Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007837.1 Hibiscus syriacus cultivar Beakdansim tig00110186_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: 1003650
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 4 of 4
Found at i:787230 original size:213 final size:212
Alignment explanation
Indices: 786824--787230 Score: 593
Period size: 217 Copynumber: 1.9 Consensus size: 212
786814 GGTTTCGGGA
* *
786824 GTAAGTGTCGAACATGAGTAGGCTCAAAATTTGCCCACGTTTTCGTGTACGTGGAGGATCTTTTA
1 GTAAGTGTCGAACATGAGTAGGCTCAAAATTTGCCAACGTTTTAGTGTACGTGGAGGATCTTTTA
*
786889 GAGACTCCCATCTCCATCCTCATGTCCAAGAATGTGTTTAGTGTTTCCATATGTACTTCAGGAAA
66 GAGAATCCCATCTCCATCCTCATGTCCAAGAATGTGTTTA-----T-CATATGTACTTCAGGAAA
* * *
786954 AATGAAGAATCGGATTATCAAAGTTTAAGCTACTCGCTTGAATCTTATACAAGCTAAGACATGTG
125 AATGAAGAATCAGATTAACAAAGTTTAAGCTACTCGCTTGAATCGTATACAAGCTAAGACATGTG
787019 AGAGTTTTAATGTGGATATCCAT
190 AGAGTTTTAATGTGGATATCCAT
* * * * * * *
787042 GTAATTGTCGGACATG-GTAGGCTCAAAATTTTCCAAGGTTTTAGTGTTCGTGGTGGGTCTTTTA
1 GTAAGTGTCGAACATGAGTAGGCTCAAAATTTGCCAACGTTTTAGTGTACGTGGAGGATCTTTTA
*
787106 GATAATCCCATCTCCATCCTCATGTCCAAGAATGTGTTTA-CATATGTACTTCAGGAAAAAAAAT
66 GAGAATCCCATCTCCATCCTCATGTCCAAGAATGTGTTTATCATATGTACTTCAGG---AAAAAT
787170 GAAGAATCAGATTAACAAAGTTTAAGCTACTCGCTTGAATCGTATACAAGCTAAGACATGT
128 GAAGAATCAGATTAACAAAGTTTAAGCTACTCGCTTGAATCGTATACAAGCTAAGACATGT
787231 AATTGTGTAT
Statistics
Matches: 172, Mismatches: 14, Indels: 11
0.87 0.07 0.06
Matches are distributed among these distances:
210 15 0.09
213 64 0.37
217 79 0.46
218 14 0.08
ACGTcount: A:0.30, C:0.17, G:0.20, T:0.32
Consensus pattern (212 bp):
GTAAGTGTCGAACATGAGTAGGCTCAAAATTTGCCAACGTTTTAGTGTACGTGGAGGATCTTTTA
GAGAATCCCATCTCCATCCTCATGTCCAAGAATGTGTTTATCATATGTACTTCAGGAAAAATGAA
GAATCAGATTAACAAAGTTTAAGCTACTCGCTTGAATCGTATACAAGCTAAGACATGTGAGAGTT
TTAATGTGGATATCCAT
Found at i:794990 original size:29 final size:28
Alignment explanation
Indices: 794925--794981 Score: 78
Period size: 29 Copynumber: 2.0 Consensus size: 28
794915 CTAAATATTC
*
794925 ATCAATATCACCCTTTAACAGACAAAGCG
1 ATCAATACCA-CCTTTAACAGACAAAGCG
*
794954 ATGAATACCACCTTCTAACAGACAAAGC
1 ATCAATACCACCTT-TAACAGACAAAGC
794982 TTCACATACA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
28 4 0.16
29 21 0.84
ACGTcount: A:0.42, C:0.28, G:0.11, T:0.19
Consensus pattern (28 bp):
ATCAATACCACCTTTAACAGACAAAGCG
Found at i:801623 original size:31 final size:30
Alignment explanation
Indices: 801594--801727 Score: 169
Period size: 31 Copynumber: 4.3 Consensus size: 30
801584 TCTTAGTAAT
*
801594 CAAAACTTAATAAAACGATAACGTAAGTAA
1 CAAAACTTAATAAAACGATAACGTAAGTGA
* * *
801624 CTAAAAGTTAATGAAACGGTAACGTAAGTGA
1 C-AAAACTTAATAAAACGATAACGTAAGTGA
**
801655 CCAAAACTTAATAAAACGATAATATAAGTGA
1 -CAAAACTTAATAAAACGATAACGTAAGTGA
*
801686 CTAAAACTTAATAAAACGATAATGTAAGTGA
1 C-AAAACTTAATAAAACGATAACGTAAGTGA
801717 CCAAAACTTAA
1 -CAAAACTTAA
801728 CTTTTTTGAA
Statistics
Matches: 90, Mismatches: 10, Indels: 7
0.84 0.09 0.07
Matches are distributed among these distances:
30 2 0.02
31 86 0.96
32 2 0.02
ACGTcount: A:0.52, C:0.13, G:0.13, T:0.22
Consensus pattern (30 bp):
CAAAACTTAATAAAACGATAACGTAAGTGA
Found at i:801691 original size:62 final size:62
Alignment explanation
Indices: 801594--801727 Score: 205
Period size: 62 Copynumber: 2.2 Consensus size: 62
801584 TCTTAGTAAT
* * * *
801594 CAAAACTTAATAAAACGATAACGTAAGTAACTAAAAGTTAATGAAACGGTAACGTAAGTGAC
1 CAAAACTTAATAAAACGATAACATAAGTAACTAAAACTTAATAAAACGATAACGTAAGTGAC
* * *
801656 CAAAACTTAATAAAACGATAATATAAGTGACTAAAACTTAATAAAACGATAATGTAAGTGAC
1 CAAAACTTAATAAAACGATAACATAAGTAACTAAAACTTAATAAAACGATAACGTAAGTGAC
801718 CAAAACTTAA
1 CAAAACTTAA
801728 CTTTTTTGAA
Statistics
Matches: 65, Mismatches: 7, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
62 65 1.00
ACGTcount: A:0.52, C:0.13, G:0.13, T:0.22
Consensus pattern (62 bp):
CAAAACTTAATAAAACGATAACATAAGTAACTAAAACTTAATAAAACGATAACGTAAGTGAC
Found at i:803379 original size:61 final size:61
Alignment explanation
Indices: 803273--803457 Score: 246
Period size: 62 Copynumber: 3.0 Consensus size: 61
803263 GTCGATAAAA
* * *
803273 GTGAAGTTATGGATGTTACTAATCCTTAGTAGTTAGGAGTCTTCAAATCTGATAAAATCACT
1 GTGAAGTTGTGGATGTTACTAATCCTTAGTAGTTAGGAGTGTTCAAATCTG-CAAAATCACT
* *
803335 GTGAAATTGTGGATGTTACTAATTC-TAGTAGTTAGGAGTGTTCAAATCTTGCAAAATCACT
1 GTGAAGTTGTGGATGTTACTAATCCTTAGTAGTTAGGAGTGTTCAAATC-TGCAAAATCACT
* * * * *
803396 GTGAAGTTGTGGATATTACTAATGCTTAGTTGTTAGGATTGTTCAAATTTGGCAAAATCACT
1 GTGAAGTTGTGGATGTTACTAATCCTTAGTAGTTAGGAGTGTTCAAATCT-GCAAAATCACT
803458 TAAATATCAT
Statistics
Matches: 109, Mismatches: 11, Indels: 6
0.87 0.09 0.05
Matches are distributed among these distances:
61 54 0.50
62 55 0.50
ACGTcount: A:0.31, C:0.11, G:0.21, T:0.37
Consensus pattern (61 bp):
GTGAAGTTGTGGATGTTACTAATCCTTAGTAGTTAGGAGTGTTCAAATCTGCAAAATCACT
Found at i:804392 original size:30 final size:30
Alignment explanation
Indices: 804356--804413 Score: 98
Period size: 30 Copynumber: 1.9 Consensus size: 30
804346 CACAATGGTC
* *
804356 AAATTAAATTAAAAGAATCGTTTAATAAAA
1 AAATTAAATTAAAAGAATCATCTAATAAAA
804386 AAATTAAATTAAAAGAATCATCTAATAA
1 AAATTAAATTAAAAGAATCATCTAATAA
804414 TAAACTTTTA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 26 1.00
ACGTcount: A:0.60, C:0.05, G:0.05, T:0.29
Consensus pattern (30 bp):
AAATTAAATTAAAAGAATCATCTAATAAAA
Found at i:804861 original size:15 final size:14
Alignment explanation
Indices: 804831--804869 Score: 51
Period size: 15 Copynumber: 2.7 Consensus size: 14
804821 GATAACACAA
*
804831 AATAAATAGTTTTT
1 AATAAATATTTTTT
804845 AATAAATATTATTTT
1 AATAAATATT-TTTT
*
804860 AATTAATATT
1 AATAAATATT
804870 CGTGTATGAT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
14 9 0.41
15 13 0.59
ACGTcount: A:0.46, C:0.00, G:0.03, T:0.51
Consensus pattern (14 bp):
AATAAATATTTTTT
Found at i:810934 original size:20 final size:20
Alignment explanation
Indices: 810909--810946 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
810899 TGTTATACAA
810909 GGGGGAATCGGTACCCTCTG
1 GGGGGAATCGGTACCCTCTG
*
810929 GGGGGAATCGGTTCCCTC
1 GGGGGAATCGGTACCCTC
810947 CGAGTACTGG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.13, C:0.26, G:0.39, T:0.21
Consensus pattern (20 bp):
GGGGGAATCGGTACCCTCTG
Found at i:813431 original size:20 final size:20
Alignment explanation
Indices: 813394--813432 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
813384 AGATTGAGTG
* * *
813394 GATTTTGATGTTGTTTGCAC
1 GATTTTAATGATGATTGCAC
813414 GATTTTAATGATGATTGCA
1 GATTTTAATGATGATTGCA
813433 AGTTTAGGAG
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.23, C:0.08, G:0.23, T:0.46
Consensus pattern (20 bp):
GATTTTAATGATGATTGCAC
Found at i:813641 original size:23 final size:21
Alignment explanation
Indices: 813611--813669 Score: 66
Period size: 20 Copynumber: 2.8 Consensus size: 21
813601 TTACCCTGTG
813611 GGGGGAATCGGTTCCCCTTCAAA
1 GGGGGAATCGGTTCCCC-TC-AA
*
813634 GGGGGAATTGGTT-CCCTCAA
1 GGGGGAATCGGTTCCCCTCAA
* *
813654 GGGGGGATCGATTCCC
1 GGGGGAATCGGTTCCC
813670 TCTGCACCAA
Statistics
Matches: 31, Mismatches: 4, Indels: 4
0.79 0.10 0.10
Matches are distributed among these distances:
20 12 0.39
21 4 0.13
22 3 0.10
23 12 0.39
ACGTcount: A:0.19, C:0.24, G:0.36, T:0.22
Consensus pattern (21 bp):
GGGGGAATCGGTTCCCCTCAA
Found at i:813658 original size:21 final size:23
Alignment explanation
Indices: 813610--813669 Score: 72
Period size: 23 Copynumber: 2.7 Consensus size: 23
813600 ATTACCCTGT
813610 GGGGGGAATCGGTTCCCCTTCAA
1 GGGGGGAATCGGTTCCCCTTCAA
* *
813633 AGGGGGAATTGGTT-CCC-TCAA
1 GGGGGGAATCGGTTCCCCTTCAA
*
813654 GGGGGG-ATCGATTCCC
1 GGGGGGAATCGGTTCCC
813670 TCTGCACCAA
Statistics
Matches: 31, Mismatches: 5, Indels: 4
0.77 0.12 0.10
Matches are distributed among these distances:
20 5 0.16
21 11 0.35
22 3 0.10
23 12 0.39
ACGTcount: A:0.18, C:0.23, G:0.37, T:0.22
Consensus pattern (23 bp):
GGGGGGAATCGGTTCCCCTTCAA
Found at i:821921 original size:61 final size:62
Alignment explanation
Indices: 821813--822057 Score: 336
Period size: 61 Copynumber: 4.0 Consensus size: 62
821803 GTCGATAAAA
* * * *
821813 GTGAAGTTGTGGATGTCACTAATCCTTAGTAGTTAGGAGTCTTCAAATCTGATAAAATCACT
1 GTGAAGTTGTGGATGTTACTAATTCTTAGTAGTTAGGAGTGTTCAAATCTGACAAAATCACT
* * *
821875 ATGAAGTTGTGGATGTTACTAATTC-TAGTAGTTAGGAGTGTTCAAATCTAATAAAATCACT
1 GTGAAGTTGTGGATGTTACTAATTCTTAGTAGTTAGGAGTGTTCAAATCTGACAAAATCACT
*
821936 GTGAA-ATGTGGATGTTACTAATTC-TAGTAGTTAGGAGTGTTCAAATCTTG-CAAAATCACT
1 GTGAAGTTGTGGATGTTACTAATTCTTAGTAGTTAGGAGTGTTCAAATC-TGACAAAATCACT
* * * * *
821996 GTGAAGTTGTGGATGTTACTAATGCTTAGTTGTTAGGATTGTTCAAATTTGGCAAAATCACT
1 GTGAAGTTGTGGATGTTACTAATTCTTAGTAGTTAGGAGTGTTCAAATCTGACAAAATCACT
822058 TAAATATCAT
Statistics
Matches: 165, Mismatches: 14, Indels: 8
0.88 0.07 0.04
Matches are distributed among these distances:
60 55 0.33
61 58 0.35
62 52 0.32
ACGTcount: A:0.31, C:0.11, G:0.22, T:0.36
Consensus pattern (62 bp):
GTGAAGTTGTGGATGTTACTAATTCTTAGTAGTTAGGAGTGTTCAAATCTGACAAAATCACT
Found at i:821974 original size:60 final size:62
Alignment explanation
Indices: 821813--822043 Score: 333
Period size: 60 Copynumber: 3.8 Consensus size: 62
821803 GTCGATAAAA
* * * *
821813 GTGAAGTTGTGGATGTCACTAATCCTTAGTAGTTAGGAGTCTTCAAATCTGATAAAATCACT
1 GTGAAGTTGTGGATGTTACTAATTCTTAGTAGTTAGGAGTGTTCAAATCTAATAAAATCACT
*
821875 ATGAAGTTGTGGATGTTACTAATTC-TAGTAGTTAGGAGTGTTCAAATCTAATAAAATCACT
1 GTGAAGTTGTGGATGTTACTAATTCTTAGTAGTTAGGAGTGTTCAAATCTAATAAAATCACT
* ***
821936 GTGAA-ATGTGGATGTTACTAATTC-TAGTAGTTAGGAGTGTTCAAATCTTGCAAAATCACT
1 GTGAAGTTGTGGATGTTACTAATTCTTAGTAGTTAGGAGTGTTCAAATCTAATAAAATCACT
* * *
821996 GTGAAGTTGTGGATGTTACTAATGCTTAGTTGTTAGGATTGTTCAAAT
1 GTGAAGTTGTGGATGTTACTAATTCTTAGTAGTTAGGAGTGTTCAAAT
822044 TTGGCAAAAT
Statistics
Matches: 153, Mismatches: 14, Indels: 4
0.89 0.08 0.02
Matches are distributed among these distances:
60 56 0.37
61 55 0.36
62 42 0.27
ACGTcount: A:0.31, C:0.11, G:0.22, T:0.36
Consensus pattern (62 bp):
GTGAAGTTGTGGATGTTACTAATTCTTAGTAGTTAGGAGTGTTCAAATCTAATAAAATCACT
Found at i:822180 original size:21 final size:21
Alignment explanation
Indices: 822154--822195 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
822144 AGGAAAATCG
* *
822154 CATGGACCATTCGTCGTCTTT
1 CATGGAACATTCGACGTCTTT
*
822175 CATGGAAGATTCGACGTCTTT
1 CATGGAACATTCGACGTCTTT
822196 TATTAAGACG
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.19, C:0.24, G:0.21, T:0.36
Consensus pattern (21 bp):
CATGGAACATTCGACGTCTTT
Found at i:824790 original size:24 final size:25
Alignment explanation
Indices: 824753--824799 Score: 69
Period size: 24 Copynumber: 1.9 Consensus size: 25
824743 AGAAACTTGG
* *
824753 AATTTTTTAGAAAATAATAATTTCA
1 AATTTTTCAGAAAAAAATAATTTCA
824778 AATTTTTCA-AAAAAAATAATTT
1 AATTTTTCAGAAAAAAATAATTT
824800 TTCAAAATTT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
24 12 0.60
25 8 0.40
ACGTcount: A:0.51, C:0.04, G:0.02, T:0.43
Consensus pattern (25 bp):
AATTTTTCAGAAAAAAATAATTTCA
Found at i:825253 original size:33 final size:33
Alignment explanation
Indices: 825186--825265 Score: 117
Period size: 33 Copynumber: 2.4 Consensus size: 33
825176 CATAAGCCAC
825186 GCGATCGACACAGCGGCAGGCTGGGCAGTGCAG
1 GCGATCGACACAGCGGCAGGCTGGGCAGTGCAG
* *
825219 GCGGTCGACACAGCGGCAGGCTGGGCCG-GTCAG
1 GCGATCGACACAGCGGCAGGCTGGGCAGTG-CAG
*
825252 GCGATCGATACAGC
1 GCGATCGACACAGC
825266 AGCGGGCTTC
Statistics
Matches: 42, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
32 1 0.02
33 41 0.98
ACGTcount: A:0.20, C:0.29, G:0.41, T:0.10
Consensus pattern (33 bp):
GCGATCGACACAGCGGCAGGCTGGGCAGTGCAG
Found at i:831034 original size:22 final size:22
Alignment explanation
Indices: 831006--831054 Score: 98
Period size: 22 Copynumber: 2.2 Consensus size: 22
830996 AATGTCGTTT
831006 AGTAGGTAGGCGGCGACCGGTG
1 AGTAGGTAGGCGGCGACCGGTG
831028 AGTAGGTAGGCGGCGACCGGTG
1 AGTAGGTAGGCGGCGACCGGTG
831050 AGTAG
1 AGTAG
831055 CTATTCGACA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 27 1.00
ACGTcount: A:0.20, C:0.16, G:0.49, T:0.14
Consensus pattern (22 bp):
AGTAGGTAGGCGGCGACCGGTG
Found at i:831821 original size:23 final size:23
Alignment explanation
Indices: 831795--831839 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
831785 CACCACAGCT
*
831795 CGTATAAATGCACCGAAGTGCCC
1 CGTAGAAATGCACCGAAGTGCCC
* *
831818 CGTAGAATTGCACCGTAGTGCC
1 CGTAGAAATGCACCGAAGTGCC
831840 ATATAATGAT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.27, C:0.29, G:0.24, T:0.20
Consensus pattern (23 bp):
CGTAGAAATGCACCGAAGTGCCC
Found at i:832088 original size:149 final size:149
Alignment explanation
Indices: 831818--832122 Score: 565
Period size: 149 Copynumber: 2.0 Consensus size: 149
831808 CGAAGTGCCC
* * *
831818 CGTAGAATTGCACCGTAGTGCCATATAATGATGTCCATAAGGACCACGTAGAATTCTTTAAGAAT
1 CGTAGACTTGCACCGTAGTGCCATATAATAATGTCCATAAGGACCACATAGAATTCTTTAAGAAT
*
831883 CATATACATATGCTAGGGATCAAGTATGTGTCTTTCCAGACTTTACACATGTTCCAAAGAATATA
66 CATATACATATGCTAGGGATCAAGTATGTGTCTTTCCAGACTTCACACATGTTCCAAAGAATATA
831948 CATATGTCCCTAAGAACCG
131 CATATGTCCCTAAGAACCG
*
831967 CGTAGACTTGCACCGTAGTGCCATATAATAATGTTCATAAGGACCACATAGAATTCTTTAAGAAT
1 CGTAGACTTGCACCGTAGTGCCATATAATAATGTCCATAAGGACCACATAGAATTCTTTAAGAAT
832032 CATATACATATGCTAGGGATCAAGTATGTGTCTTTCCAGACTTCACACATGTTCCAAAGAATATA
66 CATATACATATGCTAGGGATCAAGTATGTGTCTTTCCAGACTTCACACATGTTCCAAAGAATATA
832097 CATATGTCCCTAAGAACCG
131 CATATGTCCCTAAGAACCG
832116 CGTAGAC
1 CGTAGAC
832123 CCTCGACTCT
Statistics
Matches: 151, Mismatches: 5, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
149 151 1.00
ACGTcount: A:0.34, C:0.21, G:0.17, T:0.29
Consensus pattern (149 bp):
CGTAGACTTGCACCGTAGTGCCATATAATAATGTCCATAAGGACCACATAGAATTCTTTAAGAAT
CATATACATATGCTAGGGATCAAGTATGTGTCTTTCCAGACTTCACACATGTTCCAAAGAATATA
CATATGTCCCTAAGAACCG
Found at i:833362 original size:21 final size:21
Alignment explanation
Indices: 833338--833382 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
833328 TCTTGTTCGT
* *
833338 TTGAAGGGGTATCGGTTCCCC
1 TTGAAGGGGTACCGATTCCCC
*
833359 TTGAATGGGTACCGATTCCCC
1 TTGAAGGGGTACCGATTCCCC
833380 TTG
1 TTG
833383 CCCAGAAATC
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.16, C:0.24, G:0.29, T:0.31
Consensus pattern (21 bp):
TTGAAGGGGTACCGATTCCCC
Found at i:835951 original size:87 final size:87
Alignment explanation
Indices: 835798--836014 Score: 391
Period size: 87 Copynumber: 2.5 Consensus size: 87
835788 AAAAATTCCG
835798 AGTCGAATAAATATATTTCAGTTAAATAATATTTCATTATAATCAAGCGAGTGAATCCACTCAAA
1 AGTCGAATAAATATATTTCAGTTAAATAATATTTCATTATAATCAAGCGAGTGAATCCACTCAAA
835863 ATAATATTTCACTTCAAATTCA
66 ATAATATTTCACTTCAAATTCA
* *
835885 AGTTGAATAAATATATTTCAGTTAAATAATATTTCATTATAATCAAGCTAGTGAATCCAC-CTAA
1 AGTCGAATAAATATATTTCAGTTAAATAATATTTCATTATAATCAAGCGAGTGAATCCACTC-AA
835949 AATAATATTTCACTTCAAATTCA
65 AATAATATTTCACTTCAAATTCA
*
835972 AGTCGAATAAATATATTTCAGTTAAATAATATTTCATCATAAT
1 AGTCGAATAAATATATTTCAGTTAAATAATATTTCATTATAAT
836015 AGTTATTATT
Statistics
Matches: 125, Mismatches: 4, Indels: 2
0.95 0.03 0.02
Matches are distributed among these distances:
86 1 0.01
87 124 0.99
ACGTcount: A:0.43, C:0.13, G:0.07, T:0.36
Consensus pattern (87 bp):
AGTCGAATAAATATATTTCAGTTAAATAATATTTCATTATAATCAAGCGAGTGAATCCACTCAAA
ATAATATTTCACTTCAAATTCA
Found at i:852601 original size:10 final size:10
Alignment explanation
Indices: 852572--852678 Score: 116
Period size: 10 Copynumber: 11.1 Consensus size: 10
852562 GCTGCTGGAA
852572 AACCGGTTTG
1 AACCGGTTTG
*
852582 -ACCAGTTTTG
1 AACC-GGTTTG
852592 AACCGGTTTG
1 AACCGGTTTG
*
852602 -ACCGGTTCG
1 AACCGGTTTG
852611 AACCGGTTTG
1 AACCGGTTTG
*
852621 -ACCGGTCTG
1 AACCGGTTTG
852630 AACCGGTTTG
1 AACCGGTTTG
*
852640 -ACCGGTTCG
1 AACCGGTTTG
852649 AACCGGTTTG
1 AACCGGTTTG
*
852659 -ACCGGTCTG
1 AACCGGTTTG
*
852668 AACCGGGTTG
1 AACCGGTTTG
852678 A
1 A
852679 CCCGACCCGA
Statistics
Matches: 80, Mismatches: 11, Indels: 12
0.78 0.11 0.12
Matches are distributed among these distances:
9 35 0.44
10 42 0.52
11 3 0.04
ACGTcount: A:0.18, C:0.24, G:0.31, T:0.27
Consensus pattern (10 bp):
AACCGGTTTG
Found at i:852615 original size:19 final size:19
Alignment explanation
Indices: 852572--852680 Score: 150
Period size: 19 Copynumber: 5.7 Consensus size: 19
852562 GCTGCTGGAA
* *
852572 AACCGGTTTGACCAGTTTTG
1 AACCGGTTTGACC-GGTTCG
852592 AACCGGTTTGACCGGTTCG
1 AACCGGTTTGACCGGTTCG
852611 AACCGGTTTGACCGG-TCTG
1 AACCGGTTTGACCGGTTC-G
852630 AACCGGTTTGACCGGTTCG
1 AACCGGTTTGACCGGTTCG
852649 AACCGGTTTGACCGG-TCTG
1 AACCGGTTTGACCGGTTC-G
*
852668 AACCGGGTTGACC
1 AACCGGTTTGACC
852681 CGACCCGACT
Statistics
Matches: 83, Mismatches: 3, Indels: 7
0.89 0.03 0.08
Matches are distributed among these distances:
18 4 0.05
19 64 0.77
20 15 0.18
ACGTcount: A:0.17, C:0.26, G:0.30, T:0.27
Consensus pattern (19 bp):
AACCGGTTTGACCGGTTCG
Found at i:852640 original size:38 final size:38
Alignment explanation
Indices: 852572--852680 Score: 182
Period size: 38 Copynumber: 2.8 Consensus size: 38
852562 GCTGCTGGAA
* *
852572 AACCGGTTTGACCAGTTTTGAACCGGTTTGACCGGTTCG
1 AACCGGTTTGACC-GGTCTGAACCGGTTTGACCGGTTCG
852611 AACCGGTTTGACCGGTCTGAACCGGTTTGACCGGTTCG
1 AACCGGTTTGACCGGTCTGAACCGGTTTGACCGGTTCG
*
852649 AACCGGTTTGACCGGTCTGAACCGGGTTGACC
1 AACCGGTTTGACCGGTCTGAACCGGTTTGACC
852681 CGACCCGACT
Statistics
Matches: 67, Mismatches: 3, Indels: 1
0.94 0.04 0.01
Matches are distributed among these distances:
38 54 0.81
39 13 0.19
ACGTcount: A:0.17, C:0.26, G:0.30, T:0.27
Consensus pattern (38 bp):
AACCGGTTTGACCGGTCTGAACCGGTTTGACCGGTTCG
Found at i:852696 original size:17 final size:17
Alignment explanation
Indices: 852674--852731 Score: 107
Period size: 17 Copynumber: 3.4 Consensus size: 17
852664 TCTGAACCGG
*
852674 GTTGACCCGACCCGACT
1 GTTGACCCGACCCGACC
852691 GTTGACCCGACCCGACC
1 GTTGACCCGACCCGACC
852708 GTTGACCCGACCCGACC
1 GTTGACCCGACCCGACC
852725 GTTGACC
1 GTTGACC
852732 GTGACCGTTG
Statistics
Matches: 40, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
17 40 1.00
ACGTcount: A:0.17, C:0.43, G:0.24, T:0.16
Consensus pattern (17 bp):
GTTGACCCGACCCGACC
Found at i:852739 original size:13 final size:13
Alignment explanation
Indices: 852721--852749 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
852711 GACCCGACCC
852721 GACCGTTGACCGT
1 GACCGTTGACCGT
852734 GACCGTTGACCGT
1 GACCGTTGACCGT
852747 GAC
1 GAC
852750 TTTCTTTGAT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.17, C:0.31, G:0.31, T:0.21
Consensus pattern (13 bp):
GACCGTTGACCGT
Found at i:857133 original size:5 final size:5
Alignment explanation
Indices: 857123--857148 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
857113 TACTTATCCA
857123 AAAAT AAAAT AAAAT AAAAT AAAAT A
1 AAAAT AAAAT AAAAT AAAAT AAAAT A
857149 TTATCATAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 21 1.00
ACGTcount: A:0.81, C:0.00, G:0.00, T:0.19
Consensus pattern (5 bp):
AAAAT
Found at i:859352 original size:29 final size:29
Alignment explanation
Indices: 859298--859353 Score: 76
Period size: 29 Copynumber: 1.9 Consensus size: 29
859288 GGAGTGTGCA
* **
859298 CAAATTAAATTTCAAGATAAGTACCATCG
1 CAAATAAAATTTCAAGATAAACACCATCG
*
859327 CAAATAAAATTTTAAGATAAACACCAT
1 CAAATAAAATTTCAAGATAAACACCAT
859354 TAGTAAAATA
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
29 23 1.00
ACGTcount: A:0.50, C:0.16, G:0.07, T:0.27
Consensus pattern (29 bp):
CAAATAAAATTTCAAGATAAACACCATCG
Found at i:869437 original size:28 final size:28
Alignment explanation
Indices: 869389--869482 Score: 64
Period size: 27 Copynumber: 3.1 Consensus size: 28
869379 GAGAAAAGAA
** *
869389 TAATAAAAAAT-ATTAATATAATAATAT
1 TAATAAAAAATGAAAAAAATAATAATAT
*
869416 TAATAAAAAATGAAAAAAATAAATAAATAAA
1 TAATAAAAAATGAAAAAAAT-AAT-AAT-AT
*
869447 TATATAAAACAATGTAAAAATAAATAAAAATAT
1 TA-ATAAAA-AATG--AAAA-AAATAATAATAT
869480 TAA
1 TAA
869483 AATTAGGAGA
Statistics
Matches: 52, Mismatches: 6, Indels: 13
0.73 0.08 0.18
Matches are distributed among these distances:
27 11 0.21
28 5 0.10
29 3 0.06
30 3 0.06
31 3 0.06
32 7 0.13
33 7 0.13
34 3 0.06
35 6 0.12
36 4 0.08
ACGTcount: A:0.69, C:0.01, G:0.02, T:0.28
Consensus pattern (28 bp):
TAATAAAAAATGAAAAAAATAATAATAT
Found at i:869455 original size:24 final size:24
Alignment explanation
Indices: 869382--869472 Score: 57
Period size: 24 Copynumber: 3.9 Consensus size: 24
869372 TAAACATGAG
*
869382 AAAAGAAT-AATAAA-AAATAT-T
1 AAAAAAATAAATAAATAAATATAT
* * * *
869403 AATATAATAATATTAATAAA-AAAT
1 AAAAAAATAA-ATAAATAAATATAT
869427 GAAAAAAATAAATAAATAAATATAT
1 -AAAAAAATAAATAAATAAATATAT
* *
869452 AAAACAATGTAA-AAATAAATA
1 AAAAAAAT-AAATAAATAAATA
869473 AAAATATTAA
Statistics
Matches: 53, Mismatches: 10, Indels: 11
0.72 0.14 0.15
Matches are distributed among these distances:
21 6 0.11
22 1 0.02
23 5 0.09
24 28 0.53
25 13 0.25
ACGTcount: A:0.70, C:0.01, G:0.03, T:0.25
Consensus pattern (24 bp):
AAAAAAATAAATAAATAAATATAT
Found at i:869858 original size:34 final size:33
Alignment explanation
Indices: 869820--869906 Score: 122
Period size: 33 Copynumber: 2.6 Consensus size: 33
869810 AGTTTTACTT
869820 GGACTCAAA-ATGCTTCGGTTTTAGTGTTTCAATA
1 GGACTCAAATATG-TT-GGTTTTAGTGTTTCAATA
*
869854 GGACTTAAATATGTTGGTTTTAGTGTTTCAATA
1 GGACTCAAATATGTTGGTTTTAGTGTTTCAATA
* *
869887 TGACTCAAATAAGTTGGTTT
1 GGACTCAAATATGTTGGTTT
869907 ATTTTCTGAA
Statistics
Matches: 48, Mismatches: 4, Indels: 3
0.87 0.07 0.05
Matches are distributed among these distances:
33 35 0.73
34 10 0.21
35 3 0.06
ACGTcount: A:0.28, C:0.10, G:0.21, T:0.41
Consensus pattern (33 bp):
GGACTCAAATATGTTGGTTTTAGTGTTTCAATA
Found at i:870016 original size:9 final size:9
Alignment explanation
Indices: 869957--870018 Score: 60
Period size: 8 Copynumber: 6.9 Consensus size: 9
869947 GCCTACAAAA
869957 ATAATAAA-
1 ATAATAAAT
869965 ATAA-AAAT
1 ATAATAAAT
869973 ATAAT-AAT
1 ATAATAAAT
869981 AATAATAATAAT
1 -ATAAT-A-AAT
869993 AATAATAAAT
1 -ATAATAAAT
870003 A-AATAAAT
1 ATAATAAAT
870011 ATAATAAA
1 ATAATAAA
870019 ATGTTTTTGT
Statistics
Matches: 47, Mismatches: 0, Indels: 13
0.78 0.00 0.22
Matches are distributed among these distances:
7 3 0.06
8 19 0.40
9 12 0.26
10 3 0.06
11 1 0.02
12 9 0.19
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (9 bp):
ATAATAAAT
Found at i:870017 original size:3 final size:3
Alignment explanation
Indices: 869956--870000 Score: 67
Period size: 3 Copynumber: 15.7 Consensus size: 3
869946 GGCCTACAAA
*
869956 AAT AAT AA- AAT AAA AAT -AT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
870001 ATAAATAAAT
Statistics
Matches: 38, Mismatches: 2, Indels: 4
0.86 0.05 0.09
Matches are distributed among these distances:
2 4 0.11
3 34 0.89
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (3 bp):
AAT
Found at i:870523 original size:84 final size:83
Alignment explanation
Indices: 870363--871351 Score: 960
Period size: 84 Copynumber: 11.9 Consensus size: 83
870353 CTGAATGAAA
* * * * * * * *
870363 TCGAACTCGAAGGTCTTTG--G-CAGATATCTCTTCTTGCCTTGAGCTATGCTGCAAACGATGGT
1 TCGAACTCGAAGGTCTTTGTTGACAGATAACCCTTCTCGACTTAAGTTATGCTGTAAATGAT-GT
* * *
870425 TCCTTTG-AGCTGAGTGGAG
65 GCC-TTGAAGCTGAGCGTAG
* * * *
870444 TCGAACTCGAAGGTCTTTGTTGACAGATAACCCTTCTAGCCTTGAGTTATGCCGTAAATGATGTG
1 TCGAACTCGAAGGTCTTTGTTGACAGATAACCCTTCTCGACTTAAGTTATGCTGTAAATGATGTG
* * * *
870509 CCCTCGAAGTTGAGTGTAA
66 -CCTTGAAGCTGAGCGTAG
* * * *
870528 TCGAACTCGAGGGTCTTTG--G-CAGATAGCCCTTCTCGACTTAAGCTATGCTGCAAATGATGTG
1 TCGAACTCGAAGGTCTTTGTTGACAGATAACCCTTCTCGACTTAAGTTATGCTGTAAATGATGTG
* *
870590 CCTTGGAGTTGAGCGTAG
66 CCTTGAAGCTGAGCGTAG
* * * * *
870608 TCGAACTCGAAGGTCTTTGGTTGGCAGATAACCCTTATCGACTTATGTTATGCTGCAAATGATAT
1 TCGAACTCGAAGGTCTTT-GTTGACAGATAACCCTTCTCGACTTAAGTTATGCTGTAAATGATGT
*
870673 GCCTTGGAGCTGAGCGTAG
65 GCCTTGAAGCTGAGCGTAG
* * * * * * *
870692 TCGAAATCGAAGGTCTTTAGGTCACAGATAACCCTTCTAGTCTTGAGTTATGCTGTAAATGATAT
1 TCGAACTCGAAGGTCTTT-GTTGACAGATAACCCTTCTCGACTTAAGTTATGCTGTAAATGATGT
* * * *
870757 GCCCTCGAAGCTAAGTGTAA
65 G-CCTTGAAGCTGAGCGTAG
* * * * *
870777 TCGAACTCGAGGGTCTTTG--G-CAGATAGCCCTTCTCGACTTAAGCTATACTGCAAATGATGTG
1 TCGAACTCGAAGGTCTTTGTTGACAGATAACCCTTCTCGACTTAAGTTATGCTGTAAATGATGTG
*
870839 CCTTGGAGCTGAGCGTAG
66 CCTTGAAGCTGAGCGTAG
* * *
870857 TCAAACTCGAAGGTCTTTGGTTGACAGATAACCCTTATCGACTTAAGTTATGCTGTAAATGATAT
1 TCGAACTCGAAGGTCTTT-GTTGACAGATAACCCTTCTCGACTTAAGTTATGCTGTAAATGATGT
870922 GCCTTGAAGCTGAGCGTAG
65 GCCTTGAAGCTGAGCGTAG
* * * * * *
870941 TCGAACTCGAAGGTCTTTTGGTCACAGATAACCCTTCTAGCCTTGAGTTATGTTGTAAATGATGT
1 TCGAACTCGAAGGTC-TTTGTTGACAGATAACCCTTCTCGACTTAAGTTATGCTGTAAATGATGT
* * *
871006 GCCCTCGAAGCTGAGTGTAA
65 G-CCTTGAAGCTGAGCGTAG
* * * *
871026 TCGAACTCGAGGGTCTTTG--G-CAGATAACCCTTCTCGACTTAAGCTATACTGCAAATGATGTG
1 TCGAACTCGAAGGTCTTTGTTGACAGATAACCCTTCTCGACTTAAGTTATGCTGTAAATGATGTG
*
871088 CCTTGGAGCTGAGCGTAG
66 CCTTGAAGCTGAGCGTAG
* * *
871106 TCAAACTCGAAGGTCTTTGGTTGACAGATAACCCTTATCGACTTAAGTTATGCTGTAAATGATAT
1 TCGAACTCGAAGGTCTTT-GTTGACAGATAACCCTTCTCGACTTAAGTTATGCTGTAAATGATGT
871171 GCCTTGAAGCTGAGCGTAG
65 GCCTTGAAGCTGAGCGTAG
* * * * * * ** *
871190 TCAAACTCGAAGGTCTTTTGGTCACAGATAACCCTTCTAGCCTTGAGTTATATTGTAAATAATGT
1 TCGAACTCGAAGGTC-TTTGTTGACAGATAACCCTTCTCGACTTAAGTTATGCTGTAAATGATGT
** * *
871255 GCCCTCAAAGCTGAGTGTAA
65 G-CCTTGAAGCTGAGCGTAG
* * * * * * * *
871275 TCGAACTCGAGGGTCTTCGGTTGGCAAATAACCCTTCTTGACTTAAGTTATACTGCAAATGATAT
1 TCGAACTCGAAGGTCTT-TGTTGACAGATAACCCTTCTCGACTTAAGTTATGCTGTAAATGATGT
*
871340 GCCTTGGAGCTG
65 GCCTTGAAGCTG
871352 TGTTGAACTC
Statistics
Matches: 749, Mismatches: 136, Indels: 43
0.81 0.15 0.05
Matches are distributed among these distances:
80 90 0.12
81 126 0.17
82 1 0.00
83 8 0.01
84 397 0.53
85 127 0.17
ACGTcount: A:0.25, C:0.20, G:0.24, T:0.30
Consensus pattern (83 bp):
TCGAACTCGAAGGTCTTTGTTGACAGATAACCCTTCTCGACTTAAGTTATGCTGTAAATGATGTG
CCTTGAAGCTGAGCGTAG
Found at i:870817 original size:249 final size:249
Alignment explanation
Indices: 870432--871351 Score: 1502
Period size: 249 Copynumber: 3.7 Consensus size: 249
870422 GGTTCCTTTG
* * * * *
870432 AGCTGAGTGGAGTCGAACTCGAAGGTC-TTTGTTGACAGATAACCCTTCTAGCCTTGAGTTATGC
1 AGCTGAGCGTAGTCGAAATCGAAGGTCTTTTGGTCACAGATAACCCTTCTAGCCTTGAGTTATGC
* * *
870496 CGTAAATGATGTGCCCTCGAAGTTGAGTGTAATCGAACTCGAGGGTCTTTGGCAGATAGCCCTTC
66 TGTAAATGATGTGCCCTCGAAGCTGAGTGTAATCGAACTCGAGGGTCTTTGGCAGATAACCCTTC
* * *
870561 TCGACTTAAGCTATGCTGCAAATGATGTGCCTTGGAGTTGAGCGTAGTCGAACTCGAAGGTCTTT
131 TCGACTTAAGCTATACTGCAAATGATGTGCCTTGGAGCTGAGCGTAGTCAAACTCGAAGGTCTTT
* * *
870626 GGTTGGCAGATAACCCTTATCGACTTATGTTATGCTGCAAATGATATGCCTTGG
196 GGTTGACAGATAACCCTTATCGACTTAAGTTATGCTGCAAATGATATGCCTTGA
* *
870680 AGCTGAGCGTAGTCGAAATCGAAGGTCTTTAGGTCACAGATAACCCTTCTAGTCTTGAGTTATGC
1 AGCTGAGCGTAGTCGAAATCGAAGGTCTTTTGGTCACAGATAACCCTTCTAGCCTTGAGTTATGC
* * *
870745 TGTAAATGATATGCCCTCGAAGCTAAGTGTAATCGAACTCGAGGGTCTTTGGCAGATAGCCCTTC
66 TGTAAATGATGTGCCCTCGAAGCTGAGTGTAATCGAACTCGAGGGTCTTTGGCAGATAACCCTTC
870810 TCGACTTAAGCTATACTGCAAATGATGTGCCTTGGAGCTGAGCGTAGTCAAACTCGAAGGTCTTT
131 TCGACTTAAGCTATACTGCAAATGATGTGCCTTGGAGCTGAGCGTAGTCAAACTCGAAGGTCTTT
*
870875 GGTTGACAGATAACCCTTATCGACTTAAGTTATGCTGTAAATGATATGCCTTGA
196 GGTTGACAGATAACCCTTATCGACTTAAGTTATGCTGCAAATGATATGCCTTGA
* *
870929 AGCTGAGCGTAGTCGAACTCGAAGGTCTTTTGGTCACAGATAACCCTTCTAGCCTTGAGTTATGT
1 AGCTGAGCGTAGTCGAAATCGAAGGTCTTTTGGTCACAGATAACCCTTCTAGCCTTGAGTTATGC
870994 TGTAAATGATGTGCCCTCGAAGCTGAGTGTAATCGAACTCGAGGGTCTTTGGCAGATAACCCTTC
66 TGTAAATGATGTGCCCTCGAAGCTGAGTGTAATCGAACTCGAGGGTCTTTGGCAGATAACCCTTC
871059 TCGACTTAAGCTATACTGCAAATGATGTGCCTTGGAGCTGAGCGTAGTCAAACTCGAAGGTCTTT
131 TCGACTTAAGCTATACTGCAAATGATGTGCCTTGGAGCTGAGCGTAGTCAAACTCGAAGGTCTTT
*
871124 GGTTGACAGATAACCCTTATCGACTTAAGTTATGCTGTAAATGATATGCCTTGA
196 GGTTGACAGATAACCCTTATCGACTTAAGTTATGCTGCAAATGATATGCCTTGA
*
871178 AGCTGAGCGTAGTC-AAACTCGAAGGTCTTTTGGTCACAGATAACCCTTCTAGCCTTGAGTTATA
1 AGCTGAGCGTAGTCGAAA-TCGAAGGTCTTTTGGTCACAGATAACCCTTCTAGCCTTGAGTTATG
* * * *
871242 TTGTAAATAATGTGCCCTCAAAGCTGAGTGTAATCGAACTCGAGGGTCTTCGGTTGGCAAATAAC
65 CTGTAAATGATGTGCCCTCGAAGCTGAGTGTAATCGAACTCGAGGGTC-T---TTGGCAGATAAC
* * *
871307 CCTTCTTGACTTAAGTTATACTGCAAATGATATGCCTTGGAGCTG
126 CCTTCTCGACTTAAGCTATACTGCAAATGATGTGCCTTGGAGCTG
871352 TGTTGAACTC
Statistics
Matches: 633, Mismatches: 33, Indels: 7
0.94 0.05 0.01
Matches are distributed among these distances:
248 26 0.04
249 553 0.87
250 1 0.00
253 53 0.08
ACGTcount: A:0.26, C:0.20, G:0.24, T:0.30
Consensus pattern (249 bp):
AGCTGAGCGTAGTCGAAATCGAAGGTCTTTTGGTCACAGATAACCCTTCTAGCCTTGAGTTATGC
TGTAAATGATGTGCCCTCGAAGCTGAGTGTAATCGAACTCGAGGGTCTTTGGCAGATAACCCTTC
TCGACTTAAGCTATACTGCAAATGATGTGCCTTGGAGCTGAGCGTAGTCAAACTCGAAGGTCTTT
GGTTGACAGATAACCCTTATCGACTTAAGTTATGCTGCAAATGATATGCCTTGA
Found at i:871700 original size:110 final size:110
Alignment explanation
Indices: 871491--872136 Score: 949
Period size: 110 Copynumber: 5.9 Consensus size: 110
871481 TTGTGCAGTT
* * *
871491 TCGAGGCCAATATCATTCGCCGTGAAGTTGAAATTGACTC----TGAAACTGGAAAGTTGTTTGT
1 TCGAGTCCAATATCATTCGCTGTGAAGTTGAAATTGACTCTGAATGAAACTGAAAAGTTGTTTGT
** * * *
871552 TGACAACCAGTCGCCCCTCCGCTGTGAAGTTGAACTTGTGTTATC
66 TGACAGTCAGTCGCCCCTTCGCTGTGAAGTTGAGCTTGTGTTGTC
* * * *
871597 TCGAGTCCAATATCCTTCGCGGTGAAGTTGAAATTGACTCTAAATGAAACTGAAAAGTTTTTTGT
1 TCGAGTCCAATATCATTCGCTGTGAAGTTGAAATTGACTCTGAATGAAACTGAAAAGTTGTTTGT
* *
871662 TGACAGTCAATCACCCCTTCGCTGTGAAGTTGAGCTTGTGTTGTC
66 TGACAGTCAGTCGCCCCTTCGCTGTGAAGTTGAGCTTGTGTTGTC
* * *
871707 TCGAGTCCAATATCTTTCGCTTTGAAGTTGAAATTGACTCTGAATAAAACTGAAAAGTTGTTTGT
1 TCGAGTCCAATATCATTCGCTGTGAAGTTGAAATTGACTCTGAATGAAACTGAAAAGTTGTTTGT
* * * *
871772 TGACACTCAGACGCCCATTCGCTATGAAGTTGAGCTTGTGTTGTC
66 TGACAGTCAGTCGCCCCTTCGCTGTGAAGTTGAGCTTGTGTTGTC
* *
871817 TCGAGTCCAATATCATTCGCTGTGAAATTGAAATTGACTCTGAATGAAACTGAAAAGTTATTTGT
1 TCGAGTCCAATATCATTCGCTGTGAAGTTGAAATTGACTCTGAATGAAACTGAAAAGTTGTTTGT
* * *
871882 TGACAGTCAGCCTCCCATTCGCTGTGAAGTTGAGCTTGTGTTGTC
66 TGACAGTCAGTCGCCCCTTCGCTGTGAAGTTGAGCTTGTGTTGTC
* * * *
871927 TCAAGTCCAATATCATTCGCTGTAAAGTTGAAATTGACTCTGAATGAAATTGAAAAGTTATTTGT
1 TCGAGTCCAATATCATTCGCTGTGAAGTTGAAATTGACTCTGAATGAAACTGAAAAGTTGTTTGT
* *
871992 TGACAGTCAGTCACCCCTTCGCTGTGAAGTTGAGTTTGTGTTGTC
66 TGACAGTCAGTCGCCCCTTCGCTGTGAAGTTGAGCTTGTGTTGTC
* *
872037 TCGAGTCCAATATCCTTCGCTGTGAAGTTGAAATCGACTCTGAATGAAACTGAAAAGTTGTTTGT
1 TCGAGTCCAATATCATTCGCTGTGAAGTTGAAATTGACTCTGAATGAAACTGAAAAGTTGTTTGT
*
872102 TGACCGTCAGTCGCCCCTTCGCTGTGAAGTTGAGC
66 TGACAGTCAGTCGCCCCTTCGCTGTGAAGTTGAGC
872137 AACCACCATC
Statistics
Matches: 486, Mismatches: 50, Indels: 4
0.90 0.09 0.01
Matches are distributed among these distances:
106 37 0.08
110 449 0.92
ACGTcount: A:0.26, C:0.19, G:0.22, T:0.33
Consensus pattern (110 bp):
TCGAGTCCAATATCATTCGCTGTGAAGTTGAAATTGACTCTGAATGAAACTGAAAAGTTGTTTGT
TGACAGTCAGTCGCCCCTTCGCTGTGAAGTTGAGCTTGTGTTGTC
Found at i:876130 original size:33 final size:33
Alignment explanation
Indices: 876093--876158 Score: 114
Period size: 33 Copynumber: 2.0 Consensus size: 33
876083 AAAATGCTTC
*
876093 AGTTTTAGTGTTTCAATAGGACCCAAATACGTT
1 AGTTTTAATGTTTCAATAGGACCCAAATACGTT
*
876126 AGTTTTAATGTTTCAATAGGACTCAAATACGTT
1 AGTTTTAATGTTTCAATAGGACCCAAATACGTT
876159 GATTTATTTT
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
33 31 1.00
ACGTcount: A:0.32, C:0.14, G:0.17, T:0.38
Consensus pattern (33 bp):
AGTTTTAATGTTTCAATAGGACCCAAATACGTT
Found at i:876236 original size:3 final size:3
Alignment explanation
Indices: 876213--876286 Score: 77
Period size: 3 Copynumber: 25.3 Consensus size: 3
876203 GGCCTGCAAA
*
876213 AAT AAT AA- AAT AAA AAT -AT AAT AAT AAT AAT AAT AAT AAT AAT AAAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT -AAT
876260 AAAT AA- AAT ATAT AAT -AT AAT AA- AAT A
1 -AAT AAT AAT A-AT AAT AAT AAT AAT AAT A
876287 TTTTTATAAA
Statistics
Matches: 62, Mismatches: 2, Indels: 14
0.79 0.03 0.18
Matches are distributed among these distances:
2 10 0.16
3 42 0.68
4 10 0.16
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (3 bp):
AAT
Found at i:876474 original size:42 final size:41
Alignment explanation
Indices: 876403--876487 Score: 143
Period size: 42 Copynumber: 2.0 Consensus size: 41
876393 AGATTGGGGT
* *
876403 AATGCTTGGGGTTTTCTTTAGGTGAAGGCAACTTCCATACG
1 AATGCTTAGGGTTTTCTTTAGGTAAAGGCAACTTCCATACG
876444 AATGCTTAGGGTTTTGCTTTAGGTAAAGGCAACTTCCATACG
1 AATGCTTAGGGTTTT-CTTTAGGTAAAGGCAACTTCCATACG
876486 AA
1 AA
876488 GCGATGGAAG
Statistics
Matches: 41, Mismatches: 2, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
41 14 0.34
42 27 0.66
ACGTcount: A:0.26, C:0.16, G:0.25, T:0.33
Consensus pattern (41 bp):
AATGCTTAGGGTTTTCTTTAGGTAAAGGCAACTTCCATACG
Found at i:878675 original size:3 final size:3
Alignment explanation
Indices: 878662--878692 Score: 55
Period size: 3 Copynumber: 10.7 Consensus size: 3
878652 ATAAGATCTT
878662 TTA TT- TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
878693 TTAAATTTGA
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
2 2 0.07
3 25 0.93
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (3 bp):
TTA
Found at i:878872 original size:2 final size:2
Alignment explanation
Indices: 878867--878897 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
878857 AAAAGAGAAT
878867 TA TA 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 TA TA T
878898 TTTAGGTCAA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:880134 original size:29 final size:29
Alignment explanation
Indices: 880091--880173 Score: 139
Period size: 29 Copynumber: 2.8 Consensus size: 29
880081 CTCACCTAAC
880091 TAAATTGATGTAAGCAATGACATCATTAAT
1 TAAA-TGATGTAAGCAATGACATCATTAAT
*
880121 TAAATGATGTAAGCAATGACATCTTTAAT
1 TAAATGATGTAAGCAATGACATCATTAAT
*
880150 TAAATGATGTAAGTAATGACATCA
1 TAAATGATGTAAGCAATGACATCA
880174 ATTTAGTTTG
Statistics
Matches: 50, Mismatches: 3, Indels: 1
0.93 0.06 0.02
Matches are distributed among these distances:
29 46 0.92
30 4 0.08
ACGTcount: A:0.43, C:0.10, G:0.14, T:0.33
Consensus pattern (29 bp):
TAAATGATGTAAGCAATGACATCATTAAT
Found at i:885000 original size:29 final size:29
Alignment explanation
Indices: 884957--885039 Score: 139
Period size: 29 Copynumber: 2.8 Consensus size: 29
884947 CTCACCTAAC
884957 TAAATTGATGTAAGCAATGACATCATTAAT
1 TAAA-TGATGTAAGCAATGACATCATTAAT
*
884987 TAAATGATGTAAGCAATGACATCTTTAAT
1 TAAATGATGTAAGCAATGACATCATTAAT
*
885016 TAAATGATGTAAGTAATGACATCA
1 TAAATGATGTAAGCAATGACATCA
885040 ATTTAGTTTG
Statistics
Matches: 50, Mismatches: 3, Indels: 1
0.93 0.06 0.02
Matches are distributed among these distances:
29 46 0.92
30 4 0.08
ACGTcount: A:0.43, C:0.10, G:0.14, T:0.33
Consensus pattern (29 bp):
TAAATGATGTAAGCAATGACATCATTAAT
Found at i:893658 original size:16 final size:16
Alignment explanation
Indices: 893637--893670 Score: 59
Period size: 16 Copynumber: 2.1 Consensus size: 16
893627 TTACTATTCA
*
893637 CGTGAATAGTGAATTT
1 CGTGAATAGTGAAATT
893653 CGTGAATAGTGAAATT
1 CGTGAATAGTGAAATT
893669 CG
1 CG
893671 ATCGGCGATA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.32, C:0.09, G:0.26, T:0.32
Consensus pattern (16 bp):
CGTGAATAGTGAAATT
Found at i:898725 original size:21 final size:21
Alignment explanation
Indices: 898700--898862 Score: 109
Period size: 21 Copynumber: 8.0 Consensus size: 21
898690 TCAGTTTCCA
* *
898700 AATTCACGTTGCGATAGTCGG
1 AATTCGCGTTGCGATAGTCCG
* *
898721 AATTCGTGTTGCGATAGTCCA
1 AATTCGCGTTGCGATAGTCCG
* * ** **
898742 AAAT--CATTGCGATTTTCTA
1 AATTCGCGTTGCGATAGTCCG
898761 AATTCGCGTTGCGATAGTCCG
1 AATTCGCGTTGCGATAGTCCG
** *
898782 AATTCGCGTTGCGATTTTCTG
1 AATTCGCGTTGCGATAGTCCG
* *
898803 AATTCGCGTTACGATAGTCCA
1 AATTCGCGTTGCGATAGTCCG
* * ** **
898824 AAAT--CATTGCGATTTTCTA
1 AATTCGCGTTGCGATAGTCCG
898843 AATTCGCGTTGCGATAGTCC
1 AATTCGCGTTGCGATAGTCC
898863 AAAATCATTG
Statistics
Matches: 103, Mismatches: 35, Indels: 8
0.71 0.24 0.05
Matches are distributed among these distances:
19 26 0.25
21 77 0.75
ACGTcount: A:0.24, C:0.20, G:0.21, T:0.34
Consensus pattern (21 bp):
AATTCGCGTTGCGATAGTCCG
Found at i:898753 original size:40 final size:40
Alignment explanation
Indices: 898721--898887 Score: 262
Period size: 40 Copynumber: 4.1 Consensus size: 40
898711 CGATAGTCGG
*
898721 AATTCGTGTTGCGATAGTCCAAAATCATTGCGATTTTCTA
1 AATTCGCGTTGCGATAGTCCAAAATCATTGCGATTTTCTA
* * * *
898761 AATTCGCGTTGCGATAGTCCGAATTCGCGTTGCGATTTTCTG
1 AATTCGCGTTGCGATAGTCCAAAAT--CATTGCGATTTTCTA
*
898803 AATTCGCGTTACGATAGTCCAAAATCATTGCGATTTTCTA
1 AATTCGCGTTGCGATAGTCCAAAATCATTGCGATTTTCTA
898843 AATTCGCGTTGCGATAGTCCAAAATCATTGCGATTTTCTA
1 AATTCGCGTTGCGATAGTCCAAAATCATTGCGATTTTCTA
898883 AATTC
1 AATTC
898888 ACGACCACGA
Statistics
Matches: 114, Mismatches: 11, Indels: 4
0.88 0.09 0.03
Matches are distributed among these distances:
40 79 0.69
42 35 0.31
ACGTcount: A:0.26, C:0.20, G:0.19, T:0.36
Consensus pattern (40 bp):
AATTCGCGTTGCGATAGTCCAAAATCATTGCGATTTTCTA
Found at i:898794 original size:82 final size:82
Alignment explanation
Indices: 898700--898862 Score: 272
Period size: 82 Copynumber: 2.0 Consensus size: 82
898690 TCAGTTTCCA
* *
898700 AATTCACGTTGCGATAGTCGGAATTCGTGTTGCGATAGTCCAAAATCATTGCGATTTTCTAAATT
1 AATTCACGTTGCGATAGTCGGAATTCGCGTTACGATAGTCCAAAATCATTGCGATTTTCTAAATT
898765 CGCGTTGCGATAGTCCG
66 CGCGTTGCGATAGTCCG
* ** *
898782 AATTCGCGTTGCGATTTTCTGAATTCGCGTTACGATAGTCCAAAATCATTGCGATTTTCTAAATT
1 AATTCACGTTGCGATAGTCGGAATTCGCGTTACGATAGTCCAAAATCATTGCGATTTTCTAAATT
898847 CGCGTTGCGATAGTCC
66 CGCGTTGCGATAGTCC
898863 AAAATCATTG
Statistics
Matches: 75, Mismatches: 6, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
82 75 1.00
ACGTcount: A:0.24, C:0.20, G:0.21, T:0.34
Consensus pattern (82 bp):
AATTCACGTTGCGATAGTCGGAATTCGCGTTACGATAGTCCAAAATCATTGCGATTTTCTAAATT
CGCGTTGCGATAGTCCG
Found at i:898875 original size:19 final size:19
Alignment explanation
Indices: 898814--898876 Score: 63
Period size: 19 Copynumber: 3.2 Consensus size: 19
898804 ATTCGCGTTA
898814 CGATAGTCCAAAATCATTG
1 CGATAGTCCAAAATCATTG
** * * *
898833 CGATTTTCTAAATTCGCGTTG
1 CGATAGTCCAAAAT--CATTG
898854 CGATAGTCCAAAATCATTG
1 CGATAGTCCAAAATCATTG
898873 CGAT
1 CGAT
898877 TTTCTAAATT
Statistics
Matches: 32, Mismatches: 10, Indels: 4
0.70 0.22 0.09
Matches are distributed among these distances:
19 18 0.56
21 14 0.44
ACGTcount: A:0.30, C:0.21, G:0.17, T:0.32
Consensus pattern (19 bp):
CGATAGTCCAAAATCATTG
Found at i:899882 original size:182 final size:182
Alignment explanation
Indices: 899575--899940 Score: 723
Period size: 182 Copynumber: 2.0 Consensus size: 182
899565 CGTGTCTTCG
899575 ACACGTCCGCGCGGATACTATCTTTTTAGGGAAAATTCTTAAGAAACAAATACGAATTATAATCC
1 ACACGTCCGCGCGGATACTATCTTTTTAGGGAAAATTCTTAAGAAACAAATACGAATTATAATCC
899640 TACAACAATTAAATAAGATAAGCTTTTATTCTCAACGTGTTTATTTAAAAAAAAGAGAGAAAATT
66 TACAACAATTAAATAAGATAAGCTTTTATTCTCAACGTGTTTATTTAAAAAAAAGAGAGAAAATT
899705 CGGACTATCGCAATGATTTTGGACTATCGCAACGCGAATTCGGAAAATCGCA
131 CGGACTATCGCAATGATTTTGGACTATCGCAACGCGAATTCGGAAAATCGCA
*
899757 ACACGTCCGCGCGGATACTATCTTTTTAGGGAAAATTCTTAAGAAACAAATGCGAATTATAATCC
1 ACACGTCCGCGCGGATACTATCTTTTTAGGGAAAATTCTTAAGAAACAAATACGAATTATAATCC
899822 TACAACAATTAAATAAGATAAGCTTTTATTCTCAACGTGTTTATTTAAAAAAAAGAGAGAAAATT
66 TACAACAATTAAATAAGATAAGCTTTTATTCTCAACGTGTTTATTTAAAAAAAAGAGAGAAAATT
899887 CGGACTATCGCAATGATTTTGGACTATCGCAACGCGAATTCGGAAAATCGCA
131 CGGACTATCGCAATGATTTTGGACTATCGCAACGCGAATTCGGAAAATCGCA
899939 AC
1 AC
899941 GTGAATTTGG
Statistics
Matches: 183, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
182 183 1.00
ACGTcount: A:0.39, C:0.17, G:0.16, T:0.28
Consensus pattern (182 bp):
ACACGTCCGCGCGGATACTATCTTTTTAGGGAAAATTCTTAAGAAACAAATACGAATTATAATCC
TACAACAATTAAATAAGATAAGCTTTTATTCTCAACGTGTTTATTTAAAAAAAAGAGAGAAAATT
CGGACTATCGCAATGATTTTGGACTATCGCAACGCGAATTCGGAAAATCGCA
Found at i:899938 original size:21 final size:21
Alignment explanation
Indices: 899912--900065 Score: 177
Period size: 21 Copynumber: 7.3 Consensus size: 21
899902 ATTTTGGACT
*
899912 ATCGCAACGCGAATTCGGAAA
1 ATCGCAACGCGAATTCAGAAA
* ** **
899933 ATCGCAACGTGAATTTGGACT
1 ATCGCAACGCGAATTCAGAAA
* *
899954 ATCGCAACGCAAATTTAGAAA
1 ATCGCAACGCGAATTCAGAAA
899975 ATCG-AAGCGCGAATTCAGAAA
1 ATCGCAA-CGCGAATTCAGAAA
899996 ATCG-AAGCGCGAATTCAGAAA
1 ATCGCAA-CGCGAATTCAGAAA
* **
900017 ATCGCAGCGCGAATTCAGACT
1 ATCGCAACGCGAATTCAGAAA
900038 ATCGCAACGCGAATTCAGAAA
1 ATCGCAACGCGAATTCAGAAA
900059 ATCGCAA
1 ATCGCAA
900066 TGATTTTGGA
Statistics
Matches: 114, Mismatches: 17, Indels: 4
0.84 0.13 0.03
Matches are distributed among these distances:
20 2 0.02
21 111 0.97
22 1 0.01
ACGTcount: A:0.39, C:0.22, G:0.21, T:0.18
Consensus pattern (21 bp):
ATCGCAACGCGAATTCAGAAA
Found at i:899960 original size:42 final size:42
Alignment explanation
Indices: 899904--900098 Score: 209
Period size: 42 Copynumber: 4.7 Consensus size: 42
899894 TCGCAATGAT
*
899904 TTTGGACTATCGCAACGCGAATTCGGAAAATCGCAACGTGAA
1 TTTGGACTATCGCAACGCGAATTCAGAAAATCGCAACGTGAA
* * *
899946 TTTGGACTATCGCAACGCAAATTTAGAAAATCG-AAGCGCGAA
1 TTTGGACTATCGCAACGCGAATTCAGAAAATCGCAA-CGTGAA
** ** * *
899988 TTCAGAAAATCG-AAGCGCGAATTCAGAAAATCGCAGCGCGAA
1 TTTGGACTATCGCAA-CGCGAATTCAGAAAATCGCAACGTGAA
** *
900030 TTCAGACTATCGCAACGCGAATTCAGAAAATCGCAA--TGAT
1 TTTGGACTATCGCAACGCGAATTCAGAAAATCGCAACGTGAA
* *
900070 TTTGGACTATCGCATCGCGAATTCCGAAA
1 TTTGGACTATCGCAACGCGAATTCAGAAA
900099 CTGAGTTGTG
Statistics
Matches: 129, Mismatches: 20, Indels: 10
0.81 0.13 0.06
Matches are distributed among these distances:
40 27 0.21
41 4 0.03
42 95 0.74
43 3 0.02
ACGTcount: A:0.36, C:0.22, G:0.22, T:0.21
Consensus pattern (42 bp):
TTTGGACTATCGCAACGCGAATTCAGAAAATCGCAACGTGAA
Found at i:899996 original size:63 final size:63
Alignment explanation
Indices: 899912--900098 Score: 202
Period size: 63 Copynumber: 3.0 Consensus size: 63
899902 ATTTTGGACT
* * *
899912 ATCGCAACGCGAATTCGGAAAATCGCAACGTGAATTTGGACTATCGCAACGCAAATTTAGAAA
1 ATCGCAACGCGAATTCAGAAAATCGCAACGTGAATTTGGACTATCGCAACGCGAATTCAGAAA
* ** ** * **
899975 ATCG-AAGCGCGAATTCAGAAAATCG-AAGCGCGAATTCAGAAAATCGCAGCGCGAATTCAGACT
1 ATCGCAA-CGCGAATTCAGAAAATCGCAA-CGTGAATTTGGACTATCGCAACGCGAATTCAGAAA
* * *
900038 ATCGCAACGCGAATTCAGAAAATCGCAA--TGATTTTGGACTATCGCATCGCGAATTCCGAAA
1 ATCGCAACGCGAATTCAGAAAATCGCAACGTGAATTTGGACTATCGCAACGCGAATTCAGAAA
900099 CTGAGTTGTG
Statistics
Matches: 99, Mismatches: 21, Indels: 10
0.76 0.16 0.08
Matches are distributed among these distances:
61 23 0.23
62 4 0.04
63 68 0.69
64 4 0.04
ACGTcount: A:0.37, C:0.22, G:0.21, T:0.20
Consensus pattern (63 bp):
ATCGCAACGCGAATTCAGAAAATCGCAACGTGAATTTGGACTATCGCAACGCGAATTCAGAAA
Found at i:904916 original size:21 final size:21
Alignment explanation
Indices: 904838--904918 Score: 65
Period size: 21 Copynumber: 3.8 Consensus size: 21
904828 TAGATGGATT
904838 AAAGGGTTAAGACCTTTTGATG
1 AAAGGGTTAA-ACCTTTTGATG
* * * * * *
904860 AAATGATTTAACCGTTCGATT
1 AAAGGGTTAAACCTTTTGATG
* *
904881 AAAGGACTT-ATCCTTTTGATG
1 AAAGG-GTTAAACCTTTTGATG
904902 AAAGGGTTAAACCTTTT
1 AAAGGGTTAAACCTTTT
904919 CATAAAGTGA
Statistics
Matches: 43, Mismatches: 14, Indels: 5
0.69 0.23 0.08
Matches are distributed among these distances:
20 2 0.05
21 32 0.74
22 9 0.21
ACGTcount: A:0.32, C:0.12, G:0.20, T:0.36
Consensus pattern (21 bp):
AAAGGGTTAAACCTTTTGATG
Found at i:905610 original size:44 final size:42
Alignment explanation
Indices: 905528--905673 Score: 145
Period size: 43 Copynumber: 3.4 Consensus size: 42
905518 AATTTATTGA
* *
905528 ATTGAAAAAAATTAGGGGCATTAATCGTAAAGGTAAAAATCGAT
1 ATTGAAAAAAATTAGGGGC-TTAATTGTAAAAGTAAAAAT-GAT
* * *
905572 ATTG-AAAAAATTAGGGGTCTCAATTGTAAAAGTAAAAAATAAG
1 ATTGAAAAAAATTAGGGG-CTTAATTGTAAAAGT-AAAAATGAT
* *
905615 ATTGAAAAAAATTTGGGGCCTTAATTATAAAAGTAAAAATTG-T
1 ATTGAAAAAAATTAGGGG-CTTAATTGTAAAAGTAAAAA-TGAT
905658 GATTG-AAAAAATTAGG
1 -ATTGAAAAAAATTAGG
905674 AGCGTTATAA
Statistics
Matches: 85, Mismatches: 12, Indels: 11
0.79 0.11 0.10
Matches are distributed among these distances:
43 44 0.52
44 41 0.48
ACGTcount: A:0.49, C:0.05, G:0.19, T:0.27
Consensus pattern (42 bp):
ATTGAAAAAAATTAGGGGCTTAATTGTAAAAGTAAAAATGAT
Found at i:905789 original size:44 final size:45
Alignment explanation
Indices: 905576--905834 Score: 172
Period size: 44 Copynumber: 6.1 Consensus size: 45
905566 ATCGATATTG
* * * * * *
905576 AAAAAATTA-GGGGTCTCAATTGTAAAAGTAAAAAATAAGATTGA
1 AAAAAATTATGGAGCCTCAATTATAAAAGTAAAAAGTGAGATTAA
* * * * *
905620 AAAAAATT-TGGGGCCTTAATTATAAAAGTAAAAATTGTGATT-G
1 AAAAAATTATGGAGCCTCAATTATAAAAGTAAAAAGTGAGATTAA
*
905663 AAAAAATTA-GGAG---C-GTTATAAAAGTAAAAAGTGAGATT-A
1 AAAAAATTATGGAGCCTCAATTATAAAAGTAAAAAGTGAGATTAA
* ** * * * * *
905702 AAAAAACTAAAG-GCCTC-A--ATACAGGTATAAAGTGAAACTAA
1 AAAAAATTATGGAGCCTCAATTATAAAAGTAAAAAGTGAGATTAA
*
905743 AAAAAATTATGGAG-CTCAATTATAAAAGTAAAAAGTGGGATT-A
1 AAAAAATTATGGAGCCTCAATTATAAAAGTAAAAAGTGAGATTAA
* * * * *
905786 AAAAAATCAT-GAGCCTTAATTATAAAGGTAAAAAATAAGATTAA
1 AAAAAATTATGGAGCCTCAATTATAAAAGTAAAAAGTGAGATTAA
905830 AAAAA
1 AAAAA
905835 TAAGATCTAA
Statistics
Matches: 166, Mismatches: 36, Indels: 26
0.73 0.16 0.11
Matches are distributed among these distances:
39 30 0.18
40 17 0.10
41 13 0.08
42 6 0.04
43 44 0.27
44 56 0.34
ACGTcount: A:0.53, C:0.06, G:0.17, T:0.24
Consensus pattern (45 bp):
AAAAAATTATGGAGCCTCAATTATAAAAGTAAAAAGTGAGATTAA
Found at i:905790 original size:43 final size:44
Alignment explanation
Indices: 905576--905835 Score: 186
Period size: 43 Copynumber: 6.2 Consensus size: 44
905566 ATCGATATTG
* * * * *
905576 AAAAAATTA-GGGGTCTCAATTGTAAAAGTAAAAAATAAGATTGA
1 AAAAAATTATGGAGCCTCAATTATAAAAGTAAAAAGTGAGATT-A
* * * * *
905620 AAAAAATT-TGGGGCCTTAATTATAAAAGTAAAAATTGTGATTG
1 AAAAAATTATGGAGCCTCAATTATAAAAGTAAAAAGTGAGATTA
*
905663 AAAAAATTA-GGAG---C-GTTATAAAAGTAAAAAGTGAGATTA
1 AAAAAATTATGGAGCCTCAATTATAAAAGTAAAAAGTGAGATTA
* ** * * * * *
905702 AAAAAACTAAAG-GCCTC-A--ATACAGGTATAAAGTGAAACTAA
1 AAAAAATTATGGAGCCTCAATTATAAAAGTAAAAAGTGAGA-TTA
*
905743 AAAAAATTATGGAG-CTCAATTATAAAAGTAAAAAGTGGGATTA
1 AAAAAATTATGGAGCCTCAATTATAAAAGTAAAAAGTGAGATTA
* * * * *
905786 AAAAAATCAT-GAGCCTTAATTATAAAGGTAAAAAATAAGATTA
1 AAAAAATTATGGAGCCTCAATTATAAAAGTAAAAAGTGAGATTA
905829 AAAAAAT
1 AAAAAAT
905836 AAGATCTAAT
Statistics
Matches: 168, Mismatches: 36, Indels: 25
0.73 0.16 0.11
Matches are distributed among these distances:
39 30 0.18
40 16 0.10
41 14 0.08
42 6 0.04
43 53 0.32
44 49 0.29
ACGTcount: A:0.53, C:0.06, G:0.17, T:0.25
Consensus pattern (44 bp):
AAAAAATTATGGAGCCTCAATTATAAAAGTAAAAAGTGAGATTA
Found at i:917638 original size:23 final size:23
Alignment explanation
Indices: 917612--917661 Score: 100
Period size: 23 Copynumber: 2.2 Consensus size: 23
917602 GTTTGTATTT
917612 GTTCCTGCATTAAGTTAGCTTTG
1 GTTCCTGCATTAAGTTAGCTTTG
917635 GTTCCTGCATTAAGTTAGCTTTG
1 GTTCCTGCATTAAGTTAGCTTTG
917658 GTTC
1 GTTC
917662 TTTAAGTTGC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 27 1.00
ACGTcount: A:0.16, C:0.18, G:0.22, T:0.44
Consensus pattern (23 bp):
GTTCCTGCATTAAGTTAGCTTTG
Found at i:917668 original size:19 final size:21
Alignment explanation
Indices: 917620--917669 Score: 68
Period size: 23 Copynumber: 2.4 Consensus size: 21
917610 TTGTTCCTGC
917620 ATTAAGTTAGCTTTGGTTCCT
1 ATTAAGTTAGCTTTGGTTCCT
917641 GCATTAAGTTAGCTTTGGTT-CT
1 --ATTAAGTTAGCTTTGGTTCCT
917663 -TTAAGTT
1 ATTAAGTT
917670 GCTGATATTG
Statistics
Matches: 27, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
19 7 0.26
22 2 0.07
23 18 0.67
ACGTcount: A:0.20, C:0.12, G:0.20, T:0.48
Consensus pattern (21 bp):
ATTAAGTTAGCTTTGGTTCCT
Found at i:926680 original size:15 final size:15
Alignment explanation
Indices: 926660--926688 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
926650 CATATAAAGT
926660 TAATGTTAATGTCAC
1 TAATGTTAATGTCAC
926675 TAATGTTAATGTCA
1 TAATGTTAATGTCA
926689 AATAATTTGC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.34, C:0.10, G:0.14, T:0.41
Consensus pattern (15 bp):
TAATGTTAATGTCAC
Found at i:935847 original size:18 final size:17
Alignment explanation
Indices: 935807--935849 Score: 59
Period size: 17 Copynumber: 2.5 Consensus size: 17
935797 TAAATGTTAA
935807 ATTTTAAAAGAGATTCG
1 ATTTTAAAAGAGATTCG
* *
935824 AATTTAAAAGAGAATTTG
1 ATTTTAAAAGAG-ATTCG
935842 ATTTTAAA
1 ATTTTAAA
935850 GGAAAATAGA
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
17 11 0.50
18 11 0.50
ACGTcount: A:0.47, C:0.02, G:0.14, T:0.37
Consensus pattern (17 bp):
ATTTTAAAAGAGATTCG
Found at i:935850 original size:17 final size:19
Alignment explanation
Indices: 935806--935850 Score: 51
Period size: 18 Copynumber: 2.5 Consensus size: 19
935796 TTAAATGTTA
935806 AATTTTAAA-AGAGATTCG
1 AATTTTAAAGAGAGATTCG
* *
935824 AATTTAAAAGAGA-ATTTG
1 AATTTTAAAGAGAGATTCG
935842 -ATTTTAAAG
1 AATTTTAAAG
935851 GAAAATAGAA
Statistics
Matches: 23, Mismatches: 3, Indels: 3
0.79 0.10 0.10
Matches are distributed among these distances:
17 8 0.35
18 12 0.52
19 3 0.13
ACGTcount: A:0.47, C:0.02, G:0.16, T:0.36
Consensus pattern (19 bp):
AATTTTAAAGAGAGATTCG
Found at i:937473 original size:13 final size:13
Alignment explanation
Indices: 937455--937479 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
937445 ACGTCATTTA
937455 ATTTAAAAAAATC
1 ATTTAAAAAAATC
937468 ATTTAAAAAAAT
1 ATTTAAAAAAAT
937480 AAAAGTCCGT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.64, C:0.04, G:0.00, T:0.32
Consensus pattern (13 bp):
ATTTAAAAAAATC
Found at i:938803 original size:29 final size:30
Alignment explanation
Indices: 938745--938803 Score: 84
Period size: 29 Copynumber: 2.0 Consensus size: 30
938735 CTATTTTGAG
* *
938745 AAACGGAATGAAACATTAGACACCAGACTA
1 AAACGAAATGAAACATTAGACACCAAACTA
*
938775 AAACGAAAT-AAACATTAGACACTAAACTA
1 AAACGAAATGAAACATTAGACACCAAACTA
938804 GAAAAATAAG
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
29 18 0.69
30 8 0.31
ACGTcount: A:0.54, C:0.19, G:0.12, T:0.15
Consensus pattern (30 bp):
AAACGAAATGAAACATTAGACACCAAACTA
Found at i:939263 original size:24 final size:27
Alignment explanation
Indices: 939219--939268 Score: 70
Period size: 24 Copynumber: 2.0 Consensus size: 27
939209 TTAGGGATAG
*
939219 GAATTTGAAGTTTTTTGTAATTTCAAA
1 GAATTTGAAGTTTTTTGTAATATCAAA
939246 GAATTTG-AG-TTTTT-TAATATCAA
1 GAATTTGAAGTTTTTTGTAATATCAA
939269 TATTTTAAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
24 8 0.36
25 5 0.23
26 2 0.09
27 7 0.32
ACGTcount: A:0.34, C:0.04, G:0.14, T:0.48
Consensus pattern (27 bp):
GAATTTGAAGTTTTTTGTAATATCAAA
Found at i:943343 original size:18 final size:19
Alignment explanation
Indices: 943309--943346 Score: 60
Period size: 18 Copynumber: 2.1 Consensus size: 19
943299 ATATTTATTA
943309 ATATTTCTAATAATATAAT
1 ATATTTCTAATAATATAAT
*
943328 ATATTT-TAATATTATAAT
1 ATATTTCTAATAATATAAT
943346 A
1 A
943347 ACCAATTATA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 12 0.67
19 6 0.33
ACGTcount: A:0.47, C:0.03, G:0.00, T:0.50
Consensus pattern (19 bp):
ATATTTCTAATAATATAAT
Found at i:943450 original size:27 final size:28
Alignment explanation
Indices: 943416--943490 Score: 79
Period size: 27 Copynumber: 2.8 Consensus size: 28
943406 ATTAAAATTT
*
943416 ATATTATTTATTAATTTT-AT-AGAAATA
1 ATATTATTTATAAATTTTAATAAG-AATA
943443 ATATTA-TTA-AAATTTTAATAATGAATA
1 ATATTATTTATAAATTTTAATAA-GAATA
*
943470 ATATTATTTATATA-TTTAATA
1 ATATTATTTATAAATTTTAATA
943491 TTAATATAAT
Statistics
Matches: 41, Mismatches: 2, Indels: 9
0.79 0.04 0.17
Matches are distributed among these distances:
25 6 0.15
26 5 0.12
27 17 0.41
28 11 0.27
29 2 0.05
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.51
Consensus pattern (28 bp):
ATATTATTTATAAATTTTAATAAGAATA
Found at i:943496 original size:27 final size:27
Alignment explanation
Indices: 943416--943501 Score: 77
Period size: 27 Copynumber: 3.1 Consensus size: 27
943406 ATTAAAATTT
* *
943416 ATATTATTTAT-TAATTTTATAGAAATA
1 ATATTATTTATAT-ATTTAATATAAATA
* * *
943443 ATATTATTAAAAT-TTTAATAATGAATA
1 ATATTATTTATATATTTAAT-ATAAATA
943470 ATATTATTTATATATTTAATATTAATATA
1 ATATTATTTATATATTTAATA-TAA-ATA
943499 ATA
1 ATA
943502 ATCTAATAAT
Statistics
Matches: 46, Mismatches: 8, Indels: 8
0.74 0.13 0.13
Matches are distributed among these distances:
26 5 0.11
27 26 0.57
28 9 0.20
29 6 0.13
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (27 bp):
ATATTATTTATATATTTAATATAAATA
Found at i:943542 original size:23 final size:23
Alignment explanation
Indices: 943516--943560 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
943506 AATAATATTT
943516 TAATAAAGATATTTAAAATATAC
1 TAATAAAGATATTTAAAATATAC
* * *
943539 TAATTAATATTTTTAAAATATA
1 TAATAAAGATATTTAAAATATA
943561 ATAAAACACT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.53, C:0.02, G:0.02, T:0.42
Consensus pattern (23 bp):
TAATAAAGATATTTAAAATATAC
Found at i:943855 original size:15 final size:15
Alignment explanation
Indices: 943832--943861 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
943822 TCGTAAAACG
943832 TTTTCCAGAAAATGT
1 TTTTCCAGAAAATGT
*
943847 TTTTTCAGAAAATGT
1 TTTTCCAGAAAATGT
943862 AATTCATTTT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.33, C:0.10, G:0.13, T:0.43
Consensus pattern (15 bp):
TTTTCCAGAAAATGT
Found at i:948866 original size:38 final size:38
Alignment explanation
Indices: 948823--948974 Score: 209
Period size: 38 Copynumber: 4.0 Consensus size: 38
948813 ATGAAATCGA
948823 AAAGAACCC-AATAAACAAATTCGTGAAAATACACAAAT
1 AAAGAACCCTAA-AAACAAATTCGTGAAAATACACAAAT
*
948861 GAAGAACCCTAAAAACAAATTCGTGAAAATACACAAAT
1 AAAGAACCCTAAAAACAAATTCGTGAAAATACACAAAT
* *
948899 AAAGAACCCTAAAAATAAATTCATGAAAATATC-CAAAT
1 AAAGAACCCTAAAAACAAATTCGTGAAAATA-CACAAAT
* * * *
948937 AAAGAATCCTAGAAACAAATTCGTCAAAATACTCAAAT
1 AAAGAACCCTAAAAACAAATTCGTGAAAATACACAAAT
948975 GAAATCGAAA
Statistics
Matches: 102, Mismatches: 9, Indels: 6
0.87 0.08 0.05
Matches are distributed among these distances:
37 1 0.01
38 98 0.96
39 3 0.03
ACGTcount: A:0.56, C:0.18, G:0.08, T:0.18
Consensus pattern (38 bp):
AAAGAACCCTAAAAACAAATTCGTGAAAATACACAAAT
Found at i:950368 original size:21 final size:21
Alignment explanation
Indices: 950344--950408 Score: 71
Period size: 19 Copynumber: 3.1 Consensus size: 21
950334 ATAGTCTAAG
950344 TTCGCGTTGCGATTTTCCAAA
1 TTCGCGTTGCGATTTTCCAAA
** *
950365 TT--CGTTGCGATAGTCCAAG
1 TTCGCGTTGCGATTTTCCAAA
950384 TTCGCGTTGCGATTTATTCCAAA
1 TTCGCGTTGCGA-TT-TTCCAAA
950407 TT
1 TT
950409 TATTGCGATA
Statistics
Matches: 34, Mismatches: 6, Indels: 6
0.74 0.13 0.13
Matches are distributed among these distances:
19 16 0.47
21 10 0.29
22 1 0.03
23 7 0.21
ACGTcount: A:0.20, C:0.22, G:0.20, T:0.38
Consensus pattern (21 bp):
TTCGCGTTGCGATTTTCCAAA
Found at i:950405 original size:42 final size:42
Alignment explanation
Indices: 950333--950471 Score: 219
Period size: 42 Copynumber: 3.4 Consensus size: 42
950323 TTCGCATTGT
*
950333 GATAGTCTAAGTTCGCGTTGCGA-TT-TTCCAAATTCGTTGC
1 GATAGTCCAAGTTCGCGTTGCGATTTATTCCAAATTCGTTGC
**
950373 GATAGTCCAAGTTCGCGTTGCGATTTATTCCAAATTTATTGC
1 GATAGTCCAAGTTCGCGTTGCGATTTATTCCAAATTCGTTGC
* *
950415 GATAGTCCAAGTTCGCATTGCGATTTATTACAAATTCGTTGC
1 GATAGTCCAAGTTCGCGTTGCGATTTATTCCAAATTCGTTGC
950457 GATAGTCCAAGTTCG
1 GATAGTCCAAGTTCG
950472 TTGCAATAGT
Statistics
Matches: 90, Mismatches: 7, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
40 22 0.24
41 2 0.02
42 66 0.73
ACGTcount: A:0.24, C:0.19, G:0.21, T:0.36
Consensus pattern (42 bp):
GATAGTCCAAGTTCGCGTTGCGATTTATTCCAAATTCGTTGC
Found at i:950466 original size:61 final size:61
Alignment explanation
Indices: 950401--950528 Score: 175
Period size: 61 Copynumber: 2.1 Consensus size: 61
950391 TGCGATTTAT
* *
950401 TCCAAATTTATTGCGATAGTCCAAGTTCGCATTGCGATTTATTACAAATTCGTTGCGATAG
1 TCCAAATTCATTGCAATAGTCCAAGTTCGCATTGCGATTTATTACAAATTCGTTGCGATAG
* * * ** * *
950462 TCCAAGTTCGTTGCAATAGTCGAAGTTCGTGTTGCGATTTTTTCCAAATTCGTTGCGATAG
1 TCCAAATTCATTGCAATAGTCCAAGTTCGCATTGCGATTTATTACAAATTCGTTGCGATAG
950523 TCCAAA
1 TCCAAA
950529 ATCGCAACTA
Statistics
Matches: 57, Mismatches: 10, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
61 57 1.00
ACGTcount: A:0.26, C:0.19, G:0.20, T:0.36
Consensus pattern (61 bp):
TCCAAATTCATTGCAATAGTCCAAGTTCGCATTGCGATTTATTACAAATTCGTTGCGATAG
Found at i:950534 original size:103 final size:103
Alignment explanation
Indices: 950348--950534 Score: 275
Period size: 103 Copynumber: 1.8 Consensus size: 103
950338 TCTAAGTTCG
** * *
950348 CGTTGCGATTTTCCAAATTCGTTGCGATAGTCCAAGTTCGCGTTGCGATTTATTCCAAATTTATT
1 CGTTGCGATAGTCCAAATTCGTTGCAATAGTCCAAGTTCGCGTTGCGATTTATTCCAAATTCATT
**
950413 GCGATAGTCCAAGTTCGCATTGCGATTTATTACAAATT
66 GCGATAGTCCAAAATCGCATTGCGATTTATTACAAATT
* * * * *
950451 CGTTGCGATAGTCCAAGTTCGTTGCAATAGTCGAAGTTCGTGTTGCGATTTTTTCCAAATTCGTT
1 CGTTGCGATAGTCCAAATTCGTTGCAATAGTCCAAGTTCGCGTTGCGATTTATTCCAAATTCATT
950516 GCGATAGTCCAAAATCGCA
66 GCGATAGTCCAAAATCGCA
950535 ACTACTGGTG
Statistics
Matches: 73, Mismatches: 11, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
103 73 1.00
ACGTcount: A:0.24, C:0.20, G:0.20, T:0.36
Consensus pattern (103 bp):
CGTTGCGATAGTCCAAATTCGTTGCAATAGTCCAAGTTCGCGTTGCGATTTATTCCAAATTCATT
GCGATAGTCCAAAATCGCATTGCGATTTATTACAAATT
Found at i:950628 original size:6 final size:6
Alignment explanation
Indices: 950617--950641 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
950607 GACACGTATT
950617 ACCACG ACCACG ACCACG ACCACG A
1 ACCACG ACCACG ACCACG ACCACG A
950642 GACGGACGGC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.36, C:0.48, G:0.16, T:0.00
Consensus pattern (6 bp):
ACCACG
Found at i:951278 original size:6 final size:6
Alignment explanation
Indices: 951269--951293 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
951259 GCCGTCCGTC
951269 TCGTGG TCGTGG TCGTGG TCGTGG T
1 TCGTGG TCGTGG TCGTGG TCGTGG T
951294 AATAGTAATG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.00, C:0.16, G:0.48, T:0.36
Consensus pattern (6 bp):
TCGTGG
Found at i:951305 original size:12 final size:13
Alignment explanation
Indices: 951290--951321 Score: 50
Period size: 12 Copynumber: 2.6 Consensus size: 13
951280 GTCGTGGTCG
951290 TGGTAATAG-TAA
1 TGGTAATAGCTAA
951302 TGGTAAT-GCTAA
1 TGGTAATAGCTAA
951314 TGGTAATA
1 TGGTAATA
951322 CGTGTCTTCG
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
11 1 0.06
12 17 0.94
ACGTcount: A:0.38, C:0.03, G:0.25, T:0.34
Consensus pattern (13 bp):
TGGTAATAGCTAA
Found at i:960494 original size:19 final size:19
Alignment explanation
Indices: 960470--960596 Score: 218
Period size: 19 Copynumber: 6.7 Consensus size: 19
960460 GCTGCTGGAA
* *
960470 AACCGGTTTGACCAGTTCG
1 AACCGGTTTGACCGGTCCG
*
960489 AACCGGTTTGACCGGTTCG
1 AACCGGTTTGACCGGTCCG
960508 AACCGGTTTGACCGGTCCG
1 AACCGGTTTGACCGGTCCG
960527 AACCGGTTTGACCGGTCCG
1 AACCGGTTTGACCGGTCCG
960546 AACCGGTTTGACCGGTCCG
1 AACCGGTTTGACCGGTCCG
*
960565 AACCGGTTTGACCGGTCTG
1 AACCGGTTTGACCGGTCCG
960584 AACCGGTTTGACC
1 AACCGGTTTGACC
960597 CGACCCGACT
Statistics
Matches: 105, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
19 105 1.00
ACGTcount: A:0.17, C:0.29, G:0.30, T:0.24
Consensus pattern (19 bp):
AACCGGTTTGACCGGTCCG
Found at i:960617 original size:16 final size:17
Alignment explanation
Indices: 960591--960646 Score: 96
Period size: 17 Copynumber: 3.4 Consensus size: 17
960581 CTGAACCGGT
960591 TTGACCCGACCCGACTG
1 TTGACCCGACCCGACTG
960608 TTGA-CCGACCCGACTG
1 TTGACCCGACCCGACTG
*
960624 TTGACCCGACCCGACCG
1 TTGACCCGACCCGACTG
960641 TTGACC
1 TTGACC
960647 GTTGACCGTT
Statistics
Matches: 37, Mismatches: 1, Indels: 2
0.93 0.03 0.05
Matches are distributed among these distances:
16 16 0.43
17 21 0.57
ACGTcount: A:0.18, C:0.41, G:0.23, T:0.18
Consensus pattern (17 bp):
TTGACCCGACCCGACTG
Found at i:960648 original size:7 final size:7
Alignment explanation
Indices: 960636--960666 Score: 62
Period size: 7 Copynumber: 4.4 Consensus size: 7
960626 GACCCGACCC
960636 GACCGTT
1 GACCGTT
960643 GACCGTT
1 GACCGTT
960650 GACCGTT
1 GACCGTT
960657 GACCGTT
1 GACCGTT
960664 GAC
1 GAC
960667 TTCCTTTGAC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 24 1.00
ACGTcount: A:0.16, C:0.29, G:0.29, T:0.26
Consensus pattern (7 bp):
GACCGTT
Found at i:961607 original size:31 final size:31
Alignment explanation
Indices: 961536--961610 Score: 96
Period size: 31 Copynumber: 2.4 Consensus size: 31
961526 CTAATGTGAC
* *
961536 TCTTAGGTAGGCTCTGCGGCCCTGAGATCAT
1 TCTTAGGTAGGCCCTGCGGCCCTAAGATCAT
** **
961567 TCTCGGGTAGGCCCTGCGGCCCTAAGATGTT
1 TCTTAGGTAGGCCCTGCGGCCCTAAGATCAT
961598 TCTTAGGTAGGCC
1 TCTTAGGTAGGCC
961611 TCACGGCCCC
Statistics
Matches: 36, Mismatches: 8, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
31 36 1.00
ACGTcount: A:0.15, C:0.27, G:0.31, T:0.28
Consensus pattern (31 bp):
TCTTAGGTAGGCCCTGCGGCCCTAAGATCAT
Found at i:961618 original size:31 final size:32
Alignment explanation
Indices: 961583--961659 Score: 79
Period size: 31 Copynumber: 2.5 Consensus size: 32
961573 GTAGGCCCTG
*
961583 CGGCCCTAAGATGTTTCTTAGGTAGGC-CTCA
1 CGGCCCTAAGATGTTTCTTAGGTAGACTCTCA
* * * *
961614 CGGCCCCGAA-ATCTATCTTGGGTAGACTCTCA
1 CGG-CCCTAAGATGTTTCTTAGGTAGACTCTCA
961646 -GGCCCTAAGATGTT
1 CGGCCCTAAGATGTT
961660 CCCTTAGGGT
Statistics
Matches: 35, Mismatches: 8, Indels: 6
0.71 0.16 0.12
Matches are distributed among these distances:
30 5 0.14
31 21 0.60
32 9 0.26
ACGTcount: A:0.21, C:0.27, G:0.25, T:0.27
Consensus pattern (32 bp):
CGGCCCTAAGATGTTTCTTAGGTAGACTCTCA
Found at i:961637 original size:62 final size:62
Alignment explanation
Indices: 961536--961659 Score: 146
Period size: 62 Copynumber: 2.0 Consensus size: 62
961526 CTAATGTGAC
* * * *
961536 TCTTAGGTAGGCTCTGCGGCCCTGAGATCATTCTCGGGTAGGCCCTGC-GGCCCTAAGATGTT
1 TCTTAGGTAGGCTCTACGGCCCCGAAATCATTCTCGGGTAGACCCT-CAGGCCCTAAGATGTT
* *
961598 TCTTAGGTAGGC-CTCACGGCCCCGAAATC-TATCTTGGGTAGACTCTCAGGCCCTAAGATGTT
1 TCTTAGGTAGGCTCT-ACGGCCCCGAAATCAT-TCTCGGGTAGACCCTCAGGCCCTAAGATGTT
961660 CCCTTAGGGT
Statistics
Matches: 53, Mismatches: 6, Indels: 6
0.82 0.09 0.09
Matches are distributed among these distances:
61 4 0.08
62 49 0.92
ACGTcount: A:0.18, C:0.27, G:0.27, T:0.27
Consensus pattern (62 bp):
TCTTAGGTAGGCTCTACGGCCCCGAAATCATTCTCGGGTAGACCCTCAGGCCCTAAGATGTT
Found at i:964652 original size:20 final size:20
Alignment explanation
Indices: 964627--964664 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
964617 AAAAAATTAT
* *
964627 TTAAAATATTATTATTTTAC
1 TTAAAACATTAATATTTTAC
964647 TTAAAACATTAATATTTT
1 TTAAAACATTAATATTTT
964665 TTAACATTTT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.42, C:0.05, G:0.00, T:0.53
Consensus pattern (20 bp):
TTAAAACATTAATATTTTAC
Found at i:965023 original size:15 final size:15
Alignment explanation
Indices: 964998--965069 Score: 92
Period size: 15 Copynumber: 4.9 Consensus size: 15
964988 TAGTTTTTCA
964998 GAAAATGAATTACTG
1 GAAAATGAATTACTG
**
965013 GAATTTGAATTACTG
1 GAAAATGAATTACTG
*
965028 AAAAATGAATTACTG
1 GAAAATGAATTACTG
**
965043 GAATTTGAATTA-TG
1 GAAAATGAATTACTG
965057 GAAAATGAATTAC
1 GAAAATGAATTAC
965070 ATTTCTAGAA
Statistics
Matches: 46, Mismatches: 10, Indels: 2
0.79 0.17 0.03
Matches are distributed among these distances:
14 12 0.26
15 34 0.74
ACGTcount: A:0.44, C:0.06, G:0.18, T:0.32
Consensus pattern (15 bp):
GAAAATGAATTACTG
Found at i:965031 original size:29 final size:29
Alignment explanation
Indices: 964998--965069 Score: 126
Period size: 30 Copynumber: 2.4 Consensus size: 29
964988 TAGTTTTTCA
964998 GAAAATGAATTACTGGAATTTGAATTACTG
1 GAAAATGAATTACTGGAATTTGAATTA-TG
*
965028 AAAAATGAATTACTGGAATTTGAATTATG
1 GAAAATGAATTACTGGAATTTGAATTATG
965057 GAAAATGAATTAC
1 GAAAATGAATTAC
965070 ATTTCTAGAA
Statistics
Matches: 40, Mismatches: 2, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
29 14 0.35
30 26 0.65
ACGTcount: A:0.44, C:0.06, G:0.18, T:0.32
Consensus pattern (29 bp):
GAAAATGAATTACTGGAATTTGAATTATG
Found at i:965080 original size:20 final size:20
Alignment explanation
Indices: 965057--965101 Score: 81
Period size: 20 Copynumber: 2.2 Consensus size: 20
965047 TTGAATTATG
965057 GAAAATGAATTACATTTCTA
1 GAAAATGAATTACATTTCTA
*
965077 GAAAATGAATTACATTTCTG
1 GAAAATGAATTACATTTCTA
965097 GAAAA
1 GAAAA
965102 CATCTGGAAA
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.47, C:0.09, G:0.13, T:0.31
Consensus pattern (20 bp):
GAAAATGAATTACATTTCTA
Found at i:965447 original size:21 final size:22
Alignment explanation
Indices: 965422--965478 Score: 71
Period size: 23 Copynumber: 2.5 Consensus size: 22
965412 TATCTTTACT
*
965422 AAAATATTAT-TTAAATATATA
1 AAAATATTATATTAAATATAAA
*
965443 AAAATATCATTATTAAATATAAA
1 AAAATATTA-TATTAAATATAAA
965466 AAAATTATTATAT
1 AAAA-TATTATAT
965479 ATTATTAAAA
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
21 8 0.27
22 1 0.03
23 17 0.57
24 4 0.13
ACGTcount: A:0.58, C:0.02, G:0.00, T:0.40
Consensus pattern (22 bp):
AAAATATTATATTAAATATAAA
Found at i:965478 original size:29 final size:30
Alignment explanation
Indices: 965446--965522 Score: 99
Period size: 29 Copynumber: 2.6 Consensus size: 30
965436 ATATATAAAA
965446 ATATCATTATTAAATATAAAAAAAT-TAT-T
1 ATAT-ATTATTAAATATAAAAAAATATATCT
965475 ATATATTATTAAA-ATAAAAAAATAATATCT
1 ATATATTATTAAATATAAAAAAAT-ATATCT
965505 -TATATTATTATAATATAA
1 ATATATTATTA-AATATAA
965523 TTGATTATAT
Statistics
Matches: 43, Mismatches: 0, Indels: 8
0.84 0.00 0.16
Matches are distributed among these distances:
27 10 0.23
28 9 0.21
29 17 0.40
30 3 0.07
31 4 0.09
ACGTcount: A:0.56, C:0.03, G:0.00, T:0.42
Consensus pattern (30 bp):
ATATATTATTAAATATAAAAAAATATATCT
Found at i:965502 original size:24 final size:24
Alignment explanation
Indices: 965425--965507 Score: 78
Period size: 24 Copynumber: 3.3 Consensus size: 24
965415 CTTTACTAAA
* * *
965425 ATATTATTTAAATATATAAA-AAT
1 ATATTATTAAAATAAAAAAATAAT
965448 ATCATTATTAAATATAAAAAAATTATTAT
1 AT-ATTATTAAA-ATAAAAAAA-TA--AT
965477 ATATTATTAAAATAAAAAAATAAT
1 ATATTATTAAAATAAAAAAATAAT
*
965501 ATCTTAT
1 ATATTAT
965508 ATTATTATAA
Statistics
Matches: 50, Mismatches: 4, Indels: 11
0.77 0.06 0.17
Matches are distributed among these distances:
23 2 0.04
24 16 0.32
25 7 0.14
26 2 0.04
27 10 0.20
28 9 0.18
29 4 0.08
ACGTcount: A:0.57, C:0.02, G:0.00, T:0.41
Consensus pattern (24 bp):
ATATTATTAAAATAAAAAAATAAT
Found at i:965582 original size:50 final size:51
Alignment explanation
Indices: 965475--965588 Score: 144
Period size: 52 Copynumber: 2.3 Consensus size: 51
965465 AAAAATTATT
*
965475 ATATATTATTAAAATAAAAAAATAATATCTTATATTATTATAATATAATTGA
1 ATATATTATTAAAATAAAAAAATAATA-CTTATATTATTATAATATAATTAA
* * * *
965527 TTATATTATTAAACTAAAAATATAATA-TTATATTATTATAAATTTAA-TAA
1 ATATATTATTAAAATAAAAAAATAATACTTATATTATTAT-AATATAATTAA
965577 ATATATT-TTAAA
1 ATATATTATTAAA
965589 TATTTTAATA
Statistics
Matches: 55, Mismatches: 6, Indels: 5
0.83 0.09 0.08
Matches are distributed among these distances:
49 5 0.09
50 20 0.36
51 6 0.11
52 24 0.44
ACGTcount: A:0.53, C:0.02, G:0.01, T:0.45
Consensus pattern (51 bp):
ATATATTATTAAAATAAAAAAATAATACTTATATTATTATAATATAATTAA
Found at i:965878 original size:42 final size:42
Alignment explanation
Indices: 965781--965896 Score: 189
Period size: 42 Copynumber: 2.8 Consensus size: 42
965771 ATGAATTACA
*
965781 TTCCGGAAAACGAATTACGTGAAACAAACACG-GAAAACATT
1 TTCCGGAAAACGAATTACGTGAAACAAACACGAAAAAACATT
*
965822 TTCCGGAAAACGAATTACGTGAAACAAACACGAAAAAATATT
1 TTCCGGAAAACGAATTACGTGAAACAAACACGAAAAAACATT
* *
965864 TTCCGAAAAACGAATTACATGAAACAAACACGA
1 TTCCGGAAAACGAATTACGTGAAACAAACACGA
965897 GATTTCGAGA
Statistics
Matches: 70, Mismatches: 4, Indels: 1
0.93 0.05 0.01
Matches are distributed among these distances:
41 32 0.46
42 38 0.54
ACGTcount: A:0.49, C:0.19, G:0.15, T:0.17
Consensus pattern (42 bp):
TTCCGGAAAACGAATTACGTGAAACAAACACGAAAAAACATT
Found at i:966625 original size:28 final size:29
Alignment explanation
Indices: 966593--966663 Score: 117
Period size: 28 Copynumber: 2.5 Consensus size: 29
966583 AACATAATTA
966593 ATAGTCGAGTGACTATTTTATAAC-TTTG
1 ATAGTCGAGTGACTATTTTATAACTTTTG
966621 ATAGTCGAGTGACTATTTTATAACTTTTG
1 ATAGTCGAGTGACTATTTTATAACTTTTG
**
966650 ATAGTAAAGTGACT
1 ATAGTCGAGTGACT
966664 CAACAAAGGA
Statistics
Matches: 40, Mismatches: 2, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
28 24 0.60
29 16 0.40
ACGTcount: A:0.31, C:0.10, G:0.18, T:0.41
Consensus pattern (29 bp):
ATAGTCGAGTGACTATTTTATAACTTTTG
Found at i:969588 original size:2 final size:2
Alignment explanation
Indices: 969581--969629 Score: 98
Period size: 2 Copynumber: 24.5 Consensus size: 2
969571 ACGGAATTGC
969581 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
969623 TA TA TA T
1 TA TA TA T
969630 CAGTGGTTTT
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 47 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:992045 original size:31 final size:31
Alignment explanation
Indices: 991996--992054 Score: 82
Period size: 31 Copynumber: 1.9 Consensus size: 31
991986 ATACGAAATA
* * *
991996 AAAATTCATATATCATATTGAATATTTTGAT
1 AAAATACAGATATCATATTAAATATTTTGAT
*
992027 AAAATACAGATATTATATTAAATATTTT
1 AAAATACAGATATCATATTAAATATTTT
992055 AAAAGTATGA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
31 24 1.00
ACGTcount: A:0.46, C:0.05, G:0.05, T:0.44
Consensus pattern (31 bp):
AAAATACAGATATCATATTAAATATTTTGAT
Found at i:997013 original size:14 final size:14
Alignment explanation
Indices: 996990--997019 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
996980 TTTATTTAAA
*
996990 AAAGTTGAAAATAT
1 AAAGTAGAAAATAT
997004 AAAGTAGAAAATAT
1 AAAGTAGAAAATAT
997018 AA
1 AA
997020 TGGTAACTTT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.63, C:0.00, G:0.13, T:0.23
Consensus pattern (14 bp):
AAAGTAGAAAATAT
Found at i:998411 original size:16 final size:16
Alignment explanation
Indices: 998390--998423 Score: 59
Period size: 16 Copynumber: 2.1 Consensus size: 16
998380 TTACTATTCA
*
998390 CGTGAATAGTGAATTT
1 CGTGAATAGTGAAATT
998406 CGTGAATAGTGAAATT
1 CGTGAATAGTGAAATT
998422 CG
1 CG
998424 GTCGGCGATA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.32, C:0.09, G:0.26, T:0.32
Consensus pattern (16 bp):
CGTGAATAGTGAAATT
Done.