Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: chr2
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: 41236440
ACGTcount: A:0.31, C:0.16, G:0.16, T:0.31
Warning! 2030548 characters in sequence are not A, C, G, or T
File 81 of 106
Found at i:30728610 original size:13 final size:13
Alignment explanation
Indices: 30728592--30728616 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
30728582 AGAGAAATTG
30728592 TGATTTTATAAAA
1 TGATTTTATAAAA
30728605 TGATTTTATAAA
1 TGATTTTATAAA
30728617 TTTTTTGAAA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.44, C:0.00, G:0.08, T:0.48
Consensus pattern (13 bp):
TGATTTTATAAAA
Found at i:30740100 original size:11 final size:12
Alignment explanation
Indices: 30740085--30740113 Score: 51
Period size: 11 Copynumber: 2.5 Consensus size: 12
30740075 ATCCGTTGAA
30740085 AATTTTCAACGG
1 AATTTTCAACGG
30740097 -ATTTTCAACGG
1 AATTTTCAACGG
30740108 AATTTT
1 AATTTT
30740114 TCGTTGAAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
11 11 0.69
12 5 0.31
ACGTcount: A:0.31, C:0.14, G:0.14, T:0.41
Consensus pattern (12 bp):
AATTTTCAACGG
Found at i:30740232 original size:26 final size:26
Alignment explanation
Indices: 30740197--30740247 Score: 75
Period size: 26 Copynumber: 2.0 Consensus size: 26
30740187 AACGGAATTC
* * *
30740197 TGTTGGAAATTTCTAATGGAATTTTT
1 TGTTGAAAATTTCCAACGGAATTTTT
30740223 TGTTGAAAATTTCCAACGGAATTTT
1 TGTTGAAAATTTCCAACGGAATTTT
30740248 CATTGGAAAA
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
26 22 1.00
ACGTcount: A:0.29, C:0.08, G:0.18, T:0.45
Consensus pattern (26 bp):
TGTTGAAAATTTCCAACGGAATTTTT
Found at i:30742690 original size:6 final size:6
Alignment explanation
Indices: 30742679--30742746 Score: 109
Period size: 6 Copynumber: 11.3 Consensus size: 6
30742669 GCTCCACATG
* *
30742679 ATCTTC ATCTTC ATCTTC ATCTTT ATCTTC ATCTTC ATCTTT ATCTTC
1 ATCTTC ATCTTC ATCTTC ATCTTC ATCTTC ATCTTC ATCTTC ATCTTC
*
30742727 ATCTTC ATCATC ATCTTC AT
1 ATCTTC ATCTTC ATCTTC AT
30742747 TATCTTCTCC
Statistics
Matches: 56, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
6 56 1.00
ACGTcount: A:0.19, C:0.29, G:0.00, T:0.51
Consensus pattern (6 bp):
ATCTTC
Found at i:30748880 original size:12 final size:12
Alignment explanation
Indices: 30748863--30748893 Score: 53
Period size: 12 Copynumber: 2.6 Consensus size: 12
30748853 TGTACAAGTC
30748863 AAATTTTCAACA
1 AAATTTTCAACA
*
30748875 AAATTTCCAACA
1 AAATTTTCAACA
30748887 AAATTTT
1 AAATTTT
30748894 TCGTTGAAAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.48, C:0.16, G:0.00, T:0.35
Consensus pattern (12 bp):
AAATTTTCAACA
Found at i:30752125 original size:145 final size:144
Alignment explanation
Indices: 30751956--30752245 Score: 571
Period size: 145 Copynumber: 2.0 Consensus size: 144
30751946 TTTATTAATA
30751956 AGAAGATAACAGTTAATTAATTAACTGATAAATATAAATATTATATATGAATAATATATCAAATA
1 AGAAGATAACAGTTAATTAATTAACTGATAAATATAAATATTATATATGAATAATATATCAAATA
30752021 TAAATTTCAGAACATATACAAATTTGTCGATGAACAAAATATTTGCAAATAAATTTACAACCGTA
66 TAAATTTCAGAACATATACAAATTTGTCGATGAACAAAATATTTGCAAATAAATTTACAACCGTA
30752086 TGTGTCACGCATTC
131 TGTGTCACGCATTC
30752100 ANGAAGATAACAGTTAATTAATTAACTGATAAATATAAATATTATATATGAATAATATATCAAAT
1 A-GAAGATAACAGTTAATTAATTAACTGATAAATATAAATATTATATATGAATAATATATCAAAT
30752165 ATAAATTTCAGAACATATACAAATTTGTCGATGAACAAAATATTTGCAAATAAATTTACAACCGT
65 ATAAATTTCAGAACATATACAAATTTGTCGATGAACAAAATATTTGCAAATAAATTTACAACCGT
30752230 ATGTGTCACGCATTC
130 ATGTGTCACGCATTC
30752245 A
1 A
30752246 ACTTTATTTT
Statistics
Matches: 145, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
144 1 0.01
145 144 0.99
ACGTcount: A:0.47, C:0.11, G:0.10, T:0.32
Consensus pattern (144 bp):
AGAAGATAACAGTTAATTAATTAACTGATAAATATAAATATTATATATGAATAATATATCAAATA
TAAATTTCAGAACATATACAAATTTGTCGATGAACAAAATATTTGCAAATAAATTTACAACCGTA
TGTGTCACGCATTC
Found at i:30756744 original size:2 final size:2
Alignment explanation
Indices: 30756737--30756782 Score: 83
Period size: 2 Copynumber: 23.0 Consensus size: 2
30756727 ATGGAACTGA
*
30756737 AT AT AT AT TT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
30756779 AT AT
1 AT AT
30756783 CAGTATGCAA
Statistics
Matches: 42, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 42 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
AT
Found at i:30762092 original size:20 final size:20
Alignment explanation
Indices: 30762067--30762106 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
30762057 AGATATACGA
*
30762067 GTTCTTAACATATACTAAAT
1 GTTCTTAAAATATACTAAAT
*
30762087 GTTCTTAAAATATCCTAAAT
1 GTTCTTAAAATATACTAAAT
30762107 CTCTATGCAT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.40, C:0.15, G:0.05, T:0.40
Consensus pattern (20 bp):
GTTCTTAAAATATACTAAAT
Found at i:30771708 original size:19 final size:19
Alignment explanation
Indices: 30771677--30771718 Score: 59
Period size: 19 Copynumber: 2.2 Consensus size: 19
30771667 CATTGAAGTG
*
30771677 AAGAAGAATTTGAAGGATTC
1 AAGAAGAATTTGAAAGA-TC
30771697 AAGAAG-ATTTGAAAGATC
1 AAGAAGAATTTGAAAGATC
30771715 AAGA
1 AAGA
30771719 TTACAGTTCT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
18 6 0.29
19 9 0.43
20 6 0.29
ACGTcount: A:0.50, C:0.05, G:0.24, T:0.21
Consensus pattern (19 bp):
AAGAAGAATTTGAAAGATC
Found at i:30773418 original size:2 final size:2
Alignment explanation
Indices: 30773411--30773461 Score: 84
Period size: 2 Copynumber: 25.5 Consensus size: 2
30773401 TCATAATACA
*
30773411 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT TT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
*
30773453 AT TT AT AT A
1 AT AT AT AT A
30773462 GCATAAACCC
Statistics
Matches: 45, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
2 45 1.00
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (2 bp):
AT
Found at i:30774566 original size:4 final size:4
Alignment explanation
Indices: 30774550--30774608 Score: 54
Period size: 4 Copynumber: 15.2 Consensus size: 4
30774540 AGAAGAAAAG
* *
30774550 AGAA AG-A AG-A AGAA AGAA AG-A AGAA A-AGA GGAA AGAGA GGAA AGAA
1 AGAA AGAA AGAA AGAA AGAA AGAA AGAA AGA-A AGAA AGA-A AGAA AGAA
30774596 AGAA AGAA AGAA A
1 AGAA AGAA AGAA A
30774609 AAGAGAGAAA
Statistics
Matches: 46, Mismatches: 4, Indels: 10
0.77 0.07 0.17
Matches are distributed among these distances:
3 10 0.22
4 32 0.70
5 4 0.09
ACGTcount: A:0.69, C:0.00, G:0.31, T:0.00
Consensus pattern (4 bp):
AGAA
Found at i:30774579 original size:28 final size:28
Alignment explanation
Indices: 30774539--30774617 Score: 99
Period size: 28 Copynumber: 2.8 Consensus size: 28
30774529 GCCCATAACC
30774539 AAGAAGAAAAGAGAAAGAAGAAGAAAGA
1 AAGAAGAAAAGAGAAAGAAGAAGAAAGA
*
30774567 AAGAAGAAAAGAGGAAAG-AGAGGAAAGA
1 AAGAAGAAAAGA-GAAAGAAGAAGAAAGA
*
30774595 AAGAA-AGAAAGAAAAAGAGAGAA
1 AAGAAGA-AAAGAGAAAGA-AGAA
30774618 AGGAAATAAG
Statistics
Matches: 44, Mismatches: 3, Indels: 7
0.81 0.06 0.13
Matches are distributed among these distances:
27 5 0.11
28 31 0.70
29 8 0.18
ACGTcount: A:0.70, C:0.00, G:0.30, T:0.00
Consensus pattern (28 bp):
AAGAAGAAAAGAGAAAGAAGAAGAAAGA
Found at i:30774617 original size:14 final size:14
Alignment explanation
Indices: 30774539--30774619 Score: 52
Period size: 14 Copynumber: 6.2 Consensus size: 14
30774529 GCCCATAACC
30774539 AAGAAGAAA-AGAGA
1 AAGAA-AAAGAGAGA
* *
30774553 AAGAAGAAGAAAGA
1 AAGAAAAAGAGAGA
30774567 AAGAAGAAA-AGAG-
1 AAGAA-AAAGAGAGA
*
30774580 --GAAAGAGAG-GA
1 AAGAAAAAGAGAGA
*
30774591 AAG--AAAGAAAGA
1 AAGAAAAAGAGAGA
30774603 AAGAAAAAGAGAGA
1 AAGAAAAAGAGAGA
30774617 AAG
1 AAG
30774620 GAAATAAGGT
Statistics
Matches: 50, Mismatches: 8, Indels: 18
0.66 0.11 0.24
Matches are distributed among these distances:
10 3 0.06
11 9 0.18
12 5 0.10
13 3 0.06
14 28 0.56
15 2 0.04
ACGTcount: A:0.69, C:0.00, G:0.31, T:0.00
Consensus pattern (14 bp):
AAGAAAAAGAGAGA
Found at i:30774618 original size:10 final size:10
Alignment explanation
Indices: 30774542--30774618 Score: 52
Period size: 10 Copynumber: 7.6 Consensus size: 10
30774532 CATAACCAAG
30774542 AAGAAAAGAGA
1 AAGAAAA-AGA
*
30774553 AAGAAGAAGA
1 AAGAAAAAGA
30774563 AAGAAAGAAGAA
1 AAGAAA-AAG-A
*
30774575 AAGAGGAAAGA
1 AAGA-AAAAGA
* *
30774586 GAG-GAAAGA
1 AAGAAAAAGA
30774595 AAG--AAAGA
1 AAGAAAAAGA
30774603 AAGAAAAAGA
1 AAGAAAAAGA
*
30774613 GAGAAA
1 AAGAAA
30774619 GGAAATAAGG
Statistics
Matches: 55, Mismatches: 6, Indels: 11
0.76 0.08 0.15
Matches are distributed among these distances:
8 8 0.15
9 8 0.15
10 18 0.33
11 12 0.22
12 8 0.15
13 1 0.02
ACGTcount: A:0.70, C:0.00, G:0.30, T:0.00
Consensus pattern (10 bp):
AAGAAAAAGA
Found at i:30774619 original size:8 final size:8
Alignment explanation
Indices: 30774539--30774619 Score: 57
Period size: 8 Copynumber: 10.4 Consensus size: 8
30774529 GCCCATAACC
30774539 AAGA-AGA
1 AAGAGAGA
30774546 AA-AGAGA
1 AAGAGAGA
30774553 AAGA-AG-
1 AAGAGAGA
*
30774559 AAGAAAGA
1 AAGAGAGA
30774567 AAGA-AGA
1 AAGAGAGA
30774574 AA-AGAGGA
1 AAGAGA-GA
30774582 AAGAGAGGA
1 AAGAGA-GA
*
30774591 AAGAAAGA
1 AAGAGAGA
*
30774599 AAGAAAGAAA
1 AAG--AGAGA
30774609 AAGAGAGA
1 AAGAGAGA
30774617 AAG
1 AAG
30774620 GAAATAAGGT
Statistics
Matches: 61, Mismatches: 4, Indels: 17
0.74 0.05 0.21
Matches are distributed among these distances:
6 6 0.10
7 17 0.28
8 21 0.34
9 11 0.18
10 6 0.10
ACGTcount: A:0.69, C:0.00, G:0.31, T:0.00
Consensus pattern (8 bp):
AAGAGAGA
Found at i:30775371 original size:2 final size:2
Alignment explanation
Indices: 30775364--30775418 Score: 110
Period size: 2 Copynumber: 27.5 Consensus size: 2
30775354 ATTCCCATAA
30775364 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
30775406 AT AT AT AT AT AT A
1 AT AT AT AT AT AT A
30775419 CACGTATTGA
Statistics
Matches: 53, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 53 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:30782632 original size:12 final size:12
Alignment explanation
Indices: 30782605--30782644 Score: 57
Period size: 11 Copynumber: 3.5 Consensus size: 12
30782595 ATAACATTGG
30782605 GAAAAAGAA-AA
1 GAAAAAGAAGAA
*
30782616 GAAAAAG-GGAA
1 GAAAAAGAAGAA
30782627 GAAAAAGAAGAA
1 GAAAAAGAAGAA
30782639 GAAAAA
1 GAAAAA
30782645 ATGAAGTGTT
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
11 16 0.64
12 9 0.36
ACGTcount: A:0.75, C:0.00, G:0.25, T:0.00
Consensus pattern (12 bp):
GAAAAAGAAGAA
Found at i:30782650 original size:23 final size:22
Alignment explanation
Indices: 30782605--30782650 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 22
30782595 ATAACATTGG
*
30782605 GAAAAAGAAAAGAAAAAGGGAA
1 GAAAAAGAAAAGAAAAAAGGAA
*
30782627 GAAAAAGAAGAAGAAAAAATGAA
1 GAAAAAGAA-AAGAAAAAAGGAA
30782650 G
1 G
30782651 TGTTGAACAA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
22 9 0.43
23 12 0.57
ACGTcount: A:0.72, C:0.00, G:0.26, T:0.02
Consensus pattern (22 bp):
GAAAAAGAAAAGAAAAAAGGAA
Found at i:30785654 original size:37 final size:37
Alignment explanation
Indices: 30785613--30785733 Score: 154
Period size: 37 Copynumber: 3.1 Consensus size: 37
30785603 CATATGCATT
30785613 CATCATCATGTGTGCACTCCCTACTCGCACACTTCAA
1 CATCATCATGTGTGCACTCCCTACTCGCACACTTCAA
30785650 CATCATCATGTGTGCACTCCCACTCCCTACTCGCACAC-TCTAA
1 CATCATCATGTGTG------CACTCCCTACTCGCACACTTC-AA
* *
30785693 CATCATCATGTGTGCACTCCCTACTCGCATAGTTCAA
1 CATCATCATGTGTGCACTCCCTACTCGCACACTTCAA
30785730 CATC
1 CATC
30785734 CTCACACAAC
Statistics
Matches: 74, Mismatches: 2, Indels: 16
0.80 0.02 0.17
Matches are distributed among these distances:
37 36 0.49
38 2 0.03
42 2 0.03
43 34 0.46
ACGTcount: A:0.24, C:0.38, G:0.11, T:0.27
Consensus pattern (37 bp):
CATCATCATGTGTGCACTCCCTACTCGCACACTTCAA
Found at i:30785676 original size:43 final size:43
Alignment explanation
Indices: 30785627--30785718 Score: 159
Period size: 43 Copynumber: 2.1 Consensus size: 43
30785617 ATCATGTGTG
30785627 CACTCCCTACTCGCACACT-TCAACATCATCATGTGTGCACTCC
1 CACTCCCTACTCGCACACTCT-AACATCATCATGTGTGCACTCC
30785670 CACTCCCTACTCGCACACTCTAACATCATCATGTGTGCACTCC
1 CACTCCCTACTCGCACACTCTAACATCATCATGTGTGCACTCC
30785713 CTACTC
1 C-ACTC
30785719 GCATAGTTCA
Statistics
Matches: 47, Mismatches: 0, Indels: 3
0.94 0.00 0.06
Matches are distributed among these distances:
43 42 0.89
44 5 0.11
ACGTcount: A:0.23, C:0.42, G:0.09, T:0.26
Consensus pattern (43 bp):
CACTCCCTACTCGCACACTCTAACATCATCATGTGTGCACTCC
Found at i:30788481 original size:478 final size:467
Alignment explanation
Indices: 30787596--30788544 Score: 1592
Period size: 478 Copynumber: 2.0 Consensus size: 467
30787586 AATCACCTTA
* *
30787596 AGCACATAATTAGTCTAGGACCTATTTATAGAGCTTTATTCTCCTTCTACAAGTACACCTTTTCT
1 AGCACATAATTAGTCTAGGACCTATTTATAGAGCTCTATTCTCCTTCTACAAGTACACATTTTCT
*
30787661 TCCACATTTGAACTTTTTTTTTTTCAACACATTTTTTTTCACAATTTCACACCCCCAAACTTATT
66 TCCACATTTAAACTTTTTTTTTTTCAACACATTTTTTTTCACAATTTCACACCCCCAAACTTATT
*
30787726 TTCTTTGTATTGTAGGTAATGGGGTTAGTTTTCATGTTTTGAACTCTTTTTCTTTTTTTATATCA
131 TTCTTTGTATTGTAGGTAATGGGGTTAGTTTTCATGTTTTGAACTCTTTTTCTTTTTTTACATCA
30787791 ACGTCACCTTTCCACCTTTTTCAACATATAGCTCAATTTAAATTGCCTAAAACAATATACATGCT
196 ACGTCACCTTTCCACCTTTTTCAACATATAGCTCAATTTAAATTGCCTAAAACAATATACATGCT
*
30787856 TAGGAGTGAGGCTTGCAAAATTGAAAATTTTTATTTTAAGACTAGGCTCAATTAGTTAAACAAAT
261 TAGGAGTGAGGCTTCCAAAATTGAAAATTTTTATTTTAAGACTAGGCTCAATTAGTTAAACAAAT
*
30787921 AAAAGGGAAATTAGGCTCAAAAGTGGTATACTAAGGATAAAGATTTAACAAGGCTAACTTTTTAG
326 AAAAGGGAAATTAGGCTCAAAAGTGGTATACTAAGGATAAAGATTTAACAAGGCTAACTTTTTAA
* **
30787986 GCTCAAACAGTCCAAAGATGGACTAAATCTTCTCCCTAACTATGTATTGCCTAGAATTTCACCTC
391 GCTCAAACAGTCCAAAGATGGACTAAATCTTATCCCTAACTAACTATTGCCTAGAATTTCACCTC
30788051 AAGAGAAAATCG
456 AAGAGAAAATCG
* *
30788063 AGCACATAATTATTCTAGGACCTATTTATAGAGCTCTATTTTCCTTCTACAAGTACACATTTTCT
1 AGCACATAATTAGTCTAGGACCTATTTATAGAGCTCTATTCTCCTTCTACAAGTACACATTTTCT
30788128 TCCACATTTAAACTTTTTTTTTCTTTTTTTTCTTTCAACACATTTTTTTTCACAATTTCACACCC
66 TCCACATTTAAA----------CTTTTTTTT-TTTCAACACATTTTTTTTCACAATTTCACACCC
30788193 CCAAACTTATTTTCTTTGTATTGTAGGTAATGGGGTTAGTTTTCATGTTTTGAACTCTTTTTCTT
120 CCAAACTTATTTTCTTTGTATTGTAGGTAATGGGGTTAGTTTTCATGTTTTGAACTCTTTTTCTT
* * *
30788258 TTTTTACATCAATGTCATCTTTCCACCTTTTTCAACATTTAGCTCAATTTAAATTGCCTAAAACA
185 TTTTTACATCAACGTCACCTTTCCACCTTTTTCAACATATAGCTCAATTTAAATTGCCTAAAACA
*
30788323 ATATACATGCTTAGGAGTGAGGCTTCCAAAATTGAAAATTTTTATTTTAAGGCTAGGCTCAATTA
250 ATATACATGCTTAGGAGTGAGGCTTCCAAAATTGAAAATTTTTATTTTAAGACTAGGCTCAATTA
* * *
30788388 TTTAAACAAATAAAAGGGAAATTAGGCTCAAAAGTGGTATACTAGGGATAAAGATTTAATAAGGC
315 GTTAAACAAATAAAAGGGAAATTAGGCTCAAAAGTGGTATACTAAGGATAAAGATTTAACAAGGC
* * *
30788453 TAGCTTTTTAAGCTCAAACAGTCCAAAGATGGCCTAAATCTTATCCCTAACTAACTATTGCTTAG
380 TAACTTTTTAAGCTCAAACAGTCCAAAGATGGACTAAATCTTATCCCTAACTAACTATTGCCTAG
* *
30788518 GATTTTACCTCAAGAGAAAATCG
445 AATTTCACCTCAAGAGAAAATCG
30788541 AGCA
1 AGCA
30788545 AATTCTAGAA
Statistics
Matches: 448, Mismatches: 23, Indels: 11
0.93 0.05 0.02
Matches are distributed among these distances:
467 72 0.16
477 9 0.02
478 367 0.82
ACGTcount: A:0.31, C:0.18, G:0.13, T:0.38
Consensus pattern (467 bp):
AGCACATAATTAGTCTAGGACCTATTTATAGAGCTCTATTCTCCTTCTACAAGTACACATTTTCT
TCCACATTTAAACTTTTTTTTTTTCAACACATTTTTTTTCACAATTTCACACCCCCAAACTTATT
TTCTTTGTATTGTAGGTAATGGGGTTAGTTTTCATGTTTTGAACTCTTTTTCTTTTTTTACATCA
ACGTCACCTTTCCACCTTTTTCAACATATAGCTCAATTTAAATTGCCTAAAACAATATACATGCT
TAGGAGTGAGGCTTCCAAAATTGAAAATTTTTATTTTAAGACTAGGCTCAATTAGTTAAACAAAT
AAAAGGGAAATTAGGCTCAAAAGTGGTATACTAAGGATAAAGATTTAACAAGGCTAACTTTTTAA
GCTCAAACAGTCCAAAGATGGACTAAATCTTATCCCTAACTAACTATTGCCTAGAATTTCACCTC
AAGAGAAAATCG
Found at i:30789651 original size:21 final size:21
Alignment explanation
Indices: 30789627--30789694 Score: 91
Period size: 21 Copynumber: 3.2 Consensus size: 21
30789617 TTGACTTTGA
* *
30789627 ATGATGGCATCAGTTTTTGTC
1 ATGAAGGCATCTGTTTTTGTC
* *
30789648 ATGAAGGCATCTGATTTTGTT
1 ATGAAGGCATCTGTTTTTGTC
*
30789669 ATGAAGGCATCTGTCTTTGTC
1 ATGAAGGCATCTGTTTTTGTC
30789690 ATGAA
1 ATGAA
30789695 TTGCATGAAC
Statistics
Matches: 40, Mismatches: 7, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 40 1.00
ACGTcount: A:0.24, C:0.13, G:0.24, T:0.40
Consensus pattern (21 bp):
ATGAAGGCATCTGTTTTTGTC
Found at i:30810491 original size:15 final size:15
Alignment explanation
Indices: 30810471--30810503 Score: 50
Period size: 15 Copynumber: 2.2 Consensus size: 15
30810461 TAATGTTACA
30810471 AAAATTA-TAACTTAT
1 AAAATTATTAA-TTAT
30810486 AAAATTATTAATTAT
1 AAAATTATTAATTAT
30810501 AAA
1 AAA
30810504 TATATACCTT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 14 0.82
16 3 0.18
ACGTcount: A:0.58, C:0.03, G:0.00, T:0.39
Consensus pattern (15 bp):
AAAATTATTAATTAT
Found at i:30815241 original size:36 final size:36
Alignment explanation
Indices: 30815194--30815267 Score: 148
Period size: 36 Copynumber: 2.1 Consensus size: 36
30815184 TTGTGGTATT
30815194 AGTTTCTAGAAATGGGATTGACCGCTCTATGATTTC
1 AGTTTCTAGAAATGGGATTGACCGCTCTATGATTTC
30815230 AGTTTCTAGAAATGGGATTGACCGCTCTATGATTTC
1 AGTTTCTAGAAATGGGATTGACCGCTCTATGATTTC
30815266 AG
1 AG
30815268 CCATAAAGGT
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
36 38 1.00
ACGTcount: A:0.26, C:0.16, G:0.23, T:0.35
Consensus pattern (36 bp):
AGTTTCTAGAAATGGGATTGACCGCTCTATGATTTC
Found at i:30818388 original size:4 final size:4
Alignment explanation
Indices: 30818379--30818403 Score: 50
Period size: 4 Copynumber: 6.2 Consensus size: 4
30818369 TTTTAAATGT
30818379 TTTA TTTA TTTA TTTA TTTA TTTA T
1 TTTA TTTA TTTA TTTA TTTA TTTA T
30818404 GATATATATG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 21 1.00
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (4 bp):
TTTA
Found at i:30827080 original size:26 final size:26
Alignment explanation
Indices: 30827051--30827113 Score: 63
Period size: 26 Copynumber: 2.4 Consensus size: 26
30827041 GTATAACGAC
* *
30827051 AATATTTTTTTTTCAATATGACGTGT
1 AATATCTTTTTTTCAACATGACGTGT
* * * *
30827077 AATAACCTTTTTTGACCATGACGTGT
1 AATATCTTTTTTTCAACATGACGTGT
*
30827103 AATATGTTTTT
1 AATATCTTTTT
30827114 GTACATGGCG
Statistics
Matches: 28, Mismatches: 9, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
26 28 1.00
ACGTcount: A:0.27, C:0.11, G:0.13, T:0.49
Consensus pattern (26 bp):
AATATCTTTTTTTCAACATGACGTGT
Found at i:30827204 original size:24 final size:24
Alignment explanation
Indices: 30827168--30827229 Score: 97
Period size: 24 Copynumber: 2.6 Consensus size: 24
30827158 ACAACCTAAT
* * *
30827168 CATGGCGTGTAACATTTTTTTGTA
1 CATGGTGTATAACATGTTTTTGTA
30827192 CATGGTGTATAACATGTTTTTGTA
1 CATGGTGTATAACATGTTTTTGTA
30827216 CATGGTGTATAACA
1 CATGGTGTATAACA
30827230 ACCTAACCAT
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
24 35 1.00
ACGTcount: A:0.26, C:0.11, G:0.21, T:0.42
Consensus pattern (24 bp):
CATGGTGTATAACATGTTTTTGTA
Found at i:30827247 original size:69 final size:69
Alignment explanation
Indices: 30827091--30827275 Score: 210
Period size: 69 Copynumber: 2.6 Consensus size: 69
30827081 ACCTTTTTTG
* * * *
30827091 ACCATGACGTGTAATATGTTTTTGTACATGGCGTGTAACAACAGTTTGTTTTTTAACATGGCGTG
1 ACCATGACGTGTAACATATTTTTGTACAT-G-GTGT-ATAACA---TGTTTTTTAACATGGCGTA
30827156 TAACAACCTA
60 TAACAACCTA
* * * *
30827166 ATCATGGCGTGTAACATTTTTTTGTACATGGTGTATAACATGTTTTTGT-ACATGGTGTATAACA
1 ACCATGACGTGTAACATATTTTTGTACATGGTGTATAACATGTTTTT-TAACATGGCGTATAACA
30827230 ACCTA
65 ACCTA
**
30827235 ACCATGACGTGTAACATATTTTTGTACATGACGTATAACAT
1 ACCATGACGTGTAACATATTTTTGTACATGGTGTATAACAT
30827276 CATAACGTGT
Statistics
Matches: 97, Mismatches: 12, Indels: 8
0.83 0.10 0.07
Matches are distributed among these distances:
69 61 0.63
70 1 0.01
72 5 0.05
73 4 0.04
74 1 0.01
75 25 0.26
ACGTcount: A:0.29, C:0.15, G:0.18, T:0.37
Consensus pattern (69 bp):
ACCATGACGTGTAACATATTTTTGTACATGGTGTATAACATGTTTTTTAACATGGCGTATAACAA
CCTA
Found at i:30828344 original size:8 final size:7
Alignment explanation
Indices: 30828326--30828421 Score: 56
Period size: 7 Copynumber: 12.9 Consensus size: 7
30828316 TAATGTCTTA
30828326 TTTATTAT
1 TTTATT-T
30828334 TTTCATTT
1 TTT-ATTT
30828342 TTTATTT
1 TTTATTT
30828349 TTT-TATT
1 TTTAT-TT
**
30828356 TTT-CCT
1 TTTATTT
30828362 TTTACTTT
1 TTTA-TTT
30828370 ATTT-TTCT
1 -TTTATT-T
30828378 TTTATTT
1 TTTATTT
30828385 TTTCATTCT
1 TTT-ATT-T
30828394 TTTGATTT
1 TTT-ATTT
30828402 TCTT-TTT
1 T-TTATTT
30828409 TTTATTT
1 TTTATTT
30828416 TTTATT
1 TTTATT
30828422 AATTTATATA
Statistics
Matches: 72, Mismatches: 5, Indels: 23
0.72 0.05 0.23
Matches are distributed among these distances:
6 7 0.10
7 34 0.47
8 16 0.22
9 15 0.21
ACGTcount: A:0.12, C:0.08, G:0.01, T:0.78
Consensus pattern (7 bp):
TTTATTT
Found at i:30828372 original size:17 final size:16
Alignment explanation
Indices: 30828350--30828381 Score: 55
Period size: 17 Copynumber: 1.9 Consensus size: 16
30828340 TTTTTATTTT
30828350 TTTATTTTTCCTTTTAC
1 TTTATTTTT-CTTTTAC
30828367 TTTATTTTTCTTTTA
1 TTTATTTTTCTTTTA
30828382 TTTTTTCATT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 6 0.40
17 9 0.60
ACGTcount: A:0.12, C:0.12, G:0.00, T:0.75
Consensus pattern (16 bp):
TTTATTTTTCTTTTAC
Found at i:30836793 original size:26 final size:26
Alignment explanation
Indices: 30836717--30836837 Score: 74
Period size: 30 Copynumber: 4.7 Consensus size: 26
30836707 ATGTTATAAT
*
30836717 TAAAATA-AAAAACATTAAAATAAAATA
1 TAAAATATAAGAA-ATTAAAAT-AAATA
* *
30836744 TATAATATAAG-AATT---AGAAA-A
1 TAAAATATAAGAAATTAAAATAAATA
**
30836765 TAAAATATAAGAAATTAAAATTTATA
1 TAAAATATAAGAAATTAAAATAAATA
*
30836791 TAATATAGGTAAAAGAAATTAAAATAAATA
1 TAA-A-A--TATAAGAAATTAAAATAAATA
* *
30836821 TATAATATAAAAAATTA
1 TAAAATATAAGAAATTA
30836838 TATCAAAGAA
Statistics
Matches: 71, Mismatches: 13, Indels: 21
0.68 0.12 0.20
Matches are distributed among these distances:
21 11 0.15
22 7 0.10
23 1 0.01
25 2 0.03
26 17 0.24
27 8 0.11
28 4 0.06
29 1 0.01
30 20 0.28
ACGTcount: A:0.65, C:0.01, G:0.05, T:0.29
Consensus pattern (26 bp):
TAAAATATAAGAAATTAAAATAAATA
Found at i:30836888 original size:33 final size:34
Alignment explanation
Indices: 30836812--30836897 Score: 120
Period size: 34 Copynumber: 2.6 Consensus size: 34
30836802 AAAGAAATTA
* * * *
30836812 AAATAAATATATAATATAAAAAATTATATCAAAG
1 AAATAAAAATAAAATATATAAAATTATAACAAAG
30836846 AAATAAAAATAAAATATATAAAATTATAAC-AAG
1 AAATAAAAATAAAATATATAAAATTATAACAAAG
*
30836879 AAATGAAAATAAAATATAT
1 AAATAAAAATAAAATATAT
30836898 GACATTAAAA
Statistics
Matches: 47, Mismatches: 5, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
33 21 0.45
34 26 0.55
ACGTcount: A:0.67, C:0.02, G:0.03, T:0.27
Consensus pattern (34 bp):
AAATAAAAATAAAATATATAAAATTATAACAAAG
Found at i:30850870 original size:24 final size:24
Alignment explanation
Indices: 30850821--30850891 Score: 69
Period size: 24 Copynumber: 3.0 Consensus size: 24
30850811 TTTTTATTTT
*
30850821 ATTT-TTTAAATATATTAAT-TTATA
1 ATTTATTTAAA-ATATTAATAAT-TA
30850845 ATTTATTTAAAATATTAATAATTA
1 ATTTATTTAAAATATTAATAATTA
*
30850869 A-TAATTT-AAATATTAATATATTA
1 ATTTATTTAAAATATTAATA-ATTA
30850892 TTATAATTTA
Statistics
Matches: 42, Mismatches: 2, Indels: 7
0.82 0.04 0.14
Matches are distributed among these distances:
22 11 0.26
23 9 0.21
24 15 0.36
25 7 0.17
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (24 bp):
ATTTATTTAAAATATTAATAATTA
Found at i:30850874 original size:27 final size:25
Alignment explanation
Indices: 30850821--30850901 Score: 73
Period size: 25 Copynumber: 3.2 Consensus size: 25
30850811 TTTTTATTTT
30850821 ATTT-TTTAAATATATTAATTTATA
1 ATTTATTTAAATATATTAATTTATA
30850845 ATTTATTTAAA-ATATTAATAATTAATA
1 ATTTATTTAAATATATTAAT--TT-ATA
30850872 ATTTAAATATT-AATATATT-A-TTATA
1 ATTT--AT-TTAAATATATTAATTTATA
30850897 ATTTA
1 ATTTA
30850902 ATTATTATTA
Statistics
Matches: 49, Mismatches: 0, Indels: 17
0.74 0.00 0.26
Matches are distributed among these distances:
23 1 0.02
24 12 0.24
25 13 0.27
26 4 0.08
27 7 0.14
29 5 0.10
30 7 0.14
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (25 bp):
ATTTATTTAAATATATTAATTTATA
Found at i:30850882 original size:22 final size:24
Alignment explanation
Indices: 30850832--30850908 Score: 79
Period size: 25 Copynumber: 3.2 Consensus size: 24
30850822 TTTTTTAAAT
* * *
30850832 ATATTAATTTATAAT-TTATTTAAA
1 ATATTAATATATTATATAATTT-AA
30850856 ATATTAATA-ATTA-ATAATTTAA
1 ATATTAATATATTATATAATTTAA
30850878 ATATTAATATATTATTATAATTTAA
1 ATATTAATATATTA-TATAATTTAA
*
30850903 TTATTA
1 ATATTA
30850909 TTATTTTAAA
Statistics
Matches: 45, Mismatches: 4, Indels: 7
0.80 0.07 0.12
Matches are distributed among these distances:
22 11 0.24
23 12 0.27
24 8 0.18
25 14 0.31
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (24 bp):
ATATTAATATATTATATAATTTAA
Found at i:30853244 original size:16 final size:15
Alignment explanation
Indices: 30853178--30853240 Score: 65
Period size: 16 Copynumber: 4.0 Consensus size: 15
30853168 GTATACTTTA
30853178 ATTAAAATTTAATAT
1 ATTAAAATTTAATAT
30853193 ATTAATAATTTAATAT
1 ATTAA-AATTTAATAT
*
30853209 AGTAAACA-TTAATATT
1 ATTAAA-ATTTAATA-T
*
30853225 TTTAAAATATTAATAT
1 ATTAAAAT-TTAATAT
30853241 TTTATTTATA
Statistics
Matches: 40, Mismatches: 3, Indels: 9
0.77 0.06 0.17
Matches are distributed among these distances:
15 13 0.32
16 21 0.52
17 6 0.15
ACGTcount: A:0.51, C:0.02, G:0.02, T:0.46
Consensus pattern (15 bp):
ATTAAAATTTAATAT
Found at i:30853271 original size:17 final size:17
Alignment explanation
Indices: 30853246--30853279 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
30853236 AATATTTTAT
30853246 TTATAATTAAAACATTA
1 TTATAATTAAAACATTA
* *
30853263 TTATGATTAAAATATTA
1 TTATAATTAAAACATTA
30853280 ATTTTTATAA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.50, C:0.03, G:0.03, T:0.44
Consensus pattern (17 bp):
TTATAATTAAAACATTA
Found at i:30853273 original size:43 final size:45
Alignment explanation
Indices: 30853178--30853302 Score: 132
Period size: 43 Copynumber: 2.8 Consensus size: 45
30853168 GTATACTTTA
* *
30853178 ATTAAAAT-TTAATATATTAATAATTTA-ATATAGTAAACATTAATATT
1 ATTAAAATATTAATAT-TT-ATAATTTATAAATA--AAACATTAATATG
* * *
30853225 TTTAAAATATTAATATTT-T-ATTTATAATTAAAACATTATTATG
1 ATTAAAATATTAATATTTATAATTTATAAATAAAACATTAATATG
*
30853268 ATTAAAATATTAATTTTTATAATTTATAAATAAAA
1 ATTAAAATATTAATATTTATAATTTATAAATAAAA
30853303 TTTTAACTTT
Statistics
Matches: 66, Mismatches: 8, Indels: 10
0.79 0.10 0.12
Matches are distributed among these distances:
43 27 0.41
44 6 0.09
45 17 0.26
47 9 0.14
48 7 0.11
ACGTcount: A:0.50, C:0.02, G:0.02, T:0.47
Consensus pattern (45 bp):
ATTAAAATATTAATATTTATAATTTATAAATAAAACATTAATATG
Found at i:30857100 original size:41 final size:41
Alignment explanation
Indices: 30857044--30857150 Score: 126
Period size: 41 Copynumber: 2.6 Consensus size: 41
30857034 AGCAAACATC
* * * *
30857044 ACAAATACCATTATTTTGTAATTGATAGTGCGATAGATATT
1 ACAAATATCACTATTTTGTAATTGATAATGCGATAGATAAT
** * *
30857085 ACAAATATCACTATTTTGTAATCAATAATGTGGTAGATAAT
1 ACAAATATCACTATTTTGTAATTGATAATGCGATAGATAAT
*
30857126 ACAAATATCACTA-TTTGTAACTGAT
1 ACAAATATCACTATTTTGTAATTGAT
30857151 GGTGTAGTTT
Statistics
Matches: 55, Mismatches: 11, Indels: 1
0.82 0.16 0.01
Matches are distributed among these distances:
40 9 0.16
41 46 0.84
ACGTcount: A:0.39, C:0.11, G:0.12, T:0.37
Consensus pattern (41 bp):
ACAAATATCACTATTTTGTAATTGATAATGCGATAGATAAT
Found at i:30857440 original size:26 final size:24
Alignment explanation
Indices: 30857398--30857459 Score: 61
Period size: 26 Copynumber: 2.5 Consensus size: 24
30857388 ACATTGAATA
* * *
30857398 AAAATCACATTCTAAAACCAAAATC
1 AAAATCATATTCAAAAAACAAAA-C
*
30857423 AAAATCATATTCCAAAAAACAGAAC
1 AAAATCATATT-CAAAAAACAAAAC
30857448 AAATATCATATT
1 AAA-ATCATATT
30857460 TACTTACATA
Statistics
Matches: 31, Mismatches: 4, Indels: 3
0.82 0.11 0.08
Matches are distributed among these distances:
25 14 0.45
26 17 0.55
ACGTcount: A:0.56, C:0.19, G:0.02, T:0.23
Consensus pattern (24 bp):
AAAATCATATTCAAAAAACAAAAC
Found at i:30861986 original size:35 final size:36
Alignment explanation
Indices: 30861911--30861996 Score: 95
Period size: 36 Copynumber: 2.4 Consensus size: 36
30861901 TAACTACTAA
* *
30861911 TTAAATTAAT-AAAAACAAAAATAATAAAACTTAAAT
1 TTAAA-TAATAAAAAACAAAAATAATAAAACATAAAC
* * *
30861947 TTAAATAATAAAAAACAAAGAT-CTTAAACATAAAC
1 TTAAATAATAAAAAACAAAAATAATAAAACATAAAC
30861982 TTAAATAACTAAAAA
1 TTAAATAA-TAAAAA
30861997 TAAATATCGA
Statistics
Matches: 43, Mismatches: 5, Indels: 4
0.83 0.10 0.08
Matches are distributed among these distances:
35 21 0.49
36 22 0.51
ACGTcount: A:0.65, C:0.08, G:0.01, T:0.26
Consensus pattern (36 bp):
TTAAATAATAAAAAACAAAAATAATAAAACATAAAC
Found at i:30862025 original size:40 final size:40
Alignment explanation
Indices: 30861976--30862116 Score: 165
Period size: 40 Copynumber: 3.5 Consensus size: 40
30861966 GATCTTAAAC
* * *
30861976 ATAAACTTAAATAACTAAAAATAAATATCGATACAACGAT
1 ATAAACTTAAATAACTAAAAATAAATATCCAAACAACAAT
* * * *
30862016 ATAAACTTAAATAACTATACATAAATATCCAAATAACAAC
1 ATAAACTTAAATAACTAAAAATAAATATCCAAACAACAAT
* * * *
30862056 ATAAACTTAAATAACTAAACACAAAGATCCAAACAAATAAT
1 ATAAACTTAAATAACTAAAAATAAATATCCAAAC-AACAAT
*
30862097 ATAAACTTAAATAACCAAAA
1 ATAAACTTAAATAACTAAAA
30862117 TTATAATTTA
Statistics
Matches: 85, Mismatches: 15, Indels: 1
0.84 0.15 0.01
Matches are distributed among these distances:
40 63 0.74
41 22 0.26
ACGTcount: A:0.60, C:0.16, G:0.02, T:0.23
Consensus pattern (40 bp):
ATAAACTTAAATAACTAAAAATAAATATCCAAACAACAAT
Found at i:30862138 original size:16 final size:17
Alignment explanation
Indices: 30862117--30862152 Score: 56
Period size: 16 Copynumber: 2.2 Consensus size: 17
30862107 ATAACCAAAA
30862117 TTATAATTTATATAA-G
1 TTATAATTTATATAATG
*
30862133 TTATAATTTTTATAATG
1 TTATAATTTATATAATG
30862150 TTA
1 TTA
30862153 ACACAAAATA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 14 0.78
17 4 0.22
ACGTcount: A:0.39, C:0.00, G:0.06, T:0.56
Consensus pattern (17 bp):
TTATAATTTATATAATG
Found at i:30862647 original size:2 final size:2
Alignment explanation
Indices: 30862642--30862674 Score: 50
Period size: 2 Copynumber: 17.0 Consensus size: 2
30862632 TAATAAAATA
*
30862642 AT AT AT -T AT AT AT AT TT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
30862675 TACAATTAAT
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
1 1 0.04
2 27 0.96
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (2 bp):
AT
Found at i:30862703 original size:15 final size:17
Alignment explanation
Indices: 30862683--30862715 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 17
30862673 ATTACAATTA
30862683 ATAA-TTTTATAA-GTT
1 ATAATTTTTATAATGTT
30862698 ATAATTTTTATAATGTT
1 ATAATTTTTATAATGTT
30862715 A
1 A
30862716 ACATAAAATA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 4 0.25
16 8 0.50
17 4 0.25
ACGTcount: A:0.39, C:0.00, G:0.06, T:0.55
Consensus pattern (17 bp):
ATAATTTTTATAATGTT
Found at i:30868132 original size:17 final size:17
Alignment explanation
Indices: 30868110--30868147 Score: 53
Period size: 17 Copynumber: 2.3 Consensus size: 17
30868100 GTAGCTTACC
30868110 ATTTTTTT-AATTATTTT
1 ATTTTTTTGAATT-TTTT
30868127 ATTTTTTTGAATTTTTT
1 ATTTTTTTGAATTTTTT
30868144 -TTTT
1 ATTTT
30868148 AAAATTTTAA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
16 4 0.20
17 12 0.60
18 4 0.20
ACGTcount: A:0.18, C:0.00, G:0.03, T:0.79
Consensus pattern (17 bp):
ATTTTTTTGAATTTTTT
Found at i:30868229 original size:15 final size:16
Alignment explanation
Indices: 30868209--30868241 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
30868199 ATTTAATAAT
*
30868209 TAAATAA-ATAAAAAA
1 TAAATAATAGAAAAAA
30868224 TAAATAATAGAAAAAA
1 TAAATAATAGAAAAAA
30868240 TA
1 TA
30868242 TAAAAGAAAG
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 7 0.44
16 9 0.56
ACGTcount: A:0.76, C:0.00, G:0.03, T:0.21
Consensus pattern (16 bp):
TAAATAATAGAAAAAA
Found at i:30869647 original size:21 final size:21
Alignment explanation
Indices: 30869605--30869672 Score: 82
Period size: 21 Copynumber: 3.2 Consensus size: 21
30869595 TTGAATGGAG
* * *
30869605 GCATCAGTCCTTATCATAAAT
1 GCATCAGTCTTTGTCATGAAT
* *
30869626 GCGTCAGTCTTTGTTATGAAT
1 GCATCAGTCTTTGTCATGAAT
30869647 GCATCAGTCTTTGTCATGAATT
1 GCATCAGTCTTTGTCATGAA-T
30869669 GCAT
1 GCAT
30869673 GAACATATCC
Statistics
Matches: 39, Mismatches: 7, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
21 34 0.87
22 5 0.13
ACGTcount: A:0.25, C:0.19, G:0.18, T:0.38
Consensus pattern (21 bp):
GCATCAGTCTTTGTCATGAAT
Found at i:30873903 original size:13 final size:13
Alignment explanation
Indices: 30873885--30873909 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
30873875 TTCCAGAAAA
30873885 TTTATAAAATCAT
1 TTTATAAAATCAT
30873898 TTTATAAAATCA
1 TTTATAAAATCA
30873910 CAATTTCTTT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.48, C:0.08, G:0.00, T:0.44
Consensus pattern (13 bp):
TTTATAAAATCAT
Found at i:30879519 original size:15 final size:15
Alignment explanation
Indices: 30879501--30879547 Score: 85
Period size: 15 Copynumber: 3.1 Consensus size: 15
30879491 TGAGGTAAAG
*
30879501 GACAATGAGGAAGAT
1 GACAATAAGGAAGAT
30879516 GACAATAAGGAAGAT
1 GACAATAAGGAAGAT
30879531 GACAATAAGGAAGAT
1 GACAATAAGGAAGAT
30879546 GA
1 GA
30879548 GGAGGACTAG
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
15 31 1.00
ACGTcount: A:0.51, C:0.06, G:0.30, T:0.13
Consensus pattern (15 bp):
GACAATAAGGAAGAT
Found at i:30881100 original size:13 final size:13
Alignment explanation
Indices: 30881082--30881108 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
30881072 ATTTTCAAAA
30881082 ATTTTATAAAATC
1 ATTTTATAAAATC
30881095 ATTTTATAAAATC
1 ATTTTATAAAATC
30881108 A
1 A
30881109 CAATTTCTCT
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:0.48, C:0.07, G:0.00, T:0.44
Consensus pattern (13 bp):
ATTTTATAAAATC
Found at i:30887135 original size:5 final size:5
Alignment explanation
Indices: 30887114--30887146 Score: 50
Period size: 5 Copynumber: 6.8 Consensus size: 5
30887104 ACCTAACCTG
*
30887114 ACTTA ACTTA AC-TA ACTTA ACTTA ATTTA ACTT
1 ACTTA ACTTA ACTTA ACTTA ACTTA ACTTA ACTT
30887147 GAACCACGCA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
4 4 0.16
5 21 0.84
ACGTcount: A:0.39, C:0.18, G:0.00, T:0.42
Consensus pattern (5 bp):
ACTTA
Found at i:30888441 original size:13 final size:13
Alignment explanation
Indices: 30888423--30888449 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
30888413 ATTTTCAAAA
30888423 ATTTTATAAAATC
1 ATTTTATAAAATC
30888436 ATTTTATAAAATC
1 ATTTTATAAAATC
30888449 A
1 A
30888450 CAATTTCTCT
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:0.48, C:0.07, G:0.00, T:0.44
Consensus pattern (13 bp):
ATTTTATAAAATC
Found at i:30890852 original size:24 final size:22
Alignment explanation
Indices: 30890803--30890852 Score: 55
Period size: 24 Copynumber: 2.2 Consensus size: 22
30890793 TGTGAAAAGA
*
30890803 AAAAGAAAAAATAATGTTGAAC
1 AAAAGAAAAAATAATGTGGAAC
* *
30890825 AAAAGAAAAATTCAAATGTGGAAG
1 AAAAGAAAAAAT--AATGTGGAAC
30890849 AAAA
1 AAAA
30890853 TGTGTATTGG
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
22 11 0.48
24 12 0.52
ACGTcount: A:0.64, C:0.04, G:0.16, T:0.16
Consensus pattern (22 bp):
AAAAGAAAAAATAATGTGGAAC
Found at i:30893996 original size:17 final size:17
Alignment explanation
Indices: 30893964--30893997 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
30893954 GTATAAATAT
*
30893964 CATTTTTATTGAAAAAGA
1 CATTTTAATTGAAAAA-A
30893982 CATTTTAATTGAAAAA
1 CATTTTAATTGAAAAA
30893998 CATAATATTT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.47, C:0.06, G:0.09, T:0.38
Consensus pattern (17 bp):
CATTTTAATTGAAAAAA
Found at i:30895232 original size:19 final size:19
Alignment explanation
Indices: 30895208--30895245 Score: 67
Period size: 19 Copynumber: 2.0 Consensus size: 19
30895198 ACTTATAAAC
30895208 CTCAAATCATACTCAAATA
1 CTCAAATCATACTCAAATA
*
30895227 CTCAAATCATACTCCAATA
1 CTCAAATCATACTCAAATA
30895246 AGTCAAATGG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.45, C:0.29, G:0.00, T:0.26
Consensus pattern (19 bp):
CTCAAATCATACTCAAATA
Found at i:30906533 original size:23 final size:23
Alignment explanation
Indices: 30906503--30906547 Score: 74
Period size: 23 Copynumber: 2.0 Consensus size: 23
30906493 TATACGTATA
30906503 CCCATCATCATCATGCA-CACCAT
1 CCCATCATCATCAT-CATCACCAT
30906526 CCCATCATCATCATCATCACCA
1 CCCATCATCATCATCATCACCA
30906548 GCTCATGCGC
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
22 2 0.10
23 19 0.90
ACGTcount: A:0.31, C:0.44, G:0.02, T:0.22
Consensus pattern (23 bp):
CCCATCATCATCATCATCACCAT
Found at i:30906628 original size:43 final size:43
Alignment explanation
Indices: 30906539--30906670 Score: 151
Period size: 43 Copynumber: 3.1 Consensus size: 43
30906529 ATCATCATCA
* * *
30906539 TCATCACCAGC-TCATGCGCACTCCCTACTCGCATAT-GGCTAGG
1 TCATCACCAGCAT-ATGCGCACTCCCTACTCGCACATAGCCGA-G
* ** *
30906582 TCATCACCGGGTTATGCGCACTCCCTACTGGCACATAGCCGAG
1 TCATCACCAGCATATGCGCACTCCCTACTCGCACATAGCCGAG
**
30906625 TCATCTTCAGCATATGCGCACTCCCTACTCGCACATAGCCGAG
1 TCATCACCAGCATATGCGCACTCCCTACTCGCACATAGCCGAG
30906668 TCA
1 TCA
30906671 ATATAATTAC
Statistics
Matches: 75, Mismatches: 12, Indels: 4
0.82 0.13 0.04
Matches are distributed among these distances:
43 71 0.95
44 4 0.05
ACGTcount: A:0.22, C:0.36, G:0.19, T:0.23
Consensus pattern (43 bp):
TCATCACCAGCATATGCGCACTCCCTACTCGCACATAGCCGAG
Found at i:30908482 original size:14 final size:15
Alignment explanation
Indices: 30908457--30908498 Score: 59
Period size: 14 Copynumber: 2.8 Consensus size: 15
30908447 GTTAATAAAT
*
30908457 ATATATATATATATAA
1 ATATAAATATATAT-A
30908473 ATATAAATATA-ATA
1 ATATAAATATATATA
30908487 ATATAAATATAT
1 ATATAAATATAT
30908499 GAGAACAAAG
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
14 12 0.50
15 2 0.08
16 10 0.42
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (15 bp):
ATATAAATATATATA
Found at i:30908773 original size:24 final size:24
Alignment explanation
Indices: 30908724--30908775 Score: 61
Period size: 24 Copynumber: 2.2 Consensus size: 24
30908714 AACAAAGGAA
* * *
30908724 AGAAAAGAGAAAGAAGCAACCGAG
1 AGAAAAGAGAAAAAAGCAAACAAG
30908748 AGAAAAGAGACAAAAAG-AAACAAG
1 AGAAAAGAGA-AAAAAGCAAACAAG
30908772 AGAA
1 AGAA
30908776 GGCCAAGTGG
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
24 19 0.79
25 5 0.21
ACGTcount: A:0.65, C:0.10, G:0.25, T:0.00
Consensus pattern (24 bp):
AGAAAAGAGAAAAAAGCAAACAAG
Found at i:30909244 original size:5 final size:5
Alignment explanation
Indices: 30909222--30909276 Score: 73
Period size: 5 Copynumber: 11.6 Consensus size: 5
30909212 ACGGTGGAAG
30909222 AAAG- AAAG- AAAG- AAAGA AAAGA AAAGA AAAGA AAAGA AAAGA ACAAG-
1 AAAGA AAAGA AAAGA AAAGA AAAGA AAAGA AAAGA AAAGA AAAGA A-AAGA
30909269 AAAGA AAA
1 AAAGA AAA
30909277 ATGGGCATGC
Statistics
Matches: 48, Mismatches: 0, Indels: 5
0.91 0.00 0.09
Matches are distributed among these distances:
4 15 0.31
5 30 0.62
6 3 0.06
ACGTcount: A:0.78, C:0.02, G:0.20, T:0.00
Consensus pattern (5 bp):
AAAGA
Found at i:30916963 original size:5 final size:5
Alignment explanation
Indices: 30916955--30916987 Score: 59
Period size: 5 Copynumber: 6.8 Consensus size: 5
30916945 ACCTAACCTG
30916955 ACTTA ACTTA AC-TA ACTTA ACTTA ACTTA ACTT
1 ACTTA ACTTA ACTTA ACTTA ACTTA ACTTA ACTT
30916988 GGGCCACGCA
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
4 4 0.15
5 23 0.85
ACGTcount: A:0.39, C:0.21, G:0.00, T:0.39
Consensus pattern (5 bp):
ACTTA
Found at i:30916974 original size:14 final size:15
Alignment explanation
Indices: 30916955--30916987 Score: 59
Period size: 14 Copynumber: 2.3 Consensus size: 15
30916945 ACCTAACCTG
30916955 ACTTAACTTAAC-TA
1 ACTTAACTTAACTTA
30916969 ACTTAACTTAACTTA
1 ACTTAACTTAACTTA
30916984 ACTT
1 ACTT
30916988 GGGCCACGCA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
14 12 0.67
15 6 0.33
ACGTcount: A:0.39, C:0.21, G:0.00, T:0.39
Consensus pattern (15 bp):
ACTTAACTTAACTTA
Found at i:30917042 original size:15 final size:15
Alignment explanation
Indices: 30917022--30917067 Score: 58
Period size: 15 Copynumber: 3.1 Consensus size: 15
30917012 TTCTTAAAAC
30917022 AACTTTAAAACCAAA
1 AACTTTAAAACCAAA
30917037 AACTTTAAAATCC-AA
1 AACTTTAAAA-CCAAA
* *
30917052 AGCTTTAAAATCAAA
1 AACTTTAAAACCAAA
30917067 A
1 A
30917068 TCTCTGATCT
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
14 1 0.04
15 24 0.89
16 2 0.07
ACGTcount: A:0.57, C:0.17, G:0.02, T:0.24
Consensus pattern (15 bp):
AACTTTAAAACCAAA
Found at i:30918286 original size:13 final size:13
Alignment explanation
Indices: 30918268--30918292 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
30918258 TTTCAGAAAA
30918268 TTTATAAAATCAT
1 TTTATAAAATCAT
30918281 TTTATAAAATCA
1 TTTATAAAATCA
30918293 CAATTTCTCT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.48, C:0.08, G:0.00, T:0.44
Consensus pattern (13 bp):
TTTATAAAATCAT
Found at i:30922123 original size:126 final size:125
Alignment explanation
Indices: 30921966--30922217 Score: 495
Period size: 126 Copynumber: 2.0 Consensus size: 125
30921956 TACCTACTTT
30921966 ATCATCATAATTTTCTTTCTAGGATGAAGGTTAGCATCATCAAATAAACATGAATAGATTCTTCA
1 ATCATCATAATTTTCTTTCTAGGATGAAGGTTAGCATCATCAAATAAACATGAATAGATTCTTCA
30922031 ACAATTAATGTCCTCTTATTGAACACTCTATATGCTTTAGAAGTCGAAGAGTATCTTAGA
66 ACAATTAATGTCCTCTTATTGAACACTCTATATGCTTTAGAAGTCGAAGAGTATCTTAGA
30922091 NATCATCATAATTTTCTTTCTAGGATGAAGGTTAGCATCATCAAATAAACATGAATAGATTCTTC
1 -ATCATCATAATTTTCTTTCTAGGATGAAGGTTAGCATCATCAAATAAACATGAATAGATTCTTC
30922156 AACAATTAATGTCCTCTTATTGAACACTCTATATGCTTTAGAAGTCGAAGAGTATCTTAGA
65 AACAATTAATGTCCTCTTATTGAACACTCTATATGCTTTAGAAGTCGAAGAGTATCTTAGA
30922217 A
1 A
30922218 AGATTTCCTC
Statistics
Matches: 126, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
125 1 0.01
126 125 0.99
ACGTcount: A:0.35, C:0.16, G:0.13, T:0.35
Consensus pattern (125 bp):
ATCATCATAATTTTCTTTCTAGGATGAAGGTTAGCATCATCAAATAAACATGAATAGATTCTTCA
ACAATTAATGTCCTCTTATTGAACACTCTATATGCTTTAGAAGTCGAAGAGTATCTTAGA
Found at i:30927517 original size:21 final size:21
Alignment explanation
Indices: 30927488--30927530 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 21
30927478 TTAATGTTAC
30927488 AAATATTTGAGAAGAAAGAAG
1 AAATATTTGAGAAGAAAGAAG
* *
30927509 AAATTTTTGAGAATAAAGAAG
1 AAATATTTGAGAAGAAAGAAG
30927530 A
1 A
30927531 GTATGACTTT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.56, C:0.00, G:0.21, T:0.23
Consensus pattern (21 bp):
AAATATTTGAGAAGAAAGAAG
Found at i:30927784 original size:39 final size:39
Alignment explanation
Indices: 30927729--30927835 Score: 169
Period size: 39 Copynumber: 2.7 Consensus size: 39
30927719 ATAATTGTTT
* *
30927729 CCTTTCATAATACAACTATTCAATAGTTATATCTAATAA
1 CCTTTCATAATACAACTATTAAAAAGTTATATCTAATAA
* *
30927768 CCTTTCATAATGCAACTATAAAAAAGTTATATCTAATAA
1 CCTTTCATAATACAACTATTAAAAAGTTATATCTAATAA
*
30927807 CCTTTCTTAATACAACTATTAAAAAGTTA
1 CCTTTCATAATACAACTATTAAAAAGTTA
30927836 ATGTTTTAAT
Statistics
Matches: 61, Mismatches: 7, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
39 61 1.00
ACGTcount: A:0.43, C:0.17, G:0.04, T:0.36
Consensus pattern (39 bp):
CCTTTCATAATACAACTATTAAAAAGTTATATCTAATAA
Found at i:30930520 original size:38 final size:40
Alignment explanation
Indices: 30930434--30930536 Score: 131
Period size: 38 Copynumber: 2.6 Consensus size: 40
30930424 ACCCGGCTCA
*
30930434 TGTACATCCCCCCACATCGTGCACATAGCCGGCACCATCG
1 TGTACATCCCCCCACATCGTGCACATAGCCAGCACCATCG
* * **
30930474 TGTGCAT-CCCCCACCATCGTGCACA-A-TCAGCGTCATCG
1 TGTACATCCCCCCA-CATCGTGCACATAGCCAGCACCATCG
30930512 TGTACATCCCCCCACATCGTGCACA
1 TGTACATCCCCCCACATCGTGCACA
30930537 CGGGCACTAT
Statistics
Matches: 55, Mismatches: 6, Indels: 6
0.82 0.09 0.09
Matches are distributed among these distances:
38 25 0.45
39 13 0.24
40 17 0.31
ACGTcount: A:0.22, C:0.42, G:0.17, T:0.19
Consensus pattern (40 bp):
TGTACATCCCCCCACATCGTGCACATAGCCAGCACCATCG
Found at i:30930529 original size:19 final size:18
Alignment explanation
Indices: 30930434--30930532 Score: 54
Period size: 19 Copynumber: 5.1 Consensus size: 18
30930424 ACCCGGCTCA
30930434 TGTACATCCCCCCACATCG
1 TGTACAT-CCCCCACATCG
* **
30930453 TGCACATAGCCGGCACCATCG
1 TGTACAT--CCCCCA-CATCG
*
30930474 TGTGCATCCCCCACCATCG
1 TGTACATCCCCCA-CATCG
* ** **
30930493 TGCACAATCAGCGTCATCG
1 TGTAC-ATCCCCCACATCG
30930512 TGTACATCCCCCCACATCG
1 TGTACAT-CCCCCACATCG
30930531 TG
1 TG
30930533 CACACGGGCA
Statistics
Matches: 57, Mismatches: 19, Indels: 8
0.68 0.23 0.10
Matches are distributed among these distances:
18 2 0.04
19 37 0.65
20 8 0.14
21 10 0.18
ACGTcount: A:0.21, C:0.41, G:0.17, T:0.20
Consensus pattern (18 bp):
TGTACATCCCCCACATCG
Found at i:30933201 original size:42 final size:42
Alignment explanation
Indices: 30933145--30933249 Score: 106
Period size: 45 Copynumber: 2.4 Consensus size: 42
30933135 AAAATGAAAA
* *
30933145 TATTTAAATATTATTTAACTATAATAAATA-ATATAAAGCATAT
1 TATTGAAATATTATTTAA-TATAATAAATATA-ATAAAGAATAT
*
30933188 TATTGAATATTATTATTTGAATATAATAAATGTAATAAAGAATAT
1 TATTGAA-A-TATTATTT-AATATAATAAATATAATAAAGAATAT
* *
30933233 TATT-TAGTATTATTTAA
1 TATTGAAATATTATTTAA
30933250 ATTTAATGAA
Statistics
Matches: 53, Mismatches: 5, Indels: 10
0.78 0.07 0.15
Matches are distributed among these distances:
41 2 0.04
42 8 0.15
43 6 0.11
44 2 0.04
45 32 0.60
46 3 0.06
ACGTcount: A:0.48, C:0.02, G:0.06, T:0.45
Consensus pattern (42 bp):
TATTGAAATATTATTTAATATAATAAATATAATAAAGAATAT
Found at i:30933213 original size:45 final size:45
Alignment explanation
Indices: 30933153--30933246 Score: 120
Period size: 45 Copynumber: 2.1 Consensus size: 45
30933143 AATATTTAAA
*
30933153 TATTATTTAACTATAATAAATA-ATATAAAGCATATTATTGAATAT
1 TATTATTTAACTATAATAAATATA-ATAAAGAATATTATTGAATAT
* * *
30933198 TATTATTTGAA-TATAATAAATGTAATAAAGAATATTATTTAGTAT
1 TATTATTT-AACTATAATAAATATAATAAAGAATATTATTGAATAT
30933243 TATT
1 TATT
30933247 TAAATTTAAT
Statistics
Matches: 43, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
45 40 0.93
46 3 0.07
ACGTcount: A:0.47, C:0.02, G:0.06, T:0.45
Consensus pattern (45 bp):
TATTATTTAACTATAATAAATATAATAAAGAATATTATTGAATAT
Found at i:30933340 original size:23 final size:22
Alignment explanation
Indices: 30933284--30933357 Score: 78
Period size: 23 Copynumber: 3.3 Consensus size: 22
30933274 TTTTAATATT
*
30933284 AAATATTATTTAATTATAATAA
1 AAATATTATTAAATTATAATAA
** *
30933306 AAAGT-TTAATTAGCTTCTAATACA
1 AAA-TATT-ATTAAATTATAATA-A
30933330 AAATATTATTAAATTATAATAA
1 AAATATTATTAAATTATAATAA
30933352 AAATAT
1 AAATAT
30933358 GTTTGTATTT
Statistics
Matches: 41, Mismatches: 7, Indels: 8
0.73 0.12 0.14
Matches are distributed among these distances:
22 12 0.29
23 23 0.56
24 6 0.15
ACGTcount: A:0.53, C:0.04, G:0.03, T:0.41
Consensus pattern (22 bp):
AAATATTATTAAATTATAATAA
Found at i:30934461 original size:15 final size:14
Alignment explanation
Indices: 30934417--30934468 Score: 54
Period size: 14 Copynumber: 3.8 Consensus size: 14
30934407 ATTATAACTT
30934417 AGTTATTTTTAGT-
1 AGTTATTTTTAGTG
* * *
30934430 TGTT-TTTATAGTT
1 AGTTATTTTTAGTG
30934443 AGTTTATTTTTAGTG
1 AG-TTATTTTTAGTG
30934458 AGTTATTTTTA
1 AGTTATTTTTA
30934469 TTTTATGTTT
Statistics
Matches: 31, Mismatches: 5, Indels: 5
0.76 0.12 0.12
Matches are distributed among these distances:
12 7 0.23
13 4 0.13
14 11 0.35
15 9 0.29
ACGTcount: A:0.21, C:0.00, G:0.15, T:0.63
Consensus pattern (14 bp):
AGTTATTTTTAGTG
Found at i:30936357 original size:34 final size:34
Alignment explanation
Indices: 30936319--30936388 Score: 140
Period size: 34 Copynumber: 2.1 Consensus size: 34
30936309 ATGCATGCGA
30936319 TGGGATGCAAAATGTCTAATTAATCACTTAAATG
1 TGGGATGCAAAATGTCTAATTAATCACTTAAATG
30936353 TGGGATGCAAAATGTCTAATTAATCACTTAAATG
1 TGGGATGCAAAATGTCTAATTAATCACTTAAATG
30936387 TG
1 TG
30936389 ATATTCGACC
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
34 36 1.00
ACGTcount: A:0.37, C:0.11, G:0.19, T:0.33
Consensus pattern (34 bp):
TGGGATGCAAAATGTCTAATTAATCACTTAAATG
Found at i:30941820 original size:21 final size:18
Alignment explanation
Indices: 30941795--30941833 Score: 51
Period size: 20 Copynumber: 2.0 Consensus size: 18
30941785 TTTAATTAGA
30941795 TTAGTTTTAATTGAGTAATTT
1 TTAG-TTTAATT-AG-AATTT
30941816 TTAGTTTAATTAGAATTT
1 TTAGTTTAATTAGAATTT
30941834 AGATTTTAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
18 5 0.28
19 2 0.11
20 7 0.39
21 4 0.22
ACGTcount: A:0.31, C:0.00, G:0.13, T:0.56
Consensus pattern (18 bp):
TTAGTTTAATTAGAATTT
Found at i:30941841 original size:18 final size:18
Alignment explanation
Indices: 30941784--30941845 Score: 58
Period size: 18 Copynumber: 3.5 Consensus size: 18
30941774 TTGCTCTAAT
30941784 TTTTAATTAG-A-TTAG-
1 TTTTAATTAGAATTTAGA
**
30941799 TTTTAATTGAGTAATTTTTA
1 TTTTAATT-AG-AATTTAGA
*
30941819 GTTTAATTAGAATTTAGA
1 TTTTAATTAGAATTTAGA
30941837 TTTTAATTA
1 TTTTAATTA
30941846 TTTGAATAAA
Statistics
Matches: 36, Mismatches: 6, Indels: 7
0.73 0.12 0.14
Matches are distributed among these distances:
15 8 0.22
16 2 0.06
18 15 0.42
19 4 0.11
20 7 0.19
ACGTcount: A:0.34, C:0.00, G:0.11, T:0.55
Consensus pattern (18 bp):
TTTTAATTAGAATTTAGA
Found at i:30943361 original size:26 final size:25
Alignment explanation
Indices: 30943308--30943358 Score: 77
Period size: 25 Copynumber: 2.0 Consensus size: 25
30943298 TTTCTTGAAG
*
30943308 TCAATTTTGTAAACTCTATTTCTTT
1 TCAATTTTCTAAACTCTATTTCTTT
30943333 TCAATTTTCTAGAACTCT-TTTCTTT
1 TCAATTTTCTA-AACTCTATTTCTTT
30943358 T
1 T
30943359 TCATCGACGA
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
25 18 0.75
26 6 0.25
ACGTcount: A:0.22, C:0.18, G:0.04, T:0.57
Consensus pattern (25 bp):
TCAATTTTCTAAACTCTATTTCTTT
Found at i:30945526 original size:63 final size:61
Alignment explanation
Indices: 30945447--30945605 Score: 183
Period size: 63 Copynumber: 2.5 Consensus size: 61
30945437 TTGATGTAAC
* * *
30945447 CGTGCATGTGCGGAGTGGGCAGTGCATATGCCGATTACATGATGATGTAGTGACAAGTACAA
1 CGTGCATGTGCAGAGTGGGCAGTGCATATGCCG-TCAAATGATGATGTAGTGACAAGTACAA
* * * **
30945509 TCGTGCATATGCAGAGTGGACAGTGCATATGCCTGTCAAATGATGATGTTGTGACACTTACAA
1 -CGTGCATGTGCAGAGTGGGCAGTGCATATGCC-GTCAAATGATGATGTAGTGACAAGTACAA
* * *
30945572 CTATGCATGTGCAGAGTGGGGAGTGCACATGCCG
1 C-GTGCATGTGCAGAGTGGGCAGTGCATATGCCG
30945606 GTAATGATGT
Statistics
Matches: 81, Mismatches: 13, Indels: 5
0.82 0.13 0.05
Matches are distributed among these distances:
62 2 0.02
63 78 0.96
64 1 0.01
ACGTcount: A:0.26, C:0.18, G:0.31, T:0.25
Consensus pattern (61 bp):
CGTGCATGTGCAGAGTGGGCAGTGCATATGCCGTCAAATGATGATGTAGTGACAAGTACAA
Found at i:30946951 original size:39 final size:39
Alignment explanation
Indices: 30946908--30946991 Score: 116
Period size: 39 Copynumber: 2.2 Consensus size: 39
30946898 CTATTCAATT
30946908 GTTATAAATAACAACCTTTCATAATATAA-TAATAAAAAA
1 GTTATAAATAACAACCTTTCATAATATAACT-ATAAAAAA
** * *
30946947 GTTATATTTAATAACCTTTCATAATATAACTATTAAAAA
1 GTTATAAATAACAACCTTTCATAATATAACTATAAAAAA
30946986 GTTATA
1 GTTATA
30946992 TTTTAATAAG
Statistics
Matches: 40, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
39 39 0.98
40 1 0.03
ACGTcount: A:0.50, C:0.10, G:0.04, T:0.37
Consensus pattern (39 bp):
GTTATAAATAACAACCTTTCATAATATAACTATAAAAAA
Found at i:30946992 original size:39 final size:40
Alignment explanation
Indices: 30946920--30947000 Score: 130
Period size: 39 Copynumber: 2.0 Consensus size: 40
30946910 TATAAATAAC
30946920 AACCTTTCATAATATAATAATAAAAAAGTTATA-TTTAAT
1 AACCTTTCATAATATAATAATAAAAAAGTTATATTTTAAT
*
30946959 AACCTTTCATAATATAACT-ATTAAAAAGTTATATTTTAAT
1 AACCTTTCATAATATAA-TAATAAAAAAGTTATATTTTAAT
30946999 AA
1 AA
30947001 GGTAATTATT
Statistics
Matches: 39, Mismatches: 1, Indels: 3
0.91 0.02 0.07
Matches are distributed among these distances:
39 30 0.77
40 9 0.23
ACGTcount: A:0.49, C:0.09, G:0.02, T:0.40
Consensus pattern (40 bp):
AACCTTTCATAATATAATAATAAAAAAGTTATATTTTAAT
Found at i:30949573 original size:84 final size:84
Alignment explanation
Indices: 30949431--30949600 Score: 223
Period size: 84 Copynumber: 2.0 Consensus size: 84
30949421 GGAATGTCAC
* ** * * * *
30949431 GCTTTTGAACCTTCTGCTCTTTTGGATCTTTTTTCTGCTTTCCTTTAGCAAGTGGCTTTTTCTCA
1 GCTTTTGAACCTTCTGCTCTTTTGGAACTCCTTGCTGCTTTCCTCTAGCAAGTAGCTTTTGCTCA
*
30949496 ATACCCCTAATTCTTTCTA
66 AGACCCCTAATTCTTTCTA
* * * *
30949515 GCTTTTGACCCTTTTGCTCTTTTGGAACTCCTTGCTGTTTTCCTCTAGCAATTAGCTTTTGCTCA
1 GCTTTTGAACCTTCTGCTCTTTTGGAACTCCTTGCTGCTTTCCTCTAGCAAGTAGCTTTTGCTCA
*
30949580 AGAGCCCTAATTCTTTCTA
66 AGACCCCTAATTCTTTCTA
30949599 GC
1 GC
30949601 CGATTTGAGG
Statistics
Matches: 73, Mismatches: 13, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
84 73 1.00
ACGTcount: A:0.15, C:0.26, G:0.14, T:0.46
Consensus pattern (84 bp):
GCTTTTGAACCTTCTGCTCTTTTGGAACTCCTTGCTGCTTTCCTCTAGCAAGTAGCTTTTGCTCA
AGACCCCTAATTCTTTCTA
Found at i:30952258 original size:22 final size:20
Alignment explanation
Indices: 30952241--30952279 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
30952231 TGTTAGGGAT
30952241 TGAGTCACTGGATATTAGGG
1 TGAGTCACTGGATATTAGGG
* *
30952261 TGTGTGACTGGATATTAGG
1 TGAGTCACTGGATATTAGG
30952280 AATCGTAACC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.23, C:0.08, G:0.36, T:0.33
Consensus pattern (20 bp):
TGAGTCACTGGATATTAGGG
Found at i:30952392 original size:48 final size:48
Alignment explanation
Indices: 30952317--30952430 Score: 165
Period size: 48 Copynumber: 2.4 Consensus size: 48
30952307 GTGCCTGAAT
* * *
30952317 ATTACGTGACTAAATATTTGTTAAGCATTGCGTGACTTATTTATAGGC
1 ATTACGTGACTGAATATTTGTTAAGCATTGCGTAACTTATTTATAAGC
* * *
30952365 ATTACGTGACTGAATATTTGTTGAGCATTGCGTAACTTGTTTATAAGT
1 ATTACGTGACTGAATATTTGTTAAGCATTGCGTAACTTATTTATAAGC
*
30952413 ATTACGTCACTGAATATT
1 ATTACGTGACTGAATATT
30952431 ACGTGACTGA
Statistics
Matches: 59, Mismatches: 7, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
48 59 1.00
ACGTcount: A:0.29, C:0.12, G:0.18, T:0.40
Consensus pattern (48 bp):
ATTACGTGACTGAATATTTGTTAAGCATTGCGTAACTTATTTATAAGC
Found at i:30952393 original size:26 final size:25
Alignment explanation
Indices: 30952317--30952393 Score: 79
Period size: 26 Copynumber: 3.1 Consensus size: 25
30952307 GTGCCTGAAT
*
30952317 ATTACGTGACTAAATATTTGTTAAGC
1 ATTACGTGACT-AATATTTGTTGAGC
* * *
30952343 ATTGCGTGACT--TATTTATAG-GC
1 ATTACGTGACTAATATTTGTTGAGC
30952365 ATTACGTGACTGAATATTTGTTGAGC
1 ATTACGTGACT-AATATTTGTTGAGC
30952391 ATT
1 ATT
30952394 GCGTAACTTG
Statistics
Matches: 40, Mismatches: 7, Indels: 8
0.73 0.13 0.15
Matches are distributed among these distances:
22 12 0.30
23 6 0.15
25 7 0.17
26 15 0.38
ACGTcount: A:0.29, C:0.12, G:0.19, T:0.40
Consensus pattern (25 bp):
ATTACGTGACTAATATTTGTTGAGC
Found at i:30952432 original size:15 final size:15
Alignment explanation
Indices: 30952412--30952445 Score: 59
Period size: 15 Copynumber: 2.3 Consensus size: 15
30952402 TGTTTATAAG
30952412 TATTACGTCACTGAA
1 TATTACGTCACTGAA
*
30952427 TATTACGTGACTGAA
1 TATTACGTCACTGAA
30952442 TATT
1 TATT
30952446 TGTTGAGTAT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.32, C:0.15, G:0.15, T:0.38
Consensus pattern (15 bp):
TATTACGTCACTGAA
Found at i:30953732 original size:61 final size:61
Alignment explanation
Indices: 30953503--30953736 Score: 270
Period size: 61 Copynumber: 3.8 Consensus size: 61
30953493 GGTCTATGAG
*
30953503 CGAAATATCTATCGATAGATGATAAATATATCGATAGATACCGTTTCTTTCATCTTCCAAGTATT
1 CGAAATATCTATCGATAGATGATAAATATATCGATAGATACCG----TTTCATCTTCCAAGCATT
** * * * * ** *
30953568 CCCAATATCTATCGATAGCTTATAAATATATCGATAGCTTCTATTTCATCTTCCAAGCAAT
1 CGAAATATCTATCGATAGATGATAAATATATCGATAGATACCGTTTCATCTTCCAAGCATT
* * * * * *
30953629 CGAAATAGCTATCGATACATTATAAACATATCGATAGCTACCGTTTCATCTTCCAACCATT
1 CGAAATATCTATCGATAGATGATAAATATATCGATAGATACCGTTTCATCTTCCAAGCATT
* *
30953690 CGAAATTTCTATCGATAGAAGATAAATATATCGATAGATACCGTTTC
1 CGAAATATCTATCGATAGATGATAAATATATCGATAGATACCGTTTC
30953737 TTTCATCTTC
Statistics
Matches: 141, Mismatches: 28, Indels: 4
0.82 0.16 0.02
Matches are distributed among these distances:
61 106 0.75
65 35 0.25
ACGTcount: A:0.35, C:0.20, G:0.11, T:0.34
Consensus pattern (61 bp):
CGAAATATCTATCGATAGATGATAAATATATCGATAGATACCGTTTCATCTTCCAAGCATT
Found at i:30953843 original size:29 final size:29
Alignment explanation
Indices: 30953810--30953868 Score: 118
Period size: 29 Copynumber: 2.0 Consensus size: 29
30953800 AACCCTAACG
30953810 AAAAATCACATTCCTTATAAACGTTGCAA
1 AAAAATCACATTCCTTATAAACGTTGCAA
30953839 AAAAATCACATTCCTTATAAACGTTGCAA
1 AAAAATCACATTCCTTATAAACGTTGCAA
30953868 A
1 A
30953869 GTGATATTCC
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 30 1.00
ACGTcount: A:0.46, C:0.20, G:0.07, T:0.27
Consensus pattern (29 bp):
AAAAATCACATTCCTTATAAACGTTGCAA
Found at i:30955776 original size:23 final size:23
Alignment explanation
Indices: 30955750--30955796 Score: 58
Period size: 23 Copynumber: 2.0 Consensus size: 23
30955740 GTGATTTTAG
* *
30955750 AATAAATACTCACGTCATTCCAT
1 AATAAATACTAACGTCACTCCAT
* *
30955773 AATAACTAGTAACGTCACTCCAT
1 AATAAATACTAACGTCACTCCAT
30955796 A
1 A
30955797 TATATTACTC
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.40, C:0.26, G:0.06, T:0.28
Consensus pattern (23 bp):
AATAAATACTAACGTCACTCCAT
Found at i:30955862 original size:23 final size:23
Alignment explanation
Indices: 30955822--30955879 Score: 62
Period size: 23 Copynumber: 2.5 Consensus size: 23
30955812 AGTCAATATC
*
30955822 AACTAGTCATGCAATTCCACAAA
1 AACTAGTCACGCAATTCCACAAA
** * *
30955845 AACTAGTCACGCGCTTCCATAAT
1 AACTAGTCACGCAATTCCACAAA
*
30955868 AACTAGTAACGC
1 AACTAGTCACGC
30955880 CACTCTATAT
Statistics
Matches: 29, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
23 29 1.00
ACGTcount: A:0.38, C:0.28, G:0.12, T:0.22
Consensus pattern (23 bp):
AACTAGTCACGCAATTCCACAAA
Found at i:30957993 original size:24 final size:24
Alignment explanation
Indices: 30957966--30958014 Score: 64
Period size: 24 Copynumber: 2.0 Consensus size: 24
30957956 GCATCTGCAT
30957966 CTGCA-TCACCTGCTGGATCTCCAA
1 CTGCATTCA-CTGCTGGATCTCCAA
* *
30957990 CTGCATTGACTGTTGGATCTCCAA
1 CTGCATTCACTGCTGGATCTCCAA
30958014 C
1 C
30958015 GTTATTGCAT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
24 20 0.91
25 2 0.09
ACGTcount: A:0.20, C:0.33, G:0.18, T:0.29
Consensus pattern (24 bp):
CTGCATTCACTGCTGGATCTCCAA
Found at i:30958239 original size:24 final size:24
Alignment explanation
Indices: 30958211--30958256 Score: 65
Period size: 24 Copynumber: 1.9 Consensus size: 24
30958201 GAAGGAGAAA
* * *
30958211 CAAGAGTAGCATCATGATGAGCAG
1 CAAGAGAAGCACCATGAAGAGCAG
30958235 CAAGAGAAGCACCATGAAGAGC
1 CAAGAGAAGCACCATGAAGAGC
30958257 TACAGAAGGA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 19 1.00
ACGTcount: A:0.41, C:0.20, G:0.28, T:0.11
Consensus pattern (24 bp):
CAAGAGAAGCACCATGAAGAGCAG
Found at i:30967179 original size:31 final size:30
Alignment explanation
Indices: 30967144--30967210 Score: 84
Period size: 31 Copynumber: 2.2 Consensus size: 30
30967134 AATAATTAGT
30967144 TATAAAGACT-TATTT-GACTCAAAATAAAAAG
1 TATAAAG-CTCTATTTAG-CTCAAAAT-AAAAG
*
30967175 TATAAAGGTCTATTTAGCTCAAAATAAAAG
1 TATAAAGCTCTATTTAGCTCAAAATAAAAG
30967205 TATAAA
1 TATAAA
30967211 AGTTTGATTG
Statistics
Matches: 33, Mismatches: 1, Indels: 5
0.85 0.03 0.13
Matches are distributed among these distances:
30 12 0.36
31 20 0.61
32 1 0.03
ACGTcount: A:0.51, C:0.09, G:0.10, T:0.30
Consensus pattern (30 bp):
TATAAAGCTCTATTTAGCTCAAAATAAAAG
Found at i:30975753 original size:2 final size:2
Alignment explanation
Indices: 30975746--30975778 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
30975736 GATTATTTAG
*
30975746 TA TA TA TA TC TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
30975779 TATGTATGTA
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.45, C:0.03, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:30980465 original size:18 final size:18
Alignment explanation
Indices: 30980426--30980465 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
30980416 GTTGGTATCT
* * *
30980426 AAAGAAAAGCAAAATAAG
1 AAAGAAAAACAAAAAAAA
30980444 AAAGAAAAACAAAAAAAA
1 AAAGAAAAACAAAAAAAA
30980462 AAAG
1 AAAG
30980466 CGTACCTATG
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.80, C:0.05, G:0.12, T:0.03
Consensus pattern (18 bp):
AAAGAAAAACAAAAAAAA
Found at i:30999748 original size:28 final size:29
Alignment explanation
Indices: 30999707--30999766 Score: 68
Period size: 30 Copynumber: 2.1 Consensus size: 29
30999697 GTCTATGGGC
*
30999707 AATTTTTCAATTTT-TGGGGCAAAAATGT
1 AATTTTTCAATTTTAGGGGGCAAAAATGT
* * *
30999735 AATTTTTGACTTTTACGGGGGCAAAAGTGT
1 AATTTTTCAATTTTA-GGGGGCAAAAATGT
30999765 AA
1 AA
30999767 ATTTCAAAAA
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
28 12 0.46
30 14 0.54
ACGTcount: A:0.32, C:0.08, G:0.22, T:0.38
Consensus pattern (29 bp):
AATTTTTCAATTTTAGGGGGCAAAAATGT
Found at i:31007450 original size:21 final size:20
Alignment explanation
Indices: 31007426--31007472 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 20
31007416 ATTTTACCTT
*
31007426 TTTTTCACTTGTTTCCTTGAA
1 TTTTTCACTT-TTCCCTTGAA
*
31007447 TTTTCACACTTTTCCCTTGAA
1 TTTT-TCACTTTTCCCTTGAA
31007468 TTTTT
1 TTTTT
31007473 TCCACCTAGG
Statistics
Matches: 22, Mismatches: 3, Indels: 3
0.79 0.11 0.11
Matches are distributed among these distances:
21 17 0.77
22 5 0.23
ACGTcount: A:0.15, C:0.21, G:0.06, T:0.57
Consensus pattern (20 bp):
TTTTTCACTTTTCCCTTGAA
Found at i:31007472 original size:22 final size:22
Alignment explanation
Indices: 31007431--31007471 Score: 66
Period size: 21 Copynumber: 1.9 Consensus size: 22
31007421 ACCTTTTTTT
*
31007431 CACTTGTTTCCTTGAATTTTCA
1 CACTTGTTCCCTTGAATTTTCA
31007453 CACTT-TTCCCTTGAATTTT
1 CACTTGTTCCCTTGAATTTT
31007472 TTCCACCTAG
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 13 0.72
22 5 0.28
ACGTcount: A:0.17, C:0.24, G:0.07, T:0.51
Consensus pattern (22 bp):
CACTTGTTCCCTTGAATTTTCA
Found at i:31015219 original size:17 final size:16
Alignment explanation
Indices: 31015170--31015212 Score: 68
Period size: 17 Copynumber: 2.6 Consensus size: 16
31015160 GATTTGGGAT
31015170 TGCTCCCCCTAGATATG
1 TGCT-CCCCTAGATATG
31015187 TGCTCACCCTAGATATG
1 TGCTC-CCCTAGATATG
31015204 TGCTCCCCT
1 TGCTCCCCT
31015213 TAAATATATG
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
16 5 0.20
17 20 0.80
ACGTcount: A:0.16, C:0.37, G:0.16, T:0.30
Consensus pattern (16 bp):
TGCTCCCCTAGATATG
Found at i:31026977 original size:11 final size:13
Alignment explanation
Indices: 31026955--31026986 Score: 50
Period size: 12 Copynumber: 2.6 Consensus size: 13
31026945 GTATTATTTA
31026955 TCATTTTATTATT
1 TCATTTTATTATT
31026968 TC-TTTT-TTATT
1 TCATTTTATTATT
31026979 TCATTTTA
1 TCATTTTA
31026987 CTTTTTTTTT
Statistics
Matches: 17, Mismatches: 0, Indels: 4
0.81 0.00 0.19
Matches are distributed among these distances:
11 7 0.41
12 8 0.47
13 2 0.12
ACGTcount: A:0.19, C:0.09, G:0.00, T:0.72
Consensus pattern (13 bp):
TCATTTTATTATT
Found at i:31026997 original size:17 final size:18
Alignment explanation
Indices: 31026969--31027003 Score: 63
Period size: 17 Copynumber: 2.0 Consensus size: 18
31026959 TTTATTATTT
31026969 CTTTTTTATTTCATTTTA
1 CTTTTTTATTTCATTTTA
31026987 CTTTTTT-TTTCATTTTA
1 CTTTTTTATTTCATTTTA
31027004 TTAATATCCT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 10 0.59
18 7 0.41
ACGTcount: A:0.14, C:0.11, G:0.00, T:0.74
Consensus pattern (18 bp):
CTTTTTTATTTCATTTTA
Found at i:31027201 original size:3 final size:3
Alignment explanation
Indices: 31027193--31027235 Score: 59
Period size: 3 Copynumber: 14.3 Consensus size: 3
31027183 CCAAATAATC
* * *
31027193 TAT TAT TAT TAT TAT TAT TAT TGT CAT TAT TAT TAT TTT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
31027236 TTACTCACTA
Statistics
Matches: 34, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
3 34 1.00
ACGTcount: A:0.28, C:0.02, G:0.02, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:31028594 original size:18 final size:18
Alignment explanation
Indices: 31028567--31028613 Score: 58
Period size: 18 Copynumber: 2.6 Consensus size: 18
31028557 GATAACATTA
*
31028567 AAAAAGAAAAATCAAAAT
1 AAAAATAAAAATCAAAAT
* * *
31028585 CAAAATAAAAATGAAAGT
1 AAAAATAAAAATCAAAAT
31028603 AAAAATAAAAA
1 AAAAATAAAAA
31028614 ATTAAAATTG
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.77, C:0.04, G:0.06, T:0.13
Consensus pattern (18 bp):
AAAAATAAAAATCAAAAT
Found at i:31029485 original size:19 final size:20
Alignment explanation
Indices: 31029449--31029486 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
31029439 CATTCAAGAG
**
31029449 TTTTAACCTCTAAGGTTTTT
1 TTTTAACCAATAAGGTTTTT
31029469 TTTTAACCAATAA-GTTTT
1 TTTTAACCAATAAGGTTTT
31029487 AACATTCAAT
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
19 5 0.31
20 11 0.69
ACGTcount: A:0.26, C:0.13, G:0.08, T:0.53
Consensus pattern (20 bp):
TTTTAACCAATAAGGTTTTT
Found at i:31036785 original size:12 final size:12
Alignment explanation
Indices: 31036768--31036792 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
31036758 ATAATAATAA
31036768 ATTAGAAAAAAT
1 ATTAGAAAAAAT
31036780 ATTAGAAAAAAT
1 ATTAGAAAAAAT
31036792 A
1 A
31036793 AAAATATGTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.68, C:0.00, G:0.08, T:0.24
Consensus pattern (12 bp):
ATTAGAAAAAAT
Found at i:31038892 original size:43 final size:43
Alignment explanation
Indices: 31038844--31038996 Score: 218
Period size: 43 Copynumber: 3.6 Consensus size: 43
31038834 TCACTAGCTC
** **
31038844 ATGCGCACTCCCTACTCGCACATGGCAGGGTCATCAC-CGGGTT
1 ATGCGCACTCCCTACTCGCACATAACAGGGTCATC-CTCGACTT
* *
31038887 ATGCGCACTCCCTACTCACACATAACCGGGTCATCCTCGACTT
1 ATGCGCACTCCCTACTCGCACATAACAGGGTCATCCTCGACTT
* *
31038930 ATGCACACTCCCTACTCGCACATAACAGGGTCATCCTTGACTT
1 ATGCGCACTCCCTACTCGCACATAACAGGGTCATCCTCGACTT
31038973 ATGCGCACTCCCTACTCGCACATA
1 ATGCGCACTCCCTACTCGCACATA
31038997 GCCAAGTCAA
Statistics
Matches: 98, Mismatches: 11, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
42 1 0.01
43 97 0.99
ACGTcount: A:0.23, C:0.37, G:0.17, T:0.23
Consensus pattern (43 bp):
ATGCGCACTCCCTACTCGCACATAACAGGGTCATCCTCGACTT
Found at i:31044819 original size:11 final size:11
Alignment explanation
Indices: 31044805--31044834 Score: 51
Period size: 11 Copynumber: 2.7 Consensus size: 11
31044795 AGTTGCAAGG
31044805 AAAAAAAATGA
1 AAAAAAAATGA
*
31044816 AAAACAAATGA
1 AAAAAAAATGA
31044827 AAAAAAAA
1 AAAAAAAA
31044835 AAGAACAAAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
11 17 1.00
ACGTcount: A:0.83, C:0.03, G:0.07, T:0.07
Consensus pattern (11 bp):
AAAAAAAATGA
Found at i:31044841 original size:20 final size:20
Alignment explanation
Indices: 31044804--31044843 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 20
31044794 AAGTTGCAAG
31044804 GAAAAAAAATGAAAAACAAAT
1 GAAAAAAAA-GAAAAACAAAT
31044825 GAAAAAAAA-AAAGAACAAA
1 GAAAAAAAAGAAA-AACAAA
31044844 ACAAAAGAGA
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
19 3 0.17
20 6 0.33
21 9 0.50
ACGTcount: A:0.80, C:0.05, G:0.10, T:0.05
Consensus pattern (20 bp):
GAAAAAAAAGAAAAACAAAT
Found at i:31046457 original size:22 final size:23
Alignment explanation
Indices: 31046432--31046504 Score: 73
Period size: 21 Copynumber: 3.3 Consensus size: 23
31046422 AACCCCTTTG
*
31046432 AAACCTTCGGA-TACATTTTCTA
1 AAACCTTCCGAGTACATTTTCTA
31046454 AAACC-TCCGAGTACATTTTC--
1 AAACCTTCCGAGTACATTTTCTA
* * **
31046474 AAATCGTCTAAGTACATTTTCTA
1 AAACCTTCCGAGTACATTTTCTA
31046497 AAACCTTC
1 AAACCTTC
31046505 AGGTGCAATC
Statistics
Matches: 41, Mismatches: 6, Indels: 7
0.76 0.11 0.13
Matches are distributed among these distances:
20 4 0.10
21 17 0.41
22 14 0.34
23 6 0.15
ACGTcount: A:0.33, C:0.25, G:0.08, T:0.34
Consensus pattern (23 bp):
AAACCTTCCGAGTACATTTTCTA
Found at i:31046712 original size:21 final size:22
Alignment explanation
Indices: 31046678--31046739 Score: 72
Period size: 21 Copynumber: 2.9 Consensus size: 22
31046668 ATCTTCAAAT
* *
31046678 ACATTTTCCAAAACCTCTGAGC
1 ACATTCTCCAAAACCTCTAAGC
* *
31046700 ACATTCT-CAAAACCTCCAAGT
1 ACATTCTCCAAAACCTCTAAGC
*
31046721 ACATTCTCCAAAGCCTCTA
1 ACATTCTCCAAAACCTCTA
31046740 GGTATATTCT
Statistics
Matches: 33, Mismatches: 6, Indels: 2
0.80 0.15 0.05
Matches are distributed among these distances:
21 18 0.55
22 15 0.45
ACGTcount: A:0.34, C:0.34, G:0.06, T:0.26
Consensus pattern (22 bp):
ACATTCTCCAAAACCTCTAAGC
Found at i:31046780 original size:22 final size:22
Alignment explanation
Indices: 31046677--31046781 Score: 88
Period size: 22 Copynumber: 4.8 Consensus size: 22
31046667 AATCTTCAAA
* *
31046677 TACATTTTCCAAAACCTCTGAG
1 TACATTCTCCAAAACCTCCGAG
* *
31046699 CACATTCT-CAAAACCTCCAAG
1 TACATTCTCCAAAACCTCCGAG
* *
31046720 TACATTCTCCAAAGCCT-CTAGG
1 TACATTCTCCAAAACCTCCGA-G
* **
31046742 TATATTCTTATAAAACCTCCGAG
1 TACATTC-TCCAAAACCTCCGAG
*
31046765 TACATTCTCTAAAACCT
1 TACATTCTCCAAAACCT
31046782 TCGCGTAATC
Statistics
Matches: 65, Mismatches: 14, Indels: 8
0.75 0.16 0.09
Matches are distributed among these distances:
21 20 0.31
22 29 0.45
23 14 0.22
24 2 0.03
ACGTcount: A:0.33, C:0.30, G:0.08, T:0.30
Consensus pattern (22 bp):
TACATTCTCCAAAACCTCCGAG
Found at i:31046857 original size:32 final size:32
Alignment explanation
Indices: 31046821--31046904 Score: 159
Period size: 32 Copynumber: 2.6 Consensus size: 32
31046811 GTCTTAAAGC
31046821 CTCGGATAAGGAGTTTTTTAAAGTCATGGAGT
1 CTCGGATAAGGAGTTTTTTAAAGTCATGGAGT
31046853 CTCGGATAAGGAGTTTTTTAAAGTCATGGAGT
1 CTCGGATAAGGAGTTTTTTAAAGTCATGGAGT
31046885 CTCGGATAAGGAGTTGTTTT
1 CTCGGATAAGGAGTT-TTTT
31046905 TAACGTTGTA
Statistics
Matches: 51, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
32 47 0.92
33 4 0.08
ACGTcount: A:0.26, C:0.10, G:0.29, T:0.36
Consensus pattern (32 bp):
CTCGGATAAGGAGTTTTTTAAAGTCATGGAGT
Found at i:31048979 original size:14 final size:15
Alignment explanation
Indices: 31048942--31048981 Score: 50
Period size: 14 Copynumber: 2.8 Consensus size: 15
31048932 CTTTGATTTA
31048942 AAAAATAA-AAAACT
1 AAAAATAATAAAACT
31048956 AAAACA-AATAAAA-T
1 AAAA-ATAATAAAACT
31048970 AAAAATAATAAA
1 AAAAATAATAAA
31048982 TTAGAAAGAA
Statistics
Matches: 23, Mismatches: 0, Indels: 6
0.79 0.00 0.21
Matches are distributed among these distances:
13 1 0.04
14 17 0.74
15 5 0.22
ACGTcount: A:0.80, C:0.05, G:0.00, T:0.15
Consensus pattern (15 bp):
AAAAATAATAAAACT
Found at i:31086274 original size:21 final size:21
Alignment explanation
Indices: 31086240--31086291 Score: 61
Period size: 21 Copynumber: 2.4 Consensus size: 21
31086230 ATAGTTTTAT
*
31086240 GTTTTCAAACAAAATTGCATG
1 GTTTTCAAACAAAATAGCATG
31086261 GTTTT-AAACTAAAATAGCATG
1 GTTTTCAAAC-AAAATAGCATG
*
31086282 ATTTATCAAA
1 GTTT-TCAAA
31086292 TACTCTTCCG
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
20 4 0.15
21 18 0.69
22 1 0.04
23 3 0.12
ACGTcount: A:0.42, C:0.12, G:0.12, T:0.35
Consensus pattern (21 bp):
GTTTTCAAACAAAATAGCATG
Found at i:31088665 original size:42 final size:42
Alignment explanation
Indices: 31088560--31088683 Score: 140
Period size: 42 Copynumber: 3.0 Consensus size: 42
31088550 GTAATGATAT
*** *
31088560 TGACCCGACTATGTGCGAGTAAAAGTGTGCATAAGCCGATGC
1 TGACCCGACTATGTGCGAGTGGGAGTGCGCATAAGCCGATGC
* * *
31088602 TGACCCGGCTATGTGCGAGTGGGAGTGCGCATAAGCTGATGT
1 TGACCCGACTATGTGCGAGTGGGAGTGCGCATAAGCCGATGC
* * * * *
31088644 TGTCTCGACTATGTGCAAGTGGGAGTGCACATAAGTCGAT
1 TGACCCGACTATGTGCGAGTGGGAGTGCGCATAAGCCGAT
31088684 ACATATGAGT
Statistics
Matches: 68, Mismatches: 14, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
42 68 1.00
ACGTcount: A:0.24, C:0.19, G:0.32, T:0.24
Consensus pattern (42 bp):
TGACCCGACTATGTGCGAGTGGGAGTGCGCATAAGCCGATGC
Found at i:31092515 original size:33 final size:33
Alignment explanation
Indices: 31092471--31092556 Score: 100
Period size: 33 Copynumber: 2.6 Consensus size: 33
31092461 TTTTAATGTC
* * *
31092471 ATATATATTATTTTTATTTTTTATTATAATCTT
1 ATATATTTTATTTTTATTTTTTAATAAAATCTT
* * *
31092504 ATATATTTTATTTTCATTTCTTAATAAAATTTT
1 ATATATTTTATTTTTATTTTTTAATAAAATCTT
* *
31092537 CTATATTATATTTTTATTTT
1 ATATATTTTATTTTTATTTT
31092557 AATTTTTTTA
Statistics
Matches: 43, Mismatches: 10, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
33 43 1.00
ACGTcount: A:0.30, C:0.05, G:0.00, T:0.65
Consensus pattern (33 bp):
ATATATTTTATTTTTATTTTTTAATAAAATCTT
Found at i:31093393 original size:2 final size:2
Alignment explanation
Indices: 31093386--31093463 Score: 88
Period size: 2 Copynumber: 39.5 Consensus size: 2
31093376 ATCACTACCC
31093386 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
** ** *
31093428 -A NN NG CA TA TA CTA TA TA TA TA TA TA TA T- TA TA TA T
1 TA TA TA TA TA TA -TA TA TA TA TA TA TA TA TA TA TA TA T
31093464 TAAAGAGTAA
Statistics
Matches: 68, Mismatches: 5, Indels: 6
0.86 0.06 0.08
Matches are distributed among these distances:
1 2 0.03
2 64 0.94
3 2 0.03
ACGTcount: A:0.46, C:0.03, G:0.01, T:0.46
Consensus pattern (2 bp):
TA
Found at i:31103282 original size:28 final size:28
Alignment explanation
Indices: 31103242--31103296 Score: 74
Period size: 28 Copynumber: 2.0 Consensus size: 28
31103232 ATATTACAAA
*
31103242 CAAATAAATTACACCAAACATAAATAAG
1 CAAATAAACTACACCAAACATAAATAAG
* * *
31103270 CAAATACACTACATCAAATATAAATAA
1 CAAATAAACTACACCAAACATAAATAA
31103297 AATTTTAATC
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
28 23 1.00
ACGTcount: A:0.60, C:0.18, G:0.02, T:0.20
Consensus pattern (28 bp):
CAAATAAACTACACCAAACATAAATAAG
Found at i:31106655 original size:138 final size:137
Alignment explanation
Indices: 31106404--31106657 Score: 325
Period size: 138 Copynumber: 1.8 Consensus size: 137
31106394 AGTAAGAAGT
* * * * * *
31106404 TGAGAACTGTAGGTAGGTAGGTAGTGCCAGAGACTTTGAAGGTGAGATGGCCGATGGGGAGTGCT
1 TGAGAACCGTAGGCAGGTAGCTAGTGCCAAAGACTTTGAAGGTGAGATGGCAGATGGGGAG-GAT
* *
31106469 AGAGTGGTGACCGACTGAAAGTGCGATGCCGATGGATGATGGCAATGGGGACGGTCGGATGAAGA
65 AGAGTGGTGACCGACTGAAAGTGAGATGCCGATGGACGATGGCAATGGGGACGGTCGGATGAAGA
31106534 TTGGGGAG
130 TTGGGGAG
*
31106542 TGAGAACCGTAGGCAGGTAGCTAGTGCCAAAGACTTTGAAGGTGAGATAAGG-AG-TGCTGGA-G
1 TGAGAACCGTAGGCAGGTAGCTAGTGCCAAAGACTTTGAAGGTGAGAT--GGCAGATG-GGGAGG
* * * *
31106604 ATAGAGTGGTGACCGGCTGAAGGTGAGATGCCGATGGGCGATGGCTGATGGGGA
63 ATAGAGTGGTGACCGACTGAAAGTGAGATGCCGATGGACGATGGC-AATGGGGA
31106658 TGTCCGAATG
Statistics
Matches: 99, Mismatches: 13, Indels: 8
0.82 0.11 0.07
Matches are distributed among these distances:
137 40 0.40
138 53 0.54
139 4 0.04
140 2 0.02
ACGTcount: A:0.26, C:0.12, G:0.42, T:0.20
Consensus pattern (137 bp):
TGAGAACCGTAGGCAGGTAGCTAGTGCCAAAGACTTTGAAGGTGAGATGGCAGATGGGGAGGATA
GAGTGGTGACCGACTGAAAGTGAGATGCCGATGGACGATGGCAATGGGGACGGTCGGATGAAGAT
TGGGGAG
Found at i:31106820 original size:7 final size:7
Alignment explanation
Indices: 31106810--31106835 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
31106800 AGAGGTTGGG
31106810 TTAGCAC
1 TTAGCAC
31106817 TTAGCAC
1 TTAGCAC
31106824 TTAGCAC
1 TTAGCAC
31106831 TTAGC
1 TTAGC
31106836 CGGTCCTTGG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.27, C:0.27, G:0.15, T:0.31
Consensus pattern (7 bp):
TTAGCAC
Done.