Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008061.1 Hibiscus syriacus cultivar Beakdansim tig00110556_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: 5800122
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 16 of 26
Found at i:3102920 original size:18 final size:18
Alignment explanation
Indices: 3102899--3102943 Score: 72
Period size: 18 Copynumber: 2.5 Consensus size: 18
3102889 TCCACTTCGG
*
3102899 GAGCCATCACCTCGCCCA
1 GAGCCATCACCTCACCCA
*
3102917 GAGCTATCACCTCACCCA
1 GAGCCATCACCTCACCCA
3102935 GAGCCATCA
1 GAGCCATCA
3102944 TCTGATCGAC
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.27, C:0.44, G:0.16, T:0.13
Consensus pattern (18 bp):
GAGCCATCACCTCACCCA
Found at i:3103450 original size:20 final size:20
Alignment explanation
Indices: 3103425--3103470 Score: 56
Period size: 20 Copynumber: 2.3 Consensus size: 20
3103415 TAGTTTACTT
*
3103425 TCGCAACATGAAAATGACTA
1 TCGCAACACGAAAATGACTA
* * *
3103445 TCGCAACGCGGAAATGGCTA
1 TCGCAACACGAAAATGACTA
3103465 TCGCAA
1 TCGCAA
3103471 TGCGAAATGA
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.37, C:0.24, G:0.22, T:0.17
Consensus pattern (20 bp):
TCGCAACACGAAAATGACTA
Found at i:3103479 original size:19 final size:20
Alignment explanation
Indices: 3103436--3103491 Score: 69
Period size: 20 Copynumber: 2.9 Consensus size: 20
3103426 CGCAACATGA
3103436 AAATGACTATCGCAACGCGG
1 AAATGACTATCGCAACGCGG
* *
3103456 AAATGGCTATCGCAATGC-G
1 AAATGACTATCGCAACGCGG
**
3103475 AAATGAAAATCGCAACG
1 AAATGACTATCGCAACG
3103492 ACAAAATCGC
Statistics
Matches: 30, Mismatches: 6, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
19 14 0.47
20 16 0.53
ACGTcount: A:0.39, C:0.21, G:0.23, T:0.16
Consensus pattern (20 bp):
AAATGACTATCGCAACGCGG
Found at i:3103499 original size:14 final size:14
Alignment explanation
Indices: 3103480--3103536 Score: 60
Period size: 14 Copynumber: 3.7 Consensus size: 14
3103470 ATGCGAAATG
3103480 AAAATCGCAACGAC
1 AAAATCGCAACGAC
*
3103494 AAAATCGCAATGCGAAATG
1 AAAATCGCAA--CG--A-C
3103513 AAAATCGCAACGAC
1 AAAATCGCAACGAC
3103527 AAAATCGCAA
1 AAAATCGCAA
3103537 TGCGAAATGA
Statistics
Matches: 36, Mismatches: 2, Indels: 10
0.75 0.04 0.21
Matches are distributed among these distances:
14 20 0.56
15 1 0.03
16 2 0.06
17 2 0.06
18 1 0.03
19 10 0.28
ACGTcount: A:0.51, C:0.23, G:0.16, T:0.11
Consensus pattern (14 bp):
AAAATCGCAACGAC
Found at i:3103506 original size:33 final size:33
Alignment explanation
Indices: 3103464--3103555 Score: 175
Period size: 33 Copynumber: 2.8 Consensus size: 33
3103454 GGAAATGGCT
3103464 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
1 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
3103497 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
1 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
*
3103530 ATCGCAATGCGAAATGAAAGTCGCAA
1 ATCGCAATGCGAAATGAAAATCGCAA
3103556 TGCGATTTGT
Statistics
Matches: 58, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
33 58 1.00
ACGTcount: A:0.47, C:0.21, G:0.20, T:0.13
Consensus pattern (33 bp):
ATCGCAATGCGAAATGAAAATCGCAACGACAAA
Found at i:3103518 original size:19 final size:19
Alignment explanation
Indices: 3103464--3103560 Score: 97
Period size: 19 Copynumber: 5.6 Consensus size: 19
3103454 GGAAATGGCT
3103464 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
3103483 ATCGCAA--CG--A-CAAA
1 ATCGCAATGCGAAATGAAA
3103497 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
3103516 ATCGCAA--CG--A-CAAA
1 ATCGCAATGCGAAATGAAA
3103530 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
3103549 GTCGCAATGCGA
1 ATCGCAATGCGA
3103561 TTTGTGTTTC
Statistics
Matches: 63, Mismatches: 5, Indels: 20
0.72 0.06 0.23
Matches are distributed among these distances:
14 20 0.32
15 2 0.03
16 4 0.06
17 4 0.06
18 2 0.03
19 31 0.49
ACGTcount: A:0.45, C:0.21, G:0.21, T:0.13
Consensus pattern (19 bp):
ATCGCAATGCGAAATGAAA
Found at i:3103578 original size:19 final size:18
Alignment explanation
Indices: 3103567--3103706 Score: 89
Period size: 20 Copynumber: 7.9 Consensus size: 18
3103557 GCGATTTGTG
*
3103567 TTTCGTGTTGCGATTTCA
1 TTTCGCGTTGCGATTTCA
*
3103585 TTTCGCGTTGCGATTTTA
1 TTTCGCGTTGCGATTTCA
3103603 -TT---GTTGCGATTTTCA
1 TTTCGCGTTGCGA-TTTCA
*
3103618 TTTCGCATTGCGATTT--
1 TTTCGCGTTGCGATTTCA
*
3103634 TGT--CGTTGCGATTTGCA
1 TTTCGCGTTGCGATTT-CA
* **
3103651 TTTCGCATTGCGATAGCCA
1 TTTCGCGTTGCGAT-TTCA
*
3103670 TTTCCGCGTTGCGATAGTCA
1 TTT-CGCGTTGCGAT-TTCA
*
3103690 TTTTCGCGTTACGATTT
1 -TTTCGCGTTGCGATTT
3103707 TAAGTTTCGT
Statistics
Matches: 95, Mismatches: 14, Indels: 25
0.71 0.10 0.19
Matches are distributed among these distances:
14 17 0.18
15 4 0.04
16 4 0.04
17 4 0.04
18 19 0.20
19 20 0.21
20 24 0.25
21 3 0.03
ACGTcount: A:0.14, C:0.19, G:0.22, T:0.45
Consensus pattern (18 bp):
TTTCGCGTTGCGATTTCA
Found at i:3103610 original size:14 final size:14
Alignment explanation
Indices: 3103591--3103647 Score: 51
Period size: 14 Copynumber: 3.7 Consensus size: 14
3103581 TTCATTTCGC
3103591 GTTGCGATTTTATT
1 GTTGCGATTTTATT
3103605 GTTGCGATTTTCATTT
1 GTTGCGATTTT-A-TT
* *
3103621 CGCATTGCGATTTTGTC
1 -G--TTGCGATTTTATT
3103638 GTTGCGATTT
1 GTTGCGATTT
3103648 GCATTTCGCA
Statistics
Matches: 36, Mismatches: 2, Indels: 10
0.75 0.04 0.21
Matches are distributed among these distances:
14 20 0.56
15 1 0.03
16 3 0.08
17 2 0.06
19 10 0.28
ACGTcount: A:0.12, C:0.14, G:0.23, T:0.51
Consensus pattern (14 bp):
GTTGCGATTTTATT
Found at i:3103622 original size:33 final size:33
Alignment explanation
Indices: 3103572--3103664 Score: 143
Period size: 33 Copynumber: 2.8 Consensus size: 33
3103562 TTGTGTTTCG
*
3103572 TGTTGCGA-TTTCATTTCGCGTTGCGATTTTAT
1 TGTTGCGATTTTCATTTCGCATTGCGATTTTAT
*
3103604 TGTTGCGATTTTCATTTCGCATTGCGATTTTGT
1 TGTTGCGATTTTCATTTCGCATTGCGATTTTAT
* *
3103637 CGTTGCGATTTGCATTTCGCATTGCGAT
1 TGTTGCGATTTTCATTTCGCATTGCGAT
3103665 AGCCATTTCC
Statistics
Matches: 56, Mismatches: 4, Indels: 1
0.92 0.07 0.02
Matches are distributed among these distances:
32 8 0.14
33 48 0.86
ACGTcount: A:0.13, C:0.17, G:0.23, T:0.47
Consensus pattern (33 bp):
TGTTGCGATTTTCATTTCGCATTGCGATTTTAT
Found at i:3105600 original size:14 final size:14
Alignment explanation
Indices: 3105566--3105604 Score: 51
Period size: 14 Copynumber: 2.8 Consensus size: 14
3105556 TTGATTGTTT
3105566 AATTGATTTGTAAA
1 AATTGATTTGTAAA
*
3105580 AAATGATTTGTAAA
1 AATTGATTTGTAAA
**
3105594 TGTTGATTTGT
1 AATTGATTTGT
3105605 TTAATTGGTG
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.36, C:0.00, G:0.18, T:0.46
Consensus pattern (14 bp):
AATTGATTTGTAAA
Found at i:3106055 original size:20 final size:20
Alignment explanation
Indices: 3106030--3106121 Score: 76
Period size: 20 Copynumber: 4.5 Consensus size: 20
3106020 TTGAAGATGA
3106030 TTGCGATTTTCAGAATCTCG
1 TTGCGATTTTCAGAATCTCG
***
3106050 TTGCGAAAGTCAGAATCTCG
1 TTGCGATTTTCAGAATCTCG
* **
3106070 TTGCGATTTTGTATTATCTCG
1 TTGCGATTTT-CAGAATCTCG
** * * *
3106091 TTGCGATAGTCAGTATCGCA
1 TTGCGATTTTCAGAATCTCG
3106111 TTGCGATTTTC
1 TTGCGATTTTC
3106122 CAAATTCACA
Statistics
Matches: 54, Mismatches: 17, Indels: 2
0.74 0.23 0.03
Matches are distributed among these distances:
20 39 0.72
21 15 0.28
ACGTcount: A:0.21, C:0.18, G:0.22, T:0.39
Consensus pattern (20 bp):
TTGCGATTTTCAGAATCTCG
Found at i:3106153 original size:20 final size:21
Alignment explanation
Indices: 3106106--3106157 Score: 61
Period size: 20 Copynumber: 2.5 Consensus size: 21
3106096 ATAGTCAGTA
*
3106106 TCGCATTGCGATTTTCCAAAT
1 TCGCATTGCGATTTTACAAAT
* **
3106127 TCACATTGCGA-TTTACTTAT
1 TCGCATTGCGATTTTACAAAT
3106147 TCGCATTGCGA
1 TCGCATTGCGA
3106158 ATTAGGAAAA
Statistics
Matches: 26, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
20 16 0.62
21 10 0.38
ACGTcount: A:0.23, C:0.23, G:0.15, T:0.38
Consensus pattern (21 bp):
TCGCATTGCGATTTTACAAAT
Found at i:3106968 original size:24 final size:24
Alignment explanation
Indices: 3106941--3106994 Score: 81
Period size: 24 Copynumber: 2.2 Consensus size: 24
3106931 GTATTCGAAA
*
3106941 TTTGATCTTGGTCAATACCCGGAC
1 TTTGATATTGGTCAATACCCGGAC
* *
3106965 TTTGATATTGGTCAATACTCGGAT
1 TTTGATATTGGTCAATACCCGGAC
3106989 TTTGAT
1 TTTGAT
3106995 GATGTTTCAG
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.22, C:0.17, G:0.20, T:0.41
Consensus pattern (24 bp):
TTTGATATTGGTCAATACCCGGAC
Found at i:3107186 original size:12 final size:12
Alignment explanation
Indices: 3107169--3107193 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
3107159 ATATAATCCT
3107169 GAAGAAGAAAAA
1 GAAGAAGAAAAA
3107181 GAAGAAGAAAAA
1 GAAGAAGAAAAA
3107193 G
1 G
3107194 TCCCCGAAAA
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:0.72, C:0.00, G:0.28, T:0.00
Consensus pattern (12 bp):
GAAGAAGAAAAA
Found at i:3108713 original size:33 final size:33
Alignment explanation
Indices: 3108671--3108797 Score: 193
Period size: 33 Copynumber: 3.8 Consensus size: 33
3108661 GGAAATTACT
3108671 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
* **
3108704 ATCGCAATGCGAAATGAAAATTGCAACGCTA-A
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
* *
3108736 TTTCGCAATGCGAAATGAAAATCGCAACGAGGGA
1 -ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
3108770 ATCGCAATGCGAAATGAAAATCGCAACG
1 ATCGCAATGCGAAATGAAAATCGCAACG
3108798 CGAATTAAAT
Statistics
Matches: 83, Mismatches: 9, Indels: 4
0.86 0.09 0.04
Matches are distributed among these distances:
32 1 0.01
33 81 0.98
34 1 0.01
ACGTcount: A:0.43, C:0.19, G:0.23, T:0.16
Consensus pattern (33 bp):
ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
Found at i:3108778 original size:66 final size:66
Alignment explanation
Indices: 3108672--3108803 Score: 237
Period size: 66 Copynumber: 2.0 Consensus size: 66
3108662 GAAATTACTA
* *
3108672 TCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATGAAAATTGCAACGCTAAT
1 TCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCGCAACGCGAAT
3108737 T
66 T
*
3108738 TCGCAATGCGAAATGAAAATCGCAACGAGGGAATCGCAATGCGAAATGAAAATCGCAACGCGAAT
1 TCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCGCAACGCGAAT
3108803 T
66 T
3108804 AAATTTCGCG
Statistics
Matches: 63, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
66 63 1.00
ACGTcount: A:0.42, C:0.19, G:0.23, T:0.17
Consensus pattern (66 bp):
TCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCGCAACGCGAAT
T
Found at i:3108850 original size:19 final size:19
Alignment explanation
Indices: 3108826--3108872 Score: 85
Period size: 19 Copynumber: 2.5 Consensus size: 19
3108816 GCGATTCTCT
3108826 CGTTGCGATTTTCATTTCG
1 CGTTGCGATTTTCATTTCG
3108845 CGTTGCGATTTTCATTTCG
1 CGTTGCGATTTTCATTTCG
*
3108864 CATTGCGAT
1 CGTTGCGAT
3108873 AGTATTTTTT
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
19 27 1.00
ACGTcount: A:0.13, C:0.21, G:0.21, T:0.45
Consensus pattern (19 bp):
CGTTGCGATTTTCATTTCG
Found at i:3108998 original size:14 final size:14
Alignment explanation
Indices: 3108979--3109015 Score: 65
Period size: 14 Copynumber: 2.6 Consensus size: 14
3108969 CATCAATTAA
3108979 ACAAATCAACTTTT
1 ACAAATCAACTTTT
*
3108993 ACAAATCACCTTTT
1 ACAAATCAACTTTT
3109007 ACAAATCAA
1 ACAAATCAA
3109016 TTAAACAATC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.46, C:0.24, G:0.00, T:0.30
Consensus pattern (14 bp):
ACAAATCAACTTTT
Found at i:3110432 original size:42 final size:42
Alignment explanation
Indices: 3110386--3110465 Score: 106
Period size: 42 Copynumber: 1.9 Consensus size: 42
3110376 CGATGACAGC
* * *
3110386 GGCCTCTTGAACGGTGGGAGGGGACTCTCGAGGAATGATAGG
1 GGCCTCTTCAACGATAGGAGGGGACTCTCGAGGAATGATAGG
* * *
3110428 GGCCTCTTCAACGATAGGAGTGGACTCTTGAGGGATGA
1 GGCCTCTTCAACGATAGGAGGGGACTCTCGAGGAATGA
3110466 CAGGCGAGTC
Statistics
Matches: 32, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
42 32 1.00
ACGTcount: A:0.23, C:0.17, G:0.39, T:0.21
Consensus pattern (42 bp):
GGCCTCTTCAACGATAGGAGGGGACTCTCGAGGAATGATAGG
Found at i:3110857 original size:91 final size:92
Alignment explanation
Indices: 3110687--3110871 Score: 279
Period size: 91 Copynumber: 2.0 Consensus size: 92
3110677 ATTTCAAACT
3110687 TTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCACAGTGTTAAAGAATACATAGTTTAGC
1 TTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCACAGTGTTAAAGAATACA-AGTTTAGC
3110752 AGAATTGGCAGCAACCGAATAAATTTAC
65 AGAATTGGCAGCAACCGAATAAATTTAC
* *
3110780 TTCAACCAAAAGACAAAACAAAAAGGA-AAATATTAACTTCACAGTGTT-AATAA-AC-AGTTTA
1 TTCAACCAAAAGACAAAAC--AAA-GACAAATACTAACTTCACAGTGTTAAAGAATACAAGTTTA
*
3110841 GCAGTATTGGCAGCAACCGAATAAATTTAC
63 GCAGAATTGGCAGCAACCGAATAAATTTAC
3110871 T
1 T
3110872 AAGCAATCTA
Statistics
Matches: 86, Mismatches: 3, Indels: 8
0.89 0.03 0.08
Matches are distributed among these distances:
91 36 0.42
93 21 0.24
94 4 0.05
95 23 0.27
96 2 0.02
ACGTcount: A:0.47, C:0.17, G:0.13, T:0.23
Consensus pattern (92 bp):
TTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCACAGTGTTAAAGAATACAAGTTTAGCA
GAATTGGCAGCAACCGAATAAATTTAC
Found at i:3112569 original size:20 final size:19
Alignment explanation
Indices: 3112538--3112711 Score: 128
Period size: 19 Copynumber: 9.8 Consensus size: 19
3112528 TCTTTTGGTT
3112538 GAAATGAAAATCGCAACGA
1 GAAATGAAAATCGCAACGA
* *
3112557 GATAATGAGAATCGCAACGCG
1 GA-AATGAAAATCGCAACG-A
**
3112578 GAAATGACTATCGCAACGA
1 GAAATGAAAATCGCAACGA
*
3112597 G--A-G--AATCGCAACGC
1 GAAATGAAAATCGCAACGA
**
3112611 GAAATGACTATCGCAACGA
1 GAAATGAAAATCGCAACGA
3112630 G--A-G--AATCGCAACGCA
1 GAAATGAAAATCGCAACG-A
*
3112645 -AAATGAAAATCGCAACGC
1 GAAATGAAAATCGCAACGA
3112663 GAAATGAAAATCGCAACGA
1 GAAATGAAAATCGCAACGA
*
3112682 G--A-G--AATCGCAACGC
1 GAAATGAAAATCGCAACGA
3112696 GAAATGAAAATCGCAA
1 GAAATGAAAATCGCAA
3112712 TGCGATTTTG
Statistics
Matches: 123, Mismatches: 13, Indels: 38
0.71 0.07 0.22
Matches are distributed among these distances:
14 30 0.24
15 1 0.01
16 6 0.05
17 6 0.05
19 49 0.40
20 29 0.24
21 2 0.02
ACGTcount: A:0.45, C:0.21, G:0.23, T:0.11
Consensus pattern (19 bp):
GAAATGAAAATCGCAACGA
Found at i:3112606 original size:14 final size:14
Alignment explanation
Indices: 3112587--3112642 Score: 58
Period size: 14 Copynumber: 3.6 Consensus size: 14
3112577 GGAAATGACT
3112587 ATCGCAACGAGAGA
1 ATCGCAACGAGAGA
*
3112601 ATCGCAACGCGAAATGA
1 ATCGCAA--CGAGA-GA
3112618 CTATCGCAACGAGAGA
1 --ATCGCAACGAGAGA
3112634 ATCGCAACG
1 ATCGCAACG
3112643 CAAAATGAAA
Statistics
Matches: 35, Mismatches: 2, Indels: 10
0.74 0.04 0.21
Matches are distributed among these distances:
14 16 0.46
16 6 0.17
17 6 0.17
19 7 0.20
ACGTcount: A:0.39, C:0.25, G:0.25, T:0.11
Consensus pattern (14 bp):
ATCGCAACGAGAGA
Found at i:3112620 original size:33 final size:33
Alignment explanation
Indices: 3112563--3112661 Score: 162
Period size: 33 Copynumber: 3.0 Consensus size: 33
3112553 ACGAGATAAT
3112563 GAGAATCGCAACGCGGAAATGACTATCGCAACGA
1 GAGAATCGCAACGC-GAAATGACTATCGCAACGA
3112597 GAGAATCGCAACGCGAAATGACTATCGCAACGA
1 GAGAATCGCAACGCGAAATGACTATCGCAACGA
* **
3112630 GAGAATCGCAACGCAAAATGAAAATCGCAACG
1 GAGAATCGCAACGCGAAATGACTATCGCAACG
3112662 CGAAATGAAA
Statistics
Matches: 62, Mismatches: 3, Indels: 1
0.94 0.05 0.02
Matches are distributed among these distances:
33 48 0.77
34 14 0.23
ACGTcount: A:0.41, C:0.23, G:0.24, T:0.11
Consensus pattern (33 bp):
GAGAATCGCAACGCGAAATGACTATCGCAACGA
Found at i:3112660 original size:52 final size:52
Alignment explanation
Indices: 3112539--3112716 Score: 200
Period size: 52 Copynumber: 3.4 Consensus size: 52
3112529 CTTTTGGTTG
* * * *
3112539 AAATGAAAATCGCAACGAGATAATGAGAATCGCAACGCG-GAAAT-GACTATCGCA
1 AAATGAAAATCGCAACGCGA-AATGAAAATCGCAACGAGAG-AATCG-C-AACGCA
* * **
3112593 ACGA-GAGAATCGCAACGCGAAATGACTATCGCAACGAGAGAATCGCAACGCA
1 A-AATGAAAATCGCAACGCGAAATGAAAATCGCAACGAGAGAATCGCAACGCA
*
3112645 AAATGAAAATCGCAACGCGAAATGAAAATCGCAACGAGAGAATCGCAACGCG
1 AAATGAAAATCGCAACGCGAAATGAAAATCGCAACGAGAGAATCGCAACGCA
*
3112697 AAATGAAAATCGCAATGCGA
1 AAATGAAAATCGCAACGCGA
3112717 TTTTGGTTTC
Statistics
Matches: 107, Mismatches: 13, Indels: 10
0.82 0.10 0.08
Matches are distributed among these distances:
51 1 0.01
52 69 0.64
53 19 0.18
54 17 0.16
55 1 0.01
ACGTcount: A:0.44, C:0.21, G:0.23, T:0.12
Consensus pattern (52 bp):
AAATGAAAATCGCAACGCGAAATGAAAATCGCAACGAGAGAATCGCAACGCA
Found at i:3112678 original size:33 final size:33
Alignment explanation
Indices: 3112641--3112711 Score: 108
Period size: 33 Copynumber: 2.2 Consensus size: 33
3112631 AGAATCGCAA
3112641 CGCAA-AATGAAAATCGCAACGCGAAATGAAAAT
1 CGCAACAA-GAAAATCGCAACGCGAAATGAAAAT
* *
3112674 CGCAACGAGAGAATCGCAACGCGAAATGAAAAT
1 CGCAACAAGAAAATCGCAACGCGAAATGAAAAT
3112707 CGCAA
1 CGCAA
3112712 TGCGATTTTG
Statistics
Matches: 35, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
33 34 0.97
34 1 0.03
ACGTcount: A:0.48, C:0.21, G:0.21, T:0.10
Consensus pattern (33 bp):
CGCAACAAGAAAATCGCAACGCGAAATGAAAAT
Found at i:3112728 original size:19 final size:19
Alignment explanation
Indices: 3112706--3112778 Score: 67
Period size: 19 Copynumber: 3.8 Consensus size: 19
3112696 GAAATGAAAA
* *
3112706 TCGCAATGCGATTTTGGTT
1 TCGCATTGCGATTTTGATT
* *
3112725 TCGCGTTGCGATTTTTATT
1 TCGCATTGCGATTTTGATT
*
3112744 TCGCATTGCGATAGTT-ATT
1 TCGCATTGCGAT-TTTGATT
*
3112763 TCCGCGTTGCGATTTT
1 T-CGCATTGCGATTTT
3112779 CATTCTCGAA
Statistics
Matches: 44, Mismatches: 8, Indels: 4
0.79 0.14 0.07
Matches are distributed among these distances:
19 32 0.73
20 12 0.27
ACGTcount: A:0.14, C:0.18, G:0.23, T:0.45
Consensus pattern (19 bp):
TCGCATTGCGATTTTGATT
Found at i:3112774 original size:20 final size:19
Alignment explanation
Indices: 3112723--3112775 Score: 70
Period size: 19 Copynumber: 2.7 Consensus size: 19
3112713 GCGATTTTGG
**
3112723 TTTCGCGTTGCGATTTTTA
1 TTTCGCGTTGCGATAGTTA
*
3112742 TTTCGCATTGCGATAGTTA
1 TTTCGCGTTGCGATAGTTA
3112761 TTTCCGCGTTGCGAT
1 TTT-CGCGTTGCGAT
3112776 TTTCATTCTC
Statistics
Matches: 29, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
19 19 0.66
20 10 0.34
ACGTcount: A:0.13, C:0.19, G:0.23, T:0.45
Consensus pattern (19 bp):
TTTCGCGTTGCGATAGTTA
Found at i:3113349 original size:20 final size:19
Alignment explanation
Indices: 3113297--3113350 Score: 72
Period size: 20 Copynumber: 2.7 Consensus size: 19
3113287 GCTATGTAAA
*
3113297 TCGCATTGCGATAGTAAGAT
1 TCGCATTGCGAT-TTAAGAT
3113317 TCGCATTGCGATTTAAGTAT
1 TCGCATTGCGATTTAAG-AT
*
3113337 TCGCGTTGCGATTT
1 TCGCATTGCGATTT
3113351 TCCTAATTCG
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
19 4 0.13
20 27 0.87
ACGTcount: A:0.22, C:0.17, G:0.24, T:0.37
Consensus pattern (19 bp):
TCGCATTGCGATTTAAGAT
Found at i:3113382 original size:21 final size:21
Alignment explanation
Indices: 3113358--3113533 Score: 71
Period size: 21 Copynumber: 8.5 Consensus size: 21
3113348 TTTTCCTAAT
3113358 TCGCATTGCGAATTATGAAAA
1 TCGCATTGCGAATTATGAAAA
** * *
3113379 TCGCAACGCGAA-TACGTAAA
1 TCGCATTGCGAATTATGAAAA
* *
3113399 TCGCAATGCGAATTAGGAAAA
1 TCGCATTGCGAATTATGAAAA
* * * **
3113420 TTGCATTGTG-A-TAGTCAGTA
1 TCGCATTGCGAATTA-TGAAAA
* * *
3113440 TCGCATTGCG-ATTTTCCAAAT
1 TCGCATTGCGAATTAT-GAAAA
* * *
3113461 TCGCATTGCGATTTACT--TAT
1 TCGCATTGCGAATTA-TGAAAA
3113481 TCGCATTGCGAATTGA-GAAAA
1 TCGCATTGCGAATT-ATGAAAA
** *
3113502 TCGCAACGCGAAATT-GGAAAA
1 TCGCATTGCG-AATTATGAAAA
3113523 TCGCATTGCGA
1 TCGCATTGCGA
3113534 TAGTCATAAT
Statistics
Matches: 114, Mismatches: 30, Indels: 23
0.68 0.18 0.14
Matches are distributed among these distances:
19 2 0.02
20 46 0.40
21 59 0.52
22 6 0.05
23 1 0.01
ACGTcount: A:0.33, C:0.18, G:0.21, T:0.28
Consensus pattern (21 bp):
TCGCATTGCGAATTATGAAAA
Found at i:3113484 original size:20 final size:21
Alignment explanation
Indices: 3113440--3113491 Score: 70
Period size: 20 Copynumber: 2.5 Consensus size: 21
3113430 ATAGTCAGTA
*
3113440 TCGCATTGCGATTTTCCAAAT
1 TCGCATTGCGATTTTACAAAT
**
3113461 TCGCATTGCGA-TTTACTTAT
1 TCGCATTGCGATTTTACAAAT
3113481 TCGCATTGCGA
1 TCGCATTGCGA
3113492 ATTGAGAAAA
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
20 17 0.61
21 11 0.39
ACGTcount: A:0.21, C:0.23, G:0.17, T:0.38
Consensus pattern (21 bp):
TCGCATTGCGATTTTACAAAT
Found at i:3118888 original size:23 final size:23
Alignment explanation
Indices: 3118789--3118884 Score: 138
Period size: 23 Copynumber: 4.2 Consensus size: 23
3118779 GGAATGTGAG
3118789 ATTCACATAAGAATGAAATCCAC
1 ATTCACATAAGAATGAAATCCAC
*
3118812 ATTCACATATGAATGAAATCCAC
1 ATTCACATAAGAATGAAATCCAC
* *
3118835 ATTCTCATAAGAATGAAATCTAC
1 ATTCACATAAGAATGAAATCCAC
* * *
3118858 ATTCCCATAGGAATGAAATCTAC
1 ATTCACATAAGAATGAAATCCAC
3118881 ATTC
1 ATTC
3118885 CCATGTTTGG
Statistics
Matches: 67, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
23 67 1.00
ACGTcount: A:0.43, C:0.21, G:0.09, T:0.27
Consensus pattern (23 bp):
ATTCACATAAGAATGAAATCCAC
Found at i:3129235 original size:45 final size:45
Alignment explanation
Indices: 3129121--3129328 Score: 150
Period size: 43 Copynumber: 4.8 Consensus size: 45
3129111 CAATTTCTGT
* *
3129121 CTTTATAATAGAGACCCCTAA--TTTTTTAATTTCACTTTTTTAA
1 CTTTATAATTGAGACCCCTAAGTTTTTTTAATTTCACTTTTCTAA
*
3129164 CTTTATAATTGAGACCCTTAAGTTTTTTTAATTTCAC-TTTCTAA
1 CTTTATAATTGAGACCCCTAAGTTTTTTTAATTTCACTTTTCTAA
* * * * * * * *
3129208 TTTTCTATTTGAGGCCCCTAAGTTTTTTCAATCTCA--ATTAT-A
1 CTTTATAATTGAGACCCCTAAGTTTTTTTAATTTCACTTTTCTAA
* * * *
3129250 CATTTATAATTAAGGCCCCT-A-TTTTTTTAATCTCGA--TTTCTAC
1 C-TTTATAATTGAGACCCCTAAGTTTTTTTAATTTC-ACTTTTCTAA
* * *
3129293 CTTTATAATTAAGGCCTCTAA-TTTTTTATAATTTCA
1 CTTTATAATTGAGACCCCTAAGTTTTTT-TAATTTCA
3129329 TAAAATTCTC
Statistics
Matches: 136, Mismatches: 22, Indels: 14
0.79 0.13 0.08
Matches are distributed among these distances:
41 12 0.09
42 23 0.17
43 46 0.34
44 41 0.30
45 14 0.10
ACGTcount: A:0.27, C:0.17, G:0.07, T:0.49
Consensus pattern (45 bp):
CTTTATAATTGAGACCCCTAAGTTTTTTTAATTTCACTTTTCTAA
Found at i:3129243 original size:131 final size:129
Alignment explanation
Indices: 3128993--3129246 Score: 318
Period size: 131 Copynumber: 2.0 Consensus size: 129
3128983 TTTTTTTACT
* * **
3128993 TTTATAATTGAAGCCCCTAATTTTGTAATTTCACTTTTAACTTTATAATTGAGGCTTTTTAATAT
1 TTTATAATAGAAGCCCCTAATTTTGTAATTTCACTTTTAACTTTATAATTGAGACTCCTTAATAT
* *
3129058 TTTTCAATCTCACTTTCTATCTTTTCAATTGAGGTCCTAAGACTTTTCAATCTCAATTTCTGTC
66 TTTTCAATCTCACTTTCTATATTTTCAATTGAGGCCCTAAGACTTTTCAATCTCAATTTCTGTC
*
3129122 TTTATAATAG-AGACCCCTAATTTTTTAATTTCACTTTTTTAACTTTATAATTGAGAC-CCTTAA
1 TTTATAATAGAAG-CCCCTAATTTTGTAATTTCAC--TTTTAACTTTATAATTGAGACTCCTTAA
* * * **
3129185 GT-TTTTTTAATTTCACTTTCTA-ATTTTCTATTTGAGGCCCCTAAGTTTTTTCAATCTCAATT
63 -TATTTTTCAATCTCACTTTCTATATTTTC-AATTGAGG-CCCTAAGACTTTTCAATCTCAATT
3129247 ATACATTTAT
Statistics
Matches: 107, Mismatches: 12, Indels: 10
0.83 0.09 0.08
Matches are distributed among these distances:
128 2 0.02
129 34 0.32
130 29 0.27
131 42 0.39
ACGTcount: A:0.26, C:0.17, G:0.08, T:0.49
Consensus pattern (129 bp):
TTTATAATAGAAGCCCCTAATTTTGTAATTTCACTTTTAACTTTATAATTGAGACTCCTTAATAT
TTTTCAATCTCACTTTCTATATTTTCAATTGAGGCCCTAAGACTTTTCAATCTCAATTTCTGTC
Found at i:3129266 original size:43 final size:43
Alignment explanation
Indices: 3129219--3129319 Score: 134
Period size: 42 Copynumber: 2.4 Consensus size: 43
3129209 TTTCTATTTG
3129219 AGGCCCCTAAGTTTTTTCAATCTC-AATTATACATTTATAATTA
1 AGGCCCCTAA-TTTTTTCAATCTCGAATTATACATTTATAATTA
* * * *
3129262 AGGCCCCT-ATTTTTTTAATCTCGATTTCTACCTTTATAATTA
1 AGGCCCCTAATTTTTTCAATCTCGAATTATACATTTATAATTA
*
3129304 AGGCCTCTAATTTTTT
1 AGGCCCCTAATTTTTT
3129320 ATAATTTCAT
Statistics
Matches: 51, Mismatches: 5, Indels: 4
0.85 0.08 0.07
Matches are distributed among these distances:
41 12 0.24
42 24 0.47
43 15 0.29
ACGTcount: A:0.27, C:0.20, G:0.08, T:0.46
Consensus pattern (43 bp):
AGGCCCCTAATTTTTTCAATCTCGAATTATACATTTATAATTA
Found at i:3137774 original size:32 final size:31
Alignment explanation
Indices: 3137698--3137774 Score: 109
Period size: 33 Copynumber: 2.4 Consensus size: 31
3137688 TTTTAAACTT
* *
3137698 TATTTCAATTATCGAACTTGAAGTTTTTAAG
1 TATTTCAATTATCAAACTTGAAGTATTTAAG
*
3137729 TATTTGAATTTATCAAACTTGGAAGTATTTAAG
1 TATTTCAA-TTATCAAACTT-GAAGTATTTAAG
3137762 TATTTCAATTATC
1 TATTTCAATTATC
3137775 GTAAACTTTG
Statistics
Matches: 40, Mismatches: 4, Indels: 3
0.85 0.09 0.06
Matches are distributed among these distances:
31 7 0.17
32 15 0.38
33 18 0.45
ACGTcount: A:0.34, C:0.09, G:0.12, T:0.45
Consensus pattern (31 bp):
TATTTCAATTATCAAACTTGAAGTATTTAAG
Found at i:3137988 original size:15 final size:17
Alignment explanation
Indices: 3137962--3137993 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
3137952 TTCTATGGGA
3137962 AAAAACCGGAT-CGGAT
1 AAAAACCGGATCCGGAT
3137978 AAAAACC-GATCCGGAT
1 AAAAACCGGATCCGGAT
3137994 CGGATTGAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
15 3 0.20
16 12 0.80
ACGTcount: A:0.44, C:0.22, G:0.22, T:0.12
Consensus pattern (17 bp):
AAAAACCGGATCCGGAT
Found at i:3143907 original size:31 final size:30
Alignment explanation
Indices: 3143863--3143948 Score: 95
Period size: 31 Copynumber: 2.8 Consensus size: 30
3143853 TCAATAAAGT
3143863 TTAAAAG-TTATAAAATACTTATTAAATTTA
1 TTAAAAGATTATAAAATA-TTATTAAATTTA
*
3143893 TTAAAAGATTATAAAATTATTAATAAATTTA
1 TTAAAAGATTATAAAA-TATTATTAAATTTA
* *
3143924 TCT-AAATACTATAAAATAATTATTA
1 T-TAAAAGATTATAAAAT-ATTATTA
3143949 TATTATCGAA
Statistics
Matches: 48, Mismatches: 4, Indels: 7
0.81 0.07 0.12
Matches are distributed among these distances:
30 8 0.17
31 37 0.77
32 3 0.06
ACGTcount: A:0.52, C:0.03, G:0.02, T:0.42
Consensus pattern (30 bp):
TTAAAAGATTATAAAATATTATTAAATTTA
Found at i:3145180 original size:29 final size:29
Alignment explanation
Indices: 3145146--3145207 Score: 79
Period size: 29 Copynumber: 2.1 Consensus size: 29
3145136 ATTTATCTTT
* *
3145146 TTTTTTTTATCAAAATAGATACATAAAATA
1 TTTTTTGT-TCAAAACAGATACATAAAATA
* *
3145176 TTTTTTGTTCAAAACAGATACCTAAAGTA
1 TTTTTTGTTCAAAACAGATACATAAAATA
3145205 TTT
1 TTT
3145208 AATTTTTTCT
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
29 21 0.75
30 7 0.25
ACGTcount: A:0.40, C:0.10, G:0.06, T:0.44
Consensus pattern (29 bp):
TTTTTTGTTCAAAACAGATACATAAAATA
Found at i:3151960 original size:55 final size:54
Alignment explanation
Indices: 3151912--3152241 Score: 217
Period size: 55 Copynumber: 6.0 Consensus size: 54
3151902 TCTTTGAATG
* * *
3151912 ACGGGTCTGCTCCCTATCCCTTCAGGGAGTATAAGACTCGATCAATCTTCAACA
1 ACGGGTCTGCTCCCTATTCATTCAGGGAGTATAAGACTCGATCAATCTTCAATA
* * *
3151966 AGCGTGTCTGCTCCCTATTCATTTAGGGAGTATAAGACTCAATCAATCTTCAATAA
1 A-CGGGTCTGCTCCCTATTCATTCAGGGAGTATAAGACTCGATCAATCTTCAAT-A
* * * * *
3152022 ACGGGTCCGCTCCTTATTCGTTCAGGGAGTAT-AGAACTCGAACAATCTTCATAAA
1 ACGGGTCTGCTCCCTATTCATTCAGGGAGTATAAG-ACTCGATCAATCTTCA-ATA
* * * * * * *
3152077 ACGGGTCCGCTCTCTATTC-TACCAGAGAGTAT-GGAACTCGAACAATCTTCAACAA
1 ACGGGTCTGCTCCCTATTCAT-TCAGGGAGTATAAG-ACTCGATCAATCTTCAA-TA
* * * * *
3152132 ACGAGT-TCGCTCTCTATTTC-TTCAGAGAATAT-AGAACTCGAACAATCTTCAATAAA
1 ACGGGTCT-GCTCCCTA-TTCATTCAGGGAGTATAAG-ACTCGATCAATCTTCAAT--A
* ** * * * *
3152188 ACAGGTCCACTCTCTATTCCTTCAGAGAGTATACA-ACTCGA-AAATCTTCAATA
1 ACGGGTCTGCTCCCTATTCATTCAGGGAGTATA-AGACTCGATCAATCTTCAATA
3152241 A
1 A
3152242 ACAGGTTTGC
Statistics
Matches: 231, Mismatches: 31, Indels: 29
0.79 0.11 0.10
Matches are distributed among these distances:
53 2 0.01
54 5 0.02
55 187 0.81
56 36 0.16
58 1 0.00
ACGTcount: A:0.31, C:0.25, G:0.16, T:0.28
Consensus pattern (54 bp):
ACGGGTCTGCTCCCTATTCATTCAGGGAGTATAAGACTCGATCAATCTTCAATA
Found at i:3152068 original size:110 final size:108
Alignment explanation
Indices: 3151912--3152243 Score: 291
Period size: 110 Copynumber: 3.0 Consensus size: 108
3151902 TCTTTGAATG
* * * * * * *
3151912 ACGGGTCTGCTCCCTATCCCTTCAGGGAGTATA-AGACTCGATCAATCTTCAACAAGCGTGTCTG
1 ACGGGTCCGCTCCTTAT-TCTTCAGGGAGTATAGA-ACTCGAACAATCTTCAA-AAACGGGTCCG
** * *
3151976 CTCCCTATTC-ATTTAGGGAGTATA-AGACTC-AATCAATCTTCAATAA
63 CTCCCTATTCTA-CCAGAGAGTATAGA-ACTCGAA-CAATCTTCAACAA
3152022 ACGGGTCCGCTCCTTATTCGTTCAGGGAGTATAGAACTCGAACAATCTTCATAAAACGGGTCCGC
1 ACGGGTCCGCTCCTTATTC-TTCAGGGAGTATAGAACTCGAACAATCTTCA-AAAACGGGTCCGC
* *
3152087 TCTCTATTCTACCAGAGAGTATGGAACTCGAACAATCTTCAACAA
64 TCCCTATTCTACCAGAGAGTATAGAACTCGAACAATCTTCAACAA
* * * * *
3152132 ACGAGTTCGCT-CTCTATTTCTTCAGAGAATATAGAACTCGAACAATCTTCAATAAAACAGGTCC
1 ACGGGTCCGCTCCT-TA-TTCTTCAGGGAGTATAGAACTCGAACAATCTTC-A-AAAACGGGTCC
* * * * *
3152196 ACTCTCTATTCCT-TCAGAGAGTATACAACTCGAA-AATCTTCAATAA
62 GCTCCCTATT-CTACCAGAGAGTATAGAACTCGAACAATCTTCAACAA
3152242 AC
1 AC
3152244 AGGTTTGCTT
Statistics
Matches: 189, Mismatches: 23, Indels: 20
0.81 0.10 0.09
Matches are distributed among these distances:
109 3 0.02
110 136 0.72
111 48 0.25
112 2 0.01
ACGTcount: A:0.31, C:0.25, G:0.16, T:0.28
Consensus pattern (108 bp):
ACGGGTCCGCTCCTTATTCTTCAGGGAGTATAGAACTCGAACAATCTTCAAAAACGGGTCCGCTC
CCTATTCTACCAGAGAGTATAGAACTCGAACAATCTTCAACAA
Found at i:3152298 original size:35 final size:37
Alignment explanation
Indices: 3152252--3152327 Score: 104
Period size: 35 Copynumber: 2.1 Consensus size: 37
3152242 ACAGGTTTGC
*
3152252 TTCACTACTC-TTCTGTGAAGGCTTATGA-TGA-TTGT
1 TTCACTACTCTTTC-GTGAAGGCTTAAGATTGACTTGT
*
3152287 TTCACTGCTCTTTCGTGAAGGCTTAAGATTGACTTGT
1 TTCACTACTCTTTCGTGAAGGCTTAAGATTGACTTGT
3152324 TTCA
1 TTCA
3152328 AAGGTCAACA
Statistics
Matches: 36, Mismatches: 2, Indels: 4
0.86 0.05 0.10
Matches are distributed among these distances:
35 22 0.61
36 6 0.17
37 8 0.22
ACGTcount: A:0.20, C:0.18, G:0.20, T:0.42
Consensus pattern (37 bp):
TTCACTACTCTTTCGTGAAGGCTTAAGATTGACTTGT
Found at i:3158893 original size:21 final size:21
Alignment explanation
Indices: 3158867--3158906 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
3158857 CCCCCTTTGA
*
3158867 AGGGGAACCGATTCCCCCCAC
1 AGGGGAACCGATACCCCCCAC
*
3158888 AGGGGAATCGATACCCCCC
1 AGGGGAACCGATACCCCCC
3158907 TGGGGTTCTG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.25, C:0.40, G:0.25, T:0.10
Consensus pattern (21 bp):
AGGGGAACCGATACCCCCCAC
Found at i:3163410 original size:24 final size:24
Alignment explanation
Indices: 3163374--3163434 Score: 70
Period size: 24 Copynumber: 2.5 Consensus size: 24
3163364 CTTTCATCAT
3163374 TTTTTTCCATTTTCCATTTTTTCT-TC
1 TTTTTT-C-TTTT-CATTTTTTCTATC
*
3163400 TTTTTTCTTTTCGTTTTTTCTATC
1 TTTTTTCTTTTCATTTTTTCTATC
*
3163424 ATTTTTCTTTT
1 TTTTTTCTTTT
3163435 TTCTCATTTT
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
23 9 0.28
24 16 0.50
25 1 0.03
26 6 0.19
ACGTcount: A:0.07, C:0.18, G:0.02, T:0.74
Consensus pattern (24 bp):
TTTTTTCTTTTCATTTTTTCTATC
Found at i:3163434 original size:18 final size:17
Alignment explanation
Indices: 3163391--3163501 Score: 80
Period size: 15 Copynumber: 6.8 Consensus size: 17
3163381 CATTTTCCAT
3163391 TTTTTCTTCTTTT-TTC-
1 TTTTTCTT-TTTTCTTCA
3163407 -TTTTCGTTTTTTCTATCA
1 TTTTTC-TTTTTTCT-TCA
3163425 TTTTTCTTTTTTC-TCA
1 TTTTTCTTTTTTCTTCA
3163441 TTTTTC--TTTTCTTC-
1 TTTTTCTTTTTTCTTCA
*
3163455 TTTTTC-TTCTTC-TCA
1 TTTTTCTTTTTTCTTCA
*
3163470 TTTTTATTATTTT-TTCA
1 TTTTTCTT-TTTTCTTCA
*
3163487 TTTTTTTCTTTTTCT
1 TTTTTCT-TTTTTCT
3163502 CTTTTATTTC
Statistics
Matches: 78, Mismatches: 4, Indels: 24
0.74 0.04 0.23
Matches are distributed among these distances:
14 13 0.17
15 20 0.26
16 13 0.17
17 18 0.23
18 9 0.12
19 5 0.06
ACGTcount: A:0.06, C:0.17, G:0.01, T:0.76
Consensus pattern (17 bp):
TTTTTCTTTTTTCTTCA
Found at i:3163435 original size:41 final size:42
Alignment explanation
Indices: 3163381--3163461 Score: 112
Period size: 40 Copynumber: 2.0 Consensus size: 42
3163371 CATTTTTTTC
*
3163381 CATTTTCCATTTTTTCTTCTTTTTTCTTTTCGT-TTTTTCTAT
1 CATTTTCCATTTTTTC-TCATTTTTCTTTTCGTCTTTTTCTAT
* *
3163423 CATTTTTC-TTTTTTCTCATTTTTCTTTTCTTCTTTTTCT
1 CATTTTCCATTTTTTCTCATTTTTCTTTTCGTCTTTTTCT
3163462 TCTTCTCATT
Statistics
Matches: 35, Mismatches: 3, Indels: 3
0.85 0.07 0.07
Matches are distributed among these distances:
40 14 0.40
41 14 0.40
42 7 0.20
ACGTcount: A:0.06, C:0.20, G:0.01, T:0.73
Consensus pattern (42 bp):
CATTTTCCATTTTTTCTCATTTTTCTTTTCGTCTTTTTCTAT
Found at i:3163452 original size:14 final size:14
Alignment explanation
Indices: 3163422--3163474 Score: 63
Period size: 14 Copynumber: 3.6 Consensus size: 14
3163412 GTTTTTTCTA
3163422 TCATTTTTCTTTTTTC
1 TCATTTTTC--TTTTC
3163438 TCATTTTTCTTTTC
1 TCATTTTTCTTTTC
3163452 TTC-TTTTTCTTCTTC
1 -TCATTTTTCTT-TTC
3163467 TCATTTTT
1 TCATTTTT
3163475 ATTATTTTTT
Statistics
Matches: 34, Mismatches: 0, Indels: 7
0.83 0.00 0.17
Matches are distributed among these distances:
14 15 0.44
15 10 0.29
16 9 0.26
ACGTcount: A:0.06, C:0.21, G:0.00, T:0.74
Consensus pattern (14 bp):
TCATTTTTCTTTTC
Found at i:3163484 original size:55 final size:53
Alignment explanation
Indices: 3163392--3163501 Score: 127
Period size: 55 Copynumber: 2.0 Consensus size: 53
3163382 ATTTTCCATT
* *
3163392 TTTTCTTCTTTTTTCTTTTCGTTTTTTCTATCATTTTTC-TTTTTTCTCATTTTTC
1 TTTTCTTCTTTTTTCTTCTCATTTTTTCTAT-ATTTTTCATTTTTT-TC-TTTTTC
3163447 TTTTCTTCTTTTTCTTCTTCTCATTTTTAT-TAT-TTTTTCATTTTTTTCTTTTTC
1 TTTTCTTC-TTTT-TTCTTCTCATTTTT-TCTATATTTTTCATTTTTTTCTTTTTC
3163501 T
1 T
3163502 CTTTTATTTC
Statistics
Matches: 49, Mismatches: 2, Indels: 9
0.82 0.03 0.15
Matches are distributed among these distances:
54 7 0.14
55 16 0.33
56 10 0.20
57 15 0.31
58 1 0.02
ACGTcount: A:0.06, C:0.17, G:0.01, T:0.75
Consensus pattern (53 bp):
TTTTCTTCTTTTTTCTTCTCATTTTTTCTATATTTTTCATTTTTTTCTTTTTC
Found at i:3163505 original size:48 final size:46
Alignment explanation
Indices: 3163389--3163506 Score: 106
Period size: 46 Copynumber: 2.6 Consensus size: 46
3163379 TCCATTTTCC
* *
3163389 ATTTTTTCTTCTTTTTTC-TTTTCGTTTT-TTC-T-ATCATTTTTCTT
1 ATTTTTTCAT-TTTTTTCTTTTTCTTTTTCTTCTTCATCATTTTT-TT
* *
3163433 -TTTTCTCATTTTTCTT-TTCTTCTTTTTCTTCTTC-TCATTTTTATT
1 ATTTTTTCATTTTT-TTCTTTTTCTTTTTCTTCTTCATCATTTTT-TT
3163478 ATTTTTTCATTTTTTTCTTTTTCTCTTTT
1 ATTTTTTCATTTTTTTCTTTTTCT-TTTT
3163507 ATTTCTTCTT
Statistics
Matches: 59, Mismatches: 7, Indels: 13
0.75 0.09 0.16
Matches are distributed among these distances:
42 4 0.07
43 17 0.29
44 3 0.05
45 13 0.22
46 18 0.31
47 4 0.07
ACGTcount: A:0.07, C:0.17, G:0.01, T:0.75
Consensus pattern (46 bp):
ATTTTTTCATTTTTTTCTTTTTCTTTTTCTTCTTCATCATTTTTTT
Found at i:3163513 original size:9 final size:8
Alignment explanation
Indices: 3163390--3163513 Score: 60
Period size: 8 Copynumber: 15.1 Consensus size: 8
3163380 CCATTTTCCA
3163390 TTTTTTCT
1 TTTTTTCT
*
3163398 TCTTTT-T
1 TTTTTTCT
* *
3163405 TCTTTTCG
1 TTTTTTCT
3163413 TTTTTTCT
1 TTTTTTCT
3163421 ATCATTTTTC-
1 -T--TTTTTCT
3163431 TTTTTTCT
1 TTTTTTCT
*
3163439 CATTTTTCT
1 -TTTTTTCT
*
3163448 TTTCTTC-
1 TTTTTTCT
3163455 -TTTTTCT
1 TTTTTTCT
* *
3163462 TCTTCTCAT
1 TTTTTTC-T
*
3163471 TTTTATT-A
1 TTTT-TTCT
3163479 TTTTTTCAT
1 TTTTTTC-T
3163488 TTTTTTCT
1 TTTTTTCT
*
3163496 TTTTCTCT
1 TTTTTTCT
3163504 TTTATTTCT
1 TTT-TTTCT
3163513 T
1 T
3163514 CTTCAAGCGA
Statistics
Matches: 87, Mismatches: 16, Indels: 25
0.68 0.12 0.20
Matches are distributed among these distances:
6 5 0.06
7 15 0.17
8 35 0.40
9 25 0.29
10 1 0.01
11 6 0.07
ACGTcount: A:0.06, C:0.17, G:0.01, T:0.76
Consensus pattern (8 bp):
TTTTTTCT
Found at i:3163515 original size:48 final size:47
Alignment explanation
Indices: 3163326--3163514 Score: 135
Period size: 48 Copynumber: 3.9 Consensus size: 47
3163316 CCCCTTTTAT
* * *
3163326 TTTTCTTTATTTTTTCATTTTTCTC-TTTT-TGTTTTTCTCTTTCATCA
1 TTTT-TTTATTTTTTCATTTTTTTCTTTTTCTCTTTTTTTC-TTCATCA
* *
3163373 TTTTTTTCCA-TTTTCCATTTTTTCTTCTTTTT-TCTTTTCGTTTTTTCTATCA
1 TTTTTTT--ATTTTTTCA-TTTTT-TTCTTTTTCTCTTTT--TTTCTTC-ATCA
*
3163425 TTTTTCTT-TTTTCTCA--TTTTTC-TTTTCTTCTTTTTCTTCTTC-TCA
1 TTTTT-TTATTTTTTCATTTTTTTCTTTTTC-TCTTTTT-TTCTTCATCA
3163470 TTTTTATTATTTTTTCATTTTTTTCTTTTTCTCTTTTATTTCTTC
1 TTTTT-TTATTTTTTCATTTTTTTCTTTTTCTCTTTT-TTTCTTC
3163515 TTCAAGCGAA
Statistics
Matches: 114, Mismatches: 10, Indels: 35
0.72 0.06 0.22
Matches are distributed among these distances:
45 10 0.09
46 15 0.13
47 18 0.16
48 33 0.29
49 8 0.07
50 9 0.08
51 8 0.07
52 11 0.10
53 2 0.02
ACGTcount: A:0.07, C:0.18, G:0.01, T:0.74
Consensus pattern (47 bp):
TTTTTTTATTTTTTCATTTTTTTCTTTTTCTCTTTTTTTCTTCATCA
Found at i:3173204 original size:45 final size:46
Alignment explanation
Indices: 3173137--3173240 Score: 165
Period size: 45 Copynumber: 2.3 Consensus size: 46
3173127 CCATGCTTTG
3173137 TTATTCACAAAAATAAATCCTAACCGCATGATATCTAATTCGCATGC
1 TTATTCA-AAAAATAAATCCTAACCGCATGATATCTAATTCGCATGC
* *
3173184 TTATTCAAAAAATAAA-CCTAACCGCGTGATATCTAGTTCGCATGC
1 TTATTCAAAAAATAAATCCTAACCGCATGATATCTAATTCGCATGC
*
3173229 TTATTAAAAAAA
1 TTATTCAAAAAA
3173241 CGAAAATAAA
Statistics
Matches: 54, Mismatches: 3, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
45 38 0.70
46 9 0.17
47 7 0.13
ACGTcount: A:0.40, C:0.20, G:0.10, T:0.30
Consensus pattern (46 bp):
TTATTCAAAAAATAAATCCTAACCGCATGATATCTAATTCGCATGC
Found at i:3185682 original size:28 final size:28
Alignment explanation
Indices: 3185647--3185700 Score: 108
Period size: 28 Copynumber: 1.9 Consensus size: 28
3185637 CCATTTAAGT
3185647 AAAAATGATTAAGAAAACTAAGTATTTC
1 AAAAATGATTAAGAAAACTAAGTATTTC
3185675 AAAAATGATTAAGAAAACTAAGTATT
1 AAAAATGATTAAGAAAACTAAGTATT
3185701 CCTAAGCATA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 26 1.00
ACGTcount: A:0.56, C:0.06, G:0.11, T:0.28
Consensus pattern (28 bp):
AAAAATGATTAAGAAAACTAAGTATTTC
Found at i:3202089 original size:28 final size:28
Alignment explanation
Indices: 3202049--3202102 Score: 108
Period size: 28 Copynumber: 1.9 Consensus size: 28
3202039 TGTCATGTTA
3202049 ACATTATTATTTTTTTAACGGTAGGTTG
1 ACATTATTATTTTTTTAACGGTAGGTTG
3202077 ACATTATTATTTTTTTAACGGTAGGT
1 ACATTATTATTTTTTTAACGGTAGGT
3202103 GATCAAAATA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 26 1.00
ACGTcount: A:0.26, C:0.07, G:0.17, T:0.50
Consensus pattern (28 bp):
ACATTATTATTTTTTTAACGGTAGGTTG
Found at i:3202685 original size:30 final size:30
Alignment explanation
Indices: 3202649--3202726 Score: 93
Period size: 31 Copynumber: 2.5 Consensus size: 30
3202639 CCAAAAAGCC
* *
3202649 TAACAAATGGTCACTAATGTGATCGATTTG
1 TAACAAATAGTCACTAATATGATCGATTTG
* *
3202679 TAACAAATTAGTCATTAATATTATCGATTTG
1 TAACAAA-TAGTCACTAATATGATCGATTTG
*
3202710 TAACAAATTAATCACTA
1 TAACAAA-TAGTCACTA
3202727 GATGTTAATA
Statistics
Matches: 41, Mismatches: 6, Indels: 1
0.85 0.12 0.02
Matches are distributed among these distances:
30 7 0.17
31 34 0.83
ACGTcount: A:0.40, C:0.13, G:0.12, T:0.36
Consensus pattern (30 bp):
TAACAAATAGTCACTAATATGATCGATTTG
Found at i:3203854 original size:31 final size:31
Alignment explanation
Indices: 3203816--3203880 Score: 112
Period size: 31 Copynumber: 2.1 Consensus size: 31
3203806 CAACGGCGAG
*
3203816 TGACTAATTTGTTACAAATCGATAATATTAA
1 TGACTAATTTGTTACAAATCGATAACATTAA
*
3203847 TGACTAATTTGTTACGAATCGATAACATTAA
1 TGACTAATTTGTTACAAATCGATAACATTAA
3203878 TGA
1 TGA
3203881 TCATTGTTAG
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
31 32 1.00
ACGTcount: A:0.40, C:0.11, G:0.12, T:0.37
Consensus pattern (31 bp):
TGACTAATTTGTTACAAATCGATAACATTAA
Found at i:3207989 original size:29 final size:29
Alignment explanation
Indices: 3207947--3208017 Score: 142
Period size: 29 Copynumber: 2.4 Consensus size: 29
3207937 AAATTCTAAA
3207947 ATATTTGTATTAACTATCATCTACATTAG
1 ATATTTGTATTAACTATCATCTACATTAG
3207976 ATATTTGTATTAACTATCATCTACATTAG
1 ATATTTGTATTAACTATCATCTACATTAG
3208005 ATATTTGTATTAA
1 ATATTTGTATTAA
3208018 TAAATGTTGG
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 42 1.00
ACGTcount: A:0.35, C:0.11, G:0.07, T:0.46
Consensus pattern (29 bp):
ATATTTGTATTAACTATCATCTACATTAG
Found at i:3213272 original size:20 final size:20
Alignment explanation
Indices: 3213247--3213286 Score: 71
Period size: 20 Copynumber: 2.0 Consensus size: 20
3213237 ATGCTATTGG
*
3213247 AGGAGCTTGGGCACAATCAA
1 AGGAGCTTGGGAACAATCAA
3213267 AGGAGCTTGGGAACAATCAA
1 AGGAGCTTGGGAACAATCAA
3213287 GAGAATGTCT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.38, C:0.17, G:0.30, T:0.15
Consensus pattern (20 bp):
AGGAGCTTGGGAACAATCAA
Found at i:3213930 original size:38 final size:38
Alignment explanation
Indices: 3213884--3213969 Score: 163
Period size: 38 Copynumber: 2.3 Consensus size: 38
3213874 AAAATTATCA
*
3213884 TTGTTTTCTCCTTGGTAGATCGAGAGAAGTTGTTATTC
1 TTGTTTTCTCCTTGGTAGATCGAGAGAAGTTGTAATTC
3213922 TTGTTTTCTCCTTGGTAGATCGAGAGAAGTTGTAATTC
1 TTGTTTTCTCCTTGGTAGATCGAGAGAAGTTGTAATTC
3213960 TTGTTTTCTC
1 TTGTTTTCTC
3213970 TTTAGTTTTT
Statistics
Matches: 47, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
38 47 1.00
ACGTcount: A:0.17, C:0.14, G:0.22, T:0.47
Consensus pattern (38 bp):
TTGTTTTCTCCTTGGTAGATCGAGAGAAGTTGTAATTC
Found at i:3215674 original size:18 final size:19
Alignment explanation
Indices: 3215639--3215674 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
3215629 TTTTCTTCGA
3215639 TTATAATAATTAAATTTTT
1 TTATAATAATTAAATTTTT
*
3215658 TTATAAT-ATTTAATTTT
1 TTATAATAATTAAATTTT
3215675 AAAATACCAG
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 9 0.56
19 7 0.44
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (19 bp):
TTATAATAATTAAATTTTT
Found at i:3215796 original size:30 final size:28
Alignment explanation
Indices: 3215734--3215798 Score: 71
Period size: 27 Copynumber: 2.3 Consensus size: 28
3215724 GATATTGAAA
* *
3215734 AATAAATAAATAAATATTAAAATAATTT
1 AATATATAAATAAATAATAAAATAATTT
3215762 -ATATATAAA-AAATAGATAAAATATTATTT
1 AATATATAAATAAATA-ATAAAATA--ATTT
3215791 AATATATA
1 AATATATA
3215799 TATATTTATA
Statistics
Matches: 31, Mismatches: 2, Indels: 6
0.79 0.05 0.15
Matches are distributed among these distances:
26 5 0.16
27 15 0.48
29 4 0.13
30 7 0.23
ACGTcount: A:0.62, C:0.00, G:0.02, T:0.37
Consensus pattern (28 bp):
AATATATAAATAAATAATAAAATAATTT
Found at i:3217170 original size:3 final size:3
Alignment explanation
Indices: 3217154--3217204 Score: 72
Period size: 3 Copynumber: 17.7 Consensus size: 3
3217144 TAATATTTAT
3217154 TAA TAA -AA -AA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T-A TAAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T-AA
3217200 TAA TA
1 TAA TA
3217205 TTTAAATGAA
Statistics
Matches: 45, Mismatches: 0, Indels: 6
0.88 0.00 0.12
Matches are distributed among these distances:
2 6 0.13
3 37 0.82
4 2 0.04
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
TAA
Found at i:3223616 original size:15 final size:16
Alignment explanation
Indices: 3223596--3223625 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
3223586 ACAGAAGAAA
3223596 TGAAGTT-TCAAGTTT
1 TGAAGTTCTCAAGTTT
3223611 TGAAGTTCTCAAGTT
1 TGAAGTTCTCAAGTT
3223626 GTGGGCTTTT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 7 0.50
16 7 0.50
ACGTcount: A:0.27, C:0.10, G:0.20, T:0.43
Consensus pattern (16 bp):
TGAAGTTCTCAAGTTT
Found at i:3235001 original size:18 final size:18
Alignment explanation
Indices: 3234978--3235064 Score: 84
Period size: 18 Copynumber: 4.7 Consensus size: 18
3234968 ACTGAATATT
* *
3234978 TGTCCCGAATGATCACTA
1 TGTCCCGAAGGACCACTA
3234996 TGTCCCGAAGGACCACTA
1 TGTCCCGAAGGACCACTA
* *
3235014 TATCCCGAAGGACCACTGTT
1 TGTCCCGAAGGACCAC--TA
* * *
3235034 TGTTCCAAAGAACCACTA
1 TGTCCCGAAGGACCACTA
*
3235052 TATCCCGAAGGAC
1 TGTCCCGAAGGAC
3235065 TACTGTTTAT
Statistics
Matches: 54, Mismatches: 13, Indels: 4
0.76 0.18 0.06
Matches are distributed among these distances:
18 41 0.76
20 13 0.24
ACGTcount: A:0.30, C:0.30, G:0.18, T:0.22
Consensus pattern (18 bp):
TGTCCCGAAGGACCACTA
Found at i:3236983 original size:23 final size:22
Alignment explanation
Indices: 3236957--3236999 Score: 61
Period size: 23 Copynumber: 1.9 Consensus size: 22
3236947 TGGCTCATAG
3236957 CATGTATCA-CATATGCATATAAT
1 CATGTAT-ATCATAT-CATATAAT
3236980 CATGTATATCATATCATATA
1 CATGTATATCATATCATATA
3237000 TCTTATGTTT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
22 7 0.37
23 12 0.63
ACGTcount: A:0.40, C:0.16, G:0.07, T:0.37
Consensus pattern (22 bp):
CATGTATATCATATCATATAAT
Found at i:3238461 original size:83 final size:83
Alignment explanation
Indices: 3238329--3238490 Score: 288
Period size: 83 Copynumber: 2.0 Consensus size: 83
3238319 TTTTTTTCTT
* * * *
3238329 TTTCATAATTATAATTTAATGATTTTAATTTTTAGATTTGAGTCGAATAATATTTCTTTAACTTT
1 TTTCACAATTATAATTTAATGATTTTAATTTTTAAATTTGAGTCAAATAATATTTCTTTAACTTC
3238394 TGAGTTAAAATTTTTATA
66 TGAGTTAAAATTTTTATA
3238412 TTTCACAATTATAATTTAATGATTTTAATTTTTAAATTTGAGTCAAATAATATTTCTTTAACTTC
1 TTTCACAATTATAATTTAATGATTTTAATTTTTAAATTTGAGTCAAATAATATTTCTTTAACTTC
3238477 TGAGTTAAAATTTT
66 TGAGTTAAAATTTT
3238491 CATTTTTTAA
Statistics
Matches: 75, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
83 75 1.00
ACGTcount: A:0.35, C:0.06, G:0.07, T:0.52
Consensus pattern (83 bp):
TTTCACAATTATAATTTAATGATTTTAATTTTTAAATTTGAGTCAAATAATATTTCTTTAACTTC
TGAGTTAAAATTTTTATA
Found at i:3241154 original size:6 final size:6
Alignment explanation
Indices: 3241137--3241167 Score: 53
Period size: 6 Copynumber: 5.0 Consensus size: 6
3241127 TTCTAAACTA
3241137 CTTTTGC CTTTTC CTTTTC CTTTTC CTTTTC
1 CTTTT-C CTTTTC CTTTTC CTTTTC CTTTTC
3241168 GCTTGATATT
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
6 19 0.79
7 5 0.21
ACGTcount: A:0.00, C:0.32, G:0.03, T:0.65
Consensus pattern (6 bp):
CTTTTC
Found at i:3241974 original size:22 final size:22
Alignment explanation
Indices: 3241946--3241994 Score: 62
Period size: 22 Copynumber: 2.2 Consensus size: 22
3241936 ATATCCGAAC
* *
3241946 ATAAAATTTAAAAATTCAAAAT
1 ATAAAATATAAAAATCCAAAAT
* *
3241968 ATAAAATATAATAATCCATAAT
1 ATAAAATATAAAAATCCAAAAT
3241990 ATAAA
1 ATAAA
3241995 TAATTAATTA
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.63, C:0.06, G:0.00, T:0.31
Consensus pattern (22 bp):
ATAAAATATAAAAATCCAAAAT
Found at i:3249901 original size:31 final size:32
Alignment explanation
Indices: 3249846--3249929 Score: 98
Period size: 31 Copynumber: 2.7 Consensus size: 32
3249836 ATGATCTTTG
* * * * **
3249846 TTGTTTTTTTTTTCTATTTGTAATAGCTGTGT
1 TTGTTTATATTTTGTATTTTTAATAAATGTGT
3249878 TTGTTTATA-TTTGTATTTTTAATAAATGTGT
1 TTGTTTATATTTTGTATTTTTAATAAATGTGT
*
3249909 TTGTTTATATTTTTTATTTTT
1 TTGTTTATATTTTGTATTTTT
3249930 TAAAGTTATT
Statistics
Matches: 44, Mismatches: 7, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
31 27 0.61
32 17 0.39
ACGTcount: A:0.18, C:0.02, G:0.12, T:0.68
Consensus pattern (32 bp):
TTGTTTATATTTTGTATTTTTAATAAATGTGT
Found at i:3252089 original size:44 final size:44
Alignment explanation
Indices: 3252023--3252116 Score: 179
Period size: 44 Copynumber: 2.1 Consensus size: 44
3252013 AACATGAATC
3252023 AACATACACTTGATCTAAAAGTCATAGTATGCTAAAATGTTTCGA
1 AACA-ACACTTGATCTAAAAGTCATAGTATGCTAAAATGTTTCGA
3252068 AACAACACTTGATCTAAAAGTCATAGTATGCTAAAATGTTTCGA
1 AACAACACTTGATCTAAAAGTCATAGTATGCTAAAATGTTTCGA
3252112 AACAA
1 AACAA
3252117 GTTAGCCCAT
Statistics
Matches: 49, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
44 45 0.92
45 4 0.08
ACGTcount: A:0.43, C:0.16, G:0.13, T:0.29
Consensus pattern (44 bp):
AACAACACTTGATCTAAAAGTCATAGTATGCTAAAATGTTTCGA
Found at i:3253493 original size:25 final size:24
Alignment explanation
Indices: 3253460--3253508 Score: 62
Period size: 25 Copynumber: 2.0 Consensus size: 24
3253450 TGTTCATCTC
* *
3253460 ATTTATTTATATTATTTTTATAATA
1 ATTTATTTAAAATATTTTTA-AATA
*
3253485 ATTTCTTTAAAATATTTTTAAATA
1 ATTTATTTAAAATATTTTTAAATA
3253509 CATCTACCTA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
24 4 0.19
25 17 0.81
ACGTcount: A:0.39, C:0.02, G:0.00, T:0.59
Consensus pattern (24 bp):
ATTTATTTAAAATATTTTTAAATA
Found at i:3254721 original size:175 final size:175
Alignment explanation
Indices: 3254420--3254772 Score: 595
Period size: 175 Copynumber: 2.0 Consensus size: 175
3254410 TTTAAATTTT
*
3254420 AAATATATTATATATAACATATGGGCTCAGCCCAAACCATTTAAAACCCAATTAATAATTTAAGA
1 AAATATATTATATATAACATATGGGCTAAGCCCAAACCATTTAAAACCCAATTAATAATTTAAGA
3254485 TCTAATAACTTTTAAACTTAAATCAATATTAATTAATTAAAAAAGTATATAAAATTTTTTA-TTT
66 TCTAATAACTTTTAAACTTAAATCAATATTAATTAATTAAAAAAGTATATAAAATTTTTTATTTT
*
3254549 ATAATTATATATTATTAAAATTAATTGTAAACTGTTTTTTAATTAA
131 ATAATTATATATTATTAAAATTAATTATAAACT-TTTTTTAATTAA
*
3254595 AAATATATATATATATAACATATGGGTTAAG-CCAAACCATTTAAAACCCAATTAATAATTTAAG
1 AAATATAT-TATATATAACATATGGGCTAAGCCCAAACCATTTAAAACCCAATTAATAATTTAAG
* * *
3254659 ATCTAATAACTTTTAAACTTAAATCAATATTAATTAATTAAAAAATTTATCTGAAA-TTTTTATT
65 ATCTAATAACTTTTAAACTTAAATCAATATTAATTAATTAAAAAA-GTATATAAAATTTTTTATT
*
3254723 TTATAATTATATATTATTTAAATTAATTATAAACTTTTTTTAATTAA
129 TTATAATTATATATTATTAAAATTAATTATAAACTTTTTTTAATTAA
3254770 AAA
1 AAA
3254773 ACATTTAATT
Statistics
Matches: 168, Mismatches: 7, Indels: 6
0.93 0.04 0.03
Matches are distributed among these distances:
175 107 0.64
176 61 0.36
ACGTcount: A:0.46, C:0.08, G:0.04, T:0.41
Consensus pattern (175 bp):
AAATATATTATATATAACATATGGGCTAAGCCCAAACCATTTAAAACCCAATTAATAATTTAAGA
TCTAATAACTTTTAAACTTAAATCAATATTAATTAATTAAAAAAGTATATAAAATTTTTTATTTT
ATAATTATATATTATTAAAATTAATTATAAACTTTTTTTAATTAA
Found at i:3262100 original size:24 final size:25
Alignment explanation
Indices: 3262062--3262110 Score: 64
Period size: 24 Copynumber: 2.0 Consensus size: 25
3262052 AGTACCCATT
** *
3262062 AAAATTGAATGTTTA-GTTTTAAAA
1 AAAATTGAAACTTTATGTATTAAAA
3262086 AAAATTGAAACTTTATGTATTAAAA
1 AAAATTGAAACTTTATGTATTAAAA
3262111 CAGACCAAAA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
24 13 0.62
25 8 0.38
ACGTcount: A:0.49, C:0.02, G:0.10, T:0.39
Consensus pattern (25 bp):
AAAATTGAAACTTTATGTATTAAAA
Found at i:3267366 original size:17 final size:16
Alignment explanation
Indices: 3267336--3267386 Score: 50
Period size: 16 Copynumber: 3.1 Consensus size: 16
3267326 TTTAATAAAA
3267336 ATATTAATTAATAAATT
1 ATATTAATTAAT-AATT
* *
3267353 ATATTTATTGATAATT
1 ATATTAATTAATAATT
*
3267369 ATAATAATATAAT-ATT
1 ATATTAAT-TAATAATT
3267385 AT
1 AT
3267387 TTTTTAATGT
Statistics
Matches: 28, Mismatches: 5, Indels: 3
0.78 0.14 0.08
Matches are distributed among these distances:
16 15 0.54
17 13 0.46
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (16 bp):
ATATTAATTAATAATT
Found at i:3267423 original size:24 final size:21
Alignment explanation
Indices: 3267396--3267441 Score: 56
Period size: 22 Copynumber: 2.0 Consensus size: 21
3267386 TTTTTTAATG
3267396 TTTTAATTATATATAATATTATAC
1 TTTT-ATTATA-ATAATAT-ATAC
*
3267420 TTTTATTTTAATAATATATAC
1 TTTTATTATAATAATATATAC
3267441 T
1 T
3267442 AAATTATTAA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
21 5 0.24
22 7 0.33
23 5 0.24
24 4 0.19
ACGTcount: A:0.39, C:0.04, G:0.00, T:0.57
Consensus pattern (21 bp):
TTTTATTATAATAATATATAC
Found at i:3267438 original size:29 final size:30
Alignment explanation
Indices: 3267369--3267439 Score: 83
Period size: 29 Copynumber: 2.3 Consensus size: 30
3267359 ATTGATAATT
*
3267369 ATAATAATATAATATTATTTTTTAATGTTTTA
1 ATAAT-ATATAATATTATCTTTTAA-GTTTTA
*
3267401 ATTATATATAATATTATACTTTT-A-TTTTA
1 ATAATATATAATATTAT-CTTTTAAGTTTTA
3267430 ATAATATATA
1 ATAATATATA
3267440 CTAAATTATT
Statistics
Matches: 35, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
29 14 0.40
31 13 0.37
32 8 0.23
ACGTcount: A:0.42, C:0.01, G:0.01, T:0.55
Consensus pattern (30 bp):
ATAATATATAATATTATCTTTTAAGTTTTA
Found at i:3267438 original size:31 final size:31
Alignment explanation
Indices: 3267367--3267448 Score: 84
Period size: 31 Copynumber: 2.7 Consensus size: 31
3267357 TTATTGATAA
*
3267367 TTATAATA-ATATAATATTATTTTTTAATGT
1 TTATAATATATATAATATTATCTTTTAATGT
3267397 TT-TAATTATATATAATATTATACTTTT-AT-T
1 TTATAA-TATATATAATATTAT-CTTTTAATGT
3267427 TTAATAATATATACTAA-ATTAT
1 TT-ATAATATATA-TAATATTAT
3267449 TAATAAAATT
Statistics
Matches: 45, Mismatches: 1, Indels: 11
0.79 0.02 0.19
Matches are distributed among these distances:
29 3 0.07
30 7 0.16
31 25 0.56
32 10 0.22
ACGTcount: A:0.41, C:0.02, G:0.01, T:0.55
Consensus pattern (31 bp):
TTATAATATATATAATATTATCTTTTAATGT
Found at i:3267578 original size:37 final size:41
Alignment explanation
Indices: 3267487--3267578 Score: 102
Period size: 42 Copynumber: 2.3 Consensus size: 41
3267477 CATAACAATA
*** *
3267487 TTATTTTAATATGTAATTAATATAATTAATAATATATTATTC
1 TTATTTTAATAAACAATTAATATAATT-ATAATATATAATTC
3267529 TTATTTTAATAAACAATTAATATAATT-T-ATA-ATAATT-
1 TTATTTTAATAAACAATTAATATAATTATAATATATAATTC
*
3267566 TTATTTTCATAAA
1 TTATTTTAATAAA
3267579 ATATAATAAT
Statistics
Matches: 45, Mismatches: 5, Indels: 5
0.82 0.09 0.09
Matches are distributed among these distances:
37 12 0.27
38 5 0.11
39 3 0.07
40 1 0.02
42 24 0.53
ACGTcount: A:0.45, C:0.03, G:0.01, T:0.51
Consensus pattern (41 bp):
TTATTTTAATAAACAATTAATATAATTATAATATATAATTC
Found at i:3267636 original size:28 final size:26
Alignment explanation
Indices: 3267605--3267658 Score: 65
Period size: 26 Copynumber: 2.0 Consensus size: 26
3267595 ATTTTTATTT
3267605 ATAAAATTATATATATAA-TATTTTAATA
1 ATAAAATTA-A-ATA-AATTATTTTAATA
*
3267633 ATAACATTAAATAAATTATTTTAATA
1 ATAAAATTAAATAAATTATTTTAATA
3267659 TTTTAAAAAT
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
25 2 0.08
26 13 0.54
27 1 0.04
28 8 0.33
ACGTcount: A:0.54, C:0.02, G:0.00, T:0.44
Consensus pattern (26 bp):
ATAAAATTAAATAAATTATTTTAATA
Found at i:3267690 original size:20 final size:19
Alignment explanation
Indices: 3267659--3267698 Score: 71
Period size: 20 Copynumber: 2.1 Consensus size: 19
3267649 TATTTTAATA
3267659 TTTTAAAAATAATATTATT
1 TTTTAAAAATAATATTATT
3267678 TTTTAATAAATAATATTATT
1 TTTTAA-AAATAATATTATT
3267698 T
1 T
3267699 ATTGTATATG
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 6 0.30
20 14 0.70
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (19 bp):
TTTTAAAAATAATATTATT
Found at i:3268340 original size:2 final size:2
Alignment explanation
Indices: 3268335--3268370 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
3268325 TTTTTAAAAT
3268335 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
3268371 AATTATTATA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:3268624 original size:18 final size:19
Alignment explanation
Indices: 3268580--3268624 Score: 60
Period size: 18 Copynumber: 2.5 Consensus size: 19
3268570 TATATAATAT
*
3268580 TCATTGTTT-GGTTATTTA
1 TCATTCTTTAGGTTATTTA
3268598 TC-TTCTTTAGGTTATTTA
1 TCATTCTTTAGGTTATTTA
3268616 TCATT-TTTA
1 TCATTCTTTA
3268625 AGTTGAGGAC
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
17 5 0.21
18 17 0.71
19 2 0.08
ACGTcount: A:0.18, C:0.09, G:0.11, T:0.62
Consensus pattern (19 bp):
TCATTCTTTAGGTTATTTA
Found at i:3284282 original size:38 final size:38
Alignment explanation
Indices: 3284231--3284307 Score: 145
Period size: 38 Copynumber: 2.0 Consensus size: 38
3284221 TTTCTTTGGC
*
3284231 ATTCCTTATAATGTAAGTTAAATAAGTAATGTGGTGGA
1 ATTCCTTATAATGTAAGATAAATAAGTAATGTGGTGGA
3284269 ATTCCTTATAATGTAAGATAAATAAGTAATGTGGTGGA
1 ATTCCTTATAATGTAAGATAAATAAGTAATGTGGTGGA
3284307 A
1 A
3284308 AACTTATCAA
Statistics
Matches: 38, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
38 38 1.00
ACGTcount: A:0.39, C:0.05, G:0.21, T:0.35
Consensus pattern (38 bp):
ATTCCTTATAATGTAAGATAAATAAGTAATGTGGTGGA
Found at i:3293955 original size:13 final size:13
Alignment explanation
Indices: 3293934--3293984 Score: 50
Period size: 12 Copynumber: 3.8 Consensus size: 13
3293924 ACTCCTTGAT
*
3293934 AACCCAATTATAA
1 AACCAAATTATAA
3293947 AACCAAATTA-AA
1 AACCAAATTATAA
*
3293959 AACCCAATTAGTATA
1 AACCAAATTA-TA-A
*
3293974 AAACAAATTAT
1 AACCAAATTAT
3293985 TTGACTTTTG
Statistics
Matches: 31, Mismatches: 4, Indels: 5
0.77 0.10 0.12
Matches are distributed among these distances:
12 11 0.35
13 9 0.29
14 2 0.06
15 9 0.29
ACGTcount: A:0.57, C:0.18, G:0.02, T:0.24
Consensus pattern (13 bp):
AACCAAATTATAA
Found at i:3293960 original size:12 final size:13
Alignment explanation
Indices: 3293934--3293968 Score: 54
Period size: 12 Copynumber: 2.8 Consensus size: 13
3293924 ACTCCTTGAT
3293934 AACCCAATTATAA
1 AACCCAATTATAA
*
3293947 AACCAAATTA-AA
1 AACCCAATTATAA
3293959 AACCCAATTA
1 AACCCAATTA
3293969 GTATAAAACA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
12 11 0.55
13 9 0.45
ACGTcount: A:0.57, C:0.23, G:0.00, T:0.20
Consensus pattern (13 bp):
AACCCAATTATAA
Found at i:3293962 original size:25 final size:27
Alignment explanation
Indices: 3293934--3293983 Score: 77
Period size: 25 Copynumber: 1.9 Consensus size: 27
3293924 ACTCCTTGAT
*
3293934 AACCCAATTA-TA-AAACCAAATTAAA
1 AACCCAATTAGTATAAAACAAATTAAA
3293959 AACCCAATTAGTATAAAACAAATTA
1 AACCCAATTAGTATAAAACAAATTA
3293984 TTTGACTTTT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
25 10 0.45
26 2 0.09
27 10 0.45
ACGTcount: A:0.58, C:0.18, G:0.02, T:0.22
Consensus pattern (27 bp):
AACCCAATTAGTATAAAACAAATTAAA
Found at i:3294802 original size:29 final size:29
Alignment explanation
Indices: 3294745--3294810 Score: 73
Period size: 29 Copynumber: 2.2 Consensus size: 29
3294735 TTTATATAAA
*
3294745 ATAAAGATTAAAAAATCATTTGAACATTA-
1 ATAAA-ATTAAAAAATCATATGAACATTAC
*
3294774 ATATAAATTAAAAAATCATAT-AATTATTAC
1 ATA-AAATTAAAAAATCATATGAA-CATTAC
3294804 ATAAAAT
1 ATAAAAT
3294811 ATCAACGTAA
Statistics
Matches: 32, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
28 2 0.06
29 25 0.78
30 5 0.16
ACGTcount: A:0.58, C:0.06, G:0.03, T:0.33
Consensus pattern (29 bp):
ATAAAATTAAAAAATCATATGAACATTAC
Found at i:3296498 original size:9 final size:9
Alignment explanation
Indices: 3296486--3296526 Score: 50
Period size: 8 Copynumber: 4.8 Consensus size: 9
3296476 TTTTAGATCT
3296486 TCTTCTTAA
1 TCTTCTTAA
*
3296495 TCTTCTTTA
1 TCTTCTTAA
*
3296504 -CTTTTTAA
1 TCTTCTTAA
3296512 TCTTCTT-A
1 TCTTCTTAA
3296520 TCTTCTT
1 TCTTCTT
3296527 GTTTTTATTT
Statistics
Matches: 27, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
8 14 0.52
9 13 0.48
ACGTcount: A:0.15, C:0.22, G:0.00, T:0.63
Consensus pattern (9 bp):
TCTTCTTAA
Found at i:3296796 original size:56 final size:57
Alignment explanation
Indices: 3296697--3296820 Score: 180
Period size: 56 Copynumber: 2.2 Consensus size: 57
3296687 TTAAATATTA
*
3296697 TTTGAGAAGAAATAGATTATTTTGACGCGAATAATAACACATGTCAAAGTGGCACCG
1 TTTGATAAGAAATAGATTATTTTGACGCGAATAATAACACATGTCAAAGTGGCACCG
* * *
3296754 -TTGATAAGAAATGGATTATTTTGACTCGAATAA-AGACGCATGTCAAAGTGGCACCG
1 TTTGATAAGAAATAGATTATTTTGACGCGAATAATA-ACACATGTCAAAGTGGCACCG
3296810 TTTGATGAAGA
1 TTTGAT-AAGA
3296821 TTAACAACAA
Statistics
Matches: 60, Mismatches: 4, Indels: 5
0.87 0.06 0.07
Matches are distributed among these distances:
55 1 0.02
56 50 0.83
57 5 0.08
58 4 0.07
ACGTcount: A:0.37, C:0.13, G:0.23, T:0.27
Consensus pattern (57 bp):
TTTGATAAGAAATAGATTATTTTGACGCGAATAATAACACATGTCAAAGTGGCACCG
Found at i:3300727 original size:19 final size:19
Alignment explanation
Indices: 3300703--3300749 Score: 94
Period size: 19 Copynumber: 2.5 Consensus size: 19
3300693 TCATGGATAT
3300703 GGTAAATTATCTGACCATA
1 GGTAAATTATCTGACCATA
3300722 GGTAAATTATCTGACCATA
1 GGTAAATTATCTGACCATA
3300741 GGTAAATTA
1 GGTAAATTA
3300750 CCTTTAGATT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 28 1.00
ACGTcount: A:0.38, C:0.13, G:0.17, T:0.32
Consensus pattern (19 bp):
GGTAAATTATCTGACCATA
Found at i:3301305 original size:153 final size:152
Alignment explanation
Indices: 3300973--3301276 Score: 574
Period size: 153 Copynumber: 2.0 Consensus size: 152
3300963 GTTTCTTTTG
*
3300973 GCTTACGCTATTTCGTGACACTTATATGTTTTGTAAATCACGTGGGAAATGTCAACATGCATGGA
1 GCTTACGCTATTTCGTGAAACTTATATGTTTTGTAAATCACGTGGGAAATGTCAACATGCATGGA
3301038 ATTTAAACCGAAAAAATGAATTGCCTCAAAATCCAATTTATGTCTTTTGAAATTTTTTATGTGCG
66 ATTTAAACCGAAAAAATGAATTGCCTCAAAATCCAATTTATGTCTTTTGAAATTTTTTATGTGCG
3301103 AGGACTCGATTATATAGGCCCT
131 AGGACTCGATTATATAGGCCCT
*
3301125 GGCTTACGCTATTTCGTGACACTTATATGTTTTGTAAATCACGTGGGAAATGTCAACATGCATGG
1 -GCTTACGCTATTTCGTGAAACTTATATGTTTTGTAAATCACGTGGGAAATGTCAACATGCATGG
3301190 AATTTAAACCGAAAAAATGAATTGCCTCAAAATCCAATTTATGTC-TTTGAAATTTTTTATGTGC
65 AATTTAAACCGAAAAAATGAATTGCCTCAAAATCCAATTTATGTCTTTTGAAATTTTTTATGTGC
3301254 GAGGACTCGATTATATAGGCCCT
130 GAGGACTCGATTATATAGGCCCT
3301277 TTTACTTCTT
Statistics
Matches: 151, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
152 42 0.28
153 109 0.72
ACGTcount: A:0.31, C:0.16, G:0.18, T:0.35
Consensus pattern (152 bp):
GCTTACGCTATTTCGTGAAACTTATATGTTTTGTAAATCACGTGGGAAATGTCAACATGCATGGA
ATTTAAACCGAAAAAATGAATTGCCTCAAAATCCAATTTATGTCTTTTGAAATTTTTTATGTGCG
AGGACTCGATTATATAGGCCCT
Found at i:3312892 original size:20 final size:20
Alignment explanation
Indices: 3312847--3312944 Score: 151
Period size: 20 Copynumber: 4.7 Consensus size: 20
3312837 GCATGAGTAG
3312847 TGCATCGATGCACATGTTAAAGAA
1 TGCATCGATGCAC-TG-T--AGAA
3312871 TGCATCGATGCACTGTAGAA
1 TGCATCGATGCACTGTAGAA
3312891 TGCATCGATGCACTGTAGAA
1 TGCATCGATGCACTGTAGAA
*
3312911 TGCATCGATGCACTGTAGAT
1 TGCATCGATGCACTGTAGAA
3312931 TGCATCGATGCACT
1 TGCATCGATGCACT
3312945 TCAAGGGGAA
Statistics
Matches: 73, Mismatches: 1, Indels: 4
0.94 0.01 0.05
Matches are distributed among these distances:
20 57 0.78
22 1 0.01
23 2 0.03
24 13 0.18
ACGTcount: A:0.30, C:0.20, G:0.23, T:0.27
Consensus pattern (20 bp):
TGCATCGATGCACTGTAGAA
Found at i:3312919 original size:40 final size:42
Alignment explanation
Indices: 3312831--3312944 Score: 155
Period size: 40 Copynumber: 2.7 Consensus size: 42
3312821 TAATTTTTGT
*
3312831 ATCGATGCA-TG-AGTAGTGCATCGATGCACATGTTAAAGAATGC
1 ATCGATGCACTGTAG-AATGCATCGATGCAC-TGTT-AAGAATGC
3312874 ATCGATGCACTGTAGAATGCATCGATGCACTG-T-AGAATGC
1 ATCGATGCACTGTAGAATGCATCGATGCACTGTTAAGAATGC
*
3312914 ATCGATGCACTGTAGATTGCATCGATGCACT
1 ATCGATGCACTGTAGAATGCATCGATGCACT
3312945 TCAAGGGGAA
Statistics
Matches: 67, Mismatches: 2, Indels: 7
0.88 0.03 0.09
Matches are distributed among these distances:
40 37 0.55
42 1 0.01
43 11 0.16
44 16 0.24
45 2 0.03
ACGTcount: A:0.30, C:0.19, G:0.25, T:0.26
Consensus pattern (42 bp):
ATCGATGCACTGTAGAATGCATCGATGCACTGTTAAGAATGC
Found at i:3317078 original size:23 final size:23
Alignment explanation
Indices: 3317048--3317097 Score: 100
Period size: 23 Copynumber: 2.2 Consensus size: 23
3317038 CCTATCAAAC
3317048 GTTGTGCAAGAGCAACTGATGTG
1 GTTGTGCAAGAGCAACTGATGTG
3317071 GTTGTGCAAGAGCAACTGATGTG
1 GTTGTGCAAGAGCAACTGATGTG
3317094 GTTG
1 GTTG
3317098 CTCCATCACC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 27 1.00
ACGTcount: A:0.24, C:0.12, G:0.36, T:0.28
Consensus pattern (23 bp):
GTTGTGCAAGAGCAACTGATGTG
Found at i:3318010 original size:16 final size:17
Alignment explanation
Indices: 3317984--3318020 Score: 58
Period size: 16 Copynumber: 2.2 Consensus size: 17
3317974 ATATATATAT
*
3317984 ATATGAATTATATTAAA
1 ATATGAATTATATAAAA
3318001 ATAT-AATTATATAAAA
1 ATATGAATTATATAAAA
3318017 ATAT
1 ATAT
3318021 TTAGAAAACC
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 15 0.79
17 4 0.21
ACGTcount: A:0.57, C:0.00, G:0.03, T:0.41
Consensus pattern (17 bp):
ATATGAATTATATAAAA
Found at i:3318123 original size:22 final size:19
Alignment explanation
Indices: 3318076--3318123 Score: 51
Period size: 22 Copynumber: 2.4 Consensus size: 19
3318066 AATTTGAATC
3318076 TTAAATTTTGTCTATTTAT
1 TTAAATTTTGTCTATTTAT
* *
3318095 TTGAATTGTTTTCTCATTTATT
1 TTAAATT-TTGTCT-ATTTA-T
3318117 TTAAATT
1 TTAAATT
3318124 ATAATCATTA
Statistics
Matches: 23, Mismatches: 3, Indels: 3
0.79 0.10 0.10
Matches are distributed among these distances:
19 6 0.26
20 5 0.22
21 5 0.22
22 7 0.30
ACGTcount: A:0.25, C:0.06, G:0.06, T:0.62
Consensus pattern (19 bp):
TTAAATTTTGTCTATTTAT
Found at i:3318639 original size:2 final size:2
Alignment explanation
Indices: 3318632--3318700 Score: 120
Period size: 2 Copynumber: 34.5 Consensus size: 2
3318622 AGTTAACTTC
* *
3318632 AT AT AT AT AT AG AT AT AT AT AT AT AT AT AT AT AT AG AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
3318674 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
3318701 GTACAAAAAC
Statistics
Matches: 63, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 63 1.00
ACGTcount: A:0.51, C:0.00, G:0.03, T:0.46
Consensus pattern (2 bp):
AT
Found at i:3320247 original size:13 final size:12
Alignment explanation
Indices: 3320213--3320251 Score: 51
Period size: 12 Copynumber: 3.2 Consensus size: 12
3320203 AGAAACCATA
*
3320213 AAAAATGGTGAT
1 AAAAATGATGAT
*
3320225 AGAAATGATGAT
1 AAAAATGATGAT
3320237 AAAATATGATGAT
1 AAAA-ATGATGAT
3320250 AA
1 AA
3320252 TTTAATAAAG
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
12 13 0.57
13 10 0.43
ACGTcount: A:0.54, C:0.00, G:0.21, T:0.26
Consensus pattern (12 bp):
AAAAATGATGAT
Found at i:3320597 original size:15 final size:14
Alignment explanation
Indices: 3320577--3320613 Score: 56
Period size: 15 Copynumber: 2.6 Consensus size: 14
3320567 GAGGACTAAC
*
3320577 TTTATTTTAATTTA
1 TTTATTTTAATATA
3320591 TTTTATTTTAATATA
1 -TTTATTTTAATATA
3320606 TTTATTTT
1 TTTATTTT
3320614 CACCAATTAG
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
14 8 0.38
15 13 0.62
ACGTcount: A:0.27, C:0.00, G:0.00, T:0.73
Consensus pattern (14 bp):
TTTATTTTAATATA
Found at i:3330625 original size:18 final size:18
Alignment explanation
Indices: 3330599--3330643 Score: 81
Period size: 18 Copynumber: 2.5 Consensus size: 18
3330589 TGTCTTTCTG
*
3330599 ATGGACCTGGAATCCTAA
1 ATGGTCCTGGAATCCTAA
3330617 ATGGTCCTGGAATCCTAA
1 ATGGTCCTGGAATCCTAA
3330635 ATGGTCCTG
1 ATGGTCCTG
3330644 AAGCATTAAA
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
18 26 1.00
ACGTcount: A:0.27, C:0.22, G:0.24, T:0.27
Consensus pattern (18 bp):
ATGGTCCTGGAATCCTAA
Found at i:3336596 original size:18 final size:18
Alignment explanation
Indices: 3336569--3336620 Score: 72
Period size: 18 Copynumber: 3.0 Consensus size: 18
3336559 CTGGAATGTT
*
3336569 TATGAGGGAATTGGAATC
1 TATGAAGGAATTGGAATC
3336587 TATGAAGGAATTGGAATC
1 TATGAAGGAATTGGAATC
*
3336605 --TGTAGGAATTGGAATC
1 TATGAAGGAATTGGAATC
3336621 AAATTCTATA
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
16 15 0.47
18 17 0.53
ACGTcount: A:0.35, C:0.06, G:0.31, T:0.29
Consensus pattern (18 bp):
TATGAAGGAATTGGAATC
Found at i:3337213 original size:27 final size:28
Alignment explanation
Indices: 3337156--3337218 Score: 110
Period size: 28 Copynumber: 2.3 Consensus size: 28
3337146 GACCCGACCT
3337156 GACCCGAATATCACACTTAAAAAACCCC
1 GACCCGAATATCACACTTAAAAAACCCC
*
3337184 GACCCGAATATCACACTTAAAAAA-CTC
1 GACCCGAATATCACACTTAAAAAACCCC
3337211 GACCCGAA
1 GACCCGAA
3337219 CAAAATAAAG
Statistics
Matches: 34, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
27 10 0.29
28 24 0.71
ACGTcount: A:0.43, C:0.33, G:0.10, T:0.14
Consensus pattern (28 bp):
GACCCGAATATCACACTTAAAAAACCCC
Found at i:3337471 original size:37 final size:38
Alignment explanation
Indices: 3337384--3337472 Score: 144
Period size: 38 Copynumber: 2.3 Consensus size: 38
3337374 TTTTCACCCT
3337384 AAACCCGAACCCGACCCGACCCGAATATCACACTTAAAA
1 AAACCCG-ACCCGACCCGACCCGAATATCACACTTAAAA
* *
3337423 AAACCCAACCCGACTCGACCCGAATATCACAC-TAAAA
1 AAACCCGACCCGACCCGACCCGAATATCACACTTAAAA
3337460 AAACCCGACCCGA
1 AAACCCGACCCGA
3337473 ACAAAATAAA
Statistics
Matches: 47, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
37 17 0.36
38 24 0.51
39 6 0.13
ACGTcount: A:0.42, C:0.39, G:0.10, T:0.09
Consensus pattern (38 bp):
AAACCCGACCCGACCCGACCCGAATATCACACTTAAAA
Found at i:3337662 original size:259 final size:255
Alignment explanation
Indices: 3337183--3337687 Score: 814
Period size: 259 Copynumber: 2.0 Consensus size: 255
3337173 TAAAAAACCC
* * *
3337183 CGACCCGAATATCACACTTAAAAAACTCGACCCGAACAAAATAAAGTTTCATCCGACCCGAGCCA
1 CGACCCGAATATCACACTAAAAAAACCCGACCCGAACAAAATAAAGTTTCATCCGACCCGACCCA
* *
3337248 AATATATGAATTAGAAATCCGACCCGACCTGACCCGAAATAATAAAAAATTATTTTTTATTTAAT
66 AATATATGAATTAGAAATCCAACCCGACCCGACCCGAAATAATAAAAAATTATTTTTTATTTAAT
* ** *
3337313 AAAAACAGTGACTTAATTTGACCCGACCCGAATTATATATATTTTCGGGTCGGTCTAATTTTTTT
131 AAAAACAATGACTTAATCCGACCCGACCCGAATTATATATATTTTCGGGTCGGTCCAATTTTTTT
*
3337378 CACCCTAAACCCGAACCCGACCCGACCCGAATATCACACTTAAAAAAACCCAACCCGACT
196 CACCCTAAACCCGAACCCGACCCGACCCGAATATCAAACTTAAAAAAACCCAACCCGACT
*
3337438 CGACCCGAATATCACACTAAAAAAACCCGACCCGAACAAAATAAAGTTTCATCCGACCCGACCCG
1 CGACCCGAATATCACACTAAAAAAACCCGACCCGAACAAAATAAAGTTTCATCCGACCCGACCCA
3337503 AATATATGAATTAGAAATCCAATCCAACCCGACCCGACCCGAAATAATAAAAAATTA-TTTTTAT
66 AATATATGAATTAG--A---AATCCAACCCGACCCGACCCGAAATAATAAAAAATTATTTTTTAT
* * **
3337567 TTAATAAAAACAATGACTTAATCCGACCCGATCTGAATTATATATATTTTCGGGTCGGTCCGGTT
126 TTAATAAAAACAATGACTTAATCCGACCCGACCCGAATTATATATATTTTCGGGTCGGTCCAATT
*
3337632 TTTTTCACCCTAAACCCGAACCTGACCCGACCCGAATATCAAACTTAAAAAAACCC
191 TTTTTCACCCTAAACCCGAACCCGACCCGACCCGAATATCAAACTTAAAAAAACCC
3337688 GATCCGATCC
Statistics
Matches: 229, Mismatches: 16, Indels: 6
0.91 0.06 0.02
Matches are distributed among these distances:
255 75 0.33
257 1 0.00
259 118 0.52
260 35 0.15
ACGTcount: A:0.38, C:0.27, G:0.11, T:0.24
Consensus pattern (255 bp):
CGACCCGAATATCACACTAAAAAAACCCGACCCGAACAAAATAAAGTTTCATCCGACCCGACCCA
AATATATGAATTAGAAATCCAACCCGACCCGACCCGAAATAATAAAAAATTATTTTTTATTTAAT
AAAAACAATGACTTAATCCGACCCGACCCGAATTATATATATTTTCGGGTCGGTCCAATTTTTTT
CACCCTAAACCCGAACCCGACCCGACCCGAATATCAAACTTAAAAAAACCCAACCCGACT
Found at i:3338530 original size:11 final size:11
Alignment explanation
Indices: 3338483--3338574 Score: 62
Period size: 11 Copynumber: 8.2 Consensus size: 11
3338473 TTTCTTTTAT
*
3338483 TTTTATAATTA
1 TTTTATTATTA
* **
3338494 TTTAATTACAA
1 TTTTATTATTA
*
3338505 TTTTATT-TTGT
1 TTTTATTATT-A
3338516 TTTTATTATTA
1 TTTTATTATTA
*
3338527 TTTT-TGATATA
1 TTTTATTAT-TA
*
3338538 TTTAAATTATTA
1 TTT-TATTATTA
*
3338550 TTTTCATGATTA
1 TTTT-ATTATTA
3338562 TTTTATTATTA
1 TTTTATTATTA
3338573 TT
1 TT
3338575 ATCTTAAGTC
Statistics
Matches: 60, Mismatches: 15, Indels: 12
0.69 0.17 0.14
Matches are distributed among these distances:
10 3 0.05
11 37 0.62
12 17 0.28
13 3 0.05
ACGTcount: A:0.29, C:0.02, G:0.03, T:0.65
Consensus pattern (11 bp):
TTTTATTATTA
Found at i:3338546 original size:23 final size:22
Alignment explanation
Indices: 3338483--3338574 Score: 71
Period size: 22 Copynumber: 4.1 Consensus size: 22
3338473 TTTCTTTTAT
* **
3338483 TTTTATAATTATTTAATTACAA
1 TTTTATGATTATTTAATTATTA
* * *
3338505 TTTTAT-TTTGTTTTTATTATTA
1 TTTTATGATT-ATTTAATTATTA
3338527 TTTT-TGATATATTTAAATTATTA
1 TTTTATGAT-TATTT-AATTATTA
*
3338550 TTTTCATGATTATTTTATTATTA
1 TTTT-ATGATTATTTAATTATTA
3338573 TT
1 TT
3338575 ATCTTAAGTC
Statistics
Matches: 55, Mismatches: 9, Indels: 11
0.73 0.12 0.15
Matches are distributed among these distances:
21 3 0.05
22 22 0.40
23 21 0.38
24 5 0.09
25 4 0.07
ACGTcount: A:0.29, C:0.02, G:0.03, T:0.65
Consensus pattern (22 bp):
TTTTATGATTATTTAATTATTA
Found at i:3338572 original size:26 final size:24
Alignment explanation
Indices: 3338518--3338576 Score: 68
Period size: 23 Copynumber: 2.4 Consensus size: 24
3338508 TATTTTGTTT
3338518 TTATTATTATTTTTGATATATTTA
1 TTATTATTATTTTTGATATATTTA
*
3338542 -AATTATTATTTTCATGAT-TATTTTA
1 TTATTATTATTTT--TGATATA-TTTA
3338567 TTATTATTAT
1 TTATTATTAT
3338577 CTTAAGTCAT
Statistics
Matches: 29, Mismatches: 2, Indels: 6
0.78 0.05 0.16
Matches are distributed among these distances:
23 11 0.38
24 2 0.07
25 8 0.28
26 8 0.28
ACGTcount: A:0.31, C:0.02, G:0.03, T:0.64
Consensus pattern (24 bp):
TTATTATTATTTTTGATATATTTA
Found at i:3339454 original size:2 final size:2
Alignment explanation
Indices: 3339449--3339490 Score: 84
Period size: 2 Copynumber: 21.0 Consensus size: 2
3339439 ATTATTTTTA
3339449 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
3339491 TTCAAGTATT
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):
AT
Found at i:3345240 original size:13 final size:14
Alignment explanation
Indices: 3345210--3345242 Score: 66
Period size: 14 Copynumber: 2.4 Consensus size: 14
3345200 CCATTGCAAG
3345210 AAAATGCACCAACA
1 AAAATGCACCAACA
3345224 AAAATGCACCAACA
1 AAAATGCACCAACA
3345238 AAAAT
1 AAAAT
3345243 CCTCTAGTTC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.61, C:0.24, G:0.06, T:0.09
Consensus pattern (14 bp):
AAAATGCACCAACA
Found at i:3348462 original size:22 final size:22
Alignment explanation
Indices: 3348406--3348462 Score: 69
Period size: 22 Copynumber: 2.6 Consensus size: 22
3348396 ACATCTACAA
* **
3348406 TCTTCAAAGATAATAGATTTTC
1 TCTTCAAAGATGATAGATCCTC
*
3348428 TCTTCAAATATGATAGATCCTC
1 TCTTCAAAGATGATAGATCCTC
*
3348450 TTTTCAAAGATGA
1 TCTTCAAAGATGA
3348463 AAGCTTTATT
Statistics
Matches: 29, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
22 29 1.00
ACGTcount: A:0.35, C:0.16, G:0.11, T:0.39
Consensus pattern (22 bp):
TCTTCAAAGATGATAGATCCTC
Found at i:3349264 original size:76 final size:76
Alignment explanation
Indices: 3349138--3349364 Score: 391
Period size: 76 Copynumber: 3.0 Consensus size: 76
3349128 CCACACATCC
*
3349138 GTAAGCCCTACAGTGCAGGATGTTTTCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAAAACCT
1 GTAAGCCCTACAGTGCAGGATGTTTTCAAAAAGCCTTCGGAAGCTTTTTGATGTTTTCAAAACCT
3349203 TCGGGTCATTT
66 TCGGGTCATTT
*
3349214 GTAAGCCCTACAGTGCAGGATGTTTTCAAAAAGCCTTCGGAAGATTTTTGATGTTTTCAAAACCT
1 GTAAGCCCTACAGTGCAGGATGTTTTCAAAAAGCCTTCGGAAGCTTTTTGATGTTTTCAAAACCT
*
3349279 TCGGGTCATCT
66 TCGGGTCATTT
* * * *
3349290 GTAAGCCCTACAGTGCAAGATGTTTTAAAAAAGCCTTCGGAAGCTTTTTTATGTTTTCAAAATCT
1 GTAAGCCCTACAGTGCAGGATGTTTTCAAAAAGCCTTCGGAAGCTTTTTGATGTTTTCAAAACCT
3349355 TCGGGTCATT
66 TCGGGTCATT
3349365 CCTAAGACCT
Statistics
Matches: 142, Mismatches: 9, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
76 142 1.00
ACGTcount: A:0.26, C:0.19, G:0.21, T:0.34
Consensus pattern (76 bp):
GTAAGCCCTACAGTGCAGGATGTTTTCAAAAAGCCTTCGGAAGCTTTTTGATGTTTTCAAAACCT
TCGGGTCATTT
Found at i:3349650 original size:93 final size:93
Alignment explanation
Indices: 3349463--3349642 Score: 324
Period size: 93 Copynumber: 1.9 Consensus size: 93
3349453 TAATGAGAAT
*
3349463 AACTTGTTCAACCTTTTGCTTGAATCCATTATTCGATGGATCAACTTTTCCAGAGAAAGTTCATA
1 AACTTGTTCAACCTTTTGCTTGAATCCATTATTCGATGGATCAACATTTCCAGAGAAAGTTCATA
3349528 ATGAGAAGAACTCATCTGAAGAGAAAAG
66 ATGAGAAGAACTCATCTGAAGAGAAAAG
* *
3349556 AACTTGTTCAACCTTTTGCTTGAATCCATTATTCGATGGATCAACATTTCTAGAGGAAGTTCATA
1 AACTTGTTCAACCTTTTGCTTGAATCCATTATTCGATGGATCAACATTTCCAGAGAAAGTTCATA
*
3349621 ATGAGAATAACTCATCTGAAGA
66 ATGAGAAGAACTCATCTGAAGA
3349643 AGGAAGAAGA
Statistics
Matches: 83, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
93 83 1.00
ACGTcount: A:0.34, C:0.17, G:0.17, T:0.32
Consensus pattern (93 bp):
AACTTGTTCAACCTTTTGCTTGAATCCATTATTCGATGGATCAACATTTCCAGAGAAAGTTCATA
ATGAGAAGAACTCATCTGAAGAGAAAAG
Found at i:3349744 original size:206 final size:208
Alignment explanation
Indices: 3349390--3349765 Score: 650
Period size: 206 Copynumber: 1.8 Consensus size: 208
3349380 CAGAATGTTT
3349390 TCAACATTTTCAGAGGAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATA
1 TCAACATTTTCAGAGGAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATA
* * * * *
3349455 ATGAGAATAACTTGTTCAACCTTTTGCTTGAATCCATTATTCGATGGATCAACTTTTCCAGAGAA
66 ATGAGAAGAACTTGTTCAACCTTTTGCTCGAATCCATCACTCGATGGATAAACTTTTCCAGAGAA
3349520 AGTTCATAATGAGAAGAACTCATCTGAAGA-GAA-AAGAACTTGTTCAACCTTTTGCTTGAATCC
131 AGTTCATAATGAGAAGAACTCATCTGAAGAGGAAGAAGAACTTGTTCAACCTTTTGCTTGAATCC
3349583 ATTATTCGATGGA
196 ATTATTCGATGGA
*
3349596 TCAACA-TTTCTAGAGGAAGTTCATAATGAGAATAACTCATCTGAAGAAGGAAGAAGAAGTTCAT
1 TCAACATTTTC-AGAGGAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCAT
*
3349660 AATGAGAAGAACTTGTTCAACCTTTTGCTCGAATTCATCACTCGATGGATAAACTTTTCCAGAGA
65 AATGAGAAGAACTTGTTCAACCTTTTGCTCGAATCCATCACTCGATGGATAAACTTTTCCAGAGA
*
3349725 AAGTTCATAATGAGAAGAACTTATCTGAAGAGGAAGAAGAA
130 AAGTTCATAATGAGAAGAACTCATCTGAAGAGGAAGAAGAA
3349766 GTTAATAAAG
Statistics
Matches: 159, Mismatches: 8, Indels: 4
0.93 0.05 0.02
Matches are distributed among these distances:
205 4 0.03
206 147 0.92
207 3 0.02
208 5 0.03
ACGTcount: A:0.38, C:0.15, G:0.19, T:0.28
Consensus pattern (208 bp):
TCAACATTTTCAGAGGAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATA
ATGAGAAGAACTTGTTCAACCTTTTGCTCGAATCCATCACTCGATGGATAAACTTTTCCAGAGAA
AGTTCATAATGAGAAGAACTCATCTGAAGAGGAAGAAGAACTTGTTCAACCTTTTGCTTGAATCC
ATTATTCGATGGA
Found at i:3349812 original size:112 final size:112
Alignment explanation
Indices: 3349553--3349812 Score: 353
Period size: 113 Copynumber: 2.3 Consensus size: 112
3349543 CTGAAGAGAA
* * * * * *
3349553 AAGAACTTGTTCAACCTTTTGCTTGAATCCATTATTCGATGGATCAACATTTCTAGAGGAAGTTC
1 AAGAACTTGTTCAACCTTTTGC-TGAATCTATCACTCGATGGATAAACATTTCCAGAGAAAGTTC
* * *
3349618 ATAATGAGAATAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAG
65 ATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTAATAAAGAG
*
3349666 AAGAACTTGTTCAACCTTTTGCTCGAAT-TCATCACTCGATGGATAAACTTTTCCAGAGAAAGTT
1 AAGAACTTGTTCAACCTTTTGCT-GAATCT-ATCACTCGATGGATAAACATTTCCAGAGAAAGTT
*
3349730 CATAATGAGAAGAACTTATCTGAAG-AGGAAGAAGAAGTTAATAAAGAG
64 CATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTAATAAAGAG
* *
3349778 AAGAGCTTGTTCAACCTTTTGCATGACTCTATCAC
1 AAGAACTTGTTCAACCTTTTGC-TGAATCTATCAC
3349813 AGAAGGAGAT
Statistics
Matches: 130, Mismatches: 13, Indels: 9
0.86 0.09 0.06
Matches are distributed among these distances:
112 51 0.39
113 79 0.61
ACGTcount: A:0.37, C:0.16, G:0.19, T:0.29
Consensus pattern (112 bp):
AAGAACTTGTTCAACCTTTTGCTGAATCTATCACTCGATGGATAAACATTTCCAGAGAAAGTTCA
TAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTAATAAAGAG
Found at i:3349900 original size:23 final size:22
Alignment explanation
Indices: 3349858--3349902 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 22
3349848 CGTTCATAAT
*
3349858 GAGAAGAATTCATCTGAAGAAG
1 GAGAAGAATTCATATGAAGAAG
3349880 GAGAAGAAGTTCATAAT-AAGAAG
1 GAGAAGAA-TTCAT-ATGAAGAAG
3349903 AATTTGTTCA
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
22 8 0.40
23 11 0.55
24 1 0.05
ACGTcount: A:0.49, C:0.07, G:0.27, T:0.18
Consensus pattern (22 bp):
GAGAAGAATTCATATGAAGAAG
Found at i:3350211 original size:3 final size:3
Alignment explanation
Indices: 3350203--3350263 Score: 61
Period size: 3 Copynumber: 20.0 Consensus size: 3
3350193 TTTTTACTAT
* * * *
3350203 TTA TTA TTA TTAA TAA TTA ATA ATA TTA TTA TCA TTA TTA TTA TTTA
1 TTA TTA TTA TT-A TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA -TTA
3350250 TTA TTA TTA -TA TTA
1 TTA TTA TTA TTA TTA
3350264 CATGCCCATT
Statistics
Matches: 49, Mismatches: 6, Indels: 6
0.80 0.10 0.10
Matches are distributed among these distances:
2 2 0.04
3 42 0.86
4 5 0.10
ACGTcount: A:0.39, C:0.02, G:0.00, T:0.59
Consensus pattern (3 bp):
TTA
Found at i:3350250 original size:19 final size:18
Alignment explanation
Indices: 3350228--3350263 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
3350218 ATTAATAATA
3350228 TTATTATCATTATTATTAT
1 TTATTATCATTA-TATTAT
*
3350247 TTATTATTATTATATTA
1 TTATTATCATTATATTA
3350264 CATGCCCATT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 5 0.31
19 11 0.69
ACGTcount: A:0.33, C:0.03, G:0.00, T:0.64
Consensus pattern (18 bp):
TTATTATCATTATATTAT
Found at i:3351596 original size:23 final size:22
Alignment explanation
Indices: 3351529--3351624 Score: 70
Period size: 23 Copynumber: 4.2 Consensus size: 22
3351519 TTTATTTTTT
*
3351529 TTATTTTGATCATTATTTAATTA
1 TTATTTT-ATGATTATTTAATTA
** * * *
3351552 CAATTTTAT-TTTGTTTTTATTA
1 TTATTTTATGATT-ATTTAATTA
3351574 TTATTTT-TGATATATTTAAATTA
1 TTATTTTATGAT-TATTT-AATTA
*
3351597 TTATTTTCATGATTATTTTATTA
1 TTATTTT-ATGATTATTTAATTA
3351620 TTATT
1 TTATT
3351625 ATCTTAAGTC
Statistics
Matches: 56, Mismatches: 11, Indels: 12
0.71 0.14 0.15
Matches are distributed among these distances:
21 3 0.05
22 18 0.32
23 26 0.46
24 5 0.09
25 4 0.07
ACGTcount: A:0.28, C:0.03, G:0.04, T:0.65
Consensus pattern (22 bp):
TTATTTTATGATTATTTAATTA
Found at i:3355301 original size:30 final size:30
Alignment explanation
Indices: 3355229--3355301 Score: 110
Period size: 30 Copynumber: 2.4 Consensus size: 30
3355219 CTCGAAGGAC
3355229 CTATCCAGAGGTCATAAAGATCCTCGGTAA
1 CTATCCAGAGGTCATAAAGATCCTCGGTAA
* *
3355259 TTATCCAGAGGTCATAAAGATCCTTGGTAA
1 CTATCCAGAGGTCATAAAGATCCTCGGTAA
* *
3355289 CTGTCCATAGGTC
1 CTATCCAGAGGTC
3355302 CCGAAGAATC
Statistics
Matches: 38, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
30 38 1.00
ACGTcount: A:0.30, C:0.22, G:0.21, T:0.27
Consensus pattern (30 bp):
CTATCCAGAGGTCATAAAGATCCTCGGTAA
Found at i:3356103 original size:22 final size:20
Alignment explanation
Indices: 3356051--3356107 Score: 62
Period size: 22 Copynumber: 2.8 Consensus size: 20
3356041 TAATGAAGGT
3356051 ATGCATCGATGCACTATACA
1 ATGCATCGATGCACTATACA
* *
3356071 ATGTATCGATGCATTCT-TAACG
1 ATGCATCGATGCA--CTAT-ACA
3356093 ATGCATCGATGCACT
1 ATGCATCGATGCACT
3356108 TACTTGTGCA
Statistics
Matches: 31, Mismatches: 3, Indels: 6
0.77 0.08 0.15
Matches are distributed among these distances:
20 14 0.45
21 1 0.03
22 16 0.52
ACGTcount: A:0.30, C:0.23, G:0.18, T:0.30
Consensus pattern (20 bp):
ATGCATCGATGCACTATACA
Found at i:3357787 original size:36 final size:36
Alignment explanation
Indices: 3357740--3357812 Score: 146
Period size: 36 Copynumber: 2.0 Consensus size: 36
3357730 AGTTCTGGAA
3357740 TTAAGTGATAAAAGAATCAGCTATGGATATGTAGAT
1 TTAAGTGATAAAAGAATCAGCTATGGATATGTAGAT
3357776 TTAAGTGATAAAAGAATCAGCTATGGATATGTAGAT
1 TTAAGTGATAAAAGAATCAGCTATGGATATGTAGAT
3357812 T
1 T
3357813 ATAATTTATC
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
36 37 1.00
ACGTcount: A:0.41, C:0.05, G:0.22, T:0.32
Consensus pattern (36 bp):
TTAAGTGATAAAAGAATCAGCTATGGATATGTAGAT
Done.