Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Gbar_D07
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: 56457815
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 1765025 characters in sequence are not A, C, G, or T
File 110 of 189
Found at i:30776742 original size:38 final size:38
Alignment explanation
Indices: 30776558--30776739 Score: 202
Period size: 38 Copynumber: 4.8 Consensus size: 38
30776548 AATGTAATGT
* * *
30776558 TATTCAGGCTATGTGCCTAGCAGGCTTTGTGCCGATAA
1 TATTCGGGCTATGTGCCTAGCAGGCTTTGTGCCGGTGA
* * *
30776596 TATTCGGGCTCTATGCCTAGCAGGCTTTGTGCCGTTGA
1 TATTCGGGCTATGTGCCTAGCAGGCTTTGTGCCGGTGA
** * ** * *
30776634 TATTCGAACTATGTGTCTAATAGGATTTGTGCAGGTGA
1 TATTCGGGCTATGTGCCTAGCAGGCTTTGTGCCGGTGA
* * * *
30776672 TATTCGGGCTATGTGCCTAGCAGGCTGTGTTCTGGTGT
1 TATTCGGGCTATGTGCCTAGCAGGCTTTGTGCCGGTGA
*
30776710 TATTCGGGCTCTGTGCCTAGCAGGCTTTGT
1 TATTCGGGCTATGTGCCTAGCAGGCTTTGT
30776740 TCTAGTGTAT
Statistics
Matches: 117, Mismatches: 27, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
38 117 1.00
ACGTcount: A:0.16, C:0.19, G:0.29, T:0.35
Consensus pattern (38 bp):
TATTCGGGCTATGTGCCTAGCAGGCTTTGTGCCGGTGA
Found at i:30779015 original size:106 final size:106
Alignment explanation
Indices: 30778830--30779037 Score: 353
Period size: 106 Copynumber: 2.0 Consensus size: 106
30778820 TCACGTTTAT
* * * *
30778830 GCTTATAATTTTGTATGTGTGAAATGTATTATGACTGAATGCCAAGTTATTTGATTAAATGAATT
1 GCTTATAATTGTGAATGTGTGAAATGTATTATGACTAAATGCCAAGTTATTTGATTAAACGAATT
30778895 GATATAGTCTGGGTTGCTATGATAACATAATGAGACACCAG
66 GATATAGTCTGGGTTGCTATGATAACATAATGAGACACCAG
*
30778936 GCTTATAATTGTGAATGTGTGAAATGTATTATGACTAAATGCCAAGTTATTTGATTAAACGATTT
1 GCTTATAATTGTGAATGTGTGAAATGTATTATGACTAAATGCCAAGTTATTTGATTAAACGAATT
* *
30779001 GATATTGTCTGGGTTGCTATGATAACATAATGTGACA
66 GATATAGTCTGGGTTGCTATGATAACATAATGAGACA
30779038 TAATGCATTT
Statistics
Matches: 95, Mismatches: 7, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
106 95 1.00
ACGTcount: A:0.33, C:0.09, G:0.21, T:0.38
Consensus pattern (106 bp):
GCTTATAATTGTGAATGTGTGAAATGTATTATGACTAAATGCCAAGTTATTTGATTAAACGAATT
GATATAGTCTGGGTTGCTATGATAACATAATGAGACACCAG
Found at i:30790139 original size:346 final size:345
Alignment explanation
Indices: 30789152--30790187 Score: 2054
Period size: 345 Copynumber: 3.0 Consensus size: 345
30789142 GTTTGGAATT
30789152 GAAATTAAGGTTTACACACTAGATTGGTGTGGTGAAATCACATTTTCGGCAAATCTAGCTAGTTT
1 GAAATTAAGGTTTACACACTAGATTGGTGTGGTGAAATCACATTTTCGGCAAATCTAGCTAGTTT
30789217 TAAGTATGTATGATAGATGATTTGTGGTATGCATTTTTATATGATTTAAATGTGTTTTAGGTTCT
66 TAAGTATGTATGATAGATGATTTGTGGTATGCATTTTTATATGATTTAAATGTGTTTTAGGTTCT
30789282 TTATAATGTGTTTGTAATGTATTTAATGTGAATGCAAAGTGTCAGACTCGTTGGGATGTCCTACA
131 TTATAATGTGTTTGTAATGTATTTAATGTGAATGCAAAGTGTCAGACTCGTTGGGATGTCCTACA
30789347 TGCAAAGAAAAAGGCAAACAAATGCTTATTTGGGCTTTTGCCATTAAAGTCAAGGTTGCAAGGTG
196 TGCAAAGAAAAAGGCAAACAAATGCTTATTTGGGCTTTTGCCATTAAAGTCAAGGTTGCAAGGTG
30789412 AGTGGTTTGGTGTGCTACAATTATGCACAAATCAAAGCATTAAAGGGGAGCTTAGGTAGCCTAAT
261 AGTGGTTTGGTGTGCTACAATTATGCACAAATCAAAGCATTAAAGGGGAGCTTAGGTAGCCTAAT
30789477 CATATATACTAAGTTCCATG
326 CATATATACTAAGTTCCATG
30789497 GAAATTAAGGTTTACACACTAGATTGGTGTGGTGAAATCACATTTTCGGCAAATCTAGCTAGTTT
1 GAAATTAAGGTTTACACACTAGATTGGTGTGGTGAAATCACATTTTCGGCAAATCTAGCTAGTTT
30789562 TAAGTATGTATGATAGATGATTTGTGGTATGCATTTTTATATGATTTAAATGTGTTTTAGGTTCT
66 TAAGTATGTATGATAGATGATTTGTGGTATGCATTTTTATATGATTTAAATGTGTTTTAGGTTCT
30789627 TTATAATGTGTTTGTAATGTATTTAATGTGAATGCAAAGTGTCAGACTCGTTGGGATGTCCTACA
131 TTATAATGTGTTTGTAATGTATTTAATGTGAATGCAAAGTGTCAGACTCGTTGGGATGTCCTACA
30789692 TGCAAAGAAAAAGGCAAACAAATGCTTATTTGGGCTTTTGCCATTAAAGTCAAGGTTGCAAGGTG
196 TGCAAAGAAAAAGGCAAACAAATGCTTATTTGGGCTTTTGCCATTAAAGTCAAGGTTGCAAGGTG
30789757 AGTGGTTTGGTGTGCTACAATTATGCACAAATCAAAGCATTAAAGGGGAGCTTAGGTAGCCTAAT
261 AGTGGTTTGGTGTGCTACAATTATGCACAAATCAAAGCATTAAAGGGGAGCTTAGGTAGCCTAAT
30789822 CATATATACTAAGTTCCATG
326 CATATATACTAAGTTCCATG
*
30789842 GAAATTAAATGTTTACACACTAGATTGGTGTGGTGAAATCACATTTTCGGCAAATCTAGCTAGTT
1 GAAATT-AAGGTTTACACACTAGATTGGTGTGGTGAAATCACATTTTCGGCAAATCTAGCTAGTT
30789907 TTAAGTATGTATGATAGATGATTTGTGGTATGCATTTTTATATGATTTAAATGTGTTTTAGGTTC
65 TTAAGTATGTATGATAGATGATTTGTGGTATGCATTTTTATATGATTTAAATGTGTTTTAGGTTC
30789972 TTTATAATGTGTTTGTAATGTATTTAATGTGAATGCAAAGTGTCAGACTCGTTGGGATGTCCTAC
130 TTTATAATGTGTTTGTAATGTATTTAATGTGAATGCAAAGTGTCAGACTCGTTGGGATGTCCTAC
30790037 ATGCAAAGAAAAAGGCAAACAAATGCTTATTTGGGCTTTTGCCATTAAAGTCAAGGTTGCAAGGT
195 ATGCAAAGAAAAAGGCAAACAAATGCTTATTTGGGCTTTTGCCATTAAAGTCAAGGTTGCAAGGT
30790102 GAGTGGTTTGGTGTGCTACAATTATGCACAAATCAAAGCATTAAAGGGGAGCTTAGGTAGCCTAA
260 GAGTGGTTTGGTGTGCTACAATTATGCACAAATCAAAGCATTAAAGGGGAGCTTAGGTAGCCTAA
30790167 TCATATATACTAAGTTCCATG
325 TCATATATACTAAGTTCCATG
30790188 ACTAAGTGTT
Statistics
Matches: 689, Mismatches: 1, Indels: 1
1.00 0.00 0.00
Matches are distributed among these distances:
345 351 0.51
346 338 0.49
ACGTcount: A:0.31, C:0.12, G:0.22, T:0.35
Consensus pattern (345 bp):
GAAATTAAGGTTTACACACTAGATTGGTGTGGTGAAATCACATTTTCGGCAAATCTAGCTAGTTT
TAAGTATGTATGATAGATGATTTGTGGTATGCATTTTTATATGATTTAAATGTGTTTTAGGTTCT
TTATAATGTGTTTGTAATGTATTTAATGTGAATGCAAAGTGTCAGACTCGTTGGGATGTCCTACA
TGCAAAGAAAAAGGCAAACAAATGCTTATTTGGGCTTTTGCCATTAAAGTCAAGGTTGCAAGGTG
AGTGGTTTGGTGTGCTACAATTATGCACAAATCAAAGCATTAAAGGGGAGCTTAGGTAGCCTAAT
CATATATACTAAGTTCCATG
Found at i:30790594 original size:22 final size:22
Alignment explanation
Indices: 30790537--30790598 Score: 72
Period size: 23 Copynumber: 2.8 Consensus size: 22
30790527 AGAGGTTATA
*
30790537 TAAA-TAGTTGTGTTTGAAGCG
1 TAAATTAGTTGTGTTTGGAGCG
* * *
30790558 TATATTTGGTTGTGTTTGGAGGG
1 TA-AATTAGTTGTGTTTGGAGCG
30790581 TAAATTAGTTGTGTTTGG
1 TAAATTAGTTGTGTTTGG
30790599 CAACCATGTT
Statistics
Matches: 33, Mismatches: 6, Indels: 3
0.79 0.14 0.07
Matches are distributed among these distances:
21 2 0.06
22 15 0.45
23 16 0.48
ACGTcount: A:0.21, C:0.02, G:0.32, T:0.45
Consensus pattern (22 bp):
TAAATTAGTTGTGTTTGGAGCG
Found at i:30814780 original size:18 final size:18
Alignment explanation
Indices: 30814757--30814817 Score: 52
Period size: 18 Copynumber: 3.3 Consensus size: 18
30814747 ACAAAGGAAA
30814757 AAGCTTAATTTGGATCCT
1 AAGCTTAATTTGGATCCT
* * * *
30814775 AAGCTT-ACTAGGCTCTT
1 AAGCTTAATTTGGATCCT
30814792 CAACGGCTTAATTTGGATCCT
1 -AA--GCTTAATTTGGATCCT
30814813 AAGCT
1 AAGCT
30814818 CGCGAAAGAG
Statistics
Matches: 31, Mismatches: 8, Indels: 8
0.66 0.17 0.17
Matches are distributed among these distances:
17 7 0.23
18 11 0.35
20 6 0.19
21 7 0.23
ACGTcount: A:0.26, C:0.21, G:0.18, T:0.34
Consensus pattern (18 bp):
AAGCTTAATTTGGATCCT
Found at i:30819080 original size:20 final size:20
Alignment explanation
Indices: 30819055--30819103 Score: 66
Period size: 20 Copynumber: 2.5 Consensus size: 20
30819045 TGAGTTATTT
30819055 AAGTAAGCAAGTAAGTAAAC
1 AAGTAAGCAAGTAAGTAAAC
*
30819075 AAGTAAG-AGAGTAAGTAAAG
1 AAGTAAGCA-AGTAAGTAAAC
30819095 AAG-AAGCAA
1 AAGTAAGCAA
30819104 AGACCATGAT
Statistics
Matches: 26, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
19 5 0.19
20 21 0.81
ACGTcount: A:0.57, C:0.06, G:0.24, T:0.12
Consensus pattern (20 bp):
AAGTAAGCAAGTAAGTAAAC
Found at i:30825091 original size:28 final size:28
Alignment explanation
Indices: 30825059--30825113 Score: 92
Period size: 28 Copynumber: 2.0 Consensus size: 28
30825049 ACAGAATAAT
*
30825059 GTGGGCTTTAGCCCAATACAAAAACAAG
1 GTGGGCCTTAGCCCAATACAAAAACAAG
*
30825087 GTGGGCCTTAGCCCAATACAGAAACAA
1 GTGGGCCTTAGCCCAATACAAAAACAA
30825114 TATGCAATAT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
28 25 1.00
ACGTcount: A:0.38, C:0.24, G:0.22, T:0.16
Consensus pattern (28 bp):
GTGGGCCTTAGCCCAATACAAAAACAAG
Found at i:30825337 original size:27 final size:28
Alignment explanation
Indices: 30825273--30825337 Score: 73
Period size: 27 Copynumber: 2.4 Consensus size: 28
30825263 AACAGAGCTG
30825273 CCAGT-ACAGT-ATATGTGGCAAAGCCA
1 CCAGTAACAGTAATATGTGGCAAAGCCA
* * *
30825299 TCATTAATAGTAAT-TGTGGCAAAGCCA
1 CCAGTAACAGTAATATGTGGCAAAGCCA
*
30825326 CCCGTAACAGTA
1 CCAGTAACAGTA
30825338 CTTCCTCCAT
Statistics
Matches: 30, Mismatches: 7, Indels: 3
0.75 0.17 0.08
Matches are distributed among these distances:
26 3 0.10
27 25 0.83
28 2 0.07
ACGTcount: A:0.35, C:0.22, G:0.20, T:0.23
Consensus pattern (28 bp):
CCAGTAACAGTAATATGTGGCAAAGCCA
Found at i:30825700 original size:55 final size:55
Alignment explanation
Indices: 30825561--30826004 Score: 396
Period size: 55 Copynumber: 8.1 Consensus size: 55
30825551 GGTATTTTAG
* * * * * * *
30825561 TAATTTTGCAAATTGAAGGTATTTTGGTAA-TTTTACAAACTGAGGTTATTTAG-
1 TAATTTTACAAATCGAGGGTATTTTAGTAATTTTTACAAATTGAGGGTATTTCGA
* * *
30825614 TCATTTCACAAATCGAGGGTATTTT-GATAATTTTTACATATTGAGGGTATTTCGA
1 TAATTTTACAAATCGAGGGTATTTTAG-TAATTTTTACAAATTGAGGGTATTTCGA
* * * *
30825669 TAATTTTGCAAATTGGGGGTATTTTAGTAATTTTTACAAATCGAGGGTATTTCGA
1 TAATTTTACAAATCGAGGGTATTTTAGTAATTTTTACAAATTGAGGGTATTTCGA
* * * * * * * *
30825724 TAATTTTGCAAATCGGGGGTATTTCAATAATTTTGA-AATTTGGGGGTATTT-TA
1 TAATTTTACAAATCGAGGGTATTTTAGTAATTTTTACAAATTGAGGGTATTTCGA
* * *
30825777 GTAATTTTTACAAATCGAGGGTATTTCAATAATTTTTTGCAAATTG-GGGATATTTCGA
1 -TAA-TTTTACAAATCGAGGGTATTTTAGTAA-TTTTTACAAATTGAGGG-TATTTCGA
* *
30825835 TAATTTTACAAATCGAGGGTATTTT-GATAATTTTGA-AAATTGGGGGTATTTC-A
1 TAATTTTACAAATCGAGGGTATTTTAG-TAATTTTTACAAATTGAGGGTATTTCGA
* * *
30825888 GTAATTTTACAAA-CTAGGGGTATTTTAATAATTTTTCCAAATT-AGGGGTATTTCGA
1 -TAATTTTACAAATCGA-GGGTATTTTAGTAATTTTTACAAATTGA-GGGTATTTCGA
*
30825944 TAATTTTGCAAATCG-GGCGTATTTTAGTAA-TTTTACAAATT-AGGGGTATTTC-A
1 TAATTTTACAAATCGAGG-GTATTTTAGTAATTTTTACAAATTGA-GGGTATTTCGA
30825997 GTAATTTT
1 -TAATTTT
30826005 TTCAAGTCAG
Statistics
Matches: 327, Mismatches: 43, Indels: 41
0.80 0.10 0.10
Matches are distributed among these distances:
52 1 0.00
53 28 0.09
54 104 0.32
55 146 0.45
56 34 0.10
57 13 0.04
58 1 0.00
ACGTcount: A:0.30, C:0.08, G:0.20, T:0.42
Consensus pattern (55 bp):
TAATTTTACAAATCGAGGGTATTTTAGTAATTTTTACAAATTGAGGGTATTTCGA
Found at i:30825767 original size:82 final size:82
Alignment explanation
Indices: 30825621--30826045 Score: 377
Period size: 82 Copynumber: 5.2 Consensus size: 82
30825611 TAGTCATTTC
* * * *
30825621 ACAAATCGAGGGTATTTTGATAATTTTTACATATTGAGGGTATTTCGATAATTTTGCAAATTGGG
1 ACAAATCGAGGGTATTTCGATAA-TTTTACAAATTGGGGGTATTTCAATAATTTTG-AAATTGGG
30825686 GGTATTTTAG-TAATTTTT
64 GGTATTTTAGATAATTTTT
* *
30825704 ACAAATCGAGGGTATTTCGATAATTTTGCAAATCGGGGGTATTTCAATAATTTTGAAATTTGGGG
1 ACAAATCGAGGGTATTTCGATAATTTTACAAATTGGGGGTATTTCAATAATTTTGAAA-TTGGGG
30825769 GTATTTTAG-TAATTTTT
65 GTATTTTAGATAATTTTT
* * * * * * *
30825786 ACAAATCGAGGGTATTTCAATAATTTTTTGCAAATTGGGGATATTTCGATAATTTTACAAATCGA
1 ACAAATCGAGGGTATTTCGATAA--TTTTACAAATTGGGGGTATTTCAATAATTTT-GAAATTGG
*
30825851 GGGTATTTT-GATAATTTTG
63 GGGTATTTTAGATAATTTTT
* * * * * * *
30825870 A-AAATTGGGGGTATTTC-AGTAATTTTACAAACTAGGGGTATTTTAATAATTTTTCCAAATTAG
1 ACAAATCGAGGGTATTTCGA-TAATTTTACAAATTGGGGGTATTTCAATAA-TTTT-GAAATTGG
*
30825933 GGGTA-TTTCGATAA-TTTT
63 GGGTATTTTAGATAATTTTT
* * * * * * **
30825951 GCAAATCG-GGCGTATTT-TAGTAATTTTACAAATTAGGGGTATTTCAGTAATTTTTTCAAGTCA
1 ACAAATCGAGG-GTATTTCGA-TAATTTTACAAATTGGGGGTATTTCAATAA--TTTTGAAATTG
*
30826014 GGGGTA-TTTCGATAA-TTTT
62 GGGGTATTTTAGATAATTTTT
30826033 ACAAATCGAGGGT
1 ACAAATCGAGGGT
30826046 CTCGGTGACC
Statistics
Matches: 294, Mismatches: 35, Indels: 27
0.83 0.10 0.08
Matches are distributed among these distances:
81 32 0.11
82 165 0.56
83 47 0.16
84 47 0.16
85 3 0.01
ACGTcount: A:0.30, C:0.08, G:0.20, T:0.41
Consensus pattern (82 bp):
ACAAATCGAGGGTATTTCGATAATTTTACAAATTGGGGGTATTTCAATAATTTTGAAATTGGGGG
TATTTTAGATAATTTTT
Found at i:30826045 original size:27 final size:27
Alignment explanation
Indices: 30825561--30826045 Score: 325
Period size: 27 Copynumber: 17.7 Consensus size: 27
30825551 GGTATTTTAG
* * * * *
30825561 TAATTTTGCAAATTGAAGGTATTTTGG
1 TAATTTTACAAATCGAGGGTATTTCGA
* *
30825588 TAATTTTACAAA-CTGAGGTTATTTAG-
1 TAATTTTACAAATC-GAGGGTATTTCGA
* * *
30825614 TCATTTCACAAATCGAGGGTATTTTGA
1 TAATTTTACAAATCGAGGGTATTTCGA
* *
30825641 TAATTTTTACATATTGAGGGTATTTCGA
1 TAA-TTTTACAAATCGAGGGTATTTCGA
* * * *
30825669 TAATTTTGCAAATTGGGGGTATTT-TA
1 TAATTTTACAAATCGAGGGTATTTCGA
30825695 GTAATTTTTACAAATCGAGGGTATTTCGA
1 -TAA-TTTTACAAATCGAGGGTATTTCGA
* * *
30825724 TAATTTTGCAAATCGGGGGTATTTCAA
1 TAATTTTACAAATCGAGGGTATTTCGA
* * * *
30825751 TAATTTTGA-AATTTGGGGGTATTT-TA
1 TAATTTT-ACAAATCGAGGGTATTTCGA
*
30825777 GTAATTTTTACAAATCGAGGGTATTTCAA
1 -TAA-TTTTACAAATCGAGGGTATTTCGA
* *
30825806 TAATTTTTTGCAAATTG-GGGATATTTCGA
1 TAA--TTTTACAAATCGAGGG-TATTTCGA
*
30825835 TAATTTTACAAATCGAGGGTATTTTGA
1 TAATTTTACAAATCGAGGGTATTTCGA
* *
30825862 TAATTTTGA-AAATTGGGGGTATTTC-A
1 TAATTTT-ACAAATCGAGGGTATTTCGA
* **
30825888 GTAATTTTACAAA-CTAGGGGTATTTTAA
1 -TAATTTTACAAATCGA-GGGTATTTCGA
* *
30825916 TAATTTTTCCAAAT-TAGGGGTATTTCGA
1 TAA-TTTTACAAATCGA-GGGTATTTCGA
* *
30825944 TAATTTTGCAAATCG-GGCGTATTT-TA
1 TAATTTTACAAATCGAGG-GTATTTCGA
*
30825970 GTAATTTTACAAAT-TAGGGGTATTTC-A
1 -TAATTTTACAAATCGA-GGGTATTTCGA
* *
30825997 GTAATTTTTTCAAGTC-AGGGGTATTTCGA
1 -TAA-TTTTACAAATCGA-GGGTATTTCGA
30826026 TAATTTTACAAATCGAGGGT
1 TAATTTTACAAATCGAGGGT
30826046 CTCGGTGACC
Statistics
Matches: 368, Mismatches: 58, Indels: 64
0.75 0.12 0.13
Matches are distributed among these distances:
26 27 0.07
27 198 0.54
28 119 0.32
29 24 0.07
ACGTcount: A:0.30, C:0.08, G:0.20, T:0.42
Consensus pattern (27 bp):
TAATTTTACAAATCGAGGGTATTTCGA
Found at i:30830046 original size:17 final size:16
Alignment explanation
Indices: 30830018--30830063 Score: 62
Period size: 15 Copynumber: 3.0 Consensus size: 16
30830008 ACATTATCCC
30830018 TCATCC-CTCATCTCA
1 TCATCCTCTCATCTCA
30830033 TCATCCCTCTCATCTC-
1 TCAT-CCTCTCATCTCA
30830049 TCATCCTCTC-TCTCA
1 TCATCCTCTCATCTCA
30830064 ACTCTCTTAG
Statistics
Matches: 28, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
14 4 0.14
15 10 0.36
16 6 0.21
17 8 0.29
ACGTcount: A:0.15, C:0.48, G:0.00, T:0.37
Consensus pattern (16 bp):
TCATCCTCTCATCTCA
Found at i:30830052 original size:19 final size:19
Alignment explanation
Indices: 30830028--30830069 Score: 57
Period size: 19 Copynumber: 2.2 Consensus size: 19
30830018 TCATCCCTCA
*
30830028 TCTCATCATCCCTCTCATC
1 TCTCATCATCCCTCTCAAC
* *
30830047 TCTCATCCTCTCTCTCAAC
1 TCTCATCATCCCTCTCAAC
30830066 TCTC
1 TCTC
30830070 TTAGCTCTCA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.14, C:0.48, G:0.00, T:0.38
Consensus pattern (19 bp):
TCTCATCATCCCTCTCAAC
Found at i:30838210 original size:11 final size:11
Alignment explanation
Indices: 30838196--30838224 Score: 58
Period size: 11 Copynumber: 2.6 Consensus size: 11
30838186 AAATGATATT
30838196 TTATTATTTTA
1 TTATTATTTTA
30838207 TTATTATTTTA
1 TTATTATTTTA
30838218 TTATTAT
1 TTATTAT
30838225 ATATATAAGA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 18 1.00
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (11 bp):
TTATTATTTTA
Found at i:30838957 original size:15 final size:15
Alignment explanation
Indices: 30838932--30838966 Score: 54
Period size: 15 Copynumber: 2.4 Consensus size: 15
30838922 GACTCTATTT
*
30838932 TAATT-ATATTAGGA
1 TAATTAATATTAAGA
30838946 TAATTAATATTAAGA
1 TAATTAATATTAAGA
30838961 TAATTA
1 TAATTA
30838967 TTAAGAATTA
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:30839009 original size:10 final size:10
Alignment explanation
Indices: 30838991--30839038 Score: 53
Period size: 10 Copynumber: 4.9 Consensus size: 10
30838981 ATTGTAGGAT
30838991 TTTAT-TTTA
1 TTTATCTTTA
30839000 TTTATCTTTA
1 TTTATCTTTA
30839010 TTTATCTTTA
1 TTTATCTTTA
* ** *
30839020 ATTAAATGTA
1 TTTATCTTTA
30839030 TTTATCTTT
1 TTTATCTTT
30839039 TGGGAATTTA
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:30844499 original size:15 final size:15
Alignment explanation
Indices: 30844474--30844508 Score: 54
Period size: 15 Copynumber: 2.4 Consensus size: 15
30844464 GACTCTATTT
*
30844474 TAATT-ATATTAGGA
1 TAATTAATATTAAGA
30844488 TAATTAATATTAAGA
1 TAATTAATATTAAGA
30844503 TAATTA
1 TAATTA
30844509 TTAAGAATTA
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:30844551 original size:10 final size:10
Alignment explanation
Indices: 30844533--30844580 Score: 62
Period size: 10 Copynumber: 4.9 Consensus size: 10
30844523 ATTTTAGGAT
30844533 TTTAT-TTTA
1 TTTATCTTTA
30844542 TTTATCTTTA
1 TTTATCTTTA
30844552 TTTATCTTTA
1 TTTATCTTTA
* * *
30844562 ATTAACTGTA
1 TTTATCTTTA
30844572 TTTATCTTT
1 TTTATCTTT
30844581 TGGGAATTTA
Statistics
Matches: 32, Mismatches: 6, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
9 5 0.16
10 27 0.84
ACGTcount: A:0.23, C:0.08, G:0.02, T:0.67
Consensus pattern (10 bp):
TTTATCTTTA
Found at i:30853556 original size:50 final size:50
Alignment explanation
Indices: 30853498--30853634 Score: 238
Period size: 50 Copynumber: 2.7 Consensus size: 50
30853488 ACTGCCAATG
**
30853498 CCATGTCCCAGACATGGTCTTACGGGGGACCTCTCATCTCGGTCCCAACA
1 CCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGGTCCCAACA
* *
30853548 CCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGGTGCCAACG
1 CCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGGTCCCAACA
30853598 CCATGTCCCAGACATGGTCTTACATGGGACCTCTCAT
1 CCATGTCCCAGACATGGTCTTACATGGGACCTCTCAT
30853635 AATCTCAATG
Statistics
Matches: 83, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
50 83 1.00
ACGTcount: A:0.20, C:0.34, G:0.21, T:0.24
Consensus pattern (50 bp):
CCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGGTCCCAACA
Found at i:30854344 original size:17 final size:18
Alignment explanation
Indices: 30854318--30854357 Score: 55
Period size: 17 Copynumber: 2.3 Consensus size: 18
30854308 TTATATATAT
*
30854318 ATTTCAATTCAAATCACC
1 ATTTCAATTCAAATCACA
*
30854336 ATTTC-ATTCAATTCACA
1 ATTTCAATTCAAATCACA
30854353 ATTTC
1 ATTTC
30854358 TCATGTTCAC
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
17 15 0.75
18 5 0.25
ACGTcount: A:0.35, C:0.25, G:0.00, T:0.40
Consensus pattern (18 bp):
ATTTCAATTCAAATCACA
Found at i:30855206 original size:15 final size:15
Alignment explanation
Indices: 30855186--30855215 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
30855176 AATTTATTAT
*
30855186 ATTTCATTATTTACA
1 ATTTCATTACTTACA
30855201 ATTTCATTACTTACA
1 ATTTCATTACTTACA
30855216 TCGTTTCTTT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.33, C:0.17, G:0.00, T:0.50
Consensus pattern (15 bp):
ATTTCATTACTTACA
Found at i:30856186 original size:127 final size:127
Alignment explanation
Indices: 30855960--30856201 Score: 484
Period size: 127 Copynumber: 1.9 Consensus size: 127
30855950 TCATTTTGCC
30855960 AATTTCATCCTTGAGTTATCACTTAATTTGGTAAAATTGTGATTTAGTCCCTCAAAATTCTTCAC
1 AATTTCATCCTTGAGTTATCACTTAATTTGGTAAAATTGTGATTTAGTCCCTCAAAATTCTTCAC
30856025 CTTTTCAATTTGGTCCTAATTCATCCATATTCCTTAGTTTCTATATTATTATAATTTTTAAA
66 CTTTTCAATTTGGTCCTAATTCATCCATATTCCTTAGTTTCTATATTATTATAATTTTTAAA
30856087 AATTTCATCCTTGAGTTATCACTTAATTTGGTAAAATTGTGATTTAGTCCCTCAAAATTCTTCAC
1 AATTTCATCCTTGAGTTATCACTTAATTTGGTAAAATTGTGATTTAGTCCCTCAAAATTCTTCAC
30856152 CTTTTCAATTTGGTCCTAATTCATCCATATTCCTTAGTTTCTATATTATT
66 CTTTTCAATTTGGTCCTAATTCATCCATATTCCTTAGTTTCTATATTATT
30856202 CCACCCTTAA
Statistics
Matches: 115, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
127 115 1.00
ACGTcount: A:0.27, C:0.18, G:0.08, T:0.46
Consensus pattern (127 bp):
AATTTCATCCTTGAGTTATCACTTAATTTGGTAAAATTGTGATTTAGTCCCTCAAAATTCTTCAC
CTTTTCAATTTGGTCCTAATTCATCCATATTCCTTAGTTTCTATATTATTATAATTTTTAAA
Found at i:30859741 original size:50 final size:50
Alignment explanation
Indices: 30859633--30859879 Score: 212
Period size: 50 Copynumber: 4.8 Consensus size: 50
30859623 ATTTGGGTAA
*
30859633 AGAGATCCCATGTAAGACCATGTCTGGGACATGACATTGGCATCATTGAGATTATG
1 AGAGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCA-C--TGAG---ATG
* * *
30859689 AGAGGTCCCATGTAAGACCATGTTTGGGACATGGCGTTGGCACTGAGATG
1 AGAGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACTGAGATG
* ** * * * * *
30859739 AGAGGTCCCCCGTAAGACCATGTCTGGAACATAGCATAGGCACCGATATG
1 AGAGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACTGAGATG
* * * * * *
30859789 AGA-ACTCCCACGTAAGACCATATCTGGGATATGGCATTGGCAGT-ACAAG
1 AGAGA-TCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACTGAGATG
* * *
30859838 TA-ACATCCCATGTAAGACCATGTATGGGACATGTCATTGGCA
1 -AGAGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCA
30859880 TGTTATTATC
Statistics
Matches: 159, Mismatches: 29, Indels: 13
0.79 0.14 0.06
Matches are distributed among these distances:
49 36 0.23
50 80 0.50
53 4 0.03
55 1 0.01
56 38 0.24
ACGTcount: A:0.30, C:0.21, G:0.26, T:0.23
Consensus pattern (50 bp):
AGAGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACTGAGATG
Found at i:30866655 original size:50 final size:54
Alignment explanation
Indices: 30866531--30866679 Score: 164
Period size: 56 Copynumber: 2.8 Consensus size: 54
30866521 ATTTGGGTAA
* *
30866531 AGAGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCCTTGAGATTAGT
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCA--CATGAGATTAGT
* *
30866587 AGAGGTCCCATGTAAGACCATGTTTGGGACATGGCGTTGGCA-ATGAGA-T-G-
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACATGAGATTAGT
* * * *
30866637 AGAGGTCTC-TCGTAAGACCATGTCTGGAACATAGCATGGGCAC
1 AGAGGTCCCAT-GTAAGACCATGTCTGGGACATGGCATTGGCAC
30866680 CGATATGAGA
Statistics
Matches: 81, Mismatches: 10, Indels: 9
0.81 0.10 0.09
Matches are distributed among these distances:
49 1 0.01
50 34 0.42
51 1 0.01
52 1 0.01
53 5 0.06
56 39 0.48
ACGTcount: A:0.27, C:0.19, G:0.30, T:0.24
Consensus pattern (54 bp):
AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACATGAGATTAGT
Found at i:30866702 original size:50 final size:50
Alignment explanation
Indices: 30866531--30866724 Score: 183
Period size: 50 Copynumber: 3.8 Consensus size: 50
30866521 ATTTGGGTAA
*
30866531 AGAGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCCTTGAGATTAG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCA-CC--GAGA-T-G
* * **
30866586 TAGAGGTCCCATGTAAGACCATGTTTGGGACATGGCGTTGGCAATGAGATG
1 -AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATG
* * * * *
30866637 AGAGGTCTC-TCGTAAGACCATGTCTGGAACATAGCATGGGCACCGATATG
1 AGAGGTCCCAT-GTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATG
** * * *
30866687 AGAACTCCCATGTAAGACCATATATGGGATATGGCATT
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATT
30866725 TGAAGTACAA
Statistics
Matches: 113, Mismatches: 23, Indels: 10
0.77 0.16 0.07
Matches are distributed among these distances:
49 1 0.01
50 66 0.58
51 2 0.02
52 1 0.01
53 4 0.04
56 39 0.35
ACGTcount: A:0.28, C:0.19, G:0.28, T:0.25
Consensus pattern (50 bp):
AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATG
Found at i:30868837 original size:6 final size:6
Alignment explanation
Indices: 30868826--30868850 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
30868816 GCGATAATGT
30868826 AAAGGA AAAGGA AAAGGA AAAGGA A
1 AAAGGA AAAGGA AAAGGA AAAGGA A
30868851 TGGTTTTGAC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.68, C:0.00, G:0.32, T:0.00
Consensus pattern (6 bp):
AAAGGA
Found at i:30870205 original size:20 final size:18
Alignment explanation
Indices: 30870180--30870216 Score: 56
Period size: 20 Copynumber: 1.9 Consensus size: 18
30870170 ATTGCTAAGT
30870180 TGTAAAATGAGTTGTAAATG
1 TGTAAAAT-AGTTG-AAATG
30870200 TGTAAAATAGTTGAAAT
1 TGTAAAATAGTTGAAAT
30870217 TATGAGTTGC
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 4 0.24
19 5 0.29
20 8 0.47
ACGTcount: A:0.43, C:0.00, G:0.22, T:0.35
Consensus pattern (18 bp):
TGTAAAATAGTTGAAATG
Found at i:30870827 original size:46 final size:46
Alignment explanation
Indices: 30870777--30870948 Score: 181
Period size: 46 Copynumber: 3.7 Consensus size: 46
30870767 TGAGCATCCA
* *
30870777 AACTCGTTGAGTTGAGTTCGAGTTCACTTATGGATGCGAATGTTCG
1 AACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATGTCCG
* * * *
30870823 AACTCGTTGAGTTGAGTCTGAGTTC-GTGA--GATG-TAACTAGGCATCCG
1 AACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAA-T--G--TCCG
* * *
30870870 AGCTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCG
1 AACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATGTCCG
*
30870916 AGCTCGTTGAGTTGAGTCCGAGTTCACTTATGG
1 AACTCGTTGAGTTGAGTCCGAGTTCACTTATGG
30870949 GCGGGTTACA
Statistics
Matches: 104, Mismatches: 13, Indels: 18
0.77 0.10 0.13
Matches are distributed among these distances:
42 2 0.02
43 5 0.05
45 3 0.03
46 59 0.57
47 26 0.25
48 3 0.03
50 4 0.04
51 2 0.02
ACGTcount: A:0.21, C:0.19, G:0.30, T:0.31
Consensus pattern (46 bp):
AACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATGTCCG
Found at i:30870885 original size:93 final size:93
Alignment explanation
Indices: 30870770--30870940 Score: 270
Period size: 93 Copynumber: 1.8 Consensus size: 93
30870760 GGATGGTTGA
* * **
30870770 GCATCCAAACTCGTTGAGTTGAGTTCGAGTTCACTTATGGATGCGAATGTTCGAACTCGTTGAGT
1 GCATCCAAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAGT
*
30870835 TGAGTCTGAGTTCGTGAGATGTAACTAG
66 TGAGTCCGAGTTCGTGAGATGTAACTAG
* * *
30870863 GCATCCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAGCTCGTTGAGT
1 GCATCCAAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAGT
30870928 TGAGTCCGAGTTC
66 TGAGTCCGAGTTC
30870941 ACTTATGGGC
Statistics
Matches: 70, Mismatches: 8, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
93 70 1.00
ACGTcount: A:0.21, C:0.20, G:0.29, T:0.30
Consensus pattern (93 bp):
GCATCCAAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAGT
TGAGTCCGAGTTCGTGAGATGTAACTAG
Found at i:30881167 original size:5 final size:5
Alignment explanation
Indices: 30881157--30881218 Score: 106
Period size: 5 Copynumber: 12.2 Consensus size: 5
30881147 ATGATGCATA
*
30881157 AATAT AATAT AATAT AATAT AATAT AATAT AATAT AATAT AATAT AATAA
1 AATAT AATAT AATAT AATAT AATAT AATAT AATAT AATAT AATAT AATAT
30881207 ATATAT AATAT A
1 A-ATAT AATAT A
30881219 GTAAGATATA
Statistics
Matches: 54, Mismatches: 2, Indels: 2
0.93 0.03 0.03
Matches are distributed among these distances:
5 50 0.93
6 4 0.07
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (5 bp):
AATAT
Found at i:30882413 original size:26 final size:26
Alignment explanation
Indices: 30882384--30882437 Score: 108
Period size: 26 Copynumber: 2.1 Consensus size: 26
30882374 AATGCTTAAC
30882384 AAATATTACATTTTATTTATTTCTTT
1 AAATATTACATTTTATTTATTTCTTT
30882410 AAATATTACATTTTATTTATTTCTTT
1 AAATATTACATTTTATTTATTTCTTT
30882436 AA
1 AA
30882438 CAGGAGGACT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 28 1.00
ACGTcount: A:0.33, C:0.07, G:0.00, T:0.59
Consensus pattern (26 bp):
AAATATTACATTTTATTTATTTCTTT
Found at i:30885377 original size:15 final size:15
Alignment explanation
Indices: 30885357--30885389 Score: 57
Period size: 15 Copynumber: 2.2 Consensus size: 15
30885347 GAGGAGAGGA
30885357 AATTGAAAAGAAAAC
1 AATTGAAAAGAAAAC
*
30885372 AATTGAAAAGAACAC
1 AATTGAAAAGAAAAC
30885387 AAT
1 AAT
30885390 CAATTAAAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.64, C:0.09, G:0.12, T:0.15
Consensus pattern (15 bp):
AATTGAAAAGAAAAC
Found at i:30885786 original size:21 final size:22
Alignment explanation
Indices: 30885762--30885805 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 22
30885752 TTTTTTGAAA
30885762 AAAAATC-ATAAGAATCAAAAT
1 AAAAATCAATAAGAATCAAAAT
* *
30885783 -AAAATCAATAATAATCTAAAT
1 AAAAATCAATAAGAATCAAAAT
30885804 AA
1 AA
30885806 TATGAGAATT
Statistics
Matches: 19, Mismatches: 2, Indels: 3
0.79 0.08 0.12
Matches are distributed among these distances:
20 6 0.32
21 12 0.63
22 1 0.05
ACGTcount: A:0.66, C:0.09, G:0.02, T:0.23
Consensus pattern (22 bp):
AAAAATCAATAAGAATCAAAAT
Found at i:30892033 original size:20 final size:20
Alignment explanation
Indices: 30892008--30892045 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
30891998 ACCCCCTTTA
30892008 TTAACATAAA-AATTTAAAAT
1 TTAACA-AAATAATTTAAAAT
30892028 TTAACAAAATAATTTAAA
1 TTAACAAAATAATTTAAA
30892046 CTAGAAAAAC
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
19 3 0.18
20 14 0.82
ACGTcount: A:0.61, C:0.05, G:0.00, T:0.34
Consensus pattern (20 bp):
TTAACAAAATAATTTAAAAT
Found at i:30907196 original size:17 final size:17
Alignment explanation
Indices: 30907174--30907211 Score: 60
Period size: 17 Copynumber: 2.2 Consensus size: 17
30907164 ATGATAGGCG
30907174 TGAGAGAGGATGA-GAGA
1 TGAGAG-GGATGATGAGA
30907191 TGAGAGGGATGATGAGA
1 TGAGAGGGATGATGAGA
30907208 TGAG
1 TGAG
30907212 GGATGAGGGA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
16 6 0.30
17 14 0.70
ACGTcount: A:0.37, C:0.00, G:0.47, T:0.16
Consensus pattern (17 bp):
TGAGAGGGATGATGAGA
Found at i:30907197 original size:15 final size:15
Alignment explanation
Indices: 30907177--30907218 Score: 59
Period size: 15 Copynumber: 2.7 Consensus size: 15
30907167 ATAGGCGTGA
30907177 GAGAGGATGAGAGAT
1 GAGAGGATGAGAGAT
30907192 GAGAGGGATGATGAGAT
1 GAGA-GGATGA-GAGAT
30907209 GAG-GGATGAG
1 GAGAGGATGAG
30907219 GGATAAAGTA
Statistics
Matches: 25, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
14 1 0.04
15 10 0.40
16 6 0.24
17 8 0.32
ACGTcount: A:0.36, C:0.00, G:0.50, T:0.14
Consensus pattern (15 bp):
GAGAGGATGAGAGAT
Found at i:30909454 original size:23 final size:23
Alignment explanation
Indices: 30909422--30909473 Score: 86
Period size: 23 Copynumber: 2.3 Consensus size: 23
30909412 GCAGCAACGA
*
30909422 AGAGAAAAACGACAAGAGACTGG
1 AGAGATAAACGACAAGAGACTGG
*
30909445 AGAGATAAACGACAAGAGAGTGG
1 AGAGATAAACGACAAGAGACTGG
30909468 AGAGAT
1 AGAGAT
30909474 TTTGGGGAAA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
23 27 1.00
ACGTcount: A:0.50, C:0.10, G:0.33, T:0.08
Consensus pattern (23 bp):
AGAGATAAACGACAAGAGACTGG
Found at i:30919620 original size:6 final size:6
Alignment explanation
Indices: 30919611--30919639 Score: 58
Period size: 6 Copynumber: 4.8 Consensus size: 6
30919601 CTAAAACCAA
30919611 AAAAAT AAAAAT AAAAAT AAAAAT AAAAA
1 AAAAAT AAAAAT AAAAAT AAAAAT AAAAA
30919640 ACCTAAGATA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.86, C:0.00, G:0.00, T:0.14
Consensus pattern (6 bp):
AAAAAT
Found at i:30926003 original size:39 final size:40
Alignment explanation
Indices: 30925958--30926173 Score: 237
Period size: 39 Copynumber: 5.5 Consensus size: 40
30925948 GCTCCTCGTT
* * * *
30925958 CAAATGCCTTCGGGACATAGCCCGGTTTTAGTAACTCACA
1 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
*
30925998 C-AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCA
1 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
*
30926037 CAAATGCCTTC-GGACTTAACCCGGATTTAGTACCTCGCA
1 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
* *
30926076 CAAAGGCCTTCGGG-CTTAACCCGGAATTT-GTATCTCGCA
1 CAAATGCCTTCGGGACTTAACCCGG-ATTTAGTAACTCGCA
** * * * *
30926115 CAAATGCCTTC-GGATCTTAGTCCGGATATATTCACTTAGCA
1 CAAATGCCTTCGGGA-CTTAACCCGGATTTAGTAAC-TCGCA
30926156 CAAA-GCCTTCGGGACTTA
1 CAAATGCCTTCGGGACTTA
30926174 GCCCAGACAG
Statistics
Matches: 151, Mismatches: 17, Indels: 16
0.82 0.09 0.09
Matches are distributed among these distances:
38 2 0.01
39 102 0.68
40 36 0.24
41 11 0.07
ACGTcount: A:0.26, C:0.28, G:0.19, T:0.26
Consensus pattern (40 bp):
CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
Found at i:30932915 original size:27 final size:27
Alignment explanation
Indices: 30932885--30932945 Score: 104
Period size: 27 Copynumber: 2.3 Consensus size: 27
30932875 ATTGGTACTG
30932885 AAGGATCTATCGCGGTATTGAAAAACA
1 AAGGATCTATCGCGGTATTGAAAAACA
*
30932912 AAGGAGCTATCGCGGTATTGAAAAACA
1 AAGGATCTATCGCGGTATTGAAAAACA
*
30932939 AATGATC
1 AAGGATC
30932946 AAATGTTTAA
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
27 31 1.00
ACGTcount: A:0.41, C:0.15, G:0.23, T:0.21
Consensus pattern (27 bp):
AAGGATCTATCGCGGTATTGAAAAACA
Found at i:30943756 original size:80 final size:78
Alignment explanation
Indices: 30943672--30943843 Score: 213
Period size: 79 Copynumber: 2.2 Consensus size: 78
30943662 GGACTAAGAT
*
30943672 CCGAAGGCATTTGTGCGAG-A-TACAAGTTCCGGGTTAAGCCCCGAAGGCCTTTGTGCGAGATAC
1 CCGAAGGCATTTGTGCGAGCATTA-AA--TCCGGGTTAAGCCCCGAAGG-CATTGTGCGAGATAC
* *
30943735 TAAATCCGGGTTAAGTC
62 TAAAACCGGGCTAAGTC
* * * *
30943752 CCGAAGGCATTCGTGCGAGTCATTAAATCCGGGTTAAGTCCCGAAGGCATTGTGTGAGTTACTAA
1 CCGAAGGCATTTGTGCGAG-CATTAAATCCGGGTTAAGCCCCGAAGGCATTGTGCGAGATACTAA
*
30943817 AACCGGGCTATGTC
65 AACCGGGCTAAGTC
30943831 CCGAAGGCATTTG
1 CCGAAGGCATTTG
30943844 AACGAGGAGC
Statistics
Matches: 80, Mismatches: 9, Indels: 7
0.83 0.09 0.07
Matches are distributed among these distances:
79 38 0.47
80 37 0.46
82 3 0.04
83 2 0.03
ACGTcount: A:0.25, C:0.22, G:0.28, T:0.24
Consensus pattern (78 bp):
CCGAAGGCATTTGTGCGAGCATTAAATCCGGGTTAAGCCCCGAAGGCATTGTGCGAGATACTAAA
ACCGGGCTAAGTC
Found at i:30943834 original size:39 final size:39
Alignment explanation
Indices: 30943619--30943841 Score: 207
Period size: 40 Copynumber: 5.6 Consensus size: 39
30943609 TTGAATGCTG
* * * * * *
30943619 TCCGGGCTAAGTCCCGAAGGCTTTGTGCTAAGTGAATATA
1 TCCGGGTTAAGTCCCGAAGGCATTGTGC-GAGTTACTAAA
** * *
30943659 TCCGGACTAAGAT-CCGAAGGCATTTGTGCGAGATAC-AAGT
1 TCCGGGTTAAG-TCCCGAAGGCA-TTGTGCGAGTTACTAA-A
* * *
30943699 TCCGGGTTAAGCCCCGAAGGCCTTTGTGCGAGATACTAAA
1 TCCGGGTTAAGTCCCGAAGG-CATTGTGCGAGTTACTAAA
* *
30943739 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTCATTAAA
1 TCCGGGTTAAGTCCCGAAGGCATT-GTGCGAGTTACTAAA
*
30943779 TCCGGGTTAAGTCCCGAAGGCATTGTGTGAGTTACTAAA
1 TCCGGGTTAAGTCCCGAAGGCATTGTGCGAGTTACTAAA
* * *
30943818 ACCGGGCTATGTCCCGAAGGCATT
1 TCCGGGTTAAGTCCCGAAGGCATT
30943842 TGAACGAGGA
Statistics
Matches: 152, Mismatches: 24, Indels: 15
0.80 0.13 0.08
Matches are distributed among these distances:
39 37 0.24
40 105 0.69
41 10 0.07
ACGTcount: A:0.26, C:0.22, G:0.28, T:0.25
Consensus pattern (39 bp):
TCCGGGTTAAGTCCCGAAGGCATTGTGCGAGTTACTAAA
Found at i:30943861 original size:79 final size:80
Alignment explanation
Indices: 30943699--30943876 Score: 200
Period size: 79 Copynumber: 2.2 Consensus size: 80
30943689 AGATACAAGT
* * * *
30943699 TCCGGGTTAAGCCCCGAAGGCCTTTGTGCGAGATACTAAATCCGGGTTAAGTCCCGAAGGCATTC
1 TCCGGGTTAAGTCCCGAAGGCCATTGTGCGAGATACTAAAACCGGGCTAAGTCCCGAAGGCATTC
** *
30943764 GTGCGAGTCATTAAA
66 GAACGAGTCACTAAA
* * * *
30943779 TCCGGGTTAAGTCCCGAAGG-CATTGTGTGAGTTACTAAAACCGGGCTATGTCCCGAAGGCATTT
1 TCCGGGTTAAGTCCCGAAGGCCATTGTGCGAGATACTAAAACCGGGCTAAGTCCCGAAGGCATTC
* *
30943843 GAACGAG-GAGCTATA
66 GAACGAGTCA-CTAAA
*
30943858 TCC-GGTTAAATCCCGAAGG
1 TCCGGGTTAAGTCCCGAAGG
30943877 TACGTGATTT
Statistics
Matches: 83, Mismatches: 14, Indels: 4
0.82 0.14 0.04
Matches are distributed among these distances:
78 16 0.19
79 48 0.58
80 19 0.23
ACGTcount: A:0.26, C:0.22, G:0.28, T:0.24
Consensus pattern (80 bp):
TCCGGGTTAAGTCCCGAAGGCCATTGTGCGAGATACTAAAACCGGGCTAAGTCCCGAAGGCATTC
GAACGAGTCACTAAA
Found at i:30951657 original size:80 final size:78
Alignment explanation
Indices: 30951573--30951744 Score: 213
Period size: 79 Copynumber: 2.2 Consensus size: 78
30951563 GGACTAAGAT
*
30951573 CCGAAGGCATTTGTGCGAG-A-TACAAGTTCCGGGTTAAGCCCCGAAGGCCTTTGTGCGAGATAC
1 CCGAAGGCATTTGTGCGAGCATTA-AA--TCCGGGTTAAGCCCCGAAGG-CATTGTGCGAGATAC
* *
30951636 TAAATCCGGGTTAAGTC
62 TAAAACCGGGCTAAGTC
* * * *
30951653 CCGAAGGCATTCGTGCGAGTCATTAAATCCGGGTTAAGTCCCGAAGGCATTGTGTGAGTTACTAA
1 CCGAAGGCATTTGTGCGAG-CATTAAATCCGGGTTAAGCCCCGAAGGCATTGTGCGAGATACTAA
*
30951718 AACCGGGCTATGTC
65 AACCGGGCTAAGTC
30951732 CCGAAGGCATTTG
1 CCGAAGGCATTTG
30951745 AACGAGGAGC
Statistics
Matches: 80, Mismatches: 9, Indels: 7
0.83 0.09 0.07
Matches are distributed among these distances:
79 38 0.47
80 37 0.46
82 3 0.04
83 2 0.03
ACGTcount: A:0.25, C:0.22, G:0.28, T:0.24
Consensus pattern (78 bp):
CCGAAGGCATTTGTGCGAGCATTAAATCCGGGTTAAGCCCCGAAGGCATTGTGCGAGATACTAAA
ACCGGGCTAAGTC
Found at i:30951735 original size:39 final size:39
Alignment explanation
Indices: 30951520--30951742 Score: 207
Period size: 40 Copynumber: 5.6 Consensus size: 39
30951510 TTGAATGCTG
* * * * * *
30951520 TCCGGGCTAAGTCCCGAAGGCTTTGTGCTAAGTGAATATA
1 TCCGGGTTAAGTCCCGAAGGCATTGTGC-GAGTTACTAAA
** * *
30951560 TCCGGACTAAGAT-CCGAAGGCATTTGTGCGAGATAC-AAGT
1 TCCGGGTTAAG-TCCCGAAGGCA-TTGTGCGAGTTACTAA-A
* * *
30951600 TCCGGGTTAAGCCCCGAAGGCCTTTGTGCGAGATACTAAA
1 TCCGGGTTAAGTCCCGAAGG-CATTGTGCGAGTTACTAAA
* *
30951640 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTCATTAAA
1 TCCGGGTTAAGTCCCGAAGGCATT-GTGCGAGTTACTAAA
*
30951680 TCCGGGTTAAGTCCCGAAGGCATTGTGTGAGTTACTAAA
1 TCCGGGTTAAGTCCCGAAGGCATTGTGCGAGTTACTAAA
* * *
30951719 ACCGGGCTATGTCCCGAAGGCATT
1 TCCGGGTTAAGTCCCGAAGGCATT
30951743 TGAACGAGGA
Statistics
Matches: 152, Mismatches: 24, Indels: 15
0.80 0.13 0.08
Matches are distributed among these distances:
39 37 0.24
40 105 0.69
41 10 0.07
ACGTcount: A:0.26, C:0.22, G:0.28, T:0.25
Consensus pattern (39 bp):
TCCGGGTTAAGTCCCGAAGGCATTGTGCGAGTTACTAAA
Found at i:30955080 original size:14 final size:14
Alignment explanation
Indices: 30955061--30955088 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
30955051 GTTTAAAGAT
30955061 GATTAAAAACTAAG
1 GATTAAAAACTAAG
30955075 GATTAAAAACTAAG
1 GATTAAAAACTAAG
30955089 TAAAAAGAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.57, C:0.07, G:0.14, T:0.21
Consensus pattern (14 bp):
GATTAAAAACTAAG
Found at i:30965257 original size:15 final size:15
Alignment explanation
Indices: 30965230--30965271 Score: 57
Period size: 15 Copynumber: 2.8 Consensus size: 15
30965220 AAATCTAAAC
*
30965230 TAAATACATATTTAA
1 TAAATAAATATTTAA
* *
30965245 TAATTAAATATTTAG
1 TAAATAAATATTTAA
30965260 TAAATAAATATT
1 TAAATAAATATT
30965272 AAACTTTTCA
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
15 23 1.00
ACGTcount: A:0.52, C:0.02, G:0.02, T:0.43
Consensus pattern (15 bp):
TAAATAAATATTTAA
Found at i:30969288 original size:3 final size:3
Alignment explanation
Indices: 30969280--30969320 Score: 73
Period size: 3 Copynumber: 13.7 Consensus size: 3
30969270 CTCCGTGGGA
*
30969280 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TTT TCT TC
1 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TC
30969321 GGGATCCTAG
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
3 36 1.00
ACGTcount: A:0.00, C:0.32, G:0.00, T:0.68
Consensus pattern (3 bp):
TCT
Found at i:30971175 original size:29 final size:30
Alignment explanation
Indices: 30971116--30971176 Score: 79
Period size: 30 Copynumber: 2.1 Consensus size: 30
30971106 TGCCTTTGAA
* * *
30971116 AATATTTACAAAAAGAGACATCTAATTTTT
1 AATATTTACAAAAAGAGACAACCAAATTTT
*
30971146 AATATTTACAAAAAGTG-CAACCAAATTTT
1 AATATTTACAAAAAGAGACAACCAAATTTT
30971175 AA
1 AA
30971177 AAATAGTTCA
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
29 11 0.41
30 16 0.59
ACGTcount: A:0.49, C:0.11, G:0.07, T:0.33
Consensus pattern (30 bp):
AATATTTACAAAAAGAGACAACCAAATTTT
Found at i:30976965 original size:8 final size:8
Alignment explanation
Indices: 30976949--30976984 Score: 63
Period size: 8 Copynumber: 4.5 Consensus size: 8
30976939 CCAAAATGCA
30976949 AAATTCAC
1 AAATTCAC
*
30976957 AAATCCAC
1 AAATTCAC
30976965 AAATTCAC
1 AAATTCAC
30976973 AAATTCAC
1 AAATTCAC
30976981 AAAT
1 AAAT
30976985 AATGACTTTT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
8 26 1.00
ACGTcount: A:0.53, C:0.25, G:0.00, T:0.22
Consensus pattern (8 bp):
AAATTCAC
Found at i:30981022 original size:53 final size:52
Alignment explanation
Indices: 30980940--30981160 Score: 244
Period size: 53 Copynumber: 4.1 Consensus size: 52
30980930 AGAGGTCAAT
* * * *
30980940 AAATGATCGAAATACCTCTATAGGGTAAAATGACCAAAATACCGCCATAGGATA
1 AAATGATCAAAATACC-CCATAGGGTAAAATGACCGAAATACC-CCATAGGGTA
* * * * *
30980994 AAATGACCGAAATACCTCATAGGGTAAAATGACTGAAATAGCCCTATAGGGTA
1 AAATGATCAAAATACCCCATAGGGTAAAATGACCGAAATA-CCCCATAGGGTA
* * **
30981047 AAATAATTAAAATACCCCATAGGGTAAAATGACCGAAATACCTTTATAGGGTA
1 AAATGATCAAAATACCCCATAGGGTAAAATGACCGAAATACC-CCATAGGGTA
* * *
30981100 AAATGATCAAAATTCCCCCATAGGGTAAAATGATCGAAATACCCCCATATGGTA
1 AAATGATCAAAA-TACCCCATAGGGTAAAATGACCGAAATA-CCCCATAGGGTA
30981154 AAATGAT
1 AAATGAT
30981161 TGATATACCC
Statistics
Matches: 142, Mismatches: 21, Indels: 8
0.83 0.12 0.05
Matches are distributed among these distances:
52 2 0.01
53 81 0.57
54 57 0.40
55 2 0.01
ACGTcount: A:0.43, C:0.18, G:0.17, T:0.22
Consensus pattern (52 bp):
AAATGATCAAAATACCCCATAGGGTAAAATGACCGAAATACCCCATAGGGTA
Found at i:30981096 original size:80 final size:78
Alignment explanation
Indices: 30980940--30981159 Score: 280
Period size: 80 Copynumber: 2.7 Consensus size: 78
30980930 AGAGGTCAAT
* *
30980940 AAATGATCGAAATACCTCTATAGGGTAAAATGACCAAAATACCGCCATAGGATAAAATGACCGAA
1 AAATGATCGAAATACC-CTATAGGGTAAAATGATCAAAATACC-CCATAGGGTAAAATGACCGAA
30981005 ATACCTCATAGGGTA
64 ATACCTCATAGGGTA
* *
30981020 AAATGA-CTGAAATAGCCCTATAGGGTAAAATAATTAAAATACCCCATAGGGTAAAATGACCGAA
1 AAATGATC-GAAATA-CCCTATAGGGTAAAATGATCAAAATACCCCATAGGGTAAAATGACCGAA
*
30981084 ATACCTTTATAGGGTA
64 ATACC-TCATAGGGTA
* * * * *
30981100 AAATGATCAAAATTCCCCCATAGGGTAAAATGATCGAAATACCCCCATATGGTAAAATGA
1 AAATGATCGAAA-TACCCTATAGGGTAAAATGATCAAAATA-CCCCATAGGGTAAAATGA
30981160 TTGATATACC
Statistics
Matches: 122, Mismatches: 12, Indels: 11
0.84 0.08 0.08
Matches are distributed among these distances:
79 26 0.21
80 75 0.61
81 21 0.17
ACGTcount: A:0.44, C:0.18, G:0.17, T:0.22
Consensus pattern (78 bp):
AAATGATCGAAATACCCTATAGGGTAAAATGATCAAAATACCCCATAGGGTAAAATGACCGAAAT
ACCTCATAGGGTA
Found at i:30981160 original size:27 final size:27
Alignment explanation
Indices: 30980940--30981171 Score: 236
Period size: 27 Copynumber: 8.7 Consensus size: 27
30980930 AGAGGTCAAT
* *
30980940 AAATGATCGAAATACCTCTATAGGGTA
1 AAATGATCGAAATACCCCCATAGGGTA
* * * *
30980967 AAATGACCAAAATACCGCCATAGGATA
1 AAATGATCGAAATACCCCCATAGGGTA
* *
30980994 AAATGACCGAAATA-CCTCATAGGGTA
1 AAATGATCGAAATACCCCCATAGGGTA
* *
30981020 AAATGA-CTGAAATAGCCCTATAGGGTA
1 AAATGATC-GAAATACCCCCATAGGGTA
* **
30981047 AAATAATTAAAATA-CCCCATAGGGTA
1 AAATGATCGAAATACCCCCATAGGGTA
* ***
30981073 AAATGACCGAAATACCTTTATAGGGTA
1 AAATGATCGAAATACCCCCATAGGGTA
* *
30981100 AAATGATCAAAATTCCCCCATAGGGTA
1 AAATGATCGAAATACCCCCATAGGGTA
*
30981127 AAATGATCGAAATACCCCCATATGGTA
1 AAATGATCGAAATACCCCCATAGGGTA
* *
30981154 AAATGATTGATATACCCC
1 AAATGATCGAAATACCCC
30981172 TAGGAGATGA
Statistics
Matches: 168, Mismatches: 33, Indels: 8
0.80 0.16 0.04
Matches are distributed among these distances:
25 1 0.01
26 42 0.25
27 125 0.74
ACGTcount: A:0.43, C:0.19, G:0.16, T:0.22
Consensus pattern (27 bp):
AAATGATCGAAATACCCCCATAGGGTA
Found at i:30981357 original size:26 final size:26
Alignment explanation
Indices: 30981319--30981399 Score: 117
Period size: 26 Copynumber: 3.1 Consensus size: 26
30981309 TGGAGGAAGT
* *
30981319 ATACTATTTCTGGTAGCTTTGCTGCG
1 ATACTATTACTGGAAGCTTTGCTGCG
* *
30981345 ATACTGTTACTGGAAGCTTTGTTGCG
1 ATACTATTACTGGAAGCTTTGCTGCG
*
30981371 ATACTATTACTGGCAGCTTTGCTGCG
1 ATACTATTACTGGAAGCTTTGCTGCG
30981397 ATA
1 ATA
30981400 TTGGTGTGTT
Statistics
Matches: 48, Mismatches: 7, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
26 48 1.00
ACGTcount: A:0.20, C:0.19, G:0.23, T:0.38
Consensus pattern (26 bp):
ATACTATTACTGGAAGCTTTGCTGCG
Found at i:30981551 original size:28 final size:27
Alignment explanation
Indices: 30981510--30981580 Score: 90
Period size: 28 Copynumber: 2.6 Consensus size: 27
30981500 GTACTAATTT
*
30981510 TGTACTGGGCTAAGGCCCACACTGTTAC
1 TGTACTGGGATAAGGCCCACACTG-TAC
*
30981538 TGTATTGGGATAAGGCCCACACTGTAC
1 TGTACTGGGATAAGGCCCACACTGTAC
*
30981565 TGTTACT-GAATAAGGC
1 TG-TACTGGGATAAGGC
30981581 TCGAGCCTAG
Statistics
Matches: 38, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
27 13 0.34
28 25 0.66
ACGTcount: A:0.25, C:0.23, G:0.25, T:0.27
Consensus pattern (27 bp):
TGTACTGGGATAAGGCCCACACTGTAC
Found at i:30986815 original size:15 final size:15
Alignment explanation
Indices: 30986795--30986825 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
30986785 TACTAGGTCG
30986795 TGTAACTACCTGACT
1 TGTAACTACCTGACT
30986810 TGTAACTACCTGACT
1 TGTAACTACCTGACT
30986825 T
1 T
30986826 ACAACTAATA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.26, C:0.26, G:0.13, T:0.35
Consensus pattern (15 bp):
TGTAACTACCTGACT
Found at i:30986831 original size:15 final size:15
Alignment explanation
Indices: 30986798--30986832 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
30986788 TAGGTCGTGT
**
30986798 AACTACCTGACTTGT
1 AACTACCTGACTTAC
30986813 AACTACCTGACTTAC
1 AACTACCTGACTTAC
30986828 AACTA
1 AACTA
30986833 ATATGCCCAA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.34, C:0.29, G:0.09, T:0.29
Consensus pattern (15 bp):
AACTACCTGACTTAC
Found at i:30987845 original size:20 final size:19
Alignment explanation
Indices: 30987818--30987859 Score: 59
Period size: 20 Copynumber: 2.2 Consensus size: 19
30987808 CTTTCAAAAT
30987818 TTTCTTACTTT-CATTTGCA
1 TTTCTTACTTTCCA-TTGCA
30987837 TTTCATTACTTTCCATTGCA
1 TTTC-TTACTTTCCATTGCA
30987857 TTT
1 TTT
30987860 ACTTTCTTTA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
19 4 0.19
20 15 0.71
21 2 0.10
ACGTcount: A:0.17, C:0.21, G:0.05, T:0.57
Consensus pattern (19 bp):
TTTCTTACTTTCCATTGCA
Found at i:30992882 original size:23 final size:23
Alignment explanation
Indices: 30992850--30992900 Score: 68
Period size: 23 Copynumber: 2.3 Consensus size: 23
30992840 GCATATACTC
* * *
30992850 TTGAG-ATGATAACTCTAATGGT
1 TTGAGTATGATAACTATAACGAT
30992872 TTGAGTATGATAACTATAACGAT
1 TTGAGTATGATAACTATAACGAT
30992895 TTGAGT
1 TTGAGT
30992901 GGAACTTCTT
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
22 5 0.20
23 20 0.80
ACGTcount: A:0.33, C:0.08, G:0.22, T:0.37
Consensus pattern (23 bp):
TTGAGTATGATAACTATAACGAT
Found at i:30997514 original size:21 final size:19
Alignment explanation
Indices: 30997489--30997527 Score: 51
Period size: 19 Copynumber: 1.9 Consensus size: 19
30997479 TGTGCCATAT
30997489 TACATTCGTATATAATATTTG
1 TACATTCG-AT-TAATATTTG
*
30997510 TACATTTGATTAATATTT
1 TACATTCGATTAATATTT
30997528 AAGGTCTATG
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 8 0.47
20 2 0.12
21 7 0.41
ACGTcount: A:0.33, C:0.08, G:0.08, T:0.51
Consensus pattern (19 bp):
TACATTCGATTAATATTTG
Found at i:30999783 original size:21 final size:21
Alignment explanation
Indices: 30999744--30999783 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
30999734 TTTTGCTTGG
*
30999744 TTTAATAAGTTTTTCTTAAGA
1 TTTAATAAATTTTTCTTAAGA
30999765 TTTAATAAATTATTT-TTAA
1 TTTAATAAATT-TTTCTTAA
30999784 TTGGACTGTA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
21 14 0.82
22 3 0.18
ACGTcount: A:0.38, C:0.03, G:0.05, T:0.55
Consensus pattern (21 bp):
TTTAATAAATTTTTCTTAAGA
Found at i:31001109 original size:18 final size:17
Alignment explanation
Indices: 31001075--31001115 Score: 55
Period size: 18 Copynumber: 2.3 Consensus size: 17
31001065 AAGGCTATTT
*
31001075 TGGGTCGTGTAGGCCACA
1 TGGG-CGTGTAGCCCACA
31001093 TGGGCGTGTGAGCCCACA
1 TGGGCGTGT-AGCCCACA
31001111 TGGGC
1 TGGGC
31001116 ATGCAACATG
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
17 5 0.24
18 16 0.76
ACGTcount: A:0.15, C:0.24, G:0.41, T:0.20
Consensus pattern (17 bp):
TGGGCGTGTAGCCCACA
Found at i:31003760 original size:19 final size:19
Alignment explanation
Indices: 31003718--31003754 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
31003708 CTAAAATAAT
* *
31003718 TAATTTAAATTTTACTTGA
1 TAATTAAAATTTTAATTGA
31003737 TAATTAAAATTTTAATTG
1 TAATTAAAATTTTAATTG
31003755 GAAATTGTTT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.41, C:0.03, G:0.05, T:0.51
Consensus pattern (19 bp):
TAATTAAAATTTTAATTGA
Found at i:31008659 original size:19 final size:19
Alignment explanation
Indices: 31008637--31008703 Score: 62
Period size: 19 Copynumber: 3.3 Consensus size: 19
31008627 TTCCTCAATG
31008637 AATATGTTATTAATGCTTT
1 AATATGTTATTAATGCTTT
* * * *
31008656 AATATGCTATATATTCCTCAATG
1 AATATGTTAT-TAATGCT---TT
31008679 AATATGTTATTAATGCTTT
1 AATATGTTATTAATGCTTT
31008698 AATATG
1 AATATG
31008704 CTATCTGTTT
Statistics
Matches: 36, Mismatches: 8, Indels: 8
0.69 0.15 0.15
Matches are distributed among these distances:
19 16 0.44
20 5 0.14
22 5 0.14
23 10 0.28
ACGTcount: A:0.34, C:0.09, G:0.10, T:0.46
Consensus pattern (19 bp):
AATATGTTATTAATGCTTT
Found at i:31008671 original size:42 final size:42
Alignment explanation
Indices: 31008623--31008707 Score: 170
Period size: 42 Copynumber: 2.0 Consensus size: 42
31008613 GAAGTAACAC
31008623 TATATTCCTCAATGAATATGTTATTAATGCTTTAATATGCTA
1 TATATTCCTCAATGAATATGTTATTAATGCTTTAATATGCTA
31008665 TATATTCCTCAATGAATATGTTATTAATGCTTTAATATGCTA
1 TATATTCCTCAATGAATATGTTATTAATGCTTTAATATGCTA
31008707 T
1 T
31008708 CTGTTTTTAA
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
42 43 1.00
ACGTcount: A:0.33, C:0.12, G:0.09, T:0.46
Consensus pattern (42 bp):
TATATTCCTCAATGAATATGTTATTAATGCTTTAATATGCTA
Found at i:31008682 original size:23 final size:23
Alignment explanation
Indices: 31008623--31008684 Score: 60
Period size: 19 Copynumber: 2.9 Consensus size: 23
31008613 GAAGTAACAC
*
31008623 TATATTCCTCAATGAATATGTTA
1 TATATTCCTCAATGAATATGCTA
* * *
31008646 T-TAATGCT---TTAATATGCTA
1 TATATTCCTCAATGAATATGCTA
31008665 TATATTCCTCAATGAATATG
1 TATATTCCTCAATGAATATG
31008685 TTATTAATGC
Statistics
Matches: 28, Mismatches: 7, Indels: 8
0.65 0.16 0.19
Matches are distributed among these distances:
19 10 0.36
20 5 0.18
22 5 0.18
23 8 0.29
ACGTcount: A:0.34, C:0.13, G:0.10, T:0.44
Consensus pattern (23 bp):
TATATTCCTCAATGAATATGCTA
Found at i:31017700 original size:23 final size:23
Alignment explanation
Indices: 31017673--31017771 Score: 162
Period size: 23 Copynumber: 4.3 Consensus size: 23
31017663 AGTGTTATTG
31017673 ATCAGTGGTAGCTTCGGCTACAT
1 ATCAGTGGTAGCTTCGGCTACAT
*
31017696 TTCAGTGGTAGCTTCGGCTACAT
1 ATCAGTGGTAGCTTCGGCTACAT
* * *
31017719 TTCAGTGGTAGCTACGGCTACGT
1 ATCAGTGGTAGCTTCGGCTACAT
31017742 ATCAGTGGTAGCTTCGGCTACAT
1 ATCAGTGGTAGCTTCGGCTACAT
31017765 ATCAGTG
1 ATCAGTG
31017772 TGGCACTTAT
Statistics
Matches: 70, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
23 70 1.00
ACGTcount: A:0.20, C:0.21, G:0.27, T:0.31
Consensus pattern (23 bp):
ATCAGTGGTAGCTTCGGCTACAT
Found at i:31022247 original size:24 final size:26
Alignment explanation
Indices: 31022217--31022268 Score: 70
Period size: 26 Copynumber: 2.0 Consensus size: 26
31022207 TTTATTTTTA
*
31022217 TAATAATATTAAATTTT-AATAAAATAG
1 TAATAATA--AAATTTTGAAAAAAATAG
31022244 TAATAATAAAATTTTGAAAAAAATA
1 TAATAATAAAATTTTGAAAAAAATA
31022269 CAAAAAATAT
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
25 7 0.30
26 8 0.35
27 8 0.35
ACGTcount: A:0.60, C:0.00, G:0.04, T:0.37
Consensus pattern (26 bp):
TAATAATAAAATTTTGAAAAAAATAG
Found at i:31023008 original size:19 final size:19
Alignment explanation
Indices: 31022963--31023001 Score: 55
Period size: 19 Copynumber: 2.1 Consensus size: 19
31022953 TTGTCGAAAT
31022963 AGAAGAGAAAAATAGGAGAA
1 AGAA-AGAAAAATAGGAGAA
31022983 AGAAAGAAAAA-AGGA-AA
1 AGAAAGAAAAATAGGAGAA
31023000 AG
1 AG
31023002 GAAAAGAGAG
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
17 4 0.21
18 4 0.21
19 7 0.37
20 4 0.21
ACGTcount: A:0.69, C:0.00, G:0.28, T:0.03
Consensus pattern (19 bp):
AGAAAGAAAAATAGGAGAA
Found at i:31023019 original size:13 final size:12
Alignment explanation
Indices: 31022983--31023029 Score: 51
Period size: 12 Copynumber: 3.8 Consensus size: 12
31022973 AATAGGAGAA
31022983 AGAAAGAAAAAAG
1 AGAAA-AAAAAAG
*
31022996 -GAAAAGGAAAAG
1 AGAAAA-AAAAAG
31023008 AGAGAAAAAAAAG
1 AGA-AAAAAAAAG
31023021 AGAAAAAAA
1 AGAAAAAAA
31023030 GAGTAGATGA
Statistics
Matches: 29, Mismatches: 2, Indels: 7
0.76 0.05 0.18
Matches are distributed among these distances:
11 1 0.03
12 15 0.52
13 10 0.34
14 3 0.10
ACGTcount: A:0.77, C:0.00, G:0.23, T:0.00
Consensus pattern (12 bp):
AGAAAAAAAAAG
Found at i:31023155 original size:6 final size:6
Alignment explanation
Indices: 31023146--31023194 Score: 55
Period size: 6 Copynumber: 7.8 Consensus size: 6
31023136 AAAGAAAGAA
*
31023146 AAAAAT AAAAAT AAAAAT AGAAAAT AAAAA- AAAAGAA AAAAATT AAAAA
1 AAAAAT AAAAAT AAAAAT A-AAAAT AAAAAT AAAA-AT AAAAA-T AAAAA
31023195 ACTTAATTAG
Statistics
Matches: 38, Mismatches: 1, Indels: 7
0.83 0.02 0.15
Matches are distributed among these distances:
5 4 0.11
6 19 0.50
7 15 0.39
ACGTcount: A:0.84, C:0.00, G:0.04, T:0.12
Consensus pattern (6 bp):
AAAAAT
Found at i:31023193 original size:15 final size:15
Alignment explanation
Indices: 31023133--31023195 Score: 58
Period size: 16 Copynumber: 4.1 Consensus size: 15
31023123 GAAGAAGAAG
* *
31023133 AAGAAAGAAAGAAAA
1 AAGAAAAAAATAAAA
*
31023148 AA-ATAAAAATAAAA
1 AAGAAAAAAATAAAA
31023162 ATAGAAAATAAA-AAAA
1 A-AGAAAA-AAATAAAA
31023178 AAGAAAAAAATTAAAA
1 AAGAAAAAAA-TAAAA
31023194 AA
1 AA
31023196 CTTAATTAGA
Statistics
Matches: 39, Mismatches: 4, Indels: 9
0.75 0.08 0.17
Matches are distributed among these distances:
14 13 0.33
15 9 0.23
16 14 0.36
17 3 0.08
ACGTcount: A:0.83, C:0.00, G:0.08, T:0.10
Consensus pattern (15 bp):
AAGAAAAAAATAAAA
Found at i:31023495 original size:75 final size:75
Alignment explanation
Indices: 31023363--31023509 Score: 181
Period size: 75 Copynumber: 2.0 Consensus size: 75
31023353 ACCCAACAGG
* * * * *
31023363 CCCAGCAGCAGCATAGCAGGCCGTCCAACAGTCAGGCCCAGCGTGCGGCTTCGAGCAGCCCAGCA
1 CCCAGCAGCAGCATAGCAGGCCATCCAACAGCCAGGCCCAGCGTGCAGCTGCCAGCAGCCCAGCA
31023428 CCCAGGCAGC
66 CCCAGGCAGC
* * *
31023438 CCCAGCAGCAGCATAGCAGGCCCAT-CAACAGCCAGGCCTAGCGTGTAG-TAGCCAGCAGGCCAG
1 CCCAGCAGCAGCATAGCAGG-CCATCCAACAGCCAGGCCCAGCGTGCAGCT-GCCAGCAGCCCAG
*
31023501 CATCCAGGC
64 CACCCAGGC
31023510 CTAGCGCTCA
Statistics
Matches: 61, Mismatches: 9, Indels: 4
0.82 0.12 0.05
Matches are distributed among these distances:
74 1 0.02
75 57 0.93
76 3 0.05
ACGTcount: A:0.24, C:0.38, G:0.29, T:0.09
Consensus pattern (75 bp):
CCCAGCAGCAGCATAGCAGGCCATCCAACAGCCAGGCCCAGCGTGCAGCTGCCAGCAGCCCAGCA
CCCAGGCAGC
Found at i:31023583 original size:16 final size:16
Alignment explanation
Indices: 31023533--31023584 Score: 54
Period size: 15 Copynumber: 3.4 Consensus size: 16
31023523 GGTCCAACTG
*
31023533 CAAAAA-AAAAAGGAA
1 CAAAAAGAAAAAGAAA
* *
31023548 CAAAAGGAAAAA-AGA
1 CAAAAAGAAAAAGAAA
*
31023563 GAAAAAGAAAAAGAAA
1 CAAAAAGAAAAAGAAA
31023579 CAAAAA
1 CAAAAA
31023585 ATGCTCGAAT
Statistics
Matches: 28, Mismatches: 7, Indels: 3
0.74 0.18 0.08
Matches are distributed among these distances:
15 16 0.57
16 12 0.43
ACGTcount: A:0.79, C:0.06, G:0.15, T:0.00
Consensus pattern (16 bp):
CAAAAAGAAAAAGAAA
Found at i:31023912 original size:21 final size:22
Alignment explanation
Indices: 31023888--31023932 Score: 65
Period size: 21 Copynumber: 2.1 Consensus size: 22
31023878 AAATAGAAAA
*
31023888 TTAAAAAAAAACTCGTTT-TTT
1 TTAAAAAAAAACACGTTTATTT
*
31023909 TTAAAAAATAACACGTTTATTT
1 TTAAAAAAAAACACGTTTATTT
31023931 TT
1 TT
31023933 TGTGATTATT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
21 16 0.76
22 5 0.24
ACGTcount: A:0.42, C:0.09, G:0.04, T:0.44
Consensus pattern (22 bp):
TTAAAAAAAAACACGTTTATTT
Found at i:31024015 original size:17 final size:17
Alignment explanation
Indices: 31023993--31024204 Score: 133
Period size: 18 Copynumber: 11.4 Consensus size: 17
31023983 AAGTAATTTA
* *
31023993 TCAAAAATTTCTTTTTT
1 TCAAAAATTTCTGTGTT
31024010 TCAAAAAAATTTC-GTGTT
1 TC--AAAAATTTCTGTGTT
*
31024028 TCAAAAATTTTTGTGTT
1 TCAAAAATTTCTGTGTT
*
31024045 TCAAAAAAATTCTCGTGTT
1 TC-AAAAATTTCT-GTGTT
* *
31024064 TAAAAAATTTTCGTGTTTT
1 TCAAAAA-TTTC-TGTGTT
31024083 TCAAAAATTT-TCGTGTT
1 TCAAAAATTTCT-GTGTT
*
31024100 TCAAAATTTTCGTGTTTTTGTGTTT
1 TCAAAAATTTC-------TGTG-TT
*
31024125 TCAAAAAATTCTCGTGTT
1 TCAAAAATTTCT-GTGTT
*
31024143 TCAAAAATTTTTGTGTT
1 TCAAAAATTTCTGTGTT
31024160 TCAAAAAAATTTCTCGTGTT
1 TC--AAAAATTTCT-GTGTT
31024180 TCAAAAATTT-TCGTGTTT
1 TCAAAAATTTCT-GTG-TT
31024198 TCAAAAA
1 TCAAAAA
31024205 AATTATGGTA
Statistics
Matches: 157, Mismatches: 16, Indels: 43
0.73 0.07 0.20
Matches are distributed among these distances:
16 9 0.06
17 34 0.22
18 51 0.32
19 40 0.25
20 8 0.05
24 3 0.02
25 12 0.08
ACGTcount: A:0.32, C:0.11, G:0.10, T:0.47
Consensus pattern (17 bp):
TCAAAAATTTCTGTGTT
Found at i:31024062 original size:19 final size:18
Alignment explanation
Indices: 31024008--31024205 Score: 176
Period size: 17 Copynumber: 11.6 Consensus size: 18
31023998 AATTTCTTTT
*
31024008 TTTCAAAAAAATTTCGTG
1 TTTCAAAAAATTTTCGTG
*
31024026 TTTC-AAAAATTTTTGTG
1 TTTCAAAAAATTTTCGTG
*
31024043 TTTCAAAAAAATTCTCGTG
1 TTTC-AAAAAATTTTCGTG
31024062 TTT-AAAAAATTTTCGTG
1 TTTCAAAAAATTTTCGTG
31024079 TTTTTC-AAAAATTTTCGTG
1 --TTTCAAAAAATTTTCGTG
31024098 TTTC--AAAATTTTCGTG
1 TTTCAAAAAATTTTCGTG
*
31024114 TTT-------TTGT-GT-
1 TTTCAAAAAATTTTCGTG
*
31024123 TTTCAAAAAATTCTCGTG
1 TTTCAAAAAATTTTCGTG
*
31024141 TTTC-AAAAATTTTTGTG
1 TTTCAAAAAATTTTCGTG
31024158 TTTCAAAAAAATTTCTCGTG
1 TTTC-AAAAAATTT-TCGTG
31024178 TTTC-AAAAATTTTCGTG
1 TTTCAAAAAATTTTCGTG
31024195 TTTTCAAAAAA
1 -TTTCAAAAAA
31024206 ATTATGGTAT
Statistics
Matches: 151, Mismatches: 10, Indels: 37
0.76 0.05 0.19
Matches are distributed among these distances:
9 3 0.02
10 2 0.01
11 3 0.02
16 18 0.12
17 54 0.36
18 20 0.13
19 43 0.28
20 8 0.05
ACGTcount: A:0.32, C:0.11, G:0.11, T:0.46
Consensus pattern (18 bp):
TTTCAAAAAATTTTCGTG
Found at i:31024124 original size:43 final size:44
Alignment explanation
Indices: 31024071--31024199 Score: 136
Period size: 43 Copynumber: 3.1 Consensus size: 44
31024061 GTTTAAAAAA
*
31024071 TTTTCGTGTTTTTC-AAAAATTTTCGTGTTTC-AAAATTTTCGTG
1 TTTTCGTG-TTTTCAAAAAATTCTCGTGTTTCAAAAATTTTCGTG
*
31024114 TTTTTGTGTTTTCAAAAAATTCTCGTGTTTCAAAAA------T-
1 TTTTCGTGTTTTCAAAAAATTCTCGTGTTTCAAAAATTTTCGTG
31024151 TTTT-GTG-TTTCAAAAAAATTTCTCGTGTTTCAAAAATTTTCGTG
1 TTTTCGTGTTTTC-AAAAAA-TTCTCGTGTTTCAAAAATTTTCGTG
31024195 TTTTC
1 TTTTC
31024200 AAAAAAATTA
Statistics
Matches: 72, Mismatches: 2, Indels: 22
0.75 0.02 0.23
Matches are distributed among these distances:
35 4 0.06
36 9 0.12
37 21 0.29
38 1 0.01
42 5 0.07
43 24 0.33
44 8 0.11
ACGTcount: A:0.25, C:0.12, G:0.12, T:0.51
Consensus pattern (44 bp):
TTTTCGTGTTTTCAAAAAATTCTCGTGTTTCAAAAATTTTCGTG
Found at i:31024124 original size:79 final size:81
Alignment explanation
Indices: 31024035--31024198 Score: 253
Period size: 79 Copynumber: 2.0 Consensus size: 81
31024025 GTTTCAAAAA
***
31024035 TTTTTGTG-TTTCAAAAAAATTCTCGTGTTTAAAAAATTTTCGTGTTTTTCAAAAATTT-TCGTG
1 TTTTTGTGTTTTC-AAAAAATTCTCGTGTTTAAAAAATTTTCGTGTTTCAAAAAAATTTCTCGTG
31024098 TTTC-AAAATTTTCGTG
65 TTTCAAAAATTTTCGTG
* *
31024114 TTTTTGTGTTTTCAAAAAATTCTCGTGTTTCAAAAATTTTTGTGTTTCAAAAAAATTTCTCGTGT
1 TTTTTGTGTTTTCAAAAAATTCTCGTGTTTAAAAAATTTTCGTGTTTCAAAAAAATTTCTCGTGT
31024179 TTCAAAAATTTTCGTG
66 TTCAAAAATTTTCGTG
31024195 TTTT
1 TTTT
31024199 CAAAAAAATT
Statistics
Matches: 77, Mismatches: 5, Indels: 4
0.90 0.06 0.05
Matches are distributed among these distances:
79 48 0.62
80 13 0.17
81 16 0.21
ACGTcount: A:0.27, C:0.10, G:0.12, T:0.50
Consensus pattern (81 bp):
TTTTTGTGTTTTCAAAAAATTCTCGTGTTTAAAAAATTTTCGTGTTTCAAAAAAATTTCTCGTGT
TTCAAAAATTTTCGTG
Found at i:31024219 original size:37 final size:37
Alignment explanation
Indices: 31024114--31024255 Score: 150
Period size: 37 Copynumber: 3.9 Consensus size: 37
31024104 AATTTTCGTG
*
31024114 TTTTTGTGTTTTC-AAAAAATTCTCGTGTTTCAAAAA
1 TTTTCGTGTTTTCAAAAAAATTCTCGTGTTTCAAAAA
*
31024150 TTTTTGTG-TTTCAAAAAAATTTCTCGTGTTTCAAAAA
1 TTTTCGTGTTTTCAAAAAAA-TTCTCGTGTTTCAAAAA
* * *
31024187 TTTTCGTGTTTTCAAAAAAATTATGGTATTTC-AAAA
1 TTTTCGTGTTTTCAAAAAAATTCTCGTGTTTCAAAAA
* * * *
31024223 TTCTCTTGTTTT-AAAACAAA-ACTAGTGTTTCAA
1 TTTTCGTGTTTTCAAAA-AAATTCTCGTGTTTCAA
31024256 TCGAATCACG
Statistics
Matches: 91, Mismatches: 10, Indels: 10
0.82 0.09 0.09
Matches are distributed among these distances:
35 15 0.16
36 32 0.35
37 33 0.36
38 11 0.12
ACGTcount: A:0.33, C:0.11, G:0.11, T:0.45
Consensus pattern (37 bp):
TTTTCGTGTTTTCAAAAAAATTCTCGTGTTTCAAAAA
Found at i:31024223 original size:36 final size:37
Alignment explanation
Indices: 31023993--31024255 Score: 233
Period size: 36 Copynumber: 7.1 Consensus size: 37
31023983 AAGTAATTTA
* *
31023993 TCAAAAA-TTTCTTTTTTTCAAAAAAATT-TCGTGTT
1 TCAAAAATTTTCGTGTTTTCAAAAAAATTCTCGTGTT
*
31024028 TCAAAAATTTTTGTG-TTTCAAAAAAATTCTCGTGTT
1 TCAAAAATTTTCGTGTTTTCAAAAAAATTCTCGTGTT
* *
31024064 TAAAAAATTTTCGTGTTTTTC--AAAAATTTTCGTGTT
1 TCAAAAATTTTCGTG-TTTTCAAAAAAATTCTCGTGTT
31024100 TC-AAAATTTTCGTGTTTTTGTGTTTTC-AAAAAATTCTCGTGTT
1 TCAAAAATTTTC--------GTGTTTTCAAAAAAATTCTCGTGTT
*
31024143 TCAAAAATTTTTGTG-TTTCAAAAAAATTTCTCGTGTT
1 TCAAAAATTTTCGTGTTTTCAAAAAAA-TTCTCGTGTT
* * *
31024180 TCAAAAATTTTCGTGTTTTCAAAAAAATTATGGTATT
1 TCAAAAATTTTCGTGTTTTCAAAAAAATTCTCGTGTT
* * * *
31024217 TC-AAAATTCTCTTGTTTT-AAAACAAA-ACTAGTGTT
1 TCAAAAATTTTCGTGTTTTCAAAA-AAATTCTCGTGTT
31024252 TCAA
1 TCAA
31024256 TCGAATCACG
Statistics
Matches: 190, Mismatches: 19, Indels: 37
0.77 0.08 0.15
Matches are distributed among these distances:
35 44 0.23
36 66 0.35
37 33 0.17
38 15 0.08
42 5 0.03
43 19 0.10
44 8 0.04
ACGTcount: A:0.33, C:0.11, G:0.10, T:0.46
Consensus pattern (37 bp):
TCAAAAATTTTCGTGTTTTCAAAAAAATTCTCGTGTT
Found at i:31024680 original size:9 final size:9
Alignment explanation
Indices: 31024666--31024691 Score: 52
Period size: 9 Copynumber: 2.9 Consensus size: 9
31024656 ACGCGCATTG
31024666 TCAAAATTC
1 TCAAAATTC
31024675 TCAAAATTC
1 TCAAAATTC
31024684 TCAAAATT
1 TCAAAATT
31024692 TCTTGTTCAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 17 1.00
ACGTcount: A:0.46, C:0.19, G:0.00, T:0.35
Consensus pattern (9 bp):
TCAAAATTC
Found at i:31032057 original size:35 final size:35
Alignment explanation
Indices: 31032006--31032091 Score: 106
Period size: 35 Copynumber: 2.5 Consensus size: 35
31031996 TCAAAATAGA
* *
31032006 AGAGAAAGAGAGGAGAAAAAAAGAA-AA-AGGAAAGG
1 AGAGAAAGAAAAGAGAAAAAAA-AAGAAGAGG-AAGG
31032041 AGAGAAAGAAAAGAGAAAAAAAAAGAAGAGGAAGG
1 AGAGAAAGAAAAGAGAAAAAAAAAGAAGAGGAAGG
*
31032076 A-AGAGAGAAAAGAGAA
1 AGAGAAAGAAAAGAGAA
31032092 GAGGAGAGAC
Statistics
Matches: 46, Mismatches: 3, Indels: 5
0.85 0.06 0.09
Matches are distributed among these distances:
34 16 0.35
35 27 0.59
36 3 0.07
ACGTcount: A:0.67, C:0.00, G:0.33, T:0.00
Consensus pattern (35 bp):
AGAGAAAGAAAAGAGAAAAAAAAAGAAGAGGAAGG
Found at i:31032076 original size:40 final size:35
Alignment explanation
Indices: 31032003--31032094 Score: 85
Period size: 39 Copynumber: 2.4 Consensus size: 35
31031993 TTGTCAAAAT
*
31032003 AGAAGAGAAAGAGAGGAGAAAAAAAGAAAAAGGAAAGGAG
1 AGAA-AGAAA-AGA-GAAAAAAAAAGAAAAAGG-AA-GAG
31032043 AGAAAGAAAAGAGAAAAAAAAAGAAGAGGAAGGAAGAG
1 AGAAAGAAAAGAGAAAAAAAAAGAA-A--AAGGAAGAG
*
31032081 AGAAAAGAGAAGAG
1 AG-AAAGAAAAGAG
31032095 GAGAGACCGG
Statistics
Matches: 46, Mismatches: 2, Indels: 9
0.81 0.04 0.16
Matches are distributed among these distances:
37 12 0.26
38 9 0.20
39 17 0.37
40 8 0.17
ACGTcount: A:0.66, C:0.00, G:0.34, T:0.00
Consensus pattern (35 bp):
AGAAAGAAAAGAGAAAAAAAAAGAAAAAGGAAGAG
Found at i:31032554 original size:9 final size:8
Alignment explanation
Indices: 31032531--31032576 Score: 51
Period size: 9 Copynumber: 5.8 Consensus size: 8
31032521 CAACTACAAA
*
31032531 AAAAAAAG
1 AAAAAAGG
31032539 AGAAAAAGG
1 A-AAAAAGG
31032548 AAGAAAAGG
1 AA-AAAAGG
31032557 AAAAAA-G
1 AAAAAAGG
31032564 AAAAAA-G
1 AAAAAAGG
31032571 AAAAAA
1 AAAAAA
31032577 AAAACAAAAA
Statistics
Matches: 35, Mismatches: 1, Indels: 5
0.85 0.02 0.12
Matches are distributed among these distances:
7 14 0.40
8 6 0.17
9 15 0.43
ACGTcount: A:0.80, C:0.00, G:0.20, T:0.00
Consensus pattern (8 bp):
AAAAAAGG
Found at i:31032560 original size:23 final size:23
Alignment explanation
Indices: 31032532--31032577 Score: 65
Period size: 25 Copynumber: 1.9 Consensus size: 23
31032522 AACTACAAAA
*
31032532 AAAAAAGAGAAAAAGGAAGAAAAGG
1 AAAAAAGA-AAAAA-GAAAAAAAGG
31032557 AAAAAAGAAAAAAGAAAAAAA
1 AAAAAAGAAAAAAGAAAAAAA
31032578 AAACAAAAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
23 7 0.35
24 5 0.25
25 8 0.40
ACGTcount: A:0.80, C:0.00, G:0.20, T:0.00
Consensus pattern (23 bp):
AAAAAAGAAAAAAGAAAAAAAGG
Found at i:31032576 original size:7 final size:7
Alignment explanation
Indices: 31032528--31032580 Score: 56
Period size: 7 Copynumber: 7.6 Consensus size: 7
31032518 GTCCAACTAC
31032528 AAAAAA-
1 AAAAAAG
*
31032534 AAAAGAG
1 AAAAAAG
*
31032541 AAAAAGG
1 AAAAAAG
31032548 AAGAAAAGG
1 AA-AAAA-G
31032557 AAAAAAG
1 AAAAAAG
31032564 AAAAAAG
1 AAAAAAG
31032571 AAAAAA-
1 AAAAAAG
31032577 AAAA
1 AAAA
31032581 CAAAAAAGCC
Statistics
Matches: 40, Mismatches: 4, Indels: 6
0.80 0.08 0.12
Matches are distributed among these distances:
6 9 0.22
7 21 0.52
8 7 0.17
9 3 0.08
ACGTcount: A:0.83, C:0.00, G:0.17, T:0.00
Consensus pattern (7 bp):
AAAAAAG
Found at i:31032579 original size:25 final size:25
Alignment explanation
Indices: 31032528--31032588 Score: 63
Period size: 25 Copynumber: 2.5 Consensus size: 25
31032518 GTCCAACTAC
* *
31032528 AAAA-AAAAAAGAGAAAAAGGAAGA
1 AAAACAAAAAAGAGAAAAAGAAAAA
**
31032552 AAAGGAAAAAAGA-AAAAAGAAAAAA
1 AAAACAAAAAAGAGAAAAAG-AAAAA
31032577 AAAACAAAAAAG
1 AAAACAAAAAAG
31032589 CCCCGAATTG
Statistics
Matches: 30, Mismatches: 5, Indels: 3
0.79 0.13 0.08
Matches are distributed among these distances:
24 9 0.30
25 21 0.70
ACGTcount: A:0.82, C:0.02, G:0.16, T:0.00
Consensus pattern (25 bp):
AAAACAAAAAAGAGAAAAAGAAAAA
Found at i:31032585 original size:23 final size:23
Alignment explanation
Indices: 31032528--31032586 Score: 64
Period size: 23 Copynumber: 2.5 Consensus size: 23
31032518 GTCCAACTAC
* *
31032528 AAAAAAAAAAGAGAAAAAGGAAG
1 AAAAAAAAAAAAGAAAAAAGAAG
** *
31032551 AAAAGGAAAAAAGAAAAAAGAAA
1 AAAAAAAAAAAAGAAAAAAGAAG
31032574 AAAAAAACAAAAA
1 AAAAAAA-AAAAA
31032587 AGCCCCGAAT
Statistics
Matches: 28, Mismatches: 7, Indels: 1
0.78 0.19 0.03
Matches are distributed among these distances:
23 23 0.82
24 5 0.18
ACGTcount: A:0.83, C:0.02, G:0.15, T:0.00
Consensus pattern (23 bp):
AAAAAAAAAAAAGAAAAAAGAAG
Found at i:31032763 original size:29 final size:29
Alignment explanation
Indices: 31032731--31032788 Score: 73
Period size: 29 Copynumber: 2.0 Consensus size: 29
31032721 TACTAATAAA
* *
31032731 GCCCTTTTTTTCAA-AATTTATCGAAATGG
1 GCCCATTTTTT-AATAATTTACCGAAATGG
*
31032760 GCCCATTTTTTAATTATTTACCGAAATGG
1 GCCCATTTTTTAATAATTTACCGAAATGG
31032789 ATCTTTTTCC
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
28 2 0.08
29 23 0.92
ACGTcount: A:0.28, C:0.17, G:0.14, T:0.41
Consensus pattern (29 bp):
GCCCATTTTTTAATAATTTACCGAAATGG
Found at i:31033181 original size:23 final size:23
Alignment explanation
Indices: 31033151--31033204 Score: 99
Period size: 23 Copynumber: 2.3 Consensus size: 23
31033141 TTTGACGTTT
31033151 TTGAGCAAATAGTATAAAATCGC
1 TTGAGCAAATAGTATAAAATCGC
31033174 TTGAGCAAATAGTATAAAATCGC
1 TTGAGCAAATAGTATAAAATCGC
31033197 TTGTAGCA
1 TTG-AGCA
31033205 GGATGCTATT
Statistics
Matches: 30, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
23 26 0.87
24 4 0.13
ACGTcount: A:0.41, C:0.13, G:0.19, T:0.28
Consensus pattern (23 bp):
TTGAGCAAATAGTATAAAATCGC
Found at i:31033300 original size:149 final size:150
Alignment explanation
Indices: 31033030--31033330 Score: 541
Period size: 149 Copynumber: 2.0 Consensus size: 150
31033020 CGTTTCTGAT
31033030 CAAATAGTATAAAATCGCTTCTAGCAGGATGCTATTTGAGAAGAATTTATGAAATCGCGCCCTCG
1 CAAATAGTATAAAATCGCTTCTAGCAGGATGCTATTTGAGAAGAATTTATGAAATCGCGCCCTCG
*
31033095 TGGACGCGCTTTTGCTACAGTAGGTCACGGAAGAAATAATTATTTTTTTGACGTTTTTGAGCAAA
66 TGGACGCGCTTTTGCTACAGTAGGTCACGAAAGAAATAATTATTTTTTTGACGTTTTTGAGCAAA
31033160 TAGTATAAAATCGCTTG-AG
131 TAGTATAAAATCGCTTGTAG
* * * *
31033179 CAAATAGTATAAAATCGCTTGTAGCAGGATGCTATTTGAGAAGAATTTGTGATATCGCGCTCTCG
1 CAAATAGTATAAAATCGCTTCTAGCAGGATGCTATTTGAGAAGAATTTATGAAATCGCGCCCTCG
*
31033244 TGGACGCGCTTTTGCTACAGTAGGTCCCGAAAGAAATAATTATTTTTTTGACGTTTTTGAGCAAA
66 TGGACGCGCTTTTGCTACAGTAGGTCACGAAAGAAATAATTATTTTTTTGACGTTTTTGAGCAAA
31033309 TAGTATAAAATCGCTTGTAG
131 TAGTATAAAATCGCTTGTAG
31033329 CA
1 CA
31033331 GGATGCTATT
Statistics
Matches: 145, Mismatches: 6, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
149 141 0.97
150 4 0.03
ACGTcount: A:0.31, C:0.15, G:0.22, T:0.32
Consensus pattern (150 bp):
CAAATAGTATAAAATCGCTTCTAGCAGGATGCTATTTGAGAAGAATTTATGAAATCGCGCCCTCG
TGGACGCGCTTTTGCTACAGTAGGTCACGAAAGAAATAATTATTTTTTTGACGTTTTTGAGCAAA
TAGTATAAAATCGCTTGTAG
Found at i:31034139 original size:29 final size:29
Alignment explanation
Indices: 31034106--31034276 Score: 133
Period size: 33 Copynumber: 5.8 Consensus size: 29
31034096 TATACATCCA
*
31034106 ATTA-GGTTAAGGGTTTTAATTAAATTTGG
1 ATTAGGGTT-AGGGTTTTAATTAAATTAGG
31034135 ATTAGGGTTTTTAGGGTTTTTAATTAAATTAGG
1 ATTAGGG---TTAGGG-TTTTAATTAAATTAGG
*
31034168 -TTAGGGTTAGGGTATTTAATT--A--GGG
1 ATTAGGGTTAGGGT-TTTAATTAAATTAGG
* *
31034193 TTTA-GGTGAGGGTTTTTAATTAAATTAGG
1 ATTAGGGTTAGGG-TTTTAATTAAATTAGG
*
31034222 ATTAGGGTTTTTAGTGTTTTAAATTAAATTAGG
1 ATTAGGG---TTAGGGTTTT-AATTAAATTAGG
31034255 -TTAGGGTTAGGGTTTTTAATTA
1 ATTAGGGTTAGGG-TTTTAATTA
31034277 GGGTTTTGAA
Statistics
Matches: 116, Mismatches: 8, Indels: 36
0.73 0.05 0.22
Matches are distributed among these distances:
25 16 0.14
26 4 0.03
27 2 0.02
28 1 0.01
29 32 0.28
30 8 0.07
32 20 0.17
33 33 0.28
ACGTcount: A:0.27, C:0.00, G:0.26, T:0.46
Consensus pattern (29 bp):
ATTAGGGTTAGGGTTTTAATTAAATTAGG
Found at i:31034194 original size:25 final size:24
Alignment explanation
Indices: 31034161--31034214 Score: 65
Period size: 25 Copynumber: 2.2 Consensus size: 24
31034151 TTTTTAATTA
*
31034161 AATTAGG-TTAGGGTTAGGGTATTT
1 AATTAGGTTTA-GGTGAGGGTATTT
*
31034185 AATTAGGGTTTAGGTGAGGGTTTTT
1 AATTA-GGTTTAGGTGAGGGTATTT
31034210 AATTA
1 AATTA
31034215 AATTAGGATT
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
24 5 0.19
25 18 0.69
26 3 0.12
ACGTcount: A:0.26, C:0.00, G:0.31, T:0.43
Consensus pattern (24 bp):
AATTAGGTTTAGGTGAGGGTATTT
Found at i:31034217 original size:87 final size:86
Alignment explanation
Indices: 31034115--31034282 Score: 291
Period size: 87 Copynumber: 1.9 Consensus size: 86
31034105 AATTAGGTTA
* *
31034115 AGGGTTTTAATTAAATTTGGATTAGGGTTTTTAGGGTTTTTAATTAAATTAGGTTAGGGTTAGGG
1 AGGGTTTTAATTAAATTAGGATTAGGGTTTTTAGGGTTTTAAATTAAATTAGGTTAGGGTTAGGG
31034180 TATTTAATTAGGGTTTAGGTG
66 TATTTAATTAGGGTTTAGGTG
*
31034201 AGGGTTTTTAATTAAATTAGGATTAGGGTTTTTAGTGTTTTAAATTAAATTAGGTTAGGGTTAGG
1 AGGG-TTTTAATTAAATTAGGATTAGGGTTTTTAGGGTTTTAAATTAAATTAGGTTAGGGTTAGG
*
31034266 GTTTTTAATTAGGGTTT
65 GTATTTAATTAGGGTTT
31034283 TGAATTAATT
Statistics
Matches: 77, Mismatches: 4, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
86 4 0.05
87 73 0.95
ACGTcount: A:0.26, C:0.00, G:0.27, T:0.46
Consensus pattern (86 bp):
AGGGTTTTAATTAAATTAGGATTAGGGTTTTTAGGGTTTTAAATTAAATTAGGTTAGGGTTAGGG
TATTTAATTAGGGTTTAGGTG
Found at i:31034233 original size:25 final size:23
Alignment explanation
Indices: 31034145--31034234 Score: 72
Period size: 24 Copynumber: 3.5 Consensus size: 23
31034135 ATTAGGGTTT
31034145 TTAGGGTTTTTAATTAAATTAGG
1 TTAGGGTTTTTAATTAAATTAGG
**
31034168 TTAGGGTTAGGGTATTTAATTAGGGTTTAGG
1 TTAGGG-T----T-TTTAATTA--AATTAGG
*
31034199 TGAGGGTTTTTAATTAAATTAGG
1 TTAGGGTTTTTAATTAAATTAGG
31034222 ATTAGGGTTTTTA
1 -TTAGGGTTTTTA
31034235 GTGTTTTAAA
Statistics
Matches: 52, Mismatches: 6, Indels: 17
0.69 0.08 0.23
Matches are distributed among these distances:
23 11 0.21
24 12 0.23
25 8 0.15
26 1 0.02
28 1 0.02
29 8 0.15
30 1 0.02
31 10 0.19
ACGTcount: A:0.27, C:0.00, G:0.28, T:0.46
Consensus pattern (23 bp):
TTAGGGTTTTTAATTAAATTAGG
Found at i:31034306 original size:6 final size:6
Alignment explanation
Indices: 31034295--31034334 Score: 80
Period size: 6 Copynumber: 6.7 Consensus size: 6
31034285 AATTAATTTA
31034295 GGTTAG GGTTAG GGTTAG GGTTAG GGTTAG GGTTAG GGTT
1 GGTTAG GGTTAG GGTTAG GGTTAG GGTTAG GGTTAG GGTT
31034335 TTTAATTAGG
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 34 1.00
ACGTcount: A:0.15, C:0.00, G:0.50, T:0.35
Consensus pattern (6 bp):
GGTTAG
Found at i:31034345 original size:13 final size:13
Alignment explanation
Indices: 31034327--31034368 Score: 59
Period size: 13 Copynumber: 3.2 Consensus size: 13
31034317 AGGGTTAGGG
31034327 TTAGGGTTTTTAA
1 TTAGGGTTTTTAA
*
31034340 TTAGGGTATTTAA
1 TTAGGGTTTTTAA
31034353 TTA-GGTTTTTGAA
1 TTAGGGTTTTT-AA
31034366 TTA
1 TTA
31034369 ATTTAGGTTA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
12 6 0.23
13 20 0.77
ACGTcount: A:0.26, C:0.00, G:0.21, T:0.52
Consensus pattern (13 bp):
TTAGGGTTTTTAA
Found at i:31034353 original size:79 final size:72
Alignment explanation
Indices: 31034261--31034434 Score: 258
Period size: 79 Copynumber: 2.3 Consensus size: 72
31034251 TAGGTTAGGG
31034261 TTAGGGTTTTTAATTAGGGTTTTGAATTAATTTAGGTTAGGGTTAGGGTTAGGGTTAGGGTTAGG
1 TTAGGG-TTTTAATTAGGGTTTTGAATTAATTTAGGTTAGGGTTAGGGTTAGGGTTA-----A-G
31034326 GTTAGGGTTTTTAA
59 GTTAGGGTTTTTAA
*
31034340 TTAGGGTATTTAATTAGGTTTTTGAATTAATTTAGGTTAGGGTTAGGGTTAGGGTTAAGGTTAGG
1 TTAGGGT-TTTAATTAGGGTTTTGAATTAATTTAGGTTAGGGTTAGGGTTAGGGTTAAGGTTAGG
31034405 GTTTTTAA
65 GTTTTTAA
31034413 TTAGGGTTTTGAATTAGGGTTT
1 TTAGGGTTTT-AATTAGGGTTT
31034435 AGGTTAAGGT
Statistics
Matches: 91, Mismatches: 2, Indels: 10
0.88 0.02 0.10
Matches are distributed among these distances:
72 3 0.03
73 32 0.35
74 1 0.01
78 1 0.01
79 54 0.59
ACGTcount: A:0.22, C:0.00, G:0.32, T:0.45
Consensus pattern (72 bp):
TTAGGGTTTTAATTAGGGTTTTGAATTAATTTAGGTTAGGGTTAGGGTTAGGGTTAAGGTTAGGG
TTTTTAA
Found at i:31034385 original size:6 final size:6
Alignment explanation
Indices: 31034374--31034407 Score: 59
Period size: 6 Copynumber: 5.7 Consensus size: 6
31034364 AATTAATTTA
*
31034374 GGTTAG GGTTAG GGTTAG GGTTAA GGTTAG GGTT
1 GGTTAG GGTTAG GGTTAG GGTTAG GGTTAG GGTT
31034408 TTTAATTAGG
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
6 26 1.00
ACGTcount: A:0.18, C:0.00, G:0.47, T:0.35
Consensus pattern (6 bp):
GGTTAG
Found at i:31034418 original size:13 final size:13
Alignment explanation
Indices: 31034400--31034434 Score: 61
Period size: 13 Copynumber: 2.7 Consensus size: 13
31034390 AGGGTTAAGG
*
31034400 TTAGGGTTTTTAA
1 TTAGGGTTTTGAA
31034413 TTAGGGTTTTGAA
1 TTAGGGTTTTGAA
31034426 TTAGGGTTT
1 TTAGGGTTT
31034435 AGGTTAAGGT
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:0.20, C:0.00, G:0.29, T:0.51
Consensus pattern (13 bp):
TTAGGGTTTTGAA
Found at i:31034446 original size:50 final size:50
Alignment explanation
Indices: 31034376--31034505 Score: 167
Period size: 50 Copynumber: 2.6 Consensus size: 50
31034366 TTAATTTAGG
* * * *
31034376 TTAGGG-TTAGGGTTAGGGTTAAGGTTAGGGTTTTTAATTAGGGTTTTGAA
1 TTAGGGTTTA-GGTTAAGGTTAGGGTTAGGGTTTTTAATTAAGATTTTGAA
*
31034426 TTAGGGTTTAGGTTAAGGTTAGGGTTTGGGTTTTTAATTAAGATTTTGAA
1 TTAGGGTTTAGGTTAAGGTTAGGGTTAGGGTTTTTAATTAAGATTTTGAA
* *
31034476 TTA--ATTTAGGTTATGGTTAGGGTTAGGGTT
1 TTAGGGTTTAGGTTAAGGTTAGGGTTAGGGTT
31034506 AGGGTTTTGA
Statistics
Matches: 71, Mismatches: 8, Indels: 4
0.86 0.10 0.05
Matches are distributed among these distances:
48 24 0.34
50 44 0.62
51 3 0.04
ACGTcount: A:0.22, C:0.00, G:0.33, T:0.45
Consensus pattern (50 bp):
TTAGGGTTTAGGTTAAGGTTAGGGTTAGGGTTTTTAATTAAGATTTTGAA
Found at i:31034448 original size:73 final size:75
Alignment explanation
Indices: 31034261--31034457 Score: 249
Period size: 73 Copynumber: 2.6 Consensus size: 75
31034251 TAGGTTAGGG
* * *
31034261 TTAGGGTTTTTAATTAGGGTTTTGAATTAATTTAGGTTAGGGTTAGGGTTAGGGTTAGGGTTAGG
1 TTAGGGTATTTAATTAGGGTTTAGAATT-A---AGGTTAGGGTTAGGGTTAGGGTTAGGGTTAAG
31034326 GTTAGGGTTTTTAA
62 GTTAGGGTTTTTAA
* * *
31034340 TTAGGGTATTTAATTAGGTTTTTGAATTAA-TTTA-GGTTAGGGTTAGGGTTAGGGTTAAGGTTA
1 TTAGGGTATTTAATTAGGGTTTAGAATTAAGGTTAGGGTTAGGGTTAGGGTTAGGGTTAAGGTTA
31034403 GGGTTTTTAA
66 GGGTTTTTAA
* *
31034413 TTAGGGT-TTTGAATTAGGGTTTAG-GTTAAGGTTAGGGTTTGGGTT
1 TTAGGGTATTT-AATTAGGGTTTAGAATTAAGGTTAGGGTTAGGGTT
31034458 TTTAATTAAG
Statistics
Matches: 106, Mismatches: 9, Indels: 11
0.84 0.07 0.09
Matches are distributed among these distances:
72 7 0.07
73 59 0.56
74 12 0.11
75 1 0.01
78 1 0.01
79 26 0.25
ACGTcount: A:0.22, C:0.00, G:0.34, T:0.45
Consensus pattern (75 bp):
TTAGGGTATTTAATTAGGGTTTAGAATTAAGGTTAGGGTTAGGGTTAGGGTTAGGGTTAAGGTTA
GGGTTTTTAA
Found at i:31034449 original size:18 final size:18
Alignment explanation
Indices: 31034370--31034457 Score: 63
Period size: 18 Copynumber: 5.4 Consensus size: 18
31034360 TTTGAATTAA
*
31034370 TTTAGGTTAGGGTTAGGG
1 TTTAGGTTAAGGTTAGGG
31034388 -TTAGGGTTAAGGTTAGGG
1 TTTA-GGTTAAGGTTAGGG
31034406 TTT---TTAA--TTAGGG
1 TTTAGGTTAAGGTTAGGG
*
31034419 TTT---TGAA--TTAGGG
1 TTTAGGTTAAGGTTAGGG
31034432 TTTAGGTTAAGGTTAGGG
1 TTTAGGTTAAGGTTAGGG
*
31034450 TTTGGGTT
1 TTTAGGTT
31034458 TTTAATTAAG
Statistics
Matches: 59, Mismatches: 4, Indels: 14
0.77 0.05 0.18
Matches are distributed among these distances:
13 21 0.36
15 4 0.07
16 3 0.05
17 3 0.05
18 26 0.44
19 2 0.03
ACGTcount: A:0.19, C:0.00, G:0.38, T:0.43
Consensus pattern (18 bp):
TTTAGGTTAAGGTTAGGG
Found at i:31034551 original size:13 final size:13
Alignment explanation
Indices: 31034533--31034563 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
31034523 TAGGTTATGG
*
31034533 TTAGGGTTTTTAA
1 TTAGGGTATTTAA
31034546 TTAGGGTATTTAA
1 TTAGGGTATTTAA
31034559 TTAGG
1 TTAGG
31034564 TTAGAGTTTT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.26, C:0.00, G:0.26, T:0.48
Consensus pattern (13 bp):
TTAGGGTATTTAA
Found at i:31034671 original size:27 final size:27
Alignment explanation
Indices: 31034633--31034684 Score: 95
Period size: 27 Copynumber: 1.9 Consensus size: 27
31034623 AACTCGAAAA
*
31034633 TTTTTTATTTTATTACATCAAATAAAC
1 TTTTCTATTTTATTACATCAAATAAAC
31034660 TTTTCTATTTTATTACATCAAATAA
1 TTTTCTATTTTATTACATCAAATAA
31034685 TATTTAAATA
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
27 24 1.00
ACGTcount: A:0.37, C:0.12, G:0.00, T:0.52
Consensus pattern (27 bp):
TTTTCTATTTTATTACATCAAATAAAC
Found at i:31035108 original size:18 final size:18
Alignment explanation
Indices: 31035085--31035119 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
31035075 TGGAAAAGGA
*
31035085 TACATATAAGGGTTAGGG
1 TACATATAAGGGCTAGGG
31035103 TACATATAAGGGCTAGG
1 TACATATAAGGGCTAGG
31035120 AAACGCACCT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.34, C:0.09, G:0.31, T:0.26
Consensus pattern (18 bp):
TACATATAAGGGCTAGGG
Found at i:31035780 original size:7 final size:7
Alignment explanation
Indices: 31035770--31035794 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
31035760 TTATATACAT
31035770 AATACTA
1 AATACTA
31035777 AATACTA
1 AATACTA
31035784 AATACTA
1 AATACTA
31035791 AATA
1 AATA
31035795 TCAATCGGCT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.60, C:0.12, G:0.00, T:0.28
Consensus pattern (7 bp):
AATACTA
Found at i:31036975 original size:11 final size:11
Alignment explanation
Indices: 31036959--31037059 Score: 64
Period size: 11 Copynumber: 8.6 Consensus size: 11
31036949 TAATTTTAGA
31036959 AGGAAATTGAG
1 AGGAAATTGAG
*
31036970 AGGAAATTGAA
1 AGGAAATTGAG
*
31036981 ATGAAATATGAGTTTG
1 AGGAAAT-TGA----G
* *
31036997 AGGGAATTTTAG
1 A-GGAAATTGAG
31037009 AAGGAAATTGAG
1 -AGGAAATTGAG
31037021 A-GAAATTTG-G
1 AGGAAA-TTGAG
31037031 AAGGAAATTGAG
1 -AGGAAATTGAG
31037043 AGG-AATTGAG
1 AGGAAATTGAG
31037053 AGGAAAT
1 AGGAAAT
31037060 ATTAGAGAGG
Statistics
Matches: 70, Mismatches: 8, Indels: 24
0.69 0.08 0.24
Matches are distributed among these distances:
10 15 0.21
11 30 0.43
12 17 0.24
13 1 0.01
16 3 0.04
17 4 0.06
ACGTcount: A:0.45, C:0.00, G:0.32, T:0.24
Consensus pattern (11 bp):
AGGAAATTGAG
Found at i:31036977 original size:51 final size:51
Alignment explanation
Indices: 31036909--31037027 Score: 161
Period size: 51 Copynumber: 2.4 Consensus size: 51
31036899 TTTTAAAAAC
* * * *
31036909 GGAAATTTAGAGAAAATTGAAATTAAATATG-GATTTGAAATAATTTTAGAA
1 GGAAATTGAGAGGAAATTGAAATGAAATATGAG-TTTGAAAGAATTTTAGAA
**
31036960 GGAAATTGAGAGGAAATTGAAATGAAATATGAGTTTGAGGGAATTTTAGAA
1 GGAAATTGAGAGGAAATTGAAATGAAATATGAGTTTGAAAGAATTTTAGAA
31037011 GGAAATTGAGA-GAAATT
1 GGAAATTGAGAGGAAATT
31037028 TGGAAGGAAA
Statistics
Matches: 61, Mismatches: 6, Indels: 3
0.87 0.09 0.04
Matches are distributed among these distances:
50 6 0.10
51 54 0.89
52 1 0.02
ACGTcount: A:0.46, C:0.00, G:0.24, T:0.29
Consensus pattern (51 bp):
GGAAATTGAGAGGAAATTGAAATGAAATATGAGTTTGAAAGAATTTTAGAA
Found at i:31037027 original size:10 final size:11
Alignment explanation
Indices: 31037010--31037059 Score: 61
Period size: 10 Copynumber: 4.6 Consensus size: 11
31037000 GAATTTTAGA
31037010 AGGAAATTGAG
1 AGGAAATTGAG
31037021 A-GAAATTTG-G
1 AGGAAA-TTGAG
31037031 AAGGAAATTGAG
1 -AGGAAATTGAG
31037043 AGG-AATTGAG
1 AGGAAATTGAG
31037053 AGGAAAT
1 AGGAAAT
31037060 ATTAGAGAGG
Statistics
Matches: 34, Mismatches: 0, Indels: 10
0.77 0.00 0.23
Matches are distributed among these distances:
10 15 0.44
11 14 0.41
12 5 0.15
ACGTcount: A:0.46, C:0.00, G:0.34, T:0.20
Consensus pattern (11 bp):
AGGAAATTGAG
Found at i:31037033 original size:22 final size:22
Alignment explanation
Indices: 31036994--31037059 Score: 80
Period size: 22 Copynumber: 3.0 Consensus size: 22
31036984 AAATATGAGT
* *
31036994 TTGAGGGAATTTTAGAAGGAAA
1 TTGAGAGAAATTTAGAAGGAAA
*
31037016 TTGAGAGAAATTTGGAAGGAAA
1 TTGAGAGAAATTTAGAAGGAAA
* *
31037038 TTGAGAGGAATTGAG-AGGAAA
1 TTGAGAGAAATTTAGAAGGAAA
31037059 T
1 T
31037060 ATTAGAGAGG
Statistics
Matches: 38, Mismatches: 6, Indels: 1
0.84 0.13 0.02
Matches are distributed among these distances:
21 7 0.18
22 31 0.82
ACGTcount: A:0.42, C:0.00, G:0.33, T:0.24
Consensus pattern (22 bp):
TTGAGAGAAATTTAGAAGGAAA
Found at i:31037389 original size:29 final size:29
Alignment explanation
Indices: 31037331--31037396 Score: 73
Period size: 29 Copynumber: 2.3 Consensus size: 29
31037321 CGATTTCCCG
*
31037331 AAAAA-GGACCATTCCGGTAAATAATTAA
1 AAAAAGGGCCCATTCCGGTAAATAATTAA
* * *
31037359 AAAATGGGCCCATTTCGGTAAAT-TTTGAA
1 AAAAAGGGCCCATTCCGGTAAATAATT-AA
31037388 AAAAAGGGC
1 AAAAAGGGC
31037397 TTTTATTGGT
Statistics
Matches: 31, Mismatches: 5, Indels: 3
0.79 0.13 0.08
Matches are distributed among these distances:
28 6 0.19
29 25 0.81
ACGTcount: A:0.44, C:0.14, G:0.20, T:0.23
Consensus pattern (29 bp):
AAAAAGGGCCCATTCCGGTAAATAATTAA
Found at i:31037724 original size:17 final size:18
Alignment explanation
Indices: 31037704--31037806 Score: 81
Period size: 17 Copynumber: 5.7 Consensus size: 18
31037694 TCAAAATTTC
31037704 TTGT-TTTCAAAAAAATT
1 TTGTGTTTCAAAAAAATT
31037721 TTGTGTTTC--AAAAATT
1 TTGTGTTTCAAAAAAATT
31037737 TTAGTGTTTCAAAAAAATT
1 TT-GTGTTTCAAAAAAATT
*
31037756 CTCGTGTTT--AAAAAATAT
1 -TTGTGTTTCAAAAAAAT-T
**
31037774 CCGTGTTTTCAAAAAAATT
1 TTGTG-TTTCAAAAAAATT
* *
31037793 ATGGTATTTCAAAA
1 -TTGTGTTTCAAAA
31037807 TTCTCGTGTT
Statistics
Matches: 71, Mismatches: 5, Indels: 18
0.76 0.05 0.19
Matches are distributed among these distances:
16 9 0.13
17 22 0.31
18 8 0.11
19 22 0.31
20 10 0.14
ACGTcount: A:0.39, C:0.09, G:0.11, T:0.42
Consensus pattern (18 bp):
TTGTGTTTCAAAAAAATT
Found at i:31037752 original size:36 final size:36
Alignment explanation
Indices: 31037708--31037840 Score: 144
Period size: 36 Copynumber: 3.7 Consensus size: 36
31037698 AATTTCTTGT
* *
31037708 TTTCAAAAAAATT-TTGTGTTTCAAAAATTTTAGTG
1 TTTCAAAAAAATTCTCGTGTTTCAAAAATTTTCGTG
* * *
31037743 TTTCAAAAAAATTCTCGTGTTTAAAAAATATCCGTG
1 TTTCAAAAAAATTCTCGTGTTTCAAAAATTTTCGTG
* * * *
31037779 TTTTCAAAAAAATTATGGTATTTC-AAAATTCTCGTG
1 -TTTCAAAAAAATTCTCGTGTTTCAAAAATTTTCGTG
*
31037815 TTTTAAAAAAAATTCTCGTGTTTCAA
1 -TTTCAAAAAAATTCTCGTGTTTCAA
31037841 TCGGATCACG
Statistics
Matches: 79, Mismatches: 16, Indels: 4
0.80 0.16 0.04
Matches are distributed among these distances:
35 13 0.16
36 46 0.58
37 20 0.25
ACGTcount: A:0.38, C:0.11, G:0.11, T:0.41
Consensus pattern (36 bp):
TTTCAAAAAAATTCTCGTGTTTCAAAAATTTTCGTG
Found at i:31037825 original size:19 final size:19
Alignment explanation
Indices: 31037696--31037837 Score: 90
Period size: 19 Copynumber: 7.8 Consensus size: 19
31037686 AAAATTTATC
*
31037696 AAAATT-TCTTGTTTTCAAA
1 AAAATTCTCGTGTTTT-AAA
* *
31037715 AAAATT-TTGTG-TTT-CA
1 AAAATTCTCGTGTTTTAAA
* * *
31037731 AAAATTTTAGTGTTTCAAA
1 AAAATTCTCGTGTTTTAAA
31037750 AAAATTCTCGTG-TTT-AA
1 AAAATTCTCGTGTTTTAAA
31037767 AAAATATC-CGTGTTTTCAAA
1 AAAAT-TCTCGTGTTTT-AAA
* *
31037787 AAAATTAT-G-GTATTT--C
1 AAAATTCTCGTGT-TTTAAA
31037803 AAAATTCTCGTGTTTTAAAA
1 AAAATTCTCGTGTTTT-AAA
31037823 AAAATTCTCGTGTTT
1 AAAATTCTCGTGTTT
31037838 CAATCGGATC
Statistics
Matches: 96, Mismatches: 13, Indels: 27
0.71 0.10 0.20
Matches are distributed among these distances:
16 14 0.15
17 19 0.20
18 16 0.17
19 25 0.26
20 22 0.23
ACGTcount: A:0.37, C:0.10, G:0.11, T:0.43
Consensus pattern (19 bp):
AAAATTCTCGTGTTTTAAA
Found at i:31040503 original size:17 final size:18
Alignment explanation
Indices: 31040469--31040514 Score: 64
Period size: 17 Copynumber: 2.8 Consensus size: 18
31040459 CCGTTATGTC
31040469 CGCGACCGCGA-C--AAA
1 CGCGACCGCGACCGAAAA
31040484 CGCGA-CGCGACCGAAAA
1 CGCGACCGCGACCGAAAA
31040501 CGCGACCGCGACCG
1 CGCGACCGCGACCG
31040515 CAATTTAAAT
Statistics
Matches: 27, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
14 5 0.19
15 6 0.22
17 8 0.30
18 8 0.30
ACGTcount: A:0.28, C:0.41, G:0.30, T:0.00
Consensus pattern (18 bp):
CGCGACCGCGACCGAAAA
Found at i:31042157 original size:7 final size:7
Alignment explanation
Indices: 31042147--31042181 Score: 52
Period size: 7 Copynumber: 5.0 Consensus size: 7
31042137 ACATAAATCT
31042147 CTAACCC
1 CTAACCC
31042154 CTAACCC
1 CTAACCC
*
31042161 CTAACCT
1 CTAACCC
*
31042168 TTAACCC
1 CTAACCC
31042175 CTAACCC
1 CTAACCC
31042182 TTAAACCTTA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
7 24 1.00
ACGTcount: A:0.29, C:0.51, G:0.00, T:0.20
Consensus pattern (7 bp):
CTAACCC
Found at i:31042185 original size:14 final size:14
Alignment explanation
Indices: 31042147--31042185 Score: 60
Period size: 14 Copynumber: 2.8 Consensus size: 14
31042137 ACATAAATCT
*
31042147 CTAACCCCTAACCC
1 CTAACCCTTAACCC
*
31042161 CTAACCTTTAACCC
1 CTAACCCTTAACCC
31042175 CTAACCCTTAA
1 CTAACCCTTAA
31042186 ACCTTAAACC
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
14 22 1.00
ACGTcount: A:0.31, C:0.46, G:0.00, T:0.23
Consensus pattern (14 bp):
CTAACCCTTAACCC
Found at i:31042206 original size:21 final size:22
Alignment explanation
Indices: 31042149--31042214 Score: 82
Period size: 21 Copynumber: 3.1 Consensus size: 22
31042139 ATAAATCTCT
* *
31042149 AACCCCTAACCCCT-AACCTTT
1 AACCCCTAACCCTTAAACCTTA
31042170 AACCCCTAACCCTTAAACCTTA
1 AACCCCTAACCCTTAAACCTTA
* *
31042192 AACCCC-AACCTTTAAACCATA
1 AACCCCTAACCCTTAAACCTTA
31042213 AA
1 AA
31042215 TCATAAACCA
Statistics
Matches: 40, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
21 28 0.70
22 12 0.30
ACGTcount: A:0.38, C:0.41, G:0.00, T:0.21
Consensus pattern (22 bp):
AACCCCTAACCCTTAAACCTTA
Done.