Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008654.1 Hibiscus syriacus cultivar Beakdansim tig00111648_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: 3533819
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 10 of 18
Found at i:1801786 original size:11 final size:10
Alignment explanation
Indices: 1801762--1801802 Score: 57
Period size: 11 Copynumber: 4.0 Consensus size: 10
1801752 CGATTGCGTT
1801762 AATAAAAT-A
1 AATAAAATAA
1801771 AATAAAATAAA
1 AATAAAAT-AA
1801782 AATAAAATAA
1 AATAAAATAA
1801792 AATAATAATAA
1 AATAA-AATAA
1801803 TAGTAATAAT
Statistics
Matches: 29, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
9 8 0.28
10 7 0.24
11 14 0.48
ACGTcount: A:0.78, C:0.00, G:0.00, T:0.22
Consensus pattern (10 bp):
AATAAAATAA
Found at i:1801791 original size:16 final size:16
Alignment explanation
Indices: 1801765--1801802 Score: 60
Period size: 16 Copynumber: 2.4 Consensus size: 16
1801755 TTGCGTTAAT
1801765 AAAAT-AAATAAAATA
1 AAAATAAAATAAAATA
1801780 AAAATAAAATAAAATA
1 AAAATAAAATAAAATA
*
1801796 ATAATAA
1 AAAATAA
1801803 TAGTAATAAT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
15 5 0.24
16 16 0.76
ACGTcount: A:0.79, C:0.00, G:0.00, T:0.21
Consensus pattern (16 bp):
AAAATAAAATAAAATA
Found at i:1801800 original size:3 final size:3
Alignment explanation
Indices: 1801761--1801833 Score: 73
Period size: 3 Copynumber: 24.7 Consensus size: 3
1801751 CCGATTGCGT
*
1801761 TAA TAA -AA TAAA TAA -AA TAA AAA TAA -AA TAA -AA TAA TAA TAA
1 TAA TAA TAA T-AA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
*
1801803 TAG TAA TAA TAA CTAA TTAA TAA TAA TAA TA
1 TAA TAA TAA TAA -TAA -TAA TAA TAA TAA TA
1801834 TTAACGAGAT
Statistics
Matches: 59, Mismatches: 5, Indels: 12
0.78 0.07 0.16
Matches are distributed among these distances:
2 8 0.14
3 42 0.71
4 9 0.15
ACGTcount: A:0.68, C:0.01, G:0.01, T:0.29
Consensus pattern (3 bp):
TAA
Found at i:1802321 original size:130 final size:131
Alignment explanation
Indices: 1802060--1802420 Score: 399
Period size: 130 Copynumber: 2.8 Consensus size: 131
1802050 TCTTCAGGGT
* * * * * *
1802060 AGATTAAATTTGGAAAAAAGGGATATGCTCCACTGCACTTCAAGGTAGATCAGA--TGGAAATGT
1 AGATCAAATCTGGAAAAAGGGGATATGCTCCGCTGCTCTTCAGGGTAGATCAGATCTGGAAATGT
* * * * ** *
1802123 TAATTCACTCTACTG-TTTTTCAGGGTAGATTAAATTAAGGTAGATTTGTTCCACTTCTCCTCAG
66 TGATTCACTCCACTGCTTTTT-AGGGTAGATTGAATCAAGACAGATTTGTTCCACTTCTACTCA-
1802187 GGA
129 GGA
* *
1802190 AGATCAAATCTGGAAAAAGGGGATCTGCTCCGCTGCTCTTCAGGGTAGATCAGATCTGGAAACGT
1 AGATCAAATCTGGAAAAAGGGGATATGCTCCGCTGCTCTTCAGGGTAGATCAGATCTGGAAATGT
* *
1802255 TGATTCACTCCACTGCTTTTTAGGGTAGATTGAATCAAGACAGATTTGTTTCA-TTGCTAGTC-G
66 TGATTCACTCCACTGCTTTTTAGGGTAGATTGAATCAAGACAGATTTGTTCCACTT-CTACTCAG
1802318 GA
130 GA
* * * * * * *
1802320 AGATCAAATCTGGAAAAAGGGGATATTCTCAGCTACTATTCAGGGAAAATCAAATCTGGAAATGT
1 AGATCAAATCTGGAAAAAGGGGATATGCTCCGCTGCTCTTCAGGGTAGATCAGATCTGGAAATGT
* * * * *
1802385 TGATTCACTCCATTTCTATTCAGGGTAAATTGAATC
66 TGATTCACTCCACTGCTTTTTAGGGTAGATTGAATC
1802421 GGGTTTGATT
Statistics
Matches: 196, Mismatches: 31, Indels: 8
0.83 0.13 0.03
Matches are distributed among these distances:
130 137 0.70
131 2 0.01
132 52 0.27
133 5 0.03
ACGTcount: A:0.31, C:0.17, G:0.22, T:0.31
Consensus pattern (131 bp):
AGATCAAATCTGGAAAAAGGGGATATGCTCCGCTGCTCTTCAGGGTAGATCAGATCTGGAAATGT
TGATTCACTCCACTGCTTTTTAGGGTAGATTGAATCAAGACAGATTTGTTCCACTTCTACTCAGG
A
Found at i:1803739 original size:13 final size:13
Alignment explanation
Indices: 1803721--1803745 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1803711 TTGAACCCCT
1803721 TTTTTATTTTTTA
1 TTTTTATTTTTTA
1803734 TTTTTATTTTTT
1 TTTTTATTTTTT
1803746 CTCTTTTTTC
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:0.12, C:0.00, G:0.00, T:0.88
Consensus pattern (13 bp):
TTTTTATTTTTTA
Found at i:1803762 original size:20 final size:20
Alignment explanation
Indices: 1803741--1803777 Score: 58
Period size: 19 Copynumber: 1.9 Consensus size: 20
1803731 TTATTTTTAT
1803741 TTTTTCTCTTT-TTTCTTCA
1 TTTTTCTCTTTCTTTCTTCA
*
1803760 TTTTTCTTTTTCTTTCTT
1 TTTTTCTCTTTCTTTCTT
1803778 TCTTTCTTCT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
19 10 0.62
20 6 0.38
ACGTcount: A:0.03, C:0.19, G:0.00, T:0.78
Consensus pattern (20 bp):
TTTTTCTCTTTCTTTCTTCA
Found at i:1803770 original size:7 final size:7
Alignment explanation
Indices: 1803719--1803801 Score: 53
Period size: 7 Copynumber: 11.0 Consensus size: 7
1803709 TCTTGAACCC
1803719 CTTTTTT
1 CTTTTTT
*
1803726 ATTTTTT
1 CTTTTTT
*
1803733 ATTTTTAT
1 CTTTTT-T
1803741 -TTTTTCT
1 CTTTTT-T
1803748 CTTTTTT
1 CTTTTTT
1803755 CTTCATTTT
1 CTT--TTTT
1803764 -TCTTTTT
1 CT-TTTTT
1803771 CTTTCTTT
1 CTTT-TTT
*
1803779 CTTTCTT
1 CTTTTTT
1803786 CTTTCTTTT
1 C-TT-TTTT
1803795 CTTTTTT
1 CTTTTTT
1803802 TCCTTCATTT
Statistics
Matches: 63, Mismatches: 4, Indels: 18
0.74 0.05 0.21
Matches are distributed among these distances:
7 35 0.56
8 19 0.30
9 9 0.14
ACGTcount: A:0.05, C:0.16, G:0.00, T:0.80
Consensus pattern (7 bp):
CTTTTTT
Found at i:1803779 original size:24 final size:24
Alignment explanation
Indices: 1803741--1803811 Score: 83
Period size: 24 Copynumber: 2.9 Consensus size: 24
1803731 TTATTTTTAT
1803741 TTTTTCTCTTTTTTCTTCATTTTTC
1 TTTTTCT-TTTTTTCTTCATTTTTC
*
1803766 TTTTTCTTTCTTTCTTTC-TTCTTTC
1 TTTTTCTTTTTTTC-TTCATT-TTTC
1803791 -TTTTCTTTTTTTCCTTCATTT
1 TTTTTCTTTTTTT-CTTCATTT
1803812 GGTTTCTTCA
Statistics
Matches: 40, Mismatches: 2, Indels: 9
0.78 0.04 0.18
Matches are distributed among these distances:
24 23 0.57
25 17 0.43
ACGTcount: A:0.03, C:0.21, G:0.00, T:0.76
Consensus pattern (24 bp):
TTTTTCTTTTTTTCTTCATTTTTC
Found at i:1803788 original size:31 final size:30
Alignment explanation
Indices: 1803727--1803800 Score: 78
Period size: 32 Copynumber: 2.4 Consensus size: 30
1803717 CCCTTTTTTA
* * *
1803727 TTTTTTATTTTTATTTTTTCTCTTTTTTCT
1 TTTTTTCTTTTTATTTCTTCTCTTTCTTCT
*
1803757 TCATTTTTCTTTTTCTTTCTT-TCTTTCTTCT
1 T--TTTTTCTTTTTATTTCTTCTCTTTCTTCT
1803788 TTCTTTTCTTTTT
1 TT-TTTTCTTTTT
1803801 TTCCTTCATT
Statistics
Matches: 37, Mismatches: 4, Indels: 6
0.79 0.09 0.13
Matches are distributed among these distances:
29 1 0.03
30 11 0.30
31 10 0.27
32 15 0.41
ACGTcount: A:0.04, C:0.16, G:0.00, T:0.80
Consensus pattern (30 bp):
TTTTTTCTTTTTATTTCTTCTCTTTCTTCT
Found at i:1808102 original size:9 final size:9
Alignment explanation
Indices: 1808073--1808111 Score: 51
Period size: 9 Copynumber: 4.3 Consensus size: 9
1808063 TTATTCGTAA
*
1808073 TTTCTTTTT
1 TTTCATTTT
**
1808082 TTTCATCAT
1 TTTCATTTT
1808091 TTTCATTTT
1 TTTCATTTT
1808100 TTTCATTTT
1 TTTCATTTT
1808109 TTT
1 TTT
1808112 GGAACATGTG
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
9 25 1.00
ACGTcount: A:0.10, C:0.13, G:0.00, T:0.77
Consensus pattern (9 bp):
TTTCATTTT
Found at i:1821317 original size:19 final size:20
Alignment explanation
Indices: 1821295--1821340 Score: 67
Period size: 20 Copynumber: 2.4 Consensus size: 20
1821285 TTAATGAATA
1821295 AAATGCAATGCA-AAAAAGT
1 AAATGCAATGCAGAAAAAGT
* *
1821314 AAATGTAATGCAGAAAATGT
1 AAATGCAATGCAGAAAAAGT
1821334 AAATGCA
1 AAATGCA
1821341 TAATACTAGG
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
19 11 0.48
20 12 0.52
ACGTcount: A:0.54, C:0.09, G:0.17, T:0.20
Consensus pattern (20 bp):
AAATGCAATGCAGAAAAAGT
Found at i:1827059 original size:11 final size:11
Alignment explanation
Indices: 1827043--1827077 Score: 52
Period size: 11 Copynumber: 3.2 Consensus size: 11
1827033 AGTTTGTAAA
1827043 ATAAATATAAT
1 ATAAATATAAT
*
1827054 ATAAATATAAA
1 ATAAATATAAT
*
1827065 ATAAAAATAAT
1 ATAAATATAAT
1827076 AT
1 AT
1827078 TATTAACGAG
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
11 21 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (11 bp):
ATAAATATAAT
Found at i:1831432 original size:20 final size:18
Alignment explanation
Indices: 1831404--1831446 Score: 50
Period size: 20 Copynumber: 2.3 Consensus size: 18
1831394 GAAGTTCTAT
* *
1831404 TTTTATTTCATCTTTTTTAC
1 TTTTCTTTCA-CTATTTT-C
1831424 TTTTCTTTCACTATTTTC
1 TTTTCTTTCACTATTTTC
1831442 TTTTC
1 TTTTC
1831447 ACAATGTTAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
18 6 0.29
19 6 0.29
20 9 0.43
ACGTcount: A:0.12, C:0.19, G:0.00, T:0.70
Consensus pattern (18 bp):
TTTTCTTTCACTATTTTC
Found at i:1833591 original size:2 final size:2
Alignment explanation
Indices: 1833584--1833627 Score: 88
Period size: 2 Copynumber: 22.0 Consensus size: 2
1833574 TGTTATTTAA
1833584 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
1833626 AT
1 AT
1833628 TTTTCTTTAA
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 42 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1839512 original size:16 final size:15
Alignment explanation
Indices: 1839476--1839508 Score: 57
Period size: 15 Copynumber: 2.2 Consensus size: 15
1839466 TCCAGCAAAG
*
1839476 AAAGAAGAAGGAAAA
1 AAAGAAAAAGGAAAA
1839491 AAAGAAAAAGGAAAA
1 AAAGAAAAAGGAAAA
1839506 AAA
1 AAA
1839509 AGAATTGAAC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.79, C:0.00, G:0.21, T:0.00
Consensus pattern (15 bp):
AAAGAAAAAGGAAAA
Found at i:1844307 original size:22 final size:22
Alignment explanation
Indices: 1844278--1844332 Score: 101
Period size: 22 Copynumber: 2.5 Consensus size: 22
1844268 ATCTACACTC
1844278 TTCAAAGATGATAGATTCTCTT
1 TTCAAAGATGATAGATTCTCTT
*
1844300 TTTAAAGATGATAGATTCTCTT
1 TTCAAAGATGATAGATTCTCTT
1844322 TTCAAAGATGA
1 TTCAAAGATGA
1844333 AAGCTTTATG
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
22 31 1.00
ACGTcount: A:0.35, C:0.11, G:0.15, T:0.40
Consensus pattern (22 bp):
TTCAAAGATGATAGATTCTCTT
Found at i:1845159 original size:76 final size:76
Alignment explanation
Indices: 1845008--1845507 Score: 898
Period size: 76 Copynumber: 6.6 Consensus size: 76
1844998 CTATTTCCCA
*
1845008 CATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAA-CCTTCAGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1845072 AGCCTTAGGGT
66 AGCCTTAGGGT
*
1845083 CATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCATTTTGATGTTTTCAA
1 CATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1845148 AGCCTTAGGGT
66 AGCCTTAGGGT
*
1845159 CATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGATTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1845224 AGCCTTAGGGT
66 AGCCTTAGGGT
* *
1845235 CATCTATAAGTCCTACAGTGCATGATGTATCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1845300 AGCCTTAGGGT
66 AGCCTTAGGGT
1845311 CATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1845376 AGCCTTAGGGT
66 AGCCTTAGGGT
*
1845387 CATCTGTAAGTCCTACAGTGAATGATGTTTCCAAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCA
1 CATCTGTAAGTCCTACAGTGCATGATGTTTCC-AAAAAGCCTTCGGGAGCTTTTTGATGTTTTCA
1845452 AAGCCTTAGGGT
65 AAGCCTTAGGGT
* *
1845464 CATCTGTAAGTCCTTCAGTGCATGATGTTTTC-AAAA-CCTTCGGG
1 CATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGG
1845508 TCATCTATAA
Statistics
Matches: 410, Mismatches: 13, Indels: 5
0.96 0.03 0.01
Matches are distributed among these distances:
74 8 0.02
75 41 0.10
76 288 0.70
77 73 0.18
ACGTcount: A:0.25, C:0.20, G:0.22, T:0.34
Consensus pattern (76 bp):
CATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
AGCCTTAGGGT
Found at i:1845494 original size:45 final size:45
Alignment explanation
Indices: 1845441--1845539 Score: 162
Period size: 45 Copynumber: 2.2 Consensus size: 45
1845431 GGGAGCTTTT
* * *
1845441 TGATGTTTTCAAAGCCTTAGGGTCATCTGTAAGTCCTTCAGTGCA
1 TGATGTTTTCAAAACCTTAGGGTCATCTATAAGCCCTTCAGTGCA
*
1845486 TGATGTTTTCAAAACCTTCGGGTCATCTATAAGCCCTTCAGTGCA
1 TGATGTTTTCAAAACCTTAGGGTCATCTATAAGCCCTTCAGTGCA
1845531 TGATGTTTT
1 TGATGTTTT
1845540 TTAAGACCTC
Statistics
Matches: 50, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
45 50 1.00
ACGTcount: A:0.22, C:0.20, G:0.20, T:0.37
Consensus pattern (45 bp):
TGATGTTTTCAAAACCTTAGGGTCATCTATAAGCCCTTCAGTGCA
Found at i:1845702 original size:3 final size:3
Alignment explanation
Indices: 1845694--1845733 Score: 71
Period size: 3 Copynumber: 13.3 Consensus size: 3
1845684 TTTTTTGTTT
*
1845694 TTA TTA TTA TTA TTA TTT TTA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
1845734 ATATAAATAA
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
3 35 1.00
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (3 bp):
TTA
Found at i:1847082 original size:22 final size:22
Alignment explanation
Indices: 1847057--1847105 Score: 73
Period size: 22 Copynumber: 2.2 Consensus size: 22
1847047 ATTATTTATT
*
1847057 TATTATTTTGTTATTACTTTT-A
1 TATTATTTTATTATTA-TTTTCA
1847079 TATTATTTTATTATTATTTTCA
1 TATTATTTTATTATTATTTTCA
1847101 TATTA
1 TATTA
1847106 GTCACATAAA
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
21 4 0.16
22 21 0.84
ACGTcount: A:0.27, C:0.04, G:0.02, T:0.67
Consensus pattern (22 bp):
TATTATTTTATTATTATTTTCA
Found at i:1847104 original size:11 final size:10
Alignment explanation
Indices: 1847036--1847105 Score: 59
Period size: 11 Copynumber: 6.3 Consensus size: 10
1847026 GCTTTTTAAT
1847036 TTATTTTAATCA
1 TTATTTT-AT-A
*
1847048 TTATTTATTTA
1 TTATTT-TATA
*
1847059 TTATTTTGTTA
1 TTATTTT-ATA
1847070 TTACTTTTATA
1 TTA-TTTTATA
1847081 TTATTTTATTA
1 TTATTTTA-TA
1847092 TTATTTTCATA
1 TTATTTT-ATA
1847103 TTA
1 TTA
1847106 GTCACATAAA
Statistics
Matches: 51, Mismatches: 2, Indels: 11
0.80 0.03 0.17
Matches are distributed among these distances:
10 6 0.12
11 32 0.63
12 12 0.24
13 1 0.02
ACGTcount: A:0.27, C:0.04, G:0.01, T:0.67
Consensus pattern (10 bp):
TTATTTTATA
Found at i:1849486 original size:2 final size:2
Alignment explanation
Indices: 1849479--1849508 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
1849469 TGATATACAA
1849479 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
1849509 TAGTAATTAA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1849787 original size:29 final size:30
Alignment explanation
Indices: 1849754--1849817 Score: 94
Period size: 29 Copynumber: 2.2 Consensus size: 30
1849744 ATGTGATTTA
1849754 TTTTATTAATATATAATGATAATATA-AAG
1 TTTTATTAATATATAATGATAATATATAAG
* *
1849783 TTTTATTAATATTTAATTATAATATATAAG
1 TTTTATTAATATATAATGATAATATATAAG
*
1849813 ATTTA
1 TTTTA
1849818 AAAATAAAAT
Statistics
Matches: 31, Mismatches: 3, Indels: 1
0.89 0.09 0.03
Matches are distributed among these distances:
29 24 0.77
30 7 0.23
ACGTcount: A:0.45, C:0.00, G:0.05, T:0.50
Consensus pattern (30 bp):
TTTTATTAATATATAATGATAATATATAAG
Found at i:1850176 original size:33 final size:33
Alignment explanation
Indices: 1850138--1850202 Score: 121
Period size: 33 Copynumber: 2.0 Consensus size: 33
1850128 TTCCTTCTCC
*
1850138 AAAACTTCATTAATGTCTCCCTCCTCCTCCCCT
1 AAAACTTCATCAATGTCTCCCTCCTCCTCCCCT
1850171 AAAACTTCATCAATGTCTCCCTCCTCCTCCCC
1 AAAACTTCATCAATGTCTCCCTCCTCCTCCCC
1850203 CAATTCCTCA
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 31 1.00
ACGTcount: A:0.22, C:0.45, G:0.03, T:0.31
Consensus pattern (33 bp):
AAAACTTCATCAATGTCTCCCTCCTCCTCCCCT
Found at i:1850220 original size:30 final size:32
Alignment explanation
Indices: 1850136--1850233 Score: 101
Period size: 33 Copynumber: 3.1 Consensus size: 32
1850126 CTTTCCTTCT
* *
1850136 CCAAAACTTCATTAATGTCTCCCTCCTCCTCC
1 CCAAAACTTCATCAATATCTCCCTCCTCCTCC
*
1850168 CCTAAAACTTCATCAATGTCTCCCTCCTCCTCC
1 CC-AAAACTTCATCAATATCTCCCTCCTCCTCC
* * * *
1850201 CC-CAA-TTCCTCATTATCTCCCTCTCCCCTCC
1 CCAAAACTTCATCAATATCTCCCTC-CTCCTCC
1850232 CC
1 CC
1850234 TAAATCTCCA
Statistics
Matches: 58, Mismatches: 6, Indels: 5
0.84 0.09 0.07
Matches are distributed among these distances:
30 15 0.26
31 10 0.17
32 2 0.03
33 31 0.53
ACGTcount: A:0.18, C:0.49, G:0.02, T:0.31
Consensus pattern (32 bp):
CCAAAACTTCATCAATATCTCCCTCCTCCTCC
Found at i:1850893 original size:32 final size:32
Alignment explanation
Indices: 1850851--1850912 Score: 88
Period size: 32 Copynumber: 1.9 Consensus size: 32
1850841 TATCATTTTA
* * *
1850851 AATCTCTTACATAACACACTTCTTTCATCTTC
1 AATCTCTTACACAACAAACTCCTTTCATCTTC
*
1850883 AATCTTTTACACAACAAACTCCTTTCATCT
1 AATCTCTTACACAACAAACTCCTTTCATCT
1850913 AACCAAAAAC
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
32 26 1.00
ACGTcount: A:0.31, C:0.31, G:0.00, T:0.39
Consensus pattern (32 bp):
AATCTCTTACACAACAAACTCCTTTCATCTTC
Found at i:1853126 original size:75 final size:74
Alignment explanation
Indices: 1852993--1853148 Score: 226
Period size: 75 Copynumber: 2.1 Consensus size: 74
1852983 TCCATGTCGT
* **
1852993 TTTTTTTCAAATTTGTTAAAAATATCTAAATGTTTGATATTATTTTTAACTTTGAAA-TTAAAAA
1 TTTTTTTCAAATTTGTTAAAAATATCTAAAAGTTTGATATTATTTTTAACTTCAAAATTTAAAAA
*
1853057 AATATATATTA
66 AAT-T-TAATA
*
1853068 TTTTTTTCAAATTTGTTAAAAA-ATTCTAAAAGTTTGATATTATTTTTAACTTCAAAATTTTAAA
1 TTTTTTTCAAATTTGTTAAAAATA-TCTAAAAGTTTGATATTATTTTTAACTTCAAAATTTAAAA
1853132 AAATTTAATA
65 AAATTTAATA
1853142 TTTTTTT
1 TTTTTTT
1853149 ATTTTAATAA
Statistics
Matches: 74, Mismatches: 5, Indels: 5
0.88 0.06 0.06
Matches are distributed among these distances:
74 12 0.16
75 53 0.72
76 9 0.12
ACGTcount: A:0.40, C:0.04, G:0.04, T:0.51
Consensus pattern (74 bp):
TTTTTTTCAAATTTGTTAAAAATATCTAAAAGTTTGATATTATTTTTAACTTCAAAATTTAAAAA
AATTTAATA
Found at i:1854605 original size:19 final size:19
Alignment explanation
Indices: 1854576--1854644 Score: 122
Period size: 19 Copynumber: 3.7 Consensus size: 19
1854566 CTTAAAATCA
1854576 AAAGA-TGAAGAAGTTACG
1 AAAGATTGAAGAAGTTACG
1854594 AAAGATTGAAGAAGTTACG
1 AAAGATTGAAGAAGTTACG
1854613 AAAGATTGAAGAAGTTACG
1 AAAGATTGAAGAAGTTACG
*
1854632 AAAGATTAAAGAA
1 AAAGATTGAAGAA
1854645 AATGGGTTTT
Statistics
Matches: 49, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
18 5 0.10
19 44 0.90
ACGTcount: A:0.52, C:0.04, G:0.25, T:0.19
Consensus pattern (19 bp):
AAAGATTGAAGAAGTTACG
Found at i:1856499 original size:21 final size:19
Alignment explanation
Indices: 1856457--1856499 Score: 50
Period size: 21 Copynumber: 2.2 Consensus size: 19
1856447 TATGCACACG
*
1856457 TGATATGTGATAGAAGAAA
1 TGATATGAGATAGAAGAAA
*
1856476 TGATATGAGCATATGAATAAA
1 TGATATGAG-ATA-GAAGAAA
1856497 TGA
1 TGA
1856500 GAGTTTCCAA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
19 8 0.40
20 3 0.15
21 9 0.45
ACGTcount: A:0.47, C:0.02, G:0.23, T:0.28
Consensus pattern (19 bp):
TGATATGAGATAGAAGAAA
Found at i:1859731 original size:31 final size:31
Alignment explanation
Indices: 1859693--1859879 Score: 288
Period size: 31 Copynumber: 6.0 Consensus size: 31
1859683 AGGGTCGAGG
*
1859693 GTTTACCTATGTTCTTCGGGACATATGGATT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
*
1859724 GTTTACCTTTGTTCTTCGGGACATATGGA-T
1 GTTTACCTATGTTCTTCGGGACATATGGACT
*
1859754 CGTTTACCTATGTTCTTCGGGATATATGGACT
1 -GTTTACCTATGTTCTTCGGGACATATGGACT
1859786 GTTTACCTATGTTCTTCGGGACATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
1859817 GTTTACCTATGTTCTTCGGGACATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
* * *
1859848 GATTACCTAGGTTCTTCGGAATC-TATGGACT
1 GTTTACCTATGTTCTTCGGGA-CATATGGACT
1859879 G
1 G
1859880 GTTCTTCGGG
Statistics
Matches: 146, Mismatches: 7, Indels: 6
0.92 0.04 0.04
Matches are distributed among these distances:
30 1 0.01
31 143 0.98
32 2 0.01
ACGTcount: A:0.19, C:0.18, G:0.23, T:0.40
Consensus pattern (31 bp):
GTTTACCTATGTTCTTCGGGACATATGGACT
Found at i:1866077 original size:41 final size:41
Alignment explanation
Indices: 1866020--1866105 Score: 163
Period size: 41 Copynumber: 2.1 Consensus size: 41
1866010 TCCTACATTG
*
1866020 AATGTTGGGGTCCAAAATGCTCCTAAAAGAATATGGGTCAA
1 AATGTTGGGATCCAAAATGCTCCTAAAAGAATATGGGTCAA
1866061 AATGTTGGGATCCAAAATGCTCCTAAAAGAATATGGGTCAA
1 AATGTTGGGATCCAAAATGCTCCTAAAAGAATATGGGTCAA
1866102 AATG
1 AATG
1866106 ATCATTTTAA
Statistics
Matches: 44, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
41 44 1.00
ACGTcount: A:0.38, C:0.14, G:0.23, T:0.24
Consensus pattern (41 bp):
AATGTTGGGATCCAAAATGCTCCTAAAAGAATATGGGTCAA
Found at i:1876814 original size:3 final size:3
Alignment explanation
Indices: 1876806--1876839 Score: 50
Period size: 3 Copynumber: 10.7 Consensus size: 3
1876796 TCCAGAGTCA
1876806 TCT TCT TCTT TCT TCT TCT TCTT TCT TCT TCT TC
1 TCT TCT TC-T TCT TCT TCT TC-T TCT TCT TCT TC
1876840 ATACGTGAGA
Statistics
Matches: 29, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
3 23 0.79
4 6 0.21
ACGTcount: A:0.00, C:0.32, G:0.00, T:0.68
Consensus pattern (3 bp):
TCT
Found at i:1876822 original size:13 final size:13
Alignment explanation
Indices: 1876806--1876839 Score: 68
Period size: 13 Copynumber: 2.6 Consensus size: 13
1876796 TCCAGAGTCA
1876806 TCTTCTTCTTTCT
1 TCTTCTTCTTTCT
1876819 TCTTCTTCTTTCT
1 TCTTCTTCTTTCT
1876832 TCTTCTTC
1 TCTTCTTC
1876840 ATACGTGAGA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 21 1.00
ACGTcount: A:0.00, C:0.32, G:0.00, T:0.68
Consensus pattern (13 bp):
TCTTCTTCTTTCT
Found at i:1877337 original size:21 final size:21
Alignment explanation
Indices: 1877295--1877337 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
1877285 TTTCTGGGCT
*
1877295 AGGGGAATCGATACCCATTCA
1 AGGGGAATCGATACCCACTCA
* *
1877316 AGGGGAATCGATGCCCCCTCA
1 AGGGGAATCGATACCCACTCA
1877337 A
1 A
1877338 ACGAATATGA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.30, C:0.28, G:0.26, T:0.16
Consensus pattern (21 bp):
AGGGGAATCGATACCCACTCA
Found at i:1878112 original size:103 final size:103
Alignment explanation
Indices: 1877891--1878104 Score: 383
Period size: 103 Copynumber: 2.1 Consensus size: 103
1877881 AGGGTCTATG
*
1877891 TGGTTCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAGGTCTGGTGAGACACCTACTTGA
1 TGGTTCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAGGTCTGGTGAGACACATACTTGA
* *
1877956 TCCTTGGTATATGTATATGATTCTTAAGGAATGATATG
66 TCCTTGGCATATGTATATGATTCTTAAGGAATGATATA
* *
1877994 TGGTCCTTCGGGACATATATGTATTCTTTGGAATATGTGTGAGGTCTGGTGAGACACATACTTGA
1 TGGTTCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAGGTCTGGTGAGACACATACTTGA
1878059 TCCTTGGCATATGTATATGATTCTTAAGGAATGATATA
66 TCCTTGGCATATGTATATGATTCTTAAGGAATGATATA
1878097 TGGTTCTT
1 TGGTTCTT
1878105 ATGGACATTA
Statistics
Matches: 105, Mismatches: 6, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
103 105 1.00
ACGTcount: A:0.24, C:0.13, G:0.25, T:0.38
Consensus pattern (103 bp):
TGGTTCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAGGTCTGGTGAGACACATACTTGA
TCCTTGGCATATGTATATGATTCTTAAGGAATGATATA
Found at i:1878157 original size:23 final size:23
Alignment explanation
Indices: 1878121--1878183 Score: 83
Period size: 23 Copynumber: 2.7 Consensus size: 23
1878111 ATTATTATAT
*
1878121 GGCACTACGTTGCAATTCTACGC
1 GGCACTACGGTGCAATTCTACGC
* *
1878144 GGCACTCCGGTGCAATTCTACGT
1 GGCACTACGGTGCAATTCTACGC
1878167 GGCACTTA-GGTGCAATT
1 GGCAC-TACGGTGCAATT
1878184 ATATGAGTTG
Statistics
Matches: 35, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
23 34 0.97
24 1 0.03
ACGTcount: A:0.21, C:0.27, G:0.25, T:0.27
Consensus pattern (23 bp):
GGCACTACGGTGCAATTCTACGC
Found at i:1884270 original size:20 final size:20
Alignment explanation
Indices: 1884231--1884270 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
1884221 TCTGGGCTAG
*
1884231 GGGAATCGATACCCATTCAA
1 GGGAATCGATACCCACTCAA
*
1884251 GGGAATCGATACCCCCTCAA
1 GGGAATCGATACCCACTCAA
1884271 ACGAATATGA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.33, C:0.30, G:0.20, T:0.17
Consensus pattern (20 bp):
GGGAATCGATACCCACTCAA
Found at i:1884276 original size:20 final size:20
Alignment explanation
Indices: 1884233--1884276 Score: 52
Period size: 20 Copynumber: 2.2 Consensus size: 20
1884223 TGGGCTAGGG
* **
1884233 GAATCGATACCCATTCAAGG
1 GAATCGATACCCACTCAAAC
*
1884253 GAATCGATACCCCCTCAAAC
1 GAATCGATACCCACTCAAAC
1884273 GAAT
1 GAAT
1884277 ATGAATTTCC
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.36, C:0.30, G:0.16, T:0.18
Consensus pattern (20 bp):
GAATCGATACCCACTCAAAC
Found at i:1884323 original size:20 final size:20
Alignment explanation
Indices: 1884298--1884335 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
1884288 GAACGCTAGA
*
1884298 GGGGAATCGATACCCCCAGG
1 GGGGAACCGATACCCCCAGG
*
1884318 GGGGAACCGATTCCCCCA
1 GGGGAACCGATACCCCCA
1884336 TAATAAAAAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.24, C:0.34, G:0.32, T:0.11
Consensus pattern (20 bp):
GGGGAACCGATACCCCCAGG
Found at i:1884365 original size:17 final size:16
Alignment explanation
Indices: 1884340--1884373 Score: 50
Period size: 17 Copynumber: 2.1 Consensus size: 16
1884330 CCCCCATAAT
1884340 AAAAAAAAGAAGAAGAG
1 AAAAAAAAGAAG-AGAG
*
1884357 AAAAGAAAGAAGAGAG
1 AAAAAAAAGAAGAGAG
1884373 A
1 A
1884374 CTAAACTATC
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 5 0.31
17 11 0.69
ACGTcount: A:0.74, C:0.00, G:0.26, T:0.00
Consensus pattern (16 bp):
AAAAAAAAGAAGAGAG
Found at i:1885049 original size:103 final size:103
Alignment explanation
Indices: 1884824--1885041 Score: 391
Period size: 103 Copynumber: 2.1 Consensus size: 103
1884814 GTAGAGGGTC
* * * *
1884824 TATGTGGTTCTTCGGGATATATATGTATTCTTTGGAACATGTGTGAGGTCTGGTGAGACACCTAC
1 TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
*
1884889 TTGATCCTTGGTATATGTATATGATTCTTAAGGAATGA
66 TTGATCCTTGGCATATGTATATGATTCTTAAGGAATGA
1884927 TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
1 TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
1884992 TTGATCCTTGGCATATGTATATGATTCTTAAGGAATGA
66 TTGATCCTTGGCATATGTATATGATTCTTAAGGAATGA
1885030 TATGTGGTCCTT
1 TATGTGGTCCTT
1885042 ATGGACATTA
Statistics
Matches: 110, Mismatches: 5, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
103 110 1.00
ACGTcount: A:0.24, C:0.13, G:0.25, T:0.38
Consensus pattern (103 bp):
TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
TTGATCCTTGGCATATGTATATGATTCTTAAGGAATGA
Found at i:1885085 original size:23 final size:23
Alignment explanation
Indices: 1885058--1885120 Score: 83
Period size: 23 Copynumber: 2.7 Consensus size: 23
1885048 ATTATTATAT
1885058 GGCAC-TATGGTGCAATTCTACGC
1 GGCACTTA-GGTGCAATTCTACGC
* * *
1885081 GGCACTTCGGTGTAATTCTACGT
1 GGCACTTAGGTGCAATTCTACGC
1885104 GGCACTTAGGTGCAATT
1 GGCACTTAGGTGCAATT
1885121 ATATGAGTTG
Statistics
Matches: 34, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
23 33 0.97
24 1 0.03
ACGTcount: A:0.21, C:0.22, G:0.27, T:0.30
Consensus pattern (23 bp):
GGCACTTAGGTGCAATTCTACGC
Found at i:1888484 original size:15 final size:15
Alignment explanation
Indices: 1888466--1888522 Score: 89
Period size: 15 Copynumber: 3.9 Consensus size: 15
1888456 TTCCGGAAAA
1888466 TGAATTACTGGAATT
1 TGAATTACTGGAATT
**
1888481 TGAATTACTGGAAAA
1 TGAATTACTGGAATT
1888496 TGAATTACTGGAATT
1 TGAATTACTGGAATT
1888511 TGAATT-CTGGAA
1 TGAATTACTGGAA
1888523 AATGAATTAT
Statistics
Matches: 38, Mismatches: 4, Indels: 1
0.88 0.09 0.02
Matches are distributed among these distances:
14 6 0.16
15 32 0.84
ACGTcount: A:0.37, C:0.07, G:0.21, T:0.35
Consensus pattern (15 bp):
TGAATTACTGGAATT
Found at i:1888530 original size:29 final size:30
Alignment explanation
Indices: 1888460--1888531 Score: 137
Period size: 30 Copynumber: 2.4 Consensus size: 30
1888450 TTGTTTTTCC
1888460 GGAAAATGAATTACTGGAATTTGAATTACT
1 GGAAAATGAATTACTGGAATTTGAATTACT
1888490 GGAAAATGAATTACTGGAATTTGAATT-CT
1 GGAAAATGAATTACTGGAATTTGAATTACT
1888519 GGAAAATGAATTA
1 GGAAAATGAATTA
1888532 TATTTCTAGA
Statistics
Matches: 42, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
29 15 0.36
30 27 0.64
ACGTcount: A:0.42, C:0.06, G:0.21, T:0.32
Consensus pattern (30 bp):
GGAAAATGAATTACTGGAATTTGAATTACT
Found at i:1888573 original size:14 final size:14
Alignment explanation
Indices: 1888540--1888574 Score: 52
Period size: 14 Copynumber: 2.5 Consensus size: 14
1888530 TATATTTCTA
*
1888540 GAAAACGTTTTCCG
1 GAAAATGTTTTCCG
1888554 GAAAATGTTTTCCG
1 GAAAATGTTTTCCG
*
1888568 TAAAATG
1 GAAAATG
1888575 AATTACATTT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.34, C:0.14, G:0.20, T:0.31
Consensus pattern (14 bp):
GAAAATGTTTTCCG
Found at i:1888841 original size:21 final size:22
Alignment explanation
Indices: 1888807--1888849 Score: 61
Period size: 21 Copynumber: 2.0 Consensus size: 22
1888797 AGTATTATAT
1888807 TATATTTTAAAAATATTAATTAG
1 TATATTTT-AAAATATTAATTAG
*
1888830 TATATTTT-AAATATTTATTA
1 TATATTTTAAAATATTAATTA
1888850 AAATATTATT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
21 11 0.58
23 8 0.42
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.53
Consensus pattern (22 bp):
TATATTTTAAAATATTAATTAG
Found at i:1888855 original size:21 final size:21
Alignment explanation
Indices: 1888808--1888866 Score: 55
Period size: 23 Copynumber: 2.6 Consensus size: 21
1888798 GTATTATATT
**
1888808 ATATTTTAAAAATATTAATTAGT
1 ATATTTT--AAATATTAATTAAA
*
1888831 ATATTTTAAATATTTATTAAA
1 ATATTTTAAATATTAATTAAA
1888852 ATATTATTTAAATAT
1 ATA-T-TTTAAATAT
1888867 ATAAATATAT
Statistics
Matches: 31, Mismatches: 3, Indels: 4
0.82 0.08 0.11
Matches are distributed among these distances:
21 14 0.45
22 1 0.03
23 16 0.52
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.51
Consensus pattern (21 bp):
ATATTTTAAATATTAATTAAA
Found at i:1888890 original size:19 final size:20
Alignment explanation
Indices: 1888844--1889002 Score: 64
Period size: 20 Copynumber: 7.8 Consensus size: 20
1888834 TTTTAAATAT
1888844 TTATTAAA-ATATTATTTAA
1 TTATTAAATATATTATTTAA
* *
1888863 ATATATAAATATATTA-TTCA
1 TTAT-TAAATATATTATTTAA
* *
1888883 TTATTAAATATATAAATTT-T
1 TTATTAAATATAT-TATTTAA
*
1888903 TTATT--ATATATTATTAAA
1 TTATTAAATATATTATTTAA
* * *
1888921 ATA-AAAATATAATATCTTATA
1 TTATTAAATATATTAT-TTA-A
1888942 TTATTATAATAATTGATTATTTATA
1 TTATTA-AAT-A-T-ATTATTTA-A
* *
1888967 TATATTAAAAATATAATATT-A
1 T-TATTAAATATATTAT-TTAA
1888988 TTATTATAA-ATATTA
1 TTATTA-AATATATTA
1889003 ATAAATAAAT
Statistics
Matches: 105, Mismatches: 18, Indels: 33
0.67 0.12 0.21
Matches are distributed among these distances:
17 3 0.03
18 8 0.08
19 20 0.19
20 28 0.27
21 15 0.14
22 5 0.05
23 6 0.06
24 2 0.02
25 9 0.09
26 9 0.09
ACGTcount: A:0.48, C:0.01, G:0.01, T:0.50
Consensus pattern (20 bp):
TTATTAAATATATTATTTAA
Found at i:1888906 original size:27 final size:26
Alignment explanation
Indices: 1888853--1888915 Score: 81
Period size: 27 Copynumber: 2.3 Consensus size: 26
1888843 TTTATTAAAA
1888853 TATTATTTAAATATATAAATATATTAT
1 TATTA-TTAAATATATAAATATATTAT
* *
1888880 TCATTATTAAATATATAAATTTTTTAT
1 T-ATTATTAAATATATAAATATATTAT
1888907 TATATATTA
1 TAT-TATTA
1888916 TTAAAATAAA
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
26 2 0.06
27 26 0.81
28 4 0.12
ACGTcount: A:0.44, C:0.02, G:0.00, T:0.54
Consensus pattern (26 bp):
TATTATTAAATATATAAATATATTAT
Found at i:1889015 original size:32 final size:31
Alignment explanation
Indices: 1888946--1889013 Score: 88
Period size: 29 Copynumber: 2.2 Consensus size: 31
1888936 CTTATATTAT
*
1888946 TATAATAATTGATTATTTATATATATTAAAAA
1 TATAAT-ATTGATTATTTATAAATATTAAAAA
1888978 TATAATATT-ATTA-TTATAAATATTAATAAA
1 TATAATATTGATTATTTATAAATATTAA-AAA
1889008 TA-AATA
1 TATAATA
1889014 ATATTTGATG
Statistics
Matches: 34, Mismatches: 1, Indels: 5
0.85 0.03 0.12
Matches are distributed among these distances:
29 16 0.47
30 9 0.26
31 3 0.09
32 6 0.18
ACGTcount: A:0.53, C:0.00, G:0.01, T:0.46
Consensus pattern (31 bp):
TATAATATTGATTATTTATAAATATTAAAAA
Found at i:1889243 original size:42 final size:42
Alignment explanation
Indices: 1889191--1889307 Score: 198
Period size: 42 Copynumber: 2.8 Consensus size: 42
1889181 ATGAATTACA
*
1889191 TTCCGAAAAACCAATTACGTGAAACAAACACGGGAAAACATT
1 TTCCGAAAAACGAATTACGTGAAACAAACACGGGAAAACATT
*
1889233 TTCCGGAAAACGAATTACGTGAAACAAACACGGGAAAACATT
1 TTCCGAAAAACGAATTACGTGAAACAAACACGGGAAAACATT
* *
1889275 TTTCGAAAAATGAATTACGTGAAACAAACACGG
1 TTCCGAAAAACGAATTACGTGAAACAAACACGG
1889308 TAATTCGAAG
Statistics
Matches: 70, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
42 70 1.00
ACGTcount: A:0.46, C:0.19, G:0.17, T:0.18
Consensus pattern (42 bp):
TTCCGAAAAACGAATTACGTGAAACAAACACGGGAAAACATT
Found at i:1892029 original size:20 final size:21
Alignment explanation
Indices: 1892004--1892043 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 21
1891994 CTTTACATAG
*
1892004 TAGTATCGATGCCAT-AGGTA
1 TAGTATCGATACCATCAGGTA
*
1892024 TAGTATTGATACCATCAGGT
1 TAGTATCGATACCATCAGGT
1892044 CCCAACGGCT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 13 0.76
21 4 0.24
ACGTcount: A:0.30, C:0.15, G:0.23, T:0.33
Consensus pattern (21 bp):
TAGTATCGATACCATCAGGTA
Found at i:1892192 original size:20 final size:21
Alignment explanation
Indices: 1892154--1892194 Score: 66
Period size: 20 Copynumber: 2.0 Consensus size: 21
1892144 TGCAAAAATT
*
1892154 TCATCCCCAAACGGTTAGAAA
1 TCATCCCCAAACGGCTAGAAA
1892175 TCATCCCC-AACGGCTAGAAA
1 TCATCCCCAAACGGCTAGAAA
1892195 CGACCACAAC
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 11 0.58
21 8 0.42
ACGTcount: A:0.37, C:0.32, G:0.15, T:0.17
Consensus pattern (21 bp):
TCATCCCCAAACGGCTAGAAA
Found at i:1894606 original size:17 final size:17
Alignment explanation
Indices: 1894584--1894624 Score: 73
Period size: 17 Copynumber: 2.4 Consensus size: 17
1894574 AATTTATATC
1894584 AACTTTTCAAATGCTTT
1 AACTTTTCAAATGCTTT
1894601 AACTTTTCAAATGCTTT
1 AACTTTTCAAATGCTTT
*
1894618 AAATTTT
1 AACTTTT
1894625 TTACCTTAAT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
17 23 1.00
ACGTcount: A:0.32, C:0.15, G:0.05, T:0.49
Consensus pattern (17 bp):
AACTTTTCAAATGCTTT
Found at i:1896233 original size:158 final size:159
Alignment explanation
Indices: 1895939--1896251 Score: 493
Period size: 158 Copynumber: 2.0 Consensus size: 159
1895929 TGTTAGAAAT
*
1895939 TCCTTGGTGAGGAGCTAAGGTAGTGGAGGTAGACTTAGTTGAGAAGTCGAACCACTATAAATCAC
1 TCCTTGGTGAGGAGCTAAAGTAGTGGAGGTAGACTTA--TGAGAAGTCGAACCACTATAAATCAC
* * * *
1896004 TGTGCAATTTGTCTATCTTTCTAATCTCTTTACTCCCTAAACACTAAAACTAATTCAACACCTCT
64 TGTGCAATTTGTCTATCTTTCTAATCTCCTTACTCCATAAACACAAAAACCAATTCAACACCTCT
* *
1896069 TGGCAAACTTTTTCGGTTGTCAACTTGAGAA
129 TAGCAAACTTTTTCAGTTGTCAACTTGAGAA
* * **
1896100 TCCTTGGTGATGAGCTAAAGTAGTGGAGGTAGACTTA-GAGAAGTCGAACCATTATAAATCGTTG
1 TCCTTGGTGAGGAGCTAAAGTAGTGGAGGTAGACTTATGAGAAGTCGAACCACTATAAATCACTG
*
1896164 TGCAATTTGTCTATCTTTCTAATCTCCTTACTCCATAAACACAAAAACCAATTCAACCCCTCTTA
66 TGCAATTTGTCTATCTTTCTAATCTCCTTACTCCATAAACACAAAAACCAATTCAACACCTCTTA
1896229 GCAAACTTTTTCAGTTGTCAACT
131 GCAAACTTTTTCAGTTGTCAACT
1896252 CGAGCTTCCG
Statistics
Matches: 140, Mismatches: 12, Indels: 3
0.90 0.08 0.02
Matches are distributed among these distances:
158 105 0.75
161 35 0.25
ACGTcount: A:0.30, C:0.21, G:0.17, T:0.32
Consensus pattern (159 bp):
TCCTTGGTGAGGAGCTAAAGTAGTGGAGGTAGACTTATGAGAAGTCGAACCACTATAAATCACTG
TGCAATTTGTCTATCTTTCTAATCTCCTTACTCCATAAACACAAAAACCAATTCAACACCTCTTA
GCAAACTTTTTCAGTTGTCAACTTGAGAA
Found at i:1896839 original size:2 final size:2
Alignment explanation
Indices: 1896832--1896863 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
1896822 AATACATTAA
1896832 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
1896864 TAATATGAAA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1900223 original size:21 final size:20
Alignment explanation
Indices: 1900190--1900231 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 20
1900180 ATAATTATTT
*
1900190 AAAAAATTAAATAAAATATA
1 AAAAAATTAAATAAAAAATA
*
1900210 AAAAATATTTAATAAAAAATA
1 AAAAA-ATTAAATAAAAAATA
1900231 A
1 A
1900232 TTTTTTATAT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
20 5 0.26
21 14 0.74
ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (20 bp):
AAAAAATTAAATAAAAAATA
Found at i:1907490 original size:52 final size:52
Alignment explanation
Indices: 1907428--1907542 Score: 212
Period size: 52 Copynumber: 2.2 Consensus size: 52
1907418 GCCATTGTTT
1907428 GGCTAGCTGAATTCAGCTTTATTATACATTTATCTTTTAATTACCTTTATTC
1 GGCTAGCTGAATTCAGCTTTATTATACATTTATCTTTTAATTACCTTTATTC
*
1907480 GGCTAGCTGAATTCAGCTTTATTATACATTTATCTTTTAATTACCTTTGTTC
1 GGCTAGCTGAATTCAGCTTTATTATACATTTATCTTTTAATTACCTTTATTC
*
1907532 GACTAGCTGAA
1 GGCTAGCTGAA
1907543 GGATTCATGT
Statistics
Matches: 61, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
52 61 1.00
ACGTcount: A:0.25, C:0.17, G:0.12, T:0.45
Consensus pattern (52 bp):
GGCTAGCTGAATTCAGCTTTATTATACATTTATCTTTTAATTACCTTTATTC
Found at i:1913520 original size:110 final size:109
Alignment explanation
Indices: 1913371--1913692 Score: 392
Period size: 110 Copynumber: 3.0 Consensus size: 109
1913361 CTTGAGATTG
* *
1913371 TTTTTCTTAAAATCAATTTCATCTCGCTTGAGACGGTTTTCCCATT-AAACACAAGTTTTGAAAT
1 TTTTTCTTAAAATCAATTTCGTCTCGCTTGAGACAGTTTTCCC-TTGAAACACAAGTTTTGAAAT
* *
1913435 TGTTTCACTTGAAACCAAAATTGATCTCACTTGATATTATTTTTT
65 TATTTCACTTGAAACCAAAATTGATCTCACTTGAGATTATTTTTT
* * *
1913480 ATTTTTCTTAAAATCAA-TTCTGTCTCGCTTAAGGCAGTTTTCCCTTGAAACACAAATTTTGAAA
1 -TTTTTCTTAAAATCAATTTC-GTCTCGCTTGAGACAGTTTTCCCTTGAAACACAAGTTTTGAAA
* *
1913544 TTCTTTCACTCGAAA-CAAAATTGATCTCACTTGAGATTA----TT
64 TTATTTCACTTGAAACCAAAATTGATCTCACTTGAGATTATTTTTT
* * * * *
1913585 TTTTTCTTAAAACCAAATTTCGTCTTGCTTGAGAAAGTTTTCCCTTGAAACACAAAGTTTGGAAT
1 TTTTTCTTAAAATC-AATTTCGTCTCGCTTGAGACAGTTTTCCCTTGAAACAC-AAGTTTTGAAA
* *
1913650 TTATTTCACCTGAAACC-AAA-TGATCTCACTTGAGATTGTTTTT
64 TTATTTCACTTGAAACCAAAATTGATCTCACTTGAGATTATTTTT
1913693 GTAAAAAATA
Statistics
Matches: 182, Mismatches: 20, Indels: 21
0.82 0.09 0.09
Matches are distributed among these distances:
104 13 0.07
105 49 0.27
106 26 0.14
107 1 0.01
109 29 0.16
110 64 0.35
ACGTcount: A:0.30, C:0.18, G:0.11, T:0.41
Consensus pattern (109 bp):
TTTTTCTTAAAATCAATTTCGTCTCGCTTGAGACAGTTTTCCCTTGAAACACAAGTTTTGAAATT
ATTTCACTTGAAACCAAAATTGATCTCACTTGAGATTATTTTTT
Found at i:1913677 original size:105 final size:105
Alignment explanation
Indices: 1913349--1913727 Score: 389
Period size: 110 Copynumber: 3.6 Consensus size: 105
1913339 GCAAATATAA
* * * *
1913349 AAATGGATCTCACTTGAGA-T-TGTTTTTCTTAAAATCAATTTCATCTCGCTTGAGACGGTTTTC
1 AAATTGATCTCACTTGAGATTATTTTTTTCTTAAAATCAATTTCGTCTCGCTTGAGACAGTTTTC
* *
1913412 CCATT-AAACAC-AAGTTTTGAAATTGTTTCACTTGAAACC
66 CC-TTGAAACACAAAGTTTTGAAATTATTTCACCTGAAACC
* * *
1913451 AAAATTGATCTCACTTGATATTATTTTTTATTTTTCTTAAAATCAA-TTCTGTCTCGCTTAAGGC
1 -AAATTGATCTCACTTGAGATTA----TT-TTTTTCTTAAAATCAATTTC-GTCTCGCTTGAGAC
* *
1913515 AGTTTTCCCTTGAAACACAAA-TTTTGAAATTCTTTCA-CTCGAAACA
59 AGTTTTCCCTTGAAACACAAAGTTTTGAAATTATTTCACCT-GAAACC
* * *
1913561 AAATTGATCTCACTTGAGATTATTTTTTTCTTAAAACCAAATTTCGTCTTGCTTGAGAAAGTTTT
1 AAATTGATCTCACTTGAGATTATTTTTTTCTTAAAATC-AATTTCGTCTCGCTTGAGACAGTTTT
* *
1913626 CCCTTGAAACACAAAGTTTGGAATTTATTTCACCTGAAACC
65 CCCTTGAAACACAAAGTTTTGAAATTATTTCACCTGAAACC
* * ** * * * *
1913667 AAA-TGATCTCACTTGAGATTGTTTTTGT-AAAAAATAAATTTCATCTTGCATGAGACAGTTT
1 AAATTGATCTCACTTGAGATTATTTTTTTCTTAAAATCAATTTCGTCTCGCTTGAGACAGTTT
1913728 CCTTCTAAAC
Statistics
Matches: 232, Mismatches: 29, Indels: 30
0.80 0.10 0.10
Matches are distributed among these distances:
103 39 0.17
104 18 0.08
105 58 0.25
106 24 0.10
107 2 0.01
109 28 0.12
110 61 0.26
111 2 0.01
ACGTcount: A:0.31, C:0.17, G:0.12, T:0.40
Consensus pattern (105 bp):
AAATTGATCTCACTTGAGATTATTTTTTTCTTAAAATCAATTTCGTCTCGCTTGAGACAGTTTTC
CCTTGAAACACAAAGTTTTGAAATTATTTCACCTGAAACC
Found at i:1914913 original size:91 final size:89
Alignment explanation
Indices: 1914755--1915016 Score: 343
Period size: 91 Copynumber: 3.0 Consensus size: 89
1914745 AGGAGGTGGA
* * * * *
1914755 TCAACATTTTCAGTGGAGAGTTCATAATAAGAAGAACTCATCCAACGAGGGAGAAGAAGTTCATA
1 TCAACATTTCCAGTGGAGAGTTCATAATGAGAAGAACTCATCCAACGAGAGAGAATAAGTTCTTA
* * *
1914820 ATGAGAAGAGTTTGTTTAACCTTGG
66 ATGAGAAGAGCTTGTTCAACCAT-G
* * *
1914845 CTCAACATTTCCAGTGGAGAGTTCATAATGAGAATAAATCATCCAACGAGAAAGAATAAGTTCTT
1 -TCAACATTTCCAGTGGAGAGTTCATAATGAGAAGAACTCATCCAACGAGAGAGAATAAGTTCTT
1914910 AATGAGAAGAGCTTGTTCAACCATG
65 AATGAGAAGAGCTTGTTCAACCATG
* * *
1914935 T---CATTTCTAATGGAGAGTTCATAATGAGAAGAACTCATCCAATGAGAGAGAATAAGTT-TAT
1 TCAACATTTCCAGTGGAGAGTTCATAATGAGAAGAACTCATCCAACGAGAGAGAATAAGTTCT-T
1914996 AATGAGAAGAGCTTGTTCAAC
65 AATGAGAAGAGCTTGTTCAAC
1915017 ATTAGCTTGT
Statistics
Matches: 153, Mismatches: 17, Indels: 7
0.86 0.10 0.04
Matches are distributed among these distances:
85 1 0.01
86 73 0.48
89 1 0.01
90 1 0.01
91 77 0.50
ACGTcount: A:0.38, C:0.14, G:0.21, T:0.27
Consensus pattern (89 bp):
TCAACATTTCCAGTGGAGAGTTCATAATGAGAAGAACTCATCCAACGAGAGAGAATAAGTTCTTA
ATGAGAAGAGCTTGTTCAACCATG
Found at i:1915426 original size:17 final size:18
Alignment explanation
Indices: 1915404--1915448 Score: 58
Period size: 17 Copynumber: 2.6 Consensus size: 18
1915394 CCATTTTTTC
*
1915404 ATTTTTATTATA-TTATT
1 ATTTTTATTATATTTACT
1915421 ATTTTTATT-TATTTACT
1 ATTTTTATTATATTTACT
*
1915438 ATTATTATTAT
1 ATTTTTATTAT
1915449 TTAAAATATT
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
16 2 0.08
17 21 0.88
18 1 0.04
ACGTcount: A:0.29, C:0.02, G:0.00, T:0.69
Consensus pattern (18 bp):
ATTTTTATTATATTTACT
Found at i:1915430 original size:23 final size:23
Alignment explanation
Indices: 1915407--1915451 Score: 67
Period size: 23 Copynumber: 2.0 Consensus size: 23
1915397 TTTTTTCATT
1915407 TTTA-TTA-TATTATTATTTTTA
1 TTTATTTACTATTATTATTTTTA
1915428 TTTATTTACTATTATTATTATTTA
1 TTTATTTACTATTATTATT-TTTA
1915452 AAATATTATT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
21 4 0.19
22 3 0.14
23 10 0.48
24 4 0.19
ACGTcount: A:0.29, C:0.02, G:0.00, T:0.69
Consensus pattern (23 bp):
TTTATTTACTATTATTATTTTTA
Found at i:1915442 original size:20 final size:21
Alignment explanation
Indices: 1915407--1915451 Score: 65
Period size: 20 Copynumber: 2.2 Consensus size: 21
1915397 TTTTTTCATT
* *
1915407 TTTATTATATTATTATTTTTA
1 TTTATTATACTATTATTATTA
1915428 TTTATT-TACTATTATTATTA
1 TTTATTATACTATTATTATTA
1915448 TTTA
1 TTTA
1915452 AAATATTATT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
20 16 0.73
21 6 0.27
ACGTcount: A:0.29, C:0.02, G:0.00, T:0.69
Consensus pattern (21 bp):
TTTATTATACTATTATTATTA
Found at i:1919692 original size:29 final size:28
Alignment explanation
Indices: 1919631--1919694 Score: 76
Period size: 29 Copynumber: 2.2 Consensus size: 28
1919621 TATGTTCATA
*
1919631 ATAATAAATATTGAAAAATTTTGGACCT
1 ATAATAAATATTGAAAAATATTGGACCT
* *
1919659 CTAATAAGAGTATTGAAAAA-ATTGGACTT
1 ATAATAA-A-TATTGAAAAATATTGGACCT
1919688 ATAATAA
1 ATAATAA
1919695 CAAATAGTAA
Statistics
Matches: 30, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
28 6 0.20
29 14 0.47
30 10 0.33
ACGTcount: A:0.48, C:0.06, G:0.12, T:0.33
Consensus pattern (28 bp):
ATAATAAATATTGAAAAATATTGGACCT
Found at i:1919944 original size:30 final size:32
Alignment explanation
Indices: 1919883--1919960 Score: 115
Period size: 30 Copynumber: 2.5 Consensus size: 32
1919873 GAGTATGCCT
*
1919883 ATAATAATAAATATTAGAAGAAAATTGAACTC
1 ATAATAATAAATATTAGAAGAAAATTAAACTC
1919915 ATAATAATAAATATT-GAA-AAAATTAAACTC
1 ATAATAATAAATATTAGAAGAAAATTAAACTC
* *
1919945 ATAATAACAAGTATTA
1 ATAATAATAAATATTA
1919961 AAATTAATTG
Statistics
Matches: 42, Mismatches: 3, Indels: 3
0.88 0.06 0.06
Matches are distributed among these distances:
30 24 0.57
31 3 0.07
32 15 0.36
ACGTcount: A:0.58, C:0.06, G:0.06, T:0.29
Consensus pattern (32 bp):
ATAATAATAAATATTAGAAGAAAATTAAACTC
Found at i:1919963 original size:27 final size:28
Alignment explanation
Indices: 1919903--1919967 Score: 78
Period size: 30 Copynumber: 2.3 Consensus size: 28
1919893 ATATTAGAAG
* *
1919903 AAAATTGAACTCATAATAATAAATATTGAA
1 AAAATTAAACTCATAATAACAAATATT--A
*
1919933 AAAATTAAACTCATAATAACAAGTATT-
1 AAAATTAAACTCATAATAACAAATATTA
1919960 AAAATTAA
1 AAAATTAA
1919968 TTGGGCCTTA
Statistics
Matches: 32, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
27 8 0.25
30 24 0.75
ACGTcount: A:0.58, C:0.08, G:0.05, T:0.29
Consensus pattern (28 bp):
AAAATTAAACTCATAATAACAAATATTA
Found at i:1926596 original size:93 final size:93
Alignment explanation
Indices: 1926437--1926615 Score: 286
Period size: 93 Copynumber: 1.9 Consensus size: 93
1926427 TCATGATCTT
** * * * *
1926437 TCTACTGGAAATGTTGGTCCCTCGAGTGAGGCGTTACTGATTTAAAATATCGTGAATCGAGCAAA
1 TCTACTGGAAATGTTAATCCCTCAAGTAAGGCGTCACTGATTCAAAATATCGTGAATCGAGCAAA
1926502 GGTTGAACAAGTTCTTCATTATCAATTC
66 GGTTGAACAAGTTCTTCATTATCAATTC
* *
1926530 TCTACTGGAAATGTTAATCCCTCAAGTAAGGTGTCGCTGATTCAAAATATCGTGAATCGAGCAAA
1 TCTACTGGAAATGTTAATCCCTCAAGTAAGGCGTCACTGATTCAAAATATCGTGAATCGAGCAAA
1926595 GGTTGAACAAGTTCTTCATTA
66 GGTTGAACAAGTTCTTCATTA
1926616 CGAACTTCTT
Statistics
Matches: 78, Mismatches: 8, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
93 78 1.00
ACGTcount: A:0.31, C:0.17, G:0.21, T:0.31
Consensus pattern (93 bp):
TCTACTGGAAATGTTAATCCCTCAAGTAAGGCGTCACTGATTCAAAATATCGTGAATCGAGCAAA
GGTTGAACAAGTTCTTCATTATCAATTC
Found at i:1927154 original size:175 final size:178
Alignment explanation
Indices: 1926860--1927304 Score: 666
Period size: 175 Copynumber: 2.5 Consensus size: 178
1926850 GAGATAAAAT
** * *
1926860 TTGTTTCGAGGGAAAACTGTCTTAAGTGAGACAAAGTTTATTTTAAGAAAAACAATCTCAAGTGA
1 TTGTTTCGAGTAAAAACTGTCTCAAGCGAGACAAAGTTTATTTTAAGAAAAACAATCTCAAGTGA
*
1926925 GATGAAATTCTTGTTTCAAGTGAAACAATTTCAAATTTTATATTTCATGGGAAAC-TTCTCAAGC
66 GATGAAA-TCTTGTTTCAAGTGAAACAATTTCAAATTTTATATTTCAAGGGAAACTTTCTCAAGC
1926989 AAGATGAAATTTAC-TTTAAGAAAAACAATCTTGAGTGAAATGAAATTTC
130 AAGATGAAATTT-CTTTTAAGAAAAACAATCTTGAGTGAAATGAAATTTC
*
1927038 TTGTTTCGAGTAAAAACTGTCTCAAGCGAGACAAAATTTATTTTAAGAAAAACAATCTCAAGTGA
1 TTGTTTCGAGTAAAAACTGTCTCAAGCGAGACAAAGTTTATTTTAAGAAAAACAATCTCAAGTGA
* * *
1927103 GATG-AA-CTTGTTTCAAGTGAAACGATTTCAAATTTTATATTTCAAGGGAAACTTTCTCCAGCG
66 GATGAAATCTTGTTTCAAGTGAAACAATTTCAAATTTTATATTTCAAGGGAAACTTTCTCAAGCA
* *
1927166 AGATGAAATTTCTTTTAAGAAAAATAATCTTGAGTGATATGAAATTTC
131 AGATGAAATTTCTTTTAAGAAAAACAATCTTGAGTGAAATGAAATTTC
* * *
1927214 TTGTTTTGA-TTAAAACTGTCTCAAGCGAGACAAAGTTTGTTTTAAGAAAAACAATCTCAAGTGA
1 TTGTTTCGAGTAAAAACTGTCTCAAGCGAGACAAAGTTTATTTTAAGAAAAACAATCTCAAGTGA
* * *
1927278 GGTAAAATTTCTGTTTCAAGTGGAAAC
66 GATGAAATCT-TGTTTCAAGT-GAAAC
1927305 TGTCTCAAGC
Statistics
Matches: 243, Mismatches: 18, Indels: 11
0.89 0.07 0.04
Matches are distributed among these distances:
175 99 0.41
176 62 0.26
177 3 0.01
178 74 0.30
179 5 0.02
ACGTcount: A:0.38, C:0.12, G:0.17, T:0.33
Consensus pattern (178 bp):
TTGTTTCGAGTAAAAACTGTCTCAAGCGAGACAAAGTTTATTTTAAGAAAAACAATCTCAAGTGA
GATGAAATCTTGTTTCAAGTGAAACAATTTCAAATTTTATATTTCAAGGGAAACTTTCTCAAGCA
AGATGAAATTTCTTTTAAGAAAAACAATCTTGAGTGAAATGAAATTTC
Found at i:1927257 original size:75 final size:74
Alignment explanation
Indices: 1927151--1927764 Score: 520
Period size: 75 Copynumber: 8.2 Consensus size: 74
1927141 ATTTCAAGGG
* * * * * ** * *
1927151 AAACTTTCTCCAGCGAGATGAAATTTCTTTTAAGAAAAATAATCTTGAGTGATATGAAATTTCTT
1 AAACTGTCTCAAGCGAGA-CAAATTTGTTTTAAGAAAAACAATCTCAAGTGAGATAAAATTTC-T
* *
1927216 GTTTTGA-TTA
64 GTTTCGAGTGA
*
1927226 AAACTGTCTCAAGCGAGACAAAGTTTGTTTTAAGAAAAACAATCTCAAGTGAGGTAAAATTTCTG
1 AAACTGTCTCAAGCGAGACAAA-TTTGTTTTAAGAAAAACAATCTCAAGTGAGATAAAATTTCTG
* *
1927291 TTTCAAGTGG
65 TTTCGAGTGA
*
1927301 AAACTGTCTCAAGCGAGACAAAATTTGTTTTAAGAAAAACAATCTCAAGTGAGATAAAATATCTG
1 AAACTGTCTCAAGCGAGAC-AAATTTGTTTTAAGAAAAACAATCTCAAGTGAGATAAAATTTCTG
1927366 TTTCGAGTGA
65 TTTCGAGTGA
* * *
1927376 AAACTGTCTCAAACGAGACGAAATTTGTTTTAAGAAAAAAAAATCTCAAGTGAGATAAAATTTAT
1 AAACTGTCTCAAGCGAGAC-AAATTTGTTTTAAG-AAAAACAATCTCAAGTGAGATAAAATTTCT
*
1927441 GTTTTGAGTG-
64 GTTTCGAGTGA
*
1927451 AAACTATCTCAAGCGAGACGAAATTTGTTTTAAGAAAAACAATCTCAAGTGAGAT-AAATATTCT
1 AAACTGTCTCAAGCGAGAC-AAATTTGTTTTAAGAAAAACAATCTCAAGTGAGATAAAAT-TTCT
* *
1927515 ATTTCAAGTG-
64 GTTTCGAGTGA
* * * * ** * *
1927525 AAACTATATCAAGCAAGATAAAATTT-TTGCTTCAAGTGAAACAATCTCAAGCT-AGAT-GAATC
1 AAACTGTCTCAAGCGAGA-CAAATTTGTT--TT-AAGAAAAACAATCTCAAG-TGAGATAAAATT
** *
1927587 T-TGTTTTAAG-AA
61 TCTGTTTCGAGTGA
** * * * ** * *
1927599 AAACAATCTCAAGTGAGATAAATCTTTTGTTTATAGTGAAACTATCTCAAGCGAGATAAAAGTTT
1 AAACTGTCTCAAGCGAGACAAAT-TTGT-TTTA-AGAAAAACAATCTCAAGTGAGATAAAA-TTT
*
1927664 -TG-CTCGAGTG-
62 CTGTTTCGAGTGA
* ** *
1927674 AAACTATCTCAAGCGAGATGAATCTTGTTTTAAG-AAAACAATCTCAAGTGAGAT-AAATCTTTT
1 AAACTGTCTCAAGCGAGACAAAT-TTGTTTTAAGAAAAACAATCTCAAGTGAGATAAAAT-TTCT
1927737 GTTTCGAGT-A
64 GTTTCGAGTGA
*
1927747 AAACTATCTCAAGCGAGA
1 AAACTGTCTCAAGCGAGA
1927765 TAAAATTTTG
Statistics
Matches: 454, Mismatches: 62, Indels: 48
0.80 0.11 0.09
Matches are distributed among these distances:
70 1 0.00
71 5 0.01
72 19 0.04
73 37 0.08
74 110 0.24
75 214 0.47
76 67 0.15
77 1 0.00
ACGTcount: A:0.39, C:0.13, G:0.17, T:0.31
Consensus pattern (74 bp):
AAACTGTCTCAAGCGAGACAAATTTGTTTTAAGAAAAACAATCTCAAGTGAGATAAAATTTCTGT
TTCGAGTGA
Found at i:1927461 original size:38 final size:37
Alignment explanation
Indices: 1927226--1927802 Score: 389
Period size: 38 Copynumber: 15.5 Consensus size: 37
1927216 GTTTTGATTA
* * * * **
1927226 AAACTGTCTCAAGCGAGA-CAAAGTTTGTTTTAAGAA
1 AAACTATCTCAAGCGAGATAAAATTTTGTTTCAAGTG
* * *
1927262 AAACAATCTCAAGTGAGGTAAAATTTCTGTTTCAAGTGG
1 AAACTATCTCAAGCGAGATAAAATTT-TGTTTCAAGT-G
* * * **
1927301 AAACTGTCTCAAGCGAGACAAAA-TTTGTTTTAAGAA
1 AAACTATCTCAAGCGAGATAAAATTTTGTTTCAAGTG
* * * *
1927337 AAACAATCTCAAGTGAGATAAAATATCTGTTTCGAGTG
1 AAACTATCTCAAGCGAGATAAAAT-TTTGTTTCAAGTG
* * ** * **
1927375 AAAACTGTCTCAAACGAGACGAAA-TTTGTTTTAAGAAA
1 -AAACTATCTCAAGCGAGATAAAATTTTGTTTCAAG-TG
** * **
1927413 AAAAAATCTCAAGTGAGATAAAATTTATGTTTTGAGTG
1 AAACTATCTCAAGCGAGATAAAATTT-TGTTTCAAGTG
** * **
1927451 AAACTATCTCAAGCGAGACGAAA-TTTGTTTTAAGAA
1 AAACTATCTCAAGCGAGATAAAATTTTGTTTCAAGTG
* * * *
1927487 AAACAATCTCAAGTGAGATAAATATTCTATTTCAAGTG
1 AAACTATCTCAAGCGAGATAAA-ATTTTGTTTCAAGTG
* * *
1927525 AAACTATATCAAGCAAGATAAAATTTTTGCTTCAAGTG
1 AAACTATCTCAAGCGAGATAAAA-TTTTGTTTCAAGTG
* * * * * **
1927563 AAACAATCTCAAGCTAGAT-GAATCTTGTTTTAAGAA
1 AAACTATCTCAAGCGAGATAAAATTTTGTTTCAAGTG
* * *
1927599 AAACAATCTCAAGTGAGATAAATCTTTTGTTT-ATAGTG
1 AAACTATCTCAAGCGAGATAAA-ATTTTGTTTCA-AGTG
* *
1927637 AAACTATCTCAAGCGAGATAAAAGTTTTG-CTCGAGTG
1 AAACTATCTCAAGCGAGATAAAA-TTTTGTTTCAAGTG
* * * *
1927674 AAACTATCTCAAGCGAGAT-GAATCTTGTTTTAAG-A
1 AAACTATCTCAAGCGAGATAAAATTTTGTTTCAAGTG
* * * * *
1927709 AAACAATCTCAAGTGAGATAAATCTTTTGTTTCGAGTA
1 AAACTATCTCAAGCGAGATAAA-ATTTTGTTTCAAGTG
* *
1927747 AAACTATCTCAAGCGAGATAAAATTTTGCTTCGAGTG
1 AAACTATCTCAAGCGAGATAAAATTTTGTTTCAAGTG
*
1927784 AAACTATCTCAGGCGAGAT
1 AAACTATCTCAAGCGAGAT
1927803 GAATCTTGTT
Statistics
Matches: 409, Mismatches: 111, Indels: 41
0.73 0.20 0.07
Matches are distributed among these distances:
35 21 0.05
36 91 0.22
37 108 0.26
38 146 0.36
39 43 0.11
ACGTcount: A:0.39, C:0.13, G:0.17, T:0.30
Consensus pattern (37 bp):
AAACTATCTCAAGCGAGATAAAATTTTGTTTCAAGTG
Found at i:1927753 original size:110 final size:111
Alignment explanation
Indices: 1927226--1927813 Score: 593
Period size: 112 Copynumber: 5.3 Consensus size: 111
1927216 GTTTTGATTA
* ** * *
1927226 AAACTGTCTCAAGCGAGACAAAGT-TTGTTTTAAGAAAAACAATCTCAAGTGAGGTAAAAT-TTC
1 AAACTATCTCAAGCGAGATGAA-TCTTGTTTTAAGAAAAACAATCTCAAGTGAGAT-AAATCTTT
* * * ** **
1927289 TGTTTCAAGTGGAAACTGTCTCAAGCGAGACAAAA-TTTGTTTTAAGAA
64 TGTTTCAAGT-GAAACTATCTCAAGCGAGATAAAATTTTGCTTCGAGTG
* * * * ** * ** ** *
1927337 AAACAATCTCAAGTGAGATAAAATATCTGTTTCGAGTGAAAACTGTCTCAAACGAGACGAAA---
1 AAACTATCTCAAGCGAGAT-GAATCT-TGTTTTAAG-AAAAACAATCTCAAGTGAGA-TAAATCT
* ** ** * * *
1927399 TTTGTTTTAAGAAAAAAAAATCTCAAGTGAGATAAAATTTATGTTTTGAGTG
62 TTTGTTTCAAG-TGAAACTATCTCAAGCGAGATAAAATTT-TGCTTCGAGTG
* * *
1927451 AAACTATCTCAAGCGAGACGAAAT-TTGTTTTAAGAAAAACAATCTCAAGTGAGATAAATATTCT
1 AAACTATCTCAAGCGAGATG-AATCTTGTTTTAAGAAAAACAATCTCAAGTGAGATAAATCTTTT
* * * *
1927515 ATTTCAAGTGAAACTATATCAAGCAAGATAAAATTTTTGCTTCAAGTG
65 GTTTCAAGTGAAACTATCTCAAGCGAGATAAAA-TTTTGCTTCGAGTG
* *
1927563 AAACAATCTCAAGCTAGATGAATCTTGTTTTAAGAAAAACAATCTCAAGTGAGATAAATCTTTTG
1 AAACTATCTCAAGCGAGATGAATCTTGTTTTAAGAAAAACAATCTCAAGTGAGATAAATCTTTTG
1927628 TTT-ATAGTGAAACTATCTCAAGCGAGATAAAAGTTTTGC-TCGAGTG
66 TTTCA-AGTGAAACTATCTCAAGCGAGATAAAA-TTTTGCTTCGAGTG
1927674 AAACTATCTCAAGCGAGATGAATCTTGTTTTAAG-AAAACAATCTCAAGTGAGATAAATCTTTTG
1 AAACTATCTCAAGCGAGATGAATCTTGTTTTAAGAAAAACAATCTCAAGTGAGATAAATCTTTTG
* *
1927738 TTTCGAGTAAAACTATCTCAAGCGAGATAAAATTTTGCTTCGAGTG
66 TTTCAAGTGAAACTATCTCAAGCGAGATAAAATTTTGCTTCGAGTG
*
1927784 AAACTATCTCAGGCGAGATGAATCTTGTTT
1 AAACTATCTCAAGCGAGATGAATCTTGTTT
1927814 GAAAATATTG
Statistics
Matches: 395, Mismatches: 65, Indels: 35
0.80 0.13 0.07
Matches are distributed among these distances:
109 6 0.02
110 98 0.25
111 73 0.18
112 153 0.39
113 21 0.05
114 44 0.11
ACGTcount: A:0.39, C:0.13, G:0.17, T:0.31
Consensus pattern (111 bp):
AAACTATCTCAAGCGAGATGAATCTTGTTTTAAGAAAAACAATCTCAAGTGAGATAAATCTTTTG
TTTCAAGTGAAACTATCTCAAGCGAGATAAAATTTTGCTTCGAGTG
Found at i:1939382 original size:28 final size:27
Alignment explanation
Indices: 1939337--1939389 Score: 70
Period size: 28 Copynumber: 1.9 Consensus size: 27
1939327 AAACTTTGAG
** *
1939337 GGGTCAAATTATTTTTTTTTAATTTAA
1 GGGTCAAATTATAATTTTTAAATTTAA
1939364 GGGTCTAAATTATAATTTTTAAATTT
1 GGGTC-AAATTATAATTTTTAAATTT
1939390 TGGGGGCCAT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
27 5 0.23
28 17 0.77
ACGTcount: A:0.32, C:0.04, G:0.11, T:0.53
Consensus pattern (27 bp):
GGGTCAAATTATAATTTTTAAATTTAA
Found at i:1942610 original size:56 final size:55
Alignment explanation
Indices: 1942522--1942705 Score: 224
Period size: 56 Copynumber: 3.3 Consensus size: 55
1942512 CAGGGCCCAA
* * *
1942522 AAATCGAATATATTTATCAGTTGTTGTCATTAATAAGCATAAAAATATGGGTCCCG
1 AAATCGAATATATCTATCAGTTGTTGTCATTAAAAAGCATAAAAATA-GGGACCCG
* * * * *
1942578 AAATCGAGTATATCTATCAGTTGTTATTATTAAGAAGCATAAAAGTAGGGACCTCG
1 AAATCGAATATATCTATCAGTTGTTGTCATTAAAAAGCATAAAAATAGGGACC-CG
* * * *
1942634 GAATCAAATATATCTATCAGTTGTTGCCATTAAAAAGCATAAAAATAGGAGGCCCG
1 AAATCGAATATATCTATCAGTTGTTGTCATTAAAAAGCATAAAAATAGG-GACCCG
*
1942690 GAATCGAATATATCTA
1 AAATCGAATATATCTA
1942706 GAAAATAGGA
Statistics
Matches: 109, Mismatches: 17, Indels: 4
0.84 0.13 0.03
Matches are distributed among these distances:
55 5 0.05
56 101 0.93
57 3 0.03
ACGTcount: A:0.39, C:0.14, G:0.17, T:0.30
Consensus pattern (55 bp):
AAATCGAATATATCTATCAGTTGTTGTCATTAAAAAGCATAAAAATAGGGACCCG
Found at i:1944833 original size:20 final size:20
Alignment explanation
Indices: 1944808--1944847 Score: 80
Period size: 20 Copynumber: 2.0 Consensus size: 20
1944798 AGACATATGG
1944808 AGCAAATGTAATCCTCAGGC
1 AGCAAATGTAATCCTCAGGC
1944828 AGCAAATGTAATCCTCAGGC
1 AGCAAATGTAATCCTCAGGC
1944848 CTTTGGCTTT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.35, C:0.25, G:0.20, T:0.20
Consensus pattern (20 bp):
AGCAAATGTAATCCTCAGGC
Found at i:1944893 original size:3 final size:3
Alignment explanation
Indices: 1944885--1944910 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
1944875 CGTCAGGACC
1944885 TAT TAT TAT TAT TAT TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TA
1944911 ACGTTTTTTA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (3 bp):
TAT
Found at i:1953197 original size:17 final size:17
Alignment explanation
Indices: 1953175--1953210 Score: 72
Period size: 17 Copynumber: 2.1 Consensus size: 17
1953165 TAATTCCTAC
1953175 ATTCACCCATATTTAAA
1 ATTCACCCATATTTAAA
1953192 ATTCACCCATATTTAAA
1 ATTCACCCATATTTAAA
1953209 AT
1 AT
1953211 GTAAAAAAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.42, C:0.22, G:0.00, T:0.36
Consensus pattern (17 bp):
ATTCACCCATATTTAAA
Found at i:1956003 original size:39 final size:35
Alignment explanation
Indices: 1955960--1956050 Score: 85
Period size: 39 Copynumber: 2.4 Consensus size: 35
1955950 ATAACATAAC
1955960 TAAAAAAGAATAAAAATAGAAATAAAAATAAAACAAGAA
1 TAAAAAAGAATAAAAATAG-AAT-AAAA-AAAA-AAGAA
* * *
1955999 TAAAAACA-AAGAAAAAATAGAATAAAAGAAAAATAA
1 TAAAAA-AGAA-TAAAAATAGAATAAAAAAAAAAGAA
1956035 TAAAAAAAGAATAAAA
1 T-AAAAAAGAATAAAA
1956051 TTAATATATA
Statistics
Matches: 44, Mismatches: 4, Indels: 11
0.75 0.07 0.19
Matches are distributed among these distances:
36 10 0.23
37 10 0.23
38 4 0.09
39 11 0.25
40 9 0.20
ACGTcount: A:0.78, C:0.02, G:0.08, T:0.12
Consensus pattern (35 bp):
TAAAAAAGAATAAAAATAGAATAAAAAAAAAAGAA
Found at i:1956017 original size:17 final size:16
Alignment explanation
Indices: 1955979--1956051 Score: 51
Period size: 17 Copynumber: 4.2 Consensus size: 16
1955969 ATAAAAATAG
1955979 AAATAAAAATAAA-ACAA
1 AAATAAAAA-AAAGA-AA
*
1955996 GAATAAAAACAAAGAAA
1 AAATAAAAA-AAAGAAA
*
1956013 AAATAGAATAAAAG-AA
1 AAATA-AAAAAAAGAAA
1956029 AAATAATAAAAAAAGAATA
1 AAAT-A-AAAAAAAGAA-A
1956048 AAAT
1 AAAT
1956052 TAATATATAT
Statistics
Matches: 45, Mismatches: 6, Indels: 8
0.76 0.10 0.14
Matches are distributed among these distances:
16 6 0.13
17 29 0.64
18 5 0.11
19 5 0.11
ACGTcount: A:0.78, C:0.03, G:0.07, T:0.12
Consensus pattern (16 bp):
AAATAAAAAAAAGAAA
Found at i:1956047 original size:11 final size:11
Alignment explanation
Indices: 1955961--1956050 Score: 55
Period size: 11 Copynumber: 8.3 Consensus size: 11
1955951 TAACATAACT
1955961 AAAAAAGAATA
1 AAAAAAGAATA
*
1955972 AAAATAG---A
1 AAAAAAGAATA
*
1955980 AATAAA-AATA
1 AAAAAAGAATA
*
1955990 AAACAAGAATA
1 AAAAAAGAATA
* *
1956001 AAAACA-AAGA
1 AAAAAAGAATA
1956011 AAAAATAGAATAAA
1 AAAAA-AGAAT--A
*
1956025 AGAAAAATAATA
1 A-AAAAAGAATA
1956037 AAAAAAGAATA
1 AAAAAAGAATA
1956048 AAA
1 AAA
1956051 TTAATATATA
Statistics
Matches: 58, Mismatches: 12, Indels: 18
0.66 0.14 0.20
Matches are distributed among these distances:
8 5 0.09
10 12 0.21
11 27 0.47
12 4 0.07
14 6 0.10
15 4 0.07
ACGTcount: A:0.79, C:0.02, G:0.08, T:0.11
Consensus pattern (11 bp):
AAAAAAGAATA
Found at i:1956142 original size:39 final size:37
Alignment explanation
Indices: 1956098--1956206 Score: 91
Period size: 39 Copynumber: 2.9 Consensus size: 37
1956088 TAAAATAAGT
1956098 AATAAACAATA-ATAAGAAAAAAATAAAGATATATATA
1 AATAAACAATATATAA-AAAAAAATAAAGATATATATA
* * * * *
1956135 CATATAAATATTATGTAAAAACAAATAAATATATATATA
1 -A-ATAAACAATATATAAAAAAAAATAAAGATATATATA
* *
1956174 AATAAAC-AT-TAGAAAAACAAAAT-AATATATATA
1 AATAAACAATATATAAAAA-AAAATAAAGATATATA
1956207 AGTAGAATAA
Statistics
Matches: 58, Mismatches: 10, Indels: 9
0.75 0.13 0.12
Matches are distributed among these distances:
35 16 0.28
36 5 0.09
37 5 0.09
38 2 0.03
39 27 0.47
40 3 0.05
ACGTcount: A:0.65, C:0.05, G:0.04, T:0.27
Consensus pattern (37 bp):
AATAAACAATATATAAAAAAAAATAAAGATATATATA
Found at i:1956167 original size:35 final size:36
Alignment explanation
Indices: 1956126--1956206 Score: 96
Period size: 37 Copynumber: 2.2 Consensus size: 36
1956116 AAAAATAAAG
*
1956126 ATATATATACAT-ATAAATATTATGTAAAAAC-AAATA
1 ATATATATACATAATAAACATTA-G-AAAAACAAAATA
*
1956162 A-ATATATATATAAATAAACATTAGAAAAACAAAATA
1 ATATATATACAT-AATAAACATTAGAAAAACAAAATA
1956198 ATATATATA
1 ATATATATA
1956207 AGTAGAATAA
Statistics
Matches: 39, Mismatches: 2, Indels: 7
0.81 0.04 0.15
Matches are distributed among these distances:
35 15 0.38
36 8 0.21
37 16 0.41
ACGTcount: A:0.62, C:0.05, G:0.02, T:0.31
Consensus pattern (36 bp):
ATATATATACATAATAAACATTAGAAAAACAAAATA
Found at i:1956207 original size:33 final size:38
Alignment explanation
Indices: 1956114--1956206 Score: 115
Period size: 35 Copynumber: 2.5 Consensus size: 38
1956104 CAATAATAAG
* *
1956114 AAAA-AAATAAAGATATATATACATATAAATATTATGTA
1 AAAACAAATAAATATATATATA-ATATAAACATTATGTA
1956152 AAAACAAATAAATATATATATAA-ATAAACATTA-G-A
1 AAAACAAATAAATATATATATAATATAAACATTATGTA
1956187 AAAACAAA-ATAATATATATA
1 AAAACAAATA-AATATATATA
1956207 AGTAGAATAA
Statistics
Matches: 51, Mismatches: 2, Indels: 7
0.85 0.03 0.12
Matches are distributed among these distances:
34 1 0.02
35 19 0.37
36 1 0.02
37 9 0.18
38 5 0.10
39 16 0.31
ACGTcount: A:0.65, C:0.04, G:0.03, T:0.28
Consensus pattern (38 bp):
AAAACAAATAAATATATATATAATATAAACATTATGTA
Found at i:1956250 original size:12 final size:12
Alignment explanation
Indices: 1956221--1956305 Score: 70
Period size: 12 Copynumber: 7.2 Consensus size: 12
1956211 GAATAAAAAG
1956221 AAAATAATAATA
1 AAAATAATAATA
**
1956233 GGAATAATAATA
1 AAAATAATAATA
* *
1956245 ATAATAGTAA-A
1 AAAATAATAATA
*
1956256 AAGA-AATAATA
1 AAAATAATAATA
1956267 AAATATATATAATA
1 AAA-ATA-ATAATA
1956281 AGAAATAA-AATA
1 A-AAATAATAATA
1956293 AAAATAA-AATA
1 AAAATAATAATA
1956304 AA
1 AA
1956306 CAAATAAAAA
Statistics
Matches: 59, Mismatches: 9, Indels: 11
0.75 0.11 0.14
Matches are distributed among these distances:
10 4 0.07
11 18 0.31
12 23 0.39
13 2 0.03
14 10 0.17
15 2 0.03
ACGTcount: A:0.71, C:0.00, G:0.06, T:0.24
Consensus pattern (12 bp):
AAAATAATAATA
Found at i:1956297 original size:11 final size:11
Alignment explanation
Indices: 1956263--1956305 Score: 50
Period size: 11 Copynumber: 3.5 Consensus size: 11
1956253 AAAAAGAAAT
1956263 AATAAAATATATA
1 AATAAAA-ATA-A
1956276 TAATAAGAAATAA
1 -AATAA-AAATAA
1956289 AATAAAAATAA
1 AATAAAAATAA
1956300 AATAAA
1 AATAAA
1956306 CAAATAAAAA
Statistics
Matches: 28, Mismatches: 0, Indels: 5
0.85 0.00 0.15
Matches are distributed among these distances:
11 12 0.43
12 5 0.18
13 1 0.04
14 8 0.29
15 2 0.07
ACGTcount: A:0.74, C:0.00, G:0.02, T:0.23
Consensus pattern (11 bp):
AATAAAAATAA
Found at i:1956299 original size:21 final size:20
Alignment explanation
Indices: 1956263--1956322 Score: 59
Period size: 20 Copynumber: 3.0 Consensus size: 20
1956253 AAAAAGAAAT
* *
1956263 AATAAAATATATATAATAAGA
1 AATAAAATAAAAATAA-AAGA
*
1956284 AATAAAATAAAAATAAAATA
1 AATAAAATAAAAATAAAAGA
*
1956304 AA-CAAATAAAAAATAAAAG
1 AATAAAAT-AAAAATAAAAG
1956323 GATTAAATTT
Statistics
Matches: 33, Mismatches: 5, Indels: 3
0.80 0.12 0.07
Matches are distributed among these distances:
19 4 0.12
20 15 0.45
21 14 0.42
ACGTcount: A:0.75, C:0.02, G:0.03, T:0.20
Consensus pattern (20 bp):
AATAAAATAAAAATAAAAGA
Found at i:1958976 original size:6 final size:6
Alignment explanation
Indices: 1958957--1958996 Score: 55
Period size: 6 Copynumber: 6.5 Consensus size: 6
1958947 ACCCACCTTA
1958957 TTTCTT TTAT-TT TTTCTT TTTCTT TTTCTT TTTCTCT TTT
1 TTTCTT TT-TCTT TTTCTT TTTCTT TTTCTT TTTCT-T TTT
1958997 TTCAATTTAG
Statistics
Matches: 31, Mismatches: 0, Indels: 5
0.86 0.00 0.14
Matches are distributed among these distances:
5 1 0.03
6 25 0.81
7 5 0.16
ACGTcount: A:0.03, C:0.15, G:0.00, T:0.82
Consensus pattern (6 bp):
TTTCTT
Found at i:1967082 original size:33 final size:33
Alignment explanation
Indices: 1967035--1967110 Score: 127
Period size: 33 Copynumber: 2.3 Consensus size: 33
1967025 CACTAAATGT
*
1967035 TCTTAATGAATTCATATCTCAGGTTTTGGGTTG
1 TCTTAATGAGTTCATATCTCAGGTTTTGGGTTG
1967068 TCTTAATGAGTTCATATCTCAGGTTTTGGGTTG
1 TCTTAATGAGTTCATATCTCAGGTTTTGGGTTG
1967101 TCCTT-ATGAG
1 T-CTTAATGAG
1967111 ATAGACTTGA
Statistics
Matches: 41, Mismatches: 1, Indels: 2
0.93 0.02 0.05
Matches are distributed among these distances:
33 38 0.93
34 3 0.07
ACGTcount: A:0.20, C:0.13, G:0.22, T:0.45
Consensus pattern (33 bp):
TCTTAATGAGTTCATATCTCAGGTTTTGGGTTG
Found at i:1972799 original size:14 final size:14
Alignment explanation
Indices: 1972774--1972821 Score: 53
Period size: 14 Copynumber: 3.4 Consensus size: 14
1972764 ATTTACTTTT
1972774 TATTTATTTAATTTC
1 TATTT-TTTAATTTC
1972789 -ATTATTTTAATTTC
1 TATT-TTTTAATTTC
* *
1972803 TATTTTTTATTTTT
1 TATTTTTTAATTTC
1972817 TATTT
1 TATTT
1972822 ACATTTTCAA
Statistics
Matches: 29, Mismatches: 2, Indels: 5
0.81 0.06 0.14
Matches are distributed among these distances:
14 25 0.86
15 4 0.14
ACGTcount: A:0.23, C:0.04, G:0.00, T:0.73
Consensus pattern (14 bp):
TATTTTTTAATTTC
Found at i:1973518 original size:17 final size:18
Alignment explanation
Indices: 1973493--1973530 Score: 51
Period size: 17 Copynumber: 2.2 Consensus size: 18
1973483 TTATCCCAAT
*
1973493 TTTAGTTATTTTA-TTTA
1 TTTAGTTATTTAATTTTA
*
1973510 TTTATTTATTTAATTTTA
1 TTTAGTTATTTAATTTTA
1973528 TTT
1 TTT
1973531 CATTATACTT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
17 11 0.61
18 7 0.39
ACGTcount: A:0.24, C:0.00, G:0.03, T:0.74
Consensus pattern (18 bp):
TTTAGTTATTTAATTTTA
Found at i:1973603 original size:14 final size:14
Alignment explanation
Indices: 1973565--1973616 Score: 59
Period size: 14 Copynumber: 3.5 Consensus size: 14
1973555 AATCCCCTTT
*
1973565 TTTATTTATTACTA
1 TTTATTTATTATTA
1973579 TTACTATTTTATTATTA
1 TT--TA-TTTATTATTA
1973596 TTTATTTATTATTA
1 TTTATTTATTATTA
*
1973610 TATATTT
1 TTTATTT
1973617 TAATTCATTA
Statistics
Matches: 33, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
14 18 0.55
15 2 0.06
16 2 0.06
17 11 0.33
ACGTcount: A:0.29, C:0.04, G:0.00, T:0.67
Consensus pattern (14 bp):
TTTATTTATTATTA
Found at i:1979063 original size:11 final size:11
Alignment explanation
Indices: 1979034--1979068 Score: 52
Period size: 11 Copynumber: 3.1 Consensus size: 11
1979024 AATTCAATTA
*
1979034 TTTTATTTATT
1 TTTTATTTAAT
1979045 TGTTTATTTAAT
1 T-TTTATTTAAT
1979057 TTTTATTTAAT
1 TTTTATTTAAT
1979068 T
1 T
1979069 ATACTTCTTT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
11 12 0.55
12 10 0.45
ACGTcount: A:0.23, C:0.00, G:0.03, T:0.74
Consensus pattern (11 bp):
TTTTATTTAAT
Found at i:1979137 original size:7 final size:7
Alignment explanation
Indices: 1979100--1979142 Score: 50
Period size: 7 Copynumber: 5.7 Consensus size: 7
1979090 AACCCCCTTT
1979100 TTATTTA
1 TTATTTA
1979107 TTACTATTA
1 TTA-T-TTA
*
1979116 ATATTTA
1 TTATTTA
1979123 TTATTTTA
1 TTA-TTTA
1979131 TTATTTA
1 TTATTTA
1979138 TTATT
1 TTATT
1979143 ATATATTTTA
Statistics
Matches: 31, Mismatches: 2, Indels: 6
0.79 0.05 0.15
Matches are distributed among these distances:
7 17 0.55
8 9 0.29
9 5 0.16
ACGTcount: A:0.30, C:0.02, G:0.00, T:0.67
Consensus pattern (7 bp):
TTATTTA
Found at i:1979137 original size:15 final size:15
Alignment explanation
Indices: 1979100--1979142 Score: 59
Period size: 15 Copynumber: 2.8 Consensus size: 15
1979090 AACCCCCTTT
*
1979100 TTATTTATTACTATTA
1 TTATTTATTA-TTTTA
*
1979116 ATATTTATTATTTTA
1 TTATTTATTATTTTA
1979131 TTATTTATTATT
1 TTATTTATTATT
1979143 ATATATTTTA
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
15 15 0.62
16 9 0.38
ACGTcount: A:0.30, C:0.02, G:0.00, T:0.67
Consensus pattern (15 bp):
TTATTTATTATTTTA
Found at i:1983667 original size:10 final size:10
Alignment explanation
Indices: 1983652--1983791 Score: 114
Period size: 10 Copynumber: 14.0 Consensus size: 10
1983642 TAGCTCTTTT
*
1983652 AAAGAAAGAA
1 AAAGAAAAAA
1983662 AAAGAAAAAA
1 AAAGAAAAAA
1983672 AAA-AAAAAA
1 AAAGAAAAAA
1983681 AAA-AAAAGAA
1 AAAGAAAA-AA
1983691 AAA-AATAAAA
1 AAAGAA-AAAA
*
1983701 AAA-ATAAAA
1 AAAGAAAAAA
*
1983710 AAATAAAAAA
1 AAAGAAAAAA
1983720 AATA-AAAAAA
1 AA-AGAAAAAA
*
1983730 AAATAAAAAA
1 AAAGAAAAAA
1983740 TAAA-AAATAAA
1 -AAAGAAA-AAA
1983751 AAA-AAAATAA
1 AAAGAAAA-AA
*
1983761 AAAAAAAAAA
1 AAAGAAAAAA
1983771 AAAGAAAAAA
1 AAAGAAAAAA
*
1983781 AGGAGAAAAAA
1 A-AAGAAAAAA
1983792 TAGAAAAATG
Statistics
Matches: 115, Mismatches: 5, Indels: 19
0.83 0.04 0.14
Matches are distributed among these distances:
9 22 0.19
10 72 0.63
11 21 0.18
ACGTcount: A:0.89, C:0.00, G:0.06, T:0.06
Consensus pattern (10 bp):
AAAGAAAAAA
Found at i:1983796 original size:9 final size:8
Alignment explanation
Indices: 1983660--1983800 Score: 122
Period size: 8 Copynumber: 16.8 Consensus size: 8
1983650 TTAAAGAAAG
*
1983660 AAAAAGAA
1 AAAAATAA
1983668 AAAAA-AA
1 AAAAATAA
*
1983675 AAAAAAAA
1 AAAAATAA
*
1983683 AAAAAGAA
1 AAAAATAA
1983691 AAAAATAAA
1 AAAAAT-AA
1983700 AAAAATAA
1 AAAAATAA
1983708 AAAAATAAA
1 AAAAAT-AA
1983717 AAAAATAAA
1 AAAAAT-AA
*
1983726 AAAAAAATA
1 AAAAATA-A
1983735 AAAAATAAA
1 AAAAAT-AA
*
1983744 AAATAAAAA
1 AAA-AATAA
1983753 AAAAATAA
1 AAAAATAA
*
1983761 AAAAAAAA
1 AAAAATAA
*
1983769 AAAAAGAA
1 AAAAATAA
*
1983777 AAAAAGGAGA
1 AAAAA-TA-A
*
1983787 AAAAATAG
1 AAAAATAA
1983795 AAAAAT
1 AAAAAT
1983801 GGTCAAGTTG
Statistics
Matches: 115, Mismatches: 10, Indels: 16
0.82 0.07 0.11
Matches are distributed among these distances:
7 7 0.06
8 57 0.50
9 42 0.37
10 9 0.08
ACGTcount: A:0.88, C:0.00, G:0.05, T:0.07
Consensus pattern (8 bp):
AAAAATAA
Found at i:1983799 original size:1 final size:1
Alignment explanation
Indices: 1983660--1983781 Score: 145
Period size: 1 Copynumber: 122.0 Consensus size: 1
1983650 TTAAAGAAAG
* * * * * *
1983660 AAAAAGAAAAAAAAAAAAAAAAAAAAAAGAAAAAAATAAAAAAAATAAAAAAATAAAAAAAATAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
* * * * *
1983725 AAAAAAAATAAAAAATAAAAAATAAAAAAAAAATAAAAAAAAAAAAAAAGAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
1983782 GGAGAAAAAA
Statistics
Matches: 99, Mismatches: 22, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
1 99 1.00
ACGTcount: A:0.91, C:0.00, G:0.02, T:0.07
Consensus pattern (1 bp):
A
Found at i:1985574 original size:139 final size:139
Alignment explanation
Indices: 1985311--1985825 Score: 712
Period size: 139 Copynumber: 3.7 Consensus size: 139
1985301 AACAAATTAA
* * * * **
1985311 ATCAATATTT-CAATGGAGAGTTCATACTGAGAAGAACTCATTCGATGAGGGAGAAGAAGTTCAT
1 ATCAACATTTCCAATGGAGAGTTCATAATGAGAAGAACTCATCCGAAGAGAAAGAAGAAGTTCAT
* * *
1985375 AATGAGAAGAAATTTTTTAACCTTAGCTCGATTCATCGCATATGGAGTTGAATCAGCGACCCCTC
66 AATGAGAAGAACTTGTTCAACCTTAGCTCGATTCATCGCATATGGAGTTGAATCAGCGACCCCTC
1985440 ACTCGAGAG
131 ACTCGAGAG
** * * *
1985449 ATCAGTATTTCCAATGGAGAGTTCACAATGATAAGATCTCATCCGAAGAGAAAGAAGAAGTTCAT
1 ATCAACATTTCCAATGGAGAGTTCATAATGAGAAGAACTCATCCGAAGAGAAAGAAGAAGTTCAT
*
1985514 AATGAGAAGAACTTGTTCAACCTTAGCTCGATTCATCGCATATGGAGTTGAATCAACGACCCCTC
66 AATGAGAAGAACTTGTTCAACCTTAGCTCGATTCATCGCATATGGAGTTGAATCAGCGACCCCTC
1985579 ACTCGAGAG
131 ACTCGAGAG
* * * * *
1985588 ATCAACATTTCTAATGGAGAGTTCATAATGAGAAGAATTCATCTGATGA-AGGAGAAGAAGTTCA
1 ATCAACATTTCCAATGGAGAGTTCATAATGAGAAGAACTCATCCGAAGAGA-AAGAAGAAGTTCA
* * ** *
1985652 TAATGAGAAGAACTTGTTCAACCTTAGCTCGATTCATCACATATGAAGTTGAATCAGTAACACCT
65 TAATGAGAAGAACTTGTTCAACCTTAGCTCGATTCATCGCATATGGAGTTGAATCAGCGACCCCT
1985717 CACTCGAG-G
130 CACTCGAGAG
* * * *
1985726 CATCAACATTTCCAATGGAGAGTTCATAATGATAAGAACTCATCCGAATAGTAAGAAGAAGTTAA
1 -ATCAACATTTCCAATGGAGAGTTCATAATGAGAAGAACTCATCCGAAGAGAAAGAAGAAGTTCA
* *
1985791 CAATGAGAAGAACTTGTTCAACCTTAGTTCGATTC
65 TAATGAGAAGAACTTGTTCAACCTTAGCTCGATTC
1985826 CATCACAAGA
Statistics
Matches: 333, Mismatches: 40, Indels: 7
0.88 0.11 0.02
Matches are distributed among these distances:
138 11 0.03
139 322 0.97
ACGTcount: A:0.36, C:0.18, G:0.20, T:0.26
Consensus pattern (139 bp):
ATCAACATTTCCAATGGAGAGTTCATAATGAGAAGAACTCATCCGAAGAGAAAGAAGAAGTTCAT
AATGAGAAGAACTTGTTCAACCTTAGCTCGATTCATCGCATATGGAGTTGAATCAGCGACCCCTC
ACTCGAGAG
Found at i:1985661 original size:23 final size:22
Alignment explanation
Indices: 1985617--1985661 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 22
1985607 AGTTCATAAT
*
1985617 GAGAAGAATTCATCTGATGAAG
1 GAGAAGAATTCATATGATGAAG
1985639 GAGAAGAAGTTCATAATGA-GAAG
1 GAGAAGAA-TTCAT-ATGATGAAG
1985662 AACTTGTTCA
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
22 8 0.40
23 9 0.45
24 3 0.15
ACGTcount: A:0.44, C:0.07, G:0.29, T:0.20
Consensus pattern (22 bp):
GAGAAGAATTCATATGATGAAG
Found at i:1985825 original size:278 final size:277
Alignment explanation
Indices: 1985311--1985825 Score: 800
Period size: 278 Copynumber: 1.9 Consensus size: 277
1985301 AACAAATTAA
* * *
1985311 ATCAATATTTCAATGGAGAGTTCATACTGAGAAGAACTCATTCGATGAGGGAGAAGAAGTTCATA
1 ATCAACATTTCAATGGAGAGTTCATAATGAGAAGAACTCATTCGATGAAGGAGAAGAAGTTCATA
* * * * * *
1985376 ATGAGAAGAAATTTTTTAACCTTAGCTCGATTCATCGCATATGGAGTTGAATCAGCGACCCCTCA
66 ATGAGAAGAAATTGTTCAACCTTAGCTCGATTCATCACATATGAAGTTGAATCAGCAACACCTCA
** *
1985441 CTCGAGAGATCAGTATTTCCAATGGAGAGTTCACAATGATAAGATCTCATCCGAAGAGAAAGAAG
131 CTCGAGAGATCAACATTTCCAATGGAGAGTTCACAATGATAAGAACTCATCCGAAGAGAAAGAAG
* *
1985506 AAGTTCATAATGAGAAGAACTTGTTCAACCTTAGCTCGATTCATCGCATATGGAGTTGAATCAAC
196 AAGTTAACAATGAGAAGAACTTGTTCAACCTTAGCTCGATTCATCGCATATGGAGTTGAATCAAC
1985571 GACCCCTCACTCGAGAG
261 GACCCCTCACTCGAGAG
*
1985588 ATCAACATTTCTAATGGAGAGTTCATAATGAGAAGAATTCA-TCTGATGAAGGAGAAGAAGTTCA
1 ATCAACATTTC-AATGGAGAGTTCATAATGAGAAGAACTCATTC-GATGAAGGAGAAGAAGTTCA
* *
1985652 TAATGAGAAGAACTTGTTCAACCTTAGCTCGATTCATCACATATGAAGTTGAATCAGTAACACCT
64 TAATGAGAAGAAATTGTTCAACCTTAGCTCGATTCATCACATATGAAGTTGAATCAGCAACACCT
* * *
1985717 CACTCGAG-GCATCAACATTTCCAATGGAGAGTTCATAATGATAAGAACTCATCCGAATAGTAAG
129 CACTCGAGAG-ATCAACATTTCCAATGGAGAGTTCACAATGATAAGAACTCATCCGAAGAGAAAG
*
1985781 AAGAAGTTAACAATGAGAAGAACTTGTTCAACCTTAGTTCGATTC
193 AAGAAGTTAACAATGAGAAGAACTTGTTCAACCTTAGCTCGATTC
1985826 CATCACAAGA
Statistics
Matches: 214, Mismatches: 21, Indels: 5
0.89 0.09 0.02
Matches are distributed among these distances:
277 13 0.06
278 201 0.94
ACGTcount: A:0.36, C:0.18, G:0.20, T:0.26
Consensus pattern (277 bp):
ATCAACATTTCAATGGAGAGTTCATAATGAGAAGAACTCATTCGATGAAGGAGAAGAAGTTCATA
ATGAGAAGAAATTGTTCAACCTTAGCTCGATTCATCACATATGAAGTTGAATCAGCAACACCTCA
CTCGAGAGATCAACATTTCCAATGGAGAGTTCACAATGATAAGAACTCATCCGAAGAGAAAGAAG
AAGTTAACAATGAGAAGAACTTGTTCAACCTTAGCTCGATTCATCGCATATGGAGTTGAATCAAC
GACCCCTCACTCGAGAG
Found at i:1985878 original size:115 final size:117
Alignment explanation
Indices: 1985727--1985998 Score: 406
Period size: 115 Copynumber: 2.3 Consensus size: 117
1985717 CACTCGAGGC
* * * * *
1985727 ATCAACATTTCCAATG-GAGAGTTCATAATGATAAGAACTCATCCGAATAGTAAGAAGAAGTTAA
1 ATCAACATTTCCAATGAAAGAGTTCATAATAAGAAGAACTCATCCGAAGAGGAAGAAGAAGTTAA
*
1985791 CAATGAGAAGAACTTGTTCAACCTTAGTTCGATTCCATC-ACAA-GAAATGG
66 CAATGAGAAGAACTTGTTCAACCTTAGTTCGATTCCATCAAAAAGGAAATGG
* * * *
1985841 ATCAATATTTCCAATGAAAGAGTTCATAATAAGAAGAACTCGTCCGAAGAGGAAGAATAAGTTCA
1 ATCAACATTTCCAATGAAAGAGTTCATAATAAGAAGAACTCATCCGAAGAGGAAGAAGAAGTTAA
* *
1985906 TAATGAGAAGAACTTGTTCAACCTTAGTTCGATTCCATCATAAAAGGAGATGG
66 CAATGAGAAGAACTTGTTCAACCTTAGTTCGATTCCATCA-AAAAGGAAATGG
1985959 ATCAACATTTCCAATGAAAGAGTTCATAATAAGAAGAACT
1 ATCAACATTTCCAATGAAAGAGTTCATAATAAGAAGAACT
1985999 TGTTCAACAT
Statistics
Matches: 141, Mismatches: 13, Indels: 4
0.89 0.08 0.03
Matches are distributed among these distances:
114 15 0.11
115 78 0.55
117 3 0.02
118 45 0.32
ACGTcount: A:0.42, C:0.15, G:0.18, T:0.25
Consensus pattern (117 bp):
ATCAACATTTCCAATGAAAGAGTTCATAATAAGAAGAACTCATCCGAAGAGGAAGAAGAAGTTAA
CAATGAGAAGAACTTGTTCAACCTTAGTTCGATTCCATCAAAAAGGAAATGG
Found at i:1986063 original size:76 final size:78
Alignment explanation
Indices: 1985900--1986073 Score: 237
Period size: 76 Copynumber: 2.2 Consensus size: 78
1985890 AGGAAGAATA
*
1985900 AGTTCATAATGAGAAGAACTTGTTCAACCTTAGTTCGATTCCATCATAAAAGGAGATGGATCAAC
1 AGTTCATAATGAGAAGAACTTGTTCAACCTTAGTTCGATTCCATCACAAAAGGAGAT-GATCAAC
1985965 ATTTCCAATGAAAG
65 ATTTCCAATGAAAG
* * * *
1985979 AGTTCATAATAAGAAGAACTTGTTCAACATTTTGTTCGATTCCATCACAAAA-G-GAT-ATCAAT
1 AGTTCATAATGAGAAGAACTTGTTCAAC-CTTAGTTCGATTCCATCACAAAAGGAGATGATCAAC
* * *
1986041 ATTTCTAGTGGAAG
65 ATTTCCAATGAAAG
1986055 AGTTCATAATGAGAAGAAC
1 AGTTCATAATGAGAAGAAC
1986074 CCGTCCGAAG
Statistics
Matches: 85, Mismatches: 9, Indels: 5
0.86 0.09 0.05
Matches are distributed among these distances:
76 34 0.40
78 3 0.04
79 28 0.33
80 20 0.24
ACGTcount: A:0.39, C:0.15, G:0.17, T:0.29
Consensus pattern (78 bp):
AGTTCATAATGAGAAGAACTTGTTCAACCTTAGTTCGATTCCATCACAAAAGGAGATGATCAACA
TTTCCAATGAAAG
Found at i:1987906 original size:50 final size:49
Alignment explanation
Indices: 1987800--1987922 Score: 119
Period size: 50 Copynumber: 2.5 Consensus size: 49
1987790 TGATATCTTT
* * *
1987800 TATTTTATTTCTTTACTTT-ATATTTTAATTTATGCGATTTACTTTTTATT
1 TATTTAATTTCATTACTTTAAT-TTTTAATTTATGC-ATTTACTTTTTATA
*
1987850 TATTTAATTTCATTACTTTAATTTTTAATTTTTGC-TTTACATTTTTCA-A
1 TATTTAATTTCATTACTTTAATTTTTAATTTATGCATTTAC-TTTTT-ATA
*
1987899 TACTTTAATTTTAGTT-CTTTAATT
1 TA-TTTAATTTCA-TTACTTTAATT
1987923 ATTTCTCTTT
Statistics
Matches: 63, Mismatches: 5, Indels: 10
0.81 0.06 0.13
Matches are distributed among these distances:
48 5 0.08
49 7 0.11
50 47 0.75
51 4 0.06
ACGTcount: A:0.24, C:0.09, G:0.03, T:0.63
Consensus pattern (49 bp):
TATTTAATTTCATTACTTTAATTTTTAATTTATGCATTTACTTTTTATA
Found at i:2004883 original size:130 final size:131
Alignment explanation
Indices: 2004707--2005080 Score: 446
Period size: 130 Copynumber: 2.9 Consensus size: 131
2004697 GGAAAAAGGA
* * * * ** * * ** *
2004707 AATATTTAATTATCTTCTATCGAGAAGAAACAACCTCTCATGCCTTAAAGTAGCCATTTCTTACT
1 AATATCTAATTATTTTCAATCGAGAATAAATGACCTCTCATACCTTAAAGCAATCATTTATTACT
* * * * * ** * * *
2004772 CCAATCAAAAT-AAAAAATAGTATTATTTCCTTCTAAAATTTGATATTAATTCGAGAGGAACTGA
66 CCAATCGAAATGAAGAAATATTATTATTTCATCCTAAAATTAAATATTAATCCGAGAGAAAATGA
2004836 T
131 T
* * * *
2004837 AATATCTAATTATTTTCAATAGAGAATAAATGACCTCTCATACCTTAAAACATTCATTTATCACT
1 AATATCTAATTATTTTCAATCGAGAATAAATGACCTCTCATACCTTAAAGCAATCATTTATTACT
2004902 CCAATCGAAATGAAGAAATATTATTATTTCATCCTAAAATTAAATATTAATCCGAGAGAAAATGA
66 CCAATCGAAATGAAGAAATATTATTATTTCATCCTAAAATTAAATATTAATCCGAGAGAAAATGA
2004967 T
131 T
* * * *
2004968 AATATCCAATTATTTCCAACCGAGAATAAATGA-CTCTCATTCCTTAAAGCAATCATTTATTACT
1 AATATCTAATTATTTTCAATCGAGAATAAATGACCTCTCATACCTTAAAGCAATCATTTATTACT
* * *
2005032 CCAATCGAAATGAAGAAATATTACTATTTTATCCTAAAATTCAATATTA
66 CCAATCGAAATGAAGAAATATTATTATTTCATCCTAAAATTAAATATTA
2005081 TTCGAATGTT
Statistics
Matches: 208, Mismatches: 35, Indels: 2
0.85 0.14 0.01
Matches are distributed among these distances:
130 134 0.64
131 74 0.36
ACGTcount: A:0.41, C:0.17, G:0.08, T:0.34
Consensus pattern (131 bp):
AATATCTAATTATTTTCAATCGAGAATAAATGACCTCTCATACCTTAAAGCAATCATTTATTACT
CCAATCGAAATGAAGAAATATTATTATTTCATCCTAAAATTAAATATTAATCCGAGAGAAAATGA
T
Found at i:2008772 original size:2 final size:2
Alignment explanation
Indices: 2008765--2008795 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
2008755 TTATATGCCA
2008765 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC A
1 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC A
2008796 TATATATATA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.48, G:0.00, T:0.00
Consensus pattern (2 bp):
AC
Found at i:2011244 original size:48 final size:48
Alignment explanation
Indices: 2011166--2011382 Score: 255
Period size: 48 Copynumber: 4.5 Consensus size: 48
2011156 GGAAGACTTA
*
2011166 TTCCACTTACTCTGAA-GGAATATCAAATCTTGGAAAAGAGAGACATG
1 TTCCGCTTACTCTGAAGGGAATATCAAATCTTGGAAAAGAGAGACATG
* * * *
2011213 TTCCGCTTACTCTGAAGGTAATATCAAATCTTTGAGAAGAGAAACATG
1 TTCCGCTTACTCTGAAGGGAATATCAAATCTTGGAAAAGAGAGACATG
* * * **
2011261 TT-CGCTTACAT-TGAAGGGAATATCAGATATGGGGAAGTTGAGAGAC-TG
1 TTCCGCTTAC-TCTGAAGGGAATATCAAATCT-TGGAA-AAGAGAGACATG
* *
2011309 TTCCTCTTACTCTGAAGGGAATATCAAATCCTGGAAAAGAGAGA-ACTG
1 TTCCGCTTACTCTGAAGGGAATATCAAATCTTGGAAAAGAGAGACA-TG
2011357 TTCCGCTTACTCTGAAGGGAATATCA
1 TTCCGCTTACTCTGAAGGGAATATCA
2011383 GATTTTTTAA
Statistics
Matches: 140, Mismatches: 22, Indels: 15
0.79 0.12 0.08
Matches are distributed among these distances:
47 44 0.31
48 68 0.49
49 28 0.20
ACGTcount: A:0.34, C:0.17, G:0.22, T:0.27
Consensus pattern (48 bp):
TTCCGCTTACTCTGAAGGGAATATCAAATCTTGGAAAAGAGAGACATG
Found at i:2011567 original size:42 final size:41
Alignment explanation
Indices: 2011453--2011575 Score: 133
Period size: 42 Copynumber: 3.0 Consensus size: 41
2011443 CATGTGAAAA
* * *
2011453 CATCATGC-CTGAAAGTCTTATGGATGGCCCGAAGGACTTAT
1 CATCATGCTC-GAAAGACTTATAGATGGCCCGAAGGACTTAG
* * ** *
2011494 CATCTTGCTCGAAAGGCTTATAGATTACCCGAAGGATTTAAG
1 CATCATGCTCGAAAGACTTATAGATGGCCCGAAGGACTT-AG
2011536 CATCATGCTCGAAAGACTTACT-GATGGCCCGAAGGACTTA
1 CATCATGCTCGAAAGACTTA-TAGATGGCCCGAAGGACTTA
2011576 TAAATTTTGG
Statistics
Matches: 67, Mismatches: 12, Indels: 6
0.79 0.14 0.07
Matches are distributed among these distances:
41 32 0.48
42 34 0.51
43 1 0.01
ACGTcount: A:0.29, C:0.22, G:0.23, T:0.26
Consensus pattern (41 bp):
CATCATGCTCGAAAGACTTATAGATGGCCCGAAGGACTTAG
Found at i:2011859 original size:230 final size:230
Alignment explanation
Indices: 2011386--2011955 Score: 808
Period size: 230 Copynumber: 2.5 Consensus size: 230
2011376 AATATCAGAT
* * *
2011386 TTTTTAAAATTTCAATTTT-AGGTTTAATATGAGAAACATTTCTCATATTTCAAAAGGCATGTGA
1 TTTTCAAAATTTCAATTTTCAGATTTAATATGAGAAAC--TT-TCATATTTCAAAAGACATGTGA
* *
2011450 AAACATCATGCCTGAAAGTCTTATGGATGGCCCGAAGGACTTATCATCTTGCTCGAAAGGCTTAT
63 AAACATCATGCCCGAAAGTCTTATGGATGGCCCGAAGGACTTATCATCTTGCTCGAAAGGCTTAA
* * *
2011515 AGATTACCCGAAGGATTTAAGCATCATGCTCGAAAGACTTACTGATGGCCCGAAGGACTTATAAA
128 AGATGACCCGAAGAATTTAAGCATCATGCTCGAAAGACATACTGATGGCCCGAAGGACTTATAAA
2011580 TTTTGGAAATAGTTTACTAAGTAAGAAACCTTTCTTAC
193 TTTTGGAAATAGTTTACTAAGTAAGAAACCTTTCTTAC
2011618 TTTTCAAAATTTCAATTTTCAGATTTAATATGAGAAACTTTCATATTTCAAAAGACATGTGAAAA
1 TTTTCAAAATTTCAATTTTCAGATTTAATATGAGAAACTTTCATATTTCAAAAGACATGTGAAAA
* * *
2011683 CATCCTGCCCGAAGGTCTTATGGATGGCCTGAAGGACTTATCATCTTGCTCGAAAGGCTTAAAGA
66 CATCATGCCCGAAAGTCTTATGGATGGCCCGAAGGACTTATCATCTTGCTCGAAAGGCTTAAAGA
* *
2011748 TGACCTGAAGAATTTAAGCATCATGCTCGAAAGACATACTGAT-GCCTGAAGGACTTATAAATTT
131 TGACCCGAAGAATTTAAGCATCATGCTCGAAAGACATACTGATGGCCCGAAGGACTTATAAATTT
2011812 TGGAAATAGTTTACTAAGTAAGAAACCTTTCTTAC
196 TGGAAATAGTTTACTAAGTAAGAAACCTTTCTTAC
* * ** * *
2011847 TTTTCAAAAATTTCAAATTTTCAAATTTGA-ATGAGAAACCTTTCTCATATTTTGATAGACAAGT
1 TTTTC-AAAATTTC-AATTTTCAGATTTAATATGAGAAA-C-TT-TCATATTTCAAAAGACATGT
* * * * *
2011911 AAAAACATCATG-TCTAAAGGTCTTAT-GATGACCCAAAGGACTTAT
61 GAAAACATCATGCCCGAAA-GTCTTATGGATGGCCCGAAGGACTTAT
2011956 AAATTTTGGA
Statistics
Matches: 304, Mismatches: 27, Indels: 14
0.88 0.08 0.04
Matches are distributed among these distances:
229 60 0.20
230 139 0.46
231 16 0.05
232 39 0.13
233 50 0.16
ACGTcount: A:0.35, C:0.16, G:0.16, T:0.32
Consensus pattern (230 bp):
TTTTCAAAATTTCAATTTTCAGATTTAATATGAGAAACTTTCATATTTCAAAAGACATGTGAAAA
CATCATGCCCGAAAGTCTTATGGATGGCCCGAAGGACTTATCATCTTGCTCGAAAGGCTTAAAGA
TGACCCGAAGAATTTAAGCATCATGCTCGAAAGACATACTGATGGCCCGAAGGACTTATAAATTT
TGGAAATAGTTTACTAAGTAAGAAACCTTTCTTAC
Found at i:2018620 original size:21 final size:22
Alignment explanation
Indices: 2018590--2018643 Score: 58
Period size: 23 Copynumber: 2.5 Consensus size: 22
2018580 CGTGGGAGGT
*
2018590 ATCGATTCCC-TC-AAGGAGGGA
1 ATCGGTTCCCATCAAAGG-GGGA
*
2018611 ATTGGTTCCCATTCAAAGGGGGA
1 ATCGGTTCCCA-TCAAAGGGGGA
2018634 ATCGGTTCCC
1 ATCGGTTCCC
2018644 CTTCAAGGGG
Statistics
Matches: 27, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
21 8 0.30
23 15 0.56
24 4 0.15
ACGTcount: A:0.24, C:0.24, G:0.28, T:0.24
Consensus pattern (22 bp):
ATCGGTTCCCATCAAAGGGGGA
Found at i:2018633 original size:23 final size:22
Alignment explanation
Indices: 2018600--2018653 Score: 72
Period size: 23 Copynumber: 2.4 Consensus size: 22
2018590 ATCGATTCCC
*
2018600 TCAAGGAGGGAATTGGTTCCCAT
1 TCAAGG-GGGAATCGGTTCCCAT
*
2018623 TCAAAGGGGGAATCGGTTCCCCT
1 TC-AAGGGGGAATCGGTTCCCAT
2018646 TCAAGGGG
1 TCAAGGGG
2018654 TATCGATTCC
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
22 6 0.21
23 18 0.64
24 4 0.14
ACGTcount: A:0.24, C:0.20, G:0.33, T:0.22
Consensus pattern (22 bp):
TCAAGGGGGAATCGGTTCCCAT
Found at i:2024635 original size:22 final size:23
Alignment explanation
Indices: 2024592--2024635 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
2024582 TTTGAAACGA
*
2024592 TTTGAAATACTTTGTAAAATTAT
1 TTTGAAATAATTTGTAAAATTAT
*
2024615 TTTGAAATAATTT-TAATATTA
1 TTTGAAATAATTTGTAAAATTA
2024636 AAACTTAATT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
22 7 0.37
23 12 0.63
ACGTcount: A:0.41, C:0.02, G:0.07, T:0.50
Consensus pattern (23 bp):
TTTGAAATAATTTGTAAAATTAT
Found at i:2031709 original size:8 final size:8
Alignment explanation
Indices: 2031696--2031767 Score: 51
Period size: 8 Copynumber: 9.1 Consensus size: 8
2031686 CCTATTTTCT
2031696 TTTTCTTC
1 TTTTCTTC
2031704 TTTTCTTTC
1 TTTTC-TTC
*
2031713 TCTTTCTTT
1 T-TTTCTTC
*
2031722 TTTTCAT-
1 TTTTCTTC
**
2031729 TTTTCTAG
1 TTTTCTTC
2031737 TTTTCTTC
1 TTTTCTTC
*
2031745 ATTT-TTC
1 TTTTCTTC
*
2031752 TTTTTTTC
1 TTTTCTTC
2031760 TTTT-TTC
1 TTTTCTTC
2031767 T
1 T
2031768 AGCGAAATAT
Statistics
Matches: 52, Mismatches: 8, Indels: 9
0.75 0.12 0.13
Matches are distributed among these distances:
7 15 0.29
8 26 0.50
9 7 0.13
10 4 0.08
ACGTcount: A:0.04, C:0.18, G:0.01, T:0.76
Consensus pattern (8 bp):
TTTTCTTC
Found at i:2031712 original size:18 final size:19
Alignment explanation
Indices: 2031691--2031762 Score: 59
Period size: 18 Copynumber: 4.2 Consensus size: 19
2031681 TGAACCCTAT
2031691 TTTC-TTTTTCTTCTTTTC
1 TTTCATTTTTCTTCTTTTC
*
2031709 TTTC---TCT-TTCTTTT-
1 TTTCATTTTTCTTCTTTTC
**
2031723 TTTCATTTTTCTAGTTTTC
1 TTTCATTTTTCTTCTTTTC
*
2031742 -TTCATTTTTCTTTTTTTC
1 TTTCATTTTTCTTCTTTTC
2031760 TTT
1 TTT
2031763 TTTCTAGCGA
Statistics
Matches: 42, Mismatches: 6, Indels: 11
0.71 0.10 0.19
Matches are distributed among these distances:
14 4 0.10
15 7 0.17
16 2 0.05
17 2 0.05
18 25 0.60
19 2 0.05
ACGTcount: A:0.04, C:0.18, G:0.01, T:0.76
Consensus pattern (19 bp):
TTTCATTTTTCTTCTTTTC
Found at i:2031733 original size:15 final size:15
Alignment explanation
Indices: 2031701--2031767 Score: 73
Period size: 15 Copynumber: 4.3 Consensus size: 15
2031691 TTTCTTTTTC
*
2031701 TTCTTTTCTTTC-TCT
1 TTCTTTT-TTTCATTT
2031716 TTCTTTTTTTCATTT
1 TTCTTTTTTTCATTT
2031731 TTCTAGTTTTCTTCATTT
1 TTCT--TTTT-TTCATTT
*
2031749 TTCTTTTTTTCTTTT
1 TTCTTTTTTTCATTT
2031764 TTCT
1 TTCT
2031768 AGCGAAATAT
Statistics
Matches: 46, Mismatches: 2, Indels: 8
0.82 0.04 0.14
Matches are distributed among these distances:
14 4 0.09
15 23 0.50
16 4 0.09
17 4 0.09
18 11 0.24
ACGTcount: A:0.04, C:0.18, G:0.01, T:0.76
Consensus pattern (15 bp):
TTCTTTTTTTCATTT
Found at i:2031741 original size:33 final size:32
Alignment explanation
Indices: 2031690--2031769 Score: 99
Period size: 33 Copynumber: 2.4 Consensus size: 32
2031680 TTGAACCCTA
**
2031690 TTTTCTTTTTCTTCTTTTCTTTC-TCTTTCTTT
1 TTTTCTTTTTCTAGTTTTC-TTCATCTTTCTTT
*
2031722 TTTTCATTTTTCTAGTTTTCTTCATTTTTCTTT
1 TTTTC-TTTTTCTAGTTTTCTTCATCTTTCTTT
2031755 TTTTCTTTTTTCTAG
1 TTTTC-TTTTTCTAG
2031770 CGAAATATTT
Statistics
Matches: 42, Mismatches: 4, Indels: 3
0.86 0.08 0.06
Matches are distributed among these distances:
32 8 0.19
33 34 0.81
ACGTcount: A:0.05, C:0.17, G:0.03, T:0.75
Consensus pattern (32 bp):
TTTTCTTTTTCTAGTTTTCTTCATCTTTCTTT
Found at i:2032764 original size:21 final size:21
Alignment explanation
Indices: 2032738--2032786 Score: 80
Period size: 21 Copynumber: 2.3 Consensus size: 21
2032728 TCAGACAGAA
*
2032738 TAATCAGTCCATATTCTTCTG
1 TAATCAGTACATATTCTTCTG
*
2032759 TAATCAGTACATATTCTTTTG
1 TAATCAGTACATATTCTTCTG
2032780 TAATCAG
1 TAATCAG
2032787 AACTTTTCAG
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.29, C:0.18, G:0.10, T:0.43
Consensus pattern (21 bp):
TAATCAGTACATATTCTTCTG
Found at i:2035111 original size:29 final size:30
Alignment explanation
Indices: 2035063--2035123 Score: 79
Period size: 29 Copynumber: 2.1 Consensus size: 30
2035053 ATTTCGATCC
**
2035063 CTAAACTTTTCAAAGTTTATACTTTAGCCA
1 CTAAACTTTTCAAAACTTATACTTTAGCCA
* *
2035093 CTAAAC-TTTCAAAACTTATATTTTAGTCA
1 CTAAACTTTTCAAAACTTATACTTTAGCCA
2035122 CT
1 CT
2035124 GGTCAAAATT
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
29 21 0.78
30 6 0.22
ACGTcount: A:0.34, C:0.20, G:0.05, T:0.41
Consensus pattern (30 bp):
CTAAACTTTTCAAAACTTATACTTTAGCCA
Found at i:2045953 original size:25 final size:25
Alignment explanation
Indices: 2045925--2045980 Score: 85
Period size: 25 Copynumber: 2.2 Consensus size: 25
2045915 TTGGATTGTA
*
2045925 ATTTGGGCCAGCTGTTGGGCTCACT
1 ATTTAGGCCAGCTGTTGGGCTCACT
*
2045950 ATTTAGGCCAGTTGTTGGGCTCACT
1 ATTTAGGCCAGCTGTTGGGCTCACT
*
2045975 GTTTAG
1 ATTTAG
2045981 ACCGATTGAT
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
25 28 1.00
ACGTcount: A:0.14, C:0.20, G:0.30, T:0.36
Consensus pattern (25 bp):
ATTTAGGCCAGCTGTTGGGCTCACT
Found at i:2046063 original size:21 final size:21
Alignment explanation
Indices: 2046037--2046077 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
2046027 TGGCCTGCAA
2046037 AAATAATAAAAAGAAA-AATAT
1 AAATAA-AAAAAGAAATAATAT
2046058 AAATAAAAAAAGAAATAATA
1 AAATAAAAAAAGAAATAATA
2046078 ATATCAATAA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 9 0.47
21 10 0.53
ACGTcount: A:0.78, C:0.00, G:0.05, T:0.17
Consensus pattern (21 bp):
AAATAAAAAAAGAAATAATAT
Found at i:2046080 original size:18 final size:18
Alignment explanation
Indices: 2046038--2046080 Score: 54
Period size: 18 Copynumber: 2.4 Consensus size: 18
2046028 GGCCTGCAAA
2046038 AATAATAAAAAGAAAAAT
1 AATAATAAAAAGAAAAAT
2046056 -ATAAATAAAAA-AAGAAAT
1 AAT-AATAAAAAGAA-AAAT
2046074 AATAATA
1 AATAATA
2046081 TCAATAATAA
Statistics
Matches: 22, Mismatches: 0, Indels: 6
0.79 0.00 0.21
Matches are distributed among these distances:
17 4 0.18
18 16 0.73
19 2 0.09
ACGTcount: A:0.77, C:0.00, G:0.05, T:0.19
Consensus pattern (18 bp):
AATAATAAAAAGAAAAAT
Done.