Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Gbar_D01
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: 62811768
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 736185 characters in sequence are not A, C, G, or T
File 84 of 211
Found at i:22770940 original size:12 final size:12
Alignment explanation
Indices: 22770923--22770949 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
22770913 AAAGTGCAAA
22770923 AAAAAAAATTAT
1 AAAAAAAATTAT
22770935 AAAAAAAATTAT
1 AAAAAAAATTAT
22770947 AAA
1 AAA
22770950 TTACAAAAAC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.78, C:0.00, G:0.00, T:0.22
Consensus pattern (12 bp):
AAAAAAAATTAT
Found at i:22770950 original size:19 final size:20
Alignment explanation
Indices: 22770928--22770969 Score: 59
Period size: 19 Copynumber: 2.1 Consensus size: 20
22770918 GCAAAAAAAA
*
22770928 AAATTATAAAAA-AAATTAT
1 AAATTACAAAAACAAATTAT
*
22770947 AAATTACAAAAACATATTAT
1 AAATTACAAAAACAAATTAT
22770967 AAA
1 AAA
22770970 AATTGAAAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
19 11 0.55
20 9 0.45
ACGTcount: A:0.67, C:0.05, G:0.00, T:0.29
Consensus pattern (20 bp):
AAATTACAAAAACAAATTAT
Found at i:22771681 original size:29 final size:30
Alignment explanation
Indices: 22771631--22771687 Score: 82
Period size: 29 Copynumber: 1.9 Consensus size: 30
22771621 ATTTTATAAT
22771631 ATTTTTAAATATTGTTTTTCATAACTTTAAC
1 ATTTTTAAATATTGTTTTTCATAA-TTTAAC
*
22771662 ATTTTTATATA-T-TTTTTCATAATTTA
1 ATTTTTAAATATTGTTTTTCATAATTTA
22771688 TATAATTTAC
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
28 4 0.16
29 10 0.40
30 1 0.04
31 10 0.40
ACGTcount: A:0.32, C:0.07, G:0.02, T:0.60
Consensus pattern (30 bp):
ATTTTTAAATATTGTTTTTCATAATTTAAC
Found at i:22771805 original size:18 final size:18
Alignment explanation
Indices: 22771784--22771841 Score: 62
Period size: 18 Copynumber: 3.2 Consensus size: 18
22771774 TTTTTTTTCA
*
22771784 TTTTTATATTTTTATAAT
1 TTTTTATATTTTTATGAT
* *
22771802 TTTTAATTATTTCTATGAT
1 TTTTTA-TATTTTTATGAT
* *
22771821 TTTGTAAATTTTTATGAT
1 TTTTTATATTTTTATGAT
22771839 TTT
1 TTT
22771842 AATTATAAAA
Statistics
Matches: 32, Mismatches: 7, Indels: 2
0.78 0.17 0.05
Matches are distributed among these distances:
18 18 0.56
19 14 0.44
ACGTcount: A:0.26, C:0.02, G:0.05, T:0.67
Consensus pattern (18 bp):
TTTTTATATTTTTATGAT
Found at i:22771813 original size:27 final size:27
Alignment explanation
Indices: 22771707--22771834 Score: 84
Period size: 27 Copynumber: 4.6 Consensus size: 27
22771697 CATGTACTTT
* **
22771707 TATTTTTAATAAATTTTAATATATTTGGA
1 TATTTTT-ATAATTTTTAAT-TATTTTTA
* * *
22771736 TATTTTT-TCATGTATAA-TATTTTTCTA
1 TATTTTTATAATTTTTAATTA-TTTT-TA
* *
22771763 TATTGTTATAATTTTT-TTTCATTTTTA
1 TATTTTTATAATTTTTAATT-ATTTTTA
*
22771790 TATTTTTATAATTTTTAATTATTTCTA
1 TATTTTTATAATTTTTAATTATTTTTA
22771817 TGATTTTGTA-AATTTTTA
1 T-ATTTT-TATAATTTTTA
22771835 TGATTTTAAT
Statistics
Matches: 77, Mismatches: 14, Indels: 17
0.71 0.13 0.16
Matches are distributed among these distances:
25 2 0.03
26 3 0.04
27 37 0.48
28 25 0.32
29 10 0.13
ACGTcount: A:0.29, C:0.03, G:0.05, T:0.63
Consensus pattern (27 bp):
TATTTTTATAATTTTTAATTATTTTTA
Found at i:22771840 original size:9 final size:9
Alignment explanation
Indices: 22771754--22771841 Score: 54
Period size: 9 Copynumber: 9.6 Consensus size: 9
22771744 CATGTATAAT
*
22771754 ATTTTTCTA
1 ATTTTTATA
*
22771763 TATTGTTATA
1 -ATTTTTATA
* *
22771773 ATTTTTTTTC
1 A-TTTTTATA
22771783 ATTTTTAT-
1 ATTTTTATA
22771791 ATTTTTATA
1 ATTTTTATA
*
22771800 ATTTTTAATT
1 ATTTTT-ATA
* *
22771810 ATTTCTATG
1 ATTTTTATA
22771819 ATTTTGTA-A
1 ATTTT-TATA
*
22771828 ATTTTTATG
1 ATTTTTATA
22771837 ATTTT
1 ATTTT
22771842 AATTATAAAA
Statistics
Matches: 61, Mismatches: 12, Indels: 11
0.73 0.14 0.13
Matches are distributed among these distances:
8 10 0.16
9 29 0.48
10 22 0.36
ACGTcount: A:0.25, C:0.03, G:0.05, T:0.67
Consensus pattern (9 bp):
ATTTTTATA
Found at i:22772401 original size:10 final size:10
Alignment explanation
Indices: 22772388--22772511 Score: 57
Period size: 9 Copynumber: 12.7 Consensus size: 10
22772378 TTAATGAAAA
22772388 TATAAAATAT
1 TATAAAATAT
22772398 TATAAAA-AT
1 TATAAAATAT
* *
22772407 TTTGAAATA-
1 TATAAAATAT
22772416 TATAAAA-A-
1 TATAAAATAT
* *
22772424 CATAGAAAAAT
1 TATA-AAATAT
22772435 TATAAAATAT
1 TATAAAATAT
22772445 TATTAAAA-AT
1 TA-TAAAATAT
** **
22772455 GGTTGAATAT
1 TATAAAATAT
22772465 TAT-AAATAT
1 TATAAAATAT
**
22772474 TATTAGTATAT
1 TA-TAAAATAT
22772485 TATGAAAA-A-
1 TAT-AAAATAT
22772494 TATGAAAATAT
1 TAT-AAAATAT
22772505 TATAAAA
1 TATAAAA
22772512 ATTTAGAAAT
Statistics
Matches: 85, Mismatches: 18, Indels: 22
0.68 0.14 0.18
Matches are distributed among these distances:
8 4 0.05
9 33 0.39
10 29 0.34
11 19 0.22
ACGTcount: A:0.56, C:0.01, G:0.06, T:0.36
Consensus pattern (10 bp):
TATAAAATAT
Found at i:22772405 original size:18 final size:18
Alignment explanation
Indices: 22772341--22772441 Score: 64
Period size: 19 Copynumber: 5.4 Consensus size: 18
22772331 TATAACAAGT
*
22772341 TTATAAAATTATAAAACTCA
1 TTATAAAAATATAAAA-T-A
*
22772361 -TAGAAAAATCATAAAA-A
1 TTATAAAAAT-ATAAAATA
*
22772378 TTAATGAAAATATAAAATA
1 TT-ATAAAAATATAAAATA
* *
22772397 TTATAAAAATTTTGAAATA
1 TTATAAAAA-TATAAAATA
* *
22772416 -TATAAAAACATAGAAAAA
1 TTATAAAAATATA-AAATA
22772434 TTATAAAA
1 TTATAAAA
22772442 TATTATTAAA
Statistics
Matches: 63, Mismatches: 11, Indels: 15
0.71 0.12 0.17
Matches are distributed among these distances:
17 2 0.03
18 25 0.40
19 30 0.48
20 6 0.10
ACGTcount: A:0.62, C:0.04, G:0.04, T:0.30
Consensus pattern (18 bp):
TTATAAAAATATAAAATA
Found at i:22772452 original size:20 final size:19
Alignment explanation
Indices: 22772326--22772514 Score: 70
Period size: 20 Copynumber: 9.8 Consensus size: 19
22772316 AAATTACTAT
*
22772326 AATATTATAACAAGTT-TATA
1 AATATTATAA-AAATTATA-A
* *
22772346 AA-ATTATAAAACTCATAGA
1 AATATTATAAAAATTATA-A
* *
22772365 AAAATCATAAAAATTAATGAA
1 AATATTATAAAAATT-AT-AA
*
22772386 AATA-TA-AAATATTATAA
1 AATATTATAAAAATTATAA
**
22772403 AA-ATT-TTGAAATATATAA
1 AATATTATAAAAAT-TATAA
* *
22772421 AA-ACATAGAAAAATTATAA
1 AATA-TTATAAAAATTATAA
** **
22772440 AATATTATTAAAAATGGTTG
1 AATATTA-TAAAAATTATAA
* *
22772460 AATATTATAAATATTATTAG
1 AATATTATAAAAATTA-TAA
*
22772480 TATATTATGAAAAA-TATGAA
1 AATATTAT-AAAAATTAT-AA
22772500 AATATTATAAAAATT
1 AATATTATAAAAATT
22772515 TAGAAATGAT
Statistics
Matches: 124, Mismatches: 30, Indels: 30
0.67 0.16 0.16
Matches are distributed among these distances:
16 1 0.01
17 8 0.06
18 13 0.10
19 40 0.32
20 51 0.41
21 10 0.08
22 1 0.01
ACGTcount: A:0.57, C:0.03, G:0.06, T:0.34
Consensus pattern (19 bp):
AATATTATAAAAATTATAA
Found at i:22772468 original size:67 final size:66
Alignment explanation
Indices: 22772326--22772454 Score: 163
Period size: 65 Copynumber: 1.9 Consensus size: 66
22772316 AAATTACTAT
* * *
22772326 AATATTATAACAAGTTTATAAAATTATAAAACTCATAGAAAAATCATAAAAATTAATGAAAATAT
1 AATATTATAA-AAATTTATAAAATTATAAAACACATAGAAAAATCATAAAAATTAATAAAAATAT
22772391 AA
65 AA
* * *
22772393 AATATTATAAAAATTT-TGAAATATATAAAA-ACATAGAAAAATTATAAAATATTATTAAAAAT
1 AATATTATAAAAATTTATAAAAT-TATAAAACACATAGAAAAATCATAAAA-ATTAATAAAAAT
22772455 GGTTGAATAT
Statistics
Matches: 54, Mismatches: 6, Indels: 5
0.83 0.09 0.08
Matches are distributed among these distances:
65 22 0.41
66 22 0.41
67 10 0.19
ACGTcount: A:0.60, C:0.04, G:0.04, T:0.32
Consensus pattern (66 bp):
AATATTATAAAAATTTATAAAATTATAAAACACATAGAAAAATCATAAAAATTAATAAAAATATA
A
Found at i:22773268 original size:20 final size:20
Alignment explanation
Indices: 22773243--22773291 Score: 64
Period size: 20 Copynumber: 2.5 Consensus size: 20
22773233 GAACTAAAAC
* *
22773243 TATCGATGCCAAA-AGAAATT
1 TATCGATACCAAACA-AAATG
22773263 TATCGATACCAAACAAAATG
1 TATCGATACCAAACAAAATG
22773283 TATCGATAC
1 TATCGATAC
22773292 TTAATAAATC
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
20 25 0.96
21 1 0.04
ACGTcount: A:0.45, C:0.18, G:0.12, T:0.24
Consensus pattern (20 bp):
TATCGATACCAAACAAAATG
Found at i:22778485 original size:33 final size:32
Alignment explanation
Indices: 22778448--22778514 Score: 116
Period size: 33 Copynumber: 2.1 Consensus size: 32
22778438 CTTCATTTGG
*
22778448 GGTAGATTTAAGCTTTAACCCCTCATTCTTCTT
1 GGTAGATTCAAGCTTTAACCCCTCATTCTT-TT
22778481 GGTAGATTCAAGCTTTAACCCCTCATTCTTTT
1 GGTAGATTCAAGCTTTAACCCCTCATTCTTTT
22778513 GG
1 GG
22778515 AATATTCTTC
Statistics
Matches: 33, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
32 4 0.12
33 29 0.88
ACGTcount: A:0.21, C:0.24, G:0.15, T:0.40
Consensus pattern (32 bp):
GGTAGATTCAAGCTTTAACCCCTCATTCTTTT
Found at i:22778606 original size:174 final size:174
Alignment explanation
Indices: 22778299--22778633 Score: 494
Period size: 174 Copynumber: 1.9 Consensus size: 174
22778289 TTTGAGATCC
* *
22778299 TTCTCCTTAGTAGATTCAAGCTTTAACCCCTCATTCTTTTGGAATCTTCTTCCTCTATTAGACTT
1 TTCTCCTTAGTAGATTCAAGCTTTAACCCCTCATTCTTTTGGAATATTCTTCCTCTATTAGAATT
*** *
22778364 CAGGAATCTCTTCAATCTCCTAGCAAACATGGTTATCTCTTTGTCTTCATCCACCTCTTCTCTTG
66 CAGGAATCTCTTCAATCTCCTAGCAAACATGAACATCTCTTTGTCTTCATCCACCTCTTCGCTTG
22778429 ATTCACTATCTTCATTTGGGGTAGATTTAAGCTTTAACCCCTCA
131 ATTCACTATCTTCATTTGGGGTAGATTTAAGCTTTAACCCCTCA
* * *
22778473 TTCTTCTTGGTAGATTCAAGCTTTAACCCCTCATTCTTTTGGAATATTCTTCCTCT-TTTGAAAT
1 TTCTCCTTAGTAGATTCAAGCTTTAACCCCTCATTCTTTTGGAATATTCTTCCTCTATTAG-AAT
* * * * *
22778537 TCATGAATCTTTTGAATCTCCTAGCAAACATGAACATCTCCTTT-TGTTCATCCACCTCTTCGGT
65 TCAGGAATCTCTTCAATCTCCTAGCAAACATGAACATCT-CTTTGTCTTCATCCACCTCTTCGCT
* *
22778601 TGATTCACTATCTTCATTTGTGGTGGATTTAAG
129 TGATTCACTATCTTCATTTGGGGTAGATTTAAG
22778634 AGCAACACCA
Statistics
Matches: 143, Mismatches: 16, Indels: 4
0.88 0.10 0.02
Matches are distributed among these distances:
173 3 0.02
174 136 0.95
175 4 0.03
ACGTcount: A:0.21, C:0.25, G:0.12, T:0.42
Consensus pattern (174 bp):
TTCTCCTTAGTAGATTCAAGCTTTAACCCCTCATTCTTTTGGAATATTCTTCCTCTATTAGAATT
CAGGAATCTCTTCAATCTCCTAGCAAACATGAACATCTCTTTGTCTTCATCCACCTCTTCGCTTG
ATTCACTATCTTCATTTGGGGTAGATTTAAGCTTTAACCCCTCA
Found at i:22784898 original size:10 final size:10
Alignment explanation
Indices: 22784870--22784949 Score: 63
Period size: 10 Copynumber: 7.8 Consensus size: 10
22784860 CTTGTTTAAC
*
22784870 AAAAATGATA
1 AAAAATTATA
22784880 AAAAATTATA
1 AAAAATTATA
*
22784890 AAAAGTTAT-
1 AAAAATTATA
*
22784899 AGAAATTATTA
1 AAAAATTA-TA
**
22784910 AAATTTTATTA
1 AAAAATTA-TA
* *
22784921 AATAGTTATA
1 AAAAATTATA
22784931 AAAAATTATA
1 AAAAATTATA
22784941 AAAATATTA
1 AAAA-ATTA
22784950 AAGAGTATAG
Statistics
Matches: 55, Mismatches: 12, Indels: 5
0.76 0.17 0.07
Matches are distributed among these distances:
9 6 0.11
10 32 0.58
11 17 0.31
ACGTcount: A:0.60, C:0.00, G:0.05, T:0.35
Consensus pattern (10 bp):
AAAAATTATA
Found at i:22787350 original size:29 final size:29
Alignment explanation
Indices: 22787291--22787372 Score: 76
Period size: 29 Copynumber: 2.8 Consensus size: 29
22787281 AAAACGTTGT
* ** *
22787291 AATTTTT-TAAAATTATGAAAATATTATAA
1 AATTTTTATAAAATTAT-AAAAAAACAAAA
22787320 AATTTTTATAAAATTATAAAAAAACAAAA
1 AATTTTTATAAAATTATAAAAAAACAAAA
* *
22787349 AAATATTATTAAATATTATAAAAA
1 AATTTTTA-TAAA-ATTATAAAAA
22787373 TTTTAAAAAT
Statistics
Matches: 44, Mismatches: 6, Indels: 4
0.81 0.11 0.07
Matches are distributed among these distances:
29 21 0.48
30 13 0.30
31 10 0.23
ACGTcount: A:0.60, C:0.01, G:0.01, T:0.38
Consensus pattern (29 bp):
AATTTTTATAAAATTATAAAAAAACAAAA
Found at i:22787352 original size:30 final size:30
Alignment explanation
Indices: 22787291--22787372 Score: 62
Period size: 30 Copynumber: 2.7 Consensus size: 30
22787281 AAAACGTTGT
* ** *
22787291 AATTTTT-TAAAATTATGAAAATATTATAAA
1 AATTTTTATAAAATTAT-AAAAAAACAAAAA
*
22787321 ATTTTT-ATAAAATTATAAAAAAACAAAAA
1 AATTTTTATAAAATTATAAAAAAACAAAAA
*
22787350 AATATTATTA-AATATTATAAAAA
1 AAT-TT-TTATAAAATTATAAAAA
22787373 TTTTAAAAAT
Statistics
Matches: 41, Mismatches: 7, Indels: 7
0.75 0.13 0.13
Matches are distributed among these distances:
29 11 0.27
30 16 0.39
31 13 0.32
32 1 0.02
ACGTcount: A:0.60, C:0.01, G:0.01, T:0.38
Consensus pattern (30 bp):
AATTTTTATAAAATTATAAAAAAACAAAAA
Found at i:22789463 original size:26 final size:26
Alignment explanation
Indices: 22789434--22789537 Score: 109
Period size: 26 Copynumber: 4.0 Consensus size: 26
22789424 GCCTAGCGAG
*
22789434 CTTGAGTTTAAGTGGGTCAAAGGACC
1 CTTGAGTTTAAGTTGGTCAAAGGACC
* * **
22789460 CTTGAGTTTAAGTAGGTTAGGGGACC
1 CTTGAGTTTAAGTTGGTCAAAGGACC
* * **
22789486 CCTGAGTTTGAGTTGGTCGGAGGACC
1 CTTGAGTTTAAGTTGGTCAAAGGACC
* *
22789512 TTTGAGTTTGAGTTGGTCAAAGGACC
1 CTTGAGTTTAAGTTGGTCAAAGGACC
22789538 ATGAGTATAT
Statistics
Matches: 64, Mismatches: 14, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
26 64 1.00
ACGTcount: A:0.22, C:0.14, G:0.34, T:0.30
Consensus pattern (26 bp):
CTTGAGTTTAAGTTGGTCAAAGGACC
Found at i:22795739 original size:11 final size:11
Alignment explanation
Indices: 22795716--22795747 Score: 55
Period size: 11 Copynumber: 2.8 Consensus size: 11
22795706 ATACAATTTG
22795716 ATTAAATAATTC
1 ATTAAA-AATTC
22795728 ATTAAAAATTC
1 ATTAAAAATTC
22795739 ATTAAAAAT
1 ATTAAAAAT
22795748 AAATATAAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
11 14 0.70
12 6 0.30
ACGTcount: A:0.56, C:0.06, G:0.00, T:0.38
Consensus pattern (11 bp):
ATTAAAAATTC
Found at i:22805912 original size:25 final size:25
Alignment explanation
Indices: 22805884--22805942 Score: 73
Period size: 25 Copynumber: 2.4 Consensus size: 25
22805874 AGAGAAGAGT
* *
22805884 AAAACAAAACATAGTAGAACATAAC
1 AAAACAAAACAGAGTAGAACAGAAC
* *
22805909 AAAACATAACAGAGTAGAGCAGAAC
1 AAAACAAAACAGAGTAGAACAGAAC
*
22805934 ATAACAAAA
1 AAAACAAAA
22805943 TAGAACAGAA
Statistics
Matches: 28, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
25 28 1.00
ACGTcount: A:0.63, C:0.15, G:0.12, T:0.10
Consensus pattern (25 bp):
AAAACAAAACAGAGTAGAACAGAAC
Found at i:22805934 original size:20 final size:20
Alignment explanation
Indices: 22805906--22805954 Score: 62
Period size: 20 Copynumber: 2.5 Consensus size: 20
22805896 AGTAGAACAT
* * *
22805906 AACAAAACATAACAGAGTAG
1 AACAGAACATAACAAAATAG
*
22805926 AGCAGAACATAACAAAATAG
1 AACAGAACATAACAAAATAG
22805946 AACAGAACA
1 AACAGAACA
22805955 AAGTAGAGCA
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.61, C:0.16, G:0.14, T:0.08
Consensus pattern (20 bp):
AACAGAACATAACAAAATAG
Found at i:22805952 original size:5 final size:5
Alignment explanation
Indices: 22805899--22806213 Score: 55
Period size: 5 Copynumber: 63.0 Consensus size: 5
22805889 AAAACATAGT
* * * ** * * * *
22805899 AGAAC ATAAC AAAAC ATAAC AGAGT AGAGC AGAAC ATAAC AAAAT AGAAC
1 AGAAC AGAAC AGAAC AGAAC AGAAC AGAAC AGAAC AGAAC AGAAC AGAAC
* * * * * * * * * *
22805949 AGAAC A-AAGT AGAGC ATAAT AGAAT AGAGC AGAAC ATAAC ATAAC ATAGC
1 AGAAC AGAA-C AGAAC AGAAC AGAAC AGAAC AGAAC AGAAC AGAAC AGAAC
* * ** * *
22805999 AGAAC AGAAC TGAGAA- A-AAC ATAAC AGAAC AGAAT AGAGT GGAAC ATAAC
1 AGAAC AGAAC --AGAAC AGAAC AGAAC AGAAC AGAAC AGAAC AGAAC AGAAC
* * * * * ** *
22806049 AAAAT AGAAC A-AAGC A-AAGC AAAAC AGAAC ATAAC AGAAT AGAGT AGGAC
1 AGAAC AGAAC AGAA-C AGAA-C AGAAC AGAAC AGAAC AGAAC AGAAC AGAAC
* * * * * * * * * *
22806099 ATAAA AAAAC AGAAT AGAGC AGAGC AGAAT AGAAC AGAAC AGAAG AAAAA
1 AGAAC AGAAC AGAAC AGAAC AGAAC AGAAC AGAAC AGAAC AGAAC AGAAC
* * * * * * * * *
22806149 AAAAC ACAAC AGAAT AGAAC AGAAT AGAGC AAAAC ATAAT AGAAC TGAAC
1 AGAAC AGAAC AGAAC AGAAC AGAAC AGAAC AGAAC AGAAC AGAAC AGAAC
* * *
22806199 TGAAC TGAAC TGAAC
1 AGAAC AGAAC AGAAC
22806214 TGAGTTATAC
Statistics
Matches: 225, Mismatches: 77, Indels: 16
0.71 0.24 0.05
Matches are distributed among these distances:
3 2 0.01
4 6 0.03
5 210 0.93
6 3 0.01
7 4 0.02
ACGTcount: A:0.58, C:0.14, G:0.17, T:0.10
Consensus pattern (5 bp):
AGAAC
Found at i:22805967 original size:30 final size:30
Alignment explanation
Indices: 22805886--22805984 Score: 90
Period size: 30 Copynumber: 3.3 Consensus size: 30
22805876 AGAAGAGTAA
* * * *
22805886 AACAAAACATAGTAGAACATAACAAAACAT
1 AACAGAACAAAGTAGAACATAACAAAATAG
** * *
22805916 AACAGAGTAGAGCAGAACATAACAAAATAG
1 AACAGAACAAAGTAGAACATAACAAAATAG
* * *
22805946 AACAGAACAAAGTAGAGCATAATAGAATAG
1 AACAGAACAAAGTAGAACATAACAAAATAG
*
22805976 AGCAGAACA
1 AACAGAACA
22805985 TAACATAACA
Statistics
Matches: 54, Mismatches: 15, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
30 54 1.00
ACGTcount: A:0.59, C:0.14, G:0.16, T:0.11
Consensus pattern (30 bp):
AACAGAACAAAGTAGAACATAACAAAATAG
Found at i:22806045 original size:55 final size:56
Alignment explanation
Indices: 22806011--22806142 Score: 151
Period size: 55 Copynumber: 2.4 Consensus size: 56
22806001 AACAGAACTG
* *
22806011 AGAAAAACATAACAGAACAGAATAGAGT-GGAACATAACAAAATAGAACAAAGCAA
1 AGAAAAACAGAACAGAACAGAATAGAGTAGGAACATAACAAAACAGAACAAAGCAA
* * * * * *
22806066 AGCAAAACAGAACATAACAGAATAGAGTAGG-ACATAAAAAAACAGAATAGAGCAG
1 AGAAAAACAGAACAGAACAGAATAGAGTAGGAACATAACAAAACAGAACAAAGCAA
* * *
22806121 AGCAGAATAGAACAGAACAGAA
1 AGAAAAACAGAACAGAACAGAA
22806143 GAAAAAAAAA
Statistics
Matches: 65, Mismatches: 11, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
55 63 0.97
56 2 0.03
ACGTcount: A:0.60, C:0.13, G:0.19, T:0.08
Consensus pattern (56 bp):
AGAAAAACAGAACAGAACAGAATAGAGTAGGAACATAACAAAACAGAACAAAGCAA
Found at i:22806128 original size:15 final size:15
Alignment explanation
Indices: 22806106--22806198 Score: 69
Period size: 15 Copynumber: 6.2 Consensus size: 15
22806096 GACATAAAAA
*
22806106 AACAGAATAGAGCAG
1 AACAGAATAGAACAG
*
22806121 AGCAGAATAGAACAG
1 AACAGAATAGAACAG
* * * *
22806136 AACAGAAGAAAAAAA
1 AACAGAATAGAACAG
* * *
22806151 AACACAACAGAATAG
1 AACAGAATAGAACAG
* *
22806166 AACAGAATAGAGCAA
1 AACAGAATAGAACAG
* *
22806181 AACATAATAGAACTG
1 AACAGAATAGAACAG
22806196 AAC
1 AAC
22806199 TGAACTGAAC
Statistics
Matches: 57, Mismatches: 21, Indels: 0
0.73 0.27 0.00
Matches are distributed among these distances:
15 57 1.00
ACGTcount: A:0.60, C:0.14, G:0.18, T:0.08
Consensus pattern (15 bp):
AACAGAATAGAACAG
Found at i:22806214 original size:5 final size:5
Alignment explanation
Indices: 22806190--22806216 Score: 54
Period size: 5 Copynumber: 5.4 Consensus size: 5
22806180 AAACATAATA
22806190 GAACT GAACT GAACT GAACT GAACT GA
1 GAACT GAACT GAACT GAACT GAACT GA
22806217 GTTATACAGA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 22 1.00
ACGTcount: A:0.41, C:0.19, G:0.22, T:0.19
Consensus pattern (5 bp):
GAACT
Found at i:22808946 original size:21 final size:21
Alignment explanation
Indices: 22808920--22808960 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
22808910 AAAAATTTGG
*
22808920 ATAAAAACTTAGAAA-TAAAAA
1 ATAAAAAATTA-AAAGTAAAAA
22808941 ATAAAAAATTAAAAGTAAAA
1 ATAAAAAATTAAAAGTAAAA
22808961 CCTACTCACT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 3 0.17
21 15 0.83
ACGTcount: A:0.73, C:0.02, G:0.05, T:0.20
Consensus pattern (21 bp):
ATAAAAAATTAAAAGTAAAAA
Found at i:22825431 original size:27 final size:27
Alignment explanation
Indices: 22825381--22825481 Score: 107
Period size: 27 Copynumber: 3.7 Consensus size: 27
22825371 ACACGCTAGA
* *
22825381 AAATAGAAGCCTTTGTGATC-ATCTATG
1 AAATGGAAGCCTTTGTG-GCAATCTATG
* *
22825408 TAATGGAAGCCTTTTTGGCAATCTATG
1 AAATGGAAGCCTTTGTGGCAATCTATG
**
22825435 AAATGGAAGCCTTTGTGGTGATCTATGG
1 AAATGGAAGCCTTTGTGGCAATCTAT-G
22825463 AAA-GGAATGCCTTTGTGGC
1 AAATGGAA-GCCTTTGTGGC
22825482 GTATTCTAAA
Statistics
Matches: 62, Mismatches: 9, Indels: 5
0.82 0.12 0.07
Matches are distributed among these distances:
26 1 0.02
27 47 0.76
28 14 0.23
ACGTcount: A:0.28, C:0.14, G:0.26, T:0.33
Consensus pattern (27 bp):
AAATGGAAGCCTTTGTGGCAATCTATG
Found at i:22840218 original size:13 final size:13
Alignment explanation
Indices: 22840202--22840248 Score: 51
Period size: 13 Copynumber: 3.5 Consensus size: 13
22840192 GAGAGTAGGA
*
22840202 TTCTGTATATTTG
1 TTCTGTATATCTG
*
22840215 TTCTGCATATCTG
1 TTCTGTATATCTG
22840228 ATTCTG-ATATCTG
1 -TTCTGTATATCTG
22840241 TATCTGTA
1 T-TCTGTA
22840249 GAGGACTTAG
Statistics
Matches: 29, Mismatches: 2, Indels: 5
0.81 0.06 0.14
Matches are distributed among these distances:
12 1 0.03
13 22 0.76
14 6 0.21
ACGTcount: A:0.19, C:0.15, G:0.15, T:0.51
Consensus pattern (13 bp):
TTCTGTATATCTG
Found at i:22847923 original size:16 final size:17
Alignment explanation
Indices: 22847890--22847931 Score: 50
Period size: 17 Copynumber: 2.5 Consensus size: 17
22847880 TAAATATTAT
*
22847890 TTTTTTAATTAATTTAA
1 TTTTTTAATTAATATAA
*
22847907 TTTTTTCATTAA-ATAA
1 TTTTTTAATTAATATAA
22847923 TTTTCTTAA
1 TTTT-TTAA
22847932 CCCAATTCTA
Statistics
Matches: 21, Mismatches: 3, Indels: 2
0.81 0.12 0.08
Matches are distributed among these distances:
16 7 0.33
17 14 0.67
ACGTcount: A:0.33, C:0.05, G:0.00, T:0.62
Consensus pattern (17 bp):
TTTTTTAATTAATATAA
Found at i:22853691 original size:61 final size:62
Alignment explanation
Indices: 22853615--22853739 Score: 171
Period size: 61 Copynumber: 2.0 Consensus size: 62
22853605 TCTTATATCT
* * * * *
22853615 AAAAATTCAACAAATTTAGCCCTCAATATTTAC-AAAATTTGCCATCTAGTTCTAATTCTAA
1 AAAAAATCAACAAATTTAGCCCTAAATATTTACAAAAATTTGCAATCTAATTCTAATACTAA
* * *
22853676 AAAAAATCAATAAATTTAGCCCTAAATATTTACAAAAATTTTCAATTTAATTCTAATACTAA
1 AAAAAATCAACAAATTTAGCCCTAAATATTTACAAAAATTTGCAATCTAATTCTAATACTAA
22853738 AA
1 AA
22853740 GTTAAAAAAA
Statistics
Matches: 55, Mismatches: 8, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
61 30 0.55
62 25 0.45
ACGTcount: A:0.46, C:0.16, G:0.03, T:0.34
Consensus pattern (62 bp):
AAAAAATCAACAAATTTAGCCCTAAATATTTACAAAAATTTGCAATCTAATTCTAATACTAA
Found at i:22860260 original size:3 final size:3
Alignment explanation
Indices: 22860252--22860295 Score: 88
Period size: 3 Copynumber: 14.7 Consensus size: 3
22860242 CTTGTTTCCA
22860252 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
22860296 GAGTTGAACT
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 41 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
ATT
Found at i:22860782 original size:46 final size:46
Alignment explanation
Indices: 22860730--22860822 Score: 159
Period size: 46 Copynumber: 2.0 Consensus size: 46
22860720 AATATACTTG
* *
22860730 TTAAAGTAACTGCTCGGTTGTTGAAGTCGTTTTACTTTTCTACCTC
1 TTAAAGTAACTGCTCGGTTGTCGAAGTCGTTTTAATTTTCTACCTC
*
22860776 TTAAAGTAACTGTTCGGTTGTCGAAGTCGTTTTAATTTTCTACCTC
1 TTAAAGTAACTGCTCGGTTGTCGAAGTCGTTTTAATTTTCTACCTC
22860822 T
1 T
22860823 GGATTATTTT
Statistics
Matches: 44, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
46 44 1.00
ACGTcount: A:0.20, C:0.18, G:0.17, T:0.44
Consensus pattern (46 bp):
TTAAAGTAACTGCTCGGTTGTCGAAGTCGTTTTAATTTTCTACCTC
Found at i:22867478 original size:33 final size:32
Alignment explanation
Indices: 22867440--22867525 Score: 127
Period size: 33 Copynumber: 2.6 Consensus size: 32
22867430 ACCAAAAATT
*
22867440 TATTTTAAAAATTAAAAAAATTTATTTTAAAAA
1 TATTTT-AAAATTAAAAAAATGTATTTTAAAAA
* *
22867473 TATTTTAAAATTAAAAAAAAAGTATTTTAAAAG
1 TATTTTAAAATT-AAAAAAATGTATTTTAAAAA
22867506 TATTTTAAAATTAAAAAAAT
1 TATTTTAAAATTAAAAAAAT
22867526 AAAAAAAATA
Statistics
Matches: 48, Mismatches: 4, Indels: 3
0.87 0.07 0.05
Matches are distributed among these distances:
32 13 0.27
33 35 0.73
ACGTcount: A:0.58, C:0.00, G:0.02, T:0.40
Consensus pattern (32 bp):
TATTTTAAAATTAAAAAAATGTATTTTAAAAA
Found at i:22870637 original size:29 final size:29
Alignment explanation
Indices: 22870595--22870655 Score: 97
Period size: 29 Copynumber: 2.1 Consensus size: 29
22870585 TCTAACTTGT
*
22870595 ATCACTTCTTTACCCTTGAAGTCCGATGC
1 ATCACTTCTTTACCCTTGAAGTCCGATAC
22870624 ATCAC-TCTTTTACCCTTGAAGTCCGATAC
1 ATCACTTC-TTTACCCTTGAAGTCCGATAC
22870653 ATC
1 ATC
22870656 GCCCATCTCT
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
28 2 0.07
29 28 0.93
ACGTcount: A:0.23, C:0.31, G:0.11, T:0.34
Consensus pattern (29 bp):
ATCACTTCTTTACCCTTGAAGTCCGATAC
Found at i:22875257 original size:18 final size:17
Alignment explanation
Indices: 22875234--22875270 Score: 56
Period size: 17 Copynumber: 2.1 Consensus size: 17
22875224 ATTTATTTAG
22875234 ATCAAGAATGAATGGAAA
1 ATCAAGAA-GAATGGAAA
*
22875252 ATCAAGGAGAATGGAAA
1 ATCAAGAAGAATGGAAA
22875269 AT
1 AT
22875271 TACCAAATAT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 11 0.61
18 7 0.39
ACGTcount: A:0.54, C:0.05, G:0.24, T:0.16
Consensus pattern (17 bp):
ATCAAGAAGAATGGAAA
Found at i:22876402 original size:20 final size:20
Alignment explanation
Indices: 22876355--22876410 Score: 58
Period size: 20 Copynumber: 2.8 Consensus size: 20
22876345 AGTTTATGCT
* * * *
22876355 AAGTAAATGAAAGGGAAAGT
1 AAGTAAATGGAATGGTAAGA
*
22876375 AAGAAAATGGAATGGTAAGA
1 AAGTAAATGGAATGGTAAGA
*
22876395 AAGTAAATAGAATGGT
1 AAGTAAATGGAATGGT
22876411 TCATAGTATT
Statistics
Matches: 29, Mismatches: 7, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
20 29 1.00
ACGTcount: A:0.54, C:0.00, G:0.29, T:0.18
Consensus pattern (20 bp):
AAGTAAATGGAATGGTAAGA
Found at i:22892625 original size:28 final size:29
Alignment explanation
Indices: 22892594--22892653 Score: 77
Period size: 28 Copynumber: 2.1 Consensus size: 29
22892584 AAATTGATAT
*
22892594 AAACTTATGAAAATTA-AAAAAATCATAA
1 AAACTTATCAAAATTATAAAAAATCATAA
* * *
22892622 AAACTTATCAATATTATGAAAATTCATAA
1 AAACTTATCAAAATTATAAAAAATCATAA
22892651 AAA
1 AAA
22892654 AATCTAATAT
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
28 14 0.52
29 13 0.48
ACGTcount: A:0.60, C:0.08, G:0.03, T:0.28
Consensus pattern (29 bp):
AAACTTATCAAAATTATAAAAAATCATAA
Found at i:22892679 original size:10 final size:10
Alignment explanation
Indices: 22892544--22892763 Score: 66
Period size: 10 Copynumber: 23.3 Consensus size: 10
22892534 ATTAACAAGT
22892544 TTATAAAAAA
1 TTATAAAAAA
*
22892554 -TAT-AAAAC
1 TTATAAAAAA
22892562 TTACT-AAAAA
1 TTA-TAAAAAA
22892572 TTA-AAAAAA
1 TTATAAAAAA
22892581 -T-T--AAAA
1 TTATAAAAAA
* *
22892587 TTGATATAAAC
1 TT-ATAAAAAA
*
22892598 TTAT-GAAAA
1 TTATAAAAAA
22892607 TTA-AAAAAA
1 TTATAAAAAA
* *
22892616 TCATAAAAAC
1 TTATAAAAAA
* *
22892626 TTAT-CAATA
1 TTATAAAAAA
*
22892635 TTAT-GAAAA
1 TTATAAAAAA
22892644 TTCATAAAAAA
1 TT-ATAAAAAA
* * * *
22892655 ATCTAATATA
1 TTATAAAAAA
22892665 TTATAAAAAA
1 TTATAAAAAA
22892675 TTAT--AAAA
1 TTATAAAAAA
22892683 TTAATAAAACATA
1 TT-ATAAAA-A-A
*
22892696 TT-TAAAACA
1 TTATAAAAAA
**
22892705 TT-TAAAATT
1 TTATAAAAAA
*
22892714 TTATAAAAAT
1 TTATAAAAAA
*
22892724 TTAT-AGAAA
1 TTATAAAAAA
22892733 -T-TAAAAAA
1 TTATAAAAAA
22892741 -TATATAAAAA
1 TTATA-AAAAA
*
22892751 TTATGAAAAA
1 TTATAAAAAA
22892761 TTA
1 TTA
22892764 GAAATTATTA
Statistics
Matches: 156, Mismatches: 31, Indels: 46
0.67 0.13 0.20
Matches are distributed among these distances:
6 4 0.03
7 2 0.01
8 17 0.11
9 51 0.33
10 58 0.37
11 20 0.13
12 1 0.01
13 3 0.02
ACGTcount: A:0.60, C:0.05, G:0.02, T:0.33
Consensus pattern (10 bp):
TTATAAAAAA
Found at i:22892748 original size:28 final size:28
Alignment explanation
Indices: 22892715--22892777 Score: 76
Period size: 28 Copynumber: 2.3 Consensus size: 28
22892705 TTTAAAATTT
*
22892715 TATAAAAATTTAT-AGAAATTAAAAAATA
1 TATAAAAA-TTATGAAAAATTAAAAAATA
* *
22892743 TATAAAAATTATGAAAAATTAGAAATTA
1 TATAAAAATTATGAAAAATTAAAAAATA
22892771 T-TAAAAA
1 TATAAAAA
22892778 ACTCATTTAA
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
27 10 0.32
28 21 0.68
ACGTcount: A:0.63, C:0.00, G:0.05, T:0.32
Consensus pattern (28 bp):
TATAAAAATTATGAAAAATTAAAAAATA
Found at i:22896455 original size:23 final size:22
Alignment explanation
Indices: 22896412--22896455 Score: 54
Period size: 23 Copynumber: 1.9 Consensus size: 22
22896402 TTCTAAGTCG
22896412 ATATTCAATTCAATTCCACACCT
1 ATATTCAATTCAATT-CACACCT
22896435 ATATTCATTATTCAATT-ACAC
1 ATATTCA--ATTCAATTCACAC
22896456 TTAGTCAATT
Statistics
Matches: 19, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
23 11 0.58
25 8 0.42
ACGTcount: A:0.36, C:0.25, G:0.00, T:0.39
Consensus pattern (22 bp):
ATATTCAATTCAATTCACACCT
Found at i:22896660 original size:51 final size:50
Alignment explanation
Indices: 22896599--22896785 Score: 229
Period size: 51 Copynumber: 3.7 Consensus size: 50
22896589 TCGGTTCACA
*
22896599 TAGTAGCCTGCACATAGTACTACACATGTGACCATTATCATTCGATACACG
1 TAGTAGCCTGCACATAGTACTACACACGTGACCA-TATCATTCGATACACG
* * * * *
22896650 TAGTATCCTGCACATAGTACTACACACGTGATCGA-AACTATCTGGTATGCA--
1 TAGTAGCCTGCACATAGTACTACACACGTGA-CCATATC-AT-TCG-ATACACG
*
22896701 TAGTAGCCTGCACATAGTACTACACATGTGACC-TATCATTCCGATACACG
1 TAGTAGCCTGCACATAGTACTACACACGTGACCATATCATT-CGATACACG
22896751 TAGTAGCCTGCACATAGTACTACACACGTGACCAT
1 TAGTAGCCTGCACATAGTACTACACACGTGACCAT
22896786 CACTTTCACT
Statistics
Matches: 114, Mismatches: 13, Indels: 18
0.79 0.09 0.12
Matches are distributed among these distances:
48 5 0.04
49 3 0.03
50 37 0.32
51 61 0.54
52 4 0.04
53 4 0.04
ACGTcount: A:0.31, C:0.26, G:0.17, T:0.26
Consensus pattern (50 bp):
TAGTAGCCTGCACATAGTACTACACACGTGACCATATCATTCGATACACG
Found at i:22896777 original size:101 final size:101
Alignment explanation
Indices: 22896597--22896781 Score: 336
Period size: 101 Copynumber: 1.8 Consensus size: 101
22896587 GTTCGGTTCA
*
22896597 CATAGTAGCCTGCACATAGTACTACACATGTGACCATTATCATTCGATACACGTAGTATCCTGCA
1 CATAGTAGCCTGCACATAGTACTACACATGTGACCA-TATCATTCGATACACGTAGTAGCCTGCA
22896662 CATAGTACTACACACGTGATCGAAACTATCTGGTATG
65 CATAGTACTACACACGTGATCGAAACTATCTGGTATG
22896699 CATAGTAGCCTGCACATAGTACTACACATGTGACC-TATCATTCCGATACACGTAGTAGCCTGCA
1 CATAGTAGCCTGCACATAGTACTACACATGTGACCATATCATT-CGATACACGTAGTAGCCTGCA
22896763 CATAGTACTACACACGTGA
65 CATAGTACTACACACGTGA
22896782 CCATCACTTT
Statistics
Matches: 81, Mismatches: 1, Indels: 3
0.95 0.01 0.04
Matches are distributed among these distances:
100 7 0.09
101 39 0.48
102 35 0.43
ACGTcount: A:0.31, C:0.26, G:0.17, T:0.26
Consensus pattern (101 bp):
CATAGTAGCCTGCACATAGTACTACACATGTGACCATATCATTCGATACACGTAGTAGCCTGCAC
ATAGTACTACACACGTGATCGAAACTATCTGGTATG
Found at i:22899384 original size:144 final size:144
Alignment explanation
Indices: 22899124--22899402 Score: 459
Period size: 144 Copynumber: 1.9 Consensus size: 144
22899114 CTTCTTGAAC
* * * * *
22899124 TTTTGATCTTGCAGTTCATAATTTACTTCAACCCAATACTTGTTTTCTATTTCTCAAAATAGATA
1 TTTTGATCTTGCACTTCATAATTTAATCCAACCCAATACTTGTTTTCTATTTCCCAAAATAAATA
* * * *
22899189 TTATTTATTTAATTAATGAAATCAACTAAACTAATTTTCTAATTAAATAATTTTCTCAATCCAGT
66 TTAATTAATTAATTAATGAAATCAACTAAACTAATTTCCCAATTAAATAATTTTCTCAATCCAGT
22899254 TCTAACTAGTCCAA
131 TCTAACTAGTCCAA
22899268 TTTTGATCTTGCACTTCATAATTTAATCCAACCCAATACTTGTTTTCTATTTCCCAAAATAAATA
1 TTTTGATCTTGCACTTCATAATTTAATCCAACCCAATACTTGTTTTCTATTTCCCAAAATAAATA
* *
22899333 TTAATTAATTAATTAATTAAATCAACTAAATTAATTTCCCAATTAAATAATTTTCTCAATCCAGT
66 TTAATTAATTAATTAATGAAATCAACTAAACTAATTTCCCAATTAAATAATTTTCTCAATCCAGT
22899398 TCTAA
131 TCTAA
22899403 TTCCATTAGA
Statistics
Matches: 124, Mismatches: 11, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
144 124 1.00
ACGTcount: A:0.36, C:0.17, G:0.04, T:0.42
Consensus pattern (144 bp):
TTTTGATCTTGCACTTCATAATTTAATCCAACCCAATACTTGTTTTCTATTTCCCAAAATAAATA
TTAATTAATTAATTAATGAAATCAACTAAACTAATTTCCCAATTAAATAATTTTCTCAATCCAGT
TCTAACTAGTCCAA
Found at i:22901273 original size:10 final size:10
Alignment explanation
Indices: 22901258--22901551 Score: 64
Period size: 10 Copynumber: 30.1 Consensus size: 10
22901248 TTCTTAAAAA
22901258 TTATAATTTT
1 TTATAATTTT
**
22901268 TTATAATTCA
1 TTATAATTTT
* * *
22901278 TTAGAACTTA
1 TTATAATTTT
*
22901288 TTATGAATCTT
1 TTAT-AATTTT
*
22901299 TTATAACTTT
1 TTATAATTTT
* *
22901309 TGAAAATTTT
1 TTATAATTTT
* *
22901319 TTTTGAAAATTT
1 TTAT--AATTTT
*
22901331 TTATAAGTTT
1 TTATAATTTT
* *
22901341 ATAGAATGTTT
1 TTATAAT-TTT
22901352 TTAT-ATTTT
1 TTATAATTTT
* *
22901361 TAAT-A-TGT
1 TTATAATTTT
*
22901369 TT-T-ATCTT
1 TTATAATTTT
22901377 TTATAATTACTT
1 TTATAATT--TT
*
22901389 TTATAATTTA
1 TTATAATTTT
22901399 TTAGT-A-TTT
1 TTA-TAATTTT
22901408 TTATAA-TTT
1 TTATAATTTT
*
22901417 TTATAA-TAT
1 TTATAATTTT
* *
22901426 TTAAAAGTTT
1 TTATAATTTT
22901436 TTATGAATTTT
1 TTAT-AATTTT
* *
22901447 TT-CAA-GTT
1 TTATAATTTT
*
22901455 TTATGATTTT
1 TTATAATTTT
* **
22901465 TTGT-AGCTT
1 TTATAATTTT
*
22901474 TTATAAGTTT
1 TTATAATTTT
* *
22901484 CTATAAATATT
1 TTAT-AATTTT
*
22901495 TCAT-ATTTT
1 TTATAATTTT
22901504 TTAATAA--TT
1 TT-ATAATTTT
*
22901513 TTA-AATTTG
1 TTATAATTTT
* *
22901522 TAATAATCTT
1 TTATAATTTT
*
22901532 TTATGA-TTT
1 TTATAATTTT
22901541 TTATAATTTT
1 TTATAATTTT
22901551 T
1 T
22901552 ATGAGAAAAA
Statistics
Matches: 198, Mismatches: 63, Indels: 46
0.64 0.21 0.15
Matches are distributed among these distances:
7 4 0.02
8 12 0.06
9 58 0.29
10 79 0.40
11 27 0.14
12 18 0.09
ACGTcount: A:0.32, C:0.04, G:0.06, T:0.59
Consensus pattern (10 bp):
TTATAATTTT
Found at i:22901331 original size:12 final size:13
Alignment explanation
Indices: 22901306--22901332 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
22901296 CTTTTATAAC
22901306 TTTTGAAAATTTT
1 TTTTGAAAATTTT
22901319 TTTTGAAAATTTT
1 TTTTGAAAATTTT
22901332 T
1 T
22901333 ATAAGTTTAT
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:0.30, C:0.00, G:0.07, T:0.63
Consensus pattern (13 bp):
TTTTGAAAATTTT
Found at i:22901398 original size:19 final size:19
Alignment explanation
Indices: 22901376--22901416 Score: 55
Period size: 19 Copynumber: 2.2 Consensus size: 19
22901366 TGTTTTATCT
*
22901376 TTTATAATTACTTTTATAA
1 TTTATAAGTACTTTTATAA
* *
22901395 TTTATTAGTATTTTTATAA
1 TTTATAAGTACTTTTATAA
22901414 TTT
1 TTT
22901417 TTATAATATT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.32, C:0.02, G:0.02, T:0.63
Consensus pattern (19 bp):
TTTATAAGTACTTTTATAA
Found at i:22901420 original size:9 final size:9
Alignment explanation
Indices: 22901387--22901553 Score: 90
Period size: 9 Copynumber: 17.7 Consensus size: 9
22901377 TTATAATTAC
22901387 TTTTATAAT
1 TTTTATAAT
22901396 TTATTAGT-AT
1 TT-TTA-TAAT
22901406 TTTTATAAT
1 TTTTATAAT
22901415 TTTTATAAT
1 TTTTATAAT
* *
22901424 ATTTAAAAGT
1 TTTTATAA-T
22901434 TTTTATGAAT
1 TTTTAT-AAT
*
22901444 TTTT-TCAAG
1 TTTTAT-AAT
*
22901453 TTTTATGATT
1 TTTTAT-AAT
* **
22901463 TTTTGTAGC
1 TTTTATAAT
22901472 TTTTATAAGT
1 TTTTATAA-T
*
22901482 TTCTATAAAT
1 TTTTAT-AAT
* *
22901492 ATTTCATATT
1 -TTTTATAAT
22901502 TTTTAATAA-
1 TTTT-ATAAT
22901511 TTTTA-AAT
1 TTTTATAAT
*
22901519 TTGTAATAAT
1 TT-TTATAAT
*
22901529 CTTTTATGAT
1 -TTTTATAAT
22901539 TTTTATAAT
1 TTTTATAAT
22901548 TTTTAT
1 TTTTAT
22901554 GAGAAAAATA
Statistics
Matches: 119, Mismatches: 25, Indels: 28
0.69 0.15 0.16
Matches are distributed among these distances:
7 2 0.02
8 4 0.03
9 59 0.50
10 43 0.36
11 11 0.09
ACGTcount: A:0.31, C:0.03, G:0.06, T:0.60
Consensus pattern (9 bp):
TTTTATAAT
Found at i:22902661 original size:20 final size:20
Alignment explanation
Indices: 22902638--22902680 Score: 70
Period size: 20 Copynumber: 2.1 Consensus size: 20
22902628 CATTTTTTTA
22902638 TTTTCTTCTTTCT-TTTCCTC
1 TTTTCTT-TTTCTATTTCCTC
22902658 TTTTCTTTTTCTATTTCCTC
1 TTTTCTTTTTCTATTTCCTC
22902678 TTT
1 TTT
22902681 CAATTGAGTT
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
19 5 0.23
20 17 0.77
ACGTcount: A:0.02, C:0.26, G:0.00, T:0.72
Consensus pattern (20 bp):
TTTTCTTTTTCTATTTCCTC
Found at i:22902661 original size:26 final size:27
Alignment explanation
Indices: 22902618--22902682 Score: 64
Period size: 26 Copynumber: 2.4 Consensus size: 27
22902608 ACGTCAAATC
*
22902618 CTTTCCTTTTCAT-TTTTTTATTTTCTT
1 CTTTCCTTTTCATCTTTTCT-TTTTCTT
*
22902645 CTTT-CTTTTCCTCTTTTCTTTTTC-T
1 CTTTCCTTTTCATCTTTTCTTTTTCTT
*
22902670 ATTTCCTCTTTCA
1 CTTTCCT-TTTCA
22902683 ATTGAGTTCT
Statistics
Matches: 31, Mismatches: 4, Indels: 6
0.76 0.10 0.15
Matches are distributed among these distances:
25 4 0.13
26 14 0.45
27 13 0.42
ACGTcount: A:0.06, C:0.25, G:0.00, T:0.69
Consensus pattern (27 bp):
CTTTCCTTTTCATCTTTTCTTTTTCTT
Found at i:22903687 original size:2 final size:2
Alignment explanation
Indices: 22903682--22903719 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
22903672 TATATATATA
22903682 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
22903720 AATTTGGCGC
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.00, C:0.00, G:0.50, T:0.50
Consensus pattern (2 bp):
TG
Found at i:22905809 original size:14 final size:14
Alignment explanation
Indices: 22905790--22905823 Score: 52
Period size: 13 Copynumber: 2.4 Consensus size: 14
22905780 ATAAAATGAA
22905790 AATAAAAATCTAAT
1 AATAAAAATCTAAT
22905804 AAT-AAAATCTAAT
1 AATAAAAATCTAAT
22905817 AGATAAA
1 A-ATAAA
22905824 TACTTAACAA
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
13 11 0.61
14 5 0.28
15 2 0.11
ACGTcount: A:0.65, C:0.06, G:0.03, T:0.26
Consensus pattern (14 bp):
AATAAAAATCTAAT
Found at i:22905812 original size:13 final size:14
Alignment explanation
Indices: 22905794--22905823 Score: 53
Period size: 13 Copynumber: 2.2 Consensus size: 14
22905784 AATGAAAATA
22905794 AAAATCTAATA-AT
1 AAAATCTAATAGAT
22905807 AAAATCTAATAGAT
1 AAAATCTAATAGAT
22905821 AAA
1 AAA
22905824 TACTTAACAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 11 0.69
14 5 0.31
ACGTcount: A:0.63, C:0.07, G:0.03, T:0.27
Consensus pattern (14 bp):
AAAATCTAATAGAT
Found at i:22912910 original size:139 final size:139
Alignment explanation
Indices: 22912660--22912917 Score: 403
Period size: 139 Copynumber: 1.9 Consensus size: 139
22912650 AGAAAATGGA
22912660 AAAACGAATACTTACCGAATCGAGCGAGTTCAACCGTCAAGCACGATGAAGAAATAAAAGAAATC
1 AAAACGAATACTTACCGAATCGAGCGAGTTCAACCGTCAAGCACGATGAAGAAATAAAAGAAATC
**
22912725 AAAAGAAAAGAGGGAGGAAACAATGAAAATTTGGCAGAAAAAGGGTGAATAAACATCAGAATGAT
66 AAAAGAAAAGAGGGAGGAAACAATGAAAATTCAGCAGAAAAAGGGTGAATAAACATCAGAATGAT
22912790 TGAAGTGGC
131 TGAAGTGGC
* ** *
22912799 AAAACGAATACTTACCGAATCGAGCGAGTTCAATCGTCGAA-CACGAT-AGAGGCATAAAAGGAA
1 AAAACGAATACTTACCGAATCGAGCGAGTTCAACCGTC-AAGCACGATGA-AGAAATAAAAGAAA
* **
22912862 TCAAAAGAAAAGAGGGATGAAACAATGAAAATTCATTAGAAAAAGGGTGAATAAAC
64 TCAAAAGAAAAGAGGGAGGAAACAATGAAAATTCAGCAGAAAAAGGGTGAATAAAC
22912918 GTCAAAACAA
Statistics
Matches: 108, Mismatches: 9, Indels: 4
0.89 0.07 0.03
Matches are distributed among these distances:
138 1 0.01
139 105 0.97
140 2 0.02
ACGTcount: A:0.48, C:0.13, G:0.23, T:0.16
Consensus pattern (139 bp):
AAAACGAATACTTACCGAATCGAGCGAGTTCAACCGTCAAGCACGATGAAGAAATAAAAGAAATC
AAAAGAAAAGAGGGAGGAAACAATGAAAATTCAGCAGAAAAAGGGTGAATAAACATCAGAATGAT
TGAAGTGGC
Found at i:22914159 original size:28 final size:29
Alignment explanation
Indices: 22914116--22914171 Score: 80
Period size: 28 Copynumber: 2.0 Consensus size: 29
22914106 TGTAAAGCAA
*
22914116 GGGATAAAATTGTAAAATCTAAA-AAATAG
1 GGGATAAAATTATAAAATC-AAATAAATAG
22914145 GGGA-AAAATTATAAAATCAAATAAATA
1 GGGATAAAATTATAAAATCAAATAAATA
22914172 AAGAACAAAT
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
27 3 0.12
28 18 0.72
29 4 0.16
ACGTcount: A:0.59, C:0.04, G:0.14, T:0.23
Consensus pattern (29 bp):
GGGATAAAATTATAAAATCAAATAAATAG
Found at i:22918423 original size:20 final size:21
Alignment explanation
Indices: 22918400--22918439 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
22918390 TTTGTACTTA
*
22918400 TCTAATGTC-TTTTTCTTTCT
1 TCTAATGTCATTTATCTTTCT
*
22918420 TCTAATTTCATTTATCTTTC
1 TCTAATGTCATTTATCTTTC
22918440 CAAGTTTATT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 8 0.47
21 9 0.53
ACGTcount: A:0.15, C:0.20, G:0.03, T:0.62
Consensus pattern (21 bp):
TCTAATGTCATTTATCTTTCT
Found at i:22918516 original size:17 final size:19
Alignment explanation
Indices: 22918483--22918517 Score: 56
Period size: 17 Copynumber: 1.9 Consensus size: 19
22918473 GTATTAATAA
22918483 AAATATTAGGTTTAAAAAT
1 AAATATTAGGTTTAAAAAT
22918502 AAAT-TTAGG-TTAAAAA
1 AAATATTAGGTTTAAAAA
22918518 ACATTCGTTT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 7 0.44
18 5 0.31
19 4 0.25
ACGTcount: A:0.54, C:0.00, G:0.11, T:0.34
Consensus pattern (19 bp):
AAATATTAGGTTTAAAAAT
Found at i:22918518 original size:18 final size:19
Alignment explanation
Indices: 22918483--22918518 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
22918473 GTATTAATAA
*
22918483 AAATATTAGGTTTAAAAAT
1 AAATATTAGGTTAAAAAAT
22918502 AAAT-TTAGGTTAAAAAA
1 AAATATTAGGTTAAAAAA
22918519 CATTCGTTTA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 12 0.75
19 4 0.25
ACGTcount: A:0.56, C:0.00, G:0.11, T:0.33
Consensus pattern (19 bp):
AAATATTAGGTTAAAAAAT
Found at i:22918619 original size:20 final size:20
Alignment explanation
Indices: 22918596--22918633 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
22918586 TATTTTCAAG
22918596 TTTATA-ATATATTTTTTTCT
1 TTTATATAT-TATTTTTTTCT
22918616 TTTATATATTATTTTTTT
1 TTTATATATTATTTTTTT
22918634 GGTATTCTCC
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
20 15 0.88
21 2 0.12
ACGTcount: A:0.24, C:0.03, G:0.00, T:0.74
Consensus pattern (20 bp):
TTTATATATTATTTTTTTCT
Found at i:22921176 original size:29 final size:29
Alignment explanation
Indices: 22921143--22921210 Score: 91
Period size: 29 Copynumber: 2.3 Consensus size: 29
22921133 ATCGACAAAT
** *
22921143 GAAAAGGGATAGTTTCGGCTATCGAATAC
1 GAAAAGGGATACCTTCAGCTATCGAATAC
* *
22921172 GAAAAGGGATACCTTCAGCTATCGATTAT
1 GAAAAGGGATACCTTCAGCTATCGAATAC
22921201 GAAAAGGGAT
1 GAAAAGGGAT
22921211 GCTGACAACC
Statistics
Matches: 34, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
29 34 1.00
ACGTcount: A:0.37, C:0.13, G:0.26, T:0.24
Consensus pattern (29 bp):
GAAAAGGGATACCTTCAGCTATCGAATAC
Found at i:22921231 original size:29 final size:29
Alignment explanation
Indices: 22921199--22921358 Score: 162
Period size: 30 Copynumber: 5.4 Consensus size: 29
22921189 GCTATCGATT
* *
22921199 ATGAAAAGGGATGCTGACAACCATCAACA
1 ATGAAAAGGGATGGTGACGACCATCAACA
*
22921228 ATGAAAAGGGATGGTGACGACCATCGACA
1 ATGAAAAGGGATGGTGACGACCATCAACA
* ** * *
22921257 ATGAAAAGGGATAGCT-TTGGCTATCAA-A
1 ATGAAAAGGGAT-GGTGACGACCATCAACA
* *
22921285 TTATGAAAAGGGATGGTGATGACCATCAGATA
1 --ATGAAAAGGGATGGTGACGACCATCA-ACA
*
22921317 ATGAAAAGGGATGGTGACGACCATCGAACT
1 ATGAAAAGGGATGGTGACGACCATC-AACA
22921347 ATGAAAAGGGAT
1 ATGAAAAGGGAT
22921359 AACTTCAACT
Statistics
Matches: 108, Mismatches: 16, Indels: 13
0.79 0.12 0.09
Matches are distributed among these distances:
28 1 0.01
29 46 0.43
30 58 0.54
31 2 0.02
32 1 0.01
ACGTcount: A:0.40, C:0.14, G:0.28, T:0.19
Consensus pattern (29 bp):
ATGAAAAGGGATGGTGACGACCATCAACA
Found at i:22921293 original size:30 final size:30
Alignment explanation
Indices: 22921141--22921448 Score: 127
Period size: 30 Copynumber: 10.4 Consensus size: 30
22921131 TCATCGACAA
* * *
22921141 ATGAAAAGGGATAGTTTCGGCTATCGAA-T
1 ATGAAAAGGGATAGCTTCGACTATCAAATT
* * *
22921170 ACGAAAAGGGATACCTTC-AGCTATC-GATT
1 ATGAAAAGGGATAGCTTCGA-CTATCAAATT
* * *
22921199 ATGAAAAGGGAT-GCTGACAACCATCAACA--
1 ATGAAAAGGGATAGCT-TCGACTATCAA-ATT
* * * *
22921228 ATGAAAAGGGAT-GGTGACGACCATCGACA--
1 ATGAAAAGGGATAGCT-TCGACTATC-AAATT
* *
22921257 ATGAAAAGGGATAGCTTTGGCTATCAAATT
1 ATGAAAAGGGATAGCTTCGACTATCAAATT
* * * *
22921287 ATGAAAAGGGAT-GGTGAT-GACCATCAGATA
1 ATGAAAAGGGATAGCT--TCGACTATCAAATT
* * * * *
22921317 ATGAAAAGGGAT-GGTGACGACCATCGAACT
1 ATGAAAAGGGATAGCT-TCGACTATCAAATT
* *
22921347 ATGAAAAGGGATAACTTCAACTATCAAATT
1 ATGAAAAGGGATAGCTTCGACTATCAAATT
* * * * **
22921377 ATGAAAATGGATAGCTTCGGCTGTCGAACA
1 ATGAAAAGGGATAGCTTCGACTATCAAATT
* ** *
22921407 ATGAAAAGGGATAACTTCGGTTATCAAATC
1 ATGAAAAGGGATAGCTTCGACTATCAAATT
*
22921437 ACGAAAAGGGAT
1 ATGAAAAGGGAT
22921449 GTGTCAACCA
Statistics
Matches: 212, Mismatches: 53, Indels: 27
0.73 0.18 0.09
Matches are distributed among these distances:
28 5 0.02
29 80 0.38
30 124 0.58
31 3 0.01
ACGTcount: A:0.39, C:0.15, G:0.25, T:0.22
Consensus pattern (30 bp):
ATGAAAAGGGATAGCTTCGACTATCAAATT
Found at i:22921381 original size:60 final size:59
Alignment explanation
Indices: 22921317--22921449 Score: 140
Period size: 60 Copynumber: 2.2 Consensus size: 59
22921307 CCATCAGATA
* * *
22921317 ATGAAAAGGGATGGTGACGACCATCGAACTATGAAAAGGGATAACTTCAACTATCAAATT
1 ATGAAAAGGGATGCT-ACGACCATCGAACAATGAAAAGGGATAACTTCAACTATCAAATC
* * * ** ***
22921377 ATGAAAATGGATAGCTTCGGCTGTCGAACAATGAAAAGGGATAACTTCGGTTATCAAATC
1 ATGAAAAGGGAT-GCTACGACCATCGAACAATGAAAAGGGATAACTTCAACTATCAAATC
*
22921437 ACGAAAAGGGATG
1 ATGAAAAGGGATG
22921450 TGTCAACCAT
Statistics
Matches: 59, Mismatches: 13, Indels: 3
0.79 0.17 0.04
Matches are distributed among these distances:
59 1 0.02
60 56 0.95
61 2 0.03
ACGTcount: A:0.40, C:0.14, G:0.24, T:0.22
Consensus pattern (59 bp):
ATGAAAAGGGATGCTACGACCATCGAACAATGAAAAGGGATAACTTCAACTATCAAATC
Found at i:22921418 original size:90 final size:87
Alignment explanation
Indices: 22921172--22921388 Score: 274
Period size: 90 Copynumber: 2.5 Consensus size: 87
22921162 TATCGAATAC
* * * **
22921172 GAAAAGGGATACCTTCAGCTATC-GATTATGAAAAGGGATGCTGACAACCATCAACAATGAAAAG
1 GAAAAGGGATAACTTCAACTATCAAATTATGAAAAGGGATGCT-ATGACCATCAACAATGAAAAG
22921236 GGATGGTGACGACCATCGACAAT
65 GGATGGTGACGACCATCGACAAT
* *** * *
22921259 GAAAAGGGATAGCTTTGGCTATCAAATTATGAAAAGGGATGGTGATGACCATCAGATAATGAAAA
1 GAAAAGGGATAACTTCAACTATCAAATTATGAAAAGGGATGCT-ATGACCATCA-ACAATGAAAA
*
22921324 GGGATGGTGACGACCATCGAACTAT
64 GGGATGGTGACGACCATCG-ACAAT
*
22921349 GAAAAGGGATAACTTCAACTATCAAATTATGAAAATGGAT
1 GAAAAGGGATAACTTCAACTATCAAATTATGAAAAGGGAT
22921389 AGCTTCGGCT
Statistics
Matches: 113, Mismatches: 14, Indels: 3
0.87 0.11 0.02
Matches are distributed among these distances:
87 20 0.18
88 26 0.23
89 28 0.25
90 39 0.35
ACGTcount: A:0.40, C:0.14, G:0.24, T:0.21
Consensus pattern (87 bp):
GAAAAGGGATAACTTCAACTATCAAATTATGAAAAGGGATGCTATGACCATCAACAATGAAAAGG
GATGGTGACGACCATCGACAAT
Found at i:22929017 original size:30 final size:30
Alignment explanation
Indices: 22928866--22929222 Score: 189
Period size: 30 Copynumber: 12.0 Consensus size: 30
22928856 TCATCGACAA
* * *
22928866 ATGAAAAGGGATAGTTTGGGCTATCGAA-T
1 ATGAAAAGGGATAGCTTCGACTATCGAATT
* * *
22928895 ACGAAAAAGGATAG-TTCCGACTATTG-ATT
1 ATGAAAAGGGATAGCTT-CGACTATCGAATT
* * **
22928924 ATGAAAAGGGAT-GGTGAT-GACCATC-AACA
1 ATGAAAAGGGATAGCT--TCGACTATCGAATT
* * * * *
22928953 ATGAAAAAGGAT-GGTAACGACCATCG-ACT
1 ATGAAAAGGGATAGCT-TCGACTATCGAATT
* *
22928982 ATGAAAAGGGATAGCTTCGGCTATCCAATT
1 ATGAAAAGGGATAGCTTCGACTATCGAATT
* * *
22929012 ATGAAAAGGGAT-GGTGAT-GACCATCGAATA
1 ATGAAAAGGGATAGCT--TCGACTATCGAATT
* * * *
22929042 ATGAAAAGGGAT-GGTGACGACCATCGAACT
1 ATGAAAAGGGATAGCT-TCGACTATCGAATT
* *
22929072 ATGAAAAGGAATAGCTTCGACTATCAAATT
1 ATGAAAAGGGATAGCTTCGACTATCGAATT
* * * * *
22929102 ATGAAAAGGGAT-GGTGACGACCATTGAACT
1 ATGAAAAGGGATAGCT-TCGACTATCGAATT
* *
22929132 ATGAAAAGGGATAGCTTCGGCTATCAAATT
1 ATGAAAAGGGATAGCTTCGACTATCGAATT
* * * * *
22929162 ATGAAAAGGGATGGCTTTGGCTGTCGAACT
1 ATGAAAAGGGATAGCTTCGACTATCGAATT
* **
22929192 ATGAAAAGGGATAACTTCGGTTATCGAATT
1 ATGAAAAGGGATAGCTTCGACTATCGAATT
22929222 A
1 A
22929223 CAAAAAAGGA
Statistics
Matches: 251, Mismatches: 61, Indels: 31
0.73 0.18 0.09
Matches are distributed among these distances:
28 5 0.02
29 80 0.32
30 160 0.64
31 6 0.02
ACGTcount: A:0.37, C:0.13, G:0.26, T:0.24
Consensus pattern (30 bp):
ATGAAAAGGGATAGCTTCGACTATCGAATT
Found at i:22929077 original size:60 final size:58
Alignment explanation
Indices: 22928923--22929143 Score: 214
Period size: 60 Copynumber: 3.7 Consensus size: 58
22928913 GACTATTGAT
* * * * *
22928923 TATGAAAAGGGATGGTGATGACCATC-AACAATGAAAAAGGATGGTAACGACCATCGAC
1 TATGAAAAGGGATGGTGACGACCATCGAACTATGAAAAGGGATGGT-ATGACCATCGAA
* * * * * *
22928981 TATGAAAAGGGATAGCT-TCGGCTATCCAATTATGAAAAGGGATGGTGATGACCATCGAA
1 TATGAAAAGGGAT-GGTGACGACCATCGAACTATGAAAAGGGATGGT-ATGACCATCGAA
* * * *
22929040 TAATGAAAAGGGATGGTGACGACCATCGAACTATGAAAAGGAATAGCT-TCGACTATCAAA
1 T-ATGAAAAGGGATGGTGACGACCATCGAACTATGAAAAGGGAT-GGTAT-GACCATCGAA
*
22929100 TTATGAAAAGGGATGGTGACGACCATTGAACTATGAAAAGGGAT
1 -TATGAAAAGGGATGGTGACGACCATCGAACTATGAAAAGGGAT
22929144 AGCTTCGGCT
Statistics
Matches: 133, Mismatches: 23, Indels: 12
0.79 0.14 0.07
Matches are distributed among these distances:
58 18 0.14
59 32 0.24
60 80 0.60
61 3 0.02
ACGTcount: A:0.39, C:0.14, G:0.26, T:0.21
Consensus pattern (58 bp):
TATGAAAAGGGATGGTGACGACCATCGAACTATGAAAAGGGATGGTATGACCATCGAA
Found at i:22929105 original size:90 final size:89
Alignment explanation
Indices: 22928921--22929143 Score: 342
Period size: 90 Copynumber: 2.5 Consensus size: 89
22928911 CCGACTATTG
* *
22928921 ATTATGAAAAGGGATGGTGATGACCATC-AACAATGAAAAAGGATGGTAACGACCATCGACTATG
1 ATTATGAAAAGGGATGGTGATGACCATCGAATAATGAAAAGGGATGGTAACGACCATCGACTATG
* * *
22928985 AAAAGGGATAGCTTCGGCTATCCA
66 AAAAGGAATAGCTTCGACTATCAA
*
22929009 ATTATGAAAAGGGATGGTGATGACCATCGAATAATGAAAAGGGATGGTGACGACCATCGAACTAT
1 ATTATGAAAAGGGATGGTGATGACCATCGAATAATGAAAAGGGATGGTAACGACCATCG-ACTAT
22929074 GAAAAGGAATAGCTTCGACTATCAA
65 GAAAAGGAATAGCTTCGACTATCAA
* *
22929099 ATTATGAAAAGGGATGGTGACGACCATTGAACT-ATGAAAAGGGAT
1 ATTATGAAAAGGGATGGTGATGACCATCGAA-TAATGAAAAGGGAT
22929144 AGCTTCGGCT
Statistics
Matches: 124, Mismatches: 8, Indels: 4
0.91 0.06 0.03
Matches are distributed among these distances:
88 28 0.23
89 27 0.22
90 68 0.55
91 1 0.01
ACGTcount: A:0.39, C:0.13, G:0.26, T:0.21
Consensus pattern (89 bp):
ATTATGAAAAGGGATGGTGATGACCATCGAATAATGAAAAGGGATGGTAACGACCATCGACTATG
AAAAGGAATAGCTTCGACTATCAA
Found at i:22929170 original size:90 final size:90
Alignment explanation
Indices: 22928888--22929143 Score: 335
Period size: 90 Copynumber: 2.9 Consensus size: 90
22928878 AGTTTGGGCT
* * ** *
22928888 ATCGAA-TACGAAAAAGGATAG-TTCCGACTAT-TGATTATGAAAAGGGATGGTGATGACCA-TC
1 ATCGAACTATGAAAAGGGATAGCTT-CGACTATCAAATTATGAAAAGGGATGGTGATGACCATTG
* *
22928949 AACAATGAAAAAGGATGGTAACGACC
65 AACTATGAAAAGGGATGGTAACGACC
* * *
22928975 ATCG-ACTATGAAAAGGGATAGCTTCGGCTATCCAATTATGAAAAGGGATGGTGATGACCATCGA
1 ATCGAACTATGAAAAGGGATAGCTTCGACTATCAAATTATGAAAAGGGATGGTGATGACCATTGA
*
22929039 A-TAATGAAAAGGGATGGTGACGACC
66 ACT-ATGAAAAGGGATGGTAACGACC
* *
22929064 ATCGAACTATGAAAAGGAATAGCTTCGACTATCAAATTATGAAAAGGGATGGTGACGACCATTGA
1 ATCGAACTATGAAAAGGGATAGCTTCGACTATCAAATTATGAAAAGGGATGGTGATGACCATTGA
22929129 ACTATGAAAAGGGAT
66 ACTATGAAAAGGGAT
22929144 AGCTTCGGCT
Statistics
Matches: 147, Mismatches: 15, Indels: 11
0.85 0.09 0.06
Matches are distributed among these distances:
86 1 0.01
87 23 0.16
88 28 0.19
89 26 0.18
90 68 0.46
91 1 0.01
ACGTcount: A:0.39, C:0.14, G:0.25, T:0.21
Consensus pattern (90 bp):
ATCGAACTATGAAAAGGGATAGCTTCGACTATCAAATTATGAAAAGGGATGGTGATGACCATTGA
ACTATGAAAAGGGATGGTAACGACC
Found at i:22929191 original size:60 final size:60
Alignment explanation
Indices: 22929042--22929222 Score: 247
Period size: 60 Copynumber: 3.0 Consensus size: 60
22929032 CCATCGAATA
* *
22929042 ATGAAAAGGGATGGTGACGACCATCGAACTATGAAAAGGAATAGCTTCGACTATCAAATT
1 ATGAAAAGGGATGGTGACGACCATCGAACTATGAAAAGGGATAGCTTCGGCTATCAAATT
*
22929102 ATGAAAAGGGATGGTGACGACCATTGAACTATGAAAAGGGATAGCTTCGGCTATCAAATT
1 ATGAAAAGGGATGGTGACGACCATCGAACTATGAAAAGGGATAGCTTCGGCTATCAAATT
** * ** * * *
22929162 ATGAAAAGGGATGGCT-TTGGCTGTCGAACTATGAAAAGGGATAACTTCGGTTATCGAATT
1 ATGAAAAGGGATGG-TGACGACCATCGAACTATGAAAAGGGATAGCTTCGGCTATCAAATT
22929222 A
1 A
22929223 CAAAAAAGGA
Statistics
Matches: 108, Mismatches: 12, Indels: 2
0.89 0.10 0.02
Matches are distributed among these distances:
60 107 0.99
61 1 0.01
ACGTcount: A:0.36, C:0.13, G:0.26, T:0.24
Consensus pattern (60 bp):
ATGAAAAGGGATGGTGACGACCATCGAACTATGAAAAGGGATAGCTTCGGCTATCAAATT
Found at i:22929195 original size:90 final size:90
Alignment explanation
Indices: 22928921--22929203 Score: 322
Period size: 90 Copynumber: 3.2 Consensus size: 90
22928911 CCGACTATTG
* * * * * *
22928921 ATTATGAAAAGGGATGGTGATGACCATC-AACAATGAAAAAGGATGGTAACGACCATC-GACTAT
1 ATTATGAAAAGGGATGGTGACGACCATCGAATAATGAAAAGGGATGCTGACGACCATCAAACTAT
*
22928984 GAAAAGGGATAGCTTCGGCTATCCA
66 GAAAAGGGATAGCTTCGGCTATCAA
* * *
22929009 ATTATGAAAAGGGATGGTGATGACCATCGAATAATGAAAAGGGATGGTGACGACCATCGAACTAT
1 ATTATGAAAAGGGATGGTGACGACCATCGAATAATGAAAAGGGATGCTGACGACCATCAAACTAT
* *
22929074 GAAAAGGAATAGCTTCGACTATCAA
66 GAAAAGGGATAGCTTCGGCTATCAA
* * * * *
22929099 ATTATGAAAAGGGATGGTGACGACCATTGAACT-ATGAAAAGGGATAGCT-TCGGCTATCAAATT
1 ATTATGAAAAGGGATGGTGACGACCATCGAA-TAATGAAAAGGGAT-GCTGACGACCATCAAACT
* * * *
22929162 ATGAAAAGGGATGGCTTTGGCTGTCGA
64 ATGAAAAGGGATAGCTTCGGCTATCAA
*
22929189 ACTATGAAAAGGGAT
1 ATTATGAAAAGGGAT
22929204 AACTTCGGTT
Statistics
Matches: 169, Mismatches: 22, Indels: 6
0.86 0.11 0.03
Matches are distributed among these distances:
88 28 0.17
89 26 0.15
90 112 0.66
91 3 0.02
ACGTcount: A:0.38, C:0.13, G:0.27, T:0.22
Consensus pattern (90 bp):
ATTATGAAAAGGGATGGTGACGACCATCGAATAATGAAAAGGGATGCTGACGACCATCAAACTAT
GAAAAGGGATAGCTTCGGCTATCAA
Found at i:22931323 original size:29 final size:29
Alignment explanation
Indices: 22931279--22931345 Score: 98
Period size: 29 Copynumber: 2.3 Consensus size: 29
22931269 TTGAAAAATG
*
22931279 AAAAGGGATAGTTTCGGCTATCGAATACA
1 AAAAGGGATAGCTTCGGCTATCGAATACA
* **
22931308 AAAAGGGATAGCTTCGGCTATCGATTATG
1 AAAAGGGATAGCTTCGGCTATCGAATACA
22931337 AAAAGGGAT
1 AAAAGGGAT
22931346 GGTGACGACA
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
29 34 1.00
ACGTcount: A:0.37, C:0.12, G:0.27, T:0.24
Consensus pattern (29 bp):
AAAAGGGATAGCTTCGGCTATCGAATACA
Found at i:22931370 original size:29 final size:29
Alignment explanation
Indices: 22931334--22931495 Score: 103
Period size: 30 Copynumber: 5.5 Consensus size: 29
22931324 GCTATCGATT
*
22931334 ATGAAAAGGGATGGTGACGACAATCAACA
1 ATGAAAAGGGATAGTGACGACAATCAACA
* * * *
22931363 ATGGAAAGGGATAGTGACGACCATCGACT
1 ATGAAAAGGGATAGTGACGACAATCAACA
* * * *
22931392 ATGAAAAGGGATAACT-TCGGCTATCAA-A
1 ATGAAAAGGGAT-AGTGACGACAATCAACA
* * * * *
22931420 TTATTAAAATGGATGGTGACGACCATCGAATA
1 --ATGAAAAGGGATAGTGACGACAATC-AACA
* * * *
22931452 ATGAAAAGGGATAGTGACTGTCATTGAACT
1 ATGAAAAGGGATAGTGAC-GACAATCAACA
22931482 ATGAAAAGGGATAG
1 ATGAAAAGGGATAG
22931496 CTTCGACTAT
Statistics
Matches: 98, Mismatches: 28, Indels: 13
0.71 0.20 0.09
Matches are distributed among these distances:
29 43 0.44
30 49 0.50
31 5 0.05
32 1 0.01
ACGTcount: A:0.40, C:0.12, G:0.27, T:0.21
Consensus pattern (29 bp):
ATGAAAAGGGATAGTGACGACAATCAACA
Found at i:22931577 original size:91 final size:89
Alignment explanation
Indices: 22931308--22931590 Score: 356
Period size: 91 Copynumber: 3.2 Consensus size: 89
22931298 ATCGAATACA
* * * *
22931308 AAAAGGGATAGCTTCGGCTATC-GATTATGAAAAGGGATGGTGACGACAATC-AACAATGGAAAG
1 AAAAGGGATAGCTTCGGCTATCAAATTATTAAAATGGATGGTGACGACCATCGAACAATGGAAAG
*
22931371 GGATAGTGACGACCATCGACTATG
66 GGATAGTGACGACCATCAACTATG
* * *
22931395 AAAAGGGATAACTTCGGCTATCAAATTATTAAAATGGATGGTGACGACCATCGAATAATGAAAAG
1 AAAAGGGATAGCTTCGGCTATCAAATTATTAAAATGGATGGTGACGACCATCGAACAATGGAAAG
* *
22931460 GGATAGTGACTG-TCATTGAACTATG
66 GGATAGTGAC-GACCA-TCAACTATG
* * * *
22931485 AAAAGGGATAGCTTCGACTATCAAATTATTAAAAATGGATGGGGATGACCATCGAACAATGGAGA
1 AAAAGGGATAGCTTCGGCTATCAAATTATT-AAAATGGATGGTGACGACCATCGAACAATGGAAA
* *
22931550 GGGATGGTGACGACCATCAAATTATG
65 GGGATAGTGACGACCATC-AACTATG
*
22931576 AAAAAGGATAGCTTC
1 AAAAGGGATAGCTTC
22931591 AGCTGTCGAA
Statistics
Matches: 167, Mismatches: 22, Indels: 10
0.84 0.11 0.05
Matches are distributed among these distances:
87 21 0.13
88 25 0.15
89 22 0.13
90 38 0.23
91 61 0.37
ACGTcount: A:0.39, C:0.13, G:0.26, T:0.22
Consensus pattern (89 bp):
AAAAGGGATAGCTTCGGCTATCAAATTATTAAAATGGATGGTGACGACCATCGAACAATGGAAAG
GGATAGTGACGACCATCAACTATG
Found at i:22938926 original size:40 final size:40
Alignment explanation
Indices: 22938858--22938968 Score: 134
Period size: 40 Copynumber: 2.8 Consensus size: 40
22938848 AGATTAGGGC
* * *
22938858 ATACACAACCGACTTACATATA-TCAGGGCATATACACAAT
1 ATACACAAACGACTAACACATACT-AGGGCATATACACAAT
*
22938898 ATACACAATCGACTAACACATACTAGGGCATATACACAAT
1 ATACACAAACGACTAACACATACTAGGGCATATACACAAT
* * * *
22938938 ATACATAAAAGGCTAACACATACTAAGGCAT
1 ATACACAAACGACTAACACATACTAGGGCAT
22938969 TTAAGCATTC
Statistics
Matches: 62, Mismatches: 8, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
40 61 0.98
41 1 0.02
ACGTcount: A:0.45, C:0.23, G:0.11, T:0.21
Consensus pattern (40 bp):
ATACACAAACGACTAACACATACTAGGGCATATACACAAT
Found at i:22940615 original size:32 final size:32
Alignment explanation
Indices: 22940579--22940643 Score: 87
Period size: 32 Copynumber: 2.0 Consensus size: 32
22940569 TCTTTAAAAG
*
22940579 AAACATAA-TTATTCAATTAATATCTCTTAAAT
1 AAACATAACTT-TTCAAGTAATATCTCTTAAAT
* *
22940611 AAACATAACTTTTCAAGTAATATTTCTTGAAT
1 AAACATAACTTTTCAAGTAATATCTCTTAAAT
22940643 A
1 A
22940644 TTTATAATTC
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
32 27 0.93
33 2 0.07
ACGTcount: A:0.45, C:0.12, G:0.03, T:0.40
Consensus pattern (32 bp):
AAACATAACTTTTCAAGTAATATCTCTTAAAT
Found at i:22941419 original size:39 final size:39
Alignment explanation
Indices: 22941344--22941420 Score: 118
Period size: 39 Copynumber: 2.0 Consensus size: 39
22941334 TGACTCAAAT
* ** *
22941344 AATATAGGTTTGTACCTCATCCCTAAATTTTTAATTTTC
1 AATATAGGTTTGTACCTCATCCCCAAATGGTGAATTTTC
22941383 AATATAGGTTTGTACCTCATCCCCAAATGGTGAATTTT
1 AATATAGGTTTGTACCTCATCCCCAAATGGTGAATTTT
22941421 GGATCCCAAA
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
39 34 1.00
ACGTcount: A:0.29, C:0.18, G:0.12, T:0.42
Consensus pattern (39 bp):
AATATAGGTTTGTACCTCATCCCCAAATGGTGAATTTTC
Found at i:22942942 original size:23 final size:23
Alignment explanation
Indices: 22942909--22942986 Score: 129
Period size: 23 Copynumber: 3.4 Consensus size: 23
22942899 TTTAAGCGGA
*
22942909 TGTGTTTGGAGGGTATATTTGGT
1 TGTGTTTGGAGGCTATATTTGGT
*
22942932 TGTGTTGGGAGGCTATATTTGGT
1 TGTGTTTGGAGGCTATATTTGGT
*
22942955 TGTGTTTGGAGGCTATGTTTGGT
1 TGTGTTTGGAGGCTATATTTGGT
22942978 TGTGTTTGG
1 TGTGTTTGG
22942987 TGGATGATAG
Statistics
Matches: 51, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
23 51 1.00
ACGTcount: A:0.10, C:0.03, G:0.40, T:0.47
Consensus pattern (23 bp):
TGTGTTTGGAGGCTATATTTGGT
Found at i:22944872 original size:20 final size:20
Alignment explanation
Indices: 22944835--22944873 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
22944825 TGGGCGGTTT
*
22944835 TAGGAGGAAAGTTTGGGATA
1 TAGGAGGAAAGTTAGGGATA
22944855 TAGGA-GAAAGTTAAGGGAT
1 TAGGAGGAAAGTT-AGGGAT
22944874 TGGGGGGAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 7 0.41
20 10 0.59
ACGTcount: A:0.38, C:0.00, G:0.38, T:0.23
Consensus pattern (20 bp):
TAGGAGGAAAGTTAGGGATA
Found at i:22955532 original size:18 final size:18
Alignment explanation
Indices: 22955480--22955532 Score: 56
Period size: 18 Copynumber: 3.0 Consensus size: 18
22955470 AATCTGGCAG
22955480 ACAGA-TCAGTTACAGAT
1 ACAGATTCAGTTACAGAT
* **
22955497 ACAAATAT-AGTTTTAGAT
1 ACAGAT-TCAGTTACAGAT
22955515 ACAGATTCAGTTACAGAT
1 ACAGATTCAGTTACAGAT
22955533 GCAAATACAA
Statistics
Matches: 27, Mismatches: 6, Indels: 5
0.71 0.16 0.13
Matches are distributed among these distances:
17 5 0.19
18 21 0.78
19 1 0.04
ACGTcount: A:0.42, C:0.13, G:0.15, T:0.30
Consensus pattern (18 bp):
ACAGATTCAGTTACAGAT
Found at i:22955550 original size:36 final size:35
Alignment explanation
Indices: 22955480--22955553 Score: 94
Period size: 36 Copynumber: 2.1 Consensus size: 35
22955470 AATCTGGCAG
* ** *
22955480 ACAGATCAGTTACAGATACAAATATAGTTTTAGAT
1 ACAGATCAGTTACAGATACAAATACAAATATAGAT
*
22955515 ACAGATTCAGTTACAGATGCAAATACAAATATAGAT
1 ACAGA-TCAGTTACAGATACAAATACAAATATAGAT
22955551 ACA
1 ACA
22955554 AATCCTACCC
Statistics
Matches: 33, Mismatches: 5, Indels: 1
0.85 0.13 0.03
Matches are distributed among these distances:
35 5 0.15
36 28 0.85
ACGTcount: A:0.46, C:0.14, G:0.14, T:0.27
Consensus pattern (35 bp):
ACAGATCAGTTACAGATACAAATACAAATATAGAT
Found at i:22956022 original size:17 final size:17
Alignment explanation
Indices: 22956000--22956032 Score: 66
Period size: 17 Copynumber: 1.9 Consensus size: 17
22955990 CAGAAAATGG
22956000 GTCCACACACCCGTGTT
1 GTCCACACACCCGTGTT
22956017 GTCCACACACCCGTGT
1 GTCCACACACCCGTGT
22956033 GGCCCACACG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.18, C:0.42, G:0.18, T:0.21
Consensus pattern (17 bp):
GTCCACACACCCGTGTT
Found at i:22956039 original size:17 final size:17
Alignment explanation
Indices: 22956002--22956041 Score: 62
Period size: 17 Copynumber: 2.4 Consensus size: 17
22955992 GAAAATGGGT
* *
22956002 CCACACACCCGTGTTGT
1 CCACACACCCGTGTGGC
22956019 CCACACACCCGTGTGGC
1 CCACACACCCGTGTGGC
22956036 CCACAC
1 CCACAC
22956042 GGCCTACCTG
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
17 21 1.00
ACGTcount: A:0.20, C:0.47, G:0.17, T:0.15
Consensus pattern (17 bp):
CCACACACCCGTGTGGC
Found at i:22959271 original size:253 final size:254
Alignment explanation
Indices: 22958822--22959329 Score: 946
Period size: 253 Copynumber: 2.0 Consensus size: 254
22958812 AAAAGTATTT
22958822 TAGGGTTCCTAACAAGAAAAAGACCATAAACGGTGTAGTTTTAATTTTGGGTTTAAGATTTTTTA
1 TAGGGTTCCTAACAAGAAAAAGACCATAAACGGTGTAGTTTTAATTTTGGGTTTAAGATTTTTTA
* *
22958887 TATTAATTATAAAATGACATTAAAAGCATGTGGAAAAAATTGATGGTTAAAAAATCATACCGTTA
66 TATTAATTATAAAATGACATTAAAAGCATGTGGAAAAAAATAATGGTTAAAAAATCATACCGTTA
*
22958952 AGTTAACTGATGAGTCACCAAACTATTAGCATTTTAACAATTTTGGACTAAAAAATTTGACTAGT
131 AGTTAACTGATGAGTCACCAAACTATTAGCATTTTAACAATTTTGGACTAAAAAAATTGACTAGT
22959017 CAAGTGATCAATTTCTAACTTTTTAAAGTCAAGAAACCTAATAAGAAACTTTCTAATAA
196 CAAGTGATCAATTTCTAACTTTTTAAAGTCAAGAAACCTAATAAGAAACTTTCTAATAA
*
22959076 TAGGGTTCCTAACGAGAAAAAGACCATAAACGGTGTAG-TTTAATTTTGGGTTTAAGATTTTTTA
1 TAGGGTTCCTAACAAGAAAAAGACCATAAACGGTGTAGTTTTAATTTTGGGTTTAAGATTTTTTA
*
22959140 TATTAATTATAAAATGACATTAAAAGCATGTGGAAAAAAATAATGGTTAAAAAATCATACTGTTA
66 TATTAATTATAAAATGACATTAAAAGCATGTGGAAAAAAATAATGGTTAAAAAATCATACCGTTA
22959205 AGTTAACTGATGAGTCACCAAACTATTAGCATTTTAACAATTTTGGACTAAAAAAATTGACTAGT
131 AGTTAACTGATGAGTCACCAAACTATTAGCATTTTAACAATTTTGGACTAAAAAAATTGACTAGT
* *
22959270 CAAGTGATCATTTTCTAACTTTTTAAAGTCAAGTAACCTAATAAGAAACTTTCTAATAA
196 CAAGTGATCAATTTCTAACTTTTTAAAGTCAAGAAACCTAATAAGAAACTTTCTAATAA
22959329 T
1 T
22959330 CGGATGATCA
Statistics
Matches: 247, Mismatches: 7, Indels: 1
0.97 0.03 0.00
Matches are distributed among these distances:
253 210 0.85
254 37 0.15
ACGTcount: A:0.41, C:0.11, G:0.14, T:0.34
Consensus pattern (254 bp):
TAGGGTTCCTAACAAGAAAAAGACCATAAACGGTGTAGTTTTAATTTTGGGTTTAAGATTTTTTA
TATTAATTATAAAATGACATTAAAAGCATGTGGAAAAAAATAATGGTTAAAAAATCATACCGTTA
AGTTAACTGATGAGTCACCAAACTATTAGCATTTTAACAATTTTGGACTAAAAAAATTGACTAGT
CAAGTGATCAATTTCTAACTTTTTAAAGTCAAGAAACCTAATAAGAAACTTTCTAATAA
Found at i:22960109 original size:5 final size:5
Alignment explanation
Indices: 22960101--22960137 Score: 65
Period size: 5 Copynumber: 7.4 Consensus size: 5
22960091 GTTTTGTTTC
*
22960101 TTTTA TTTTA TTTTA TTTTA TTTCA TTTTA TTTTA TT
1 TTTTA TTTTA TTTTA TTTTA TTTTA TTTTA TTTTA TT
22960138 CTTTTGAAAA
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
5 30 1.00
ACGTcount: A:0.19, C:0.03, G:0.00, T:0.78
Consensus pattern (5 bp):
TTTTA
Found at i:22973721 original size:2 final size:2
Alignment explanation
Indices: 22973714--22973750 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
22973704 AGTTCATGAT
22973714 TA TA TA TA TA TA TA 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 TA TA T
22973751 TTTATGTTCG
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:22975683 original size:43 final size:43
Alignment explanation
Indices: 22975626--22975809 Score: 201
Period size: 43 Copynumber: 4.3 Consensus size: 43
22975616 TTTTAGAAAT
* * * *
22975626 AAACGCCGCTAAAGACCAAGACATTTAGTGGCGCTTTTACAAC
1 AAACACCGCTAAAGACCAAGACCTTTAGCGGCGCTTTTCCAAC
* *
22975669 AAACACCGCTAAAGACCAAGACCTTTAACGACGCTTTTCCAAC
1 AAACACCGCTAAAGACCAAGACCTTTAGCGGCGCTTTTCCAAC
* * *
22975712 AAACACCGCTAAAGACCATGACCTTTAGCAGCGCTTTTCCCAC
1 AAACACCGCTAAAGACCAAGACCTTTAGCGGCGCTTTTCCAAC
* * ** * *
22975755 AAACGCCACTAAAGAATAA-ACCTTTACCGGCGCTTCTCGCAA-
1 AAACACCGCTAAAGACCAAGACCTTTAGCGGCGCTTTTC-CAAC
*
22975797 AAACGCCGCTAAA
1 AAACACCGCTAAA
22975810 AACATAACCT
Statistics
Matches: 119, Mismatches: 21, Indels: 3
0.83 0.15 0.02
Matches are distributed among these distances:
42 28 0.24
43 91 0.76
ACGTcount: A:0.35, C:0.31, G:0.15, T:0.19
Consensus pattern (43 bp):
AAACACCGCTAAAGACCAAGACCTTTAGCGGCGCTTTTCCAAC
Found at i:22975801 original size:42 final size:42
Alignment explanation
Indices: 22975732--22975822 Score: 103
Period size: 42 Copynumber: 2.2 Consensus size: 42
22975722 AAAGACCATG
* * * *
22975732 ACCTTTAGCAGCGCTTTTCCCACAAACGCCACTAAAGA-ATAA
1 ACCTTTACCAGCGCTTCTCCCAAAAACGCCACTAAAAACAT-A
* * *
22975774 ACCTTTACCGGCGCTTCTCGCAAAAACGCCGCTAAAAACATA
1 ACCTTTACCAGCGCTTCTCCCAAAAACGCCACTAAAAACATA
22975816 ACCTTTA
1 ACCTTTA
22975823 AAAAATATAT
Statistics
Matches: 41, Mismatches: 7, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
42 39 0.95
43 2 0.05
ACGTcount: A:0.34, C:0.32, G:0.12, T:0.22
Consensus pattern (42 bp):
ACCTTTACCAGCGCTTCTCCCAAAAACGCCACTAAAAACATA
Found at i:22977829 original size:11 final size:11
Alignment explanation
Indices: 22977813--22977837 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
22977803 TATATTTTAG
22977813 AAAAAAATAAT
1 AAAAAAATAAT
22977824 AAAAAAATAAT
1 AAAAAAATAAT
22977835 AAA
1 AAA
22977838 TAATAAAAGG
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:0.84, C:0.00, G:0.00, T:0.16
Consensus pattern (11 bp):
AAAAAAATAAT
Found at i:22981619 original size:7 final size:7
Alignment explanation
Indices: 22981607--22981682 Score: 55
Period size: 7 Copynumber: 10.7 Consensus size: 7
22981597 ACTAATTAAT
22981607 CTAAACC
1 CTAAACC
22981614 CTAAACC
1 CTAAACC
**
22981621 CTATCCC
1 CTAAACC
22981628 CTAAACC
1 CTAAACC
* *
22981635 ATAAATC
1 CTAAACC
* *
22981642 ATAAAAC
1 CTAAACC
*
22981649 AT-AACC
1 CTAAACC
22981655 CTAAAACC
1 CT-AAACC
22981663 CTAAACCC
1 CTAAA-CC
*
22981671 CTAACCC
1 CTAAACC
22981678 CTAAA
1 CTAAA
22981683 ATTTAAATCT
Statistics
Matches: 55, Mismatches: 11, Indels: 6
0.76 0.15 0.08
Matches are distributed among these distances:
6 4 0.07
7 39 0.71
8 12 0.22
ACGTcount: A:0.45, C:0.38, G:0.00, T:0.17
Consensus pattern (7 bp):
CTAAACC
Found at i:22981826 original size:16 final size:17
Alignment explanation
Indices: 22981790--22981831 Score: 68
Period size: 16 Copynumber: 2.5 Consensus size: 17
22981780 CTCTATAATC
22981790 ATTATTTTAATATATTAA
1 ATTA-TTTAATATATTAA
22981808 ATTATTTAATATA-TAA
1 ATTATTTAATATATTAA
22981824 ATTATTTA
1 ATTATTTA
22981832 TAAATAATTT
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
16 11 0.46
17 9 0.38
18 4 0.17
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (17 bp):
ATTATTTAATATATTAA
Found at i:22982033 original size:7 final size:7
Alignment explanation
Indices: 22982018--22982111 Score: 73
Period size: 7 Copynumber: 13.4 Consensus size: 7
22982008 CTTAATCTAT
*
22982018 AACCTTA
1 AACCATA
22982025 AACCATA
1 AACCATA
22982032 AACCATA
1 AACCATA
* *
22982039 ACCCCTA
1 AACCATA
22982046 AATCC-TA
1 AA-CCATA
*
22982053 AACCTTA
1 AACCATA
22982060 AACCATA
1 AACCATA
**
22982067 AACTTTA
1 AACCATA
22982074 AACCATA
1 AACCATA
* *
22982081 ACCCCTA
1 AACCATA
*
22982088 ACCCATA
1 AACCATA
*
22982095 ATCCATA
1 AACCATA
*
22982102 AACCTTA
1 AACCATA
22982109 AAC
1 AAC
22982112 TCTATGCCAT
Statistics
Matches: 70, Mismatches: 15, Indels: 4
0.79 0.17 0.04
Matches are distributed among these distances:
6 2 0.03
7 66 0.94
8 2 0.03
ACGTcount: A:0.46, C:0.33, G:0.00, T:0.21
Consensus pattern (7 bp):
AACCATA
Found at i:22982047 original size:14 final size:14
Alignment explanation
Indices: 22982018--22982146 Score: 89
Period size: 14 Copynumber: 9.2 Consensus size: 14
22982008 CTTAATCTAT
* *
22982018 AACCTTAAACCATA
1 AACCATAAACCCTA
*
22982032 AACCATAACCCCTA
1 AACCATAAACCCTA
*
22982046 AATCC-TAAACCTTA
1 AA-CCATAAACCCTA
**
22982060 AACCATAAACTTTA
1 AACCATAAACCCTA
*
22982074 AACCATAACCCCTA
1 AACCATAAACCCTA
* * *
22982088 ACCCATAATCCATA
1 AACCATAAACCCTA
* *
22982102 AACCTTAAACTCTA
1 AACCATAAACCCTA
** *
22982116 TGCCATATACCCTA
1 AACCATAAACCCTA
* *
22982130 AACCAAAAACCTTA
1 AACCATAAACCCTA
22982144 AAC
1 AAC
22982147 TATAGAGATA
Statistics
Matches: 86, Mismatches: 27, Indels: 4
0.74 0.23 0.03
Matches are distributed among these distances:
13 2 0.02
14 82 0.95
15 2 0.02
ACGTcount: A:0.45, C:0.33, G:0.01, T:0.22
Consensus pattern (14 bp):
AACCATAAACCCTA
Found at i:22982054 original size:21 final size:21
Alignment explanation
Indices: 22981938--22982132 Score: 73
Period size: 21 Copynumber: 9.3 Consensus size: 21
22981928 AATAATTAAT
* *
22981938 CTAAACCCTAAATCATAAACCC
1 CTAAACTCTAAACCAT-AACCC
* *
22981960 CT-AACTCTTAACCCTCAACCC
1 CTAAACTCTAAACCAT-AACCC
* * * *
22981981 CTTACCCCTAAACCTTAAACCC
1 CTAAACTCTAAACCAT-AACCC
* *
22982003 C--AACTCTTAATCTATAA-CC
1 CTAAACTC-TAAACCATAACCC
*
22982022 TTAAAC-CATAAACCATAACCC
1 CTAAACTC-TAAACCATAACCC
* *
22982043 CTAAA-TCCTAAACCTTAAACC
1 CTAAACT-CTAAACCATAACCC
* *
22982064 ATAAACTTTAAACCATAACCC
1 CTAAACTCTAAACCATAACCC
* * *
22982085 CT-AACCCATAATCCATAAACC
1 CTAAACTC-TAAACCATAACCC
* **
22982106 TTAAACTCTATGCCATATA-CC
1 CTAAACTCTAAACCATA-ACCC
22982127 CTAAAC
1 CTAAAC
22982133 CAAAAACCTT
Statistics
Matches: 126, Mismatches: 36, Indels: 23
0.68 0.19 0.12
Matches are distributed among these distances:
19 2 0.02
20 17 0.13
21 83 0.66
22 24 0.19
ACGTcount: A:0.40, C:0.36, G:0.01, T:0.24
Consensus pattern (21 bp):
CTAAACTCTAAACCATAACCC
Found at i:22982088 original size:35 final size:35
Alignment explanation
Indices: 22982018--22982146 Score: 107
Period size: 35 Copynumber: 3.7 Consensus size: 35
22982008 CTTAATCTAT
* * * *
22982018 AACCTTAAACCATAAACCATAACCCCTAAATCCTA
1 AACCTTAAACCATAAACCTTAAACCATAAACCCTA
* *
22982053 AACCTTAAACCATAAACTTTAAACCATAACCCCTA
1 AACCTTAAACCATAAACCTTAAACCATAAACCCTA
* * * ** *
22982088 ACCCATAATCCATAAACCTTAAACTC-TATGCCATA
1 AACCTTAAACCATAAACCTTAAAC-CATAAACCCTA
* * *
22982123 TACCCTAAACCAAAAACCTTAAAC
1 AACCTTAAACCATAAACCTTAAAC
22982147 TATAGAGATA
Statistics
Matches: 75, Mismatches: 18, Indels: 2
0.79 0.19 0.02
Matches are distributed among these distances:
35 74 0.99
36 1 0.01
ACGTcount: A:0.45, C:0.33, G:0.01, T:0.22
Consensus pattern (35 bp):
AACCTTAAACCATAAACCTTAAACCATAAACCCTA
Found at i:22982104 original size:42 final size:42
Alignment explanation
Indices: 22982030--22982112 Score: 114
Period size: 42 Copynumber: 2.0 Consensus size: 42
22982020 CCTTAAACCA
* *
22982030 TAAACCATAACCCCTAAATCCTAAACCTTAAACCATAAACTT
1 TAAACCATAACCCCTAAACCCTAAACCATAAACCATAAACTT
* *
22982072 TAAACCATAACCCCT-AACCCATAATCCATAAACCTTAAACT
1 TAAACCATAACCCCTAAACCC-TAAACCATAAACCATAAACT
22982113 CTATGCCATA
Statistics
Matches: 36, Mismatches: 4, Indels: 2
0.86 0.10 0.05
Matches are distributed among these distances:
41 4 0.11
42 32 0.89
ACGTcount: A:0.45, C:0.33, G:0.00, T:0.23
Consensus pattern (42 bp):
TAAACCATAACCCCTAAACCCTAAACCATAAACCATAAACTT
Found at i:22982122 original size:42 final size:42
Alignment explanation
Indices: 22982030--22982133 Score: 113
Period size: 42 Copynumber: 2.5 Consensus size: 42
22982020 CCTTAAACCA
* * *
22982030 TAAACCATAACCCCTAAATCCTAAACCTTAAACCATAAACTT
1 TAAACCATAACCCCTAAACCCTAAACCATAAACCATAAACTC
* *
22982072 TAAACCATAACCCCT-AACCCATAATCCATAAACCTTAAACTC
1 TAAACCATAACCCCTAAACCC-TAAACCATAAACCATAAACTC
**
22982114 TATGCCATATA-CCCTAAACC
1 TAAACCATA-ACCCCTAAACC
22982134 AAAAACCTTA
Statistics
Matches: 52, Mismatches: 7, Indels: 5
0.81 0.11 0.08
Matches are distributed among these distances:
41 4 0.08
42 43 0.83
43 5 0.10
ACGTcount: A:0.42, C:0.34, G:0.01, T:0.23
Consensus pattern (42 bp):
TAAACCATAACCCCTAAACCCTAAACCATAAACCATAAACTC
Found at i:22982513 original size:41 final size:41
Alignment explanation
Indices: 22982453--22982570 Score: 173
Period size: 42 Copynumber: 2.9 Consensus size: 41
22982443 AAATGTTTTT
*
22982453 GCAGCGCTTTTCCAAAAACGCCGCTAAAGCCCTGAGCATTA
1 GCAGCGCTTCTCCAAAAACGCCGCTAAAGCCCTGAGCATTA
* * *
22982494 GCGGCGCTTCTCCAAAAACGCCGCTAAATCCCTTGAGTATTA
1 GCAGCGCTTCTCCAAAAACGCCGCTAAAGCCC-TGAGCATTA
* *
22982536 GCAGCGCTTCTCCAAAAACACCTCTAAAGCCCTGA
1 GCAGCGCTTCTCCAAAAACGCCGCTAAAGCCCTGA
22982571 AAGGTCAAAA
Statistics
Matches: 68, Mismatches: 8, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
41 32 0.47
42 36 0.53
ACGTcount: A:0.29, C:0.33, G:0.18, T:0.20
Consensus pattern (41 bp):
GCAGCGCTTCTCCAAAAACGCCGCTAAAGCCCTGAGCATTA
Found at i:22986130 original size:3 final size:3
Alignment explanation
Indices: 22986122--22986182 Score: 52
Period size: 3 Copynumber: 19.3 Consensus size: 3
22986112 ATATATAGGT
* * *
22986122 ATA ATA ATA TTA ATA TTTA AT- ATA ATA ATAA ATA ATA CTA ATA ATA
1 ATA ATA ATA ATA ATA -ATA ATA ATA ATA AT-A ATA ATA ATA ATA ATA
22986168 ATA CAGTA ATA ATA A
1 ATA -A-TA ATA ATA A
22986183 CAATTTAACA
Statistics
Matches: 47, Mismatches: 6, Indels: 10
0.75 0.10 0.16
Matches are distributed among these distances:
2 2 0.04
3 36 0.77
4 7 0.15
5 2 0.04
ACGTcount: A:0.59, C:0.03, G:0.02, T:0.36
Consensus pattern (3 bp):
ATA
Found at i:22986165 original size:16 final size:15
Alignment explanation
Indices: 22986139--22986168 Score: 51
Period size: 16 Copynumber: 1.9 Consensus size: 15
22986129 TATTAATATT
22986139 TAATATAATAATAAA
1 TAATATAATAATAAA
22986154 TAATACTAATAATAA
1 TAATA-TAATAATAA
22986169 TACAGTAATA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 5 0.36
16 9 0.64
ACGTcount: A:0.63, C:0.03, G:0.00, T:0.33
Consensus pattern (15 bp):
TAATATAATAATAAA
Found at i:22988111 original size:88 final size:87
Alignment explanation
Indices: 22987998--22988297 Score: 404
Period size: 88 Copynumber: 3.4 Consensus size: 87
22987988 AAGACTGATG
* * * *
22987998 TCTTCGATCTGCTTCGCTGCCAGTACAAGAAGGCAAGATCTG-TCATTTTCGACCTACTCCACTG
1 TCTTCGATCTGCTTCTCTGTCAGTACAGGAAGGCAAGATCTGCT-ATTTTC-ACCTACTCCACTA
**
22988062 CTGCCCAGTAAGACAAGGCTGGTA
64 CTGCCCAGGGAGACAAGGCTGGTA
* * * * *
22988086 TCTTCGATCTGCTTCTCTGTCAGTACAGGAAGGCAAAATCTACTATCTTCAGCCTATTCTACTAC
1 TCTTCGATCTGCTTCTCTGTCAGTACAGGAAGGCAAGATCTGCTATTTTCA-CCTACTCCACTAC
*
22988151 TACCCAGGGAGACAAGGCTGGTA
65 TGCCCAGGGAGACAAGGCTGGTA
* * * * *
22988174 TCTTCGATATGCTTCTCCGTCAGTACAGGAAGACAAGATTTGCTATTTTCAACCTGCTCCACTAC
1 TCTTCGATCTGCTTCTCTGTCAGTACAGGAAGGCAAGATCTGCTATTTTC-ACCTACTCCACTAC
22988239 TGCCCAGGGAGACAAGGCTGGTA
65 TGCCCAGGGAGACAAGGCTGGTA
22988262 TCTTCGATCTGCTTCTCTGTCAGTACAGGAAGGCAA
1 TCTTCGATCTGCTTCTCTGTCAGTACAGGAAGGCAA
22988298 TACCTACTAT
Statistics
Matches: 183, Mismatches: 26, Indels: 6
0.85 0.12 0.03
Matches are distributed among these distances:
87 1 0.01
88 180 0.98
89 2 0.01
ACGTcount: A:0.25, C:0.27, G:0.21, T:0.28
Consensus pattern (87 bp):
TCTTCGATCTGCTTCTCTGTCAGTACAGGAAGGCAAGATCTGCTATTTTCACCTACTCCACTACT
GCCCAGGGAGACAAGGCTGGTA
Found at i:22988210 original size:44 final size:44
Alignment explanation
Indices: 22988071--22988293 Score: 107
Period size: 44 Copynumber: 5.1 Consensus size: 44
22988061 GCTGCCCAGT
* *
22988071 AAGACAAGGCTGGTATCTTCGATCTGCTTCTCTGTCAGTACAGG
1 AAGACAAGGCTGGTATCTTCGATATGCTTCTCCGTCAGTACAGG
* ** ** * * * * **
22988115 AAGGCAAAATCTACTATCTTCAGCCTATTCTACTAC-T-A-CCCAGG
1 AAGAC-AAGGCTGGTATCTTC-G-ATATGCTTCTCCGTCAGTACAGG
*
22988159 GAGACAAGGCTGGTATCTTCGATATGCTTCTCCGTCAGTACAGG
1 AAGACAAGGCTGGTATCTTCGATATGCTTCTCCGTCAGTACAGG
** * * * * * * **
22988203 AAGACAAGATTTGCTATTTTC-A-A-CCTGCTCCACTACTGCCCAGG
1 AAGACAAG-GCTGGTATCTTCGATATGCTTCTCC-GT-CAGTACAGG
* * *
22988247 GAGACAAGGCTGGTATCTTCGATCTGCTTCTCTGTCAGTACAGG
1 AAGACAAGGCTGGTATCTTCGATATGCTTCTCCGTCAGTACAGG
22988291 AAG
1 AAG
22988294 GCAATACCTA
Statistics
Matches: 117, Mismatches: 50, Indels: 24
0.61 0.26 0.13
Matches are distributed among these distances:
41 8 0.07
42 8 0.07
43 22 0.19
44 45 0.38
45 21 0.18
46 7 0.06
47 6 0.05
ACGTcount: A:0.26, C:0.25, G:0.22, T:0.28
Consensus pattern (44 bp):
AAGACAAGGCTGGTATCTTCGATATGCTTCTCCGTCAGTACAGG
Found at i:22989477 original size:21 final size:23
Alignment explanation
Indices: 22989420--22989479 Score: 65
Period size: 21 Copynumber: 2.7 Consensus size: 23
22989410 AGACCACCAC
22989420 ATGCCCTATTCTGATCAACATTCT
1 ATGCCCTATTCTGATC-ACATTCT
* *
22989444 AAG--CTACTCTGATCAC-TTCT
1 ATGCCCTATTCTGATCACATTCT
22989464 -TGCCCTATTCTGATCA
1 ATGCCCTATTCTGATCA
22989480 AAATTTGAGC
Statistics
Matches: 30, Mismatches: 4, Indels: 7
0.73 0.10 0.17
Matches are distributed among these distances:
19 1 0.03
20 4 0.13
21 13 0.43
22 10 0.33
24 2 0.07
ACGTcount: A:0.23, C:0.30, G:0.10, T:0.37
Consensus pattern (23 bp):
ATGCCCTATTCTGATCACATTCT
Found at i:22989582 original size:15 final size:15
Alignment explanation
Indices: 22989562--22989605 Score: 56
Period size: 15 Copynumber: 3.0 Consensus size: 15
22989552 CCTTAGCCTC
22989562 TCCATTTTTATTTTT
1 TCCATTTTTATTTTT
22989577 TCCATTTTTCA-TTTT
1 TCCATTTTT-ATTTTT
*
22989592 T-CATTTTCATTTTT
1 TCCATTTTTATTTTT
22989606 ATTTTCATTT
Statistics
Matches: 26, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
13 1 0.04
14 10 0.38
15 14 0.54
16 1 0.04
ACGTcount: A:0.14, C:0.16, G:0.00, T:0.70
Consensus pattern (15 bp):
TCCATTTTTATTTTT
Found at i:22989584 original size:7 final size:6
Alignment explanation
Indices: 22989582--22989616 Score: 52
Period size: 6 Copynumber: 5.7 Consensus size: 6
22989572 TTTTTTCCAT
*
22989582 TTTTCA TTTTTCA TTTTCA TTTTTA TTTTCA TTTT
1 TTTTCA -TTTTCA TTTTCA TTTTCA TTTTCA TTTT
22989617 TTCAAATTTT
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
6 20 0.77
7 6 0.23
ACGTcount: A:0.14, C:0.11, G:0.00, T:0.74
Consensus pattern (6 bp):
TTTTCA
Found at i:22989609 original size:12 final size:13
Alignment explanation
Indices: 22989582--22989617 Score: 65
Period size: 12 Copynumber: 2.8 Consensus size: 13
22989572 TTTTTTCCAT
22989582 TTTTCATTTTTCA
1 TTTTCATTTTTCA
22989595 TTTTCATTTTT-A
1 TTTTCATTTTTCA
22989607 TTTTCATTTTT
1 TTTTCATTTTT
22989618 TCAAATTTTT
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
12 12 0.52
13 11 0.48
ACGTcount: A:0.14, C:0.11, G:0.00, T:0.75
Consensus pattern (13 bp):
TTTTCATTTTTCA
Found at i:22989617 original size:7 final size:7
Alignment explanation
Indices: 22989564--22989617 Score: 62
Period size: 7 Copynumber: 8.0 Consensus size: 7
22989554 TTAGCCTCTC
22989564 CATTTTT
1 CATTTTT
22989571 -ATTTTTT
1 CA-TTTTT
22989578 CCATTTTT
1 -CATTTTT
22989586 CATTTTT
1 CATTTTT
22989593 CA-TTTT
1 CATTTTT
22989599 CATTTTT
1 CATTTTT
22989606 -A-TTTT
1 CATTTTT
22989611 CATTTTT
1 CATTTTT
22989618 TCAAATTTTT
Statistics
Matches: 41, Mismatches: 0, Indels: 12
0.77 0.00 0.23
Matches are distributed among these distances:
5 4 0.10
6 9 0.22
7 22 0.54
8 5 0.12
9 1 0.02
ACGTcount: A:0.15, C:0.13, G:0.00, T:0.72
Consensus pattern (7 bp):
CATTTTT
Found at i:22990136 original size:10 final size:10
Alignment explanation
Indices: 22990121--22990193 Score: 57
Period size: 10 Copynumber: 7.4 Consensus size: 10
22990111 CGGTAGAGGT
22990121 TTTTTGTTTC
1 TTTTTGTTTC
*
22990131 TTTTTGTTTT
1 TTTTTGTTTC
*
22990141 TGTTTTTTATTC
1 T-TTTTGT-TTC
22990153 TTTTTG-TTC
1 TTTTTGTTTC
22990162 TTTTT-TCTT-
1 TTTTTGT-TTC
22990171 TTTTTG-TTC
1 TTTTTGTTTC
22990180 TTTTT-TGTTC
1 TTTTTGT-TTC
22990190 TTTT
1 TTTT
22990194 CTTTTTTTCT
Statistics
Matches: 51, Mismatches: 4, Indels: 16
0.72 0.06 0.23
Matches are distributed among these distances:
8 2 0.04
9 18 0.35
10 19 0.37
11 9 0.18
12 3 0.06
ACGTcount: A:0.01, C:0.08, G:0.08, T:0.82
Consensus pattern (10 bp):
TTTTTGTTTC
Found at i:22990193 original size:37 final size:36
Alignment explanation
Indices: 22990120--22990212 Score: 107
Period size: 37 Copynumber: 2.5 Consensus size: 36
22990110 CCGGTAGAGG
* *
22990120 TTTTTTGTTTCTTTTTGTTTTTGTTTTTTATTCTTTT-
1 TTTTTT-TTTCTTTTT-TTGTTCTTTTTTATTCTTTTC
*
22990157 TGTTCTTTTTTCTTTTTTTGTTCTTTTTTGTTCTTTTC
1 T-TT-TTTTTTCTTTTTTTGTTCTTTTTTATTCTTTTC
22990195 TTTTTTTCTTCTTTTTTT
1 TTTTTTT-TTCTTTTTTT
22990213 TACATTGAAT
Statistics
Matches: 49, Mismatches: 3, Indels: 8
0.82 0.05 0.13
Matches are distributed among these distances:
36 4 0.08
37 30 0.61
38 12 0.24
39 3 0.06
ACGTcount: A:0.01, C:0.10, G:0.06, T:0.83
Consensus pattern (36 bp):
TTTTTTTTTCTTTTTTTGTTCTTTTTTATTCTTTTC
Found at i:22990199 original size:16 final size:15
Alignment explanation
Indices: 22990120--22990213 Score: 86
Period size: 16 Copynumber: 6.2 Consensus size: 15
22990110 CCGGTAGAGG
22990120 TTTTTTGTTTCTTTTT
1 TTTTTTG-TTCTTTTT
*
22990136 GTTTTTGTT-TTTTAT
1 TTTTTTGTTCTTTT-T
22990151 TCTTTTTGTTCTTTTT
1 T-TTTTTGTTCTTTTT
* * *
22990167 TCTTTT-TT-TGTTC
1 TTTTTTGTTCTTTTT
22990180 TTTTTTGTTCTTTTCT
1 TTTTTTGTTCTTTT-T
*
22990196 TTTTTTCTTCTTTTT
1 TTTTTTGTTCTTTTT
22990211 TTT
1 TTT
22990214 ACATTGAATC
Statistics
Matches: 63, Mismatches: 9, Indels: 13
0.74 0.11 0.15
Matches are distributed among these distances:
13 8 0.13
14 8 0.13
15 14 0.22
16 29 0.46
17 4 0.06
ACGTcount: A:0.01, C:0.10, G:0.06, T:0.83
Consensus pattern (15 bp):
TTTTTTGTTCTTTTT
Found at i:22990211 original size:26 final size:27
Alignment explanation
Indices: 22990143--22990211 Score: 97
Period size: 26 Copynumber: 2.6 Consensus size: 27
22990133 TTTGTTTTTG
22990143 TTTTTTATTC-TTTTTGTTCTTTTTTCT
1 TTTTTTATTCTTTTTTGTTC-TTTTTCT
*
22990170 TTTTTTGTTCTTTTTTGTTC-TTTTCT
1 TTTTTTATTCTTTTTTGTTCTTTTTCT
*
22990196 TTTTTTCTTCTTTTTT
1 TTTTTTATTCTTTTTT
22990212 TTACATTGAA
Statistics
Matches: 39, Mismatches: 2, Indels: 3
0.89 0.05 0.07
Matches are distributed among these distances:
26 21 0.54
27 9 0.23
28 9 0.23
ACGTcount: A:0.01, C:0.12, G:0.04, T:0.83
Consensus pattern (27 bp):
TTTTTTATTCTTTTTTGTTCTTTTTCT
Found at i:22996006 original size:21 final size:20
Alignment explanation
Indices: 22995974--22996012 Score: 51
Period size: 21 Copynumber: 1.9 Consensus size: 20
22995964 TTATCCATTT
* *
22995974 TTATTGTTAACATTTGGTCC
1 TTATTGTCAACATATGGTCC
22995994 TTATATGTCAACATATGGT
1 TTAT-TGTCAACATATGGT
22996013 ACATGTGACA
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 4 0.25
21 12 0.75
ACGTcount: A:0.26, C:0.13, G:0.15, T:0.46
Consensus pattern (20 bp):
TTATTGTCAACATATGGTCC
Found at i:23007416 original size:44 final size:45
Alignment explanation
Indices: 23007335--23007432 Score: 135
Period size: 44 Copynumber: 2.2 Consensus size: 45
23007325 AAGACTTGTA
**
23007335 TCTTCGATCTACTTCACCACCAATATGGGAAGACAAGATCTGTTT
1 TCTTCGATCTACTTCACCACCAATACAGGAAGACAAGATCTGTTT
* * *
23007380 TCTTCTATCTACTTCA-CGCCAATACATGAAGACAAGATCTGTTT
1 TCTTCGATCTACTTCACCACCAATACAGGAAGACAAGATCTGTTT
*
23007424 TTTTCGATC
1 TCTTCGATC
23007433 GATTCCACTG
Statistics
Matches: 46, Mismatches: 7, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
44 31 0.67
45 15 0.33
ACGTcount: A:0.28, C:0.24, G:0.13, T:0.35
Consensus pattern (45 bp):
TCTTCGATCTACTTCACCACCAATACAGGAAGACAAGATCTGTTT
Found at i:23007677 original size:88 final size:88
Alignment explanation
Indices: 23007584--23007838 Score: 226
Period size: 88 Copynumber: 2.9 Consensus size: 88
23007574 ACCAGTATGG
* * * *
23007584 GAAGATAAAATATG-TATATTCGATCCACTTCGCTACC-GATATAGGAAGACAGGACCTACTATC
1 GAAGATAAAATATGCTATATTCGATCCACTCCACCACCAG-TATAGGAAGACAAGACCT-CTATC
23007647 TTTGATCTACTTCACGCCAGTACAT
64 TTTGATCTACTTCACGCCAGTACAT
* * * * * * * * * *
23007672 GAAGATAAGATCTGCTTTCTTCGATCTACTCCACCACCAGTATGGGGAGACAAGATCTGTTTCTT
1 GAAGATAAAATATGCTATATTCGATCCACTCCACCACCAGTATAGGAAGACAAGACCTCTATCTT
23007737 TGATCTACTTCACGCCAGTACAT
66 TGATCTACTTCACGCCAGTACAT
* * * * * * * * * * * *
23007760 GAAGACAAGATCTACTTTCTTCGATCTACTCCACCACCAGTATGGGGAGACAAGATCTGTTTTCT
1 GAAGATAAAATATGCTATATTCGATCCACTCCACCACCAGTATAGGAAGACAAGACCT-CTATCT
*
23007825 TCGATCTACTTCAC
65 TTGATCTACTTCAC
23007839 CACCAGTATG
Statistics
Matches: 146, Mismatches: 18, Indels: 5
0.86 0.11 0.03
Matches are distributed among these distances:
88 96 0.66
89 49 0.34
90 1 0.01
ACGTcount: A:0.29, C:0.25, G:0.17, T:0.30
Consensus pattern (88 bp):
GAAGATAAAATATGCTATATTCGATCCACTCCACCACCAGTATAGGAAGACAAGACCTCTATCTT
TGATCTACTTCACGCCAGTACAT
Found at i:23007698 original size:44 final size:45
Alignment explanation
Indices: 23007626--23007998 Score: 360
Period size: 44 Copynumber: 8.4 Consensus size: 45
23007616 CTACCGATAT
* * * * * *
23007626 AGGAAGACAGGACCTACTATCTTTGATCTACTTCA-CGCCAGTAC
1 AGGAAGACAAGATCTGCTTTCTTCGATCTACTTCACCACCAGTAC
* * * *
23007670 ATGAAGATAAGATCTGCTTTCTTCGATCTACTCCACCACCAGTAT
1 AGGAAGACAAGATCTGCTTTCTTCGATCTACTTCACCACCAGTAC
* * * *
23007715 GGGGAGACAAGATCTG-TTTCTTTGATCTACTTCA-CGCCAGTAC
1 AGGAAGACAAGATCTGCTTTCTTCGATCTACTTCACCACCAGTAC
* * * *
23007758 ATGAAGACAAGATCTACTTTCTTCGATCTACTCCACCACCAGTAT
1 AGGAAGACAAGATCTGCTTTCTTCGATCTACTTCACCACCAGTAC
* * * *
23007803 GGGGAGACAAGATCTGTTTTCTTCGATCTACTTCACCACCAGTAT
1 AGGAAGACAAGATCTGCTTTCTTCGATCTACTTCACCACCAGTAC
* * * *
23007848 GGGAAGACAAGATCTGCTATCTTTGATCTACTTCA-CGCCAGTAC
1 AGGAAGACAAGATCTGCTTTCTTCGATCTACTTCACCACCAGTAC
* * *
23007892 ATGAAGACAAGATCTGCTTTCTTCGATCTACTCCACCACCAGTAT
1 AGGAAGACAAGATCTGCTTTCTTCGATCTACTTCACCACCAGTAC
* * * * * * * *
23007937 GGGGAGACAAGATCTG-TATATTCGATCCACTTCACTACCAATAT
1 AGGAAGACAAGATCTGCTTTCTTCGATCTACTTCACCACCAGTAC
* *
23007981 AGGAAGATAGGATCTGCT
1 AGGAAGACAAGATCTGCT
23007999 GCTTTTCAAC
Statistics
Matches: 266, Mismatches: 58, Indels: 9
0.80 0.17 0.03
Matches are distributed among these distances:
43 19 0.07
44 130 0.49
45 117 0.44
ACGTcount: A:0.28, C:0.25, G:0.18, T:0.28
Consensus pattern (45 bp):
AGGAAGACAAGATCTGCTTTCTTCGATCTACTTCACCACCAGTAC
Found at i:23007727 original size:45 final size:45
Alignment explanation
Indices: 23007672--23007998 Score: 365
Period size: 45 Copynumber: 7.4 Consensus size: 45
23007662 GCCAGTACAT
*
23007672 GAAGATAAGATCTGCTTTCTTCGATCTACTCCACCACCAGTATGG
1 GAAGACAAGATCTGCTTTCTTCGATCTACTCCACCACCAGTATGG
* * * * ***
23007717 GGAGACAAGATCTG-TTTCTTTGATCTACTTCA-CGCCAGTACAT
1 GAAGACAAGATCTGCTTTCTTCGATCTACTCCACCACCAGTATGG
*
23007760 GAAGACAAGATCTACTTTCTTCGATCTACTCCACCACCAGTATGG
1 GAAGACAAGATCTGCTTTCTTCGATCTACTCCACCACCAGTATGG
* * *
23007805 GGAGACAAGATCTGTTTTCTTCGATCTACTTCACCACCAGTATGG
1 GAAGACAAGATCTGCTTTCTTCGATCTACTCCACCACCAGTATGG
* * * * ***
23007850 GAAGACAAGATCTGCTATCTTTGATCTACTTCA-CGCCAGTACAT
1 GAAGACAAGATCTGCTTTCTTCGATCTACTCCACCACCAGTATGG
23007894 GAAGACAAGATCTGCTTTCTTCGATCTACTCCACCACCAGTATGG
1 GAAGACAAGATCTGCTTTCTTCGATCTACTCCACCACCAGTATGG
* * * * * * * *
23007939 GGAGACAAGATCTG-TATATTCGATCCACTTCACTACCAATATAG
1 GAAGACAAGATCTGCTTTCTTCGATCTACTCCACCACCAGTATGG
* *
23007983 GAAGATAGGATCTGCT
1 GAAGACAAGATCTGCT
23007999 GCTTTTCAAC
Statistics
Matches: 232, Mismatches: 46, Indels: 8
0.81 0.16 0.03
Matches are distributed among these distances:
43 19 0.08
44 103 0.44
45 110 0.47
ACGTcount: A:0.28, C:0.25, G:0.18, T:0.29
Consensus pattern (45 bp):
GAAGACAAGATCTGCTTTCTTCGATCTACTCCACCACCAGTATGG
Found at i:23007923 original size:134 final size:133
Alignment explanation
Indices: 23007678--23007998 Score: 509
Period size: 133 Copynumber: 2.4 Consensus size: 133
23007668 ACATGAAGAT
* * *
23007678 AAGATCTGCTTTCTTCGATCTACTCCACCACCAGTATGGGGAGACAAGATCTG-TTTCTTTGATC
1 AAGATCTG-TTTCTTCGATCTACTTCACCACCAGTATGGGAAGACAAGATCTGCTATCTTTGATC
23007742 TACTTCACGCCAGTACATGAAGACAAGATCTACTTTCTTCGATCTACTCCACCACCAGTATGGGG
65 TACTTCACGCCAGTACATGAAGACAAGATCTACTTTCTTCGATCTACTCCACCACCAGTATGGGG
23007807 AGAC
130 AGAC
23007811 AAGATCTGTTTTCTTCGATCTACTTCACCACCAGTATGGGAAGACAAGATCTGCTATCTTTGATC
1 AAGATCTG-TTTCTTCGATCTACTTCACCACCAGTATGGGAAGACAAGATCTGCTATCTTTGATC
*
23007876 TACTTCACGCCAGTACATGAAGACAAGATCTGCTTTCTTCGATCTACTCCACCACCAGTATGGGG
65 TACTTCACGCCAGTACATGAAGACAAGATCTACTTTCTTCGATCTACTCCACCACCAGTATGGGG
23007941 AGAC
130 AGAC
* * * * * * * *
23007945 AAGATCTGTATATTCGATCCACTTCACTACCAATATAGGAAGATAGGATCTGCT
1 AAGATCTGTTTCTTCGATCTACTTCACCACCAGTATGGGAAGACAAGATCTGCT
23007999 GCTTTTCAAC
Statistics
Matches: 174, Mismatches: 13, Indels: 2
0.92 0.07 0.01
Matches are distributed among these distances:
133 88 0.51
134 86 0.49
ACGTcount: A:0.28, C:0.26, G:0.18, T:0.29
Consensus pattern (133 bp):
AAGATCTGTTTCTTCGATCTACTTCACCACCAGTATGGGAAGACAAGATCTGCTATCTTTGATCT
ACTTCACGCCAGTACATGAAGACAAGATCTACTTTCTTCGATCTACTCCACCACCAGTATGGGGA
GAC
Found at i:23016089 original size:20 final size:20
Alignment explanation
Indices: 23016060--23016099 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
23016050 TAAAGGTCTT
* *
23016060 TAATGTATATGATGTGATGC
1 TAATGCATATGATGCGATGC
23016080 TAATGCATATGATGCGATGC
1 TAATGCATATGATGCGATGC
23016100 ATGAGGTGAA
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:0.30, C:0.10, G:0.25, T:0.35
Consensus pattern (20 bp):
TAATGCATATGATGCGATGC
Found at i:23021112 original size:34 final size:34
Alignment explanation
Indices: 23021060--23021127 Score: 118
Period size: 34 Copynumber: 2.0 Consensus size: 34
23021050 TACATTTATT
23021060 AAGGCTAAATTTATAGTAAATAGTGAAAATTGAA
1 AAGGCTAAATTTATAGTAAATAGTGAAAATTGAA
* *
23021094 AAGGTTAAGTTTATAGTAAATAGTGAAAATTGAA
1 AAGGCTAAATTTATAGTAAATAGTGAAAATTGAA
23021128 CTGCAGAAGA
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
34 32 1.00
ACGTcount: A:0.49, C:0.01, G:0.19, T:0.31
Consensus pattern (34 bp):
AAGGCTAAATTTATAGTAAATAGTGAAAATTGAA
Found at i:23026872 original size:29 final size:29
Alignment explanation
Indices: 23026829--23026935 Score: 114
Period size: 29 Copynumber: 3.8 Consensus size: 29
23026819 AACATGCCAG
* *
23026829 AAAAAGGAAGTCTTTATGGCAATCTATGA
1 AAAAAGGAAGCCTTTGTGGCAATCTATGA
* * *
23026858 AAAAATGAAGCCTTTGTGGCGATATATG-
1 AAAAAGGAAGCCTTTGTGGCAATCTATGA
23026886 AAAAAGGAAGCCTTTTGTGGCGAA-CTAT-A
1 AAAAAGGAAGCC-TTTGTGGC-AATCTATGA
*
23026915 AAAAA-AAAGCCTTTGTGGCAA
1 AAAAAGGAAGCCTTTGTGGCAA
23026936 ACTCTGTATA
Statistics
Matches: 66, Mismatches: 9, Indels: 9
0.79 0.11 0.11
Matches are distributed among these distances:
26 2 0.03
27 8 0.12
28 16 0.24
29 39 0.59
30 1 0.02
ACGTcount: A:0.40, C:0.12, G:0.22, T:0.25
Consensus pattern (29 bp):
AAAAAGGAAGCCTTTGTGGCAATCTATGA
Found at i:23029519 original size:17 final size:17
Alignment explanation
Indices: 23029497--23029529 Score: 66
Period size: 17 Copynumber: 1.9 Consensus size: 17
23029487 GTAATAAAAT
23029497 GGGTGAACGAACCACCG
1 GGGTGAACGAACCACCG
23029514 GGGTGAACGAACCACC
1 GGGTGAACGAACCACC
23029530 AAGGTTTTTG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.30, C:0.30, G:0.33, T:0.06
Consensus pattern (17 bp):
GGGTGAACGAACCACCG
Found at i:23029899 original size:15 final size:15
Alignment explanation
Indices: 23029879--23029910 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
23029869 CATTTCACTA
*
23029879 TTATGTCTTTTGTAT
1 TTATGTCTTTTATAT
23029894 TTATGTCTTTTATAT
1 TTATGTCTTTTATAT
23029909 TT
1 TT
23029911 TGCATGCATA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.16, C:0.06, G:0.09, T:0.69
Consensus pattern (15 bp):
TTATGTCTTTTATAT
Done.