Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009462.1 Hibiscus syriacus cultivar Beakdansim tig00113725_pilon, whole genome shotgun sequence
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: 20687664
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 19 of 91
Found at i:3827750 original size:37 final size:35
Alignment explanation
Indices: 3827667--3827826 Score: 139
Period size: 37 Copynumber: 4.4 Consensus size: 35
3827657 CTCAAAATAC
*
3827667 AAATTTTATCTCACTTGAGATAGTTTAC-CT-AAAA
1 AAATTTTATCTCACTTGAGACAGTTT-CTCTCAAAA
* **
3827701 AAATATCGTCTCACTTGAGACAGTTTCTCTCGAAACA
1 AAATTTTATCTCACTTGAGACAGTTTCTCTC-AAA-A
* *
3827738 AAATTTTATCTCACTAGAGATAGTTT-TCCTCAAAA
1 AAATTTTATCTCACTTGAGACAGTTTCT-CTCAAAA
*
3827773 ACAATTTT-TCGTCTTACTCGAGACAGTTTCTCTCGAAATA
1 A-AATTTTATC-TC--ACTTGAGACAGTTTCTCTC-AAA-A
3827813 AAATTTTATCTCAC
1 AAATTTTATCTCAC
3827827 ATATTTTTTC
Statistics
Matches: 102, Mismatches: 11, Indels: 23
0.75 0.08 0.17
Matches are distributed among these distances:
33 1 0.01
34 24 0.24
35 4 0.04
36 15 0.15
37 27 0.26
38 15 0.15
39 12 0.12
40 4 0.04
ACGTcount: A:0.34, C:0.20, G:0.10, T:0.36
Consensus pattern (35 bp):
AAATTTTATCTCACTTGAGACAGTTTCTCTCAAAA
Found at i:3827750 original size:71 final size:74
Alignment explanation
Indices: 3827667--3827826 Score: 236
Period size: 75 Copynumber: 2.2 Consensus size: 74
3827657 CTCAAAATAC
* *
3827667 AAATTTTATCTCACTTGAGATAGTTTACCT-AAAAA-AA-TATCGTCTCACTTGAGACAGTTTCT
1 AAATTTTATCTCACTAGAGATAGTTTACCTCAAAAACAATTATCGTCTCACTCGAGACAGTTTCT
3827729 CTCGAAACA
66 CTCGAAACA
* * *
3827738 AAATTTTATCTCACTAGAGATAGTTTTCCTCAAAAACAATTTTTCGTCTTACTCGAGACAGTTTC
1 AAATTTTATCTCACTAGAGATAGTTTACCTCAAAAACAA-TTATCGTCTCACTCGAGACAGTTTC
*
3827803 TCTCGAAATA
65 TCTCGAAACA
3827813 AAATTTTATCTCAC
1 AAATTTTATCTCAC
3827827 ATATTTTTTC
Statistics
Matches: 79, Mismatches: 6, Indels: 4
0.89 0.07 0.04
Matches are distributed among these distances:
71 28 0.35
72 5 0.06
73 2 0.03
75 44 0.56
ACGTcount: A:0.34, C:0.20, G:0.10, T:0.36
Consensus pattern (74 bp):
AAATTTTATCTCACTAGAGATAGTTTACCTCAAAAACAATTATCGTCTCACTCGAGACAGTTTCT
CTCGAAACA
Found at i:3827968 original size:72 final size:72
Alignment explanation
Indices: 3827706--3828060 Score: 239
Period size: 72 Copynumber: 4.9 Consensus size: 72
3827696 TAAAAAAATA
** * * **
3827706 TCGTCTCACTTGAGACAGTTTCTCTCGAAAC-AAAATTTTATCTCACTAGAGATAGTTTTCCTCA
1 TCGTCTCACTCAAGACAGTTTCTCTCGAAACAAAAATTTCATTTCACTTTAGATA-TTTT-CTC-
***
3827770 AAAACAATTTT
63 TTGA-AATTTT
* * * * * *
3827781 TCGTCTTACTCGAGACAGTTTCTCTCGAAA-TAAAATTTTATCTCAC-----ATATTTTTTCTTG
1 TCGTCTCACTCAAGACAGTTTCTCTCGAAACAAAAATTTCATTTCACTTTAGATATTTTCTCTTG
*
3827840 AAATAAATT
66 AAAT--TTT
* * * *** * * *
3827849 TCGTTTCATTTAAGACAACCTC-CTTGAAACAAAAAATTGT-ATATCACTTTAGATATTTTCCCT
1 TCGTCTCACTCAAGACAGTTTCTCTCGAAAC-AAAAATT-TCATTTCACTTTAGATATTTTCTCT
3827912 TGAACATTTT
64 TGAA-ATTTT
* *
3827922 T-GTCTCACTCAAGATAGTTTCTCTCGAAACAAAAATTTCATTTCACTTGAGATATTTTCTCTTG
1 TCGTCTCACTCAAGACAGTTTCTCTCGAAACAAAAATTTCATTTCACTTTAGATATTTTCTCTTG
3827986 AAATTTT
66 AAATTTT
* * * * *
3827993 TCTTCTCACTCGAGACATTTTCTCTCGAAACCAAAATTGC-TTCTCAC-TTATGATATTTTCTCT
1 TCGTCTCACTCAAGACAGTTTCTCTCGAAACAAAAATTTCATT-TCACTTTA-GATATTTTCTCT
3828056 TGAAA
64 TGAAA
3828061 ATATCGTCTC
Statistics
Matches: 224, Mismatches: 39, Indels: 37
0.75 0.13 0.12
Matches are distributed among these distances:
66 3 0.01
67 7 0.03
68 18 0.08
69 16 0.07
70 4 0.02
71 11 0.05
72 97 0.43
73 10 0.04
74 13 0.06
75 45 0.20
ACGTcount: A:0.30, C:0.20, G:0.09, T:0.40
Consensus pattern (72 bp):
TCGTCTCACTCAAGACAGTTTCTCTCGAAACAAAAATTTCATTTCACTTTAGATATTTTCTCTTG
AAATTTT
Found at i:3828687 original size:21 final size:17
Alignment explanation
Indices: 3828643--3828684 Score: 84
Period size: 17 Copynumber: 2.5 Consensus size: 17
3828633 AAGTTCTGTT
3828643 TTTCTTTCATCTCCATA
1 TTTCTTTCATCTCCATA
3828660 TTTCTTTCATCTCCATA
1 TTTCTTTCATCTCCATA
3828677 TTTCTTTC
1 TTTCTTTC
3828685 TTTATTTTCA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 25 1.00
ACGTcount: A:0.14, C:0.29, G:0.00, T:0.57
Consensus pattern (17 bp):
TTTCTTTCATCTCCATA
Found at i:3829355 original size:17 final size:17
Alignment explanation
Indices: 3829319--3829370 Score: 59
Period size: 17 Copynumber: 3.0 Consensus size: 17
3829309 TTATTTTCTC
* *
3829319 TTTATTTATTATTAAATA
1 TTTATTT-TTTTTAATTA
3829337 TTTATTTTTTTTAATTA
1 TTTATTTTTTTTAATTA
**
3829354 TTTATTTACTTTAATTA
1 TTTATTTTTTTTAATTA
3829371 ATTTTAAAAT
Statistics
Matches: 30, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
17 23 0.77
18 7 0.23
ACGTcount: A:0.31, C:0.02, G:0.00, T:0.67
Consensus pattern (17 bp):
TTTATTTTTTTTAATTA
Found at i:3829520 original size:26 final size:25
Alignment explanation
Indices: 3829475--3829524 Score: 66
Period size: 25 Copynumber: 2.0 Consensus size: 25
3829465 CTCTATACTA
*
3829475 TATTTATTTATTTGAGAATTATGAAT
1 TATTTATTTATTTGAAAATT-TGAAT
3829501 TATTT-TTTATTTGAAAAATTTGAA
1 TATTTATTTATTTG-AAAATTTGAA
3829525 ACTCATCAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
25 12 0.55
26 10 0.45
ACGTcount: A:0.36, C:0.00, G:0.10, T:0.54
Consensus pattern (25 bp):
TATTTATTTATTTGAAAATTTGAAT
Found at i:3833031 original size:16 final size:15
Alignment explanation
Indices: 3833012--3833049 Score: 58
Period size: 15 Copynumber: 2.5 Consensus size: 15
3833002 AGGATATTCT
3833012 AAAAAAGAAATAAAAA
1 AAAAAAGAAA-AAAAA
3833028 AAAAAAGAAAAAAAA
1 AAAAAAGAAAAAAAA
*
3833043 AGAAAAG
1 AAAAAAG
3833050 TGTTCGAAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
15 11 0.52
16 10 0.48
ACGTcount: A:0.87, C:0.00, G:0.11, T:0.03
Consensus pattern (15 bp):
AAAAAAGAAAAAAAA
Found at i:3854000 original size:4 final size:4
Alignment explanation
Indices: 3853991--3854019 Score: 51
Period size: 4 Copynumber: 7.5 Consensus size: 4
3853981 TTACTTATCC
3853991 AAAT AAAT AAAT AAAT AAAT AAA- AAAT AA
1 AAAT AAAT AAAT AAAT AAAT AAAT AAAT AA
3854020 GAAGATGTTT
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
3 3 0.12
4 21 0.88
ACGTcount: A:0.79, C:0.00, G:0.00, T:0.21
Consensus pattern (4 bp):
AAAT
Found at i:3854137 original size:31 final size:31
Alignment explanation
Indices: 3854100--3854284 Score: 134
Period size: 31 Copynumber: 6.1 Consensus size: 31
3854090 TTATAATATT
*
3854100 AATAAAATAAAAATATTTATATCACTAATAA
1 AATAAAATAAAAATATTTATATCAATAATAA
* * *
3854131 AATAAAATAAAAATCTTTATAACATTAATAA
1 AATAAAATAAAAATATTTATATCAATAATAA
** *** * *
3854162 AAT-ATTTAATTTTGATTTA-AT--ATGATAT
1 AATAAAATAAAAAT-ATTTATATCAATAATAA
* * *
3854190 TATAAAA-AACAATA-ATA-AT-AATAATAA
1 AATAAAATAAAAATATTTATATCAATAATAA
** *
3854217 AACTAAAACTAATGATATTTATATCATTAATAA
1 AA-TAAAA-TAAAAATATTTATATCAATAATAA
3854250 AATAAAATAAAAATATTTATATCAATAATAA
1 AATAAAATAAAAATATTTATATCAATAATAA
3854281 AATA
1 AATA
3854285 TTACATTAAA
Statistics
Matches: 115, Mismatches: 30, Indels: 18
0.71 0.18 0.11
Matches are distributed among these distances:
26 4 0.03
27 7 0.06
28 14 0.12
29 1 0.01
30 11 0.10
31 62 0.54
32 7 0.06
33 9 0.08
ACGTcount: A:0.58, C:0.05, G:0.02, T:0.35
Consensus pattern (31 bp):
AATAAAATAAAAATATTTATATCAATAATAA
Found at i:3854160 original size:26 final size:26
Alignment explanation
Indices: 3854081--3854165 Score: 80
Period size: 31 Copynumber: 3.0 Consensus size: 26
3854071 TAACAATAAT
*
3854081 AAAATAGTATTATAATATTAATAAAATA
1 AAAATA-T-TTATAACATTAATAAAATA
*
3854109 AAAATATTTATATCACTAATAAAATAAAATA
1 AAAATATTTATA--AC--AT-TAATAAAATA
*
3854140 AAAATCTTTATAACATTAATAAAATA
1 AAAATATTTATAACATTAATAAAATA
3854166 TTTAATTTTG
Statistics
Matches: 48, Mismatches: 4, Indels: 12
0.75 0.06 0.19
Matches are distributed among these distances:
26 14 0.29
27 3 0.06
28 7 0.15
29 2 0.04
30 2 0.04
31 20 0.42
ACGTcount: A:0.60, C:0.05, G:0.01, T:0.34
Consensus pattern (26 bp):
AAAATATTTATAACATTAATAAAATA
Found at i:3854323 original size:119 final size:120
Alignment explanation
Indices: 3854112--3854333 Score: 308
Period size: 119 Copynumber: 1.9 Consensus size: 120
3854102 TAAAATAAAA
* * **
3854112 ATATTTATATCACTAATAAAATAAAATAAAAATCTTTATAACATTAATAAAATATTTAATTTTGA
1 ATATTTATATCACTAATAAAATAAAATAAAAATATTTATAACAATAATAAAATATTTAATTTAAA
* *
3854177 TTTAATATGATATTATAAAAAACAATAAT-AATAATAATAAAACTAAAACTAATG
66 TTGAATATCATATTATAAAAAACAATAATAAATAATAATAAAACTAAAACTAATG
* *
3854231 ATATTTATATCATTAATAAAATAAAATAAAAATATTTATATCAATAATAAAATA-TTACA-TTAA
1 ATATTTATATCACTAATAAAATAAAATAAAAATATTTATAACAATAATAAAATATTTA-ATTTAA
*
3854294 ATTGAATA-CATATTATAAAAATATTAATAATAAATAATAA
65 ATTGAATATCATATTATAAAAA-A-CAATAATAAATAATAA
3854334 AAATGAACAA
Statistics
Matches: 90, Mismatches: 9, Indels: 7
0.85 0.08 0.07
Matches are distributed among these distances:
117 12 0.13
118 13 0.14
119 57 0.63
120 8 0.09
ACGTcount: A:0.57, C:0.05, G:0.02, T:0.36
Consensus pattern (120 bp):
ATATTTATATCACTAATAAAATAAAATAAAAATATTTATAACAATAATAAAATATTTAATTTAAA
TTGAATATCATATTATAAAAAACAATAATAAATAATAATAAAACTAAAACTAATG
Found at i:3855785 original size:37 final size:37
Alignment explanation
Indices: 3855739--3855850 Score: 170
Period size: 37 Copynumber: 3.0 Consensus size: 37
3855729 AACATAACGT
* * * * *
3855739 TAGAATTTTATTAGGATTTAAACTCCTAAAAATATGA
1 TAGAGTTTTACTATGATTCAAACTCCTAAAAATAGGA
3855776 TAGAGTTTTACTATGATTCAAACTCCTAAAAATAGGA
1 TAGAGTTTTACTATGATTCAAACTCCTAAAAATAGGA
*
3855813 TAGAGTTCTACTATGATTCAAACTCCTAAAAATAGGA
1 TAGAGTTTTACTATGATTCAAACTCCTAAAAATAGGA
3855850 T
1 T
3855851 CCACAAGCAT
Statistics
Matches: 69, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
37 69 1.00
ACGTcount: A:0.41, C:0.12, G:0.12, T:0.34
Consensus pattern (37 bp):
TAGAGTTTTACTATGATTCAAACTCCTAAAAATAGGA
Found at i:3856556 original size:36 final size:36
Alignment explanation
Indices: 3856472--3856664 Score: 106
Period size: 36 Copynumber: 5.4 Consensus size: 36
3856462 TATATATATA
* * *
3856472 TATACTATT-TTTTTA-TGTTTTATTTATTATATATATA
1 TATA-TATTATTTTTACTTTTTTA-TTATTAT-TTTATT
3856509 TATATATTATTTTTACTTTTTTATTATTATTTTATT
1 TATATATTATTTTTACTTTTTTATTATTATTTTATT
3856545 TATATATTA-TTTT-CTTCTTTT-TCT-TTA-TTT-TT
1 TATATATTATTTTTACTT-TTTTAT-TATTATTTTATT
* * *
3856577 TA-ATAAT-TTTTTACATATTTTTTTTATTTATTTTACT
1 TATATATTATTTTTAC-T-TTTTTATTA-TTATTTTATT
* * *
3856614 TACTATTTTATTTTTGCTTTCTTTATCT-TATCTTTTATT
1 TA-TATATTATTTTTACTTT-TTTAT-TAT-TATTTTATT
3856653 TA-AT-TTATTTTT
1 TATATATTATTTTT
3856665 TTCTTCATTT
Statistics
Matches: 126, Mismatches: 11, Indels: 39
0.72 0.06 0.22
Matches are distributed among these distances:
31 8 0.06
32 5 0.04
33 9 0.07
34 9 0.07
35 12 0.10
36 28 0.22
37 22 0.17
38 9 0.07
39 17 0.13
40 7 0.06
ACGTcount: A:0.23, C:0.06, G:0.01, T:0.70
Consensus pattern (36 bp):
TATATATTATTTTTACTTTTTTATTATTATTTTATT
Found at i:3856565 original size:37 final size:36
Alignment explanation
Indices: 3856466--3856578 Score: 115
Period size: 36 Copynumber: 3.1 Consensus size: 36
3856456 TATATATATA
* *
3856466 TATATATATACTATTTTTT-TATGTTTTATTTATTATATA
1 TATATATATATTATTTTTTCT-T-TTTTA-TTATTAT-TT
*
3856505 TATATATATATTATTTTTACTTTTTTATTATTATTT
1 TATATATATATTATTTTTTCTTTTTTATTATTATTT
*
3856541 TATTTATATATTATTTTCTTCTTTTTCT-TTATT-TTT
1 TATATATATATTATTTT-TTCTTTTT-TATTATTATTT
3856577 TA
1 TA
3856579 ATAATTTTTT
Statistics
Matches: 66, Mismatches: 5, Indels: 9
0.82 0.06 0.11
Matches are distributed among these distances:
36 22 0.33
37 19 0.29
38 6 0.09
39 18 0.27
40 1 0.02
ACGTcount: A:0.26, C:0.04, G:0.01, T:0.69
Consensus pattern (36 bp):
TATATATATATTATTTTTTCTTTTTTATTATTATTT
Found at i:3856669 original size:27 final size:27
Alignment explanation
Indices: 3856639--3856703 Score: 78
Period size: 27 Copynumber: 2.4 Consensus size: 27
3856629 GCTTTCTTTA
* *
3856639 TCTTATCTTTTATTTAATTTATTTTTT
1 TCTTATCTTTTATTCAATTTATTTATT
*
3856666 TCTTCAT-TTTAATTCAATTTATTTATT
1 TCTT-ATCTTTTATTCAATTTATTTATT
*
3856693 TCTTACCTTTT
1 TCTTATCTTTT
3856704 TATCTAACAT
Statistics
Matches: 31, Mismatches: 5, Indels: 4
0.77 0.12 0.10
Matches are distributed among these distances:
26 1 0.03
27 28 0.90
28 2 0.06
ACGTcount: A:0.20, C:0.12, G:0.00, T:0.68
Consensus pattern (27 bp):
TCTTATCTTTTATTCAATTTATTTATT
Found at i:3857745 original size:15 final size:15
Alignment explanation
Indices: 3857725--3857755 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
3857715 GGGGTAGGAC
3857725 TTTTTATTTTCATTA
1 TTTTTATTTTCATTA
*
3857740 TTTTTATTTTTATTA
1 TTTTTATTTTCATTA
3857755 T
1 T
3857756 CCTTGCCTCA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.19, C:0.03, G:0.00, T:0.77
Consensus pattern (15 bp):
TTTTTATTTTCATTA
Found at i:3859713 original size:17 final size:17
Alignment explanation
Indices: 3859693--3859725 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
3859683 AAAGAGAAGA
3859693 AAAAAGCAAA-GAAAAAC
1 AAAAA-CAAAGGAAAAAC
3859710 AAAAACAAAGGAAAAA
1 AAAAACAAAGGAAAAA
3859726 GTGAAGAAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 4 0.27
17 11 0.73
ACGTcount: A:0.79, C:0.09, G:0.12, T:0.00
Consensus pattern (17 bp):
AAAAACAAAGGAAAAAC
Found at i:3860783 original size:32 final size:32
Alignment explanation
Indices: 3860746--3860837 Score: 130
Period size: 32 Copynumber: 2.9 Consensus size: 32
3860736 TGAGAAACAT
* * *
3860746 TTGGGGAATCTTTGAAGATTCAACATCAAATG
1 TTGGGGCATCTTTGGAGATTCAACATCAAATA
* *
3860778 TTGGGGCATTTTTGGAGATTCAACATCGAATA
1 TTGGGGCATCTTTGGAGATTCAACATCAAATA
*
3860810 TTGGGGCATCTTTGGGGATTCAACATCA
1 TTGGGGCATCTTTGGAGATTCAACATCA
3860838 TGATGTGAAT
Statistics
Matches: 52, Mismatches: 8, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
32 52 1.00
ACGTcount: A:0.28, C:0.14, G:0.25, T:0.33
Consensus pattern (32 bp):
TTGGGGCATCTTTGGAGATTCAACATCAAATA
Found at i:3861503 original size:36 final size:36
Alignment explanation
Indices: 3861453--3861532 Score: 133
Period size: 36 Copynumber: 2.2 Consensus size: 36
3861443 AATTTACTCA
* *
3861453 AAACAAAGTTTTGTCTCTCTTTAGATAGTTTCCCTTG
1 AAACAAA-TTTTGTCTCTCTTGAGACAGTTTCCCTTG
3861490 AAACAAATTTTGTCTCTCTTGAGACAGTTTCCCTTG
1 AAACAAATTTTGTCTCTCTTGAGACAGTTTCCCTTG
3861526 AAACAAA
1 AAACAAA
3861533 ATCTTTGAAT
Statistics
Matches: 41, Mismatches: 2, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
36 34 0.83
37 7 0.17
ACGTcount: A:0.30, C:0.20, G:0.12, T:0.38
Consensus pattern (36 bp):
AAACAAATTTTGTCTCTCTTGAGACAGTTTCCCTTG
Found at i:3861648 original size:36 final size:37
Alignment explanation
Indices: 3861545--3861705 Score: 191
Period size: 37 Copynumber: 4.4 Consensus size: 37
3861535 CTTTGAATCT
* *
3861545 GTTTTCCTTGAAACAAA-TTTTGTCTCCCTTGAGACA
1 GTTTCCCTTGAAACAAAGTTTTGTCTCTCTTGAGACA
** * * *
3861581 GTTTCTTTTGGAACTAAGTATTGTCTCTCTTGAGACA
1 GTTTCCCTTGAAACAAAGTTTTGTCTCTCTTGAGACA
* * *
3861618 ATTTCTCTTTAAACAAA-TTTTGTCTCTCTTGAGACA
1 GTTTCCCTTGAAACAAAGTTTTGTCTCTCTTGAGACA
* *
3861654 ATTTCCCTTGAAACAAAGTTTTGTCTCACTTGAGACA
1 GTTTCCCTTGAAACAAAGTTTTGTCTCTCTTGAGACA
*
3861691 GTTTCTCTTGAAACA
1 GTTTCCCTTGAAACA
3861706 CCAATCTTTG
Statistics
Matches: 105, Mismatches: 18, Indels: 3
0.83 0.14 0.02
Matches are distributed among these distances:
36 45 0.43
37 60 0.57
ACGTcount: A:0.26, C:0.20, G:0.14, T:0.40
Consensus pattern (37 bp):
GTTTCCCTTGAAACAAAGTTTTGTCTCTCTTGAGACA
Found at i:3861678 original size:73 final size:73
Alignment explanation
Indices: 3861547--3861705 Score: 221
Period size: 73 Copynumber: 2.2 Consensus size: 73
3861537 TTGAATCTGT
* ** * * *
3861547 TTTC-CTTGAAACAAATTTTGTCTCCCTTGAGACAGTTTCTTTTGGAACTAAGTATTGTCTCTCT
1 TTTCTCTTGAAACAAATTTTGTCTCCCTTGAGACAATTTCCCTTGAAACAAAGTATTGTCTCACT
3861611 TGAGACAA
66 TGAGACAA
* * *
3861619 TTTCTCTTTAAACAAATTTTGTCTCTCTTGAGACAATTTCCCTTGAAACAAAGTTTTGTCTCACT
1 TTTCTCTTGAAACAAATTTTGTCTCCCTTGAGACAATTTCCCTTGAAACAAAGTATTGTCTCACT
*
3861684 TGAGACAG
66 TGAGACAA
3861692 TTTCTCTTGAAACA
1 TTTCTCTTGAAACA
3861706 CCAATCTTTG
Statistics
Matches: 75, Mismatches: 11, Indels: 1
0.86 0.13 0.01
Matches are distributed among these distances:
72 4 0.05
73 71 0.95
ACGTcount: A:0.26, C:0.20, G:0.13, T:0.40
Consensus pattern (73 bp):
TTTCTCTTGAAACAAATTTTGTCTCCCTTGAGACAATTTCCCTTGAAACAAAGTATTGTCTCACT
TGAGACAA
Found at i:3861866 original size:36 final size:35
Alignment explanation
Indices: 3861758--3861876 Score: 204
Period size: 34 Copynumber: 3.4 Consensus size: 35
3861748 CCTTGGGACA
*
3861758 GTTTCTCTTGAAACAAAAAAAAAACCTTTGAAATT
1 GTTTCTCTTGAAACACAAAAAAAACCTTTGAAATT
3861793 GTTTCTCTTGAAACAC-AAAAAAACCTTTGAAATT
1 GTTTCTCTTGAAACACAAAAAAAACCTTTGAAATT
*
3861827 GTTTCTCTTGAAACACAAAAAACAACCTTTGAAAAT
1 GTTTCTCTTGAAACACAAAAAA-AACCTTTGAAATT
3861863 GTTTCTCTTGAAAC
1 GTTTCTCTTGAAAC
3861877 CCAAGACCTT
Statistics
Matches: 80, Mismatches: 2, Indels: 3
0.94 0.02 0.04
Matches are distributed among these distances:
34 34 0.43
35 20 0.25
36 26 0.32
ACGTcount: A:0.41, C:0.18, G:0.09, T:0.32
Consensus pattern (35 bp):
GTTTCTCTTGAAACACAAAAAAAACCTTTGAAATT
Found at i:3862513 original size:37 final size:37
Alignment explanation
Indices: 3862467--3862578 Score: 197
Period size: 37 Copynumber: 3.0 Consensus size: 37
3862457 AACATAACGT
*
3862467 TAGAATTTTACTAGGATTCAAACTCCTAAAAATAGGA
1 TAGAGTTTTACTAGGATTCAAACTCCTAAAAATAGGA
3862504 TAGAGTTTTACTAGGATTCAAACTCCTAAAAATAGGA
1 TAGAGTTTTACTAGGATTCAAACTCCTAAAAATAGGA
* *
3862541 TAGAGTTCTACTATGATTCAAACTCCTAAAAATAGGA
1 TAGAGTTTTACTAGGATTCAAACTCCTAAAAATAGGA
3862578 T
1 T
3862579 CCACAAGCAT
Statistics
Matches: 72, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
37 72 1.00
ACGTcount: A:0.41, C:0.14, G:0.14, T:0.30
Consensus pattern (37 bp):
TAGAGTTTTACTAGGATTCAAACTCCTAAAAATAGGA
Found at i:3863126 original size:2 final size:2
Alignment explanation
Indices: 3863121--3863192 Score: 58
Period size: 2 Copynumber: 36.5 Consensus size: 2
3863111 TTTTTTAGAT
* * * * *
3863121 TA TA TA TA TA TA TA TA TA TA TA TA TT TA CTA TT TT TT TA T- TT
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA -TA TA TA TA TA TA TA
* *
3863163 TT TA TT TA T- 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 T
3863193 TATTTTTACT
Statistics
Matches: 60, Mismatches: 7, Indels: 6
0.82 0.10 0.08
Matches are distributed among these distances:
1 2 0.03
2 56 0.93
3 2 0.03
ACGTcount: A:0.38, C:0.01, G:0.00, T:0.61
Consensus pattern (2 bp):
TA
Found at i:3863126 original size:24 final size:25
Alignment explanation
Indices: 3863081--3863129 Score: 73
Period size: 25 Copynumber: 2.0 Consensus size: 25
3863071 ATTTTTTACA
*
3863081 TTTTCTTTTTTACTTTAGTATATAT
1 TTTTCTTTTTTACATTAGTATATAT
*
3863106 TTTTCTTTTTTAGATTA-TATATAT
1 TTTTCTTTTTTACATTAGTATATAT
3863130 ATATATATAT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
24 7 0.32
25 15 0.68
ACGTcount: A:0.22, C:0.06, G:0.04, T:0.67
Consensus pattern (25 bp):
TTTTCTTTTTTACATTAGTATATAT
Found at i:3863254 original size:24 final size:23
Alignment explanation
Indices: 3863186--3863260 Score: 64
Period size: 24 Copynumber: 3.1 Consensus size: 23
3863176 TATATATATA
*
3863186 TATATATTATTTTTACTTTTTA-T
1 TATATATT-TTTTTTCTTTTTATT
*
3863209 TAT-TATTTTATTTATTTGTTTTATT
1 TATATATTTT-TTT-TCT-TTTTATT
*
3863234 TATATATTTTTTCTTCTTTTTCTT
1 TATATATTTTTT-TTCTTTTTATT
3863258 TAT
1 TAT
3863261 TTTTTATATT
Statistics
Matches: 42, Mismatches: 4, Indels: 11
0.74 0.07 0.19
Matches are distributed among these distances:
21 2 0.05
22 7 0.17
23 4 0.10
24 14 0.33
25 8 0.19
26 7 0.17
ACGTcount: A:0.20, C:0.05, G:0.01, T:0.73
Consensus pattern (23 bp):
TATATATTTTTTTTCTTTTTATT
Found at i:3866114 original size:20 final size:20
Alignment explanation
Indices: 3866091--3866130 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
3866081 CCATTATAAT
*
3866091 TGTTGATATGACATTTCACG
1 TGTTGATATGACAATTCACG
* *
3866111 TGTTTATGTGACAATTCACG
1 TGTTGATATGACAATTCACG
3866131 ATACTAACAT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.25, C:0.15, G:0.20, T:0.40
Consensus pattern (20 bp):
TGTTGATATGACAATTCACG
Found at i:3866671 original size:30 final size:30
Alignment explanation
Indices: 3866631--3866688 Score: 80
Period size: 30 Copynumber: 1.9 Consensus size: 30
3866621 TCGATTATTT
* *
3866631 TAAAAGATAATTATATAATAAGTTTCGATA
1 TAAAAGATAATTAGATAATAAATTTCGATA
* *
3866661 TAAAATATAATTAGGTAATAAATTTCGA
1 TAAAAGATAATTAGATAATAAATTTCGA
3866689 CTAATACAAA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
30 24 1.00
ACGTcount: A:0.50, C:0.03, G:0.10, T:0.36
Consensus pattern (30 bp):
TAAAAGATAATTAGATAATAAATTTCGATA
Found at i:3866743 original size:25 final size:25
Alignment explanation
Indices: 3866696--3866743 Score: 60
Period size: 25 Copynumber: 1.9 Consensus size: 25
3866686 CGACTAATAC
* * *
3866696 AAAATTTTTAAGTCTTGAATAATTT
1 AAAATTTGTAAATCTAGAATAATTT
*
3866721 AAAATTTGTAAATCTAGATTAAT
1 AAAATTTGTAAATCTAGAATAAT
3866744 CCAGTAAAAT
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
25 19 1.00
ACGTcount: A:0.44, C:0.04, G:0.08, T:0.44
Consensus pattern (25 bp):
AAAATTTGTAAATCTAGAATAATTT
Found at i:3867329 original size:21 final size:21
Alignment explanation
Indices: 3867303--3867351 Score: 73
Period size: 21 Copynumber: 2.3 Consensus size: 21
3867293 TGACTATCGT
3867303 AATGCGATTTT-CCAATTTCGC
1 AATGCGATTTTCCCAA-TTCGC
*
3867324 ATTGCGATTTTCCCAATTCGC
1 AATGCGATTTTCCCAATTCGC
3867345 AATGCGA
1 AATGCGA
3867352 ATAAGTAAAT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
21 21 0.84
22 4 0.16
ACGTcount: A:0.24, C:0.24, G:0.16, T:0.35
Consensus pattern (21 bp):
AATGCGATTTTCCCAATTCGC
Found at i:3867366 original size:20 final size:21
Alignment explanation
Indices: 3867341--3867392 Score: 70
Period size: 21 Copynumber: 2.5 Consensus size: 21
3867331 TTTTCCCAAT
*
3867341 TCGCAATGCGAA-TAAGTAAA
1 TCGCAATGCGAATTAAGAAAA
**
3867361 TCGCAATGCGAATTTGGAAAA
1 TCGCAATGCGAATTAAGAAAA
3867382 TCGCAATGCGA
1 TCGCAATGCGA
3867393 TACTGACTAT
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
20 12 0.43
21 16 0.57
ACGTcount: A:0.38, C:0.17, G:0.23, T:0.21
Consensus pattern (21 bp):
TCGCAATGCGAATTAAGAAAA
Found at i:3867371 original size:41 final size:41
Alignment explanation
Indices: 3867320--3867535 Score: 116
Period size: 41 Copynumber: 5.3 Consensus size: 41
3867310 TTTTCCAATT
* *
3867320 TCGCATTGCGATTTTCCCAATTCGCAATGCGAATAAGTAAA
1 TCGCAATGCGATTTTCCTAATTCGCAATGCGAATAAGTAAA
* *** * * *
3867361 TCGCAATGCGAATTTGGAAAATCGCAATGCG-AT-ACTGACTA
1 TCGCAATGCGATTTTCCTAATTCGCAATGCGAATAAGT-A-AA
* * * * * *
3867402 TCGCAATGCAATTTTCCTAATTCGCATTGTGATTTACGT-AT
1 TCGCAATGCGATTTTCCTAATTCGCAATGCGA-ATAAGTAAA
** * * *
3867443 TCGCGTTACGATTTTCATAATTCGCAATGCGAATACGTAAA
1 TCGCAATGCGATTTTCCTAATTCGCAATGCGAATAAGTAAA
* * *** * * *
3867484 TCGCAACGC-AATTAAGTAAATCGCAATGCGAATTAGGAAAA
1 TCGCAATGCGATTTTCCTAATTCGCAATGCGAA-TAAGTAAA
3867525 TCGCAATGCGA
1 TCGCAATGCGA
3867536 ATACGTAAAT
Statistics
Matches: 125, Mismatches: 42, Indels: 15
0.69 0.23 0.08
Matches are distributed among these distances:
39 2 0.02
40 26 0.21
41 94 0.75
42 1 0.01
43 1 0.01
44 1 0.01
ACGTcount: A:0.33, C:0.20, G:0.19, T:0.29
Consensus pattern (41 bp):
TCGCAATGCGATTTTCCTAATTCGCAATGCGAATAAGTAAA
Found at i:3867436 original size:21 final size:21
Alignment explanation
Indices: 3867412--3867468 Score: 53
Period size: 20 Copynumber: 2.8 Consensus size: 21
3867402 TCGCAATGCA
* **
3867412 ATTTTCCTAATTCGCATTGTG
1 ATTTTCATAATTCGCATTACG
* * *
3867433 ATTTACGT-ATTCGCGTTACG
1 ATTTTCATAATTCGCATTACG
3867453 ATTTTCATAATTCGCA
1 ATTTTCATAATTCGCA
3867469 ATGCGAATAC
Statistics
Matches: 27, Mismatches: 8, Indels: 2
0.73 0.22 0.05
Matches are distributed among these distances:
20 15 0.56
21 12 0.44
ACGTcount: A:0.23, C:0.19, G:0.14, T:0.44
Consensus pattern (21 bp):
ATTTTCATAATTCGCATTACG
Found at i:3867489 original size:20 final size:21
Alignment explanation
Indices: 3867464--3867560 Score: 128
Period size: 20 Copynumber: 4.8 Consensus size: 21
3867454 TTTTCATAAT
3867464 TCGCAATGCGAA-TACGTAAA
1 TCGCAATGCGAATTACGTAAA
* *
3867484 TCGCAACGC-AATTAAGTAAA
1 TCGCAATGCGAATTACGTAAA
* *
3867504 TCGCAATGCGAATTAGGAAAA
1 TCGCAATGCGAATTACGTAAA
3867525 TCGCAATGCGAA-TACGTAAA
1 TCGCAATGCGAATTACGTAAA
*
3867545 TCGCAATGCGATTTAC
1 TCGCAATGCGAATTAC
3867561 ATAACGCCAT
Statistics
Matches: 66, Mismatches: 8, Indels: 5
0.84 0.10 0.06
Matches are distributed among these distances:
19 2 0.03
20 40 0.61
21 24 0.36
ACGTcount: A:0.39, C:0.20, G:0.20, T:0.22
Consensus pattern (21 bp):
TCGCAATGCGAATTACGTAAA
Found at i:3867544 original size:41 final size:40
Alignment explanation
Indices: 3867464--3867555 Score: 123
Period size: 41 Copynumber: 2.3 Consensus size: 40
3867454 TTTTCATAAT
*
3867464 TCGCAATGCGAATACGTAAATCGCAACGCAATTAAGTAAA
1 TCGCAATGCGAATACGAAAATCGCAACGCAATTAAGTAAA
* * *
3867504 TCGCAATGCGAATTAGGAAAATCGCAATGCGAA-TACGTAAA
1 TCGCAATGCGAA-TACGAAAATCGCAACGC-AATTAAGTAAA
3867545 TCGCAATGCGA
1 TCGCAATGCGA
3867556 TTTACATAAC
Statistics
Matches: 46, Mismatches: 4, Indels: 3
0.87 0.08 0.06
Matches are distributed among these distances:
40 12 0.26
41 32 0.70
42 2 0.04
ACGTcount: A:0.40, C:0.20, G:0.21, T:0.20
Consensus pattern (40 bp):
TCGCAATGCGAATACGAAAATCGCAACGCAATTAAGTAAA
Found at i:3867821 original size:27 final size:27
Alignment explanation
Indices: 3867764--3867816 Score: 70
Period size: 27 Copynumber: 1.9 Consensus size: 27
3867754 CATCGCCGAC
* *
3867764 GAAATCCCTCACAACCATTCACAGTCA
1 GAAATCCCTCACAACCATTCAAAATCA
*
3867791 GAAATCCCTCACAATCATTCAGAAAT
1 GAAATCCCTCACAACCATTCA-AAAT
3867817 GGAAAATCAA
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
27 20 0.91
28 2 0.09
ACGTcount: A:0.40, C:0.32, G:0.08, T:0.21
Consensus pattern (27 bp):
GAAATCCCTCACAACCATTCAAAATCA
Found at i:3868162 original size:19 final size:19
Alignment explanation
Indices: 3868138--3868268 Score: 165
Period size: 19 Copynumber: 7.4 Consensus size: 19
3868128 GAAAATCGTA
3868138 TTGCGATTTTCATTTCGCG
1 TTGCGATTTTCATTTCGCG
3868157 TTGCGATTTTCATTTCGCG
1 TTGCGATTTTCATTTCGCG
3868176 TTGCGATTTTCATTTCGCG
1 TTGCGATTTTCATTTCGCG
3868195 TTGCGA--TTC-TTT--CG
1 TTGCGATTTTCATTTCGCG
3868209 TTGCGATTTTCATTTCGCG
1 TTGCGATTTTCATTTCGCG
*
3868228 TTGCGA--TTC---TCTCG
1 TTGCGATTTTCATTTCGCG
**
3868242 TTGCGATAGTCATTTCGCG
1 TTGCGATTTTCATTTCGCG
3868261 TTGCGATT
1 TTGCGATT
3868269 CTCTCATTAC
Statistics
Matches: 98, Mismatches: 4, Indels: 20
0.80 0.03 0.16
Matches are distributed among these distances:
14 18 0.18
16 8 0.08
17 9 0.09
19 63 0.64
ACGTcount: A:0.11, C:0.21, G:0.22, T:0.46
Consensus pattern (19 bp):
TTGCGATTTTCATTTCGCG
Found at i:3868212 original size:14 final size:14
Alignment explanation
Indices: 3868193--3868248 Score: 58
Period size: 14 Copynumber: 3.6 Consensus size: 14
3868183 TTTCATTTCG
3868193 CGTTGCGATTCTTT
1 CGTTGCGATTCTTT
3868207 CGTTGCGATTTTCATTT
1 CGTTGCGA--TTC-TTT
*
3868224 CGCGTTGCGATTCTCT
1 --CGTTGCGATTCTTT
3868240 CGTTGCGAT
1 CGTTGCGAT
3868249 AGTCATTTCG
Statistics
Matches: 36, Mismatches: 1, Indels: 10
0.77 0.02 0.21
Matches are distributed among these distances:
14 17 0.47
16 5 0.14
17 6 0.17
19 8 0.22
ACGTcount: A:0.09, C:0.23, G:0.23, T:0.45
Consensus pattern (14 bp):
CGTTGCGATTCTTT
Found at i:3868213 original size:33 final size:33
Alignment explanation
Indices: 3868138--3868305 Score: 201
Period size: 33 Copynumber: 4.9 Consensus size: 33
3868128 GAAAATCGTA
*
3868138 TTGCGATTTTCATTTCGCGTTGCGATTTTCATTTCGCG
1 TTGCGATTTTCATTTCGCGTTGCGA--TTC---TCTCG
*
3868176 TTGCGATTTTCATTTCGCGTTGCGATTCTTTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
3868209 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
** *
3868242 TTGCGATAGTCATTTCGCGTTGCGATTCTCTCA
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
* ** *
3868275 TTACGATAGTCATTTCCGTGTTGCGATTCTC
1 TTGCGATTTTCATTT-CGCGTTGCGATTCTC
3868306 ATTATCTCGT
Statistics
Matches: 121, Mismatches: 8, Indels: 6
0.90 0.06 0.04
Matches are distributed among these distances:
33 79 0.65
34 14 0.12
36 3 0.02
38 25 0.21
ACGTcount: A:0.12, C:0.23, G:0.21, T:0.45
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
Found at i:3868263 original size:52 final size:52
Alignment explanation
Indices: 3868146--3868268 Score: 157
Period size: 52 Copynumber: 2.4 Consensus size: 52
3868136 TATTGCGATT
3868146 TTCATTTCGCGTTGCGATTTTCATTTCGCGTTGCGATTTTCATTTCGCGTTGCGA
1 TTCATTTCGCGTTGCGATTTTCATTTCGCGTTGCGA-TTTC--TTCGCGTTGCGA
*
3868201 TTC-TTT--CGTTGCGATTTTCATTTCGCGTTGCGA-TTC-TCTCGTTGCGA
1 TTCATTTCGCGTTGCGATTTTCATTTCGCGTTGCGATTTCTTCGCGTTGCGA
3868248 TAGTCATTTCGCGTTGCGATT
1 T--TCATTTCGCGTTGCGATT
3868269 CTCTCATTAC
Statistics
Matches: 62, Mismatches: 1, Indels: 13
0.82 0.01 0.17
Matches are distributed among these distances:
47 11 0.18
49 2 0.03
50 6 0.10
52 37 0.60
54 3 0.05
55 3 0.05
ACGTcount: A:0.11, C:0.22, G:0.22, T:0.46
Consensus pattern (52 bp):
TTCATTTCGCGTTGCGATTTTCATTTCGCGTTGCGATTTCTTCGCGTTGCGA
Found at i:3868307 original size:20 final size:20
Alignment explanation
Indices: 3868284--3868330 Score: 53
Period size: 20 Copynumber: 2.4 Consensus size: 20
3868274 ATTACGATAG
3868284 TCATTTCCGT-GTTGCGATTC
1 TCATTTCC-TCGTTGCGATTC
*
3868304 TCATTAT-CTCGTTGCGATTT
1 TCATT-TCCTCGTTGCGATTC
3868324 TCATTTC
1 TCATTTC
3868331 AACCAAAAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 6
0.77 0.03 0.20
Matches are distributed among these distances:
19 2 0.09
20 20 0.87
21 1 0.04
ACGTcount: A:0.13, C:0.23, G:0.15, T:0.49
Consensus pattern (20 bp):
TCATTTCCTCGTTGCGATTC
Found at i:3870678 original size:20 final size:20
Alignment explanation
Indices: 3870653--3870695 Score: 77
Period size: 20 Copynumber: 2.1 Consensus size: 20
3870643 AATAGTTTCT
3870653 GAAAATGAAAATCGCAACAC
1 GAAAATGAAAATCGCAACAC
*
3870673 GAAAATGAAAATCGCAACGC
1 GAAAATGAAAATCGCAACAC
3870693 GAA
1 GAA
3870696 TTTGACTATC
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.53, C:0.19, G:0.19, T:0.09
Consensus pattern (20 bp):
GAAAATGAAAATCGCAACAC
Found at i:3871287 original size:41 final size:41
Alignment explanation
Indices: 3871168--3871305 Score: 161
Period size: 41 Copynumber: 3.4 Consensus size: 41
3871158 CGCTTTGAAA
* * *
3871168 ATCGCATTGCGATTATGTATTATCTCGTTGCGAAAGTCAGT
1 ATCGCGTTGCGATTTTGTATTATCGCGTTGCGAAAGTCAGT
* * ** * * *
3871209 ATTGAGTTGCGAAATT-AAGTATCGAGTTGCGAAAGTCAGT
1 ATCGCGTTGCGATTTTGTATTATCGCGTTGCGAAAGTCAGT
*
3871249 ATCGCGTTGCGATTTTGTATTATCGCGTTGCGATAGTCAGT
1 ATCGCGTTGCGATTTTGTATTATCGCGTTGCGAAAGTCAGT
*
3871290 ACCGCGTTGCGATTTT
1 ATCGCGTTGCGATTTT
3871306 CCAAATTCGC
Statistics
Matches: 77, Mismatches: 19, Indels: 2
0.79 0.19 0.02
Matches are distributed among these distances:
40 32 0.42
41 45 0.58
ACGTcount: A:0.23, C:0.16, G:0.25, T:0.36
Consensus pattern (41 bp):
ATCGCGTTGCGATTTTGTATTATCGCGTTGCGAAAGTCAGT
Found at i:3871302 original size:20 final size:20
Alignment explanation
Indices: 3871188--3871301 Score: 104
Period size: 20 Copynumber: 5.7 Consensus size: 20
3871178 GATTATGTAT
*
3871188 TATCTCGTTGCGAAAGTCAG
1 TATCGCGTTGCGAAAGTCAG
* * * *
3871208 TATTGAGTTGCGAAATTAAG
1 TATCGCGTTGCGAAAGTCAG
*
3871228 TATCGAGTTGCGAAAGTCAG
1 TATCGCGTTGCGAAAGTCAG
** *
3871248 TATCGCGTTGCGATTTTGT-AT
1 TATCGCGTTGCGA--AAGTCAG
*
3871269 TATCGCGTTGCGATAGTCAG
1 TATCGCGTTGCGAAAGTCAG
*
3871289 TACCGCGTTGCGA
1 TATCGCGTTGCGA
3871302 TTTTCCAAAT
Statistics
Matches: 76, Mismatches: 15, Indels: 6
0.78 0.15 0.06
Matches are distributed among these distances:
19 3 0.04
20 57 0.75
21 14 0.18
22 2 0.03
ACGTcount: A:0.24, C:0.17, G:0.27, T:0.32
Consensus pattern (20 bp):
TATCGCGTTGCGAAAGTCAG
Found at i:3871321 original size:41 final size:41
Alignment explanation
Indices: 3871235--3871323 Score: 108
Period size: 41 Copynumber: 2.2 Consensus size: 41
3871225 AAGTATCGAG
* * ** * *
3871235 TTGCGAAAGTCAGTATCGCGTTGCGATTTTGTATTATCGCG
1 TTGCGATAGTCAGTACCGCGTTGCGATTTTCAAATATCGCA
3871276 TTGCGATAGTCAGTACCGCGTTGCGATTTTCCAAAT-TCGCA
1 TTGCGATAGTCAGTACCGCGTTGCGATTTT-CAAATATCGCA
3871317 TTGCGAT
1 TTGCGAT
3871324 TTACTTATTC
Statistics
Matches: 41, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
41 39 0.95
42 2 0.05
ACGTcount: A:0.20, C:0.20, G:0.25, T:0.35
Consensus pattern (41 bp):
TTGCGATAGTCAGTACCGCGTTGCGATTTTCAAATATCGCA
Found at i:3871322 original size:21 final size:20
Alignment explanation
Indices: 3871296--3871342 Score: 58
Period size: 20 Copynumber: 2.3 Consensus size: 20
3871286 CAGTACCGCG
*
3871296 TTGCGATTTTCCAAATTCGCA
1 TTGCGA-TTTACAAATTCGCA
**
3871317 TTGCGATTTACTTATTCGCA
1 TTGCGATTTACAAATTCGCA
3871337 TTGCGA
1 TTGCGA
3871343 ATTGGGAAAA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
20 17 0.74
21 6 0.26
ACGTcount: A:0.21, C:0.21, G:0.17, T:0.40
Consensus pattern (20 bp):
TTGCGATTTACAAATTCGCA
Found at i:3871384 original size:21 final size:22
Alignment explanation
Indices: 3871332--3871384 Score: 74
Period size: 21 Copynumber: 2.5 Consensus size: 22
3871322 ATTTACTTAT
3871332 TCGCATTGCG-AATTGGGAAAA
1 TCGCATTGCGAAATTGGGAAAA
**
3871353 TCGCAACGCGAAATT-GGAAAA
1 TCGCATTGCGAAATTGGGAAAA
3871374 TCGCATTGCGA
1 TCGCATTGCGA
3871385 TAGTCATAAT
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
21 23 0.85
22 4 0.15
ACGTcount: A:0.34, C:0.19, G:0.26, T:0.21
Consensus pattern (22 bp):
TCGCATTGCGAAATTGGGAAAA
Found at i:3874358 original size:25 final size:25
Alignment explanation
Indices: 3874330--3874381 Score: 61
Period size: 25 Copynumber: 2.1 Consensus size: 25
3874320 AAAAATAAAT
3874330 AAAT-ATTAATAAAACATTTATCTAA
1 AAATAATTAA-AAAACATTTATCTAA
* * *
3874355 AAATAATTTAAAAATATTTATTTAA
1 AAATAATTAAAAAACATTTATCTAA
3874380 AA
1 AA
3874382 TATCAGAAAA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
25 19 0.83
26 4 0.17
ACGTcount: A:0.58, C:0.04, G:0.00, T:0.38
Consensus pattern (25 bp):
AAATAATTAAAAAACATTTATCTAA
Found at i:3875981 original size:3 final size:3
Alignment explanation
Indices: 3875968--3876001 Score: 54
Period size: 3 Copynumber: 12.0 Consensus size: 3
3875958 ATTTATTTAT
3875968 TAA TAA T-A TAA TAA T-A TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
3876002 AAAAATGAAA
Statistics
Matches: 29, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
2 4 0.14
3 25 0.86
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (3 bp):
TAA
Found at i:3875981 original size:8 final size:8
Alignment explanation
Indices: 3875968--3876000 Score: 57
Period size: 8 Copynumber: 4.0 Consensus size: 8
3875958 ATTTATTTAT
3875968 TAATAATA
1 TAATAATA
3875976 TAATAATA
1 TAATAATA
3875984 TAATAATAA
1 TAATAAT-A
3875993 TAATAATA
1 TAATAATA
3876001 AAAAAATGAA
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
8 16 0.67
9 8 0.33
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (8 bp):
TAATAATA
Found at i:3876188 original size:45 final size:46
Alignment explanation
Indices: 3876130--3876342 Score: 333
Period size: 45 Copynumber: 4.7 Consensus size: 46
3876120 GATGGAAATG
*
3876130 TTGAAAACATCATGCACTGAAGGACTTACAGATGACCCGAATG-TT
1 TTGAAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGTTT
* *
3876175 TTGAAAACATCATGCACTGAAGGGCTTACAGATGACCTGAAGGTTT
1 TTGAAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGTTT
* * *
3876221 TTGAAAACATCATGCATTGAAGGGCTTACAGATGA-CCTAAGGTTT
1 TTGAAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGTTT
*
3876266 TTGAAAACATCATGCACTGAAAGACTTACAGATGACCCGAAGG-TT
1 TTGAAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGTTT
*
3876311 TTGAAAACATCATGCATTGAAGGACTTACAGA
1 TTGAAAACATCATGCACTGAAGGACTTACAGA
3876343 CGTAGGAAAT
Statistics
Matches: 154, Mismatches: 12, Indels: 4
0.91 0.07 0.02
Matches are distributed among these distances:
45 112 0.73
46 42 0.27
ACGTcount: A:0.36, C:0.18, G:0.21, T:0.25
Consensus pattern (46 bp):
TTGAAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGTTT
Found at i:3876285 original size:91 final size:90
Alignment explanation
Indices: 3876130--3876342 Score: 338
Period size: 91 Copynumber: 2.4 Consensus size: 90
3876120 GATGGAAATG
* *
3876130 TTGAAAACATCATGCACTGAAGGACTTACAGATGACCCGAATGTTTTGAAAACATCATGCACTGA
1 TTGAAAACATCATGCATTGAAGGACTTACAGATGACCCGAAGGTTTTGAAAACATCATGCACTGA
* * *
3876195 AGGGCTTACAGATGACCTGAAGGTTT
66 AAGACTTACAGATGACCCGAAGG-TT
* *
3876221 TTGAAAACATCATGCATTGAAGGGCTTACAGATGA-CCTAAGGTTTTTGAAAACATCATGCACTG
1 TTGAAAACATCATGCATTGAAGGACTTACAGATGACCCGAAGG-TTTTGAAAACATCATGCACTG
3876285 AAAGACTTACAGATGACCCGAAGGTT
65 AAAGACTTACAGATGACCCGAAGGTT
3876311 TTGAAAACATCATGCATTGAAGGACTTACAGA
1 TTGAAAACATCATGCATTGAAGGACTTACAGA
3876343 CGTAGGAAAT
Statistics
Matches: 113, Mismatches: 8, Indels: 3
0.91 0.06 0.02
Matches are distributed among these distances:
90 38 0.34
91 75 0.66
ACGTcount: A:0.36, C:0.18, G:0.21, T:0.25
Consensus pattern (90 bp):
TTGAAAACATCATGCATTGAAGGACTTACAGATGACCCGAAGGTTTTGAAAACATCATGCACTGA
AAGACTTACAGATGACCCGAAGGTT
Found at i:3877027 original size:22 final size:20
Alignment explanation
Indices: 3877002--3877052 Score: 68
Period size: 19 Copynumber: 2.5 Consensus size: 20
3876992 AATAAAGCTT
*
3877002 TCATCTTTGAAAAGAGAATCTA
1 TCATCTTTG--AAGAAAATCTA
3877024 TCATCTTTG-AGAAAATCTA
1 TCATCTTTGAAGAAAATCTA
3877043 TCATCTTTGA
1 TCATCTTTGA
3877053 GGAATGTAGA
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
19 18 0.67
22 9 0.33
ACGTcount: A:0.35, C:0.16, G:0.12, T:0.37
Consensus pattern (20 bp):
TCATCTTTGAAGAAAATCTA
Found at i:3877470 original size:54 final size:54
Alignment explanation
Indices: 3877409--3877539 Score: 136
Period size: 54 Copynumber: 2.4 Consensus size: 54
3877399 ATGACCATAT
* * * * *
3877409 ATTCATCCTTTCTTGTGGCTTCTACCCAGATTTTCGTAAAGCTTTTGATAACAC
1 ATTCATCCTTTCTTGTGGCTTCTACACAGATGTTCATAAAGCATTTGACAACAC
* * * **
3877463 ATTCATCCATTCCTGTGACTTCTGTACAGATGTTCATAAAGCATTTGACAACAC
1 ATTCATCCTTTCTTGTGGCTTCTACACAGATGTTCATAAAGCATTTGACAACAC
* * * *
3877517 ATTTATCTTTTCTTTTGGTTTCT
1 ATTCATCCTTTCTTGTGGCTTCT
3877540 GGACAAATAT
Statistics
Matches: 60, Mismatches: 17, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
54 60 1.00
ACGTcount: A:0.23, C:0.22, G:0.12, T:0.43
Consensus pattern (54 bp):
ATTCATCCTTTCTTGTGGCTTCTACACAGATGTTCATAAAGCATTTGACAACAC
Found at i:3880710 original size:20 final size:20
Alignment explanation
Indices: 3880685--3880735 Score: 102
Period size: 20 Copynumber: 2.5 Consensus size: 20
3880675 TAATGAAGGC
3880685 ATGCATCGATGCACTACACT
1 ATGCATCGATGCACTACACT
3880705 ATGCATCGATGCACTACACT
1 ATGCATCGATGCACTACACT
3880725 ATGCATCGATG
1 ATGCATCGATG
3880736 TACCCCTTGA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.29, C:0.27, G:0.18, T:0.25
Consensus pattern (20 bp):
ATGCATCGATGCACTACACT
Found at i:3887734 original size:18 final size:17
Alignment explanation
Indices: 3887711--3887758 Score: 78
Period size: 17 Copynumber: 2.8 Consensus size: 17
3887701 CTTGGTTCAA
3887711 TTTTTTCCTTCTTTCCCT
1 TTTTTTCCTT-TTTCCCT
*
3887729 TTTTTTCCTTTTTTCCT
1 TTTTTTCCTTTTTCCCT
3887746 TTTTTTCCTTTTT
1 TTTTTTCCTTTTT
3887759 TTTTTTTTTT
Statistics
Matches: 29, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
17 19 0.66
18 10 0.34
ACGTcount: A:0.00, C:0.25, G:0.00, T:0.75
Consensus pattern (17 bp):
TTTTTTCCTTTTTCCCT
Found at i:3887748 original size:7 final size:8
Alignment explanation
Indices: 3887711--3887759 Score: 62
Period size: 9 Copynumber: 5.8 Consensus size: 8
3887701 CTTGGTTCAA
3887711 TTTTTTCC
1 TTTTTTCC
*
3887719 TTCTTTCCC
1 TT-TTTTCC
3887728 TTTTTTTCC
1 -TTTTTTCC
3887737 TTTTTTCC
1 TTTTTTCC
3887745 TTTTTTTCC
1 -TTTTTTCC
3887754 TTTTTT
1 TTTTTT
3887760 TTTTTTTTTT
Statistics
Matches: 36, Mismatches: 2, Indels: 6
0.82 0.05 0.14
Matches are distributed among these distances:
8 16 0.44
9 18 0.50
10 2 0.06
ACGTcount: A:0.00, C:0.24, G:0.00, T:0.76
Consensus pattern (8 bp):
TTTTTTCC
Found at i:3887759 original size:18 final size:18
Alignment explanation
Indices: 3887728--3887897 Score: 200
Period size: 16 Copynumber: 9.9 Consensus size: 18
3887718 CTTCTTTCCC
**
3887728 TTTTTTTCC-TTTTTTCC
1 TTTTTTTCCTTTTTTTTT
3887745 TTTTTTTCCTTTTTTTTT
1 TTTTTTTCCTTTTTTTTT
3887763 TTTTTTT--TTTTTTTTT
1 TTTTTTTCCTTTTTTTTT
3887779 TTTTTTT--TTTTTTGTTT
1 TTTTTTTCCTTTTTT-TTT
3887796 TTTTTTT--TTTTTTTTT
1 TTTTTTTCCTTTTTTTTT
3887812 TTTTTTT--TTTTTTTTT
1 TTTTTTTCCTTTTTTTTT
3887828 TTTTTTT--TTTTTTTTT
1 TTTTTTTCCTTTTTTTTT
**
3887844 TTTTTTTTTTTTTTTTTT
1 TTTTTTTCCTTTTTTTTT
3887862 TTTTTTTCCTTTTTTTTTTT
1 TTTTTTTCC--TTTTTTTTT
3887882 TTTTTTTCCTTTTTTT
1 TTTTTTTCCTTTTTTT
3887898 CAAGTATAAT
Statistics
Matches: 143, Mismatches: 4, Indels: 11
0.91 0.03 0.07
Matches are distributed among these distances:
16 64 0.45
17 25 0.17
18 36 0.25
20 18 0.13
ACGTcount: A:0.00, C:0.06, G:0.01, T:0.94
Consensus pattern (18 bp):
TTTTTTTCCTTTTTTTTT
Found at i:3887897 original size:1 final size:1
Alignment explanation
Indices: 3887754--3887888 Score: 243
Period size: 1 Copynumber: 135.0 Consensus size: 1
3887744 CTTTTTTTCC
*
3887754 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTGTTTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
**
3887819 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTCCTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
3887884 TTTTT
1 TTTTT
3887889 CCTTTTTTTC
Statistics
Matches: 130, Mismatches: 4, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
1 130 1.00
ACGTcount: A:0.00, C:0.01, G:0.01, T:0.98
Consensus pattern (1 bp):
T
Found at i:3892909 original size:36 final size:33
Alignment explanation
Indices: 3892835--3892909 Score: 87
Period size: 36 Copynumber: 2.2 Consensus size: 33
3892825 TTTCTTAATA
3892835 TTAAAAATAAATAAATATAAATTAAACATTTAT
1 TTAAAAATAAATAAATATAAATTAAACATTTAT
* * * *
3892868 CTAAAAATAATTAAAATATAATTTAAAAATATTTAT
1 TTAAAAATAAAT-AAATATAAATT--AAACATTTAT
3892904 TTAAAA
1 TTAAAA
3892910 TATCTGAAAA
Statistics
Matches: 34, Mismatches: 5, Indels: 3
0.81 0.12 0.07
Matches are distributed among these distances:
33 10 0.29
34 10 0.29
36 14 0.41
ACGTcount: A:0.60, C:0.03, G:0.00, T:0.37
Consensus pattern (33 bp):
TTAAAAATAAATAAATATAAATTAAACATTTAT
Found at i:3901581 original size:3 final size:3
Alignment explanation
Indices: 3901575--3901614 Score: 80
Period size: 3 Copynumber: 13.3 Consensus size: 3
3901565 TGGAGAGACA
3901575 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG A
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG A
3901615 GAGTTATTAT
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 37 1.00
ACGTcount: A:0.68, C:0.00, G:0.33, T:0.00
Consensus pattern (3 bp):
AAG
Found at i:3903064 original size:2 final size:2
Alignment explanation
Indices: 3903006--3903047 Score: 84
Period size: 2 Copynumber: 21.0 Consensus size: 2
3902996 TTTAGATTAT
3903006 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
3903048 CTTACCCTAA
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:3906863 original size:20 final size:19
Alignment explanation
Indices: 3906840--3906946 Score: 51
Period size: 20 Copynumber: 5.5 Consensus size: 19
3906830 CTATCTCAAG
3906840 CGAGATGAAATATTCTATTT
1 CGAG-TGAAATATTCTATTT
**
3906860 CGAGTGAAACTA-TCTCA-AG
1 CGAGTGAAA-TATTCT-ATTT
* *
3906879 CGAGATGAAATCTTCTGTTT
1 CGAG-TGAAATATTCTATTT
**
3906899 CGAGTGAAACTA-TCTCA-AG
1 CGAGTGAAA-TATTCT-ATTT
* *
3906918 CGAGATGAAATCTTCTGTTT
1 CGAG-TGAAATATTCTATTT
3906938 CGAGTGAAA
1 CGAGTGAAA
3906947 CTATCTCAAG
Statistics
Matches: 63, Mismatches: 14, Indels: 21
0.64 0.14 0.21
Matches are distributed among these distances:
19 31 0.49
20 32 0.51
ACGTcount: A:0.33, C:0.16, G:0.21, T:0.31
Consensus pattern (19 bp):
CGAGTGAAATATTCTATTT
Found at i:3907175 original size:20 final size:19
Alignment explanation
Indices: 3907120--3907176 Score: 53
Period size: 20 Copynumber: 2.9 Consensus size: 19
3907110 AAGCGAAATA
3907120 AAATCTTCTGTTTCGAGTG
1 AAATCTTCTGTTTCGAGTG
****
3907139 AAA-CTATCTCAAGCGAGATG
1 AAATCT-TCTGTTTCGAG-TG
3907159 AAATCTTCTGTTTCGAGT
1 AAATCTTCTGTTTCGAGT
3907177 TAAACTATCT
Statistics
Matches: 27, Mismatches: 8, Indels: 6
0.66 0.20 0.15
Matches are distributed among these distances:
18 2 0.07
19 11 0.41
20 12 0.44
21 2 0.07
ACGTcount: A:0.28, C:0.18, G:0.19, T:0.35
Consensus pattern (19 bp):
AAATCTTCTGTTTCGAGTG
Found at i:3907199 original size:39 final size:39
Alignment explanation
Indices: 3906749--3907191 Score: 645
Period size: 39 Copynumber: 11.4 Consensus size: 39
3906739 GTTTTAAGGA
* * *
3906749 AAACAATCTCAAGTGAGATGATATCTTCTGTTTCGAGTG
1 AAACTATCTCAAGCGAGATGAAATCTTCTGTTTCGAGTG
* * * *
3906788 AAACTAGCTCAAGTGAGATGAAATATTTTGTTTC-ATGTG
1 AAACTATCTCAAGCGAGATGAAATCTTCTGTTTCGA-GTG
* *
3906827 AAACTATCTCAAGCGAGATGAAATATTCTATTTCGAGTG
1 AAACTATCTCAAGCGAGATGAAATCTTCTGTTTCGAGTG
3906866 AAACTATCTCAAGCGAGATGAAATCTTCTGTTTCGAGTG
1 AAACTATCTCAAGCGAGATGAAATCTTCTGTTTCGAGTG
3906905 AAACTATCTCAAGCGAGATGAAATCTTCTGTTTCGAGTG
1 AAACTATCTCAAGCGAGATGAAATCTTCTGTTTCGAGTG
** *
3906944 AAACTATCTCAAGATAGATAAAATCTTCTGTTTCGAGTG
1 AAACTATCTCAAGCGAGATGAAATCTTCTGTTTCGAGTG
* * *
3906983 AAACTATCTCAAGCGAGATAAAATCTTCTATTTCGTGTG
1 AAACTATCTCAAGCGAGATGAAATCTTCTGTTTCGAGTG
* * *
3907022 AAATTATCTCAAGCGAGATAAAATATTCTGTTTCGAGTG
1 AAACTATCTCAAGCGAGATGAAATCTTCTGTTTCGAGTG
* * * *
3907061 AAACTATCTCAAACGAGATAAAATCTTATTTTTCGAGTG
1 AAACTATCTCAAGCGAGATGAAATCTTCTGTTTCGAGTG
* *
3907100 AAACTATCTCAAGCGAAATAAAATCTTCTGTTTCGAGTG
1 AAACTATCTCAAGCGAGATGAAATCTTCTGTTTCGAGTG
*
3907139 AAACTATCTCAAGCGAGATGAAATCTTCTGTTTCGAGTT
1 AAACTATCTCAAGCGAGATGAAATCTTCTGTTTCGAGTG
3907178 AAACTATCTCAAGC
1 AAACTATCTCAAGC
3907192 TTGATGAATA
Statistics
Matches: 368, Mismatches: 34, Indels: 4
0.91 0.08 0.01
Matches are distributed among these distances:
38 1 0.00
39 366 0.99
40 1 0.00
ACGTcount: A:0.34, C:0.16, G:0.17, T:0.32
Consensus pattern (39 bp):
AAACTATCTCAAGCGAGATGAAATCTTCTGTTTCGAGTG
Found at i:3911335 original size:8 final size:9
Alignment explanation
Indices: 3911317--3911355 Score: 51
Period size: 9 Copynumber: 4.2 Consensus size: 9
3911307 TTTAAAAAAT
3911317 AAAATTAAA
1 AAAATTAAA
3911326 AAAATTAAA
1 AAAATTAAA
*
3911335 AAAATAGAAA
1 AAAAT-TAAA
*
3911345 AAAAATAAA
1 AAAATTAAA
3911354 AA
1 AA
3911356 TAAAATAAAC
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
9 19 0.73
10 7 0.27
ACGTcount: A:0.82, C:0.00, G:0.03, T:0.15
Consensus pattern (9 bp):
AAAATTAAA
Found at i:3911349 original size:23 final size:23
Alignment explanation
Indices: 3911305--3911360 Score: 58
Period size: 23 Copynumber: 2.3 Consensus size: 23
3911295 TAATAAACCT
* *
3911305 AATTTAAAAAATAAAATTAAAAA
1 AATTAAAAAAATAAAATAAAAAA
*
3911328 AATTAAAAAAATAGAAAAAAAATAA
1 AATTAAAAAAATA-AAATAAAA-AA
*
3911353 AAATAAAA
1 AATTAAAA
3911361 TAAACATAAA
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
23 12 0.44
24 6 0.22
25 9 0.33
ACGTcount: A:0.79, C:0.00, G:0.02, T:0.20
Consensus pattern (23 bp):
AATTAAAAAAATAAAATAAAAAA
Found at i:3911444 original size:22 final size:20
Alignment explanation
Indices: 3911404--3911454 Score: 66
Period size: 22 Copynumber: 2.4 Consensus size: 20
3911394 ATAAAAGTAC
3911404 TAAACTAAAAGGGAATAAAT
1 TAAACTAAAAGGGAATAAAT
*
3911424 TAAACATAAAATGGGACTAAAT
1 TAAAC-TAAAA-GGGAATAAAT
3911446 TCAAACTAA
1 T-AAACTAA
3911455 TCGAAATTCA
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
20 5 0.19
21 5 0.19
22 13 0.48
23 4 0.15
ACGTcount: A:0.57, C:0.10, G:0.12, T:0.22
Consensus pattern (20 bp):
TAAACTAAAAGGGAATAAAT
Found at i:3911463 original size:16 final size:18
Alignment explanation
Indices: 3911442--3911480 Score: 55
Period size: 16 Copynumber: 2.2 Consensus size: 18
3911432 AAATGGGACT
3911442 AAATTCAAA-CT-AATCG
1 AAATTCAAAGCTAAATCG
3911458 AAATTCAAAGGCTAAATCG
1 AAATTCAAA-GCTAAATCG
3911477 AAAT
1 AAAT
3911481 AAAATAAAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
16 9 0.45
18 2 0.10
19 9 0.45
ACGTcount: A:0.51, C:0.15, G:0.10, T:0.23
Consensus pattern (18 bp):
AAATTCAAAGCTAAATCG
Found at i:3915630 original size:21 final size:20
Alignment explanation
Indices: 3915589--3915631 Score: 52
Period size: 21 Copynumber: 2.1 Consensus size: 20
3915579 CTTAATCCAA
*
3915589 AAATCTAAACATAAATTCCT
1 AAATCTAAACATAAATCCCT
3915609 AAATCTAATAC-TCAAATCCCT
1 AAATCTAA-ACAT-AAATCCCT
3915630 AA
1 AA
3915632 TCCTGATCCC
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
20 9 0.45
21 11 0.55
ACGTcount: A:0.49, C:0.23, G:0.00, T:0.28
Consensus pattern (20 bp):
AAATCTAAACATAAATCCCT
Found at i:3915934 original size:40 final size:43
Alignment explanation
Indices: 3915862--3915958 Score: 103
Period size: 40 Copynumber: 2.3 Consensus size: 43
3915852 AACAAACAAA
* * **
3915862 TTCGCAATGCG-ATTTCAAATTCGCAACACGAAC-T-CCAA-T
1 TTCGCAACGCGAATTTCAAATTCACAACACGAACATGAAAATT
** *
3915901 TTCGCAACGCGAATTTGGAATTCACAACTCGAACATGAAAATT
1 TTCGCAACGCGAATTTCAAATTCACAACACGAACATGAAAATT
3915944 TTCGCAACGCGAATT
1 TTCGCAACGCGAATT
3915959 ACCGATATAG
Statistics
Matches: 47, Mismatches: 7, Indels: 4
0.81 0.12 0.07
Matches are distributed among these distances:
39 10 0.21
40 18 0.38
41 1 0.02
42 2 0.04
43 16 0.34
ACGTcount: A:0.34, C:0.25, G:0.15, T:0.26
Consensus pattern (43 bp):
TTCGCAACGCGAATTTCAAATTCACAACACGAACATGAAAATT
Found at i:3916014 original size:49 final size:49
Alignment explanation
Indices: 3915942--3916075 Score: 232
Period size: 49 Copynumber: 2.7 Consensus size: 49
3915932 AACATGAAAA
* *
3915942 TTTTCGCAACGCGAATTACCGATATAGGTAAACATAGTTGCGAAATCCG
1 TTTTCGCAACGAGAATTACCGATATAGGTAAACACAGTTGCGAAATCCG
*
3915991 TTTTCACAACGAGAATTACCGATATAGGTAAACACAGTTGCGAAATCCG
1 TTTTCGCAACGAGAATTACCGATATAGGTAAACACAGTTGCGAAATCCG
*
3916040 TTTTCGCAACTAGAATTACCGATATAGGTAAACACA
1 TTTTCGCAACGAGAATTACCGATATAGGTAAACACA
3916076 ACTATTCACA
Statistics
Matches: 80, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
49 80 1.00
ACGTcount: A:0.36, C:0.20, G:0.18, T:0.26
Consensus pattern (49 bp):
TTTTCGCAACGAGAATTACCGATATAGGTAAACACAGTTGCGAAATCCG
Found at i:3916181 original size:13 final size:13
Alignment explanation
Indices: 3916157--3916189 Score: 50
Period size: 13 Copynumber: 2.5 Consensus size: 13
3916147 TCGAATTTAC
3916157 CAATTACGCAACT
1 CAATTACGCAACT
3916170 CGAATT-CGCAACT
1 C-AATTACGCAACT
3916183 CAATTAC
1 CAATTAC
3916190 CGATATAGGT
Statistics
Matches: 18, Mismatches: 0, Indels: 4
0.82 0.00 0.18
Matches are distributed among these distances:
12 4 0.22
13 10 0.56
14 4 0.22
ACGTcount: A:0.36, C:0.30, G:0.09, T:0.24
Consensus pattern (13 bp):
CAATTACGCAACT
Found at i:3916902 original size:20 final size:19
Alignment explanation
Indices: 3916879--3916933 Score: 74
Period size: 20 Copynumber: 2.8 Consensus size: 19
3916869 ATTCTAATTC
3916879 TGTGTTGCGAATTTGGAAAT
1 TGTGTTGCGAATTTGG-AAT
* *
3916899 TGTGTTGCGAAATTGGAGT
1 TGTGTTGCGAATTTGGAAT
3916918 TCGTGTTGCGAATTTG
1 T-GTGTTGCGAATTTG
3916934 TTGGTTATTT
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
19 3 0.10
20 28 0.90
ACGTcount: A:0.20, C:0.07, G:0.33, T:0.40
Consensus pattern (19 bp):
TGTGTTGCGAATTTGGAAT
Found at i:3929397 original size:13 final size:12
Alignment explanation
Indices: 3929370--3929405 Score: 63
Period size: 13 Copynumber: 2.9 Consensus size: 12
3929360 AGTTTATAAC
3929370 TTTTCTTTTTTT
1 TTTTCTTTTTTT
3929382 TTTTCTTTTTTCT
1 TTTTCTTTTTT-T
3929395 TTTTCTTTTTT
1 TTTTCTTTTTT
3929406 GGCTTTCGTA
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
12 11 0.48
13 12 0.52
ACGTcount: A:0.00, C:0.11, G:0.00, T:0.89
Consensus pattern (12 bp):
TTTTCTTTTTTT
Found at i:3929972 original size:3 final size:3
Alignment explanation
Indices: 3929966--3930012 Score: 51
Period size: 3 Copynumber: 15.3 Consensus size: 3
3929956 TTATTATTAG
* *
3929966 AAT AAT AAT AAT AAT AAT AAAT ATT AAT TAT AGA- AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT -AAT AAT AAT AAT A-AT AAT AAT AAT AAT
3930012 A
1 A
3930013 CGAGAAAATA
Statistics
Matches: 37, Mismatches: 4, Indels: 6
0.79 0.09 0.13
Matches are distributed among these distances:
2 1 0.03
3 32 0.86
4 4 0.11
ACGTcount: A:0.64, C:0.00, G:0.02, T:0.34
Consensus pattern (3 bp):
AAT
Found at i:3941079 original size:18 final size:18
Alignment explanation
Indices: 3941056--3941103 Score: 87
Period size: 18 Copynumber: 2.7 Consensus size: 18
3941046 ATGCAAAATA
*
3941056 GGTACCGATACTCAAAGG
1 GGTACCAATACTCAAAGG
3941074 GGTACCAATACTCAAAGG
1 GGTACCAATACTCAAAGG
3941092 GGTACCAATACT
1 GGTACCAATACT
3941104 ACTTTACACA
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
18 29 1.00
ACGTcount: A:0.35, C:0.23, G:0.23, T:0.19
Consensus pattern (18 bp):
GGTACCAATACTCAAAGG
Found at i:3943543 original size:40 final size:39
Alignment explanation
Indices: 3943497--3943633 Score: 116
Period size: 40 Copynumber: 3.4 Consensus size: 39
3943487 GTTTCTGCAC
* * *
3943497 TCGCAACACGAATTTC-TTTCTCCTAATGTGATTTTCAAAT
1 TCGCAACACGAATTTCAATTC-CC-AACGTGATTTCCAAAT
* * *
3943537 TCGCAACGCGATTTTCAAATTCGCAACGTGATTTCCAAAT
1 TCGCAACACGAATTTC-AATTCCCAACGTGATTTCCAAAT
* **
3943577 TCGCAACACAGAATTTCAAATTCACAAC-TCGATTTCTGAAT
1 TCGCAACAC-GAATTTC-AATTCCCAACGT-GATTTCCAAAT
*
3943618 TCGCAACGCGAATTTC
1 TCGCAACACGAATTTC
3943634 TTTTTCGCAA
Statistics
Matches: 81, Mismatches: 12, Indels: 8
0.80 0.12 0.08
Matches are distributed among these distances:
40 44 0.54
41 34 0.42
42 3 0.04
ACGTcount: A:0.31, C:0.25, G:0.12, T:0.32
Consensus pattern (39 bp):
TCGCAACACGAATTTCAATTCCCAACGTGATTTCCAAAT
Found at i:3943549 original size:20 final size:20
Alignment explanation
Indices: 3943526--3943633 Score: 119
Period size: 20 Copynumber: 5.3 Consensus size: 20
3943516 CTCCTAATGT
3943526 GATTTTCAAATTCGCAACGC
1 GATTTTCAAATTCGCAACGC
*
3943546 GATTTTCAAATTCGCAACGT
1 GATTTTCAAATTCGCAACGC
* *
3943566 GATTTCCAAATTCGCAACAC
1 GATTTTCAAATTCGCAACGC
* * *
3943586 AGAATTTCAAATTCACAACTC
1 -GATTTTCAAATTCGCAACGC
*
3943607 GA-TTTCTGAATTCGCAACGC
1 GATTTTC-AAATTCGCAACGC
*
3943627 GAATTTC
1 GATTTTC
3943634 TTTTTCGCAA
Statistics
Matches: 74, Mismatches: 11, Indels: 5
0.82 0.12 0.06
Matches are distributed among these distances:
19 4 0.05
20 50 0.68
21 20 0.27
ACGTcount: A:0.32, C:0.24, G:0.13, T:0.31
Consensus pattern (20 bp):
GATTTTCAAATTCGCAACGC
Found at i:3943611 original size:41 final size:40
Alignment explanation
Indices: 3943524--3943633 Score: 141
Period size: 41 Copynumber: 2.7 Consensus size: 40
3943514 TTCTCCTAAT
* * *
3943524 GTGATTTTCAAATTCGCAACGCGATTTTCAAATTCGCAAC
1 GTGATTTCCAAATTCGCAACGCGAATTTCAAATTCACAAC
*
3943564 GTGATTTCCAAATTCGCAACACAGAATTTCAAATTCACAAC
1 GTGATTTCCAAATTCGCAACGC-GAATTTCAAATTCACAAC
**
3943605 -TCGATTTCTGAATTCGCAACGCGAATTTC
1 GT-GATTTCCAAATTCGCAACGCGAATTTC
3943634 TTTTTCGCAA
Statistics
Matches: 61, Mismatches: 7, Indels: 4
0.85 0.10 0.06
Matches are distributed among these distances:
40 28 0.46
41 33 0.54
ACGTcount: A:0.32, C:0.24, G:0.14, T:0.31
Consensus pattern (40 bp):
GTGATTTCCAAATTCGCAACGCGAATTTCAAATTCACAAC
Found at i:3943673 original size:20 final size:20
Alignment explanation
Indices: 3943617--3943665 Score: 64
Period size: 20 Copynumber: 2.5 Consensus size: 20
3943607 GATTTCTGAA
* *
3943617 TTCGCAACGCGAA-TTTCTTT
1 TTCGCAACAC-AAGTTTCCTT
3943637 TTCGCAACACAAGTTTCCTT
1 TTCGCAACACAAGTTTCCTT
3943657 TTCGCAACA
1 TTCGCAACA
3943666 AGATTTTCTA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
19 2 0.08
20 24 0.92
ACGTcount: A:0.24, C:0.29, G:0.12, T:0.35
Consensus pattern (20 bp):
TTCGCAACACAAGTTTCCTT
Found at i:3943699 original size:40 final size:40
Alignment explanation
Indices: 3943655--3943746 Score: 121
Period size: 40 Copynumber: 2.3 Consensus size: 40
3943645 ACAAGTTTCC
* *
3943655 TTTTCGCAACAAGATTTTCTAAATCGCAACATGAATTTTG
1 TTTTCGCAACAAGATTTTCGAAATCGCAACATGAATTTTA
* ** *
3943695 TTTTCGAAACTCGATTTTCGAATTCGCAACATGAATTTTA
1 TTTTCGCAACAAGATTTTCGAAATCGCAACATGAATTTTA
*
3943735 ATTTCGCAACAA
1 TTTTCGCAACAA
3943747 CTTTTATTTT
Statistics
Matches: 42, Mismatches: 10, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
40 42 1.00
ACGTcount: A:0.33, C:0.18, G:0.12, T:0.37
Consensus pattern (40 bp):
TTTTCGCAACAAGATTTTCGAAATCGCAACATGAATTTTA
Found at i:3943742 original size:20 final size:20
Alignment explanation
Indices: 3943656--3943763 Score: 66
Period size: 20 Copynumber: 5.5 Consensus size: 20
3943646 CAAGTTTCCT
* *
3943656 TTTCGCAACAAGATTTTCTAA
1 TTTCGCAACATGAATTT-TAA
* **
3943677 -ATCGCAACATGAATTTTGT
1 TTTCGCAACATGAATTTTAA
*
3943696 TTTCGAAAC-TCG-ATTTTCGAA
1 TTTCGCAACAT-GAATTTT--AA
3943717 -TTCGCAACATGAATTTTAA
1 TTTCGCAACATGAATTTTAA
* *
3943736 TTTCGCAACA--ACTTTTAT
1 TTTCGCAACATGAATTTTAA
3943754 TTTCGCAACA
1 TTTCGCAACA
3943764 GAAATATTTT
Statistics
Matches: 68, Mismatches: 12, Indels: 17
0.70 0.12 0.18
Matches are distributed among these distances:
18 16 0.24
19 9 0.13
20 37 0.54
21 6 0.09
ACGTcount: A:0.31, C:0.19, G:0.11, T:0.38
Consensus pattern (20 bp):
TTTCGCAACATGAATTTTAA
Found at i:3947038 original size:18 final size:18
Alignment explanation
Indices: 3947015--3947050 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
3947005 AAGAAAAAGG
3947015 AAATCAAAATCACAATCA
1 AAATCAAAATCACAATCA
*
3947033 AAATCAAAATCCCAATCA
1 AAATCAAAATCACAATCA
3947051 CAACCAGCTT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.58, C:0.25, G:0.00, T:0.17
Consensus pattern (18 bp):
AAATCAAAATCACAATCA
Found at i:3947353 original size:20 final size:20
Alignment explanation
Indices: 3947328--3947399 Score: 117
Period size: 20 Copynumber: 3.6 Consensus size: 20
3947318 TCGCAACGTG
* *
3947328 AATTTGACTTTCGTGTTGCT
1 AATTTGACTTTCGCGTTGCA
*
3947348 AATTTGACTTTCGCGTTGCG
1 AATTTGACTTTCGCGTTGCA
3947368 AATTTGACTTTCGCGTTGCA
1 AATTTGACTTTCGCGTTGCA
3947388 AATTTGACTTTC
1 AATTTGACTTTC
3947400 CCAACAATCG
Statistics
Matches: 49, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 49 1.00
ACGTcount: A:0.18, C:0.18, G:0.19, T:0.44
Consensus pattern (20 bp):
AATTTGACTTTCGCGTTGCA
Found at i:3947441 original size:20 final size:20
Alignment explanation
Indices: 3947416--3947458 Score: 77
Period size: 20 Copynumber: 2.1 Consensus size: 20
3947406 ATCGCAATAC
*
3947416 GAATTTGATTTTTGCGTTGT
1 GAATTTGATTTTCGCGTTGT
3947436 GAATTTGATTTTCGCGTTGT
1 GAATTTGATTTTCGCGTTGT
3947456 GAA
1 GAA
3947459 AGTGTATCTT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.19, C:0.07, G:0.26, T:0.49
Consensus pattern (20 bp):
GAATTTGATTTTCGCGTTGT
Found at i:3948948 original size:21 final size:21
Alignment explanation
Indices: 3948922--3949019 Score: 110
Period size: 21 Copynumber: 4.7 Consensus size: 21
3948912 GTGAATCGGA
* *
3948922 CTCTTGAACGGTGGGAGGCGC
1 CTCTTGAACGATGAGAGGCGC
*
3948943 CTCTTGAACGATGAGAGGGGC
1 CTCTTGAACGATGAGAGGCGC
3948964 CTCTTGAACGATGAGA-GCTGC
1 CTCTTGAACGATGAGAGGC-GC
* * *
3948985 CTCTTTAATGAT-AGGAGGGGC
1 CTCTTGAACGATGA-GAGGCGC
3949006 CTCTTGAACGATGA
1 CTCTTGAACGATGA
3949020 CAGGTGAATC
Statistics
Matches: 64, Mismatches: 9, Indels: 7
0.80 0.11 0.09
Matches are distributed among these distances:
20 2 0.03
21 60 0.94
22 2 0.03
ACGTcount: A:0.22, C:0.20, G:0.34, T:0.23
Consensus pattern (21 bp):
CTCTTGAACGATGAGAGGCGC
Found at i:3948987 original size:42 final size:42
Alignment explanation
Indices: 3948922--3949019 Score: 128
Period size: 42 Copynumber: 2.3 Consensus size: 42
3948912 GTGAATCGGA
* *
3948922 CTCTTGAACGGTGGGAGGCGCCTCTTGAACGAT-GAGAGGGGC
1 CTCTTGAACGATGAGAGGCGCCTCTTGAACGATAG-GAGGGGC
* *
3948964 CTCTTGAACGATGAGA-GCTGCCTCTTTAATGATAGGAGGGGC
1 CTCTTGAACGATGAGAGGC-GCCTCTTGAACGATAGGAGGGGC
3949006 CTCTTGAACGATGA
1 CTCTTGAACGATGA
3949020 CAGGTGAATC
Statistics
Matches: 50, Mismatches: 4, Indels: 4
0.86 0.07 0.07
Matches are distributed among these distances:
41 2 0.04
42 47 0.94
43 1 0.02
ACGTcount: A:0.22, C:0.20, G:0.34, T:0.23
Consensus pattern (42 bp):
CTCTTGAACGATGAGAGGCGCCTCTTGAACGATAGGAGGGGC
Found at i:3949446 original size:21 final size:21
Alignment explanation
Indices: 3949422--3949471 Score: 55
Period size: 21 Copynumber: 2.4 Consensus size: 21
3949412 ACCATTGTCG
*
3949422 TCACGTAAAGTACCGACCCCA
1 TCACGTAAAGCACCGACCCCA
* * *
3949443 TCACGCAAAGCACTGACCTCA
1 TCACGTAAAGCACCGACCCCA
*
3949464 TCATGTAA
1 TCACGTAA
3949472 CTCCCCTAAC
Statistics
Matches: 23, Mismatches: 6, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.34, C:0.34, G:0.14, T:0.18
Consensus pattern (21 bp):
TCACGTAAAGCACCGACCCCA
Found at i:3949661 original size:42 final size:42
Alignment explanation
Indices: 3949586--3949681 Score: 129
Period size: 42 Copynumber: 2.3 Consensus size: 42
3949576 GTGATGGAAT
* * * * *
3949586 AGGTGATGGCTCTCGTTGTGGAGGTGTATAATCGGCTTGATC
1 AGGTGATGGCTCACGGTGTCGAGGTGTAGAATCGGCTCGATC
* *
3949628 AGGTGATGGCTCAGGGTGTCGAGTTGTAGAATCGGCTCGATC
1 AGGTGATGGCTCACGGTGTCGAGGTGTAGAATCGGCTCGATC
3949670 AGGTGATGGCTC
1 AGGTGATGGCTC
3949682 TCGAAGTGGG
Statistics
Matches: 47, Mismatches: 7, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
42 47 1.00
ACGTcount: A:0.18, C:0.16, G:0.38, T:0.29
Consensus pattern (42 bp):
AGGTGATGGCTCACGGTGTCGAGGTGTAGAATCGGCTCGATC
Found at i:3950018 original size:20 final size:21
Alignment explanation
Indices: 3949988--3950064 Score: 88
Period size: 20 Copynumber: 3.8 Consensus size: 21
3949978 ATATGTCCGC
3949988 ATTCTGTGTTGCGAATTACAAT
1 ATTC-GTGTTGCGAATTACAAT
*
3950010 -TTCGTGTTGCGATTTAC-AT
1 ATTCGTGTTGCGAATTACAAT
*
3950029 ATTCGCGTTGCGAATTAC-AT
1 ATTCGTGTTGCGAATTACAAT
* *
3950049 ATTCGCGTTGCAAATT
1 ATTCGTGTTGCGAATT
3950065 TCAAAACTGA
Statistics
Matches: 50, Mismatches: 4, Indels: 4
0.86 0.07 0.07
Matches are distributed among these distances:
19 2 0.04
20 45 0.90
21 3 0.06
ACGTcount: A:0.23, C:0.17, G:0.19, T:0.40
Consensus pattern (21 bp):
ATTCGTGTTGCGAATTACAAT
Found at i:3953528 original size:16 final size:15
Alignment explanation
Indices: 3953497--3953537 Score: 64
Period size: 16 Copynumber: 2.7 Consensus size: 15
3953487 TTATATTATT
3953497 ATTATTATTATAATA
1 ATTATTATTATAATA
3953512 ATTATTATTATTAATA
1 ATTATTATTA-TAATA
*
3953528 AATATTATTA
1 ATTATTATTA
3953538 CAGGCCCAAA
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
15 10 0.42
16 14 0.58
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (15 bp):
ATTATTATTATAATA
Found at i:3953537 original size:3 final size:3
Alignment explanation
Indices: 3953481--3953524 Score: 54
Period size: 3 Copynumber: 14.7 Consensus size: 3
3953471 TTCATTTGAA
* *
3953481 TAT TAT T-T ATAT TAT TAT TAT TAT TAT AAT AAT TAT TAT TAT TA
1 TAT TAT TAT -TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
3953525 ATAAATATTA
Statistics
Matches: 37, Mismatches: 2, Indels: 4
0.86 0.05 0.09
Matches are distributed among these distances:
2 1 0.03
3 35 0.95
4 1 0.03
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (3 bp):
TAT
Found at i:3954652 original size:13 final size:13
Alignment explanation
Indices: 3954634--3954658 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
3954624 AATTTCTTTT
3954634 AATTTGATATAAG
1 AATTTGATATAAG
3954647 AATTTGATATAA
1 AATTTGATATAA
3954659 TTTTAATCTA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.48, C:0.00, G:0.12, T:0.40
Consensus pattern (13 bp):
AATTTGATATAAG
Found at i:3954889 original size:3 final size:3
Alignment explanation
Indices: 3954881--3954910 Score: 51
Period size: 3 Copynumber: 10.0 Consensus size: 3
3954871 TTTATTTTTA
*
3954881 ATT ATT ATT ACT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
3954911 TAACCATAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.33, C:0.03, G:0.00, T:0.63
Consensus pattern (3 bp):
ATT
Found at i:3955129 original size:20 final size:19
Alignment explanation
Indices: 3955104--3955145 Score: 57
Period size: 20 Copynumber: 2.2 Consensus size: 19
3955094 TTATTTTATA
3955104 AATTATATATTAATTGTTTT
1 AATTATATATTAATT-TTTT
* *
3955124 AATTATTTATTTATTTTTT
1 AATTATATATTAATTTTTT
3955143 AAT
1 AAT
3955146 ATCAAAGAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
19 7 0.35
20 13 0.65
ACGTcount: A:0.33, C:0.00, G:0.02, T:0.64
Consensus pattern (19 bp):
AATTATATATTAATTTTTT
Found at i:3955135 original size:120 final size:117
Alignment explanation
Indices: 3955001--3955236 Score: 285
Period size: 120 Copynumber: 2.0 Consensus size: 117
3954991 TTTAATCCTA
** * * * *
3955001 TTTTAATATTTATTTATTTTCCAATATTTAAGAAAGGA-CAATCTTAAAATAACTGGATGTCCAT
1 TTTTAATATTTATTTATTTTCCAATATCAAAGAAAAGAGCAATCTTAAAACAACTAGAAGTCC-T
* * *
3955065 TTTCTGATATTTTTAAATAAATAAATATCTTATTTTATAAATTATATATTAATTG
65 TTTATGATATTTCTAAATAAATAAATATCTTA-TTTATAAA-TATATATAAATTG
** * ** *
3955120 TTTTAATTATTTATTTATTTTTTAATATCAAAGAAAAGAGCTATCTTAAGGCAACTAGAAGTTCT
1 TTTTAA-TATTTATTTATTTTCCAATATCAAAGAAAAGAGCAATCTTAAAACAACTAGAAGTCCT
*
3955185 TTTATGATATTTCTAAATAAATAAATATTTTATTTATAAATATATATAAATT
65 TTTATGATATTTCTAAATAAATAAATATCTTATTTATAAATATATATAAATT
3955237 AATATATATA
Statistics
Matches: 99, Mismatches: 16, Indels: 5
0.82 0.13 0.04
Matches are distributed among these distances:
118 11 0.11
119 14 0.14
120 57 0.58
121 17 0.17
ACGTcount: A:0.40, C:0.07, G:0.07, T:0.47
Consensus pattern (117 bp):
TTTTAATATTTATTTATTTTCCAATATCAAAGAAAAGAGCAATCTTAAAACAACTAGAAGTCCTT
TTATGATATTTCTAAATAAATAAATATCTTATTTATAAATATATATAAATTG
Found at i:3959241 original size:15 final size:15
Alignment explanation
Indices: 3959223--3959253 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
3959213 GATCAATACC
3959223 TTTGCATACATGCAT
1 TTTGCATACATGCAT
*
3959238 TTTGCATACATTCAT
1 TTTGCATACATGCAT
3959253 T
1 T
3959254 ATTCATTACA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.26, C:0.19, G:0.10, T:0.45
Consensus pattern (15 bp):
TTTGCATACATGCAT
Found at i:3966097 original size:101 final size:101
Alignment explanation
Indices: 3965942--3966127 Score: 372
Period size: 101 Copynumber: 1.8 Consensus size: 101
3965932 ATCGCTTCGT
3965942 ATTTTGAGAGAAACAAAATTGGATGAATCTGAATGGATCCAAGCTAGATTTCATCAGTTGAACCT
1 ATTTTGAGAGAAACAAAATTGGATGAATCTGAATGGATCCAAGCTAGATTTCATCAGTTGAACCT
3966007 TATTGAGGAGAAAAGATTGAGAACATCTACTGGGGC
66 TATTGAGGAGAAAAGATTGAGAACATCTACTGGGGC
3966043 ATTTTGAGAGAAACAAAATTGGATGAATCTGAATGGATCCAAGCTAGATTTCATCAGTTGAACCT
1 ATTTTGAGAGAAACAAAATTGGATGAATCTGAATGGATCCAAGCTAGATTTCATCAGTTGAACCT
3966108 TATTGAGGAGAAAAGATTGA
66 TATTGAGGAGAAAAGATTGA
3966128 AAGCTATTTA
Statistics
Matches: 85, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
101 85 1.00
ACGTcount: A:0.38, C:0.12, G:0.23, T:0.27
Consensus pattern (101 bp):
ATTTTGAGAGAAACAAAATTGGATGAATCTGAATGGATCCAAGCTAGATTTCATCAGTTGAACCT
TATTGAGGAGAAAAGATTGAGAACATCTACTGGGGC
Found at i:3966413 original size:1 final size:1
Alignment explanation
Indices: 3966409--3966479 Score: 61
Period size: 1 Copynumber: 71.0 Consensus size: 1
3966399 AGAAAAAATG
* * * * * * * * *
3966409 AAAAAAAGAAAAAAAGAAAAAAAAGAAGAAAAAAAAAGAAGAAAAAAAAGAAAAAAAAAAGAGAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
3966474 AAAAAA
1 AAAAAA
3966480 GGGGGTCAAG
Statistics
Matches: 52, Mismatches: 18, Indels: 0
0.74 0.26 0.00
Matches are distributed among these distances:
1 52 1.00
ACGTcount: A:0.87, C:0.00, G:0.13, T:0.00
Consensus pattern (1 bp):
A
Found at i:3966415 original size:9 final size:8
Alignment explanation
Indices: 3966398--3966478 Score: 87
Period size: 8 Copynumber: 10.2 Consensus size: 8
3966388 ATTATGCTTG
3966398 AAGAAAAA
1 AAGAAAAA
*
3966406 ATGAAAAA
1 AAGAAAAA
3966414 AAGAAAAA
1 AAGAAAAA
3966422 AAGAAAAAA
1 AAG-AAAAA
3966431 AAGAAGAAA
1 AAGAA-AAA
*
3966440 AA-AAAAG
1 AAGAAAAA
3966447 AAGAAAAA
1 AAGAAAAA
*
3966455 AA-AGAAA
1 AAGAAAAA
3966462 AA-AAAAA
1 AAGAAAAA
*
3966469 GAGAAAAA
1 AAGAAAAA
3966477 AA
1 AA
3966479 AGGGGGTCAA
Statistics
Matches: 61, Mismatches: 8, Indels: 8
0.79 0.10 0.10
Matches are distributed among these distances:
7 15 0.25
8 33 0.54
9 13 0.21
ACGTcount: A:0.85, C:0.00, G:0.14, T:0.01
Consensus pattern (8 bp):
AAGAAAAA
Found at i:3966429 original size:25 final size:24
Alignment explanation
Indices: 3966401--3966480 Score: 101
Period size: 25 Copynumber: 3.3 Consensus size: 24
3966391 ATGCTTGAAG
*
3966401 AAAAAATGAAAAAAAGAAAAAAAGA
1 AAAAAAAGAAAAAAA-AAAAAAAGA
*
3966426 AAAAAAAGAAGAAAAAAAAAGAAGA
1 AAAAAAAGAA-AAAAAAAAAAAAGA
*
3966451 AAAAAAAG--AAAAAAAAAAGAGA
1 AAAAAAAGAAAAAAAAAAAAAAGA
3966473 AAAAAAAG
1 AAAAAAAG
3966481 GGGGTCAAGA
Statistics
Matches: 50, Mismatches: 4, Indels: 5
0.85 0.07 0.08
Matches are distributed among these distances:
22 20 0.40
25 25 0.50
26 5 0.10
ACGTcount: A:0.85, C:0.00, G:0.14, T:0.01
Consensus pattern (24 bp):
AAAAAAAGAAAAAAAAAAAAAAGA
Found at i:3966441 original size:13 final size:13
Alignment explanation
Indices: 3966401--3966479 Score: 89
Period size: 12 Copynumber: 6.5 Consensus size: 13
3966391 ATGCTTGAAG
*
3966401 AAAAAATGAA-AA
1 AAAAAAAGAAGAA
*
3966413 AAAGAAAAAAAG-A
1 AAA-AAAAGAAGAA
3966426 AAAAAAAGAAGAA
1 AAAAAAAGAAGAA
3966439 AAAAAAAGAAG-A
1 AAAAAAAGAAGAA
3966451 AAAAAAAG-A-AA
1 AAAAAAAGAAGAA
3966462 AAAAAAAG-AGAA
1 AAAAAAAGAAGAA
3966474 AAAAAA
1 AAAAAA
3966480 GGGGGTCAAG
Statistics
Matches: 59, Mismatches: 3, Indels: 10
0.82 0.04 0.14
Matches are distributed among these distances:
11 11 0.19
12 27 0.46
13 21 0.36
ACGTcount: A:0.86, C:0.00, G:0.13, T:0.01
Consensus pattern (13 bp):
AAAAAAAGAAGAA
Found at i:3966442 original size:22 final size:22
Alignment explanation
Indices: 3966417--3966480 Score: 94
Period size: 22 Copynumber: 2.9 Consensus size: 22
3966407 TGAAAAAAAG
3966417 AAAAAAAGAAAAAAAAGAAG-AA
1 AAAAAAAGAAAAAAAA-AAGAAA
3966439 AAAAAAAGAAGAAAAAAAAGAAA
1 AAAAAAAGAA-AAAAAAAAGAAA
*
3966462 AAAAAAAGAGAAAAAAAAG
1 AAAAAAAGAAAAAAAAAAG
3966481 GGGGTCAAGA
Statistics
Matches: 39, Mismatches: 1, Indels: 4
0.89 0.02 0.09
Matches are distributed among these distances:
22 22 0.56
23 17 0.44
ACGTcount: A:0.86, C:0.00, G:0.14, T:0.00
Consensus pattern (22 bp):
AAAAAAAGAAAAAAAAAAGAAA
Found at i:3967416 original size:114 final size:114
Alignment explanation
Indices: 3967211--3967547 Score: 575
Period size: 114 Copynumber: 3.0 Consensus size: 114
3967201 TGCCACGTTA
* *
3967211 TCATGGTAGAAATAAGGAAACCCAAAAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGG
1 TCATAGTAGAAATAAGGAAACCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGG
3967276 TTTGGTATGAACCCCAGAACCAATCATTAGATTTGAAAGATGAATTTAC
66 TTTGGTATGAACCCCAGAACCAATCATTAGATTTGAAAGATGAATTTAC
* *
3967325 TCATAGTAGAAATAAGGAGACCCAATAGCATCTTCTGGAAGTGTTATTTGAGTTATCTGATCTGG
1 TCATAGTAGAAATAAGGAAACCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGG
* *
3967390 TTTGGTATGAACCCTAGAACCAATCATTAGATTTGAAAGATGAATTTGC
66 TTTGGTATGAACCCCAGAACCAATCATTAGATTTGAAAGATGAATTTAC
* *
3967439 TCATAGTAGAAATAAGAAAACCCAATAGCATCTTTTGGAAGTGTTCTTTGAGTTATCTGATCTGG
1 TCATAGTAGAAATAAGGAAACCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGG
* * *
3967504 TTCGGTAGGAACCCCAGAACCAATCATTAGAATTGAAAGATGAA
66 TTTGGTATGAACCCCAGAACCAATCATTAGATTTGAAAGATGAA
3967548 CTGCATGATC
Statistics
Matches: 209, Mismatches: 14, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
114 209 1.00
ACGTcount: A:0.34, C:0.15, G:0.20, T:0.31
Consensus pattern (114 bp):
TCATAGTAGAAATAAGGAAACCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGG
TTTGGTATGAACCCCAGAACCAATCATTAGATTTGAAAGATGAATTTAC
Found at i:3968600 original size:24 final size:23
Alignment explanation
Indices: 3968557--3968603 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 23
3968547 GTTCATAATG
3968557 AGAAGAACTCATATGAAGAAGAA
1 AGAAGAACTCATATGAAGAAGAA
*
3968580 AGAAGAAGTTCATAATG-AGAAGAA
1 AGAAGAA-CTCAT-ATGAAGAAGAA
3968604 CTTGTTTAAC
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
23 7 0.33
24 11 0.52
25 3 0.14
ACGTcount: A:0.55, C:0.06, G:0.23, T:0.15
Consensus pattern (23 bp):
AGAAGAACTCATATGAAGAAGAA
Found at i:3968776 original size:113 final size:113
Alignment explanation
Indices: 3968510--3968837 Score: 415
Period size: 113 Copynumber: 3.0 Consensus size: 113
3968500 CATTTGATGC
* * *
3968510 AAATCCATCATTTGATGGATCAACTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATATGAAG
1 AAATTCATCACTTGATGGATCAACTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAG
*
3968575 AAGAAAGAAGAAGTTCATAATGAGAAGAACTTGTTTAACCTTTTGCTT
66 AAGAAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGCTT
* ** * * * * ** *
3968623 AAATTCTTCACCCGGTGGATCAGCAGTGT-CAGTTAGAGTTCATAATGAGAAGAACTCATCTGAA
1 AAATTCATCACTTGATGGATCAAC-TTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAA
* *
3968687 GAAGAAAGAAGAAATTCATAATGAGAAGAATTTGTTCAACCTTTTGCTT
65 GAAGAAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGCTT
3968736 AAATTCATCACTTGATGGATCAACTTTTCCAGAGAAAGTTCATAAT---------TCATCTGAAG
1 AAATTCATCACTTGATGGATCAACTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAG
* *
3968792 AAGGAAGAAGAAGTTCATAATGAGAAGAGCTTGTTCAACCTTTTGC
66 AAGAAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGC
3968838 ATGACTCTAT
Statistics
Matches: 183, Mismatches: 30, Indels: 13
0.81 0.13 0.06
Matches are distributed among these distances:
104 52 0.28
112 2 0.01
113 127 0.69
114 2 0.01
ACGTcount: A:0.38, C:0.15, G:0.19, T:0.29
Consensus pattern (113 bp):
AAATTCATCACTTGATGGATCAACTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAG
AAGAAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGCTT
Found at i:3969239 original size:3 final size:3
Alignment explanation
Indices: 3969175--3969226 Score: 81
Period size: 3 Copynumber: 17.7 Consensus size: 3
3969165 TTCATTTGAA
3969175 TAT TAT T-T ATAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T-T
1 TAT TAT TAT -TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
3969219 TAT TAT TA
1 TAT TAT TA
3969227 ATAAATATTA
Statistics
Matches: 46, Mismatches: 0, Indels: 6
0.88 0.00 0.12
Matches are distributed among these distances:
2 3 0.07
3 42 0.91
4 1 0.02
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:3970787 original size:20 final size:19
Alignment explanation
Indices: 3970762--3970803 Score: 57
Period size: 20 Copynumber: 2.2 Consensus size: 19
3970752 TTATTTTATA
3970762 AATTATATATTAATTGTTTT
1 AATTATATATTAATT-TTTT
* *
3970782 AATTATTTATTTATTTTTT
1 AATTATATATTAATTTTTT
3970801 AAT
1 AAT
3970804 ATCAAAGAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
19 7 0.35
20 13 0.65
ACGTcount: A:0.33, C:0.00, G:0.02, T:0.64
Consensus pattern (19 bp):
AATTATATATTAATTTTTT
Found at i:3970888 original size:10 final size:10
Alignment explanation
Indices: 3970873--3970927 Score: 56
Period size: 10 Copynumber: 5.3 Consensus size: 10
3970863 ATAAATATTT
*
3970873 TATTTATAAA
1 TATTTATATA
*
3970883 TATTTATAAA
1 TATTTATATA
*
3970893 TTAATATATATA
1 -T-ATTTATATA
*
3970905 TATATATATA
1 TATTTATATA
3970915 TATTTATATA
1 TATTTATATA
3970925 TAT
1 TAT
3970928 ATTTCATAAT
Statistics
Matches: 40, Mismatches: 3, Indels: 4
0.85 0.06 0.09
Matches are distributed among these distances:
10 31 0.77
11 2 0.05
12 7 0.17
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (10 bp):
TATTTATATA
Found at i:3970903 original size:2 final size:2
Alignment explanation
Indices: 3970896--3970929 Score: 59
Period size: 2 Copynumber: 17.0 Consensus size: 2
3970886 TTATAAATTA
*
3970896 AT AT AT AT AT AT AT AT AT AT AT TT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
3970930 TTCATAATTA
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (2 bp):
AT
Found at i:3977079 original size:25 final size:23
Alignment explanation
Indices: 3977034--3977081 Score: 60
Period size: 25 Copynumber: 2.0 Consensus size: 23
3977024 GGGCTATGGT
*
3977034 TTGGGCTAAGTTTGGATCGGTTG
1 TTGGGCTAAGTTTGGACCGGTTG
*
3977057 TTGGGCTCAATGTTTGGGCCGGTTG
1 TTGGGCT-AA-GTTTGGACCGGTTG
3977082 GCTTTACAAT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
23 7 0.33
24 2 0.10
25 12 0.57
ACGTcount: A:0.10, C:0.12, G:0.40, T:0.38
Consensus pattern (23 bp):
TTGGGCTAAGTTTGGACCGGTTG
Found at i:3978113 original size:83 final size:83
Alignment explanation
Indices: 3977971--3978398 Score: 694
Period size: 83 Copynumber: 5.2 Consensus size: 83
3977961 TATGGATGAC
3977971 CCCGAAGGACTTATCATCTTGCTCGAAAGGCTTATAGATGACCTGAAGGATTTACTCATCATGCT
1 CCCGAAGGACTTATCATCTTGCTCGAAAGGCTTATAGATGACCTGAAGGATTTACTCATCATGCT
3978036 CGAAAGACTTACTGATGG
66 CGAAAGACTTACTGATGG
* * *
3978054 CCCGAAGGACTTATCATGTTACTCGAAAGGCTTATAGATGACCTGAAGGATTTATTCATCATGCT
1 CCCGAAGGACTTATCATCTTGCTCGAAAGGCTTATAGATGACCTGAAGGATTTACTCATCATGCT
*
3978119 CAAAAGACTTACTGATGG
66 CGAAAGACTTACTGATGG
* * *
3978137 CCCGAATGACTTATCATCTTGCTCGAAATGCTTATAGATAACCTGAAGGATTTACTCATCATGCT
1 CCCGAAGGACTTATCATCTTGCTCGAAAGGCTTATAGATGACCTGAAGGATTTACTCATCATGCT
*
3978202 CGAAATACTTACTGATGG
66 CGAAAGACTTACTGATGG
* * * * *
3978220 CCCGGAGAACTTAACATCTTGCTCAAAAGGCTTATTGATGACCTGAAGGATTTACTCATCATGCT
1 CCCGAAGGACTTATCATCTTGCTCGAAAGGCTTATAGATGACCTGAAGGATTTACTCATCATGCT
*
3978285 CAAAAGACTTACTGATGG
66 CGAAAGACTTACTGATGG
* * *
3978303 TCCGAATGACTTATCATCTTGCTCGAAAGGCTTATAGATGACCTAAAGGATTTACTCATCATGCT
1 CCCGAAGGACTTATCATCTTGCTCGAAAGGCTTATAGATGACCTGAAGGATTTACTCATCATGCT
3978368 CGAAAGACTTACTGATGG
66 CGAAAGACTTACTGATGG
*
3978386 CCCGAATGACTTA
1 CCCGAAGGACTTA
3978399 CCAATTTTGG
Statistics
Matches: 313, Mismatches: 32, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
83 313 1.00
ACGTcount: A:0.30, C:0.21, G:0.19, T:0.29
Consensus pattern (83 bp):
CCCGAAGGACTTATCATCTTGCTCGAAAGGCTTATAGATGACCTGAAGGATTTACTCATCATGCT
CGAAAGACTTACTGATGG
Found at i:3978683 original size:233 final size:233
Alignment explanation
Indices: 3978298--3979331 Score: 1358
Period size: 233 Copynumber: 4.4 Consensus size: 233
3978288 AAGACTTACT
* * * ** **
3978298 GATGGTCCGAATGACTTATCATCTTGCTCGAAAGGCTTATAGATGACCTAAAGGATTTACTCATC
1 GATGGCCCGAATGACTTATCATCTTGCTTGAAAGACTTATAGATGACCCGAAGGATTTAAGCATC
* *
3978363 ATGCTCGAAAGACTTACTGATGGCCCGAATGACTTACCAATTTTGGAAATAATTTACTAGGTAAG
66 ATGCTCGAAAGACTTACTGATGGCCCGAAGGACTTACCAATTTTGGAAATAGTTTACTAGGTAAG
* * *
3978428 AAACTTTTCTTACTTTTCAAAAATTTCAATTTTCAGATTTAAATGAGAAACTTTCCTTATTTTTT
131 AAACTTTTCTTACTTTTCAAAAATTTCAATTTTCAGATTTAAATGAGAAACTTTTCTCATTTTTC
3978493 GAAAAACATGTGAAAACATCATGCCCGAAGGTCTTATG
196 GAAAAACATGTGAAAACATCATGCCCGAAGGTCTTATG
* * * * *
3978531 GATGGCTCGAAGGACTTATCATCTTGCTTGAAAGACTTATAGATGACCCGTAGGATTTAAGTATT
1 GATGGCCCGAATGACTTATCATCTTGCTTGAAAGACTTATAGATGACCCGAAGGATTTAAGCATC
* ** * *
3978596 ATGTTCGAAAGACTTACTGATGGCCCGAAGGACACACCAATTTTGGAAATAGTTTACTAAGTGAG
66 ATGCTCGAAAGACTTACTGATGGCCCGAAGGACTTACCAATTTTGGAAATAGTTTACTAGGTAAG
*
3978661 AAACTTTTCTTACTTTTCAAAAATTTCAATTTTCA-ATTTTAAATGAGAAACTTTTCTCTTTTTT
131 AAACTTTTCTTACTTTTCAAAAATTTCAATTTTCAGA-TTTAAATGAGAAACTTTTCTCATTTTT
* * *
3978725 CGAAAAACATGTGAAAACATCCTACCTGAAGGTCTTATG
195 CGAAAAACATGTGAAAACATCATGCCCGAAGGTCTTATG
** * * **
3978764 GATGGCTTGAAAGACTTATCATCTTG-TTCAAAAGACTTGCAGATGACCCGAAGGATTTAAGCAT
1 GATGGCCCGAATGACTTATCATCTTGCTT-GAAAGACTTATAGATGACCCGAAGGATTTAAGCAT
* * *
3978828 CATGATCGAAAGACTTACTGATGGCCCGAAGGACTTACCAATTTTGAAAATAGTTTACTAGGTAT
65 CATGCTCGAAAGACTTACTGATGGCCCGAAGGACTTACCAATTTTGGAAATAGTTTACTAGGTAA
* * * * *
3978893 GAAATTTTTTTTTTACTTTT-AAAAACTTTCAATTTTCATATTTAAATGAGAAAATTTTCACATT
130 GAAA--CTTTTCTTACTTTTCAAAAA-TTTCAATTTTCAGATTTAAATGAGAAACTTTTCTCATT
* * *
3978957 TTTCAAAAAACATGTGAAAACATCCTGCCCGAAGGTCTTACG
192 TTTCGAAAAACATGTGAAAACATCATGCCCGAAGGTCTTATG
* **
3978999 GATAGCCCGAATGACTTATCATCTTGCTTGAAAGACTTATAGATGACCCGAATAATTTAAGCATC
1 GATGGCCCGAATGACTTATCATCTTGCTTGAAAGACTTATAGATGACCCGAAGGATTTAAGCATC
* * * * * *
3979064 ATGCTCGAAAGACATAATAATAGCTCAAAGGACTTACCAATTTTGGAAATAGTTTACTAGGTAAG
66 ATGCTCGAAAGACTTACTGATGGCCCGAAGGACTTACCAATTTTGGAAATAGTTTACTAGGTAAG
* * * * ** *
3979129 AAGCTTTTCTTACTTTTC-CAAATTTAAATTTTTAGATTTAAATGAGAAACTTTAATCATTTTTT
131 AAACTTTTCTTACTTTTCAAAAATTTCAATTTTCAGATTTAAATGAGAAACTTTTCTCATTTTTC
* * *
3979193 G-AAAGCATGTGAAAACATCATTCCTGAAGGTCTTATG
196 GAAAAACATGTGAAAACATCATGCCCGAAGGTCTTATG
* * * * * * *
3979230 GATGGCCCGAATGTCTTATCATCTTGCTCGAAAGACTTACATATTACCCGAAAGATTTAAACATC
1 GATGGCCCGAATGACTTATCATCTTGCTTGAAAGACTTATAGATGACCCGAAGGATTTAAGCATC
*
3979295 ATGCTCGAAAGACTTACTAATGGCCCGAAGGACTTAC
66 ATGCTCGAAAGACTTACTGATGGCCCGAAGGACTTAC
3979332 TAAGTAAAAA
Statistics
Matches: 693, Mismatches: 100, Indels: 18
0.85 0.12 0.02
Matches are distributed among these distances:
231 119 0.17
232 37 0.05
233 335 0.48
234 5 0.01
235 194 0.28
236 3 0.00
ACGTcount: A:0.34, C:0.17, G:0.16, T:0.33
Consensus pattern (233 bp):
GATGGCCCGAATGACTTATCATCTTGCTTGAAAGACTTATAGATGACCCGAAGGATTTAAGCATC
ATGCTCGAAAGACTTACTGATGGCCCGAAGGACTTACCAATTTTGGAAATAGTTTACTAGGTAAG
AAACTTTTCTTACTTTTCAAAAATTTCAATTTTCAGATTTAAATGAGAAACTTTTCTCATTTTTC
GAAAAACATGTGAAAACATCATGCCCGAAGGTCTTATG
Found at i:3986611 original size:23 final size:23
Alignment explanation
Indices: 3986580--3986637 Score: 91
Period size: 23 Copynumber: 2.5 Consensus size: 23
3986570 TGAAACTATG
3986580 CTACGTGAA-AGTAAACTATGTGT
1 CTACGTGAATA-TAAACTATGTGT
*
3986603 CTACATGAATATAAACTATGTGT
1 CTACGTGAATATAAACTATGTGT
3986626 CTACGTGAATAT
1 CTACGTGAATAT
3986638 GTGAAAAGAT
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
23 31 0.97
24 1 0.03
ACGTcount: A:0.36, C:0.14, G:0.17, T:0.33
Consensus pattern (23 bp):
CTACGTGAATATAAACTATGTGT
Found at i:3986772 original size:28 final size:28
Alignment explanation
Indices: 3986740--3986813 Score: 139
Period size: 28 Copynumber: 2.6 Consensus size: 28
3986730 ATAGGATATA
*
3986740 GTGGTCCTACGGGACATATTTGTTCTAC
1 GTGGTCCTACGGGACATATGTGTTCTAC
3986768 GTGGTCCTACGGGACATATGTGTTCTAC
1 GTGGTCCTACGGGACATATGTGTTCTAC
3986796 GTGGTCCTACGGGACATA
1 GTGGTCCTACGGGACATA
3986814 GTGGTCATAT
Statistics
Matches: 45, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
28 45 1.00
ACGTcount: A:0.19, C:0.22, G:0.28, T:0.31
Consensus pattern (28 bp):
GTGGTCCTACGGGACATATGTGTTCTAC
Found at i:3986818 original size:46 final size:46
Alignment explanation
Indices: 3986768--3986859 Score: 166
Period size: 46 Copynumber: 2.0 Consensus size: 46
3986758 TTTGTTCTAC
*
3986768 GTGGTCCTACGGGACATATGTGTTCTACGTGGTCCTACGGGACATA
1 GTGGTCATACGGGACATATGTGTTCTACGTGGTCCTACGGGACATA
*
3986814 GTGGTCATATGGGACATATGTGTTCTACGTGGTCCTACGGGACATA
1 GTGGTCATACGGGACATATGTGTTCTACGTGGTCCTACGGGACATA
3986860 TGTGTTCAAC
Statistics
Matches: 44, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
46 44 1.00
ACGTcount: A:0.21, C:0.20, G:0.30, T:0.29
Consensus pattern (46 bp):
GTGGTCATACGGGACATATGTGTTCTACGTGGTCCTACGGGACATA
Found at i:3986819 original size:18 final size:18
Alignment explanation
Indices: 3986796--3986831 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
3986786 TGTGTTCTAC
*
3986796 GTGGTCCTACGGGACATA
1 GTGGTCATACGGGACATA
*
3986814 GTGGTCATATGGGACATA
1 GTGGTCATACGGGACATA
3986832 TGTGTTCTAC
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.25, C:0.17, G:0.33, T:0.25
Consensus pattern (18 bp):
GTGGTCATACGGGACATA
Found at i:3986838 original size:74 final size:74
Alignment explanation
Indices: 3986737--3986903 Score: 298
Period size: 74 Copynumber: 2.3 Consensus size: 74
3986727 CATATAGGAT
* *
3986737 ATAGTGGTCCTACGGGACATATTTGTTCTACGTGGTCCTACGGGACATATGTGTTCTACGTGGTC
1 ATAGTGGTCCTACGGGACATATGTGTTCTACGTGGTCCTACGGGACATATGTGTTCAACGTGGTC
3986802 CTACGGGAC
66 CTACGGGAC
* *
3986811 ATAGTGGTCATATGGGACATATGTGTTCTACGTGGTCCTACGGGACATATGTGTTCAACGTGGTC
1 ATAGTGGTCCTACGGGACATATGTGTTCTACGTGGTCCTACGGGACATATGTGTTCAACGTGGTC
3986876 CTACGGGAC
66 CTACGGGAC
3986885 ATAGTGGTCCTACGGGACA
1 ATAGTGGTCCTACGGGACA
3986904 AATTCTACGC
Statistics
Matches: 87, Mismatches: 6, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
74 87 1.00
ACGTcount: A:0.21, C:0.20, G:0.29, T:0.29
Consensus pattern (74 bp):
ATAGTGGTCCTACGGGACATATGTGTTCTACGTGGTCCTACGGGACATATGTGTTCAACGTGGTC
CTACGGGAC
Found at i:3986855 original size:28 final size:28
Alignment explanation
Indices: 3986814--3986887 Score: 121
Period size: 28 Copynumber: 2.6 Consensus size: 28
3986804 ACGGGACATA
* * *
3986814 GTGGTCATATGGGACATATGTGTTCTAC
1 GTGGTCCTACGGGACATATGTGTTCAAC
3986842 GTGGTCCTACGGGACATATGTGTTCAAC
1 GTGGTCCTACGGGACATATGTGTTCAAC
3986870 GTGGTCCTACGGGACATA
1 GTGGTCCTACGGGACATA
3986888 GTGGTCCTAC
Statistics
Matches: 43, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
28 43 1.00
ACGTcount: A:0.22, C:0.19, G:0.30, T:0.30
Consensus pattern (28 bp):
GTGGTCCTACGGGACATATGTGTTCAAC
Done.