Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold138
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: 1735418
ACGTcount: A:0.34, C:0.17, G:0.16, T:0.33
Warning! 2489 characters in sequence are not A, C, G, or T
File 11 of 11
Found at i:1564625 original size:13 final size:13
Alignment explanation
Indices: 1564607--1564631 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1564597 ACATATTGCA
1564607 GTATCGATACATT
1 GTATCGATACATT
1564620 GTATCGATACAT
1 GTATCGATACAT
1564632 GACCAAATGT
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:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
GTATCGATACATT
Found at i:1564644 original size:20 final size:22
Alignment explanation
Indices: 1564619--1564671 Score: 67
Period size: 21 Copynumber: 2.5 Consensus size: 22
1564609 ATCGATACAT
*
1564619 TGTATCGATACATGAC-CA-AA
1 TGTATCGATACATGACAAAGAA
*
1564639 TGTATCGATAC-TTACAAAGAA
1 TGTATCGATACATGACAAAGAA
1564660 TGTATCGATACA
1 TGTATCGATACA
1564672 GGTAATTGGC
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
19 3 0.11
20 12 0.43
21 13 0.46
ACGTcount: A:0.40, C:0.17, G:0.15, T:0.28
Consensus pattern (22 bp):
TGTATCGATACATGACAAAGAA
Found at i:1564775 original size:33 final size:32
Alignment explanation
Indices: 1564712--1564779 Score: 102
Period size: 33 Copynumber: 2.1 Consensus size: 32
1564702 CCTTAACTGT
*
1564712 TTGTATCGATACATACAAGATGTATTGATACA
1 TTGTATCGATACATACAAGATGTATCGATACA
1564744 TTGTATCGATACATGACTAA-ATGTATCGATACA
1 TTGTATCGATACAT-AC-AAGATGTATCGATACA
1564777 TTG
1 TTG
1564780 GCTTGTAACG
Statistics
Matches: 33, Mismatches: 1, Indels: 3
0.89 0.03 0.08
Matches are distributed among these distances:
32 14 0.42
33 17 0.52
34 2 0.06
ACGTcount: A:0.35, C:0.13, G:0.16, T:0.35
Consensus pattern (32 bp):
TTGTATCGATACATACAAGATGTATCGATACA
Found at i:1574671 original size:21 final size:21
Alignment explanation
Indices: 1574647--1574693 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 21
1574637 GATAAAGTAT
*
1574647 TGTATCAACACATTGATGAAA
1 TGTATCAACACATTGATAAAA
* * *
1574668 TGTATCGACACCTTGTTAAAA
1 TGTATCAACACATTGATAAAA
1574689 TGTAT
1 TGTAT
1574694 TGATACCTAG
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.36, C:0.15, G:0.15, T:0.34
Consensus pattern (21 bp):
TGTATCAACACATTGATAAAA
Found at i:1580789 original size:79 final size:78
Alignment explanation
Indices: 1580643--1580859 Score: 219
Period size: 79 Copynumber: 2.7 Consensus size: 78
1580633 AATGGGGCTA
* * * *
1580643 GAGTATCCCCGATTATGAAAAATCGGTGTTCT-AGAAATAAAAATCAGGG-TTGGAGTATCCCCT
1 GAGTATCCCCGATTATGAGAAATCAGTATTTTGA-AAAT-AAAATC-GGGATTGGAGTAT-CCCT
*
1580706 CGAAAATAATAG-GGTTG
62 CGAAAATAA-AGTGATTG
*
1580723 GAGTATCCCTGATTAT-AGAGAATCAGTATTTTGAAAATAAAATCGGGATTGGAGTATCCCTGCG
1 GAGTATCCCCGATTATGAGA-AATCAGTATTTTGAAAATAAAATCGGGATTGGAGTATCCCT-CG
*
1580787 AAAATAACGTGATTG
64 AAAATAAAGTGATTG
* ** * *
1580802 GAGTATCCCCGATTGTGAGAAATTGGTGTTTTGGAAATAAAATC-GGAGTTGGAGTATC
1 GAGTATCCCCGATTATGAGAAATCAGTATTTTGAAAATAAAATCGGGA-TTGGAGTATC
1580860 ACCGATTGCG
Statistics
Matches: 117, Mismatches: 13, Indels: 15
0.81 0.09 0.10
Matches are distributed among these distances:
78 11 0.09
79 74 0.63
80 31 0.26
81 1 0.01
ACGTcount: A:0.34, C:0.13, G:0.25, T:0.29
Consensus pattern (78 bp):
GAGTATCCCCGATTATGAGAAATCAGTATTTTGAAAATAAAATCGGGATTGGAGTATCCCTCGAA
AATAAAGTGATTG
Found at i:1580859 original size:51 final size:51
Alignment explanation
Indices: 1580799--1580913 Score: 158
Period size: 51 Copynumber: 2.3 Consensus size: 51
1580789 AATAACGTGA
* * * *
1580799 TTGGAGTATCCCCGATTGTGAGAAATTGGTGTTTTGGAAATAAAATCGGAG
1 TTGGAGTATCCCCGATTGCGAGAAATTGATATTTTAGAAATAAAATCGGAG
* *
1580850 TTGGAGTATCACCGATTGCGAGAAATTGATATTTTAGAAATAAAATCGGGG
1 TTGGAGTATCCCCGATTGCGAGAAATTGATATTTTAGAAATAAAATCGGAG
* *
1580901 TTGAAATATCCCC
1 TTGGAGTATCCCC
1580914 TCGGAAATAA
Statistics
Matches: 55, Mismatches: 9, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
51 55 1.00
ACGTcount: A:0.32, C:0.12, G:0.25, T:0.30
Consensus pattern (51 bp):
TTGGAGTATCCCCGATTGCGAGAAATTGATATTTTAGAAATAAAATCGGAG
Found at i:1580927 original size:28 final size:28
Alignment explanation
Indices: 1580896--1580959 Score: 74
Period size: 28 Copynumber: 2.3 Consensus size: 28
1580886 GAAATAAAAT
**
1580896 CGGGGTTGAAATATCCCCTCGGAAATAA
1 CGGGGTTGAAATATCCCCGAGGAAATAA
* * * *
1580924 CGGGATTGGAGTATCCCCGATGAAATAA
1 CGGGGTTGAAATATCCCCGAGGAAATAA
1580952 CGGGGTTG
1 CGGGGTTG
1580960 GAGTACCCCC
Statistics
Matches: 29, Mismatches: 7, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
28 29 1.00
ACGTcount: A:0.28, C:0.19, G:0.31, T:0.22
Consensus pattern (28 bp):
CGGGGTTGAAATATCCCCGAGGAAATAA
Found at i:1580960 original size:28 final size:28
Alignment explanation
Indices: 1580917--1580972 Score: 94
Period size: 28 Copynumber: 2.0 Consensus size: 28
1580907 TATCCCCTCG
*
1580917 GAAATAACGGGATTGGAGTATCCCCGAT
1 GAAATAACGGGATTGGAGTACCCCCGAT
*
1580945 GAAATAACGGGGTTGGAGTACCCCCGAT
1 GAAATAACGGGATTGGAGTACCCCCGAT
1580973 TATGAAAAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
28 26 1.00
ACGTcount: A:0.30, C:0.20, G:0.30, T:0.20
Consensus pattern (28 bp):
GAAATAACGGGATTGGAGTACCCCCGAT
Found at i:1581177 original size:51 final size:52
Alignment explanation
Indices: 1581054--1581178 Score: 128
Period size: 51 Copynumber: 2.4 Consensus size: 52
1581044 TATCCCCAAT
* * * * **
1581054 GAAAAATTGGTGTTTTGAAAATAAAATCGGAGTTGGAGTATCCCCGATTGCT
1 GAAAAATTGATGTTTTGGAAATGAAATCAGAGTTGGAGTATCCCCGATTGAA
* * * * * *
1581106 G-TAAATCGATGCTTTAGAAATGAAATCAGAGTTGGGGTATCCTCGATT-AA
1 GAAAAATTGATGTTTTGGAAATGAAATCAGAGTTGGAGTATCCCCGATTGAA
1581156 GAAAAATTGATGTTTTGGAAATG
1 GAAAAATTGATGTTTTGGAAATG
1581179 GAACCGGGAT
Statistics
Matches: 56, Mismatches: 16, Indels: 3
0.75 0.21 0.04
Matches are distributed among these distances:
50 1 0.02
51 54 0.96
52 1 0.02
ACGTcount: A:0.34, C:0.10, G:0.25, T:0.31
Consensus pattern (52 bp):
GAAAAATTGATGTTTTGGAAATGAAATCAGAGTTGGAGTATCCCCGATTGAA
Found at i:1583512 original size:20 final size:20
Alignment explanation
Indices: 1583487--1583541 Score: 76
Period size: 20 Copynumber: 2.8 Consensus size: 20
1583477 AAAATGCCTG
*
1583487 AATGTATCGATACATTGTA-A
1 AATGTATCGATACAATG-AGA
*
1583507 AATGTATCGATACAATGAGC
1 AATGTATCGATACAATGAGA
1583527 AATGTATCGATACAA
1 AATGTATCGATACAA
1583542 ATTGTGAGAA
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
19 1 0.03
20 31 0.97
ACGTcount: A:0.42, C:0.13, G:0.16, T:0.29
Consensus pattern (20 bp):
AATGTATCGATACAATGAGA
Found at i:1598533 original size:20 final size:21
Alignment explanation
Indices: 1598489--1598534 Score: 62
Period size: 20 Copynumber: 2.3 Consensus size: 21
1598479 CCAAAACATA
1598489 AAAAATGACTAAAATGATCTT
1 AAAAATGACTAAAATGATCTT
1598510 -AAAATGTA-TAAAATGA-CTT
1 AAAAATG-ACTAAAATGATCTT
1598529 AAAAAT
1 AAAAAT
1598535 CTCTAGGTCA
Statistics
Matches: 23, Mismatches: 0, Indels: 5
0.82 0.00 0.18
Matches are distributed among these distances:
19 3 0.13
20 19 0.83
21 1 0.04
ACGTcount: A:0.57, C:0.07, G:0.09, T:0.28
Consensus pattern (21 bp):
AAAAATGACTAAAATGATCTT
Found at i:1599460 original size:20 final size:20
Alignment explanation
Indices: 1599430--1599476 Score: 60
Period size: 22 Copynumber: 2.2 Consensus size: 20
1599420 TGGATAATCT
1599430 TTTTATTCTTT-TTTTTTCTC
1 TTTT-TTCTTTCTTTTTTCTC
1599450 TCTTTTTCTTTCCTTTTTTCTC
1 T-TTTTTCTTT-CTTTTTTCTC
1599472 TTTTT
1 TTTTT
1599477 AGTTTTTTTA
Statistics
Matches: 24, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
20 7 0.29
21 7 0.29
22 10 0.42
ACGTcount: A:0.02, C:0.19, G:0.00, T:0.79
Consensus pattern (20 bp):
TTTTTTCTTTCTTTTTTCTC
Found at i:1599901 original size:21 final size:21
Alignment explanation
Indices: 1599855--1599914 Score: 70
Period size: 21 Copynumber: 2.9 Consensus size: 21
1599845 AAAACCTCAT
*
1599855 ATTGTATCAATACAA-A-GCA
1 ATTGTATCGATACAATATGCA
*
1599874 CATTGTATTGATACAATATGCA
1 -ATTGTATCGATACAATATGCA
*
1599896 ATTGTATCGATATAATATG
1 ATTGTATCGATACAATATG
1599915 TCTTATGCCA
Statistics
Matches: 34, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
20 13 0.38
21 18 0.53
22 3 0.09
ACGTcount: A:0.40, C:0.12, G:0.13, T:0.35
Consensus pattern (21 bp):
ATTGTATCGATACAATATGCA
Found at i:1602575 original size:20 final size:20
Alignment explanation
Indices: 1602550--1602603 Score: 63
Period size: 20 Copynumber: 2.7 Consensus size: 20
1602540 TTATCATTGT
* *
1602550 TTGTATCGATACATGGTACA
1 TTGTATCGATACATAGTAAA
*
1602570 TTGTATCGATATATAGTAAA
1 TTGTATCGATACATAGTAAA
**
1602590 AAGTATCGATACAT
1 TTGTATCGATACAT
1602604 TGTCCTAACG
Statistics
Matches: 28, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
20 28 1.00
ACGTcount: A:0.37, C:0.11, G:0.17, T:0.35
Consensus pattern (20 bp):
TTGTATCGATACATAGTAAA
Found at i:1607008 original size:50 final size:50
Alignment explanation
Indices: 1606933--1607044 Score: 181
Period size: 50 Copynumber: 2.2 Consensus size: 50
1606923 CCACAATTTA
* *
1606933 TATCGATACATTCTGGGTTTTACCCAAATGTATCGATACATTAT-TCATTG
1 TATCGATACATTCTGAGTTTTACCCAAATGTATCGATACATT-TCTCAATG
*
1606983 TATCGATACATTCTGAGTTTTACCCAGATGTATCGATACATTTCTCAATG
1 TATCGATACATTCTGAGTTTTACCCAAATGTATCGATACATTTCTCAATG
1607033 TATCGATACATT
1 TATCGATACATT
1607045 TAGGCATTTT
Statistics
Matches: 58, Mismatches: 3, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
49 1 0.02
50 57 0.98
ACGTcount: A:0.29, C:0.19, G:0.13, T:0.39
Consensus pattern (50 bp):
TATCGATACATTCTGAGTTTTACCCAAATGTATCGATACATTTCTCAATG
Found at i:1609768 original size:20 final size:20
Alignment explanation
Indices: 1609745--1609817 Score: 101
Period size: 20 Copynumber: 3.6 Consensus size: 20
1609735 ACAATTCAAA
1609745 GTATCGATACATGTTGCAAT
1 GTATCGATACATGTTGCAAT
****
1609765 GTATCGATACATGAAAAAAAT
1 GTATCGATACATG-TTGCAAT
1609786 GTATCGATACATGTTGCAAT
1 GTATCGATACATGTTGCAAT
1609806 GTATCGATACAT
1 GTATCGATACAT
1609818 AAAAAGGATG
Statistics
Matches: 44, Mismatches: 8, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
20 28 0.64
21 16 0.36
ACGTcount: A:0.37, C:0.14, G:0.18, T:0.32
Consensus pattern (20 bp):
GTATCGATACATGTTGCAAT
Found at i:1609788 original size:21 final size:21
Alignment explanation
Indices: 1609762--1609838 Score: 86
Period size: 21 Copynumber: 3.7 Consensus size: 21
1609752 TACATGTTGC
1609762 AATGTATCGATACATGAAAAA
1 AATGTATCGATACATGAAAAA
****
1609783 AATGTATCGATACATG-TTGC
1 AATGTATCGATACATGAAAAA
1609803 AATGTATCGATACAT-AAAAA
1 AATGTATCGATACATGAAAAA
*
1609823 GGATGTATCGATACAT
1 -AATGTATCGATACAT
1609839 TTCTTGGCAG
Statistics
Matches: 45, Mismatches: 9, Indels: 4
0.78 0.16 0.07
Matches are distributed among these distances:
20 15 0.33
21 30 0.67
ACGTcount: A:0.43, C:0.12, G:0.17, T:0.29
Consensus pattern (21 bp):
AATGTATCGATACATGAAAAA
Found at i:1609796 original size:41 final size:41
Alignment explanation
Indices: 1609745--1609838 Score: 163
Period size: 41 Copynumber: 2.3 Consensus size: 41
1609735 ACAATTCAAA
1609745 GTATCGATACATGTTGCAATGTATCGATACATGAAAAA-AAT
1 GTATCGATACATGTTGCAATGTATCGATACAT-AAAAAGAAT
*
1609786 GTATCGATACATGTTGCAATGTATCGATACATAAAAAGGAT
1 GTATCGATACATGTTGCAATGTATCGATACATAAAAAGAAT
1609827 GTATCGATACAT
1 GTATCGATACAT
1609839 TTCTTGGCAG
Statistics
Matches: 51, Mismatches: 1, Indels: 2
0.94 0.02 0.04
Matches are distributed among these distances:
40 5 0.10
41 46 0.90
ACGTcount: A:0.39, C:0.13, G:0.18, T:0.30
Consensus pattern (41 bp):
GTATCGATACATGTTGCAATGTATCGATACATAAAAAGAAT
Found at i:1609895 original size:13 final size:13
Alignment explanation
Indices: 1609877--1609902 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1609867 TACAGAAAGT
1609877 ATGTATCGATACA
1 ATGTATCGATACA
1609890 ATGTATCGATACA
1 ATGTATCGATACA
1609903 CAAAAAATTG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:1609900 original size:32 final size:33
Alignment explanation
Indices: 1609859--1609922 Score: 94
Period size: 32 Copynumber: 2.0 Consensus size: 33
1609849 TAGCCAAACT
* **
1609859 TGTATCGATACAGAAAGTA-TGTATCGATACAA
1 TGTATCGATACACAAAAAATTGTATCGATACAA
1609891 TGTATCGATACACAAAAAATTGTATCGATACA
1 TGTATCGATACACAAAAAATTGTATCGATACA
1609923 TTGGCTTGTA
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
32 16 0.57
33 12 0.43
ACGTcount: A:0.42, C:0.14, G:0.16, T:0.28
Consensus pattern (33 bp):
TGTATCGATACACAAAAAATTGTATCGATACAA
Found at i:1613984 original size:15 final size:15
Alignment explanation
Indices: 1613964--1613994 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
1613954 TAAAAATGTC
*
1613964 CAAAATGAGGAAGCT
1 CAAAATGAAGAAGCT
1613979 CAAAATGAAGAAGCT
1 CAAAATGAAGAAGCT
1613994 C
1 C
1613995 CAAACGAAAT
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:0.48, C:0.16, G:0.23, T:0.13
Consensus pattern (15 bp):
CAAAATGAAGAAGCT
Found at i:1616091 original size:13 final size:13
Alignment explanation
Indices: 1616073--1616111 Score: 69
Period size: 13 Copynumber: 3.0 Consensus size: 13
1616063 ACATTTTTCC
1616073 TTGTATCGATACA
1 TTGTATCGATACA
1616086 TTGTATCGATACA
1 TTGTATCGATACA
*
1616099 CTGTATCGATACA
1 TTGTATCGATACA
1616112 GGGTGATTAT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
13 25 1.00
ACGTcount: A:0.31, C:0.18, G:0.15, T:0.36
Consensus pattern (13 bp):
TTGTATCGATACA
Found at i:1618583 original size:20 final size:20
Alignment explanation
Indices: 1618553--1618624 Score: 92
Period size: 20 Copynumber: 3.6 Consensus size: 20
1618543 ACAATTCAAA
1618553 GTATC-ATACATGTTGCAAT
1 GTATCGATACATGTTGCAAT
****
1618572 GTATCGATACATGAAAAAAAT
1 GTATCGATACATG-TTGCAAT
1618593 GTATCGATACATGTTGCAAT
1 GTATCGATACATGTTGCAAT
1618613 GTATCGATACAT
1 GTATCGATACAT
1618625 AAAAAGGATG
Statistics
Matches: 43, Mismatches: 8, Indels: 3
0.80 0.15 0.06
Matches are distributed among these distances:
19 5 0.12
20 22 0.51
21 16 0.37
ACGTcount: A:0.38, C:0.14, G:0.17, T:0.32
Consensus pattern (20 bp):
GTATCGATACATGTTGCAAT
Found at i:1618595 original size:21 final size:21
Alignment explanation
Indices: 1618569--1618645 Score: 86
Period size: 21 Copynumber: 3.7 Consensus size: 21
1618559 TACATGTTGC
1618569 AATGTATCGATACATGAAAAA
1 AATGTATCGATACATGAAAAA
****
1618590 AATGTATCGATACATG-TTGC
1 AATGTATCGATACATGAAAAA
1618610 AATGTATCGATACAT-AAAAA
1 AATGTATCGATACATGAAAAA
*
1618630 GGATGTATCGATACAT
1 -AATGTATCGATACAT
1618646 TTCTTGGCAG
Statistics
Matches: 45, Mismatches: 9, Indels: 4
0.78 0.16 0.07
Matches are distributed among these distances:
20 15 0.33
21 30 0.67
ACGTcount: A:0.43, C:0.12, G:0.17, T:0.29
Consensus pattern (21 bp):
AATGTATCGATACATGAAAAA
Found at i:1618609 original size:41 final size:41
Alignment explanation
Indices: 1618553--1618645 Score: 154
Period size: 41 Copynumber: 2.3 Consensus size: 41
1618543 ACAATTCAAA
1618553 GTATC-ATACATGTTGCAATGTATCGATACATGAAAAA-AAT
1 GTATCGATACATGTTGCAATGTATCGATACAT-AAAAAGAAT
*
1618593 GTATCGATACATGTTGCAATGTATCGATACATAAAAAGGAT
1 GTATCGATACATGTTGCAATGTATCGATACATAAAAAGAAT
1618634 GTATCGATACAT
1 GTATCGATACAT
1618646 TTCTTGGCAG
Statistics
Matches: 50, Mismatches: 1, Indels: 3
0.93 0.02 0.06
Matches are distributed among these distances:
40 10 0.20
41 40 0.80
ACGTcount: A:0.40, C:0.13, G:0.17, T:0.30
Consensus pattern (41 bp):
GTATCGATACATGTTGCAATGTATCGATACATAAAAAGAAT
Found at i:1618702 original size:13 final size:13
Alignment explanation
Indices: 1618684--1618709 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1618674 TACAGAAAGT
1618684 ATGTATCGATACA
1 ATGTATCGATACA
1618697 ATGTATCGATACA
1 ATGTATCGATACA
1618710 CAAAAAATTG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:1618707 original size:32 final size:33
Alignment explanation
Indices: 1618666--1618729 Score: 94
Period size: 32 Copynumber: 2.0 Consensus size: 33
1618656 TAGCCAAACT
* **
1618666 TGTATCGATACAGAAAGTA-TGTATCGATACAA
1 TGTATCGATACACAAAAAATTGTATCGATACAA
1618698 TGTATCGATACACAAAAAATTGTATCGATACA
1 TGTATCGATACACAAAAAATTGTATCGATACA
1618730 TTGGCTTGTA
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
32 16 0.57
33 12 0.43
ACGTcount: A:0.42, C:0.14, G:0.16, T:0.28
Consensus pattern (33 bp):
TGTATCGATACACAAAAAATTGTATCGATACAA
Found at i:1619584 original size:78 final size:78
Alignment explanation
Indices: 1619455--1619602 Score: 217
Period size: 78 Copynumber: 1.9 Consensus size: 78
1619445 ATAAGCTTTC
* * * *
1619455 AGGATACTCTAACCTCGGTTTTATTTCTGAAACATCAATTTTTCATAATCGGGGATACTCCAACC
1 AGGATACTCCAACCCCGGTTTTATTTCTAAAACATCAATTTTTCACAATCGGGGATACTCCAACC
1619520 CCATTATTTCGAA
66 CCATTATTTCGAA
* * *
1619533 AGGATACTCCAACCCCGGTTTTATTT-TCAAAACATCGATTTTTCACCATCGGGGATGCTCCAAC
1 AGGATACTCCAACCCCGGTTTTATTTCT-AAAACATCAATTTTTCACAATCGGGGATACTCCAAC
1619597 CCCATT
65 CCCATT
1619603 TTTATCTCCA
Statistics
Matches: 62, Mismatches: 7, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
77 1 0.02
78 61 0.98
ACGTcount: A:0.28, C:0.26, G:0.14, T:0.32
Consensus pattern (78 bp):
AGGATACTCCAACCCCGGTTTTATTTCTAAAACATCAATTTTTCACAATCGGGGATACTCCAACC
CCATTATTTCGAA
Found at i:1621668 original size:4 final size:4
Alignment explanation
Indices: 1621659--1621696 Score: 58
Period size: 4 Copynumber: 9.5 Consensus size: 4
1621649 TTTGAGGTGC
* *
1621659 TTAT TTAT TTAT TTAT TCAT TTGT TTAT TTAT TTAT TT
1 TTAT TTAT TTAT TTAT TTAT TTAT TTAT TTAT TTAT TT
1621697 TGTTTTGTTT
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
4 30 1.00
ACGTcount: A:0.21, C:0.03, G:0.03, T:0.74
Consensus pattern (4 bp):
TTAT
Found at i:1621685 original size:16 final size:16
Alignment explanation
Indices: 1621661--1621701 Score: 55
Period size: 16 Copynumber: 2.5 Consensus size: 16
1621651 TGAGGTGCTT
*
1621661 ATTTATTTATTTATTC
1 ATTTGTTTATTTATTC
*
1621677 ATTTGTTTATTTATTT
1 ATTTGTTTATTTATTC
1621693 ATTTTGTTT
1 A-TTTGTTT
1621702 TGTTTTGTAC
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
16 15 0.68
17 7 0.32
ACGTcount: A:0.20, C:0.02, G:0.05, T:0.73
Consensus pattern (16 bp):
ATTTGTTTATTTATTC
Found at i:1631936 original size:1 final size:1
Alignment explanation
Indices: 1631932--1631975 Score: 52
Period size: 1 Copynumber: 44.0 Consensus size: 1
1631922 TCCTTTTTCT
* * * *
1631932 AAAAAACAAAAAAAAATAAAAAAATAAAAAAAAAGAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
1631976 GAGAAAAGAA
Statistics
Matches: 35, Mismatches: 8, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
1 35 1.00
ACGTcount: A:0.91, C:0.02, G:0.02, T:0.05
Consensus pattern (1 bp):
A
Found at i:1631947 original size:10 final size:10
Alignment explanation
Indices: 1631939--1631990 Score: 61
Period size: 10 Copynumber: 5.1 Consensus size: 10
1631929 TCTAAAAAAC
1631939 AAAAAAAA-A
1 AAAAAAAAGA
* *
1631948 TAAAAAAATA
1 AAAAAAAAGA
1631958 AAAAAAAAGA
1 AAAAAAAAGA
1631968 AAAAAAAAGA
1 AAAAAAAAGA
1631978 GAAAAGAAAAGA
1 -AAAA-AAAAGA
1631990 A
1 A
1631991 CCTACTTAAG
Statistics
Matches: 37, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
9 7 0.19
10 19 0.51
11 5 0.14
12 6 0.16
ACGTcount: A:0.87, C:0.00, G:0.10, T:0.04
Consensus pattern (10 bp):
AAAAAAAAGA
Found at i:1631955 original size:18 final size:18
Alignment explanation
Indices: 1631932--1631987 Score: 69
Period size: 18 Copynumber: 3.2 Consensus size: 18
1631922 TCCTTTTTCT
*
1631932 AAAAAACAAAAAAAAATA
1 AAAAAACAAAAAAAAAGA
*
1631950 AAAAAATAAAAAAAAAGA
1 AAAAAACAAAAAAAAAGA
* *
1631968 AAAAAA-AAGAGAAAAGA
1 AAAAAACAAAAAAAAAGA
1631985 AAA
1 AAA
1631988 GAACCTACTT
Statistics
Matches: 34, Mismatches: 4, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
17 12 0.35
18 22 0.65
ACGTcount: A:0.88, C:0.02, G:0.07, T:0.04
Consensus pattern (18 bp):
AAAAAACAAAAAAAAAGA
Found at i:1631980 original size:12 final size:12
Alignment explanation
Indices: 1631957--1631989 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
1631947 ATAAAAAAAT
1631957 AAAAAAAA-AGA
1 AAAAAAAAGAGA
1631968 AAAAAAAAGAGA
1 AAAAAAAAGAGA
*
1631980 AAAGAAAAGA
1 AAAAAAAAGA
1631990 ACCTACTTAA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
11 8 0.40
12 12 0.60
ACGTcount: A:0.85, C:0.00, G:0.15, T:0.00
Consensus pattern (12 bp):
AAAAAAAAGAGA
Found at i:1632585 original size:31 final size:31
Alignment explanation
Indices: 1632542--1632610 Score: 120
Period size: 31 Copynumber: 2.2 Consensus size: 31
1632532 CTAAGAATGA
1632542 ACTCTTAAGGTTATTATTGGTAGGGCTTAGG
1 ACTCTTAAGGTTATTATTGGTAGGGCTTAGG
*
1632573 ACTCTTAGGGTTATTATTGGTAGGGCTTAGG
1 ACTCTTAAGGTTATTATTGGTAGGGCTTAGG
*
1632604 ACCCTTA
1 ACTCTTA
1632611 CGAACAGAGA
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
31 36 1.00
ACGTcount: A:0.22, C:0.13, G:0.28, T:0.38
Consensus pattern (31 bp):
ACTCTTAAGGTTATTATTGGTAGGGCTTAGG
Found at i:1633095 original size:61 final size:61
Alignment explanation
Indices: 1632983--1633680 Score: 877
Period size: 61 Copynumber: 11.4 Consensus size: 61
1632973 AACATTTTAT
* * * * *
1632983 CCTTTCAGTCCTCATAGAGCAGAACAC--TTTCCTTTCAGAAGCCCACACAAGTTGGTGACA
1 CCTTTCAGTCCTCAAAGAGCAGGACGCTTTTTCCTTTTA-AAGCCCACACAAGTTGGTGGCA
* * * *
1633043 -CTTTCCAGTCCTCAAAGAGTAGGATGCTTTTTCCTTTTAAAGCCCACGCAAGTTGGTAGCA
1 CCTTT-CAGTCCTCAAAGAGCAGGACGCTTTTTCCTTTTAAAGCCCACACAAGTTGGTGGCA
* * **
1633104 CCTTCCAGTCCTCAAAGAGTAGGACATTTTTTCCTTTTAAAGCCCACACAAGTTGGTGGCA
1 CCTTTCAGTCCTCAAAGAGCAGGACGCTTTTTCCTTTTAAAGCCCACACAAGTTGGTGGCA
* * *
1633165 TCTTTCAGTCCTCAATGAGCAGGACGCCTTTTCCTTTTAAAGCCCACACAAGTTGGTGGCA
1 CCTTTCAGTCCTCAAAGAGCAGGACGCTTTTTCCTTTTAAAGCCCACACAAGTTGGTGGCA
* * **
1633226 CCTTCCAGTCTTCAAAGAATAGGACGCCTTTTT-CTTTTAAAGCCCACACAAGTTGGTGGCA
1 CCTTTCAGTCCTCAAAGAGCAGGACG-CTTTTTCCTTTTAAAGCCCACACAAGTTGGTGGCA
* * *
1633287 CC-TTCTAGTCCTCAAAGAGTAAGACACTTTTTCCTTTTAAAGCCCACACAAGTTGGTGGCA
1 CCTTTC-AGTCCTCAAAGAGCAGGACGCTTTTTCCTTTTAAAGCCCACACAAGTTGGTGGCA
* * * *
1633348 CCTTCCAGTCCTCAAAGAACAGGATGCCTTTTCCTTTTAAAGCCCACACAAGTTGGTGGCA
1 CCTTTCAGTCCTCAAAGAGCAGGACGCTTTTTCCTTTTAAAGCCCACACAAGTTGGTGGCA
* *
1633409 CCTTTCAGTCCTCAAAGAGCCAGGATGCCTTTTCCTTTTAAAGCCCACACAAGTTGGTGGCA
1 CCTTTCAGTCCTCAAAGAG-CAGGACGCTTTTTCCTTTTAAAGCCCACACAAGTTGGTGGCA
* * *
1633471 CCATTCAATCCTCAAAGAGTAGGACGCTTTTTCCTTTTAAAGCCCACACAAGTTGGTGGCA
1 CCTTTCAGTCCTCAAAGAGCAGGACGCTTTTTCCTTTTAAAGCCCACACAAGTTGGTGGCA
* * * *
1633532 CCTTTCAGTCCTCAAAGAGCAAGATGCCTTTTCCTTTTAAAGCCCATACAAGTTGGTGGCA
1 CCTTTCAGTCCTCAAAGAGCAGGACGCTTTTTCCTTTTAAAGCCCACACAAGTTGGTGGCA
* * * * * * *
1633593 CCTTTCAGTCTTTAAAAAGCAGGATG-TCTTTTCCTTTTAGAGCCTACATAAGTTGGTGGCA
1 CCTTTCAGTCCTCAAAGAGCAGGACGCT-TTTTCCTTTTAAAGCCCACACAAGTTGGTGGCA
* * * *
1633654 CCTTTTAGTTCTCAAATAGCAAGACGC
1 CCTTTCAGTCCTCAAAGAGCAGGACGC
1633681 ACTTCATTTC
Statistics
Matches: 556, Mismatches: 71, Indels: 20
0.86 0.11 0.03
Matches are distributed among these distances:
59 4 0.01
60 25 0.04
61 449 0.81
62 78 0.14
ACGTcount: A:0.26, C:0.27, G:0.18, T:0.29
Consensus pattern (61 bp):
CCTTTCAGTCCTCAAAGAGCAGGACGCTTTTTCCTTTTAAAGCCCACACAAGTTGGTGGCA
Found at i:1633757 original size:41 final size:41
Alignment explanation
Indices: 1633703--1633845 Score: 196
Period size: 41 Copynumber: 3.5 Consensus size: 41
1633693 TCTTTTATCT
* * * *
1633703 TTTGTCTTTAAAGAGTAAGATGCATTTTATTTCCTTTTCCC
1 TTTGTCCTCAAAGAGTAGGATGCAATTTATTTCCTTTTCCC
*
1633744 TTTGTCCTCAAAGAGCAGGATGCAATTTATTTCCTTTTCCC
1 TTTGTCCTCAAAGAGTAGGATGCAATTTATTTCCTTTTCCC
* * * *
1633785 TTTGTCCTCAAAGAATGGGACGCACTTTATTTCCTTTTCCC
1 TTTGTCCTCAAAGAGTAGGATGCAATTTATTTCCTTTTCCC
*
1633826 TTTGTCCTCAAAGAGCAGGA
1 TTTGTCCTCAAAGAGTAGGA
1633846 CAGATTTAAT
Statistics
Matches: 89, Mismatches: 13, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
41 89 1.00
ACGTcount: A:0.22, C:0.22, G:0.15, T:0.40
Consensus pattern (41 bp):
TTTGTCCTCAAAGAGTAGGATGCAATTTATTTCCTTTTCCC
Found at i:1634635 original size:20 final size:20
Alignment explanation
Indices: 1634584--1634636 Score: 61
Period size: 20 Copynumber: 2.6 Consensus size: 20
1634574 TTTTACCCAG
*
1634584 ATGTATCGATACATTTTTCA
1 ATGTATCGATACATTTCTCA
* * *
1634604 CTATATTGATACATTTCTCA
1 ATGTATCGATACATTTCTCA
*
1634624 ATGTATCAATACA
1 ATGTATCGATACA
1634637 ATCAAGCATT
Statistics
Matches: 25, Mismatches: 8, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.34, C:0.17, G:0.08, T:0.42
Consensus pattern (20 bp):
ATGTATCGATACATTTCTCA
Found at i:1637185 original size:79 final size:79
Alignment explanation
Indices: 1636989--1637186 Score: 252
Period size: 79 Copynumber: 2.5 Consensus size: 79
1636979 TCATTCATGT
* * ** * * * *
1636989 TTTTATTTCTAAAATACCAATTTTTCACCATCGGGGATACTCCAACCCTGTTGTTTCCGAGGGGA
1 TTTTATTTCTAAAACACCGATTTTTCATAATCGGGGATACTCCAACCCTATTATTTCCAAAGGGA
1637054 TACTCCAACCCCGA
66 TACTCCAACCCCGA
* * *
1637068 TTTTATTTCTAAAACACCGATTGTCCATAATCGAGGATACTCCAACCCTATTATTTCCAAAGGGA
1 TTTTATTTCTAAAACACCGATTTTTCATAATCGGGGATACTCCAACCCTATTATTTCCAAAGGGA
* *
1637133 TACTCTAACCCCGG
66 TACTCCAACCCCGA
* **
1637147 TTTTATTTCTAAAACATCGATTTTTCATTGTCGGGGATAC
1 TTTTATTTCTAAAACACCGATTTTTCATAATCGGGGATAC
1637187 CCTAATCCCA
Statistics
Matches: 100, Mismatches: 19, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
79 100 1.00
ACGTcount: A:0.27, C:0.25, G:0.14, T:0.34
Consensus pattern (79 bp):
TTTTATTTCTAAAACACCGATTTTTCATAATCGGGGATACTCCAACCCTATTATTTCCAAAGGGA
TACTCCAACCCCGA
Found at i:1637232 original size:51 final size:51
Alignment explanation
Indices: 1637129--1637237 Score: 132
Period size: 51 Copynumber: 2.1 Consensus size: 51
1637119 TATTTCCAAA
* * ***
1637129 GGGATACTCTAACCCCGGTTTTATTTCTAAAACATCGATTTTTCATTGTCG
1 GGGATACCCTAACCCCAGTTTTATTTCTAAAACATCGATTTTTCACCATCG
*
1637180 GGGATACCCTAATCCCAGTTTTATTT-TCAAAACATCGA-TTTTCAACCATCG
1 GGGATACCCTAACCCCAGTTTTATTTCT-AAAACATCGATTTTTC-ACCATCG
1637231 GGGATAC
1 GGGATAC
1637238 TCCAACCTCG
Statistics
Matches: 50, Mismatches: 6, Indels: 4
0.83 0.10 0.07
Matches are distributed among these distances:
50 6 0.12
51 44 0.88
ACGTcount: A:0.27, C:0.23, G:0.16, T:0.35
Consensus pattern (51 bp):
GGGATACCCTAACCCCAGTTTTATTTCTAAAACATCGATTTTTCACCATCG
Found at i:1637393 original size:210 final size:208
Alignment explanation
Indices: 1637010--1637396 Score: 508
Period size: 210 Copynumber: 1.9 Consensus size: 208
1637000 AAATACCAAT
* **
1637010 TTTTCACCATCGGGGATACTCCAACCCTGTTGTTTCCGAGGGGATACTCCAACCCCGATTTTATT
1 TTTTCACCATCGGGGATACTCCAACCCTGTTATTTCCGAGCAGATACTCCAACCCCGATTTTATT
** * * *
1637075 TCTAAAACACCGATTGTCCATAATCGAGGATACTCCAACCCTATTATTTCCAAAGGGATACTCTA
66 TCTAAAACAAAGATTGTCCAAAATCGAGGATACTCCAACCCCATTATTTCCAAAGGGATACTCCA
* ***
1637140 ACCCCGGTTTTATTTCTAAAACATCGATTTTTCATTGTCGGGGATACCCTAATCCCAGTTTTATT
131 ACCCCGGTTTTATTTCCAAAACATCGATTTTTCACCATCGGGGATACCCTAATCCCAGTTTTATT
1637205 TTCAAAACATCGA
196 TTCAAAACATCGA
**
1637218 TTTTCAACCATCGGGGATACTCCAA-CCTCGTTATTTTTGAGCAGATACTCCAACCCC-AGTTTT
1 TTTTC-ACCATCGGGGATACTCCAACCCT-GTTATTTCCGAGCAGATACTCCAACCCCGA-TTTT
* * * * * * * *
1637281 GATTTCTAAAGCAAATATTTTTCAAAATCGAGGATACTCCAACCCCGTTATTTTCGAGGGGATAC
63 -ATTTCTAAAACAAAGATTGTCCAAAATCGAGGATACTCCAACCCCATTATTTCCAAAGGGATAC
* *
1637346 TCCGACCTCGGTTTTATTTCCAAAACATCGATTTTTCACCATCGGGGATAC
127 TCCAACCCCGGTTTTATTTCCAAAACATCGATTTTTCACCATCGGGGATAC
1637397 TACAACCCTA
Statistics
Matches: 151, Mismatches: 24, Indels: 6
0.83 0.13 0.03
Matches are distributed among these distances:
208 9 0.06
209 46 0.30
210 96 0.64
ACGTcount: A:0.27, C:0.26, G:0.15, T:0.33
Consensus pattern (208 bp):
TTTTCACCATCGGGGATACTCCAACCCTGTTATTTCCGAGCAGATACTCCAACCCCGATTTTATT
TCTAAAACAAAGATTGTCCAAAATCGAGGATACTCCAACCCCATTATTTCCAAAGGGATACTCCA
ACCCCGGTTTTATTTCCAAAACATCGATTTTTCACCATCGGGGATACCCTAATCCCAGTTTTATT
TTCAAAACATCGA
Found at i:1637404 original size:79 final size:78
Alignment explanation
Indices: 1637179--1637528 Score: 348
Period size: 79 Copynumber: 4.4 Consensus size: 78
1637169 TTTCATTGTC
* *
1637179 GGGGATAC-CCTAATCCCAGTTTTATTTTCAAAACATCGA-TTTTCAACCATCGGGGATACTCCA
1 GGGGATACTCC-AA-CCCAGTTTTATTTCCAAAACATCGATTTTTC-ACCATCGGGGATACTACA
* * *
1637242 ACCTCGTTATTTTTGA
63 ACCCCATTATTTTCGA
** * * *** ** * *
1637258 GCAGATACTCCAACCCCAGTTTTGATTTCTAAAGCAAATATTTTTCAAAATCGAGGATACTCCAA
1 GGGGATACTCCAA-CCCAGTTTT-ATTTCCAAAACATCGATTTTTCACCATCGGGGATACTACAA
*
1637323 CCCCGTTATTTTCGA
64 CCCCATTATTTTCGA
* *
1637338 GGGGATACTCCGACCTCGGTTTTATTTCCAAAACATCGATTTTTCACCATCGGGGATACTACAAC
1 GGGGATACTCCAACC-CAGTTTTATTTCCAAAACATCGATTTTTCACCATCGGGGATACTACAAC
*
1637403 CCTATTA-TTTCTGA
65 CCCATTATTTTC-GA
* *
1637417 GGGGATACTCCAACCCTAGTTTTATTTCCAAAACATCAATTTTTCACCATCTGGGATACTACAAC
1 GGGGATACTCCAACCC-AGTTTTATTTCCAAAACATCGATTTTTCACCATCGGGGATACTACAAC
*
1637482 CCCATTATTTTCAA
65 CCCATTATTTTCGA
* * *
1637496 GGTGATGCTCCAATCCC-GTTTTTATCTCCAAAA
1 GGGGATACTCCAA-CCCAG-TTTTATTTCCAAAA
1637529 TATTAAATTT
Statistics
Matches: 224, Mismatches: 38, Indels: 18
0.80 0.14 0.06
Matches are distributed among these distances:
78 6 0.03
79 149 0.67
80 64 0.29
81 5 0.02
ACGTcount: A:0.28, C:0.25, G:0.14, T:0.33
Consensus pattern (78 bp):
GGGGATACTCCAACCCAGTTTTATTTCCAAAACATCGATTTTTCACCATCGGGGATACTACAACC
CCATTATTTTCGA
Found at i:1642478 original size:15 final size:14
Alignment explanation
Indices: 1642458--1642490 Score: 50
Period size: 13 Copynumber: 2.4 Consensus size: 14
1642448 GTATCGATAC
1642458 ATACAAGATGTATCG
1 ATACAA-ATGTATCG
1642473 ATAC-AATGTATCG
1 ATACAAATGTATCG
1642486 ATACA
1 ATACA
1642491 TGACCAAATT
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
13 12 0.71
14 1 0.06
15 4 0.24
ACGTcount: A:0.42, C:0.15, G:0.15, T:0.27
Consensus pattern (14 bp):
ATACAAATGTATCG
Found at i:1642483 original size:13 final size:13
Alignment explanation
Indices: 1642465--1642490 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1642455 TACATACAAG
1642465 ATGTATCGATACA
1 ATGTATCGATACA
1642478 ATGTATCGATACA
1 ATGTATCGATACA
1642491 TGACCAAATT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:1642509 original size:34 final size:32
Alignment explanation
Indices: 1642447--1642511 Score: 96
Period size: 34 Copynumber: 2.0 Consensus size: 32
1642437 CTTAACTGTT
1642447 TGTATCGATACATACAAGATGTATCGATACAA
1 TGTATCGATACATACAAGATGTATCGATACAA
1642479 TGTATCGATACATGACCAA-ATTGTATCGATACA
1 TGTATCGATACAT-A-CAAGA-TGTATCGATACA
1642512 TTGGTTTGTA
Statistics
Matches: 30, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
32 13 0.43
33 2 0.07
34 15 0.50
ACGTcount: A:0.38, C:0.17, G:0.15, T:0.29
Consensus pattern (32 bp):
TGTATCGATACATACAAGATGTATCGATACAA
Found at i:1644108 original size:3 final size:3
Alignment explanation
Indices: 1644090--1644123 Score: 50
Period size: 3 Copynumber: 11.3 Consensus size: 3
1644080 CATCAAGGAC
* *
1644090 GAT GAA GAT AAT GAT GAT GAT GAT GAT GAT GAT G
1 GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT G
1644124 GTGACTCAGA
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.38, C:0.00, G:0.32, T:0.29
Consensus pattern (3 bp):
GAT
Found at i:1648447 original size:52 final size:52
Alignment explanation
Indices: 1648247--1648427 Score: 317
Period size: 52 Copynumber: 3.5 Consensus size: 52
1648237 CGAAATATGA
* * *
1648247 AAATTCGCCTGCATGTATCGATACATTTCATAGTGTATCGATACATCTGGGT
1 AAATTTGCCTGCATGTATCGATACATTTTATAGTGTATCGATACATCTGGGC
*
1648299 AAATTTGCCTGCATGTATCGATACCTTTTATAGTGTATCGATACATCTGGGC
1 AAATTTGCCTGCATGTATCGATACATTTTATAGTGTATCGATACATCTGGGC
*
1648351 AAATTTGCCTGCATGTATCGATACATTTTATAGTGTATCGATACATCGGGGC
1 AAATTTGCCTGCATGTATCGATACATTTTATAGTGTATCGATACATCTGGGC
1648403 AAATTTGCCTGCATGTATCGATACA
1 AAATTTGCCTGCATGTATCGATACA
1648428 AAGATCAGTG
Statistics
Matches: 123, Mismatches: 6, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
52 123 1.00
ACGTcount: A:0.27, C:0.19, G:0.19, T:0.35
Consensus pattern (52 bp):
AAATTTGCCTGCATGTATCGATACATTTTATAGTGTATCGATACATCTGGGC
Found at i:1648454 original size:13 final size:13
Alignment explanation
Indices: 1648436--1648460 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1648426 CAAAGATCAG
1648436 TGTATCGATACAA
1 TGTATCGATACAA
1648449 TGTATCGATACA
1 TGTATCGATACA
1648461 TTTGAGTAAT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:1655053 original size:320 final size:320
Alignment explanation
Indices: 1654471--1655073 Score: 951
Period size: 320 Copynumber: 1.9 Consensus size: 320
1654461 AGGGGGAGAT
*
1654471 TGTTAGGATCTTGGTTTTCATATAACAAAGGATTGAATAAAACCGAAAATTAATTTGAAAATCCA
1 TGTTAGGATCTTGGTTTTCATATAACAAAGGATTGAATAAAACCGAAAATTAATTTGAAAATACA
* ** * * *
1654536 AAAATGTGTTTTATTCATTTAAGTACTTTATAAATTTTGTGCTAAATGATTTTTAACTCACTAAA
66 AAAATATGTTTTATTCAACTAAGTACTTTATAAATTTTGTACCAAATGATTTTTAACTCACCAAA
1654601 TGTTTTCTAGATAAGTATAAATGTTTTCAAGGCTTAAAATGATTGATTTTTAAGTTAAAAATAAA
131 TGTTTTCTAGATAAGTATAAATGTTTTCAAGGCTTAAAATGATTGATTTTTAAGTTAAAAATAAA
* * *
1654666 TCAAAGTTTCGATACATAGGTATTTGTATCGATACATTAATGTTGACTAAGGCTACAAAGGTCAA
196 TCAAAGTATCAATACATAGGTATTTGTATCGATACATTAAGGTTGACTAAGGCTACAAAGGTCAA
*
1654731 AACCCTCAAACGTATCGATACACCTTCGGATGTATCGATACATAATGCACAGTATCGATA
261 AACCCTCAAAAGTATCGATACACCTTCGGATGTATCGATACATAATGCACAGTATCGATA
* * *
1654791 TGTTAGGATCTTGGTTTTGATATAACAAAGGATTGAATAAAACCGGAAATTATTTTGAAAATAAC
1 TGTTAGGATCTTGGTTTTCATATAACAAAGGATTGAATAAAACCGAAAATTAATTTGAAAAT-AC
* * * *
1654856 AATAATATGTTTTATTCAACTAAGTGCTTTATAAATTTTGTACCAAATGATTTTTGATTCACCAA
65 AAAAATATGTTTTATTCAACTAAGTACTTTATAAATTTTGTACCAAATGATTTTTAACTCACCAA
*
1654921 ATGTTTTCTAGTTAAGGT-TAAATGTTTTCAAGGCTTAAAATGATTGATTTTTAAGTT-AAAATA
130 ATGTTTTCTAGATAA-GTATAAATGTTTTCAAGGCTTAAAATGATTGATTTTTAAGTTAAAAATA
* * *
1654984 TATCAAAGTATCAATACATAGGTATTTGTATCGATACATTAAGGTTGACTTAGGCTA-AAATTGT
194 AATCAAAGTATCAATACATAGGTATTTGTATCGATACATTAAGGTTGACTAAGGCTACAAA-GGT
*
1655048 CAAAACCCTTAAAAGTATCGATACAC
258 CAAAACCCTCAAAAGTATCGATACAC
1655074 AATTCAAAGT
Statistics
Matches: 257, Mismatches: 23, Indels: 6
0.90 0.08 0.02
Matches are distributed among these distances:
319 3 0.01
320 143 0.56
321 109 0.42
322 2 0.01
ACGTcount: A:0.37, C:0.12, G:0.14, T:0.36
Consensus pattern (320 bp):
TGTTAGGATCTTGGTTTTCATATAACAAAGGATTGAATAAAACCGAAAATTAATTTGAAAATACA
AAAATATGTTTTATTCAACTAAGTACTTTATAAATTTTGTACCAAATGATTTTTAACTCACCAAA
TGTTTTCTAGATAAGTATAAATGTTTTCAAGGCTTAAAATGATTGATTTTTAAGTTAAAAATAAA
TCAAAGTATCAATACATAGGTATTTGTATCGATACATTAAGGTTGACTAAGGCTACAAAGGTCAA
AACCCTCAAAAGTATCGATACACCTTCGGATGTATCGATACATAATGCACAGTATCGATA
Found at i:1655191 original size:13 final size:13
Alignment explanation
Indices: 1655173--1655198 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1655163 TACACCAAGT
1655173 ATGTATCGATACA
1 ATGTATCGATACA
1655186 ATGTATCGATACA
1 ATGTATCGATACA
1655199 CAAAAAAAAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:1657453 original size:21 final size:21
Alignment explanation
Indices: 1657420--1657464 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 21
1657410 TTGCAAGTTG
*
1657420 AAATAAAGAAGTTGGCTAATGA
1 AAATAAAGAAGTTAGCTAA-GA
*
1657442 AAATAATG-AGTTAGCTAAGA
1 AAATAAAGAAGTTAGCTAAGA
1657462 AAA
1 AAA
1657465 ATGAAAACTT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 5 0.24
21 9 0.43
22 7 0.33
ACGTcount: A:0.53, C:0.04, G:0.20, T:0.22
Consensus pattern (21 bp):
AAATAAAGAAGTTAGCTAAGA
Found at i:1659287 original size:15 final size:15
Alignment explanation
Indices: 1659267--1659297 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
1659257 TAAAAATGTC
*
1659267 CAAAATGAGGAAGCT
1 CAAAATGAAGAAGCT
1659282 CAAAATGAAGAAGCT
1 CAAAATGAAGAAGCT
1659297 C
1 C
1659298 CAAACGAAAT
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:0.48, C:0.16, G:0.23, T:0.13
Consensus pattern (15 bp):
CAAAATGAAGAAGCT
Found at i:1661392 original size:13 final size:13
Alignment explanation
Indices: 1661374--1661399 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1661364 ACATTTTTCT
1661374 TTGTATCGATACA
1 TTGTATCGATACA
1661387 TTGTATCGATACA
1 TTGTATCGATACA
1661400 GGGTGATTAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TTGTATCGATACA
Found at i:1666401 original size:79 final size:78
Alignment explanation
Indices: 1666208--1666423 Score: 213
Period size: 79 Copynumber: 2.7 Consensus size: 78
1666198 GGGGCCAGAG
* * ** * * *
1666208 TATCCCCGATTATGGAAAATTGGTATTCCAGAAATAAAACCGGGGTTGGAGTATCCCTTCGGAAA
1 TATCCCTGATTATAGAAAATCAGTATT-TAGAAATAAAACCGGGGTTGGAGTATCCCCTCGAAAA
*
1666273 TAACAGAGTTGGAG
65 TAACAGAGTTGGAA
* *
1666287 TATCCCTGATTATAGAAAATCAGTATTTTGAAAATAAAATCGGGGTTGGAGTATCCCCTCGAAAA
1 TATCCCTGATTATAGAAAATCAGTATTTAG-AAATAAAACCGGGGTTGGAGTATCCCCTCGAAAA
1666352 TAAC-GAGGTTGGAA
65 TAACAGA-GTTGGAA
* * * ** *
1666366 TATTCTTGATTGT-GAAAAATC-GATGATTTAGAAATAAGGCCGGGGTTGAAGTATCCCC
1 TATCCCTGATTATAG-AAAATCAG-T-ATTTAGAAATAAAACCGGGGTTGGAGTATCCCC
1666424 CGATTATGAG
Statistics
Matches: 114, Mismatches: 18, Indels: 10
0.80 0.13 0.07
Matches are distributed among these distances:
78 5 0.04
79 104 0.91
80 5 0.04
ACGTcount: A:0.34, C:0.15, G:0.24, T:0.28
Consensus pattern (78 bp):
TATCCCTGATTATAGAAAATCAGTATTTAGAAATAAAACCGGGGTTGGAGTATCCCCTCGAAAAT
AACAGAGTTGGAA
Found at i:1666495 original size:51 final size:51
Alignment explanation
Indices: 1666410--1666526 Score: 153
Period size: 51 Copynumber: 2.3 Consensus size: 51
1666400 TAAGGCCGGG
* * *
1666410 GTTGAAGTATCCCCCGATTATGAGAAATTAATATTTTGAAAATAAAATCGAA
1 GTTGGAGTAT-CCCCGATTATGAAAAATTAATATTTTAAAAATAAAATCGAA
* * * *
1666462 GTTGGAGTATCCCCGATTGTGAAAAATTGATATTTTAAAAATAAAATTGAG
1 GTTGGAGTATCCCCGATTATGAAAAATTAATATTTTAAAAATAAAATCGAA
*
1666513 GTTGGAATATCCCC
1 GTTGGAGTATCCCC
1666527 TAAGAAATAA
Statistics
Matches: 57, Mismatches: 8, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
51 48 0.84
52 9 0.16
ACGTcount: A:0.38, C:0.12, G:0.18, T:0.32
Consensus pattern (51 bp):
GTTGGAGTATCCCCGATTATGAAAAATTAATATTTTAAAAATAAAATCGAA
Found at i:1666712 original size:51 final size:51
Alignment explanation
Indices: 1666650--1666818 Score: 185
Period size: 51 Copynumber: 3.3 Consensus size: 51
1666640 AAATAATGGG
* * *
1666650 GTTGGAGTATCCCCAATTGTGAAAAATTGGTGTTTTGGAAATAAAATCGGA
1 GTTGGAGTATCCCCGATTGAGAAAAATTGATGTTTTGGAAATAAAATCGGA
* ** * * * *
1666701 GTTGGAGTATCCCCGATTGCGGTAAATCGATGCTTTAGAAATAAAATTGGA
1 GTTGGAGTATCCCCGATTGAGAAAAATTGATGTTTTGGAAATAAAATCGGA
* * * ** * *
1666752 GTTGGAGTATCCTCGATTAAGAAAAATTGATGTGTTGGAAATGGAACCGGG
1 GTTGGAGTATCCCCGATTGAGAAAAATTGATGTTTTGGAAATAAAATCGGA
1666803 GTTGGAGTATCCCCGA
1 GTTGGAGTATCCCCGA
1666819 GATGAAAAAT
Statistics
Matches: 94, Mismatches: 24, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
51 94 1.00
ACGTcount: A:0.31, C:0.12, G:0.28, T:0.29
Consensus pattern (51 bp):
GTTGGAGTATCCCCGATTGAGAAAAATTGATGTTTTGGAAATAAAATCGGA
Found at i:1669144 original size:20 final size:20
Alignment explanation
Indices: 1669119--1669157 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
1669109 AAAAAGCCTG
*
1669119 AATGTATCGATACATTGTAA
1 AATGTATCGATACAATGTAA
1669139 AATGTATCGATACAATGTA
1 AATGTATCGATACAATGTA
1669158 TTGATACAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.41, C:0.10, G:0.15, T:0.33
Consensus pattern (20 bp):
AATGTATCGATACAATGTAA
Found at i:1669156 original size:33 final size:33
Alignment explanation
Indices: 1669119--1669186 Score: 102
Period size: 33 Copynumber: 2.1 Consensus size: 33
1669109 AAAAAGCCTG
*
1669119 AATGTATCGATACATTGTAA-AATGTATCGATAC
1 AATGTATCGATACAATG-AACAATGTATCGATAC
*
1669152 AATGTATTGATACAATGAACAATGTATCGATAC
1 AATGTATCGATACAATGAACAATGTATCGATAC
1669185 AA
1 AA
1669187 ATTGTGAAAA
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
32 2 0.06
33 30 0.94
ACGTcount: A:0.43, C:0.12, G:0.15, T:0.31
Consensus pattern (33 bp):
AATGTATCGATACAATGAACAATGTATCGATAC
Found at i:1669186 original size:13 final size:13
Alignment explanation
Indices: 1669139--1669168 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
1669129 TACATTGTAA
1669139 AATGTATCGATAC
1 AATGTATCGATAC
*
1669152 AATGTATTGATAC
1 AATGTATCGATAC
1669165 AATG
1 AATG
1669169 AACAATGTAT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.40, C:0.10, G:0.17, T:0.33
Consensus pattern (13 bp):
AATGTATCGATAC
Found at i:1671085 original size:19 final size:19
Alignment explanation
Indices: 1671061--1671116 Score: 76
Period size: 19 Copynumber: 2.9 Consensus size: 19
1671051 TGTATCAATA
*
1671061 CATTGTATCGATACATGTT
1 CATTGTATCGATACATGCT
**
1671080 CATTGTATCGATACACACT
1 CATTGTATCGATACATGCT
1671099 CAATTGTATCGATACATG
1 C-ATTGTATCGATACATG
1671117 AACTAGCAAT
Statistics
Matches: 31, Mismatches: 5, Indels: 1
0.84 0.14 0.03
Matches are distributed among these distances:
19 17 0.55
20 14 0.45
ACGTcount: A:0.30, C:0.20, G:0.14, T:0.36
Consensus pattern (19 bp):
CATTGTATCGATACATGCT
Found at i:1677423 original size:7 final size:7
Alignment explanation
Indices: 1677407--1677440 Score: 59
Period size: 7 Copynumber: 4.9 Consensus size: 7
1677397 CATCTTTAAC
*
1677407 TTCTTTT
1 TTCTTCT
1677414 TTCTTCT
1 TTCTTCT
1677421 TTCTTCT
1 TTCTTCT
1677428 TTCTTCT
1 TTCTTCT
1677435 TTCTTC
1 TTCTTC
1677441 ACGTTTTAAT
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
7 26 1.00
ACGTcount: A:0.00, C:0.26, G:0.00, T:0.74
Consensus pattern (7 bp):
TTCTTCT
Found at i:1678697 original size:128 final size:131
Alignment explanation
Indices: 1678498--1678859 Score: 332
Period size: 140 Copynumber: 2.7 Consensus size: 131
1678488 AATAATTTTC
* * *
1678498 TTATTAAAATTAAAATATTGAGTAATTTTA-TT-CT-TTTTCTTATTTATCTTG-AACTCCTTAT
1 TTATT-AAATTAAAATATTGACTAATTTTATTTATTATTTTCTTATTAATCTTGAAAC-CCTTAT
* * *
1678559 TAACGCAAACTTTTTTAATTTATATATTTTTGAACTAATTTTTAAACT-A-T-TTT-T-AATGAA
64 TAATGTAAACTTTTTTAATTTATATATTTTTGAACTAACTTTTAAACTAAGTATTTATAAATG-A
1678619 ATTT
128 ATTT
*
1678623 TTATTAAATTAAAATATTGACTAATCTTTATTTATTATTTTCTTATTAACCTTGAAACCCTTATT
1 TTATTAAATTAAAATATTGACTAAT-TTTATTTATTATTTTCTTATTAATCTTGAAACCCTTATT
* * *
1678688 AATGTAAACTTTTTTAATAGATATATAATTTTTATTATTAACTAACTTTTAATCTAAGTATTTAT
65 AATGTAAACTTTTTTAAT---T-TAT-A-TATT-TT-TGAACTAACTTTTAAACTAAGTATTTAT
*
1678753 AAATGATTTT
122 AAATGAATTT
* * * **
1678763 TTATTAAATTAAAATA-TGAATTAATTTCTATTTATTATTTTCTTACTAATTTTGAAGTCCTTAT
1 TTATTAAATTAAAATATTG-ACTAATTT-TATTTATTATTTTCTTATTAATCTTGAAACCCTTAT
* *
1678827 TAATCTAAA-TTTTCCTTAATTTATTTATCTTTT
64 TAATGTAAACTTTT--TTAATTTATATAT-TTTT
1678860 TATTAATATT
Statistics
Matches: 194, Mismatches: 20, Indels: 37
0.77 0.08 0.15
Matches are distributed among these distances:
124 19 0.10
125 9 0.05
126 2 0.01
127 1 0.01
128 38 0.20
129 3 0.02
131 1 0.01
132 3 0.02
133 1 0.01
134 4 0.02
135 6 0.03
136 16 0.08
137 4 0.02
138 2 0.01
139 11 0.06
140 65 0.34
141 9 0.05
ACGTcount: A:0.34, C:0.09, G:0.04, T:0.53
Consensus pattern (131 bp):
TTATTAAATTAAAATATTGACTAATTTTATTTATTATTTTCTTATTAATCTTGAAACCCTTATTA
ATGTAAACTTTTTTAATTTATATATTTTTGAACTAACTTTTAAACTAAGTATTTATAAATGAATT
T
Found at i:1678860 original size:140 final size:141
Alignment explanation
Indices: 1678620--1678910 Score: 342
Period size: 140 Copynumber: 2.1 Consensus size: 141
1678610 TTTAATGAAA
*
1678620 TTTTTATTAAATTAAAATATTGACTAATCTTTATTTATTATTTTCTTATTAACCTTGAAACCCTT
1 TTTTTATTAAATTAAAATATTGACTAATCTTTATTTATTATTTTCTTACTAACCTTGAAACCCTT
*
1678685 ATTAATGTAAACTTTTTTAATAGATATATAATTTTTA-T-TATTAACTAACTTTTAATCTAAGTA
66 ATTAATCTAAACTTTTTTAATAGATATATAATTTTTATTATATTAA-TAACTTTTAATCTAAGTA
1678748 TTTATAAATGAT
130 TTTATAAATGAT
* ** **
1678760 TTTTTATTAAATTAAAATA-TGAATTAAT-TTCTATTTATTATTTTCTTACTAATTTTGAAGTCC
1 TTTTTATTAAATTAAAATATTG-ACTAATCTT-TATTTATTATTTTCTTACTAACCTTGAAACCC
** * * * *
1678823 TTATTAATCTAAA-TTTTCCTTAATTTATTTAT-CTTTTTATTAATATTAATTATTTTTAATCTA
64 TTATTAATCTAAACTTTT--TTAATAGATATATAATTTTTATT-ATATTAATAACTTTTAATCTA
* * *
1678886 AGTTTTTATTAATTAT
126 AGTATTTATAAATGAT
1678902 TTTTTATTA
1 TTTTTATTA
1678911 TGATAAGATA
Statistics
Matches: 128, Mismatches: 16, Indels: 12
0.82 0.10 0.08
Matches are distributed among these distances:
139 8 0.06
140 69 0.54
141 11 0.09
142 34 0.27
143 6 0.05
ACGTcount: A:0.34, C:0.08, G:0.03, T:0.55
Consensus pattern (141 bp):
TTTTTATTAAATTAAAATATTGACTAATCTTTATTTATTATTTTCTTACTAACCTTGAAACCCTT
ATTAATCTAAACTTTTTTAATAGATATATAATTTTTATTATATTAATAACTTTTAATCTAAGTAT
TTATAAATGAT
Found at i:1679828 original size:31 final size:31
Alignment explanation
Indices: 1679793--1679855 Score: 99
Period size: 31 Copynumber: 2.0 Consensus size: 31
1679783 TAATAAAAAT
* * *
1679793 AATATTTTTAAAAAATGTATAAAATAATTTA
1 AATATTATTAAAAAATATAAAAAATAATTTA
1679824 AATATTATTAAAAAATATAAAAAATAATTTA
1 AATATTATTAAAAAATATAAAAAATAATTTA
1679855 A
1 A
1679856 CAATATACTC
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
31 29 1.00
ACGTcount: A:0.60, C:0.00, G:0.02, T:0.38
Consensus pattern (31 bp):
AATATTATTAAAAAATATAAAAAATAATTTA
Found at i:1680203 original size:18 final size:16
Alignment explanation
Indices: 1680146--1680207 Score: 56
Period size: 18 Copynumber: 3.8 Consensus size: 16
1680136 AATTATACAT
*
1680146 ATTAAATAATAAA-TA
1 ATTAAAAAATAAATTA
* *
1680161 ATTAAAAATTATATTA
1 ATTAAAAAATAAATTA
1680177 ATGTTAAAAAATAAATTA
1 A--TTAAAAAATAAATTA
1680195 A-TATAAAAATAAA
1 ATTA-AAAAATAAA
1680208 AAAATAAAGG
Statistics
Matches: 38, Mismatches: 5, Indels: 7
0.76 0.10 0.14
Matches are distributed among these distances:
15 12 0.32
16 12 0.32
18 14 0.37
ACGTcount: A:0.65, C:0.00, G:0.02, T:0.34
Consensus pattern (16 bp):
ATTAAAAAATAAATTA
Found at i:1680204 original size:16 final size:15
Alignment explanation
Indices: 1680146--1680207 Score: 54
Period size: 16 Copynumber: 3.8 Consensus size: 15
1680136 AATTATACAT
1680146 ATTAAATAATAAA-TA
1 ATTAAA-AATAAATTA
*
1680161 ATTAAAAATTATATTA
1 ATTAAAAA-TAAATTA
1680177 ATGTTAAAAAATAAATTA
1 A--TT-AAAAATAAATTA
1680195 ATATAAAAATAAA
1 AT-TAAAAATAAA
1680208 AAAATAAAGG
Statistics
Matches: 39, Mismatches: 2, Indels: 11
0.75 0.04 0.21
Matches are distributed among these distances:
14 2 0.05
15 9 0.23
16 13 0.33
17 1 0.03
18 9 0.23
19 5 0.13
ACGTcount: A:0.65, C:0.00, G:0.02, T:0.34
Consensus pattern (15 bp):
ATTAAAAATAAATTA
Found at i:1683599 original size:21 final size:22
Alignment explanation
Indices: 1683562--1683607 Score: 76
Period size: 21 Copynumber: 2.1 Consensus size: 22
1683552 AAAGCATCTT
1683562 TGCTAAAAGTACATGTATGATG
1 TGCTAAAAGTACATGTATGATG
*
1683584 TGCTAAAA-TGCATGTATGATG
1 TGCTAAAAGTACATGTATGATG
1683605 TGC
1 TGC
1683608 CAAAGTATCT
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
21 15 0.65
22 8 0.35
ACGTcount: A:0.33, C:0.11, G:0.24, T:0.33
Consensus pattern (22 bp):
TGCTAAAAGTACATGTATGATG
Found at i:1684190 original size:4 final size:4
Alignment explanation
Indices: 1684181--1684207 Score: 54
Period size: 4 Copynumber: 6.8 Consensus size: 4
1684171 AATTTATATA
1684181 AAAT AAAT AAAT AAAT AAAT AAAT AAA
1 AAAT AAAT AAAT AAAT AAAT AAAT AAA
1684208 AATGAGAATT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 23 1.00
ACGTcount: A:0.78, C:0.00, G:0.00, T:0.22
Consensus pattern (4 bp):
AAAT
Found at i:1685295 original size:13 final size:13
Alignment explanation
Indices: 1685277--1685302 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1685267 CAATTTTTTG
1685277 TGTATCGATACAT
1 TGTATCGATACAT
1685290 TGTATCGATACAT
1 TGTATCGATACAT
1685303 ACTTGCTGTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:1686042 original size:21 final size:21
Alignment explanation
Indices: 1686001--1686044 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
1685991 CTCTCCTTTA
* *
1686001 TCTCCCCCGTTTATTAATAAT
1 TCTCCCCCGTTAATCAATAAT
1686022 TCTCCCCC-TTAATCAAGTAAT
1 TCTCCCCCGTTAATCAA-TAAT
1686043 TC
1 TC
1686045 ATATCAAAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
20 6 0.30
21 14 0.70
ACGTcount: A:0.25, C:0.32, G:0.05, T:0.39
Consensus pattern (21 bp):
TCTCCCCCGTTAATCAATAAT
Found at i:1687867 original size:13 final size:13
Alignment explanation
Indices: 1687849--1687874 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1687839 ATAATCACCC
1687849 TGTATCGATACAA
1 TGTATCGATACAA
1687862 TGTATCGATACAA
1 TGTATCGATACAA
1687875 AGAAAAAATG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:1689964 original size:15 final size:15
Alignment explanation
Indices: 1689944--1689974 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
1689934 ATTTCGTTTG
*
1689944 GAGCTTCTTCATTTT
1 GAGCTTCCTCATTTT
1689959 GAGCTTCCTCATTTT
1 GAGCTTCCTCATTTT
1689974 G
1 G
1689975 GACATTTTTA
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:0.13, C:0.23, G:0.16, T:0.48
Consensus pattern (15 bp):
GAGCTTCCTCATTTT
Found at i:1691805 original size:21 final size:21
Alignment explanation
Indices: 1691776--1691820 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 21
1691766 AAGTTTTCAT
*
1691776 TTTTCTTAGCTAAC-TCATTA
1 TTTTCTTAGCCAACTTCATTA
*
1691796 TTTTCATTAGCCAACTTCTTTA
1 TTTTC-TTAGCCAACTTCATTA
1691818 TTT
1 TTT
1691821 CAACTTGCAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 5 0.24
21 8 0.38
22 8 0.38
ACGTcount: A:0.22, C:0.20, G:0.04, T:0.53
Consensus pattern (21 bp):
TTTTCTTAGCCAACTTCATTA
Found at i:1694056 original size:13 final size:13
Alignment explanation
Indices: 1694038--1694063 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1694028 CAATTTTTTG
1694038 TGTATCGATACAT
1 TGTATCGATACAT
1694051 TGTATCGATACAT
1 TGTATCGATACAT
1694064 ACTTGCTGTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:1694929 original size:25 final size:25
Alignment explanation
Indices: 1694893--1694942 Score: 66
Period size: 25 Copynumber: 2.0 Consensus size: 25
1694883 TTTTTTAAAA
*
1694893 AAAAAATGATAAAAATG-ATTTTTT
1 AAAAAATAATAAAAATGTATTTTTT
*
1694917 AAAAAATAAATAAATATGTATTTTTT
1 AAAAAAT-AATAAAAATGTATTTTTT
1694943 TAATTATAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
24 7 0.32
25 8 0.36
26 7 0.32
ACGTcount: A:0.54, C:0.00, G:0.06, T:0.40
Consensus pattern (25 bp):
AAAAAATAATAAAAATGTATTTTTT
Found at i:1696883 original size:19 final size:20
Alignment explanation
Indices: 1696859--1696911 Score: 72
Period size: 19 Copynumber: 2.7 Consensus size: 20
1696849 ATCGATAAAA
**
1696859 TGTATCGATACATGTTC-AT
1 TGTATCGATACATGGACAAT
1696878 TGTATCGATACATGGACAAT
1 TGTATCGATACATGGACAAT
*
1696898 TGCATCGATACATG
1 TGTATCGATACATG
1696912 AAACTGGCAG
Statistics
Matches: 30, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
19 15 0.50
20 15 0.50
ACGTcount: A:0.30, C:0.17, G:0.19, T:0.34
Consensus pattern (20 bp):
TGTATCGATACATGGACAAT
Found at i:1696904 original size:20 final size:19
Alignment explanation
Indices: 1696862--1696911 Score: 64
Period size: 20 Copynumber: 2.6 Consensus size: 19
1696852 GATAAAATGT
** *
1696862 ATCGATACATGTTCATTGT
1 ATCGATACATGGACATTGC
1696881 ATCGATACATGGACAATTGC
1 ATCGATACATGGAC-ATTGC
1696901 ATCGATACATG
1 ATCGATACATG
1696912 AAACTGGCAG
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
19 12 0.44
20 15 0.56
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Consensus pattern (19 bp):
ATCGATACATGGACATTGC
Found at i:1696998 original size:33 final size:33
Alignment explanation
Indices: 1696941--1697003 Score: 92
Period size: 33 Copynumber: 1.9 Consensus size: 33
1696931 TACCACTGTT
*
1696941 TGTATCGATACATGGTACATTGTATCGATATAA
1 TGTATCGATACATGATACATTGTATCGATATAA
*
1696974 TGTATCGATACATGATGGCA-TGTATCGATA
1 TGTATCGATACATGAT-ACATTGTATCGATA
1697004 CATTGCTTCA
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
33 25 0.93
34 2 0.07
ACGTcount: A:0.32, C:0.13, G:0.21, T:0.35
Consensus pattern (33 bp):
TGTATCGATACATGATACATTGTATCGATATAA
Found at i:1703238 original size:22 final size:21
Alignment explanation
Indices: 1703200--1703240 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
1703190 ATCAAATCTT
* *
1703200 CTTCAAATTTCTTATTTTTCA
1 CTTCAAAATACTTATTTTTCA
1703221 CTTCAAAATACTTCATTTTT
1 CTTCAAAATACTT-ATTTTT
1703241 TTATCAAAAT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 11 0.65
22 6 0.35
ACGTcount: A:0.27, C:0.20, G:0.00, T:0.54
Consensus pattern (21 bp):
CTTCAAAATACTTATTTTTCA
Found at i:1708823 original size:25 final size:25
Alignment explanation
Indices: 1708768--1708823 Score: 62
Period size: 25 Copynumber: 2.3 Consensus size: 25
1708758 TTTATGATAA
*
1708768 TTAATTTT--AATTTTAATTTTCTC
1 TTAATTTTAAAATTTTAATTTTATC
* *
1708791 TTAATTTTAAAATTTTTATTTTATT
1 TTAATTTTAAAATTTTAATTTTATC
*
1708816 TTATTTTT
1 TTAATTTT
1708824 GAACTAGTTT
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
23 8 0.30
25 19 0.70
ACGTcount: A:0.27, C:0.04, G:0.00, T:0.70
Consensus pattern (25 bp):
TTAATTTTAAAATTTTAATTTTATC
Found at i:1709964 original size:12 final size:13
Alignment explanation
Indices: 1709941--1709969 Score: 51
Period size: 12 Copynumber: 2.3 Consensus size: 13
1709931 GATTTTGATA
1709941 AATTTAGTATTTT
1 AATTTAGTATTTT
1709954 AATTT-GTATTTT
1 AATTTAGTATTTT
1709966 AATT
1 AATT
1709970 ATTTAGGAAC
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 11 0.69
13 5 0.31
ACGTcount: A:0.31, C:0.00, G:0.07, T:0.62
Consensus pattern (13 bp):
AATTTAGTATTTT
Found at i:1714344 original size:30 final size:31
Alignment explanation
Indices: 1714291--1714354 Score: 94
Period size: 30 Copynumber: 2.1 Consensus size: 31
1714281 TAGAATTGTT
*
1714291 TTTCATGCATTTGGATTTTATTTAAAGACCA
1 TTTCATGCATTTGGATATTATTTAAAGACCA
* *
1714322 TTTCATGCATTT-TATATTATTTAGAGACCA
1 TTTCATGCATTTGGATATTATTTAAAGACCA
1714352 TTT
1 TTT
1714355 TGCACACTTG
Statistics
Matches: 30, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
30 18 0.60
31 12 0.40
ACGTcount: A:0.28, C:0.12, G:0.11, T:0.48
Consensus pattern (31 bp):
TTTCATGCATTTGGATATTATTTAAAGACCA
Found at i:1718551 original size:33 final size:33
Alignment explanation
Indices: 1718514--1718612 Score: 155
Period size: 32 Copynumber: 3.0 Consensus size: 33
1718504 AGTAGCTTAA
1718514 ATTGTATCGATACAAAAAAATATGTATCGATAC
1 ATTGTATCGATACAAAAAAATATGTATCGATAC
1718547 ATTGTATCGATAC-AAAAAATATGTATCGATAC
1 ATTGTATCGATACAAAAAAATATGTATCGATAC
* ***
1718579 ATTGTATCGATACAACACTTTATGTATCGATAC
1 ATTGTATCGATACAAAAAAATATGTATCGATAC
1718612 A
1 A
1718613 AATCATTGAA
Statistics
Matches: 61, Mismatches: 4, Indels: 2
0.91 0.06 0.03
Matches are distributed among these distances:
32 32 0.52
33 29 0.48
ACGTcount: A:0.41, C:0.14, G:0.12, T:0.32
Consensus pattern (33 bp):
ATTGTATCGATACAAAAAAATATGTATCGATAC
Found at i:1718554 original size:13 final size:13
Alignment explanation
Indices: 1718536--1718592 Score: 60
Period size: 13 Copynumber: 3.9 Consensus size: 13
1718526 CAAAAAAATA
1718536 TGTATCGATACAT
1 TGTATCGATACAT
1718549 TGTATCGATACAAAAAAT
1 TGTATCGATAC-----AT
1718567 ATGTATCGATACAT
1 -TGTATCGATACAT
1718581 TGTATCGATACA
1 TGTATCGATACA
1718593 ACACTTTATG
Statistics
Matches: 38, Mismatches: 0, Indels: 12
0.76 0.00 0.24
Matches are distributed among these distances:
13 23 0.61
14 2 0.05
18 2 0.05
19 11 0.29
ACGTcount: A:0.39, C:0.14, G:0.14, T:0.33
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:1718573 original size:19 final size:18
Alignment explanation
Indices: 1718512--1718579 Score: 74
Period size: 19 Copynumber: 3.9 Consensus size: 18
1718502 GCAGTAGCTT
1718512 AAATTGTATCGATACAAAA
1 AAATTGTATCGATAC-AAA
1718531 AAATATGTATCGATAC---
1 AAAT-TGTATCGATACAAA
1718547 --ATTGTATCGATACAAA
1 AAATTGTATCGATACAAA
1718563 AAATATGTATCGATACA
1 AAAT-TGTATCGATACA
1718580 TTGTATCGAT
Statistics
Matches: 42, Mismatches: 0, Indels: 14
0.75 0.00 0.25
Matches are distributed among these distances:
13 11 0.26
14 2 0.05
18 2 0.05
19 16 0.38
20 11 0.26
ACGTcount: A:0.47, C:0.12, G:0.12, T:0.29
Consensus pattern (18 bp):
AAATTGTATCGATACAAA
Found at i:1719445 original size:29 final size:30
Alignment explanation
Indices: 1719366--1719445 Score: 110
Period size: 29 Copynumber: 2.7 Consensus size: 30
1719356 AAGCTTAAGA
*
1719366 AATTAAAAGTCAACTAAAA-AATGAAAAAG
1 AATTAAAAGTCAACTAAAACACTGAAAAAG
* *
1719395 AATTAAAAGCCAACTAAAACACT-AAAAGG
1 AATTAAAAGTCAACTAAAACACTGAAAAAG
*
1719424 AATTAAAAGTTAACTAAAACAC
1 AATTAAAAGTCAACTAAAACAC
1719446 CATAACTTCC
Statistics
Matches: 45, Mismatches: 5, Indels: 2
0.87 0.10 0.04
Matches are distributed among these distances:
29 43 0.96
30 2 0.04
ACGTcount: A:0.61, C:0.12, G:0.09, T:0.17
Consensus pattern (30 bp):
AATTAAAAGTCAACTAAAACACTGAAAAAG
Found at i:1721502 original size:16 final size:15
Alignment explanation
Indices: 1721477--1721506 Score: 51
Period size: 16 Copynumber: 1.9 Consensus size: 15
1721467 TGAAAAAGAA
1721477 TTTTTTATTATTTTC
1 TTTTTTATTATTTTC
1721492 TTTTGTTATTATTTT
1 TTTT-TTATTATTTT
1721507 TTATTTTTTT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 4 0.29
16 10 0.71
ACGTcount: A:0.13, C:0.03, G:0.03, T:0.80
Consensus pattern (15 bp):
TTTTTTATTATTTTC
Found at i:1722720 original size:16 final size:17
Alignment explanation
Indices: 1722701--1722734 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
1722691 TTGCTTTCAG
1722701 TTGTTG-CTGCTGGAGT
1 TTGTTGTCTGCTGGAGT
*
1722717 TTGTTGTTTGCTGGAGT
1 TTGTTGTCTGCTGGAGT
1722734 T
1 T
1722735 GCTACTGGTG
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 6 0.38
17 10 0.62
ACGTcount: A:0.06, C:0.09, G:0.35, T:0.50
Consensus pattern (17 bp):
TTGTTGTCTGCTGGAGT
Found at i:1723104 original size:138 final size:138
Alignment explanation
Indices: 1722948--1723236 Score: 535
Period size: 138 Copynumber: 2.1 Consensus size: 138
1722938 CAGCCCCCCA
* *
1722948 CATG-TTGTATGCTTCATGATTTTCTCCATGTGGCCTCCAATTCATTTTGTTTACCATATTTTTC
1 CATGATTGCATGCTTCATGATTTTCTCCATGTGGCCTCCAATTCATTTTGTTTACCATATGTTTC
1723012 TGCATGATTTGCATCTCCCATCACTTTTTCATTTGCACGTTGCTTTGCTTTCTTTCCATTTGCTT
66 TGCATGATTTGCATCTCCCATCACTTTTTCATTTGCACGTTGCTTTGCTTTCTTTCCATTTGCTT
1723077 GTGTTCCT
131 GTGTTCCT
*
1723085 CATGATTGCATGCTTCATGATTTTCTCCATGTGGCCTCCAATTCATTTTGTTTGCCATATGTTTC
1 CATGATTGCATGCTTCATGATTTTCTCCATGTGGCCTCCAATTCATTTTGTTTACCATATGTTTC
*
1723150 TTCATGATTTGCATCTCCCATCACTTTTTCATTTGCACGTTGCTTTGCTTTCTTTCCATTTGCTT
66 TGCATGATTTGCATCTCCCATCACTTTTTCATTTGCACGTTGCTTTGCTTTCTTTCCATTTGCTT
1723215 GTGTTCCT
131 GTGTTCCT
1723223 CATGATTGCATGCT
1 CATGATTGCATGCT
1723237 ACATTGCATT
Statistics
Matches: 147, Mismatches: 4, Indels: 1
0.97 0.03 0.01
Matches are distributed among these distances:
137 4 0.03
138 143 0.97
ACGTcount: A:0.14, C:0.24, G:0.14, T:0.48
Consensus pattern (138 bp):
CATGATTGCATGCTTCATGATTTTCTCCATGTGGCCTCCAATTCATTTTGTTTACCATATGTTTC
TGCATGATTTGCATCTCCCATCACTTTTTCATTTGCACGTTGCTTTGCTTTCTTTCCATTTGCTT
GTGTTCCT
Found at i:1725029 original size:125 final size:125
Alignment explanation
Indices: 1724137--1726606 Score: 1848
Period size: 125 Copynumber: 19.6 Consensus size: 125
1724127 TAAATGAGGT
* * * * * * * * *
1724137 AGTCTTCAGGGTTAAATCTGACAAGCAGACTGAGGGATAGAAAAGTCTCCAAGGTCAAAGCCAAC
1 AGTCTCCAGGGTCAAAGCCGACAGGCAGACT-AGGG-TAGGAAAGTCTTCAGGGTCAAAGCCGAC
* * * * * * * *
1724202 AGGTAGACTTTAGATGATAGGAAAGTCTCCAAGGTTAAAGCCGATAGGCAGACAAAGGGCAAGAA
64 AGGCAGAC--TA-AGGGTAAGAAAGTCTCCAAGGTCAAAGCCGACAGGCAGACTAAGGG-AAGGA
1724267 A
125 A
* * * * * *
1724268 AGTCTCCAGGGTCAAAGTCGAAAGGCAGACTAAGAGATAGGAAAGTCTTCAAGGTCAAAACTGAC
1 AGTCTCCAGGGTCAAAGCCGACAGGCAGACT-AG-GGTAGGAAAGTCTTCAGGGTCAAAGCCGAC
* * * * *
1724333 AGGCAGACTAAGGGATAGGAAAGTCTCCAAGGTAAAAGCCAACAGGCAGACTAAGGGATGAAA
64 AGGCAGACTAAGGG-TAAGAAAGTCTCCAAGGTCAAAGCCGACAGGCAGACTAAGGGAAGGAA
* * * * * * * * *
1724396 AGTCTCTAGGGTCCCAA-CCGACAAGCAGACTAAGGGAATGAAAGTCTCCAAGGTTAAAGCCAAC
1 AGTCTCCAGGGT-CAAAGCCGACAGGCAGACT-AGGGTAGGAAAGTCTTCAGGGTCAAAGCCGAC
* * * * * * *
1724460 AGGCAGACTAAGGG-AATGAAAATCTTCAAGGTCAAAACCGACAAGCAGACTAAAGCAATGAA
64 AGGCAGACTAAGGGTAA-GAAAGTCTCCAAGGTCAAAGCCGACAGGCAGACTAAGGGAAGGAA
* * ** * *
1724522 AGTCTCCAAGATCAAAGCCGACAGGCAGACTAAGGAAATGAAAGT-TTCTAGGGTCAAAGCCGAT
1 AGTCTCCAGGGTCAAAGCCGACAGGCAGACT-AGGGTAGGAAAGTCTTC-AGGGTCAAAGCCGAC
* * * * *
1724586 AGGCAGACTGAGGGTAAAAAAGTCTCTAAGGTCAAAGCCGACAGGCAGACTAAAGGTAGGAA
64 AGGCAGACTAAGGGTAAGAAAGTCTCCAAGGTCAAAGCCGACAGGCAGACTAAGGGAAGGAA
* * * * * * *
1724648 AGTCTCTAGGGTCAAAACCGAAAGGCAGACTAAGGGAAAGCAAGTC-TCTAGGGTCAAAACCGAC
1 AGTCTCCAGGGTCAAAGCCGACAGGCAGACT-AGGGTAGGAAAGTCTTC-AGGGTCAAAGCCGAC
* * * * *
1724712 AGGCAGACTAAGGG-AAGAAAAGTCTCTAGGGTCAAACCCAATAGGCAGACTAAGGGAAGGAA
64 AGGCAGACTAAGGGTAAG-AAAGTCTCCAAGGTCAAAGCCGACAGGCAGACTAAGGGAAGGAA
* * * *
1724774 AGCCTCCAGGGTCAAAGCCGACAGGCAGACTAAGGGGAATGAAAGTC-TCTAGGGTCAAAGCTGA
1 AGTCTCCAGGGTCAAAGCCGACAGGCAGACT-A-GGGTAGGAAAGTCTTC-AGGGTCAAAGCCGA
* * * ** * *
1724838 TAGACAGACTAAGAG-AACGAAAAGTCTCCAAGGTCAAAATCGACAGGCAGACTAAGAGAAAGAA
63 CAGGCAGACTAAGGGTAA-G-AAAGTCTCCAAGGTCAAAGCCGACAGGCAGACTAAGGGAAGGAA
* * * *
1724902 AGTCTCCA-GGTCAAAGCAGACAGGCAGACTGAAGGTAGGAAAGTCTTCAAGGTCAAAGCTGACA
1 AGTCTCCAGGGTCAAAGCCGACAGGCAGACT-AGGGTAGGAAAGTCTTCAGGGTCAAAGCCGACA
* * * * * * * *
1724966 GGTAGACTGAGGGTAAGAAAGTCTCAAATGTCAAAGCCGACAAGCAAACTGAGGGTAGGAA
65 GGCAGACTAAGGGTAAGAAAGTCTCCAAGGTCAAAGCCGACAGGCAGACTAAGGGAAGGAA
* ** *
1725027 AGTCTCTAAAGTCAAAGCCGACAAGAGGTAGACTGAGGGTA-GAGAAGTCTTCAGGGTCAAAGCC
1 AGTCTCCAGGGTCAAAGCCGAC---AGGCAGACT-AGGGTAGGA-AAGTCTTCAGGGTCAAAGCC
* * * * * * * * *
1725091 GACAGGCAGACTTAGGGTAGGGAAGTCTCTAGGGTTAAAGCAGATAGGCAGACTTAGGGAAGG-A
61 GACAGGCAGACTAAGGGTAAGAAAGTCTCCAAGGTCAAAGCCGACAGGCAGACTAAGGGAAGGAA
** * * * * * *
1725155 AGTCTTTAGGGTCAAGGCCGACATGCAAACTAAGGGTAGGGAAGTCTTCAAGGTCAAAGCCGATA
1 AGTCTCCAGGGTCAAAGCCGACAGGCAGACT-AGGGTAGGAAAGTCTTCAGGGTCAAAGCCGACA
* * * * * *
1725220 GGCAAACTAAGGGTAGGAAAGTCTTCAGGGTCAAAGCCGACAGGCAGACTTAGGGAACGAA
65 GGCAGACTAAGGGTAAGAAAGTCTCCAAGGTCAAAGCCGACAGGCAGACTAAGGGAAGGAA
* * * * * * * * *
1725281 AGTCTCTAGGGTCAAAACTGACAAGCATACTAGGGGTAGTAAAGTCTCCAGGGTCAAAGTCGATA
1 AGTCTCCAGGGTCAAAGCCGACAGGCAGACTA-GGGTAGGAAAGTCTTCAGGGTCAAAGCCGACA
* * * * *** * * *
1725346 AGCAGACTTAGAG-AACGAAAGTCTCCCGAGGTCAAAATTGACAGGCAAACTAAGGGTAGGGA
65 GGCAGACTAAGGGTAA-GAAAGTCT-CCAAGGTCAAAGCCGACAGGCAGACTAAGGGAAGGAA
* * * * * * * * *
1725408 ACTCTCCTGGGTCAAAGCTGACAGGCAAACTTAGGG-AAGCAAGTCTCCAAGGTCAAAGCCGATA
1 AGTCTCCAGGGTCAAAGCCGACAGGCAGAC-TAGGGTAGGAAAGTCTTCAGGGTCAAAGCCGACA
* * * * * * *
1725472 GGCAGACTAAGGGTAGGGAAGTTTCCAAGGTCAAAGTCGATAGACAGACTTAGGGAAGGAA
65 GGCAGACTAAGGGTAAGAAAGTCTCCAAGGTCAAAGCCGACAGGCAGACTAAGGGAAGGAA
* * * * * * * *
1725533 AGTCTCGAGGGTCAAAACTGACAAGCAGACTGGGGTA-GAGAAGTCTCCAGGGTCAAAGCTGATA
1 AGTCTCCAGGGTCAAAGCCGACAGGCAGACTAGGGTAGGA-AAGTCTTCAGGGTCAAAGCCGACA
* * * ** * * * *
1725597 GGCAGACTTAGGG-AAGAAAAGTCTCCTGAGGTCAAAACTAATAGGCAAACTAAGGGTAGGGA
65 GGCAGACTAAGGGTAAG-AAAGTCTCC-AAGGTCAAAGCCGACAGGCAGACTAAGGGAAGGAA
* * * * * * *
1725659 ACTCTCCTGGGTCAAAGCCGACAGGCAAACTTAGGGAAGG-AAGTC-TCTGGGGTCAAAGTCGAT
1 AGTCTCCAGGGTCAAAGCCGACAGGCAGAC-TAGGGTAGGAAAGTCTTC-AGGGTCAAAGCCGAC
* * * * * *
1725722 AGGCAGACTAAGGGTAGGGAAGTTTTCAAGGTCAAAGCCGATAGGTAGACTTAA-GGAAGGAA
64 AGGCAGACTAAGGGTAAGAAAGTCTCCAAGGTCAAAGCCGACAGGCAGAC-TAAGGGAAGGAA
* *** * * *
1725784 AGTCTCGAGGGTCAAAATTGACAAGCAGACTGGGGTA-GAGAAGTCTGCAGGGTCAAAGCCGACA
1 AGTCTCCAGGGTCAAAGCCGACAGGCAGACTAGGGTAGGA-AAGTCTTCAGGGTCAAAGCCGACA
* *
1725848 GGCAGACTAAGGGTAA-AAAGTCTCCAGGGTCAAAGCCGACAGGCAGACTAAGGGTAGGAA
65 GGCAGACTAAGGGTAAGAAAGTCTCCAAGGTCAAAGCCGACAGGCAGACTAAGGGAAGGAA
* * * * * *
1725908 AGTCTCCAGGGTCAAAGTCGACAGGAAGACTTAGGGTAGGGAAGTCTCCAAGGTCAAAGCTGACA
1 AGTCTCCAGGGTCAAAGCCGACAGGCAGAC-TAGGGTAGGAAAGTCTTCAGGGTCAAAGCCGACA
* * * * * * * * * * * *
1725973 GGAAAACTTAGGG-AAGGAAGTGTCCAGGGTTAAAGCCAACAAGCAAACTAAGGGTAGGGA
65 GGCAGACTAAGGGTAAGAAAGTCTCCAAGGTCAAAGCCGACAGGCAGACTAAGGGAAGGAA
* ** * ** *
1726033 AGTCTCCAGGGTCAAAGCCGACAGGCAGACTAAGGGAAAAAAAGTC-TCTGGGGTCAAAGCTAAT
1 AGTCTCCAGGGTCAAAGCCGACAGGCAGACT-AGGGTAGGAAAGTCTTC-AGGGTCAAAGCCGAC
* * * *
1726097 AAGCAGACTAAGGG--AGAAAAGTCTCCAAGATCAAAGCCGACAGGCAGACTGAGGGTAGGAA
64 AGGCAGACTAAGGGTAAG-AAAGTCTCCAAGGTCAAAGCCGACAGGCAGACTAAGGGAAGGAA
* * * * ** * * **
1726158 AGTCTCTAAGGTCAAAGTCGACAGGCAGACTGAGGGGAAAAAAGTCTCCAAGGTCAAAGCCGATG
1 AGTCTCCAGGGTCAAAGCCGACAGGCAGACT-AGGGTAGGAAAGTCTTCAGGGTCAAAGCCGACA
* * * * * *
1726223 GGCAGACTAAGGG-AAGGGAAGTTTCCATGGTCAAAG-CGATAGGCAGACTGAGGGAAAGAA
65 GGCAGACTAAGGGTAA-GAAAGTCTCCAAGGTCAAAGCCGACAGGCAGACTAAGGGAAGGAA
* * * * *
1726283 AGTCTCCAAGGTCAAAGCCGACAGGCAGACTGAGGGTAGGGAAGTC-TCTAGGGTTAATGCCGAT
1 AGTCTCCAGGGTCAAAGCCGACAGGCAGACT-AGGGTAGGAAAGTCTTC-AGGGTCAAAGCCGAC
** * * * * * * *
1726347 AAACAGACTGAGGGTAGGAAAGTCTCCAGGGTCAAAGCCAACAAGCAGACTAAGGGTAGGGA
64 AGGCAGACTAAGGGTAAGAAAGTCTCCAAGGTCAAAGCCGACAGGCAGACTAAGGGAAGGAA
* * * * * * *
1726409 AGTCTCCAAGGTCAAAGTCGATAGGCAAATTTAGGGAAGG-AAGTCTCCAGGGTCAAAGCCGACA
1 AGTCTCCAGGGTCAAAGCCGACAGGCAGA-CTAGGGTAGGAAAGTCTTCAGGGTCAAAGCCGACA
* * * * * * *
1726473 GGCAGACTTAGGGTAGGGAAGTCT-CTAGTGTCAAAGCCGACAGGCAGACTTAGGGTAGGGA
65 GGCAGACTAAGGGTAAGAAAGTCTCCAAG-GTCAAAGCCGACAGGCAGACTAAGGGAAGGAA
* * * *
1726534 AGTCTCTAGGGTCAAAGCCGACAGGCAGACTTAGGGTGGGGAAGTC-TCAAAGGTCAAAGCCGAC
1 AGTCTCCAGGGTCAAAGCCGACAGGCAGAC-TAGGGTAGGAAAGTCTTC-AGGGTCAAAGCCGAC
*
1726598 AAGCAGACT
64 AGGCAGACT
1726607 TAGAGAAGGA
Statistics
Matches: 1872, Mismatches: 411, Indels: 117
0.78 0.17 0.05
Matches are distributed among these distances:
123 4 0.00
124 79 0.04
125 738 0.39
126 602 0.32
127 167 0.09
128 101 0.05
129 124 0.07
131 56 0.03
132 1 0.00
ACGTcount: A:0.36, C:0.18, G:0.30, T:0.15
Consensus pattern (125 bp):
AGTCTCCAGGGTCAAAGCCGACAGGCAGACTAGGGTAGGAAAGTCTTCAGGGTCAAAGCCGACAG
GCAGACTAAGGGTAAGAAAGTCTCCAAGGTCAAAGCCGACAGGCAGACTAAGGGAAGGAA
Found at i:1726607 original size:42 final size:42
Alignment explanation
Indices: 1724137--1726609 Score: 1716
Period size: 42 Copynumber: 58.8 Consensus size: 42
1724127 TAAATGAGGT
* * * * * * **
1724137 AGTCTTCAGGGTTAAATCTGACAAGCAGACTGAGGGATAGAAA
1 AGTCTCCAGGGTCAAAGCCGACAGGCAGACTTAGGG-TAGGGA
* * * * *
1724180 AGTCTCCAAGGTCAAAGCCAACAGGTAGACTTTAGATGATAGGAA
1 AGTCTCCAGGGTCAAAGCCGACAGGCAGAC-TTAG--GGTAGGGA
* * * ** * **
1724225 AGTCTCCAAGGTTAAAGCCGATAGGCAGACAAAGGGCAAGAAA
1 AGTCTCCAGGGTCAAAGCCGACAGGCAGACTTAGGG-TAGGGA
* * * * *
1724268 AGTCTCCAGGGTCAAAGTCGAAAGGCAGACTAAGAGATAGGAA
1 AGTCTCCAGGGTCAAAGCCGACAGGCAGACTTAG-GGTAGGGA
* * * * * *
1724311 AGTCTTCAAGGTCAAAACTGACAGGCAGACTAAGGGATAGGAA
1 AGTCTCCAGGGTCAAAGCCGACAGGCAGACTTAGGG-TAGGGA
* * * * **
1724354 AGTCTCCAAGGTAAAAGCCAACAGGCAGACTAAGGG-ATGAAA
1 AGTCTCCAGGGTCAAAGCCGACAGGCAGACTTAGGGTA-GGGA
* * * * * * *
1724396 AGTCTCTAGGGTCCCAA-CCGACAAGCAGACTAAGGGAATGAA
1 AGTCTCCAGGGT-CAAAGCCGACAGGCAGACTTAGGGTAGGGA
* * * * * * *
1724438 AGTCTCCAAGGTTAAAGCCAACAGGCAGACTAAGGGAATGAA
1 AGTCTCCAGGGTCAAAGCCGACAGGCAGACTTAGGGTAGGGA
* * * * * * * ** * *
1724480 AATCTTCAAGGTCAAAACCGACAAGCAGACTAAAGCAATGAA
1 AGTCTCCAGGGTCAAAGCCGACAGGCAGACTTAGGGTAGGGA
* * * ** * *
1724522 AGTCTCCAAGATCAAAGCCGACAGGCAGACTAAGGAAATGAA
1 AGTCTCCAGGGTCAAAGCCGACAGGCAGACTTAGGGTAGGGA
* * * * ***
1724564 AGTTTCTAGGGTCAAAGCCGATAGGCAGACTGAGGGTAAAAA
1 AGTCTCCAGGGTCAAAGCCGACAGGCAGACTTAGGGTAGGGA
* * * * *
1724606 AGTCTCTAAGGTCAAAGCCGACAGGCAGACTAAAGGTAGGAA
1 AGTCTCCAGGGTCAAAGCCGACAGGCAGACTTAGGGTAGGGA
* * * * * * *
1724648 AGTCTCTAGGGTCAAAACCGAAAGGCAGACTAAGGGAAAGCA
1 AGTCTCCAGGGTCAAAGCCGACAGGCAGACTTAGGGTAGGGA
* * * * **
1724690 AGTCTCTAGGGTCAAAACCGACAGGCAGACTAAGGGAAGAAA
1 AGTCTCCAGGGTCAAAGCCGACAGGCAGACTTAGGGTAGGGA
* * * * * * *
1724732 AGTCTCTAGGGTCAAACCCAATAGGCAGACTAAGGGAAGGAA
1 AGTCTCCAGGGTCAAAGCCGACAGGCAGACTTAGGGTAGGGA
* * * * *
1724774 AGCCTCCAGGGTCAAAGCCGACAGGCAGACTAAGGGGAATGAA
1 AGTCTCCAGGGTCAAAGCCGACAGGCAGACTTA-GGGTAGGGA
* * * * * * * **
1724817 AGTCTCTAGGGTCAAAGCTGATAGACAGACTAAGAGAACGAAA
1 AGTCTCCAGGGTCAAAGCCGACAGGCAGACTTAGGGTA-GGGA
* ** * * * * *
1724860 AGTCTCCAAGGTCAAAATCGACAGGCAGACTAAGAGAAAGAA
1 AGTCTCCAGGGTCAAAGCCGACAGGCAGACTTAGGGTAGGGA
* * * *
1724902 AGTCTCCA-GGTCAAAGCAGACAGGCAGACTGAAGGTAGGAA
1 AGTCTCCAGGGTCAAAGCCGACAGGCAGACTTAGGGTAGGGA
* * * * * * *
1724943 AGTCTTCAAGGTCAAAGCTGACAGGTAGACTGAGGGTAAGAA
1 AGTCTCCAGGGTCAAAGCCGACAGGCAGACTTAGGGTAGGGA
* ** * * * *
1724985 AGTCTCAAATGTCAAAGCCGACAAGCAAACTGAGGGTAGGAA
1 AGTCTCCAGGGTCAAAGCCGACAGGCAGACTTAGGGTAGGGA
* ** * * *
1725027 AGTCTCTAAAGTCAAAGCCGACAAGAGGTAGACTGAGGGTAGAGA
1 AGTCTCCAGGGTCAAAGCCGAC---AGGCAGACTTAGGGTAGGGA
*
1725072 AGTCTTCAGGGTCAAAGCCGACAGGCAGACTTAGGGTAGGGA
1 AGTCTCCAGGGTCAAAGCCGACAGGCAGACTTAGGGTAGGGA
* * * * *
1725114 AGTCTCTAGGGTTAAAGCAGATAGGCAGACTTAGGG-AAGGA
1 AGTCTCCAGGGTCAAAGCCGACAGGCAGACTTAGGGTAGGGA
** * * * *
1725155 AGTCTTTAGGGTCAAGGCCGACATGCAAACTAAGGGTAGGGA
1 AGTCTCCAGGGTCAAAGCCGACAGGCAGACTTAGGGTAGGGA
* * * * * *
1725197 AGTCTTCAAGGTCAAAGCCGATAGGCAAACTAAGGGTAGGAA
1 AGTCTCCAGGGTCAAAGCCGACAGGCAGACTTAGGGTAGGGA
* * * *
1725239 AGTCTTCAGGGTCAAAGCCGACAGGCAGACTTAGGGAACGAA
1 AGTCTCCAGGGTCAAAGCCGACAGGCAGACTTAGGGTAGGGA
* * * * * **
1725281 AGTCTCTAGGGTCAAAACTGACAAGCATAC-TAGGGGTAGTAA
1 AGTCTCCAGGGTCAAAGCCGACAGGCAGACTTA-GGGTAGGGA
* * * * * * *
1725323 AGTCTCCAGGGTCAAAGTCGATAAGCAGACTTAGAGAACGAA
1 AGTCTCCAGGGTCAAAGCCGACAGGCAGACTTAGGGTAGGGA
* *** * *
1725365 AGTCTCCCGAGGTCAAAATTGACAGGCAAACTAAGGGTAGGGA
1 AGTCTCCAG-GGTCAAAGCCGACAGGCAGACTTAGGGTAGGGA
* * * * * *
1725408 ACTCTCCTGGGTCAAAGCTGACAGGCAAACTTAGGG-AAGCA
1 AGTCTCCAGGGTCAAAGCCGACAGGCAGACTTAGGGTAGGGA
* * *
1725449 AGTCTCCAAGGTCAAAGCCGATAGGCAGACTAAGGGTAGGGA
1 AGTCTCCAGGGTCAAAGCCGACAGGCAGACTTAGGGTAGGGA
* * * * * * *
1725491 AGTTTCCAAGGTCAAAGTCGATAGACAGACTTAGGGAAGGAA
1 AGTCTCCAGGGTCAAAGCCGACAGGCAGACTTAGGGTAGGGA
* * * * * *
1725533 AGTCTCGAGGGTCAAAACTGACAAGCAGAC-TGGGGTAGAGA
1 AGTCTCCAGGGTCAAAGCCGACAGGCAGACTTAGGGTAGGGA
* * * **
1725574 AGTCTCCAGGGTCAAAGCTGATAGGCAGACTTAGGGAAGAAA
1 AGTCTCCAGGGTCAAAGCCGACAGGCAGACTTAGGGTAGGGA
* * ** * * *
1725616 AGTCTCCTGAGGTCAAAACTAATAGGCAAACTAAGGGTAGGGA
1 AGTCTCCAG-GGTCAAAGCCGACAGGCAGACTTAGGGTAGGGA
* * * *
1725659 ACTCTCCTGGGTCAAAGCCGACAGGCAAACTTAGGG-AAGGA
1 AGTCTCCAGGGTCAAAGCCGACAGGCAGACTTAGGGTAGGGA
** * * *
1725700 AGTCTCTGGGGTCAAAGTCGATAGGCAGACTAAGGGTAGGGA
1 AGTCTCCAGGGTCAAAGCCGACAGGCAGACTTAGGGTAGGGA
* * * * * * * *
1725742 AGTTTTCAAGGTCAAAGCCGATAGGTAGACTTAAGGAAGGAA
1 AGTCTCCAGGGTCAAAGCCGACAGGCAGACTTAGGGTAGGGA
* *** * * *
1725784 AGTCTCGAGGGTCAAAATTGACAAGCAGAC-TGGGGTAGAGA
1 AGTCTCCAGGGTCAAAGCCGACAGGCAGACTTAGGGTAGGGA
* * **
1725825 AGTCTGCAGGGTCAAAGCCGACAGGCAGACTAAGGGTA-AAA
1 AGTCTCCAGGGTCAAAGCCGACAGGCAGACTTAGGGTAGGGA
* *
1725866 AGTCTCCAGGGTCAAAGCCGACAGGCAGACTAAGGGTAGGAA
1 AGTCTCCAGGGTCAAAGCCGACAGGCAGACTTAGGGTAGGGA
* *
1725908 AGTCTCCAGGGTCAAAGTCGACAGGAAGACTTAGGGTAGGGA
1 AGTCTCCAGGGTCAAAGCCGACAGGCAGACTTAGGGTAGGGA
* * * * *
1725950 AGTCTCCAAGGTCAAAGCTGACAGGAAAACTTAGGG-AAGGA
1 AGTCTCCAGGGTCAAAGCCGACAGGCAGACTTAGGGTAGGGA
* * * * * *
1725991 AGTGTCCAGGGTTAAAGCCAACAAGCAAACTAAGGGTAGGGA
1 AGTCTCCAGGGTCAAAGCCGACAGGCAGACTTAGGGTAGGGA
* * ***
1726033 AGTCTCCAGGGTCAAAGCCGACAGGCAGACTAAGGGAAAAAA
1 AGTCTCCAGGGTCAAAGCCGACAGGCAGACTTAGGGTAGGGA
** ** * * * **
1726075 AGTCTCTGGGGTCAAAGCTAATAAGCAGACTAAGGG-AGAAA
1 AGTCTCCAGGGTCAAAGCCGACAGGCAGACTTAGGGTAGGGA
* * * *
1726116 AGTCTCCAAGATCAAAGCCGACAGGCAGACTGAGGGTAGGAA
1 AGTCTCCAGGGTCAAAGCCGACAGGCAGACTTAGGGTAGGGA
* * * * * ***
1726158 AGTCTCTAAGGTCAAAGTCGACAGGCAGACTGAGGGGAAAAA
1 AGTCTCCAGGGTCAAAGCCGACAGGCAGACTTAGGGTAGGGA
* ** * *
1726200 AGTCTCCAAGGTCAAAGCCGATGGGCAGACTAAGGGAAGGGA
1 AGTCTCCAGGGTCAAAGCCGACAGGCAGACTTAGGGTAGGGA
* * * * * * *
1726242 AGTTTCCATGGTCAAAG-CGATAGGCAGACTGAGGGAAAGAA
1 AGTCTCCAGGGTCAAAGCCGACAGGCAGACTTAGGGTAGGGA
* *
1726283 AGTCTCCAAGGTCAAAGCCGACAGGCAGACTGAGGGTAGGGA
1 AGTCTCCAGGGTCAAAGCCGACAGGCAGACTTAGGGTAGGGA
* * * * ** * *
1726325 AGTCTCTAGGGTTAATGCCGATAAACAGACTGAGGGTAGGAA
1 AGTCTCCAGGGTCAAAGCCGACAGGCAGACTTAGGGTAGGGA
* * *
1726367 AGTCTCCAGGGTCAAAGCCAACAAGCAGACTAAGGGTAGGGA
1 AGTCTCCAGGGTCAAAGCCGACAGGCAGACTTAGGGTAGGGA
* * * * * *
1726409 AGTCTCCAAGGTCAAAGTCGATAGGCAAATTTAGGG-AAGGA
1 AGTCTCCAGGGTCAAAGCCGACAGGCAGACTTAGGGTAGGGA
1726450 AGTCTCCAGGGTCAAAGCCGACAGGCAGACTTAGGGTAGGGA
1 AGTCTCCAGGGTCAAAGCCGACAGGCAGACTTAGGGTAGGGA
* *
1726492 AGTCTCTAGTGTCAAAGCCGACAGGCAGACTTAGGGTAGGGA
1 AGTCTCCAGGGTCAAAGCCGACAGGCAGACTTAGGGTAGGGA
* *
1726534 AGTCTCTAGGGTCAAAGCCGACAGGCAGACTTAGGGTGGGGA
1 AGTCTCCAGGGTCAAAGCCGACAGGCAGACTTAGGGTAGGGA
* * *
1726576 AGTCTCAAAGGTCAAAGCCGACAAGCAGACTTAG
1 AGTCTCCAGGGTCAAAGCCGACAGGCAGACTTAG
1726610 AGAAGGAACC
Statistics
Matches: 1972, Mismatches: 428, Indels: 61
0.80 0.17 0.02
Matches are distributed among these distances:
41 369 0.19
42 1270 0.64
43 262 0.13
44 6 0.00
45 64 0.03
46 1 0.00
ACGTcount: A:0.36, C:0.18, G:0.30, T:0.15
Consensus pattern (42 bp):
AGTCTCCAGGGTCAAAGCCGACAGGCAGACTTAGGGTAGGGA
Found at i:1726607 original size:84 final size:84
Alignment explanation
Indices: 1724137--1726617 Score: 2057
Period size: 84 Copynumber: 29.5 Consensus size: 84
1724127 TAAATGAGGT
* * * * * * * * *
1724137 AGTCTTCAGGGTTAAATCTGACAAGCAGACTGAGGGATAGAAAAGTCTCCAAGGTCAAAGCCAAC
1 AGTCTCCAGGGTCAAAGCCGACAGGCAGACTTAGGGA-AGGAAAGTCTCCAGGGTCAAAGCCGAC
* * *
1724202 AGGTAGACTTTAGATGATAGGAA
65 AGGCAGAC--TA-AGGGTAGGAA
* * * ** * * *
1724225 AGTCTCCAAGGTTAAAGCCGATAGGCAGACAAAGGGCAAGAAAAGTCTCCAGGGTCAAAGTCGAA
1 AGTCTCCAGGGTCAAAGCCGACAGGCAGACTTAGGG-AAGGAAAGTCTCCAGGGTCAAAGCCGAC
*
1724290 AGGCAGACTAAGAGATAGGAA
65 AGGCAGACTAAG-GGTAGGAA
* * * * * * * *
1724311 AGTCTTCAAGGTCAAAACTGACAGGCAGACTAAGGGATAGGAAAGTCTCCAAGGTAAAAGCCAAC
1 AGTCTCCAGGGTCAAAGCCGACAGGCAGACTTAGGGA-AGGAAAGTCTCCAGGGTCAAAGCCGAC
*
1724376 AGGCAGACTAAGGG-ATGAAA
65 AGGCAGACTAAGGGTA-GGAA
* * * * * * * *
1724396 AGTCTCTAGGGTCCCAA-CCGACAAGCAGACTAAGGGAATGAAAGTCTCCAAGGTTAAAGCCAAC
1 AGTCTCCAGGGT-CAAAGCCGACAGGCAGACTTAGGGAAGGAAAGTCTCCAGGGTCAAAGCCGAC
* *
1724460 AGGCAGACTAAGGGAATGAA
65 AGGCAGACTAAGGGTAGGAA
* * * * * * * * * * *
1724480 AATCTTCAAGGTCAAAACCGACAAGCAGACTAAAGCAATGAAAGTCTCCAAGATCAAAGCCGACA
1 AGTCTCCAGGGTCAAAGCCGACAGGCAGACTTAGGGAAGGAAAGTCTCCAGGGTCAAAGCCGACA
** *
1724545 GGCAGACTAAGGAAATGAA
66 GGCAGACTAAGGGTAGGAA
* * * * * * *
1724564 AGTTTCTAGGGTCAAAGCCGATAGGCAGACTGAGGGTAA-AAAAGTCTCTAAGGTCAAAGCCGAC
1 AGTCTCCAGGGTCAAAGCCGACAGGCAGACTTAGGG-AAGGAAAGTCTCCAGGGTCAAAGCCGAC
*
1724628 AGGCAGACTAAAGGTAGGAA
65 AGGCAGACTAAGGGTAGGAA
* * * * * * * *
1724648 AGTCTCTAGGGTCAAAACCGAAAGGCAGACTAAGGGAAAGCAAGTCTCTAGGGTCAAAACCGACA
1 AGTCTCCAGGGTCAAAGCCGACAGGCAGACTTAGGGAAGGAAAGTCTCCAGGGTCAAAGCCGACA
* *
1724713 GGCAGACTAAGGGAAGAAA
66 GGCAGACTAAGGGTAGGAA
* * * * * *
1724732 AGTCTCTAGGGTCAAACCCAATAGGCAGACTAAGGGAAGGAAAGCCTCCAGGGTCAAAGCCGACA
1 AGTCTCCAGGGTCAAAGCCGACAGGCAGACTTAGGGAAGGAAAGTCTCCAGGGTCAAAGCCGACA
* *
1724797 GGCAGACTAAGGGGAATGAA
66 GGCAGACTAA-GGGTAGGAA
* * * * * * * * **
1724817 AGTCTCTAGGGTCAAAGCTGATAGACAGACTAAGAGAACGAAAAGTCTCCAAGGTCAAAATCGAC
1 AGTCTCCAGGGTCAAAGCCGACAGGCAGACTTAGGGAA-GGAAAGTCTCCAGGGTCAAAGCCGAC
* * *
1724882 AGGCAGACTAAGAGAAAGAA
65 AGGCAGACTAAGGGTAGGAA
* * * * * * *
1724902 AGTCTCCA-GGTCAAAGCAGACAGGCAGACTGAAGGTAGGAAAGTCTTCAAGGTCAAAGCTGACA
1 AGTCTCCAGGGTCAAAGCCGACAGGCAGACTTAGGGAAGGAAAGTCTCCAGGGTCAAAGCCGACA
* * *
1724966 GGTAGACTGAGGGTAAGAA
66 GGCAGACTAAGGGTAGGAA
* ** * * * * * **
1724985 AGTCTCAAATGTCAAAGCCGACAAGCAAACTGAGGGTAGGAAAGTCTCTAAAGTCAAAGCCGACA
1 AGTCTCCAGGGTCAAAGCCGACAGGCAGACTTAGGGAAGGAAAGTCTCCAGGGTCAAAGCCGAC-
* *
1725050 AGAGGTAGACTGAGGGTA-GAGA
65 --AGGCAGACTAAGGGTAGGA-A
* * * * * * *
1725072 AGTCTTCAGGGTCAAAGCCGACAGGCAGACTTAGGGTAGGGAAGTCTCTAGGGTTAAAGCAGATA
1 AGTCTCCAGGGTCAAAGCCGACAGGCAGACTTAGGGAAGGAAAGTCTCCAGGGTCAAAGCCGACA
* *
1725137 GGCAGACTTAGGGAAGG-A
66 GGCAGACTAAGGGTAGGAA
** * * * * * * * * *
1725155 AGTCTTTAGGGTCAAGGCCGACATGCAAACTAAGGGTAGGGAAGTCTTCAAGGTCAAAGCCGATA
1 AGTCTCCAGGGTCAAAGCCGACAGGCAGACTTAGGGAAGGAAAGTCTCCAGGGTCAAAGCCGACA
*
1725220 GGCAAACTAAGGGTAGGAA
66 GGCAGACTAAGGGTAGGAA
* * * * *
1725239 AGTCTTCAGGGTCAAAGCCGACAGGCAGACTTAGGGAACGAAAGTCTCTAGGGTCAAAACTGACA
1 AGTCTCCAGGGTCAAAGCCGACAGGCAGACTTAGGGAAGGAAAGTCTCCAGGGTCAAAGCCGACA
* * * *
1725304 AGCATACTAGGGGTAGTAA
66 GGCAGACTAAGGGTAGGAA
* * * * * * ***
1725323 AGTCTCCAGGGTCAAAGTCGATAAGCAGACTTAGAGAACGAAAGTCTCCCGAGGTCAAAATTGAC
1 AGTCTCCAGGGTCAAAGCCGACAGGCAGACTTAGGGAAGGAAAGTCTCCAG-GGTCAAAGCCGAC
* *
1725388 AGGCAAACTAAGGGTAGGGA
65 AGGCAGACTAAGGGTAGGAA
* * * * * * *
1725408 ACTCTCCTGGGTCAAAGCTGACAGGCAAACTTAGGGAA-GCAAGTCTCCAAGGTCAAAGCCGATA
1 AGTCTCCAGGGTCAAAGCCGACAGGCAGACTTAGGGAAGGAAAGTCTCCAGGGTCAAAGCCGACA
*
1725472 GGCAGACTAAGGGTAGGGA
66 GGCAGACTAAGGGTAGGAA
* * * * * * * *
1725491 AGTTTCCAAGGTCAAAGTCGATAGACAGACTTAGGGAAGGAAAGTCTCGAGGGTCAAAACTGACA
1 AGTCTCCAGGGTCAAAGCCGACAGGCAGACTTAGGGAAGGAAAGTCTCCAGGGTCAAAGCCGACA
* *
1725556 AGCAGACT-GGGGTA-GAGA
66 GGCAGACTAAGGGTAGGA-A
* * * * * ** *
1725574 AGTCTCCAGGGTCAAAGCTGATAGGCAGACTTAGGGAAGAAAAGTCTCCTGAGGTCAAAACTAAT
1 AGTCTCCAGGGTCAAAGCCGACAGGCAGACTTAGGGAAGGAAAGTCTCCAG-GGTCAAAGCCGAC
* *
1725639 AGGCAAACTAAGGGTAGGGA
65 AGGCAGACTAAGGGTAGGAA
* * * ** * *
1725659 ACTCTCCTGGGTCAAAGCCGACAGGCAAACTTAGGGAAGG-AAGTCTCTGGGGTCAAAGTCGATA
1 AGTCTCCAGGGTCAAAGCCGACAGGCAGACTTAGGGAAGGAAAGTCTCCAGGGTCAAAGCCGACA
*
1725723 GGCAGACTAAGGGTAGGGA
66 GGCAGACTAAGGGTAGGAA
* * * * * * * ***
1725742 AGTTTTCAAGGTCAAAGCCGATAGGTAGACTTAAGGAAGGAAAGTCTCGAGGGTCAAAATTGACA
1 AGTCTCCAGGGTCAAAGCCGACAGGCAGACTTAGGGAAGGAAAGTCTCCAGGGTCAAAGCCGACA
* *
1725807 AGCAGACT-GGGGTA-GAGA
66 GGCAGACTAAGGGTAGGA-A
* *
1725825 AGTCTGCAGGGTCAAAGCCGACAGGCAGACTAAGGGTAA--AAAGTCTCCAGGGTCAAAGCCGAC
1 AGTCTCCAGGGTCAAAGCCGACAGGCAGACTTAGGG-AAGGAAAGTCTCCAGGGTCAAAGCCGAC
1725888 AGGCAGACTAAGGGTAGGAA
65 AGGCAGACTAAGGGTAGGAA
* * * * * *
1725908 AGTCTCCAGGGTCAAAGTCGACAGGAAGACTTAGGGTAGGGAAGTCTCCAAGGTCAAAGCTGACA
1 AGTCTCCAGGGTCAAAGCCGACAGGCAGACTTAGGGAAGGAAAGTCTCCAGGGTCAAAGCCGACA
* * * *
1725973 GGAAAACTTAGGGAAGG-A
66 GGCAGACTAAGGGTAGGAA
* * * * * * * *
1725991 AGTGTCCAGGGTTAAAGCCAACAAGCAAACTAAGGGTAGGGAAGTCTCCAGGGTCAAAGCCGACA
1 AGTCTCCAGGGTCAAAGCCGACAGGCAGACTTAGGGAAGGAAAGTCTCCAGGGTCAAAGCCGACA
* **
1726056 GGCAGACTAAGGGAAAAAA
66 GGCAGACTAAGGGTAGGAA
** ** * * * * * *
1726075 AGTCTCTGGGGTCAAAGCTAATAAGCAGACTAAGGG-AGAAAAGTCTCCAAGATCAAAGCCGACA
1 AGTCTCCAGGGTCAAAGCCGACAGGCAGACTTAGGGAAGGAAAGTCTCCAGGGTCAAAGCCGACA
*
1726139 GGCAGACTGAGGGTAGGAA
66 GGCAGACTAAGGGTAGGAA
* * * * * * *
1726158 AGTCTCTAAGGTCAAAGTCGACAGGCAGACTGAGGGGAA-AAAAGTCTCCAAGGTCAAAGCCGAT
1 AGTCTCCAGGGTCAAAGCCGACAGGCAGACTTA-GGGAAGGAAAGTCTCCAGGGTCAAAGCCGAC
* * *
1726222 GGGCAGACTAAGGGAAGGGA
65 AGGCAGACTAAGGGTAGGAA
* * * * * *
1726242 AGTTTCCATGGTCAAAG-CGATAGGCAGACTGAGGGAAAGAAAGTCTCCAAGGTCAAAGCCGACA
1 AGTCTCCAGGGTCAAAGCCGACAGGCAGACTTAGGGAAGGAAAGTCTCCAGGGTCAAAGCCGACA
* *
1726306 GGCAGACTGAGGGTAGGGA
66 GGCAGACTAAGGGTAGGAA
* * * * ** * * *
1726325 AGTCTCTAGGGTTAATGCCGATAAACAGACTGAGGGTAGGAAAGTCTCCAGGGTCAAAGCCAACA
1 AGTCTCCAGGGTCAAAGCCGACAGGCAGACTTAGGGAAGGAAAGTCTCCAGGGTCAAAGCCGACA
* *
1726390 AGCAGACTAAGGGTAGGGA
66 GGCAGACTAAGGGTAGGAA
* * * * *
1726409 AGTCTCCAAGGTCAAAGTCGATAGGCAAATTTAGGGAAGG-AAGTCTCCAGGGTCAAAGCCGACA
1 AGTCTCCAGGGTCAAAGCCGACAGGCAGACTTAGGGAAGGAAAGTCTCCAGGGTCAAAGCCGACA
* *
1726473 GGCAGACTTAGGGTAGGGA
66 GGCAGACTAAGGGTAGGAA
* * * * *
1726492 AGTCTCTAGTGTCAAAGCCGACAGGCAGACTTAGGGTAGGGAAGTCTCTAGGGTCAAAGCCGACA
1 AGTCTCCAGGGTCAAAGCCGACAGGCAGACTTAGGGAAGGAAAGTCTCCAGGGTCAAAGCCGACA
* * *
1726557 GGCAGACTTAGGGTGGGGA
66 GGCAGACTAAGGGTAGGAA
* * * *
1726576 AGTCTCAAAGGTCAAAGCCGACAAGCAGACTTAGAGAAGGAA
1 AGTCTCCAGGGTCAAAGCCGACAGGCAGACTTAGGGAAGGAA
1726618 CCATAAGTTT
Statistics
Matches: 1969, Mismatches: 387, Indels: 78
0.81 0.16 0.03
Matches are distributed among these distances:
82 36 0.02
83 627 0.32
84 879 0.45
85 189 0.10
86 111 0.06
87 68 0.03
88 58 0.03
89 1 0.00
ACGTcount: A:0.36, C:0.18, G:0.30, T:0.15
Consensus pattern (84 bp):
AGTCTCCAGGGTCAAAGCCGACAGGCAGACTTAGGGAAGGAAAGTCTCCAGGGTCAAAGCCGACA
GGCAGACTAAGGGTAGGAA
Found at i:1728857 original size:13 final size:13
Alignment explanation
Indices: 1728839--1728864 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1728829 CATTTTTTTG
1728839 TGTATCGATACAT
1 TGTATCGATACAT
1728852 TGTATCGATACAT
1 TGTATCGATACAT
1728865 ACTTTGTGTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:1728876 original size:32 final size:33
Alignment explanation
Indices: 1728819--1728882 Score: 103
Period size: 32 Copynumber: 2.0 Consensus size: 33
1728809 TACAAGCCAA
**
1728819 TGTATCGATACATTTTTTTGTGTATCGATACAT
1 TGTATCGATACATTACTTTGTGTATCGATACAT
1728852 TGTATCGATACA-TACTTTGTGTATCGATACA
1 TGTATCGATACATTACTTTGTGTATCGATACA
1728883 AGTTTGGCTA
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
32 17 0.59
33 12 0.41
ACGTcount: A:0.27, C:0.14, G:0.16, T:0.44
Consensus pattern (33 bp):
TGTATCGATACATTACTTTGTGTATCGATACAT
Found at i:1730962 original size:21 final size:20
Alignment explanation
Indices: 1730933--1730975 Score: 50
Period size: 20 Copynumber: 2.1 Consensus size: 20
1730923 GACTAGTGTG
* *
1730933 GGGACTGCCCGGTTGTGACCT
1 GGGACTG-CCGGTCGCGACCT
*
1730954 GGGAGTGCCGGTCGCGACCT
1 GGGACTGCCGGTCGCGACCT
1730974 GG
1 GG
1730976 TGGTGCTGCC
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
20 13 0.68
21 6 0.32
ACGTcount: A:0.09, C:0.28, G:0.44, T:0.19
Consensus pattern (20 bp):
GGGACTGCCGGTCGCGACCT
Found at i:1731425 original size:13 final size:13
Alignment explanation
Indices: 1731407--1731444 Score: 67
Period size: 13 Copynumber: 2.9 Consensus size: 13
1731397 ATAATCCCCT
1731407 TGTATCGATACAG
1 TGTATCGATACAG
*
1731420 TGTATCGATACAT
1 TGTATCGATACAG
1731433 TGTATCGATACA
1 TGTATCGATACA
1731445 AAGAAAAATG
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
13 24 1.00
ACGTcount: A:0.32, C:0.16, G:0.18, T:0.34
Consensus pattern (13 bp):
TGTATCGATACAG
Done.