCAACTTTAGT
Found at i:66411406 original size:30 final size:30
Alignment explanation
Indices: 66411335--66411417 Score: 89
Period size: 30 Copynumber: 2.7 Consensus size: 30
66411325 CTTTTGTTTC
* *
66411335 AATTTCTTTTTCATCTTCTTTTTCACTCTCA
1 AATTTCTTTTTCTTC-TCTTTTTCAATCTCA
66411366 AATTTC-TTTTCGTTCTCTTTTTCAATCTC-
1 AATTTCTTTTTC-TTCTCTTTTTCAATCTCA
* *
66411395 ATTTTCTTTTTCATTTTCTTTTT
1 AATTTCTTTTTC-TTCTCTTTTT
66411418 GCTTTTCAAA
Statistics
Matches: 45, Mismatches: 5, Indels: 5
0.82 0.09 0.09
Matches are distributed among these distances:
29 5 0.11
30 32 0.71
31 8 0.18
ACGTcount: A:0.13, C:0.22, G:0.01, T:0.64
Consensus pattern (30 bp):
AATTTCTTTTTCTTCTCTTTTTCAATCTCA
Found at i:66411417 original size:18 final size:18
Alignment explanation
Indices: 66411368--66411423 Score: 51
Period size: 18 Copynumber: 3.1 Consensus size: 18
66411358 CACTCTCAAA
* *
66411368 TTTC-TTTTCGTTCTCTT
1 TTTCATTTTCATTTTCTT
* *
66411385 TTTCAATCTCATTTTCTT
1 TTTCATTTTCATTTTCTT
*
66411403 TTTCATTTTCTTTTTGCTT
1 TTTCATTTTCATTTT-CTT
66411422 TT
1 TT
66411424 CAAAGGCTTT
Statistics
Matches: 30, Mismatches: 7, Indels: 2
0.77 0.18 0.05
Matches are distributed among these distances:
17 4 0.13
18 21 0.70
19 5 0.17
ACGTcount: A:0.07, C:0.20, G:0.04, T:0.70
Consensus pattern (18 bp):
TTTCATTTTCATTTTCTT
Found at i:66411424 original size:12 final size:12
Alignment explanation
Indices: 66411393--66411417 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
66411383 TTTTTCAATC
66411393 TCATTTTCTTTT
1 TCATTTTCTTTT
66411405 TCATTTTCTTTT
1 TCATTTTCTTTT
66411417 T
1 T
66411418 GCTTTTCAAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.08, C:0.16, G:0.00, T:0.76
Consensus pattern (12 bp):
TCATTTTCTTTT
Found at i:66411435 original size:12 final size:12
Alignment explanation
Indices: 66411420--66411450 Score: 62
Period size: 12 Copynumber: 2.6 Consensus size: 12
66411410 TTCTTTTTGC
66411420 TTTTCAAAGGCT
1 TTTTCAAAGGCT
66411432 TTTTCAAAGGCT
1 TTTTCAAAGGCT
66411444 TTTTCAA
1 TTTTCAA
66411451 GTTCTCTCAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.26, C:0.16, G:0.13, T:0.45
Consensus pattern (12 bp):
TTTTCAAAGGCT
Found at i:66411521 original size:16 final size:14
Alignment explanation
Indices: 66411498--66411561 Score: 65
Period size: 16 Copynumber: 4.2 Consensus size: 14
66411488 CTCTTGCCTC
66411498 TCTTTTCTTTTTATT
1 TCTTTTCTTTTT-TT
*
66411513 TCATTTTCTTTTTCT
1 TC-TTTTCTTTTTTT
66411528 TCTTTTGCTTTTTCTT
1 TCTTTT-CTTTTT-TT
*
66411544 TCCTTTTCTTTATTT
1 T-CTTTTCTTTTTTT
66411559 TCT
1 TCT
66411562 CTTTACAAGA
Statistics
Matches: 42, Mismatches: 3, Indels: 9
0.78 0.06 0.17
Matches are distributed among these distances:
14 6 0.14
15 14 0.33
16 17 0.40
17 5 0.12
ACGTcount: A:0.05, C:0.19, G:0.02, T:0.75
Consensus pattern (14 bp):
TCTTTTCTTTTTTT
Found at i:66412487 original size:11 final size:11
Alignment explanation
Indices: 66412471--66412519 Score: 50
Period size: 10 Copynumber: 4.6 Consensus size: 11
66412461 CATTAAACAC
66412471 TTTTTTTCAGA
1 TTTTTTTCAGA
*
66412482 TTTTTTT-TGAA
1 TTTTTTTCAG-A
*
66412493 TTTTTTTGA-A
1 TTTTTTTCAGA
66412503 TTTTTTTC-GA
1 TTTTTTTCAGA
66412513 TTTTTTT
1 TTTTTTT
66412520 TTTACTTGTA
Statistics
Matches: 32, Mismatches: 3, Indels: 7
0.76 0.07 0.17
Matches are distributed among these distances:
10 17 0.53
11 15 0.47
ACGTcount: A:0.14, C:0.04, G:0.08, T:0.73
Consensus pattern (11 bp):
TTTTTTTCAGA
Found at i:66412520 original size:11 final size:10
Alignment explanation
Indices: 66412483--66412519 Score: 58
Period size: 10 Copynumber: 3.7 Consensus size: 10
66412473 TTTTTCAGAT
66412483 TTTTTTTGAA
1 TTTTTTTGAA
66412493 TTTTTTTGAA
1 TTTTTTTGAA
66412503 TTTTTTTCG-A
1 TTTTTTT-GAA
66412513 TTTTTTT
1 TTTTTTT
66412520 TTTACTTGTA
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
10 25 0.96
11 1 0.04
ACGTcount: A:0.14, C:0.03, G:0.08, T:0.76
Consensus pattern (10 bp):
TTTTTTTGAA
Found at i:66414264 original size:30 final size:30
Alignment explanation
Indices: 66414230--66414326 Score: 81
Period size: 30 Copynumber: 3.2 Consensus size: 30
66414220 TAAACTAATA
*
66414230 TGAGCTAAGCTTTAGCTTGTGAGCTAAAGT
1 TGAGCTAAGCTTTAGCTCGTGAGCTAAAGT
* * * * * *
66414260 TGAGCTGAGGC-TAAACTCCTAAGCTGAAGT
1 TGAGCT-AAGCTTTAGCTCGTGAGCTAAAGT
* *
66414290 TGAGCTAAGGTTTAGCTCGTGAGTTGAAAG-
1 TGAGCTAAGCTTTAGCTCGTGAGCT-AAAGT
66414320 TGAGCTA
1 TGAGCTA
66414327 GGAGTGAGCT
Statistics
Matches: 49, Mismatches: 15, Indels: 6
0.70 0.21 0.09
Matches are distributed among these distances:
29 2 0.04
30 41 0.84
31 6 0.12
ACGTcount: A:0.28, C:0.14, G:0.29, T:0.29
Consensus pattern (30 bp):
TGAGCTAAGCTTTAGCTCGTGAGCTAAAGT
Found at i:66414748 original size:14 final size:14
Alignment explanation
Indices: 66414709--66414739 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
66414699 TTCATATCCC
*
66414709 TTCATTCATACCAT
1 TTCATTCCTACCAT
66414723 TTCATTCCTACCAT
1 TTCATTCCTACCAT
66414737 TTC
1 TTC
66414740 GTTCGTACCC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.23, C:0.32, G:0.00, T:0.45
Consensus pattern (14 bp):
TTCATTCCTACCAT
Found at i:66419162 original size:30 final size:29
Alignment explanation
Indices: 66419113--66419193 Score: 94
Period size: 30 Copynumber: 2.8 Consensus size: 29
66419103 TTTTGTTTCA
66419113 ATTTCTTTTTCA-TCTTCTTTTTCACTCTC
1 ATTTCTTTTTCATTC-TCTTTTTCACTCTC
* *
66419142 AAATTT-TTTTTCGTTCTCTTTTTCAGTCTC
1 --ATTTCTTTTTCATTCTCTTTTTCACTCTC
*
66419172 ATTTCTTTTTCATTTTCTTTTT
1 ATTTCTTTTTCATTCTCTTTTT
66419194 GCTTTTCAAA
Statistics
Matches: 44, Mismatches: 4, Indels: 6
0.81 0.07 0.11
Matches are distributed among these distances:
28 4 0.09
29 15 0.34
30 19 0.43
31 6 0.14
ACGTcount: A:0.11, C:0.21, G:0.02, T:0.65
Consensus pattern (29 bp):
ATTTCTTTTTCATTCTCTTTTTCACTCTC
Found at i:66419282 original size:15 final size:14
Alignment explanation
Indices: 66419259--66419320 Score: 70
Period size: 15 Copynumber: 4.2 Consensus size: 14
66419249 TGTCTGCCTC
66419259 TCTTTTCTTTTTATT
1 TCTTTTCTTTTT-TT
* *
66419274 TCATTTCTTTTTCT
1 TCTTTTCTTTTTTT
66419288 TCTTTTGCTTTTTCTT
1 TCTTTT-CTTTTT-TT
*
66419304 TCTTTTCTTTATTT
1 TCTTTTCTTTTTTT
66419318 TCT
1 TCT
66419321 CTTTACAAGA
Statistics
Matches: 40, Mismatches: 5, Indels: 5
0.80 0.10 0.10
Matches are distributed among these distances:
14 11 0.28
15 22 0.55
16 7 0.17
ACGTcount: A:0.05, C:0.18, G:0.02, T:0.76
Consensus pattern (14 bp):
TCTTTTCTTTTTTT
Found at i:66419300 original size:16 final size:15
Alignment explanation
Indices: 66419259--66419313 Score: 76
Period size: 15 Copynumber: 3.7 Consensus size: 15
66419249 TGTCTGCCTC
*
66419259 TCTTTTCTTTTTATT
1 TCTTTTCTTTTTCTT
*
66419274 TCATTTCTTTTTC-T
1 TCTTTTCTTTTTCTT
66419288 TCTTTTGCTTTTTCTT
1 TCTTTT-CTTTTTCTT
66419304 TCTTTTCTTT
1 TCTTTTCTTT
66419314 ATTTTCTCTT
Statistics
Matches: 35, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
14 6 0.17
15 22 0.63
16 7 0.20
ACGTcount: A:0.04, C:0.18, G:0.02, T:0.76
Consensus pattern (15 bp):
TCTTTTCTTTTTCTT
Found at i:66420165 original size:11 final size:11
Alignment explanation
Indices: 66420149--66420201 Score: 54
Period size: 12 Copynumber: 4.7 Consensus size: 11
66420139 ATTAAACACT
66420149 TTTTTTTTAGA
1 TTTTTTTTAGA
66420160 TTTTTTTT-GA
1 TTTTTTTTAGA
*
66420170 ATTTTTTTATGA
1 TTTTTTTTA-GA
* *
66420182 ATTTTTTTCGAA
1 TTTTTTTTAG-A
66420194 TTTTTTTT
1 TTTTTTTT
66420202 GACTTGTATA
Statistics
Matches: 36, Mismatches: 3, Indels: 5
0.82 0.07 0.11
Matches are distributed among these distances:
10 9 0.25
11 9 0.25
12 18 0.50
ACGTcount: A:0.17, C:0.02, G:0.08, T:0.74
Consensus pattern (11 bp):
TTTTTTTTAGA
Found at i:66420182 original size:12 final size:11
Alignment explanation
Indices: 66420148--66420203 Score: 76
Period size: 11 Copynumber: 4.9 Consensus size: 11
66420138 CATTAAACAC
*
66420148 TTTTTTTTTAGA
1 TTTTTTTTGA-A
66420160 TTTTTTTTGAA
1 TTTTTTTTGAA
66420171 TTTTTTTATGAA
1 TTTTTTT-TGAA
*
66420183 TTTTTTTCGAA
1 TTTTTTTTGAA
66420194 TTTTTTTTGA
1 TTTTTTTTGA
66420204 CTTGTATAAC
Statistics
Matches: 40, Mismatches: 3, Indels: 3
0.87 0.07 0.07
Matches are distributed among these distances:
11 20 0.50
12 20 0.50
ACGTcount: A:0.18, C:0.02, G:0.09, T:0.71
Consensus pattern (11 bp):
TTTTTTTTGAA
Found at i:66420185 original size:23 final size:21
Alignment explanation
Indices: 66420150--66420200 Score: 75
Period size: 23 Copynumber: 2.3 Consensus size: 21
66420140 TTAAACACTT
*
66420150 TTTTTTTAGATTTTTTTTGAA
1 TTTTTTTAGATTTTTTTCGAA
66420171 TTTTTTTATGAATTTTTTTCGAA
1 TTTTTTTA-G-ATTTTTTTCGAA
66420194 TTTTTTT
1 TTTTTTT
66420201 TGACTTGTAT
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
21 8 0.30
22 1 0.04
23 18 0.67
ACGTcount: A:0.18, C:0.02, G:0.08, T:0.73
Consensus pattern (21 bp):
TTTTTTTAGATTTTTTTCGAA
Found at i:66421940 original size:30 final size:30
Alignment explanation
Indices: 66421906--66422002 Score: 81
Period size: 30 Copynumber: 3.2 Consensus size: 30
66421896 TAAACTAATA
*
66421906 TGAGCTAAGCTTTAGCTTGTGAGCTAAAGT
1 TGAGCTAAGCTTTAGCTCGTGAGCTAAAGT
* * * * * *
66421936 TGAGCTGAGGC-TAAACTCCTAAGCTGAAGT
1 TGAGCT-AAGCTTTAGCTCGTGAGCTAAAGT
* *
66421966 TGAGCTAAGGTTTAGCTCGTGAGTTGAAAG-
1 TGAGCTAAGCTTTAGCTCGTGAGCT-AAAGT
66421996 TGAGCTA
1 TGAGCTA
66422003 GGAGTGAGCT
Statistics
Matches: 49, Mismatches: 15, Indels: 6
0.70 0.21 0.09
Matches are distributed among these distances:
29 2 0.04
30 41 0.84
31 6 0.12
ACGTcount: A:0.28, C:0.14, G:0.29, T:0.29
Consensus pattern (30 bp):
TGAGCTAAGCTTTAGCTCGTGAGCTAAAGT
Found at i:66422424 original size:14 final size:14
Alignment explanation
Indices: 66422366--66422424 Score: 57
Period size: 14 Copynumber: 4.2 Consensus size: 14
66422356 ACATAAATCG
*
66422366 ACCAATTCGTTCAT
1 ACCATTTCGTTCAT
*
66422380 ATCC-CTTCGTTCAT
1 A-CCATTTCGTTCAT
* *
66422394 ACCATTTCATTCCT
1 ACCATTTCGTTCAT
*
66422408 ACCATTTCGTTCGT
1 ACCATTTCGTTCAT
66422422 ACC
1 ACC
66422425 CCTCTTTCTA
Statistics
Matches: 37, Mismatches: 6, Indels: 4
0.79 0.13 0.09
Matches are distributed among these distances:
13 2 0.05
14 33 0.89
15 2 0.05
ACGTcount: A:0.20, C:0.34, G:0.07, T:0.39
Consensus pattern (14 bp):
ACCATTTCGTTCAT
Found at i:66432462 original size:15 final size:15
Alignment explanation
Indices: 66432442--66432478 Score: 67
Period size: 15 Copynumber: 2.5 Consensus size: 15
66432432 CATAAATCAC
66432442 TTTTTTTTTC-GAAT
1 TTTTTTTTTCGGAAT
66432456 TTTTTTTTTCGGAAT
1 TTTTTTTTTCGGAAT
66432471 TTTTTTTT
1 TTTTTTTT
66432479 CAAACTTGTA
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
14 10 0.45
15 12 0.55
ACGTcount: A:0.11, C:0.05, G:0.08, T:0.76
Consensus pattern (15 bp):
TTTTTTTTTCGGAAT
Found at i:66435029 original size:15 final size:15
Alignment explanation
Indices: 66435009--66435056 Score: 53
Period size: 15 Copynumber: 3.3 Consensus size: 15
66434999 TCAAAGATGG
66435009 GTTTATGGATATGAA
1 GTTTATGGATATGAA
* * *
66435024 GTTTATGTAGATG-G
1 GTTTATGGATATGAA
*
66435038 GTTTATGGATATAAA
1 GTTTATGGATATGAA
66435053 GTTT
1 GTTT
66435057 TTGTAGGTTT
Statistics
Matches: 25, Mismatches: 7, Indels: 2
0.74 0.21 0.06
Matches are distributed among these distances:
14 10 0.40
15 15 0.60
ACGTcount: A:0.29, C:0.00, G:0.27, T:0.44
Consensus pattern (15 bp):
GTTTATGGATATGAA
Found at i:66435043 original size:14 final size:14
Alignment explanation
Indices: 66435003--66435046 Score: 52
Period size: 14 Copynumber: 3.1 Consensus size: 14
66434993 AAGGATTCAA
66435003 AGATGGGTTTATGG
1 AGATGGGTTTATGG
* * *
66435017 ATATGAAGTTTATGT
1 AGATG-GGTTTATGG
66435032 AGATGGGTTTATGG
1 AGATGGGTTTATGG
66435046 A
1 A
66435047 TATAAAGTTT
Statistics
Matches: 23, Mismatches: 6, Indels: 2
0.74 0.19 0.06
Matches are distributed among these distances:
14 12 0.52
15 11 0.48
ACGTcount: A:0.27, C:0.00, G:0.34, T:0.39
Consensus pattern (14 bp):
AGATGGGTTTATGG
Found at i:66435072 original size:29 final size:29
Alignment explanation
Indices: 66435003--66435062 Score: 102
Period size: 29 Copynumber: 2.1 Consensus size: 29
66434993 AAGGATTCAA
*
66435003 AGATGGGTTTATGGATATGAAGTTTATGT
1 AGATGGGTTTATGGATATAAAGTTTATGT
*
66435032 AGATGGGTTTATGGATATAAAGTTTTTGT
1 AGATGGGTTTATGGATATAAAGTTTATGT
66435061 AG
1 AG
66435063 GTTTGGTTAT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
29 29 1.00
ACGTcount: A:0.28, C:0.00, G:0.30, T:0.42
Consensus pattern (29 bp):
AGATGGGTTTATGGATATAAAGTTTATGT
Found at i:66436087 original size:14 final size:14
Alignment explanation
Indices: 66436045--66436089 Score: 56
Period size: 14 Copynumber: 3.3 Consensus size: 14
66436035 TTAAAGAAGC
66436045 AACTCATTAAATTA
1 AACTCATTAAATTA
* *
66436059 AATTCATCAAA-TA
1 AACTCATTAAATTA
*
66436072 AACTCATTTAATTA
1 AACTCATTAAATTA
66436086 AACT
1 AACT
66436090 AAGATGAGTT
Statistics
Matches: 25, Mismatches: 5, Indels: 2
0.78 0.16 0.06
Matches are distributed among these distances:
13 10 0.40
14 15 0.60
ACGTcount: A:0.49, C:0.16, G:0.00, T:0.36
Consensus pattern (14 bp):
AACTCATTAAATTA
Found at i:66438610 original size:18 final size:18
Alignment explanation
Indices: 66438569--66438614 Score: 56
Period size: 18 Copynumber: 2.6 Consensus size: 18
66438559 TCTTTTTCAT
* *
66438569 TCTCTTTTTCAATCTTAT
1 TCTCTTTTTCAATCTCAA
* *
66438587 TTTCTTTTTCACTCTCAA
1 TCTCTTTTTCAATCTCAA
66438605 TCTCTTTTTC
1 TCTCTTTTTC
66438615 TTTTTCTTTC
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.13, C:0.26, G:0.00, T:0.61
Consensus pattern (18 bp):
TCTCTTTTTCAATCTCAA
Found at i:66438620 original size:24 final size:24
Alignment explanation
Indices: 66438540--66438617 Score: 86
Period size: 24 Copynumber: 3.2 Consensus size: 24
66438530 CTTGTTCACA
*
66438540 TTCTTTCTCTCTCTCAAACTCTTT
1 TTCTTTCTCTCTCTCAATCTCTTT
* * *
66438564 TTCATTCTCTTTTTCAATCT-TATT
1 TTCTTTCTCTCTCTCAATCTCT-TT
* *
66438588 TTCTTTTTCACTCTCAATCTCTTT
1 TTCTTTCTCTCTCTCAATCTCTTT
66438612 TTCTTT
1 TTCTTT
66438618 TTCTTTCATT
Statistics
Matches: 43, Mismatches: 9, Indels: 4
0.77 0.16 0.07
Matches are distributed among these distances:
23 1 0.02
24 41 0.95
25 1 0.02
ACGTcount: A:0.13, C:0.27, G:0.00, T:0.60
Consensus pattern (24 bp):
TTCTTTCTCTCTCTCAATCTCTTT
Found at i:66439931 original size:15 final size:15
Alignment explanation
Indices: 66439911--66439958 Score: 53
Period size: 15 Copynumber: 3.3 Consensus size: 15
66439901 TCAAAGATGG
66439911 GTTTATGGATATGAA
1 GTTTATGGATATGAA
* * *
66439926 GTTTATGTAGATG-G
1 GTTTATGGATATGAA
*
66439940 GTTTATGGATATAAA
1 GTTTATGGATATGAA
66439955 GTTT
1 GTTT
66439959 TTGTAGGTTT
Statistics
Matches: 25, Mismatches: 7, Indels: 2
0.74 0.21 0.06
Matches are distributed among these distances:
14 10 0.40
15 15 0.60
ACGTcount: A:0.29, C:0.00, G:0.27, T:0.44
Consensus pattern (15 bp):
GTTTATGGATATGAA
Found at i:66439945 original size:14 final size:14
Alignment explanation
Indices: 66439905--66439948 Score: 52
Period size: 14 Copynumber: 3.1 Consensus size: 14
66439895 AAGGATTCAA
66439905 AGATGGGTTTATGG
1 AGATGGGTTTATGG
* * *
66439919 ATATGAAGTTTATGT
1 AGATG-GGTTTATGG
66439934 AGATGGGTTTATGG
1 AGATGGGTTTATGG
66439948 A
1 A
66439949 TATAAAGTTT
Statistics
Matches: 23, Mismatches: 6, Indels: 2
0.74 0.19 0.06
Matches are distributed among these distances:
14 12 0.52
15 11 0.48
ACGTcount: A:0.27, C:0.00, G:0.34, T:0.39
Consensus pattern (14 bp):
AGATGGGTTTATGG
Found at i:66439974 original size:29 final size:29
Alignment explanation
Indices: 66439905--66439964 Score: 102
Period size: 29 Copynumber: 2.1 Consensus size: 29
66439895 AAGGATTCAA
*
66439905 AGATGGGTTTATGGATATGAAGTTTATGT
1 AGATGGGTTTATGGATATAAAGTTTATGT
*
66439934 AGATGGGTTTATGGATATAAAGTTTTTGT
1 AGATGGGTTTATGGATATAAAGTTTATGT
66439963 AG
1 AG
66439965 GTTTGGTTAT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
29 29 1.00
ACGTcount: A:0.28, C:0.00, G:0.30, T:0.42
Consensus pattern (29 bp):
AGATGGGTTTATGGATATAAAGTTTATGT
Found at i:66440990 original size:14 final size:14
Alignment explanation
Indices: 66440948--66440992 Score: 56
Period size: 14 Copynumber: 3.3 Consensus size: 14
66440938 TTAAAGAAGC
66440948 AACTCATTAAATTA
1 AACTCATTAAATTA
* *
66440962 AATTCATCAAA-TA
1 AACTCATTAAATTA
*
66440975 AACTCATTTAATTA
1 AACTCATTAAATTA
66440989 AACT
1 AACT
66440993 AAGATGAGTT
Statistics
Matches: 25, Mismatches: 5, Indels: 2
0.78 0.16 0.06
Matches are distributed among these distances:
13 10 0.40
14 15 0.60
ACGTcount: A:0.49, C:0.16, G:0.00, T:0.36
Consensus pattern (14 bp):
AACTCATTAAATTA
Found at i:66443688 original size:30 final size:30
Alignment explanation
Indices: 66443654--66443750 Score: 90
Period size: 30 Copynumber: 3.2 Consensus size: 30
66443644 TAAACTAAAA
66443654 TGAGCTAAGCTTTAGCTCGTGAGCTAAAGT
1 TGAGCTAAGCTTTAGCTCGTGAGCTAAAGT
* * * * * *
66443684 TGAGCTGAGGC-TAAACTCCTAAGCTGAAGT
1 TGAGCT-AAGCTTTAGCTCGTGAGCTAAAGT
* *
66443714 TGAGCTAAGGTTTAGCTCGTGAGTTGAAAG-
1 TGAGCTAAGCTTTAGCTCGTGAGCT-AAAGT
66443744 TGAGCTA
1 TGAGCTA
66443751 GGAGTGAGCT
Statistics
Matches: 50, Mismatches: 14, Indels: 6
0.71 0.20 0.09
Matches are distributed among these distances:
29 2 0.04
30 42 0.84
31 6 0.12
ACGTcount: A:0.28, C:0.15, G:0.29, T:0.28
Consensus pattern (30 bp):
TGAGCTAAGCTTTAGCTCGTGAGCTAAAGT
Found at i:66445822 original size:30 final size:30
Alignment explanation
Indices: 66445719--66445816 Score: 97
Period size: 30 Copynumber: 3.3 Consensus size: 30
66445709 AGCTCACTCC
*
66445719 TAGCTCATATTCAGCTCACGAGCTAAACCT
1 TAGCTCATCTTCAGCTCACGAGCTAAACCT
* * * * * *
66445749 TAGCTCAGCTTCAGCTTAGGAGTTTAATCT
1 TAGCTCATCTTCAGCTCACGAGCTAAACCT
* * * *
66445779 CAGCTCAACTTTAGCTCACGAGCTAAAGCT
1 TAGCTCATCTTCAGCTCACGAGCTAAACCT
66445809 TAGCTCAT
1 TAGCTCAT
66445817 TTTTAGTTTA
Statistics
Matches: 51, Mismatches: 17, Indels: 0
0.75 0.25 0.00
Matches are distributed among these distances:
30 51 1.00
ACGTcount: A:0.28, C:0.27, G:0.16, T:0.30
Consensus pattern (30 bp):
TAGCTCATCTTCAGCTCACGAGCTAAACCT
Found at i:66446885 original size:19 final size:19
Alignment explanation
Indices: 66446861--66446900 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
66446851 AGCTCCCATG
66446861 TAGCTCCACACCAGCTCAT
1 TAGCTCCACACCAGCTCAT
***
66446880 TAGCTCGGGACCAGCTCAT
1 TAGCTCCACACCAGCTCAT
66446899 TA
1 TA
66446901 TCAGCTCACG
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.25, C:0.35, G:0.17, T:0.23
Consensus pattern (19 bp):
TAGCTCCACACCAGCTCAT
Found at i:66449116 original size:14 final size:14
Alignment explanation
Indices: 66449069--66449116 Score: 60
Period size: 14 Copynumber: 3.4 Consensus size: 14
66449059 GTACGAATGG
*
66449069 AATGGTAGGAACGA
1 AATGGTAGGAACAA
*
66449083 AAGGGTAGGAACAA
1 AATGGTAGGAACAA
*
66449097 AATGGTATGAACAA
1 AATGGTAGGAACAA
*
66449111 ATTGGT
1 AATGGT
66449117 CGGTTTAGGT
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
14 29 1.00
ACGTcount: A:0.44, C:0.06, G:0.31, T:0.19
Consensus pattern (14 bp):
AATGGTAGGAACAA
Found at i:66453468 original size:21 final size:19
Alignment explanation
Indices: 66453442--66453505 Score: 58
Period size: 21 Copynumber: 3.2 Consensus size: 19
66453432 CTCTTGCCTC
66453442 TCTTTTCCTTTTATTTTGTTT
1 TCTTTT-CTTTT-TTTTGTTT
*
66453463 TCTTTT-TCTTCTTTTGCTTTT
1 TCTTTTCT-TTTTTTTG--TTT
*
66453484 TCTTTTCTTTTCTTTGTTT
1 TCTTTTCTTTTTTTTGTTT
66453503 TCT
1 TCT
66453506 CTTTACAAAA
Statistics
Matches: 36, Mismatches: 3, Indels: 10
0.73 0.06 0.20
Matches are distributed among these distances:
19 12 0.33
20 2 0.06
21 21 0.58
22 1 0.03
ACGTcount: A:0.02, C:0.17, G:0.05, T:0.77
Consensus pattern (19 bp):
TCTTTTCTTTTTTTTGTTT
Found at i:66453491 original size:5 final size:5
Alignment explanation
Indices: 66453442--66453498 Score: 53
Period size: 5 Copynumber: 11.0 Consensus size: 5
66453432 CTCTTGCCTC
* * *
66453442 TCTTT TCCTTT TATTT TGTTT TCTTT T-TCT TCTTT TGCTTTT TCTTT
1 TCTTT T-CTTT TCTTT TCTTT TCTTT TCTTT TCTTT T-C-TTT TCTTT
66453489 TCTTT TCTTT
1 TCTTT TCTTT
66453499 GTTTTCTCTT
Statistics
Matches: 43, Mismatches: 5, Indels: 8
0.77 0.09 0.14
Matches are distributed among these distances:
4 3 0.07
5 29 0.67
6 7 0.16
7 4 0.09
ACGTcount: A:0.02, C:0.18, G:0.04, T:0.77
Consensus pattern (5 bp):
TCTTT
Found at i:66453508 original size:21 final size:20
Alignment explanation
Indices: 66453440--66453509 Score: 72
Period size: 20 Copynumber: 3.4 Consensus size: 20
66453430 GCCTCTTGCC
66453440 TCTCTTTTCCTTTTATTTTGTTT
1 TCTCTTTT-C-TTT-TTTTGTTT
*
66453463 TCT-TTTTCTTCTTTTGCTTT
1 TCTCTTTTCTTTTTTTG-TTT
66453483 T-TCTTTTCTTTTCTTTGTTT
1 TCTCTTTTCTTTT-TTTGTTT
66453503 TCTCTTT
1 TCTCTTT
66453510 ACAAAAATGT
Statistics
Matches: 41, Mismatches: 2, Indels: 10
0.77 0.04 0.19
Matches are distributed among these distances:
19 6 0.15
20 18 0.44
21 10 0.24
22 4 0.10
23 3 0.07
ACGTcount: A:0.01, C:0.19, G:0.04, T:0.76
Consensus pattern (20 bp):
TCTCTTTTCTTTTTTTGTTT
Found at i:66454455 original size:10 final size:11
Alignment explanation
Indices: 66454412--66454460 Score: 59
Period size: 11 Copynumber: 4.7 Consensus size: 11
66454402 TAAATCACTT
66454412 TTTTTTTC--A
1 TTTTTTTCGAA
66454421 TTTTTTT-GAA
1 TTTTTTTCGAA
66454431 TTTTTTTCGAA
1 TTTTTTTCGAA
**
66454442 TTTTTTTCGGT
1 TTTTTTTCGAA
66454453 TTTTTTTC
1 TTTTTTTC
66454461 AAACTTGTAT
Statistics
Matches: 35, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
9 7 0.20
10 8 0.23
11 20 0.57
ACGTcount: A:0.10, C:0.08, G:0.08, T:0.73
Consensus pattern (11 bp):
TTTTTTTCGAA
Found at i:66457795 original size:14 final size:14
Alignment explanation
Indices: 66457748--66457795 Score: 60
Period size: 14 Copynumber: 3.4 Consensus size: 14
66457738 GTACGAATGG
*
66457748 AATGGTAGGAACGA
1 AATGGTAGGAACAA
*
66457762 AAGGGTAGGAACAA
1 AATGGTAGGAACAA
*
66457776 AATGGTATGAACAA
1 AATGGTAGGAACAA
*
66457790 ATTGGT
1 AATGGT
66457796 CGGTTTAGGT
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
14 29 1.00
ACGTcount: A:0.44, C:0.06, G:0.31, T:0.19
Consensus pattern (14 bp):
AATGGTAGGAACAA
Found at i:66462845 original size:13 final size:13
Alignment explanation
Indices: 66462827--66462851 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
66462817 AATAGTTGTG
66462827 TGTTATTTAATTA
1 TGTTATTTAATTA
66462840 TGTTATTTAATT
1 TGTTATTTAATT
66462852 TTGTAGGTTG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.28, C:0.00, G:0.08, T:0.64
Consensus pattern (13 bp):
TGTTATTTAATTA
Found at i:66464584 original size:14 final size:14
Alignment explanation
Indices: 66464526--66464584 Score: 57
Period size: 14 Copynumber: 4.2 Consensus size: 14
66464516 ACCTAAATCG
*
66464526 ACCAATTCGTTCAT
1 ACCATTTCGTTCAT
*
66464540 ATCCCTTT-GTTCAT
1 A-CCATTTCGTTCAT
* *
66464554 ACCATTTCATTCCT
1 ACCATTTCGTTCAT
*
66464568 ACCATTTCGTTCGT
1 ACCATTTCGTTCAT
66464582 ACC
1 ACC
66464585 CCTCTTTCTA
Statistics
Matches: 36, Mismatches: 7, Indels: 4
0.77 0.15 0.09
Matches are distributed among these distances:
13 5 0.14
14 27 0.75
15 4 0.11
ACGTcount: A:0.20, C:0.32, G:0.07, T:0.41
Consensus pattern (14 bp):
ACCATTTCGTTCAT
Found at i:66471729 original size:10 final size:10
Alignment explanation
Indices: 66471714--66471740 Score: 54
Period size: 10 Copynumber: 2.7 Consensus size: 10
66471704 TACTCCTTCA
66471714 AGCTCAAATC
1 AGCTCAAATC
66471724 AGCTCAAATC
1 AGCTCAAATC
66471734 AGCTCAA
1 AGCTCAA
66471741 CTTCAACTTA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 17 1.00
ACGTcount: A:0.41, C:0.30, G:0.11, T:0.19
Consensus pattern (10 bp):
AGCTCAAATC
Found at i:66474122 original size:21 final size:21
Alignment explanation
Indices: 66474096--66474153 Score: 62
Period size: 21 Copynumber: 2.7 Consensus size: 21
66474086 AATGAGAGCG
**
66474096 GAAAAAGAAAGGCAAGAAAAT
1 GAAAAAGAAAGAAAAGAAAAT
* *
66474117 GAAAAAGAGAGAAAAGAAATT
1 GAAAAAGAAAGAAAAGAAAAT
*
66474138 GAAAGAGAAAAGAAAA
1 GAAAAAG-AAAGAAAA
66474154 AGAGTTGTGA
Statistics
Matches: 30, Mismatches: 6, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
21 23 0.77
22 7 0.23
ACGTcount: A:0.69, C:0.02, G:0.24, T:0.05
Consensus pattern (21 bp):
GAAAAAGAAAGAAAAGAAAAT
Found at i:66475693 original size:71 final size:71
Alignment explanation
Indices: 66475605--66475768 Score: 310
Period size: 71 Copynumber: 2.3 Consensus size: 71
66475595 GAGATGTATC
66475605 CCATGTAGACAAGAGAGCTACGTGAAAGATAAATGTAGCTAGGTCGCATGCGTGATTCCAAGTGA
1 CCATGTAGACAAGAGAGCTACGTGAAAGATAAATGTAGCTAGGTCGCATGCGTGATTCCAAGTGA
66475670 AGGACA
66 AGGACA
*
66475676 CCATGTAGACAAGAGAGCTACGTGAAAGATAAATGTAGCTGGGTCGCATGCGTGATTCCAAGTGA
1 CCATGTAGACAAGAGAGCTACGTGAAAGATAAATGTAGCTAGGTCGCATGCGTGATTCCAAGTGA
*
66475741 CGGACA
66 AGGACA
66475747 CCATGTAGACAAGAGAGCTACG
1 CCATGTAGACAAGAGAGCTACG
66475769 AGACAAATCG
Statistics
Matches: 91, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
71 91 1.00
ACGTcount: A:0.34, C:0.18, G:0.29, T:0.19
Consensus pattern (71 bp):
CCATGTAGACAAGAGAGCTACGTGAAAGATAAATGTAGCTAGGTCGCATGCGTGATTCCAAGTGA
AGGACA
Found at i:66483292 original size:70 final size:71
Alignment explanation
Indices: 66483141--66483303 Score: 310
Period size: 70 Copynumber: 2.3 Consensus size: 71
66483131 GAGATGTATC
66483141 CCATGTAGACAAGAGAGCTACGTGAAAGATAAATGTAGCTAGGTCGCATGCGTGATTCCAAGTGA
1 CCATGTAGACAAGAGAGCTACGTGAAAGATAAATGTAGCTAGGTCGCATGCGTGATTCCAAGTGA
66483206 AGGACA
66 AGGACA
66483212 CCATGTAGACAAGAGAGCTACGTGAAAGATAAATGTAGCT-GGTCGCATGCGTGATTCCAAGTGA
1 CCATGTAGACAAGAGAGCTACGTGAAAGATAAATGTAGCTAGGTCGCATGCGTGATTCCAAGTGA
*
66483276 CGGACA
66 AGGACA
66483282 CCATGTAGACAAGAGAGCTACG
1 CCATGTAGACAAGAGAGCTACG
66483304 AGACAAATCG
Statistics
Matches: 91, Mismatches: 1, Indels: 1
0.98 0.01 0.01
Matches are distributed among these distances:
70 51 0.56
71 40 0.44
ACGTcount: A:0.34, C:0.18, G:0.28, T:0.19
Consensus pattern (71 bp):
CCATGTAGACAAGAGAGCTACGTGAAAGATAAATGTAGCTAGGTCGCATGCGTGATTCCAAGTGA
AGGACA
Found at i:66495653 original size:15 final size:15
Alignment explanation
Indices: 66495607--66495654 Score: 53
Period size: 15 Copynumber: 3.3 Consensus size: 15
66495597 AAACCTACAA
*
66495607 AAACTTTATATCCAT
1 AAACTTCATATCCAT
* * *
66495622 AAA-TCCATCTACAT
1 AAACTTCATATCCAT
66495636 AAACTTCATATCCAT
1 AAACTTCATATCCAT
66495651 AAAC
1 AAAC
66495655 CCACCTTTGA
Statistics
Matches: 25, Mismatches: 7, Indels: 2
0.74 0.21 0.06
Matches are distributed among these distances:
14 10 0.40
15 15 0.60
ACGTcount: A:0.44, C:0.25, G:0.00, T:0.31
Consensus pattern (15 bp):
AAACTTCATATCCAT
Found at i:66496508 original size:17 final size:17
Alignment explanation
Indices: 66496466--66496508 Score: 54
Period size: 17 Copynumber: 2.5 Consensus size: 17
66496456 TGCACTTAAG
66496466 CCATTCATGCATTCTAT
1 CCATTCATGCATTCTAT
66496483 -CATTCCATGCATT-TGAT
1 CCATT-CATGCATTCT-AT
66496500 CCATTCATG
1 CCATTCATG
66496509 GACTAGCCTT
Statistics
Matches: 23, Mismatches: 0, Indels: 6
0.79 0.00 0.21
Matches are distributed among these distances:
16 5 0.22
17 14 0.61
18 4 0.17
ACGTcount: A:0.23, C:0.28, G:0.09, T:0.40
Consensus pattern (17 bp):
CCATTCATGCATTCTAT
Found at i:66496935 original size:30 final size:30
Alignment explanation
Indices: 66496901--66496997 Score: 99
Period size: 30 Copynumber: 3.2 Consensus size: 30
66496891 TAAACTAAAA
66496901 TGAGCTAAGCTTTAGCTCGTGAGCTAAAGT
1 TGAGCTAAGCTTTAGCTCGTGAGCTAAAGT
* * * * *
66496931 TGAGCTAAGGC-TAAACTCCTAAGCTGAAGT
1 TGAGCTAA-GCTTTAGCTCGTGAGCTAAAGT
* *
66496961 TGAGCTAAGGTTTAGCTCGTGAGTTGAAAG-
1 TGAGCTAAGCTTTAGCTCGTGAGCT-AAAGT
66496991 TGAGCTA
1 TGAGCTA
66496998 GGAATGAGCT
Statistics
Matches: 52, Mismatches: 12, Indels: 6
0.74 0.17 0.09
Matches are distributed among these distances:
29 1 0.02
30 46 0.88
31 5 0.10
ACGTcount: A:0.29, C:0.15, G:0.28, T:0.28
Consensus pattern (30 bp):
TGAGCTAAGCTTTAGCTCGTGAGCTAAAGT
Found at i:66498703 original size:30 final size:31
Alignment explanation
Indices: 66498669--66498765 Score: 101
Period size: 30 Copynumber: 3.2 Consensus size: 31
66498659 AGCTCACTCC
*
66498669 TAGCTC-ACTTTCAACTCACGAGCTAAACCT
1 TAGCTCAACTTTCAGCTCACGAGCTAAACCT
* * * * *
66498699 TAGCTCAAC-TTCAGCTTAGGAGTTTAGCCT
1 TAGCTCAACTTTCAGCTCACGAGCTAAACCT
* *
66498729 CAGCTCAACTTT-AGCTCACGAGCTAAAGCT
1 TAGCTCAACTTTCAGCTCACGAGCTAAACCT
66498759 TAGCTCA
1 TAGCTCA
66498766 TTTTAGTTTA
Statistics
Matches: 51, Mismatches: 14, Indels: 4
0.74 0.20 0.06
Matches are distributed among these distances:
30 47 0.92
31 4 0.08
ACGTcount: A:0.28, C:0.29, G:0.15, T:0.28
Consensus pattern (31 bp):
TAGCTCAACTTTCAGCTCACGAGCTAAACCT
Found at i:66500886 original size:14 final size:14
Alignment explanation
Indices: 66500864--66500908 Score: 65
Period size: 14 Copynumber: 3.3 Consensus size: 14
66500854 TTAAAGAAGC
66500864 AACTCATTAAATTA
1 AACTCATTAAATTA
*
66500878 AATTCATTAAA-TA
1 AACTCATTAAATTA
*
66500891 AACTCATTTAATTA
1 AACTCATTAAATTA
66500905 AACT
1 AACT
66500909 AAGATGAGTT
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
13 11 0.41
14 16 0.59
ACGTcount: A:0.49, C:0.13, G:0.00, T:0.38
Consensus pattern (14 bp):
AACTCATTAAATTA
Found at i:66500945 original size:22 final size:22
Alignment explanation
Indices: 66500920--66500989 Score: 60
Period size: 22 Copynumber: 3.3 Consensus size: 22
66500910 AGATGAGTTG
66500920 TATTAATGACTAGCAACTCATT
1 TATTAATGACTAGCAACTCATT
*
66500942 TATTAA--ACTA--AGA-TGAGTT
1 TATTAATGACTAGCA-ACTCA-TT
*
66500961 GTATTAATGACCAGCAACTCATT
1 -TATTAATGACTAGCAACTCATT
66500984 TATTAA
1 TATTAA
66500990 ATTAAGATGA
Statistics
Matches: 37, Mismatches: 3, Indels: 16
0.66 0.05 0.29
Matches are distributed among these distances:
18 3 0.08
19 3 0.08
20 10 0.27
22 15 0.41
23 3 0.08
24 3 0.08
ACGTcount: A:0.39, C:0.14, G:0.11, T:0.36
Consensus pattern (22 bp):
TATTAATGACTAGCAACTCATT
Found at i:66500952 original size:42 final size:42
Alignment explanation
Indices: 66500891--66501038 Score: 260
Period size: 42 Copynumber: 3.5 Consensus size: 42
66500881 TCATTAAATA
*
66500891 AACTCATTTAATTAAACTAAGATGAGTTGTATTAATGACTAGC
1 AACTCATTT-ATTAAACTAAGATGAGTTGTATTAATGACCAGC
66500934 AACTCATTTATTAAACTAAGATGAGTTGTATTAATGACCAGC
1 AACTCATTTATTAAACTAAGATGAGTTGTATTAATGACCAGC
* *
66500976 AACTCATTTATTAAATTAAGATGAGTTGTATTAATGACCAGG
1 AACTCATTTATTAAACTAAGATGAGTTGTATTAATGACCAGC
66501018 AACTCATTTATTAAACTAAGA
1 AACTCATTTATTAAACTAAGA
66501039 GGCTTAAATA
Statistics
Matches: 101, Mismatches: 4, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
42 92 0.91
43 9 0.09
ACGTcount: A:0.40, C:0.12, G:0.14, T:0.34
Consensus pattern (42 bp):
AACTCATTTATTAAACTAAGATGAGTTGTATTAATGACCAGC
Found at i:66500965 original size:20 final size:20
Alignment explanation
Indices: 66500901--66500967 Score: 59
Period size: 20 Copynumber: 3.2 Consensus size: 20
66500891 AACTCATTTA
66500901 ATTAAACTAAGATGAGTTGT
1 ATTAAACTAAGATGAGTTGT
*
66500921 ATTAATGACT-AGCAACTCA-TT-T
1 ATTAA--ACTAAG--A-TGAGTTGT
66500943 ATTAAACTAAGATGAGTTGT
1 ATTAAACTAAGATGAGTTGT
66500963 ATTAA
1 ATTAA
66500968 TGACCAGCAA
Statistics
Matches: 37, Mismatches: 2, Indels: 16
0.67 0.04 0.29
Matches are distributed among these distances:
18 2 0.05
19 3 0.08
20 14 0.38
21 4 0.11
22 9 0.24
23 3 0.08
24 2 0.05
ACGTcount: A:0.40, C:0.09, G:0.15, T:0.36
Consensus pattern (20 bp):
ATTAAACTAAGATGAGTTGT
Found at i:66504133 original size:21 final size:21
Alignment explanation
Indices: 66504100--66504173 Score: 50
Period size: 21 Copynumber: 3.6 Consensus size: 21
66504090 AAGACACTCA
**
66504100 TTTTTTCAATTTCCTTCTCTT
1 TTTTTTCTTTTTCCTTCTCTT
66504121 TTTTTTCTTTTT-CTT-TAC-T
1 TTTTTTCTTTTTCCTTCT-CTT
**
66504140 GATTTTC-TTTTCAC-TCTCTT
1 TTTTTTCTTTTTC-CTTCTCTT
66504160 TTGTTTTCTTTTTC
1 TT-TTTTCTTTTTC
66504174 TGATTTTTTT
Statistics
Matches: 40, Mismatches: 6, Indels: 13
0.68 0.10 0.22
Matches are distributed among these distances:
18 4 0.10
19 9 0.22
20 7 0.17
21 15 0.38
22 5 0.12
ACGTcount: A:0.07, C:0.20, G:0.03, T:0.70
Consensus pattern (21 bp):
TTTTTTCTTTTTCCTTCTCTT
Found at i:66506318 original size:13 final size:13
Alignment explanation
Indices: 66506302--66506336 Score: 61
Period size: 13 Copynumber: 2.7 Consensus size: 13
66506292 TTTTCAGATT
66506302 TTTTTTTTTTCAA
1 TTTTTTTTTTCAA
*
66506315 TTTTTTTTTTCGA
1 TTTTTTTTTTCAA
66506328 TTTTTTTTT
1 TTTTTTTTT
66506337 GAAACTTACT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 21 1.00
ACGTcount: A:0.09, C:0.06, G:0.03, T:0.83
Consensus pattern (13 bp):
TTTTTTTTTTCAA
Found at i:66507526 original size:14 final size:14
Alignment explanation
Indices: 66507504--66507548 Score: 65
Period size: 14 Copynumber: 3.3 Consensus size: 14
66507494 TTAAAGAAGC
66507504 AACTCATTAAATTA
1 AACTCATTAAATTA
*
66507518 AATTCATTAAA-TA
1 AACTCATTAAATTA
*
66507531 AACTCATTTAATTA
1 AACTCATTAAATTA
66507545 AACT
1 AACT
66507549 AAGATGAGTT
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
13 11 0.41
14 16 0.59
ACGTcount: A:0.49, C:0.13, G:0.00, T:0.38
Consensus pattern (14 bp):
AACTCATTAAATTA
Found at i:66507592 original size:42 final size:42
Alignment explanation
Indices: 66507531--66507636 Score: 194
Period size: 42 Copynumber: 2.5 Consensus size: 42
66507521 TCATTAAATA
66507531 AACTCATTTAATTAAACTAAGATGAGTTGTAATAATGACCAGC
1 AACTCATTT-ATTAAACTAAGATGAGTTGTAATAATGACCAGC
*
66507574 AACTCATTTATTAAACTAAGATGAGTTGTATTAATGACCAGC
1 AACTCATTTATTAAACTAAGATGAGTTGTAATAATGACCAGC
66507616 AACTCATTTATTAAACTAAGA
1 AACTCATTTATTAAACTAAGA
66507637 GGCTTAAATG
Statistics
Matches: 62, Mismatches: 1, Indels: 1
0.97 0.02 0.02
Matches are distributed among these distances:
42 53 0.85
43 9 0.15
ACGTcount: A:0.42, C:0.14, G:0.12, T:0.32
Consensus pattern (42 bp):
AACTCATTTATTAAACTAAGATGAGTTGTAATAATGACCAGC
Found at i:66511734 original size:20 final size:20
Alignment explanation
Indices: 66511711--66511757 Score: 58
Period size: 20 Copynumber: 2.4 Consensus size: 20
66511701 AGCTCCATTC
66511711 AGCTCAATTAAGCTCATTTG
1 AGCTCAATTAAGCTCATTTG
* * **
66511731 AGCTCATTTCAGCTTGTTTG
1 AGCTCAATTAAGCTCATTTG
66511751 AGCTCAA
1 AGCTCAA
66511758 CCGAGCTTAC
Statistics
Matches: 22, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.26, C:0.21, G:0.17, T:0.36
Consensus pattern (20 bp):
AGCTCAATTAAGCTCATTTG
Found at i:66513761 original size:14 final size:14
Alignment explanation
Indices: 66513719--66513763 Score: 56
Period size: 14 Copynumber: 3.3 Consensus size: 14
66513709 TTAAAGAAGC
66513719 AACTCATTAAATTA
1 AACTCATTAAATTA
* *
66513733 AATTCATCAAA-TA
1 AACTCATTAAATTA
*
66513746 AACTCATTTAATTA
1 AACTCATTAAATTA
66513760 AACT
1 AACT
66513764 AAGATGAGTT
Statistics
Matches: 25, Mismatches: 5, Indels: 2
0.78 0.16 0.06
Matches are distributed among these distances:
13 10 0.40
14 15 0.60
ACGTcount: A:0.49, C:0.16, G:0.00, T:0.36
Consensus pattern (14 bp):
AACTCATTAAATTA
Found at i:66516234 original size:18 final size:18
Alignment explanation
Indices: 66516209--66516254 Score: 65
Period size: 18 Copynumber: 2.6 Consensus size: 18
66516199 TCTTTTTCGT
*
66516209 TCTCTTTTTCAATCTCAT
1 TCTCTTTTTCAATCTCAA
* *
66516227 TTTCTTTTTCACTCTCAA
1 TCTCTTTTTCAATCTCAA
66516245 TCTCTTTTTC
1 TCTCTTTTTC
66516255 TTTTTCTTTC
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.13, C:0.28, G:0.00, T:0.59
Consensus pattern (18 bp):
TCTCTTTTTCAATCTCAA
Found at i:66516255 original size:24 final size:24
Alignment explanation
Indices: 66516190--66516260 Score: 79
Period size: 24 Copynumber: 3.0 Consensus size: 24
66516180 TTTTTTCTCT
* * * *
66516190 CTCTCAAACTCTTTTTCGTTCTCT
1 CTCTCAATCTCTTTTTCTTTTTCA
* * *
66516214 TTTTCAATCTCATTTTCTTTTTCA
1 CTCTCAATCTCTTTTTCTTTTTCA
66516238 CTCTCAATCTCTTTTTCTTTTTC
1 CTCTCAATCTCTTTTTCTTTTTC
66516261 TTTCATTTCT
Statistics
Matches: 37, Mismatches: 10, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
24 37 1.00
ACGTcount: A:0.13, C:0.28, G:0.01, T:0.58
Consensus pattern (24 bp):
CTCTCAATCTCTTTTTCTTTTTCA
Found at i:66519779 original size:30 final size:30
Alignment explanation
Indices: 66519693--66519780 Score: 88
Period size: 30 Copynumber: 2.9 Consensus size: 30
66519683 CTAGCTCACT
* *
66519693 TTCAACTCACGAGCTAAACCTTATCTCAAC
1 TTCAGCTCACGAGCTAAAGCTTATCTCAAC
* * ** *
66519723 TTCAGCTTAGGAG-TTTAGCCTCATCTCAAC
1 TTCAGCTCACGAGCTAAAG-CTTATCTCAAC
*
66519753 TTTAGCTCACGAGCTAAAGCTTATCTCA
1 TTCAGCTCACGAGCTAAAGCTTATCTCA
66519781 TTTTAGTTTA
Statistics
Matches: 43, Mismatches: 13, Indels: 4
0.72 0.22 0.07
Matches are distributed among these distances:
29 2 0.05
30 38 0.88
31 3 0.07
ACGTcount: A:0.28, C:0.28, G:0.12, T:0.31
Consensus pattern (30 bp):
TTCAGCTCACGAGCTAAAGCTTATCTCAAC
Found at i:66522326 original size:5 final size:5
Alignment explanation
Indices: 66522316--66522375 Score: 54
Period size: 5 Copynumber: 11.6 Consensus size: 5
66522306 AAGAGAAAAC
66522316 AAAGA AAAGA AAAGAA AAAGAA AAAGA AAA-A GAAA-A AAAGA AAATGA
1 AAAGA AAAGA AAAG-A AAAG-A AAAGA AAAGA -AAAGA AAAGA AAA-GA
66522363 AATA-A AAAGA AAA
1 AA-AGA AAAGA AAA
66522376 AGAGGCAAGA
Statistics
Matches: 49, Mismatches: 0, Indels: 12
0.80 0.00 0.20
Matches are distributed among these distances:
4 5 0.10
5 28 0.57
6 15 0.31
7 1 0.02
ACGTcount: A:0.82, C:0.00, G:0.15, T:0.03
Consensus pattern (5 bp):
AAAGA
Found at i:66522336 original size:6 final size:6
Alignment explanation
Indices: 66522316--66522378 Score: 62
Period size: 6 Copynumber: 10.8 Consensus size: 6
66522306 AAGAGAAAAC
*
66522316 AAAG-A AAAG-A AAAGAA AAAGAA AAAGAA AAAGAA AAA-AA GAAA-ATG
1 AAAGAA AAAGAA AAAGAA AAAGAA AAAGAA AAAGAA AAAGAA -AAAGA-A
*
66522362 AAATAA AAAGAA AAAGA
1 AAAGAA AAAGAA AAAGA
66522379 GGCAAGAGGC
Statistics
Matches: 51, Mismatches: 3, Indels: 7
0.84 0.05 0.11
Matches are distributed among these distances:
5 11 0.22
6 39 0.76
7 1 0.02
ACGTcount: A:0.81, C:0.00, G:0.16, T:0.03
Consensus pattern (6 bp):
AAAGAA
Found at i:66522357 original size:36 final size:37
Alignment explanation
Indices: 66522309--66522378 Score: 108
Period size: 36 Copynumber: 1.9 Consensus size: 37
66522299 TCTTGTAAAG
66522309 AGAAAACAAAGAAAA-GAAAAGAAAAAGAAAAAGAAAA
1 AGAAAACAAAGAAAATG-AAAGAAAAAGAAAAAGAAAA
*
66522346 AGAAAA-AAAGAAAATGAAATAAAAAGAAAAAGA
1 AGAAAACAAAGAAAATGAAAGAAAAAGAAAAAGA
66522379 GGCAAGAGGC
Statistics
Matches: 31, Mismatches: 1, Indels: 3
0.89 0.03 0.09
Matches are distributed among these distances:
36 24 0.77
37 7 0.23
ACGTcount: A:0.80, C:0.01, G:0.16, T:0.03
Consensus pattern (37 bp):
AGAAAACAAAGAAAATGAAAGAAAAAGAAAAAGAAAA
Found at i:66522454 original size:11 final size:12
Alignment explanation
Indices: 66522424--66522454 Score: 53
Period size: 12 Copynumber: 2.6 Consensus size: 12
66522414 TTGAGAGAAC
66522424 TTGAAAAAGCCT
1 TTGAAAAAGCCT
*
66522436 TTGAAAAATCCT
1 TTGAAAAAGCCT
66522448 TTGAAAA
1 TTGAAAA
66522455 GCAAAAAGAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.45, C:0.13, G:0.13, T:0.29
Consensus pattern (12 bp):
TTGAAAAAGCCT
Found at i:66522465 original size:12 final size:12
Alignment explanation
Indices: 66522457--66522481 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
66522447 TTTGAAAAGC
66522457 AAAAAGAAAATG
1 AAAAAGAAAATG
66522469 AAAAAGAAAATG
1 AAAAAGAAAATG
66522481 A
1 A
66522482 GATTGAAAAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.76, C:0.00, G:0.16, T:0.08
Consensus pattern (12 bp):
AAAAAGAAAATG
Found at i:66522478 original size:18 final size:18
Alignment explanation
Indices: 66522451--66522506 Score: 51
Period size: 18 Copynumber: 3.1 Consensus size: 18
66522441 AAATCCTTTG
66522451 AAAAGCAAAAAGAAAATGA
1 AAAAG-AAAAAGAAAATGA
* * *
66522470 AAAAGAAAATGAGATTGA
1 AAAAGAAAAAGAAAATGA
* *
66522488 AAAAGAGAACGAAAA-GA
1 AAAAGAAAAAGAAAATGA
66522505 AA
1 AA
66522507 TTTGAGAGTG
Statistics
Matches: 30, Mismatches: 7, Indels: 2
0.77 0.18 0.05
Matches are distributed among these distances:
17 4 0.13
18 21 0.70
19 5 0.17
ACGTcount: A:0.70, C:0.04, G:0.20, T:0.07
Consensus pattern (18 bp):
AAAAGAAAAAGAAAATGA
Found at i:66522491 original size:30 final size:31
Alignment explanation
Indices: 66522457--66522538 Score: 105
Period size: 30 Copynumber: 2.7 Consensus size: 31
66522447 TTTGAAAAGC
*
66522457 AAAAAGAAAATGAAAAAGAAA-ATGAGATTG
1 AAAAAGAAAATGAAAAAGAAATATGAGAGTG
* * *
66522487 AAAAAGAGAACG-AAAAGAAATTTGAGAGTG
1 AAAAAGAAAATGAAAAAGAAATATGAGAGTG
*
66522517 AAAAAGAAGATGAAAAAGAAAT
1 AAAAAGAAAATGAAAAAGAAAT
66522539 TGAAACAAAA
Statistics
Matches: 43, Mismatches: 7, Indels: 3
0.81 0.13 0.06
Matches are distributed among these distances:
29 8 0.19
30 26 0.60
31 9 0.21
ACGTcount: A:0.65, C:0.01, G:0.22, T:0.12
Consensus pattern (31 bp):
AAAAAGAAAATGAAAAAGAAATATGAGAGTG
Found at i:66524664 original size:30 final size:30
Alignment explanation
Indices: 66524578--66524665 Score: 79
Period size: 30 Copynumber: 2.9 Consensus size: 30
66524568 CACTCTCACT
* * *
66524578 TTCAACTCACGAGCTAAACCTTATCTCAAC
1 TTCAGCTCACGAGCTAAAGCTTAGCTCAAC
* * ** *
66524608 TTCAGCTTAGGAG-TTTAGCCTCAGCTCAAC
1 TTCAGCTCACGAGCTAAAG-CTTAGCTCAAC
*
66524638 TTTAGCTCACGAGCTAAAGCTTAGCTCA
1 TTCAGCTCACGAGCTAAAGCTTAGCTCA
66524666 TTTTAGTTTA
Statistics
Matches: 42, Mismatches: 14, Indels: 4
0.70 0.23 0.07
Matches are distributed among these distances:
29 2 0.05
30 37 0.88
31 3 0.07
ACGTcount: A:0.28, C:0.28, G:0.15, T:0.28
Consensus pattern (30 bp):
TTCAGCTCACGAGCTAAAGCTTAGCTCAAC
Found at i:66526512 original size:14 final size:14
Alignment explanation
Indices: 66526470--66526514 Score: 56
Period size: 14 Copynumber: 3.3 Consensus size: 14
66526460 TTAAAGAAGC
66526470 AACTCATTAAATTA
1 AACTCATTAAATTA
* *
66526484 AATTCATCAAA-TA
1 AACTCATTAAATTA
*
66526497 AACTCATTTAATTA
1 AACTCATTAAATTA
66526511 AACT
1 AACT
66526515 AAGATGAGTT
Statistics
Matches: 25, Mismatches: 5, Indels: 2
0.78 0.16 0.06
Matches are distributed among these distances:
13 10 0.40
14 15 0.60
ACGTcount: A:0.49, C:0.16, G:0.00, T:0.36
Consensus pattern (14 bp):
AACTCATTAAATTA
Found at i:66537727 original size:21 final size:20
Alignment explanation
Indices: 66537688--66537736 Score: 62
Period size: 21 Copynumber: 2.4 Consensus size: 20
66537678 ATCAGCTCAC
*
66537688 TTGAGCTCGTTTTAACTCGT
1 TTGAGCTCGATTTAACTCGT
*
66537708 TTGAGCTCGAATTTAGCTCGT
1 TTGAGCTCG-ATTTAACTCGT
*
66537729 TTCAGCTC
1 TTGAGCTC
66537737 ATTCCTTTTT
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
20 9 0.36
21 16 0.64
ACGTcount: A:0.16, C:0.22, G:0.20, T:0.41
Consensus pattern (20 bp):
TTGAGCTCGATTTAACTCGT
Found at i:66540590 original size:9 final size:10
Alignment explanation
Indices: 66540583--66540644 Score: 65
Period size: 11 Copynumber: 6.0 Consensus size: 10
66540573 AAGAGAAAAC
66540583 AAAGAAAAGA
1 AAAGAAAAGA
66540593 AAAGAAAAGAA
1 AAAGAAAAG-A
66540604 AAAGCAAAAGA
1 AAAG-AAAAGA
*
66540615 AGA-AAAAGA
1 AAAGAAAAGA
66540624 AAACGAAATA-A
1 AAA-GAAA-AGA
66540635 AAAGAAAAGA
1 AAAGAAAAGA
66540645 GAGGCAAGAG
Statistics
Matches: 44, Mismatches: 2, Indels: 12
0.76 0.03 0.21
Matches are distributed among these distances:
9 9 0.20
10 14 0.32
11 15 0.34
12 6 0.14
ACGTcount: A:0.77, C:0.03, G:0.18, T:0.02
Consensus pattern (10 bp):
AAAGAAAAGA
Found at i:66540603 original size:15 final size:14
Alignment explanation
Indices: 66540576--66540644 Score: 66
Period size: 16 Copynumber: 4.6 Consensus size: 14
66540566 TTTTGTAAAG
* *
66540576 AGAAAACAAAGAAA
1 AGAAAAGAAAAAAA
66540590 AGAAAAGAAAAGAAAA
1 AGAAAAG-AAA-AAAA
*
66540606 AGCAAAAGAAGAAAA
1 AG-AAAAGAAAAAAA
66540621 AGAAAACGAAATAAAA
1 AGAAAA-GAAA-AAAA
66540637 AGAAAAGA
1 AGAAAAGA
66540645 GAGGCAAGAG
Statistics
Matches: 46, Mismatches: 4, Indels: 9
0.78 0.07 0.15
Matches are distributed among these distances:
14 10 0.22
15 14 0.30
16 17 0.37
17 5 0.11
ACGTcount: A:0.77, C:0.04, G:0.17, T:0.01
Consensus pattern (14 bp):
AGAAAAGAAAAAAA
Found at i:66540612 original size:6 final size:5
Alignment explanation
Indices: 66540583--66540644 Score: 65
Period size: 5 Copynumber: 12.0 Consensus size: 5
66540573 AAGAGAAAAC
*
66540583 AAAGA AAAGA AAAGA AAAGAA AAAGCA AAAGA AGA-A AAAGA AAACGA
1 AAAGA AAAGA AAAGA AAAG-A AAAG-A AAAGA AAAGA AAAGA AAA-GA
66540630 AATA-A AAAGA AAAGA
1 AA-AGA AAAGA AAAGA
66540645 GAGGCAAGAG
Statistics
Matches: 49, Mismatches: 3, Indels: 10
0.79 0.05 0.16
Matches are distributed among these distances:
4 4 0.08
5 30 0.61
6 14 0.29
7 1 0.02
ACGTcount: A:0.77, C:0.03, G:0.18, T:0.02
Consensus pattern (5 bp):
AAAGA
Found at i:66540624 original size:31 final size:30
Alignment explanation
Indices: 66540587--66540644 Score: 82
Period size: 31 Copynumber: 1.9 Consensus size: 30
66540577 GAAAACAAAG
66540587 AAAAGAAAA-GAAAAGAAAAAGCAAAAGAAGA
1 AAAAGAAAACG-AAAGAAAAAG-AAAAGAAGA
*
66540618 AAAAGAAAACGAAATAAAAAGAAAAGA
1 AAAAGAAAACGAAAGAAAAAGAAAAGA
66540645 GAGGCAAGAG
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
30 6 0.24
31 18 0.72
32 1 0.04
ACGTcount: A:0.78, C:0.03, G:0.17, T:0.02
Consensus pattern (30 bp):
AAAAGAAAACGAAAGAAAAAGAAAAGAAGA
Found at i:66540724 original size:11 final size:12
Alignment explanation
Indices: 66540692--66540722 Score: 62
Period size: 12 Copynumber: 2.6 Consensus size: 12
66540682 TTGAGAGAAC
66540692 TTGAAAAAGCCT
1 TTGAAAAAGCCT
66540704 TTGAAAAAGCCT
1 TTGAAAAAGCCT
66540716 TTGAAAA
1 TTGAAAA
66540723 GCAAAAAGAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.45, C:0.13, G:0.16, T:0.26
Consensus pattern (12 bp):
TTGAAAAAGCCT
Found at i:66540759 original size:30 final size:29
Alignment explanation
Indices: 66540725--66540806 Score: 83
Period size: 30 Copynumber: 2.8 Consensus size: 29
66540715 TTTGAAAAGC
*
66540725 AAAAAGAAAATGAAAAATAAAATGAGATTG
1 AAAAAGAAAATGAAAAA-AAAATGAGAGTG
* * **
66540755 AAAAAGAGAACGAAAAGAAATCTGAGAGTG
1 AAAAAGAAAATGAAAA-AAAAATGAGAGTG
* *
66540785 AAAAAGAAGATGAAAAAGAAAT
1 AAAAAGAAAATGAAAAAAAAAT
66540807 TGAAACAAAA
Statistics
Matches: 40, Mismatches: 11, Indels: 3
0.74 0.20 0.06
Matches are distributed among these distances:
29 3 0.08
30 36 0.90
31 1 0.03
ACGTcount: A:0.65, C:0.02, G:0.21, T:0.12
Consensus pattern (29 bp):
AAAAAGAAAATGAAAAAAAAATGAGAGTG
Found at i:66542780 original size:37 final size:37
Alignment explanation
Indices: 66542727--66542800 Score: 139
Period size: 37 Copynumber: 2.0 Consensus size: 37
66542717 TATAAAAGAA
66542727 GTCTTACCCGGACATAATCTCCACACGTAGTCATCGG
1 GTCTTACCCGGACATAATCTCCACACGTAGTCATCGG
*
66542764 GTCTTACCCGGTCATAATCTCCACACGTAGTCATCGG
1 GTCTTACCCGGACATAATCTCCACACGTAGTCATCGG
66542801 TCTCACCTGA
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
37 36 1.00
ACGTcount: A:0.23, C:0.32, G:0.19, T:0.26
Consensus pattern (37 bp):
GTCTTACCCGGACATAATCTCCACACGTAGTCATCGG
Found at i:66542967 original size:49 final size:49
Alignment explanation
Indices: 66542912--66543084 Score: 247
Period size: 49 Copynumber: 3.4 Consensus size: 49
66542902 TTTTACATTA
*
66542912 GCCATTAGGCCTTATCACATATACATACACTTTCACATTCACCACATCG
1 GCCATTAGGCCTTATCACATATACATACACTTTCACATTCATCACATCG
66542961 GCCATTAGGCCAATGGCCTTATCACATATACATACACTTTCACATTCATCACATCG
1 GCCATT------A-GGCCTTATCACATATACATACACTTTCACATTCATCACATCG
* *
66543017 GCCATTAGGCCTTATCACATATACATACACTTTCACATTCATCGCATTG
1 GCCATTAGGCCTTATCACATATACATACACTTTCACATTCATCACATCG
*
66543066 GCCATTCGGCCTTATCACA
1 GCCATTAGGCCTTATCACA
66543085 CATATATGTA
Statistics
Matches: 113, Mismatches: 4, Indels: 14
0.86 0.03 0.11
Matches are distributed among these distances:
49 64 0.57
50 1 0.01
55 1 0.01
56 47 0.42
ACGTcount: A:0.29, C:0.31, G:0.10, T:0.29
Consensus pattern (49 bp):
GCCATTAGGCCTTATCACATATACATACACTTTCACATTCATCACATCG
Found at i:66542968 original size:56 final size:56
Alignment explanation
Indices: 66542907--66543071 Score: 229
Period size: 56 Copynumber: 3.1 Consensus size: 56
66542897 ATATATTTTA
*
66542907 CATTAGCCATTAGGCCTTATCACATATACATACACTTTCACATTCACCACATCGGC
1 CATTAGCCATTAGGCCTTATCACATATACATACACTTTCACATTCATCACATCGGC
*
66542963 CATTAGGCCAAT-GGCCTTATCACATATACATACACTTTCACATTCATCACATC-G-
1 CATTA-GCCATTAGGCCTTATCACATATACATACACTTTCACATTCATCACATCGGC
* *
66543017 -----GCCATTAGGCCTTATCACATATACATACACTTTCACATTCATCGCATTGGC
1 CATTAGCCATTAGGCCTTATCACATATACATACACTTTCACATTCATCACATCGGC
66543068 CATT
1 CATT
66543072 CGGCCTTATC
Statistics
Matches: 96, Mismatches: 5, Indels: 17
0.81 0.04 0.14
Matches are distributed among these distances:
48 5 0.05
49 39 0.41
50 1 0.01
55 1 0.01
56 45 0.47
57 5 0.05
ACGTcount: A:0.30, C:0.30, G:0.10, T:0.30
Consensus pattern (56 bp):
CATTAGCCATTAGGCCTTATCACATATACATACACTTTCACATTCATCACATCGGC
Found at i:66546910 original size:30 final size:31
Alignment explanation
Indices: 66546876--66546970 Score: 97
Period size: 30 Copynumber: 3.2 Consensus size: 31
66546866 AGCTCACTCC
*
66546876 TAGCTC-ACTTTCAACTCACGAGCTAAACCT
1 TAGCTCAACTTTCAGCTCACGAGCTAAACCT
* * * * *
66546906 TAGCTCAAC-TTCAGCTTAGGAGTTTAGCCT
1 TAGCTCAACTTTCAGCTCACGAGCTAAACCT
* *
66546936 CAGCTCAACTTT-AGCTCACGAGCTAAAGCT
1 TAGCTCAACTTTCAGCTCACGAGCTAAACCT
66546966 TAGCT
1 TAGCT
66546971 TATTTTAGTT
Statistics
Matches: 49, Mismatches: 14, Indels: 4
0.73 0.21 0.06
Matches are distributed among these distances:
30 45 0.92
31 4 0.08
ACGTcount: A:0.27, C:0.28, G:0.16, T:0.28
Consensus pattern (31 bp):
TAGCTCAACTTTCAGCTCACGAGCTAAACCT
Found at i:66548570 original size:13 final size:13
Alignment explanation
Indices: 66548552--66548580 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
66548542 AACAGTTGTG
66548552 TGTTATTTAATTA
1 TGTTATTTAATTA
66548565 TGTTATTTAATTA
1 TGTTATTTAATTA
66548578 TGT
1 TGT
66548581 AGGTTAGCCA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.28, C:0.00, G:0.10, T:0.62
Consensus pattern (13 bp):
TGTTATTTAATTA
Found at i:66552410 original size:91 final size:92
Alignment explanation
Indices: 66552301--66552468 Score: 295
Period size: 92 Copynumber: 1.8 Consensus size: 92
66552291 GCCCCTAAGT
*
66552301 GAACTCGGACTCAACTCAACGAGCTCGG-CGTTCGCATCCATAAGTGAACTC-GACTCAACTCAA
1 GAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCAT-AGTGAACTCGGACTCAACTCAA
66552364 CGAGTTCGGATGCCTAGTTACATCTCAC
65 CGAGTTCGGATGCCTAGTTACATCTCAC
*
66552392 GAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCATAGTGAACTCGGACTCAACTCAAC
1 GAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAGTGAACTCGGACTCAACTCAAC
66552457 GAGTTCGGATGC
66 GAGTTCGGATGC
66552469 TCAACCATCC
Statistics
Matches: 73, Mismatches: 2, Indels: 3
0.94 0.03 0.04
Matches are distributed among these distances:
91 36 0.49
92 37 0.51
ACGTcount: A:0.28, C:0.30, G:0.21, T:0.21
Consensus pattern (92 bp):
GAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAGTGAACTCGGACTCAACTCAAC
GAGTTCGGATGCCTAGTTACATCTCAC
Found at i:66552456 original size:45 final size:46
Alignment explanation
Indices: 66552296--66552465 Score: 201
Period size: 45 Copynumber: 3.7 Consensus size: 46
66552286 TAACCGCCCC
* *
66552296 TAAGTGAACTCGGACTCAACTCAACGAGCTCGG-CGTTCGCATCCA
1 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCA
*
66552341 TAAGTGAACTC-GACTCAACTCAACGAGTTCGGATGCCTAGTT-ACAT-C-
1 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGA---C-A-TTCGCATCCA
* *
66552388 TCA-CGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCA
1 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCA
66552433 T-AGTGAACTCGGACTCAACTCAACGAGTTCGGA
1 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGA
66552466 TGCTCAACCA
Statistics
Matches: 107, Mismatches: 7, Indels: 22
0.79 0.05 0.16
Matches are distributed among these distances:
42 2 0.02
43 4 0.04
44 23 0.21
45 41 0.38
46 6 0.06
47 24 0.22
48 2 0.02
49 3 0.03
50 2 0.02
ACGTcount: A:0.29, C:0.29, G:0.21, T:0.22
Consensus pattern (46 bp):
TAAGTGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCA
Found at i:66552921 original size:30 final size:30
Alignment explanation
Indices: 66552887--66552946 Score: 93
Period size: 30 Copynumber: 2.0 Consensus size: 30
66552877 ATTTAATACG
66552887 AACTTTGGAAAAATTACACTTTTGCCCCTA
1 AACTTTGGAAAAATTACACTTTTGCCCCTA
* * *
66552917 AACTTTTGCATAATTACACTTTTGCCCCTA
1 AACTTTGGAAAAATTACACTTTTGCCCCTA
66552947 GGCTCGGGAA
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
30 27 1.00
ACGTcount: A:0.30, C:0.25, G:0.08, T:0.37
Consensus pattern (30 bp):
AACTTTGGAAAAATTACACTTTTGCCCCTA
Found at i:66568329 original size:46 final size:46
Alignment explanation
Indices: 66568262--66568434 Score: 183
Period size: 46 Copynumber: 3.7 Consensus size: 46
66568252 AACTCGCCCC
* * *
66568262 TAAGTGAACTCGGACTCAACTCAATGAGCTCGGGCGTTCGCATCCA
1 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGACGTTCGCATCCA
* *
66568308 TAAGTGAACTCGGACTCAACTCAACGAGTTCGAATGCCTAGTT-ACAT-C-
1 TAAGTGAACTCGGACTCAACTCAACGAGTTCG---GAC--GTTCGCATCCA
* * * *
66568356 TCA-CGAACTCAGACTCAACTCAACGAGTTCGGACATTCGCATCCA
1 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGACGTTCGCATCCA
*
66568401 TAGGTGAACTCGGACTCAACTCAACGAGTTCGGA
1 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGA
66568435 TGCTCAACCA
Statistics
Matches: 104, Mismatches: 14, Indels: 18
0.76 0.10 0.13
Matches are distributed among these distances:
42 2 0.02
43 3 0.03
44 3 0.03
45 1 0.01
46 58 0.56
47 26 0.25
48 2 0.02
49 3 0.03
50 3 0.03
51 3 0.03
ACGTcount: A:0.29, C:0.28, G:0.21, T:0.22
Consensus pattern (46 bp):
TAAGTGAACTCGGACTCAACTCAACGAGTTCGGACGTTCGCATCCA
Found at i:66568376 original size:93 final size:93
Alignment explanation
Indices: 66568267--66568437 Score: 279
Period size: 93 Copynumber: 1.8 Consensus size: 93
66568257 GCCCCTAAGT
* * * *
66568267 GAACTCGGACTCAACTCAATGAGCTCGGGCGTTCGCATCCATAAGTGAACTCGGACTCAACTCAA
1 GAACTCAGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
66568332 CGAGTTCGAATGCCTAGTTACATCTCAC
66 CGAGTTCGAATGCCTAGTTACATCTCAC
* *
66568360 GAACTCAGACTCAACTCAACGAGTTCGGACATTCGCATCCATAGGTGAACTCGGACTCAACTCAA
1 GAACTCAGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
*
66568425 CGAGTTCGGATGC
66 CGAGTTCGAATGC
66568438 TCAACCATCC
Statistics
Matches: 71, Mismatches: 7, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
93 71 1.00
ACGTcount: A:0.29, C:0.29, G:0.21, T:0.22
Consensus pattern (93 bp):
GAACTCAGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
CGAGTTCGAATGCCTAGTTACATCTCAC
Found at i:66568891 original size:30 final size:30
Alignment explanation
Indices: 66568857--66568916 Score: 93
Period size: 30 Copynumber: 2.0 Consensus size: 30
66568847 ATTTAATACG
66568857 AACTTTGGAAAAATTACACTTTTGCCCCTA
1 AACTTTGGAAAAATTACACTTTTGCCCCTA
* * *
66568887 AACTTTTGCATAATTACACTTTTGCCCCTA
1 AACTTTGGAAAAATTACACTTTTGCCCCTA
66568917 GGCTCGGGAA
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
30 27 1.00
ACGTcount: A:0.30, C:0.25, G:0.08, T:0.37
Consensus pattern (30 bp):
AACTTTGGAAAAATTACACTTTTGCCCCTA
Found at i:66572133 original size:14 final size:14
Alignment explanation
Indices: 66572116--66572150 Score: 52
Period size: 14 Copynumber: 2.5 Consensus size: 14
66572106 TAATTCAGTG
66572116 AAAAAAATTCGTAC
1 AAAAAAATTCGTAC
* *
66572130 AAAAAATTTCGTAT
1 AAAAAAATTCGTAC
66572144 AAAAAAA
1 AAAAAAA
66572151 AGAACATATA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.63, C:0.09, G:0.06, T:0.23
Consensus pattern (14 bp):
AAAAAAATTCGTAC
Found at i:66573591 original size:14 final size:14
Alignment explanation
Indices: 66573574--66573604 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
66573564 TGGATAGTTG
66573574 AAGAAAGGCTAAGA
1 AAGAAAGGCTAAGA
*
66573588 AAGAAAGGTTAAGA
1 AAGAAAGGCTAAGA
66573602 AAG
1 AAG
66573605 GTTCAAATAG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.58, C:0.03, G:0.29, T:0.10
Consensus pattern (14 bp):
AAGAAAGGCTAAGA
Found at i:66574795 original size:30 final size:31
Alignment explanation
Indices: 66574761--66574857 Score: 101
Period size: 30 Copynumber: 3.2 Consensus size: 31
66574751 AGCTCACTCC
*
66574761 TAGCTC-ACTTTCAACTCACGAGCTAAACCT
1 TAGCTCAACTTTCAGCTCACGAGCTAAACCT
* * * * *
66574791 TAGCTCAAC-TTCAGCTTAGGAGTTTAGCCT
1 TAGCTCAACTTTCAGCTCACGAGCTAAACCT
* *
66574821 CAGCTCAACTTT-AGCTCACGAGCTAAAGCT
1 TAGCTCAACTTTCAGCTCACGAGCTAAACCT
66574851 TAGCTCA
1 TAGCTCA
66574858 TTTTAGTTTA
Statistics
Matches: 51, Mismatches: 14, Indels: 4
0.74 0.20 0.06
Matches are distributed among these distances:
30 47 0.92
31 4 0.08
ACGTcount: A:0.28, C:0.29, G:0.15, T:0.28
Consensus pattern (31 bp):
TAGCTCAACTTTCAGCTCACGAGCTAAACCT
Found at i:66576610 original size:18 final size:16
Alignment explanation
Indices: 66576588--66576627 Score: 53
Period size: 17 Copynumber: 2.4 Consensus size: 16
66576578 AAAAAAATTC
* *
66576588 AAAAAAAAATTTTGAA
1 AAAAAAAAAATCTGAA
66576604 AAGAAAAAAAATCTGAA
1 AA-AAAAAAAATCTGAA
66576621 AAAAAAA
1 AAAAAAA
66576628 GTGTTTAATG
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
16 7 0.33
17 14 0.67
ACGTcount: A:0.75, C:0.03, G:0.07, T:0.15
Consensus pattern (16 bp):
AAAAAAAAAATCTGAA
Found at i:66587940 original size:30 final size:30
Alignment explanation
Indices: 66587855--66587951 Score: 97
Period size: 30 Copynumber: 3.2 Consensus size: 30
66587845 TAAACTAAAA
* * *
66587855 TGAGCTAAGCTTTAGCTCGTGAGCTAAAGT
1 TGAGCTAAGGTTTAGCTCATGAGCTGAAGT
* * * * * *
66587885 TGAGCTGAGGCTAAACTCCTAAGCTGAAGT
1 TGAGCTAAGGTTTAGCTCATGAGCTGAAGT
66587915 TGAGCTAAGGTTTAGCTCATGAGCTGAA-T
1 TGAGCTAAGGTTTAGCTCATGAGCTGAAGT
66587944 ATGAGCTA
1 -TGAGCTA
66587952 GGAGTGAGCT
Statistics
Matches: 52, Mismatches: 14, Indels: 2
0.76 0.21 0.03
Matches are distributed among these distances:
29 1 0.02
30 51 0.98
ACGTcount: A:0.29, C:0.16, G:0.27, T:0.28
Consensus pattern (30 bp):
TGAGCTAAGGTTTAGCTCATGAGCTGAAGT
Found at i:66589804 original size:14 final size:14
Alignment explanation
Indices: 66589782--66589829 Score: 60
Period size: 14 Copynumber: 3.4 Consensus size: 14
66589772 ACCTAAACCG
* *
66589782 ACCAATTTGTTCAT
1 ACCATTTTGTTCCT
66589796 ACCATTTTGTTCCT
1 ACCATTTTGTTCCT
* *
66589810 ACCCTTTCGTTCCT
1 ACCATTTTGTTCCT
66589824 ACCATT
1 ACCATT
66589830 CCATTCGTAA
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
14 29 1.00
ACGTcount: A:0.19, C:0.31, G:0.06, T:0.44
Consensus pattern (14 bp):
ACCATTTTGTTCCT
Found at i:66591763 original size:30 final size:30
Alignment explanation
Indices: 66591711--66591796 Score: 104
Period size: 30 Copynumber: 2.9 Consensus size: 30
66591701 TTCTTTTGTT
*
66591711 TCAATTTCTTTTTCA-TCTTCTTTTTCACTC
1 TCAATTTCTTTTTCATTC-TCTTTTTCAATC
*
66591741 TCAAATTTC-TTTTCGTTCTCTTTTTCAATC
1 TC-AATTTCTTTTTCATTCTCTTTTTCAATC
* *
66591771 TCATTTTCTTTTTCATTTTCTTTTTC
1 TCAATTTCTTTTTCATTCTCTTTTTC
66591797 TTTTCAAAGG
Statistics
Matches: 48, Mismatches: 5, Indels: 6
0.81 0.08 0.10
Matches are distributed among these distances:
29 5 0.10
30 35 0.73
31 8 0.17
ACGTcount: A:0.13, C:0.23, G:0.01, T:0.63
Consensus pattern (30 bp):
TCAATTTCTTTTTCATTCTCTTTTTCAATC
Found at i:66591782 original size:18 final size:18
Alignment explanation
Indices: 66591759--66591800 Score: 57
Period size: 18 Copynumber: 2.3 Consensus size: 18
66591749 CTTTTCGTTC
66591759 TCTTTTTCAATCTCATTT
1 TCTTTTTCAATCTCATTT
* * *
66591777 TCTTTTTCATTTTCTTTT
1 TCTTTTTCAATCTCATTT
66591795 TCTTTT
1 TCTTTT
66591801 CAAAGGCTTT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.10, C:0.19, G:0.00, T:0.71
Consensus pattern (18 bp):
TCTTTTTCAATCTCATTT
Found at i:66591786 original size:12 final size:12
Alignment explanation
Indices: 66591771--66591801 Score: 55
Period size: 12 Copynumber: 2.7 Consensus size: 12
66591761 TTTTTCAATC
66591771 TCATTTTCTTTT
1 TCATTTTCTTTT
66591783 TCATTTTCTTTT
1 TCATTTTCTTTT
66591795 TC-TTTTC
1 TCATTTTC
66591802 AAAGGCTTTT
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
11 5 0.26
12 14 0.74
ACGTcount: A:0.06, C:0.19, G:0.00, T:0.74
Consensus pattern (12 bp):
TCATTTTCTTTT
Found at i:66591812 original size:12 final size:12
Alignment explanation
Indices: 66591797--66591827 Score: 62
Period size: 12 Copynumber: 2.6 Consensus size: 12
66591787 TTTCTTTTTC
66591797 TTTTCAAAGGCT
1 TTTTCAAAGGCT
66591809 TTTTCAAAGGCT
1 TTTTCAAAGGCT
66591821 TTTTCAA
1 TTTTCAA
66591828 GTTCTCTCAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.26, C:0.16, G:0.13, T:0.45
Consensus pattern (12 bp):
TTTTCAAAGGCT
Found at i:66591917 original size:21 final size:21
Alignment explanation
Indices: 66591893--66591942 Score: 66
Period size: 21 Copynumber: 2.4 Consensus size: 21
66591883 TTTTATTTCA
66591893 TTTTCTTTT-TATTCTTTTGTT
1 TTTTCTTTTCTATTC-TTTGTT
*
66591914 TTTTCTTTTCTTTTCTTTGTT
1 TTTTCTTTTCTATTCTTTGTT
*
66591935 TTCTCTTT
1 TTTTCTTT
66591943 ACAAGAATGT
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
21 22 0.85
22 4 0.15
ACGTcount: A:0.02, C:0.14, G:0.04, T:0.80
Consensus pattern (21 bp):
TTTTCTTTTCTATTCTTTGTT
Found at i:66591921 original size:12 final size:13
Alignment explanation
Indices: 66591875--66591927 Score: 54
Period size: 12 Copynumber: 3.8 Consensus size: 13
66591865 CTCTTGCCTC
66591875 TCTTTTCTTTTTATT
1 TCTTTTC-TTTTA-T
66591890 TCATTTTCTTTTTAT
1 TC-TTTTC-TTTTAT
*
66591905 TCTTTTGTTTT-T
1 TCTTTTCTTTTAT
66591917 TCTTTTCTTTT
1 TCTTTTCTTTT
66591928 CTTTGTTTTC
Statistics
Matches: 35, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
12 11 0.31
13 4 0.11
14 4 0.11
15 5 0.14
16 11 0.31
ACGTcount: A:0.06, C:0.13, G:0.02, T:0.79
Consensus pattern (13 bp):
TCTTTTCTTTTAT
Found at i:66596185 original size:18 final size:18
Alignment explanation
Indices: 66596164--66596213 Score: 73
Period size: 18 Copynumber: 2.8 Consensus size: 18
66596154 AAACTCTTTT
66596164 TCATTCTCTTTTTCAATC
1 TCATTCTCTTTTTCAATC
* *
66596182 TCATTTTCTTTTTCACTC
1 TCATTCTCTTTTTCAATC
*
66596200 TCAATCTCTTTTTC
1 TCATTCTCTTTTTC
66596214 TTTTTCTTTC
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 28 1.00
ACGTcount: A:0.14, C:0.28, G:0.00, T:0.58
Consensus pattern (18 bp):
TCATTCTCTTTTTCAATC
Found at i:66596219 original size:24 final size:24
Alignment explanation
Indices: 66596139--66596216 Score: 93
Period size: 24 Copynumber: 3.2 Consensus size: 24
66596129 CTTGTTCACA
*
66596139 TTCTTTCTCTCTCTCAAACTCTTT
1 TTCTTTCTCTCTCTCAATCTCTTT
* * * *
66596163 TTCATTCTCTTTTTCAATCTCATT
1 TTCTTTCTCTCTCTCAATCTCTTT
* *
66596187 TTCTTTTTCACTCTCAATCTCTTT
1 TTCTTTCTCTCTCTCAATCTCTTT
66596211 TTCTTT
1 TTCTTT
66596217 TTCTTTCATT
Statistics
Matches: 43, Mismatches: 11, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
24 43 1.00
ACGTcount: A:0.13, C:0.28, G:0.00, T:0.59
Consensus pattern (24 bp):
TTCTTTCTCTCTCTCAATCTCTTT
Found at i:66597313 original size:9 final size:9
Alignment explanation
Indices: 66597299--66597330 Score: 64
Period size: 9 Copynumber: 3.6 Consensus size: 9
66597289 TTGTTTGAAA
66597299 TTTTTTTCG
1 TTTTTTTCG
66597308 TTTTTTTCG
1 TTTTTTTCG
66597317 TTTTTTTCG
1 TTTTTTTCG
66597326 TTTTT
1 TTTTT
66597331 ATTTTGAAAC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 23 1.00
ACGTcount: A:0.00, C:0.09, G:0.09, T:0.81
Consensus pattern (9 bp):
TTTTTTTCG
Done.