Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold287
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: 1864789
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.31
Warning! 140151 characters in sequence are not A, C, G, or T
File 6 of 7
Found at i:1414873 original size:24 final size:24
Alignment explanation
Indices: 1414810--1414887 Score: 95
Period size: 24 Copynumber: 3.2 Consensus size: 24
1414800 ATAATAACCA
*
1414810 TTTCATTGATATCCTTTTTGACCT
1 TTTCATTGGTATCCTTTTTGACCT
* *
1414834 TTTCAATGGTAACCTTTTTGACCT
1 TTTCATTGGTATCCTTTTTGACCT
**
1414858 TTTCATTCGG-ATCCTTTTCAACCT
1 TTTCATT-GGTATCCTTTTTGACCT
1414882 TTTCAT
1 TTTCAT
1414888 GGTTTCAGGA
Statistics
Matches: 46, Mismatches: 7, Indels: 2
0.84 0.13 0.04
Matches are distributed among these distances:
24 44 0.96
25 2 0.04
ACGTcount: A:0.18, C:0.23, G:0.09, T:0.50
Consensus pattern (24 bp):
TTTCATTGGTATCCTTTTTGACCT
Found at i:1427174 original size:25 final size:25
Alignment explanation
Indices: 1427146--1427203 Score: 66
Period size: 25 Copynumber: 2.3 Consensus size: 25
1427136 ATTTTTCTCC
*
1427146 TAAA-TTTCAATTTTATTTAATTATT
1 TAAATTTTCAA-TTTATTGAATTATT
*
1427171 TAAATTTTTAATTTATTGAATTA-T
1 TAAATTTTCAATTTATTGAATTATT
1427195 TAATATTTT
1 TAA-ATTTT
1427204 ATACTAATTA
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
24 4 0.14
25 20 0.69
26 5 0.17
ACGTcount: A:0.36, C:0.02, G:0.02, T:0.60
Consensus pattern (25 bp):
TAAATTTTCAATTTATTGAATTATT
Found at i:1432531 original size:21 final size:22
Alignment explanation
Indices: 1432515--1432568 Score: 67
Period size: 22 Copynumber: 2.5 Consensus size: 22
1432505 GTAACAGTTT
1432515 AGATA-AAATGCAGAACAGATC
1 AGATACAAATGCAGAACAGATC
* *
1432536 AGATACAGATGCAGAATAGATC
1 AGATACAAATGCAGAACAGATC
1432558 AGA-ATCAAATG
1 AGATA-CAAATG
1432569 TAGTTTCCTA
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
21 6 0.21
22 22 0.79
ACGTcount: A:0.50, C:0.13, G:0.20, T:0.17
Consensus pattern (22 bp):
AGATACAAATGCAGAACAGATC
Found at i:1436940 original size:13 final size:13
Alignment explanation
Indices: 1436922--1436946 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1436912 TAATTTATAT
1436922 GTGTGAAAATTTC
1 GTGTGAAAATTTC
1436935 GTGTGAAAATTT
1 GTGTGAAAATTT
1436947 TATCGTTTGT
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:0.04, G:0.24, T:0.40
Consensus pattern (13 bp):
GTGTGAAAATTTC
Found at i:1440262 original size:4 final size:4
Alignment explanation
Indices: 1440253--1440297 Score: 74
Period size: 4 Copynumber: 11.5 Consensus size: 4
1440243 CGAGCCCCCC
*
1440253 TTAT TTAT TTAT TTAT TTAT TTAT TTAT TTA- TTAT TCAT TTAT TT
1 TTAT TTAT TTAT TTAT TTAT TTAT TTAT TTAT TTAT TTAT TTAT TT
1440298 TCCAGAAAAT
Statistics
Matches: 38, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
3 3 0.08
4 35 0.92
ACGTcount: A:0.24, C:0.02, G:0.00, T:0.73
Consensus pattern (4 bp):
TTAT
Found at i:1440697 original size:180 final size:181
Alignment explanation
Indices: 1440385--1440745 Score: 715
Period size: 180 Copynumber: 2.0 Consensus size: 181
1440375 TTTAAAACAC
1440385 ACATGTTGATTAAACTAGATATTTGAACACTTTAATTCAAAAATTATCCAATTTTCCAAATTGAT
1 ACATGTTGATTAAACTAGATATTTGAACACTTTAATTCAAAAATTATCCAATTTTCCAAATTGAT
1440450 TAGCAATGAAATTAGAGGCTCAATTTCAAACAATTAATGAATAAACCAATATAAGAATGAACAGA
66 TAGCAATGAAATTAGAGGCTCAATTTCAAACAATTAATGAATAAACCAATATAAGAATGAACAGA
1440515 TGTGAAAGAAAAACATGCAGCAAAAGAAAATCTACCATGCATACTAACAAA
131 TGTGAAAGAAAAACATGCAGCAAAAGAAAATCTACCATGCATACTAACAAA
1440566 ACATGTTGA-TAAACTAGATATTTGAACACTTTAATTCAAAAATTATCCAATTTTCCAAATTGAT
1 ACATGTTGATTAAACTAGATATTTGAACACTTTAATTCAAAAATTATCCAATTTTCCAAATTGAT
1440630 TAGCAATGAAATTAGAGGCTCAATTTCAAACAATTAATGAATAAACCAATATAAGAATGAACAGA
66 TAGCAATGAAATTAGAGGCTCAATTTCAAACAATTAATGAATAAACCAATATAAGAATGAACAGA
1440695 TGTGAAAGAAAAACATGCAGCAAAAGAAAATCTACCATGCATACTAACAAA
131 TGTGAAAGAAAAACATGCAGCAAAAGAAAATCTACCATGCATACTAACAAA
1440746 TTATCAAAAT
Statistics
Matches: 180, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
180 171 0.95
181 9 0.05
ACGTcount: A:0.48, C:0.14, G:0.12, T:0.26
Consensus pattern (181 bp):
ACATGTTGATTAAACTAGATATTTGAACACTTTAATTCAAAAATTATCCAATTTTCCAAATTGAT
TAGCAATGAAATTAGAGGCTCAATTTCAAACAATTAATGAATAAACCAATATAAGAATGAACAGA
TGTGAAAGAAAAACATGCAGCAAAAGAAAATCTACCATGCATACTAACAAA
Found at i:1447034 original size:12 final size:12
Alignment explanation
Indices: 1447017--1447041 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
1447007 TGTTATTTCG
1447017 GGTCGGTTAACC
1 GGTCGGTTAACC
1447029 GGTCGGTTAACC
1 GGTCGGTTAACC
1447041 G
1 G
1447042 AATGAACACC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.16, C:0.24, G:0.36, T:0.24
Consensus pattern (12 bp):
GGTCGGTTAACC
Found at i:1452648 original size:29 final size:30
Alignment explanation
Indices: 1452591--1452846 Score: 128
Period size: 30 Copynumber: 8.6 Consensus size: 30
1452581 AGTCGAAGCT
*
1452591 ATCCCTTTTCATTATTTGATGGTCGTCACC
1 ATCCCTTTTCATTATTTGATGGCCGTCACC
*
1452621 ATCCCTTTTCATTA-TTGATGGCCTTCACC
1 ATCCCTTTTCATTATTTGATGGCCGTCACC
* * * * **
1452650 ATCCCTTTTCATAATTTGATAGCTG-AAGTT
1 ATCCCTTTTCATTATTTGATGGCCGTCA-CC
** * ** * *
1452680 ATCCCTTTTCACAATTCGATAACCG-AAGCT
1 ATCCCTTTTCATTATTTGATGGCCGTCA-CC
* ** * * *
1452710 ATCCCTTATCACAATTCGATAGCCAG--AGCT
1 ATCCCTTTTCATTATTTGATGGCC-GTCA-CC
* * *
1452740 ATCCCTTTTCATTGTTCGATGGCCATCACC
1 ATCCCTTTTCATTATTTGATGGCCGTCACC
** *
1452770 ATCCCTTTTCATTA-TTGATGTTTCGTTACC
1 ATCCCTTTTCATTATTTGATG-GCCGTCACC
* * *** *
1452800 ATCCCTTTTCATAATTTGATAGCCGAGGCA
1 ATCCCTTTTCATTATTTGATGGCCGTCACC
1452830 ATCCCTTTTCATTATTT
1 ATCCCTTTTCATTATTT
1452847 TGATAACCGA
Statistics
Matches: 181, Mismatches: 38, Indels: 14
0.78 0.16 0.06
Matches are distributed among these distances:
29 32 0.18
30 142 0.78
31 7 0.04
ACGTcount: A:0.22, C:0.27, G:0.12, T:0.39
Consensus pattern (30 bp):
ATCCCTTTTCATTATTTGATGGCCGTCACC
Found at i:1452774 original size:60 final size:60
Alignment explanation
Indices: 1452621--1452776 Score: 149
Period size: 60 Copynumber: 2.6 Consensus size: 60
1452611 GGTCGTCACC
* * * * * *
1452621 ATCCCTTTTCATTATT-GATGGCCTTCACCATCCCTTTTCATAATTTGATAGCTGAAGTT
1 ATCCCTTTTCATTATTCGATGGCCATCACCATCCCTTATCACAATTCGATAGCAGAAGCT
** ** *
1452680 ATCCCTTTTCACAATTCGATAACCGA--AGCTATCCCTTATCACAATTCGATAGCCAG-AGCT
1 ATCCCTTTTCATTATTCGATGGCC-ATCA-CCATCCCTTATCACAATTCGATAG-CAGAAGCT
*
1452740 ATCCCTTTTCATTGTTCGATGGCCATCACCATCCCTT
1 ATCCCTTTTCATTATTCGATGGCCATCACCATCCCTT
1452777 TTCATTATTG
Statistics
Matches: 74, Mismatches: 17, Indels: 11
0.73 0.17 0.11
Matches are distributed among these distances:
59 16 0.22
60 55 0.74
61 3 0.04
ACGTcount: A:0.24, C:0.29, G:0.12, T:0.36
Consensus pattern (60 bp):
ATCCCTTTTCATTATTCGATGGCCATCACCATCCCTTATCACAATTCGATAGCAGAAGCT
Found at i:1452849 original size:31 final size:31
Alignment explanation
Indices: 1452800--1452874 Score: 100
Period size: 31 Copynumber: 2.5 Consensus size: 31
1452790 TTTCGTTACC
*
1452800 ATCCCTTTTCA-TAATTTGATAGCCG-AGGCA
1 ATCCCTTTTCATTAATTTGATAACCGAAGG-A
* *
1452830 ATCCCTTTTCATTATTTTGATAACCGAAGGT
1 ATCCCTTTTCATTAATTTGATAACCGAAGGA
1452861 ATCCCTTTTCATTA
1 ATCCCTTTTCATTA
1452875 GCCAATGATC
Statistics
Matches: 40, Mismatches: 3, Indels: 3
0.87 0.07 0.07
Matches are distributed among these distances:
30 11 0.28
31 26 0.65
32 3 0.08
ACGTcount: A:0.25, C:0.23, G:0.12, T:0.40
Consensus pattern (31 bp):
ATCCCTTTTCATTAATTTGATAACCGAAGGA
Found at i:1454052 original size:13 final size:13
Alignment explanation
Indices: 1454025--1454077 Score: 54
Period size: 13 Copynumber: 4.2 Consensus size: 13
1454015 TTATAGTAGG
1454025 GTCACA-GACCGT
1 GTCACACGACCGT
*
1454037 GTCACACGATCGT
1 GTCACACGACCGT
* * *
1454050 GTCTCACGCCCGG
1 GTCACACGACCGT
*
1454063 GTCACACGCCCGT
1 GTCACACGACCGT
1454076 GT
1 GT
1454078 GCCAGGCCGT
Statistics
Matches: 33, Mismatches: 7, Indels: 1
0.80 0.17 0.02
Matches are distributed among these distances:
12 6 0.18
13 27 0.82
ACGTcount: A:0.17, C:0.38, G:0.26, T:0.19
Consensus pattern (13 bp):
GTCACACGACCGT
Found at i:1456147 original size:8 final size:8
Alignment explanation
Indices: 1456136--1456165 Score: 51
Period size: 8 Copynumber: 3.8 Consensus size: 8
1456126 TTTATCCTTA
1456136 TTTACCAT
1 TTTACCAT
1456144 TTTACCAT
1 TTTACCAT
1456152 TTTACCAT
1 TTTACCAT
*
1456160 GTTACC
1 TTTACC
1456166 CTTTAAAGAC
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
8 21 1.00
ACGTcount: A:0.23, C:0.27, G:0.03, T:0.47
Consensus pattern (8 bp):
TTTACCAT
Found at i:1465871 original size:19 final size:20
Alignment explanation
Indices: 1465844--1465891 Score: 62
Period size: 19 Copynumber: 2.5 Consensus size: 20
1465834 TCTATATAGC
*
1465844 GAAAGAGAAAAGAAGAAAAA
1 GAAAGAGAAAAGAACAAAAA
*
1465864 GAAA-AGAAAAGAACAAAAG
1 GAAAGAGAAAAGAACAAAAA
*
1465883 GAAGGAGAA
1 GAAAGAGAA
1465892 CGAGAAAGGA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
19 16 0.67
20 8 0.33
ACGTcount: A:0.71, C:0.02, G:0.27, T:0.00
Consensus pattern (20 bp):
GAAAGAGAAAAGAACAAAAA
Found at i:1474356 original size:5 final size:5
Alignment explanation
Indices: 1474346--1474379 Score: 68
Period size: 5 Copynumber: 6.8 Consensus size: 5
1474336 TTAAGAAAAT
1474346 GATTA GATTA GATTA GATTA GATTA GATTA GATT
1 GATTA GATTA GATTA GATTA GATTA GATTA GATT
1474380 TAGTGTCTGA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 29 1.00
ACGTcount: A:0.38, C:0.00, G:0.21, T:0.41
Consensus pattern (5 bp):
GATTA
Found at i:1476501 original size:8 final size:8
Alignment explanation
Indices: 1476488--1476544 Score: 51
Period size: 8 Copynumber: 6.8 Consensus size: 8
1476478 ATTAAGCTCT
1476488 TTTAAAAA
1 TTTAAAAA
*
1476496 TTTAAAAT
1 TTTAAAAA
1476504 TATTAAAAA
1 T-TTAAAAA
* *
1476513 TATAAAAG
1 TTTAAAAA
1476521 TTATAAAAA
1 TT-TAAAAA
*
1476530 TTTTAAAA
1 TTTAAAAA
1476538 TTATAAA
1 TT-TAAA
1476545 TTTTTTATTA
Statistics
Matches: 38, Mismatches: 8, Indels: 5
0.75 0.16 0.10
Matches are distributed among these distances:
8 21 0.55
9 17 0.45
ACGTcount: A:0.60, C:0.00, G:0.02, T:0.39
Consensus pattern (8 bp):
TTTAAAAA
Found at i:1476542 original size:17 final size:16
Alignment explanation
Indices: 1476490--1476544 Score: 74
Period size: 17 Copynumber: 3.2 Consensus size: 16
1476480 TAAGCTCTTT
1476490 TAAAAATTTAAAATTA
1 TAAAAATTTAAAATTA
*
1476506 TTAAAAATATAAAAGTTA
1 -TAAAAATTTAAAA-TTA
1476524 TAAAAATTTTAAAATTA
1 TAAAAA-TTTAAAATTA
1476541 TAAA
1 TAAA
1476545 TTTTTTATTA
Statistics
Matches: 34, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
17 25 0.74
18 9 0.26
ACGTcount: A:0.62, C:0.00, G:0.02, T:0.36
Consensus pattern (16 bp):
TAAAAATTTAAAATTA
Found at i:1479161 original size:30 final size:31
Alignment explanation
Indices: 1479096--1479161 Score: 80
Period size: 31 Copynumber: 2.2 Consensus size: 31
1479086 TTAAAATGAT
* * *
1479096 AATTTCATGTATATATTTAGATCACAATCAA
1 AATTTCATGAATATAATCAGATCACAATCAA
* *
1479127 AATTTCATGAATATAATCATATCA-AATTAA
1 AATTTCATGAATATAATCAGATCACAATCAA
1479157 AATTT
1 AATTT
1479162 ACATATAATT
Statistics
Matches: 30, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
30 10 0.33
31 20 0.67
ACGTcount: A:0.45, C:0.11, G:0.05, T:0.39
Consensus pattern (31 bp):
AATTTCATGAATATAATCAGATCACAATCAA
Found at i:1480082 original size:30 final size:31
Alignment explanation
Indices: 1480026--1480084 Score: 93
Period size: 31 Copynumber: 1.9 Consensus size: 31
1480016 AATTGGTTTT
* *
1480026 TTATTTTAAAAATTCAAAAAATTATAAAAAA
1 TTATTTTAAAAAGTCAAAAAAGTATAAAAAA
1480057 TTATTTTAAAAAGTC-AAAAAGTATAAAA
1 TTATTTTAAAAAGTCAAAAAAGTATAAAA
1480085 GCATAAAAAT
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
30 12 0.46
31 14 0.54
ACGTcount: A:0.59, C:0.03, G:0.03, T:0.34
Consensus pattern (31 bp):
TTATTTTAAAAAGTCAAAAAAGTATAAAAAA
Found at i:1485467 original size:7 final size:7
Alignment explanation
Indices: 1485455--1485493 Score: 55
Period size: 7 Copynumber: 5.9 Consensus size: 7
1485445 TCAAAAATTA
1485455 TAAAAAT
1 TAAAAAT
1485462 TAAAAAT
1 TAAAAAT
1485469 T-AAAAT
1 TAAAAAT
1485475 T-AAAAT
1 TAAAAAT
*
1485481 TAAAATT
1 TAAAAAT
1485488 TAAAAA
1 TAAAAA
1485494 ATATAAAAAG
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
6 12 0.41
7 17 0.59
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (7 bp):
TAAAAAT
Found at i:1485501 original size:7 final size:6
Alignment explanation
Indices: 1485457--1485492 Score: 54
Period size: 6 Copynumber: 5.7 Consensus size: 6
1485447 AAAAATTATA
1485457 AAAATT AAAAATT AAAATT AAAATT AAAATTT AAAA
1 AAAATT -AAAATT AAAATT AAAATT AAAA-TT AAAA
1485493 AATATAAAAA
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
6 16 0.57
7 12 0.43
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (6 bp):
AAAATT
Found at i:1485983 original size:3 final size:3
Alignment explanation
Indices: 1485977--1486013 Score: 74
Period size: 3 Copynumber: 12.3 Consensus size: 3
1485967 TTCTTTGTTT
1485977 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T
1486014 TTTCACTAAA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 34 1.00
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (3 bp):
TAA
Found at i:1493325 original size:21 final size:21
Alignment explanation
Indices: 1493301--1493343 Score: 86
Period size: 21 Copynumber: 2.0 Consensus size: 21
1493291 ATTAAAAATA
1493301 TAAAAAAATATATTTTAATTT
1 TAAAAAAATATATTTTAATTT
1493322 TAAAAAAATATATTTTAATTT
1 TAAAAAAATATATTTTAATTT
1493343 T
1 T
1493344 GCATACATGT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (21 bp):
TAAAAAAATATATTTTAATTT
Found at i:1494277 original size:28 final size:29
Alignment explanation
Indices: 1494231--1494286 Score: 87
Period size: 28 Copynumber: 2.0 Consensus size: 29
1494221 GAGAAGGGGG
* *
1494231 GGGGGATGGGGGGGTAGGAAAAGTTTTGA
1 GGGGGAAGGGAGGGTAGGAAAAGTTTTGA
1494260 GGGGGAAGGGAGGG-AGGAAAAGTTTTG
1 GGGGGAAGGGAGGGTAGGAAAAGTTTTG
1494287 GGGAAAAGTA
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
28 13 0.52
29 12 0.48
ACGTcount: A:0.27, C:0.00, G:0.55, T:0.18
Consensus pattern (29 bp):
GGGGGAAGGGAGGGTAGGAAAAGTTTTGA
Found at i:1496882 original size:33 final size:33
Alignment explanation
Indices: 1496840--1496905 Score: 123
Period size: 33 Copynumber: 2.0 Consensus size: 33
1496830 TGAGAAAGAA
1496840 GAAAAAAAATGAAGTTTTTAGAAAAAAAATTGG
1 GAAAAAAAATGAAGTTTTTAGAAAAAAAATTGG
*
1496873 GAAAAAAAATGAAGTTTTTAGAAAAAAATTTGG
1 GAAAAAAAATGAAGTTTTTAGAAAAAAAATTGG
1496906 TTTAAATAAG
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 32 1.00
ACGTcount: A:0.56, C:0.00, G:0.18, T:0.26
Consensus pattern (33 bp):
GAAAAAAAATGAAGTTTTTAGAAAAAAAATTGG
Found at i:1497307 original size:3 final size:3
Alignment explanation
Indices: 1497299--1497396 Score: 58
Period size: 3 Copynumber: 32.3 Consensus size: 3
1497289 ATTTTTGCTA
* * *
1497299 TAT TAT TAT TA- AAT TAAT TAAT TAAT TAAT TAT TAT CAT TAG TAT TAT
1 TAT TAT TAT TAT TAT T-AT T-AT T-AT T-AT TAT TAT TAT TAT TAT TAT
* * * * * *
1497347 TAT T-T T-T TAT TAT TAT CAT CAT CAT CAT TAT TAT TAA TAT TAA TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1497393 TAT T
1 TAT T
1497397 GTTAAATTGT
Statistics
Matches: 80, Mismatches: 12, Indels: 6
0.82 0.12 0.06
Matches are distributed among these distances:
2 5 0.06
3 60 0.75
4 15 0.19
ACGTcount: A:0.38, C:0.05, G:0.01, T:0.56
Consensus pattern (3 bp):
TAT
Found at i:1497646 original size:13 final size:13
Alignment explanation
Indices: 1497628--1497653 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1497618 GAAACAATCC
1497628 CTAAAAATCAGTA
1 CTAAAAATCAGTA
1497641 CTAAAAATCAGTA
1 CTAAAAATCAGTA
1497654 ACTTCCTAAG
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:0.54, C:0.15, G:0.08, T:0.23
Consensus pattern (13 bp):
CTAAAAATCAGTA
Found at i:1499819 original size:38 final size:38
Alignment explanation
Indices: 1499770--1499925 Score: 312
Period size: 38 Copynumber: 4.1 Consensus size: 38
1499760 TAAAGTATTG
1499770 TTCATTCTCAAAAAAGGTAACATCCCGAGAGATAAACA
1 TTCATTCTCAAAAAAGGTAACATCCCGAGAGATAAACA
1499808 TTCATTCTCAAAAAAGGTAACATCCCGAGAGATAAACA
1 TTCATTCTCAAAAAAGGTAACATCCCGAGAGATAAACA
1499846 TTCATTCTCAAAAAAGGTAACATCCCGAGAGATAAACA
1 TTCATTCTCAAAAAAGGTAACATCCCGAGAGATAAACA
1499884 TTCATTCTCAAAAAAGGTAACATCCCGAGAGATAAACA
1 TTCATTCTCAAAAAAGGTAACATCCCGAGAGATAAACA
1499922 TTCA
1 TTCA
1499926 GCGTAAGGTA
Statistics
Matches: 118, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
38 118 1.00
ACGTcount: A:0.44, C:0.21, G:0.13, T:0.22
Consensus pattern (38 bp):
TTCATTCTCAAAAAAGGTAACATCCCGAGAGATAAACA
Found at i:1503029 original size:35 final size:35
Alignment explanation
Indices: 1502985--1503054 Score: 122
Period size: 35 Copynumber: 2.0 Consensus size: 35
1502975 AATCAACTAG
1502985 GTACCAATTTTGGGCGTATCGAGAGTGCTAATCCT
1 GTACCAATTTTGGGCGTATCGAGAGTGCTAATCCT
* *
1503020 GTACCAATTTTGGGCGTATTGAGGGTGCTAATCCT
1 GTACCAATTTTGGGCGTATCGAGAGTGCTAATCCT
1503055 TCCTCGTGTG
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
35 33 1.00
ACGTcount: A:0.21, C:0.19, G:0.27, T:0.33
Consensus pattern (35 bp):
GTACCAATTTTGGGCGTATCGAGAGTGCTAATCCT
Found at i:1510818 original size:25 final size:25
Alignment explanation
Indices: 1510795--1510971 Score: 219
Period size: 25 Copynumber: 7.0 Consensus size: 25
1510785 ACTGCAGAGA
* *
1510795 CTTATCAGATGATTCACCATAGAGG
1 CTTATCAGATGATTCACCACAAAGG
* * **
1510820 TTTATCAGATAATTTGCCACAAAGG
1 CTTATCAGATGATTCACCACAAAGG
*
1510845 CTTATCAGATGATTCGCCACAAAGG
1 CTTATCAGATGATTCACCACAAAGG
* *
1510870 CTTATCAAATGATTCACCATAAAGG
1 CTTATCAGATGATTCACCACAAAGG
1510895 CTTATCAGATGATTCAGCACCACAAAGG
1 CTTATCAGATGATT---CACCACAAAGG
**
1510923 CTTATCAGATGATTTGCCACAAAGG
1 CTTATCAGATGATTCACCACAAAGG
*
1510948 CTTATCAGATAATTCACCACAAAG
1 CTTATCAGATGATTCACCACAAAG
1510972 ACTTCACGTA
Statistics
Matches: 130, Mismatches: 19, Indels: 6
0.84 0.12 0.04
Matches are distributed among these distances:
25 106 0.82
28 24 0.18
ACGTcount: A:0.36, C:0.21, G:0.16, T:0.27
Consensus pattern (25 bp):
CTTATCAGATGATTCACCACAAAGG
Found at i:1510943 original size:78 final size:75
Alignment explanation
Indices: 1510795--1510971 Score: 255
Period size: 78 Copynumber: 2.3 Consensus size: 75
1510785 ACTGCAGAGA
* * *
1510795 CTTATCAGATGATTCACCATAGAGGTTTATCAGATAATTTGCCACAAAGGCTTATCAGATGATTC
1 CTTATCAGATGATTCACCATAAAGGCTTATCAGATAATTAGCCACAAAGGCTTATCAGATGATTC
1510860 GCCACAAAGG
66 GCCACAAAGG
* *
1510870 CTTATCAAATGATTCACCATAAAGGCTTATCAGATGATTCAGCACCACAAAGGCTTATCAGATGA
1 CTTATCAGATGATTCACCATAAAGGCTTATCAGATAATT-AG--CCACAAAGGCTTATCAGATGA
*
1510935 TTTGCCACAAAGG
63 TTCGCCACAAAGG
* *
1510948 CTTATCAGATAATTCACCACAAAG
1 CTTATCAGATGATTCACCATAAAG
1510972 ACTTCACGTA
Statistics
Matches: 90, Mismatches: 9, Indels: 3
0.88 0.09 0.03
Matches are distributed among these distances:
75 35 0.39
76 1 0.01
78 54 0.60
ACGTcount: A:0.36, C:0.21, G:0.16, T:0.27
Consensus pattern (75 bp):
CTTATCAGATGATTCACCATAAAGGCTTATCAGATAATTAGCCACAAAGGCTTATCAGATGATTC
GCCACAAAGG
Found at i:1513219 original size:164 final size:165
Alignment explanation
Indices: 1512909--1513239 Score: 551
Period size: 164 Copynumber: 2.0 Consensus size: 165
1512899 CGATAGTGAC
*
1512909 TAATTCAAACAATCATCTTAATTAAGGTTACTAAATTGAGAAAAAAAATTTAGAGTGACCAAAAT
1 TAATTCAAACAATCATCTTAATTAAGGTGACTAAATTGAGAAAAAAAATTTAGAGTGACCAAAAT
* *
1512974 ATGATAAACTCTATTTTAGAGTGACCATGGGCATAAGTTACCTTTAATTTAATTGTTTTAATTTT
66 ATGACAAACCCTATTTTAGAGTGACCATGGGCATAAGTTACCTTTAATTTAATTGTTTTAATTTT
1513039 TATTTTGAAGCAAATAAGATTAAATTTGTTAAGTT
131 TATTTTGAAGCAAATAAGATTAAATTTGTTAAGTT
*
1513074 TAATTCAAACAATTATCTTAATTAAGGTGACTAAATTGAG-AAAAAAA-TT-GAGTGACCAAAAT
1 TAATTCAAACAATCATCTTAATTAAGGTGACTAAATTGAGAAAAAAAATTTAGAGTGACCAAAAT
* *
1513136 ATGACAAACCCTATTTTAGAGTGACCATGGGTATAGGGTTACCCTTTAATTTAATTGTTTTAATT
66 ATGACAAACCCTATTTTAGAGTGACCATGGGCATA-AGTTA-CCTTTAATTTAATTGTTTTAATT
* *
1513201 TTTATTTTGAATCAAATAAGATTAAATTTGTTAATTT
129 TTTATTTTGAAGCAAATAAGATTAAATTTGTTAAGTT
1513238 TA
1 TA
1513240 GACTTAAAAC
Statistics
Matches: 156, Mismatches: 8, Indels: 5
0.92 0.05 0.03
Matches are distributed among these distances:
162 45 0.29
163 6 0.04
164 67 0.43
165 38 0.24
ACGTcount: A:0.39, C:0.09, G:0.13, T:0.38
Consensus pattern (165 bp):
TAATTCAAACAATCATCTTAATTAAGGTGACTAAATTGAGAAAAAAAATTTAGAGTGACCAAAAT
ATGACAAACCCTATTTTAGAGTGACCATGGGCATAAGTTACCTTTAATTTAATTGTTTTAATTTT
TATTTTGAAGCAAATAAGATTAAATTTGTTAAGTT
Found at i:1513265 original size:4 final size:4
Alignment explanation
Indices: 1513256--1513290 Score: 54
Period size: 4 Copynumber: 9.0 Consensus size: 4
1513246 AAACTTAATA
*
1513256 TATT TATT TATT T-TT TATT TATA TATT TATT TATT
1 TATT TATT TATT TATT TATT TATT TATT TATT TATT
1513291 GAAAGCAAAA
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
3 3 0.11
4 25 0.89
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (4 bp):
TATT
Found at i:1515423 original size:57 final size:57
Alignment explanation
Indices: 1515347--1515461 Score: 162
Period size: 57 Copynumber: 2.0 Consensus size: 57
1515337 GATATAACAA
* *
1515347 TGAAATGAATTGTGTGAAA-TGTGTA-TACTCTTATAGATTGATAATAGAATATGATAT
1 TGAAATGAACTATGTGAAATTG-GTATTA-TCTTATAGATTGATAATAGAATATGATAT
* *
1515404 TGAAATGAACTATGTGAAATTGGTATTATCTTATGGATTGATGATAGAATATGATAT
1 TGAAATGAACTATGTGAAATTGGTATTATCTTATAGATTGATAATAGAATATGATAT
1515461 T
1 T
1515462 TGAGATGAGT
Statistics
Matches: 52, Mismatches: 4, Indels: 4
0.87 0.07 0.07
Matches are distributed among these distances:
57 48 0.92
58 4 0.08
ACGTcount: A:0.37, C:0.03, G:0.20, T:0.39
Consensus pattern (57 bp):
TGAAATGAACTATGTGAAATTGGTATTATCTTATAGATTGATAATAGAATATGATAT
Found at i:1521590 original size:18 final size:18
Alignment explanation
Indices: 1521567--1521602 Score: 56
Period size: 18 Copynumber: 2.0 Consensus size: 18
1521557 TTAACTTAAT
1521567 TAAAGTTTAAA-TTTAAAC
1 TAAAG-TTAAAGTTTAAAC
1521585 TAAAGTTAAAGTTTAAAC
1 TAAAGTTAAAGTTTAAAC
1521603 AAAATGATGA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 5 0.29
18 12 0.71
ACGTcount: A:0.50, C:0.06, G:0.08, T:0.36
Consensus pattern (18 bp):
TAAAGTTAAAGTTTAAAC
Found at i:1522580 original size:15 final size:16
Alignment explanation
Indices: 1522562--1522592 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
1522552 TATCACAACA
1522562 TCAATC-ATAACATAG
1 TCAATCAATAACATAG
1522577 TCAATCAATAACATAG
1 TCAATCAATAACATAG
1522593 ATATTGTCCC
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 6 0.40
16 9 0.60
ACGTcount: A:0.48, C:0.19, G:0.06, T:0.26
Consensus pattern (16 bp):
TCAATCAATAACATAG
Found at i:1524641 original size:20 final size:19
Alignment explanation
Indices: 1524628--1524742 Score: 113
Period size: 20 Copynumber: 5.8 Consensus size: 19
1524618 CAGGGGTATT
1524628 GAAGTACAAACAGGGGCAC
1 GAAGTACAAACAGGGGCAC
* *
1524647 GTAAGTGCAATCAGGGGCAC
1 G-AAGTACAAACAGGGGCAC
1524667 TGAAGTACAAACAGGGGCAC
1 -GAAGTACAAACAGGGGCAC
* ** *
1524687 GTAAGTGCAATTAGGGGTACC
1 G-AAGTACAAACAGGGGCA-C
1524708 GAAGTACAAACAGGGGCAC
1 GAAGTACAAACAGGGGCAC
* *
1524727 GTAAGTGCAATCAGGG
1 G-AAGTACAAACAGGG
1524743 TATAATTTAC
Statistics
Matches: 77, Mismatches: 14, Indels: 9
0.77 0.14 0.09
Matches are distributed among these distances:
19 4 0.05
20 70 0.91
21 3 0.04
ACGTcount: A:0.36, C:0.18, G:0.33, T:0.13
Consensus pattern (19 bp):
GAAGTACAAACAGGGGCAC
Found at i:1524643 original size:40 final size:40
Alignment explanation
Indices: 1524611--1524742 Score: 203
Period size: 40 Copynumber: 3.3 Consensus size: 40
1524601 GGGAACCGAT
*
1524611 GTGCATTCAGGGGTATTGAAGTACAAACAGGGGCACGTAA
1 GTGCATTCAGGGGTACTGAAGTACAAACAGGGGCACGTAA
* *
1524651 GTGCAATCAGGGGCACTGAAGTACAAACAGGGGCACGTAA
1 GTGCATTCAGGGGTACTGAAGTACAAACAGGGGCACGTAA
*
1524691 GTGCAATT-AGGGGTACCGAAGTACAAACAGGGGCACGTAA
1 GTGC-ATTCAGGGGTACTGAAGTACAAACAGGGGCACGTAA
*
1524731 GTGCAATCAGGG
1 GTGCATTCAGGG
1524743 TATAATTTAC
Statistics
Matches: 83, Mismatches: 7, Indels: 4
0.88 0.07 0.04
Matches are distributed among these distances:
39 2 0.02
40 79 0.95
41 2 0.02
ACGTcount: A:0.33, C:0.17, G:0.33, T:0.16
Consensus pattern (40 bp):
GTGCATTCAGGGGTACTGAAGTACAAACAGGGGCACGTAA
Found at i:1528509 original size:333 final size:326
Alignment explanation
Indices: 1527897--1528554 Score: 1199
Period size: 333 Copynumber: 2.0 Consensus size: 326
1527887 ACCTAAGTTA
1527897 CAAGAAAACATGATTCAACATAACCTTTTTGCGATTAACCATTTATGCATTAATCCTTAAGTCCT
1 CAAGAAAACATGATTCAACATAACCTTTTTGCGATTAACCATTTATGCATTAATCCTTAAGTCCT
1527962 TTATCTCTGGGATGGACACAAGTTATGGAATAGTCACACTTGCATAGTCCATCCCATGTTCCTTG
66 TTATCTCTGGGATGGACACAAGTTATGGAATAGTCACACTTGCATAGTCCATCCCATGTTCCTTG
*
1528027 ATATCTTGAGTAGACTATGGTATACAAATAAGTACAACATCTCATATCAGCTTATTTGAGCATGC
131 ATATCTTGAGTAGACTATGATATACAAATAAGTACAACATCTCATATCAGCTTATTTGAGCATGC
1528092 CCATGCATTTCTAGTCTCACTCAATCAAGTGGCCTAAGATATTACTCCCATTATGTAGGAGGGAC
196 CCATGCATTTCTAGTCTCACTCAATCAAGTGGCCTAAGATATTACTCCCATTATGTAGGAGGGAC
1528157 TTATCCTATATCGATCAACCATATCCCTCTACATAGATCGTGGCATATCCAACATCAACCTTTAT
261 TTATCCTATATCGATCAACCATAT-CC-CT-C-T--AT-GTGGCATATCCAACATCAACCTTTAT
1528222 AGAACAAT
319 AGAACAAT
* *
1528230 CAAGATAACATGATTCAACATAACCTTTTTGTGATTAACCATTTATGCATTAATCCTTAAGTCCT
1 CAAGAAAACATGATTCAACATAACCTTTTTGCGATTAACCATTTATGCATTAATCCTTAAGTCCT
1528295 TTATCTCTGGGATGGACACAAGTTATGGAATAGTCACACTTGCATAGTCCATCCCATGTTCCTTG
66 TTATCTCTGGGATGGACACAAGTTATGGAATAGTCACACTTGCATAGTCCATCCCATGTTCCTTG
*
1528360 ATATCTTGAGTAGACTATGATATACAAATAAGTACAACATCTCATATCAGCTTATTTGAGCATGG
131 ATATCTTGAGTAGACTATGATATACAAATAAGTACAACATCTCATATCAGCTTATTTGAGCATGC
1528425 CCATGCATTTCTAGTCTCACTCAATCAAGTGGCCTAAGATATTACTCCCATTATGTAGGAGGGAC
196 CCATGCATTTCTAGTCTCACTCAATCAAGTGGCCTAAGATATTACTCCCATTATGTAGGAGGGAC
* *
1528490 TTATCCTATATCGATCAACCATATCCCTCTATGTGGTATATCCAACATCAGCCTTTATAGAACAA
261 TTATCCTATATCGATCAACCATATCCCTCTATGTGGCATATCCAACATCAACCTTTATAGAACAA
1528555 CCAGTTACGG
Statistics
Matches: 319, Mismatches: 6, Indels: 7
0.96 0.02 0.02
Matches are distributed among these distances:
326 31 0.10
327 2 0.01
329 1 0.00
330 1 0.00
331 2 0.01
332 2 0.01
333 280 0.88
ACGTcount: A:0.31, C:0.22, G:0.14, T:0.32
Consensus pattern (326 bp):
CAAGAAAACATGATTCAACATAACCTTTTTGCGATTAACCATTTATGCATTAATCCTTAAGTCCT
TTATCTCTGGGATGGACACAAGTTATGGAATAGTCACACTTGCATAGTCCATCCCATGTTCCTTG
ATATCTTGAGTAGACTATGATATACAAATAAGTACAACATCTCATATCAGCTTATTTGAGCATGC
CCATGCATTTCTAGTCTCACTCAATCAAGTGGCCTAAGATATTACTCCCATTATGTAGGAGGGAC
TTATCCTATATCGATCAACCATATCCCTCTATGTGGCATATCCAACATCAACCTTTATAGAACAA
T
Found at i:1537158 original size:24 final size:24
Alignment explanation
Indices: 1537103--1537172 Score: 72
Period size: 24 Copynumber: 2.9 Consensus size: 24
1537093 TACAGCTCTT
* *
1537103 ATGAGCTTCCCGTTATACA-GCCCGA
1 ATGAGCTTCCCG-T-TACATGGCTGA
*
1537128 ATAAGCTTCCCGTTACATGGCTGA
1 ATGAGCTTCCCGTTACATGGCTGA
*
1537152 ATGAGCTTCCCG-TATATGGCT
1 ATGAGCTTCCCGTTACATGGCT
1537173 CGAGAGAGAG
Statistics
Matches: 39, Mismatches: 5, Indels: 4
0.81 0.10 0.08
Matches are distributed among these distances:
23 12 0.31
24 16 0.41
25 11 0.28
ACGTcount: A:0.23, C:0.27, G:0.21, T:0.29
Consensus pattern (24 bp):
ATGAGCTTCCCGTTACATGGCTGA
Found at i:1541940 original size:57 final size:57
Alignment explanation
Indices: 1541867--1542040 Score: 269
Period size: 57 Copynumber: 3.1 Consensus size: 57
1541857 AACTAATTTT
* *
1541867 ATATAACATTGAAATGAA-TTGTGTGAAATGGGTATGATATTATAGATTGATAATAGA
1 ATATAACATGGAAATGAACTT-TGTGAAATTGGTATGATATTATAGATTGATAATAGA
*
1541924 ATATTACATGGAAATGAACTTTGTGAAATTGGTATGATATTATAGATTGATAATAGA
1 ATATAACATGGAAATGAACTTTGTGAAATTGGTATGATATTATAGATTGATAATAGA
* * * *
1541981 ATATGACATGGAAATGAACTTTGTGAAATTGGTATGATCTTATGGATTGATGATAGA
1 ATATAACATGGAAATGAACTTTGTGAAATTGGTATGATATTATAGATTGATAATAGA
1542038 ATA
1 ATA
1542041 AGATGTTTAA
Statistics
Matches: 109, Mismatches: 7, Indels: 2
0.92 0.06 0.02
Matches are distributed among these distances:
57 107 0.98
58 2 0.02
ACGTcount: A:0.40, C:0.03, G:0.21, T:0.36
Consensus pattern (57 bp):
ATATAACATGGAAATGAACTTTGTGAAATTGGTATGATATTATAGATTGATAATAGA
Found at i:1550423 original size:102 final size:103
Alignment explanation
Indices: 1550306--1550510 Score: 394
Period size: 102 Copynumber: 2.0 Consensus size: 103
1550296 TTTTATTATT
1550306 TTCTTTACAATATAATTTTATAATTATTAATTTAAAATTTTATAAATTATAAAGAAAAACACAAA
1 TTCTTTACAATATAATTTTATAATTATTAATTTAAAATTTTATAAATTATAAAGAAAAACACAAA
1550371 CCCGTGGCTTCGCATTGTCTATACCTTGCTTTTAATGG
66 CCCGTGGCTTCGCATTGTCTATACCTTGCTTTTAATGG
*
1550409 TTCTTTACAA-ATAATTTTATAATTATTGATTTAAAATTTTATAAATTATAAAGAAAAACACAAA
1 TTCTTTACAATATAATTTTATAATTATTAATTTAAAATTTTATAAATTATAAAGAAAAACACAAA
1550473 CCCGTGGCTTCGCATTGTCTATACCTTGCTTTTAATGG
66 CCCGTGGCTTCGCATTGTCTATACCTTGCTTTTAATGG
1550511 CAGCACTGTA
Statistics
Matches: 101, Mismatches: 1, Indels: 1
0.98 0.01 0.01
Matches are distributed among these distances:
102 91 0.90
103 10 0.10
ACGTcount: A:0.37, C:0.14, G:0.09, T:0.40
Consensus pattern (103 bp):
TTCTTTACAATATAATTTTATAATTATTAATTTAAAATTTTATAAATTATAAAGAAAAACACAAA
CCCGTGGCTTCGCATTGTCTATACCTTGCTTTTAATGG
Found at i:1556216 original size:42 final size:42
Alignment explanation
Indices: 1556052--1556216 Score: 179
Period size: 43 Copynumber: 3.9 Consensus size: 42
1556042 TACCGTAACA
* * * * * *
1556052 ATGCCATATCCCAGATATGGTCTTACATGTAATCTCGTATCA
1 ATGCAATATCCCAGACATGGTCTTACACGAAATCTCATATCG
* * *
1556094 ATGTCAATAGCCCAGCCATGGTCTTACACGAAATCACATATCG
1 ATG-CAATATCCCAGACATGGTCTTACACGAAATCTCATATCG
*
1556137 ATGCGAATGTCCCAGACATGGTCTTACAC-AAATTCTCATATCG
1 ATGC-AATATCCCAGACATGGTCTTACACGAAA-TCTCATATCG
* * *
1556180 ATGCCATATCCCAGATATGGTCTTACACGTAATCTCA
1 ATGCAATATCCCAGACATGGTCTTACACGAAATCTCA
1556217 GAAACCCTAA
Statistics
Matches: 102, Mismatches: 17, Indels: 8
0.80 0.13 0.06
Matches are distributed among these distances:
42 33 0.32
43 69 0.68
ACGTcount: A:0.30, C:0.26, G:0.15, T:0.28
Consensus pattern (42 bp):
ATGCAATATCCCAGACATGGTCTTACACGAAATCTCATATCG
Found at i:1556821 original size:21 final size:19
Alignment explanation
Indices: 1556786--1556829 Score: 52
Period size: 20 Copynumber: 2.2 Consensus size: 19
1556776 TCACTTTATA
1556786 AAATATTAAAATCTAACAT
1 AAATATTAAAATCTAACAT
* *
1556805 CAAATATTCATAATCTATCAT
1 -AAATATT-AAAATCTAACAT
1556826 AAAT
1 AAAT
1556830 CATCAATTTA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 11 0.52
21 10 0.48
ACGTcount: A:0.52, C:0.14, G:0.00, T:0.34
Consensus pattern (19 bp):
AAATATTAAAATCTAACAT
Found at i:1561939 original size:25 final size:24
Alignment explanation
Indices: 1561876--1561945 Score: 68
Period size: 24 Copynumber: 2.9 Consensus size: 24
1561866 GTGGGATAAC
*
1561876 AATGCTCACACGAGCTGTGAATAT
1 AATGCTCACACGAGCTATGAATAT
* * ** *
1561900 AATGATCCCTTGAGCTATGATTAT
1 AATGCTCACACGAGCTATGAATAT
*
1561924 AAATGCTCACACGAGCTGTGAA
1 -AATGCTCACACGAGCTATGAA
1561946 AATGGGCATA
Statistics
Matches: 33, Mismatches: 12, Indels: 1
0.72 0.26 0.02
Matches are distributed among these distances:
24 18 0.55
25 15 0.45
ACGTcount: A:0.33, C:0.20, G:0.20, T:0.27
Consensus pattern (24 bp):
AATGCTCACACGAGCTATGAATAT
Found at i:1565851 original size:45 final size:45
Alignment explanation
Indices: 1565780--1565910 Score: 147
Period size: 45 Copynumber: 2.9 Consensus size: 45
1565770 GGTTGTATGC
* * * *
1565780 CTAAAATGATTAAGACCGTAGTTAAAAGATGCTATGACATCA-AGA
1 CTAAAATGAGTAGGACCATAGCTAAAAGATGCTATGACATCATA-A
*
1565825 CTAAAATGAGTAGGACCATAGCTAAAAGATGTTATGACATCATAA
1 CTAAAATGAGTAGGACCATAGCTAAAAGATGCTATGACATCATAA
* * * * * *
1565870 CTGAAATGGGTAGGGCCATAACTGAAAGATGCTATGGCATC
1 CTAAAATGAGTAGGACCATAGCTAAAAGATGCTATGACATC
1565911 GTTGATTGTC
Statistics
Matches: 73, Mismatches: 12, Indels: 2
0.84 0.14 0.02
Matches are distributed among these distances:
45 72 0.99
46 1 0.01
ACGTcount: A:0.40, C:0.15, G:0.21, T:0.24
Consensus pattern (45 bp):
CTAAAATGAGTAGGACCATAGCTAAAAGATGCTATGACATCATAA
Found at i:1569015 original size:27 final size:27
Alignment explanation
Indices: 1568985--1569051 Score: 80
Period size: 27 Copynumber: 2.5 Consensus size: 27
1568975 TAGTCCAATG
*
1568985 GGACGTTAAAGACGGGACACTCTGATA
1 GGACGTTAAACACGGGACACTCTGATA
* ** *
1569012 GGACGTTAAACATGGGGTAGTCTGATA
1 GGACGTTAAACACGGGACACTCTGATA
*
1569039 GGACGTCAAACAC
1 GGACGTTAAACAC
1569052 TGGGTAGCCC
Statistics
Matches: 33, Mismatches: 7, Indels: 0
0.82 0.17 0.00
Matches are distributed among these distances:
27 33 1.00
ACGTcount: A:0.33, C:0.18, G:0.30, T:0.19
Consensus pattern (27 bp):
GGACGTTAAACACGGGACACTCTGATA
Found at i:1573908 original size:24 final size:25
Alignment explanation
Indices: 1573878--1573940 Score: 74
Period size: 24 Copynumber: 2.6 Consensus size: 25
1573868 GCGGGATAAC
*
1573878 AATGCTCACACGAGCTGTGAATAT-
1 AATGCTCACACGAGCTATGAATATA
* ** *
1573902 AATGCTCTCTTGAGCTATGAATGTA
1 AATGCTCACACGAGCTATGAATATA
1573927 AATGCTCACACGAG
1 AATGCTCACACGAG
1573941 TTGTAAAAAT
Statistics
Matches: 30, Mismatches: 8, Indels: 1
0.77 0.21 0.03
Matches are distributed among these distances:
24 19 0.63
25 11 0.37
ACGTcount: A:0.32, C:0.21, G:0.21, T:0.27
Consensus pattern (25 bp):
AATGCTCACACGAGCTATGAATATA
Found at i:1587184 original size:35 final size:35
Alignment explanation
Indices: 1587138--1587206 Score: 129
Period size: 35 Copynumber: 2.0 Consensus size: 35
1587128 GTTTATATAA
*
1587138 TCAAGTAATTTACATGTCAAACTTACAAATGCATC
1 TCAAGTAATTTACATGTCAAACTTAAAAATGCATC
1587173 TCAAGTAATTTACATGTCAAACTTAAAAATGCAT
1 TCAAGTAATTTACATGTCAAACTTAAAAATGCAT
1587207 GACCAACAAT
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
35 33 1.00
ACGTcount: A:0.42, C:0.17, G:0.09, T:0.32
Consensus pattern (35 bp):
TCAAGTAATTTACATGTCAAACTTAAAAATGCATC
Found at i:1597508 original size:12 final size:12
Alignment explanation
Indices: 1597486--1597524 Score: 53
Period size: 12 Copynumber: 3.2 Consensus size: 12
1597476 AAAAATTTAA
1597486 TATATTTAATTT
1 TATATTTAATTT
1597498 TAT-TATTAATTAT
1 TATAT-TTAATT-T
1597511 TATATTTAATTT
1 TATATTTAATTT
1597523 TA
1 TA
1597525 GAAAATATTT
Statistics
Matches: 24, Mismatches: 0, Indels: 6
0.80 0.00 0.20
Matches are distributed among these distances:
11 1 0.04
12 12 0.50
13 10 0.42
14 1 0.04
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (12 bp):
TATATTTAATTT
Found at i:1600260 original size:14 final size:13
Alignment explanation
Indices: 1600230--1600256 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
1600220 AAATATGATT
1600230 ATAATCCCATTAA
1 ATAATCCCATTAA
1600243 ATAATCCCATTAA
1 ATAATCCCATTAA
1600256 A
1 A
1600257 ATAAGTAACC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.48, C:0.22, G:0.00, T:0.30
Consensus pattern (13 bp):
ATAATCCCATTAA
Found at i:1608352 original size:3 final size:3
Alignment explanation
Indices: 1608344--1608382 Score: 78
Period size: 3 Copynumber: 13.0 Consensus size: 3
1608334 TTTACTAGTG
1608344 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1608383 GCTCTTGCCA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 36 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:1616718 original size:13 final size:13
Alignment explanation
Indices: 1616700--1616755 Score: 91
Period size: 13 Copynumber: 4.5 Consensus size: 13
1616690 AATTTTGAAT
1616700 TATTTAGTGATAA
1 TATTTAGTGATAA
1616713 TATTTAGTGATAA
1 TATTTAGTGATAA
1616726 TATTTAG-GAT--
1 TATTTAGTGATAA
1616736 TATTTAGTGATAA
1 TATTTAGTGATAA
1616749 TATTTAG
1 TATTTAG
1616756 GAAAAATTTA
Statistics
Matches: 40, Mismatches: 0, Indels: 6
0.87 0.00 0.13
Matches are distributed among these distances:
10 7 0.17
11 3 0.08
12 3 0.08
13 27 0.68
ACGTcount: A:0.36, C:0.00, G:0.16, T:0.48
Consensus pattern (13 bp):
TATTTAGTGATAA
Found at i:1616739 original size:23 final size:23
Alignment explanation
Indices: 1616713--1616757 Score: 90
Period size: 23 Copynumber: 2.0 Consensus size: 23
1616703 TTAGTGATAA
1616713 TATTTAGTGATAATATTTAGGAT
1 TATTTAGTGATAATATTTAGGAT
1616736 TATTTAGTGATAATATTTAGGA
1 TATTTAGTGATAATATTTAGGA
1616758 AAAATTTAGC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.36, C:0.00, G:0.18, T:0.47
Consensus pattern (23 bp):
TATTTAGTGATAATATTTAGGAT
Found at i:1619585 original size:3 final size:3
Alignment explanation
Indices: 1619577--1619607 Score: 55
Period size: 3 Copynumber: 10.7 Consensus size: 3
1619567 CATATATATG
1619577 AAT AAT AAT AAT AAT -AT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1619608 ATAAATGAGC
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
2 2 0.07
3 25 0.93
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:1619597 original size:14 final size:14
Alignment explanation
Indices: 1619578--1619611 Score: 61
Period size: 14 Copynumber: 2.5 Consensus size: 14
1619568 ATATATATGA
1619578 ATAATAATAATAAT
1 ATAATAATAATAAT
1619592 ATAATAATAATAAT
1 ATAATAATAATAAT
1619606 A-AATAA
1 ATAATAA
1619612 ATGAGCAAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
13 5 0.25
14 15 0.75
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (14 bp):
ATAATAATAATAAT
Found at i:1621386 original size:90 final size:90
Alignment explanation
Indices: 1621256--1621765 Score: 457
Period size: 90 Copynumber: 5.8 Consensus size: 90
1621246 TAATCCGCTT
* * * *
1621256 CACTGTAATCTCA-GG-GATTGGATTATCAGA-TTCAATCTGCTCCGCTGTAGTCTCCGGGAGAT
1 CACTGTAATCTCAGGGAGATAGGATTA-CTGACTTCAATCTGCTCCGCTGTAATCTCAGGGAGAT
*
1621318 AAGATCTGAAATTCTTCGGTCTGCTC
65 AAGATCTGAAATTCTTCAGTCTGCTC
*
1621344 CACTGTAATCTCAGGGAGATAGGATTACT-ATCTTCAATCTGCTCCGCTGTAATCTCAAGGAGAT
1 CACTGTAATCTCAGGGAGATAGGATTACTGA-CTTCAATCTGCTCCGCTGTAATCTCAGGGAGAT
1621408 AAGATCTGAAATTCTTCAGTCTGCTC
65 AAGATCTGAAATTCTTCAGTCTGCTC
* * * * * ** *
1621434 CACTGTAATCTCAGGGAGATAAGA--CCTGA-TGCGATCTACTCTACTGTAA-CTTCAGAGAGAT
1 CACTGTAATCTCAGGGAGATAGGATTACTGACTTCAATCTGCTCCGCTGTAATC-TCAGGGAGAT
** * *
1621495 AAGATCCT-TTATT-TT-AATCCGCTC
65 AAGAT-CTGAAATTCTTCAGTCTGCTC
* **
1621519 CACTGTAATCTCAGGGAGATAGGATTACT-AGCTTCGATCTGCTCTACTGTAATCTCAGGGAGAT
1 CACTGTAATCTCAGGGAGATAGGATTACTGA-CTTCAATCTGCTCCGCTGTAATCTCAGGGAGAT
* * *
1621583 AAGA-CTGACATTCTTCGGTCTGTTC
65 AAGATCTGAAATTCTTCAGTCTGCTC
* * * * * * * * *
1621608 CACTGTAATCTCAGGGAAATAAGA--CCTGAC-GCGATCTACTCTGCTGTAA-CTTTAGAGAGAT
1 CACTGTAATCTCAGGGAGATAGGATTACTGACTTCAATCTGCTCCGCTGTAATC-TCAGGGAGAT
** * **
1621669 AAGATCAT-TCATT-TT-AATCCACTC
65 AAGATC-TGAAATTCTTCAGTCTGCTC
* *
1621693 CACTGTAATATCAGGGAGATAGGATTACTAACTTCAATCTGCTCCGCTGTAATCTCAGGGAGATA
1 CACTGTAATCTCAGGGAGATAGGATTACTGACTTCAATCTGCTCCGCTGTAATCTCAGGGAGATA
1621758 AGATCTGA
66 AGATCTGA
1621766 CACGATCTAC
Statistics
Matches: 342, Mismatches: 56, Indels: 48
0.77 0.13 0.11
Matches are distributed among these distances:
85 56 0.16
86 36 0.11
87 49 0.14
88 82 0.24
89 33 0.10
90 86 0.25
ACGTcount: A:0.28, C:0.22, G:0.20, T:0.30
Consensus pattern (90 bp):
CACTGTAATCTCAGGGAGATAGGATTACTGACTTCAATCTGCTCCGCTGTAATCTCAGGGAGATA
AGATCTGAAATTCTTCAGTCTGCTC
Found at i:1621394 original size:44 final size:44
Alignment explanation
Indices: 1621286--1621890 Score: 322
Period size: 44 Copynumber: 13.8 Consensus size: 44
1621276 GATTATCAGA
* * * *
1621286 TTCAATCTGCTCCGCTGTAGTCTCCGGGAGATAAGATCTGA-AATTC
1 TTCAATCTGCTCCACTGTAATCTCAGGGAGATAAGAT-T-ACTA-TC
** *
1621332 TTCGGTCTGCTCCACTGTAATCTCAGGGAGATAGGATTACTATC
1 TTCAATCTGCTCCACTGTAATCTCAGGGAGATAAGATTACTATC
* * *
1621376 TTCAATCTGCTCCGCTGTAATCTCAAGGAGATAAGATCTGA-AATTC
1 TTCAATCTGCTCCACTGTAATCTCAGGGAGATAAGAT-T-ACTA-TC
* *
1621422 TTCAGTCTGCTCCACTGTAATCTCAGGGAGATAAGA--CCTGA--
1 TTCAATCTGCTCCACTGTAATCTCAGGGAGATAAGATTACT-ATC
* * * * * *
1621463 TGCGATCTACTCTACTGTAA-CTTCAGAGAGATAAGATCCT-TTAT-
1 TTCAATCTGCTCCACTGTAATC-TCAGGGAGATAAGAT--TACTATC
* * * *
1621507 TTTAATCCGCTCCACTGTAATCTCAGGGAGATAGGATTACTAGC
1 TTCAATCTGCTCCACTGTAATCTCAGGGAGATAAGATTACTATC
* * *
1621551 TTCGATCTGCTCTACTGTAATCTCAGGGAGATAAGACTGAC-ATTC
1 TTCAATCTGCTCCACTGTAATCTCAGGGAGATAAGA-TTACTA-TC
** * * *
1621596 TTCGGTCTGTTCCACTGTAATCTCAGGGAAATAAGA--CCTGA-C
1 TTCAATCTGCTCCACTGTAATCTCAGGGAGATAAGATTACT-ATC
* * * ** * * * *
1621638 -GCGATCTACTCTGCTGTAA-CTTTAGAGAGATAAGATCATTCAT-
1 TTCAATCTGCTCCACTGTAATC-TCAGGGAGATAAGATTACT-ATC
* ** * * *
1621681 TTTAATCCACTCCACTGTAATATCAGGGAGATAGGATTACTAAC
1 TTCAATCTGCTCCACTGTAATCTCAGGGAGATAAGATTACTATC
*
1621725 TTCAATCTGCTCCGCTGTAATCTCAGGGAGATAAGA-T-CTGA-C
1 TTCAATCTGCTCCACTGTAATCTCAGGGAGATAAGATTACT-ATC
* * * * * * *
1621767 -ACGATCTACTCTACTGTAAAT-TCAGAGAGAAAAGATCCT-TTAT-
1 TTCAATCTGCTCCACTGT-AATCTCAGGGAGATAAGAT--TACTATC
* *** *
1621810 TTTAATCCATTCCACTGTAATCTCAGGGAGATAGGATTACTAAT-
1 TTCAATCTGCTCCACTGTAATCTCAGGGAGATAAGATTACT-ATC
* *
1621854 TTCAATCTACTCCGCTGTAATCTCAGGGAGATAAGAT
1 TTCAATCTGCTCCACTGTAATCTCAGGGAGATAAGAT
1621891 CTTTTAATCC
Statistics
Matches: 422, Mismatches: 101, Indels: 74
0.71 0.17 0.12
Matches are distributed among these distances:
40 2 0.00
41 76 0.18
42 10 0.02
43 13 0.03
44 213 0.50
45 41 0.10
46 67 0.16
ACGTcount: A:0.29, C:0.22, G:0.19, T:0.31
Consensus pattern (44 bp):
TTCAATCTGCTCCACTGTAATCTCAGGGAGATAAGATTACTATC
Found at i:1621667 original size:174 final size:175
Alignment explanation
Indices: 1621340--1621767 Score: 696
Period size: 174 Copynumber: 2.5 Consensus size: 175
1621330 TCTTCGGTCT
* *
1621340 GCTCCACTGTAATCTCAGGGAGATAGGATTACTATCTTCAATCTGCTCCGCTGTAATCTCAAGGA
1 GCTCCACTGTAATCTCAGGGAGATAGGATTACTAACTTCAATCTGCTCCGCTGTAATCTCAGGGA
* * *
1621405 GATAAGATCTGAAATTCTTCAGTCTGCTCCACTGTAATCTCAGGGAGATAAGACCTGATGCGATC
66 GATAAGATCTGACATTCTTCAGTCTGCTCCACTGTAATCTCAGGGAAATAAGACCTGACGCGATC
* *
1621470 TACTCTACTGTAACTTCAGAGAGATAAGATCCTTTATTTTAATCC
131 TACTCTACTGTAACTTCAGAGAGATAAGATCATTCATTTTAATCC
* * **
1621515 GCTCCACTGTAATCTCAGGGAGATAGGATTACTAGCTTCGATCTGCTCTACTGTAATCTCAGGGA
1 GCTCCACTGTAATCTCAGGGAGATAGGATTACTAACTTCAATCTGCTCCGCTGTAATCTCAGGGA
* *
1621580 GATAAGA-CTGACATTCTTCGGTCTGTTCCACTGTAATCTCAGGGAAATAAGACCTGACGCGATC
66 GATAAGATCTGACATTCTTCAGTCTGCTCCACTGTAATCTCAGGGAAATAAGACCTGACGCGATC
* *
1621644 TACTCTGCTGTAACTTTAGAGAGATAAGATCATTCATTTTAATCC
131 TACTCTACTGTAACTTCAGAGAGATAAGATCATTCATTTTAATCC
* *
1621689 ACTCCACTGTAATATCAGGGAGATAGGATTACTAACTTCAATCTGCTCCGCTGTAATCTCAGGGA
1 GCTCCACTGTAATCTCAGGGAGATAGGATTACTAACTTCAATCTGCTCCGCTGTAATCTCAGGGA
1621754 GATAAGATCTGACA
66 GATAAGATCTGACA
1621768 CGATCTACTC
Statistics
Matches: 232, Mismatches: 20, Indels: 2
0.91 0.08 0.01
Matches are distributed among these distances:
174 159 0.69
175 73 0.31
ACGTcount: A:0.29, C:0.22, G:0.19, T:0.30
Consensus pattern (175 bp):
GCTCCACTGTAATCTCAGGGAGATAGGATTACTAACTTCAATCTGCTCCGCTGTAATCTCAGGGA
GATAAGATCTGACATTCTTCAGTCTGCTCCACTGTAATCTCAGGGAAATAAGACCTGACGCGATC
TACTCTACTGTAACTTCAGAGAGATAAGATCATTCATTTTAATCC
Found at i:1621772 original size:129 final size:129
Alignment explanation
Indices: 1621601--1621892 Score: 449
Period size: 129 Copynumber: 2.3 Consensus size: 129
1621591 CATTCTTCGG
* * * * * * * *
1621601 TCTGTTCCACTGTAATCTCAGGGAAATAAGACCTGACGCGATCTACTCTGCTGTAACTTTAGAGA
1 TCTGCTCCGCTGTAATCTCAGGGAGATAAGATCTGACACGATCTACTCTACTGTAAATTCAGAGA
*
1621666 GATAAGATCATTCATTTTAATCCACTCCACTGTAATATCAGGGAGATAGGATTACTAACTTCAA
66 GAAAAGATCATTCATTTTAATCCACTCCACTGTAATATCAGGGAGATAGGATTACTAACTTCAA
1621730 TCTGCTCCGCTGTAATCTCAGGGAGATAAGATCTGACACGATCTACTCTACTGTAAATTCAGAGA
1 TCTGCTCCGCTGTAATCTCAGGGAGATAAGATCTGACACGATCTACTCTACTGTAAATTCAGAGA
* * * * *
1621795 GAAAAGATCCTTTATTTTAATCCATTCCACTGTAATCTCAGGGAGATAGGATTACTAATTTCAA
66 GAAAAGATCATTCATTTTAATCCACTCCACTGTAATATCAGGGAGATAGGATTACTAACTTCAA
*
1621859 TCTACTCCGCTGTAATCTCAGGGAGATAAGATCT
1 TCTGCTCCGCTGTAATCTCAGGGAGATAAGATCT
1621893 TTTAATCCGC
Statistics
Matches: 148, Mismatches: 15, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
129 148 1.00
ACGTcount: A:0.31, C:0.21, G:0.17, T:0.30
Consensus pattern (129 bp):
TCTGCTCCGCTGTAATCTCAGGGAGATAAGATCTGACACGATCTACTCTACTGTAAATTCAGAGA
GAAAAGATCATTCATTTTAATCCACTCCACTGTAATATCAGGGAGATAGGATTACTAACTTCAA
Found at i:1622041 original size:86 final size:86
Alignment explanation
Indices: 1621893--1622143 Score: 425
Period size: 86 Copynumber: 2.9 Consensus size: 86
1621883 GATAAGATCT
* *
1621893 TTTAATCC-GCTCCACTGCAACCAATGAAGGCAAGAC-TTGTTTTCGATCTTCTTCGCTGTTAAT
1 TTTAA-CCAGCTCCACTGCAACCAATGAAGGCAAGGCTTTGTTTTCGATCTGCTTCGCTGTTAAT
*
1621956 TCAGGAAGGCAAGATCTGCTTC
65 GCAGGAAGGCAAGATCTGCTTC
* *
1621978 TTTAACCAGCTCCATTGCAACCAATGAAGGCAAGGCTTTGTTTTCGATCTGCTTCGTTGTTAATG
1 TTTAACCAGCTCCACTGCAACCAATGAAGGCAAGGCTTTGTTTTCGATCTGCTTCGCTGTTAATG
1622043 CAGGAAGGCAAGATCTGCTTC
66 CAGGAAGGCAAGATCTGCTTC
*
1622064 TTTAACCAGCTCCACTGTAACCAATGAAGGCAAGGCTTTGTTTTCGATCTGCTTCGCTGTTAATG
1 TTTAACCAGCTCCACTGCAACCAATGAAGGCAAGGCTTTGTTTTCGATCTGCTTCGCTGTTAATG
1622129 CAGGAAGGCAAGATC
66 CAGGAAGGCAAGATC
1622144 NNNNNNNNNN
Statistics
Matches: 156, Mismatches: 8, Indels: 3
0.93 0.05 0.02
Matches are distributed among these distances:
84 2 0.01
85 31 0.20
86 123 0.79
ACGTcount: A:0.25, C:0.23, G:0.21, T:0.31
Consensus pattern (86 bp):
TTTAACCAGCTCCACTGCAACCAATGAAGGCAAGGCTTTGTTTTCGATCTGCTTCGCTGTTAATG
CAGGAAGGCAAGATCTGCTTC
Found at i:1622050 original size:43 final size:43
Alignment explanation
Indices: 1622003--1622140 Score: 129
Period size: 43 Copynumber: 3.2 Consensus size: 43
1621993 TGCAACCAAT
*
1622003 GAAGGCAAGGCTTTGTTTTCGATCTGCTTCGTTGTTAATGCAG
1 GAAGGCAAGGCTTTGTTTTCGATCTGCTTCGCTGTTAATGCAG
* * ** * * * * * *
1622046 GAAGGCAA-GATCTGCTTCTTTAACCAGCTCCACTG-TAA-CCAAT
1 GAAGGCAAGGCTTTG-TT-TTCGATCTGCTTCGCTGTTAATGC-AG
1622089 GAAGGCAAGGCTTTGTTTTCGATCTGCTTCGCTGTTAATGCAG
1 GAAGGCAAGGCTTTGTTTTCGATCTGCTTCGCTGTTAATGCAG
1622132 GAAGGCAAG
1 GAAGGCAAG
1622141 ATCNNNNNNN
Statistics
Matches: 68, Mismatches: 21, Indels: 12
0.67 0.21 0.12
Matches are distributed among these distances:
42 16 0.24
43 37 0.54
44 15 0.22
ACGTcount: A:0.24, C:0.20, G:0.25, T:0.30
Consensus pattern (43 bp):
GAAGGCAAGGCTTTGTTTTCGATCTGCTTCGCTGTTAATGCAG
Found at i:1623668 original size:21 final size:21
Alignment explanation
Indices: 1623642--1623688 Score: 60
Period size: 21 Copynumber: 2.2 Consensus size: 21
1623632 GGTATAGCAA
1623642 GATCACCGT-ATGCCCCAATCT
1 GATCA-CGTCATGCCCCAATCT
* *
1623663 GATCACTTCATGCCCCATTCT
1 GATCACGTCATGCCCCAATCT
1623684 GATCA
1 GATCA
1623689 ATATTTGAGC
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
20 2 0.09
21 21 0.91
ACGTcount: A:0.23, C:0.36, G:0.13, T:0.28
Consensus pattern (21 bp):
GATCACGTCATGCCCCAATCT
Found at i:1623791 original size:8 final size:8
Alignment explanation
Indices: 1623780--1623819 Score: 50
Period size: 7 Copynumber: 5.2 Consensus size: 8
1623770 CCATTTTTAC
1623780 TTTTTCAT
1 TTTTTCAT
1623788 TTTTTCA-
1 TTTTTCAT
1623795 TTTTTCA-
1 TTTTTCAT
1623802 TTTTT-AT
1 TTTTTCAT
1623809 TTTTCTCAT
1 TTTT-TCAT
1623818 TT
1 TT
1623820 CTTTTTCTTT
Statistics
Matches: 29, Mismatches: 0, Indels: 5
0.85 0.00 0.15
Matches are distributed among these distances:
6 1 0.03
7 16 0.55
8 8 0.28
9 4 0.14
ACGTcount: A:0.12, C:0.12, G:0.00, T:0.75
Consensus pattern (8 bp):
TTTTTCAT
Found at i:1623796 original size:22 final size:21
Alignment explanation
Indices: 1623771--1623834 Score: 71
Period size: 22 Copynumber: 3.0 Consensus size: 21
1623761 TTAGCCTCTC
1623771 CATTTTTACTTTTTCATTTTTT
1 CATTTTT-CTTTTTCATTTTTT
1623793 CATTTTTCATTTTT-ATTTTTCT
1 CATTTTTC-TTTTTCATTTTT-T
*
1623815 CA--TTTCTTTTTCTTTTTTT
1 CATTTTTCTTTTTCATTTTTT
1623834 C
1 C
1623835 TTCTTTTTTT
Statistics
Matches: 38, Mismatches: 1, Indels: 9
0.79 0.02 0.19
Matches are distributed among these distances:
19 7 0.18
20 9 0.24
21 7 0.18
22 15 0.39
ACGTcount: A:0.11, C:0.16, G:0.00, T:0.73
Consensus pattern (21 bp):
CATTTTTCTTTTTCATTTTTT
Found at i:1623798 original size:15 final size:14
Alignment explanation
Indices: 1623771--1623836 Score: 64
Period size: 14 Copynumber: 4.8 Consensus size: 14
1623761 TTAGCCTCTC
*
1623771 CATTTTTACTTTTT
1 CATTTTTTCTTTTT
1623785 CATTTTTTCATTTTT
1 CATTTTTTC-TTTTT
*
1623800 CA-TTTTTATTTTT
1 CATTTTTTCTTTTT
**
1623813 C-TCATTTCTTTTT
1 CATTTTTTCTTTTT
*
1623826 CTTTTTTTCTT
1 CATTTTTTCTT
1623837 CTTTTTTTGT
Statistics
Matches: 42, Mismatches: 7, Indels: 6
0.76 0.13 0.11
Matches are distributed among these distances:
13 15 0.36
14 20 0.48
15 7 0.17
ACGTcount: A:0.11, C:0.15, G:0.00, T:0.74
Consensus pattern (14 bp):
CATTTTTTCTTTTT
Found at i:1623832 original size:7 final size:7
Alignment explanation
Indices: 1623771--1623813 Score: 54
Period size: 7 Copynumber: 6.1 Consensus size: 7
1623761 TTAGCCTCTC
1623771 CATTTTT
1 CATTTTT
1623778 -ACTTTTT
1 CA-TTTTT
1623785 CATTTTTT
1 CA-TTTTT
1623793 CATTTTT
1 CATTTTT
1623800 CATTTTT
1 CATTTTT
1623807 -ATTTTT
1 CATTTTT
1623813 C
1 C
1623814 TCATTTCTTT
Statistics
Matches: 32, Mismatches: 1, Indels: 6
0.82 0.03 0.15
Matches are distributed among these distances:
6 7 0.22
7 17 0.53
8 8 0.25
ACGTcount: A:0.14, C:0.14, G:0.00, T:0.72
Consensus pattern (7 bp):
CATTTTT
Found at i:1633363 original size:10 final size:11
Alignment explanation
Indices: 1633327--1633357 Score: 53
Period size: 11 Copynumber: 2.8 Consensus size: 11
1633317 CTAATTTCAC
1633327 ATTTAAAAATT
1 ATTTAAAAATT
1633338 ATTTAAAAATT
1 ATTTAAAAATT
*
1633349 GTTTAAAAA
1 ATTTAAAAA
1633358 AATTTATCTA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
11 19 1.00
ACGTcount: A:0.55, C:0.00, G:0.03, T:0.42
Consensus pattern (11 bp):
ATTTAAAAATT
Found at i:1635285 original size:132 final size:132
Alignment explanation
Indices: 1635125--1635907 Score: 1128
Period size: 132 Copynumber: 6.0 Consensus size: 132
1635115 GATATAGGAT
* * * *
1635125 TTGGTTGCTTAAATCTGCTTCCCGCTATCTTGGCAAGATAAGATTTGTCGTCTTTGATCTGCTCC
1 TTGGTGGCTTAAATCTGCTTCCCACTATCTTGGAAAGATAAGATTTGCCGTCTTTGATCTGCTCC
* * *
1635190 ACTACTGCTTAGGGAGATAAGAACTACAATCTTCAACCTACTCCGCTGCTGCTCAGGGAGACAAG
66 ACTACTGCTTAGGGAGATAAGATCTACAATCTTCAACCTTCTCCGCTGCTGCTCAAGGAGACAAG
1635255 GC
131 GC
* * *
1635257 TTGGTGGCTTAAATCTGTTTCCCACTATCTTGGAAA-ATAAGATTTGCTGTCTTCGATCTGCTCC
1 TTGGTGGCTTAAATCTGCTTCCCACTATCTTGGAAAGATAAGATTTGCCGTCTTTGATCTGCTCC
* * * *
1635321 ACTACTGCTTAGGGAGATAAGATCTACAATATTCAACCTTCTCTGCTGCTGCTCAGGGAAACAAG
66 ACTACTGCTTAGGGAGATAAGATCTACAATCTTCAACCTTCTCCGCTGCTGCTCAAGGAGACAAG
1635386 GC
131 GC
* * * *
1635388 TTGGTGGCTTAAATCTGCTTCCTACTATTTTGGAAAGATAAGATTTGCCGTCTTCGATTTGCTCC
1 TTGGTGGCTTAAATCTGCTTCCCACTATCTTGGAAAGATAAGATTTGCCGTCTTTGATCTGCTCC
* * *
1635453 ACTACTGCTTAGGGAGATATGATCT---A----CAGCCTCCTCCGCTGCTGCTCAAGGAGACAAG
66 ACTACTGCTTAGGGAGATAAGATCTACAATCTTCAACCTTCTCCGCTGCTGCTCAAGGAGACAAG
1635511 GC
131 GC
* * *
1635513 TTTGTGGCTTAAATGTGCTTCCCACTATCTTGGAAAGATAAGACTTGCCGTCTTTGATCTGCTCC
1 TTGGTGGCTTAAATCTGCTTCCCACTATCTTGGAAAGATAAGATTTGCCGTCTTTGATCTGCTCC
* *
1635578 ACTACTGCTTAGGGAGATAAGATCTACAATCTTCAACCTTCTTCGCTGCTGCTCAGGGAGACAAG
66 ACTACTGCTTAGGGAGATAAGATCTACAATCTTCAACCTTCTCCGCTGCTGCTCAAGGAGACAAG
1635643 GC
131 GC
* * *
1635645 TTGGTGGCTTAAATCTGCTTCCCACTATTTTGGAAAGATAAGATTTGCCGTCTTTCATTTGCTCC
1 TTGGTGGCTTAAATCTGCTTCCCACTATCTTGGAAAGATAAGATTTGCCGTCTTTGATCTGCTCC
* * *
1635710 ATTACTGCTTAGGGAGATAGGATCT---A----CAACCTCCTCCGCTGCTGCTCAAGGAGACAAG
66 ACTACTGCTTAGGGAGATAAGATCTACAATCTTCAACCTTCTCCGCTGCTGCTCAAGGAGACAAG
1635768 GC
131 GC
** *
1635770 TTTATGGCTTAAATCTGCTTCCCACTATCTTGGAAAGATAAGACTTGCCGTCTTTGATCTGCTCC
1 TTGGTGGCTTAAATCTGCTTCCCACTATCTTGGAAAGATAAGATTTGCCGTCTTTGATCTGCTCC
* *
1635835 ACTACTGCTTAGGGAGATAAGATCTACAATCTTCAACCTTCTCCGCTGTTGCTCAAGGAGACAAT
66 ACTACTGCTTAGGGAGATAAGATCTACAATCTTCAACCTTCTCCGCTGCTGCTCAAGGAGACAAG
1635900 GC
131 GC
1635902 TTGGTG
1 TTGGTG
1635908 TTTCACCAGT
Statistics
Matches: 577, Mismatches: 59, Indels: 30
0.87 0.09 0.05
Matches are distributed among these distances:
125 224 0.39
128 2 0.00
129 2 0.00
131 120 0.21
132 229 0.40
ACGTcount: A:0.24, C:0.24, G:0.21, T:0.31
Consensus pattern (132 bp):
TTGGTGGCTTAAATCTGCTTCCCACTATCTTGGAAAGATAAGATTTGCCGTCTTTGATCTGCTCC
ACTACTGCTTAGGGAGATAAGATCTACAATCTTCAACCTTCTCCGCTGCTGCTCAAGGAGACAAG
GC
Found at i:1635342 original size:44 final size:44
Alignment explanation
Indices: 1635160--1635471 Score: 121
Period size: 44 Copynumber: 7.1 Consensus size: 44
1635150 TATCTTGGCA
**
1635160 AGATAAGATTTG-TCGTCTTTGATCTGCTCCACTACTGCTTAGGG
1 AGATAAGATTTGCT-GTCTTCAATCTGCTCCACTACTGCTTAGGG
** * ** * * * * *
1635204 AGATAAGAACTACAATCTTCAACCTACTCCGCTGCTGCTCAGGG
1 AGATAAGATTTGCTGTCTTCAATCTGCTCCACTACTGCTTAGGG
* ** * * * * *
1635248 AGACAAGGCTTGGTGGCTTAAATCTGTTTCCCACTA-T-CTT-GGA
1 AGATAAGATTTGCTGTCTTCAATCTG-CT-CCACTACTGCTTAGGG
* *
1635291 AAATAAGATTTGCTGTCTTCGATCTGCTCCACTACTGCTTAGGG
1 AGATAAGATTTGCTGTCTTCAATCTGCTCCACTACTGCTTAGGG
* * ** * * * ** * *
1635335 AGATAAGATCTACAATATTCAACCTTCTCTGCTGCTGCTCAGGG
1 AGATAAGATTTGCTGTCTTCAATCTGCTCCACTACTGCTTAGGG
* * ** * * * * ** * *
1635379 AAACAAGGCTTGGTGGCTTAAATCTGCTTC-CTACTATTTTGGAA
1 AGATAAGATTTGCTGTCTTCAATCTGCTCCACTACTGCTTAGG-G
* * *
1635423 AGATAAGATTTGCCGTCTTCGATTTGCTCCACTACTGCTTAGGG
1 AGATAAGATTTGCTGTCTTCAATCTGCTCCACTACTGCTTAGGG
1635467 AGATA
1 AGATA
1635472 TGATCTACAG
Statistics
Matches: 171, Mismatches: 89, Indels: 16
0.62 0.32 0.06
Matches are distributed among these distances:
41 6 0.04
42 2 0.01
43 30 0.18
44 118 0.69
45 11 0.06
46 4 0.02
ACGTcount: A:0.25, C:0.22, G:0.21, T:0.32
Consensus pattern (44 bp):
AGATAAGATTTGCTGTCTTCAATCTGCTCCACTACTGCTTAGGG
Found at i:1635551 original size:125 final size:125
Alignment explanation
Indices: 1635125--1635863 Score: 978
Period size: 125 Copynumber: 5.8 Consensus size: 125
1635115 GATATAGGAT
* * * * *
1635125 TTGGTTGCTTAAATCTGCTTCCCGCTATCTTGGCAAGATAAGATTTGTCGTCTTTGATCTGCTCC
1 TTGGTGGCTTAAATCTGCTTCCCACTATCTTGGAAAGATAAGATTTGCCGTCTTCGATCTGCTCC
* *
1635190 ACTACTGCTTAGGGAGATAAGAACTACAATCTTCAACCTACTCCGCTGCTGCTCAGGGAGACAAG
66 ACTACTGCTTAGGGAGATAAG-------ATCTACAACCTCCTCCGCTGCTGCTCAGGGAGACAAG
1635255 GC
124 GC
* *
1635257 TTGGTGGCTTAAATCTGTTTCCCACTATCTTGGAAA-ATAAGATTTGCTGTCTTCGATCTGCTCC
1 TTGGTGGCTTAAATCTGCTTCCCACTATCTTGGAAAGATAAGATTTGCCGTCTTCGATCTGCTCC
* * *
1635321 ACTACTGCTTAGGGAGATAAGATCTACAATATTCAACCTTCTCTGCTGCTGCTCAGGGAAACAAG
66 ACTACTGCTTAGGGAGATAAGA--T-C--TA--CAACCTCCTCCGCTGCTGCTCAGGGAGACAAG
1635386 GC
124 GC
* * *
1635388 TTGGTGGCTTAAATCTGCTTCCTACTATTTTGGAAAGATAAGATTTGCCGTCTTCGATTTGCTCC
1 TTGGTGGCTTAAATCTGCTTCCCACTATCTTGGAAAGATAAGATTTGCCGTCTTCGATCTGCTCC
* * *
1635453 ACTACTGCTTAGGGAGATATGATCTACAGCCTCCTCCGCTGCTGCTCAAGGAGACAAGGC
66 ACTACTGCTTAGGGAGATAAGATCTACAACCTCCTCCGCTGCTGCTCAGGGAGACAAGGC
* * * *
1635513 TTTGTGGCTTAAATGTGCTTCCCACTATCTTGGAAAGATAAGACTTGCCGTCTTTGATCTGCTCC
1 TTGGTGGCTTAAATCTGCTTCCCACTATCTTGGAAAGATAAGATTTGCCGTCTTCGATCTGCTCC
*
1635578 ACTACTGCTTAGGGAGATAAGATCTACAATCTTCAACCTTCTTCGCTGCTGCTCAGGGAGACAAG
66 ACTACTGCTTAGGGAGATAAGATCTACAA-C--C-TCC-TC--CGCTGCTGCTCAGGGAGACAAG
1635643 GC
124 GC
* *
1635645 TTGGTGGCTTAAATCTGCTTCCCACTATTTTGGAAAGATAAGATTTGCCGTCTTTC-ATTTGCTC
1 TTGGTGGCTTAAATCTGCTTCCCACTATCTTGGAAAGATAAGATTTGCCGTC-TTCGATCTGCTC
* * *
1635709 CATTACTGCTTAGGGAGATAGGATCTACAACCTCCTCCGCTGCTGCTCAAGGAGACAAGGC
65 CACTACTGCTTAGGGAGATAAGATCTACAACCTCCTCCGCTGCTGCTCAGGGAGACAAGGC
** * *
1635770 TTTATGGCTTAAATCTGCTTCCCACTATCTTGGAAAGATAAGACTTGCCGTCTTTGATCTGCTCC
1 TTGGTGGCTTAAATCTGCTTCCCACTATCTTGGAAAGATAAGATTTGCCGTCTTCGATCTGCTCC
1635835 ACTACTGCTTAGGGAGATAAGATCTACAA
66 ACTACTGCTTAGGGAGATAAGATCTACAA
1635864 TCTTCAACCT
Statistics
Matches: 539, Mismatches: 51, Indels: 41
0.85 0.08 0.06
Matches are distributed among these distances:
124 3 0.01
125 220 0.41
126 2 0.00
127 5 0.01
128 3 0.01
129 5 0.01
130 3 0.01
131 111 0.21
132 185 0.34
133 2 0.00
ACGTcount: A:0.24, C:0.24, G:0.21, T:0.31
Consensus pattern (125 bp):
TTGGTGGCTTAAATCTGCTTCCCACTATCTTGGAAAGATAAGATTTGCCGTCTTCGATCTGCTCC
ACTACTGCTTAGGGAGATAAGATCTACAACCTCCTCCGCTGCTGCTCAGGGAGACAAGGC
Found at i:1635631 original size:257 final size:257
Alignment explanation
Indices: 1635125--1635907 Score: 1212
Period size: 257 Copynumber: 3.0 Consensus size: 257
1635115 GATATAGGAT
* * * * * * *
1635125 TTGGTTGCTTAAATCTGCTTCCCGCTATCTTGGCAAGATAAGATTTGTCGTCTTTGATCTGCTCC
1 TTGGTGGCTTAAATCTGCTTCCCACTATTTTGGAAAGATAAGATTTGCCGTCTTCGATTTGCTCC
* * * *
1635190 ACTACTGCTTAGGGAGATAAGAACTACAATCTTCAACCTACTCCGCTGCTGCTCAGGGAGACAAG
66 ACTACTGCTTAGGGAGAT----A-T--GATCTACAACCTCCTCCGCTGCTGCTCAAGGAGACAAG
* * * * *
1635255 GCTTGGTGGCTTAAATCTGTTTCCCACTATCTTGGAAA-ATAAGATTTGCTGTCTTCGATCTGCT
124 GCTTTGTGGCTTAAATCTGCTTCCCACTATCTTGGAAAGATAAGACTTGCCGTCTTTGATCTGCT
* *
1635319 CCACTACTGCTTAGGGAGATAAGATCTACAATATTCAACCTTC-TCTGCTGCTGCTCAGGGAAAC
189 CCACTACTGCTTAGGGAGATAAGATCTACAATCTTCAACCTTCTTC-GCTGCTGCTCAGGGAGAC
1635383 AAGGC
253 AAGGC
*
1635388 TTGGTGGCTTAAATCTGCTTCCTACTATTTTGGAAAGATAAGATTTGCCGTCTTCGATTTGCTCC
1 TTGGTGGCTTAAATCTGCTTCCCACTATTTTGGAAAGATAAGATTTGCCGTCTTCGATTTGCTCC
*
1635453 ACTACTGCTTAGGGAGATATGATCTACAGCCTCCTCCGCTGCTGCTCAAGGAGACAAGGCTTTGT
66 ACTACTGCTTAGGGAGATATGATCTACAACCTCCTCCGCTGCTGCTCAAGGAGACAAGGCTTTGT
*
1635518 GGCTTAAATGTGCTTCCCACTATCTTGGAAAGATAAGACTTGCCGTCTTTGATCTGCTCCACTAC
131 GGCTTAAATCTGCTTCCCACTATCTTGGAAAGATAAGACTTGCCGTCTTTGATCTGCTCCACTAC
1635583 TGCTTAGGGAGATAAGATCTACAATCTTCAACCTTCTTCGCTGCTGCTCAGGGAGACAAGGC
196 TGCTTAGGGAGATAAGATCTACAATCTTCAACCTTCTTCGCTGCTGCTCAGGGAGACAAGGC
1635645 TTGGTGGCTTAAATCTGCTTCCCACTATTTTGGAAAGATAAGATTTGCCGTCTTTC-ATTTGCTC
1 TTGGTGGCTTAAATCTGCTTCCCACTATTTTGGAAAGATAAGATTTGCCGTC-TTCGATTTGCTC
* * *
1635709 CATTACTGCTTAGGGAGATAGGATCTACAACCTCCTCCGCTGCTGCTCAAGGAGACAAGGCTTTA
65 CACTACTGCTTAGGGAGATATGATCTACAACCTCCTCCGCTGCTGCTCAAGGAGACAAGGCTTTG
1635774 TGGCTTAAATCTGCTTCCCACTATCTTGGAAAGATAAGACTTGCCGTCTTTGATCTGCTCCACTA
130 TGGCTTAAATCTGCTTCCCACTATCTTGGAAAGATAAGACTTGCCGTCTTTGATCTGCTCCACTA
* * * *
1635839 CTGCTTAGGGAGATAAGATCTACAATCTTCAACCTTCTCCGCTGTTGCTCAAGGAGACAATGC
195 CTGCTTAGGGAGATAAGATCTACAATCTTCAACCTTCTTCGCTGCTGCTCAGGGAGACAAGGC
1635902 TTGGTG
1 TTGGTG
1635908 TTTCACCAGT
Statistics
Matches: 486, Mismatches: 31, Indels: 12
0.92 0.06 0.02
Matches are distributed among these distances:
256 68 0.14
257 336 0.69
258 6 0.01
259 1 0.00
263 75 0.15
ACGTcount: A:0.24, C:0.24, G:0.21, T:0.31
Consensus pattern (257 bp):
TTGGTGGCTTAAATCTGCTTCCCACTATTTTGGAAAGATAAGATTTGCCGTCTTCGATTTGCTCC
ACTACTGCTTAGGGAGATATGATCTACAACCTCCTCCGCTGCTGCTCAAGGAGACAAGGCTTTGT
GGCTTAAATCTGCTTCCCACTATCTTGGAAAGATAAGACTTGCCGTCTTTGATCTGCTCCACTAC
TGCTTAGGGAGATAAGATCTACAATCTTCAACCTTCTTCGCTGCTGCTCAGGGAGACAAGGC
Found at i:1653586 original size:23 final size:23
Alignment explanation
Indices: 1653560--1653606 Score: 67
Period size: 23 Copynumber: 2.0 Consensus size: 23
1653550 TTTGGTGTGA
* **
1653560 TAGTTGTGGATATTTAGGATTGT
1 TAGTTGTGCATACCTAGGATTGT
1653583 TAGTTGTGCATACCTAGGATTGT
1 TAGTTGTGCATACCTAGGATTGT
1653606 T
1 T
1653607 TGTATTATTA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.21, C:0.06, G:0.28, T:0.45
Consensus pattern (23 bp):
TAGTTGTGCATACCTAGGATTGT
Found at i:1662629 original size:19 final size:19
Alignment explanation
Indices: 1662605--1662643 Score: 69
Period size: 19 Copynumber: 2.1 Consensus size: 19
1662595 GTACATAGAA
*
1662605 TTTAATTGTTTTGTTTGTG
1 TTTAATTATTTTGTTTGTG
1662624 TTTAATTATTTTGTTTGTG
1 TTTAATTATTTTGTTTGTG
1662643 T
1 T
1662644 GGTTTATGCT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.13, C:0.00, G:0.18, T:0.69
Consensus pattern (19 bp):
TTTAATTATTTTGTTTGTG
Found at i:1668360 original size:25 final size:25
Alignment explanation
Indices: 1668326--1668399 Score: 89
Period size: 25 Copynumber: 3.0 Consensus size: 25
1668316 TAAATACCTG
** *
1668326 ATTCTGTATGATGCCTTCGTGGCGT
1 ATTCTGTATGACACCTTCGTGGCAT
*
1668351 ATTCTGTATGACACCTTTGTGGCAT
1 ATTCTGTATGACACCTTCGTGGCAT
*
1668376 ATTCTGTTTGAC-CCTT-GTGGCAT
1 ATTCTGTATGACACCTTCGTGGCAT
1668399 A
1 A
1668400 ATCTACTTAG
Statistics
Matches: 44, Mismatches: 5, Indels: 2
0.86 0.10 0.04
Matches are distributed among these distances:
23 8 0.18
24 4 0.09
25 32 0.73
ACGTcount: A:0.16, C:0.20, G:0.23, T:0.41
Consensus pattern (25 bp):
ATTCTGTATGACACCTTCGTGGCAT
Found at i:1670707 original size:16 final size:17
Alignment explanation
Indices: 1670682--1670714 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
1670672 AATAAACGTT
*
1670682 ATAAATAAACAA-TAAA
1 ATAAACAAACAACTAAA
1670698 ATAAACAAACAACTAAA
1 ATAAACAAACAACTAAA
1670715 CCAATCAAGA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 11 0.73
17 4 0.27
ACGTcount: A:0.73, C:0.12, G:0.00, T:0.15
Consensus pattern (17 bp):
ATAAACAAACAACTAAA
Found at i:1671084 original size:198 final size:197
Alignment explanation
Indices: 1670741--1671142 Score: 669
Period size: 198 Copynumber: 2.0 Consensus size: 197
1670731 ACTTGTTTCG
* *
1670741 GGGTAGTAATTAACTTCGGGTCTGGATTTTAGGGTGAATTAGCTATTAACTAACCAACTAATACC
1 GGGTTGTAATTAACTTCGGGTCTGGATTTTAGGGTGAATTAGCTATTAACTAACCAACTAATAAC
* *
1670806 TCCCGGCCTCTAACTGATTAATTAATTGATTGATACTTGGTCATCTCCTTACCTCACTTTCTCAA
66 TCCCAGCCTCTAACTGATTAATTAATTGATTGATACTTGGTCATCTACTTACCTCACTTTCTCAA
* *
1670871 GCAAGATAAATTACGATTTACTCGGAAAACTTATCTCTCGACCTTGTTTAACTTTTGATTACTTC
131 GCAAGATAAATTACGATTTACTCGAAAAACTTATATCTCGACCTTGTTTAACTTTTGA-TACTTC
1670936 CTA
195 CTA
* * *
1670939 GGGTTGTAATTAACTTCGGGTCTGGCTTTTTGGGTGAATTAGCTATTAACTAACCATCTAATAAC
1 GGGTTGTAATTAACTTCGGGTCTGGATTTTAGGGTGAATTAGCTATTAACTAACCAACTAATAAC
** *
1671004 TCTTAGCCTCTAACTGATTAATTAATTGATTGATACTTGGTTATCTACTTACCTCACTTTCTCAA
66 TCCCAGCCTCTAACTGATTAATTAATTGATTGATACTTGGTCATCTACTTACCTCACTTTCTCAA
* *
1671069 GCAAGATAAATTACGATTTACTCGAAAAACTTATATGTTGACCTTGTTTAACTTTTGATACTTCC
131 GCAAGATAAATTACGATTTACTCGAAAAACTTATATCTCGACCTTGTTTAACTTTTGATACTTCC
1671134 TA
196 TA
1671136 GGGTTGT
1 GGGTTGT
1671143 CAAGCCTAGG
Statistics
Matches: 190, Mismatches: 14, Indels: 1
0.93 0.07 0.00
Matches are distributed among these distances:
197 16 0.08
198 174 0.92
ACGTcount: A:0.28, C:0.19, G:0.15, T:0.38
Consensus pattern (197 bp):
GGGTTGTAATTAACTTCGGGTCTGGATTTTAGGGTGAATTAGCTATTAACTAACCAACTAATAAC
TCCCAGCCTCTAACTGATTAATTAATTGATTGATACTTGGTCATCTACTTACCTCACTTTCTCAA
GCAAGATAAATTACGATTTACTCGAAAAACTTATATCTCGACCTTGTTTAACTTTTGATACTTCC
TA
Found at i:1672948 original size:102 final size:102
Alignment explanation
Indices: 1672766--1672963 Score: 254
Period size: 102 Copynumber: 1.9 Consensus size: 102
1672756 ACAATCAACA
* * * ** * *
1672766 CCTCTTTTCCCCCACTAGTAACGTGGGTAATCGTCTCACCCTTTTGTCTATGACTCTTCCATTCT
1 CCTCTTTTCCCCAAATAGTAACGTGGGTAATCATCTCACCCTACTGTCTACGACTCTTCCAATCT
* * *
1672831 TTCAGTGAGGTATAAAATTCATAAATTATTGTGTCGG
66 TTCAGTGAGGCATAAAAGTCATAAACTATTGTGTCGG
* * *
1672868 CCTCTTTTCCCCAAATAGTAATGTGGGTAATCATCTCACCCTACTGTCTACGATTTTTCCAATCT
1 CCTCTTTTCCCCAAATAGTAACGTGGGTAATCATCTCACCCTACTGTCTACGACTCTTCCAATCT
*
1672933 TTTAG-GAAGGCATAAAAGTCATAAACTATTG
66 TTCAGTG-AGGCATAAAAGTCATAAACTATTG
1672964 CGCCAATCGC
Statistics
Matches: 81, Mismatches: 14, Indels: 2
0.84 0.14 0.02
Matches are distributed among these distances:
101 1 0.01
102 80 0.99
ACGTcount: A:0.25, C:0.24, G:0.15, T:0.36
Consensus pattern (102 bp):
CCTCTTTTCCCCAAATAGTAACGTGGGTAATCATCTCACCCTACTGTCTACGACTCTTCCAATCT
TTCAGTGAGGCATAAAAGTCATAAACTATTGTGTCGG
Found at i:1676800 original size:30 final size:30
Alignment explanation
Indices: 1676745--1676806 Score: 76
Period size: 31 Copynumber: 2.1 Consensus size: 30
1676735 CACTAAGCAA
1676745 GTTTCATATACATGTATCATCCATTT-CAT
1 GTTTCATATACATGTATCATCCATTTCCAT
1676774 GTTTCAATATATCATGTAAT-AT-CATTTCCAT
1 GTTTC-ATATA-CATGT-ATCATCCATTTCCAT
1676805 GT
1 GT
1676807 ATCTCATGTA
Statistics
Matches: 29, Mismatches: 0, Indels: 6
0.83 0.00 0.17
Matches are distributed among these distances:
29 5 0.17
30 10 0.34
31 12 0.41
32 2 0.07
ACGTcount: A:0.29, C:0.18, G:0.08, T:0.45
Consensus pattern (30 bp):
GTTTCATATACATGTATCATCCATTTCCAT
Found at i:1676994 original size:25 final size:25
Alignment explanation
Indices: 1676958--1677075 Score: 125
Period size: 25 Copynumber: 4.8 Consensus size: 25
1676948 GTACATGTAT
* * *
1676958 GCTCATAAGAGCTGTGAATTGGTATA
1 GCTCATACGAGCTGAGAATCGGTA-A
*
1676984 -CTCTTACGAGCTGTA-AATCGGTAA
1 GCTCATACGAGCTG-AGAATCGGTAA
* *
1677008 GCTCATAAGAGCTGAGAATCGATAA
1 GCTCATACGAGCTGAGAATCGGTAA
* *
1677033 GCTCTTACGAGCTG-CAATCGGTAA
1 GCTCATACGAGCTGAGAATCGGTAA
1677057 GCTCATACGAGCTGAGAAT
1 GCTCATACGAGCTGAGAAT
1677076 TTGTAATCCC
Statistics
Matches: 75, Mismatches: 13, Indels: 9
0.77 0.13 0.09
Matches are distributed among these distances:
24 23 0.31
25 52 0.69
ACGTcount: A:0.31, C:0.19, G:0.25, T:0.25
Consensus pattern (25 bp):
GCTCATACGAGCTGAGAATCGGTAA
Found at i:1677071 original size:49 final size:50
Alignment explanation
Indices: 1676958--1677075 Score: 168
Period size: 50 Copynumber: 2.4 Consensus size: 50
1676948 GTACATGTAT
* * *
1676958 GCTCATAAGAGCTGTGAATTGGTATACTCTTACGAGCTGTAAATCGGTAA
1 GCTCATAAGAGCTGAGAATCGATATACTCTTACGAGCTGTAAATCGGTAA
*
1677008 GCTCATAAGAGCTGAGAATCGATA-AGCTCTTACGAGCTG-CAATCGGTAA
1 GCTCATAAGAGCTGAGAATCGATATA-CTCTTACGAGCTGTAAATCGGTAA
*
1677057 GCTCATACGAGCTGAGAAT
1 GCTCATAAGAGCTGAGAAT
1677076 TTGTAATCCC
Statistics
Matches: 62, Mismatches: 5, Indels: 3
0.89 0.07 0.04
Matches are distributed among these distances:
49 28 0.45
50 34 0.55
ACGTcount: A:0.31, C:0.19, G:0.25, T:0.25
Consensus pattern (50 bp):
GCTCATAAGAGCTGAGAATCGATATACTCTTACGAGCTGTAAATCGGTAA
Found at i:1696971 original size:25 final size:26
Alignment explanation
Indices: 1696934--1696984 Score: 61
Period size: 25 Copynumber: 2.0 Consensus size: 26
1696924 GATGTAAATC
1696934 AGAAAAATATCTT-T-AGAAATTTTCT
1 AGAAAAATATCTTCTGAG-AATTTTCT
* *
1696959 AGAATAATCTCTTCTGAGAATTTTCT
1 AGAAAAATATCTTCTGAGAATTTTCT
1696985 CTCTACAACT
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
25 11 0.50
26 9 0.41
27 2 0.09
ACGTcount: A:0.37, C:0.12, G:0.10, T:0.41
Consensus pattern (26 bp):
AGAAAAATATCTTCTGAGAATTTTCT
Found at i:1700627 original size:20 final size:19
Alignment explanation
Indices: 1700595--1700646 Score: 68
Period size: 20 Copynumber: 2.6 Consensus size: 19
1700585 AATTAGTGTT
1700595 TTTTAAATAATTTTTAAAA
1 TTTTAAATAATTTTTAAAA
*
1700614 TTTTAAATATATTTTTAGAA
1 TTTTAAATA-ATTTTTAAAA
1700634 TTATCTAAATAAT
1 TT-T-TAAATAAT
1700647 AAGTATCAAC
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
19 9 0.31
20 11 0.38
21 3 0.10
22 6 0.21
ACGTcount: A:0.44, C:0.02, G:0.02, T:0.52
Consensus pattern (19 bp):
TTTTAAATAATTTTTAAAA
Found at i:1700839 original size:30 final size:30
Alignment explanation
Indices: 1700799--1700855 Score: 87
Period size: 30 Copynumber: 1.9 Consensus size: 30
1700789 AATAAATCAT
* *
1700799 TAACGTTAGTGAACATATTGTAATTTTCAA
1 TAACATTAGTGAACACATTGTAATTTTCAA
*
1700829 TAACATTAGTGATCACATTGTAATTTT
1 TAACATTAGTGAACACATTGTAATTTT
1700856 TTAAAGTTCA
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
30 24 1.00
ACGTcount: A:0.35, C:0.11, G:0.12, T:0.42
Consensus pattern (30 bp):
TAACATTAGTGAACACATTGTAATTTTCAA
Found at i:1711335 original size:43 final size:43
Alignment explanation
Indices: 1711269--1711598 Score: 430
Period size: 43 Copynumber: 7.7 Consensus size: 43
1711259 TTTTAGAAAT
* * * * * *
1711269 AAACGCCACTATAGACCATGACCTTTAGTGGCACTTTTCCCAC
1 AAACGCCGCTATAGATCAAGACCTTTAGCGGCGCTTTTTCCAC
* *
1711312 AAACGCCGCTATAGATCAGGACCTTTAGCGGCGCTTTCTCCAC
1 AAACGCCGCTATAGATCAAGACCTTTAGCGGCGCTTTTTCCAC
* * * *
1711355 AAACGCCGCTATAGATCAGGACCATTAGCGGTGC-TTTTGCAC
1 AAACGCCGCTATAGATCAAGACCTTTAGCGGCGCTTTTTCCAC
* ** *
1711397 AAATGCCGCTATAG-TCAAGACCTTTAGCGGTACTTTTTTGCAC
1 AAACGCCGCTATAGATCAAGACCTTTAGCGGCGC-TTTTTCCAC
* * *
1711440 AAACGCCGCTATAGATCAAGACCTTTAGTGGCACCTTTTCCAC
1 AAACGCCGCTATAGATCAAGACCTTTAGCGGCGCTTTTTCCAC
1711483 AAACGCCGCTATAGATCAAGACCTTTAGCGGCGCTTTTTCCAC
1 AAACGCCGCTATAGATCAAGACCTTTAGCGGCGCTTTTTCCAC
* *
1711526 AAACGCCGCTATAGTTCAAGACCTTCAGCGGCGCTTTTTCCAC
1 AAACGCCGCTATAGATCAAGACCTTTAGCGGCGCTTTTTCCAC
**
1711569 AAACGCTACTATAGATCAAGACCTTTAGCG
1 AAACGCCGCTATAGATCAAGACCTTTAGCG
1711599 ACACTTCTCG
Statistics
Matches: 255, Mismatches: 29, Indels: 6
0.88 0.10 0.02
Matches are distributed among these distances:
41 16 0.06
42 19 0.07
43 203 0.80
44 17 0.07
ACGTcount: A:0.27, C:0.29, G:0.18, T:0.26
Consensus pattern (43 bp):
AAACGCCGCTATAGATCAAGACCTTTAGCGGCGCTTTTTCCAC
Found at i:1711511 original size:128 final size:129
Alignment explanation
Indices: 1711269--1711598 Score: 432
Period size: 128 Copynumber: 2.6 Consensus size: 129
1711259 TTTTAGAAAT
* ** * * * * *
1711269 AAACGCCACTATAGACCATGACCTTTAGTGGCACTTTTCCCACAAACGCCGCTATAGATCAGGAC
1 AAACGCCGCTATAGTTCAAGACCTTCAGCGGCACTTTTTCCACAAACGCCGCTATAGATCAAGAC
* * * *
1711334 CTTTAGCGGCGCTTTCTCCACAAACGCCGCTATAGATCAGGACCATTAGCGGTGC-TTTTGCAC
66 CTTTAGCGGCCCTTTCTCCACAAACGCCGCTATAGATCAAGACCATTAGCGGCGCTTTTTCCAC
* * * *
1711397 AAATGCCGCTATAG-TCAAGACCTTTAGCGGTACTTTTTTGCACAAACGCCGCTATAGATCAAGA
1 AAACGCCGCTATAGTTCAAGACCTTCAGCGGCAC-TTTTTCCACAAACGCCGCTATAGATCAAGA
* *
1711461 CCTTTAGTGGCACCTTT-TCCACAAACGCCGCTATAGATCAAGACCTTTAGCGGCGCTTTTTCCA
65 CCTTTAGCGGC-CCTTTCTCCACAAACGCCGCTATAGATCAAGACCATTAGCGGCGCTTTTTCCA
1711525 C
129 C
* **
1711526 AAACGCCGCTATAGTTCAAGACCTTCAGCGGCGCTTTTTCCACAAACGCTACTATAGATCAAGAC
1 AAACGCCGCTATAGTTCAAGACCTTCAGCGGCACTTTTTCCACAAACGCCGCTATAGATCAAGAC
1711591 CTTTAGCG
66 CTTTAGCG
1711599 ACACTTCTCG
Statistics
Matches: 175, Mismatches: 23, Indels: 7
0.85 0.11 0.03
Matches are distributed among these distances:
127 15 0.09
128 85 0.49
129 59 0.34
130 16 0.09
ACGTcount: A:0.27, C:0.29, G:0.18, T:0.26
Consensus pattern (129 bp):
AAACGCCGCTATAGTTCAAGACCTTCAGCGGCACTTTTTCCACAAACGCCGCTATAGATCAAGAC
CTTTAGCGGCCCTTTCTCCACAAACGCCGCTATAGATCAAGACCATTAGCGGCGCTTTTTCCAC
Found at i:1713072 original size:40 final size:40
Alignment explanation
Indices: 1713009--1713093 Score: 109
Period size: 40 Copynumber: 2.1 Consensus size: 40
1712999 TAGCTTGAAT
* * *
1713009 ATCAACACTTCAATATTTAATATGTAAGGAATTATCAAAA
1 ATCAACACTTCAATATTTAATATGCAAGAAATTAACAAAA
* *
1713049 ATCAACATTTCAATAATTT-ATATGCAAGAAATTAACACAA
1 ATCAACACTTCAAT-ATTTAATATGCAAGAAATTAACAAAA
1713089 ATCAA
1 ATCAA
1713094 TCTTACAACA
Statistics
Matches: 39, Mismatches: 5, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
40 35 0.90
41 4 0.10
ACGTcount: A:0.49, C:0.14, G:0.06, T:0.31
Consensus pattern (40 bp):
ATCAACACTTCAATATTTAATATGCAAGAAATTAACAAAA
Found at i:1713265 original size:86 final size:84
Alignment explanation
Indices: 1713090--1713355 Score: 282
Period size: 86 Copynumber: 3.1 Consensus size: 84
1713080 TTAACACAAA
* * * * * * ** *
1713090 TCAATCTTACAACAGTTTATGTGAAACAAATTACCAAAAATCAATTATTCATAGTTCATATATTT
1 TCAATTTTATAACAATTTATATGCAACAAATTAACAAAAATCAATGGTTCA-AGTTCATGTATTT
*** * *
1713155 ACCGGCAATAGGGCTAAATCT
65 ACCAAAAATA-GACTAAATTT
*
1713176 TCAATTTCTATAACGATTTATATGCAACAAATTAACAAAAATCAATGGTTCAAGTTCATGTATTT
1 TCAATTT-TATAACAATTTATATGCAACAAATTAACAAAAATCAATGGTTCAAGTTCATGTATTT
*
1713241 ACCAAAAATCAGACTAATTTT
65 ACCAAAAAT-AGACTAAATTT
* * *
1713262 TCAATATTTATAACAACTTATATGCAACAAATTAGCAAAAAT-AGATGGTTCAAGTTCATGCATT
1 TCAAT-TTTATAACAATTTATATGCAACAAATTAACAAAAATCA-ATGGTTCAAGTTCATGTATT
*
1713326 TACCAACAAGTAGACTAAATTT
64 TACCAA-AAATAGACTAAATTT
1713348 TCAATTTT
1 TCAATTTT
1713356 CAATTTTTAA
Statistics
Matches: 153, Mismatches: 22, Indels: 11
0.82 0.12 0.06
Matches are distributed among these distances:
85 4 0.03
86 107 0.70
87 42 0.27
ACGTcount: A:0.41, C:0.16, G:0.09, T:0.34
Consensus pattern (84 bp):
TCAATTTTATAACAATTTATATGCAACAAATTAACAAAAATCAATGGTTCAAGTTCATGTATTTA
CCAAAAATAGACTAAATTT
Found at i:1713850 original size:167 final size:168
Alignment explanation
Indices: 1713553--1713856 Score: 389
Period size: 167 Copynumber: 1.8 Consensus size: 168
1713543 TTTTAAATGC
* ** * * *
1713553 AACAAATTAGCACAAATTAACAATTCAAGTTCATATATTCACCAAAAACCAGACTAAATTTTCAA
1 AACAAATTAGCAAAAACCAACAATTCAAGTGCATATATACACCAAAAACCAGACTAAATTTCCAA
* ** * * *
1713618 TTTTTATAAAATAAGAGGATGGAAGTCTAACAAAATAAAGTTTCAAATGAAATTCAGACTTACAC
66 TTTTTACAAAATAAGAGGATCAAAGTCTAACAAAATAAAGTTTCAAACGAAATTCAAAATTACAC
1713683 CATTAAGTAAATAAGAGTTTTAAACTATCGGAGATCAA
131 CATTAAGTAAATAAGAGTTTTAAACTATCGGAGATCAA
** *
1713721 AACAAATTAGCAAAAACCAACTGTTCAAGTGCATGTATACACCAAAAA-CAGGA-TCAAATTTCC
1 AACAAATTAGCAAAAACCAACAATTCAAGTGCATATATACACCAAAAACCA-GACT-AAATTTCC
* * * * *
1713784 AA-TTTTGCAAATTAAGAGGATCAAATTCTAACAAATTAAAGTTTCCAACGAAATTCAAAATTAC
64 AATTTTTACAAAATAAGAGGATCAAAGTCTAACAAAATAAAGTTTCAAACGAAATTCAAAATTAC
1713848 ACCATTAAG
129 ACCATTAAG
1713857 ATCATATTAT
Statistics
Matches: 114, Mismatches: 20, Indels: 5
0.82 0.14 0.04
Matches are distributed among these distances:
167 63 0.55
168 51 0.45
ACGTcount: A:0.47, C:0.16, G:0.11, T:0.27
Consensus pattern (168 bp):
AACAAATTAGCAAAAACCAACAATTCAAGTGCATATATACACCAAAAACCAGACTAAATTTCCAA
TTTTTACAAAATAAGAGGATCAAAGTCTAACAAAATAAAGTTTCAAACGAAATTCAAAATTACAC
CATTAAGTAAATAAGAGTTTTAAACTATCGGAGATCAA
Found at i:1714011 original size:62 final size:62
Alignment explanation
Indices: 1713938--1714065 Score: 256
Period size: 62 Copynumber: 2.1 Consensus size: 62
1713928 GCAAAACCTC
1713938 CATATGAATGAACAAATGTAGTTCTTATAATATAAATAATCAAAAGGAGCAATAATCTAAAA
1 CATATGAATGAACAAATGTAGTTCTTATAATATAAATAATCAAAAGGAGCAATAATCTAAAA
1714000 CATATGAATGAACAAATGTAGTTCTTATAATATAAATAATCAAAAGGAGCAATAATCTAAAA
1 CATATGAATGAACAAATGTAGTTCTTATAATATAAATAATCAAAAGGAGCAATAATCTAAAA
1714062 CATA
1 CATA
1714066 CCTTTTTTTA
Statistics
Matches: 66, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
62 66 1.00
ACGTcount: A:0.52, C:0.10, G:0.11, T:0.27
Consensus pattern (62 bp):
CATATGAATGAACAAATGTAGTTCTTATAATATAAATAATCAAAAGGAGCAATAATCTAAAA
Found at i:1716378 original size:19 final size:19
Alignment explanation
Indices: 1716350--1716395 Score: 67
Period size: 19 Copynumber: 2.4 Consensus size: 19
1716340 AAAATATAAA
1716350 TTTTAGTTTTT-TATTTCAT
1 TTTTA-TTTTTGTATTTCAT
*
1716369 TTTTATTTTTGTATTTTAT
1 TTTTATTTTTGTATTTCAT
1716388 TTTTATTT
1 TTTTATTT
1716396 CTTATAATTT
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
18 5 0.20
19 20 0.80
ACGTcount: A:0.15, C:0.02, G:0.04, T:0.78
Consensus pattern (19 bp):
TTTTATTTTTGTATTTCAT
Found at i:1716762 original size:7 final size:7
Alignment explanation
Indices: 1716750--1716809 Score: 79
Period size: 7 Copynumber: 8.6 Consensus size: 7
1716740 ACTAACTAAT
1716750 CTAAACC
1 CTAAACC
1716757 CTAAACC
1 CTAAACC
1716764 CTAAACC
1 CTAAACC
1716771 CT-AACC
1 CTAAACC
*
1716777 C-AACCC
1 CTAAACC
1716783 CTAAATCC
1 CTAAA-CC
1716791 CTAAACC
1 CTAAACC
1716798 CTAAATCC
1 CTAAA-CC
1716806 CTAA
1 CTAA
1716810 CTCTTAACCC
Statistics
Matches: 47, Mismatches: 2, Indels: 7
0.84 0.04 0.12
Matches are distributed among these distances:
6 9 0.19
7 25 0.53
8 13 0.28
ACGTcount: A:0.40, C:0.43, G:0.00, T:0.17
Consensus pattern (7 bp):
CTAAACC
Found at i:1716824 original size:7 final size:7
Alignment explanation
Indices: 1716750--1716837 Score: 54
Period size: 7 Copynumber: 12.6 Consensus size: 7
1716740 ACTAACTAAT
*
1716750 CTAAACC
1 CTAACCC
*
1716757 CTAAACC
1 CTAACCC
*
1716764 CTAAACC
1 CTAACCC
1716771 CTAA-CC
1 CTAACCC
1716777 C-AACCC
1 CTAACCC
*
1716783 CTAAATCC
1 CT-AACCC
*
1716791 CTAAACC
1 CTAACCC
*
1716798 CTAAATCC
1 CT-AACCC
*
1716806 CTAACTC
1 CTAACCC
*
1716813 TTAACCC
1 CTAACCC
*
1716820 CTAACCT
1 CTAACCC
*
1716827 CTAACCT
1 CTAACCC
1716834 CTAA
1 CTAA
1716838 ACCTTAAATC
Statistics
Matches: 68, Mismatches: 9, Indels: 8
0.80 0.11 0.09
Matches are distributed among these distances:
5 2 0.03
6 6 0.09
7 48 0.71
8 12 0.18
ACGTcount: A:0.36, C:0.43, G:0.00, T:0.20
Consensus pattern (7 bp):
CTAACCC
Found at i:1716888 original size:15 final size:15
Alignment explanation
Indices: 1716852--1716899 Score: 62
Period size: 15 Copynumber: 3.3 Consensus size: 15
1716842 TAAATCTCAA
* *
1716852 CCCTTAAACTATAAT
1 CCCTTAATCCATAAT
1716867 CCC-TAATCCATAAT
1 CCCTTAATCCATAAT
*
1716881 CCCTTAATCCATACT
1 CCCTTAATCCATAAT
1716896 CCCT
1 CCCT
1716900 AAACCTTACA
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
14 12 0.41
15 17 0.59
ACGTcount: A:0.31, C:0.38, G:0.00, T:0.31
Consensus pattern (15 bp):
CCCTTAATCCATAAT
Found at i:1717371 original size:41 final size:41
Alignment explanation
Indices: 1717326--1717419 Score: 107
Period size: 41 Copynumber: 2.3 Consensus size: 41
1717316 ATTAGTGATG
* *
1717326 CTTTTCCAAAAAAACAGCTAAAGCCTCGAGCATTAGCGGCA
1 CTTTTCCAAAAAAACAGCTAAAGCCCCGAGCATTAGCAGCA
* ** * * *
1717367 CTTTTCCAAACATGCCGTTAAAGCCCCGAGCATTAGCAGCG
1 CTTTTCCAAAAAAACAGCTAAAGCCCCGAGCATTAGCAGCA
*
1717408 CTTTTTCAAAAA
1 CTTTTCCAAAAA
1717420 CGCCGCTAAT
Statistics
Matches: 43, Mismatches: 10, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
41 43 1.00
ACGTcount: A:0.33, C:0.28, G:0.16, T:0.23
Consensus pattern (41 bp):
CTTTTCCAAAAAAACAGCTAAAGCCCCGAGCATTAGCAGCA
Found at i:1717434 original size:41 final size:40
Alignment explanation
Indices: 1717342--1717477 Score: 139
Period size: 41 Copynumber: 3.3 Consensus size: 40
1717332 CAAAAAAACA
* * * * *
1717342 GCTAAAGCCTCGAGCATTAGCGGCACTTTTCCAAACATGCC
1 GCTAAAGCCCCGAGCATTAGC-GCGCTTTTTCAAAAACGCC
*
1717383 GTTAAAGCCCCGAGCATTAGCAGCGCTTTTTCAAAAACGCC
1 GCTAAAGCCCCGAGCATTAGC-GCGCTTTTTCAAAAACGCC
* * *
1717424 GCTAATGCCCC-ATGCATTAGCGATGCTTTTTGAAAAACGCC
1 GCTAAAGCCCCGA-GCATTAGCG-CGCTTTTTCAAAAACGCC
*
1717465 ACTAAAGCCCCGA
1 GCTAAAGCCCCGA
1717478 AAACTCAAAA
Statistics
Matches: 79, Mismatches: 13, Indels: 5
0.81 0.13 0.05
Matches are distributed among these distances:
40 2 0.03
41 76 0.96
42 1 0.01
ACGTcount: A:0.29, C:0.30, G:0.19, T:0.22
Consensus pattern (40 bp):
GCTAAAGCCCCGAGCATTAGCGCGCTTTTTCAAAAACGCC
Found at i:1726461 original size:17 final size:16
Alignment explanation
Indices: 1726441--1726509 Score: 61
Period size: 17 Copynumber: 4.2 Consensus size: 16
1726431 AAAATAATAT
1726441 TATTTTATTAGATTTAA
1 TATTTTATTA-ATTTAA
**
1726458 TATTAGATTTAATTTAA
1 TATTTTA-TTAATTTAA
* *
1726475 TATTTATCTTAA--TAG
1 TATTT-TATTAATTTAA
1726490 TATTTTATTAATTTAA
1 TATTTTATTAATTTAA
1726506 TATT
1 TATT
1726510 AAAGTGATTA
Statistics
Matches: 40, Mismatches: 8, Indels: 9
0.70 0.14 0.16
Matches are distributed among these distances:
14 5 0.12
15 7 0.17
16 6 0.15
17 19 0.47
18 3 0.08
ACGTcount: A:0.36, C:0.01, G:0.04, T:0.58
Consensus pattern (16 bp):
TATTTTATTAATTTAA
Found at i:1726463 original size:12 final size:12
Alignment explanation
Indices: 1726446--1726470 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
1726436 AATATTATTT
1726446 TATTAGATTTAA
1 TATTAGATTTAA
1726458 TATTAGATTTAA
1 TATTAGATTTAA
1726470 T
1 T
1726471 TTAATATTTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.40, C:0.00, G:0.08, T:0.52
Consensus pattern (12 bp):
TATTAGATTTAA
Found at i:1732942 original size:29 final size:29
Alignment explanation
Indices: 1732886--1732945 Score: 84
Period size: 29 Copynumber: 2.1 Consensus size: 29
1732876 TAGTTTTCAT
**
1732886 ATTTTAATAATTATTTATTCGGCTTATAA
1 ATTTTAATAATTATTTATTCGGAATATAA
* *
1732915 ATTTTAATATTTATTTATTTGGAATATAA
1 ATTTTAATAATTATTTATTCGGAATATAA
1732944 AT
1 AT
1732946 CATAAATTTA
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
29 27 1.00
ACGTcount: A:0.37, C:0.03, G:0.07, T:0.53
Consensus pattern (29 bp):
ATTTTAATAATTATTTATTCGGAATATAA
Found at i:1733327 original size:20 final size:21
Alignment explanation
Indices: 1733278--1733336 Score: 84
Period size: 20 Copynumber: 2.9 Consensus size: 21
1733268 CCAACATCAC
* *
1733278 AAATGATTTTAAAATTATTAA
1 AAATTATTTTAAAATCATTAA
1733299 AAATTATTTTAAAATCATT-A
1 AAATTATTTTAAAATCATTAA
*
1733319 AATTTATTTTAAAATCAT
1 AAATTATTTTAAAATCAT
1733337 CATCATCATC
Statistics
Matches: 35, Mismatches: 3, Indels: 1
0.90 0.08 0.03
Matches are distributed among these distances:
20 18 0.51
21 17 0.49
ACGTcount: A:0.49, C:0.03, G:0.02, T:0.46
Consensus pattern (21 bp):
AAATTATTTTAAAATCATTAA
Found at i:1733340 original size:3 final size:3
Alignment explanation
Indices: 1733332--1733367 Score: 72
Period size: 3 Copynumber: 12.0 Consensus size: 3
1733322 TTATTTTAAA
1733332 ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC
1 ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC
1733368 TCCATTGTTT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 33 1.00
ACGTcount: A:0.33, C:0.33, G:0.00, T:0.33
Consensus pattern (3 bp):
ATC
Found at i:1734377 original size:29 final size:30
Alignment explanation
Indices: 1734344--1734420 Score: 122
Period size: 28 Copynumber: 2.6 Consensus size: 30
1734334 AAAATAATTT
*
1734344 AATAATTTTATTAATTTTATATTTC-AAAA
1 AATAATTTTAATAATTTTATATTTCAAAAA
*
1734373 AATAA-TTCAATAATTTTATATTTCAAAAA
1 AATAATTTTAATAATTTTATATTTCAAAAA
1734402 AATAATTTTAATAATTTTA
1 AATAATTTTAATAATTTTA
1734421 AAAGTATTTT
Statistics
Matches: 43, Mismatches: 3, Indels: 3
0.88 0.06 0.06
Matches are distributed among these distances:
28 17 0.40
29 14 0.33
30 12 0.28
ACGTcount: A:0.48, C:0.04, G:0.00, T:0.48
Consensus pattern (30 bp):
AATAATTTTAATAATTTTATATTTCAAAAA
Found at i:1735127 original size:20 final size:19
Alignment explanation
Indices: 1735104--1735164 Score: 56
Period size: 20 Copynumber: 3.3 Consensus size: 19
1735094 AATATTATTA
1735104 AAAATTATAAAATAGTAAAT
1 AAAATTATAAAATAGT-AAT
* * *
1735124 AAAATTAAAAAAT-TTCAAG
1 AAAATTATAAAATAGT-AAT
1735143 AAAATT-TAAAA-AGTAAT
1 AAAATTATAAAATAGTAAT
1735160 AAAAT
1 AAAAT
1735165 CATTTAAAAT
Statistics
Matches: 33, Mismatches: 7, Indels: 5
0.73 0.16 0.11
Matches are distributed among these distances:
17 7 0.21
18 5 0.15
19 9 0.27
20 12 0.36
ACGTcount: A:0.66, C:0.02, G:0.05, T:0.28
Consensus pattern (19 bp):
AAAATTATAAAATAGTAAT
Found at i:1735488 original size:37 final size:37
Alignment explanation
Indices: 1735447--1735527 Score: 108
Period size: 37 Copynumber: 2.2 Consensus size: 37
1735437 AATTATTTAA
1735447 ACCTTTTAAGCTACACATGTAAGAAAATAATTAATAC
1 ACCTTTTAAGCTACACATGTAAGAAAATAATTAATAC
* * * * *
1735484 ACCTTTTAGGTTACGCATGTAATAAAATAATTGATAC
1 ACCTTTTAAGCTACACATGTAAGAAAATAATTAATAC
*
1735521 ACATTTT
1 ACCTTTT
1735528 TTAATTGGAT
Statistics
Matches: 38, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
37 38 1.00
ACGTcount: A:0.41, C:0.15, G:0.10, T:0.35
Consensus pattern (37 bp):
ACCTTTTAAGCTACACATGTAAGAAAATAATTAATAC
Found at i:1736426 original size:14 final size:14
Alignment explanation
Indices: 1736407--1736435 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
1736397 TTTTTTTTTG
1736407 TTAGGGTTAGGGTT
1 TTAGGGTTAGGGTT
1736421 TTAGGGTTAGGGTT
1 TTAGGGTTAGGGTT
1736435 T
1 T
1736436 CCAACCACTT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.14, C:0.00, G:0.41, T:0.45
Consensus pattern (14 bp):
TTAGGGTTAGGGTT
Found at i:1741909 original size:172 final size:172
Alignment explanation
Indices: 1741623--1741972 Score: 628
Period size: 172 Copynumber: 2.0 Consensus size: 172
1741613 CTTGAGACTC
*
1741623 GCATCATTCCCCCATTCCTCAAGAAGATTCATCCTCGAATCGTCAGTTGCACAGAAAGAAAAGGG
1 GCATCATTCCCCCATTCCTCAAGAAGATTCATCCTCAAATCGTCAGTTGCACAGAAAGAAAAGGG
*
1741688 ATTAGATTAAATAACAATAAAATGAATAAAATACTTACCTAAGCTTTCTTGTGCGCCAAAACTAT
66 ATTAGATTAAATAACAATAAAATAAATAAAATACTTACCTAAGCTTTCTTGTGCGCCAAAACTAT
* *
1741753 CTCTAGGATCAAATATATGATTTTGACCTGCCAAATCAGCAT
131 CTCTAGGATCAAAGATATGATTTTGACCTCCCAAATCAGCAT
* * *
1741795 GCATCATTCCTCCATTCCTCAAGAAGATTCATCCTCAAATCTTCAGTTGCACAGAAAGAAAATGG
1 GCATCATTCCCCCATTCCTCAAGAAGATTCATCCTCAAATCGTCAGTTGCACAGAAAGAAAAGGG
1741860 ATTAGATTAAATAACAATAAAATAAATAAAATACTTACCTAAGCTTTCTTGTGCGCCAAAACTAT
66 ATTAGATTAAATAACAATAAAATAAATAAAATACTTACCTAAGCTTTCTTGTGCGCCAAAACTAT
1741925 CTCTAGGATCAAAGATATGATTTTGACCTCCCAAATCAGCAT
131 CTCTAGGATCAAAGATATGATTTTGACCTCCCAAATCAGCAT
*
1741967 GGATCA
1 GCATCA
1741973 AGTATTTCTC
Statistics
Matches: 170, Mismatches: 8, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
172 170 1.00
ACGTcount: A:0.38, C:0.21, G:0.13, T:0.28
Consensus pattern (172 bp):
GCATCATTCCCCCATTCCTCAAGAAGATTCATCCTCAAATCGTCAGTTGCACAGAAAGAAAAGGG
ATTAGATTAAATAACAATAAAATAAATAAAATACTTACCTAAGCTTTCTTGTGCGCCAAAACTAT
CTCTAGGATCAAAGATATGATTTTGACCTCCCAAATCAGCAT
Found at i:1742078 original size:160 final size:161
Alignment explanation
Indices: 1741896--1742218 Score: 639
Period size: 160 Copynumber: 2.0 Consensus size: 161
1741886 TAAAATACTT
1741896 ACCTAAGCTTTCTTGTGCGCCAAAACTATCTCTAGGATCAAAGATATGATTTTGACCTCCCAAAT
1 ACCTAAGCTTTCTTGTGCGCCAAAACTATCTCTAGGATCAAAGATATGATTTTGACCTCCCAAAT
1741961 CAGCATGGATCAAGTATTTCTCCTTCAAAAACAAATCATCAACACTAAACAAAGAAATATTAGGC
66 CAGCATGGATCAAGTATTTCTCCTTCAAAAACAAATCATCAACACTAAACAAAGAAATATTAGGC
1742026 ACATGAGTCTTCAAGTAAAAAATAACCTGTA
131 ACATGAGTCTTCAAGTAAAAAATAACCTGTA
1742057 ACCTAAGCTTT-TTGTGCGCCAAAACTATCTCTAGGATCAAAGATATGATTTTGACCTCCCAAAT
1 ACCTAAGCTTTCTTGTGCGCCAAAACTATCTCTAGGATCAAAGATATGATTTTGACCTCCCAAAT
1742121 CAGCATGGATCAAGTATTTCTCCTTCAAAAACAAATCATCAACACTAAACAAAGAAATATTAGGC
66 CAGCATGGATCAAGTATTTCTCCTTCAAAAACAAATCATCAACACTAAACAAAGAAATATTAGGC
1742186 ACATGAGTCTTCAAGTAAAAAATAACCTGTA
131 ACATGAGTCTTCAAGTAAAAAATAACCTGTA
1742217 AC
1 AC
1742219 TTTCTTTGAA
Statistics
Matches: 162, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
160 151 0.93
161 11 0.07
ACGTcount: A:0.39, C:0.22, G:0.12, T:0.27
Consensus pattern (161 bp):
ACCTAAGCTTTCTTGTGCGCCAAAACTATCTCTAGGATCAAAGATATGATTTTGACCTCCCAAAT
CAGCATGGATCAAGTATTTCTCCTTCAAAAACAAATCATCAACACTAAACAAAGAAATATTAGGC
ACATGAGTCTTCAAGTAAAAAATAACCTGTA
Found at i:1745808 original size:32 final size:32
Alignment explanation
Indices: 1745771--1745836 Score: 132
Period size: 32 Copynumber: 2.1 Consensus size: 32
1745761 TCAAAGTGAG
1745771 TTTCGAAGTCGAGAGATAGATCTTCAAACGCC
1 TTTCGAAGTCGAGAGATAGATCTTCAAACGCC
1745803 TTTCGAAGTCGAGAGATAGATCTTCAAACGCC
1 TTTCGAAGTCGAGAGATAGATCTTCAAACGCC
1745835 TT
1 TT
1745837 GAAGACATAT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 34 1.00
ACGTcount: A:0.30, C:0.21, G:0.21, T:0.27
Consensus pattern (32 bp):
TTTCGAAGTCGAGAGATAGATCTTCAAACGCC
Found at i:1746790 original size:20 final size:20
Alignment explanation
Indices: 1746753--1746790 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
1746743 GAGGAAGTGT
**
1746753 ATTTTGGCAGTTTTACTGTA
1 ATTTTGGCAGTTAAACTGTA
1746773 ATTTTGGCAGTTAAACTG
1 ATTTTGGCAGTTAAACTG
1746791 CAATATATGT
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:0.11, G:0.21, T:0.45
Consensus pattern (20 bp):
ATTTTGGCAGTTAAACTGTA
Found at i:1749350 original size:20 final size:20
Alignment explanation
Indices: 1749322--1749366 Score: 63
Period size: 20 Copynumber: 2.2 Consensus size: 20
1749312 TAATGTGTCT
*
1749322 TGTCCTAACCAAATTAATTG
1 TGTCTTAACCAAATTAATTG
**
1749342 TGTCTTAACTTAATTAATTG
1 TGTCTTAACCAAATTAATTG
1749362 TGTCT
1 TGTCT
1749367 AGTTTTAATT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.29, C:0.16, G:0.11, T:0.44
Consensus pattern (20 bp):
TGTCTTAACCAAATTAATTG
Found at i:1750320 original size:45 final size:45
Alignment explanation
Indices: 1750262--1750381 Score: 159
Period size: 45 Copynumber: 2.6 Consensus size: 45
1750252 GACCTTTTTG
* *
1750262 ATCCATTTTCGTACCAAAACCTATACCCTTTCGTGCCTACACCAAA
1 ATCCA-TTTCGTACCAAAACCTATACCATTTCGTACCTACACCAAA
* * *
1750308 ATCCATTTCGTACCAAAACCTATACCATTTTGTACCTATACCAAG
1 ATCCATTTCGTACCAAAACCTATACCATTTCGTACCTACACCAAA
** *
1750353 CCCCATTTCGTACCAAAACCAATACCATT
1 ATCCATTTCGTACCAAAACCTATACCATT
1750382 CCCTAACTAA
Statistics
Matches: 66, Mismatches: 8, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
45 61 0.92
46 5 0.08
ACGTcount: A:0.33, C:0.33, G:0.06, T:0.28
Consensus pattern (45 bp):
ATCCATTTCGTACCAAAACCTATACCATTTCGTACCTACACCAAA
Found at i:1750337 original size:22 final size:22
Alignment explanation
Indices: 1750268--1750381 Score: 102
Period size: 22 Copynumber: 5.1 Consensus size: 22
1750258 TTTGATCCAT
* *
1750268 TTTCGTACCAAAACCTATACCC
1 TTTCGTACCAAAACCAATACCA
* * * *
1750290 TTTCGTGCCTACACCAAAATCCA
1 TTTCGTACCAAAACCAATA-CCA
*
1750313 TTTCGTACCAAAACCTATACCA
1 TTTCGTACCAAAACCAATACCA
* * * **
1750335 TTTTGTACCTATACCAAGCCCCA
1 TTTCGTACCAAAACCAA-TACCA
1750358 TTTCGTACCAAAACCAATACCA
1 TTTCGTACCAAAACCAATACCA
1750380 TT
1 TT
1750382 CCCTAACTAA
Statistics
Matches: 68, Mismatches: 22, Indels: 4
0.72 0.23 0.04
Matches are distributed among these distances:
22 35 0.51
23 33 0.49
ACGTcount: A:0.32, C:0.33, G:0.06, T:0.28
Consensus pattern (22 bp):
TTTCGTACCAAAACCAATACCA
Found at i:1753865 original size:26 final size:27
Alignment explanation
Indices: 1753816--1753866 Score: 77
Period size: 26 Copynumber: 1.9 Consensus size: 27
1753806 CAATCGAGAG
*
1753816 AAAAAGTAAAAGAAAATAGTGAAAATC
1 AAAAAGTAAAAGAAAATAGAGAAAATC
*
1753843 AAAAAG-AAAAGAAAATTGAGAAAA
1 AAAAAGTAAAAGAAAATAGAGAAAA
1753867 AAAGAGGCAA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
26 16 0.73
27 6 0.27
ACGTcount: A:0.71, C:0.02, G:0.16, T:0.12
Consensus pattern (27 bp):
AAAAAGTAAAAGAAAATAGAGAAAATC
Found at i:1757192 original size:20 final size:20
Alignment explanation
Indices: 1757164--1757209 Score: 65
Period size: 20 Copynumber: 2.3 Consensus size: 20
1757154 TAATGTGTCT
*
1757164 TGTCCTAACCGAATTAATTG
1 TGTCTTAACCGAATTAATTG
**
1757184 TGTCTTAACTTAATTAATTG
1 TGTCTTAACCGAATTAATTG
1757204 TGTCTT
1 TGTCTT
1757210 GTTTTAATTA
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.26, C:0.15, G:0.13, T:0.46
Consensus pattern (20 bp):
TGTCTTAACCGAATTAATTG
Found at i:1757940 original size:45 final size:45
Alignment explanation
Indices: 1757853--1757970 Score: 137
Period size: 45 Copynumber: 2.6 Consensus size: 45
1757843 CCTTTTTGAT
* * *
1757853 CCATTTTCGTACCAAAACCTATACCCTTTCATGCCTACACCAAAAT
1 CCATTTT-GTACCAAAACCTATACCATTTCATACCTACACCAAAAC
* * * * *
1757899 TCATTTTGTACCAAAACCTATACCATTTCGTATCTATACCAAACC
1 CCATTTTGTACCAAAACCTATACCATTTCATACCTACACCAAAAC
* *
1757944 CCATTTCGTACCAAAACCAATACCATT
1 CCATTTTGTACCAAAACCTATACCATT
1757971 CCCTAACTAA
Statistics
Matches: 61, Mismatches: 11, Indels: 1
0.84 0.15 0.01
Matches are distributed among these distances:
45 55 0.90
46 6 0.10
ACGTcount: A:0.34, C:0.32, G:0.04, T:0.30
Consensus pattern (45 bp):
CCATTTTGTACCAAAACCTATACCATTTCATACCTACACCAAAAC
Found at i:1757962 original size:23 final size:21
Alignment explanation
Indices: 1757900--1757970 Score: 61
Period size: 22 Copynumber: 3.2 Consensus size: 21
1757890 CACCAAAATT
* *
1757900 CATTTTGTACCAAAACCTATAC
1 CATTTCGTACCAAAACC-AAAC
* * *
1757922 CATTTCGTATCTATACCAAACCC
1 CATTTCGTACCAAAACCAAA--C
1757945 CATTTCGTACCAAAACCAATAC
1 CATTTCGTACCAAAACCAA-AC
1757967 CATT
1 CATT
1757971 CCCTAACTAA
Statistics
Matches: 38, Mismatches: 8, Indels: 6
0.73 0.15 0.12
Matches are distributed among these distances:
21 2 0.05
22 18 0.47
23 17 0.45
24 1 0.03
ACGTcount: A:0.35, C:0.31, G:0.04, T:0.30
Consensus pattern (21 bp):
CATTTCGTACCAAAACCAAAC
Found at i:1761615 original size:24 final size:24
Alignment explanation
Indices: 1761570--1761616 Score: 58
Period size: 24 Copynumber: 2.0 Consensus size: 24
1761560 ATCTTTTTCT
*
1761570 GGGTCTTCCATCAGATATTCCTCG
1 GGGTCTTCCATCAGATACTCCTCG
* * *
1761594 GGGTCTTCCTTCGGATCCTCCTC
1 GGGTCTTCCATCAGATACTCCTC
1761617 TAAATCTTCT
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
24 19 1.00
ACGTcount: A:0.11, C:0.34, G:0.21, T:0.34
Consensus pattern (24 bp):
GGGTCTTCCATCAGATACTCCTCG
Found at i:1767635 original size:57 final size:58
Alignment explanation
Indices: 1767571--1767685 Score: 160
Period size: 57 Copynumber: 2.0 Consensus size: 58
1767561 ATTTTGCCCT
* * * * *
1767571 ACTTGAGTCACTTTAAGACCCACATATGTATCTTGGACTCTTAATTAATTTTA-TTAA
1 ACTTGAGTAACCTTAAGACCCACATATATAACTTGGACTCGTAATTAATTTTAGTTAA
* *
1767628 ACTTGAGTAACCTTAAGGCCCACGTATATAACTTGGACTCGTAATTAATTTTAGTTAA
1 ACTTGAGTAACCTTAAGACCCACATATATAACTTGGACTCGTAATTAATTTTAGTTAA
1767686 TAAGCTAAAT
Statistics
Matches: 50, Mismatches: 7, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
57 46 0.92
58 4 0.08
ACGTcount: A:0.32, C:0.17, G:0.13, T:0.37
Consensus pattern (58 bp):
ACTTGAGTAACCTTAAGACCCACATATATAACTTGGACTCGTAATTAATTTTAGTTAA
Found at i:1767861 original size:2 final size:2
Alignment explanation
Indices: 1767854--1767884 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
1767844 TAGCCAAAAT
1767854 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
1767885 GTGTATATAT
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:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:1767893 original size:2 final size:2
Alignment explanation
Indices: 1767888--1767917 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
1767878 TCTCTCTGTG
1767888 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1767918 ACACATCTAC
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):
TA
Found at i:1778918 original size:20 final size:20
Alignment explanation
Indices: 1778853--1778908 Score: 67
Period size: 20 Copynumber: 2.8 Consensus size: 20
1778843 TAGCACTACG
* *
1778853 GTGCTCCTGATAGTACTGTC
1 GTGCTCCTGATAGTACTATA
* * *
1778873 GTACTCCTGTTAGCACTATA
1 GTGCTCCTGATAGTACTATA
1778893 GTGCTCCTGATAGTAC
1 GTGCTCCTGATAGTAC
1778909 ATTTGTGCTC
Statistics
Matches: 28, Mismatches: 8, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
20 28 1.00
ACGTcount: A:0.20, C:0.25, G:0.21, T:0.34
Consensus pattern (20 bp):
GTGCTCCTGATAGTACTATA
Done.