Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Gbar_A01
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: 115637255
ACGTcount: A:0.31, C:0.17, G:0.17, T:0.31
Warning! 5450143 characters in sequence are not A, C, G, or T
File 198 of 349
Found at i:64090215 original size:13 final size:12
Alignment explanation
Indices: 64090177--64090218 Score: 59
Period size: 12 Copynumber: 3.4 Consensus size: 12
64090167 TATACAAGTT
64090177 AAAAAAATCAAA
1 AAAAAAATCAAA
64090189 AAAAAAATTC-AA
1 AAAAAAA-TCAAA
64090201 AAAAAAATCGAAA
1 AAAAAAATC-AAA
64090214 AAAAA
1 AAAAA
64090219 GAGTGATTTA
Statistics
Matches: 27, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
11 2 0.07
12 16 0.59
13 9 0.33
ACGTcount: A:0.81, C:0.07, G:0.02, T:0.10
Consensus pattern (12 bp):
AAAAAAATCAAA
Found at i:64095456 original size:19 final size:19
Alignment explanation
Indices: 64095432--64095471 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
64095422 AGCTCCCATG
64095432 TAGCTCCACACCAGCTCAT
1 TAGCTCCACACCAGCTCAT
***
64095451 TAGCTCGGGACCAGCTCAT
1 TAGCTCCACACCAGCTCAT
64095470 TA
1 TA
64095472 TCAGCTCACG
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.25, C:0.35, G:0.17, T:0.23
Consensus pattern (19 bp):
TAGCTCCACACCAGCTCAT
Found at i:64096734 original size:14 final size:14
Alignment explanation
Indices: 64096712--64096759 Score: 60
Period size: 14 Copynumber: 3.4 Consensus size: 14
64096702 ACCTAAATCG
* *
64096712 ACCAATTTGTTCAT
1 ACCATTTTGTTCCT
64096726 ACCATTTTGTTCCT
1 ACCATTTTGTTCCT
* *
64096740 ACCCTTTCGTTCCT
1 ACCATTTTGTTCCT
64096754 ACCATT
1 ACCATT
64096760 CCATTCGTAC
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
14 29 1.00
ACGTcount: A:0.19, C:0.31, G:0.06, T:0.44
Consensus pattern (14 bp):
ACCATTTTGTTCCT
Found at i:64098568 original size:21 final size:20
Alignment explanation
Indices: 64098534--64098601 Score: 66
Period size: 21 Copynumber: 3.2 Consensus size: 20
64098524 ACATTCTTGT
64098534 AAAGAGAAAA-CAAAGAAAAGA
1 AAAGA-AAAAGCAAA-AAAAGA
*
64098555 AAAGAAAAAGCAAAAGAAGAA
1 AAAGAAAAAGCAAAAAAAG-A
* *
64098576 AAAGAAAACGAAATAAAAAGA
1 AAAGAAAAAGCAA-AAAAAGA
64098597 AAAGA
1 AAAGA
64098602 GAGGCAAAAG
Statistics
Matches: 40, Mismatches: 4, Indels: 6
0.80 0.08 0.12
Matches are distributed among these distances:
20 8 0.20
21 27 0.68
22 5 0.12
ACGTcount: A:0.76, C:0.04, G:0.18, T:0.01
Consensus pattern (20 bp):
AAAGAAAAAGCAAAAAAAGA
Found at i:64098569 original size:6 final size:5
Alignment explanation
Indices: 64098545--64098601 Score: 55
Period size: 5 Copynumber: 11.0 Consensus size: 5
64098535 AAGAGAAAAC
*
64098545 AAAGA AAAGA AAAGAA AAAGCA AAAGA AGA-A AAAGA AAACGA AATA-A
1 AAAGA AAAGA AAAG-A AAAG-A AAAGA AAAGA AAAGA AAA-GA AA-AGA
64098592 AAAGA AAAGA
1 AAAGA AAAGA
64098602 GAGGCAAAAG
Statistics
Matches: 44, Mismatches: 3, Indels: 10
0.77 0.05 0.18
Matches are distributed among these distances:
4 4 0.09
5 25 0.57
6 14 0.32
7 1 0.02
ACGTcount: A:0.77, C:0.04, G:0.18, T:0.02
Consensus pattern (5 bp):
AAAGA
Found at i:64098576 original size:15 final size:14
Alignment explanation
Indices: 64098545--64098601 Score: 60
Period size: 16 Copynumber: 3.7 Consensus size: 14
64098535 AAGAGAAAAC
64098545 AAAGAAAAGAAAAGAA
1 AAAGAAAAG--AAGAA
64098561 AAAGCAAAAGAAGAA
1 AAAG-AAAAGAAGAA
*
64098576 AAAGAAAACGAAATAA
1 AAAGAAAA-G-AAGAA
64098592 AAAGAAAAGA
1 AAAGAAAAGA
64098602 GAGGCAAAAG
Statistics
Matches: 37, Mismatches: 1, Indels: 8
0.80 0.02 0.17
Matches are distributed among these distances:
14 5 0.14
15 11 0.30
16 16 0.43
17 5 0.14
ACGTcount: A:0.77, C:0.04, G:0.18, T:0.02
Consensus pattern (14 bp):
AAAGAAAAGAAGAA
Found at i:64098696 original size:12 final size:12
Alignment explanation
Indices: 64098681--64098768 Score: 52
Period size: 12 Copynumber: 7.3 Consensus size: 12
64098671 TTTGAAAAGC
64098681 AAAAAGAAAATG
1 AAAAAGAAAATG
64098693 AAAAAGAAAATG
1 AAAAAGAAAATG
* ** *
64098705 AGATTGAAAAAG
1 AAAAAGAAAATG
* *
64098717 AGAACGAAAA-G
1 AAAAAGAAAATG
** * *
64098728 AAATTTGACAGTG
1 AAA-AAGAAAATG
*
64098741 AAAAAGAAGATG
1 AAAAAGAAAATG
*
64098753 AAAAAGAAATTG
1 AAAAAGAAAATG
64098765 AAAA
1 AAAA
64098769 CAAAAGAATC
Statistics
Matches: 56, Mismatches: 18, Indels: 4
0.72 0.23 0.05
Matches are distributed among these distances:
11 3 0.05
12 49 0.88
13 4 0.07
ACGTcount: A:0.65, C:0.02, G:0.20, T:0.12
Consensus pattern (12 bp):
AAAAAGAAAATG
Found at i:64098702 original size:18 final size:18
Alignment explanation
Indices: 64098675--64098730 Score: 51
Period size: 18 Copynumber: 3.1 Consensus size: 18
64098665 AAAGTCTTTG
64098675 AAAAGCAAAAAGAAAATGA
1 AAAAG-AAAAAGAAAATGA
* * *
64098694 AAAAGAAAATGAGATTGA
1 AAAAGAAAAAGAAAATGA
* *
64098712 AAAAGAGAACGAAAA-GA
1 AAAAGAAAAAGAAAATGA
64098729 AA
1 AA
64098731 TTTGACAGTG
Statistics
Matches: 30, Mismatches: 7, Indels: 2
0.77 0.18 0.05
Matches are distributed among these distances:
17 4 0.13
18 21 0.70
19 5 0.17
ACGTcount: A:0.70, C:0.04, G:0.20, T:0.07
Consensus pattern (18 bp):
AAAAGAAAAAGAAAATGA
Found at i:64098715 original size:30 final size:31
Alignment explanation
Indices: 64098681--64098762 Score: 96
Period size: 30 Copynumber: 2.7 Consensus size: 31
64098671 TTTGAAAAGC
* *
64098681 AAAAAGAAAATGAAAAAGAAA-ATGAGATTG
1 AAAAAGAAAATGAAAAAGAAATATGACAGTG
* * *
64098711 AAAAAGAGAACG-AAAAGAAATTTGACAGTG
1 AAAAAGAAAATGAAAAAGAAATATGACAGTG
*
64098741 AAAAAGAAGATGAAAAAGAAAT
1 AAAAAGAAAATGAAAAAGAAAT
64098763 TGAAAACAAA
Statistics
Matches: 42, Mismatches: 8, Indels: 3
0.79 0.15 0.06
Matches are distributed among these distances:
29 8 0.19
30 25 0.60
31 9 0.21
ACGTcount: A:0.65, C:0.02, G:0.21, T:0.12
Consensus pattern (31 bp):
AAAAAGAAAATGAAAAAGAAATATGACAGTG
Found at i:64101007 original size:30 final size:30
Alignment explanation
Indices: 64100973--64101070 Score: 90
Period size: 30 Copynumber: 3.3 Consensus size: 30
64100963 AGCTCACTCC
64100973 TAGCTCATATTCAGCTCACGAGCTAAACCT
1 TAGCTCATATTCAGCTCACGAGCTAAACCT
** * * * * *
64101003 TAGCTCAGCTTCAGCTTAGGAGTTTAATCT
1 TAGCTCATATTCAGCTCACGAGCTAAACCT
* * *
64101033 CAGCTCA-ACTTTAGCTCACGAGCTAAAGCT
1 TAGCTCATA-TTCAGCTCACGAGCTAAACCT
64101063 TAGCTCAT
1 TAGCTCAT
64101071 TTTAGTTTAA
Statistics
Matches: 50, Mismatches: 16, Indels: 3
0.72 0.23 0.04
Matches are distributed among these distances:
30 50 1.00
ACGTcount: A:0.28, C:0.27, G:0.16, T:0.30
Consensus pattern (30 bp):
TAGCTCATATTCAGCTCACGAGCTAAACCT
Found at i:64103703 original size:21 final size:20
Alignment explanation
Indices: 64103669--64103736 Score: 66
Period size: 21 Copynumber: 3.2 Consensus size: 20
64103659 ACATTCTTGT
64103669 AAAGAGAAAA-CAAAGAAAAGA
1 AAAGA-AAAAGCAAA-AAAAGA
*
64103690 AAAGAAAAAGCAAAAGAAGAA
1 AAAGAAAAAGCAAAAAAAG-A
* *
64103711 AAAGAAAACGAAATAAAAAGA
1 AAAGAAAAAGCAA-AAAAAGA
64103732 AAAGA
1 AAAGA
64103737 GAGGCAAGAG
Statistics
Matches: 40, Mismatches: 4, Indels: 6
0.80 0.08 0.12
Matches are distributed among these distances:
20 8 0.20
21 27 0.68
22 5 0.12
ACGTcount: A:0.76, C:0.04, G:0.18, T:0.01
Consensus pattern (20 bp):
AAAGAAAAAGCAAAAAAAGA
Found at i:64103704 original size:6 final size:5
Alignment explanation
Indices: 64103680--64103736 Score: 55
Period size: 5 Copynumber: 11.0 Consensus size: 5
64103670 AAGAGAAAAC
*
64103680 AAAGA AAAGA AAAGAA AAAGCA AAAGA AGA-A AAAGA AAACGA AATA-A
1 AAAGA AAAGA AAAG-A AAAG-A AAAGA AAAGA AAAGA AAA-GA AA-AGA
64103727 AAAGA AAAGA
1 AAAGA AAAGA
64103737 GAGGCAAGAG
Statistics
Matches: 44, Mismatches: 3, Indels: 10
0.77 0.05 0.18
Matches are distributed among these distances:
4 4 0.09
5 25 0.57
6 14 0.32
7 1 0.02
ACGTcount: A:0.77, C:0.04, G:0.18, T:0.02
Consensus pattern (5 bp):
AAAGA
Found at i:64103711 original size:15 final size:14
Alignment explanation
Indices: 64103680--64103736 Score: 60
Period size: 16 Copynumber: 3.7 Consensus size: 14
64103670 AAGAGAAAAC
64103680 AAAGAAAAGAAAAGAA
1 AAAGAAAAG--AAGAA
64103696 AAAGCAAAAGAAGAA
1 AAAG-AAAAGAAGAA
*
64103711 AAAGAAAACGAAATAA
1 AAAGAAAA-G-AAGAA
64103727 AAAGAAAAGA
1 AAAGAAAAGA
64103737 GAGGCAAGAG
Statistics
Matches: 37, Mismatches: 1, Indels: 8
0.80 0.02 0.17
Matches are distributed among these distances:
14 5 0.14
15 11 0.30
16 16 0.43
17 5 0.14
ACGTcount: A:0.77, C:0.04, G:0.18, T:0.02
Consensus pattern (14 bp):
AAAGAAAAGAAGAA
Found at i:64103830 original size:12 final size:12
Alignment explanation
Indices: 64103815--64103902 Score: 52
Period size: 12 Copynumber: 7.3 Consensus size: 12
64103805 TTTGAAAAGC
64103815 AAAAAGAAAATG
1 AAAAAGAAAATG
64103827 AAAAAGAAAATG
1 AAAAAGAAAATG
* ** *
64103839 AGATTGAAAAAG
1 AAAAAGAAAATG
* *
64103851 AGAACGAAAA-G
1 AAAAAGAAAATG
** * *
64103862 AAATTTGAGAGTG
1 AAA-AAGAAAATG
*
64103875 AAAAAGAAGATG
1 AAAAAGAAAATG
*
64103887 AAAAAGAAATTG
1 AAAAAGAAAATG
64103899 AAAA
1 AAAA
64103903 CAAAAGAATC
Statistics
Matches: 56, Mismatches: 18, Indels: 4
0.72 0.23 0.05
Matches are distributed among these distances:
11 3 0.05
12 49 0.88
13 4 0.07
ACGTcount: A:0.65, C:0.01, G:0.22, T:0.12
Consensus pattern (12 bp):
AAAAAGAAAATG
Found at i:64103836 original size:18 final size:18
Alignment explanation
Indices: 64103809--64103864 Score: 51
Period size: 18 Copynumber: 3.1 Consensus size: 18
64103799 AAAAGCTTTG
64103809 AAAAGCAAAAAGAAAATGA
1 AAAAG-AAAAAGAAAATGA
* * *
64103828 AAAAGAAAATGAGATTGA
1 AAAAGAAAAAGAAAATGA
* *
64103846 AAAAGAGAACGAAAA-GA
1 AAAAGAAAAAGAAAATGA
64103863 AA
1 AA
64103865 TTTGAGAGTG
Statistics
Matches: 30, Mismatches: 7, Indels: 2
0.77 0.18 0.05
Matches are distributed among these distances:
17 4 0.13
18 21 0.70
19 5 0.17
ACGTcount: A:0.70, C:0.04, G:0.20, T:0.07
Consensus pattern (18 bp):
AAAAGAAAAAGAAAATGA
Found at i:64103851 original size:30 final size:31
Alignment explanation
Indices: 64103815--64103896 Score: 105
Period size: 30 Copynumber: 2.7 Consensus size: 31
64103805 TTTGAAAAGC
*
64103815 AAAAAGAAAATGAAAAAGAAA-ATGAGATTG
1 AAAAAGAAAATGAAAAAGAAATATGAGAGTG
* * *
64103845 AAAAAGAGAACG-AAAAGAAATTTGAGAGTG
1 AAAAAGAAAATGAAAAAGAAATATGAGAGTG
*
64103875 AAAAAGAAGATGAAAAAGAAAT
1 AAAAAGAAAATGAAAAAGAAAT
64103897 TGAAAACAAA
Statistics
Matches: 43, Mismatches: 7, Indels: 3
0.81 0.13 0.06
Matches are distributed among these distances:
29 8 0.19
30 26 0.60
31 9 0.21
ACGTcount: A:0.65, C:0.01, G:0.22, T:0.12
Consensus pattern (31 bp):
AAAAAGAAAATGAAAAAGAAATATGAGAGTG
Found at i:64106203 original size:30 final size:30
Alignment explanation
Indices: 64106120--64106204 Score: 80
Period size: 30 Copynumber: 2.8 Consensus size: 30
64106110 GCTCATATTC
*
64106120 AGCTCACGAGCTAAACCTTAGCTCAGCTTT
1 AGCTCACGAGCTAAACCTTAGCTCAACTTT
* * * * ** *
64106150 AGCTTAGGAGTTTAATATCAGCTCAACTTT
1 AGCTCACGAGCTAAACCTTAGCTCAACTTT
* *
64106180 AGCTCATGAGCTAAAGCTTAGCTCA
1 AGCTCACGAGCTAAACCTTAGCTCA
64106205 TTTTAGTTTA
Statistics
Matches: 40, Mismatches: 15, Indels: 0
0.73 0.27 0.00
Matches are distributed among these distances:
30 40 1.00
ACGTcount: A:0.29, C:0.24, G:0.18, T:0.29
Consensus pattern (30 bp):
AGCTCACGAGCTAAACCTTAGCTCAACTTT
Found at i:64111345 original size:16 final size:16
Alignment explanation
Indices: 64111326--64111368 Score: 59
Period size: 16 Copynumber: 2.7 Consensus size: 16
64111316 GCAAATCCTG
*
64111326 AAATGTCGAAATGCCA
1 AAATGTTGAAATGCCA
* *
64111342 AAATTTTGAAATGTCA
1 AAATGTTGAAATGCCA
64111358 AAATGTTGAAA
1 AAATGTTGAAA
64111369 GAATGGCAAC
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
16 23 1.00
ACGTcount: A:0.47, C:0.09, G:0.16, T:0.28
Consensus pattern (16 bp):
AAATGTTGAAATGCCA
Found at i:64112962 original size:31 final size:31
Alignment explanation
Indices: 64112918--64113088 Score: 270
Period size: 31 Copynumber: 5.5 Consensus size: 31
64112908 TTTAATGGTT
** *
64112918 ACTGGGCATAAGCCTTTTCATAAATCATATC
1 ACTGGGCCGAAGCCTTATCATAAATCATATC
*
64112949 ACTGGGCTGAAGCCTTATCATAAATCATATC
1 ACTGGGCCGAAGCCTTATCATAAATCATATC
64112980 ACTGGGCCGAAGCCTTATCATAAATCATATC
1 ACTGGGCCGAAGCCTTATCATAAATCATATC
64113011 ACTGGGCCGAAGCCTTATCATAAATCATATC
1 ACTGGGCCGAAGCCTTATCATAAATCATATC
* * * *
64113042 TCTGGGCCGACGTCTTTTCATAAATCATATC
1 ACTGGGCCGAAGCCTTATCATAAATCATATC
64113073 ACTGGGCCGAAGCCTT
1 ACTGGGCCGAAGCCTT
64113089 TACTGTAAAC
Statistics
Matches: 129, Mismatches: 11, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
31 129 1.00
ACGTcount: A:0.29, C:0.25, G:0.17, T:0.29
Consensus pattern (31 bp):
ACTGGGCCGAAGCCTTATCATAAATCATATC
Found at i:64113364 original size:25 final size:24
Alignment explanation
Indices: 64113295--64113376 Score: 94
Period size: 24 Copynumber: 3.4 Consensus size: 24
64113285 CTGGAGGCCT
* *
64113295 AGCCTCTTTTAAT-AACTAGGGCAA
1 AGCC-CTTTTGATAAACTGGGGCAA
64113319 AGCCCTTTTGATAAACTGGGGCAA
1 AGCCCTTTTGATAAACTGGGGCAA
* * *
64113343 AGCCCTTTTCGGTAAATTGGGGCAT
1 AGCCCTTTT-GATAAACTGGGGCAA
64113368 AGCCCTTTT
1 AGCCCTTTT
64113377 AGCACTTCCT
Statistics
Matches: 51, Mismatches: 5, Indels: 3
0.86 0.08 0.05
Matches are distributed among these distances:
23 7 0.14
24 23 0.45
25 21 0.41
ACGTcount: A:0.26, C:0.22, G:0.22, T:0.30
Consensus pattern (24 bp):
AGCCCTTTTGATAAACTGGGGCAA
Found at i:64114248 original size:27 final size:27
Alignment explanation
Indices: 64114186--64114250 Score: 87
Period size: 27 Copynumber: 2.4 Consensus size: 27
64114176 GGGCATATTC
64114186 GTCATTTTACCATACAGGGGTATTACG
1 GTCATTTTACCATACAGGGGTATTACG
* *
64114213 GTCACTTTACCCTACAGGGGCT-TTACG
1 GTCATTTTACCATACAGGGG-TATTACG
*
64114240 GTCTTTTTACC
1 GTCATTTTACC
64114251 TTTAGGGGTA
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
27 32 0.97
28 1 0.03
ACGTcount: A:0.20, C:0.25, G:0.20, T:0.35
Consensus pattern (27 bp):
GTCATTTTACCATACAGGGGTATTACG
Found at i:64114333 original size:27 final size:27
Alignment explanation
Indices: 64114303--64114410 Score: 94
Period size: 27 Copynumber: 3.9 Consensus size: 27
64114293 GTAAATCTAC
64114303 AAACCAAGGGTATTTCAGTAATTTTGT
1 AAACCAAGGGTATTTCAGTAATTTTGT
*
64114330 AAACCAATGGTATTTCTA-TAATTTT-T
1 AAACCAAGGGTATTTC-AGTAATTTTGT
* **
64114356 AGAAAGTCAAGGGTATTTTTGTAATTTTGT
1 --AAA-CCAAGGGTATTTCAGTAATTTTGT
* * **
64114386 AAATCAGGGGTATTTTGGTAATTTT
1 AAACCAAGGGTATTTCAGTAATTTT
64114411 ACAAAATGAG
Statistics
Matches: 68, Mismatches: 7, Indels: 12
0.78 0.08 0.14
Matches are distributed among these distances:
26 1 0.01
27 42 0.62
28 7 0.10
29 17 0.25
30 1 0.01
ACGTcount: A:0.31, C:0.07, G:0.19, T:0.43
Consensus pattern (27 bp):
AAACCAAGGGTATTTCAGTAATTTTGT
Found at i:64114423 original size:27 final size:27
Alignment explanation
Indices: 64114365--64114489 Score: 130
Period size: 27 Copynumber: 4.6 Consensus size: 27
64114355 TAGAAAGTCA
* **
64114365 AGGGTATTTTTGTAATTTT-GTAAATC
1 AGGGTATTTTGGTAATTTTACAAAATC
*
64114391 AGGGGTATTTTGGTAATTTTACAAAATG
1 A-GGGTATTTTGGTAATTTTACAAAATC
* * *
64114419 AGGGTATTTCGGTAATTTCAC-AAACC
1 AGGGTATTTTGGTAATTTTACAAAATC
*
64114445 AGTGGTATTTTGGTAATTTTACAAACT-
1 AG-GGTATTTTGGTAATTTTACAAAATC
64114472 AGGGGTATTTTGGTAATT
1 A-GGGTATTTTGGTAATT
64114490 CTACCCTATA
Statistics
Matches: 82, Mismatches: 12, Indels: 9
0.80 0.12 0.09
Matches are distributed among these distances:
26 6 0.07
27 68 0.83
28 8 0.10
ACGTcount: A:0.29, C:0.07, G:0.22, T:0.42
Consensus pattern (27 bp):
AGGGTATTTTGGTAATTTTACAAAATC
Found at i:64114483 original size:81 final size:81
Alignment explanation
Indices: 64114367--64114522 Score: 208
Period size: 81 Copynumber: 1.9 Consensus size: 81
64114357 GAAAGTCAAG
* ** * *
64114367 GGTATTTTTGTAATTTTGTAAATCAGGGGTATTTTGGTAATTTTACAAAAT-GAGGGTATTTCGG
1 GGTATTTTGGTAATTTTACAAATCAGGGGTATTTTGGTAATTCTACAAAATAG-GGGTATTTCAG
64114431 TAATTTCACAAACCAGT
65 TAATTTCACAAACCAGT
***
64114448 GGTATTTTGGTAATTTTACAAA-CTAGGGGTATTTTGGTAATTCTACCCTATAGGGGTATTTCAG
1 GGTATTTTGGTAATTTTACAAATC-AGGGGTATTTTGGTAATTCTACAAAATAGGGGTATTTCAG
64114512 TAATTTCACAA
65 TAATTTCACAA
64114523 TCGAGGGTAA
Statistics
Matches: 65, Mismatches: 8, Indels: 4
0.84 0.10 0.05
Matches are distributed among these distances:
80 1 0.02
81 63 0.97
82 1 0.02
ACGTcount: A:0.29, C:0.10, G:0.21, T:0.40
Consensus pattern (81 bp):
GGTATTTTGGTAATTTTACAAATCAGGGGTATTTTGGTAATTCTACAAAATAGGGGTATTTCAGT
AATTTCACAAACCAGT
Found at i:64114529 original size:27 final size:27
Alignment explanation
Indices: 64114387--64114555 Score: 107
Period size: 27 Copynumber: 6.3 Consensus size: 27
64114377 TAATTTTGTA
* *
64114387 AATC-AGGGGTATTTTGGTAATTTTACAA
1 AATCGAGGGGTATTTCGGTAA-TTT-CAC
64114415 AAT-GA-GGGTATTTCGGTAATTTCAC
1 AATCGAGGGGTATTTCGGTAATTTCAC
* * * * *
64114440 AAACCAGTGGTATTTTGGTAATTTTAC
1 AATCGAGGGGTATTTCGGTAATTTCAC
* * * *
64114467 AAACTAGGGGTATTTTGGTAATTCTACCC
1 AATCGAGGGGTATTTCGGTAATT-T-CAC
* *
64114496 TAT--AGGGGTATTTCAGTAATTTCAC
1 AATCGAGGGGTATTTCGGTAATTTCAC
***
64114521 AATCGA-GGGTAAAACGGTAATTTCAC
1 AATCGAGGGGTATTTCGGTAATTTCAC
*
64114547 AATTGAGGG
1 AATCGAGGG
64114556 TAAAACAGTA
Statistics
Matches: 111, Mismatches: 22, Indels: 17
0.74 0.15 0.11
Matches are distributed among these distances:
25 8 0.07
26 26 0.23
27 70 0.63
28 5 0.05
29 2 0.02
ACGTcount: A:0.31, C:0.12, G:0.22, T:0.35
Consensus pattern (27 bp):
AATCGAGGGGTATTTCGGTAATTTCAC
Found at i:64114540 original size:26 final size:26
Alignment explanation
Indices: 64114509--64114595 Score: 113
Period size: 26 Copynumber: 3.3 Consensus size: 26
64114499 AGGGGTATTT
64114509 CAGTAATTTCACAATCGAGGGTAAAA
1 CAGTAATTTCACAATCGAGGGTAAAA
* *
64114535 CGGTAATTTCACAATTGAGGGTAAAA
1 CAGTAATTTCACAATCGAGGGTAAAA
* *
64114561 CAGTAATTCTGTA-AATCAAGGGTAAAA
1 CAGTAATT-T-CACAATCGAGGGTAAAA
64114588 CAGTAATT
1 CAGTAATT
64114596 CTATAAATCG
Statistics
Matches: 53, Mismatches: 6, Indels: 3
0.85 0.10 0.05
Matches are distributed among these distances:
26 31 0.58
27 21 0.40
28 1 0.02
ACGTcount: A:0.41, C:0.13, G:0.20, T:0.26
Consensus pattern (26 bp):
CAGTAATTTCACAATCGAGGGTAAAA
Found at i:64114587 original size:27 final size:27
Alignment explanation
Indices: 64114552--64114611 Score: 102
Period size: 27 Copynumber: 2.2 Consensus size: 27
64114542 TTCACAATTG
*
64114552 AGGGTAAAACAGTAATTCTGTAAATCA
1 AGGGTAAAACAGTAATTCTATAAATCA
*
64114579 AGGGTAAAACAGTAATTCTATAAATCG
1 AGGGTAAAACAGTAATTCTATAAATCA
64114606 AGGGTA
1 AGGGTA
64114612 CTTTGGTAAT
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
27 31 1.00
ACGTcount: A:0.43, C:0.10, G:0.22, T:0.25
Consensus pattern (27 bp):
AGGGTAAAACAGTAATTCTATAAATCA
Found at i:64116997 original size:31 final size:31
Alignment explanation
Indices: 64116927--64117092 Score: 269
Period size: 31 Copynumber: 5.2 Consensus size: 31
64116917 CTGGGTATAT
*
64116927 AAGCCTTTTCATAAATCATATCACTGGGCTGACCG
1 AAGCCTTATCATAAATCATATCACT-GG--G-CCG
64116962 AAGCCTTATCATAAATCATATCACTGGGCCG
1 AAGCCTTATCATAAATCATATCACTGGGCCG
64116993 AAGCCTTATCATAAATCATATCACTGGGCCG
1 AAGCCTTATCATAAATCATATCACTGGGCCG
*
64117024 AAGCCTTATCATAAATCATATCTCTGGGCCG
1 AAGCCTTATCATAAATCATATCACTGGGCCG
*
64117055 ACGCCTTATCATAAATCATATCACTGGGCCG
1 AAGCCTTATCATAAATCATATCACTGGGCCG
64117086 AAGCCTT
1 AAGCCTT
64117093 TACTGTAAAC
Statistics
Matches: 126, Mismatches: 5, Indels: 4
0.93 0.04 0.03
Matches are distributed among these distances:
31 99 0.79
32 1 0.01
34 2 0.02
35 24 0.19
ACGTcount: A:0.30, C:0.27, G:0.16, T:0.27
Consensus pattern (31 bp):
AAGCCTTATCATAAATCATATCACTGGGCCG
Found at i:64117330 original size:23 final size:24
Alignment explanation
Indices: 64117299--64117355 Score: 89
Period size: 24 Copynumber: 2.4 Consensus size: 24
64117289 CTGGAGGCCT
64117299 AGCCTCTTTTAAT-AACTGGGGCAA
1 AGCC-CTTTTAATAAACTGGGGCAA
*
64117323 AGCCCTTTTGATAAACTGGGGCAA
1 AGCCCTTTTAATAAACTGGGGCAA
64117347 AGCCCTTTT
1 AGCCCTTTT
64117356 CGGTAAATTA
Statistics
Matches: 31, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
23 7 0.23
24 24 0.77
ACGTcount: A:0.26, C:0.23, G:0.21, T:0.30
Consensus pattern (24 bp):
AGCCCTTTTAATAAACTGGGGCAA
Found at i:64117369 original size:25 final size:24
Alignment explanation
Indices: 64117299--64117380 Score: 85
Period size: 24 Copynumber: 3.4 Consensus size: 24
64117289 CTGGAGGCCT
* *
64117299 AGCCTCTTTTAAT-AACTGGGGCAA
1 AGCC-CTTTTGATAAACTAGGGCAA
*
64117323 AGCCCTTTTGATAAACTGGGGCAA
1 AGCCCTTTTGATAAACTAGGGCAA
* * *
64117347 AGCCCTTTTCGGTAAATTAGGGCAT
1 AGCCCTTTT-GATAAACTAGGGCAA
64117372 AGCCCTTTT
1 AGCCCTTTT
64117381 AGCACTTCCT
Statistics
Matches: 51, Mismatches: 5, Indels: 3
0.86 0.08 0.05
Matches are distributed among these distances:
23 7 0.14
24 24 0.47
25 20 0.39
ACGTcount: A:0.26, C:0.22, G:0.22, T:0.30
Consensus pattern (24 bp):
AGCCCTTTTGATAAACTAGGGCAA
Found at i:64118085 original size:27 final size:27
Alignment explanation
Indices: 64118055--64118119 Score: 69
Period size: 27 Copynumber: 2.4 Consensus size: 27
64118045 GGGCATATTT
64118055 GTCATTTTACCATACAAGGG-TATTACG
1 GTCATTTTACCATACAAGGGCT-TTACG
* * * *
64118082 GTCACTTTACCCTACAGGGGCTTTACT
1 GTCATTTTACCATACAAGGGCTTTACG
*
64118109 GTCTTTTTACC
1 GTCATTTTACC
64118120 TATTAGGTGT
Statistics
Matches: 31, Mismatches: 6, Indels: 2
0.79 0.15 0.05
Matches are distributed among these distances:
27 30 0.97
28 1 0.03
ACGTcount: A:0.22, C:0.25, G:0.17, T:0.37
Consensus pattern (27 bp):
GTCATTTTACCATACAAGGGCTTTACG
Found at i:64118281 original size:27 final size:27
Alignment explanation
Indices: 64118153--64118392 Score: 155
Period size: 27 Copynumber: 8.8 Consensus size: 27
64118143 CATCCTACAA
* * * * *
64118153 GGGTGTTTTGGTAAATCTACAAACCAA
1 GGGTATTTTGGTAATTTTACAAATCAG
* ** * *
64118180 GGGTATTTTAGTAATTTTGTAAACCAA
1 GGGTATTTTGGTAATTTTACAAATCAG
* * * *
64118207 TGGTATTTCT-ATAATTTTTAGAAAGTCAA
1 GGGTATTT-TGGTAA-TTTTACAAA-TCAG
* **
64118236 GGGTATTTTTGTAATTTTATGAATCAG
1 GGGTATTTTGGTAATTTTACAAATCAG
*
64118263 GGGTATTTTGGTAATTTTACAAAT-TG
1 GGGTATTTTGGTAATTTTACAAATCAG
* * *
64118289 AGGGTATTTCGGTAATTTCACAAACCAG
1 -GGGTATTTTGGTAATTTTACAAATCAG
*
64118317 TGGTATTTTGGTAATTTTACAAA-CTAG
1 GGGTATTTTGGTAATTTTACAAATC-AG
* **
64118344 GGGTATTTTGGTAATTCTACCCTAT-AG
1 GGGTATTTTGGTAATTTTA-CAAATCAG
* *
64118371 GGGTATTTTAGTAATTTCACAA
1 GGGTATTTTGGTAATTTTACAA
64118393 TTGAGGGTAA
Statistics
Matches: 168, Mismatches: 36, Indels: 19
0.75 0.16 0.09
Matches are distributed among these distances:
26 3 0.02
27 133 0.79
28 19 0.11
29 13 0.08
ACGTcount: A:0.30, C:0.10, G:0.20, T:0.40
Consensus pattern (27 bp):
GGGTATTTTGGTAATTTTACAAATCAG
Found at i:64118375 original size:81 final size:81
Alignment explanation
Indices: 64118237--64118392 Score: 199
Period size: 81 Copynumber: 1.9 Consensus size: 81
64118227 GAAAGTCAAG
* ** * * *
64118237 GGTATTTTTGTAATTTTATGAATCAGGGGTATTTTGGTAATTTTACAAATTGAGGGTATTTCGGT
1 GGTATTTTGGTAATTTTACAAATCAGGGGTATTTTGGTAATTCTACAAATAGAGGGTATTTCAGT
64118302 AATTTCACAAACCAGT
66 AATTTCACAAACCAGT
** *
64118318 GGTATTTTGGTAATTTTACAAA-CTAGGGGTATTTTGGTAATTCTACCCTATAG-GGGTATTTTA
1 GGTATTTTGGTAATTTTACAAATC-AGGGGTATTTTGGTAATTCTA-CAAATAGAGGGTATTTCA
64118381 GTAATTTCACAA
64 GTAATTTCACAA
64118393 TTGAGGGTAA
Statistics
Matches: 64, Mismatches: 9, Indels: 4
0.83 0.12 0.05
Matches are distributed among these distances:
80 1 0.02
81 59 0.92
82 4 0.06
ACGTcount: A:0.28, C:0.10, G:0.21, T:0.42
Consensus pattern (81 bp):
GGTATTTTGGTAATTTTACAAATCAGGGGTATTTTGGTAATTCTACAAATAGAGGGTATTTCAGT
AATTTCACAAACCAGT
Found at i:64118410 original size:26 final size:26
Alignment explanation
Indices: 64118381--64118465 Score: 91
Period size: 26 Copynumber: 3.2 Consensus size: 26
64118371 GGGTATTTTA
*
64118381 GTAATTTCACAATTGAGGGTAAAACG
1 GTAATTTCACAATCGAGGGTAAAACG
**
64118407 GTAATTTCACAATCGAGGGTAAAATA
1 GTAATTTCACAATCGAGGGTAAAACG
* * *
64118433 GTAATTCTGTA-AATCAAGGGTAAAACA
1 GTAATT-T-CACAATCGAGGGTAAAACG
64118460 GTAATT
1 GTAATT
64118466 CTATAAATCG
Statistics
Matches: 51, Mismatches: 6, Indels: 3
0.85 0.10 0.05
Matches are distributed among these distances:
26 29 0.57
27 21 0.41
28 1 0.02
ACGTcount: A:0.41, C:0.11, G:0.20, T:0.28
Consensus pattern (26 bp):
GTAATTTCACAATCGAGGGTAAAACG
Found at i:64118455 original size:27 final size:27
Alignment explanation
Indices: 64118395--64118481 Score: 106
Period size: 27 Copynumber: 3.3 Consensus size: 27
64118385 TTTCACAATT
* *
64118395 GAGGGTAAAACGGTAATT-TCA-CAATC
1 GAGGGTAAAACAGTAATTCT-ATAAATC
* *
64118421 GAGGGTAAAATAGTAATTCTGTAAATC
1 GAGGGTAAAACAGTAATTCTATAAATC
*
64118448 AAGGGTAAAACAGTAATTCTATAAATC
1 GAGGGTAAAACAGTAATTCTATAAATC
64118475 GAGGGTA
1 GAGGGTA
64118482 CTTTGGTAAT
Statistics
Matches: 51, Mismatches: 8, Indels: 3
0.82 0.13 0.05
Matches are distributed among these distances:
26 16 0.31
27 35 0.69
ACGTcount: A:0.41, C:0.10, G:0.23, T:0.25
Consensus pattern (27 bp):
GAGGGTAAAACAGTAATTCTATAAATC
Found at i:64121533 original size:20 final size:21
Alignment explanation
Indices: 64121510--64121556 Score: 53
Period size: 20 Copynumber: 2.3 Consensus size: 21
64121500 AGCTCCGTCC
*
64121510 AGCTCAA-TTCAGCTCATTTG
1 AGCTCAATTTAAGCTCATTTG
* *
64121530 AGCT-AATTTAAGTTCGTTTG
1 AGCTCAATTTAAGCTCATTTG
64121550 AGCTCAA
1 AGCTCAA
64121557 CCGAGCTTAC
Statistics
Matches: 22, Mismatches: 3, Indels: 3
0.79 0.11 0.11
Matches are distributed among these distances:
19 2 0.09
20 18 0.82
21 2 0.09
ACGTcount: A:0.28, C:0.19, G:0.17, T:0.36
Consensus pattern (21 bp):
AGCTCAATTTAAGCTCATTTG
Found at i:64124132 original size:16 final size:16
Alignment explanation
Indices: 64124109--64124173 Score: 64
Period size: 16 Copynumber: 4.1 Consensus size: 16
64124099 AAGAGAAAAC
64124109 AAAG-AAAAGAAAAGA
1 AAAGAAAAAGAAAAGA
64124124 AAAGAAAAAGCAAAAGA
1 AAAGAAAAAG-AAAAGA
*
64124141 AGA-AAAAAGAAAATG-
1 AAAGAAAAAGAAAA-GA
*
64124156 AAATAAAAAGAAAGAGA
1 AAAGAAAAAGAAA-AGA
64124173 A
1 A
64124174 GCAAGAGGCA
Statistics
Matches: 42, Mismatches: 2, Indels: 10
0.78 0.04 0.19
Matches are distributed among these distances:
15 10 0.24
16 22 0.52
17 10 0.24
ACGTcount: A:0.77, C:0.02, G:0.18, T:0.03
Consensus pattern (16 bp):
AAAGAAAAAGAAAAGA
Found at i:64124138 original size:6 final size:5
Alignment explanation
Indices: 64124109--64124173 Score: 62
Period size: 5 Copynumber: 12.2 Consensus size: 5
64124099 AAGAGAAAAC
64124109 AAAGA AAAGA AAAGA AAAGAA AAAGCA AAAGA AGAA-A AAAGA AAATGA
1 AAAGA AAAGA AAAGA AAAG-A AAAG-A AAAGA A-AAGA AAAGA AAA-GA
64124157 AATA-A AAAGA AAGAGA A
1 AA-AGA AAAGA AA-AGA A
64124174 GCAAGAGGCA
Statistics
Matches: 52, Mismatches: 1, Indels: 13
0.79 0.02 0.20
Matches are distributed among these distances:
4 3 0.06
5 28 0.54
6 20 0.38
7 1 0.02
ACGTcount: A:0.77, C:0.02, G:0.18, T:0.03
Consensus pattern (5 bp):
AAAGA
Found at i:64124151 original size:32 final size:32
Alignment explanation
Indices: 64124113--64124174 Score: 83
Period size: 32 Copynumber: 1.9 Consensus size: 32
64124103 GAAAACAAAG
64124113 AAAAGAAAA-GAAAAGAAAAAGCAAA-AGAAGAA
1 AAAAGAAAATG-AAAGAAAAAG-AAAGAGAAGAA
*
64124145 AAAAGAAAATGAAATAAAAAGAAAGAGAAG
1 AAAAGAAAATGAAAGAAAAAGAAAGAGAAG
64124175 CAAGAGGCAA
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
31 3 0.11
32 23 0.85
33 1 0.04
ACGTcount: A:0.76, C:0.02, G:0.19, T:0.03
Consensus pattern (32 bp):
AAAAGAAAATGAAAGAAAAAGAAAGAGAAGAA
Found at i:64124289 original size:30 final size:31
Alignment explanation
Indices: 64124239--64124309 Score: 85
Period size: 30 Copynumber: 2.4 Consensus size: 31
64124229 TTTGAAAAGA
* *
64124239 AAAAAGAAA-ATGAGATTGAAAAAG-AGAATG
1 AAAAAGAAATTTGAGAGTGAAAAAGAAG-ATG
*
64124269 -AAAAGAAATTTGAGAGTGAAAAGGAAGATG
1 AAAAAGAAATTTGAGAGTGAAAAAGAAGATG
64124299 AAAAAGAAATT
1 AAAAAGAAATT
64124310 GAAACAAAAG
Statistics
Matches: 35, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
29 8 0.23
30 15 0.43
31 12 0.34
ACGTcount: A:0.61, C:0.00, G:0.24, T:0.15
Consensus pattern (31 bp):
AAAAAGAAATTTGAGAGTGAAAAAGAAGATG
Found at i:64125188 original size:30 final size:29
Alignment explanation
Indices: 64125093--64125189 Score: 70
Period size: 30 Copynumber: 3.2 Consensus size: 29
64125083 AGCTCACTCC
* *
64125093 TAGCTC-ACTTTCAACTCACGAGCTAAACCT
1 TAGCTCAACTTT-AGCTCACGA-CTAAAGCT
* * * * **
64125123 TAGCTCAACTTCAGCTTAGGAGTTTAGCCT
1 TAGCTCAACTTTAGCTCACGACTAAAG-CT
*
64125153 CAGCTCAACTTTAGCTCACGACCTAAAGCT
1 TAGCTCAACTTTAGCTCACGA-CTAAAGCT
64125183 TAGCTCA
1 TAGCTCA
64125190 TTTTAGTTTA
Statistics
Matches: 48, Mismatches: 16, Indels: 6
0.69 0.23 0.09
Matches are distributed among these distances:
29 2 0.04
30 39 0.81
31 7 0.15
ACGTcount: A:0.28, C:0.30, G:0.14, T:0.28
Consensus pattern (29 bp):
TAGCTCAACTTTAGCTCACGACTAAAGCT
Found at i:64126890 original size:24 final size:26
Alignment explanation
Indices: 64126861--64126908 Score: 82
Period size: 24 Copynumber: 1.9 Consensus size: 26
64126851 TTATACAAGT
64126861 AAAAAAAA-TTCGAAAA-AAAAAATC
1 AAAAAAAATTTCGAAAAGAAAAAATC
64126885 AAAAAAAATTTCGAAAAGAAAAAA
1 AAAAAAAATTTCGAAAAGAAAAAA
64126909 AAAATCTGAA
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
24 8 0.36
25 8 0.36
26 6 0.27
ACGTcount: A:0.75, C:0.06, G:0.06, T:0.12
Consensus pattern (26 bp):
AAAAAAAATTTCGAAAAGAAAAAATC
Found at i:64126912 original size:24 final size:23
Alignment explanation
Indices: 64126861--64126912 Score: 70
Period size: 25 Copynumber: 2.2 Consensus size: 23
64126851 TTATACAAGT
64126861 AAAAAAAATTCGAAAAAAAAAATC
1 AAAAAAAATTCGAAAAAAAAAA-C
*
64126885 AAAAAAAATTTCGAAAAGAAAAA-
1 AAAAAAAA-TTCGAAAAAAAAAAC
64126908 AAAAA
1 AAAAA
64126913 TCTGAAAAAA
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
23 5 0.19
24 8 0.31
25 13 0.50
ACGTcount: A:0.77, C:0.06, G:0.06, T:0.12
Consensus pattern (23 bp):
AAAAAAAATTCGAAAAAAAAAAC
Found at i:64126924 original size:18 final size:20
Alignment explanation
Indices: 64126885--64126924 Score: 57
Period size: 20 Copynumber: 2.1 Consensus size: 20
64126875 AAAAAAAATC
*
64126885 AAAAAAAATTTCGAAAAGAA
1 AAAAAAAATCTCGAAAAGAA
64126905 AAAAAAAATCT-GAAAA-AA
1 AAAAAAAATCTCGAAAAGAA
64126923 AA
1 AA
64126925 GTGTTTAATG
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
18 4 0.21
19 5 0.26
20 10 0.53
ACGTcount: A:0.75, C:0.05, G:0.07, T:0.12
Consensus pattern (20 bp):
AAAAAAAATCTCGAAAAGAA
Found at i:64132246 original size:15 final size:15
Alignment explanation
Indices: 64132226--64132280 Score: 69
Period size: 15 Copynumber: 3.8 Consensus size: 15
64132216 ACTCTCCTCA
*
64132226 TTCTTTTCTTTCTTT
1 TTCTTTTCTCTCTTT
*
64132241 TTCTTTTCACTCTTT
1 TTCTTTTCTCTCTTT
*
64132256 TTGTTTT-TCTCTTT
1 TTCTTTTCTCTCTTT
64132270 TTCTTTT-TCTC
1 TTCTTTTCTCTC
64132281 GATCAATAGA
Statistics
Matches: 35, Mismatches: 5, Indels: 1
0.85 0.12 0.02
Matches are distributed among these distances:
14 16 0.46
15 19 0.54
ACGTcount: A:0.02, C:0.22, G:0.02, T:0.75
Consensus pattern (15 bp):
TTCTTTTCTCTCTTT
Found at i:64134341 original size:17 final size:17
Alignment explanation
Indices: 64134307--64134341 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
64134297 TTCTCTTTTT
*
64134307 TTTTTTTTAATTCCGAA
1 TTTTTTTTAATACCGAA
*
64134324 TTTTTTTTAATACTGAA
1 TTTTTTTTAATACCGAA
64134341 T
1 T
64134342 ACACAAAGAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.26, C:0.09, G:0.06, T:0.60
Consensus pattern (17 bp):
TTTTTTTTAATACCGAA
Found at i:64136046 original size:9 final size:10
Alignment explanation
Indices: 64136039--64136095 Score: 55
Period size: 11 Copynumber: 5.5 Consensus size: 10
64136029 ATCAGAAAAC
64136039 AAAGAAAAGA
1 AAAGAAAAGA
64136049 AAAGAAAAAGCA
1 AAAG-AAAAG-A
*
64136061 AAAGAAGA-A
1 AAAGAAAAGA
64136070 AAAGAAAATGA
1 AAAGAAAA-GA
64136081 AATA-AAAAGA
1 AA-AGAAAAGA
64136091 AAAGA
1 AAAGA
64136096 GAGGTAAGAG
Statistics
Matches: 39, Mismatches: 2, Indels: 12
0.74 0.04 0.23
Matches are distributed among these distances:
9 9 0.23
10 9 0.23
11 15 0.38
12 6 0.15
ACGTcount: A:0.77, C:0.02, G:0.18, T:0.04
Consensus pattern (10 bp):
AAAGAAAAGA
Found at i:64136063 original size:6 final size:5
Alignment explanation
Indices: 64136039--64136095 Score: 55
Period size: 5 Copynumber: 11.0 Consensus size: 5
64136029 ATCAGAAAAC
*
64136039 AAAGA AAAGA AAAGAA AAAGCA AAAGA AGA-A AAAGA AAATGA AATA-A
1 AAAGA AAAGA AAAG-A AAAG-A AAAGA AAAGA AAAGA AAA-GA AA-AGA
64136086 AAAGA AAAGA
1 AAAGA AAAGA
64136096 GAGGTAAGAG
Statistics
Matches: 44, Mismatches: 3, Indels: 10
0.77 0.05 0.18
Matches are distributed among these distances:
4 4 0.09
5 25 0.57
6 14 0.32
7 1 0.02
ACGTcount: A:0.77, C:0.02, G:0.18, T:0.04
Consensus pattern (5 bp):
AAAGA
Found at i:64136070 original size:15 final size:14
Alignment explanation
Indices: 64136039--64136095 Score: 60
Period size: 16 Copynumber: 3.7 Consensus size: 14
64136029 ATCAGAAAAC
64136039 AAAGAAAAGAAAAGAA
1 AAAGAAAAG--AAGAA
64136055 AAAGCAAAAGAAGAA
1 AAAG-AAAAGAAGAA
*
64136070 AAAGAAAATGAAATAA
1 AAAGAAAA-G-AAGAA
64136086 AAAGAAAAGA
1 AAAGAAAAGA
64136096 GAGGTAAGAG
Statistics
Matches: 37, Mismatches: 1, Indels: 8
0.80 0.02 0.17
Matches are distributed among these distances:
14 5 0.14
15 11 0.30
16 16 0.43
17 5 0.14
ACGTcount: A:0.77, C:0.02, G:0.18, T:0.04
Consensus pattern (14 bp):
AAAGAAAAGAAGAA
Found at i:64136172 original size:12 final size:12
Alignment explanation
Indices: 64136164--64136188 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
64136154 TTTGAAAAGC
64136164 AAAAAGAAAATG
1 AAAAAGAAAATG
64136176 AAAAAGAAAATG
1 AAAAAGAAAATG
64136188 A
1 A
64136189 GATTGAAAAA
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:0.76, C:0.00, G:0.16, T:0.08
Consensus pattern (12 bp):
AAAAAGAAAATG
Found at i:64136185 original size:18 final size:18
Alignment explanation
Indices: 64136158--64136213 Score: 51
Period size: 18 Copynumber: 3.1 Consensus size: 18
64136148 AAAGCCTTTG
64136158 AAAAGCAAAAAGAAAATGA
1 AAAAG-AAAAAGAAAATGA
* * *
64136177 AAAAGAAAATGAGATTGA
1 AAAAGAAAAAGAAAATGA
* *
64136195 AAAAGAGAACGAAAA-GA
1 AAAAGAAAAAGAAAATGA
64136212 AA
1 AA
64136214 TTTGAGAGTG
Statistics
Matches: 30, Mismatches: 7, Indels: 2
0.77 0.18 0.05
Matches are distributed among these distances:
17 4 0.13
18 21 0.70
19 5 0.17
ACGTcount: A:0.70, C:0.04, G:0.20, T:0.07
Consensus pattern (18 bp):
AAAAGAAAAAGAAAATGA
Found at i:64136198 original size:30 final size:31
Alignment explanation
Indices: 64136164--64136245 Score: 105
Period size: 30 Copynumber: 2.7 Consensus size: 31
64136154 TTTGAAAAGC
*
64136164 AAAAAGAAAATGAAAAAGAAA-ATGAGATTG
1 AAAAAGAAAATGAAAAAGAAATATGAGAGTG
* * *
64136194 AAAAAGAGAACG-AAAAGAAATTTGAGAGTG
1 AAAAAGAAAATGAAAAAGAAATATGAGAGTG
*
64136224 AAAAAGAATATGAAAAAGAAAT
1 AAAAAGAAAATGAAAAAGAAAT
64136246 TGAAATAAAA
Statistics
Matches: 43, Mismatches: 7, Indels: 3
0.81 0.13 0.06
Matches are distributed among these distances:
29 8 0.19
30 26 0.60
31 9 0.21
ACGTcount: A:0.65, C:0.01, G:0.21, T:0.13
Consensus pattern (31 bp):
AAAAAGAAAATGAAAAAGAAATATGAGAGTG
Found at i:64139129 original size:21 final size:22
Alignment explanation
Indices: 64139090--64139133 Score: 63
Period size: 21 Copynumber: 2.0 Consensus size: 22
64139080 ATGCATACTC
64139090 CTTCAAGCTCAAATCAGCTCAA
1 CTTCAAGCTCAAATCAGCTCAA
* *
64139112 CTTCAA-CTCAACTTAGCTCAA
1 CTTCAAGCTCAAATCAGCTCAA
64139133 C
1 C
64139134 GAGCTCGTTT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
21 14 0.70
22 6 0.30
ACGTcount: A:0.34, C:0.34, G:0.07, T:0.25
Consensus pattern (22 bp):
CTTCAAGCTCAAATCAGCTCAA
Found at i:64139674 original size:47 final size:45
Alignment explanation
Indices: 64139609--64139697 Score: 160
Period size: 47 Copynumber: 1.9 Consensus size: 45
64139599 ATAGGATGAG
64139609 ATAAGGCTAAAGATGCGGAAGCTTTCAAATGGTTTTAAAAGGTGATA
1 ATAAGGCTAAAGATGCGGAAGCTTT-AAATGGTTTT-AAAGGTGATA
64139656 ATAAGGCTAAAGATGCGGAAGCTTTAAATGGTTTTAAAGGTG
1 ATAAGGCTAAAGATGCGGAAGCTTTAAATGGTTTTAAAGGTG
64139698 GCTAAGGATG
Statistics
Matches: 42, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
45 7 0.17
46 10 0.24
47 25 0.60
ACGTcount: A:0.37, C:0.08, G:0.27, T:0.28
Consensus pattern (45 bp):
ATAAGGCTAAAGATGCGGAAGCTTTAAATGGTTTTAAAGGTGATA
Found at i:64140081 original size:7 final size:7
Alignment explanation
Indices: 64140069--64140098 Score: 60
Period size: 7 Copynumber: 4.3 Consensus size: 7
64140059 ATTCAAATGA
64140069 TCAAAAG
1 TCAAAAG
64140076 TCAAAAG
1 TCAAAAG
64140083 TCAAAAG
1 TCAAAAG
64140090 TCAAAAG
1 TCAAAAG
64140097 TC
1 TC
64140099 CTTTACAAAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 23 1.00
ACGTcount: A:0.53, C:0.17, G:0.13, T:0.17
Consensus pattern (7 bp):
TCAAAAG
Found at i:64141145 original size:30 final size:30
Alignment explanation
Indices: 64141111--64141207 Score: 106
Period size: 30 Copynumber: 3.2 Consensus size: 30
64141101 TAAACTAAAA
*
64141111 TGAGCTAAGTTTTAGCTCGTGAGCTAAAGT
1 TGAGCTAAGGTTTAGCTCGTGAGCTAAAGT
* * * * * * *
64141141 TGAGCTGAGGCTAAACTCCTAAGCTGAAGT
1 TGAGCTAAGGTTTAGCTCGTGAGCTAAAGT
64141171 TGAGCTAAGGTTTAGCTCGTGAGCTAAA-T
1 TGAGCTAAGGTTTAGCTCGTGAGCTAAAGT
64141200 ATGAGCTA
1 -TGAGCTA
64141208 GGAGTGAGCT
Statistics
Matches: 51, Mismatches: 15, Indels: 2
0.75 0.22 0.03
Matches are distributed among these distances:
29 1 0.02
30 50 0.98
ACGTcount: A:0.29, C:0.15, G:0.27, T:0.29
Consensus pattern (30 bp):
TGAGCTAAGGTTTAGCTCGTGAGCTAAAGT
Found at i:64143404 original size:12 final size:12
Alignment explanation
Indices: 64143389--64143419 Score: 62
Period size: 12 Copynumber: 2.6 Consensus size: 12
64143379 TTCTTTTTGC
64143389 TTTTCAAAGGCT
1 TTTTCAAAGGCT
64143401 TTTTCAAAGGCT
1 TTTTCAAAGGCT
64143413 TTTTCAA
1 TTTTCAA
64143420 GTTCTCTCAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.26, C:0.16, G:0.13, T:0.45
Consensus pattern (12 bp):
TTTTCAAAGGCT
Found at i:64143496 original size:6 final size:6
Alignment explanation
Indices: 64143480--64143529 Score: 50
Period size: 6 Copynumber: 8.2 Consensus size: 6
64143470 TTTCTTTTTA
*
64143480 TTTCAT TTTCTT TTTCTT CTCTTGCTT TTTCTT TTTC-T TTTC-T TTTCTT
1 TTTCTT TTTCTT TTTCTT -T-TT-CTT TTTCTT TTTCTT TTTCTT TTTCTT
64143529 T
1 T
64143530 GTTTTCTCTT
Statistics
Matches: 39, Mismatches: 1, Indels: 8
0.81 0.02 0.17
Matches are distributed among these distances:
5 10 0.26
6 20 0.51
7 3 0.08
8 3 0.08
9 3 0.08
ACGTcount: A:0.02, C:0.20, G:0.02, T:0.76
Consensus pattern (6 bp):
TTTCTT
Found at i:64143512 original size:37 final size:37
Alignment explanation
Indices: 64143469--64143539 Score: 101
Period size: 37 Copynumber: 1.9 Consensus size: 37
64143459 CTTGCCTCTC
64143469 TTTTCTTTTT-ATTTCATTTTCTTT-TTCTTCTCTTGCT
1 TTTTCTTTTTCATTTC-TTTTCTTTGTT-TTCTCTTGCT
*
64143506 TTTTCTTTTTCTTTTCTTTTCTTTGTTTTCTCTT
1 TTTTCTTTTTCATTTCTTTTCTTTGTTTTCTCTT
64143540 TACAAGAATG
Statistics
Matches: 31, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
37 25 0.81
38 6 0.19
ACGTcount: A:0.03, C:0.18, G:0.03, T:0.76
Consensus pattern (37 bp):
TTTTCTTTTTCATTTCTTTTCTTTGTTTTCTCTTGCT
Found at i:64143540 original size:16 final size:16
Alignment explanation
Indices: 64143465--64143525 Score: 63
Period size: 16 Copynumber: 3.8 Consensus size: 16
64143455 GCCTCTTGCC
*
64143465 TCTCTTTTCTTTTTAT
1 TCTCTTTTCTTTTTCT
64143481 T-TCATTTTCTTTTTCT
1 TCTC-TTTTCTTTTTCT
*
64143497 TCTC-TTGCTTTTTCTT
1 TCTCTTTTCTTTTTC-T
*
64143513 TTTCTTTTCTTTT
1 TCTCTTTTCTTTT
64143526 CTTTGTTTTC
Statistics
Matches: 37, Mismatches: 4, Indels: 7
0.77 0.08 0.15
Matches are distributed among these distances:
15 11 0.30
16 17 0.46
17 9 0.24
ACGTcount: A:0.03, C:0.20, G:0.02, T:0.75
Consensus pattern (16 bp):
TCTCTTTTCTTTTTCT
Found at i:64144478 original size:11 final size:12
Alignment explanation
Indices: 64144452--64144495 Score: 56
Period size: 11 Copynumber: 3.7 Consensus size: 12
64144442 TTTAACTCGA
64144452 TTTTTTTTGTCAC
1 TTTTTTTT-TCAC
64144465 TTTTTTTTTC-C
1 TTTTTTTTTCAC
64144476 TTTTTTTTTCGA-
1 TTTTTTTTTC-AC
64144488 TTTTTTTT
1 TTTTTTTT
64144496 GAATTTTTTT
Statistics
Matches: 29, Mismatches: 0, Indels: 5
0.85 0.00 0.15
Matches are distributed among these distances:
11 11 0.38
12 10 0.34
13 8 0.28
ACGTcount: A:0.05, C:0.11, G:0.05, T:0.80
Consensus pattern (12 bp):
TTTTTTTTTCAC
Found at i:64144628 original size:14 final size:12
Alignment explanation
Indices: 64144600--64144642 Score: 54
Period size: 10 Copynumber: 3.6 Consensus size: 12
64144590 CAAAAAAAAA
64144600 TTTTTTTTTGA-
1 TTTTTTTTTGAT
64144611 -TTTTTTTTGACT
1 TTTTTTTTTGA-T
64144623 TCTTTTTTTTGAT
1 T-TTTTTTTTGAT
64144636 TTTTTTT
1 TTTTTTT
64144643 CGTTACGAAC
Statistics
Matches: 28, Mismatches: 0, Indels: 7
0.80 0.00 0.20
Matches are distributed among these distances:
10 10 0.36
12 6 0.21
13 2 0.07
14 10 0.36
ACGTcount: A:0.07, C:0.05, G:0.07, T:0.81
Consensus pattern (12 bp):
TTTTTTTTTGAT
Found at i:64146351 original size:30 final size:29
Alignment explanation
Indices: 64146252--64146353 Score: 98
Period size: 30 Copynumber: 3.4 Consensus size: 29
64146242 CGAGTTTAAA
*
64146252 CTAAAATGAGCTAA-GTTTAGCTCGTGAG
1 CTAAATTGAGCTAAGGTTTAGCTCGTGAG
* * * * * *
64146280 CTAAAGTTGAGCTGAGGCTAAACTCCTAAG
1 CTAAA-TTGAGCTAAGGTTTAGCTCGTGAG
*
64146310 CTGAAGTTGAGCTAAGGTTTAGCTCGTGAG
1 CT-AAATTGAGCTAAGGTTTAGCTCGTGAG
64146340 CTAAATATGAGCTA
1 CTAAAT-TGAGCTA
64146354 GGAGTGAGCT
Statistics
Matches: 55, Mismatches: 15, Indels: 6
0.72 0.20 0.08
Matches are distributed among these distances:
28 5 0.09
29 10 0.18
30 38 0.69
31 2 0.04
ACGTcount: A:0.31, C:0.16, G:0.25, T:0.27
Consensus pattern (29 bp):
CTAAATTGAGCTAAGGTTTAGCTCGTGAG
Found at i:64148546 original size:12 final size:12
Alignment explanation
Indices: 64148531--64148561 Score: 62
Period size: 12 Copynumber: 2.6 Consensus size: 12
64148521 TTCTTTTTGC
64148531 TTTTCAAAGGCT
1 TTTTCAAAGGCT
64148543 TTTTCAAAGGCT
1 TTTTCAAAGGCT
64148555 TTTTCAA
1 TTTTCAA
64148562 GTTCTCTCAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.26, C:0.16, G:0.13, T:0.45
Consensus pattern (12 bp):
TTTTCAAAGGCT
Found at i:64148631 original size:6 final size:6
Alignment explanation
Indices: 64148622--64148671 Score: 59
Period size: 6 Copynumber: 8.2 Consensus size: 6
64148612 TTTCTTTTTA
64148622 TTTCTT TTTCTT TTTCTT CTCTTGCTT TTTCTT TTTC-T TTTC-T TTTCTT
1 TTTCTT TTTCTT TTTCTT -T-TT-CTT TTTCTT TTTCTT TTTCTT TTTCTT
64148671 T
1 T
64148672 GTTTTCTCTT
Statistics
Matches: 40, Mismatches: 0, Indels: 8
0.83 0.00 0.17
Matches are distributed among these distances:
5 10 0.25
6 21 0.52
7 3 0.08
8 3 0.08
9 3 0.08
ACGTcount: A:0.00, C:0.20, G:0.02, T:0.78
Consensus pattern (6 bp):
TTTCTT
Found at i:64148633 original size:21 final size:20
Alignment explanation
Indices: 64148609--64148671 Score: 63
Period size: 21 Copynumber: 3.0 Consensus size: 20
64148599 CTCTTGCCTC
64148609 TCTTTTCTTTTTATTTCTTTT
1 TCTTTTCTTTTT-TTTCTTTT
* * *
64148630 TCTTTTTCTTCTCTTGCTTTT
1 TC-TTTTCTTTTTTTTCTTTT
64148651 TCTTTTTCTTTTCTTTTCTTT
1 TC-TTTTCTTTT-TTTTCTTT
64148672 GTTTTCTCTT
Statistics
Matches: 34, Mismatches: 6, Indels: 3
0.79 0.14 0.07
Matches are distributed among these distances:
21 20 0.59
22 14 0.41
ACGTcount: A:0.02, C:0.19, G:0.02, T:0.78
Consensus pattern (20 bp):
TCTTTTCTTTTTTTTCTTTT
Found at i:64148654 original size:37 final size:37
Alignment explanation
Indices: 64148611--64148681 Score: 101
Period size: 37 Copynumber: 1.9 Consensus size: 37
64148601 CTTGCCTCTC
64148611 TTTTCTTTTTA-TTTCTTTTTCTTT-TTCTTCTCTTGCT
1 TTTTCTTTTTATTTTC-TTTTCTTTGTT-TTCTCTTGCT
*
64148648 TTTTCTTTTTCTTTTCTTTTCTTTGTTTTCTCTT
1 TTTTCTTTTTATTTTCTTTTCTTTGTTTTCTCTT
64148682 TACAAGAATG
Statistics
Matches: 31, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
37 25 0.81
38 6 0.19
ACGTcount: A:0.01, C:0.18, G:0.03, T:0.77
Consensus pattern (37 bp):
TTTTCTTTTTATTTTCTTTTCTTTGTTTTCTCTTGCT
Found at i:64148681 original size:27 final size:26
Alignment explanation
Indices: 64148609--64148682 Score: 89
Period size: 27 Copynumber: 2.8 Consensus size: 26
64148599 CTCTTGCCTC
64148609 TCTTTTCTTT-TTATTTCTTTTTCTTT
1 TCTTTTCTTTGTT-TTTCTTTTTCTTT
*
64148635 T-TCTTCTCTTGCTTTTTCTTTTTCTTT
1 TCTTTTCT-TTG-TTTTTCTTTTTCTTT
64148662 TCTTTTCTTTGTTTTCTCTTT
1 TCTTTTCTTTGTTTT-TCTTT
64148683 ACAAGAATGT
Statistics
Matches: 41, Mismatches: 2, Indels: 9
0.79 0.04 0.17
Matches are distributed among these distances:
25 5 0.12
26 7 0.17
27 22 0.54
28 7 0.17
ACGTcount: A:0.01, C:0.19, G:0.03, T:0.77
Consensus pattern (26 bp):
TCTTTTCTTTGTTTTTCTTTTTCTTT
Found at i:64149722 original size:22 final size:20
Alignment explanation
Indices: 64149690--64149738 Score: 53
Period size: 20 Copynumber: 2.3 Consensus size: 20
64149680 GCCAAATTTA
64149690 TGAACTATTTTAATACATTAGTG
1 TGAAC-ATTTTAAT-CATT-GTG
* *
64149713 TGAACATTTTTATTATTGTG
1 TGAACATTTTAATCATTGTG
64149733 TGAACA
1 TGAACA
64149739 CCTAGATGCC
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
20 9 0.38
21 3 0.12
22 7 0.29
23 5 0.21
ACGTcount: A:0.33, C:0.08, G:0.14, T:0.45
Consensus pattern (20 bp):
TGAACATTTTAATCATTGTG
Found at i:64151825 original size:10 final size:10
Alignment explanation
Indices: 64151783--64151828 Score: 56
Period size: 10 Copynumber: 4.6 Consensus size: 10
64151773 AGCTCCGTCC
* *
64151783 AGCTCAATTC
1 AGCTCATTTG
64151793 AGCTCATTTG
1 AGCTCATTTG
*
64151803 AGATCATTTG
1 AGCTCATTTG
*
64151813 AGCTCGTTTG
1 AGCTCATTTG
64151823 AGCTCA
1 AGCTCA
64151829 ACTGAGCTTA
Statistics
Matches: 30, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
10 30 1.00
ACGTcount: A:0.24, C:0.22, G:0.20, T:0.35
Consensus pattern (10 bp):
AGCTCATTTG
Found at i:64151834 original size:20 final size:20
Alignment explanation
Indices: 64151783--64151836 Score: 63
Period size: 20 Copynumber: 2.7 Consensus size: 20
64151773 AGCTCCGTCC
*
64151783 AGCTCAATTCAGCTCATTTG
1 AGCTCAATTGAGCTCATTTG
* * *
64151803 AGATCATTTGAGCTCGTTTG
1 AGCTCAATTGAGCTCATTTG
*
64151823 AGCTCAACTGAGCT
1 AGCTCAATTGAGCT
64151837 TACTTTCAGT
Statistics
Matches: 27, Mismatches: 7, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
20 27 1.00
ACGTcount: A:0.24, C:0.22, G:0.20, T:0.33
Consensus pattern (20 bp):
AGCTCAATTGAGCTCATTTG
Found at i:64153813 original size:13 final size:13
Alignment explanation
Indices: 64153795--64153819 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
64153785 TGGTCATCAT
64153795 GGTGTGAACACAA
1 GGTGTGAACACAA
64153808 GGTGTGAACACA
1 GGTGTGAACACA
64153820 TGATCAATAC
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:0.36, C:0.16, G:0.32, T:0.16
Consensus pattern (13 bp):
GGTGTGAACACAA
Found at i:64155026 original size:27 final size:28
Alignment explanation
Indices: 64154982--64155050 Score: 72
Period size: 27 Copynumber: 2.5 Consensus size: 28
64154972 GAACATATTA
*
64154982 AAAAT-ATGTAATAGACTAAGACACA-TT
1 AAAATCATGTATTA-ACTAAGACACATTT
* *
64155009 AAAATCATGTATTAACTATGACATATTT
1 AAAATCATGTATTAACTAAGACACATTT
*
64155037 AAAA-CATGCATTAA
1 AAAATCATGTATTAA
64155051 AATTAAACAC
Statistics
Matches: 36, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
27 23 0.64
28 13 0.36
ACGTcount: A:0.49, C:0.12, G:0.09, T:0.30
Consensus pattern (28 bp):
AAAATCATGTATTAACTAAGACACATTT
Found at i:64155203 original size:20 final size:19
Alignment explanation
Indices: 64155178--64155226 Score: 62
Period size: 20 Copynumber: 2.5 Consensus size: 19
64155168 AAAAAATAGA
64155178 ATCAAGCTAAATGAGCTATC
1 ATCAAGCTAAATGAGCTA-C
* *
64155198 ATCAAGCCTAATTGAGCTAG
1 ATCAAG-CTAAATGAGCTAC
64155218 ATCAAGCTA
1 ATCAAGCTA
64155227 GATCAGCTTG
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
19 3 0.12
20 12 0.46
21 11 0.42
ACGTcount: A:0.39, C:0.20, G:0.16, T:0.24
Consensus pattern (19 bp):
ATCAAGCTAAATGAGCTAC
Found at i:64164782 original size:23 final size:22
Alignment explanation
Indices: 64164731--64164782 Score: 54
Period size: 23 Copynumber: 2.3 Consensus size: 22
64164721 CCTCGTCTTT
*
64164731 TTCTTTTGTTTCTTTTTCTAAC
1 TTCTTTTCTTTCTTTTTCTAAC
64164753 -TCATTTTCTCTTCTTTCTTC-AAC
1 TTC-TTTTCT-TTCTTT-TTCTAAC
64164776 TTCTTTT
1 TTCTTTT
64164783 TCAATTTCTT
Statistics
Matches: 25, Mismatches: 1, Indels: 7
0.76 0.03 0.21
Matches are distributed among these distances:
21 2 0.08
22 5 0.20
23 13 0.52
24 5 0.20
ACGTcount: A:0.10, C:0.23, G:0.02, T:0.65
Consensus pattern (22 bp):
TTCTTTTCTTTCTTTTTCTAAC
Found at i:64164791 original size:12 final size:12
Alignment explanation
Indices: 64164740--64164794 Score: 51
Period size: 12 Copynumber: 4.6 Consensus size: 12
64164730 TTTCTTTTGT
64164740 TTCTTTTTCTAAC
1 TTCTTTTTC-AAC
* *
64164753 -TCATTTTC-TC
1 TTCTTTTTCAAC
64164763 TTCTTTCTTCAAC
1 TTCTTT-TTCAAC
*
64164776 TTCTTTTTCAAT
1 TTCTTTTTCAAC
64164788 TTCTTTT
1 TTCTTTT
64164795 CTGTTTCACA
Statistics
Matches: 34, Mismatches: 5, Indels: 7
0.74 0.11 0.15
Matches are distributed among these distances:
10 1 0.03
11 4 0.12
12 22 0.65
13 7 0.21
ACGTcount: A:0.13, C:0.24, G:0.00, T:0.64
Consensus pattern (12 bp):
TTCTTTTTCAAC
Found at i:64164801 original size:17 final size:18
Alignment explanation
Indices: 64164776--64164813 Score: 51
Period size: 17 Copynumber: 2.2 Consensus size: 18
64164766 TTTCTTCAAC
* *
64164776 TTCTTTTTCA-ATTTCTT
1 TTCTGTTTCACATTCCTT
64164793 TTCTGTTTCACATTCCTT
1 TTCTGTTTCACATTCCTT
64164811 TTC
1 TTC
64164814 ACTCTCAATC
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
17 9 0.50
18 9 0.50
ACGTcount: A:0.11, C:0.24, G:0.03, T:0.63
Consensus pattern (18 bp):
TTCTGTTTCACATTCCTT
Found at i:64168200 original size:11 final size:12
Alignment explanation
Indices: 64168177--64168201 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
64168167 AAAAGAGAAG
64168177 AAATTCAAAAAA
1 AAATTCAAAAAA
64168189 AAATTCAAAAAA
1 AAATTCAAAAAA
64168201 A
1 A
64168202 TCGAAAAAAA
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:0.76, C:0.08, G:0.00, T:0.16
Consensus pattern (12 bp):
AAATTCAAAAAA
Found at i:64168235 original size:23 final size:23
Alignment explanation
Indices: 64168195--64168247 Score: 61
Period size: 23 Copynumber: 2.3 Consensus size: 23
64168185 AAAAAAATTC
* *
64168195 AAAAAAATCGAAAAAAAAGAAGT
1 AAAAAAATCGAAAAAAAAAAAGA
***
64168218 AAAAAAATCGAGTTAAAAAAAGA
1 AAAAAAATCGAAAAAAAAAAAGA
64168241 AAAAAAA
1 AAAAAAA
64168248 GTGAAAAGTC
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
23 25 1.00
ACGTcount: A:0.75, C:0.04, G:0.11, T:0.09
Consensus pattern (23 bp):
AAAAAAATCGAAAAAAAAAAAGA
Found at i:64168247 original size:26 final size:23
Alignment explanation
Indices: 64168195--64168247 Score: 61
Period size: 26 Copynumber: 2.2 Consensus size: 23
64168185 AAAAAAATTC
**
64168195 AAAAAAATCGAAAAAAAAGAAGT
1 AAAAAAATCGAAAAAAAAGAAAA
64168218 AAAAAAATCGAGTTAAAAAAAGAAAA
1 AAAAAAATCGA---AAAAAAAGAAAA
64168244 AAAA
1 AAAA
64168248 GTGAAAAGTC
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
23 11 0.44
26 14 0.56
ACGTcount: A:0.75, C:0.04, G:0.11, T:0.09
Consensus pattern (23 bp):
AAAAAAATCGAAAAAAAAGAAAA
Found at i:64169297 original size:6 final size:6
Alignment explanation
Indices: 64169265--64169372 Score: 67
Period size: 6 Copynumber: 17.7 Consensus size: 6
64169255 AAAGAAATTG
* * ** *
64169265 AAAG-A AAACAA AAAGAA AACGAA AAAGAA AAAGAA ATTGCA AAAGAA
1 AAAGAA AAAGAA AAAGAA AAAGAA AAAGAA AAAGAA AAAGAA AAAGAA
* ** * * *
64169312 AAAGAA ATCA-AA AAAGTG AGAGAA AAAGAA AATGAAGA AAAGAA AATTGAA
1 AAAGAA A-AAGAA AAAGAA AAAGAA AAAGAA AAAG-A-A AAAGAA AA-AGAA
64169363 AAAGAA AAAG
1 AAAGAA AAAG
64169373 CGAAAAAAGA
Statistics
Matches: 75, Mismatches: 22, Indels: 11
0.69 0.20 0.10
Matches are distributed among these distances:
5 4 0.05
6 59 0.79
7 8 0.11
8 4 0.05
ACGTcount: A:0.72, C:0.04, G:0.18, T:0.06
Consensus pattern (6 bp):
AAAGAA
Found at i:64169352 original size:14 final size:13
Alignment explanation
Indices: 64169333--64169370 Score: 51
Period size: 13 Copynumber: 2.8 Consensus size: 13
64169323 AAAAGTGAGA
64169333 GAAAAAGAAAA-T
1 GAAAAAGAAAATT
64169345 GAAGAAAAGAAAATT
1 G-A-AAAAGAAAATT
64169360 GAAAAAGAAAA
1 GAAAAAGAAAA
64169371 AGCGAAAAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 5
0.82 0.00 0.18
Matches are distributed among these distances:
12 1 0.04
13 10 0.43
14 10 0.43
15 2 0.09
ACGTcount: A:0.74, C:0.00, G:0.18, T:0.08
Consensus pattern (13 bp):
GAAAAAGAAAATT
Found at i:64169407 original size:12 final size:12
Alignment explanation
Indices: 64169376--64169407 Score: 55
Period size: 12 Copynumber: 2.7 Consensus size: 12
64169366 GAAAAAGCGA
*
64169376 AAAAAGAATTTG
1 AAAAAGAGTTTG
64169388 AAAAAGAGTTTG
1 AAAAAGAGTTTG
64169400 AAAAAGAG
1 AAAAAGAG
64169408 AAGAGTGAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.59, C:0.00, G:0.22, T:0.19
Consensus pattern (12 bp):
AAAAAGAGTTTG
Found at i:64173176 original size:6 final size:6
Alignment explanation
Indices: 64173165--64173202 Score: 60
Period size: 6 Copynumber: 6.3 Consensus size: 6
64173155 AGTTGTAAAG
64173165 TTTTAT TTTTAT TTTTAT TTTTAT TTTT-T TATTTAT TT
1 TTTTAT TTTTAT TTTTAT TTTTAT TTTTAT T-TTTAT TT
64173203 ATTTACTTAG
Statistics
Matches: 30, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
5 2 0.07
6 26 0.87
7 2 0.07
ACGTcount: A:0.16, C:0.00, G:0.00, T:0.84
Consensus pattern (6 bp):
TTTTAT
Found at i:64178139 original size:30 final size:30
Alignment explanation
Indices: 64178053--64178150 Score: 88
Period size: 30 Copynumber: 3.3 Consensus size: 30
64178043 TTAAACTAAA
* *
64178053 ATGAGCTAAGCTTTAGCTCATGAGCTAAAG
1 ATGAGCTAAGATTTAGCTCATGAGCTGAAG
* * * * * *
64178083 TTGAGCTGAGATTAAACTCCTAAGCTGAAG
1 ATGAGCTAAGATTTAGCTCATGAGCTGAAG
* * * *
64178113 CTGAGCTAAGGTTTAGCTCGTGAGCTGAAT
1 ATGAGCTAAGATTTAGCTCATGAGCTGAAG
64178143 ATGAGCTA
1 ATGAGCTA
64178151 GGAGTGAGCT
Statistics
Matches: 51, Mismatches: 17, Indels: 0
0.75 0.25 0.00
Matches are distributed among these distances:
30 51 1.00
ACGTcount: A:0.31, C:0.16, G:0.26, T:0.28
Consensus pattern (30 bp):
ATGAGCTAAGATTTAGCTCATGAGCTGAAG
Found at i:64178836 original size:30 final size:30
Alignment explanation
Indices: 64178741--64178837 Score: 88
Period size: 30 Copynumber: 3.2 Consensus size: 30
64178731 AGCTCACTCC
*
64178741 TAGCTC-ACTTTCAACTCACGAGCTAAACCT
1 TAGCTCAACTTT-AGCTCACGAGCTAAACCT
* * * * * *
64178771 TAGCTCAACTTCAGCTTAGGAGTTTAATCT
1 TAGCTCAACTTTAGCTCACGAGCTAAACCT
* * *
64178801 CAGCTCAACTTTAGCTCACAAGCTAAAGCT
1 TAGCTCAACTTTAGCTCACGAGCTAAACCT
64178831 TAGCTCA
1 TAGCTCA
64178838 TTTTAGTTTA
Statistics
Matches: 50, Mismatches: 16, Indels: 2
0.74 0.24 0.03
Matches are distributed among these distances:
30 46 0.92
31 4 0.08
ACGTcount: A:0.30, C:0.28, G:0.13, T:0.29
Consensus pattern (30 bp):
TAGCTCAACTTTAGCTCACGAGCTAAACCT
Found at i:64180250 original size:4 final size:4
Alignment explanation
Indices: 64180241--64180268 Score: 56
Period size: 4 Copynumber: 7.0 Consensus size: 4
64180231 TTAAACTAAG
64180241 TAAA TAAA TAAA TAAA TAAA TAAA TAAA
1 TAAA TAAA TAAA TAAA TAAA TAAA TAAA
64180269 AATAAAACTT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 24 1.00
ACGTcount: A:0.75, C:0.00, G:0.00, T:0.25
Consensus pattern (4 bp):
TAAA
Found at i:64181673 original size:23 final size:22
Alignment explanation
Indices: 64181621--64181673 Score: 56
Period size: 23 Copynumber: 2.4 Consensus size: 22
64181611 TCCACGTCTT
*
64181621 TTTCTTTTGTTTCTTTTTCTAA
1 TTTCTTTTCTTTCTTTTTCTAA
64181643 -TTCATTTTCTCTTCTTTCTTC-AA
1 TTTC-TTTTCT-TTCTTT-TTCTAA
64181666 TTTCTTTT
1 TTTCTTTT
64181674 TCACTCTCAT
Statistics
Matches: 26, Mismatches: 1, Indels: 7
0.76 0.03 0.21
Matches are distributed among these distances:
21 3 0.12
22 5 0.19
23 12 0.46
24 6 0.23
ACGTcount: A:0.09, C:0.19, G:0.02, T:0.70
Consensus pattern (22 bp):
TTTCTTTTCTTTCTTTTTCTAA
Found at i:64184017 original size:4 final size:4
Alignment explanation
Indices: 64184008--64184035 Score: 56
Period size: 4 Copynumber: 7.0 Consensus size: 4
64183998 TTAAACTAAG
64184008 TAAA TAAA TAAA TAAA TAAA TAAA TAAA
1 TAAA TAAA TAAA TAAA TAAA TAAA TAAA
64184036 AATAAAACTT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 24 1.00
ACGTcount: A:0.75, C:0.00, G:0.00, T:0.25
Consensus pattern (4 bp):
TAAA
Found at i:64186126 original size:9 final size:10
Alignment explanation
Indices: 64186119--64186175 Score: 55
Period size: 11 Copynumber: 5.5 Consensus size: 10
64186109 AAGAGAAAAT
64186119 AAAGAAAAGA
1 AAAGAAAAGA
64186129 AAAGAAAAAGCA
1 AAAG-AAAAG-A
*
64186141 AAAGAAGA-A
1 AAAGAAAAGA
64186150 AAAGAAAATGA
1 AAAGAAAA-GA
64186161 AATA-AAAAGA
1 AA-AGAAAAGA
64186171 AAAGA
1 AAAGA
64186176 GAGGCAAGAG
Statistics
Matches: 39, Mismatches: 2, Indels: 12
0.74 0.04 0.23
Matches are distributed among these distances:
9 9 0.23
10 9 0.23
11 15 0.38
12 6 0.15
ACGTcount: A:0.77, C:0.02, G:0.18, T:0.04
Consensus pattern (10 bp):
AAAGAAAAGA
Found at i:64186143 original size:6 final size:5
Alignment explanation
Indices: 64186119--64186175 Score: 55
Period size: 5 Copynumber: 11.0 Consensus size: 5
64186109 AAGAGAAAAT
*
64186119 AAAGA AAAGA AAAGAA AAAGCA AAAGA AGA-A AAAGA AAATGA AATA-A
1 AAAGA AAAGA AAAG-A AAAG-A AAAGA AAAGA AAAGA AAA-GA AA-AGA
64186166 AAAGA AAAGA
1 AAAGA AAAGA
64186176 GAGGCAAGAG
Statistics
Matches: 44, Mismatches: 3, Indels: 10
0.77 0.05 0.18
Matches are distributed among these distances:
4 4 0.09
5 25 0.57
6 14 0.32
7 1 0.02
ACGTcount: A:0.77, C:0.02, G:0.18, T:0.04
Consensus pattern (5 bp):
AAAGA
Found at i:64186150 original size:15 final size:14
Alignment explanation
Indices: 64186119--64186175 Score: 60
Period size: 16 Copynumber: 3.7 Consensus size: 14
64186109 AAGAGAAAAT
64186119 AAAGAAAAGAAAAGAA
1 AAAGAAAAG--AAGAA
64186135 AAAGCAAAAGAAGAA
1 AAAG-AAAAGAAGAA
*
64186150 AAAGAAAATGAAATAA
1 AAAGAAAA-G-AAGAA
64186166 AAAGAAAAGA
1 AAAGAAAAGA
64186176 GAGGCAAGAG
Statistics
Matches: 37, Mismatches: 1, Indels: 8
0.80 0.02 0.17
Matches are distributed among these distances:
14 5 0.14
15 11 0.30
16 16 0.43
17 5 0.14
ACGTcount: A:0.77, C:0.02, G:0.18, T:0.04
Consensus pattern (14 bp):
AAAGAAAAGAAGAA
Found at i:64186252 original size:12 final size:12
Alignment explanation
Indices: 64186244--64186268 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
64186234 TTTGAAAAGC
64186244 AAAAAGAAAATG
1 AAAAAGAAAATG
64186256 AAAAAGAAAATG
1 AAAAAGAAAATG
64186268 A
1 A
64186269 GATTGAAAAA
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:0.76, C:0.00, G:0.16, T:0.08
Consensus pattern (12 bp):
AAAAAGAAAATG
Found at i:64186265 original size:18 final size:18
Alignment explanation
Indices: 64186238--64186293 Score: 51
Period size: 18 Copynumber: 3.1 Consensus size: 18
64186228 AAAGCCTTTG
64186238 AAAAGCAAAAAGAAAATGA
1 AAAAG-AAAAAGAAAATGA
* * *
64186257 AAAAGAAAATGAGATTGA
1 AAAAGAAAAAGAAAATGA
* *
64186275 AAAAGAGAACGAAAA-GA
1 AAAAGAAAAAGAAAATGA
64186292 AA
1 AA
64186294 TTTGAGAGTG
Statistics
Matches: 30, Mismatches: 7, Indels: 2
0.77 0.18 0.05
Matches are distributed among these distances:
17 4 0.13
18 21 0.70
19 5 0.17
ACGTcount: A:0.70, C:0.04, G:0.20, T:0.07
Consensus pattern (18 bp):
AAAAGAAAAAGAAAATGA
Found at i:64186278 original size:30 final size:31
Alignment explanation
Indices: 64186244--64186325 Score: 105
Period size: 30 Copynumber: 2.7 Consensus size: 31
64186234 TTTGAAAAGC
*
64186244 AAAAAGAAAATGAAAAAGAAA-ATGAGATTG
1 AAAAAGAAAATGAAAAAGAAATATGAGAGTG
* * *
64186274 AAAAAGAGAACG-AAAAGAAATTTGAGAGTG
1 AAAAAGAAAATGAAAAAGAAATATGAGAGTG
*
64186304 AAAAAGAAGATGAAAAAGAAAT
1 AAAAAGAAAATGAAAAAGAAAT
64186326 TGAAACAAAA
Statistics
Matches: 43, Mismatches: 7, Indels: 3
0.81 0.13 0.06
Matches are distributed among these distances:
29 8 0.19
30 26 0.60
31 9 0.21
ACGTcount: A:0.65, C:0.01, G:0.22, T:0.12
Consensus pattern (31 bp):
AAAAAGAAAATGAAAAAGAAATATGAGAGTG
Found at i:64188460 original size:30 final size:31
Alignment explanation
Indices: 64188426--64188522 Score: 101
Period size: 30 Copynumber: 3.2 Consensus size: 31
64188416 AGCTCACTCC
*
64188426 TAGCTC-ACTTTCAACTCACGAGCTAAACCT
1 TAGCTCAACTTTCAGCTCACGAGCTAAACCT
* * * * *
64188456 TAGCTCAAC-TTCAGCTTAGGAGTTTAGCCT
1 TAGCTCAACTTTCAGCTCACGAGCTAAACCT
* *
64188486 CAGCTCAACTTT-AGCTCACGAGCTAAAGCT
1 TAGCTCAACTTTCAGCTCACGAGCTAAACCT
64188516 TAGCTCA
1 TAGCTCA
64188523 TTTTAGTTTA
Statistics
Matches: 51, Mismatches: 14, Indels: 4
0.74 0.20 0.06
Matches are distributed among these distances:
30 47 0.92
31 4 0.08
ACGTcount: A:0.28, C:0.29, G:0.15, T:0.28
Consensus pattern (31 bp):
TAGCTCAACTTTCAGCTCACGAGCTAAACCT
Found at i:64190456 original size:20 final size:20
Alignment explanation
Indices: 64190433--64190486 Score: 63
Period size: 20 Copynumber: 2.7 Consensus size: 20
64190423 AGTTTTTCCC
*
64190433 AGCTCGATTTAGCTCACATG
1 AGCTCAATTTAGCTCACATG
* ***
64190453 AGCTTAATTTAGCTCGTTTG
1 AGCTCAATTTAGCTCACATG
64190473 AGCTCAATTTAGCT
1 AGCTCAATTTAGCT
64190487 TACTTTAGCT
Statistics
Matches: 28, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
20 28 1.00
ACGTcount: A:0.24, C:0.20, G:0.19, T:0.37
Consensus pattern (20 bp):
AGCTCAATTTAGCTCACATG
Found at i:64190468 original size:30 final size:30
Alignment explanation
Indices: 64190433--64190506 Score: 98
Period size: 30 Copynumber: 2.5 Consensus size: 30
64190423 AGTTTTTCCC
64190433 AGCTCGATTT-AGCTCACA-TGAGCTTAATTT
1 AGCTCG-TTTGAGCTCA-ATTGAGCTTAATTT
* *
64190463 AGCTCGTTTGAGCTCAATTTAGCTTACTTT
1 AGCTCGTTTGAGCTCAATTGAGCTTAATTT
64190493 AGCTCGTTTGAGCT
1 AGCTCGTTTGAGCT
64190507 TGGCTTAAGT
Statistics
Matches: 40, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
29 4 0.10
30 36 0.90
ACGTcount: A:0.22, C:0.20, G:0.19, T:0.39
Consensus pattern (30 bp):
AGCTCGTTTGAGCTCAATTGAGCTTAATTT
Found at i:64190496 original size:20 final size:20
Alignment explanation
Indices: 64190433--64190497 Score: 53
Period size: 20 Copynumber: 3.2 Consensus size: 20
64190423 AGTTTTTCCC
* * * *
64190433 AGCTCGATTTAGCTCACATG
1 AGCTCAATTTAGCTTACTTT
*
64190453 AGCTTAATTTAGC-T-CGTTT
1 AGCTCAATTTAGCTTAC-TTT
64190472 GAGCTCAATTTAGCTTACTTT
1 -AGCTCAATTTAGCTTACTTT
64190493 AGCTC
1 AGCTC
64190498 GTTTGAGCTT
Statistics
Matches: 35, Mismatches: 6, Indels: 8
0.71 0.12 0.16
Matches are distributed among these distances:
18 1 0.03
19 1 0.03
20 28 0.80
21 4 0.11
22 1 0.03
ACGTcount: A:0.23, C:0.22, G:0.17, T:0.38
Consensus pattern (20 bp):
AGCTCAATTTAGCTTACTTT
Found at i:64192155 original size:19 final size:19
Alignment explanation
Indices: 64192102--64192157 Score: 60
Period size: 19 Copynumber: 2.9 Consensus size: 19
64192092 TATTAGATTT
*
64192102 AAAAAAAAAGAGAATAAATTC
1 AAAAAAAAAG-GAA-AAAATC
**
64192123 -AAAAAAAATTAAAAAATC
1 AAAAAAAAAGGAAAAAATC
64192141 AAAAAAAAAGGAAAAAA
1 AAAAAAAAAGGAAAAAA
64192158 AAGAAGTGAC
Statistics
Matches: 29, Mismatches: 5, Indels: 4
0.76 0.13 0.11
Matches are distributed among these distances:
18 5 0.17
19 16 0.55
20 8 0.28
ACGTcount: A:0.79, C:0.04, G:0.07, T:0.11
Consensus pattern (19 bp):
AAAAAAAAAGGAAAAAATC
Found at i:64192156 original size:20 final size:20
Alignment explanation
Indices: 64192102--64192158 Score: 55
Period size: 20 Copynumber: 2.9 Consensus size: 20
64192092 TATTAGATTT
* *
64192102 AAAAAAAAAGAGAATAAATTC
1 AAAAAAAAAG-GAAAAAAATC
**
64192123 -AAAAAAAA-TTAAAAAATC
1 AAAAAAAAAGGAAAAAAATC
64192141 AAAAAAAAAGGAAAAAAA
1 AAAAAAAAAGGAAAAAAA
64192159 AGAAGTGACA
Statistics
Matches: 28, Mismatches: 6, Indels: 5
0.72 0.15 0.13
Matches are distributed among these distances:
18 6 0.21
19 8 0.29
20 14 0.50
ACGTcount: A:0.79, C:0.04, G:0.07, T:0.11
Consensus pattern (20 bp):
AAAAAAAAAGGAAAAAAATC
Found at i:64193249 original size:18 final size:18
Alignment explanation
Indices: 64193223--64193326 Score: 82
Period size: 18 Copynumber: 5.6 Consensus size: 18
64193213 AAATTGAAAG
*
64193223 AAAACAAAAAGAAAACGA
1 AAAAGAAAAAGAAAACGA
** *
64193241 AAAAGAAAAAGAAATTGC
1 AAAAGAAAAAGAAAACGA
*
64193259 AAAAGAAAAAGAAATCGA
1 AAAAGAAAAAGAAAACGA
** * *
64193277 AAAAGTGAGAGAAAAAGA
1 AAAAGAAAAAGAAAACGA
* *
64193295 AAATGAAGAAAAGAAAATTGA
1 AAAAG-A-AAAAGAAAA-CGA
64193316 AAAAGAAAAAG
1 AAAAGAAAAAG
64193327 CGAAAAAAGA
Statistics
Matches: 66, Mismatches: 17, Indels: 5
0.75 0.19 0.06
Matches are distributed among these distances:
18 47 0.71
19 5 0.08
20 8 0.12
21 6 0.09
ACGTcount: A:0.71, C:0.04, G:0.18, T:0.07
Consensus pattern (18 bp):
AAAAGAAAAAGAAAACGA
Found at i:64193251 original size:6 final size:6
Alignment explanation
Indices: 64193219--64193326 Score: 74
Period size: 6 Copynumber: 17.7 Consensus size: 6
64193209 AAAGAAATTG
* * ** *
64193219 AAAG-A AAACAA AAAGAA AACGAA AAAGAA AAAGAA ATTGCA AAAGAA
1 AAAGAA AAAGAA AAAGAA AAAGAA AAAGAA AAAGAA AAAGAA AAAGAA
** ** * * *
64193266 AAAGAA ATCGAA AAAGTG AGAGAA AAAGAA AATGAAGA AAAGAA AATTGAA
1 AAAGAA AAAGAA AAAGAA AAAGAA AAAGAA AAAG-A-A AAAGAA AA-AGAA
64193317 AAAGAA AAAG
1 AAAGAA AAAG
64193327 CGAAAAAAGA
Statistics
Matches: 75, Mismatches: 24, Indels: 7
0.71 0.23 0.07
Matches are distributed among these distances:
5 3 0.04
6 61 0.81
7 7 0.09
8 4 0.05
ACGTcount: A:0.71, C:0.04, G:0.19, T:0.06
Consensus pattern (6 bp):
AAAGAA
Found at i:64193308 original size:14 final size:13
Alignment explanation
Indices: 64193287--64193324 Score: 51
Period size: 13 Copynumber: 2.8 Consensus size: 13
64193277 AAAAGTGAGA
64193287 GAAAAAGAAAA-T
1 GAAAAAGAAAATT
64193299 GAAGAAAAGAAAATT
1 G-A-AAAAGAAAATT
64193314 GAAAAAGAAAA
1 GAAAAAGAAAA
64193325 AGCGAAAAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 5
0.82 0.00 0.18
Matches are distributed among these distances:
12 1 0.04
13 10 0.43
14 10 0.43
15 2 0.09
ACGTcount: A:0.74, C:0.00, G:0.18, T:0.08
Consensus pattern (13 bp):
GAAAAAGAAAATT
Found at i:64193338 original size:21 final size:21
Alignment explanation
Indices: 64193288--64193338 Score: 50
Period size: 21 Copynumber: 2.4 Consensus size: 21
64193278 AAAGTGAGAG
*
64193288 AAAAAGAAAATGAAGAAAAGA
1 AAAAAGAAAAAGAAGAAAAGA
** *
64193309 AAATTGAAAAAGAA-AAAGCGA
1 AAAAAGAAAAAGAAGAAA-AGA
64193330 AAAAAGAAA
1 AAAAAGAAA
64193339 TTGAAAGAGA
Statistics
Matches: 23, Mismatches: 6, Indels: 2
0.74 0.19 0.06
Matches are distributed among these distances:
20 3 0.13
21 20 0.87
ACGTcount: A:0.75, C:0.02, G:0.18, T:0.06
Consensus pattern (21 bp):
AAAAAGAAAAAGAAGAAAAGA
Found at i:64193378 original size:33 final size:33
Alignment explanation
Indices: 64193341--64193403 Score: 85
Period size: 33 Copynumber: 1.9 Consensus size: 33
64193331 AAAAGAAATT
64193341 GAAAGAGAG-CT-TGAAAAGAAATCAAGTGAAAAA
1 GAAAGAGAGTCTGT-AAAAGAAA-CAAGTGAAAAA
*
64193374 GAAAGAGAGTCTGTAAAAGAAACGAGTGAA
1 GAAAGAGAGTCTGTAAAAGAAACAAGTGAA
64193404 GTGAGTAATC
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
33 16 0.59
34 10 0.37
35 1 0.04
ACGTcount: A:0.54, C:0.06, G:0.27, T:0.13
Consensus pattern (33 bp):
GAAAGAGAGTCTGTAAAAGAAACAAGTGAAAAA
Found at i:64195215 original size:19 final size:20
Alignment explanation
Indices: 64195191--64195229 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 20
64195181 TCGATTTAGC
64195191 TCACA-TGAGCTTGTTGAGA
1 TCACAGTGAGCTTGTTGAGA
64195210 TCACATGTGAGCTTGTTGAG
1 TCACA-GTGAGCTTGTTGAG
64195230 CTGAGATTGA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 5 0.28
21 13 0.72
ACGTcount: A:0.23, C:0.15, G:0.28, T:0.33
Consensus pattern (20 bp):
TCACAGTGAGCTTGTTGAGA
Found at i:64196768 original size:20 final size:20
Alignment explanation
Indices: 64196745--64196791 Score: 58
Period size: 20 Copynumber: 2.4 Consensus size: 20
64196735 AGGTTAAGAT
*
64196745 TGAGCTGAATTGAGCTTGAA
1 TGAGCTGAATTGAGCTCGAA
* * *
64196765 TGAGTTGACTTGAGCTCGAG
1 TGAGCTGAATTGAGCTCGAA
64196785 TGAGCTG
1 TGAGCTG
64196792 GAAACAAGCT
Statistics
Matches: 22, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.23, C:0.13, G:0.34, T:0.30
Consensus pattern (20 bp):
TGAGCTGAATTGAGCTCGAA
Found at i:64198512 original size:48 final size:48
Alignment explanation
Indices: 64198457--64198562 Score: 137
Period size: 48 Copynumber: 2.2 Consensus size: 48
64198447 TTGTCTTTTC
*
64198457 TTTCTTTTTCAATTT-TCTCT-TTTTCCTCACA-CTTTTGTTCAATCTCAA
1 TTTCTTTTTCAATTTCTCTCTCTTTT--TCACATCCTTT-TTCAATCTCAA
* *
64198505 TTTCTTTTTCGATTTCTTTCTCTTTTTCACATCCTTTTTCAATCTCAA
1 TTTCTTTTTCAATTTCTCTCTCTTTTTCACATCCTTTTTCAATCTCAA
64198553 TTTCTTTTTC
1 TTTCTTTTTC
64198563 CATGACACTC
Statistics
Matches: 52, Mismatches: 3, Indels: 6
0.85 0.05 0.10
Matches are distributed among these distances:
48 40 0.77
49 8 0.15
50 4 0.08
ACGTcount: A:0.14, C:0.25, G:0.02, T:0.59
Consensus pattern (48 bp):
TTTCTTTTTCAATTTCTCTCTCTTTTTCACATCCTTTTTCAATCTCAA
Found at i:64199604 original size:11 final size:10
Alignment explanation
Indices: 64199590--64199629 Score: 53
Period size: 10 Copynumber: 3.8 Consensus size: 10
64199580 ACTTTTCACT
64199590 TTTTTTTGTTC
1 TTTTTTT-TTC
*
64199601 TTTTCTTTTAC
1 TTTT-TTTTTC
64199612 TTTTTTTTTC
1 TTTTTTTTTC
64199622 TTTTTTTT
1 TTTTTTTT
64199630 GCTCACTTCT
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
10 13 0.50
11 10 0.38
12 3 0.12
ACGTcount: A:0.03, C:0.10, G:0.03, T:0.85
Consensus pattern (10 bp):
TTTTTTTTTC
Found at i:64199627 original size:23 final size:24
Alignment explanation
Indices: 64199581--64199644 Score: 71
Period size: 21 Copynumber: 2.7 Consensus size: 24
64199571 ACTCGCAATA
64199581 CTTTTCACTTTTTTTTGTTCTTTT
1 CTTTTCACTTTTTTTTGTTCTTTT
64199605 CTTTT-AC-TTTTTTT-TTCTTTT
1 CTTTTCACTTTTTTTTGTTCTTTT
*
64199626 TTTTGCTCACTTCTTTTTT
1 CTTT--TCACTT-TTTTTT
64199645 TTTTGAATTT
Statistics
Matches: 34, Mismatches: 1, Indels: 8
0.79 0.02 0.19
Matches are distributed among these distances:
21 10 0.29
22 7 0.21
23 3 0.09
24 7 0.21
25 1 0.03
26 6 0.18
ACGTcount: A:0.05, C:0.17, G:0.03, T:0.75
Consensus pattern (24 bp):
CTTTTCACTTTTTTTTGTTCTTTT
Found at i:64199628 original size:24 final size:24
Alignment explanation
Indices: 64199581--64199644 Score: 62
Period size: 24 Copynumber: 2.7 Consensus size: 24
64199571 ACTCGCAATA
*
64199581 CTTTTCACTTTTTTTTGTTCTTTT
1 CTTTTCACTTTTTTTTCTTCTTTT
64199605 CTTTT-ACTTTTTTTTTCTT-TTTT
1 CTTTTCAC-TTTTTTTTCTTCTTTT
*
64199628 -TTGCTCACTTCTTTTTT
1 CTT-TTCACTT-TTTTTT
64199645 TTTTGAATTT
Statistics
Matches: 34, Mismatches: 2, Indels: 8
0.77 0.05 0.18
Matches are distributed among these distances:
22 2 0.06
23 9 0.26
24 23 0.68
ACGTcount: A:0.05, C:0.17, G:0.03, T:0.75
Consensus pattern (24 bp):
CTTTTCACTTTTTTTTCTTCTTTT
Found at i:64201184 original size:20 final size:20
Alignment explanation
Indices: 64201161--64201207 Score: 58
Period size: 20 Copynumber: 2.4 Consensus size: 20
64201151 AGGTTAAGAT
*
64201161 TGAGCTGAATTGAGCTTGAA
1 TGAGCTGAATTGAGCTCGAA
* * *
64201181 TGAGTTGACTTGAGCTCGAG
1 TGAGCTGAATTGAGCTCGAA
64201201 TGAGCTG
1 TGAGCTG
64201208 GAAACAAGCT
Statistics
Matches: 22, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.23, C:0.13, G:0.34, T:0.30
Consensus pattern (20 bp):
TGAGCTGAATTGAGCTCGAA
Found at i:64203652 original size:24 final size:24
Alignment explanation
Indices: 64203625--64203673 Score: 89
Period size: 24 Copynumber: 2.0 Consensus size: 24
64203615 GAACGTATAC
*
64203625 CTAAACATATATTCTTGAATCAAA
1 CTAAAAATATATTCTTGAATCAAA
64203649 CTAAAAATATATTCTTGAATCAAA
1 CTAAAAATATATTCTTGAATCAAA
64203673 C
1 C
64203674 ATTCAATTTC
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.47, C:0.16, G:0.04, T:0.33
Consensus pattern (24 bp):
CTAAAAATATATTCTTGAATCAAA
Found at i:64218910 original size:7 final size:7
Alignment explanation
Indices: 64218890--64218919 Score: 51
Period size: 7 Copynumber: 4.1 Consensus size: 7
64218880 TAAACTAAGT
64218890 AAATAAA
1 AAATAAA
64218897 TAAATAAA
1 -AAATAAA
64218905 AAATAAA
1 AAATAAA
64218912 AAATAAA
1 AAATAAA
64218919 A
1 A
64218920 CTTTACAACT
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
7 15 0.68
8 7 0.32
ACGTcount: A:0.83, C:0.00, G:0.00, T:0.17
Consensus pattern (7 bp):
AAATAAA
Found at i:64220310 original size:23 final size:22
Alignment explanation
Indices: 64220258--64220310 Score: 56
Period size: 23 Copynumber: 2.4 Consensus size: 22
64220248 TCCACGTCTT
*
64220258 TTTCTTTTGTTTCTTTTTCTAA
1 TTTCTTTTCTTTCTTTTTCTAA
64220280 -TTCATTTTCTCTTCTTTCTTC-AA
1 TTTC-TTTTCT-TTCTTT-TTCTAA
64220303 TTTCTTTT
1 TTTCTTTT
64220311 TCACTCTCAA
Statistics
Matches: 26, Mismatches: 1, Indels: 7
0.76 0.03 0.21
Matches are distributed among these distances:
21 3 0.12
22 5 0.19
23 12 0.46
24 6 0.23
ACGTcount: A:0.09, C:0.19, G:0.02, T:0.70
Consensus pattern (22 bp):
TTTCTTTTCTTTCTTTTTCTAA
Found at i:64222690 original size:14 final size:15
Alignment explanation
Indices: 64222664--64222692 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
64222654 AAAACTAAGT
64222664 AAATAATAAATAAAA
1 AAATAATAAATAAAA
64222679 AAATAA-AAATAAAA
1 AAATAATAAATAAAA
64222693 CTTTACAACT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 8 0.57
15 6 0.43
ACGTcount: A:0.83, C:0.00, G:0.00, T:0.17
Consensus pattern (15 bp):
AAATAATAAATAAAA
Found at i:64230262 original size:23 final size:24
Alignment explanation
Indices: 64230222--64230269 Score: 80
Period size: 23 Copynumber: 2.0 Consensus size: 24
64230212 GAAATTGAAT
*
64230222 GTTTGATTCAAGAATATATTTTTA
1 GTTTGATTCAAGAATATATGTTTA
64230246 GTTTGATTC-AGAATATATGTTTA
1 GTTTGATTCAAGAATATATGTTTA
64230269 G
1 G
64230270 GTATACGTTC
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
23 14 0.61
24 9 0.39
ACGTcount: A:0.31, C:0.04, G:0.17, T:0.48
Consensus pattern (24 bp):
GTTTGATTCAAGAATATATGTTTA
Found at i:64243788 original size:21 final size:21
Alignment explanation
Indices: 64243739--64243805 Score: 71
Period size: 21 Copynumber: 3.1 Consensus size: 21
64243729 CCTCTTTGAA
* * *
64243739 CCATAACCAATTCGTACCAAATA
1 CCAT-ACCATTTCATACC-AATT
*
64243762 CCATACTATTTCATACCAATT
1 CCATACCATTTCATACCAATT
*
64243783 CCATACCATTTCGTACCAATT
1 CCATACCATTTCATACCAATT
64243804 CC
1 CC
64243806 CAAATACCAA
Statistics
Matches: 38, Mismatches: 6, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
21 24 0.63
22 10 0.26
23 4 0.11
ACGTcount: A:0.34, C:0.33, G:0.03, T:0.30
Consensus pattern (21 bp):
CCATACCATTTCATACCAATT
Found at i:64244130 original size:12 final size:12
Alignment explanation
Indices: 64244104--64244149 Score: 65
Period size: 13 Copynumber: 3.7 Consensus size: 12
64244094 ATAGGTGCGT
*
64244104 AAAAAAAGTTCGA
1 AAAAAAAATT-GA
64244117 AAAAAAAATTGAA
1 AAAAAAAATTG-A
64244130 AAAAAAAATTGA
1 AAAAAAAATTGA
64244142 AAAAAAAA
1 AAAAAAAA
64244150 ATTTGCATAC
Statistics
Matches: 31, Mismatches: 1, Indels: 3
0.89 0.03 0.09
Matches are distributed among these distances:
12 10 0.32
13 21 0.68
ACGTcount: A:0.76, C:0.02, G:0.09, T:0.13
Consensus pattern (12 bp):
AAAAAAAATTGA
Done.