Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Dt_chr1
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: 96304692
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.32
Warning! 2448173 characters in sequence are not A, C, G, or T
File 192 of 313
Found at i:58944473 original size:19 final size:18
Alignment explanation
Indices: 58944422--58944532 Score: 55
Period size: 19 Copynumber: 5.7 Consensus size: 18
58944412 TGTAAGTATG
*
58944422 ATAAAAA-TGATAAAAAT
1 ATAAAAACTTATAAAAAT
** *
58944439 ATTAAAATTTTATATAAGCAT
1 A-TAAAAACTTATA-AA-AAT
58944460 ATAAATAACTTATAAAAAT
1 ATAAA-AACTTATAAAAAT
* *
58944479 ATAAACACTTATAACAATT
1 ATAAAAACTTATAA-AAAT
*
58944498 ATTAAAAATTTTATTATAAAAAT
1 A-TAAAAA----CTTATAAAAAT
58944521 ATAAAAA-TTATA
1 ATAAAAACTTATA
58944533 TATATACATA
Statistics
Matches: 72, Mismatches: 11, Indels: 22
0.69 0.10 0.21
Matches are distributed among these distances:
17 6 0.08
18 13 0.18
19 15 0.21
20 13 0.18
21 9 0.12
22 6 0.08
23 4 0.06
24 6 0.08
ACGTcount: A:0.59, C:0.05, G:0.02, T:0.35
Consensus pattern (18 bp):
ATAAAAACTTATAAAAAT
Found at i:58944549 original size:25 final size:23
Alignment explanation
Indices: 58944500--58944560 Score: 81
Period size: 25 Copynumber: 2.7 Consensus size: 23
58944490 TAACAATTAT
*
58944500 TAAAAATTTTAT-TATAAAAATA
1 TAAAAATTATATATATAAAAATA
58944522 TAAAAATTATATATATACATAAATA
1 TAAAAATTATATATATA-A-AAATA
58944547 TAAAAATTAT-TATA
1 TAAAAATTATATATA
58944561 AAACTCGTTC
Statistics
Matches: 35, Mismatches: 1, Indels: 4
0.88 0.03 0.10
Matches are distributed among these distances:
22 11 0.31
23 4 0.11
24 5 0.14
25 15 0.43
ACGTcount: A:0.59, C:0.02, G:0.00, T:0.39
Consensus pattern (23 bp):
TAAAAATTATATATATAAAAATA
Found at i:58951395 original size:42 final size:42
Alignment explanation
Indices: 58951336--58951443 Score: 216
Period size: 42 Copynumber: 2.6 Consensus size: 42
58951326 ATTTTCTCCG
58951336 AAATCGCGTCCACGTCAGCGCGATGTCAGGGGACGTGTTAGC
1 AAATCGCGTCCACGTCAGCGCGATGTCAGGGGACGTGTTAGC
58951378 AAATCGCGTCCACGTCAGCGCGATGTCAGGGGACGTGTTAGC
1 AAATCGCGTCCACGTCAGCGCGATGTCAGGGGACGTGTTAGC
58951420 AAATCGCGTCCACGTCAGCGCGAT
1 AAATCGCGTCCACGTCAGCGCGAT
58951444 TACTTATGTG
Statistics
Matches: 66, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
42 66 1.00
ACGTcount: A:0.22, C:0.28, G:0.31, T:0.19
Consensus pattern (42 bp):
AAATCGCGTCCACGTCAGCGCGATGTCAGGGGACGTGTTAGC
Found at i:58957006 original size:27 final size:27
Alignment explanation
Indices: 58956976--58957153 Score: 205
Period size: 27 Copynumber: 6.6 Consensus size: 27
58956966 ATATTGAGTC
* * * *
58956976 CGCACACTCAGTGCTATATAATCAACT
1 CGCACACTTAGTGCTACATAGTCAAAT
* *
58957003 CGCACACTTAGTGCTACGTAATCAAAT
1 CGCACACTTAGTGCTACATAGTCAAAT
58957030 CGCACACTTAGTGCTACATAGTCAAACT
1 CGCACACTTAGTGCTACATAGTCAAA-T
** * *
58957058 CGCACACTTAGTGCCGCATGGTCAATT
1 CGCACACTTAGTGCTACATAGTCAAAT
* **
58957085 CGCACACTTAGTGC-ATCATATTCATTT
1 CGCACACTTAGTGCTA-CATAGTCAAAT
*
58957112 CGCACACTTAGTGCAACATAGTCAAAT
1 CGCACACTTAGTGCTACATAGTCAAAT
58957139 CGCACACTTAGTGCT
1 CGCACACTTAGTGCT
58957154 GTACAATTTA
Statistics
Matches: 130, Mismatches: 18, Indels: 6
0.84 0.12 0.04
Matches are distributed among these distances:
27 106 0.82
28 24 0.18
ACGTcount: A:0.30, C:0.28, G:0.15, T:0.27
Consensus pattern (27 bp):
CGCACACTTAGTGCTACATAGTCAAAT
Found at i:58957115 original size:82 final size:81
Alignment explanation
Indices: 58956997--58957152 Score: 233
Period size: 82 Copynumber: 1.9 Consensus size: 81
58956987 TGCTATATAA
* *
58956997 TCAACTCGCACACTTAGTGCTACGTAATCAAATCGCACACTTAGTGCTACATAGTCAAACTCGCA
1 TCAACTCGCACACTTAGTGCTACATAATCAAATCGCACACTTAGTGCAACATAGTCAAA-TCGCA
58957062 CACTTAGTGCCGCATGG
65 CACTTAGTGCCGCATGG
* * **
58957079 TCAATTCGCACACTTAGTGC-ATCATATTCATTTCGCACACTTAGTGCAACATAGTCAAATCGCA
1 TCAACTCGCACACTTAGTGCTA-CATAATCAAATCGCACACTTAGTGCAACATAGTCAAATCGCA
58957143 CACTTAGTGC
65 CACTTAGTGC
58957153 TGTACAATTT
Statistics
Matches: 67, Mismatches: 6, Indels: 3
0.88 0.08 0.04
Matches are distributed among these distances:
81 16 0.24
82 51 0.76
ACGTcount: A:0.29, C:0.28, G:0.15, T:0.27
Consensus pattern (81 bp):
TCAACTCGCACACTTAGTGCTACATAATCAAATCGCACACTTAGTGCAACATAGTCAAATCGCAC
ACTTAGTGCCGCATGG
Found at i:58976942 original size:27 final size:29
Alignment explanation
Indices: 58976912--58976973 Score: 69
Period size: 27 Copynumber: 2.2 Consensus size: 29
58976902 GTAATCGGAC
*
58976912 AAAAGAAAG-AAAAGAGAAA-GGAA-GTAG
1 AAAAGAAAGAAAAAGA-AAAGGGAATGAAG
*
58976939 AAAA-AAATAAAAAGAAAAGGGAATGAAG
1 AAAAGAAAGAAAAAGAAAAGGGAATGAAG
58976967 AAAAGAA
1 AAAAGAA
58976974 GGACATCAAA
Statistics
Matches: 29, Mismatches: 2, Indels: 6
0.78 0.05 0.16
Matches are distributed among these distances:
26 6 0.21
27 14 0.48
28 7 0.24
29 2 0.07
ACGTcount: A:0.71, C:0.00, G:0.24, T:0.05
Consensus pattern (29 bp):
AAAAGAAAGAAAAAGAAAAGGGAATGAAG
Found at i:58977054 original size:20 final size:20
Alignment explanation
Indices: 58977029--58977067 Score: 78
Period size: 20 Copynumber: 1.9 Consensus size: 20
58977019 ATTTAACAGA
58977029 TAACACACAAAATGAATCTT
1 TAACACACAAAATGAATCTT
58977049 TAACACACAAAATGAATCT
1 TAACACACAAAATGAATCT
58977068 CTATCGTCTG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.51, C:0.21, G:0.05, T:0.23
Consensus pattern (20 bp):
TAACACACAAAATGAATCTT
Found at i:58986289 original size:29 final size:29
Alignment explanation
Indices: 58986234--58986289 Score: 69
Period size: 29 Copynumber: 1.9 Consensus size: 29
58986224 CACAGTATGC
*
58986234 CACATAGCCTAACACACGGTCGAGTGGTT
1 CACATAGCCTAACACACGGGCGAGTGGTT
* *
58986263 CACATGGCCTATA-ACACGGGCGTGTGG
1 CACATAGCCTA-ACACACGGGCGAGTGG
58986290 CATCGACAAC
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
29 22 0.96
30 1 0.04
ACGTcount: A:0.25, C:0.27, G:0.29, T:0.20
Consensus pattern (29 bp):
CACATAGCCTAACACACGGGCGAGTGGTT
Found at i:58986766 original size:11 final size:11
Alignment explanation
Indices: 58986746--58986801 Score: 51
Period size: 11 Copynumber: 4.9 Consensus size: 11
58986736 CAAAGTAATC
*
58986746 GAAAAAAGAAA
1 GAAAAGAGAAA
58986757 GAAAAGAGAAA
1 GAAAAGAGAAA
*
58986768 GGAAGTAGAAGAAA
1 -GAA-AAG-AGAAA
*
58986782 -AAAAGAAAAA
1 GAAAAGAGAAA
58986792 GAAAAGAGAA
1 GAAAAGAGAA
58986802 TGAAGGAAAG
Statistics
Matches: 36, Mismatches: 5, Indels: 8
0.73 0.10 0.16
Matches are distributed among these distances:
10 4 0.11
11 20 0.56
12 5 0.14
13 2 0.06
14 5 0.14
ACGTcount: A:0.73, C:0.00, G:0.25, T:0.02
Consensus pattern (11 bp):
GAAAAGAGAAA
Found at i:58986813 original size:33 final size:33
Alignment explanation
Indices: 58986747--58986813 Score: 84
Period size: 33 Copynumber: 2.0 Consensus size: 33
58986737 AAAGTAATCG
*
58986747 AAAAAAGAAAGAAAAGAGAAAGGAAGTAGAAGA
1 AAAAAAGAAAGAAAAGAGAAAGGAAGGAGAAGA
*
58986780 AAAAAAGAAAAAGAAAAGAG-AATGAAGGA-AAGA
1 AAAAAAG--AAAGAAAAGAGAAAGGAAGGAGAAGA
58986813 A
1 A
58986814 GGACGTCAAA
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
33 12 0.40
34 7 0.23
35 11 0.37
ACGTcount: A:0.72, C:0.00, G:0.25, T:0.03
Consensus pattern (33 bp):
AAAAAAGAAAGAAAAGAGAAAGGAAGGAGAAGA
Found at i:58999022 original size:16 final size:17
Alignment explanation
Indices: 58999001--58999065 Score: 69
Period size: 17 Copynumber: 3.7 Consensus size: 17
58998991 GAATATTCAC
58999001 TTATGTTTTATTTT-TA
1 TTATGTTTTATTTTATA
58999017 TTATGTTTTCATTATTATA
1 TTATGTTTT-ATT-TTATA
** *
58999036 TTAACCTTTTATTTTATT
1 TT-ATGTTTTATTTTATA
58999054 TTATGTTTTATT
1 TTATGTTTTATT
58999066 AATTAAAAGA
Statistics
Matches: 40, Mismatches: 5, Indels: 7
0.77 0.10 0.13
Matches are distributed among these distances:
16 9 0.22
17 11 0.28
18 8 0.20
19 7 0.17
20 5 0.12
ACGTcount: A:0.22, C:0.05, G:0.05, T:0.69
Consensus pattern (17 bp):
TTATGTTTTATTTTATA
Found at i:59006517 original size:22 final size:22
Alignment explanation
Indices: 59006491--59006532 Score: 59
Period size: 22 Copynumber: 1.9 Consensus size: 22
59006481 AGTAAATAAA
59006491 AATATAT-TAGTAAATAATTAAT
1 AATATATCT-GTAAATAATTAAT
*
59006513 AATATATCTTTAAATAATTA
1 AATATATCTGTAAATAATTA
59006533 TCAGGTTGAT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
22 17 0.94
23 1 0.06
ACGTcount: A:0.52, C:0.02, G:0.02, T:0.43
Consensus pattern (22 bp):
AATATATCTGTAAATAATTAAT
Found at i:59014177 original size:99 final size:98
Alignment explanation
Indices: 59014048--59014231 Score: 323
Period size: 99 Copynumber: 1.9 Consensus size: 98
59014038 TGGCAAATGC
*
59014048 AAATGCCATTTTCTTTTACCCCTTTAAATTTATATGTTATCAAATATAAAAGAGAGAAGATAAGT
1 AAATGCCATTTTCTTTTACCCCCTTAAATTTATATGTTATCAAATATAAAAGAGAGAAGATAAGT
59014113 TATCATTTTCTTTAAAGTGCTCGCCTTTAAAGA
66 TATCATTTTCTTTAAAGTGCTCGCCTTTAAAGA
* *
59014146 AAATGCCATTTTCTTTTTACCCCCTTAAATTTATATGTTATCAAATATAAAAGCGAGAAGATAGG
1 AAATGCCATTTTC-TTTTACCCCCTTAAATTTATATGTTATCAAATATAAAAGAGAGAAGATAAG
*
59014211 TTATCATTTTCTTTAATGTGC
65 TTATCATTTTCTTTAAAGTGC
59014232 CCTGTAAAGG
Statistics
Matches: 81, Mismatches: 4, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
98 13 0.16
99 68 0.84
ACGTcount: A:0.34, C:0.15, G:0.11, T:0.40
Consensus pattern (98 bp):
AAATGCCATTTTCTTTTACCCCCTTAAATTTATATGTTATCAAATATAAAAGAGAGAAGATAAGT
TATCATTTTCTTTAAAGTGCTCGCCTTTAAAGA
Found at i:59019827 original size:18 final size:19
Alignment explanation
Indices: 59019793--59019829 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 19
59019783 AGGGGTGTGC
59019793 AAAATTCGGTTAAAACCGAA
1 AAAATTCGGTT-AAACCGAA
59019813 AAAATTCGGTT-AACCGA
1 AAAATTCGGTTAAACCGA
59019830 CCGGATTCGG
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 6 0.35
20 11 0.65
ACGTcount: A:0.46, C:0.16, G:0.16, T:0.22
Consensus pattern (19 bp):
AAAATTCGGTTAAACCGAA
Found at i:59020050 original size:13 final size:13
Alignment explanation
Indices: 59020032--59020058 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
59020022 CCTCCAGGCT
59020032 CTAAGCCCAAGAA
1 CTAAGCCCAAGAA
59020045 CTAAGCCCAAGAA
1 CTAAGCCCAAGAA
59020058 C
1 C
59020059 AATTCATGTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.44, C:0.33, G:0.15, T:0.07
Consensus pattern (13 bp):
CTAAGCCCAAGAA
Found at i:59020073 original size:7 final size:7
Alignment explanation
Indices: 59020061--59020119 Score: 73
Period size: 7 Copynumber: 8.3 Consensus size: 7
59020051 CCAAGAACAA
59020061 TTCATGT
1 TTCATGT
59020068 TTCATGT
1 TTCATGT
59020075 TTCATGT
1 TTCATGT
*
59020082 TTCACGAT
1 TTCATG-T
59020090 TTCATGT
1 TTCATGT
**
59020097 TTCATAC
1 TTCATGT
*
59020104 TGCATGT
1 TTCATGT
59020111 TTCATGT
1 TTCATGT
59020118 TT
1 TT
59020120 TCTTCTGTAC
Statistics
Matches: 43, Mismatches: 8, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
7 37 0.86
8 6 0.14
ACGTcount: A:0.17, C:0.17, G:0.14, T:0.53
Consensus pattern (7 bp):
TTCATGT
Found at i:59020409 original size:37 final size:37
Alignment explanation
Indices: 59020366--59020471 Score: 158
Period size: 37 Copynumber: 2.9 Consensus size: 37
59020356 TGTGTTAAAG
*
59020366 ACTTATGTAATGTTTTTAATTATTTAGTGATTCAAAA
1 ACTTATGTAATGTTTTTAATTATATAGTGATTCAAAA
* * * *
59020403 ATTTATGTAATGTTTTTAGTTATGTAGTGATTCAAAG
1 ACTTATGTAATGTTTTTAATTATATAGTGATTCAAAA
*
59020440 ACTTATGTAATTTTTTTAATTATATAGTGATT
1 ACTTATGTAATGTTTTTAATTATATAGTGATT
59020472 TAAATCGGTT
Statistics
Matches: 61, Mismatches: 8, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
37 61 1.00
ACGTcount: A:0.32, C:0.04, G:0.13, T:0.51
Consensus pattern (37 bp):
ACTTATGTAATGTTTTTAATTATATAGTGATTCAAAA
Found at i:59020490 original size:9 final size:9
Alignment explanation
Indices: 59020471--59020563 Score: 143
Period size: 9 Copynumber: 10.4 Consensus size: 9
59020461 ATATAGTGAT
59020471 TTAAATCGG
1 TTAAATCGG
* *
59020480 TTAAGTTGG
1 TTAAATCGG
59020489 TTAAATCGG
1 TTAAATCGG
59020498 TTAAATCGG
1 TTAAATCGG
59020507 TTAAATCGG
1 TTAAATCGG
59020516 TTAAATCGG
1 TTAAATCGG
*
59020525 TTAAGTCGG
1 TTAAATCGG
59020534 TT-AATCGG
1 TTAAATCGG
*
59020542 TTAAATAGG
1 TTAAATCGG
59020551 TTAAATCGG
1 TTAAATCGG
59020560 TTAA
1 TTAA
59020564 TTTTTAACCA
Statistics
Matches: 75, Mismatches: 8, Indels: 2
0.88 0.09 0.02
Matches are distributed among these distances:
8 7 0.09
9 68 0.91
ACGTcount: A:0.32, C:0.09, G:0.24, T:0.35
Consensus pattern (9 bp):
TTAAATCGG
Found at i:59021632 original size:23 final size:23
Alignment explanation
Indices: 59021605--59021655 Score: 77
Period size: 23 Copynumber: 2.2 Consensus size: 23
59021595 AAAATATTTT
59021605 TGTAATATCC-CGAAAATTACTAC
1 TGTAATA-CCTCGAAAATTACTAC
59021628 TGTAATACCTCGAAAATTACTAC
1 TGTAATACCTCGAAAATTACTAC
*
59021651 AGTAA
1 TGTAA
59021656 GAAAGTAGGT
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
22 2 0.08
23 24 0.92
ACGTcount: A:0.41, C:0.20, G:0.10, T:0.29
Consensus pattern (23 bp):
TGTAATACCTCGAAAATTACTAC
Found at i:59023621 original size:175 final size:175
Alignment explanation
Indices: 59023330--59023680 Score: 702
Period size: 175 Copynumber: 2.0 Consensus size: 175
59023320 AAATGTCAAA
59023330 ACATGACCAAGTTGCATGAAATGAATTTTTTTATTATTTAAATTAATAAATTGAATGAAATATTA
1 ACATGACCAAGTTGCATGAAATGAATTTTTTTATTATTTAAATTAATAAATTGAATGAAATATTA
59023395 ATTTAGATCAAAATTGGGTGGAAATTCGAGGAAAATAGAAAATTACCAAAATGTAACCTGGTAAG
66 ATTTAGATCAAAATTGGGTGGAAATTCGAGGAAAATAGAAAATTACCAAAATGTAACCTGGTAAG
59023460 TTCGTATGAACTATATTCTGTATAATTTTAATTAAAGTGAATGTT
131 TTCGTATGAACTATATTCTGTATAATTTTAATTAAAGTGAATGTT
59023505 ACATGACCAAGTTGCATGAAATGAATTTTTTTATTATTTAAATTAATAAATTGAATGAAATATTA
1 ACATGACCAAGTTGCATGAAATGAATTTTTTTATTATTTAAATTAATAAATTGAATGAAATATTA
59023570 ATTTAGATCAAAATTGGGTGGAAATTCGAGGAAAATAGAAAATTACCAAAATGTAACCTGGTAAG
66 ATTTAGATCAAAATTGGGTGGAAATTCGAGGAAAATAGAAAATTACCAAAATGTAACCTGGTAAG
59023635 TTCGTATGAACTATATTCTGTATAATTTTAATTAAAGTGAATGTT
131 TTCGTATGAACTATATTCTGTATAATTTTAATTAAAGTGAATGTT
59023680 A
1 A
59023681 TTTGGTGATG
Statistics
Matches: 176, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
175 176 1.00
ACGTcount: A:0.41, C:0.07, G:0.15, T:0.36
Consensus pattern (175 bp):
ACATGACCAAGTTGCATGAAATGAATTTTTTTATTATTTAAATTAATAAATTGAATGAAATATTA
ATTTAGATCAAAATTGGGTGGAAATTCGAGGAAAATAGAAAATTACCAAAATGTAACCTGGTAAG
TTCGTATGAACTATATTCTGTATAATTTTAATTAAAGTGAATGTT
Found at i:59025124 original size:64 final size:64
Alignment explanation
Indices: 59025042--59025165 Score: 178
Period size: 64 Copynumber: 1.9 Consensus size: 64
59025032 TGACAAAAAA
* *
59025042 TGTATTGTCTTGTTACATCAATAATC-TACTTATTTACATTTGACCAAAAAATGAATAAATTATT
1 TGTATTGTATTGTTACATCAATAA-CATACTTATTTACATTTGACCAAAAAATAAATAAATTATT
* * **
59025106 TGTATTGTATTTTTACATCAATAACATACTTATTTACATTTTATTAAAAAATAAATAAAT
1 TGTATTGTATTGTTACATCAATAACATACTTATTTACATTTGACCAAAAAATAAATAAAT
59025166 AAATAGTTTG
Statistics
Matches: 53, Mismatches: 6, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
63 1 0.02
64 52 0.98
ACGTcount: A:0.40, C:0.10, G:0.06, T:0.44
Consensus pattern (64 bp):
TGTATTGTATTGTTACATCAATAACATACTTATTTACATTTGACCAAAAAATAAATAAATTATT
Found at i:59028274 original size:51 final size:51
Alignment explanation
Indices: 59028213--59028312 Score: 148
Period size: 51 Copynumber: 2.0 Consensus size: 51
59028203 AATTATTTAA
59028213 AAATAGGGATTTAAGAGAAATTTA-AGAGGAACTTGAGAGCAAATTGAGATT
1 AAATAGGGATTTAAGAGAAATTTAGA-AGGAACTTGAGAGCAAATTGAGATT
* * * *
59028264 AAATATGGATTTGAGAGAAATTTGGAAGGAATTTGAGAGCAAATTGAGA
1 AAATAGGGATTTAAGAGAAATTTAGAAGGAACTTGAGAGCAAATTGAGA
59028313 GGAAATTTAG
Statistics
Matches: 44, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
51 43 0.98
52 1 0.02
ACGTcount: A:0.44, C:0.03, G:0.27, T:0.26
Consensus pattern (51 bp):
AAATAGGGATTTAAGAGAAATTTAGAAGGAACTTGAGAGCAAATTGAGATT
Found at i:59028286 original size:11 final size:11
Alignment explanation
Indices: 59028272--59028347 Score: 77
Period size: 11 Copynumber: 6.8 Consensus size: 11
59028262 TTAAATATGG
59028272 ATTTGAGAGAA
1 ATTTGAGAGAA
*
59028283 ATTTG-GAAGGA
1 ATTTGAG-AGAA
59028294 ATTTGAGAGCAA
1 ATTTGAGAG-AA
59028306 A-TTGAGAGGAA
1 ATTTGAGA-GAA
59028317 ATTT-AGAGAA
1 ATTTGAGAGAA
*
59028327 AATTGAGAGGAA
1 ATTTGAGA-GAA
59028339 ATTTGAGAG
1 ATTTGAGAG
59028348 GGGATTAGTT
Statistics
Matches: 54, Mismatches: 4, Indels: 14
0.75 0.06 0.19
Matches are distributed among these distances:
10 7 0.13
11 31 0.57
12 16 0.30
ACGTcount: A:0.43, C:0.01, G:0.30, T:0.25
Consensus pattern (11 bp):
ATTTGAGAGAA
Found at i:59028297 original size:22 final size:22
Alignment explanation
Indices: 59028272--59028347 Score: 95
Period size: 22 Copynumber: 3.4 Consensus size: 22
59028262 TTAAATATGG
59028272 ATTTGAGAGAAATTTG-GAAGG-A
1 ATTTGAGAGAAA-TTGAG-AGGAA
59028294 ATTTGAGAGCAAATTGAGAGGAA
1 ATTTGAGAG-AAATTGAGAGGAA
59028317 ATTT-AGAGAAAATTGAGAGGAA
1 ATTTGAGAG-AAATTGAGAGGAA
59028339 ATTTGAGAG
1 ATTTGAGAG
59028348 GGGATTAGTT
Statistics
Matches: 49, Mismatches: 1, Indels: 7
0.86 0.02 0.12
Matches are distributed among these distances:
22 36 0.73
23 13 0.27
ACGTcount: A:0.43, C:0.01, G:0.30, T:0.25
Consensus pattern (22 bp):
ATTTGAGAGAAATTGAGAGGAA
Found at i:59028333 original size:33 final size:35
Alignment explanation
Indices: 59028272--59028348 Score: 97
Period size: 33 Copynumber: 2.3 Consensus size: 35
59028262 TTAAATATGG
* * *
59028272 ATTTGAGA-GAAATTTGGAAGGAATTTGAGAGCAA
1 ATTTGAGAGGAAATTTAGAAGAAAATTGAGAGCAA
*
59028306 A-TTGAGAGGAAATTTAG-AGAAAATTGAGAGGAA
1 ATTTGAGAGGAAATTTAGAAGAAAATTGAGAGCAA
59028339 ATTTGAGAGG
1 ATTTGAGAGG
59028349 GGATTAGTTT
Statistics
Matches: 37, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
33 20 0.54
34 17 0.46
ACGTcount: A:0.43, C:0.01, G:0.31, T:0.25
Consensus pattern (35 bp):
ATTTGAGAGGAAATTTAGAAGAAAATTGAGAGCAA
Found at i:59041959 original size:7 final size:7
Alignment explanation
Indices: 59041949--59041977 Score: 58
Period size: 7 Copynumber: 4.1 Consensus size: 7
59041939 CCTAAAACCT
59041949 ACCCAAA
1 ACCCAAA
59041956 ACCCAAA
1 ACCCAAA
59041963 ACCCAAA
1 ACCCAAA
59041970 ACCCAAA
1 ACCCAAA
59041977 A
1 A
59041978 GACCCAACTA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 22 1.00
ACGTcount: A:0.59, C:0.41, G:0.00, T:0.00
Consensus pattern (7 bp):
ACCCAAA
Found at i:59042231 original size:133 final size:133
Alignment explanation
Indices: 59041993--59042258 Score: 523
Period size: 133 Copynumber: 2.0 Consensus size: 133
59041983 AACTAACAAA
59041993 ACTACACCCAGCCTAGAAAGATCAAACCCAATACCCTAAAACATACCCAAAAGACCCAATTACAA
1 ACTACACCCAGCCTAGAAAGATCAAACCCAATACCCTAAAACATACCCAAAAGACCCAATTACAA
59042058 GCCCAAACACCCTGACCCAACGACTTAAACTAACCCAAAGACCAATCAGCAAAAAAAACCTAGGT
66 GCCCAAACACCCTGACCCAACGACTTAAACTAACCCAAAGACCAATCAGCAAAAAAAACCTAGGT
59042123 GCG
131 GCG
59042126 ACTACACCCAGCCTAGAAAGATCAAACCCAATACCCTAAAACATACCCAAAAGACCCAATTACAA
1 ACTACACCCAGCCTAGAAAGATCAAACCCAATACCCTAAAACATACCCAAAAGACCCAATTACAA
*
59042191 GCCCAAACACCCTGACCCAACGACTTAAACTAACCCAAAGACCAATCAGCAAAAAAACCCTAGGT
66 GCCCAAACACCCTGACCCAACGACTTAAACTAACCCAAAGACCAATCAGCAAAAAAAACCTAGGT
59042256 GCG
131 GCG
59042259 CTGCACCTAG
Statistics
Matches: 132, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
133 132 1.00
ACGTcount: A:0.45, C:0.34, G:0.10, T:0.11
Consensus pattern (133 bp):
ACTACACCCAGCCTAGAAAGATCAAACCCAATACCCTAAAACATACCCAAAAGACCCAATTACAA
GCCCAAACACCCTGACCCAACGACTTAAACTAACCCAAAGACCAATCAGCAAAAAAAACCTAGGT
GCG
Found at i:59042549 original size:248 final size:248
Alignment explanation
Indices: 59042111--59042610 Score: 982
Period size: 248 Copynumber: 2.0 Consensus size: 248
59042101 AATCAGCAAA
59042111 AAAAACCTAGGTGCGACTACACCCAGCCTAGAAAGATCAAACCCAATACCCTAAAACATACCCAA
1 AAAAACCTAGGTGCGACTACACCCAGCCTAGAAAGATCAAACCCAATACCCTAAAACATACCCAA
59042176 AAGACCCAATTACAAGCCCAAACACCCTGACCCAACGACTTAAACTAACCCAAAGACCAATCAGC
66 AAGACCCAATTACAAGCCCAAACACCCTGACCCAACGACTTAAACTAACCCAAAGACCAATCAGC
59042241 AAAAAAACCCTAGGTGCGCTGCACCTAGGTTTTTTGACTGCTGCCATCGCCCTTGTCGCATCACC
131 AAAAAAACCCTAGGTGCGCTGCACCTAGGTTTTTTGACTGCTGCCATCGCCCTTGTCGCATCACC
59042306 TTTGCCACCGACCCACCACCGCCACTTGCCCACATGCGCCATCGAGTGCCTGC
196 TTTGCCACCGACCCACCACCGCCACTTGCCCACATGCGCCATCGAGTGCCTGC
59042359 AAAAACCTAGGTGCGACTACACCCAGCCTAGAAAGATCAAACCCAATACCCTAAAACATACCCAA
1 AAAAACCTAGGTGCGACTACACCCAGCCTAGAAAGATCAAACCCAATACCCTAAAACATACCCAA
59042424 AAGACCCAATTACAAGCCCAAACACCCTGACCCAACGACTTAAACTAACCCAAAGACCAATCAGC
66 AAGACCCAATTACAAGCCCAAACACCCTGACCCAACGACTTAAACTAACCCAAAGACCAATCAGC
* *
59042489 AAAAAACCCCTAGGTGCGCTGCCCCTAGGTTTTTTGACTGCTGCCATCGCCCTTGTCGCATCACC
131 AAAAAAACCCTAGGTGCGCTGCACCTAGGTTTTTTGACTGCTGCCATCGCCCTTGTCGCATCACC
59042554 TTTGCCACCGACCCACCACCGCCACTTGCCCACATGCGCCATCGAGTGCCTGC
196 TTTGCCACCGACCCACCACCGCCACTTGCCCACATGCGCCATCGAGTGCCTGC
59042607 AAAA
1 AAAA
59042611 CAATAAAAGA
Statistics
Matches: 250, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
248 250 1.00
ACGTcount: A:0.32, C:0.37, G:0.14, T:0.16
Consensus pattern (248 bp):
AAAAACCTAGGTGCGACTACACCCAGCCTAGAAAGATCAAACCCAATACCCTAAAACATACCCAA
AAGACCCAATTACAAGCCCAAACACCCTGACCCAACGACTTAAACTAACCCAAAGACCAATCAGC
AAAAAAACCCTAGGTGCGCTGCACCTAGGTTTTTTGACTGCTGCCATCGCCCTTGTCGCATCACC
TTTGCCACCGACCCACCACCGCCACTTGCCCACATGCGCCATCGAGTGCCTGC
Found at i:59043686 original size:21 final size:23
Alignment explanation
Indices: 59043661--59043704 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 23
59043651 TTTTATATTT
59043661 CATTTTTTT-T-ATATATACATA
1 CATTTTTTTATAATATATACATA
*
59043682 CATTTTTTTATAATATATGCATA
1 CATTTTTTTATAATATATACATA
59043705 TACGTACATG
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
21 9 0.45
22 1 0.05
23 10 0.50
ACGTcount: A:0.34, C:0.09, G:0.02, T:0.55
Consensus pattern (23 bp):
CATTTTTTTATAATATATACATA
Found at i:59044078 original size:44 final size:44
Alignment explanation
Indices: 59043995--59044080 Score: 111
Period size: 44 Copynumber: 2.0 Consensus size: 44
59043985 TAATTTATCT
* * *
59043995 ATATATATACATACTTACATATTTTTATATTTAATAATTTTAAA
1 ATATATATACATACATACATATTTTCATATTTAACAATTTTAAA
* *
59044039 ATATGTATACATACATACAT-TTTTCATATTTTCACAATTTTA
1 ATATATATACATACATACATATTTTCATA-TTTAACAATTTTA
59044081 TGTGCATACA
Statistics
Matches: 36, Mismatches: 5, Indels: 2
0.84 0.12 0.05
Matches are distributed among these distances:
43 7 0.19
44 29 0.81
ACGTcount: A:0.40, C:0.10, G:0.01, T:0.49
Consensus pattern (44 bp):
ATATATATACATACATACATATTTTCATATTTAACAATTTTAAA
Found at i:59044132 original size:7 final size:7
Alignment explanation
Indices: 59044122--59044151 Score: 60
Period size: 7 Copynumber: 4.3 Consensus size: 7
59044112 TTTTACAATT
59044122 TTATTCA
1 TTATTCA
59044129 TTATTCA
1 TTATTCA
59044136 TTATTCA
1 TTATTCA
59044143 TTATTCA
1 TTATTCA
59044150 TT
1 TT
59044152 CATTTACTTA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 23 1.00
ACGTcount: A:0.27, C:0.13, G:0.00, T:0.60
Consensus pattern (7 bp):
TTATTCA
Found at i:59048188 original size:84 final size:84
Alignment explanation
Indices: 59048047--59048245 Score: 398
Period size: 84 Copynumber: 2.4 Consensus size: 84
59048037 AGAAATTGTG
59048047 AAATCGCGCCCTCGTGGACGCGATTTCGCTATAGTTGGTCATGTAGGAAATAATTTTTTTTGACG
1 AAATCGCGCCCTCGTGGACGCGATTTCGCTATAGTTGGTCATGTAGGAAATAATTTTTTTTGACG
59048112 TTTCTAAGCAAACAGTGTC
66 TTTCTAAGCAAACAGTGTC
59048131 AAATCGCGCCCTCGTGGACGCGATTTCGCTATAGTTGGTCATGTAGGAAATAATTTTTTTTGACG
1 AAATCGCGCCCTCGTGGACGCGATTTCGCTATAGTTGGTCATGTAGGAAATAATTTTTTTTGACG
59048196 TTTCTAAGCAAACAGTGTC
66 TTTCTAAGCAAACAGTGTC
59048215 AAATCGCGCCCTCGTGGACGCGATTTCGCTA
1 AAATCGCGCCCTCGTGGACGCGATTTCGCTA
59048246 CAGTAGCAAG
Statistics
Matches: 115, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
84 115 1.00
ACGTcount: A:0.24, C:0.21, G:0.23, T:0.32
Consensus pattern (84 bp):
AAATCGCGCCCTCGTGGACGCGATTTCGCTATAGTTGGTCATGTAGGAAATAATTTTTTTTGACG
TTTCTAAGCAAACAGTGTC
Found at i:59053994 original size:29 final size:30
Alignment explanation
Indices: 59053960--59054017 Score: 91
Period size: 29 Copynumber: 2.0 Consensus size: 30
59053950 TGAAAATATT
59053960 AAAAATTTTAAAATTAT-TTAAAAAAAATA
1 AAAAATTTTAAAATTATCTTAAAAAAAATA
* *
59053989 AAAAATTTTAAATTTTTCTTAAAAAAAAT
1 AAAAATTTTAAAATTATCTTAAAAAAAAT
59054018 GAAATTTAAT
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
29 15 0.58
30 11 0.42
ACGTcount: A:0.60, C:0.02, G:0.00, T:0.38
Consensus pattern (30 bp):
AAAAATTTTAAAATTATCTTAAAAAAAATA
Found at i:59054089 original size:22 final size:22
Alignment explanation
Indices: 59054059--59054100 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
59054049 ATTTGGAGAT
*
59054059 TTTTTGAAGGAAATTGAGAGGA
1 TTTTAGAAGGAAATTGAGAGGA
*
59054081 TTTTAGAAGGAATTTGAGAG
1 TTTTAGAAGGAAATTGAGAG
59054101 TTTGAGAGAA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.36, C:0.00, G:0.31, T:0.33
Consensus pattern (22 bp):
TTTTAGAAGGAAATTGAGAGGA
Found at i:59054107 original size:30 final size:30
Alignment explanation
Indices: 59054072--59054130 Score: 91
Period size: 30 Copynumber: 2.0 Consensus size: 30
59054062 TTGAAGGAAA
* *
59054072 TTGAGAGGATTTTAGAAGGAATTTGAGAGT
1 TTGAGAGAATTTTAGAAGGAAATTGAGAGT
*
59054102 TTGAGAGAATTTTGGAAGGAAATTGAGAG
1 TTGAGAGAATTTTAGAAGGAAATTGAGAG
59054131 AAATTTTGAA
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
30 26 1.00
ACGTcount: A:0.36, C:0.00, G:0.34, T:0.31
Consensus pattern (30 bp):
TTGAGAGAATTTTAGAAGGAAATTGAGAGT
Found at i:59054127 original size:22 final size:21
Alignment explanation
Indices: 59054102--59054158 Score: 78
Period size: 22 Copynumber: 2.6 Consensus size: 21
59054092 ATTTGAGAGT
59054102 TTGAGAGAATTTTGGAAGGAAA
1 TTGAGAGAATTTT-GAAGGAAA
*
59054124 TTGAGAGAAATTTTGAAGGGAA
1 TTGAGAG-AATTTTGAAGGAAA
*
59054146 TTAAGAGAATTTT
1 TTGAGAGAATTTT
59054159 TAAAAGGAAT
Statistics
Matches: 32, Mismatches: 2, Indels: 3
0.86 0.05 0.08
Matches are distributed among these distances:
21 6 0.19
22 20 0.62
23 6 0.19
ACGTcount: A:0.40, C:0.00, G:0.28, T:0.32
Consensus pattern (21 bp):
TTGAGAGAATTTTGAAGGAAA
Found at i:59054159 original size:22 final size:22
Alignment explanation
Indices: 59054105--59054169 Score: 76
Period size: 22 Copynumber: 3.0 Consensus size: 22
59054095 TGAGAGTTTG
* * *
59054105 AGAGAATTTTGGAAGGAAATTG
1 AGAGAATTTTTGAAGGGAATTA
*
59054127 AGAGAAATTTTGAAGGGAATTA
1 AGAGAATTTTTGAAGGGAATTA
* *
59054149 AGAGAATTTTTAAAAGGAATT
1 AGAGAATTTTTGAAGGGAATT
59054170 TTTTTGTGAA
Statistics
Matches: 36, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
22 36 1.00
ACGTcount: A:0.45, C:0.00, G:0.26, T:0.29
Consensus pattern (22 bp):
AGAGAATTTTTGAAGGGAATTA
Found at i:59058197 original size:37 final size:37
Alignment explanation
Indices: 59058147--59058225 Score: 122
Period size: 37 Copynumber: 2.1 Consensus size: 37
59058137 TTATTACGAA
* * *
59058147 GTCTTACCCGGACATAATCTCCACACGAAGTTATCGG
1 GTCTTACCCGGACAAAATCCCCACACGAAGTCATCGG
*
59058184 GTCTTACCCGGACAAAATCCCCACACGTAGTCATCGG
1 GTCTTACCCGGACAAAATCCCCACACGAAGTCATCGG
59058221 GTCTT
1 GTCTT
59058226 TAGAGCTCGG
Statistics
Matches: 38, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
37 38 1.00
ACGTcount: A:0.25, C:0.32, G:0.19, T:0.24
Consensus pattern (37 bp):
GTCTTACCCGGACAAAATCCCCACACGAAGTCATCGG
Found at i:59058422 original size:47 final size:47
Alignment explanation
Indices: 59058344--59058758 Score: 704
Period size: 47 Copynumber: 8.7 Consensus size: 47
59058334 CCCTTCGGGA
* * * * * *
59058344 CTTATCACATTTATACACTTTCACATCCATCACGTTGGCCACTCGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
* *
59058391 CCTGTCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
59058438 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
59058485 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
*
59058532 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAAGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
*
59058579 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAAGC
1 CTTATCAC--ATATATACACTTTCACATTCATCACATCGGCCATTAGGC
59058628 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCAC--ATATATACACTTTCACATTCATCACATCGGCCATTAGGC
59058677 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
59058724 CTTATCACATATATACACTTTCACATTCATCACAT
1 CTTATCACATATATACACTTTCACATTCATCACAT
59058759 AGAATCCTAA
Statistics
Matches: 354, Mismatches: 12, Indels: 4
0.96 0.03 0.01
Matches are distributed among these distances:
47 259 0.73
49 95 0.27
ACGTcount: A:0.30, C:0.30, G:0.08, T:0.32
Consensus pattern (47 bp):
CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
Found at i:59058690 original size:192 final size:188
Alignment explanation
Indices: 59058344--59058758 Score: 704
Period size: 192 Copynumber: 2.2 Consensus size: 188
59058334 CCCTTCGGGA
* * * * ** *
59058344 CTTATCACATTTATACACTTTCACATCCATCACGTTGGCCACTCGGCCCTGTCACATATATACAC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCACTAAGCCCTATCACATATATACAC
*
59058409 TTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATACACTTTCACATTCATCACATC
66 TTTCACATTCATCACATCGGCCATTAAGCCTTATCACATATATACACTTTCACATTCATCACATC
59058474 GGCCATTAGGCCTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
131 GGCCATTAGGCCTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
* *
59058532 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAAGCCTTATCACATATATATAC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCACTAAGCCCTATCAC--ATATATAC
59058597 ACTTTCACATTCATCACATCGGCCATTAAGCCTTATCACATATATATACACTTTCACATTCATCA
64 ACTTTCACATTCATCACATCGGCCATTAAGCCTTATCAC--ATATATACACTTTCACATTCATCA
59058662 CATCGGCCATTAGGCCTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
127 CATCGGCCATTAGGCCTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
59058724 CTTATCACATATATACACTTTCACATTCATCACAT
1 CTTATCACATATATACACTTTCACATTCATCACAT
59058759 AGAATCCTAA
Statistics
Matches: 213, Mismatches: 10, Indels: 4
0.94 0.04 0.02
Matches are distributed among these distances:
188 46 0.22
190 46 0.22
192 121 0.57
ACGTcount: A:0.30, C:0.30, G:0.08, T:0.32
Consensus pattern (188 bp):
CTTATCACATATATACACTTTCACATTCATCACATCGGCCACTAAGCCCTATCACATATATACAC
TTTCACATTCATCACATCGGCCATTAAGCCTTATCACATATATACACTTTCACATTCATCACATC
GGCCATTAGGCCTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
Found at i:59061913 original size:40 final size:40
Alignment explanation
Indices: 59061862--59062049 Score: 286
Period size: 40 Copynumber: 4.7 Consensus size: 40
59061852 TTATTATTAT
* *
59061862 CGGATATATCACTAGCACGAATGCTCTTCGGAACTTAGTC
1 CGGATACATCACTAGCACGAATGCTCTTCGGAACTTAGCC
* * *
59061902 CGGATACATCACTAGCATGAATGCTCTTCGGGATTTAGCC
1 CGGATACATCACTAGCACGAATGCTCTTCGGAACTTAGCC
* * *
59061942 CGGATATATCACTAGCACCAATGCTCTTCGGAACTTAGTC
1 CGGATACATCACTAGCACGAATGCTCTTCGGAACTTAGCC
* *
59061982 CGGATACATCACTAGCACGAATGCTCTTTGGGACTTAGCC
1 CGGATACATCACTAGCACGAATGCTCTTCGGAACTTAGCC
59062022 CGGATACATCACTAGCACGAATGCTCTT
1 CGGATACATCACTAGCACGAATGCTCTT
59062050 NNNNNNNNNN
Statistics
Matches: 132, Mismatches: 16, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
40 132 1.00
ACGTcount: A:0.27, C:0.27, G:0.20, T:0.27
Consensus pattern (40 bp):
CGGATACATCACTAGCACGAATGCTCTTCGGAACTTAGCC
Found at i:59061995 original size:80 final size:80
Alignment explanation
Indices: 59061862--59062049 Score: 331
Period size: 80 Copynumber: 2.4 Consensus size: 80
59061852 TTATTATTAT
*
59061862 CGGATATATCACTAGCACGAATGCTCTTCGGAACTTAGTCCGGATACATCACTAGCATGAATGCT
1 CGGATATATCACTAGCACGAATGCTCTTCGGAACTTAGTCCGGATACATCACTAGCACGAATGCT
*
59061927 CTTCGGGATTTAGCC
66 CTTCGGGACTTAGCC
*
59061942 CGGATATATCACTAGCACCAATGCTCTTCGGAACTTAGTCCGGATACATCACTAGCACGAATGCT
1 CGGATATATCACTAGCACGAATGCTCTTCGGAACTTAGTCCGGATACATCACTAGCACGAATGCT
*
59062007 CTTTGGGACTTAGCC
66 CTTCGGGACTTAGCC
*
59062022 CGGATACATCACTAGCACGAATGCTCTT
1 CGGATATATCACTAGCACGAATGCTCTT
59062050 NNNNNNNNNN
Statistics
Matches: 102, Mismatches: 6, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
80 102 1.00
ACGTcount: A:0.27, C:0.27, G:0.20, T:0.27
Consensus pattern (80 bp):
CGGATATATCACTAGCACGAATGCTCTTCGGAACTTAGTCCGGATACATCACTAGCACGAATGCT
CTTCGGGACTTAGCC
Found at i:59067225 original size:16 final size:16
Alignment explanation
Indices: 59067206--59067243 Score: 76
Period size: 16 Copynumber: 2.4 Consensus size: 16
59067196 TTGAATTCGT
59067206 TTGTGAATTAATTCAC
1 TTGTGAATTAATTCAC
59067222 TTGTGAATTAATTCAC
1 TTGTGAATTAATTCAC
59067238 TTGTGA
1 TTGTGA
59067244 CATTCAATAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 22 1.00
ACGTcount: A:0.29, C:0.11, G:0.16, T:0.45
Consensus pattern (16 bp):
TTGTGAATTAATTCAC
Found at i:59068968 original size:21 final size:22
Alignment explanation
Indices: 59068926--59068998 Score: 64
Period size: 21 Copynumber: 3.4 Consensus size: 22
59068916 TTGTTTCTTG
*
59068926 TTTATTAT-TATTA-TTAGTTAT
1 TTTATTATCTATTATTTA-CTAT
*
59068947 TTTATTCTCT-TTATTTACTA-
1 TTTATTATCTATTATTTACTAT
*
59068967 TTTATTATCTATTATTTTCTAT
1 TTTATTATCTATTATTTACTAT
59068989 TCTTAGTTAT
1 T-TTA-TTAT
59068999 ATTCTTTTAT
Statistics
Matches: 42, Mismatches: 4, Indels: 9
0.76 0.07 0.16
Matches are distributed among these distances:
20 9 0.21
21 21 0.50
22 5 0.12
23 3 0.07
24 4 0.10
ACGTcount: A:0.23, C:0.08, G:0.03, T:0.66
Consensus pattern (22 bp):
TTTATTATCTATTATTTACTAT
Found at i:59072259 original size:26 final size:26
Alignment explanation
Indices: 59072228--59072278 Score: 93
Period size: 26 Copynumber: 2.0 Consensus size: 26
59072218 TCTCGAATGA
59072228 CTATCTTGATGAGAACATTTACATGG
1 CTATCTTGATGAGAACATTTACATGG
*
59072254 CTATCTTGATGAGACCATTTACATG
1 CTATCTTGATGAGAACATTTACATG
59072279 ACTCAACCTA
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 24 1.00
ACGTcount: A:0.29, C:0.18, G:0.18, T:0.35
Consensus pattern (26 bp):
CTATCTTGATGAGAACATTTACATGG
Found at i:59082168 original size:10 final size:10
Alignment explanation
Indices: 59082155--59082199 Score: 54
Period size: 10 Copynumber: 4.4 Consensus size: 10
59082145 CTAAGATGTG
*
59082155 AATTGAATTG
1 AATTGAATTA
59082165 AATTGAATATA
1 AATTGAAT-TA
*
59082176 AATTGTATTA
1 AATTGAATTA
*
59082186 AATTGAGTTA
1 AATTGAATTA
59082196 AATT
1 AATT
59082200 TACTTGTATA
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
10 22 0.73
11 8 0.27
ACGTcount: A:0.44, C:0.00, G:0.13, T:0.42
Consensus pattern (10 bp):
AATTGAATTA
Found at i:59082179 original size:21 final size:20
Alignment explanation
Indices: 59082155--59082199 Score: 54
Period size: 21 Copynumber: 2.2 Consensus size: 20
59082145 CTAAGATGTG
*
59082155 AATTGAATTGAATTGAATATA
1 AATTGAATTAAATTGAAT-TA
* *
59082176 AATTGTATTAAATTGAGTTA
1 AATTGAATTAAATTGAATTA
59082196 AATT
1 AATT
59082200 TACTTGTATA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
20 6 0.29
21 15 0.71
ACGTcount: A:0.44, C:0.00, G:0.13, T:0.42
Consensus pattern (20 bp):
AATTGAATTAAATTGAATTA
Found at i:59082869 original size:24 final size:23
Alignment explanation
Indices: 59082842--59082889 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 23
59082832 TACCCTTTAT
59082842 TGGCTCGCATAAGCTTTCCGATTA
1 TGGCTCGCATAAGCTTTCCG-TTA
** *
59082866 TGGCTCTTATGAGCTTTCCGTTA
1 TGGCTCGCATAAGCTTTCCGTTA
59082889 T
1 T
59082890 ACAGCCTGGA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
23 4 0.19
24 17 0.81
ACGTcount: A:0.17, C:0.23, G:0.21, T:0.40
Consensus pattern (23 bp):
TGGCTCGCATAAGCTTTCCGTTA
Found at i:59088054 original size:14 final size:14
Alignment explanation
Indices: 59088035--59088069 Score: 52
Period size: 14 Copynumber: 2.5 Consensus size: 14
59088025 AACAGTTTTA
*
59088035 ACTATACTAGAATG
1 ACTATACTAAAATG
59088049 ACTATACTAAAATG
1 ACTATACTAAAATG
*
59088063 ACCATAC
1 ACTATAC
59088070 ATAGTAAATA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.46, C:0.20, G:0.09, T:0.26
Consensus pattern (14 bp):
ACTATACTAAAATG
Found at i:59093625 original size:22 final size:23
Alignment explanation
Indices: 59093572--59093627 Score: 69
Period size: 22 Copynumber: 2.5 Consensus size: 23
59093562 CCCGTTTTTA
* * *
59093572 ATTAAAATTAAAATTATTTTTTT
1 ATTAAAATTAAAACTATATTGTT
*
59093595 AATAAAATTAAAACTA-ATTGTT
1 ATTAAAATTAAAACTATATTGTT
59093617 ATTAAAATTAA
1 ATTAAAATTAA
59093628 TTGTTAGTAA
Statistics
Matches: 28, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
22 14 0.50
23 14 0.50
ACGTcount: A:0.52, C:0.02, G:0.02, T:0.45
Consensus pattern (23 bp):
ATTAAAATTAAAACTATATTGTT
Found at i:59093640 original size:16 final size:16
Alignment explanation
Indices: 59093603--59093642 Score: 62
Period size: 16 Copynumber: 2.5 Consensus size: 16
59093593 TTAATAAAAT
* *
59093603 TAAAACTAATTGTTAT
1 TAAAATTAATTGTTAG
59093619 TAAAATTAATTGTTAG
1 TAAAATTAATTGTTAG
59093635 TAAAATTA
1 TAAAATTA
59093643 TCAAATTATT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
16 22 1.00
ACGTcount: A:0.47, C:0.03, G:0.07, T:0.42
Consensus pattern (16 bp):
TAAAATTAATTGTTAG
Found at i:59093712 original size:66 final size:67
Alignment explanation
Indices: 59093631--59093773 Score: 243
Period size: 68 Copynumber: 2.1 Consensus size: 67
59093621 AAATTAATTG
* *
59093631 TTAGTAAAATTATCAAATTATTAATTG-TTAATTGTATTAATTTTTGTAATAAAATCTAACATTT
1 TTAGTAAAATTATCAAATTATTAATTGATTAATTGTATTAATTGTTGTAACAAAATCTAACATTT
59093695 GA
66 GA
*
59093697 TTAGTAAATTTATCAAATTATTAATTGTATTAATTGTATTAATTGTTGTAACAAAATCTAACATT
1 TTAGTAAAATTATCAAATTATTAATTG-ATTAATTGTATTAATTGTTGTAACAAAATCTAACATT
59093762 TGA
65 TGA
59093765 TTAGTAAAA
1 TTAGTAAAA
59093774 CAAACTTGAT
Statistics
Matches: 71, Mismatches: 4, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
66 26 0.37
68 45 0.63
ACGTcount: A:0.41, C:0.05, G:0.08, T:0.45
Consensus pattern (67 bp):
TTAGTAAAATTATCAAATTATTAATTGATTAATTGTATTAATTGTTGTAACAAAATCTAACATTT
GA
Found at i:59093727 original size:9 final size:9
Alignment explanation
Indices: 59093715--59093742 Score: 56
Period size: 9 Copynumber: 3.1 Consensus size: 9
59093705 TTTATCAAAT
59093715 TATTAATTG
1 TATTAATTG
59093724 TATTAATTG
1 TATTAATTG
59093733 TATTAATTG
1 TATTAATTG
59093742 T
1 T
59093743 TGTAACAAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 19 1.00
ACGTcount: A:0.32, C:0.00, G:0.11, T:0.57
Consensus pattern (9 bp):
TATTAATTG
Found at i:59094041 original size:12 final size:12
Alignment explanation
Indices: 59094022--59094051 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
59094012 CTCCCATATT
59094022 TCGGGCGGGTCG
1 TCGGGCGGGTCG
*
59094034 TTGGGCGGGTCG
1 TCGGGCGGGTCG
59094046 TCGGGC
1 TCGGGC
59094052 CGGGCCGGGC
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
12 16 1.00
ACGTcount: A:0.00, C:0.23, G:0.57, T:0.20
Consensus pattern (12 bp):
TCGGGCGGGTCG
Found at i:59096543 original size:10 final size:11
Alignment explanation
Indices: 59096518--59096542 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
59096508 ATTTGGGAGC
59096518 AAAATGAGTGA
1 AAAATGAGTGA
59096529 AAAATGAGTGA
1 AAAATGAGTGA
59096540 AAA
1 AAA
59096543 TCAGAAAATC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.60, C:0.00, G:0.24, T:0.16
Consensus pattern (11 bp):
AAAATGAGTGA
Found at i:59106707 original size:21 final size:22
Alignment explanation
Indices: 59106683--59106724 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 22
59106673 TATTTTACTT
59106683 ATTTAATAAAAT-TTTATTTTA
1 ATTTAATAAAATGTTTATTTTA
* *
59106704 ATTTCATAATATGTTTATTTT
1 ATTTAATAAAATGTTTATTTT
59106725 TATAACACAT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 10 0.56
22 8 0.44
ACGTcount: A:0.36, C:0.02, G:0.02, T:0.60
Consensus pattern (22 bp):
ATTTAATAAAATGTTTATTTTA
Found at i:59110235 original size:70 final size:70
Alignment explanation
Indices: 59110151--59110290 Score: 253
Period size: 70 Copynumber: 2.0 Consensus size: 70
59110141 AAAACATAAA
*
59110151 ACATGAAAAAAGTTCATTATCTTTGCCGAAAATACAAAAGAAAAATAAAGAAAAAGAACAAGTTG
1 ACATGAAAAAAGTTCATCATCTTTGCCGAAAATACAAAAGAAAAATAAAGAAAAAGAACAAGTTG
59110216 GTTCG
66 GTTCG
* *
59110221 ACATGCAAAAAGTTCATCATCTTTGTCGAAAATACAAAAGAAAAATAAAGAAAAAGAACAAGTTG
1 ACATGAAAAAAGTTCATCATCTTTGCCGAAAATACAAAAGAAAAATAAAGAAAAAGAACAAGTTG
59110286 GTTCG
66 GTTCG
59110291 GCCTTGTTTT
Statistics
Matches: 67, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
70 67 1.00
ACGTcount: A:0.51, C:0.12, G:0.16, T:0.21
Consensus pattern (70 bp):
ACATGAAAAAAGTTCATCATCTTTGCCGAAAATACAAAAGAAAAATAAAGAAAAAGAACAAGTTG
GTTCG
Found at i:59118854 original size:31 final size:31
Alignment explanation
Indices: 59118816--59118876 Score: 122
Period size: 31 Copynumber: 2.0 Consensus size: 31
59118806 CTCTTTACTG
59118816 ATTAGTTTTTGGTAAAGCATGTCACTTACCA
1 ATTAGTTTTTGGTAAAGCATGTCACTTACCA
59118847 ATTAGTTTTTGGTAAAGCATGTCACTTACC
1 ATTAGTTTTTGGTAAAGCATGTCACTTACC
59118877 GATAGAAATC
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 30 1.00
ACGTcount: A:0.28, C:0.16, G:0.16, T:0.39
Consensus pattern (31 bp):
ATTAGTTTTTGGTAAAGCATGTCACTTACCA
Found at i:59119391 original size:5 final size:5
Alignment explanation
Indices: 59119381--59119412 Score: 64
Period size: 5 Copynumber: 6.4 Consensus size: 5
59119371 ACCCAAATGC
59119381 TTTAT TTTAT TTTAT TTTAT TTTAT TTTAT TT
1 TTTAT TTTAT TTTAT TTTAT TTTAT TTTAT TT
59119413 CACTTAGTTT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 27 1.00
ACGTcount: A:0.19, C:0.00, G:0.00, T:0.81
Consensus pattern (5 bp):
TTTAT
Found at i:59119755 original size:40 final size:40
Alignment explanation
Indices: 59119672--59119765 Score: 118
Period size: 40 Copynumber: 2.4 Consensus size: 40
59119662 TTTGGATGAC
*
59119672 AAACGCCGCTAAAAATCAAGCATTAGCGGCGCAAAGCATA
1 AAACGCCGCTAAAAATCAAGCATTAGCGGCGCAAAGCAAA
* * ***
59119712 AAACGCCGCTAAAGATCTAGCATTAGCGGCG-ATCCTCAAA
1 AAACGCCGCTAAAAATCAAGCATTAGCGGCGCA-AAGCAAA
59119752 AAACGCCGCTAAAA
1 AAACGCCGCTAAAA
59119766 GTCAGACATA
Statistics
Matches: 46, Mismatches: 7, Indels: 2
0.84 0.13 0.04
Matches are distributed among these distances:
39 1 0.02
40 45 0.98
ACGTcount: A:0.40, C:0.27, G:0.19, T:0.14
Consensus pattern (40 bp):
AAACGCCGCTAAAAATCAAGCATTAGCGGCGCAAAGCAAA
Found at i:59120191 original size:114 final size:114
Alignment explanation
Indices: 59119817--59120476 Score: 810
Period size: 114 Copynumber: 5.8 Consensus size: 114
59119807 GAACATCATT
* * * * *
59119817 AGCGTCGCAAAATCTCTTAACCAAAACGCAGTGTTTTGGTC-TAGATGTATATTAGAATTAGTGT
1 AGCGCCGCAAAATATCTTAACCAAAACGCAGAG-TTTGGTCTTA-AGGTATATTAGAATTAGTGG
* * * * * *
59119881 CGATTATAGGAAAACACCGCTAAAG-AAAGTATTAGCGGCG-ATCGCCAAA
64 CGCTTATGGGAAAACGCCGCTAAAGCATAGTATTAGCGGCGCGTCGTCAAA
* * * *
59119930 CA-CGCCGCAACATATCTTAACCAAAATGCAGAGTTTGGTCTTTATGTATATTAGAATTAGTGGC
1 -AGCGCCGCAAAATATCTTAACCAAAACGCAGAGTTTGGTCTTAAGGTATATTAGAATTAGTGGC
* ** * * ** * *
59119994 GCATATGAAAAAACTCCACTAAAGCA-AGTATTAGCGGCGATTTGTGAAA
65 GCTTATGGGAAAACGCCGCTAAAGCATAGTATTAGCGGCGCGTCGTCAAA
* * *
59120043 AGCGCCTCAAAATATATTAACCAAAACGCAGAGTTTGGTCTTAAGGTATATTAGAATTAGTAGCG
1 AGCGCCGCAAAATATCTTAACCAAAACGCAGAGTTTGGTCTTAAGGTATATTAGAATTAGTGGCG
* * *
59120108 CTTATGGGAAAACGCCGCTAACGCATAGTATTAGTGGCGTGTCGTCAAA
66 CTTATGGGAAAACGCCGCTAAAGCATAGTATTAGCGGCGCGTCGTCAAA
* * * *
59120157 AGCGCCGCAACATATCTTAACCAAAACGCAGAGTTTGGTCTTGAGGTATACTAGAATTAGTGGTG
1 AGCGCCGCAAAATATCTTAACCAAAACGCAGAGTTTGGTCTTAAGGTATATTAGAATTAGTGGCG
* *
59120222 TTTATTGGAAAACGCCGCTAAAGCATAGTATTAGCGGCGCGTCGTCAAA
66 CTTATGGGAAAACGCCGCTAAAGCATAGTATTAGCGGCGCGTCGTCAAA
* *
59120271 AGCGTCGCAACATATCTTAACCAAAACGCAGAGTTTGGTCTTAAGGTATATTAGAATTAGTGGCG
1 AGCGCCGCAAAATATCTTAACCAAAACGCAGAGTTTGGTCTTAAGGTATATTAGAATTAGTGGCG
** * * *
59120336 CTTATTCGAAAACGCCGCTAATGCATAGTATTAGCGGCGCGTCATTC-GA
66 CTTATGGGAAAACGCCGCTAAAGCATAGTATTAGCGGCGCGTC-GTCAAA
* * *
59120385 AGCGCCGCAAAATATCTTAACCAAAATGCAGAGTTTGGTCTTGAGGTACATTAGAATTAGTGGCG
1 AGCGCCGCAAAATATCTTAACCAAAACGCAGAGTTTGGTCTTAAGGTATATTAGAATTAGTGGCG
* *
59120450 CTTATGGGAAAACGCTGCTAATGCATA
66 CTTATGGGAAAACGCCGCTAAAGCATA
59120477 CAAGCGCCGC
Statistics
Matches: 475, Mismatches: 65, Indels: 12
0.86 0.12 0.02
Matches are distributed among these distances:
112 58 0.12
113 108 0.23
114 307 0.65
115 2 0.00
ACGTcount: A:0.33, C:0.18, G:0.22, T:0.26
Consensus pattern (114 bp):
AGCGCCGCAAAATATCTTAACCAAAACGCAGAGTTTGGTCTTAAGGTATATTAGAATTAGTGGCG
CTTATGGGAAAACGCCGCTAAAGCATAGTATTAGCGGCGCGTCGTCAAA
Found at i:59120454 original size:342 final size:340
Alignment explanation
Indices: 59119817--59120476 Score: 903
Period size: 342 Copynumber: 1.9 Consensus size: 340
59119807 GAACATCATT
* * * * *
59119817 AGCGTCGCAAAATCTCTTAACCAAAACGCAGTGTTTTGGTCTAGATGTATATTAGAATTAGTGTC
1 AGCGCCGCAAAATATCTTAACCAAAACGCAGAGTTTTGGTCTAGAGGTATACTAGAATTAGTGTC
59119882 GATTATAGGAAAACACCGCTAAAGAAAGTATTAGCGGCGATCGCCAAACACGCCGCAACATATCT
66 GATTATAGGAAAACACCGCTAAAGAAAGTATTAGCGGCGATCGCCAAACACGCCGCAACATATCT
* * * *
59119947 TAACCAAAATGCAGAGTTTGGTCTTTATGTATATTAGAATTAGTGGCGCATATGAAAAAACTCCA
131 TAACCAAAACGCAGAGTTTGGTCTTAAGGTATATTAGAATTAGTGGCGCATATGAAAAAACGCCA
* ** *
59120012 CTAAAGCAAGTATTAGCGGCGATTTGTGAAAAGCGCCTCAAAATATATTAACCAAAACGCAGAGT
196 CTAAAGCAAGTATTAGCGGCGAGTCATGAAAAGCGCCGCAAAATATATTAACCAAAACGCAGAGT
*
59120077 TTGGTCTTAAGGTATATTAGAATTAGTAGCGCTTATGGGAAAACGCCGCTAACGCATAGTATTAG
261 TTGGTCTTAAGGTACATTAGAATTAGTAGCGCTTATGGGAAAACGCCGCTAACGCATAGTATTAG
59120142 TGGCGTGTCGTCAAA
326 TGGCGTGTCGTCAAA
* *
59120157 AGCGCCGCAACATATCTTAACCAAAACGCAGAG-TTTGGTCTTGAGGTATACTAGAATTAGTGGT
1 AGCGCCGCAAAATATCTTAACCAAAACGCAGAGTTTTGGTCTAGAGGTATACTAGAATTAGT-GT
* * * * * * *
59120221 -GTTTATTGGAAAACGCCGCTAAAGCATAGTATTAGCGGCGCGTCGTCAAA-AGCGTCGCAACAT
65 CGATTATAGGAAAACACCGCTAAAG-AAAGTATTAGCGGCG-ATCGCCAAACA-CGCCGCAACAT
* ***
59120284 ATCTTAACCAAAACGCAGAGTTTGGTCTTAAGGTATATTAGAATTAGTGGCGCTTATTCGAAAAC
127 ATCTTAACCAAAACGCAGAGTTTGGTCTTAAGGTATATTAGAATTAGTGGCGCATATGAAAAAAC
* * * *** * *
59120349 GCCGCTAATGCATAGTATTAGCGGCGCGTCATTCGAAGCGCCGCAAAATATCTTAACCAAAATGC
192 GCCACTAAAGCA-AGTATTAGCGGCGAGTCATGAAAAGCGCCGCAAAATATATTAACCAAAACGC
* * * *
59120414 AGAGTTTGGTCTTGAGGTACATTAGAATTAGTGGCGCTTATGGGAAAACGCTGCTAATGCATA
256 AGAGTTTGGTCTTAAGGTACATTAGAATTAGTAGCGCTTATGGGAAAACGCCGCTAACGCATA
59120477 CAAGCGCCGC
Statistics
Matches: 276, Mismatches: 39, Indels: 8
0.85 0.12 0.02
Matches are distributed among these distances:
339 46 0.17
340 46 0.17
341 84 0.30
342 100 0.36
ACGTcount: A:0.33, C:0.18, G:0.22, T:0.26
Consensus pattern (340 bp):
AGCGCCGCAAAATATCTTAACCAAAACGCAGAGTTTTGGTCTAGAGGTATACTAGAATTAGTGTC
GATTATAGGAAAACACCGCTAAAGAAAGTATTAGCGGCGATCGCCAAACACGCCGCAACATATCT
TAACCAAAACGCAGAGTTTGGTCTTAAGGTATATTAGAATTAGTGGCGCATATGAAAAAACGCCA
CTAAAGCAAGTATTAGCGGCGAGTCATGAAAAGCGCCGCAAAATATATTAACCAAAACGCAGAGT
TTGGTCTTAAGGTACATTAGAATTAGTAGCGCTTATGGGAAAACGCCGCTAACGCATAGTATTAG
TGGCGTGTCGTCAAA
Found at i:59120895 original size:7 final size:7
Alignment explanation
Indices: 59120885--59120969 Score: 64
Period size: 7 Copynumber: 12.0 Consensus size: 7
59120875 AGAGTTTTGA
59120885 GTTTAGG
1 GTTTAGG
*
59120892 GTTTATG
1 GTTTAGG
* *
59120899 ATGTA-G
1 GTTTAGG
*
59120905 GTTTTGG
1 GTTTAGG
*
59120912 TGTTTTGG
1 -GTTTAGG
59120920 GTTTAGG
1 GTTTAGG
*
59120927 GTTTAGAA
1 GTTTAG-G
59120935 GTTTAGG
1 GTTTAGG
*
59120942 GTTTAAG
1 GTTTAGG
*
59120949 GTTTGGG
1 GTTTAGG
*
59120956 GTTTGGG
1 GTTTAGG
59120963 GTTTAGG
1 GTTTAGG
59120970 CCGCTTTAGT
Statistics
Matches: 62, Mismatches: 13, Indels: 6
0.77 0.16 0.07
Matches are distributed among these distances:
6 3 0.05
7 46 0.74
8 13 0.21
ACGTcount: A:0.14, C:0.00, G:0.40, T:0.46
Consensus pattern (7 bp):
GTTTAGG
Found at i:59120938 original size:15 final size:14
Alignment explanation
Indices: 59120920--59120959 Score: 53
Period size: 15 Copynumber: 2.8 Consensus size: 14
59120910 GGTGTTTTGG
59120920 GTTTAGGGTTTAGAA
1 GTTTAGGGTTTA-AA
*
59120935 GTTTAGGGTTTAAG
1 GTTTAGGGTTTAAA
*
59120949 GTTTGGGGTTT
1 GTTTAGGGTTT
59120960 GGGGTTTAGG
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
14 11 0.48
15 12 0.52
ACGTcount: A:0.17, C:0.00, G:0.38, T:0.45
Consensus pattern (14 bp):
GTTTAGGGTTTAAA
Found at i:59123411 original size:36 final size:36
Alignment explanation
Indices: 59123345--59123414 Score: 113
Period size: 36 Copynumber: 1.9 Consensus size: 36
59123335 ATAATTTTAG
** *
59123345 ATTATTAAGAATAAAATTATATGTGGAAGTGTATTT
1 ATTATTAAGAATAAAATTATATCCGAAAGTGTATTT
59123381 ATTATTAAGAATAAAATTATATCCGAAAGTGTAT
1 ATTATTAAGAATAAAATTATATCCGAAAGTGTAT
59123415 ATAAATTTAT
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
36 31 1.00
ACGTcount: A:0.44, C:0.03, G:0.14, T:0.39
Consensus pattern (36 bp):
ATTATTAAGAATAAAATTATATCCGAAAGTGTATTT
Found at i:59125018 original size:21 final size:21
Alignment explanation
Indices: 59124995--59125061 Score: 116
Period size: 21 Copynumber: 3.2 Consensus size: 21
59124985 GGCAGCAAAG
*
59124995 GAAGCAGAGGCTGCAACGAGG
1 GAAGCAGAGGCTGCAACGAGA
59125016 GAAGCAGAGGCTGCAACGAGA
1 GAAGCAGAGGCTGCAACGAGA
*
59125037 GAAGCAGAGGCTGCAGCGAGA
1 GAAGCAGAGGCTGCAACGAGA
59125058 GAAG
1 GAAG
59125062 AAGTGAGAGA
Statistics
Matches: 44, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 44 1.00
ACGTcount: A:0.36, C:0.18, G:0.42, T:0.04
Consensus pattern (21 bp):
GAAGCAGAGGCTGCAACGAGA
Found at i:59125619 original size:42 final size:40
Alignment explanation
Indices: 59125461--59125752 Score: 239
Period size: 42 Copynumber: 7.0 Consensus size: 40
59125451 ATTTTTTCTA
* * * **
59125461 AAAGCGCCGCTAAA-AGTCATGTTCTATAGCGGCGTTTGTGA
1 AAAGCGCCGCTAAAGA-ACATGATCTTTAGCGGCGTTT-TTT
* *
59125502 AGTAAGCGCCGCTAAAGAACATTA-CTTTTAGCGGCGTTTGTAGTG
1 A--AAGCGCCGCTAAAGAACATGATC-TTTAGCGGCGTTT-T--TT
* *
59125547 AAAGTGCCGCTAAAGAACATGATCTGTAGCGGCGTTTTTT
1 AAAGCGCCGCTAAAGAACATGATCTTTAGCGGCGTTTTTT
* *
59125587 ACCAAGCGCCGCTATAGAACATTA-CTTTTAGCGGCGTTTTTGTT
1 A--AAGCGCCGCTAAAGAACATGATC-TTTAGCGGCG-TTTT-TT
*
59125631 TAAGCGCCGCTAAAGAACATGATCTTTAGCGGCGTCTTTTTT
1 AAAGCGCCGCTAAAGAACATGATCTTTAGCGGCG--TTTTTT
* * * *
59125673 TAAGTGCCGCTAAAGGACATGATCTTTAGCGGTGCTTTTTT
1 AAAGCGCCGCTAAAGAACATGATCTTTAGCGGCG-TTTTTT
** * *
59125714 GTAGCGCCACTAAAGAACATGACCTTTAGCGGCGTTTTT
1 AAAGCGCCGCTAAAGAACATGATCTTTAGCGGCGTTTTT
59125753 CTGTAAGCGC
Statistics
Matches: 209, Mismatches: 28, Indels: 29
0.79 0.11 0.11
Matches are distributed among these distances:
40 7 0.03
41 36 0.17
42 91 0.44
43 70 0.33
44 4 0.02
45 1 0.00
ACGTcount: A:0.25, C:0.20, G:0.24, T:0.31
Consensus pattern (40 bp):
AAAGCGCCGCTAAAGAACATGATCTTTAGCGGCGTTTTTT
Found at i:59125701 original size:84 final size:84
Alignment explanation
Indices: 59125462--59125752 Score: 313
Period size: 84 Copynumber: 3.5 Consensus size: 84
59125452 TTTTTTCTAA
* * * ** *
59125462 AAGCGCCGCTAAA-AGTCATGTTCTATAGCGGCGTTTGTGAAGTAAGCGCCGCTAAAGAACATTA
1 AAGCGCCGCTAAAGA-ACATGATCTTTAGCGGCGTTT-TTTACTAAGCGCCGCTAAAGAACATTA
* *
59125526 CTTTTAGCGGCGTTTGTAGTGA
64 CTTTTAGCGGCGTTT-TTGTGT
* * * *
59125548 AAGTGCCGCTAAAGAACATGATCTGTAGCGGCGTTTTTTACCAAGCGCCGCTATAGAACATTACT
1 AAGCGCCGCTAAAGAACATGATCTTTAGCGGCGTTTTTTACTAAGCGCCGCTAAAGAACATTACT
*
59125613 TTTAGCGGCGTTTTTGTTT
66 TTTAGCGGCGTTTTTGTGT
* * * *
59125632 AAGCGCCGCTAAAGAACATGATCTTTAGCGGCGTCTTTTT-TTAAGTGCCGCTAAAGGACATGA-
1 AAGCGCCGCTAAAGAACATGATCTTTAGCGGCGT-TTTTTACTAAGCGCCGCTAAAGAACATTAC
*
59125695 TCTTTAGCGGTGCTTTTT-TGT
65 T-TTTAGCGGCG-TTTTTGTGT
* *
59125716 -AGCGCCACTAAAGAACATGACCTTTAGCGGCGTTTTT
1 AAGCGCCGCTAAAGAACATGATCTTTAGCGGCGTTTTT
59125753 CTGTAAGCGC
Statistics
Matches: 177, Mismatches: 24, Indels: 12
0.83 0.11 0.06
Matches are distributed among these distances:
82 4 0.02
83 32 0.18
84 63 0.36
85 47 0.27
86 30 0.17
87 1 0.01
ACGTcount: A:0.25, C:0.20, G:0.24, T:0.31
Consensus pattern (84 bp):
AAGCGCCGCTAAAGAACATGATCTTTAGCGGCGTTTTTTACTAAGCGCCGCTAAAGAACATTACT
TTTAGCGGCGTTTTTGTGT
Found at i:59125727 original size:41 final size:42
Alignment explanation
Indices: 59125503--59125762 Score: 257
Period size: 42 Copynumber: 6.2 Consensus size: 42
59125493 CGTTTGTGAA
* *
59125503 GTAAGCGCCGCTAAAGAACATTA-CTTTTAGCGGCG-TTTGTAGT
1 GTAAGCGCCGCTAAAGAACATGATC-TTTAGCGGCGCTTT-T-TT
* * *
59125546 GAAAGTGCCGCTAAAGAACATGATCTGTAGCGGCG-TTTTTT
1 GTAAGCGCCGCTAAAGAACATGATCTTTAGCGGCGCTTTTTT
** * *
59125587 ACCAAGCGCCGCTATAGAACATTA-CTTTTAGCGGCG-TTTTTGT
1 -GTAAGCGCCGCTAAAGAACATGATC-TTTAGCGGCGCTTTTT-T
*
59125630 TTAAGCGCCGCTAAAGAACATGATCTTTAGCGGCGTCTTTTTT
1 GTAAGCGCCGCTAAAGAACATGATCTTTAGCGGCG-CTTTTTT
* * *
59125673 -TAAGTGCCGCTAAAGGACATGATCTTTAGCGGTGCTTTTTT
1 GTAAGCGCCGCTAAAGAACATGATCTTTAGCGGCGCTTTTTT
* *
59125714 GT-AGCGCCACTAAAGAACATGACCTTTAGCGGCG-TTTTTCT
1 GTAAGCGCCGCTAAAGAACATGATCTTTAGCGGCGCTTTTT-T
59125755 GTAAGCGC
1 GTAAGCGC
59125763 TGCAAAAGTT
Statistics
Matches: 184, Mismatches: 23, Indels: 21
0.81 0.10 0.09
Matches are distributed among these distances:
40 5 0.03
41 39 0.21
42 99 0.54
43 35 0.19
44 6 0.03
ACGTcount: A:0.24, C:0.20, G:0.24, T:0.32
Consensus pattern (42 bp):
GTAAGCGCCGCTAAAGAACATGATCTTTAGCGGCGCTTTTTT
Found at i:59129878 original size:18 final size:18
Alignment explanation
Indices: 59129857--59129894 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 18
59129847 TAAAATTCTT
59129857 TAAATAATAAT-TTAAATA
1 TAAA-AATAATATTAAATA
*
59129875 TAAAAATAGTATTAAATA
1 TAAAAATAATATTAAATA
59129893 TA
1 TA
59129895 TTTAACAGTT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
17 5 0.28
18 13 0.72
ACGTcount: A:0.61, C:0.00, G:0.03, T:0.37
Consensus pattern (18 bp):
TAAAAATAATATTAAATA
Found at i:59131360 original size:13 final size:13
Alignment explanation
Indices: 59131342--59131407 Score: 90
Period size: 13 Copynumber: 5.5 Consensus size: 13
59131332 TAGGTTTTTC
59131342 CTAAATATTATCA
1 CTAAATATTATCA
59131355 CTAAATA--ATC-
1 CTAAATATTATCA
59131365 CTAAATATTATCA
1 CTAAATATTATCA
59131378 CTAAATA--ATC-
1 CTAAATATTATCA
59131388 CTAAATATTATCA
1 CTAAATATTATCA
59131401 CTAAATA
1 CTAAATA
59131408 ATTCAAATTT
Statistics
Matches: 47, Mismatches: 0, Indels: 12
0.80 0.00 0.20
Matches are distributed among these distances:
10 14 0.30
11 6 0.13
12 6 0.13
13 21 0.45
ACGTcount: A:0.48, C:0.17, G:0.00, T:0.35
Consensus pattern (13 bp):
CTAAATATTATCA
Found at i:59131367 original size:23 final size:23
Alignment explanation
Indices: 59131340--59131409 Score: 140
Period size: 23 Copynumber: 3.0 Consensus size: 23
59131330 GCTAGGTTTT
59131340 TCCTAAATATTATCACTAAATAA
1 TCCTAAATATTATCACTAAATAA
59131363 TCCTAAATATTATCACTAAATAA
1 TCCTAAATATTATCACTAAATAA
59131386 TCCTAAATATTATCACTAAATAA
1 TCCTAAATATTATCACTAAATAA
59131409 T
1 T
59131410 TCAAATTTTA
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 47 1.00
ACGTcount: A:0.47, C:0.17, G:0.00, T:0.36
Consensus pattern (23 bp):
TCCTAAATATTATCACTAAATAA
Found at i:59132353 original size:24 final size:24
Alignment explanation
Indices: 59132324--59132371 Score: 96
Period size: 24 Copynumber: 2.0 Consensus size: 24
59132314 TTTTCCAAAG
59132324 ATAATTTGGATTTTTTATTATTAC
1 ATAATTTGGATTTTTTATTATTAC
59132348 ATAATTTGGATTTTTTATTATTAC
1 ATAATTTGGATTTTTTATTATTAC
59132372 TCATAAAGTG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.29, C:0.04, G:0.08, T:0.58
Consensus pattern (24 bp):
ATAATTTGGATTTTTTATTATTAC
Found at i:59137692 original size:26 final size:28
Alignment explanation
Indices: 59137656--59137729 Score: 109
Period size: 28 Copynumber: 2.8 Consensus size: 28
59137646 AAAAATAAAA
59137656 ATTTACCAAAATAT-TAT-AATTTTTTT
1 ATTTACCAAAATATATATAAATTTTTTT
* *
59137682 ATTTACTAAAAAATATATAAATTTTTTT
1 ATTTACCAAAATATATATAAATTTTTTT
59137710 ATTTACCAAAATATAT-TAAA
1 ATTTACCAAAATATATATAAA
59137730 AAAAATCTGC
Statistics
Matches: 42, Mismatches: 4, Indels: 3
0.86 0.08 0.06
Matches are distributed among these distances:
26 12 0.29
27 7 0.17
28 23 0.55
ACGTcount: A:0.46, C:0.07, G:0.00, T:0.47
Consensus pattern (28 bp):
ATTTACCAAAATATATATAAATTTTTTT
Found at i:59137920 original size:11 final size:11
Alignment explanation
Indices: 59137888--59137927 Score: 55
Period size: 11 Copynumber: 3.7 Consensus size: 11
59137878 GTTGTTACAG
59137888 AAAAGAAGAG-
1 AAAAGAAGAGA
*
59137898 AAAAGGAGAGA
1 AAAAGAAGAGA
*
59137909 AAAAGAATAGA
1 AAAAGAAGAGA
59137920 AAAAGAAG
1 AAAAGAAG
59137928 GTATATTTTT
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
10 9 0.36
11 16 0.64
ACGTcount: A:0.70, C:0.00, G:0.28, T:0.03
Consensus pattern (11 bp):
AAAAGAAGAGA
Found at i:59137989 original size:19 final size:21
Alignment explanation
Indices: 59137951--59137989 Score: 55
Period size: 19 Copynumber: 2.0 Consensus size: 21
59137941 AAATTTTGAT
*
59137951 TATATTGTTGTTATTATTTTG
1 TATATTGTTGTTAATATTTTG
59137972 TATATT-TTG-TAATATTTT
1 TATATTGTTGTTAATATTTT
59137990 TTATTTTAGT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 8 0.47
20 3 0.18
21 6 0.35
ACGTcount: A:0.23, C:0.00, G:0.10, T:0.67
Consensus pattern (21 bp):
TATATTGTTGTTAATATTTTG
Found at i:59138091 original size:17 final size:19
Alignment explanation
Indices: 59138069--59138107 Score: 64
Period size: 19 Copynumber: 2.2 Consensus size: 19
59138059 TTGTTGTTGT
59138069 TGTTATT-A-GTATTAAGA
1 TGTTATTAATGTATTAAGA
59138086 TGTTATTAATGTATTAAGA
1 TGTTATTAATGTATTAAGA
59138105 TGT
1 TGT
59138108 AACTTAGTAA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
17 7 0.35
18 1 0.05
19 12 0.60
ACGTcount: A:0.33, C:0.00, G:0.18, T:0.49
Consensus pattern (19 bp):
TGTTATTAATGTATTAAGA
Found at i:59138870 original size:18 final size:18
Alignment explanation
Indices: 59138827--59138871 Score: 63
Period size: 18 Copynumber: 2.5 Consensus size: 18
59138817 TTGACATGGT
*
59138827 TGGTGGTGAAGAAGAAGG
1 TGGTGGCGAAGAAGAAGG
**
59138845 TGCCGGCGAAGAAGAAGG
1 TGGTGGCGAAGAAGAAGG
59138863 TGGTGGCGA
1 TGGTGGCGA
59138872 TCATTGGGAT
Statistics
Matches: 22, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.29, C:0.09, G:0.49, T:0.13
Consensus pattern (18 bp):
TGGTGGCGAAGAAGAAGG
Found at i:59144653 original size:38 final size:36
Alignment explanation
Indices: 59144598--59144792 Score: 146
Period size: 38 Copynumber: 5.1 Consensus size: 36
59144588 TAAAATTACT
* *
59144598 TTTTTTTTCTTTTTTTCCTTCCTTCCCTCTTTTCTTC
1 TTTTTTTTCTTTCTTTCCTTCCTTTCCT-TTTTCTTC
*
59144635 TTTTTTTTCTTCTCTTTCCTTTTCTTTCCTTCTTTCTT-
1 TTTTTTTTCTT-TCTTTCC-TTCCTTTCCTT-TTTCTTC
* *
59144673 TCTTTTTTC-TTCTCTT--TTCTTTTCCTTTTCTTCTTC
1 TTTTTTTTCTTTCT-TTCCTTCCTTTCC-TTT-TTCTTC
*
59144709 TTATTTCTTTCTTTCTTTCTCTTCTCCTTTCCTTTTCTTTTC
1 TT-TTT-TTTCTTTCTTTC-C-T-TCCTTTCCTTTT-TCTTC
* *
59144751 TTCTTTTTCTTTCTTTCCTCTCCTTTCTTTCTTTCTTTC
1 TTTTTTTTCTTTCTTTCCT-TCCTTTCCTT-TTTC-TTC
59144790 TTT
1 TTT
59144793 CTTTCCCTCT
Statistics
Matches: 127, Mismatches: 13, Indels: 34
0.73 0.07 0.20
Matches are distributed among these distances:
34 8 0.06
35 7 0.06
36 4 0.03
37 17 0.13
38 33 0.26
39 26 0.20
40 12 0.09
41 3 0.02
42 10 0.08
43 7 0.06
ACGTcount: A:0.01, C:0.28, G:0.00, T:0.71
Consensus pattern (36 bp):
TTTTTTTTCTTTCTTTCCTTCCTTTCCTTTTTCTTC
Found at i:59144668 original size:18 final size:17
Alignment explanation
Indices: 59144603--59144796 Score: 111
Period size: 16 Copynumber: 11.4 Consensus size: 17
59144593 TTACTTTTTT
59144603 TTTCTTTT-TTTCCTTC
1 TTTCTTTTCTTTCCTTC
* ** *
59144619 CTTC-CCTCTTTTCTTC
1 TTTCTTTTCTTTCCTTC
*
59144635 TTTTTTTTC-TT-C-TC
1 TTTCTTTTCTTTCCTTC
59144649 TTTCCTTTTCTTTCCTTC
1 TTT-CTTTTCTTTCCTTC
*
59144667 TTTC-TTTCTTT-TTTC
1 TTTCTTTTCTTTCCTTC
*
59144682 TTCTCTTTTCTTTTCCTTT
1 TT-TCTTTTC-TTTCCTTC
* *
59144701 TCTTCTTCTTATTTCTTTC
1 T-TTCTT-TTCTTTCCTTC
59144720 TTTCTTTCTCTTCTCC-T-
1 TTTCTTT-TCTT-TCCTTC
* *
59144737 TTCCTTTTCTTTTCTTC
1 TTTCTTTTCTTTCCTTC
*
59144754 TTTTTCTTTCTTTCCTCTCC
1 TTTCT-TTTCTTTCCT-T-C
*
59144774 TTTC-TTTCTTTCTTTC
1 TTTCTTTTCTTTCCTTC
59144790 TTTCTTT
1 TTTCTTT
59144797 CCCTCTCTTT
Statistics
Matches: 134, Mismatches: 24, Indels: 39
0.68 0.12 0.20
Matches are distributed among these distances:
14 5 0.04
15 14 0.10
16 35 0.26
17 21 0.16
18 35 0.26
19 17 0.13
20 7 0.05
ACGTcount: A:0.01, C:0.29, G:0.00, T:0.71
Consensus pattern (17 bp):
TTTCTTTTCTTTCCTTC
Found at i:59144671 original size:4 final size:4
Alignment explanation
Indices: 59144640--59144797 Score: 101
Period size: 4 Copynumber: 37.0 Consensus size: 4
59144630 TCTTCTTTTT
*
59144640 TTTC TTCTC TTTCC TTTTC TTTC CTTC TTTC TTTC TTT- TTTC TTCTC
1 TTTC TT-TC TTT-C -TTTC TTTC TTTC TTTC TTTC TTTC TTTC TT-TC
*
59144687 TTTTC TTTTCC TTT- TCTTC -TTC -TTA TTTC TTTC TTTC TTTC TCTTC
1 -TTTC -TTT-C TTTC T-TTC TTTC TTTC TTTC TTTC TTTC TTTC T-TTC
* * *
59144733 -TCC TTTCC TTTTC TTTTC TTCTT TTTC TTTC TTTCC TCTCC TTTC TTTC
1 TTTC TTT-C -TTTC -TTTC TT-TC TTTC TTTC TTT-C T-TTC TTTC TTTC
59144782 TTTC TTTC TTTC TTTC
1 TTTC TTTC TTTC TTTC
59144798 CCTCTCTTTC
Statistics
Matches: 127, Mismatches: 10, Indels: 34
0.74 0.06 0.20
Matches are distributed among these distances:
3 11 0.09
4 72 0.57
5 34 0.27
6 10 0.08
ACGTcount: A:0.01, C:0.29, G:0.00, T:0.70
Consensus pattern (4 bp):
TTTC
Found at i:59144691 original size:48 final size:44
Alignment explanation
Indices: 59144645--59144795 Score: 158
Period size: 44 Copynumber: 3.5 Consensus size: 44
59144635 TTTTTTTTCT
59144645 TCTCTTTCCTTTTCTTTCCTTCTTTCTTTCTTT-TTTCTTCTCTT-T
1 TCTCTTTCCTTTTCTTT-CTTC-TT-TTTCTTTCTTTCTTCTCTTCT
59144690 TCT-TTTCCTTTTC-TTCTTCTTATTTCTTTCTTTCTT-TC-TCT
1 TCTCTTTCCTTTTCTTTCTTCTT-TTTCTTTCTTTCTTCTCTTCT
*
59144731 TCTCCTTTCCTTTTCTTTTCTTCTTTTTCTTTCTTTCCTCTCCTTTCT
1 TCT-CTTTCCTTTTC-TTTCTTCTTTTTCTTTCTTTCTTCT-C-TTCT
59144779 T-TCTTT-C-TTTCTTTCTT
1 TCTCTTTCCTTTTCTTTCTT
59144796 TCCCTCTCTT
Statistics
Matches: 94, Mismatches: 2, Indels: 22
0.80 0.02 0.19
Matches are distributed among these distances:
40 1 0.01
41 15 0.16
42 10 0.11
43 18 0.19
44 27 0.29
45 13 0.14
46 5 0.05
47 1 0.01
48 4 0.04
ACGTcount: A:0.01, C:0.29, G:0.00, T:0.70
Consensus pattern (44 bp):
TCTCTTTCCTTTTCTTTCTTCTTTTTCTTTCTTTCTTCTCTTCT
Found at i:59144748 original size:30 final size:29
Alignment explanation
Indices: 59144712--59144808 Score: 92
Period size: 30 Copynumber: 3.3 Consensus size: 29
59144702 CTTCTTCTTA
59144712 TTTCTTTCTTTCTTTCTCTTCTCCTTTCCT
1 TTTCTTTCTTTCTTTCTCTTCT-CTTTCCT
*
59144742 TTTCTTT-TCTTCTTTTTCTT-TCTTTCCT
1 TTTCTTTCT-TTCTTTCTCTTCTCTTTCCT
* * *
59144770 CTCCTTTCTTTCTTTCT-TTCTTTCTTTCCC
1 TTTCTTTCTTTCTTTCTCTTC--TCTTTCCT
*
59144800 TCTCTTTCT
1 TTTCTTTCT
59144809 GCCCCCCACC
Statistics
Matches: 54, Mismatches: 8, Indels: 10
0.75 0.11 0.14
Matches are distributed among these distances:
27 2 0.04
28 19 0.35
29 3 0.06
30 30 0.56
ACGTcount: A:0.00, C:0.32, G:0.00, T:0.68
Consensus pattern (29 bp):
TTTCTTTCTTTCTTTCTCTTCTCTTTCCT
Found at i:59144796 original size:48 final size:46
Alignment explanation
Indices: 59144668--59144766 Score: 66
Period size: 43 Copynumber: 2.2 Consensus size: 46
59144658 CTTTCCTTCT
* *
59144668 TTCTTTCTTTTTTC-TTCTCTT-TTCTTTTCCTTTTC-TTCTT-C-
1 TTCTTTCTTTTTTCTTTCTTTTCTTCTTTTTCTTTTCTTTCTTCCT
* * * * *
59144709 TTATTTCTTTCTTTCTTTCTCTTC-TCCTTTCCTTTTCTTTTCTTCTTT
1 TTCTTTCTTT-TTTCTTTCTTTTCTTCTTTTTCTTTTC-TTTCTTC-CT
59144757 TTCTTTCTTT
1 TTCTTTCTTT
59144767 CCTCTCCTTT
Statistics
Matches: 46, Mismatches: 4, Indels: 9
0.78 0.07 0.15
Matches are distributed among these distances:
41 9 0.20
42 4 0.09
43 19 0.41
45 5 0.11
48 9 0.20
ACGTcount: A:0.01, C:0.26, G:0.00, T:0.73
Consensus pattern (46 bp):
TTCTTTCTTTTTTCTTTCTTTTCTTCTTTTTCTTTTCTTTCTTCCT
Found at i:59144807 original size:18 final size:17
Alignment explanation
Indices: 59144640--59144808 Score: 79
Period size: 18 Copynumber: 9.8 Consensus size: 17
59144630 TCTTCTTTTT
*
59144640 TTTCTTCTCTTTCCTTTTC
1 TTTCCTCTCTTT-C-TTTC
59144659 TTTCCT-TCTTTCTTTC
1 TTTCCTCTCTTTCTTTC
*
59144675 TTT--TTTCTTCTCTTTTC
1 TTTCCTCTCTT-TC-TTTC
*
59144692 TTTTC-CT-TTTC-TTC
1 TTTCCTCTCTTTCTTTC
** *
59144706 TTCTTATTTCTTTCTTTC
1 TT-TCCTCTCTTTCTTTC
59144724 TTTCTCTTCTCCTTTCCTTTTC
1 TTTC-C-TCT-CTTT-C-TTTC
* *
59144746 TTTTCTTCTTTTTCTTTC
1 -TTTCCTCTCTTTCTTTC
59144764 TTTCCTCTC---CTTTC
1 TTTCCTCTCTTTCTTTC
*
59144778 TTT-CTTTCTTTCTTTC
1 TTTCCTCTCTTTCTTTC
59144794 TTTCCCTCTCTTTCT
1 TTT-CCTCTCTTTCT
59144809 GCCCCCCACC
Statistics
Matches: 117, Mismatches: 13, Indels: 41
0.68 0.08 0.24
Matches are distributed among these distances:
13 4 0.03
14 14 0.12
15 6 0.05
16 20 0.17
17 22 0.19
18 24 0.21
19 8 0.07
20 7 0.06
21 4 0.03
22 4 0.03
23 4 0.03
ACGTcount: A:0.01, C:0.30, G:0.00, T:0.69
Consensus pattern (17 bp):
TTTCCTCTCTTTCTTTC
Found at i:59144870 original size:27 final size:27
Alignment explanation
Indices: 59144840--59144915 Score: 98
Period size: 27 Copynumber: 2.8 Consensus size: 27
59144830 CATTATTAAC
59144840 TGGTGCCGCCAATGGCATTGGCACCAT
1 TGGTGCCGCCAATGGCATTGGCACCAT
** * *
59144867 TGGTGCCGCCAATGGTTTTGGTACCTT
1 TGGTGCCGCCAATGGCATTGGCACCAT
**
59144894 TGGTGCCGCCAATACCATTGGC
1 TGGTGCCGCCAATGGCATTGGC
59144916 GTGACCCCCG
Statistics
Matches: 40, Mismatches: 9, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
27 40 1.00
ACGTcount: A:0.16, C:0.28, G:0.29, T:0.28
Consensus pattern (27 bp):
TGGTGCCGCCAATGGCATTGGCACCAT
Found at i:59145001 original size:25 final size:26
Alignment explanation
Indices: 59144967--59145018 Score: 79
Period size: 27 Copynumber: 2.0 Consensus size: 26
59144957 TTTTGTTTTT
59144967 TTATATA-TTTCGGTAAATAAAAAAA
1 TTATATATTTTCGGTAAATAAAAAAA
*
59144992 TTATATATTTTTTGGTAAATAAAAAAA
1 TTATATA-TTTTCGGTAAATAAAAAAA
59145019 AGTTATAACA
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
25 7 0.29
27 17 0.71
ACGTcount: A:0.50, C:0.02, G:0.08, T:0.40
Consensus pattern (26 bp):
TTATATATTTTCGGTAAATAAAAAAA
Found at i:59145025 original size:27 final size:26
Alignment explanation
Indices: 59144967--59145025 Score: 75
Period size: 27 Copynumber: 2.2 Consensus size: 26
59144957 TTTTGTTTTT
59144967 TTATATATTTCGGTAAATAAAAAAA-
1 TTATATATTTCGGTAAATAAAAAAAG
*
59144992 TTATATATTTTTTGGTAAATAAAAAAAAG
1 TTATATA--TTTCGGTAAAT-AAAAAAAG
59145021 TTATA
1 TTATA
59145026 ACATTTTGGT
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
25 7 0.24
27 10 0.34
28 7 0.24
29 5 0.17
ACGTcount: A:0.49, C:0.02, G:0.08, T:0.41
Consensus pattern (26 bp):
TTATATATTTCGGTAAATAAAAAAAG
Found at i:59145032 original size:28 final size:27
Alignment explanation
Indices: 59144968--59145038 Score: 81
Period size: 28 Copynumber: 2.6 Consensus size: 27
59144958 TTTGTTTTTT
* *
59144968 TATATATTTCGGTAAATAAAAAAATTA
1 TATACATTTTGGTAAATAAAAAAATTA
**
59144995 TATATTTTTTGGTAAATAAAAAAAAGTTA
1 TATACATTTTGGTAAAT-AAAAAAA-TTA
59145024 TA-ACATTTTGGTAAA
1 TATACATTTTGGTAAA
59145039 AATTTTTTAT
Statistics
Matches: 38, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
27 15 0.39
28 18 0.47
29 5 0.13
ACGTcount: A:0.48, C:0.03, G:0.10, T:0.39
Consensus pattern (27 bp):
TATACATTTTGGTAAATAAAAAAATTA
Found at i:59147524 original size:41 final size:41
Alignment explanation
Indices: 59147462--59147546 Score: 161
Period size: 41 Copynumber: 2.1 Consensus size: 41
59147452 AAATTGAGTG
59147462 ATTCGAGGTGTATTTCAAAGCTAAGAGATAGATCTTCGAAC
1 ATTCGAGGTGTATTTCAAAGCTAAGAGATAGATCTTCGAAC
*
59147503 ATTCGAGGTGTATTTCGAAGCTAAGAGATAGATCTTCGAAC
1 ATTCGAGGTGTATTTCAAAGCTAAGAGATAGATCTTCGAAC
59147544 ATT
1 ATT
59147547 GGATCCCATC
Statistics
Matches: 43, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
41 43 1.00
ACGTcount: A:0.33, C:0.14, G:0.22, T:0.31
Consensus pattern (41 bp):
ATTCGAGGTGTATTTCAAAGCTAAGAGATAGATCTTCGAAC
Found at i:59147542 original size:21 final size:21
Alignment explanation
Indices: 59147479--59147542 Score: 62
Period size: 21 Copynumber: 3.1 Consensus size: 21
59147469 GTGTATTTCA
59147479 AAGCTAAGAGATAGATCTTCG
1 AAGCTAAGAGATAGATCTTCG
** *
59147500 AA-CATTCGAGGT-GTAT-TTCG
1 AAGC-TAAGAGATAG-ATCTTCG
59147520 AAGCTAAGAGATAGATCTTCG
1 AAGCTAAGAGATAGATCTTCG
59147541 AA
1 AA
59147543 CATTGGATCC
Statistics
Matches: 32, Mismatches: 6, Indels: 10
0.67 0.12 0.21
Matches are distributed among these distances:
20 15 0.47
21 17 0.53
ACGTcount: A:0.36, C:0.14, G:0.23, T:0.27
Consensus pattern (21 bp):
AAGCTAAGAGATAGATCTTCG
Found at i:59151670 original size:98 final size:98
Alignment explanation
Indices: 59151496--59151692 Score: 367
Period size: 98 Copynumber: 2.0 Consensus size: 98
59151486 GTACAATAAA
*
59151496 ACTTTAAAAGAACATCCACTTATCCAAGATTTAAGAAATCACACCCAATATGTTAGGGCACAATT
1 ACTTTAAAAGAACATCCACTTATCCAAGATTTAAGAAATCACACCCAATACGTTAGGGCACAATT
*
59151561 CCTCTAGAATCCCAAACTCGGAATATTTCCTTT
66 CCTCTAAAATCCCAAACTCGGAATATTTCCTTT
59151594 ACTTTAAAAGAACATCCACTTATCCAAGATTTAAGAAATCACACCCAATACGTTAGGGCACAATT
1 ACTTTAAAAGAACATCCACTTATCCAAGATTTAAGAAATCACACCCAATACGTTAGGGCACAATT
*
59151659 CCTTTAAAATCCCAAACTCGGAATATTTCCTTT
66 CCTCTAAAATCCCAAACTCGGAATATTTCCTTT
59151692 A
1 A
59151693 TTATTTTTAA
Statistics
Matches: 96, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
98 96 1.00
ACGTcount: A:0.38, C:0.24, G:0.10, T:0.28
Consensus pattern (98 bp):
ACTTTAAAAGAACATCCACTTATCCAAGATTTAAGAAATCACACCCAATACGTTAGGGCACAATT
CCTCTAAAATCCCAAACTCGGAATATTTCCTTT
Found at i:59152622 original size:22 final size:20
Alignment explanation
Indices: 59152593--59152644 Score: 52
Period size: 22 Copynumber: 2.5 Consensus size: 20
59152583 AAAATATTTT
*
59152593 TAAA-AAAAAATAGAAATAAA
1 TAAATAAAAAACA-AAATAAA
*
59152613 TAAATGAAAACAACAAAATATA
1 TAAAT-AAAA-AACAAAATAAA
59152635 TAAATAAAAA
1 TAAATAAAAA
59152645 CGAATTATAG
Statistics
Matches: 27, Mismatches: 2, Indels: 6
0.77 0.06 0.17
Matches are distributed among these distances:
20 5 0.19
21 4 0.15
22 15 0.56
23 3 0.11
ACGTcount: A:0.75, C:0.04, G:0.04, T:0.17
Consensus pattern (20 bp):
TAAATAAAAAACAAAATAAA
Found at i:59152629 original size:129 final size:130
Alignment explanation
Indices: 59152423--59152671 Score: 412
Period size: 129 Copynumber: 1.9 Consensus size: 130
59152413 TAAATATAAA
*** *
59152423 AATATTAAAAATAGATATACGTACACATAAAAATATTTGTTTTTTAAAAAATATAAATAAATAAA
1 AATATTAAAAATAGATATACGTACACATAAAAATATTTGTTTAAAAAAAAATAGAAATAAATAAA
*
59152488 TGAAAACAACAAAATATATAAATAAAAACTAATTACAGAAAAAAAAGAAATAATTATAATAATTA
66 TGAAAACAACAAAATATATAAATAAAAACGAATTACAG-AAAAAAAGAAATAATTATAATAATTA
59152553 C
130 C
*
59152554 AATATTAAAAATAGATATACGTACATATAAAAATA-TT-TTTAAAAAAAAATAGAAATAAATAAA
1 AATATTAAAAATAGATATACGTACACATAAAAATATTTGTTTAAAAAAAAATAGAAATAAATAAA
*
59152617 TGAAAACAACAAAATATATAAATAAAAACGAATTATAGAAAAAAAGAAATAATTA
66 TGAAAACAACAAAATATATAAATAAAAACGAATTACAGAAAAAAAGAAATAATTA
59152672 CATTATGGAA
Statistics
Matches: 111, Mismatches: 7, Indels: 3
0.92 0.06 0.02
Matches are distributed among these distances:
128 17 0.15
129 58 0.52
130 2 0.02
131 34 0.31
ACGTcount: A:0.63, C:0.05, G:0.05, T:0.27
Consensus pattern (130 bp):
AATATTAAAAATAGATATACGTACACATAAAAATATTTGTTTAAAAAAAAATAGAAATAAATAAA
TGAAAACAACAAAATATATAAATAAAAACGAATTACAGAAAAAAAGAAATAATTATAATAATTAC
Found at i:59158757 original size:79 final size:81
Alignment explanation
Indices: 59158648--59158830 Score: 223
Period size: 79 Copynumber: 2.3 Consensus size: 81
59158638 TACTCGTTCA
* *
59158648 AATGCCTTCGGGACATAGCCCGG-TTATAGTAACTCGCACAAATGCCTTCGGGA-CTTAACCCGG
1 AATGCCTTCGGGACTTAGCCCGGAATATAGTAACTCGCACAAATGCCTTC-GGATCTTAACCCGG
* *
59158711 ATTTAGTAAC-TCGCACC
65 ATATAGTAACTTAGCA-C
* **
59158728 AATGCCTTCGGG-CTTAGCCCGGAAT-TAGTATCTCGCACAAATGCCTTCGGATCTTAGTCCGGA
1 AATGCCTTCGGGACTTAGCCCGGAATATAGTAACTCGCACAAATGCCTTCGGATCTTAACCCGGA
* *
59158791 TATGGTCACTTAGCAC
66 TATAGTAACTTAGCAC
*
59158807 AAAGCCTTCGGGACTTAGCCCGGA
1 AATGCCTTCGGGACTTAGCCCGGA
59158831 CATCATTCGA
Statistics
Matches: 89, Mismatches: 10, Indels: 8
0.83 0.09 0.07
Matches are distributed among these distances:
78 3 0.03
79 58 0.65
80 28 0.31
ACGTcount: A:0.25, C:0.28, G:0.23, T:0.25
Consensus pattern (81 bp):
AATGCCTTCGGGACTTAGCCCGGAATATAGTAACTCGCACAAATGCCTTCGGATCTTAACCCGGA
TATAGTAACTTAGCAC
Found at i:59158830 original size:40 final size:40
Alignment explanation
Indices: 59158627--59158830 Score: 229
Period size: 40 Copynumber: 5.1 Consensus size: 40
59158617 CGGAATTTAA
** *
59158627 CCGGATATAGCT-ACTCGTTCAAATGCCTTCGGGACATAGC
1 CCGGATATAG-TAACTCGCACAAATGCCTTCGGGACTTAGC
* *
59158667 CCGGTTATAGTAACTCGCACAAATGCCTTCGGGACTTAAC
1 CCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGC
* *
59158707 CCGGATTTAGTAACTCGCACCAATGCCTTCGGG-CTTAGC
1 CCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGC
* *
59158746 CCGGA-ATTAGTATCTCGCACAAATGCCTTC-GGATCTTAGT
1 CCGGATA-TAGTAACTCGCACAAATGCCTTCGGGA-CTTAGC
* * *
59158786 CCGGATATGGTCACTTAGCACAAA-GCCTTCGGGACTTAGC
1 CCGGATATAGTAAC-TCGCACAAATGCCTTCGGGACTTAGC
59158826 CCGGA
1 CCGGA
59158831 CATCATTCGA
Statistics
Matches: 139, Mismatches: 18, Indels: 14
0.81 0.11 0.08
Matches are distributed among these distances:
38 2 0.01
39 32 0.23
40 93 0.67
41 12 0.09
ACGTcount: A:0.25, C:0.28, G:0.23, T:0.25
Consensus pattern (40 bp):
CCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGC
Found at i:59165211 original size:13 final size:13
Alignment explanation
Indices: 59165189--59165228 Score: 53
Period size: 13 Copynumber: 3.1 Consensus size: 13
59165179 ATGTGAAAAG
*
59165189 GAATAATTGAAAT
1 GAATACTTGAAAT
59165202 GAATACTTGAAAT
1 GAATACTTGAAAT
* *
59165215 GAAGACGTGAAAT
1 GAATACTTGAAAT
59165228 G
1 G
59165229 TTAAACAAAT
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
13 24 1.00
ACGTcount: A:0.47, C:0.05, G:0.23, T:0.25
Consensus pattern (13 bp):
GAATACTTGAAAT
Found at i:59168760 original size:16 final size:16
Alignment explanation
Indices: 59168739--59168774 Score: 72
Period size: 16 Copynumber: 2.2 Consensus size: 16
59168729 TTTAGTTCGC
59168739 TGTATTGGATTAGAGG
1 TGTATTGGATTAGAGG
59168755 TGTATTGGATTAGAGG
1 TGTATTGGATTAGAGG
59168771 TGTA
1 TGTA
59168775 ATATCAAATC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.25, C:0.00, G:0.36, T:0.39
Consensus pattern (16 bp):
TGTATTGGATTAGAGG
Found at i:59169209 original size:15 final size:15
Alignment explanation
Indices: 59169189--59169219 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
59169179 GTCATGTAAG
59169189 TGAAAGGTCAAGAGT
1 TGAAAGGTCAAGAGT
59169204 TGAAAGGTCAAGAGT
1 TGAAAGGTCAAGAGT
59169219 T
1 T
59169220 ATATTATTTT
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:0.39, C:0.06, G:0.32, T:0.23
Consensus pattern (15 bp):
TGAAAGGTCAAGAGT
Found at i:59169409 original size:17 final size:17
Alignment explanation
Indices: 59169376--59169414 Score: 53
Period size: 18 Copynumber: 2.3 Consensus size: 17
59169366 TAAGCTTTTG
59169376 ATTTTATATGAGAGAAC
1 ATTTTATATGAGAGAAC
*
59169393 AATTTTATAT-TGAGAAC
1 -ATTTTATATGAGAGAAC
59169410 ATTTT
1 ATTTT
59169415 CCACAATTTG
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
16 5 0.25
17 6 0.30
18 9 0.45
ACGTcount: A:0.38, C:0.05, G:0.13, T:0.44
Consensus pattern (17 bp):
ATTTTATATGAGAGAAC
Found at i:59170180 original size:15 final size:15
Alignment explanation
Indices: 59170156--59170185 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
59170146 TGGAGATCGA
*
59170156 GGAAATGGTCGTGGT
1 GGAAAAGGTCGTGGT
59170171 GGAAAAGGTCGTGGT
1 GGAAAAGGTCGTGGT
59170186 CAAGAAGGGA
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:0.23, C:0.07, G:0.47, T:0.23
Consensus pattern (15 bp):
GGAAAAGGTCGTGGT
Found at i:59173253 original size:92 final size:91
Alignment explanation
Indices: 59173157--59173365 Score: 253
Period size: 92 Copynumber: 2.3 Consensus size: 91
59173147 TAATTATAAC
* * * * *
59173157 TAATAAATTATATTTTATGAATTTTTATAATTTAAAATTA-TAATTATTACATATAATTTAATAA
1 TAATAAATTATATTATATGAATTTATACAATTTAAAATAATTAA-TATTAAATATAATTTAAT-A
* *
59173221 TTAATAT-TAAATTTCATAAAATTCTTGA
64 GTAATATAT-AATTTCATAAAATTCTTAA
* *
59173249 TAATAAATTTTCTTATATGAATTTATACAATTTAAAATAATTAATATTAAATATAATTTAATAGT
1 TAATAAATTATATTATATGAATTTATACAATTTAAAATAATTAATATTAAATATAATTTAATAGT
*
59173314 GATATATAATTTCATAAAATTCTTAA
66 AATATATAATTTCATAAAATTCTTAA
*
59173340 TAATAAAATGT-TCTTATATGAATTTA
1 TAAT-AAAT-TATATTATATGAATTTA
59173366 CTAAAATCAA
Statistics
Matches: 103, Mismatches: 10, Indels: 8
0.85 0.08 0.07
Matches are distributed among these distances:
91 28 0.27
92 71 0.69
93 4 0.04
ACGTcount: A:0.46, C:0.04, G:0.03, T:0.47
Consensus pattern (91 bp):
TAATAAATTATATTATATGAATTTATACAATTTAAAATAATTAATATTAAATATAATTTAATAGT
AATATATAATTTCATAAAATTCTTAA
Found at i:59186160 original size:3 final size:3
Alignment explanation
Indices: 59186152--59186177 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
59186142 TTTTCCTTTG
59186152 TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TT
59186178 TGATATGAAG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:59187764 original size:73 final size:73
Alignment explanation
Indices: 59187677--59187821 Score: 263
Period size: 73 Copynumber: 2.0 Consensus size: 73
59187667 GTAGGATTAC
* *
59187677 CGTTAGGGAGATAACGGAACTTAACGGAAGAGTGATCACTTCGTAACAAAATAATAACATAAGTG
1 CGTTAGGGAGATAACGAAACTTAACGGAAGAGTGACCACTTCGTAACAAAATAATAACATAAGTG
59187742 ACTAAAAT
66 ACTAAAAT
*
59187750 CGTTAGGGAGATAACGAAACTTAATGGAAGAGTGACCACTTCGTAACAAAATAATAACATAAGTG
1 CGTTAGGGAGATAACGAAACTTAACGGAAGAGTGACCACTTCGTAACAAAATAATAACATAAGTG
59187815 ACTAAAA
66 ACTAAAA
59187822 CGTAACATTT
Statistics
Matches: 69, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
73 69 1.00
ACGTcount: A:0.45, C:0.14, G:0.20, T:0.21
Consensus pattern (73 bp):
CGTTAGGGAGATAACGAAACTTAACGGAAGAGTGACCACTTCGTAACAAAATAATAACATAAGTG
ACTAAAAT
Found at i:59190294 original size:21 final size:22
Alignment explanation
Indices: 59190268--59190313 Score: 58
Period size: 21 Copynumber: 2.1 Consensus size: 22
59190258 TGCTTGTATG
* * *
59190268 TGATTTTCACTTC-GTGTCTAC
1 TGATTTGCACTACGGTGCCTAC
59190289 TGATTTGCACTACGGTGCCTAC
1 TGATTTGCACTACGGTGCCTAC
59190311 TGA
1 TGA
59190314 GTCACACTTC
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
21 11 0.52
22 10 0.48
ACGTcount: A:0.17, C:0.24, G:0.20, T:0.39
Consensus pattern (22 bp):
TGATTTGCACTACGGTGCCTAC
Found at i:59193106 original size:9 final size:9
Alignment explanation
Indices: 59193092--59193167 Score: 116
Period size: 9 Copynumber: 8.4 Consensus size: 9
59193082 TTTGGTTAAA
59193092 AATTAACCG
1 AATTAACCG
*
59193101 AATTAACTG
1 AATTAACCG
59193110 AATTAACCG
1 AATTAACCG
* *
59193119 GATTATCCG
1 AATTAACCG
59193128 AATTAACCG
1 AATTAACCG
*
59193137 AATTACCCG
1 AATTAACCG
59193146 AATTAACCG
1 AATTAACCG
59193155 AATTAACCG
1 AATTAACCG
59193164 AATT
1 AATT
59193168 GAATCACTAT
Statistics
Matches: 59, Mismatches: 8, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
9 59 1.00
ACGTcount: A:0.41, C:0.21, G:0.12, T:0.26
Consensus pattern (9 bp):
AATTAACCG
Found at i:59199785 original size:20 final size:20
Alignment explanation
Indices: 59199757--59199910 Score: 89
Period size: 20 Copynumber: 7.7 Consensus size: 20
59199747 GAAGAAATGA
* *
59199757 CCCTGTTTGCACATCTGTGC
1 CCCTATTTGCACTTCTGTGC
* * *
59199777 CCCTATTTGTACTTCAGTAC
1 CCCTATTTGCACTTCTGTGC
* *
59199797 CCCTGA-ATGCACATCTGTGC
1 CCCT-ATTTGCACTTCTGTGC
* * * * *
59199817 CCCTGTTTGTAGTTCGGTAC
1 CCCTATTTGCACTTCTGTGC
* * *
59199837 CCCTGA-ATGCACATATGTGC
1 CCCT-ATTTGCACTTCTGTGC
* * *
59199857 CCCTATTTGTACTTCGGTAC
1 CCCTATTTGCACTTCTGTGC
*
59199877 CCCTATTTGCACTTCTATGC
1 CCCTATTTGCACTTCTGTGC
59199897 CCCTGA-TTGCACTT
1 CCCT-ATTTGCACTT
59199911 TCATGCTCCT
Statistics
Matches: 94, Mismatches: 35, Indels: 10
0.68 0.25 0.07
Matches are distributed among these distances:
19 1 0.01
20 91 0.97
21 2 0.02
ACGTcount: A:0.16, C:0.32, G:0.17, T:0.35
Consensus pattern (20 bp):
CCCTATTTGCACTTCTGTGC
Found at i:59199900 original size:40 final size:40
Alignment explanation
Indices: 59199764--59199880 Score: 198
Period size: 40 Copynumber: 2.9 Consensus size: 40
59199754 TGACCCTGTT
*
59199764 TGCACATCTGTGCCCCTATTTGTACTTCAGTACCCCTGAA
1 TGCACATCTGTGCCCCTATTTGTACTTCGGTACCCCTGAA
* *
59199804 TGCACATCTGTGCCCCTGTTTGTAGTTCGGTACCCCTGAA
1 TGCACATCTGTGCCCCTATTTGTACTTCGGTACCCCTGAA
*
59199844 TGCACATATGTGCCCCTATTTGTACTTCGGTACCCCT
1 TGCACATCTGTGCCCCTATTTGTACTTCGGTACCCCT
59199881 ATTTGCACTT
Statistics
Matches: 71, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
40 71 1.00
ACGTcount: A:0.17, C:0.32, G:0.18, T:0.33
Consensus pattern (40 bp):
TGCACATCTGTGCCCCTATTTGTACTTCGGTACCCCTGAA
Found at i:59199916 original size:20 final size:21
Alignment explanation
Indices: 59199883--59199931 Score: 75
Period size: 20 Copynumber: 2.4 Consensus size: 21
59199873 GTACCCCTAT
59199883 TTGCAC-TTCTATGCCCCTGA
1 TTGCACTTTCTATGCCCCTGA
*
59199903 TTGCACTTTC-ATGCTCCTGA
1 TTGCACTTTCTATGCCCCTGA
59199923 TTGCACTTT
1 TTGCACTTT
59199932 GGTGCGCCTG
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
20 24 0.89
21 3 0.11
ACGTcount: A:0.14, C:0.31, G:0.14, T:0.41
Consensus pattern (21 bp):
TTGCACTTTCTATGCCCCTGA
Found at i:59199928 original size:80 final size:80
Alignment explanation
Indices: 59199757--59199907 Score: 196
Period size: 80 Copynumber: 1.9 Consensus size: 80
59199747 GAAGAAATGA
* * *
59199757 CCCTGTTTGCACATCTGTGCCCCTATTTGTACTTCAGTACCCCTGAATGCACATCTGTGCCCCTG
1 CCCTGATTGCACATATGTGCCCCTATTTGTACTTCAGTACCCCTGAATGCACATCTATGCCCCTG
* * *
59199822 TTTGTAGTTCGGTAC
66 ATTGCAGTTCGATAC
* * * *
59199837 CCCTGAATGCACATATGTGCCCCTATTTGTACTTCGGTACCCCT-ATTTGCACTTCTATGCCCCT
1 CCCTGATTGCACATATGTGCCCCTATTTGTACTTCAGTACCCCTGA-ATGCACATCTATGCCCCT
59199901 GATTGCA
65 GATTGCA
59199908 CTTTCATGCT
Statistics
Matches: 61, Mismatches: 9, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
79 1 0.02
80 60 0.98
ACGTcount: A:0.17, C:0.32, G:0.17, T:0.34
Consensus pattern (80 bp):
CCCTGATTGCACATATGTGCCCCTATTTGTACTTCAGTACCCCTGAATGCACATCTATGCCCCTG
ATTGCAGTTCGATAC
Found at i:59199941 original size:20 final size:20
Alignment explanation
Indices: 59199883--59199941 Score: 66
Period size: 20 Copynumber: 3.0 Consensus size: 20
59199873 GTACCCCTAT
*
59199883 TTGCAC-TTCTATGCCCCTGA
1 TTGCACTTTC-ATGCGCCTGA
*
59199903 TTGCACTTTCATGCTCCTGA
1 TTGCACTTTCATGCGCCTGA
**
59199923 TTGCACTTTGGTGCGCCTG
1 TTGCACTTTCATGCGCCTG
59199942 TTATGCATCT
Statistics
Matches: 34, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
20 31 0.91
21 3 0.09
ACGTcount: A:0.12, C:0.31, G:0.20, T:0.37
Consensus pattern (20 bp):
TTGCACTTTCATGCGCCTGA
Found at i:59202748 original size:9 final size:9
Alignment explanation
Indices: 59202734--59202758 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
59202724 AAGAAAATTA
59202734 ATGGTTTAT
1 ATGGTTTAT
59202743 ATGGTTTAT
1 ATGGTTTAT
59202752 ATGGTTT
1 ATGGTTT
59202759 TTCTCTATCA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 16 1.00
ACGTcount: A:0.20, C:0.00, G:0.24, T:0.56
Consensus pattern (9 bp):
ATGGTTTAT
Found at i:59203711 original size:6 final size:6
Alignment explanation
Indices: 59203700--59203733 Score: 50
Period size: 6 Copynumber: 5.5 Consensus size: 6
59203690 AATCCATTTG
*
59203700 TTTTAT TTTTAT TTTTAT GTTTAT TTCTTAT TTT
1 TTTTAT TTTTAT TTTTAT TTTTAT TT-TTAT TTT
59203734 CTTAGTCTTA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
6 19 0.76
7 6 0.24
ACGTcount: A:0.15, C:0.03, G:0.03, T:0.79
Consensus pattern (6 bp):
TTTTAT
Found at i:59204399 original size:32 final size:32
Alignment explanation
Indices: 59204361--59204431 Score: 94
Period size: 30 Copynumber: 2.3 Consensus size: 32
59204351 TCTAGTTGCT
* *
59204361 TTTTTAAAATATTTACAAAAAGAGGC-ATCTAA
1 TTTTTAAAATATTTACAAAAAGA-GCAACCAAA
59204393 TTTTT--AATATTTACAAAAAGAGCAACCAAA
1 TTTTTAAAATATTTACAAAAAGAGCAACCAAA
59204423 TTTTTAAAA
1 TTTTTAAAA
59204432 ATAATTCAAT
Statistics
Matches: 34, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
29 2 0.06
30 25 0.74
32 7 0.21
ACGTcount: A:0.48, C:0.10, G:0.07, T:0.35
Consensus pattern (32 bp):
TTTTTAAAATATTTACAAAAAGAGCAACCAAA
Found at i:59211098 original size:21 final size:20
Alignment explanation
Indices: 59211069--59211114 Score: 51
Period size: 21 Copynumber: 2.3 Consensus size: 20
59211059 CGAAATGCAA
59211069 TCAACCTAACA-TGAATTAAAT
1 TCAACCTAA-ATTG-ATTAAAT
*
59211090 TCAAGCTAAATTGATTAAAT
1 TCAACCTAAATTGATTAAAT
59211110 T-AACC
1 TCAACC
59211115 ATTCCAACAA
Statistics
Matches: 22, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
19 3 0.14
20 9 0.41
21 10 0.45
ACGTcount: A:0.46, C:0.17, G:0.07, T:0.30
Consensus pattern (20 bp):
TCAACCTAAATTGATTAAAT
Found at i:59212534 original size:43 final size:43
Alignment explanation
Indices: 59212446--59212544 Score: 128
Period size: 43 Copynumber: 2.3 Consensus size: 43
59212436 AGTTTGGAAT
* * *
59212446 TTCACCAATGGGCAAATTGTATGAATTCTTCTTCGATATACTA
1 TTCACCAATGGGCAAATTGTATAAAGTCTACTTCGATATACTA
* * *
59212489 TTCACCAACGGGCAAATTGTATAAAGTCTACTTTTG-TATAGTA
1 TTCACCAATGGGCAAATTGTATAAAGTCTAC-TTCGATATACTA
59212532 TTCACCAATGGGC
1 TTCACCAATGGGC
59212545 GAACTAAGTT
Statistics
Matches: 48, Mismatches: 7, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
43 45 0.94
44 3 0.06
ACGTcount: A:0.30, C:0.19, G:0.16, T:0.34
Consensus pattern (43 bp):
TTCACCAATGGGCAAATTGTATAAAGTCTACTTCGATATACTA
Found at i:59227519 original size:37 final size:37
Alignment explanation
Indices: 59227469--59227543 Score: 132
Period size: 37 Copynumber: 2.0 Consensus size: 37
59227459 TGGGACAAGG
* *
59227469 TGTCGTCCCCAGCCATGCAATCATGAGACCCAGTCTC
1 TGTCGTCACCAGCCATACAATCATGAGACCCAGTCTC
59227506 TGTCGTCACCAGCCATACAATCATGAGACCCAGTCTC
1 TGTCGTCACCAGCCATACAATCATGAGACCCAGTCTC
59227543 T
1 T
59227544 TTAGCAAGTG
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
37 36 1.00
ACGTcount: A:0.24, C:0.36, G:0.17, T:0.23
Consensus pattern (37 bp):
TGTCGTCACCAGCCATACAATCATGAGACCCAGTCTC
Found at i:59229697 original size:17 final size:19
Alignment explanation
Indices: 59229677--59229718 Score: 54
Period size: 17 Copynumber: 2.3 Consensus size: 19
59229667 AATGGATTAG
59229677 GAAAAA-ATCAAG-AAGA-A
1 GAAAAAGAT-AAGAAAGATA
59229694 GAAAAAGATAAGAAAGATA
1 GAAAAAGATAAGAAAGATA
59229713 GAAAAA
1 GAAAAA
59229719 CTCAGAGAAT
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
17 9 0.41
18 6 0.27
19 7 0.32
ACGTcount: A:0.71, C:0.02, G:0.19, T:0.07
Consensus pattern (19 bp):
GAAAAAGATAAGAAAGATA
Found at i:59229699 original size:18 final size:19
Alignment explanation
Indices: 59229678--59229718 Score: 50
Period size: 18 Copynumber: 2.2 Consensus size: 19
59229668 ATGGATTAGG
59229678 AAAAAATCAAG-AAGA-AGA
1 AAAAAAT-AAGAAAGATAGA
*
59229696 AAAAGATAAGAAAGATAGA
1 AAAAAATAAGAAAGATAGA
59229715 AAAA
1 AAAA
59229719 CTCAGAGAAT
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
17 3 0.15
18 10 0.50
19 7 0.35
ACGTcount: A:0.73, C:0.02, G:0.17, T:0.07
Consensus pattern (19 bp):
AAAAAATAAGAAAGATAGA
Found at i:59237854 original size:154 final size:155
Alignment explanation
Indices: 59237615--59237896 Score: 451
Period size: 155 Copynumber: 1.8 Consensus size: 155
59237605 TTTTTTTTTT
* * * *
59237615 AAAAAAAGAGGAAGTTTAGATTTTTAAAAATAAAAATATGTTTTTTAGTCATTTTACAGGAAAAT
1 AAAAAAAGAGAAAGTTTAGATTTTAAAAAATAAAAATATGTTTTTTAGTCATTTTAAAGGAAAAG
* *
59237680 TTTAAATTTTTAAAATAAAGTTTTGAT-ATTTTTCAACTATTTCGAAATAAAGCTTTGATTTTAA
66 TTTAAAATTTTAAAACAAAGTTTTGATCATTTTTCAACTATTTCGAAATAAAGCTTTGATTTTAA
59237744 AAAAAATAGTGATTTTTTATAATTA
131 AAAAAATAGTGATTTTTTATAATTA
*
59237769 AAAAAAAGGAGAAAGTTTAGATTTTAAAAAATAATAATAT-TTTTTTAGTCATTTTAAAGGAAAA
1 AAAAAAA-GAGAAAGTTTAGATTTTAAAAAATAAAAATATGTTTTTTAGTCATTTTAAAGGAAAA
* * *
59237833 GTTTAAAATTTTAAAACAAAGTTTTGATCTTTTTTCAATTATTTCGAAATAAAGCTTTGGTTTT
65 GTTTAAAATTTTAAAACAAAGTTTTGATCATTTTTCAACTATTTCGAAATAAAGCTTTGATTTT
59237897 TAAGAAAACT
Statistics
Matches: 116, Mismatches: 10, Indels: 3
0.90 0.08 0.02
Matches are distributed among these distances:
154 55 0.47
155 61 0.53
ACGTcount: A:0.43, C:0.04, G:0.11, T:0.42
Consensus pattern (155 bp):
AAAAAAAGAGAAAGTTTAGATTTTAAAAAATAAAAATATGTTTTTTAGTCATTTTAAAGGAAAAG
TTTAAAATTTTAAAACAAAGTTTTGATCATTTTTCAACTATTTCGAAATAAAGCTTTGATTTTAA
AAAAAATAGTGATTTTTTATAATTA
Done.