Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold488
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: 153219
ACGTcount: A:0.31, C:0.14, G:0.15, T:0.33
Warning! 10576 characters in sequence are not A, C, G, or T
Found at i:745 original size:15 final size:15
Alignment explanation
Indices: 720--754 Score: 54
Period size: 15 Copynumber: 2.4 Consensus size: 15
710 AACTCTATTT
*
720 TAATT-ATATTAGGA
1 TAATTAATATTAAGA
734 TAATTAATATTAAGA
1 TAATTAATATTAAGA
749 TAATTA
1 TAATTA
755 TTAAGGATTA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 5 0.26
15 14 0.74
ACGTcount: A:0.49, C:0.00, G:0.09, T:0.43
Consensus pattern (15 bp):
TAATTAATATTAAGA
Found at i:797 original size:10 final size:10
Alignment explanation
Indices: 779--826 Score: 53
Period size: 10 Copynumber: 4.9 Consensus size: 10
769 ATTTTAGTAT
779 TTTAT-TTTA
1 TTTATCTTTA
788 TTTATCTTTA
1 TTTATCTTTA
798 TTTATCTTTA
1 TTTATCTTTA
* ** *
808 ATTAAATGTA
1 TTTATCTTTA
818 TTTATCTTT
1 TTTATCTTT
827 TGGGAGTTTA
Statistics
Matches: 30, Mismatches: 8, Indels: 1
0.77 0.21 0.03
Matches are distributed among these distances:
9 5 0.17
10 25 0.83
ACGTcount: A:0.25, C:0.06, G:0.02, T:0.67
Consensus pattern (10 bp):
TTTATCTTTA
Found at i:2972 original size:168 final size:168
Alignment explanation
Indices: 2678--3356 Score: 1045
Period size: 168 Copynumber: 4.0 Consensus size: 168
2668 CTTTGGGAAC
* * *
2678 TCATGCTTATGTTCCTTACCCTCATCTTGTTTTTCCTTGTACTCGGGTATTTTTGGATATTCGAC
1 TCATGTTTATGTTCCTTACCCTCATCTTGCTTTTCCTTGTACTCGGGTATTTTCGGATATTCGAC
** * **
2743 TTCGTGTTTCTCGTGCTCTTTAGGCTTTTCCCCTTTGGGGAAATTAGGTTTTTCTTTCTCGTACG
66 TTCGTGTTTCTCGTGCTCTTTAGGCTTTTCCAATTTGGGGAACTCGGGTTTTTCTTTCTCGTAC-
* *
2808 T-TTCGTGCTCCTTCGATTCGTGTGACTCGTGGCACTCC
130 TCTTCGTGCTCCTTCGATTCGTGTGACTCGTGGTACTCT
* * * * *
2846 TCATGTTTATGATCCCTACCCTCATCTTGCTTTTCCTTATACTCGGTTATTTTCAGATATTCGAC
1 TCATGTTTATGTTCCTTACCCTCATCTTGCTTTTCCTTGTACTCGGGTATTTTCGGATATTCGAC
* * * *
2911 TTCGTGTTACTCATGATCTTTAGGCTTTTCCAATTTGAGGAACTCGGGTTTTTCTTTCTCGTACT
66 TTCGTGTTTCTCGTGCTCTTTAGGCTTTTCCAATTTGGGGAACTCGGGTTTTTCTTTCTCGTACT
* *
2976 CTTCATGCTCCTTCAATTCGTGTGACTCGTGGTACTCT
131 CTTCGTGCTCCTTCGATTCGTGTGACTCGTGGTACTCT
*
3014 TCATGTTTATGTTCCTTACCCTCATCTTGCTTTTCCTTGTACTCGGGTATTTCCGGATATTCGAC
1 TCATGTTTATGTTCCTTACCCTCATCTTGCTTTTCCTTGTACTCGGGTATTTTCGGATATTCGAC
*
3079 TTCGTGTTTCTCGTGCTCTTTAGGCTTTTCCAATTTGGGGAACTCGGGCTTTTCTTTCTCGTACT
66 TTCGTGTTTCTCGTGCTCTTTAGGCTTTTCCAATTTGGGGAACTCGGGTTTTTCTTTCTCGTACT
* * *
3144 TTTCGTGCTCCTTCGATTCGCGTGATTCGTGGTACTCT
131 CTTCGTGCTCCTTCGATTCGTGTGACTCGTGGTACTCT
* *
3182 TCATGTTTATGTTCCTTACCCTCATCTTGGTTTTCCTTGTACTCGGGTATTTTTGGATATTCGAC
1 TCATGTTTATGTTCCTTACCCTCATCTTGCTTTTCCTTGTACTCGGGTATTTTCGGATATTCGAC
* * *
3247 TTCGTGTTTTTCGTGCTCTTTAGGCTTTTCCAATTTGGGGAACTCGGGTTTTTCTTTTTGGTACT
66 TTCGTGTTTCTCGTGCTCTTTAGGCTTTTCCAATTTGGGGAACTCGGGTTTTTCTTTCTCGTACT
* *
3312 CTTCCTGCTCCTTCGATTTGTGTGACTCGTGGTACTCT
131 CTTCGTGCTCCTTCGATTCGTGTGACTCGTGGTACTCT
3350 TCATGTT
1 TCATGTT
3357 GCTTGCAGGG
Statistics
Matches: 461, Mismatches: 49, Indels: 2
0.90 0.10 0.00
Matches are distributed among these distances:
167 1 0.00
168 460 1.00
ACGTcount: A:0.12, C:0.24, G:0.19, T:0.46
Consensus pattern (168 bp):
TCATGTTTATGTTCCTTACCCTCATCTTGCTTTTCCTTGTACTCGGGTATTTTCGGATATTCGAC
TTCGTGTTTCTCGTGCTCTTTAGGCTTTTCCAATTTGGGGAACTCGGGTTTTTCTTTCTCGTACT
CTTCGTGCTCCTTCGATTCGTGTGACTCGTGGTACTCT
Found at i:5681 original size:24 final size:24
Alignment explanation
Indices: 5649--5698 Score: 91
Period size: 24 Copynumber: 2.1 Consensus size: 24
5639 AATAAGATTG
*
5649 AACTTTCACCTTGGGGTCAAAGGC
1 AACTTTCACCTCGGGGTCAAAGGC
5673 AACTTTCACCTCGGGGTCAAAGGC
1 AACTTTCACCTCGGGGTCAAAGGC
5697 AA
1 AA
5699 TTGCTATGGC
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.28, C:0.26, G:0.24, T:0.22
Consensus pattern (24 bp):
AACTTTCACCTCGGGGTCAAAGGC
Found at i:7521 original size:2 final size:2
Alignment explanation
Indices: 7514--7541 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
7504 AAAATTTAAG
7514 TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA
7542 GGTATTTAAC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:7930 original size:12 final size:12
Alignment explanation
Indices: 7913--7937 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
7903 TTGTATCACC
7913 AATCATAATTAT
1 AATCATAATTAT
7925 AATCATAATTAT
1 AATCATAATTAT
7937 A
1 A
7938 CTAATAAATA
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:0.52, C:0.08, G:0.00, T:0.40
Consensus pattern (12 bp):
AATCATAATTAT
Found at i:13630 original size:24 final size:23
Alignment explanation
Indices: 13570--13638 Score: 70
Period size: 24 Copynumber: 2.9 Consensus size: 23
13560 ATAAATTATT
13570 TATAAAATTTAATTTAT-ATATAA
1 TATAAAATTTAATTTATGA-ATAA
13593 -ATAAAAATTGTAATTTATGAATAA
1 TAT-AAAATT-TAATTTATGAATAA
* *
13617 TATAAACTTATAATTTAAGAAT
1 TATAAAATT-TAATTTATGAAT
13639 CGATGCTAAA
Statistics
Matches: 39, Mismatches: 3, Indels: 7
0.80 0.06 0.14
Matches are distributed among these distances:
22 2 0.05
23 6 0.15
24 28 0.72
25 3 0.08
ACGTcount: A:0.52, C:0.01, G:0.04, T:0.42
Consensus pattern (23 bp):
TATAAAATTTAATTTATGAATAA
Found at i:15331 original size:25 final size:25
Alignment explanation
Indices: 15294--15405 Score: 93
Period size: 25 Copynumber: 4.5 Consensus size: 25
15284 GGCTCACCAC
*
15294 AGCTCGTATGAGCTTACCGATTTAT
1 AGCTCGTAGGAGCTTACCGATTTAT
**
15319 AGCTCGTAGGAGCTTACCGATTTGC
1 AGCTCGTAGGAGCTTACCGATTTAT
* * * *
15344 AGTTCATAGGAACTTTCCGATATT-T
1 AGCTCGTAGGAGCTTACCGAT-TTAT
* * *
15369 AGCTCGGAAGAGCTTACTG-TTTAT
1 AGCTCGTAGGAGCTTACCGATTTAT
* *
15393 CGCTCGTATGAGC
1 AGCTCGTAGGAGC
15406 CTACATGTAC
Statistics
Matches: 67, Mismatches: 18, Indels: 5
0.74 0.20 0.06
Matches are distributed among these distances:
23 2 0.03
24 12 0.18
25 51 0.76
26 2 0.03
ACGTcount: A:0.23, C:0.21, G:0.23, T:0.33
Consensus pattern (25 bp):
AGCTCGTAGGAGCTTACCGATTTAT
Found at i:26115 original size:64 final size:64
Alignment explanation
Indices: 26009--26128 Score: 177
Period size: 64 Copynumber: 1.9 Consensus size: 64
25999 CTAGCATCTC
* * **
26009 GATCGGTATTGATCATGCATGTGTTGCGGACATACCGCAGCTCTTTGTGAGCGTCCTATTATAT
1 GATCGGTATTGATCATGCATGTATTGCGGACATACCACAGCTCTTAATGAGCGTCCTATTATAT
* * *
26073 GATCGGTATTGATCCTGCATGTATTGTGGACATACCATAGCTCTTAATGAGCGTCC
1 GATCGGTATTGATCATGCATGTATTGCGGACATACCACAGCTCTTAATGAGCGTCC
26129 CAATATTTGG
Statistics
Matches: 49, Mismatches: 7, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
64 49 1.00
ACGTcount: A:0.22, C:0.21, G:0.24, T:0.33
Consensus pattern (64 bp):
GATCGGTATTGATCATGCATGTATTGCGGACATACCACAGCTCTTAATGAGCGTCCTATTATAT
Found at i:28214 original size:20 final size:20
Alignment explanation
Indices: 28179--28217 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
28169 TCTACACTTT
*
28179 TGAAAATTTTGAAAGTTTTC
1 TGAAAATTTTCAAAGTTTTC
*
28199 TGAAAATTTTCTAAGTTTT
1 TGAAAATTTTCAAAGTTTT
28218 AGATTTAGTC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.33, C:0.05, G:0.13, T:0.49
Consensus pattern (20 bp):
TGAAAATTTTCAAAGTTTTC
Found at i:28480 original size:25 final size:25
Alignment explanation
Indices: 28452--28546 Score: 129
Period size: 25 Copynumber: 3.8 Consensus size: 25
28442 GGACTCATCA
*
28452 CAGCTCGTATGAGCTTACCGATTTG
1 CAGCTCGTAGGAGCTTACCGATTTG
* *
28477 CAGCTCGTAAGAGCTTACCAATTTG
1 CAGCTCGTAGGAGCTTACCGATTTG
*
28502 CAGCTCGTAGGAGCTTACTGATATT-
1 CAGCTCGTAGGAGCTTACCGAT-TTG
*
28527 CAGCTCGGAGGAGCTTACCG
1 CAGCTCGTAGGAGCTTACCG
28547 TTTATCGCTC
Statistics
Matches: 62, Mismatches: 7, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
25 60 0.97
26 2 0.03
ACGTcount: A:0.23, C:0.24, G:0.25, T:0.27
Consensus pattern (25 bp):
CAGCTCGTAGGAGCTTACCGATTTG
Found at i:31220 original size:46 final size:46
Alignment explanation
Indices: 31133--31289 Score: 172
Period size: 46 Copynumber: 3.4 Consensus size: 46
31123 TAATAGTGCA
* * ** * *
31133 TGGTCACCCGTTAGGGTTGAACCTACCCAAATTGAAA-AATAATGTT
1 TGGTCACCCGTTAAGGTTGGACCTATACAAA-TCAAACAATAATGTC
* * **
31179 TGGTCACCCGTTAGGGTTGGACTTATATGAATCAAACAATAATGTC
1 TGGTCACCCGTTAAGGTTGGACCTATACAAATCAAACAATAATGTC
* * *
31225 TGGTCACCCGTTAAGGTTGGACCTATACAAATCAGATAATAGTGTC
1 TGGTCACCCGTTAAGGTTGGACCTATACAAATCAAACAATAATGTC
*
31271 TGGTCACCCATTAAGGTTG
1 TGGTCACCCGTTAAGGTTG
31290 AAATAACATA
Statistics
Matches: 94, Mismatches: 16, Indels: 2
0.84 0.14 0.02
Matches are distributed among these distances:
45 4 0.04
46 90 0.96
ACGTcount: A:0.30, C:0.19, G:0.22, T:0.29
Consensus pattern (46 bp):
TGGTCACCCGTTAAGGTTGGACCTATACAAATCAAACAATAATGTC
Found at i:34494 original size:25 final size:25
Alignment explanation
Indices: 34437--34483 Score: 69
Period size: 25 Copynumber: 1.9 Consensus size: 25
34427 TGGCTCTCAC
* *
34437 GAGCTTCCCATTATATGGTTCTTGT
1 GAGCTTCCCATTATATAGCTCTTGT
34462 GAGCTTCCCATTA-ATAGCTCTT
1 GAGCTTCCCATTATATAGCTCTT
34484 CGGAGCATTC
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
24 7 0.35
25 13 0.65
ACGTcount: A:0.19, C:0.23, G:0.17, T:0.40
Consensus pattern (25 bp):
GAGCTTCCCATTATATAGCTCTTGT
Found at i:36270 original size:43 final size:43
Alignment explanation
Indices: 36161--36288 Score: 141
Period size: 43 Copynumber: 3.0 Consensus size: 43
36151 TAAAAGCTGC
* * * * *
36161 ACAGAAGCACATAAGTGCTAAACGGAAACCCATAAGGATT-GA
1 ACAGAAGCTCAAAAGAGCTAAACGGAAACCCATAAGGGTTAAA
* * *
36203 ACAGAAGCTCATAGGAGCTAAACGGAAACCCAAAAGGGTTAAA
1 ACAGAAGCTCAAAAGAGCTAAACGGAAACCCATAAGGGTTAAA
** * *
36246 ACTTAAGCTCAAAAGAGCTGAACGGAAACCCATTAGGGTTAAA
1 ACAGAAGCTCAAAAGAGCTAAACGGAAACCCATAAGGGTTAAA
36289 CTAAAACTCA
Statistics
Matches: 72, Mismatches: 13, Indels: 1
0.84 0.15 0.01
Matches are distributed among these distances:
42 35 0.49
43 37 0.51
ACGTcount: A:0.45, C:0.19, G:0.22, T:0.15
Consensus pattern (43 bp):
ACAGAAGCTCAAAAGAGCTAAACGGAAACCCATAAGGGTTAAA
Found at i:37381 original size:44 final size:43
Alignment explanation
Indices: 37313--37561 Score: 308
Period size: 44 Copynumber: 5.7 Consensus size: 43
37303 AGCAGTAACA
* *
37313 GTAACAGTATTCAACACACAAAGTGTCGAATCTGTAATAGTACG
1 GTAACAGTATTCGACACACAAAGTGCCGAATC-GTAATAGTACG
* *
37357 GTAATAGTATTCGACACACAAAGTGCCAAATCGATAATAGTACG
1 GTAACAGTATTCGACACACAAAGTGCCGAATCG-TAATAGTACG
*
37401 GTAACAGTATTTGACACACAAAGTGCCGAATCGGTAATAGTAACG
1 GTAACAGTATTCGACACACAAAGTGCCGAATC-GTAATAGT-ACG
* *
37446 GTAACAGTATTCGACACACAAAGTGCCGAATC--AGTA--ACA
1 GTAACAGTATTCGACACACAAAGTGCCGAATCGTAATAGTACG
* * *
37485 GTAACAGTATTCGACACACAAAGTGCCGAATATGTAACAGTAACA
1 GTAACAGTATTCGACACACAAAGTGCCGAAT-CGTAATAGT-ACG
* *
37530 GTAATAGTATTCGACACATAAAGTGCCGAATC
1 GTAACAGTATTCGACACACAAAGTGCCGAATC
37562 AGCAACAGTA
Statistics
Matches: 180, Mismatches: 16, Indels: 18
0.84 0.07 0.08
Matches are distributed among these distances:
39 33 0.18
42 5 0.03
43 1 0.01
44 74 0.41
45 67 0.37
ACGTcount: A:0.40, C:0.19, G:0.19, T:0.22
Consensus pattern (43 bp):
GTAACAGTATTCGACACACAAAGTGCCGAATCGTAATAGTACG
Found at i:37444 original size:39 final size:39
Alignment explanation
Indices: 37305--37584 Score: 236
Period size: 44 Copynumber: 6.6 Consensus size: 39
37295 GTAACGGTAG
* *
37305 CAGTAACAGTAACAGTATTCAACACACAAAGTGTCGAAT
1 CAGTAACAGTAACAGTATTCGACACACAAAGTGCCGAAT
* * * *
37344 CTGTAATAGTACGGTAATAGTATTCGACACACAAAGTGCCAAAT
1 C---AGTA--ACAGTAACAGTATTCGACACACAAAGTGCCGAAT
* * *
37388 CGATAATAGTACGGTAACAGTATTTGACACACAAAGTGCCGAAT
1 C---AGTA--ACAGTAACAGTATTCGACACACAAAGTGCCGAAT
*
37432 CGGTAATAGTAACGGTAACAGTATTCGACACACAAAGTGCCGAAT
1 C------AGTAACAGTAACAGTATTCGACACACAAAGTGCCGAAT
37477 CAGTAACAGTAACAGTATTCGACACACAAAGTGCCGAATATGT
1 CAGTAACAGTAACAGTATTCGACACACAAAGTGCCG-A-A--T
* *
37520 AACAGTAACAGTAATAGTATTCGACACATAAAGTGCCGAAT
1 --CAGTAACAGTAACAGTATTCGACACACAAAGTGCCGAAT
* *
37561 CAGCAACAGTAACAGTAGTCGACA
1 CAGTAACAGTAACAGTATTCGACA
37585 TATAAATGCC
Statistics
Matches: 207, Mismatches: 20, Indels: 28
0.81 0.08 0.11
Matches are distributed among these distances:
39 56 0.27
40 1 0.00
41 2 0.01
42 3 0.01
43 2 0.01
44 70 0.34
45 68 0.33
47 5 0.02
ACGTcount: A:0.40, C:0.20, G:0.19, T:0.21
Consensus pattern (39 bp):
CAGTAACAGTAACAGTATTCGACACACAAAGTGCCGAAT
Found at i:37462 original size:45 final size:45
Alignment explanation
Indices: 37306--37577 Score: 326
Period size: 45 Copynumber: 6.2 Consensus size: 45
37296 TAACGGTAGC
* * *
37306 AGTAACAGTAACAGTATTCAACACACAAAGTGTCGAATCTGTAAT
1 AGTAACAGTAACAGTATTCGACACACAAAGTGCCGAATCGGTAAT
* * * *
37351 AGT-ACGGTAATAGTATTCGACACACAAAGTGCCAAATCGATAAT
1 AGTAACAGTAACAGTATTCGACACACAAAGTGCCGAATCGGTAAT
* *
37395 AGT-ACGGTAACAGTATTTGACACACAAAGTGCCGAATCGGTAAT
1 AGTAACAGTAACAGTATTCGACACACAAAGTGCCGAATCGGTAAT
*
37439 AGTAACGGTAACAGTATTCGACACACAAAGTGCCGAATC------
1 AGTAACAGTAACAGTATTCGACACACAAAGTGCCGAATCGGTAAT
** *
37478 AGTAACAGTAACAGTATTCGACACACAAAGTGCCGAATATGTAAC
1 AGTAACAGTAACAGTATTCGACACACAAAGTGCCGAATCGGTAAT
* * * * *
37523 AGTAACAGTAATAGTATTCGACACATAAAGTGCCGAATCAGCAAC
1 AGTAACAGTAACAGTATTCGACACACAAAGTGCCGAATCGGTAAT
37568 AGTAACAGTA
1 AGTAACAGTA
37578 GTCGACATAT
Statistics
Matches: 201, Mismatches: 19, Indels: 14
0.86 0.08 0.06
Matches are distributed among these distances:
39 37 0.18
44 77 0.38
45 87 0.43
ACGTcount: A:0.41, C:0.19, G:0.19, T:0.21
Consensus pattern (45 bp):
AGTAACAGTAACAGTATTCGACACACAAAGTGCCGAATCGGTAAT
Found at i:37514 original size:84 final size:84
Alignment explanation
Indices: 37305--37584 Score: 382
Period size: 84 Copynumber: 3.3 Consensus size: 84
37295 GTAACGGTAG
* *
37305 CAGTAACAGTAACAGTATTCAACACACAAAGTGTCGAATCTGTAATAGT-ACGGTAATAGTATTC
1 CAGTAACAGTAACAGTATTCGACACACAAAGTGCCGAATCTGTAATAGTAACGGTAATAGTATTC
*
37369 GACACACAAAGTGCCAAAT
66 GACACACAAAGTGCCGAAT
* * * * *
37388 CGATAATAGTACGGTAACAGTATTTGACACACAAAGTGCCGAATCGGTAATAGTAACGGTAACAG
1 C---AGTA--ACAGTAACAGTATTCGACACACAAAGTGCCGAATCTGTAATAGTAACGGTAATAG
37453 TATTCGACACACAAAGTGCCGAAT
61 TATTCGACACACAAAGTGCCGAAT
* * *
37477 CAGTAACAGTAACAGTATTCGACACACAAAGTGCCGAATATGTAACAGTAACAGTAATAGTATTC
1 CAGTAACAGTAACAGTATTCGACACACAAAGTGCCGAATCTGTAATAGTAACGGTAATAGTATTC
*
37542 GACACATAAAGTGCCGAAT
66 GACACACAAAGTGCCGAAT
* *
37561 CAGCAACAGTAACAGTAGTCGACA
1 CAGTAACAGTAACAGTATTCGACA
37585 TATAAATGCC
Statistics
Matches: 172, Mismatches: 19, Indels: 11
0.85 0.09 0.05
Matches are distributed among these distances:
83 1 0.01
84 93 0.54
86 6 0.03
88 39 0.23
89 33 0.19
ACGTcount: A:0.40, C:0.20, G:0.19, T:0.21
Consensus pattern (84 bp):
CAGTAACAGTAACAGTATTCGACACACAAAGTGCCGAATCTGTAATAGTAACGGTAATAGTATTC
GACACACAAAGTGCCGAAT
Found at i:37522 original size:33 final size:36
Alignment explanation
Indices: 37401--37526 Score: 114
Period size: 39 Copynumber: 3.2 Consensus size: 36
37391 TAATAGTACG
*
37401 GTAACAGTATTTGACACACAAAGTGCCGAATCGGTAATAGTAA
1 GTAACAGTATTCGACACACAAAGTGCCGAATC------AGT-A
37444 CGGTAACAGTATTCGACACACAAAGTGCCGAATCAGTAACA
1 --GTAACAGTATTCGACACACAAAGTGCCGAATCAGT---A
37485 GTAACAGTATTCGACACACAAAGTGCCGAAT-A-T-
1 GTAACAGTATTCGACACACAAAGTGCCGAATCAGTA
37518 GTAACAGTA
1 GTAACAGTA
37527 ACAGTAATAG
Statistics
Matches: 77, Mismatches: 2, Indels: 16
0.81 0.02 0.17
Matches are distributed among these distances:
33 9 0.12
37 1 0.01
38 1 0.01
39 34 0.44
41 1 0.01
45 31 0.40
ACGTcount: A:0.40, C:0.20, G:0.20, T:0.21
Consensus pattern (36 bp):
GTAACAGTATTCGACACACAAAGTGCCGAATCAGTA
Found at i:37822 original size:40 final size:40
Alignment explanation
Indices: 37777--37863 Score: 106
Period size: 40 Copynumber: 2.2 Consensus size: 40
37767 AATTCATAAC
* *
37777 TTCAGTAAATTCACAGTTCAA-TGCAATA-TACATAACAATA
1 TTCAGTAAATTCACAATTCAACT-CAATACT-CAAAACAATA
* *
37817 TTCAGTAACTTCACAATTCAACTCAGTACTCAAAACAATA
1 TTCAGTAAATTCACAATTCAACTCAATACTCAAAACAATA
37857 TTCAGTA
1 TTCAGTA
37864 TTCCATAATT
Statistics
Matches: 41, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
40 39 0.95
41 2 0.05
ACGTcount: A:0.43, C:0.21, G:0.07, T:0.30
Consensus pattern (40 bp):
TTCAGTAAATTCACAATTCAACTCAATACTCAAAACAATA
Found at i:44476 original size:40 final size:41
Alignment explanation
Indices: 44403--44483 Score: 121
Period size: 40 Copynumber: 2.0 Consensus size: 41
44393 TGTTACTAAA
* *
44403 TACTGCATGATTGCTACTGATACTATGATGGGCTAAGGCCC
1 TACTGCATGATTGATACTGATACTAAGATGGGCTAAGGCCC
44444 TACTGCAT-ATTTGATACTG-TACTAAGATGGGCTAAGGCCC
1 TACTGCATGA-TTGATACTGATACTAAGATGGGCTAAGGCCC
44484 AAACTATTAC
Statistics
Matches: 37, Mismatches: 2, Indels: 3
0.88 0.05 0.07
Matches are distributed among these distances:
40 21 0.57
41 16 0.43
ACGTcount: A:0.26, C:0.21, G:0.23, T:0.30
Consensus pattern (41 bp):
TACTGCATGATTGATACTGATACTAAGATGGGCTAAGGCCC
Found at i:54980 original size:40 final size:41
Alignment explanation
Indices: 54902--54982 Score: 114
Period size: 40 Copynumber: 2.0 Consensus size: 41
54892 TGTTACTAAA
*
54902 TACTGCATGATTGCTACTGATACTATGATGGGCTAAGGCCC
1 TACTGCATGATTGATACTGATACTATGATGGGCTAAGGCCC
54943 TACTGCAT-ATTTGATACTG-TACTGA-GATGGGCTAAGGCCC
1 TACTGCATGA-TTGATACTGATACT-ATGATGGGCTAAGGCCC
54983 AAACTGTTAC
Statistics
Matches: 37, Mismatches: 1, Indels: 5
0.86 0.02 0.12
Matches are distributed among these distances:
40 20 0.54
41 17 0.46
ACGTcount: A:0.25, C:0.21, G:0.25, T:0.30
Consensus pattern (41 bp):
TACTGCATGATTGATACTGATACTATGATGGGCTAAGGCCC
Found at i:55722 original size:15 final size:16
Alignment explanation
Indices: 55698--55744 Score: 62
Period size: 15 Copynumber: 3.0 Consensus size: 16
55688 AAATTCATGA
55698 AAATG-ATGATATATG
1 AAATGAATGATATATG
*
55713 AAAT-ATTGATATAATG
1 AAATGAATGATAT-ATG
55729 AAATGAATGATATATG
1 AAATGAATGATATATG
55745 TTTATGAAGA
Statistics
Matches: 27, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
15 10 0.37
16 10 0.37
17 7 0.26
ACGTcount: A:0.49, C:0.00, G:0.17, T:0.34
Consensus pattern (16 bp):
AAATGAATGATATATG
Found at i:56977 original size:415 final size:415
Alignment explanation
Indices: 56203--57025 Score: 1146
Period size: 415 Copynumber: 2.0 Consensus size: 415
56193 GAAAGTAAAG
* * * * **
56203 AAATGCAAATGAAAATAAAAAAATTTGGAAGAGTTAAAGTTGTTTAAAATCCTACTATGCTAGGA
1 AAATGCAAATGAAAATAAAAAAACTTGAAAGAGTTAAAGTTATATAAAATCCTACTAAACTAGGA
* *
56268 ATAATATGTATAAGTGATGCTGTGGATTTATTCACCTTGTGAGTTATCGAATATAACTTCACGAG
66 ATAACATGTATAAGTGATGCTGTGGATTTATTCACATTGTGAGTTATCGAATATAACTTCACGAG
* *
56333 TATTGCAGTATCAATAGTAGATTATTCTTGATATGTATAAATTTCATATATGAAATTAATTGATA
131 TATTGCAGTATCAATAGTAGATTATTCTTGATATGTATAAATTTCATATATGAAATGAATTAATA
* * ** * ** *
56398 TGATTAAAGTTTATACGAGCTTACTAAGCATTTATTGCTTACGTAGTTGTTTTCCTTTACTTTCC
196 TGATTAAAGATTACACGAGCTTACTAAGCATCCATTGCTTACGTAGTTGTTTTCATTTACCCTAC
* *
56463 AGATTATCGGAAGCTCGACCGGGTTGGAAGCTTGTCAGAGATATATCACACTATCCATCATTTCT
261 AAATTATCGGAAGCTCGACCGGGTTGGAAGCTTGTCAGAGATATATCACACTATCCATCAGTTCT
* * * *
56528 ATTGGTACTTTCGTATGTTTTAATTTTGGTTATAATGGCATATATAGGTAATCTGGTTAATGTTG
326 ATCGGTACTTTCGAATGTTTTAATTTTCGTTATAATGGCATATATAGGTAATCTGGTTAATGATG
*
56593 GCCTATATGTATTTTGTTGAGATTA
391 GCCTATATGTAATTTGTTGAGATTA
* * *
56618 AAATGCAAATGAAAATAAAGAAACTTGAAAGAGTTAAAGTTATATAAAATCCTACTAAACTTGGG
1 AAATGCAAATGAAAATAAAAAAACTTGAAAGAGTTAAAGTTATATAAAATCCTACTAAACTAGGA
* *
56683 ATAACATGTATAAGTGATGTTGTGGATTTATTCACATTGTGAGTTGAT-GAATATAACTTCATGA
66 ATAACATGTATAAGTGATGCTGTGGATTTATTCACATTGTGAGTT-ATCGAATATAACTTCACGA
** * * * * *
56747 GTATTGTGGTATCAATATTGGATTATTCTTGATATGTATAGATTTCATATTTGCAATGAATTAAT
130 GTATTGCAGTATCAATAGTAGATTATTCTTGATATGTATAAATTTCATATATGAAATGAATTAAT
* *
56812 ATGATTAAAGATTACACGAGCTTACTAAGCATCCATTGCTTACGTATTTGTTTTTATTTACCCTA
195 ATGATTAAAGATTACACGAGCTTACTAAGCATCCATTGCTTACGTAGTTGTTTTCATTTACCCTA
** ** **
56877 CAAATTATCGGAAGCTCGATTGGGTTGGAAGCTTGTC-GAAGATATATCACACTATCTTTTGGTT
260 CAAATTATCGGAAGCTCGACCGGGTTGGAAGCTTGTCAG-AGATATATCACACTATCCATCAGTT
* * * * * * *
56941 CTATCGGTACTTTTGAATGTTTTGATTTTCGTTATAATGGCATGTGTAGGTATTTTGTTTAATGA
324 CTATCGGTACTTTCGAATGTTTTAATTTTCGTTATAATGGCATATATAGGTAATCTGGTTAATGA
57006 TGGCCTATATGTAATTTGTT
389 TGGCCTATATGTAATTTGTT
57026 AAGTTTAGCC
Statistics
Matches: 354, Mismatches: 52, Indels: 4
0.86 0.13 0.01
Matches are distributed among these distances:
414 1 0.00
415 351 0.99
416 2 0.01
ACGTcount: A:0.31, C:0.11, G:0.18, T:0.39
Consensus pattern (415 bp):
AAATGCAAATGAAAATAAAAAAACTTGAAAGAGTTAAAGTTATATAAAATCCTACTAAACTAGGA
ATAACATGTATAAGTGATGCTGTGGATTTATTCACATTGTGAGTTATCGAATATAACTTCACGAG
TATTGCAGTATCAATAGTAGATTATTCTTGATATGTATAAATTTCATATATGAAATGAATTAATA
TGATTAAAGATTACACGAGCTTACTAAGCATCCATTGCTTACGTAGTTGTTTTCATTTACCCTAC
AAATTATCGGAAGCTCGACCGGGTTGGAAGCTTGTCAGAGATATATCACACTATCCATCAGTTCT
ATCGGTACTTTCGAATGTTTTAATTTTCGTTATAATGGCATATATAGGTAATCTGGTTAATGATG
GCCTATATGTAATTTGTTGAGATTA
Found at i:62525 original size:20 final size:20
Alignment explanation
Indices: 62500--62540 Score: 66
Period size: 20 Copynumber: 2.1 Consensus size: 20
62490 ATTTTCTTGC
*
62500 TATTTTTTT-ACTATTTTGT
1 TATTTTTTTCACTAATTTGT
62519 TATTTTTTTCACTAATTTGT
1 TATTTTTTTCACTAATTTGT
62539 TA
1 TA
62541 CAATTTCACT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
19 9 0.45
20 11 0.55
ACGTcount: A:0.20, C:0.07, G:0.05, T:0.68
Consensus pattern (20 bp):
TATTTTTTTCACTAATTTGT
Found at i:62527 original size:11 final size:11
Alignment explanation
Indices: 62479--62546 Score: 50
Period size: 11 Copynumber: 6.4 Consensus size: 11
62469 TAAAAAAGTA
*
62479 ATTTTTTTATT
1 ATTTTTTTACT
* *
62490 ATTTTCTTGCT
1 ATTTTTTTACT
62501 ATTTTTTTACT
1 ATTTTTTTACT
*
62512 ATTTTGTTA-T
1 ATTTTTTTACT
*
62522 -TTTTTTCACT
1 ATTTTTTTACT
* * *
62532 AATTTGTTACA
1 ATTTTTTTACT
62543 ATTT
1 ATTT
62547 CACTATTATG
Statistics
Matches: 42, Mismatches: 13, Indels: 4
0.71 0.22 0.07
Matches are distributed among these distances:
9 6 0.14
10 2 0.05
11 34 0.81
ACGTcount: A:0.19, C:0.09, G:0.04, T:0.68
Consensus pattern (11 bp):
ATTTTTTTACT
Found at i:62728 original size:18 final size:18
Alignment explanation
Indices: 62707--62748 Score: 59
Period size: 18 Copynumber: 2.3 Consensus size: 18
62697 GAAATATTTA
*
62707 TTTTAATAT-TTTTAGCAT
1 TTTTAATATATTATA-CAT
62725 TTTTAATATATTATACAT
1 TTTTAATATATTATACAT
62743 TTTTAA
1 TTTTAA
62749 AAATTTTATA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
18 18 0.82
19 4 0.18
ACGTcount: A:0.33, C:0.05, G:0.02, T:0.60
Consensus pattern (18 bp):
TTTTAATATATTATACAT
Found at i:71121 original size:25 final size:25
Alignment explanation
Indices: 71093--71363 Score: 136
Period size: 25 Copynumber: 10.8 Consensus size: 25
71083 AGCATGTAAT
* ** *
71093 CGGGAAGCTCTTTTGAGCCATGTAA
1 CGGGAAGCTCATGCGAGCCATATAA
* **
71118 CGGGAAGCTCATGTGAGCTGTATAA
1 CGGGAAGCTCATGCGAGCCATATAA
* *
71143 TGGGAAGCTCTTGCGAGCCA-ATAA
1 CGGGAAGCTCATGCGAGCCATATAA
*
71167 TCGGGAAGCTCATACGAGCCATA-AA
1 -CGGGAAGCTCATGCGAGCCATATAA
* * * *
71192 CGGGAAGCTTATGTGAGCCAAATAT
1 CGGGAAGCTCATGCGAGCCATATAA
* * * * *
71217 CGGTAATCTTATGAGAGCCATATAT
1 CGGGAAGCTCATGCGAGCCATATAA
* * *
71242 CGAGAAGCTCGTGAGAGCCATATAA
1 CGGGAAGCTCATGCGAGCCATATAA
** * *
71267 CCAGAAGCTCAAGAGAGAGCCAT-TAA
1 CGGGAAGCTC-A-TGCGAGCCATATAA
* * * *
71293 TCGAGAAGCTCATGAGAGCTAAATAA
1 -CGGGAAGCTCATGCGAGCCATATAA
* * * * *
71319 TGGGAAGCTCGTGAGAGCTA-AGTAT
1 CGGGAAGCTCATGCGAGCCATA-TAA
* *
71344 CGGGAAGCTCGTGAGAGCCA
1 CGGGAAGCTCATGCGAGCCA
71364 AATAGTGGGA
Statistics
Matches: 197, Mismatches: 41, Indels: 16
0.78 0.16 0.06
Matches are distributed among these distances:
24 23 0.12
25 148 0.75
26 8 0.04
27 18 0.09
ACGTcount: A:0.32, C:0.19, G:0.28, T:0.21
Consensus pattern (25 bp):
CGGGAAGCTCATGCGAGCCATATAA
Found at i:71299 original size:27 final size:26
Alignment explanation
Indices: 71229--71310 Score: 89
Period size: 27 Copynumber: 3.1 Consensus size: 26
71219 GTAATCTTAT
*
71229 GAGAGCCA-TATATCGAGAAGCTC-GT
1 GAGAGCCATTA-ATCGAGAAGCTCAGA
*
71254 GAGAGCCATATAA-CCAGAAGCTCAAGA
1 GAGAGCCAT-TAATCGAGAAGCTC-AGA
71281 GAGAGCCATTAATCGAGAAGCTCATGA
1 GAGAGCCATTAATCGAGAAGCTCA-GA
71308 GAG
1 GAG
71311 CTAAATAATG
Statistics
Matches: 48, Mismatches: 3, Indels: 10
0.79 0.05 0.16
Matches are distributed among these distances:
25 17 0.35
26 5 0.10
27 26 0.54
ACGTcount: A:0.38, C:0.20, G:0.27, T:0.16
Consensus pattern (26 bp):
GAGAGCCATTAATCGAGAAGCTCAGA
Found at i:71326 original size:52 final size:52
Alignment explanation
Indices: 71229--71367 Score: 142
Period size: 52 Copynumber: 2.7 Consensus size: 52
71219 GTAATCTTAT
* *
71229 GAGAGCCATATATCGAGAAGCTCGTGAGAGCCATATAACCAGAAGCTCAAGA
1 GAGAGCCATATATCGAGAAGCTCATGAGAGCCAAATAACCAGAAGCTCAAGA
* *** *
71281 GAGAGCCAT-TAATCGAGAAGCTCATGAGAGCTAAATAATGGGAAGCTC--GT
1 GAGAGCCATAT-ATCGAGAAGCTCATGAGAGCCAAATAACCAGAAGCTCAAGA
* * *
71331 GAGAGCTA-AGTATCGGGAAGCTCGTGAGAGCCAAATA
1 GAGAGCCATA-TATCGAGAAGCTCATGAGAGCCAAATA
71368 GTGGGATACT
Statistics
Matches: 73, Mismatches: 11, Indels: 8
0.79 0.12 0.09
Matches are distributed among these distances:
50 31 0.42
51 2 0.03
52 40 0.55
ACGTcount: A:0.37, C:0.18, G:0.28, T:0.17
Consensus pattern (52 bp):
GAGAGCCATATATCGAGAAGCTCATGAGAGCCAAATAACCAGAAGCTCAAGA
Found at i:71373 original size:25 final size:24
Alignment explanation
Indices: 71297--71373 Score: 100
Period size: 25 Copynumber: 3.1 Consensus size: 24
71287 CATTAATCGA
*
71297 GAAGCTCATGAGAGCTAAATAATGG
1 GAAGCTCGTGAGAGCTAAAT-ATGG
*
71322 GAAGCTCGTGAGAGCTAAGTATCGG
1 GAAGCTCGTGAGAGCTAAATAT-GG
*
71347 GAAGCTCGTGAGAGCCAAATAGTGG
1 GAAGCTCGTGAGAGCTAAATA-TGG
71372 GA
1 GA
71374 TACTCATAAG
Statistics
Matches: 46, Mismatches: 4, Indels: 4
0.85 0.07 0.07
Matches are distributed among these distances:
24 2 0.04
25 43 0.93
26 1 0.02
ACGTcount: A:0.34, C:0.14, G:0.34, T:0.18
Consensus pattern (24 bp):
GAAGCTCGTGAGAGCTAAATATGG
Found at i:75474 original size:98 final size:99
Alignment explanation
Indices: 75352--75553 Score: 397
Period size: 98 Copynumber: 2.1 Consensus size: 99
75342 TATATTATAA
75352 ATATTAATTAAATTATATTTACATGTATCTTTATTATATGTCAAAATAAAAATTTTAGTATGAGC
1 ATATTAATTAAATTATATTTACATGTATCTTTATTATATGTCAAAATAAAAATTTTAGTATGAGC
75417 AAAACATACATCACGACTCAAATGTCATGTTATT
66 AAAACATACATCACGACTCAAATGTCATGTTATT
75451 ATATTAATT-AATTATATTTACATGTATCTTTATTATATGTCAAAATAAAAATTTTAGTATGAGC
1 ATATTAATTAAATTATATTTACATGTATCTTTATTATATGTCAAAATAAAAATTTTAGTATGAGC
75515 AAAACATACATCACGACTCAAATGTCATGTTATT
66 AAAACATACATCACGACTCAAATGTCATGTTATT
75549 ATATT
1 ATATT
75554 GGCATGTATC
Statistics
Matches: 103, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
98 94 0.91
99 9 0.09
ACGTcount: A:0.41, C:0.11, G:0.08, T:0.40
Consensus pattern (99 bp):
ATATTAATTAAATTATATTTACATGTATCTTTATTATATGTCAAAATAAAAATTTTAGTATGAGC
AAAACATACATCACGACTCAAATGTCATGTTATT
Found at i:98485 original size:26 final size:25
Alignment explanation
Indices: 98450--98504 Score: 83
Period size: 26 Copynumber: 2.2 Consensus size: 25
98440 TTACAGTATA
98450 AAAATAAATAAAATAAATAATATTTT
1 AAAATAAATAAAATAAATAAT-TTTT
* *
98476 AAAATGAATAAAATAATTAATTTTT
1 AAAATAAATAAAATAAATAATTTTT
98501 AAAA
1 AAAA
98505 CATATTCCTC
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
25 8 0.30
26 19 0.70
ACGTcount: A:0.64, C:0.00, G:0.02, T:0.35
Consensus pattern (25 bp):
AAAATAAATAAAATAAATAATTTTT
Found at i:107919 original size:98 final size:98
Alignment explanation
Indices: 107750--107945 Score: 374
Period size: 98 Copynumber: 2.0 Consensus size: 98
107740 ACAAGCTTAT
* *
107750 GTATTTATACACAAGTACTGCCAATATACACTAGGAAACTAGCAGGAAACTCCTCTTCCTAAAGT
1 GTATTTATACACAAGTACAGCCAATATACACTAGGAAACTAGCAGGAAACTCCTCCTCCTAAAGT
107815 TTGTCCTAAAATGAAGCTTAAAATCTGGCCTAA
66 TTGTCCTAAAATGAAGCTTAAAATCTGGCCTAA
107848 GTATTTATACACAAGTACAGCCAATATACACTAGGAAACTAGCAGGAAACTCCTCCTCCTAAAGT
1 GTATTTATACACAAGTACAGCCAATATACACTAGGAAACTAGCAGGAAACTCCTCCTCCTAAAGT
107913 TTGTCCTAAAATGAAGCTTAAAATCTGGCCTAA
66 TTGTCCTAAAATGAAGCTTAAAATCTGGCCTAA
107946 AATCAAGGTC
Statistics
Matches: 96, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
98 96 1.00
ACGTcount: A:0.37, C:0.22, G:0.14, T:0.27
Consensus pattern (98 bp):
GTATTTATACACAAGTACAGCCAATATACACTAGGAAACTAGCAGGAAACTCCTCCTCCTAAAGT
TTGTCCTAAAATGAAGCTTAAAATCTGGCCTAA
Found at i:113252 original size:30 final size:30
Alignment explanation
Indices: 113216--113272 Score: 105
Period size: 30 Copynumber: 1.9 Consensus size: 30
113206 CTTCCTGATA
*
113216 AAACCAACATATAGAACATCATTTTACATG
1 AAACCAACAAATAGAACATCATTTTACATG
113246 AAACCAACAAATAGAACATCATTTTAC
1 AAACCAACAAATAGAACATCATTTTAC
113273 TTTTATGTTG
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
30 26 1.00
ACGTcount: A:0.49, C:0.21, G:0.05, T:0.25
Consensus pattern (30 bp):
AAACCAACAAATAGAACATCATTTTACATG
Found at i:114608 original size:31 final size:31
Alignment explanation
Indices: 114571--114634 Score: 101
Period size: 31 Copynumber: 2.1 Consensus size: 31
114561 TTGAAAATGG
*
114571 AAAACACTAAAGAAAATGTGTTCGATTGAAA
1 AAAACACTAAAGAAAACGTGTTCGATTGAAA
* *
114602 AAAACACTACAGAAAACGTGTTTGATTGAAA
1 AAAACACTAAAGAAAACGTGTTCGATTGAAA
114633 AA
1 AA
114635 TTAAAAATTG
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
31 30 1.00
ACGTcount: A:0.52, C:0.11, G:0.16, T:0.22
Consensus pattern (31 bp):
AAAACACTAAAGAAAACGTGTTCGATTGAAA
Found at i:120692 original size:18 final size:17
Alignment explanation
Indices: 120671--120705 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
120661 TTATTATTAA
*
120671 ATATATTTTAATTAAAAT
1 ATATAATTTAA-TAAAAT
120689 ATATAATTTAATAAAAT
1 ATATAATTTAATAAAAT
120706 TCTTAATAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 6 0.38
18 10 0.62
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (17 bp):
ATATAATTTAATAAAAT
Found at i:122636 original size:129 final size:129
Alignment explanation
Indices: 122501--122759 Score: 484
Period size: 129 Copynumber: 2.0 Consensus size: 129
122491 GGGTTGAGAA
*
122501 AAAAAAAGACCAGGGCAAAAGAACCAGAACAAGTATGTTGCTGAAAAAATTTGGCTTCTAATGTA
1 AAAAAAAGA-CAGGGCAAAAGAACCAGAACAAGTATGTTACTGAAAAAATTTGGCTTCTAATGTA
122566 AGATGCAATTTGAGAAATTCATTGC-TCTGAATTTGAGAAATTTATACCAGTGAGAACGTAAGAT
65 AGATGCAATTTGAGAAATTCATTGCTTC-GAATTTGAGAAATTTATACCAGTGAGAACGTAAGAT
122630 G
129 G
122631 AAAAAAAGACAGGGCAAAAGAACCAGAACAAGTATGTTACTGAAAAAATTTGGCTTCTAATGTAA
1 AAAAAAAGACAGGGCAAAAGAACCAGAACAAGTATGTTACTGAAAAAATTTGGCTTCTAATGTAA
122696 GATGCAATTTGAGAAATTCATTGCTTCGAATTTGAGAAATTTATACCAGTGAGAACGTAAGATG
66 GATGCAATTTGAGAAATTCATTGCTTCGAATTTGAGAAATTTATACCAGTGAGAACGTAAGATG
122760 CATTTTTGCG
Statistics
Matches: 127, Mismatches: 1, Indels: 3
0.97 0.01 0.02
Matches are distributed among these distances:
129 116 0.91
130 11 0.09
ACGTcount: A:0.42, C:0.12, G:0.20, T:0.25
Consensus pattern (129 bp):
AAAAAAAGACAGGGCAAAAGAACCAGAACAAGTATGTTACTGAAAAAATTTGGCTTCTAATGTAA
GATGCAATTTGAGAAATTCATTGCTTCGAATTTGAGAAATTTATACCAGTGAGAACGTAAGATG
Found at i:125831 original size:16 final size:15
Alignment explanation
Indices: 125811--125844 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
125801 AAAATTTAAG
125811 ATTTTTAAAACATTT
1 ATTTTTAAAACATTT
* *
125826 ATTTTTACAATATTT
1 ATTTTTAAAACATTT
125841 ATTT
1 ATTT
125845 AAAATTTACA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.35, C:0.06, G:0.00, T:0.59
Consensus pattern (15 bp):
ATTTTTAAAACATTT
Found at i:130671 original size:16 final size:17
Alignment explanation
Indices: 130646--130679 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 17
130636 ATTTTAATTT
*
130646 TTTTATAATTAT-AAAA
1 TTTTAAAATTATGAAAA
130662 TTTTAAAATTATGAAAA
1 TTTTAAAATTATGAAAA
130679 T
1 T
130680 ATATTTTAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 11 0.69
17 5 0.31
ACGTcount: A:0.50, C:0.00, G:0.03, T:0.47
Consensus pattern (17 bp):
TTTTAAAATTATGAAAA
Found at i:132059 original size:17 final size:18
Alignment explanation
Indices: 132037--132075 Score: 62
Period size: 17 Copynumber: 2.2 Consensus size: 18
132027 AAATTTTATC
*
132037 AAATTTATTTTA-AAACT
1 AAATTTATTTGATAAACT
132054 AAATTTATTTGATAAACT
1 AAATTTATTTGATAAACT
132072 AAAT
1 AAAT
132076 GTAAAATTAA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
17 11 0.55
18 9 0.45
ACGTcount: A:0.49, C:0.05, G:0.03, T:0.44
Consensus pattern (18 bp):
AAATTTATTTGATAAACT
Found at i:137517 original size:14 final size:16
Alignment explanation
Indices: 137498--137529 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
137488 ATTTATAGAA
137498 ATTTT-AAA-TTTTAT
1 ATTTTAAAATTTTTAT
137512 ATTTTAAAATTTTTAT
1 ATTTTAAAATTTTTAT
137528 AT
1 AT
137530 GATTTGAGGA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
14 5 0.31
15 3 0.19
16 8 0.50
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (16 bp):
ATTTTAAAATTTTTAT
Found at i:139940 original size:138 final size:139
Alignment explanation
Indices: 139691--139968 Score: 524
Period size: 138 Copynumber: 2.0 Consensus size: 139
139681 CTCTTTTCCT
139691 CCTTTAACTTGTTTTAGGATTGTAATAGCCCGATTTTAGGCCTAGTCGGAACAGTGGTTTCGGGA
1 CCTTTAACTTGTTTTAGGATTGTAATAGCCCGATTTTAGGCCTAGTCGGAACAGTGGTTTCGGGA
139756 CCACAAATCCGACGAGAGAAAAAAAATGTAATCGCCTGAATTTTCAGAGGTGTCGGAACGGTGAT
66 CCACAAATCCGACGAGAGAAAAAAAATGTAATCGCCTGAATTTTCAGAGGTGTCGGAACGGTGAT
139821 TCGAGATCA
131 TCGAGATCA
139830 CCTTTAACTTG-TTTAGGATTGTAATAGCCCGATTTTAGGCCTAGTCGGAACAGTGGTTTCGGGA
1 CCTTTAACTTGTTTTAGGATTGTAATAGCCCGATTTTAGGCCTAGTCGGAACAGTGGTTTCGGGA
*
139894 CCACAAATCCGACGAGAGAAAAAAAATTTAAAT-GCCTGAATTTTCAGAGGTGTCGGAACGGTGA
66 CCACAAATCCGACGAGAGAAAAAAAATGT-AATCGCCTGAATTTTCAGAGGTGTCGGAACGGTGA
139958 TTCGAGATCA
130 TTCGAGATCA
139968 C
1 C
139969 TAAATTCGAC
Statistics
Matches: 137, Mismatches: 1, Indels: 3
0.97 0.01 0.02
Matches are distributed among these distances:
138 123 0.90
139 14 0.10
ACGTcount: A:0.30, C:0.18, G:0.25, T:0.27
Consensus pattern (139 bp):
CCTTTAACTTGTTTTAGGATTGTAATAGCCCGATTTTAGGCCTAGTCGGAACAGTGGTTTCGGGA
CCACAAATCCGACGAGAGAAAAAAAATGTAATCGCCTGAATTTTCAGAGGTGTCGGAACGGTGAT
TCGAGATCA
Found at i:147039 original size:408 final size:408
Alignment explanation
Indices: 146224--146988 Score: 1530
Period size: 408 Copynumber: 1.9 Consensus size: 408
146214 CTTTATTAGT
146224 TTGCCATCTAGTATTATGTTTTATTGTATTAATAGATTCTGAATAATATTCTTCAAACCATTCAA
1 TTGCCATCTAGTATTATGTTTTATTGTATTAATAGATTCTGAATAATATTCTTCAAACCATTCAA
146289 ACAATTTTATATGGATTTTATGGGTATTCATAAATTCATAATATTCTTGAAGAATGCTTTCTTTT
66 ACAATTTTATATGGATTTTATGGGTATTCATAAATTCATAATATTCTTGAAGAATGCTTTCTTTT
146354 TTATCATTTTAATTTTTAAAGTAATCTTCTCTTTTTTGCTTTTTTGTTAGAATAGAAGTGCTTTC
131 TTATCATTTTAATTTTTAAAGTAATCTTCTCTTTTTTGCTTTTTTGTTAGAATAGAAGTGCTTTC
146419 TATACCATTCTTTGTTTATCTCAAAAGTTTTTTCTAAAACAAATATTTCTGAATTTTCTTATTGT
196 TATACCATTCTTTGTTTATCTCAAAAGTTTTTTCTAAAACAAATATTTCTGAATTTTCTTATTGT
146484 CTTGCATTATTAGCCACTGATGATTATGTTGGTGACATATTAGGTGAATTTTGGGGACTCTCTTC
261 CTTGCATTATTAGCCACTGATGATTATGTTGGTGACATATTAGGTGAATTTTGGGGACTCTCTTC
146549 CTGTCTGGCATAGATAGGTTGAGCTATATTTGAGGAATTATCTATTCCTTGTAAATTAGTTCTAG
326 CTGTCTGGCATAGATAGGTTGAGCTATATTTGAGGAATTATCTATTCCTTGTAAATTAGTTCTAG
146614 ATGTTGTTGGGATAGAAG
391 ATGTTGTTGGGATAGAAG
146632 TTGCCATCTAGTATTATGTTTTATTGTATTAATAGATTCTGAATAATATTCTTCAAACCATTCAA
1 TTGCCATCTAGTATTATGTTTTATTGTATTAATAGATTCTGAATAATATTCTTCAAACCATTCAA
146697 ACAATTTTATATGGATTTTATGGGTATTCATAAATTCATAATATTCTTGAAGAATGCTTTCTTTT
66 ACAATTTTATATGGATTTTATGGGTATTCATAAATTCATAATATTCTTGAAGAATGCTTTCTTTT
146762 TTATCATTTTAATTTTTAAAGTAATCTTCTCTTTTTTGCTTTTTTGTTAGAATAGAAGTGCTTTC
131 TTATCATTTTAATTTTTAAAGTAATCTTCTCTTTTTTGCTTTTTTGTTAGAATAGAAGTGCTTTC
146827 TATACCATTCTTTGTTTATCTCAAAAGTTTTTTCTAAAACAAATATTTCTGAATTTTCTTATTGT
196 TATACCATTCTTTGTTTATCTCAAAAGTTTTTTCTAAAACAAATATTTCTGAATTTTCTTATTGT
146892 CTTGCATTATTAGCCACTGATGATTATGTTGGTGACATATTAGGTGAATTTTGGGGACTCTCTTC
261 CTTGCATTATTAGCCACTGATGATTATGTTGGTGACATATTAGGTGAATTTTGGGGACTCTCTTC
146957 CTGTCTGGCATAGATAGGTTGAGCTATATTTG
326 CTGTCTGGCATAGATAGGTTGAGCTATATTTG
146989 CGNNNNNNNN
Statistics
Matches: 357, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
408 357 1.00
ACGTcount: A:0.27, C:0.12, G:0.14, T:0.46
Consensus pattern (408 bp):
TTGCCATCTAGTATTATGTTTTATTGTATTAATAGATTCTGAATAATATTCTTCAAACCATTCAA
ACAATTTTATATGGATTTTATGGGTATTCATAAATTCATAATATTCTTGAAGAATGCTTTCTTTT
TTATCATTTTAATTTTTAAAGTAATCTTCTCTTTTTTGCTTTTTTGTTAGAATAGAAGTGCTTTC
TATACCATTCTTTGTTTATCTCAAAAGTTTTTTCTAAAACAAATATTTCTGAATTTTCTTATTGT
CTTGCATTATTAGCCACTGATGATTATGTTGGTGACATATTAGGTGAATTTTGGGGACTCTCTTC
CTGTCTGGCATAGATAGGTTGAGCTATATTTGAGGAATTATCTATTCCTTGTAAATTAGTTCTAG
ATGTTGTTGGGATAGAAG
Found at i:151246 original size:22 final size:22
Alignment explanation
Indices: 151216--151258 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
151206 ACACCAAAAC
* * *
151216 AGGCTTTTAGCGGCGTTTTTTT
1 AGGCCTTTAGAGGCGCTTTTTT
151238 AGGCCTTTAGAGGCGCTTTTT
1 AGGCCTTTAGAGGCGCTTTTT
151259 AGCGCCGCTA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.12, C:0.16, G:0.28, T:0.44
Consensus pattern (22 bp):
AGGCCTTTAGAGGCGCTTTTTT
Found at i:151382 original size:43 final size:43
Alignment explanation
Indices: 151321--151545 Score: 299
Period size: 43 Copynumber: 5.2 Consensus size: 43
151311 CTAAAGAACG
* *
151321 CGCCACTAAAGACTAAGACCTTTAGCGGCGCTTTTCCCACAAA
1 CGCCGCTAAAGACCAAGACCTTTAGCGGCGCTTTTCCCACAAA
*
151364 CGCCGCTAAAGACCAAGACCTTTAGCGGCGCTTTACCCACAAA
1 CGCCGCTAAAGACCAAGACCTTTAGCGGCGCTTTTCCCACAAA
*
151407 CGCCGCTAAAGACCAAGACCTTTAGCGGCGCTTTACCCACAAA
1 CGCCGCTAAAGACCAAGACCTTTAGCGGCGCTTTTCCCACAAA
* * ** *
151450 CGCCGCTATAGATCGTGACCTTTAGCAGCGCTTATT-CCACAAA
1 CGCCGCTAAAGACCAAGACCTTTAGCGGCGCTT-TTCCCACAAA
* * ** **
151493 CGCCGCTAAAGATCATGACCTTTAGCAACGCTTTTGTCACAAA
1 CGCCGCTAAAGACCAAGACCTTTAGCGGCGCTTTTCCCACAAA
151536 CGCCGCTAAA
1 CGCCGCTAAA
151546 AATATAACCT
Statistics
Matches: 167, Mismatches: 13, Indels: 4
0.91 0.07 0.02
Matches are distributed among these distances:
42 2 0.01
43 164 0.98
44 1 0.01
ACGTcount: A:0.29, C:0.32, G:0.18, T:0.20
Consensus pattern (43 bp):
CGCCGCTAAAGACCAAGACCTTTAGCGGCGCTTTTCCCACAAA
Done.