Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008018.1 Hibiscus syriacus cultivar Beakdansim tig00110485_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: 927418
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 2 of 5
Found at i:181883 original size:32 final size:32
Alignment explanation
Indices: 181838--181900 Score: 99
Period size: 32 Copynumber: 2.0 Consensus size: 32
181828 TATTAATTGC
* * *
181838 ACCGAATTTGTGCCTTCCATTTTTGACTTGGA
1 ACCGAATTCGTGCCTCCCATTTCTGACTTGGA
181870 ACCGAATTCGTGCCTCCCATTTCTGACTTGG
1 ACCGAATTCGTGCCTCCCATTTCTGACTTGG
181901 CGCCTTAACT
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
32 28 1.00
ACGTcount: A:0.17, C:0.27, G:0.19, T:0.37
Consensus pattern (32 bp):
ACCGAATTCGTGCCTCCCATTTCTGACTTGGA
Found at i:189258 original size:9 final size:9
Alignment explanation
Indices: 189244--189268 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
189234 TACCTTACAT
189244 AATAAAATA
1 AATAAAATA
189253 AATAAAATA
1 AATAAAATA
189262 AATAAAA
1 AATAAAA
189269 ATTATAAAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 16 1.00
ACGTcount: A:0.80, C:0.00, G:0.00, T:0.20
Consensus pattern (9 bp):
AATAAAATA
Found at i:195933 original size:21 final size:21
Alignment explanation
Indices: 195909--195951 Score: 50
Period size: 21 Copynumber: 2.0 Consensus size: 21
195899 ATTATTACTA
* *
195909 TAAAAATATAATATAAAATTT
1 TAAAAACATAATACAAAATTT
* *
195930 TAAATACATATTACAAAATTT
1 TAAAAACATAATACAAAATTT
195951 T
1 T
195952 CGATGAAATA
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.56, C:0.05, G:0.00, T:0.40
Consensus pattern (21 bp):
TAAAAACATAATACAAAATTT
Found at i:199365 original size:31 final size:30
Alignment explanation
Indices: 199306--199365 Score: 77
Period size: 30 Copynumber: 2.0 Consensus size: 30
199296 GATTTAGTTA
* *
199306 GTAACCAAATTATAAGATTTTAAAAGTTTG
1 GTAACCAAAGTATAAGATTTAAAAAGTTTG
199336 GTAACCAAAGTATAA-ACTTTGAAAAAGTTT
1 GTAACCAAAGTATAAGA-TTT-AAAAAGTTT
199366 AGGGACCAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
29 1 0.04
30 17 0.65
31 8 0.31
ACGTcount: A:0.45, C:0.08, G:0.13, T:0.33
Consensus pattern (30 bp):
GTAACCAAAGTATAAGATTTAAAAAGTTTG
Found at i:204998 original size:60 final size:58
Alignment explanation
Indices: 204771--205010 Score: 223
Period size: 60 Copynumber: 4.1 Consensus size: 58
204761 GTAATATAAT
* * * * * *
204771 TATGTGTTTAATTTTAGGTATTAAGATATTGGGAGATTTACATACTTATACCGATGTAAG
1 TATGCGTTTATTTTTAGGTA-CAA-ATATTGAGAGATGTACATACTTACACCGATGTAAG
* * ** * **
204831 CATGCTTTTATTTTTAGGTACTAAGATATTGAGAGATACACATATTTACACAAATGTAA-
1 TATGCGTTTATTTTTAGGTAC-AA-ATATTGAGAGATGTACATACTTACACCGATGTAAG
* * * *
204890 TCATGTGTTTATTTTTAGGTA-TAATATTGAGAGGTGTACATACTTACACCGGTGTAAG
1 T-ATGCGTTTATTTTTAGGTACAAATATTGAGAGATGTACATACTTACACCGATGTAAG
* * *
204948 TATGCGTTTATATTTAGGTAGCAATATATTGAGAGATGTACATATTTACACCGGTGTAAG
1 TATGCGTTTATTTTTAGGTA-CAA-ATATTGAGAGATGTACATACTTACACCGATGTAAG
205008 TAT
1 TAT
205011 ATGTTAATTG
Statistics
Matches: 146, Mismatches: 28, Indels: 12
0.78 0.15 0.06
Matches are distributed among these distances:
57 44 0.30
58 2 0.01
59 1 0.01
60 99 0.68
ACGTcount: A:0.32, C:0.10, G:0.19, T:0.39
Consensus pattern (58 bp):
TATGCGTTTATTTTTAGGTACAAATATTGAGAGATGTACATACTTACACCGATGTAAG
Found at i:205006 original size:117 final size:120
Alignment explanation
Indices: 204750--204998 Score: 317
Period size: 117 Copynumber: 2.1 Consensus size: 120
204740 AAATACAGAA
** * * * *
204750 ACATATTTACAGTAATATAATTATGTGTTTAATTTTAGGTATTAAGATATTGGGAGATTTACATA
1 ACATATTTACACAAATGTAATCATGTGTTTAATTTTAGGTATTAAGATATTGAGAGATGTACATA
* * *
204815 CTTATACCGATGTAAGCATGCTTTTATTTTTAGGTACTAAGATATTGAGAGATAC
66 CTTACACCGATGTAAGCATGCGTTTATATTTAGGTACTAAGATATTGAGAGATAC
* *
204870 ACATATTTACACAAATGTAATCATGTGTTTATTTTTAGGTA-T-A-ATATTGAGAGGTGTACATA
1 ACATATTTACACAAATGTAATCATGTGTTTAATTTTAGGTATTAAGATATTGAGAGATGTACATA
* * * **
204932 CTTACACCGGTGTAAGTATGCGTTTATATTTAGGTAGC-AATATATTGAGAGATGT
66 CTTACACCGATGTAAGCATGCGTTTATATTTAGGTA-CTAAGATATTGAGAGATAC
204987 ACATATTTACAC
1 ACATATTTACAC
204999 CGGTGTAAGT
Statistics
Matches: 112, Mismatches: 16, Indels: 5
0.84 0.12 0.04
Matches are distributed among these distances:
117 73 0.65
118 2 0.02
119 1 0.01
120 36 0.32
ACGTcount: A:0.34, C:0.10, G:0.17, T:0.39
Consensus pattern (120 bp):
ACATATTTACACAAATGTAATCATGTGTTTAATTTTAGGTATTAAGATATTGAGAGATGTACATA
CTTACACCGATGTAAGCATGCGTTTATATTTAGGTACTAAGATATTGAGAGATAC
Found at i:205126 original size:13 final size:13
Alignment explanation
Indices: 205098--205140 Score: 61
Period size: 13 Copynumber: 3.4 Consensus size: 13
205088 AATTAATAAA
*
205098 AAAATATATTAT-
1 AAAATATTTTATG
205110 AAAATATTTTATG
1 AAAATATTTTATG
*
205123 AAAATCTTTTATG
1 AAAATATTTTATG
205136 AAAAT
1 AAAAT
205141 TAATCTTAAC
Statistics
Matches: 28, Mismatches: 2, Indels: 1
0.90 0.06 0.03
Matches are distributed among these distances:
12 11 0.39
13 17 0.61
ACGTcount: A:0.51, C:0.02, G:0.05, T:0.42
Consensus pattern (13 bp):
AAAATATTTTATG
Found at i:210848 original size:15 final size:17
Alignment explanation
Indices: 210818--210851 Score: 54
Period size: 15 Copynumber: 2.1 Consensus size: 17
210808 ACTCATTAAT
210818 AATATTTTTATATATAA
1 AATATTTTTATATATAA
210835 AATA-TTTTAT-TATAA
1 AATATTTTTATATATAA
210850 AA
1 AA
210852 AATATGTTAT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 7 0.41
16 6 0.35
17 4 0.24
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (17 bp):
AATATTTTTATATATAA
Found at i:210853 original size:17 final size:18
Alignment explanation
Indices: 210818--210861 Score: 56
Period size: 17 Copynumber: 2.6 Consensus size: 18
210808 ACTCATTAAT
*
210818 AATATTTT-TATATATAA
1 AATATTTTATATATAAAA
210835 AATATTTTAT-TATAAAA
1 AATATTTTATATATAAAA
*
210852 AATATGTTAT
1 AATATTTTAT
210862 GAAAAATATG
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
17 23 0.96
18 1 0.04
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (18 bp):
AATATTTTATATATAAAA
Found at i:211267 original size:2 final size:2
Alignment explanation
Indices: 211251--211286 Score: 56
Period size: 2 Copynumber: 18.0 Consensus size: 2
211241 GCCAAACAGG
211251 AT AT A- AT AGT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT A-T AT AT AT AT AT AT AT AT AT AT AT AT AT
211287 TCTCAAATAT
Statistics
Matches: 32, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
1 1 0.03
2 29 0.91
3 2 0.06
ACGTcount: A:0.50, C:0.00, G:0.03, T:0.47
Consensus pattern (2 bp):
AT
Found at i:211971 original size:194 final size:196
Alignment explanation
Indices: 211638--212219 Score: 1078
Period size: 194 Copynumber: 3.0 Consensus size: 196
211628 AAGACACATT
211638 TTGCTTCATATGATCTGATTTAAGTTTTTAATTGGTTTGAGCTTAAAATATGTATTTAATATATA
1 TTGCTTCATATGATCTGATTTAAGTTTTTAATTGGTTTGAGCTTAAAATATGTATTT-A-ATATA
211703 TATAATATATTTAATATTTTTGGTTACTTTGATTAGTTACCCGATTTTAAACCGAATTAACCATT
64 TATAATATATTTAATATTTTTGGTTACTTTGATTAGTTACCCGATTTTAAACCGAATTAACCATT
*
211768 AATCGAATATTGAAAAAAATAACTATTCCCCGAATGAATTAATCAAACTAATTCGATCCGGTTGT
129 AATCGAATATTGAAAAAAATAACTATTCCCCGAATGAATTAATCGAACTAATTCGATCCGGTTGT
211833 GTC
194 GTC
211836 TTGCTTCATATGATCTGATTTAAGTTTTTAATTGGTTTGAGCTTAAAATATGTATTTAATATATA
1 TTGCTTCATATGATCTGATTTAAGTTTTTAATTGGTTTGAGCTTAAAATATGTATTTAATATATA
*
211901 T-A-ATATTTAATATTTTTGGTTACTTTGATTAGTTACCCGATTTTAAACCGAATTAACTATTAA
66 TAATATATTTAATATTTTTGGTTACTTTGATTAGTTACCCGATTTTAAACCGAATTAACCATTAA
*
211964 TCGAATATTGAAAAAAATAACTATTCCCCGAATGAATTAATCGAACTAATTCGATCCAGTTGTGT
131 TCGAATATTGAAAAAAATAACTATTCCCCGAATGAATTAATCGAACTAATTCGATCCGGTTGTGT
212029 C
196 C
212030 TTGCTTCATATGATCTGATTTAAGTTTTTAATTGGTTTGAGCTTAAAATATGTATTTAATATATA
1 TTGCTTCATATGATCTGATTTAAGTTTTTAATTGGTTTGAGCTTAAAATATGTATTTAATATATA
*
212095 TAATATATTTAATATTTTTGGTTACTTTGATTAGTTAGCCGATTTTAAACCGAATTAACCATTAA
66 TAATATATTTAATATTTTTGGTTACTTTGATTAGTTACCCGATTTTAAACCGAATTAACCATTAA
* *
212160 TCGAATATTGAAAAAAATAACTATTCCCCAAATGCATTAATCGAACTAATTCGATCCGGT
131 TCGAATATTGAAAAAAATAACTATTCCCCGAATGAATTAATCGAACTAATTCGATCCGGT
212220 CGATTAATTC
Statistics
Matches: 374, Mismatches: 8, Indels: 6
0.96 0.02 0.02
Matches are distributed among these distances:
194 190 0.51
195 2 0.01
196 124 0.33
197 1 0.00
198 57 0.15
ACGTcount: A:0.34, C:0.12, G:0.12, T:0.41
Consensus pattern (196 bp):
TTGCTTCATATGATCTGATTTAAGTTTTTAATTGGTTTGAGCTTAAAATATGTATTTAATATATA
TAATATATTTAATATTTTTGGTTACTTTGATTAGTTACCCGATTTTAAACCGAATTAACCATTAA
TCGAATATTGAAAAAAATAACTATTCCCCGAATGAATTAATCGAACTAATTCGATCCGGTTGTGT
C
Found at i:212772 original size:76 final size:76
Alignment explanation
Indices: 212646--212807 Score: 272
Period size: 76 Copynumber: 2.1 Consensus size: 76
212636 TGTGTCTTCA
* *
212646 ACGTGGGGACCAGCTTTGTTATGTTTGGTAGCAGGAAGTTTGTAGCAAAATAAGGAATTCATGGG
1 ACGTGGGGACCAGCTTTGTTATGTTTGGTAGCAGGAAGTTTGCAGCAAAATAAGGAAATCATGGG
212711 AAGAATAATGC
66 AAGAATAATGC
* *
212722 ACGTGGGGACCAGCTTTGTTATGTTTGGTAGCATGATA-TTTGCAGGAAAATAAGGAAATCATGG
1 ACGTGGGGACCAGCTTTGTTATGTTTGGTAGCAGGA-AGTTTGCAGCAAAATAAGGAAATCATGG
212786 GAAGAATAATGC
65 GAAGAATAATGC
212798 ACGTGGGGAC
1 ACGTGGGGAC
212808 GGGAATGAGA
Statistics
Matches: 81, Mismatches: 4, Indels: 2
0.93 0.05 0.02
Matches are distributed among these distances:
76 80 0.99
77 1 0.01
ACGTcount: A:0.31, C:0.11, G:0.31, T:0.27
Consensus pattern (76 bp):
ACGTGGGGACCAGCTTTGTTATGTTTGGTAGCAGGAAGTTTGCAGCAAAATAAGGAAATCATGGG
AAGAATAATGC
Found at i:215568 original size:28 final size:27
Alignment explanation
Indices: 215530--215885 Score: 152
Period size: 28 Copynumber: 12.7 Consensus size: 27
215520 ATTACTATTA
* *
215530 TTAAATTATTAAACTTTAATCATTAAAG
1 TTAAATAATTAAA-TTAAATCATTAAAG
215558 TTAAATAATTATTAA-TAAATCATTAAAG
1 TTAAATAATTA--AATTAAATCATTAAAG
* * * * * *
215586 TTTAATTATTAAAGTGAATTAATTATTA-
1 TTAAATAATTAAA-TTAAATCATTA-AAG
* *
215614 TTAAATCATTAAAGTTAAATAATTATTAA-
1 TTAAATAATTAAA-TTAAATCATTA--AAG
* *
215643 -TAAATCATTAAAGTTAAATTATTAAAG
1 TTAAATAATTAAA-TTAAATCATTAAAG
* * *
215670 TGAAGTAATTATTATTAAATCATTAAAG
1 TTAAATAATTA-AATTAAATCATTAAAG
* * * *
215698 TTAAATCATTAAAGTTAAGTAATTATTA-
1 TTAAATAATTAAA-TTAAATCATTA-AAG
* *
215726 TTAAAGTATTTAATTTAAATCATTAAAG
1 TTAAA-TAATTAAATTAAATCATTAAAG
* * *
215754 TTAAATAATTATTATTAAAGT-ATTTAAT
1 TTAAATAATTA-AATTAAA-TCATTAAAG
* * *
215782 TTAAATCATTAAAGTTAAATAATTATTA-
1 TTAAATAATTAAA-TTAAATCATTA-AAG
* * * *
215810 TGAAATCATTAAAGTTAAATAATTATTA-
1 TTAAATAATTAAA-TTAAATCATTA-AAG
* * *
215838 TTAAATCATTAAATTTAAATGATTAAAT
1 TTAAATAATTAAA-TTAAATCATTAAAG
*
215866 TTAAATAATTATTATTAAAT
1 TTAAATAATTA-AATTAAAT
215886 ATATACTCGA
Statistics
Matches: 260, Mismatches: 48, Indels: 40
0.75 0.14 0.11
Matches are distributed among these distances:
26 4 0.02
27 10 0.04
28 231 0.89
29 13 0.05
30 2 0.01
ACGTcount: A:0.49, C:0.03, G:0.05, T:0.43
Consensus pattern (27 bp):
TTAAATAATTAAATTAAATCATTAAAG
Found at i:215627 original size:42 final size:42
Alignment explanation
Indices: 215525--215638 Score: 156
Period size: 42 Copynumber: 2.7 Consensus size: 42
215515 ATATCATTAC
* * * *
215525 TATTATTAAATTATTAAACTTTAATCATTAAAGTTAAATAAT
1 TATTATTAAATCATTAAAGTTTAATAATTAAAGTGAAATAAT
* * *
215567 TATTAATAAATCATTAAAGTTTAATTATTAAAGTGAATTAAT
1 TATTATTAAATCATTAAAGTTTAATAATTAAAGTGAAATAAT
*
215609 TATTATTAAATCATTAAAGTTAAATAATTA
1 TATTATTAAATCATTAAAGTTTAATAATTA
215639 TTAATAAATC
Statistics
Matches: 63, Mismatches: 9, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
42 63 1.00
ACGTcount: A:0.48, C:0.04, G:0.04, T:0.44
Consensus pattern (42 bp):
TATTATTAAATCATTAAAGTTTAATAATTAAAGTGAAATAAT
Found at i:215633 original size:70 final size:70
Alignment explanation
Indices: 215547--215708 Score: 297
Period size: 70 Copynumber: 2.3 Consensus size: 70
215537 ATTAAACTTT
* *
215547 AATCATTAAAGTTAAATAATTATTAATAAATCATTAAAGTTTAATTATTAAAGTGAATTAATTAT
1 AATCATTAAAGTTAAATAATTATTAATAAATCATTAAAGTTAAATTATTAAAGTGAAGTAATTAT
215612 TATTA
66 TATTA
215617 AATCATTAAAGTTAAATAATTATTAATAAATCATTAAAGTTAAATTATTAAAGTGAAGTAATTAT
1 AATCATTAAAGTTAAATAATTATTAATAAATCATTAAAGTTAAATTATTAAAGTGAAGTAATTAT
215682 TATTA
66 TATTA
*
215687 AATCATTAAAGTTAAATCATTA
1 AATCATTAAAGTTAAATAATTA
215709 AAGTTAAGTA
Statistics
Matches: 89, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
70 89 1.00
ACGTcount: A:0.49, C:0.04, G:0.06, T:0.41
Consensus pattern (70 bp):
AATCATTAAAGTTAAATAATTATTAATAAATCATTAAAGTTAAATTATTAAAGTGAAGTAATTAT
TATTA
Found at i:215647 original size:84 final size:82
Alignment explanation
Indices: 215525--215809 Score: 201
Period size: 84 Copynumber: 3.4 Consensus size: 82
215515 ATATCATTAC
* * * *
215525 TATTATTAAATTATTAAACTTTAATCATTA--AAGTTAAATAATTATTAATAAATCATTAAAGTT
1 TATTATTAAATCATTAAAGTTAAATAATTATTAA--TAAATAATTATTAATAAATCATTAAAGTT
* *
215588 TAATTATTAAAGTGAATTAAT
64 TAATTATT-AA-TAAAATAAT
* *
215609 TATTATTAAATCATTAAAGTTAAATAATTATTAATAAATCATTA--AAGTTAAATTATTAAAGTG
1 TATTATTAAATCATTAAAGTTAAATAATTATTAATAAATAATTATTAA--TAAATCATTAAAGT-
* * *
215672 AAGTAATTATT-ATTAAATCAT
63 --TTAATTATTAATAAAATAAT
* * * *
215693 TA-AAGTTAAATCATTAAAGTTAAGTAATTATTATTAAAGTATTTAATT--TAAATCATTAAAGT
1 TATTA-TTAAATCATTAAAGTTAAATAATTATTAATAAA-TAATT-ATTAATAAATCATTAAAGT
* * *
215755 TAAATAATTATTATTAAAGTATT
63 T---TAATTATTAATAAAATAAT
*
215778 TAAT-TTAAATCATTAAAGTTAAATAATTATTA
1 TATTATTAAATCATTAAAGTTAAATAATTATTA
215810 TGAAATCATT
Statistics
Matches: 160, Mismatches: 24, Indels: 34
0.73 0.11 0.16
Matches are distributed among these distances:
82 2 0.01
83 1 0.01
84 135 0.84
85 11 0.07
86 3 0.02
87 8 0.05
ACGTcount: A:0.48, C:0.03, G:0.06, T:0.43
Consensus pattern (82 bp):
TATTATTAAATCATTAAAGTTAAATAATTATTAATAAATAATTATTAATAAATCATTAAAGTTTA
ATTATTAATAAAATAAT
Found at i:215843 original size:42 final size:42
Alignment explanation
Indices: 215614--215834 Score: 311
Period size: 42 Copynumber: 5.3 Consensus size: 42
215604 TTAATTATTA
*
215614 TTAAATCATTAAAGTTAAATAATTATTAATAAATCATTAAAG
1 TTAAATCATTAAAGTTAAATAATTATTATTAAATCATTAAAG
* * *
215656 TTAAATTATTAAAGTGAAGTAATTATTATTAAATCATTAAAG
1 TTAAATCATTAAAGTTAAATAATTATTATTAAATCATTAAAG
* * *
215698 TTAAATCATTAAAGTTAAGTAATTATTATTAAAGT-ATTTAAT
1 TTAAATCATTAAAGTTAAATAATTATTATTAAA-TCATTAAAG
* *
215740 TTAAATCATTAAAGTTAAATAATTATTATTAAAGT-ATTTAAT
1 TTAAATCATTAAAGTTAAATAATTATTATTAAA-TCATTAAAG
*
215782 TTAAATCATTAAAGTTAAATAATTATTATGAAATCATTAAAG
1 TTAAATCATTAAAGTTAAATAATTATTATTAAATCATTAAAG
*
215824 TTAAATAATTA
1 TTAAATCATTA
215835 TTATTAAATC
Statistics
Matches: 164, Mismatches: 13, Indels: 4
0.91 0.07 0.02
Matches are distributed among these distances:
41 1 0.01
42 162 0.99
43 1 0.01
ACGTcount: A:0.49, C:0.03, G:0.06, T:0.42
Consensus pattern (42 bp):
TTAAATCATTAAAGTTAAATAATTATTATTAAATCATTAAAG
Found at i:215850 original size:8 final size:7
Alignment explanation
Indices: 215724--215887 Score: 62
Period size: 6 Copynumber: 23.4 Consensus size: 7
215714 AAGTAATTAT
215724 TATTAAA
1 TATTAAA
*
215731 GTATTTAA
1 -TATTAAA
215739 T-TTAAA
1 TATTAAA
215745 TCATTAAA
1 T-ATTAAA
*
215753 -GTTAAA
1 TATTAAA
*
215759 TAATT-AT
1 T-ATTAAA
215766 TATTAAA
1 TATTAAA
*
215773 GTATTTAA
1 -TATTAAA
215781 T-TTAAA
1 TATTAAA
215787 TCATTAAA
1 T-ATTAAA
*
215795 -GTTAAA
1 TATTAAA
*
215801 TAATT-AT
1 T-ATTAAA
*
215808 TATGAAA
1 TATTAAA
215815 TCATTAAA
1 T-ATTAAA
*
215823 -GTTAAA
1 TATTAAA
*
215829 TAATT-AT
1 T-ATTAAA
215836 TATTAAA
1 TATTAAA
215843 TCATTAAA
1 T-ATTAAA
215851 T-TTAAA
1 TATTAAA
215857 TGATTAAA
1 T-ATTAAA
215865 T-TTAAA
1 TATTAAA
*
215871 TAATT-AT
1 T-ATTAAA
215878 TATTAAA
1 TATTAAA
215885 TAT
1 TAT
215888 ATACTCGAGT
Statistics
Matches: 115, Mismatches: 20, Indels: 43
0.65 0.11 0.24
Matches are distributed among these distances:
6 48 0.42
7 19 0.17
8 48 0.42
ACGTcount: A:0.49, C:0.02, G:0.04, T:0.45
Consensus pattern (7 bp):
TATTAAA
Found at i:223602 original size:3 final size:3
Alignment explanation
Indices: 223596--223659 Score: 78
Period size: 3 Copynumber: 21.0 Consensus size: 3
223586 TTAGTTTTTT
*
223596 TTA TTA TTA TTTA TTA TTA TTA TTA TTA ATA TTA TTA TTA TTTA TTA
1 TTA TTA TTA -TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA -TTA TTA
223643 TTAA TT- TTA TTA -TA TTA
1 TT-A TTA TTA TTA TTA TTA
223660 CAGGCCCAAT
Statistics
Matches: 54, Mismatches: 2, Indels: 10
0.82 0.03 0.15
Matches are distributed among these distances:
2 4 0.07
3 41 0.76
4 9 0.17
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
TTA
Found at i:223634 original size:31 final size:30
Alignment explanation
Indices: 223596--223659 Score: 103
Period size: 31 Copynumber: 2.1 Consensus size: 30
223586 TTAGTTTTTT
223596 TTATTATTATTTATTATT-ATTATTATTAATA
1 TTATTATTATTTATTATTAATT-TTATT-ATA
223627 TTATTATTATTTATTATTAATTTTATTATA
1 TTATTATTATTTATTATTAATTTTATTATA
223657 TTA
1 TTA
223660 CAGGCCCAAT
Statistics
Matches: 32, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
30 6 0.19
31 23 0.72
32 3 0.09
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (30 bp):
TTATTATTATTTATTATTAATTTTATTATA
Found at i:225469 original size:26 final size:27
Alignment explanation
Indices: 225416--225469 Score: 83
Period size: 27 Copynumber: 2.0 Consensus size: 27
225406 ATATTTCTAA
225416 ATAAATAAATATTTTATTTATAAATAT
1 ATAAATAAATATTTTATTTATAAATAT
* *
225443 ATAAATTAATATTTT-TTTATAATTAT
1 ATAAATAAATATTTTATTTATAAATAT
225469 A
1 A
225470 ATTTTGAAAT
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
26 11 0.44
27 14 0.56
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (27 bp):
ATAAATAAATATTTTATTTATAAATAT
Found at i:230670 original size:2 final size:2
Alignment explanation
Indices: 230663--230692 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
230653 TTATCCTTTA
230663 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
230693 CTTTTGTTGT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:231035 original size:18 final size:18
Alignment explanation
Indices: 230986--231029 Score: 52
Period size: 18 Copynumber: 2.4 Consensus size: 18
230976 CTCATCCAGC
* * *
230986 AAAGAAAGAAGAAGGAAA
1 AAAGAAAAAAAAAAGAAA
231004 AAAGAAAAAAAAAAGAAA
1 AAAGAAAAAAAAAAGAAA
*
231022 AAGGAAAA
1 AAAGAAAA
231030 GGAAAATTAA
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.80, C:0.00, G:0.20, T:0.00
Consensus pattern (18 bp):
AAAGAAAAAAAAAAGAAA
Found at i:235051 original size:24 final size:24
Alignment explanation
Indices: 235007--235056 Score: 66
Period size: 24 Copynumber: 2.1 Consensus size: 24
234997 ATAAAGAACC
*
235007 AAAATAAACTTAAATATACCATTA
1 AAAATAAACTTAAACATACCATTA
*
235031 AAAATAAAGTTTAAACA-ACCATTA
1 AAAATAAA-CTTAAACATACCATTA
235055 AA
1 AA
235057 TCAACCACCA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
24 17 0.74
25 6 0.26
ACGTcount: A:0.60, C:0.12, G:0.02, T:0.26
Consensus pattern (24 bp):
AAAATAAACTTAAACATACCATTA
Found at i:245333 original size:24 final size:24
Alignment explanation
Indices: 245289--245338 Score: 66
Period size: 24 Copynumber: 2.1 Consensus size: 24
245279 ATAAGGAACC
*
245289 AAAATAAACTTAAATATACCATTA
1 AAAATAAACTTAAACATACCATTA
*
245313 AAAATAAAGTTTAAACA-ACCATTA
1 AAAATAAA-CTTAAACATACCATTA
245337 AA
1 AA
245339 TCAACCACCA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
24 17 0.74
25 6 0.26
ACGTcount: A:0.60, C:0.12, G:0.02, T:0.26
Consensus pattern (24 bp):
AAAATAAACTTAAACATACCATTA
Found at i:247349 original size:54 final size:54
Alignment explanation
Indices: 247267--247428 Score: 270
Period size: 54 Copynumber: 3.0 Consensus size: 54
247257 CAATGATTGA
*
247267 GAACATCTGAGCAGAAACCACAGGAAATGATGAATGTGTTGTCAAATGTTTTAC
1 GAACATCTGAGCAGAAGCCACAGGAAATGATGAATGTGTTGTCAAATGTTTTAC
*
247321 GAACATCTGAGCAGAAGCCACAGGAAATGATGAATGTGTTGTCAAATGTTTTAT
1 GAACATCTGAGCAGAAGCCACAGGAAATGATGAATGTGTTGTCAAATGTTTTAC
* * **
247375 GAACATCTGAGCAGAAGCCACAGGAAAGGATGAATGCGCCGTCAAATGTTTTAC
1 GAACATCTGAGCAGAAGCCACAGGAAATGATGAATGTGTTGTCAAATGTTTTAC
247429 AAACCTGCTA
Statistics
Matches: 101, Mismatches: 7, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
54 101 1.00
ACGTcount: A:0.36, C:0.16, G:0.24, T:0.24
Consensus pattern (54 bp):
GAACATCTGAGCAGAAGCCACAGGAAATGATGAATGTGTTGTCAAATGTTTTAC
Found at i:247823 original size:22 final size:22
Alignment explanation
Indices: 247792--247846 Score: 74
Period size: 22 Copynumber: 2.5 Consensus size: 22
247782 ATCTACACTC
*
247792 TTCAAAGATGATAGATTCCCTT
1 TTCAAAGATGACAGATTCCCTT
* *
247814 TTTAAAGATGACAGATTCTCTT
1 TTCAAAGATGACAGATTCCCTT
*
247836 TTCAAAAATGA
1 TTCAAAGATGA
247847 AAGCTTTATC
Statistics
Matches: 28, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 28 1.00
ACGTcount: A:0.36, C:0.15, G:0.13, T:0.36
Consensus pattern (22 bp):
TTCAAAGATGACAGATTCCCTT
Found at i:248439 original size:113 final size:113
Alignment explanation
Indices: 248241--249145 Score: 1460
Period size: 113 Copynumber: 8.0 Consensus size: 113
248231 TTTAGAAAAG
* *
248241 TTGAATTCATTATTCGATGGATTAACATTACCAGGTCAAGTTCATAATGAGAAGAACTCATCTGA
1 TTGAATTCATCATTCGATGGATCAACATTACCAGGTCAAGTTCATAATGAGAAGAACTCATCTGA
248306 AGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACTTTTCGC
66 AGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACTTTTCGC
*
248354 TTGAATTCATCATTCGATGGATCAGCATTACCAGGTCAAGTTCATAATGAGAAGAACTCATCTGA
1 TTGAATTCATCATTCGATGGATCAACATTACCAGGTCAAGTTCATAATGAGAAGAACTCATCTGA
*
248419 AGAAGGAATAAGAAGTTCATAATGAGAAGAACTTGTTCAACTTTTCGC
66 AGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACTTTTCGC
*
248467 TTGAATTCATCATTCGATGGATCAGCATTACCAGGTCAAGTTCATAATGAGAAGAACTCATCTGA
1 TTGAATTCATCATTCGATGGATCAACATTACCAGGTCAAGTTCATAATGAGAAGAACTCATCTGA
248532 AGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACTTTTCGC
66 AGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACTTTTCGC
*
248580 TTGAATTCATCATTTGATGGATCAACATTACCAGGTCAAGTTCATAATGAGAAGAACTCATCTGA
1 TTGAATTCATCATTCGATGGATCAACATTACCAGGTCAAGTTCATAATGAGAAGAACTCATCTGA
248645 AGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACTTTTCGC
66 AGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACTTTTCGC
*
248693 TTGAATTCATCATTCGATGGATCAGCATTACCAGGTCAAGTTCATAATGAGAAGAACTCATCTGA
1 TTGAATTCATCATTCGATGGATCAACATTACCAGGTCAAGTTCATAATGAGAAGAACTCATCTGA
248758 AGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACTTTTCGC
66 AGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACTTTTCGC
* *
248806 TTGAATTCATCATTCGATGGATCAGCATTACCAGGTCAAGTTCATATTGAGAAGAACTCATCTGA
1 TTGAATTCATCATTCGATGGATCAACATTACCAGGTCAAGTTCATAATGAGAAGAACTCATCTGA
* * * *
248871 AGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTATTCAACCTTTTTGT
66 AGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAA-CTTTTCGC
*
248920 TTGAATTCATCATTTGATGGATCAACATTACCAGGT-AGAGTTCATAATGAGAAGAACTCGTCAT
1 TTGAATTCATCATTCGATGGATCAACATTACCAGGTCA-AGTTCATAATGAGAAGAA--C-TCAT
* * *
248984 CTGAAGAAGAAAGAAGAAATTCATAATGAGAAGAATTTGTTCAACCTTTT-GC
62 CTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAA-CTTTTCGC
** * * * * * *
249036 TCAAATCCATCACTT-GATGGATCAACTTTTCCAGAG-AAAATTCATAATGAGAAGAACTTATCT
1 TTGAATTCATCA-TTCGATGGATCAACATTACCAG-GTCAAGTTCATAATGAGAAGAACTCATCT
*
249099 GAAGAA-GAAGAAGAAGTTCATAATGAGAAGAGCTTGTTCAACCTTTT
64 GAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAA-CTTTT
249146 GCATAACTCT
Statistics
Matches: 752, Mismatches: 32, Indels: 17
0.94 0.04 0.02
Matches are distributed among these distances:
112 37 0.05
113 557 0.74
114 58 0.08
116 45 0.06
117 55 0.07
ACGTcount: A:0.37, C:0.15, G:0.19, T:0.29
Consensus pattern (113 bp):
TTGAATTCATCATTCGATGGATCAACATTACCAGGTCAAGTTCATAATGAGAAGAACTCATCTGA
AGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACTTTTCGC
Found at i:249249 original size:17 final size:17
Alignment explanation
Indices: 249191--249250 Score: 50
Period size: 17 Copynumber: 3.4 Consensus size: 17
249181 CAGCATTTCC
* *
249191 AGAAGGAGTTCATAATG
1 AGAAGAAGTTCATAAGG
* *
249208 AGAAGAA-CTCATCTGAAGA
1 AGAAGAAGTTCA--T-AAGG
249227 AGAAGAAGTTCATAAGG
1 AGAAGAAGTTCATAAGG
249244 AGAAGAA
1 AGAAGAA
249251 TTTGTTCAAC
Statistics
Matches: 33, Mismatches: 6, Indels: 8
0.70 0.13 0.17
Matches are distributed among these distances:
16 3 0.09
17 16 0.48
18 2 0.06
19 9 0.27
20 3 0.09
ACGTcount: A:0.48, C:0.08, G:0.27, T:0.17
Consensus pattern (17 bp):
AGAAGAAGTTCATAAGG
Found at i:249301 original size:120 final size:121
Alignment explanation
Indices: 249076--249294 Score: 318
Period size: 120 Copynumber: 1.8 Consensus size: 121
249066 CCAGAGAAAA
* * *
249076 TTCATAATGAGAAGAACTTATCTGAAGAAGAAGAAGAAGTTCATAATGAGAAGAGCTTGTTCAAC
1 TTCATAATGAGAAGAACTCATCT--AGAAGAAGAAGAAGTTCATAAGGAGAAGAACTTGTTCAAC
*
249141 CTTTTGCATAACTCTATCACAGAAGGAGATATATCATCATCAGCATTTCCAGAAGGAG
64 CTTTTGCATAACTCTATCACAGAAGGAGATAAATCATCATCAGCATTTCCAGAAGGAG
* *
249199 TTCATAATGAGAAGAACTCATCT-GAAGAAGAAGAAGTTCATAAGGAGAAGAATTTGTTCAACTT
1 TTCATAATGAGAAGAACTCATCTAGAAGAAGAAGAAGTTCATAAGGAGAAGAACTTGTTCAACCT
*
249263 TTTGC-TAGATTAC-ATCACAGAAGGAGATAAAT
66 TTTGCATA-ACT-CTATCACAGAAGGAGATAAAT
249295 TGTCATCCCT
Statistics
Matches: 87, Mismatches: 7, Indels: 7
0.86 0.07 0.07
Matches are distributed among these distances:
119 2 0.02
120 62 0.71
121 1 0.01
123 22 0.25
ACGTcount: A:0.40, C:0.14, G:0.20, T:0.26
Consensus pattern (121 bp):
TTCATAATGAGAAGAACTCATCTAGAAGAAGAAGAAGTTCATAAGGAGAAGAACTTGTTCAACCT
TTTGCATAACTCTATCACAGAAGGAGATAAATCATCATCAGCATTTCCAGAAGGAG
Found at i:249488 original size:3 final size:3
Alignment explanation
Indices: 249482--249535 Score: 67
Period size: 3 Copynumber: 18.0 Consensus size: 3
249472 TTTTGGTTTT
*
249482 TTA TTA TTA TTA TTA TTA TTA ATA TTA TTA TTTA TTA TTAA TT- TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA -TTA TTA TT-A TTA TTA
249528 TTA -TA TTA
1 TTA TTA TTA
249536 CAGGCCCAAT
Statistics
Matches: 45, Mismatches: 2, Indels: 8
0.82 0.04 0.15
Matches are distributed among these distances:
2 4 0.09
3 35 0.78
4 6 0.13
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (3 bp):
TTA
Found at i:251217 original size:20 final size:19
Alignment explanation
Indices: 251192--251233 Score: 57
Period size: 20 Copynumber: 2.2 Consensus size: 19
251182 CTATTTTATA
251192 AATTATATATTAATTGTTTT
1 AATTATATATTAATT-TTTT
* *
251212 AATTATTTATTTATTTTTT
1 AATTATATATTAATTTTTT
251231 AAT
1 AAT
251234 ATCGAAGAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
19 7 0.35
20 13 0.65
ACGTcount: A:0.33, C:0.00, G:0.02, T:0.64
Consensus pattern (19 bp):
AATTATATATTAATTTTTT
Found at i:251229 original size:119 final size:119
Alignment explanation
Indices: 251088--251325 Score: 293
Period size: 120 Copynumber: 2.0 Consensus size: 119
251078 ATTTTAATCC
* * * *
251088 TGTTTTAATATTTATTTATTTTTCAATAT-TAAGAAAGGA-CAGTCTTAAAACAACTGGATGTCC
1 TGTTTTAATATTTATTTATTTTTCAATATCGAAGAAAAGAGCAGTCTTAAAACAACTAGAAGT-C
* * *
251151 ATTTTTTGATATTTTTAAATAAATAAATATCCTATTTTATAAAT-TATATATTAAT
65 ATTTTCTGATATTTCTAAATAAATAAATATCCTA-TTTATAAATATATAAATTAAT
* * *** *
251206 TGTTTTAATTATTTATTTATTTTTTAATATCGAAGAAAAGAGCTGTCTTAAGGTATCTAGAAGTC
1 TGTTTTAA-TATTTATTTATTTTTCAATATCGAAGAAAAGAGCAGTCTTAAAACAACTAGAAGTC
**
251271 ATTTTCTGATATTTCTAAATAAATAAATATTTTATTTATAAATATATAAATTAAT
65 ATTTTCTGATATTTCTAAATAAATAAATATCCTATTTATAAATATATAAATTAAT
251326 ATTTTTTTAT
Statistics
Matches: 101, Mismatches: 15, Indels: 6
0.83 0.12 0.05
Matches are distributed among these distances:
118 8 0.08
119 29 0.29
120 49 0.49
121 15 0.15
ACGTcount: A:0.38, C:0.07, G:0.08, T:0.47
Consensus pattern (119 bp):
TGTTTTAATATTTATTTATTTTTCAATATCGAAGAAAAGAGCAGTCTTAAAACAACTAGAAGTCA
TTTTCTGATATTTCTAAATAAATAAATATCCTATTTATAAATATATAAATTAAT
Found at i:251342 original size:26 final size:27
Alignment explanation
Indices: 251289--251342 Score: 83
Period size: 27 Copynumber: 2.0 Consensus size: 27
251279 ATATTTCTAA
251289 ATAAATAAATATTTTATTTATAAATAT
1 ATAAATAAATATTTTATTTATAAATAT
* *
251316 ATAAATTAATATTTT-TTTATAATTAT
1 ATAAATAAATATTTTATTTATAAATAT
251342 A
1 A
251343 ATTTTGAAAT
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
26 11 0.44
27 14 0.56
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (27 bp):
ATAAATAAATATTTTATTTATAAATAT
Found at i:256005 original size:35 final size:36
Alignment explanation
Indices: 255952--256020 Score: 95
Period size: 35 Copynumber: 1.9 Consensus size: 36
255942 TAGCGGCACA
* * *
255952 ATTTCTTGTGGGATTGATT-ATTGTCATTTTCGTCC
1 ATTTCTTGTGGGACTGATTAATTGCCAATTTCGTCC
*
255987 ATTTCTTGTGGGCCTGATTAATTGCCAATTTCGT
1 ATTTCTTGTGGGACTGATTAATTGCCAATTTCGT
256021 TTTTGAGTAT
Statistics
Matches: 29, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
35 17 0.59
36 12 0.41
ACGTcount: A:0.16, C:0.16, G:0.20, T:0.48
Consensus pattern (36 bp):
ATTTCTTGTGGGACTGATTAATTGCCAATTTCGTCC
Found at i:260427 original size:18 final size:17
Alignment explanation
Indices: 260388--260435 Score: 53
Period size: 18 Copynumber: 2.7 Consensus size: 17
260378 GGTAAATCAG
260388 GTTTTTGTAATTCTGGA
1 GTTTTTGTAATTCTGGA
*
260405 ATTTTTGGTAATTC-GAGA
1 GTTTTT-GTAATTCTG-GA
260423 GTTTTGTGTAATT
1 GTTTT-TGTAATT
260436 TTGGTTTTGG
Statistics
Matches: 26, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
17 6 0.23
18 19 0.73
19 1 0.04
ACGTcount: A:0.21, C:0.04, G:0.23, T:0.52
Consensus pattern (17 bp):
GTTTTTGTAATTCTGGA
Found at i:260787 original size:75 final size:75
Alignment explanation
Indices: 260664--260808 Score: 229
Period size: 75 Copynumber: 1.9 Consensus size: 75
260654 CTCATCAGGC
* *
260664 TTTGGTAATTCAGGAACTTCAGGCTTTGACAATTCTGGCACCTTTGGAAACTCAGGAACCTTAGG
1 TTTGGTAATTCAGGAACTTCAGGCTTTGACAACTCTGACACCTTTGGAAACTCAGGAACCTTAGG
260729 CAATTTAAGT
66 CAATTTAAGT
* * *
260739 TTTGGTAATTTAGGAACTTCGGGCTTTGGCAACTCTGAC-CCTGTTGGAAACTCAGGAACCTTAG
1 TTTGGTAATTCAGGAACTTCAGGCTTTGACAACTCTGACACCT-TTGGAAACTCAGGAACCTTAG
260803 GCAATT
65 GCAATT
260809 CAGGAACTTT
Statistics
Matches: 64, Mismatches: 5, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
74 3 0.05
75 61 0.95
ACGTcount: A:0.26, C:0.19, G:0.23, T:0.32
Consensus pattern (75 bp):
TTTGGTAATTCAGGAACTTCAGGCTTTGACAACTCTGACACCTTTGGAAACTCAGGAACCTTAGG
CAATTTAAGT
Found at i:260813 original size:18 final size:18
Alignment explanation
Indices: 260790--260830 Score: 73
Period size: 18 Copynumber: 2.3 Consensus size: 18
260780 TGTTGGAAAC
260790 TCAGGAACCTTAGGCAAT
1 TCAGGAACCTTAGGCAAT
*
260808 TCAGGAACTTTAGGCAAT
1 TCAGGAACCTTAGGCAAT
260826 TCAGG
1 TCAGG
260831 CTTAGGTAAC
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.32, C:0.20, G:0.24, T:0.24
Consensus pattern (18 bp):
TCAGGAACCTTAGGCAAT
Found at i:260845 original size:33 final size:33
Alignment explanation
Indices: 260798--260863 Score: 78
Period size: 33 Copynumber: 2.0 Consensus size: 33
260788 ACTCAGGAAC
*
260798 CTTAGGCAATTCAGGAACTTTAGGCAATTCAGG
1 CTTAGGCAACTCAGGAACTTTAGGCAATTCAGG
* * * * *
260831 CTTAGGTAACTCAGGCATTTTAGGTATTTCAGG
1 CTTAGGCAACTCAGGAACTTTAGGCAATTCAGG
260864 TTTCGGAATT
Statistics
Matches: 27, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
33 27 1.00
ACGTcount: A:0.27, C:0.17, G:0.24, T:0.32
Consensus pattern (33 bp):
CTTAGGCAACTCAGGAACTTTAGGCAATTCAGG
Found at i:262010 original size:14 final size:14
Alignment explanation
Indices: 261991--262099 Score: 98
Period size: 14 Copynumber: 8.6 Consensus size: 14
261981 GTAATCTGTC
261991 CATTTATGTTCGTT
1 CATTTATGTTCGTT
*
262005 CATTTATGTCCGTT
1 CATTTATGTTCGTT
262019 CATTTATG-TC---
1 CATTTATGTTCGTT
*
262029 CATGTATGTTCGTT
1 CATTTATGTTCGTT
262043 CATTTATGTTCG--
1 CATTTATGTTCGTT
*
262055 --TGTATGTTCGTT
1 CATTTATGTTCGTT
262067 CATTTATGTTCG--
1 CATTTATGTTCGTT
*
262079 --TGTATGTTCGTT
1 CATTTATGTTCGTT
262091 CATTTATGT
1 CATTTATGT
262100 ATGTATATGT
Statistics
Matches: 75, Mismatches: 8, Indels: 24
0.70 0.07 0.22
Matches are distributed among these distances:
10 25 0.33
11 2 0.03
13 1 0.01
14 47 0.63
ACGTcount: A:0.15, C:0.15, G:0.17, T:0.53
Consensus pattern (14 bp):
CATTTATGTTCGTT
Found at i:262075 original size:38 final size:38
Alignment explanation
Indices: 261988--262079 Score: 116
Period size: 38 Copynumber: 2.4 Consensus size: 38
261978 TTGGTAATCT
*
261988 GTCCATTTATGTTCGTTCATTTATGTCCGTTCATTTAT
1 GTCCATTTATGTTCGTTCATTTATGTCCGTTCATTTAC
* *
262026 GTCCATGTATGTTCGTTCATTTATGTTCGTGT-ATGTT-C
1 GTCCATTTATGTTCGTTCATTTATGTCCGT-TCAT-TTAC
*
262064 GTTCATTTATGTTCGT
1 GTCCATTTATGTTCGT
262080 GTATGTTCGT
Statistics
Matches: 47, Mismatches: 5, Indels: 4
0.84 0.09 0.07
Matches are distributed among these distances:
38 44 0.94
39 3 0.06
ACGTcount: A:0.14, C:0.16, G:0.17, T:0.52
Consensus pattern (38 bp):
GTCCATTTATGTTCGTTCATTTATGTCCGTTCATTTAC
Found at i:262111 original size:24 final size:24
Alignment explanation
Indices: 262009--262099 Score: 155
Period size: 24 Copynumber: 3.8 Consensus size: 24
261999 TTCGTTCATT
* * *
262009 TATGTCCGTTCATTTATGTCCATG
1 TATGTTCGTTCATTTATGTTCGTG
262033 TATGTTCGTTCATTTATGTTCGTG
1 TATGTTCGTTCATTTATGTTCGTG
262057 TATGTTCGTTCATTTATGTTCGTG
1 TATGTTCGTTCATTTATGTTCGTG
262081 TATGTTCGTTCATTTATGT
1 TATGTTCGTTCATTTATGT
262100 ATGTATATGT
Statistics
Matches: 64, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 64 1.00
ACGTcount: A:0.14, C:0.14, G:0.19, T:0.53
Consensus pattern (24 bp):
TATGTTCGTTCATTTATGTTCGTG
Found at i:265403 original size:3 final size:3
Alignment explanation
Indices: 265397--265426 Score: 60
Period size: 3 Copynumber: 10.0 Consensus size: 3
265387 ATCTGCTGCT
265397 GGA GGA GGA GGA GGA GGA GGA GGA GGA GGA
1 GGA GGA GGA GGA GGA GGA GGA GGA GGA GGA
265427 AGTGGTTTCT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.33, C:0.00, G:0.67, T:0.00
Consensus pattern (3 bp):
GGA
Found at i:265593 original size:33 final size:32
Alignment explanation
Indices: 265504--265596 Score: 96
Period size: 33 Copynumber: 2.8 Consensus size: 32
265494 TTCCTACCTT
265504 ATTAACCTGGCTAGTTCGCGTAGGCTCAGGCAG
1 ATTAACCTGGCTAGTT-GCGTAGGCTCAGGCAG
* * * * *
265537 ATTAACCTGGCTCGCCTGGGTAGGCTCCGGCCG
1 ATTAACCTGGCTAG-TTGCGTAGGCTCAGGCAG
* *
265570 ATTAACCTGGCTTGTGTGTGTAGGCTC
1 ATTAACCTGGCTAGT-TGCGTAGGCTC
265597 TGACCGACTA
Statistics
Matches: 50, Mismatches: 8, Indels: 4
0.81 0.13 0.06
Matches are distributed among these distances:
33 49 0.98
34 1 0.02
ACGTcount: A:0.16, C:0.26, G:0.31, T:0.27
Consensus pattern (32 bp):
ATTAACCTGGCTAGTTGCGTAGGCTCAGGCAG
Found at i:265899 original size:48 final size:47
Alignment explanation
Indices: 265823--266001 Score: 200
Period size: 48 Copynumber: 3.7 Consensus size: 47
265813 CGTTTCCTTG
* * *
265823 GGCGTTTGCATAAACAGCGTTTGCGTTTCTTTCGGAGGTGGAGGTACC
1 GGCGGTTGCATAAACAGCGTCTGCGTTTCTTTCGGAGGCGGAGGT-CC
* ** *
265871 GGCGGTTGCATAAATAGCGTCTGCGTTTCTTTAAGAGGCGGAGGCGCC
1 GGCGGTTGCATAAACAGCGTCTGCGTTTCTTTCGGAGGCGGAGG-TCC
* * * *
265919 GGTGGCTGCATAGACAGAGGT-TGCGTTTCTTTCGGAGGCGGATGCGT-C
1 GGCGGTTGCATAAACAG-CGTCTGCGTTTCTTTCGGAGGCGGA-G-GTCC
265967 GGCGGTTGCATAAACAGCGTCTGCGTTTCTTTCGG
1 GGCGGTTGCATAAACAGCGTCTGCGTTTCTTTCGG
266002 CGCCGGTGGT
Statistics
Matches: 107, Mismatches: 19, Indels: 10
0.79 0.14 0.07
Matches are distributed among these distances:
47 2 0.02
48 101 0.94
49 3 0.03
50 1 0.01
ACGTcount: A:0.16, C:0.20, G:0.35, T:0.28
Consensus pattern (47 bp):
GGCGGTTGCATAAACAGCGTCTGCGTTTCTTTCGGAGGCGGAGGTCC
Found at i:266031 original size:39 final size:38
Alignment explanation
Indices: 265970--266108 Score: 147
Period size: 39 Copynumber: 3.7 Consensus size: 38
265960 ATGCGTCGGC
*
265970 GGTTGCATAAACAGCGTCTGCGTTTCTTTCGGCGCCGGT
1 GGTTGCATAAACAGAGTCTGCGTTTCTTTCGGCG-CGGT
* * * * *
266009 GGTTGCATAAAAAGAGTTTGCGTCTCTTTCGGAG-GCT
1 GGTTGCATAAACAGAGTCTGCGTTTCTTTCGGCGCGGT
* * * *
266046 -GTTGCATGAACAGAGTTTGTGTTTCTTTCGGCGGCGGC
1 GGTTGCATAAACAGAGTCTGCGTTTCTTTCGGC-GCGGT
*
266084 GGTTGCATAAACAGCGTCTGCGTTT
1 GGTTGCATAAACAGAGTCTGCGTTT
266109 GAGGCGGCTG
Statistics
Matches: 80, Mismatches: 17, Indels: 6
0.78 0.17 0.06
Matches are distributed among these distances:
36 27 0.34
37 3 0.04
38 1 0.01
39 49 0.61
ACGTcount: A:0.17, C:0.20, G:0.31, T:0.32
Consensus pattern (38 bp):
GGTTGCATAAACAGAGTCTGCGTTTCTTTCGGCGCGGT
Found at i:268341 original size:37 final size:38
Alignment explanation
Indices: 268261--268341 Score: 96
Period size: 37 Copynumber: 2.2 Consensus size: 38
268251 AACAAGTTGA
* *
268261 AAAATATTTATATATTTTCTTTAAAAAATTTAAATTCAT
1 AAAA-ATTTATATATTTTCTTTAAAAAATTGAAAATCAT
*
268300 -AAAATTTATATAATTTT-TTTACAAAATTGAAAAT-AT
1 AAAAATTTATAT-ATTTTCTTTAAAAAATTGAAAATCAT
268336 AAAAAT
1 AAAAAT
268342 GTTTAATGAA
Statistics
Matches: 37, Mismatches: 3, Indels: 6
0.80 0.07 0.13
Matches are distributed among these distances:
36 2 0.05
37 27 0.73
38 8 0.22
ACGTcount: A:0.51, C:0.04, G:0.01, T:0.44
Consensus pattern (38 bp):
AAAAATTTATATATTTTCTTTAAAAAATTGAAAATCAT
Found at i:269094 original size:9 final size:9
Alignment explanation
Indices: 269079--269150 Score: 78
Period size: 9 Copynumber: 7.8 Consensus size: 9
269069 TTTTACTTTA
269079 ATTATTACTT
1 ATTATTA-TT
269089 -TTATTATT
1 ATTATTATT
269097 ATTATTATT
1 ATTATTATT
269106 ATTATTATT
1 ATTATTATT
269115 ATTATATATAT
1 ATTAT-TAT-T
269126 ATATATT-TT
1 AT-TATTATT
269135 A-TATGTATT
1 ATTAT-TATT
269144 ATTATTA
1 ATTATTA
269151 AAAAATAAAA
Statistics
Matches: 55, Mismatches: 0, Indels: 15
0.79 0.00 0.21
Matches are distributed among these distances:
7 3 0.05
8 3 0.05
9 35 0.64
10 7 0.13
11 4 0.07
12 3 0.05
ACGTcount: A:0.35, C:0.01, G:0.01, T:0.62
Consensus pattern (9 bp):
ATTATTATT
Found at i:269100 original size:6 final size:6
Alignment explanation
Indices: 269079--269150 Score: 78
Period size: 6 Copynumber: 11.7 Consensus size: 6
269069 TTTTACTTTA
269079 ATTATT ACTT-TT ATTATT ATTATT ATTATT ATTATT ATTATAT ATATATAT
1 ATTATT A-TTATT ATTATT ATTATT ATTATT ATTATT ATTAT-T AT-TAT-T
269130 ATT-TT A-TATGT ATTATT ATTA
1 ATTATT ATTAT-T ATTATT ATTA
269151 AAAAATAAAA
Statistics
Matches: 59, Mismatches: 0, Indels: 14
0.81 0.00 0.19
Matches are distributed among these distances:
4 1 0.02
5 5 0.08
6 37 0.63
7 9 0.15
8 7 0.12
ACGTcount: A:0.35, C:0.01, G:0.01, T:0.62
Consensus pattern (6 bp):
ATTATT
Found at i:269116 original size:15 final size:16
Alignment explanation
Indices: 269090--269150 Score: 74
Period size: 15 Copynumber: 3.9 Consensus size: 16
269080 TTATTACTTT
269090 TATTATTATTATTAT-
1 TATTATTATTATTATA
269105 TATTATTATTATTATA
1 TATTATTATTATTATA
269121 TATATATATATT-TTATA
1 TAT-TAT-TATTATTATA
*
269138 T-GTATTATTATTA
1 TATTATTATTATTA
269151 AAAAATAAAA
Statistics
Matches: 41, Mismatches: 1, Indels: 8
0.82 0.02 0.16
Matches are distributed among these distances:
14 4 0.10
15 21 0.51
16 3 0.07
17 9 0.22
18 4 0.10
ACGTcount: A:0.36, C:0.00, G:0.02, T:0.62
Consensus pattern (16 bp):
TATTATTATTATTATA
Found at i:269160 original size:6 final size:6
Alignment explanation
Indices: 269151--269177 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
269141 ATTATTATTA
269151 AAAAAT AAAAAT AAAAAT AAAAAT AAA
1 AAAAAT AAAAAT AAAAAT AAAAAT AAA
269178 TAAATATTAC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.85, C:0.00, G:0.00, T:0.15
Consensus pattern (6 bp):
AAAAAT
Found at i:271118 original size:114 final size:113
Alignment explanation
Indices: 270906--271118 Score: 238
Period size: 114 Copynumber: 1.9 Consensus size: 113
270896 TTTTTTTATG
* *
270906 TTTATTTATTTTTCAATATTAAGAAAAGATAATCTTAAAGTAATGATGTCCATTTTCTGATATTT
1 TTTATTTATTTTTCAATATTAAGAAAAGATAATCTTAAAGCAATGAAGTCCATTTTCTGATATTT
* ****
270971 TAAATAAATAAATATTTTTTATTATTTTTATATAAATGTTTTATTAATA
66 TAAATAAATAAATA-TTCTTATTATAAAAATATAAATGTTTTATTAATA
* *
271020 TTTATTTATTTTTTAATATTAAGAAAAGAGCT-ATCTTAAAGCACCTAGAAG--CACTTTTCTGA
1 TTTATTTATTTTTCAATATTAAGAAAAGA--TAATCTTAAAGCA-AT-GAAGTCCA-TTTTCTGA
*
271082 TATTTCTAAGTAAATAAATA-TCTTATT-TAAAAATATA
61 TATTT-TAAATAAATAAATATTCTTATTATAAAAATATA
271119 GTTATATTAT
Statistics
Matches: 83, Mismatches: 10, Indels: 12
0.79 0.10 0.11
Matches are distributed among these distances:
114 34 0.41
115 18 0.22
116 15 0.18
117 16 0.19
ACGTcount: A:0.39, C:0.07, G:0.07, T:0.46
Consensus pattern (113 bp):
TTTATTTATTTTTCAATATTAAGAAAAGATAATCTTAAAGCAATGAAGTCCATTTTCTGATATTT
TAAATAAATAAATATTCTTATTATAAAAATATAAATGTTTTATTAATA
Found at i:271657 original size:32 final size:32
Alignment explanation
Indices: 271616--271678 Score: 99
Period size: 32 Copynumber: 1.9 Consensus size: 32
271606 TTTCAAAATT
271616 TATATATATACTTATTATTTTAATAATATTTATA
1 TATATATATA-TTATT-TTTTAATAATATTTATA
*
271650 TATATATATATTATTTTTTATTAATATTT
1 TATATATATATTATTTTTTAATAATATTT
271679 TTGTTTTATT
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
32 13 0.46
33 5 0.18
34 10 0.36
ACGTcount: A:0.38, C:0.02, G:0.00, T:0.60
Consensus pattern (32 bp):
TATATATATATTATTTTTTAATAATATTTATA
Found at i:276843 original size:9 final size:8
Alignment explanation
Indices: 276821--276903 Score: 89
Period size: 8 Copynumber: 10.0 Consensus size: 8
276811 TATTATACTT
276821 GGAAAAAA
1 GGAAAAAA
276829 GGAAAAAA
1 GGAAAAAA
276837 GGAAAAAAA
1 GG-AAAAAA
276846 GGAAAAAA
1 GGAAAAAA
276854 GGAAAAAA
1 GGAAAAAA
*
276862 -GTAAAAA
1 GGAAAAAA
276869 GG-AAAAA
1 GGAAAAAA
276876 GGAAGAAAA
1 GGAA-AAAA
276885 TGAAGAAAAAA
1 -G--GAAAAAA
*
276896 AGAAAAAA
1 GGAAAAAA
276904 AAAAATTGAA
Statistics
Matches: 66, Mismatches: 2, Indels: 14
0.80 0.02 0.17
Matches are distributed among these distances:
7 13 0.20
8 33 0.50
9 12 0.18
10 1 0.02
11 4 0.06
12 3 0.05
ACGTcount: A:0.75, C:0.00, G:0.23, T:0.02
Consensus pattern (8 bp):
GGAAAAAA
Found at i:276845 original size:17 final size:17
Alignment explanation
Indices: 276823--276875 Score: 83
Period size: 17 Copynumber: 3.2 Consensus size: 17
276813 TTATACTTGG
276823 AAAAAAGGAAAAAAGGA
1 AAAAAAGGAAAAAAGGA
276840 AAAAAAGGAAAAAAGG-
1 AAAAAAGGAAAAAAGGA
*
276856 AAAAAA-GTAAAAAGGA
1 AAAAAAGGAAAAAAGGA
276872 AAAA
1 AAAA
276876 GGAAGAAAAT
Statistics
Matches: 34, Mismatches: 1, Indels: 3
0.89 0.03 0.08
Matches are distributed among these distances:
15 8 0.24
16 10 0.29
17 16 0.47
ACGTcount: A:0.77, C:0.00, G:0.21, T:0.02
Consensus pattern (17 bp):
AAAAAAGGAAAAAAGGA
Found at i:276884 original size:17 final size:18
Alignment explanation
Indices: 276824--276894 Score: 66
Period size: 17 Copynumber: 4.3 Consensus size: 18
276814 TATACTTGGA
276824 AAAAAGGAAAAAAGGAA-
1 AAAAAGGAAAAAAGGAAG
276841 AAAAAGGAAAAAAGG-A-
1 AAAAAGGAAAAAAGGAAG
*
276857 AAAAA-GTAAAAA-G--G
1 AAAAAGGAAAAAAGGAAG
*
276871 AAAAAGGAAGAAAATGAAG
1 AAAAAGGAA-AAAAGGAAG
276890 AAAAA
1 AAAAA
276895 AAGAAAAAAA
Statistics
Matches: 46, Mismatches: 2, Indels: 10
0.79 0.03 0.17
Matches are distributed among these distances:
14 6 0.13
15 8 0.17
16 10 0.22
17 16 0.35
19 6 0.13
ACGTcount: A:0.75, C:0.00, G:0.23, T:0.03
Consensus pattern (18 bp):
AAAAAGGAAAAAAGGAAG
Found at i:277402 original size:32 final size:32
Alignment explanation
Indices: 277362--277423 Score: 97
Period size: 32 Copynumber: 1.9 Consensus size: 32
277352 TCTGGAAACA
* *
277362 AGAAGTATCTCTACGAGATGAGCCTAACAACG
1 AGAAGTATCTCTACAAGATGAGCATAACAACG
*
277394 AGAAGTATCTCTACAATATGAGCATAACAA
1 AGAAGTATCTCTACAAGATGAGCATAACAA
277424 TCATTTCTTC
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
32 27 1.00
ACGTcount: A:0.42, C:0.19, G:0.18, T:0.21
Consensus pattern (32 bp):
AGAAGTATCTCTACAAGATGAGCATAACAACG
Found at i:279975 original size:22 final size:22
Alignment explanation
Indices: 279947--279992 Score: 92
Period size: 22 Copynumber: 2.1 Consensus size: 22
279937 CATTTTGAAT
279947 GCGTGTATTAGCTAATGTTGGG
1 GCGTGTATTAGCTAATGTTGGG
279969 GCGTGTATTAGCTAATGTTGGG
1 GCGTGTATTAGCTAATGTTGGG
279991 GC
1 GC
279993 ATGCTGAAGG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.17, C:0.11, G:0.37, T:0.35
Consensus pattern (22 bp):
GCGTGTATTAGCTAATGTTGGG
Found at i:282108 original size:73 final size:73
Alignment explanation
Indices: 281989--282745 Score: 1282
Period size: 73 Copynumber: 10.4 Consensus size: 73
281979 CTATTTCCAA
** *
281989 CATCTGTAAGACCTACAGTGCATGATGTTTTCAAAAAGCCTTCGGGAGCTTTTTGATCCTAAAAC
1 CATCTGTAAGACCTACAGTGCATGATGTTTTCAAAAAGCCTTCGGGAGCTTTTTGATTTTAAAGC
282054 CGT-AGGGT
66 C-TCAGGGT
* * *
282062 CATCTGTAAGACCTACAGTGCATGATGTTTTCAAAAAGCCTTCGGGAGCTTTTTTATCTTAAAAC
1 CATCTGTAAGACCTACAGTGCATGATGTTTTCAAAAAGCCTTCGGGAGCTTTTTGATTTTAAAGC
282127 CTCAGGGT
66 CTCAGGGT
* * **
282135 CATCTATAAGACCTACAGTGCATGATGTTTTCAAAAAGCCTTTGGGAGCTTTTTGATCGTAAAGC
1 CATCTGTAAGACCTACAGTGCATGATGTTTTCAAAAAGCCTTCGGGAGCTTTTTGATTTTAAAGC
282200 CTCAGGGT
66 CTCAGGGT
282208 CATCTGTAAGACCTACAGTGCATGATGTTTTCAAAAAGCCTTCGGGAGCTTTTTGATTTTAAAGC
1 CATCTGTAAGACCTACAGTGCATGATGTTTTCAAAAAGCCTTCGGGAGCTTTTTGATTTTAAAGC
282273 CTCAGGGT
66 CTCAGGGT
**
282281 CATCTGTAAGACCTACAGTGCATGAAATTTTCAAAAAGCCTTCGGGAGCTTTTTGATTTTAAAGC
1 CATCTGTAAGACCTACAGTGCATGATGTTTTCAAAAAGCCTTCGGGAGCTTTTTGATTTTAAAGC
282346 CTCAGGGT
66 CTCAGGGT
* * * * **
282354 CATTTGTAAGACCTACATTGCATGATATTTTCAAAAAGCCTTTGACAGCTTTTTGATTTTAAAGC
1 CATCTGTAAGACCTACAGTGCATGATGTTTTCAAAAAGCCTTCGGGAGCTTTTTGATTTTAAAGC
282419 CTCAGGGT
66 CTCAGGGT
282427 CATCTGTAAGACCTACAGTGCATGATGTTTTCAAAAAGCCTTCGGGAGCTTTTTGATTTTAAAGC
1 CATCTGTAAGACCTACAGTGCATGATGTTTTCAAAAAGCCTTCGGGAGCTTTTTGATTTTAAAGC
282492 CTCAGGGT
66 CTCAGGGT
* *
282500 CATCTGTAAGACCTATAGTGCATGATGTTTTCAAAAAGCCTTCGGGAGCTTTTAGATTTTAAAGC
1 CATCTGTAAGACCTACAGTGCATGATGTTTTCAAAAAGCCTTCGGGAGCTTTTTGATTTTAAAGC
282565 CTCAGGGT
66 CTCAGGGT
* *
282573 CATCTGTAAGACCTACAGTGCATGATATTTTCAAGAAGCCTTCGGGAGCTTTTTGATTTTAAAGC
1 CATCTGTAAGACCTACAGTGCATGATGTTTTCAAAAAGCCTTCGGGAGCTTTTTGATTTTAAAGC
282638 CTCAGGGT
66 CTCAGGGT
*
282646 CATCTGTAAGACCTACAATGCATGATGTTTTCAAAAAGCCTTCGGGAGCTTTTTGATTTTAAAGC
1 CATCTGTAAGACCTACAGTGCATGATGTTTTCAAAAAGCCTTCGGGAGCTTTTTGATTTTAAAGC
282711 CTCAGGGT
66 CTCAGGGT
*
282719 CATCTGTAAGACCTACAGTGCAAGATG
1 CATCTGTAAGACCTACAGTGCATGATG
282746 ATAAGACCTC
Statistics
Matches: 647, Mismatches: 36, Indels: 2
0.94 0.05 0.00
Matches are distributed among these distances:
72 1 0.00
73 646 1.00
ACGTcount: A:0.27, C:0.19, G:0.21, T:0.32
Consensus pattern (73 bp):
CATCTGTAAGACCTACAGTGCATGATGTTTTCAAAAAGCCTTCGGGAGCTTTTTGATTTTAAAGC
CTCAGGGT
Found at i:282931 original size:12 final size:12
Alignment explanation
Indices: 282914--282940 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
282904 ATTTCTCATT
282914 TTACTTTAATTA
1 TTACTTTAATTA
282926 TTACTTTAATTA
1 TTACTTTAATTA
282938 TTA
1 TTA
282941 TTATTATTAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.33, C:0.07, G:0.00, T:0.59
Consensus pattern (12 bp):
TTACTTTAATTA
Found at i:286541 original size:29 final size:30
Alignment explanation
Indices: 286499--286559 Score: 97
Period size: 29 Copynumber: 2.1 Consensus size: 30
286489 AGGGTAATAC
* *
286499 TAAAGTTACCAAGTCAACCCCCACT-CTAT
1 TAAACTTACCAAGTCAAACCCCACTACTAT
286528 TAAACTTACCAAGTCAAACCCCACTACTAT
1 TAAACTTACCAAGTCAAACCCCACTACTAT
286558 TA
1 TA
286560 TTTTAAATCA
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
29 23 0.79
30 6 0.21
ACGTcount: A:0.38, C:0.33, G:0.05, T:0.25
Consensus pattern (30 bp):
TAAACTTACCAAGTCAAACCCCACTACTAT
Found at i:287001 original size:20 final size:21
Alignment explanation
Indices: 286954--287002 Score: 64
Period size: 20 Copynumber: 2.4 Consensus size: 21
286944 AAAATAGTTT
286954 AATAAAAAACTTTAAAAAAAA
1 AATAAAAAACTTTAAAAAAAA
* * *
286975 AAGAAAAAA-TTTTAATAAAA
1 AATAAAAAACTTTAAAAAAAA
286995 AATAAAAA
1 AATAAAAA
287003 GATAATCATT
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
20 16 0.67
21 8 0.33
ACGTcount: A:0.76, C:0.02, G:0.02, T:0.20
Consensus pattern (21 bp):
AATAAAAAACTTTAAAAAAAA
Found at i:287002 original size:21 final size:21
Alignment explanation
Indices: 286957--286996 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
286947 ATAGTTTAAT
286957 AAAAAACTTTAAAAAAAAAAG
1 AAAAAACTTTAAAAAAAAAAG
* *
286978 AAAAAATTTTAATAAAAAA
1 AAAAAACTTTAAAAAAAAA
286997 TAAAAAGATA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.75, C:0.03, G:0.03, T:0.20
Consensus pattern (21 bp):
AAAAAACTTTAAAAAAAAAAG
Found at i:296069 original size:16 final size:16
Alignment explanation
Indices: 296048--296079 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
296038 CTCATTCGAA
296048 CTAGAATCGAGAATTT
1 CTAGAATCGAGAATTT
296064 CTAGAATCGAGAATTT
1 CTAGAATCGAGAATTT
296080 TTGGCTCATC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.38, C:0.12, G:0.19, T:0.31
Consensus pattern (16 bp):
CTAGAATCGAGAATTT
Found at i:318707 original size:2 final size:2
Alignment explanation
Indices: 318700--318739 Score: 73
Period size: 2 Copynumber: 20.5 Consensus size: 2
318690 AATAATTTAT
318700 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T- TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
318740 TTATGACTAC
Statistics
Matches: 37, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.03
2 36 0.97
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (2 bp):
TA
Found at i:320077 original size:3 final size:3
Alignment explanation
Indices: 320048--320100 Score: 70
Period size: 3 Copynumber: 17.0 Consensus size: 3
320038 TTGGGTTTTG
* *
320048 TAA TAT TAA TAAA TAA TATA TAT TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA T-AA TAA TA-A TAA TAA TAA TAA TAA TAA TAA TAA TAA
320095 TAA TAA
1 TAA TAA
320101 ATTTTAAAAT
Statistics
Matches: 44, Mismatches: 4, Indels: 4
0.85 0.08 0.08
Matches are distributed among these distances:
3 38 0.86
4 6 0.14
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (3 bp):
TAA
Found at i:320444 original size:124 final size:123
Alignment explanation
Indices: 320311--320537 Score: 337
Period size: 124 Copynumber: 1.8 Consensus size: 123
320301 GACCTATTTC
* * * * * * * *
320311 CTTCTGTGATAGAGTCATTCAAAAGGTTGAATAAGTTCTTCTTATTTTGAACTTCTTCTTTCTTT
1 CTTCTGTGATAGAATCATGCAAAAGGTTGAACAAGCTCTTCTCATTGTGAACTTCTTC-TTCCTC
* * *
320376 TTCAGATGAGTTTTTCTTATTATGAACTTTCTCTGGAAAGGTTTATGCTAATCTATCTG
65 TTCAAATAAGTTCTTCTTATTATGAACTTTCTCTGGAAAGGTTTATGCTAATCTATCTG
*
320435 CTTCTGTGATAGAATTATGCAAAAGGTTGAACAAGCTCTTCTCATTGTGAACTTCTTCTTCCTCT
1 CTTCTGTGATAGAATCATGCAAAAGGTTGAACAAGCTCTTCTCATTGTGAACTTCTTCTTCCTCT
320500 TCAAATAAGTTCTTCTTATTATGAACTTTCTCTGGAAA
66 TCAAATAAGTTCTTCTTATTATGAACTTTCTCTGGAAA
320538 TGTTGATCCA
Statistics
Matches: 91, Mismatches: 12, Indels: 1
0.88 0.12 0.01
Matches are distributed among these distances:
123 40 0.44
124 51 0.56
ACGTcount: A:0.25, C:0.17, G:0.15, T:0.44
Consensus pattern (123 bp):
CTTCTGTGATAGAATCATGCAAAAGGTTGAACAAGCTCTTCTCATTGTGAACTTCTTCTTCCTCT
TCAAATAAGTTCTTCTTATTATGAACTTTCTCTGGAAAGGTTTATGCTAATCTATCTG
Found at i:320910 original size:113 final size:113
Alignment explanation
Indices: 320453--321090 Score: 903
Period size: 113 Copynumber: 5.7 Consensus size: 113
320443 ATAGAATTAT
** * * * * *
320453 GCAAAAGGTTGAACAAGCTCTTCTCATTGTGAACTTCTTCTTCC-TCTTCAAATAAGTTCTTCTT
1 GCAAAAGGTTGAACAAATTCTTCTCATTATGAATTTCTTCTTCCTTCTTCAGATGAGTTCTTCTC
* * *
320517 ATTATGAACTTTCTCTGGAAATGTTGATCCATCAAGTGATGAATTTGA
66 ATTATGAACTTTCTCTGGAAAAGCTGATCCATCAAGTGATGGATTTGA
* * * *
320565 ACAAAAGGTTAAACAAGTTCTTCTCATTATGAACTTT-TTCTTCCTTCTTCAGATGAATT-TTCT
1 GCAAAAGGTTGAACAAATTCTTCTCATTATGAA-TTTCTTCTTCCTTCTTCAGATGAGTTCTTCT
* **
320628 CATTATGAACTCTAACTGGAAAAGCTGATCCATCAAGTGATGGATTTGA
65 CATTATGAACTTTCTCTGGAAAAGCTGATCCATCAAGTGATGGATTTGA
* *
320677 GCATAAGGTTGAACAAATTCTTCTCATTATGAATTTCTTCTTCCTCCTTCAAGTAATGAGTTCTT
1 GCAAAAGGTTGAACAAATTCTTCTCATTATGAATTTCTTCTTCCTTCTTC-AG--ATGAGTTCTT
* * *
320742 CTCATTATGAACTCTAC-CTGGAAAAGTTGATCCATCAAATGATGGATTTGA
63 CTCATTATGAACT-TTCTCTGGAAAAGCTGATCCATCAAGTGATGGATTTGA
320793 GCAAAAGGTTGAACAAATTCTTCTCATTATGAATTTCTTCTTCCTTCTTCAGATGAGTTCTTCTC
1 GCAAAAGGTTGAACAAATTCTTCTCATTATGAATTTCTTCTTCCTTCTTCAGATGAGTTCTTCTC
* *
320858 ATTATGAACTTTCTCTGGCAAAGCTAATCCATCAAGTGATGGATTTGA
66 ATTATGAACTTTCTCTGGAAAAGCTGATCCATCAAGTGATGGATTTGA
* *
320906 GCAAAAGGTTGAACAAATTCTTCTCATTATGAATTTATTCTTCCTTCTTCAGATGAGTTCTTCTT
1 GCAAAAGGTTGAACAAATTCTTCTCATTATGAATTTCTTCTTCCTTCTTCAGATGAGTTCTTCTC
* *
320971 ATTATGAACTTTCTCTGGCAAAGCTAATCCATCAAGTGATGGATTTGA
66 ATTATGAACTTTCTCTGGAAAAGCTGATCCATCAAGTGATGGATTTGA
* * *
321019 GCAAAA-GTTGAACAAGTTCTTCTTATTATGAACTTCTTCTT-C-TCTTCAGATGAGTTCTTCTC
1 GCAAAAGGTTGAACAAATTCTTCTCATTATGAATTTCTTCTTCCTTCTTCAGATGAGTTCTTCTC
321081 ATTATGAACT
66 ATTATGAACT
321091 CTAACTGACA
Statistics
Matches: 477, Mismatches: 40, Indels: 20
0.89 0.07 0.04
Matches are distributed among these distances:
110 29 0.06
111 4 0.01
112 156 0.33
113 185 0.39
115 8 0.02
116 95 0.20
ACGTcount: A:0.29, C:0.19, G:0.15, T:0.38
Consensus pattern (113 bp):
GCAAAAGGTTGAACAAATTCTTCTCATTATGAATTTCTTCTTCCTTCTTCAGATGAGTTCTTCTC
ATTATGAACTTTCTCTGGAAAAGCTGATCCATCAAGTGATGGATTTGA
Found at i:321588 original size:95 final size:95
Alignment explanation
Indices: 321425--321622 Score: 396
Period size: 95 Copynumber: 2.1 Consensus size: 95
321415 CAACATGTTA
321425 ATTCTGATAACAACTCATCTGATTATGAAGTGATCTTTCAAGATGATTTCACAGATATCGATAGT
1 ATTCTGATAACAACTCATCTGATTATGAAGTGATCTTTCAAGATGATTTCACAGATATCGATAGT
321490 TCTTTTAATACCGAGAAATCTTGAATTCTG
66 TCTTTTAATACCGAGAAATCTTGAATTCTG
321520 ATTCTGATAACAACTCATCTGATTATGAAGTGATCTTTCAAGATGATTTCACAGATATCGATAGT
1 ATTCTGATAACAACTCATCTGATTATGAAGTGATCTTTCAAGATGATTTCACAGATATCGATAGT
321585 TCTTTTAATACCGAGAAATCTTGAATTCTG
66 TCTTTTAATACCGAGAAATCTTGAATTCTG
321615 ATTCTGAT
1 ATTCTGAT
321623 GAGGAGAATA
Statistics
Matches: 103, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
95 103 1.00
ACGTcount: A:0.32, C:0.16, G:0.15, T:0.37
Consensus pattern (95 bp):
ATTCTGATAACAACTCATCTGATTATGAAGTGATCTTTCAAGATGATTTCACAGATATCGATAGT
TCTTTTAATACCGAGAAATCTTGAATTCTG
Found at i:322177 original size:83 final size:83
Alignment explanation
Indices: 322038--322425 Score: 731
Period size: 83 Copynumber: 4.7 Consensus size: 83
322028 CTGTTGTTCA
* *
322038 TACCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCAATGAGCACATTCCTCTTCC
1 TACCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCACATTACTCTTCC
322103 AAATTCAATGATTGATTT
66 AAATTCAATGATTGATTT
*
322121 TACCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCACATTATTCTTCC
1 TACCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCACATTACTCTTCC
322186 AAATTCAATGATTGATTT
66 AAATTCAATGATTGATTT
*
322204 TACCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCACATTATTCTTCC
1 TACCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCACATTACTCTTCC
322269 AAATTCAATGATTGATTT
66 AAATTCAATGATTGATTT
322287 TACCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCACATTACTCTTCC
1 TACCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCACATTACTCTTCC
322352 AAATTCAATGATTGATTT
66 AAATTCAATGATTGATTT
*
322370 TACCAAACCAGATCAGATAACTCAAAGAACACTTCCATAAGATGCTATGAGCACAT
1 TACCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCACAT
322426 GGTATTTGTT
Statistics
Matches: 300, Mismatches: 5, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
83 300 1.00
ACGTcount: A:0.39, C:0.23, G:0.12, T:0.26
Consensus pattern (83 bp):
TACCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCACATTACTCTTCC
AAATTCAATGATTGATTT
Found at i:322269 original size:166 final size:166
Alignment explanation
Indices: 321949--322425 Score: 774
Period size: 166 Copynumber: 2.8 Consensus size: 166
321939 GGTTTTATAT
* * * *
321949 CAAACCAAATCAGAGAACTCAAAGAACACTTCCAGAAGATGCTATTAGCACATTCCTCTTCCAAA
1 CAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCACATTACTCTTCCAAA
* *
322014 TTCAATAACTGGTTCTGTTGTTCATACCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAG
66 TTC---AA-T-GAT-TGAT-TT--TACCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAG
* *
322079 ATGCAATGAGCACATTCCTCTTCCAAATTCAATGATTGATTTTAC
122 ATGCTATGAGCACATTACTCTTCCAAATTCAATGATTGATTTTAC
*
322124 CAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCACATTATTCTTCCAAA
1 CAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCACATTACTCTTCCAAA
322189 TTCAATGATTGATTTTACCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGA
66 TTCAATGATTGATTTTACCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGA
*
322254 GCACATTATTCTTCCAAATTCAATGATTGATTTTAC
131 GCACATTACTCTTCCAAATTCAATGATTGATTTTAC
322290 CAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCACATTACTCTTCCAAA
1 CAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCACATTACTCTTCCAAA
*
322355 TTCAATGATTGATTTTACCAAACCAGATCAGATAACTCAAAGAACACTTCCATAAGATGCTATGA
66 TTCAATGATTGATTTTACCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGA
322420 GCACAT
131 GCACAT
322426 GGTATTTGTT
Statistics
Matches: 290, Mismatches: 12, Indels: 9
0.93 0.04 0.03
Matches are distributed among these distances:
166 217 0.75
168 2 0.01
169 3 0.01
170 2 0.01
171 1 0.00
172 2 0.01
175 63 0.22
ACGTcount: A:0.39, C:0.23, G:0.12, T:0.26
Consensus pattern (166 bp):
CAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCACATTACTCTTCCAAA
TTCAATGATTGATTTTACCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGA
GCACATTACTCTTCCAAATTCAATGATTGATTTTAC
Found at i:322396 original size:249 final size:255
Alignment explanation
Indices: 321949--322425 Score: 795
Period size: 249 Copynumber: 1.9 Consensus size: 255
321939 GGTTTTATAT
* *
321949 CAAACCAAATCAGAGAACTCAAAGAACACTTCCAGAAGATGCTATTAGCACATTCCTCTTCCAAA
1 CAAACCAAATCAGAGAACTCAAAGAACACTTCCAGAAGATGCTATGAGCACATTACTCTTCCAAA
* *
322014 TTCAATAACTGGTTCTGTTGTTCATACCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAG
66 TTC-A-AACTGGATCTGATGTT-ATACCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAG
*
322079 ATGCAATGAGCACATTCCTCTTCCAAATTCAATGATTGATTTTACCAAACCAGATCAGATAACTC
128 ATGCAATGAGCACATTACTCTTCCAAATTCAATGATTGATTTTACCAAACCAGATCAGATAACTC
322144 AAAGAACACTTCCAGAAGATGCTATGAGCACATTATTCTTCCAAATTCAATGATTGATTTTAC
193 AAAGAACACTTCCAGAAGATGCTATGAGCACATTATTCTTCCAAATTCAATGATTGATTTTAC
* * *
322207 CAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCACATTATTCTTCCAAA
1 CAAACCAAATCAGAGAACTCAAAGAACACTTCCAGAAGATGCTATGAGCACATTACTCTTCCAAA
322272 TTC-AA-T-GAT-TGAT-TT-TACCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATG
66 TTCAAACTGGATCTGATGTTATACCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATG
*
322331 CTATGAGCACATTACTCTTCCAAATTCAATGATTGATTTTACCAAACCAGATCAGATAACTCAAA
131 CAATGAGCACATTACTCTTCCAAATTCAATGATTGATTTTACCAAACCAGATCAGATAACTCAAA
*
322396 GAACACTTCCATAAGATGCTATGAGCACAT
196 GAACACTTCCAGAAGATGCTATGAGCACAT
322426 GGTATTTGTT
Statistics
Matches: 209, Mismatches: 10, Indels: 9
0.92 0.04 0.04
Matches are distributed among these distances:
249 136 0.65
251 2 0.01
252 3 0.01
253 2 0.01
254 1 0.00
255 2 0.01
258 63 0.30
ACGTcount: A:0.39, C:0.23, G:0.12, T:0.26
Consensus pattern (255 bp):
CAAACCAAATCAGAGAACTCAAAGAACACTTCCAGAAGATGCTATGAGCACATTACTCTTCCAAA
TTCAAACTGGATCTGATGTTATACCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATG
CAATGAGCACATTACTCTTCCAAATTCAATGATTGATTTTACCAAACCAGATCAGATAACTCAAA
GAACACTTCCAGAAGATGCTATGAGCACATTATTCTTCCAAATTCAATGATTGATTTTAC
Found at i:323658 original size:7 final size:7
Alignment explanation
Indices: 323646--323710 Score: 66
Period size: 7 Copynumber: 9.4 Consensus size: 7
323636 CTTGACCCCC
323646 CTTTTTT
1 CTTTTTT
323653 CTTTTTT
1 CTTTTTT
323660 C---TTT
1 CTTTTTT
323664 CTTTTTT
1 CTTTTTT
323671 CTTTTCTT
1 CTTTT-TT
*
323679 TTTTTTT
1 CTTTTTT
323686 CTTTCTTT
1 CTTT-TTT
323694 -TTTTTT
1 CTTTTTT
323700 CTTTTTCT
1 CTTTTT-T
323708 CTT
1 CTT
323711 CAAGCATAAT
Statistics
Matches: 49, Mismatches: 2, Indels: 13
0.77 0.03 0.20
Matches are distributed among these distances:
4 4 0.08
6 3 0.06
7 29 0.59
8 13 0.27
ACGTcount: A:0.00, C:0.17, G:0.00, T:0.83
Consensus pattern (7 bp):
CTTTTTT
Found at i:323666 original size:11 final size:11
Alignment explanation
Indices: 323646--323710 Score: 73
Period size: 10 Copynumber: 5.9 Consensus size: 11
323636 CTTGACCCCC
323646 CTTTTTTCTTT
1 CTTTTTTCTTT
323657 -TTTCTTTCTTT
1 CTTT-TTTCTTT
*
323668 TTTCTTTTCTTT
1 CTT-TTTTCTTT
323680 -TTTTTTCTTT
1 CTTTTTTCTTT
323690 CTTTTTT-TTT
1 CTTTTTTCTTT
323700 CTTTTTCTCTT
1 CTTTTT-TCTT
323711 CAAGCATAAT
Statistics
Matches: 48, Mismatches: 0, Indels: 11
0.81 0.00 0.19
Matches are distributed among these distances:
10 20 0.42
11 16 0.33
12 11 0.23
13 1 0.02
ACGTcount: A:0.00, C:0.17, G:0.00, T:0.83
Consensus pattern (11 bp):
CTTTTTTCTTT
Found at i:323682 original size:14 final size:14
Alignment explanation
Indices: 323646--323704 Score: 73
Period size: 14 Copynumber: 4.0 Consensus size: 14
323636 CTTGACCCCC
*
323646 CTTTTTTCTTTTTT
1 CTTTTTTTTTTTTT
323660 CTTTCTTTTTTCTTTT
1 CTTT-TTTTTT-TTTT
*
323676 CTTTTTTTTTCTTT
1 CTTTTTTTTTTTTT
323690 CTTTTTTTTTCTTTT
1 CTTTTTTTTT-TTTT
323705 TCTCTTCAAG
Statistics
Matches: 39, Mismatches: 3, Indels: 5
0.83 0.06 0.11
Matches are distributed among these distances:
14 17 0.44
15 14 0.36
16 8 0.21
ACGTcount: A:0.00, C:0.15, G:0.00, T:0.85
Consensus pattern (14 bp):
CTTTTTTTTTTTTT
Found at i:323707 original size:30 final size:30
Alignment explanation
Indices: 323646--323704 Score: 95
Period size: 29 Copynumber: 2.0 Consensus size: 30
323636 CTTGACCCCC
323646 CTTTTTTCTTTTTTCTTTCTTTTTTCTTTT
1 CTTTTTTCTTTTTTCTTTCTTTTTTCTTTT
323676 CTTTTTT-TTTCTTTCTTT-TTTTTTCTTTT
1 CTTTTTTCTTT-TTTCTTTCTTTTTTCTTTT
323705 TCTCTTCAAG
Statistics
Matches: 28, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
29 14 0.50
30 14 0.50
ACGTcount: A:0.00, C:0.15, G:0.00, T:0.85
Consensus pattern (30 bp):
CTTTTTTCTTTTTTCTTTCTTTTTTCTTTT
Found at i:331057 original size:15 final size:15
Alignment explanation
Indices: 331034--331065 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
331024 TGAAATGAAT
331034 AATGAATGTATGCAA
1 AATGAATGTATGCAA
*
331049 AATGCATGTATGCAA
1 AATGAATGTATGCAA
331064 AA
1 AA
331066 AGGTATTGAT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.47, C:0.09, G:0.19, T:0.25
Consensus pattern (15 bp):
AATGAATGTATGCAA
Found at i:334878 original size:21 final size:20
Alignment explanation
Indices: 334848--334887 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 20
334838 ATAATCCTAT
*
334848 TATTTCAAAATTATAAAAAAA
1 TATTT-AAAAATATAAAAAAA
334869 TATTTAAAAATATCAAAAA
1 TATTTAAAAATAT-AAAAA
334888 GGACTTCTAG
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 7 0.41
21 10 0.59
ACGTcount: A:0.62, C:0.05, G:0.00, T:0.33
Consensus pattern (20 bp):
TATTTAAAAATATAAAAAAA
Found at i:336419 original size:3 final size:3
Alignment explanation
Indices: 336390--336433 Score: 52
Period size: 3 Copynumber: 14.0 Consensus size: 3
336380 TTGGGTTTTG
* *
336390 TAA TAT TAA TAAA TAA TATA TAT TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA T-AA TAA TA-A TAA TAA TAA TAA TAA TAA TAA TAA
336434 ATTTTAAAAT
Statistics
Matches: 35, Mismatches: 4, Indels: 4
0.81 0.09 0.09
Matches are distributed among these distances:
3 29 0.83
4 6 0.17
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (3 bp):
TAA
Found at i:343441 original size:31 final size:30
Alignment explanation
Indices: 343403--343460 Score: 107
Period size: 31 Copynumber: 1.9 Consensus size: 30
343393 CCCCTGTATT
343403 TTCCACCATTTTTGGGTCAGAAAAAAAAACA
1 TTCCACCATTTTTGGGTCA-AAAAAAAAACA
343434 TTCCACCATTTTTGGGTCAAAAAAAAA
1 TTCCACCATTTTTGGGTCAAAAAAAAA
343461 CATAATATCC
Statistics
Matches: 27, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
30 8 0.30
31 19 0.70
ACGTcount: A:0.41, C:0.19, G:0.12, T:0.28
Consensus pattern (30 bp):
TTCCACCATTTTTGGGTCAAAAAAAAAACA
Found at i:346617 original size:28 final size:28
Alignment explanation
Indices: 346575--346631 Score: 71
Period size: 28 Copynumber: 2.0 Consensus size: 28
346565 GCCTCTATTT
* *
346575 ATATTATATTGTCGA-CCCATTGTTTGAA
1 ATATTATATTATCGAGCCCA-TGCTTGAA
*
346603 ATATTATGTTATCGAGCCCATGCTTGAA
1 ATATTATATTATCGAGCCCATGCTTGAA
346631 A
1 A
346632 GTAAGGATGA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
28 21 0.84
29 4 0.16
ACGTcount: A:0.30, C:0.16, G:0.16, T:0.39
Consensus pattern (28 bp):
ATATTATATTATCGAGCCCATGCTTGAA
Found at i:348323 original size:24 final size:24
Alignment explanation
Indices: 348289--348335 Score: 76
Period size: 24 Copynumber: 2.0 Consensus size: 24
348279 TCGAAAAGTT
*
348289 ACTTTTTAAAGTGTTGTATAAAAA
1 ACTTTTAAAAGTGTTGTATAAAAA
*
348313 ACTTTTAAAAGTGTTGTTTAAAA
1 ACTTTTAAAAGTGTTGTATAAAA
348336 GTGTAATTTA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.40, C:0.04, G:0.13, T:0.43
Consensus pattern (24 bp):
ACTTTTAAAAGTGTTGTATAAAAA
Found at i:351237 original size:25 final size:25
Alignment explanation
Indices: 351203--351277 Score: 132
Period size: 25 Copynumber: 3.0 Consensus size: 25
351193 GAGTAGGGGA
* *
351203 TTAGGGTTTGAAACCCTAATTTGTT
1 TTAGGGTTTGAAACCCTAATCTGAT
351228 TTAGGGTTTGAAACCCTAATCTGAT
1 TTAGGGTTTGAAACCCTAATCTGAT
351253 TTAGGGTTTGAAACCCTAATCTGAT
1 TTAGGGTTTGAAACCCTAATCTGAT
351278 GGGTTGTTGG
Statistics
Matches: 48, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 48 1.00
ACGTcount: A:0.27, C:0.15, G:0.20, T:0.39
Consensus pattern (25 bp):
TTAGGGTTTGAAACCCTAATCTGAT
Found at i:351382 original size:3 final size:3
Alignment explanation
Indices: 351363--351415 Score: 65
Period size: 3 Copynumber: 18.0 Consensus size: 3
351353 ATGTAAAATG
* *
351363 TAA TAT TAA TAA T-A TAA TAA TAAA TAA TAA TAA TAA TTA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA T-AA TAA TAA TAA TAA TAA TAA TAA
351408 TAA -AA TAA
1 TAA TAA TAA
351416 CGATAAAAAA
Statistics
Matches: 43, Mismatches: 4, Indels: 6
0.81 0.08 0.11
Matches are distributed among these distances:
2 4 0.09
3 36 0.84
4 3 0.07
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (3 bp):
TAA
Found at i:351390 original size:15 final size:17
Alignment explanation
Indices: 351369--351415 Score: 62
Period size: 17 Copynumber: 2.8 Consensus size: 17
351359 AATGTAATAT
351369 TAATAATATAATAA-TA
1 TAATAATATAATAATTA
351385 -AATAATAATAATAATTA
1 TAATAAT-ATAATAATTA
*
351402 TAATAATAAAATAA
1 TAATAATATAATAA
351416 CGATAAAAAA
Statistics
Matches: 27, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
15 6 0.22
16 7 0.26
17 8 0.30
18 6 0.22
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (17 bp):
TAATAATATAATAATTA
Found at i:351633 original size:43 final size:42
Alignment explanation
Indices: 351572--351898 Score: 216
Period size: 43 Copynumber: 7.5 Consensus size: 42
351562 TGTTGGGGAC
* * * *
351572 GACACTGCTCATACGTGATGAAGAGTTTGGGTCGTCTAAAGGT
1 GACACGGCTCCTACGTGATGAAGAGTTT-GGCCATCTAAAGGT
351615 GACACGGCTCCTACGTGATGAAGAGTTCTTGGCCATCTAAAGGT
1 GACACGGCTCCTACGTGATGAAGAG-T-TTGGCCATCTAAAGGT
* * * ** *** *
351659 GATAACACGGTTCCTACGTGACGAGGACGGCTGTTTATCT-ATGGTT
1 G---ACACGGCTCCTACGTGATGAAGA-GTTTGGCCATCTAAAGG-T
* * **
351705 GACACGGCTCCTACGTGATGAGGAGATCTGG---TCT-GGGGAT
1 GACACGGCTCCTACGTGATGAAGAG-TTTGGCCATCTAAAGG-T
* *
351745 GACACGGCTCATACGTGATGAAGAGTTCTGGCCATCTAAAAGT
1 GACACGGCTCCTACGTGATGAAGAGTT-TGGCCATCTAAAGGT
351788 GACACGGCTCCTACGTGATGAAGAGTTCTTGGCCATCTAAAGGT
1 GACACGGCTCCTACGTGATGAAGAG-T-TTGGCCATCTAAAGGT
* * ** ** *
351832 GATAACACGGTTCCTACGTGATGAGGACGGCTGGTTATCT-ATGGTT
1 G---ACACGGCTCCTACGTGATGAAGA-GTTTGGCCATCTAAAGG-T
351878 GACACGGCTCCTACGTGATGA
1 GACACGGCTCCTACGTGATGA
351899 GGAGATCTGG
Statistics
Matches: 228, Mismatches: 36, Indels: 40
0.75 0.12 0.13
Matches are distributed among these distances:
39 1 0.00
40 32 0.14
42 1 0.00
43 94 0.41
44 31 0.14
45 9 0.04
46 17 0.07
47 41 0.18
48 2 0.01
ACGTcount: A:0.24, C:0.20, G:0.29, T:0.26
Consensus pattern (42 bp):
GACACGGCTCCTACGTGATGAAGAGTTTGGCCATCTAAAGGT
Found at i:351840 original size:130 final size:128
Alignment explanation
Indices: 351614--351858 Score: 298
Period size: 130 Copynumber: 1.9 Consensus size: 128
351604 CGTCTAAAGG
* * *
351614 TGACACGGCTCCTACGTGATGAAGAGTTCTTGGCCATCTAAAGGTGATAACACGGTTCCTACGTG
1 TGACACGGCTCATACGTGATGAAGAGTTCTTGGCCATCTAAAAGTG--AACACGGCTCCTACGTG
* *** * *
351679 ACGAGGACGGCTGTTTATCTATGGTTGACACGGCTCCTACGTGATGAGGAGATCTGGTCTGGGGA
64 ACGAAGACGGCTGGCCATCTAAGGTTAACACGGCTCCTACGTGATGAGGAGATCTGGTCTGGGGA
*
351744 TGACACGGCTCATACGTGATGAAGAGTTC-TGGCCATCTAAAAGTG-ACACGGCTCCTACGTGAT
1 TGACACGGCTCATACGTGATGAAGAGTTCTTGGCCATCTAAAAGTGAACACGGCTCCTACGTGAC
* *
351807 GAAGA-GTTCTTGGCCATCTAAAGGTGATAACACGGTTCCTACGTGATGAGGA
66 GAAGACG-GC-TGGCCATCT-AAGGT--TAACACGGCTCCTACGTGATGAGGA
351859 CGGCTGGTTA
Statistics
Matches: 98, Mismatches: 12, Indels: 10
0.82 0.10 0.08
Matches are distributed among these distances:
125 1 0.01
126 21 0.21
127 6 0.06
128 4 0.04
129 15 0.15
130 51 0.52
ACGTcount: A:0.25, C:0.21, G:0.29, T:0.25
Consensus pattern (128 bp):
TGACACGGCTCATACGTGATGAAGAGTTCTTGGCCATCTAAAAGTGAACACGGCTCCTACGTGAC
GAAGACGGCTGGCCATCTAAGGTTAACACGGCTCCTACGTGATGAGGAGATCTGGTCTGGGGA
Found at i:351872 original size:173 final size:173
Alignment explanation
Indices: 351565--351938 Score: 642
Period size: 173 Copynumber: 2.2 Consensus size: 173
351555 TATTGGTTGT
* * * * *
351565 TGGGGACGACACTGCTCATACGTGATGAAGAGTTTGGGTCGTCTAAAGGTGACACGGCTCCTACG
1 TGGGGATGACACGGCTCATACGTGATGAAGAGTTTGGGCCATCTAAAAGTGACACGGCTCCTACG
*
351630 TGATGAAGAGTTCTTGGCCATCTAAAGGTGATAACACGGTTCCTACGTGACGAGGACGGCTGTTT
66 TGATGAAGAGTTCTTGGCCATCTAAAGGTGATAACACGGTTCCTACGTGACGAGGACGGCTGGTT
351695 ATCTATGGTTGACACGGCTCCTACGTGATGAGGAGATCTGGTC
131 ATCTATGGTTGACACGGCTCCTACGTGATGAGGAGATCTGGTC
351738 TGGGGATGACACGGCTCATACGTGATGAAGAGTTCT-GGCCATCTAAAAGTGACACGGCTCCTAC
1 TGGGGATGACACGGCTCATACGTGATGAAGAGTT-TGGGCCATCTAAAAGTGACACGGCTCCTAC
*
351802 GTGATGAAGAGTTCTTGGCCATCTAAAGGTGATAACACGGTTCCTACGTGATGAGGACGGCTGGT
65 GTGATGAAGAGTTCTTGGCCATCTAAAGGTGATAACACGGTTCCTACGTGACGAGGACGGCTGGT
351867 TATCTATGGTTGACACGGCTCCTACGTGATGAGGAGATCTGGTC
130 TATCTATGGTTGACACGGCTCCTACGTGATGAGGAGATCTGGTC
* * *
351911 TGGGGATGACACGGTTCCTACATGATGA
1 TGGGGATGACACGGCTCATACGTGATGA
351939 GGACGGCTGG
Statistics
Matches: 190, Mismatches: 10, Indels: 2
0.94 0.05 0.01
Matches are distributed among these distances:
173 189 0.99
174 1 0.01
ACGTcount: A:0.24, C:0.20, G:0.30, T:0.26
Consensus pattern (173 bp):
TGGGGATGACACGGCTCATACGTGATGAAGAGTTTGGGCCATCTAAAAGTGACACGGCTCCTACG
TGATGAAGAGTTCTTGGCCATCTAAAGGTGATAACACGGTTCCTACGTGACGAGGACGGCTGGTT
ATCTATGGTTGACACGGCTCCTACGTGATGAGGAGATCTGGTC
Found at i:351899 original size:43 final size:41
Alignment explanation
Indices: 351610--351941 Score: 199
Period size: 43 Copynumber: 7.7 Consensus size: 41
351600 GGGTCGTCTA
* *
351610 AAGG-TGACACGGCTCCTACGTGATGAAGAGTTCTTGGCCATCT
1 AAGGTTGACACGGCTCCTACGTGATGAGGAGATC-TGG--ATCT
* * * * *
351653 AAAGGTGATAACACGGTTCCTACGTGACGAGGACG-GCTGTTTATCT
1 -AAGGT--TGACACGGCTCCTACGTGATGAGGA-GATCTG--GATCT
*
351699 ATGGTTGACACGGCTCCTACGTGATGAGGAGATCTGG-TCT
1 AAGGTTGACACGGCTCCTACGTGATGAGGAGATCTGGATCT
** * * * *
351739 GGGGATGACACGGCTCATACGTGATGAAGAGTTCTGGCCATCT
1 AAGGTTGACACGGCTCCTACGTGATGAGGAGATCTGG--ATCT
* * *
351782 AAAAG-TGACACGGCTCCTACGTGATGAAGAGTTCTTGGCCATCT
1 -AAGGTTGACACGGCTCCTACGTGATGAGGAGATC-TGG--ATCT
* * *
351826 AAAGGTGATAACACGGTTCCTACGTGATGAGGACG-GCTGGTTATCT
1 -AAGGT--TGACACGGCTCCTACGTGATGAGGA-GATCTGG--ATCT
*
351872 ATGGTTGACACGGCTCCTACGTGATGAGGAGATCTGG-TCT
1 AAGGTTGACACGGCTCCTACGTGATGAGGAGATCTGGATCT
** * * *
351912 GGGGATGACACGGTTCCTACATGATGAGGA
1 AAGGTTGACACGGCTCCTACGTGATGAGGA
351942 CGGCTGGCCA
Statistics
Matches: 233, Mismatches: 38, Indels: 38
0.75 0.12 0.12
Matches are distributed among these distances:
40 62 0.27
42 2 0.01
43 83 0.36
44 18 0.08
45 8 0.03
46 13 0.06
47 45 0.19
48 2 0.01
ACGTcount: A:0.24, C:0.20, G:0.30, T:0.25
Consensus pattern (41 bp):
AAGGTTGACACGGCTCCTACGTGATGAGGAGATCTGGATCT
Found at i:352007 original size:28 final size:27
Alignment explanation
Indices: 351967--352060 Score: 91
Period size: 28 Copynumber: 3.4 Consensus size: 27
351957 AAGAGTTATG
* *
351967 GTTTCAAGAGAAACCAAATTAAAGATTT
1 GTTTCAAAAGAAA-CAAATCAAAGATTT
* *
351995 GTTTCAAAAGAAACAAACCCAAAGATTC
1 GTTTCAAAAGAAACAAA-TCAAAGATTT
* *
352023 GTTTCAAGA-AAACAACTCAAAGATGTGT
1 GTTTCAAAAGAAACAAATCAAAGAT-T-T
352051 GTTTCAAAAG
1 GTTTCAAAAG
352061 CAACTGTCTC
Statistics
Matches: 53, Mismatches: 9, Indels: 7
0.77 0.13 0.10
Matches are distributed among these distances:
26 7 0.13
27 11 0.21
28 35 0.66
ACGTcount: A:0.46, C:0.15, G:0.15, T:0.24
Consensus pattern (27 bp):
GTTTCAAAAGAAACAAATCAAAGATTT
Found at i:352651 original size:31 final size:30
Alignment explanation
Indices: 352587--352661 Score: 80
Period size: 31 Copynumber: 2.4 Consensus size: 30
352577 ATAGAAAATG
*
352587 TTTCAAGTGAAACGACTCAAAAATGGTTTTA
1 TTTCAAGTGAAACAACTCAAAAAT-GTTTTA
*
352618 TTTCAAGTGAAACAAACTCAAAGAT-TTTGTA
1 TTTCAAGTGAAAC-AACTCAAAAATGTTT-TA
* *
352649 TTTCTAGAGAAAC
1 TTTCAAGTGAAAC
352662 TGCCTCAAGA
Statistics
Matches: 38, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
30 3 0.08
31 26 0.68
32 9 0.24
ACGTcount: A:0.40, C:0.13, G:0.15, T:0.32
Consensus pattern (30 bp):
TTTCAAGTGAAACAACTCAAAAATGTTTTA
Found at i:352826 original size:63 final size:64
Alignment explanation
Indices: 352758--352879 Score: 183
Period size: 64 Copynumber: 1.9 Consensus size: 64
352748 GTGGGTATTT
* * *
352758 TCAAAAGAAGTTGTC-TCGAGAGACAAAATTTTGTTTCAAAGGAAACAAACTCAAAGATTTTTC
1 TCAAAAGAAATTGTCATCAAGAGACAAAATTTTGTTTCAAAAGAAACAAACTCAAAGATTTTTC
* * *
352821 TCAAAAGAAATTGTCATTAAGAGATAAAATTTTGTTTCAAAAGAAACAGACTCAAAGAT
1 TCAAAAGAAATTGTCATCAAGAGACAAAATTTTGTTTCAAAAGAAACAAACTCAAAGAT
352880 GTATCTCATC
Statistics
Matches: 52, Mismatches: 6, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
63 14 0.27
64 38 0.73
ACGTcount: A:0.45, C:0.12, G:0.15, T:0.28
Consensus pattern (64 bp):
TCAAAAGAAATTGTCATCAAGAGACAAAATTTTGTTTCAAAAGAAACAAACTCAAAGATTTTTC
Found at i:353159 original size:66 final size:68
Alignment explanation
Indices: 353071--353271 Score: 239
Period size: 70 Copynumber: 3.0 Consensus size: 68
353061 AAAGATTTAC
** * * * * *
353071 TTCAAAAGAAACGGTCTCAAGAGATACAAAATTCAT-TTT-AAGAGAAACAGATTCAAAGA-TTT
1 TTCAAAAGAAACTATCTTAAGAGAGACAAAATT-ATGTTTCAAAAGAAACAAACTCAAAGATTTT
353133 TTGT
65 TTGT
* *
353137 TTCAAAAGAAATTATCTTAAGAGAGACAAAATTTTGTTTCAAAAGAAACAAACTCAAAGATTTTT
1 TTCAAAAGAAACTATCTTAAGAGAGACAAAATTATGTTTCAAAAGAAACAAACTCAAAGA--TTT
353202 TTTGT
64 TTTGT
* * *
353207 TTCAAAAGAAACTATCTTAAGAGAGA-AAAATTTTGTTTCCAAATAAACAAACTCAAAGATTTTT
1 TTCAAAAGAAACTATCTTAAGAGAGACAAAATTATGTTTCAAAAGAAACAAACTCAAAGATTTTT
353271 T
66 T
353272 CCAAAAGAAA
Statistics
Matches: 118, Mismatches: 12, Indels: 9
0.85 0.09 0.06
Matches are distributed among these distances:
65 1 0.01
66 31 0.26
67 23 0.19
69 31 0.26
70 32 0.27
ACGTcount: A:0.45, C:0.11, G:0.12, T:0.32
Consensus pattern (68 bp):
TTCAAAAGAAACTATCTTAAGAGAGACAAAATTATGTTTCAAAAGAAACAAACTCAAAGATTTTT
TGT
Found at i:353180 original size:37 final size:36
Alignment explanation
Indices: 353131--353254 Score: 128
Period size: 36 Copynumber: 3.5 Consensus size: 36
353121 ATTCAAAGAT
*
353131 TTTTGTTTCAAAAGAAATTATCTTAAGAGAGACAAAA
1 TTTTGTTTCAAAAGAAACTATCTTAAGAGAGA-AAAA
* * * ****
353168 TTTTGTTTCAAAAGAAACAAAC-TCA-A-AGATTTT
1 TTTTGTTTCAAAAGAAACTATCTTAAGAGAGAAAAA
353201 TTTTGTTTCAAAAGAAACTATCTTAAGAGAGAAAAA
1 TTTTGTTTCAAAAGAAACTATCTTAAGAGAGAAAAA
* *
353237 TTTTGTTTCCAAATAAAC
1 TTTTGTTTCAAAAGAAAC
353255 AAACTCAAAG
Statistics
Matches: 67, Mismatches: 17, Indels: 7
0.74 0.19 0.08
Matches are distributed among these distances:
33 20 0.30
34 5 0.07
35 2 0.03
36 21 0.31
37 19 0.28
ACGTcount: A:0.44, C:0.10, G:0.11, T:0.35
Consensus pattern (36 bp):
TTTTGTTTCAAAAGAAACTATCTTAAGAGAGAAAAA
Found at i:353256 original size:69 final size:70
Alignment explanation
Indices: 353071--353271 Score: 252
Period size: 69 Copynumber: 2.9 Consensus size: 70
353061 AAAGATTTAC
** * * * * * *
353071 TTCAAAAGAAACGGTCTCAAGAGATACAAAATTCAT-TTT-AAGAGAAACAGATTCAAAGA---T
1 TTCAAAAGAAACTATCTTAAGAGAGACAAAATT-TTGTTTCAAAAGAAACAAACTCAAAGATTTT
353131 TTTTGT
65 TTTTGT
*
353137 TTCAAAAGAAATTATCTTAAGAGAGACAAAATTTTGTTTCAAAAGAAACAAACTCAAAGATTTTT
1 TTCAAAAGAAACTATCTTAAGAGAGACAAAATTTTGTTTCAAAAGAAACAAACTCAAAGATTTTT
353202 TTTGT
66 TTTGT
* *
353207 TTCAAAAGAAACTATCTTAAGAGAGA-AAAATTTTGTTTCCAAATAAACAAACTCAAAGATTTTT
1 TTCAAAAGAAACTATCTTAAGAGAGACAAAATTTTGTTTCAAAAGAAACAAACTCAAAGATTTTT
353271 T
66 T
353272 CCAAAAGAAA
Statistics
Matches: 118, Mismatches: 12, Indels: 7
0.86 0.09 0.05
Matches are distributed among these distances:
65 1 0.01
66 31 0.26
67 17 0.14
69 37 0.31
70 32 0.27
ACGTcount: A:0.45, C:0.11, G:0.12, T:0.32
Consensus pattern (70 bp):
TTCAAAAGAAACTATCTTAAGAGAGACAAAATTTTGTTTCAAAAGAAACAAACTCAAAGATTTTT
TTTGT
Found at i:353308 original size:31 final size:28
Alignment explanation
Indices: 353242--353299 Score: 91
Period size: 28 Copynumber: 2.1 Consensus size: 28
353232 AAAAATTTTG
*
353242 TTTCC-AAATAAACAAACTCAAAGATTT
1 TTTCCAAAAGAAACAAACTCAAAGATTT
*
353269 TTTCCAAAAGAAACAATCTCAAAGATTT
1 TTTCCAAAAGAAACAAACTCAAAGATTT
353297 TTT
1 TTT
353300 TTCACAAAAT
Statistics
Matches: 28, Mismatches: 2, Indels: 1
0.90 0.06 0.03
Matches are distributed among these distances:
27 5 0.18
28 23 0.82
ACGTcount: A:0.45, C:0.17, G:0.05, T:0.33
Consensus pattern (28 bp):
TTTCCAAAAGAAACAAACTCAAAGATTT
Found at i:353516 original size:28 final size:28
Alignment explanation
Indices: 353386--353654 Score: 167
Period size: 29 Copynumber: 9.5 Consensus size: 28
353376 CAAAACTTTG
* * *
353386 TTTCAAAATAAATAGACTCAAAGA--TT
1 TTTCAAAAGAAACAAACTCAAAGATTTT
*
353412 TTTCAAAAGAAAC-GACTCAAAGATATTT
1 TTTCAAAAGAAACAAACTCAAAGAT-TTT
* * *
353440 ATTCAAAAGGAACAAACTCCAAGATTTT
1 TTTCAAAAGAAACAAACTCAAAGATTTT
*
353468 TATTCAAAAGGAACAAACTCAAAGATTTT
1 T-TTCAAAAGAAACAAACTCAAAGATTTT
* ** * **
353497 TTTCAAGAGAAACTGTCTCAAGAGACAAAAATCGT
1 TTTCAAAAGAAA------CAA-ACTCAAAGATTTT
* * * *
353532 TTT-AAGATAAATAGACTCAAAGA-TTT
1 TTTCAAAAGAAACAAACTCAAAGATTTT
353558 TTTCAAAAGAAAC-AACTCAAAGATATTT
1 TTTCAAAAGAAACAAACTCAAAGAT-TTT
* * *
353586 ATTCGAAATG-AACAAACTCCAAGATTTT
1 TTTC-AAAAGAAACAAACTCAAAGATTTT
*
353614 TATTCAAAAGGAACAAACTCAAAGA-TTT
1 T-TTCAAAAGAAACAAACTCAAAGATTTT
*
353642 TTTCAAGAGAAAC
1 TTTCAAAAGAAAC
353655 TGTCTCAAGA
Statistics
Matches: 189, Mismatches: 35, Indels: 37
0.72 0.13 0.14
Matches are distributed among these distances:
25 10 0.05
26 24 0.13
27 22 0.12
28 46 0.24
29 66 0.35
34 10 0.05
35 11 0.06
ACGTcount: A:0.47, C:0.14, G:0.11, T:0.28
Consensus pattern (28 bp):
TTTCAAAAGAAACAAACTCAAAGATTTT
Found at i:353558 original size:145 final size:145
Alignment explanation
Indices: 353340--353697 Score: 571
Period size: 146 Copynumber: 2.5 Consensus size: 145
353330 CTTGTTTCAG
* * * * *
353340 ACTCAAAGA-TTTTTC-A-CGAAATTGTCTCAAGAGAGACAAAACTTTGTTTCAAAATAAATAGA
1 ACTCAAAGATTTTTTCAAGAGAAACTGTCTC-A-AGAGACAAAA-ATCGTTTTAAAATAAATAGA
*
353402 CTCAAAGA-TTTTTCAAAAGAAACGACTCAAAGATATTTATTCAAAAGGAACAAACTCCAAGATT
63 CTCAAAGATTTTTTCAAAAGAAACAACTCAAAGATATTTATTCAAAAGGAACAAACTCCAAGATT
353466 TTTATTCAAAAGGAACAA
128 TTTATTCAAAAGGAACAA
*
353484 ACTCAAAGATTTTTTTCAAGAGAAACTGTCTCAAGAGACAAAAATCGTTTTAAGATAAATAGACT
1 ACTCAAAGA-TTTTTTCAAGAGAAACTGTCTCAAGAGACAAAAATCGTTTTAAAATAAATAGACT
* *
353549 CAAAGATTTTTTCAAAAGAAACAACTCAAAGATATTTATTCGAAATGAACAAACTCCAAGATTTT
65 CAAAGATTTTTTCAAAAGAAACAACTCAAAGATATTTATTCAAAAGGAACAAACTCCAAGATTTT
353614 TATTCAAAAGGAACAA
130 TATTCAAAAGGAACAA
353630 ACTCAAAGATTTTTTCAAGAGAAACTGTCTCAAGAGACAAAAATCGTTTTAAAATAAATAGACTC
1 ACTCAAAGATTTTTTCAAGAGAAACTGTCTCAAGAGACAAAAATCGTTTTAAAATAAATAGACTC
353695 AAA
66 AAA
353698 TATTGTCGAT
Statistics
Matches: 199, Mismatches: 10, Indels: 9
0.91 0.05 0.04
Matches are distributed among these distances:
144 9 0.05
145 82 0.41
146 96 0.48
147 2 0.01
148 10 0.05
ACGTcount: A:0.46, C:0.15, G:0.12, T:0.27
Consensus pattern (145 bp):
ACTCAAAGATTTTTTCAAGAGAAACTGTCTCAAGAGACAAAAATCGTTTTAAAATAAATAGACTC
AAAGATTTTTTCAAAAGAAACAACTCAAAGATATTTATTCAAAAGGAACAAACTCCAAGATTTTT
ATTCAAAAGGAACAA
Found at i:354009 original size:36 final size:36
Alignment explanation
Indices: 353898--354016 Score: 93
Period size: 36 Copynumber: 3.4 Consensus size: 36
353888 AGAAAATGAT
** * *
353898 GTCTCAAGCGAGATGAAATTTG-CTTTA-AGATATA-
1 GTCTCAAGCGAGACAAAATTTGTTTTTAGAGA-AAAC
** **
353932 GTCTCAAATGAGACAAAATTTGTTTTTAGAGAAATT
1 GTCTCAAGCGAGACAAAATTTGTTTTTAGAGAAAAC
* *
353968 GTCTCAAGCGAGACAAAGTTTGTTTTT-GATAAAAC
1 GTCTCAAGCGAGACAAAATTTGTTTTTAGAGAAAAC
*
354003 GATCTCAAGTGAGA
1 G-TCTCAAGCGAGA
354017 TCAACTTTGT
Statistics
Matches: 67, Mismatches: 14, Indels: 6
0.77 0.16 0.07
Matches are distributed among these distances:
34 18 0.27
35 11 0.16
36 38 0.57
ACGTcount: A:0.36, C:0.12, G:0.20, T:0.32
Consensus pattern (36 bp):
GTCTCAAGCGAGACAAAATTTGTTTTTAGAGAAAAC
Found at i:354080 original size:102 final size:103
Alignment explanation
Indices: 353968--354184 Score: 255
Period size: 104 Copynumber: 2.1 Consensus size: 103
353958 TAGAGAAATT
* * *
353968 GTCTCAAGCGAGACAAAGTTTGTTTTTGATA-AAAC--GATCTCAA-GTGAGATCAACTTTG-TT
1 GTCTCAAGCGAGACAAA-ATTG-TTTTGAAAGAAACAACATCT-AAGGTGAGATCAACTTTGTTT
* * *
354028 TAATGTGAAACAAATTCGAAATTTGGATCTCAGAGGGAAAAG
63 TAA-GTGAAACAAATTCAAAATTTGGATCTCAAAGGAAAAAG
* *
354070 GTCTCAAGCGAGACAAAATTGTTTTGAAAGAAACAACAATCTAAGGTGAGATTAATTTTGTTTTA
1 GTCTCAAGCGAGACAAAATTGTTTTGAAAGAAACAAC-ATCTAAGGTGAGATCAACTTTGTTTTA
* * *
354135 AGTGAATCAAATTCAAAATTTGTATCTCAAAGGAAAAAT
65 AGTGAAACAAATTCAAAATTTGGATCTCAAAGGAAAAAG
354174 GTCTCAAGCGA
1 GTCTCAAGCGA
354185 CGCAATTTGT
Statistics
Matches: 98, Mismatches: 11, Indels: 10
0.82 0.09 0.08
Matches are distributed among these distances:
100 7 0.07
101 7 0.07
102 17 0.17
103 2 0.02
104 60 0.61
105 5 0.05
ACGTcount: A:0.39, C:0.12, G:0.19, T:0.29
Consensus pattern (103 bp):
GTCTCAAGCGAGACAAAATTGTTTTGAAAGAAACAACATCTAAGGTGAGATCAACTTTGTTTTAA
GTGAAACAAATTCAAAATTTGGATCTCAAAGGAAAAAG
Found at i:354655 original size:4 final size:4
Alignment explanation
Indices: 354639--354696 Score: 86
Period size: 4 Copynumber: 15.2 Consensus size: 4
354629 ATGCAAATTT
*
354639 TATG TAT- TATG TATG TATG --TG TATA TATG TATG TATG TATG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
354684 TATG TATG TATG T
1 TATG TATG TATG T
354697 TTTCTCGATC
Statistics
Matches: 49, Mismatches: 2, Indels: 6
0.86 0.04 0.11
Matches are distributed among these distances:
2 2 0.04
3 3 0.06
4 44 0.90
ACGTcount: A:0.26, C:0.00, G:0.22, T:0.52
Consensus pattern (4 bp):
TATG
Found at i:355907 original size:12 final size:11
Alignment explanation
Indices: 355879--355916 Score: 58
Period size: 11 Copynumber: 3.4 Consensus size: 11
355869 CCTCTTTTTG
*
355879 TTCTTTGCTTT
1 TTCTTTGATTT
355890 TTCTTTGATTT
1 TTCTTTGATTT
355901 TTGCTTTGATTT
1 TT-CTTTGATTT
355913 TTCT
1 TTCT
355917 CTCTGCTCTT
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
11 14 0.56
12 11 0.44
ACGTcount: A:0.05, C:0.13, G:0.11, T:0.71
Consensus pattern (11 bp):
TTCTTTGATTT
Found at i:362757 original size:25 final size:25
Alignment explanation
Indices: 362723--362797 Score: 132
Period size: 25 Copynumber: 3.0 Consensus size: 25
362713 GAGTAGGGGA
* *
362723 TTAGGGTTTGAAACCCTAATTTGTT
1 TTAGGGTTTGAAACCCTAATCTGAT
362748 TTAGGGTTTGAAACCCTAATCTGAT
1 TTAGGGTTTGAAACCCTAATCTGAT
362773 TTAGGGTTTGAAACCCTAATCTGAT
1 TTAGGGTTTGAAACCCTAATCTGAT
362798 GGGTTGTTGG
Statistics
Matches: 48, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 48 1.00
ACGTcount: A:0.27, C:0.15, G:0.20, T:0.39
Consensus pattern (25 bp):
TTAGGGTTTGAAACCCTAATCTGAT
Found at i:362903 original size:3 final size:3
Alignment explanation
Indices: 362884--362936 Score: 65
Period size: 3 Copynumber: 18.0 Consensus size: 3
362874 ATGTAAAATG
* *
362884 TAA TAT TAA TAA T-A TAA TAA TAAA TAA TAA TAA TAA TTA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA T-AA TAA TAA TAA TAA TAA TAA TAA
362929 TAA -AA TAA
1 TAA TAA TAA
362937 CGATAAAAAA
Statistics
Matches: 43, Mismatches: 4, Indels: 6
0.81 0.08 0.11
Matches are distributed among these distances:
2 4 0.09
3 36 0.84
4 3 0.07
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (3 bp):
TAA
Found at i:362911 original size:15 final size:17
Alignment explanation
Indices: 362890--362936 Score: 62
Period size: 17 Copynumber: 2.8 Consensus size: 17
362880 AATGTAATAT
362890 TAATAATATAATAA-TA
1 TAATAATATAATAATTA
362906 -AATAATAATAATAATTA
1 TAATAAT-ATAATAATTA
*
362923 TAATAATAAAATAA
1 TAATAATATAATAA
362937 CGATAAAAAA
Statistics
Matches: 27, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
15 6 0.22
16 7 0.26
17 8 0.30
18 6 0.22
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (17 bp):
TAATAATATAATAATTA
Found at i:363150 original size:27 final size:28
Alignment explanation
Indices: 363109--363170 Score: 92
Period size: 27 Copynumber: 2.3 Consensus size: 28
363099 ACTTAAATTA
*
363109 TAATAAA-AATATAAAATAGTTATTAAG
1 TAATAAATAATATAAAATAATTATTAAG
*
363136 TAATAAATAAT-TAAAATAATTATTGAG
1 TAATAAATAATATAAAATAATTATTAAG
363163 TAATAAAT
1 TAATAAAT
363171 TATTTTTTAA
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
27 29 0.91
28 3 0.09
ACGTcount: A:0.58, C:0.00, G:0.06, T:0.35
Consensus pattern (28 bp):
TAATAAATAATATAAAATAATTATTAAG
Found at i:367010 original size:33 final size:34
Alignment explanation
Indices: 366973--367040 Score: 111
Period size: 34 Copynumber: 2.0 Consensus size: 34
366963 ATTTTAAAAA
*
366973 AAATTAAGTT-GAGTCAAATTTAGGTTTAAGATG
1 AAATTAAGTTAGAGTCAAATTTAGGTATAAGATG
*
367006 AAATTAAGTTAGAGTCAATTTTAGGTATAAGATG
1 AAATTAAGTTAGAGTCAAATTTAGGTATAAGATG
367040 A
1 A
367041 TTTTTTTTAA
Statistics
Matches: 32, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
33 10 0.31
34 22 0.69
ACGTcount: A:0.41, C:0.03, G:0.21, T:0.35
Consensus pattern (34 bp):
AAATTAAGTTAGAGTCAAATTTAGGTATAAGATG
Found at i:367124 original size:35 final size:33
Alignment explanation
Indices: 367058--367149 Score: 127
Period size: 35 Copynumber: 2.8 Consensus size: 33
367048 TAATTTTTCT
367058 AGAT-AATAATATAAT-TTTTATATATATTTAG
1 AGATAAATAATATAATATTTTATATATATTTAG
*
367089 AGATAAATATTATAATATTTGTATTATATATTTAG
1 AGATAAATAATATAATATTT-TA-TATATATTTAG
*
367124 AGATAAATACTATAATATTTT-TATAT
1 AGATAAATAATATAATATTTTATATAT
367150 TTTTCAATTA
Statistics
Matches: 55, Mismatches: 2, Indels: 7
0.86 0.03 0.11
Matches are distributed among these distances:
31 4 0.07
32 15 0.27
33 3 0.05
34 3 0.05
35 30 0.55
ACGTcount: A:0.45, C:0.01, G:0.07, T:0.48
Consensus pattern (33 bp):
AGATAAATAATATAATATTTTATATATATTTAG
Found at i:376947 original size:32 final size:31
Alignment explanation
Indices: 376874--376949 Score: 80
Period size: 31 Copynumber: 2.4 Consensus size: 31
376864 CTAATGTGAC
* *
376874 TCTTAGGTAGGCTCTGCAGCCCTGAGATCAT
1 TCTTAGGTAGGCCCTGCAGCCCTAAGATCAT
** * **
376905 TCTCGGGTAGGCCCTGCGGCCCTAAGATGTGT
1 TCTTAGGTAGGCCCTGCAGCCCTAAGAT-CAT
376937 TCTTAGGTAGGCC
1 TCTTAGGTAGGCC
376950 ACGTGGCCCC
Statistics
Matches: 35, Mismatches: 9, Indels: 1
0.78 0.20 0.02
Matches are distributed among these distances:
31 23 0.66
32 12 0.34
ACGTcount: A:0.16, C:0.26, G:0.30, T:0.28
Consensus pattern (31 bp):
TCTTAGGTAGGCCCTGCAGCCCTAAGATCAT
Found at i:377993 original size:20 final size:19
Alignment explanation
Indices: 377953--377989 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
377943 TGATGACACA
*
377953 TATATTAATAGGAAAAAAT
1 TATATTAATAGAAAAAAAT
377972 TATATTAATAGAAAAAAA
1 TATATTAATAGAAAAAAA
377990 ATTAAATTTT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.62, C:0.00, G:0.08, T:0.30
Consensus pattern (19 bp):
TATATTAATAGAAAAAAAT
Found at i:381547 original size:21 final size:22
Alignment explanation
Indices: 381508--381549 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 22
381498 TATTTTTAAA
*
381508 ATCTATCCATTATCCTTATCCT
1 ATCTACCCATTATCCTTATCCT
381530 ATCTACCCATTA-CCTTATCC
1 ATCTACCCATTATCCTTATCC
381550 CTGCTGACAT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 8 0.42
22 11 0.58
ACGTcount: A:0.24, C:0.36, G:0.00, T:0.40
Consensus pattern (22 bp):
ATCTACCCATTATCCTTATCCT
Found at i:382908 original size:30 final size:27
Alignment explanation
Indices: 382872--382927 Score: 76
Period size: 30 Copynumber: 2.0 Consensus size: 27
382862 TTTCTTAAAA
382872 TCCATAATCCATTAATCTCTTAATCTCATT
1 TCCATAATCCA-TAATCT-TTAAT-TCATT
*
382902 TCCATAATCTATAATCTTTAATTCAT
1 TCCATAATCCATAATCTTTAATTCAT
382928 AAAGGACTTA
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
27 4 0.16
28 5 0.20
29 6 0.24
30 10 0.40
ACGTcount: A:0.32, C:0.23, G:0.00, T:0.45
Consensus pattern (27 bp):
TCCATAATCCATAATCTTTAATTCATT
Found at i:392665 original size:57 final size:58
Alignment explanation
Indices: 392596--392708 Score: 210
Period size: 57 Copynumber: 1.9 Consensus size: 58
392586 TCGCCATCAA
392596 GTCCCACTCCATCTACTTCAATTCCCTCAAT-CGCGGCTTCGACCTCGAATTCAAGTC
1 GTCCCACTCCATCTACTTCAATTCCCTCAATACGCGGCTTCGACCTCGAATTCAAGTC
392653 GTCCCACTCCATCTACTTCAATTCCCTCAATCACGCGGCTTCGACCTCGAATTCAA
1 GTCCCACTCCATCTACTTCAATTCCCTCAAT-ACGCGGCTTCGACCTCGAATTCAA
392709 ACTCGCCGAT
Statistics
Matches: 54, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
57 31 0.57
59 23 0.43
ACGTcount: A:0.22, C:0.39, G:0.12, T:0.27
Consensus pattern (58 bp):
GTCCCACTCCATCTACTTCAATTCCCTCAATACGCGGCTTCGACCTCGAATTCAAGTC
Found at i:403853 original size:27 final size:27
Alignment explanation
Indices: 403822--403889 Score: 122
Period size: 27 Copynumber: 2.6 Consensus size: 27
403812 TATATTTACA
403822 AAATCATATCTCTATAGGAATGGTAAC
1 AAATCATATCTCTATAGGAATGGTAAC
403849 AAATCATATCTCTATAGGAATGGTAAC
1 AAATCATATCTCTATAGGAATGGTAAC
403876 AAATC--ATCTCTATA
1 AAATCATATCTCTATA
403890 ATTCCTATAC
Statistics
Matches: 41, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
25 9 0.22
27 32 0.78
ACGTcount: A:0.41, C:0.16, G:0.12, T:0.31
Consensus pattern (27 bp):
AAATCATATCTCTATAGGAATGGTAAC
Found at i:407465 original size:27 final size:27
Alignment explanation
Indices: 407434--407528 Score: 158
Period size: 27 Copynumber: 3.6 Consensus size: 27
407424 TCTATTTACA
407434 AAATCATATCTCTATAGGAATGGGAAC
1 AAATCATATCTCTATAGGAATGGGAAC
407461 AAATCATATCTCTATAGGAATGGGAAC
1 AAATCATATCTCTATAGGAATGGGAAC
* *
407488 AAATCATATCTCTATAAGAATGGTAAC
1 AAATCATATCTCTATAGGAATGGGAAC
407515 AAATC--ATCTCTATA
1 AAATCATATCTCTATA
407529 ATTCCTACAC
Statistics
Matches: 66, Mismatches: 2, Indels: 2
0.94 0.03 0.03
Matches are distributed among these distances:
25 9 0.14
27 57 0.86
ACGTcount: A:0.42, C:0.16, G:0.14, T:0.28
Consensus pattern (27 bp):
AAATCATATCTCTATAGGAATGGGAAC
Found at i:410818 original size:28 final size:28
Alignment explanation
Indices: 410772--410827 Score: 94
Period size: 28 Copynumber: 2.0 Consensus size: 28
410762 CCGACTATTC
410772 GAATTAAATATTCTGATATTTATAATGA
1 GAATTAAATATTCTGATATTTATAATGA
* *
410800 GAATTAAATATTTTTATATTTATAATGA
1 GAATTAAATATTCTGATATTTATAATGA
410828 AAATATTTGA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
28 26 1.00
ACGTcount: A:0.43, C:0.02, G:0.09, T:0.46
Consensus pattern (28 bp):
GAATTAAATATTCTGATATTTATAATGA
Found at i:414229 original size:22 final size:23
Alignment explanation
Indices: 414204--414260 Score: 66
Period size: 23 Copynumber: 2.6 Consensus size: 23
414194 TAAATTATTT
414204 TATTTTAACATTATAT-ATC-TAA
1 TATTTTAA-ATTATATCATCATAA
*
414226 TA-TTTAAATTATTTCATCATAA
1 TATTTTAAATTATATCATCATAA
*
414248 TATTCTAAATTAT
1 TATTTTAAATTAT
414261 TGATTTCTTA
Statistics
Matches: 30, Mismatches: 2, Indels: 5
0.81 0.05 0.14
Matches are distributed among these distances:
20 6 0.20
21 8 0.27
22 7 0.23
23 9 0.30
ACGTcount: A:0.40, C:0.09, G:0.00, T:0.51
Consensus pattern (23 bp):
TATTTTAAATTATATCATCATAA
Found at i:419832 original size:2 final size:2
Alignment explanation
Indices: 419825--419867 Score: 86
Period size: 2 Copynumber: 21.5 Consensus size: 2
419815 AAGTAACATC
419825 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
419867 A
1 A
419868 ATTAATTAAT
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:421620 original size:2 final size:2
Alignment explanation
Indices: 421615--421641 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
421605 TCACACATCG
421615 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
421642 TACATACATT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:421853 original size:28 final size:28
Alignment explanation
Indices: 421780--421858 Score: 113
Period size: 28 Copynumber: 2.8 Consensus size: 28
421770 GTGTAGAATT
* *
421780 TGTCCCGAAGGACCACATAGAAGACATA
1 TGTCCCGAAGGACCACGTAGAACACATA
* *
421808 TGTCCCAAAAGACCACGTAGAACACATA
1 TGTCCCGAAGGACCACGTAGAACACATA
*
421836 TGTCCCGAAGGACTACGTAGAAC
1 TGTCCCGAAGGACCACGTAGAAC
421859 CCTCGACTTT
Statistics
Matches: 44, Mismatches: 7, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
28 44 1.00
ACGTcount: A:0.38, C:0.27, G:0.20, T:0.15
Consensus pattern (28 bp):
TGTCCCGAAGGACCACGTAGAACACATA
Done.