Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008531.1 Hibiscus syriacus cultivar Beakdansim tig00111409_pilon, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 3817888
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 9 of 19
Found at i:1598615 original size:8 final size:8
Alignment explanation
Indices: 1598602--1598629 Score: 56
Period size: 8 Copynumber: 3.5 Consensus size: 8
1598592 AGTTTCTCTC
1598602 ATATGTAT
1 ATATGTAT
1598610 ATATGTAT
1 ATATGTAT
1598618 ATATGTAT
1 ATATGTAT
1598626 ATAT
1 ATAT
1598630 ATATTTCCCC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 20 1.00
ACGTcount: A:0.39, C:0.00, G:0.11, T:0.50
Consensus pattern (8 bp):
ATATGTAT
Found at i:1603456 original size:31 final size:28
Alignment explanation
Indices: 1603421--1603485 Score: 76
Period size: 31 Copynumber: 2.2 Consensus size: 28
1603411 GGTATTATTA
* *
1603421 TATTTTTATGTAGTATAAATATATTCTATAG
1 TATTTATATATAGTAT--ATATATT-TATAG
*
1603452 TATTTATATATAGTATATATATTTATAT
1 TATTTATATATAGTATATATATTTATAG
1603480 TATTTA
1 TATTTA
1603486 GTCTTTATAT
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
28 10 0.32
29 7 0.23
31 14 0.45
ACGTcount: A:0.37, C:0.02, G:0.06, T:0.55
Consensus pattern (28 bp):
TATTTATATATAGTATATATATTTATAG
Found at i:1603523 original size:24 final size:25
Alignment explanation
Indices: 1603465--1603523 Score: 77
Period size: 24 Copynumber: 2.4 Consensus size: 25
1603455 TTATATATAG
1603465 TATATATATTTATATTATTTAGTCTT
1 TATATA-ATTTATATTATTTAGTCTT
* *
1603491 TATAT-ATTTATATTTTTTA-TTTT
1 TATATAATTTATATTATTTAGTCTT
1603514 TATATAATTT
1 TATATAATTT
1603524 TATAGTAGGT
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
23 8 0.27
24 17 0.57
26 5 0.17
ACGTcount: A:0.31, C:0.02, G:0.02, T:0.66
Consensus pattern (25 bp):
TATATAATTTATATTATTTAGTCTT
Found at i:1604317 original size:64 final size:62
Alignment explanation
Indices: 1604240--1604418 Score: 191
Period size: 64 Copynumber: 2.8 Consensus size: 62
1604230 TGGAACACTT
* * * **
1604240 AGTGCATCGGTGCACCAAGTGTGCATCGATGCATAAAATGCATTCGATGTTTGAA-AATAGCCTG
1 AGTGCATC-GTGCA-TAAGTGTGCATCGATGCATGAAATGCATTCGATGTTTGAATAA-AACCCA
* * *
1604304 AGTGAATCAGTGCAT-TGCTTGTGCATCGATGCATGAAATGCATTCGATGTTTTAATAAAACCCA
1 AGTGCATC-GTGCATAAG--TGTGCATCGATGCATGAAATGCATTCGATGTTTGAATAAAACCCA
*
1604368 AGTGCATCGATGCATAGAGAGTGCATCGATGCATGAAATGCATTCGATGTT
1 AGTGCATCG-TGCATA-AGTGTGCATCGATGCATGAAATGCATTCGATGTT
1604419 CAATTTATTC
Statistics
Matches: 97, Mismatches: 12, Indels: 12
0.80 0.10 0.10
Matches are distributed among these distances:
62 1 0.01
63 1 0.01
64 92 0.95
65 2 0.02
66 1 0.01
ACGTcount: A:0.30, C:0.17, G:0.24, T:0.28
Consensus pattern (62 bp):
AGTGCATCGTGCATAAGTGTGCATCGATGCATGAAATGCATTCGATGTTTGAATAAAACCCA
Found at i:1607185 original size:44 final size:44
Alignment explanation
Indices: 1607096--1607192 Score: 117
Period size: 44 Copynumber: 2.2 Consensus size: 44
1607086 GCTCTTGTGC
* * *
1607096 ATCGATGCACATTCAAGGGCGTGCATTGGTGCATCAGCTCATGT
1 ATCGATGCACATTCAAGGGCATGCATCGGTGCATCAGCTAATGT
* *
1607140 ATCGATGCACATTCAAAGGG-ATGCATCGGTGCA-CTGTTAAGTGT
1 ATCGATGCACATTC-AAGGGCATGCATCGGTGCATCAGCTAA-TGT
1607184 ATCGATGCA
1 ATCGATGCA
1607193 TTAAGCACAA
Statistics
Matches: 46, Mismatches: 5, Indels: 4
0.84 0.09 0.07
Matches are distributed among these distances:
43 4 0.09
44 37 0.80
45 5 0.11
ACGTcount: A:0.26, C:0.21, G:0.27, T:0.27
Consensus pattern (44 bp):
ATCGATGCACATTCAAGGGCATGCATCGGTGCATCAGCTAATGT
Found at i:1613097 original size:73 final size:73
Alignment explanation
Indices: 1612978--1613122 Score: 184
Period size: 73 Copynumber: 2.0 Consensus size: 73
1612968 AAGTGTGTAT
* ** * * ***
1612978 CGATGCATAAAATGCATTCGATGTTTGAAAATAGCCTGAGTGCATCGGTGCATTGCTTGTGCATC
1 CGATGCATAAAATGCATTCGATGTTTGAAAATAACCCAAGTGCATCGATGCATAGAGAGTGCATC
1613043 GATGCATC
66 GATGCATC
* *
1613051 CGATGCATGAAATGCATTCGATGTTTTAATAA-AACCCAAGTGCATCGATGCATAGAGAGTGCAT
1 CGATGCATAAAATGCATTCGATGTTTGAA-AATAACCCAAGTGCATCGATGCATAGAGAGTGCAT
1613115 CGATGCAT
65 CGATGCAT
1613123 AGAGAGTGCA
Statistics
Matches: 61, Mismatches: 10, Indels: 2
0.84 0.14 0.03
Matches are distributed among these distances:
73 59 0.97
74 2 0.03
ACGTcount: A:0.30, C:0.19, G:0.23, T:0.28
Consensus pattern (73 bp):
CGATGCATAAAATGCATTCGATGTTTGAAAATAACCCAAGTGCATCGATGCATAGAGAGTGCATC
GATGCATC
Found at i:1613113 original size:19 final size:19
Alignment explanation
Indices: 1613089--1613141 Score: 106
Period size: 19 Copynumber: 2.8 Consensus size: 19
1613079 ATAAAACCCA
1613089 AGTGCATCGATGCATAGAG
1 AGTGCATCGATGCATAGAG
1613108 AGTGCATCGATGCATAGAG
1 AGTGCATCGATGCATAGAG
1613127 AGTGCATCGATGCAT
1 AGTGCATCGATGCAT
1613142 GAAATGCATT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 34 1.00
ACGTcount: A:0.30, C:0.17, G:0.30, T:0.23
Consensus pattern (19 bp):
AGTGCATCGATGCATAGAG
Found at i:1613572 original size:2 final size:2
Alignment explanation
Indices: 1613463--1613556 Score: 85
Period size: 2 Copynumber: 48.5 Consensus size: 2
1613453 CAGTTATTTT
1613463 TA TA TA GTA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T- TA TA
1 TA TA TA -TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
* *
1613505 -A TA T- TT TA TA TA -A TA TA TA GTA TA AA TA TA T- TA TCA T- TA
1 TA TA TA TA TA TA TA TA TA TA TA -TA TA TA TA TA TA TA T-A TA TA
1613544 TCA TA T- TA TA TA T
1 T-A TA TA TA TA TA T
1613557 TTTAGTGTAT
Statistics
Matches: 78, Mismatches: 3, Indels: 22
0.76 0.03 0.21
Matches are distributed among these distances:
1 7 0.09
2 63 0.81
3 8 0.10
ACGTcount: A:0.46, C:0.02, G:0.02, T:0.50
Consensus pattern (2 bp):
TA
Found at i:1616527 original size:23 final size:24
Alignment explanation
Indices: 1616488--1616532 Score: 58
Period size: 23 Copynumber: 1.9 Consensus size: 24
1616478 TTTAAAAATT
1616488 TTGCTTCCTACCGCAAA-CCCTCA
1 TTGCTTCCTACCGCAAAGCCCTCA
*
1616511 TTGCTTCCT-CTCTCAAAGCCCT
1 TTGCTTCCTAC-CGCAAAGCCCT
1616533 TACCCCCACC
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
22 1 0.05
23 14 0.74
24 4 0.21
ACGTcount: A:0.18, C:0.42, G:0.09, T:0.31
Consensus pattern (24 bp):
TTGCTTCCTACCGCAAAGCCCTCA
Found at i:1624225 original size:60 final size:60
Alignment explanation
Indices: 1624161--1624275 Score: 151
Period size: 60 Copynumber: 1.9 Consensus size: 60
1624151 ATTATGAATA
* ** * *
1624161 TCATTCTAAATTAGTACTTAAAC-TTTTGAACATTTTAATTTTATTCCCAAACTATTACCT
1 TCATTCAAAATTAGTACCCAAACTTTTTGAACATTCTAATTTCA-TCCCAAACTATTACCT
* *
1624221 TCATTCAAAATTGGTCCCCAAACTTTTTGAACATTCTAATTTCATCCCAAACTAT
1 TCATTCAAAATTAGTACCCAAACTTTTTGAACATTCTAATTTCATCCCAAACTAT
1624276 ATGTATATAC
Statistics
Matches: 47, Mismatches: 7, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
60 29 0.62
61 18 0.38
ACGTcount: A:0.33, C:0.22, G:0.04, T:0.41
Consensus pattern (60 bp):
TCATTCAAAATTAGTACCCAAACTTTTTGAACATTCTAATTTCATCCCAAACTATTACCT
Found at i:1624723 original size:17 final size:18
Alignment explanation
Indices: 1624693--1624726 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
1624683 CATACTATGC
*
1624693 AATTCACTCTTGAAATTA
1 AATTCACTCATGAAATTA
1624711 AATT-ACTCATGAAATT
1 AATTCACTCATGAAATT
1624727 GGGAAGAAAA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 11 0.73
18 4 0.27
ACGTcount: A:0.41, C:0.15, G:0.06, T:0.38
Consensus pattern (18 bp):
AATTCACTCATGAAATTA
Found at i:1626494 original size:16 final size:13
Alignment explanation
Indices: 1626472--1626507 Score: 72
Period size: 13 Copynumber: 2.8 Consensus size: 13
1626462 GTTCCAGAGT
1626472 TTTCTTCTTCTCC
1 TTTCTTCTTCTCC
1626485 TTTCTTCTTCTCC
1 TTTCTTCTTCTCC
1626498 TTTCTTCTTC
1 TTTCTTCTTC
1626508 ATACGTAAGA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 23 1.00
ACGTcount: A:0.00, C:0.36, G:0.00, T:0.64
Consensus pattern (13 bp):
TTTCTTCTTCTCC
Found at i:1629753 original size:60 final size:59
Alignment explanation
Indices: 1629615--1629782 Score: 205
Period size: 60 Copynumber: 2.8 Consensus size: 59
1629605 ATTTTTATTT
* * *
1629615 TAAATTGGTCTTTAAACTTTT-AACTATTTTAATTTCATCCCTAATTATGAATATCATTC
1 TAAATTGGTCCTTAAACTTTTGAAC-ATTTTAATTTCATCCCAAACTATGAATATCATTC
* * * *
1629674 TAAATTAGTACTTAAACTTTTGAACATTTTAATTTCATCCCCAAACTATTACCT-TCATTC
1 TAAATTGGTCCTTAAACTTTTGAACATTTTAATTTCAT-CCCAAACTATGA-ATATCATTC
* *
1629734 TAAATTGGTCCTCAAACTTTTTGAACATTCTAATTTCATCCCAAACTAT
1 TAAATTGGTCCTTAAAC-TTTTGAACATTTTAATTTCATCCCAAACTAT
1629783 ATGTATATAC
Statistics
Matches: 94, Mismatches: 11, Indels: 7
0.84 0.10 0.06
Matches are distributed among these distances:
59 31 0.33
60 42 0.45
61 21 0.22
ACGTcount: A:0.33, C:0.20, G:0.05, T:0.43
Consensus pattern (59 bp):
TAAATTGGTCCTTAAACTTTTGAACATTTTAATTTCATCCCAAACTATGAATATCATTC
Found at i:1630248 original size:17 final size:18
Alignment explanation
Indices: 1630218--1630251 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
1630208 CTTACGATGC
*
1630218 AATTCACTCTTGAAATTA
1 AATTCACTCATGAAATTA
1630236 AATT-ACTCATGAAATT
1 AATTCACTCATGAAATT
1630252 GGGAAGAAAA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 11 0.73
18 4 0.27
ACGTcount: A:0.41, C:0.15, G:0.06, T:0.38
Consensus pattern (18 bp):
AATTCACTCATGAAATTA
Found at i:1637995 original size:16 final size:15
Alignment explanation
Indices: 1637973--1638003 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
1637963 ATTTTTTAAG
1637973 TTAT-TTTTATAAAA
1 TTATATTTTATAAAA
1637987 TTATATTTTATAAAA
1 TTATATTTTATAAAA
1638002 TT
1 TT
1638004 TTGAAATTAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 4 0.25
15 12 0.75
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (15 bp):
TTATATTTTATAAAA
Found at i:1638793 original size:37 final size:37
Alignment explanation
Indices: 1638738--1638829 Score: 114
Period size: 37 Copynumber: 2.5 Consensus size: 37
1638728 TTCGAGTTGG
* * * * *
1638738 GTGGAGGATGTAT-ATTTTTGGGTCGGATTGAATCGA
1 GTGGAGGATATATAATTTTTAGATCAGATCGAATCGA
* *
1638774 GTGGAAGATATATAATTTTTAGATCAGATCGGATCGA
1 GTGGAGGATATATAATTTTTAGATCAGATCGAATCGA
1638811 GTGGAGGATATATAATTTT
1 GTGGAGGATATATAATTTT
1638830 CAGGTCATAT
Statistics
Matches: 47, Mismatches: 8, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
36 11 0.23
37 36 0.77
ACGTcount: A:0.29, C:0.05, G:0.29, T:0.36
Consensus pattern (37 bp):
GTGGAGGATATATAATTTTTAGATCAGATCGAATCGA
Found at i:1638807 original size:42 final size:41
Alignment explanation
Indices: 1638763--1638847 Score: 97
Period size: 37 Copynumber: 2.1 Consensus size: 41
1638753 TTTTGGGTCG
*
1638763 GATTGAATCGAGTGGAAGATATATAATTTTTAGATCAGATC
1 GATTGAATCGAGTGGAAGATATATAATTTTCAGATCAGATC
* * *
1638804 G---G-ATCGAGTGGAGGATATATAATTTTCAGGTCATATC
1 GATTGAATCGAGTGGAAGATATATAATTTTCAGATCAGATC
1638841 AGATTGA
1 -GATTGA
1638848 CAGAAAACGC
Statistics
Matches: 35, Mismatches: 4, Indels: 9
0.73 0.08 0.19
Matches are distributed among these distances:
37 31 0.89
38 2 0.06
41 2 0.06
ACGTcount: A:0.34, C:0.08, G:0.25, T:0.33
Consensus pattern (41 bp):
GATTGAATCGAGTGGAAGATATATAATTTTCAGATCAGATC
Found at i:1639529 original size:59 final size:59
Alignment explanation
Indices: 1639422--1639533 Score: 138
Period size: 59 Copynumber: 1.9 Consensus size: 59
1639412 TTGAATGATC
* * *
1639422 ATTTTGTAACTTTTGATAGTTAAGGACTCAACAAAGCAACACCTTATAGTTGAGGAATT
1 ATTTTGTAACTTTTAATAGTGAAGGACTCAACAAAGCAACACCATATAGTTGAGGAATT
* * *
1639481 ATTTTGTAACTTTTAATAGTCGGA-GACTCAACAAAGTAATGA-CATATAGTTGA
1 ATTTTGTAACTTTTAATAGT-GAAGGACTCAACAAAGCAA-CACCATATAGTTGA
1639534 ATGATCATTT
Statistics
Matches: 45, Mismatches: 6, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
59 43 0.96
60 2 0.04
ACGTcount: A:0.37, C:0.12, G:0.17, T:0.34
Consensus pattern (59 bp):
ATTTTGTAACTTTTAATAGTGAAGGACTCAACAAAGCAACACCATATAGTTGAGGAATT
Found at i:1640684 original size:14 final size:13
Alignment explanation
Indices: 1640660--1640699 Score: 53
Period size: 13 Copynumber: 3.0 Consensus size: 13
1640650 CAGTTAAAAA
1640660 TTATAAAATATTT
1 TTATAAAATATTT
* *
1640673 TTATTTAAATATTA
1 TTA-TAAAATATTT
1640687 TTATAAAATATTT
1 TTATAAAATATTT
1640700 ATTTTTCTAT
Statistics
Matches: 22, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
13 11 0.50
14 11 0.50
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (13 bp):
TTATAAAATATTT
Found at i:1640701 original size:14 final size:14
Alignment explanation
Indices: 1640659--1640702 Score: 56
Period size: 14 Copynumber: 3.2 Consensus size: 14
1640649 TCAGTTAAAA
1640659 ATTATAAAATATTT
1 ATTATAAAATATTT
*
1640673 -TTATTTAAATA-TT
1 ATTA-TAAAATATTT
1640686 ATTATAAAATATTT
1 ATTATAAAATATTT
1640700 ATT
1 ATT
1640703 TTTCTATTTT
Statistics
Matches: 25, Mismatches: 2, Indels: 6
0.76 0.06 0.18
Matches are distributed among these distances:
13 11 0.44
14 14 0.56
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (14 bp):
ATTATAAAATATTT
Found at i:1645779 original size:17 final size:16
Alignment explanation
Indices: 1645715--1645834 Score: 80
Period size: 17 Copynumber: 6.9 Consensus size: 16
1645705 ATTCTAAATG
*
1645715 TTTACATTTATCATATA
1 TTTACA-TTATCAGATA
1645732 TTTCACCATTATCAGATGA
1 TTT-A-CATTATCAGAT-A
*
1645751 TTTTCAGTTATCAGATA
1 TTTACA-TTATCAGATA
1645768 TTTACATATATCAGATGA
1 TTTACAT-TATCAGAT-A
* *
1645786 -TTGCAGTTATAAGATA
1 TTTACA-TTATCAGATA
* *
1645802 TTTACAGATATCATATA
1 TTTACA-TTATCAGATA
1645819 TTTTACAGTTATCAGA
1 -TTTACA-TTATCAGA
1645835 CACAAATTAA
Statistics
Matches: 83, Mismatches: 11, Indels: 17
0.75 0.10 0.15
Matches are distributed among these distances:
16 2 0.02
17 42 0.51
18 33 0.40
19 6 0.07
ACGTcount: A:0.35, C:0.12, G:0.10, T:0.42
Consensus pattern (16 bp):
TTTACATTATCAGATA
Found at i:1645801 original size:34 final size:35
Alignment explanation
Indices: 1645741--1645814 Score: 114
Period size: 34 Copynumber: 2.1 Consensus size: 35
1645731 ATTTCACCAT
* * *
1645741 TATCAGATGATTTTCAGTTATCAGATATTTACATA
1 TATCAGATGATTTGCAGTTATAAGATATTTACAGA
1645776 TATCAGATGA-TTGCAGTTATAAGATATTTACAGA
1 TATCAGATGATTTGCAGTTATAAGATATTTACAGA
1645810 TATCA
1 TATCA
1645815 TATATTTTAC
Statistics
Matches: 36, Mismatches: 3, Indels: 1
0.90 0.08 0.03
Matches are distributed among these distances:
34 26 0.72
35 10 0.28
ACGTcount: A:0.36, C:0.11, G:0.14, T:0.39
Consensus pattern (35 bp):
TATCAGATGATTTGCAGTTATAAGATATTTACAGA
Found at i:1655723 original size:64 final size:64
Alignment explanation
Indices: 1655651--1655782 Score: 219
Period size: 64 Copynumber: 2.1 Consensus size: 64
1655641 ATATTGTTCT
*
1655651 ATCAGTACTGATACTAAAGGCTTAATATGGGAAGAAACAACTGTGTAGTATCAATACTTATACA
1 ATCAGTACTGATACTAAAGGCTTAATATGAGAAGAAACAACTGTGTAGTATCAATACTTATACA
* * * *
1655715 ATCAGTACTGATACTATATGCTTAATATGAGAAGAAACAGCTGTGTAGTATCGATACTTATACA
1 ATCAGTACTGATACTAAAGGCTTAATATGAGAAGAAACAACTGTGTAGTATCAATACTTATACA
1655779 ATCA
1 ATCA
1655783 ATATCGATAC
Statistics
Matches: 63, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
64 63 1.00
ACGTcount: A:0.39, C:0.14, G:0.17, T:0.30
Consensus pattern (64 bp):
ATCAGTACTGATACTAAAGGCTTAATATGAGAAGAAACAACTGTGTAGTATCAATACTTATACA
Found at i:1656308 original size:54 final size:54
Alignment explanation
Indices: 1656226--1656558 Score: 452
Period size: 54 Copynumber: 6.2 Consensus size: 54
1656216 TATCAGTACA
*
1656226 ATGTGTGCAATTCACGGAATTCATCATGAGTTGATGAATAACCATACATGCACT
1 ATGTGTGCAATTCACGGAATTCATCATGAGTTGATGAACAACCATACATGCACT
*** * *
1656280 ATGTGTGCAATTCATTAAATTCATCATGAGTTGATCAACAACCGTACATGCACT
1 ATGTGTGCAATTCACGGAATTCATCATGAGTTGATGAACAACCATACATGCACT
* * * *
1656334 ATGTGTACAATTTACGGAATTCATCATGAGTTGATGAACATCCATACAGGCACT
1 ATGTGTGCAATTCACGGAATTCATCATGAGTTGATGAACAACCATACATGCACT
* * * * *
1656388 ATGTGCGTAATTCACGAAATTCATCATGAGTTGATGAACAACCGTACGTGCACT
1 ATGTGTGCAATTCACGGAATTCATCATGAGTTGATGAACAACCATACATGCACT
*
1656442 ATGTGTGCAATTCACGGAATTCATCATGAGTTGATGAACAACCATAC-CGACACT
1 ATGTGTGCAATTCACGGAATTCATCATGAGTTGATGAACAACCATACATG-CACT
* * * * *
1656496 ATGTGTGCAATTCACGGAATTAATCATGAGTTGATGAACTACCGTATAAGCACT
1 ATGTGTGCAATTCACGGAATTCATCATGAGTTGATGAACAACCATACATGCACT
*
1656550 AAGTGTGCA
1 ATGTGTGCA
1656559 TCTTAATAAA
Statistics
Matches: 242, Mismatches: 35, Indels: 4
0.86 0.12 0.01
Matches are distributed among these distances:
53 1 0.00
54 240 0.99
55 1 0.00
ACGTcount: A:0.33, C:0.19, G:0.19, T:0.29
Consensus pattern (54 bp):
ATGTGTGCAATTCACGGAATTCATCATGAGTTGATGAACAACCATACATGCACT
Found at i:1662641 original size:19 final size:21
Alignment explanation
Indices: 1662613--1662659 Score: 62
Period size: 19 Copynumber: 2.3 Consensus size: 21
1662603 TGCAAAAATG
*
1662613 GTATCAGTACCATA-ATAG-A
1 GTATCGGTACCATAGATAGTA
1662632 GTATCGGTACCATAGTATAGTA
1 GTATCGGTACCATAG-ATAGTA
1662654 GTATCG
1 GTATCG
1662660 ATACTATGGT
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
19 13 0.54
21 4 0.17
22 7 0.29
ACGTcount: A:0.34, C:0.15, G:0.21, T:0.30
Consensus pattern (21 bp):
GTATCGGTACCATAGATAGTA
Found at i:1663097 original size:54 final size:54
Alignment explanation
Indices: 1663015--1663394 Score: 455
Period size: 54 Copynumber: 7.3 Consensus size: 54
1663005 TGTACGACAG
* *
1663015 GCACTATGT-TCGCAATTCACGAAATTCATCATGAGTTGATGAACAATCGTACAT
1 GCACTATGTGT-GCAATTCACGGAATTCATCATGAGTTGATGAACAACCGTACAT
* *
1663069 GCACTATGTGTGCAATTCACGGAATTCATCATGAGTTGATGAACAACCATACAG
1 GCACTATGTGTGCAATTCACGGAATTCATCATGAGTTGATGAACAACCGTACAT
*
1663123 GCACTATGTGTG-------C--AA-T--TCATGAGTTGATCAACAACCGTACAT
1 GCACTATGTGTGCAATTCACGGAATTCATCATGAGTTGATGAACAACCGTACAT
* * * * *
1663165 GCACTATGTGTACAATTTACGGAATTCATCATGAGTTGGTGAACATCCGTACAG
1 GCACTATGTGTGCAATTCACGGAATTCATCATGAGTTGATGAACAACCGTACAT
* * * *
1663219 GCACTATGTGCGCAATTCACGAAACTCATCATGAGTTGATGAACAACCGTACGT
1 GCACTATGTGTGCAATTCACGGAATTCATCATGAGTTGATGAACAACCGTACAT
* *
1663273 GCACTATGTGTGCAATTCACGGAATTCATCATGAGTTGATGAACAACCATAC-C
1 GCACTATGTGTGCAATTCACGGAATTCATCATGAGTTGATGAACAACCGTACAT
* * * *
1663326 GACACTATGTGTGCAATTCACGGAATTAATCATGAGTTGATGAACTACCGTATAA
1 G-CACTATGTGTGCAATTCACGGAATTCATCATGAGTTGATGAACAACCGTACAT
*
1663381 GCACTAAGTGTGCA
1 GCACTATGTGTGCA
1663395 TCTTAATAAA
Statistics
Matches: 279, Mismatches: 32, Indels: 30
0.82 0.09 0.09
Matches are distributed among these distances:
42 34 0.12
44 1 0.00
45 2 0.01
47 1 0.00
49 1 0.00
51 2 0.01
52 1 0.00
53 1 0.00
54 234 0.84
55 2 0.01
ACGTcount: A:0.32, C:0.21, G:0.20, T:0.27
Consensus pattern (54 bp):
GCACTATGTGTGCAATTCACGGAATTCATCATGAGTTGATGAACAACCGTACAT
Found at i:1663156 original size:42 final size:42
Alignment explanation
Indices: 1663097--1663181 Score: 134
Period size: 42 Copynumber: 2.0 Consensus size: 42
1663087 ACGGAATTCA
* *
1663097 TCATGAGTTGATGAACAACCATACAGGCACTATGTGTGCAAT
1 TCATGAGTTGATCAACAACCATACAGGCACTATGTGTACAAT
* *
1663139 TCATGAGTTGATCAACAACCGTACATGCACTATGTGTACAAT
1 TCATGAGTTGATCAACAACCATACAGGCACTATGTGTACAAT
1663181 T
1 T
1663182 TACGGAATTC
Statistics
Matches: 39, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
42 39 1.00
ACGTcount: A:0.33, C:0.20, G:0.19, T:0.28
Consensus pattern (42 bp):
TCATGAGTTGATCAACAACCATACAGGCACTATGTGTACAAT
Found at i:1663165 original size:96 final size:96
Alignment explanation
Indices: 1663043--1663345 Score: 399
Period size: 96 Copynumber: 3.0 Consensus size: 96
1663033 ACGAAATTCA
*
1663043 TCATGAGTTGATGAACAATCGTACATGCACTATGTGTGCAATTCACGGAATTCATCATGAGTTGA
1 TCATGAGTTGATGAACAACCGTACATGCACTATGTGTGCAATTCACGGAATTCATCATGAGTTGA
1663108 TGAACAACCATACAGGCACTATGTGTGCAAT
66 TGAACAACCATACAGGCACTATGTGTGCAAT
* * * *
1663139 TCATGAGTTGATCAACAACCGTACATGCACTATGTGTACAATTTACGGAATTCATCATGAGTTGG
1 TCATGAGTTGATGAACAACCGTACATGCACTATGTGTGCAATTCACGGAATTCATCATGAGTTGA
* * *
1663204 TGAACATCCGTACAGGCACTATGTGCGCAATTCACGAAACT
66 TGAACAACCATACAGGCACTATGT--G----T---GCAA-T
*
1663245 CATCATGAGTTGATGAACAACCGTACGTGCACTATGTGTGCAATTCACGGAATTCATCATGAGTT
1 --TCATGAGTTGATGAACAACCGTACATGCACTATGTGTGCAATTCACGGAATTCATCATGAGTT
* *
1663310 GATGAACAACCATACCGACACTATGTGTGCAAT
64 GATGAACAACCATACAGGCACTATGTGTGCAAT
1663343 TCA
1 TCA
1663346 CGGAATTAAT
Statistics
Matches: 177, Mismatches: 18, Indels: 24
0.81 0.08 0.11
Matches are distributed among these distances:
96 85 0.48
98 2 0.01
99 3 0.02
102 2 0.01
105 3 0.02
106 2 0.01
108 80 0.45
ACGTcount: A:0.32, C:0.21, G:0.20, T:0.27
Consensus pattern (96 bp):
TCATGAGTTGATGAACAACCGTACATGCACTATGTGTGCAATTCACGGAATTCATCATGAGTTGA
TGAACAACCATACAGGCACTATGTGTGCAAT
Found at i:1664397 original size:3 final size:3
Alignment explanation
Indices: 1664389--1664488 Score: 164
Period size: 3 Copynumber: 32.3 Consensus size: 3
1664379 AGGTTTGTAA
1664389 AAT AAT AAT AAT AAT AAT AAT AAT AAGT AAAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AA-T -AAT AAT AAT AAT AAT AAT
1664436 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AATT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA-T AAT AAT
*
1664482 CAT AAT A
1 AAT AAT A
1664489 TTAACGAGAT
Statistics
Matches: 92, Mismatches: 2, Indels: 6
0.92 0.02 0.06
Matches are distributed among these distances:
3 85 0.92
4 5 0.05
5 2 0.02
ACGTcount: A:0.65, C:0.01, G:0.01, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:1668949 original size:17 final size:17
Alignment explanation
Indices: 1668929--1669004 Score: 82
Period size: 17 Copynumber: 4.4 Consensus size: 17
1668919 GATTTTCAAT
1668929 TATCAGATATTTACAGA
1 TATCAGATATTTACAGA
* *
1668946 TATCGGAT-TATTACAGT
1 TATCAGATAT-TTACAGA
*
1668963 TATCAGATATTTACAAA
1 TATCAGATATTTACAGA
* *
1668980 TATCAAATATTTTACAGT
1 TATCAGATA-TTTACAGA
1668998 TATCAGA
1 TATCAGA
1669005 CACAAATTAA
Statistics
Matches: 47, Mismatches: 9, Indels: 5
0.77 0.15 0.08
Matches are distributed among these distances:
16 1 0.02
17 33 0.70
18 13 0.28
ACGTcount: A:0.39, C:0.12, G:0.11, T:0.38
Consensus pattern (17 bp):
TATCAGATATTTACAGA
Found at i:1668967 original size:34 final size:35
Alignment explanation
Indices: 1668911--1669004 Score: 111
Period size: 34 Copynumber: 2.7 Consensus size: 35
1668901 AATTCACTGT
* * *
1668911 TATCAAATGAT-TTTCAATTATCAGATATTTACAGA
1 TATCAAAT-ATATTACAGTTATCAGATATTTACAAA
**
1668946 TATCGGAT-TATTACAGTTATCAGATATTTACAAA
1 TATCAAATATATTACAGTTATCAGATATTTACAAA
*
1668980 TATCAAATATTTTACAGTTATCAGA
1 TATCAAATATATTACAGTTATCAGA
1669005 CACAAATTAA
Statistics
Matches: 49, Mismatches: 8, Indels: 4
0.80 0.13 0.07
Matches are distributed among these distances:
33 1 0.02
34 27 0.55
35 21 0.43
ACGTcount: A:0.39, C:0.12, G:0.10, T:0.39
Consensus pattern (35 bp):
TATCAAATATATTACAGTTATCAGATATTTACAAA
Found at i:1669001 original size:18 final size:18
Alignment explanation
Indices: 1668890--1669002 Score: 72
Period size: 17 Copynumber: 6.4 Consensus size: 18
1668880 AAATGTTGGT
* * *
1668890 AGTTATCAAACAATTCAC
1 AGTTATCAAATATTTTAC
*
1668908 TGTTATCAAATGATTTT-C
1 AGTTATCAAAT-ATTTTAC
* *
1668926 AATTATCAGATA-TTTAC
1 AGTTATCAAATATTTTAC
* ** *
1668943 AGATATCGGAT-TATTAC
1 AGTTATCAAATATTTTAC
*
1668960 AGTTATCAGATA-TTTAC
1 AGTTATCAAATATTTTAC
**
1668977 AAATATCAAATATTTTAC
1 AGTTATCAAATATTTTAC
1668995 AGTTATCA
1 AGTTATCA
1669003 GACACAAATT
Statistics
Matches: 71, Mismatches: 19, Indels: 10
0.71 0.19 0.10
Matches are distributed among these distances:
16 3 0.04
17 36 0.51
18 29 0.41
19 3 0.04
ACGTcount: A:0.39, C:0.13, G:0.09, T:0.39
Consensus pattern (18 bp):
AGTTATCAAATATTTTAC
Found at i:1672389 original size:3 final size:3
Alignment explanation
Indices: 1672381--1672436 Score: 103
Period size: 3 Copynumber: 18.7 Consensus size: 3
1672371 TTTATGGTTA
*
1672381 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AGT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1672429 AAT AAT AA
1 AAT AAT AA
1672437 AAAGTAAACA
Statistics
Matches: 51, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
3 51 1.00
ACGTcount: A:0.66, C:0.00, G:0.02, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:1673855 original size:3 final size:3
Alignment explanation
Indices: 1673837--1673906 Score: 88
Period size: 3 Copynumber: 22.0 Consensus size: 3
1673827 TTTGGGCCTG
1673837 TAA TATA TAA TAAA TAA TAA TAA TAA TAA TAA TAA TAAA TAAA TAA TAA
1 TAA TA-A TAA T-AA TAA TAA TAA TAA TAA TAA TAA T-AA T-AA TAA TAA
1673886 TAA TAAA TAA -AA TAA TAA TAA
1 TAA T-AA TAA TAA TAA TAA TAA
1673907 ATATAAAAAA
Statistics
Matches: 62, Mismatches: 0, Indels: 10
0.86 0.00 0.14
Matches are distributed among these distances:
2 2 0.03
3 44 0.71
4 16 0.26
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
TAA
Found at i:1673870 original size:29 final size:29
Alignment explanation
Indices: 1673838--1673909 Score: 112
Period size: 29 Copynumber: 2.5 Consensus size: 29
1673828 TTGGGCCTGT
1673838 AATATATAATAAATAATAATAAT-AATAAT
1 AATA-ATAATAAATAATAATAATAAATAAT
1673867 AATAATAAATAAATAATAATAATAAATAA-
1 AATAAT-AATAAATAATAATAATAAATAAT
1673896 AATAATAATAAATA
1 AATAATAATAAATA
1673910 TAAAAAAAAC
Statistics
Matches: 41, Mismatches: 0, Indels: 5
0.89 0.00 0.11
Matches are distributed among these distances:
28 10 0.24
29 26 0.63
30 5 0.12
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (29 bp):
AATAATAATAAATAATAATAATAAATAAT
Found at i:1673929 original size:16 final size:16
Alignment explanation
Indices: 1673905--1673935 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
1673895 AAATAATAAT
1673905 AAATATAAAAAAAACC
1 AAATATAAAAAAAACC
*
1673921 AAATGTAAAAAAAAC
1 AAATATAAAAAAAAC
1673936 TAGTGTCTTC
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.74, C:0.10, G:0.03, T:0.13
Consensus pattern (16 bp):
AAATATAAAAAAAACC
Found at i:1674619 original size:113 final size:113
Alignment explanation
Indices: 1674421--1675048 Score: 811
Period size: 113 Copynumber: 5.5 Consensus size: 113
1674411 GTCGAACAAA
* * *
1674421 TTCTTCTCATTATGAACTTCCTT-TGGAAATGCTGATCCATCAAGTGATGTATTTGAGCAAAAGG
1 TTCTTCTCATTATGAACTT-TTTCTGGAAAAGCTGATCCATCAAGTGATGGATTTGAGCAAAAGG
*
1674485 TTGAACAAACTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAG
65 TTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAG
1674534 TTCTTCTCATTATGAACTTTTTCTGGAAAAGCTGATCCATCAAGTGATGGATTTGAGCAAAAGGT
1 TTCTTCTCATTATGAACTTTTTCTGGAAAAGCTGATCCATCAAGTGATGGATTTGAGCAAAAGGT
* * *
1674599 TGAACAAACTCTTCTCATTATAAACTTCTTTTTCCTTCTTCAGATGAG
66 TGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAG
* *
1674647 TTCTTCTCATTATGGACTTTTTCTGGAAAAGCTGATCCATCAAGTGATGGATTTGAGTAAAAGGT
1 TTCTTCTCATTATGAACTTTTTCTGGAAAAGCTGATCCATCAAGTGATGGATTTGAGCAAAAGGT
* *
1674712 TGAACAAGTTCTTCTTATTATGAACTTCTTCTTCCTTCTTCAGATGAG
66 TGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAG
* * ** * *
1674760 TTCTTCTCATTATGAACTTTCTCTGGAAAAGCTGATGCTGATTTATCTCCTTCTGTGATAGAATT
1 TTCTTCTCATTATGAACTTTTTCTGGAAAAGCTGAT-C-----CA--T-C--AAGTGATGGATTT
* * *
1674825 -ATGCAAAAGGTTGAACAAATTCTTCTCATTATGAATTTCTTCTTCC-TCTTCAAATAAG
55 GA-GCAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAG
** * * ** **
1674883 TTCTTCTCATTATGAAC---TTCTGGAAAATTTGATCTATCGAA-TGATGAATTCAAATAAAAGG
1 TTCTTCTCATTATGAACTTTTTCTGGAAAAGCTGATCCATC-AAGTGATGGATTTGAGCAAAAGG
1674944 TTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAG
65 TTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAG
* *
1674993 TTCTTCTCATTATGAACTTTTTCTGGAAAAGCTGATCCATCAAATGATGTATTTGA
1 TTCTTCTCATTATGAACTTTTTCTGGAAAAGCTGATCCATCAAGTGATGGATTTGA
1675049 ATCTTTGCTA
Statistics
Matches: 450, Mismatches: 46, Indels: 38
0.84 0.09 0.07
Matches are distributed among these distances:
109 47 0.10
110 28 0.06
111 1 0.00
112 5 0.01
113 272 0.60
114 3 0.01
119 2 0.00
120 13 0.03
121 1 0.00
122 1 0.00
123 28 0.06
124 49 0.11
ACGTcount: A:0.28, C:0.18, G:0.15, T:0.39
Consensus pattern (113 bp):
TTCTTCTCATTATGAACTTTTTCTGGAAAAGCTGATCCATCAAGTGATGGATTTGAGCAAAAGGT
TGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAG
Found at i:1675474 original size:22 final size:22
Alignment explanation
Indices: 1675449--1675503 Score: 83
Period size: 22 Copynumber: 2.5 Consensus size: 22
1675439 GATAAAGCTT
*
1675449 TCATCTTTGAAAAGAGAATCTG
1 TCATCTTTGAAAAGAGAATCTA
* *
1675471 TCATCTTTAAAAAGGGAATCTA
1 TCATCTTTGAAAAGAGAATCTA
1675493 TCATCTTTGAA
1 TCATCTTTGAA
1675504 GAGTGTAGAT
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
22 29 1.00
ACGTcount: A:0.36, C:0.15, G:0.15, T:0.35
Consensus pattern (22 bp):
TCATCTTTGAAAAGAGAATCTA
Found at i:1676002 original size:54 final size:53
Alignment explanation
Indices: 1675870--1676074 Score: 245
Period size: 54 Copynumber: 3.9 Consensus size: 53
1675860 ATAATCACTG
* * *
1675870 GTTCGTAAAACATTTGACAATACATTCATCTTTTCCTGTGGTTTCTG-TC-GA
1 GTTCGTAAAACATTTGACAACACATTCATCCTTTCCTGTGGCTTCTGCTCAGA
* * * ** *
1675921 GAT-GTAAAACACTTGACAACACATTCATCTTTTTTTATGGCTTCTGCTCAGA
1 GTTCGTAAAACATTTGACAACACATTCATCCTTTCCTGTGGCTTCTGCTCAGA
* *
1675973 TGTTCGTAAAACATTTGACAACACATTCATCCTTTCTTGTGGTTTCTGCTCAGA
1 -GTTCGTAAAACATTTGACAACACATTCATCCTTTCCTGTGGCTTCTGCTCAGA
* * *
1676027 CGTTCGTAAAGCGTTTGACAACACATTCATCCTTTTCTGTGGCTTCTG
1 -GTTCGTAAAACATTTGACAACACATTCATCCTTTCCTGTGGCTTCTG
1676075 TCGAGATTTC
Statistics
Matches: 131, Mismatches: 19, Indels: 5
0.85 0.12 0.03
Matches are distributed among these distances:
50 37 0.28
51 4 0.03
52 2 0.02
53 2 0.02
54 86 0.66
ACGTcount: A:0.24, C:0.22, G:0.16, T:0.39
Consensus pattern (53 bp):
GTTCGTAAAACATTTGACAACACATTCATCCTTTCCTGTGGCTTCTGCTCAGA
Found at i:1678247 original size:115 final size:116
Alignment explanation
Indices: 1677984--1678445 Score: 792
Period size: 115 Copynumber: 4.0 Consensus size: 116
1677974 ATGCAGTTCT
* * * * *
1677984 TCTTTCAATTCCAATGATTGG-TTCTGGGGTTCCTACCGAACCAGATCAGATAACTCAAAGAACA
1 TCTTTCAAATCCAATGATTGGTTTTTGGGGTTCATACCAAACCAAATCAGATAACTCAAAGAACA
1678048 CTTCCAGAAGATGCTATTGGGGCTCCTTA-TTCTACTATGAGCAA-ATTCA
66 CTTCCAGAAGATGCTATTGGGGCTCCTTATTTCTACTATGAGCAACATTCA
*
1678097 TCTTTCAACTCCAATGATTGGTTTTTGGGGTTCATACCAAACCAAATCAGATAACTCAAAGAACA
1 TCTTTCAAATCCAATGATTGGTTTTTGGGGTTCATACCAAACCAAATCAGATAACTCAAAGAACA
*
1678162 CTTCTAGAAGATGCTATTGGGGCTCCTTATTTCTACTATGAGCAA-ATTCA
66 CTTCCAGAAGATGCTATTGGGGCTCCTTATTTCTACTATGAGCAACATTCA
1678212 TCTTTCAAATCCAATGATTGGTTTTTGGGGTTCATACCAAACCAAATCAGATAACTCAAAGAACA
1 TCTTTCAAATCCAATGATTGGTTTTTGGGGTTCATACCAAACCAAATCAGATAACTCAAAGAACA
*
1678277 CTTCCAGAAGATGCTATTGGGGCTCTTTATTTCTACTATGA-CAACATTCA
66 CTTCCAGAAGATGCTATTGGGGCTCCTTATTTCTACTATGAGCAACATTCA
* *
1678327 TCTTGCAAATCCAATGATTGGTTTTTAGGGTTCATACCAAACCAAATCAGATAACTCAAAGAACA
1 TCTTTCAAATCCAATGATTGGTTTTTGGGGTTCATACCAAACCAAATCAGATAACTCAAAGAACA
1678392 CTTCCAGAAGATGCTATTGGGGCTCCTTATTTCTACTATGAG-AACATTCA
66 CTTCCAGAAGATGCTATTGGGGCTCCTTATTTCTACTATGAGCAACATTCA
1678442 TCTT
1 TCTT
1678446 GCTCCAGTTA
Statistics
Matches: 333, Mismatches: 12, Indels: 6
0.95 0.03 0.02
Matches are distributed among these distances:
113 20 0.06
114 70 0.21
115 243 0.73
ACGTcount: A:0.31, C:0.21, G:0.16, T:0.32
Consensus pattern (116 bp):
TCTTTCAAATCCAATGATTGGTTTTTGGGGTTCATACCAAACCAAATCAGATAACTCAAAGAACA
CTTCCAGAAGATGCTATTGGGGCTCCTTATTTCTACTATGAGCAACATTCA
Found at i:1680553 original size:1 final size:1
Alignment explanation
Indices: 1680542--1680603 Score: 79
Period size: 1 Copynumber: 62.0 Consensus size: 1
1680532 TATTTCTCCC
* * * * *
1680542 TTTTTTCTTTTTTCTTTTTTTCTTTTTTTTTCTTTTTTTTTTTTTTTTTTTTTTCTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
1680604 CTTCTTTCTT
Statistics
Matches: 51, Mismatches: 10, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
1 51 1.00
ACGTcount: A:0.00, C:0.08, G:0.00, T:0.92
Consensus pattern (1 bp):
T
Found at i:1680562 original size:15 final size:15
Alignment explanation
Indices: 1680542--1680637 Score: 101
Period size: 15 Copynumber: 6.7 Consensus size: 15
1680532 TATTTCTCCC
1680542 TTTTTTCTTTTTTCT
1 TTTTTTCTTTTTTCT
1680557 TTTTTTCTTTTTT-T
1 TTTTTTCTTTTTTCT
*
1680571 TTCTTT-TTTTTT-T
1 TTTTTTCTTTTTTCT
1680584 TTTTTT-TTTTTTCT
1 TTTTTTCTTTTTTCT
*
1680598 TTTTTTCTTCTTTCT
1 TTTTTTCTTTTTTCT
** ***
1680613 TTGCTGGATTTTTCT
1 TTTTTTCTTTTTTCT
1680628 TTTTTTCTTT
1 TTTTTTCTTT
1680638 GTTGGATGAG
Statistics
Matches: 65, Mismatches: 14, Indels: 4
0.78 0.17 0.05
Matches are distributed among these distances:
13 18 0.28
14 13 0.20
15 34 0.52
ACGTcount: A:0.01, C:0.11, G:0.03, T:0.84
Consensus pattern (15 bp):
TTTTTTCTTTTTTCT
Found at i:1680624 original size:23 final size:24
Alignment explanation
Indices: 1680598--1680644 Score: 62
Period size: 23 Copynumber: 2.0 Consensus size: 24
1680588 TTTTTTTTCT
1680598 TTTTTTC-TTCTTTCTTTGCTGGA
1 TTTTTTCTTTCTTTCTTTGCTGGA
* *
1680621 -TTTTTCTTTTTTTCTTTGTTGGA
1 TTTTTTCTTTCTTTCTTTGCTGGA
1680644 T
1 T
1680645 GAGTATAAGA
Statistics
Matches: 20, Mismatches: 2, Indels: 3
0.80 0.08 0.12
Matches are distributed among these distances:
22 6 0.30
23 14 0.70
ACGTcount: A:0.04, C:0.13, G:0.13, T:0.70
Consensus pattern (24 bp):
TTTTTTCTTTCTTTCTTTGCTGGA
Found at i:1680632 original size:7 final size:7
Alignment explanation
Indices: 1680541--1680614 Score: 82
Period size: 7 Copynumber: 10.6 Consensus size: 7
1680531 CTATTTCTCC
1680541 CTTTTTT
1 CTTTTTT
1680548 CTTTTTT
1 CTTTTTT
1680555 CTTTTTTT
1 C-TTTTTT
1680563 CTTTTTT
1 CTTTTTT
1680570 -TTTCTTT
1 CTTT-TTT
1680577 -TTTTTT
1 CTTTTTT
1680583 -TTTTTT
1 CTTTTTT
*
1680589 TTTTTTT
1 CTTTTTT
1680596 CTTTTTTT
1 C-TTTTTT
*
1680604 CTTCTTT
1 CTTTTTT
1680611 CTTT
1 CTTT
1680615 GCTGGATTTT
Statistics
Matches: 60, Mismatches: 3, Indels: 8
0.85 0.04 0.11
Matches are distributed among these distances:
6 12 0.20
7 34 0.57
8 14 0.23
ACGTcount: A:0.00, C:0.12, G:0.00, T:0.88
Consensus pattern (7 bp):
CTTTTTT
Found at i:1680637 original size:8 final size:8
Alignment explanation
Indices: 1680542--1680606 Score: 89
Period size: 8 Copynumber: 8.1 Consensus size: 8
1680532 TATTTCTCCC
1680542 TTTTTTC-
1 TTTTTTCT
1680549 TTTTTTCT
1 TTTTTTCT
1680557 TTTTTTCTTT
1 TTTTTTC--T
1680567 TTTTTTCT
1 TTTTTTCT
1680575 TTTTTT-T
1 TTTTTTCT
*
1680582 TTTTTTTT
1 TTTTTTCT
1680590 TTTTTTCT
1 TTTTTTCT
1680598 TTTTTTCT
1 TTTTTTCT
1680606 T
1 T
1680607 CTTTCTTTGC
Statistics
Matches: 53, Mismatches: 1, Indels: 7
0.87 0.02 0.11
Matches are distributed among these distances:
7 14 0.26
8 31 0.58
10 8 0.15
ACGTcount: A:0.00, C:0.09, G:0.00, T:0.91
Consensus pattern (8 bp):
TTTTTTCT
Found at i:1683213 original size:14 final size:14
Alignment explanation
Indices: 1683196--1683234 Score: 53
Period size: 14 Copynumber: 2.8 Consensus size: 14
1683186 TAAAAGTATG
1683196 AATGCAAAATGAAA
1 AATGCAAAATGAAA
*
1683210 AATGCAAAGATGCAA
1 AATGCAAA-ATGAAA
1683225 AATG-AAAATG
1 AATGCAAAATG
1683235 CATATATGAA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
13 3 0.13
14 11 0.48
15 9 0.39
ACGTcount: A:0.59, C:0.08, G:0.18, T:0.15
Consensus pattern (14 bp):
AATGCAAAATGAAA
Found at i:1687244 original size:18 final size:17
Alignment explanation
Indices: 1687223--1687256 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
1687213 AAAAAAATAT
1687223 TAATAAATAATATAAAAA
1 TAATAAATAATA-AAAAA
*
1687241 TAATAAGTAATAAAAA
1 TAATAAATAATAAAAA
1687257 TTTGAAAGAA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 4 0.27
18 11 0.73
ACGTcount: A:0.71, C:0.00, G:0.03, T:0.26
Consensus pattern (17 bp):
TAATAAATAATAAAAAA
Found at i:1688066 original size:3 final size:3
Alignment explanation
Indices: 1688058--1688101 Score: 79
Period size: 3 Copynumber: 14.7 Consensus size: 3
1688048 TTTATGGTTC
*
1688058 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AGT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1688102 AAAGTAAACA
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
3 39 1.00
ACGTcount: A:0.66, C:0.00, G:0.02, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:1689522 original size:3 final size:3
Alignment explanation
Indices: 1689504--1689572 Score: 75
Period size: 3 Copynumber: 22.0 Consensus size: 3
1689494 TTTGGGCCTG
* *
1689504 TAA TATA TAA TAAA TAA TAA TAT TAG TAA TAA TAA TAA TAAA TAA TAA
1 TAA TA-A TAA T-AA TAA TAA TAA TAA TAA TAA TAA TAA T-AA TAA TAA
* *
1689552 TAA TAA AAA AAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA
1689573 ATATAAAAAA
Statistics
Matches: 58, Mismatches: 5, Indels: 6
0.84 0.07 0.09
Matches are distributed among these distances:
3 49 0.84
4 9 0.16
ACGTcount: A:0.67, C:0.00, G:0.01, T:0.32
Consensus pattern (3 bp):
TAA
Found at i:1689541 original size:25 final size:23
Alignment explanation
Indices: 1689503--1689572 Score: 74
Period size: 25 Copynumber: 3.0 Consensus size: 23
1689493 ATTTGGGCCT
1689503 GTAATATATAATAAATAATAATATTA
1 GTAATA-ATAATAAATAATAATA--A
1689529 GTAATAATAAT-AATAAATAATAA
1 GTAATAATAATAAAT-AATAATAA
*
1689552 -TAATAA-AAAAAATAATAATAA
1 GTAATAATAATAAATAATAATAA
1689573 ATATAAAAAA
Statistics
Matches: 41, Mismatches: 1, Indels: 9
0.80 0.02 0.18
Matches are distributed among these distances:
21 10 0.24
22 9 0.22
23 1 0.02
24 3 0.07
25 12 0.29
26 6 0.15
ACGTcount: A:0.66, C:0.00, G:0.03, T:0.31
Consensus pattern (23 bp):
GTAATAATAATAAATAATAATAA
Found at i:1689544 original size:28 final size:28
Alignment explanation
Indices: 1689504--1689575 Score: 99
Period size: 28 Copynumber: 2.5 Consensus size: 28
1689494 TTTGGGCCTG
* **
1689504 TAATATATAATAAATAATAATATTAGTAA
1 TAATA-ATAATAAATAATAATAATAAAAA
1689533 TAATAATAATAAATAATAATAATAAAAA
1 TAATAATAATAAATAATAATAATAAAAA
*
1689561 AAATAATAATAAATA
1 TAATAATAATAAATA
1689576 TAAAAAAACC
Statistics
Matches: 39, Mismatches: 4, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
28 34 0.87
29 5 0.13
ACGTcount: A:0.67, C:0.00, G:0.01, T:0.32
Consensus pattern (28 bp):
TAATAATAATAAATAATAATAATAAAAA
Found at i:1690538 original size:17 final size:17
Alignment explanation
Indices: 1690499--1690573 Score: 50
Period size: 17 Copynumber: 4.5 Consensus size: 17
1690489 GTCCGGTCTT
*
1690499 ATTATTAT-TATTATAT
1 ATTATTATATATTATAC
*
1690515 ATAATTATATATTATAC
1 ATTATTATATATTATAC
* *
1690532 GTTATTACATA-TATA-
1 ATTATTATATATTATAC
*
1690547 ATAATATTATATTATTA-AT
1 AT--TATTATA-TATTATAC
1690566 ATTATTAT
1 ATTATTAT
1690574 TTACAAAGCC
Statistics
Matches: 46, Mismatches: 7, Indels: 11
0.72 0.11 0.17
Matches are distributed among these distances:
15 1 0.02
16 11 0.24
17 27 0.59
18 3 0.07
19 4 0.09
ACGTcount: A:0.43, C:0.03, G:0.01, T:0.53
Consensus pattern (17 bp):
ATTATTATATATTATAC
Found at i:1690538 original size:27 final size:25
Alignment explanation
Indices: 1690498--1690573 Score: 77
Period size: 27 Copynumber: 3.0 Consensus size: 25
1690488 CGTCCGGTCT
1690498 TATTATTATTATTATATATAATTATA
1 TATTA-TATTATTATATATAATTATA
1690524 TATTATACGTTATTACATATATAA-TA-A
1 TATTATA--TTATT--ATATATAATTATA
*
1690551 TATTATATTATTA-ATATTATTAT
1 TATTATATTATTATATATAATTAT
1690574 TTACAAAGCC
Statistics
Matches: 43, Mismatches: 1, Indels: 14
0.74 0.02 0.24
Matches are distributed among these distances:
22 5 0.12
23 3 0.07
25 7 0.16
26 5 0.12
27 13 0.30
28 2 0.05
29 8 0.19
ACGTcount: A:0.42, C:0.03, G:0.01, T:0.54
Consensus pattern (25 bp):
TATTATATTATTATATATAATTATA
Found at i:1699112 original size:20 final size:20
Alignment explanation
Indices: 1699069--1699114 Score: 56
Period size: 20 Copynumber: 2.3 Consensus size: 20
1699059 TCTAGAAAAT
* * *
1699069 TAAATCCTCCGGGTGATTTA
1 TAAAACCTCCGGGTCATCTA
*
1699089 TAAAACCTCCGGGTCATCTG
1 TAAAACCTCCGGGTCATCTA
1699109 TAAAAC
1 TAAAAC
1699115 GTCAGGGTAG
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.30, C:0.24, G:0.17, T:0.28
Consensus pattern (20 bp):
TAAAACCTCCGGGTCATCTA
Found at i:1699272 original size:3 final size:3
Alignment explanation
Indices: 1699264--1699371 Score: 62
Period size: 3 Copynumber: 35.3 Consensus size: 3
1699254 TGTCCGATCA
* *
1699264 TAT TAT TAT TAT TA- TAA TAT TAT TAT TAA TAT TAT TAT ATAT ATAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT -TAT -TAT
* * * * *
1699310 AAT TAT ATAT TA- TACGT TAT TA- TAT ATAA TAA TAA TAA TAT TA- TAT
1 TAT TAT -TAT TAT TA--T TAT TAT TAT -TAT TAT TAT TAT TAT TAT TAT
*
1699356 TAT TAA TAT TAT TAT T
1 TAT TAT TAT TAT TAT T
1699372 TACAAAGCCC
Statistics
Matches: 87, Mismatches: 9, Indels: 18
0.76 0.08 0.16
Matches are distributed among these distances:
2 8 0.09
3 65 0.75
4 12 0.14
5 2 0.02
ACGTcount: A:0.44, C:0.01, G:0.01, T:0.55
Consensus pattern (3 bp):
TAT
Found at i:1699285 original size:17 final size:17
Alignment explanation
Indices: 1699264--1699371 Score: 66
Period size: 17 Copynumber: 6.4 Consensus size: 17
1699254 TGTCCGATCA
* *
1699264 TATTATTATTATTATAA
1 TATTATTATTATAATAT
1699281 TATTATTA-T-TAATAT
1 TATTATTATTATAATAT
1699296 TATTA-TA-TAT-ATAT
1 TATTATTATTATAATAT
* *
1699310 AATTATATATTATACGTTAT
1 TATTAT-TATTATA--ATAT
* * *
1699330 TATATATAATAATAATAA
1 TAT-TATTATTATAATAT
1699348 TATTA-TATTATTAATAT
1 TATTATTATTA-TAATAT
1699365 TATTATT
1 TATTATT
1699372 TACAAAGCCC
Statistics
Matches: 69, Mismatches: 12, Indels: 19
0.69 0.12 0.19
Matches are distributed among these distances:
14 11 0.16
15 10 0.14
16 6 0.09
17 23 0.33
18 6 0.09
20 10 0.14
21 3 0.04
ACGTcount: A:0.44, C:0.01, G:0.01, T:0.55
Consensus pattern (17 bp):
TATTATTATTATAATAT
Found at i:1699286 original size:14 final size:14
Alignment explanation
Indices: 1699267--1699371 Score: 80
Period size: 14 Copynumber: 7.7 Consensus size: 14
1699257 CCGATCATAT
1699267 TATTATTATTATAA
1 TATTATTATTATAA
1699281 TATTATTA-T-TAA
1 TATTATTATTATAA
1699293 TATTATTA-TATATA
1 TATTATTATTATA-A
* *
1699307 TATAATTA-TATAT
1 TATTATTATTATAA
1699320 TA-TACGTTATTAT-A
1 TATTA--TTATTATAA
* * *
1699334 TATAATAATAATAA
1 TATTATTATTATAA
1699348 TATTA-TATTATTAA
1 TATTATTATTA-TAA
1699362 TATTATTATT
1 TATTATTATT
1699372 TACAAAGCCC
Statistics
Matches: 72, Mismatches: 10, Indels: 17
0.73 0.10 0.17
Matches are distributed among these distances:
12 13 0.18
13 13 0.18
14 38 0.53
15 8 0.11
ACGTcount: A:0.44, C:0.01, G:0.01, T:0.54
Consensus pattern (14 bp):
TATTATTATTATAA
Found at i:1700699 original size:3 final size:3
Alignment explanation
Indices: 1700691--1700737 Score: 53
Period size: 3 Copynumber: 16.3 Consensus size: 3
1700681 TAATGTAGAC
* * *
1700691 ATT ATT ATT AAT ATT A-T ATT -TT AGT ATT ATT ATT AAT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1700737 A
1 A
1700738 ATAATAATAA
Statistics
Matches: 36, Mismatches: 6, Indels: 4
0.78 0.13 0.09
Matches are distributed among these distances:
2 4 0.11
3 32 0.89
ACGTcount: A:0.38, C:0.00, G:0.02, T:0.60
Consensus pattern (3 bp):
ATT
Found at i:1700706 original size:12 final size:12
Alignment explanation
Indices: 1700691--1700740 Score: 73
Period size: 12 Copynumber: 4.1 Consensus size: 12
1700681 TAATGTAGAC
1700691 ATTATTATTAAT
1 ATTATTATTAAT
* *
1700703 ATTATATTTTAGT
1 ATTAT-TATTAAT
1700716 ATTATTATTAAT
1 ATTATTATTAAT
1700728 ATTATTATTAAT
1 ATTATTATTAAT
1700740 A
1 A
1700741 ATAATAATAA
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
12 23 0.70
13 10 0.30
ACGTcount: A:0.40, C:0.00, G:0.02, T:0.58
Consensus pattern (12 bp):
ATTATTATTAAT
Found at i:1700709 original size:37 final size:36
Alignment explanation
Indices: 1700667--1700740 Score: 87
Period size: 37 Copynumber: 2.0 Consensus size: 36
1700657 TTTTAATCTT
1700667 TTATATTATAATATTA-ATGTAGACATTATTATTAATA
1 TTATATTATAATATTATAT-TA-ACATTATTATTAATA
* * *
1700704 TTATATTTTAGTATTATTATTAATATTATTATTAATA
1 TTATATTATAATATTA-TATTAACATTATTATTAATA
1700741 ATAATAATAA
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
37 28 0.88
38 2 0.06
39 2 0.06
ACGTcount: A:0.41, C:0.01, G:0.04, T:0.54
Consensus pattern (36 bp):
TTATATTATAATATTATATTAACATTATTATTAATA
Found at i:1703123 original size:28 final size:27
Alignment explanation
Indices: 1703091--1703147 Score: 87
Period size: 28 Copynumber: 2.1 Consensus size: 27
1703081 TTATAATTCT
*
1703091 TTATTTTCAAAATTTTTATATATACTTA
1 TTATTTTCAAAATATTTATATATA-TTA
*
1703119 TTATTTTCATAATATTTATATATATTA
1 TTATTTTCAAAATATTTATATATATTA
1703146 TT
1 TT
1703148 TTATTAATGT
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
27 5 0.19
28 22 0.81
ACGTcount: A:0.35, C:0.05, G:0.00, T:0.60
Consensus pattern (27 bp):
TTATTTTCAAAATATTTATATATATTA
Found at i:1703155 original size:24 final size:22
Alignment explanation
Indices: 1703116--1703170 Score: 60
Period size: 24 Copynumber: 2.5 Consensus size: 22
1703106 TTATATATAC
1703116 TTATTATTTTCATAATATTTATA
1 TTATTATTTTCATAATATTT-TA
*
1703139 TATATTATTTT-ATTAATGTTTTA
1 T-TATTATTTTCA-TAATATTTTA
1703162 TT-TTATTTT
1 TTATTATTTT
1703171 TCAAGTATTA
Statistics
Matches: 29, Mismatches: 1, Indels: 6
0.81 0.03 0.17
Matches are distributed among these distances:
21 7 0.24
22 1 0.03
23 5 0.17
24 16 0.55
ACGTcount: A:0.29, C:0.02, G:0.02, T:0.67
Consensus pattern (22 bp):
TTATTATTTTCATAATATTTTA
Found at i:1706008 original size:37 final size:37
Alignment explanation
Indices: 1705958--1706061 Score: 136
Period size: 37 Copynumber: 2.8 Consensus size: 37
1705948 CTTTTCGTCC
* *
1705958 TACTAGGATTCAAACTCCTAAAAATAGGATATAATTT
1 TACTAGGATTCAAACTCCTAAAAATAGGATAGAATTA
* *
1705995 TCCTAGGATTCAAACTCCTAAAAATAGGATAGAGTTA
1 TACTAGGATTCAAACTCCTAAAAATAGGATAGAATTA
** * *
1706032 TACTATTATTTAAACTCCTAAAGATAGGAT
1 TACTAGGATTCAAACTCCTAAAAATAGGAT
1706062 CCACAAGCAT
Statistics
Matches: 58, Mismatches: 9, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
37 58 1.00
ACGTcount: A:0.41, C:0.14, G:0.12, T:0.32
Consensus pattern (37 bp):
TACTAGGATTCAAACTCCTAAAAATAGGATAGAATTA
Found at i:1706497 original size:22 final size:22
Alignment explanation
Indices: 1706451--1706506 Score: 69
Period size: 22 Copynumber: 2.5 Consensus size: 22
1706441 AATTTAACCC
*
1706451 TTATTAT-TTATATGTATATAT
1 TTATTATATTTTATGTATATAT
* *
1706472 TTATTATATTTTATTTATTTAT
1 TTATTATATTTTATGTATATAT
1706494 TTATTATAATTTT
1 TTATTAT-ATTTT
1706507 TTTCTCATTT
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
21 7 0.23
22 18 0.60
23 5 0.17
ACGTcount: A:0.30, C:0.00, G:0.02, T:0.68
Consensus pattern (22 bp):
TTATTATATTTTATGTATATAT
Found at i:1706687 original size:31 final size:31
Alignment explanation
Indices: 1706637--1706798 Score: 78
Period size: 31 Copynumber: 5.4 Consensus size: 31
1706627 CCTAACGTTA
**
1706637 TATATATTTATATTCTTACT-TTATTTTATTT
1 TATATATTTATATGATTACTATT-TTTTATTT
* *
1706668 TATATATTTCTATGATTACTATTTTTTA-GT
1 TATATATTTATATGATTACTATTTTTTATTT
* *
1706698 TA-ATA-TTATATG-TATATTTATTTTTCA-TT
1 TATATATTTATATGAT-TA-CTATTTTTTATTT
* * **
1706727 TATTTA-TTATTATTATTACTATTTAGTATTT
1 TATATATTTA-TATGATTACTATTTTTTATTT
*
1706758 TAT-TATATTATA-CA-TAC-ATTTTTATATTT
1 TATATAT-TTATATGATTACTATTTTT-TATTT
*
1706787 T-TATATATATAT
1 TATATATTTATAT
1706799 TTTTTTATTA
Statistics
Matches: 101, Mismatches: 18, Indels: 26
0.70 0.12 0.18
Matches are distributed among these distances:
27 1 0.01
28 17 0.17
29 26 0.26
30 17 0.17
31 34 0.34
32 6 0.06
ACGTcount: A:0.30, C:0.05, G:0.02, T:0.62
Consensus pattern (31 bp):
TATATATTTATATGATTACTATTTTTTATTT
Found at i:1706810 original size:25 final size:25
Alignment explanation
Indices: 1706755--1706832 Score: 83
Period size: 22 Copynumber: 3.3 Consensus size: 25
1706745 CTATTTAGTA
* *
1706755 TTTTATTATATTATACATAC-ATTT
1 TTTTATTATTTTATATATACTATTT
*
1706779 TTATA-T-TTTTATATATA-TATTT
1 TTTTATTATTTTATATATACTATTT
*
1706801 TTTTATTATTTTATTTATACTATTT
1 TTTTATTATTTTATATATACTATTT
*
1706826 ATTTATT
1 TTTTATT
1706833 TTCATTATAT
Statistics
Matches: 44, Mismatches: 6, Indels: 7
0.77 0.11 0.12
Matches are distributed among these distances:
22 17 0.39
23 2 0.05
24 14 0.32
25 11 0.25
ACGTcount: A:0.29, C:0.04, G:0.00, T:0.67
Consensus pattern (25 bp):
TTTTATTATTTTATATATACTATTT
Found at i:1706818 original size:28 final size:32
Alignment explanation
Indices: 1706779--1706845 Score: 83
Period size: 29 Copynumber: 2.3 Consensus size: 32
1706769 ACATACATTT
1706779 TTATA-TT-TTTATA-TATATATTT-TTTT-A
1 TTATATTTATTTATACTATATATTTATTTTCA
*
1706806 TTAT-TTTATTTATACTATTTATTTATTTTCA
1 TTATATTTATTTATACTATATATTTATTTTCA
1706837 TTATATTTA
1 TTATATTTA
1706846 GTTTCATTGC
Statistics
Matches: 33, Mismatches: 1, Indels: 7
0.80 0.02 0.17
Matches are distributed among these distances:
27 6 0.18
28 6 0.18
29 8 0.24
30 4 0.12
31 5 0.15
32 4 0.12
ACGTcount: A:0.28, C:0.03, G:0.00, T:0.69
Consensus pattern (32 bp):
TTATATTTATTTATACTATATATTTATTTTCA
Found at i:1706819 original size:22 final size:22
Alignment explanation
Indices: 1706714--1706844 Score: 58
Period size: 22 Copynumber: 6.0 Consensus size: 22
1706704 TATATGTATA
*
1706714 TTTATT-TTTCATTTAT-TTATT
1 TTTATTATTTTATTTATATT-TT
* *
1706735 ATTATTATTACTATTTAGTATTTT
1 TTTATTATT-TTATTTA-TATTTT
* * ** *
1706759 ATTA-TATTATACATACATTTT
1 TTTATTATTTTATTTATATTTT
* *
1706780 TATATT-TTTATATATATATTTT
1 TTTATTATTT-TATTTATATTTT
* *
1706802 TTTATTATTTTATTTATA-CTA
1 TTTATTATTTTATTTATATTTT
1706823 TTTATTTATTTTCA-TTATATTT
1 TTTA-TTATTTT-ATTTATATTT
1706845 AGTTTCATTG
Statistics
Matches: 83, Mismatches: 17, Indels: 18
0.70 0.14 0.15
Matches are distributed among these distances:
21 19 0.23
22 41 0.49
23 14 0.17
24 7 0.08
25 2 0.02
ACGTcount: A:0.28, C:0.05, G:0.01, T:0.66
Consensus pattern (22 bp):
TTTATTATTTTATTTATATTTT
Found at i:1706842 original size:46 final size:46
Alignment explanation
Indices: 1706755--1706842 Score: 108
Period size: 46 Copynumber: 1.9 Consensus size: 46
1706745 CTATTTAGTA
*
1706755 TTTTATTATATTATACATACATTTTTATATTTTTATATATATATTT
1 TTTTATTATATTATACATACATTTTTATATTTTCATATATATATTT
* **
1706801 TTTTATTATTTTATTTATACTATTTATT-TATTTTCAT-TATAT
1 TTTTATTATATTATACATAC-ATTT-TTATATTTTCATATATAT
1706843 TTAGTTTCAT
Statistics
Matches: 36, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
46 22 0.61
47 12 0.33
48 2 0.06
ACGTcount: A:0.30, C:0.05, G:0.00, T:0.66
Consensus pattern (46 bp):
TTTTATTATATTATACATACATTTTTATATTTTCATATATATATTT
Found at i:1709136 original size:13 final size:13
Alignment explanation
Indices: 1709118--1709145 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
1709108 GTATGCTCCG
1709118 TGACGTTCTATTT
1 TGACGTTCTATTT
1709131 TGACGTTCTATTT
1 TGACGTTCTATTT
1709144 TG
1 TG
1709146 GGCTTGAAGA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.14, C:0.14, G:0.18, T:0.54
Consensus pattern (13 bp):
TGACGTTCTATTT
Found at i:1710873 original size:11 final size:11
Alignment explanation
Indices: 1710857--1710893 Score: 74
Period size: 11 Copynumber: 3.4 Consensus size: 11
1710847 AACAAAAAAG
1710857 AAAAGAAGAAA
1 AAAAGAAGAAA
1710868 AAAAGAAGAAA
1 AAAAGAAGAAA
1710879 AAAAGAAGAAA
1 AAAAGAAGAAA
1710890 AAAA
1 AAAA
1710894 AGGAACAAAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 26 1.00
ACGTcount: A:0.84, C:0.00, G:0.16, T:0.00
Consensus pattern (11 bp):
AAAAGAAGAAA
Found at i:1710904 original size:12 final size:11
Alignment explanation
Indices: 1710845--1710895 Score: 57
Period size: 11 Copynumber: 4.5 Consensus size: 11
1710835 CAAAAAGGAT
*
1710845 AAAACAAAAAA
1 AAAAGAAAAAA
*
1710856 GAAAAGAAGAAA
1 -AAAAGAAAAAA
*
1710868 AAAAGAAGAAA
1 AAAAGAAAAAA
1710879 AAAAGAAGAAAA
1 AAAAGAA-AAAA
1710891 AAAAG
1 AAAAG
1710896 GAACAAAAAT
Statistics
Matches: 35, Mismatches: 3, Indels: 2
0.88 0.08 0.05
Matches are distributed among these distances:
11 18 0.51
12 17 0.49
ACGTcount: A:0.82, C:0.02, G:0.16, T:0.00
Consensus pattern (11 bp):
AAAAGAAAAAA
Found at i:1711766 original size:23 final size:22
Alignment explanation
Indices: 1711739--1711801 Score: 72
Period size: 24 Copynumber: 2.8 Consensus size: 22
1711729 TGAAAGAGAC
1711739 AATATTTTCAAAACTTTTTATT
1 AATATTTTCAAAACTTTTTATT
* *
1711761 AAATATTTTTCGAAACTCTTTATT
1 -AATA-TTTTCAAAACTTTTTATT
* *
1711785 GATATTTTCAGAACTTT
1 AATATTTTCAAAACTTT
1711802 GAAAATAAAA
Statistics
Matches: 33, Mismatches: 6, Indels: 3
0.79 0.14 0.07
Matches are distributed among these distances:
22 10 0.30
23 7 0.21
24 16 0.48
ACGTcount: A:0.33, C:0.11, G:0.05, T:0.51
Consensus pattern (22 bp):
AATATTTTCAAAACTTTTTATT
Found at i:1713293 original size:106 final size:106
Alignment explanation
Indices: 1712441--1713292 Score: 1285
Period size: 106 Copynumber: 8.0 Consensus size: 106
1712431 ATATCGTGCC
* * * *
1712441 ACTCGAGACAACACAAGTTTAACTTCACAACGAAGGGACGGCTGGTTGTCAACAAACAACTTCCC
1 ACTCCAGACAACACAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCC
*
1712506 AAATTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
* *
1712547 ACTCCAGACAACACAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAAATTCTC
1 ACTCCAGACAACACAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCC
*
1712612 AATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
* * * *
1712653 ACTCCAGACAACGCAAGTTCAACTTCACGATGAAGGGACCGCTGGTTGTCAATAAACAATTTCCC
1 ACTCCAGACAACACAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCC
1712718 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
* * * ** * * *
1712759 ACTCAAGACAACGCAAGTTCAACTTCATGAAAAAGGGATCGCTGGTTGTCAATAAACAAGTTCCC
1 ACTCCAGACAACACAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCC
* *
1712824 AATTTCAGAGTCAATTTCAACTTCACAGCAAAGGATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
* * *
1712865 ACTCCAGACAA-AGCAAGTTCAACTTCACGATGAAGGGACCGCTGGTTGTCAACAAATAACTTCT
1 ACTCCAGACAACA-CAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCC
* *
1712929 CAATTTCAGAGCCAATTTCAACTTCACAACAAAGGATATTGG
65 CAATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
* *
1712971 ACTCCAGATAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCC
1 ACTCCAGACAACACAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCC
1713036 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
* * * *
1713077 ACTCCAGACAACGCAAGTTCAACTTCAGGATGAAGGGACCGCTGGTTGTCAACAAACAATTTCCC
1 ACTCCAGACAACACAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCC
* * *
1713142 AATTTCGGAGCCAATTTCAACTTCACAACAAAGGATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
* * * *
1713183 ACTCGAGACAACACAAGTTCAACTTCACAACGAAGGGACTGCTGGTTGTCAACAAACAATTTCCC
1 ACTCCAGACAACACAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCC
* * *
1713248 GATTCCAGAGCCAATTTCAACTTCAC-GACGGAGGATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAG-CGAAGGATATTGG
1713289 ACTC
1 ACTC
1713293 GGAACAATGC
Statistics
Matches: 683, Mismatches: 60, Indels: 6
0.91 0.08 0.01
Matches are distributed among these distances:
106 683 1.00
ACGTcount: A:0.35, C:0.25, G:0.18, T:0.23
Consensus pattern (106 bp):
ACTCCAGACAACACAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCC
AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
Found at i:1714785 original size:22 final size:22
Alignment explanation
Indices: 1714758--1714817 Score: 57
Period size: 24 Copynumber: 2.6 Consensus size: 22
1714748 CTATTTAGTA
1714758 TTTTATTATATTATACATACAT
1 TTTTATTATATTATACATACAT
* * **
1714780 TTTTATATTTATATATATATATTT
1 TTTTAT-TATAT-TATACATACAT
*
1714804 TTTTATTATTTTAT
1 TTTTATTATATTAT
1714818 TTATACTATT
Statistics
Matches: 30, Mismatches: 6, Indels: 4
0.75 0.15 0.10
Matches are distributed among these distances:
22 9 0.30
23 7 0.23
24 14 0.47
ACGTcount: A:0.32, C:0.03, G:0.00, T:0.65
Consensus pattern (22 bp):
TTTTATTATATTATACATACAT
Found at i:1714788 original size:24 final size:24
Alignment explanation
Indices: 1714761--1714817 Score: 64
Period size: 22 Copynumber: 2.5 Consensus size: 24
1714751 TTTAGTATTT
1714761 TATTATATTATACATACATTTTTA
1 TATTATATTATACATACATTTTTA
* * *
1714785 TATT-TA-TATATATATATTTTTT
1 TATTATATTATACATACATTTTTA
*
1714807 TATTATTTTAT
1 TATTATATTAT
1714818 TTATACTATT
Statistics
Matches: 27, Mismatches: 4, Indels: 4
0.77 0.11 0.11
Matches are distributed among these distances:
22 17 0.63
23 3 0.11
24 7 0.26
ACGTcount: A:0.33, C:0.04, G:0.00, T:0.63
Consensus pattern (24 bp):
TATTATATTATACATACATTTTTA
Found at i:1714951 original size:25 final size:25
Alignment explanation
Indices: 1714922--1715019 Score: 69
Period size: 25 Copynumber: 3.8 Consensus size: 25
1714912 TTTGTATATA
1714922 TATTTTATCTTCATTTATTTTATTT
1 TATTTTATCTTCATTTATTTTATTT
*
1714947 TATTTTA--TTCAATTTTATTTTTTTT
1 TATTTTATCTTC-A-TTTATTTTATTT
* * *
1714972 TGTTTCATC--CAATTATTTTATGTT
1 TATTTTATCTTCATTTATTTTAT-TT
1714996 TATTATTATTGGCTTCATTTATTT
1 TATT-TTA-T--CTTCATTTATTT
1715020 CCTTAGTTTA
Statistics
Matches: 54, Mismatches: 8, Indels: 17
0.68 0.10 0.22
Matches are distributed among these distances:
23 11 0.20
24 7 0.13
25 26 0.48
26 1 0.02
28 1 0.02
30 8 0.15
ACGTcount: A:0.20, C:0.08, G:0.04, T:0.67
Consensus pattern (25 bp):
TATTTTATCTTCATTTATTTTATTT
Found at i:1714972 original size:5 final size:5
Alignment explanation
Indices: 1714922--1714971 Score: 50
Period size: 5 Copynumber: 10.2 Consensus size: 5
1714912 TTTGTATATA
* * *
1714922 TATTT TATCTT CA-TT TATTT TATTT TATTT TATTC AATTT TATTT T-TTT
1 TATTT TAT-TT TATTT TATTT TATTT TATTT TATTT TATTT TATTT TATTT
1714971 T
1 T
1714972 TGTTTCATCC
Statistics
Matches: 37, Mismatches: 6, Indels: 5
0.77 0.12 0.10
Matches are distributed among these distances:
4 7 0.19
5 27 0.73
6 3 0.08
ACGTcount: A:0.20, C:0.06, G:0.00, T:0.74
Consensus pattern (5 bp):
TATTT
Found at i:1719441 original size:75 final size:75
Alignment explanation
Indices: 1719302--1719474 Score: 229
Period size: 75 Copynumber: 2.3 Consensus size: 75
1719292 ATTAATAAGA
* * * * *
1719302 AGCAAATGTTGGGGCATGTTGAAAGCCCCTCTCAATCAGAATCATGAATGTTGATGTATTTTGAA
1 AGCAAATGTTGGGGCATGCTGAAAGCCCCTCTCAATCAGAATCAAGAATGTTGACGCATATTGAA
*
1719367 CATTTATATT
66 CACTTATATT
* * *
1719377 AGCAAATGCTGGGGCATACTGAAAGCCCCTCTCAATCAGAATGAAGAATGTTGACGCATATTGAA
1 AGCAAATGTTGGGGCATGCTGAAAGCCCCTCTCAATCAGAATCAAGAATGTTGACGCATATTGAA
** *
1719442 TGCTTGTATT
66 CACTTATATT
*
1719452 AGCCAATGTTGGGGCATGCTGAA
1 AGCAAATGTTGGGGCATGCTGAA
1719475 GGTCTATATC
Statistics
Matches: 83, Mismatches: 15, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
75 83 1.00
ACGTcount: A:0.31, C:0.17, G:0.23, T:0.29
Consensus pattern (75 bp):
AGCAAATGTTGGGGCATGCTGAAAGCCCCTCTCAATCAGAATCAAGAATGTTGACGCATATTGAA
CACTTATATT
Found at i:1721393 original size:73 final size:73
Alignment explanation
Indices: 1721270--1722038 Score: 1171
Period size: 73 Copynumber: 10.5 Consensus size: 73
1721260 CTATTTCCAA
* *
1721270 CATCTGTAAGCCCTACAGTGCATGATGTTTTCAAAAAGCCTTCGGAAGCTTTTTGATCTTAAAGC
1 CATCTGTAAGACCTACAGTGCATGATGTTTTCAAAAAGCCTTCGGGAGCTTTTTGATCTTAAAGC
1721335 CTCAGGGT
66 CTCAGGGT
1721343 CATCTGTAAGACCTACAGTGCATGATGTTTTCAAAAAGCCTTCGGGAGCTTTTTGATCTTAAAGC
1 CATCTGTAAGACCTACAGTGCATGATGTTTTCAAAAAGCCTTCGGGAGCTTTTTGATCTTAAAGC
1721408 CTCAGGGT
66 CTCAGGGT
* * * * * * *
1721416 CATATGTAAGAACTATAGTGTATGATGTTTTCAAAAAGCCTCCGGGAGGTTTTTGATCTTAAATC
1 CATCTGTAAGACCTACAGTGCATGATGTTTTCAAAAAGCCTTCGGGAGCTTTTTGATCTTAAAGC
1721481 CTCAGGGT
66 CTCAGGGT
* * * * *
1721489 CATCTGTAAGACCTGCAGTGCAGGATGTTTTCAAAAAGCCTTCGGAAGGTTTTTGAAGTTTTTAA
1 CATCTGTAAGACCTACAGTGCATGATGTTTTCAAAAAGCCTTCGGGAGCTTTTTG-A--TCTTAA
1721554 AGCCTCAGGGT
63 AGCCTCAGGGT
* *
1721565 CATCTGTAAGACCTACAGTGCATGATGTTTTCAAAAAGCCTTCGGAATCTTTTTGATCTTAAAGC
1 CATCTGTAAGACCTACAGTGCATGATGTTTTCAAAAAGCCTTCGGGAGCTTTTTGATCTTAAAGC
1721630 CTCAGGGT
66 CTCAGGGT
* * * *
1721638 CATCTGTAAGACCTACAGTGCATGATGTTTTCAAAAAGCCTCCGAGATCTTTTTGATCTTAAATC
1 CATCTGTAAGACCTACAGTGCATGATGTTTTCAAAAAGCCTTCGGGAGCTTTTTGATCTTAAAGC
1721703 CTCAGGGT
66 CTCAGGGT
* * * * *
1721711 CATCTTTAAGACCTGCAGTGCAGGATGTTTTCAAAAAGCCTTTGGGAGCTTTTTGAAGTTTTTAA
1 CATCTGTAAGACCTACAGTGCATGATGTTTTCAAAAAGCCTTCGGGAGCTTTTTG-A--TCTTAA
*
1721776 AACCTCAGGGT
63 AGCCTCAGGGT
* *
1721787 CATCTATAAGACCTACAGTGCATGATGTTTTCAAAAAGCCTTCGGGAGCTTTTTAATCTTAAAGC
1 CATCTGTAAGACCTACAGTGCATGATGTTTTCAAAAAGCCTTCGGGAGCTTTTTGATCTTAAAGC
1721852 CTCAGGGT
66 CTCAGGGT
*
1721860 CATCTGTAAGACCTACAGTGCATGATGTTTTCAAAAAGCCTTCGGGAGCTTTTTGATTTTAAAGC
1 CATCTGTAAGACCTACAGTGCATGATGTTTTCAAAAAGCCTTCGGGAGCTTTTTGATCTTAAAGC
* *
1721925 CTCATGAT
66 CTCAGGGT
* *
1721933 CATCTGTAAG-CTTACAGTCCATGATGTTTTCAAAAAGCCTTCGGGAGCTTTTTGATCTTAAAGC
1 CATCTGTAAGACCTACAGTGCATGATGTTTTCAAAAAGCCTTCGGGAGCTTTTTGATCTTAAAGC
1721997 CTCAGGGT
66 CTCAGGGT
*
1722005 CATCTGTAAGACCTACAGTGCATGGTGTTTTCAA
1 CATCTGTAAGACCTACAGTGCATGATGTTTTCAA
1722039 CATTTCAATC
Statistics
Matches: 632, Mismatches: 57, Indels: 14
0.90 0.08 0.02
Matches are distributed among these distances:
72 67 0.11
73 430 0.68
74 2 0.00
75 2 0.00
76 131 0.21
ACGTcount: A:0.27, C:0.20, G:0.21, T:0.33
Consensus pattern (73 bp):
CATCTGTAAGACCTACAGTGCATGATGTTTTCAAAAAGCCTTCGGGAGCTTTTTGATCTTAAAGC
CTCAGGGT
Found at i:1721665 original size:222 final size:219
Alignment explanation
Indices: 1721270--1722038 Score: 1189
Period size: 222 Copynumber: 3.5 Consensus size: 219
1721260 CTATTTCCAA
* *
1721270 CATCTGTAAGCCCTACAGTGCATGATGTTTTCAAAAAGCCTTCGGAAGCTTTTTGATCTTAAAGC
1 CATCTGTAAGACCTACAGTGCAGGATGTTTTCAAAAAGCCTTCGGAAGCTTTTTGATCTTAAAGC
1721335 CTCAGGGTCATCTGTAAGACCTACAGTGCATGATGTTTTCAAAAAGCCTTCGGGAGCTTTTTGAT
66 CTCAGGGTCATCTGTAAGACCTACAGTGCATGATGTTTTCAAAAAGCCTTCGGGAGCTTTTTGAT
* * * * *
1721400 CTTAAAGCCTCAGGGTCATATGTAAGAACTATAGTGTATGATGTTTTCAAAAAGCCTCCGGGAGG
131 CTTAAAGCCTCAGGGTCATCTGTAAGACCTACAGTGCATGATGTTTTCAAAAAGCCTCCGGGAGC
1721465 TTTTTGATCTTAAATCCTCAGGGT
196 TTTTTGATCTTAAATCCTCAGGGT
* * *
1721489 CATCTGTAAGACCTGCAGTGCAGGATGTTTTCAAAAAGCCTTCGGAAGGTTTTTGAAGTTTTTAA
1 CATCTGTAAGACCTACAGTGCAGGATGTTTTCAAAAAGCCTTCGGAAGCTTTTTG-A--TCTTAA
* *
1721554 AGCCTCAGGGTCATCTGTAAGACCTACAGTGCATGATGTTTTCAAAAAGCCTTCGGAATCTTTTT
63 AGCCTCAGGGTCATCTGTAAGACCTACAGTGCATGATGTTTTCAAAAAGCCTTCGGGAGCTTTTT
*
1721619 GATCTTAAAGCCTCAGGGTCATCTGTAAGACCTACAGTGCATGATGTTTTCAAAAAGCCTCCGAG
128 GATCTTAAAGCCTCAGGGTCATCTGTAAGACCTACAGTGCATGATGTTTTCAAAAAGCCTCCGGG
*
1721684 ATCTTTTTGATCTTAAATCCTCAGGGT
193 AGCTTTTTGATCTTAAATCCTCAGGGT
* * * * *
1721711 CATCTTTAAGACCTGCAGTGCAGGATGTTTTCAAAAAGCCTTTGGGAGCTTTTTGAAGTTTTTAA
1 CATCTGTAAGACCTACAGTGCAGGATGTTTTCAAAAAGCCTTCGGAAGCTTTTTG-A--TCTTAA
* *
1721776 AACCTCAGGGTCATCTATAAGACCTACAGTGCATGATGTTTTCAAAAAGCCTTCGGGAGCTTTTT
63 AGCCTCAGGGTCATCTGTAAGACCTACAGTGCATGATGTTTTCAAAAAGCCTTCGGGAGCTTTTT
* *
1721841 AATCTTAAAGCCTCAGGGTCATCTGTAAGACCTACAGTGCATGATGTTTTCAAAAAGCCTTCGGG
128 GATCTTAAAGCCTCAGGGTCATCTGTAAGACCTACAGTGCATGATGTTTTCAAAAAGCCTCCGGG
* * * *
1721906 AGCTTTTTGATTTTAAAGCCTCATGAT
193 AGCTTTTTGATCTTAAATCCTCAGGGT
* * * *
1721933 CATCTGTAAG-CTTACAGTCCATGATGTTTTCAAAAAGCCTTCGGGAGCTTTTTGATCTTAAAGC
1 CATCTGTAAGACCTACAGTGCAGGATGTTTTCAAAAAGCCTTCGGAAGCTTTTTGATCTTAAAGC
*
1721997 CTCAGGGTCATCTGTAAGACCTACAGTGCATGGTGTTTTCAA
66 CTCAGGGTCATCTGTAAGACCTACAGTGCATGATGTTTTCAA
1722039 CATTTCAATC
Statistics
Matches: 507, Mismatches: 40, Indels: 7
0.92 0.07 0.01
Matches are distributed among these distances:
218 47 0.09
219 51 0.10
220 2 0.00
221 39 0.08
222 368 0.73
ACGTcount: A:0.27, C:0.20, G:0.21, T:0.33
Consensus pattern (219 bp):
CATCTGTAAGACCTACAGTGCAGGATGTTTTCAAAAAGCCTTCGGAAGCTTTTTGATCTTAAAGC
CTCAGGGTCATCTGTAAGACCTACAGTGCATGATGTTTTCAAAAAGCCTTCGGGAGCTTTTTGAT
CTTAAAGCCTCAGGGTCATCTGTAAGACCTACAGTGCATGATGTTTTCAAAAAGCCTCCGGGAGC
TTTTTGATCTTAAATCCTCAGGGT
Found at i:1721851 original size:295 final size:294
Alignment explanation
Indices: 1721270--1722038 Score: 1195
Period size: 295 Copynumber: 2.6 Consensus size: 294
1721260 CTATTTCCAA
*
1721270 CATCTGTAAGCCCTACAGTGCATGATGTTTTCAAAAAGCCTTCGGAAGCTTTTTGATCTTAAAGC
1 CATCTGTAAGACCTACAGTGCATGATGTTTTCAAAAAGCCTTCGGAAGCTTTTTGATCTTAAAGC
1721335 CTCAGGGTCATCTGTAAGACCTACAGTGCATGATGTTTTCAAAAAGCCTTCGGGAGCTTTTTGAT
66 CTCAGGGTCATCTGTAAGACCTACAGTGCATGATGTTTTCAAAAAGCCTTCGGGAGCTTTTTGAT
* * * * * *
1721400 CTTAAAGCCTCAGGGTCATATGTAAGAACTATAGTGTATGATGTTTTCAAAAAGCCTCCGGGAGG
131 CTTAAAGCCTCAGGGTCATCTGTAAGACCTACAGTGCAGGATGTTTTCAAAAAGCCTCCGGGAGC
* * *
1721465 TTTTTGATCTTAAATCCTCAGGGTCATCTGTAAGACCTGCAGTGCAGGATGTTTTCAAAAAGCCT
196 TTTTTGATCTTAAAACCTCAGGGTCATCTATAAGACCTACAGTGCAGGATGTTTTCAAAAAGCCT
* *
1721530 TCGGAAGGTTTTTGAAGTTTTTAAAGCCTCAGGGT
261 TCGGAAGCTTTTTGAAG-TCTTAAAGCCTCAGGGT
*
1721565 CATCTGTAAGACCTACAGTGCATGATGTTTTCAAAAAGCCTTCGGAATCTTTTTGATCTTAAAGC
1 CATCTGTAAGACCTACAGTGCATGATGTTTTCAAAAAGCCTTCGGAAGCTTTTTGATCTTAAAGC
* * *
1721630 CTCAGGGTCATCTGTAAGACCTACAGTGCATGATGTTTTCAAAAAGCCTCCGAGATCTTTTTGAT
66 CTCAGGGTCATCTGTAAGACCTACAGTGCATGATGTTTTCAAAAAGCCTTCGGGAGCTTTTTGAT
* * * **
1721695 CTTAAATCCTCAGGGTCATCTTTAAGACCTGCAGTGCAGGATGTTTTCAAAAAGCCTTTGGGAGC
131 CTTAAAGCCTCAGGGTCATCTGTAAGACCTACAGTGCAGGATGTTTTCAAAAAGCCTCCGGGAGC
* *
1721760 TTTTTGAAGTTTTTAAAACCTCAGGGTCATCTATAAGACCTACAGTGCATGATGTTTTCAAAAAG
196 TTTTTG-A--TCTTAAAACCTCAGGGTCATCTATAAGACCTACAGTGCAGGATGTTTTCAAAAAG
*
1721825 CCTTCGGGAGCTTTTT-AA-TCTTAAAGCCTCAGGGT
258 CCTTCGGAAGCTTTTTGAAGTCTTAAAGCCTCAGGGT
* *
1721860 CATCTGTAAGACCTACAGTGCATGATGTTTTCAAAAAGCCTTCGGGAGCTTTTTGATTTTAAAGC
1 CATCTGTAAGACCTACAGTGCATGATGTTTTCAAAAAGCCTTCGGAAGCTTTTTGATCTTAAAGC
* * * *
1721925 CTCATGATCATCTGTAAG-CTTACAGTCCATGATGTTTTCAAAAAGCCTTCGGGAGCTTTTTGAT
66 CTCAGGGTCATCTGTAAGACCTACAGTGCATGATGTTTTCAAAAAGCCTTCGGGAGCTTTTTGAT
1721989 CTTAAAGCCTCAGGGTCATCTGTAAGACCTACAGTGCATGG-TGTTTTCAA
131 CTTAAAGCCTCAGGGTCATCTGTAAGACCTACAGTGCA-GGATGTTTTCAA
1722039 CATTTCAATC
Statistics
Matches: 433, Mismatches: 37, Indels: 9
0.90 0.08 0.02
Matches are distributed among these distances:
294 85 0.20
295 281 0.65
296 1 0.00
297 2 0.00
298 64 0.15
ACGTcount: A:0.27, C:0.20, G:0.21, T:0.33
Consensus pattern (294 bp):
CATCTGTAAGACCTACAGTGCATGATGTTTTCAAAAAGCCTTCGGAAGCTTTTTGATCTTAAAGC
CTCAGGGTCATCTGTAAGACCTACAGTGCATGATGTTTTCAAAAAGCCTTCGGGAGCTTTTTGAT
CTTAAAGCCTCAGGGTCATCTGTAAGACCTACAGTGCAGGATGTTTTCAAAAAGCCTCCGGGAGC
TTTTTGATCTTAAAACCTCAGGGTCATCTATAAGACCTACAGTGCAGGATGTTTTCAAAAAGCCT
TCGGAAGCTTTTTGAAGTCTTAAAGCCTCAGGGT
Found at i:1722189 original size:3 final size:3
Alignment explanation
Indices: 1722161--1722209 Score: 66
Period size: 3 Copynumber: 17.0 Consensus size: 3
1722151 TTTCATCTTT
* *
1722161 TTA TTA ATA TTA -TA TT- TTA GTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1722207 TTA
1 TTA
1722210 ATAAATAAAT
Statistics
Matches: 40, Mismatches: 4, Indels: 4
0.83 0.08 0.08
Matches are distributed among these distances:
2 4 0.10
3 36 0.90
ACGTcount: A:0.35, C:0.00, G:0.02, T:0.63
Consensus pattern (3 bp):
TTA
Found at i:1727008 original size:13 final size:14
Alignment explanation
Indices: 1726990--1727022 Score: 50
Period size: 13 Copynumber: 2.4 Consensus size: 14
1726980 GAGTGACGAT
1726990 TATTATATAAT-AA
1 TATTATATAATAAA
*
1727003 TATTATATTATAAA
1 TATTATATAATAAA
1727017 TATTAT
1 TATTAT
1727023 TATTTATAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
13 10 0.56
14 8 0.44
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (14 bp):
TATTATATAATAAA
Found at i:1727032 original size:16 final size:16
Alignment explanation
Indices: 1726988--1727032 Score: 56
Period size: 16 Copynumber: 2.8 Consensus size: 16
1726978 CCGAGTGACG
1726988 ATTA-TTATATAATAAT
1 ATTATTTATA-AATAAT
*
1727004 ATTATATTATAAATATT
1 ATTAT-TTATAAATAAT
1727021 ATTATTTATAAA
1 ATTATTTATAAA
1727033 GCCCGAAGGC
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
16 11 0.42
17 10 0.38
18 5 0.19
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (16 bp):
ATTATTTATAAATAAT
Found at i:1734686 original size:22 final size:22
Alignment explanation
Indices: 1734652--1734709 Score: 80
Period size: 22 Copynumber: 2.6 Consensus size: 22
1734642 TATATCTACA
* *
1734652 TTTTGCAAGGATGATAGATTCTC
1 TTTT-CAAAGATGATAGATTATC
*
1734675 TTTTCAAAGATGATATATTATC
1 TTTTCAAAGATGATAGATTATC
1734697 TTTTCAAAGATGA
1 TTTTCAAAGATGA
1734710 AAGCTTTATT
Statistics
Matches: 32, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
22 28 0.88
23 4 0.12
ACGTcount: A:0.33, C:0.10, G:0.16, T:0.41
Consensus pattern (22 bp):
TTTTCAAAGATGATAGATTATC
Found at i:1735388 original size:83 final size:83
Alignment explanation
Indices: 1735244--1735405 Score: 279
Period size: 83 Copynumber: 2.0 Consensus size: 83
1735234 AGCAAAATCA
* * *
1735244 AAATTTGAACTCCACGAAAGAGTAGTGGAACGGATTTTTCAGTAAAGTATGAAATCTTCACAGAA
1 AAATCTGAACTCCACAAAAGAGTAGTGGAACAGATTTTTCAGTAAAGTATGAAATCTTCACAGAA
1735309 GAGTAATGAAGTAAAAGC
66 GAGTAATGAAGTAAAAGC
*
1735327 AAATCTGAACTCCACAAAAGAGTTGTGGAACAGATTTTTCAGTAAAGTATGAAATCTTCACAGAA
1 AAATCTGAACTCCACAAAAGAGTAGTGGAACAGATTTTTCAGTAAAGTATGAAATCTTCACAGAA
*
1735392 GAGTAGTGAAGTAA
66 GAGTAATGAAGTAA
1735406 TCCAATGGTG
Statistics
Matches: 74, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
83 74 1.00
ACGTcount: A:0.42, C:0.12, G:0.21, T:0.25
Consensus pattern (83 bp):
AAATCTGAACTCCACAAAAGAGTAGTGGAACAGATTTTTCAGTAAAGTATGAAATCTTCACAGAA
GAGTAATGAAGTAAAAGC
Found at i:1735518 original size:83 final size:84
Alignment explanation
Indices: 1735422--1735607 Score: 254
Period size: 83 Copynumber: 2.2 Consensus size: 84
1735412 GGTGAGTATG
* * *
1735422 ATCTTCACGGAAGAGTAGTGAAATTAGATTCTCGTTCATTTTCACGGAA-AAGTAGTGGAATGA-
1 ATCTTCACGGAAGAGTAGTGAAATTAGATTCTCATTCATTTTCACAGAAGAA-TAGTGGAA-CAT
1735485 ATTTTTCAACAAAGTATGA-A
64 ATTTTTCAACAAAGTATGAGA
* * *
1735505 ATCTTCACGGAAGAGTAGTGAAGTTAGATTCTCATTCGTTTTCATAGAAGAATAGTGGAACATAT
1 ATCTTCACGGAAGAGTAGTGAAATTAGATTCTCATTCATTTTCACAGAAGAATAGTGGAACATAT
*
1735570 TTTTCAGCAAAGTATGAGA
66 TTTTCAACAAAGTATGAGA
*
1735589 A-CTTCACGAAAGAGTAGTG
1 ATCTTCACGGAAGAGTAGTG
1735608 GAGTAATCCA
Statistics
Matches: 92, Mismatches: 8, Indels: 6
0.87 0.08 0.06
Matches are distributed among these distances:
82 1 0.01
83 87 0.95
84 4 0.04
ACGTcount: A:0.35, C:0.12, G:0.22, T:0.31
Consensus pattern (84 bp):
ATCTTCACGGAAGAGTAGTGAAATTAGATTCTCATTCATTTTCACAGAAGAATAGTGGAACATAT
TTTTCAACAAAGTATGAGA
Found at i:1736122 original size:13 final size:14
Alignment explanation
Indices: 1736104--1736136 Score: 50
Period size: 13 Copynumber: 2.4 Consensus size: 14
1736094 GAGTGATGAT
1736104 TATTATATAAT-AA
1 TATTATATAATAAA
*
1736117 TATTATATTATAAA
1 TATTATATAATAAA
1736131 TATTAT
1 TATTAT
1736137 TATTTATAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
13 10 0.56
14 8 0.44
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (14 bp):
TATTATATAATAAA
Found at i:1736146 original size:16 final size:16
Alignment explanation
Indices: 1736102--1736146 Score: 56
Period size: 16 Copynumber: 2.8 Consensus size: 16
1736092 TCGAGTGATG
1736102 ATTA-TTATATAATAAT
1 ATTATTTATA-AATAAT
*
1736118 ATTATATTATAAATATT
1 ATTAT-TTATAAATAAT
1736135 ATTATTTATAAA
1 ATTATTTATAAA
1736147 GCCCGAAGGC
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
16 11 0.42
17 10 0.38
18 5 0.19
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (16 bp):
ATTATTTATAAATAAT
Found at i:1736235 original size:21 final size:21
Alignment explanation
Indices: 1736209--1736249 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
1736199 GGTTACAAAG
* *
1736209 CAAGGCACACAGGCCTGATTA
1 CAAGGCACACAAGCCCGATTA
1736230 CAAGGCACACAAGCCCGATT
1 CAAGGCACACAAGCCCGATT
1736250 CAGATTCAAG
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.34, C:0.32, G:0.22, T:0.12
Consensus pattern (21 bp):
CAAGGCACACAAGCCCGATTA
Found at i:1738416 original size:21 final size:21
Alignment explanation
Indices: 1738392--1738431 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
1738382 TAACAAAGGT
* *
1738392 AGTACCGATACTCCCTGTAGG
1 AGTACCAATACTCACTGTAGG
*
1738413 AGTATCAATACTCACTGTA
1 AGTACCAATACTCACTGTA
1738432 CTGGGCATTT
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.30, C:0.25, G:0.17, T:0.28
Consensus pattern (21 bp):
AGTACCAATACTCACTGTAGG
Found at i:1741790 original size:20 final size:20
Alignment explanation
Indices: 1741765--1741802 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
1741755 CTTTACATAG
1741765 TAGTATCGATACCATAAGCT
1 TAGTATCGATACCATAAGCT
*
1741785 TAGTATCGATACCGTAAG
1 TAGTATCGATACCATAAG
1741803 GCCCAACAGC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.34, C:0.18, G:0.18, T:0.29
Consensus pattern (20 bp):
TAGTATCGATACCATAAGCT
Found at i:1744411 original size:18 final size:18
Alignment explanation
Indices: 1744388--1744422 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
1744378 GTTCTTAAGG
*
1744388 AGTGGTCCTTCTGGACAT
1 AGTGGTCCTTCAGGACAT
1744406 AGTGGTCCTTCAGGACA
1 AGTGGTCCTTCAGGACA
1744423 AGTTTAAGAG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.20, C:0.23, G:0.29, T:0.29
Consensus pattern (18 bp):
AGTGGTCCTTCAGGACAT
Found at i:1747853 original size:23 final size:21
Alignment explanation
Indices: 1747818--1747860 Score: 68
Period size: 23 Copynumber: 2.0 Consensus size: 21
1747808 AGCATAGTAT
1747818 AAATAATAAATATAGTTTTTG
1 AAATAATAAATATAGTTTTTG
1747839 AAATATATAATATATAGTTTTT
1 AAATA-ATAA-ATATAGTTTTT
1747861 AAAACAGTTT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
21 5 0.25
22 4 0.20
23 11 0.55
ACGTcount: A:0.47, C:0.00, G:0.07, T:0.47
Consensus pattern (21 bp):
AAATAATAAATATAGTTTTTG
Found at i:1747963 original size:100 final size:100
Alignment explanation
Indices: 1747856--1748057 Score: 289
Period size: 103 Copynumber: 2.0 Consensus size: 100
1747846 TAATATATAG
*
1747856 TTTTTAAAACAGTTTTGAAAACATATAGTATATAGTTTTTTAAAATAATTTTGAAAACG-TATAA
1 TTTTTAAAACAGTTTTGAAAACATATAGTATATAG-TTTTTAAAACAATTTTGAAAACGATATAA
*
1747920 TATAGTTTTTAAAATAATTTTGAAAACGTATATATT
65 TATAGTTTTTAAAACAATTTTGAAAACGTATATATT
* * **
1747956 TTTTTAAAATAGTTTTGAAAACGTATAGTATATAGTTTTTAAAACGGTTTTGAAAACGTATATAT
1 TTTTTAAAACAGTTTTGAAAACATATAGTATATAGTTTTTAAAACAATTTTGAAAACG---ATAT
**
1748021 AATATAGTTTTTAAAACGGTTTTGAAAACGTATATAT
63 AATATAGTTTTTAAAACAATTTTGAAAACGTATATAT
1748058 AATATAGTTT
Statistics
Matches: 90, Mismatches: 8, Indels: 5
0.87 0.08 0.05
Matches are distributed among these distances:
99 20 0.22
100 33 0.37
103 37 0.41
ACGTcount: A:0.41, C:0.04, G:0.11, T:0.43
Consensus pattern (100 bp):
TTTTTAAAACAGTTTTGAAAACATATAGTATATAGTTTTTAAAACAATTTTGAAAACGATATAAT
ATAGTTTTTAAAACAATTTTGAAAACGTATATATT
Found at i:1747973 original size:64 final size:65
Alignment explanation
Indices: 1747850--1748020 Score: 236
Period size: 64 Copynumber: 2.6 Consensus size: 65
1747840 AATATATAAT
*
1747850 ATATAGTTTTTAAAACAGTTTTGAAAACATATAGTATATAGTTTTTTAAAATAATTTTGAAAACG
1 ATATAGTTTTTAAAACAGTTTTGAAAAC-----GTATATATTTTTTTAAAATAATTTTGAAAACG
1747915 TATA-
61 TATAG
* * *
1747919 ATATAGTTTTTAAAATAATTTTGAAAACGTATATATTTTTTTAAAATAGTTTTGAAAACGTATAG
1 ATATAGTTTTTAAAACAGTTTTGAAAACGTATATATTTTTTTAAAATAATTTTGAAAACGTATAG
*
1747984 TATATAGTTTTTAAAACGGTTTTGAAAACGTATATAT
1 -ATATAGTTTTTAAAACAGTTTTGAAAACGTATATAT
1748021 AATATAGTTT
Statistics
Matches: 93, Mismatches: 7, Indels: 7
0.87 0.07 0.07
Matches are distributed among these distances:
64 34 0.37
66 33 0.35
69 26 0.28
ACGTcount: A:0.42, C:0.04, G:0.11, T:0.43
Consensus pattern (65 bp):
ATATAGTTTTTAAAACAGTTTTGAAAACGTATATATTTTTTTAAAATAATTTTGAAAACGTATAG
Found at i:1748026 original size:37 final size:36
Alignment explanation
Indices: 1747841--1748073 Score: 256
Period size: 37 Copynumber: 6.6 Consensus size: 36
1747831 AGTTTTTGAA
1747841 ATATATAATATATAGTTTTTAAAACAGTTTTGAAAAC-
1 ATATAT-A-ATATAGTTTTTAAAACAGTTTTGAAAACG
* *
1747878 ATATAGT-ATATAGTTTTTTAAAATAATTTTGAAAACG
1 ATATA-TAATATAG-TTTTTAAAACAGTTTTGAAAACG
* *
1747915 ---TATAATATAGTTTTTAAAATAATTTTGAAAACG
1 ATATATAATATAGTTTTTAAAACAGTTTTGAAAACG
*
1747948 -TATAT-AT-T--TTTTTAAAATAGTTTTGAAAACG
1 ATATATAATATAGTTTTTAAAACAGTTTTGAAAACG
*
1747979 -TATAGT-ATATAGTTTTTAAAACGGTTTTGAAAACG
1 ATATA-TAATATAGTTTTTAAAACAGTTTTGAAAACG
*
1748014 TATATATAATATAGTTTTTAAAACGGTTTTGAAAACG
1 -ATATATAATATAGTTTTTAAAACAGTTTTGAAAACG
1748051 TATATATAATATAGTTTTTAAAA
1 -ATATATAATATAGTTTTTAAAA
1748074 AATGGTTTTT
Statistics
Matches: 178, Mismatches: 5, Indels: 26
0.85 0.02 0.12
Matches are distributed among these distances:
31 26 0.15
32 3 0.02
33 26 0.15
34 10 0.06
35 30 0.17
36 21 0.12
37 61 0.34
38 1 0.01
ACGTcount: A:0.42, C:0.04, G:0.11, T:0.43
Consensus pattern (36 bp):
ATATATAATATAGTTTTTAAAACAGTTTTGAAAACG
Found at i:1748134 original size:29 final size:29
Alignment explanation
Indices: 1748075--1748143 Score: 77
Period size: 29 Copynumber: 2.3 Consensus size: 29
1748065 TTTTTAAAAA
1748075 ATGGTTTTTAAAAATATATTAATATATTAT
1 ATGGTTTTTAAAAATATATT-ATATATTAT
** *
1748105 ATGGTTTTTGGAAATATAATT-TATGTTAT
1 ATGGTTTTTAAAAATAT-ATTATATATTAT
*
1748134 ATAGTTTTTA
1 ATGGTTTTTA
1748144 TTATTTTTAT
Statistics
Matches: 33, Mismatches: 5, Indels: 3
0.80 0.12 0.07
Matches are distributed among these distances:
29 15 0.45
30 15 0.45
31 3 0.09
ACGTcount: A:0.36, C:0.00, G:0.12, T:0.52
Consensus pattern (29 bp):
ATGGTTTTTAAAAATATATTATATATTAT
Found at i:1748152 original size:9 final size:9
Alignment explanation
Indices: 1748138--1748167 Score: 51
Period size: 9 Copynumber: 3.2 Consensus size: 9
1748128 TGTTATATAG
1748138 TTTTTATTA
1 TTTTTATTA
1748147 TTTTTATTA
1 TTTTTATTA
1748156 TTTATTATTA
1 TTT-TTATTA
1748166 TT
1 TT
1748168 ATTCCATATA
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
9 12 0.60
10 8 0.40
ACGTcount: A:0.23, C:0.00, G:0.00, T:0.77
Consensus pattern (9 bp):
TTTTTATTA
Found at i:1748159 original size:16 final size:16
Alignment explanation
Indices: 1748140--1748201 Score: 54
Period size: 16 Copynumber: 3.8 Consensus size: 16
1748130 TTATATAGTT
1748140 TTTATTATTTTTATTA
1 TTTATTATTTTTATTA
*
1748156 TTTATTATTATTATTCCA
1 TTTATTATTTTTATT--A
* * *
1748174 TATATTAAGTTATATTA
1 TTTATT-ATTTTTATTA
1748191 -TTATTATTTTT
1 TTTATTATTTTT
1748202 TTTTATTAAA
Statistics
Matches: 35, Mismatches: 8, Indels: 7
0.70 0.16 0.14
Matches are distributed among these distances:
15 4 0.11
16 18 0.51
17 1 0.03
18 6 0.17
19 6 0.17
ACGTcount: A:0.29, C:0.03, G:0.02, T:0.66
Consensus pattern (16 bp):
TTTATTATTTTTATTA
Found at i:1748166 original size:13 final size:13
Alignment explanation
Indices: 1748144--1748209 Score: 51
Period size: 13 Copynumber: 4.7 Consensus size: 13
1748134 ATAGTTTTTA
*
1748144 TTATTTTTATTAT
1 TTATTATTATTAT
1748157 TTATTATTATTAT
1 TTATTATTATTAT
*
1748170 TCCATATATTAAGTTAT
1 T-TAT-TATT-A-TTAT
*
1748187 ATTATTATTATTTT
1 -TTATTATTATTAT
*
1748201 TTTTTATTA
1 TTATTATTA
1748210 AATAAATTTT
Statistics
Matches: 43, Mismatches: 5, Indels: 10
0.74 0.09 0.17
Matches are distributed among these distances:
13 21 0.49
14 5 0.12
15 5 0.12
16 5 0.12
17 6 0.14
18 1 0.02
ACGTcount: A:0.29, C:0.03, G:0.02, T:0.67
Consensus pattern (13 bp):
TTATTATTATTAT
Found at i:1749387 original size:18 final size:16
Alignment explanation
Indices: 1749364--1749410 Score: 60
Period size: 16 Copynumber: 2.8 Consensus size: 16
1749354 CAAATTCTTC
1749364 TTTAATATTTTTTTCCAA
1 TTTAATATTTTTTT--AA
1749382 TTTAAT-TATTTTTTAA
1 TTTAATAT-TTTTTTAA
1749398 TTTAATATTTTTT
1 TTTAATATTTTTT
1749411 CCTTTTTTCT
Statistics
Matches: 27, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
16 13 0.48
17 2 0.07
18 12 0.44
ACGTcount: A:0.28, C:0.04, G:0.00, T:0.68
Consensus pattern (16 bp):
TTTAATATTTTTTTAA
Found at i:1749399 original size:16 final size:15
Alignment explanation
Indices: 1749364--1749410 Score: 58
Period size: 18 Copynumber: 2.9 Consensus size: 15
1749354 CAAATTCTTC
1749364 TTTAATATTTTTTTCCAA
1 TTTAATA-TTTTTT--AA
1749382 TTTAATTATTTTTTAA
1 TTTAA-TATTTTTTAA
1749398 TTTAATATTTTTT
1 TTTAATATTTTTT
1749411 CCTTTTTTCT
Statistics
Matches: 28, Mismatches: 0, Indels: 5
0.85 0.00 0.15
Matches are distributed among these distances:
15 8 0.29
16 7 0.25
18 11 0.39
19 2 0.07
ACGTcount: A:0.28, C:0.04, G:0.00, T:0.68
Consensus pattern (15 bp):
TTTAATATTTTTTAA
Found at i:1749438 original size:18 final size:18
Alignment explanation
Indices: 1749403--1749445 Score: 54
Period size: 18 Copynumber: 2.4 Consensus size: 18
1749393 TTTAATTTAA
1749403 TATT-TTTTCCTTTTTTC
1 TATTATTTTCCTTTTTTC
*
1749420 TTTTATTTT-CTTTTATTC
1 TATTATTTTCCTTTT-TTC
1749438 TATTATTT
1 TATTATTT
1749446 AACATTAATT
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
17 8 0.36
18 14 0.64
ACGTcount: A:0.12, C:0.12, G:0.00, T:0.77
Consensus pattern (18 bp):
TATTATTTTCCTTTTTTC
Found at i:1761620 original size:25 final size:23
Alignment explanation
Indices: 1761592--1761637 Score: 74
Period size: 23 Copynumber: 1.9 Consensus size: 23
1761582 ATAGCATAAT
1761592 ATATATAATAAATATAGTTTTTGAA
1 ATATATAAT--ATATAGTTTTTGAA
1761617 ATATATAATATATAGTTTTTG
1 ATATATAATATATAGTTTTTG
1761638 GAAACTTACT
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
23 12 0.57
25 9 0.43
ACGTcount: A:0.43, C:0.00, G:0.09, T:0.48
Consensus pattern (23 bp):
ATATATAATATATAGTTTTTGAA
Found at i:1761702 original size:35 final size:34
Alignment explanation
Indices: 1761624--1761835 Score: 261
Period size: 35 Copynumber: 6.1 Consensus size: 34
1761614 GAAATATATA
* * *
1761624 ATATATAGTTTTTGGAAACTTACTTTTAAAAACGTAT
1 ATATATAGTTTTT--AAA-ATAGTTTTGAAAACGTAT
* *
1761661 AATATATAATTTTTAAAATAGTTTTGAAAACATAT
1 -ATATATAGTTTTTAAAATAGTTTTGAAAACGTAT
*
1761696 AGTATATAGTTTTTTAAAATAATTTTGAAAACGTAT
1 A-TATATAG-TTTTTAAAATAGTTTTGAAAACGTAT
*
1761732 A-ATATAGTTTTTAAAATAATTTTGAAAACGTAT
1 ATATATAGTTTTTAAAATAGTTTTGAAAACGTAT
1761765 ATA-AT--TTTTTAAAATAGTTTTGAAAACGTAT
1 ATATATAGTTTTTAAAATAGTTTTGAAAACGTAT
*
1761796 AGTATATAGTTTTTAAAATAGTTTTGAAAATGTAT
1 A-TATATAGTTTTTAAAATAGTTTTGAAAACGTAT
1761831 ATATA
1 ATATA
1761836 ATATGGTTTT
Statistics
Matches: 157, Mismatches: 10, Indels: 18
0.85 0.05 0.10
Matches are distributed among these distances:
31 26 0.17
32 2 0.01
33 31 0.20
34 12 0.08
35 46 0.29
36 28 0.18
38 12 0.08
ACGTcount: A:0.43, C:0.03, G:0.10, T:0.44
Consensus pattern (34 bp):
ATATATAGTTTTTAAAATAGTTTTGAAAACGTAT
Found at i:1761776 original size:64 final size:65
Alignment explanation
Indices: 1761647--1761833 Score: 250
Period size: 64 Copynumber: 2.8 Consensus size: 65
1761637 GGAAACTTAC
* * *
1761647 TTTTAAAAACGTATAATATATAATTTTTAAAATAGTTTTGAAAACATATAGTATATAGTTTTTTA
1 TTTTGAAAACGTAT-ATATATAGTTTTTAAAATAGTTTTGAAAAC-----GTATATAATTTTTTA
1761712 AAATAA
60 AAATAA
* *
1761718 TTTTGAAAACGTATA-ATATAGTTTTTAAAATAATTTTGAAAACGTATATAATTTTTTAAAATAG
1 TTTTGAAAACGTATATATATAGTTTTTAAAATAGTTTTGAAAACGTATATAATTTTTTAAAATAA
*
1761782 TTTTGAAAACGTATAGTATATAGTTTTTAAAATAGTTTTGAAAATGTATATA
1 TTTTGAAAACGTATA-TATATAGTTTTTAAAATAGTTTTGAAAACGTATATA
1761834 TAATATGGTT
Statistics
Matches: 107, Mismatches: 7, Indels: 9
0.87 0.06 0.07
Matches are distributed among these distances:
64 34 0.32
66 33 0.31
69 26 0.24
70 1 0.01
71 13 0.12
ACGTcount: A:0.44, C:0.03, G:0.10, T:0.44
Consensus pattern (65 bp):
TTTTGAAAACGTATATATATAGTTTTTAAAATAGTTTTGAAAACGTATATAATTTTTTAAAATAA
Found at i:1761939 original size:10 final size:10
Alignment explanation
Indices: 1761917--1761984 Score: 50
Period size: 10 Copynumber: 6.3 Consensus size: 10
1761907 TATATAGTTT
1761917 TTATTATTT-
1 TTATTATTTA
1761926 TTATTATTTA
1 TTATTATTTA
1761936 TTATTATTTCA
1 TTATTATTT-A
*
1761947 TATAGTAGGTTATA
1 T-TATTA--TT-TA
1761961 TTATT-TTTA
1 TTATTATTTA
1761970 TTTAGTTATTTA
1 -TTA-TTATTTA
1761982 TTA
1 TTA
1761985 AATTTTAACA
Statistics
Matches: 48, Mismatches: 2, Indels: 16
0.73 0.03 0.24
Matches are distributed among these distances:
9 11 0.23
10 14 0.29
11 7 0.15
12 8 0.17
13 3 0.06
14 4 0.08
15 1 0.02
ACGTcount: A:0.28, C:0.01, G:0.06, T:0.65
Consensus pattern (10 bp):
TTATTATTTA
Found at i:1763183 original size:6 final size:7
Alignment explanation
Indices: 1763166--1763219 Score: 63
Period size: 7 Copynumber: 7.6 Consensus size: 7
1763156 AATTTAATAT
1763166 TTTTTCA
1 TTTTTCA
1763173 TTTTTCA
1 TTTTTCA
*
1763180 TTTTTCG
1 TTTTTCA
*
1763187 TTTTTCG
1 TTTTTCA
*
1763194 TTTTTCG
1 TTTTTCA
*
1763201 TTTTTCGT
1 TTTTTC-A
1763209 TTTTTCA
1 TTTTTCA
1763216 TTTT
1 TTTT
1763220 AATTTTATTA
Statistics
Matches: 43, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
7 37 0.86
8 6 0.14
ACGTcount: A:0.06, C:0.13, G:0.07, T:0.74
Consensus pattern (7 bp):
TTTTTCA
Found at i:1763192 original size:21 final size:22
Alignment explanation
Indices: 1763165--1763219 Score: 85
Period size: 21 Copynumber: 2.5 Consensus size: 22
1763155 TAATTTAATA
1763165 TTTTTTCATTTTTCATTTTTCG
1 TTTTTTCATTTTTCATTTTTCG
* *
1763187 -TTTTTCGTTTTTCGTTTTTCG
1 TTTTTTCATTTTTCATTTTTCG
1763208 TTTTTTCATTTT
1 TTTTTTCATTTT
1763220 AATTTTATTA
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
21 19 0.66
22 10 0.34
ACGTcount: A:0.05, C:0.13, G:0.07, T:0.75
Consensus pattern (22 bp):
TTTTTTCATTTTTCATTTTTCG
Found at i:1765158 original size:31 final size:30
Alignment explanation
Indices: 1765107--1765174 Score: 100
Period size: 31 Copynumber: 2.2 Consensus size: 30
1765097 CAACAGTTAC
* * *
1765107 GTTGGGGACCATATTGCAAATGGACTAAAT
1 GTTGGGGAACATATTACAAATGAACTAAAT
1765137 GTTGAGGGAACATATTACAAATGAACTAAAT
1 GTTG-GGGAACATATTACAAATGAACTAAAT
1765168 GTTGGGG
1 GTTGGGG
1765175 GATTATATTG
Statistics
Matches: 34, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
30 7 0.21
31 27 0.79
ACGTcount: A:0.35, C:0.10, G:0.28, T:0.26
Consensus pattern (30 bp):
GTTGGGGAACATATTACAAATGAACTAAAT
Found at i:1766892 original size:2 final size:2
Alignment explanation
Indices: 1766885--1766926 Score: 84
Period size: 2 Copynumber: 21.0 Consensus size: 2
1766875 AATAAACAAC
1766885 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1766927 TAGCAGCTCC
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1767125 original size:29 final size:29
Alignment explanation
Indices: 1767092--1767151 Score: 120
Period size: 29 Copynumber: 2.1 Consensus size: 29
1767082 TGAACTTTTC
1767092 TAAAACTTGCAATACAATCCCCCAACATT
1 TAAAACTTGCAATACAATCCCCCAACATT
1767121 TAAAACTTGCAATACAATCCCCCAACATT
1 TAAAACTTGCAATACAATCCCCCAACATT
1767150 TA
1 TA
1767152 GTCCATTTAC
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 31 1.00
ACGTcount: A:0.42, C:0.30, G:0.03, T:0.25
Consensus pattern (29 bp):
TAAAACTTGCAATACAATCCCCCAACATT
Found at i:1767225 original size:31 final size:31
Alignment explanation
Indices: 1767190--1767250 Score: 97
Period size: 31 Copynumber: 2.0 Consensus size: 31
1767180 TTACGTCGAA
1767190 GACCATATTGCAAACAGA-CTAAATGTTGGGG
1 GACCATATTGCAAA-AGAGCTAAATGTTGGGG
*
1767221 GACCATATTGCAAATGAGCTAAATGTTGGG
1 GACCATATTGCAAAAGAGCTAAATGTTGGG
1767251 TGACTGTATT
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
30 2 0.07
31 26 0.93
ACGTcount: A:0.34, C:0.15, G:0.26, T:0.25
Consensus pattern (31 bp):
GACCATATTGCAAAAGAGCTAAATGTTGGGG
Found at i:1768755 original size:17 final size:16
Alignment explanation
Indices: 1768733--1768776 Score: 52
Period size: 16 Copynumber: 2.7 Consensus size: 16
1768723 GAATAAAAAA
*
1768733 TTAAATAAATTATTTGT
1 TTAAATAAATTA-TTAT
*
1768750 TTAAATAAAATATTAT
1 TTAAATAAATTATTAT
*
1768766 TTAAATTAATT
1 TTAAATAAATT
1768777 TTAAACTCTT
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
16 12 0.52
17 11 0.48
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (16 bp):
TTAAATAAATTATTAT
Found at i:1768770 original size:16 final size:17
Alignment explanation
Indices: 1768733--1768771 Score: 53
Period size: 17 Copynumber: 2.4 Consensus size: 17
1768723 GAATAAAAAA
* *
1768733 TTAAATAAATTATTTGT
1 TTAAATAAAATATTTAT
1768750 TTAAATAAAATA-TTAT
1 TTAAATAAAATATTTAT
1768766 TTAAAT
1 TTAAAT
1768772 TAATTTTAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
16 9 0.45
17 11 0.55
ACGTcount: A:0.49, C:0.00, G:0.03, T:0.49
Consensus pattern (17 bp):
TTAAATAAAATATTTAT
Found at i:1768770 original size:29 final size:30
Alignment explanation
Indices: 1768715--1768773 Score: 84
Period size: 29 Copynumber: 2.0 Consensus size: 30
1768705 CTTTTAAAAG
1768715 TTTGTTTAGAATAAAAAATTAAATAAATTA
1 TTTGTTTAGAATAAAAAATTAAATAAATTA
* **
1768745 TTTGTTTA-AATAAAATATTATTTAAATTA
1 TTTGTTTAGAATAAAAAATTAAATAAATTA
1768774 ATTTTAAACT
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
29 18 0.69
30 8 0.31
ACGTcount: A:0.49, C:0.00, G:0.05, T:0.46
Consensus pattern (30 bp):
TTTGTTTAGAATAAAAAATTAAATAAATTA
Found at i:1768978 original size:29 final size:28
Alignment explanation
Indices: 1768945--1769007 Score: 81
Period size: 28 Copynumber: 2.2 Consensus size: 28
1768935 ATAAAATCGG
*
1768945 TTAATTCAGTTCAATTAATAATTTTCAAA
1 TTAATTCAGTTCAATT-ACAATTTTCAAA
**
1768974 TTAATTCAGTTCGGTTACAATTTTCAAA
1 TTAATTCAGTTCAATTACAATTTTCAAA
*
1769002 TAAATT
1 TTAATT
1769008 TCGATTCGAA
Statistics
Matches: 30, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
28 16 0.53
29 14 0.47
ACGTcount: A:0.38, C:0.11, G:0.06, T:0.44
Consensus pattern (28 bp):
TTAATTCAGTTCAATTACAATTTTCAAA
Found at i:1769225 original size:104 final size:105
Alignment explanation
Indices: 1769103--1769330 Score: 318
Period size: 106 Copynumber: 2.2 Consensus size: 105
1769093 CAAATTACCG
*
1769103 AATTTTTGCTTCGATTAATTTGGTTAATAATTTT-AAAAAAAAT-AGTTAATTC-AGTTCGGTTA
1 AATTTTTGCTTCGATTAATTTGGTTAATAATTTTAAAAAAAAATCAGTTAA-TCGAGTTCAGTTA
* * *
1769165 ATAATTTTCATATTGATTGGGTTCGGTTAATAATTTTCAAAT
65 ATAA-TTTCAAATTAATTAGGTTCGGTTAATAATTTTCAAAT
* * *
1769207 AATTTTTGCTTCAATTAATTTGGTTAATAATTTTCAAAAAAAAATCGGTTAATCGGGTTCAGTTA
1 AATTTTTGCTTCGATTAATTTGGTTAATAATTTT-AAAAAAAAATCAGTTAATCGAGTTCAGTTA
*
1769272 ATAATTTCAAATTAATTAGGTTTGGTTAATAATTTTCAAAT
65 ATAATTTCAAATTAATTAGGTTCGGTTAATAATTTTCAAAT
* *
1769313 AAATTTTGGTTCGATTAA
1 AATTTTTGCTTCGATTAA
1769331 CCGAACCGAA
Statistics
Matches: 109, Mismatches: 11, Indels: 6
0.87 0.09 0.05
Matches are distributed among these distances:
104 33 0.30
106 59 0.54
107 17 0.16
ACGTcount: A:0.35, C:0.07, G:0.13, T:0.45
Consensus pattern (105 bp):
AATTTTTGCTTCGATTAATTTGGTTAATAATTTTAAAAAAAAATCAGTTAATCGAGTTCAGTTAA
TAATTTCAAATTAATTAGGTTCGGTTAATAATTTTCAAAT
Done.