Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold211
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: 2193984
ACGTcount: A:0.31, C:0.16, G:0.16, T:0.31
Warning! 112243 characters in sequence are not A, C, G, or T
File 3 of 6
Found at i:829481 original size:20 final size:19
Alignment explanation
Indices: 829416--829662 Score: 101
Period size: 20 Copynumber: 12.3 Consensus size: 19
829406 CACATATGTG
829416 CCCCTGTTTGTACCTCGGTA
1 CCCCTGTTTGTACCTCGG-A
* * * * *
829436 CCCTTGATTGCACATATGTG-
1 CCCCTGTTTGTACCT-CG-GA
829456 CCCCTGTTTGTACCTCGGCA
1 CCCCTGTTTGTACCTCGG-A
* * *
829476 CCCCTGATTGCACATACGTG-
1 CCCCTGTTTGTACCT-CG-GA
829496 CCCCTGTTTGTACCATACGTG-
1 CCCCTGTTTGTACC-T-CG-GA
829517 CCCCTGTTTGTACCTCGGTA
1 CCCCTGTTTGTACCTCGG-A
* * *
829537 CCCCTGATTGCACATACGTG-
1 CCCCTGTTTGTACCT-CG-GA
*
829557 CCCCTGTTTGTACCTCGATA
1 CCCCTGTTTGTACCTCG-GA
* * * *
829577 CCCCTGATTGCACATACATG-
1 CCCCTGTTTGTACCT-C-GGA
829597 CCCCTGTTTGTACCTCGGTA
1 CCCCTGTTTGTACCTCGG-A
* * *
829617 CCCCTGATTGCACATACGTG-
1 CCCCTGTTTGTACCT-CG-GA
*
829637 CCCCTGTTTGTACCTCAGTA
1 CCCCTGTTTGTACCTC-GGA
829657 CCCCTG
1 CCCCTG
829663 ATTGCACATA
Statistics
Matches: 167, Mismatches: 40, Indels: 40
0.68 0.16 0.16
Matches are distributed among these distances:
18 3 0.02
19 7 0.04
20 125 0.75
21 28 0.17
22 4 0.02
ACGTcount: A:0.15, C:0.35, G:0.19, T:0.31
Consensus pattern (19 bp):
CCCCTGTTTGTACCTCGGA
Found at i:829547 original size:141 final size:141
Alignment explanation
Indices: 829368--829650 Score: 494
Period size: 141 Copynumber: 2.0 Consensus size: 141
829358 CTTGATTGCA
* *
829368 CATACGTGCCCCTGTTTGTACCTCGGTACCATTGATTGCACATATGTGCCCCTGTTTGTACCTCG
1 CATACGTGCCCCTGTTTGTACCTCGGTACCACTGATTGCACATACGTGCCCCTGTTTGTACCTCG
* * **
829433 GTACCCTTGATTGCACATATGTGCCCCTGTTTGTACCTCGGCACCCCTGATTGCACATACGTGCC
66 ATACCCCTGATTGCACATACATGCCCCTGTTTGTACCTCGGCACCCCTGATTGCACATACGTGCC
829498 CCTGTTTGTAC
131 CCTGTTTGTAC
*
829509 CATACGTGCCCCTGTTTGTACCTCGGTACCCCTGATTGCACATACGTGCCCCTGTTTGTACCTCG
1 CATACGTGCCCCTGTTTGTACCTCGGTACCACTGATTGCACATACGTGCCCCTGTTTGTACCTCG
*
829574 ATACCCCTGATTGCACATACATGCCCCTGTTTGTACCTCGGTACCCCTGATTGCACATACGTGCC
66 ATACCCCTGATTGCACATACATGCCCCTGTTTGTACCTCGGCACCCCTGATTGCACATACGTGCC
829639 CCTGTTTGTAC
131 CCTGTTTGTAC
829650 C
1 C
829651 TCAGTACCCC
Statistics
Matches: 134, Mismatches: 8, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
141 134 1.00
ACGTcount: A:0.16, C:0.34, G:0.19, T:0.31
Consensus pattern (141 bp):
CATACGTGCCCCTGTTTGTACCTCGGTACCACTGATTGCACATACGTGCCCCTGTTTGTACCTCG
ATACCCCTGATTGCACATACATGCCCCTGTTTGTACCTCGGCACCCCTGATTGCACATACGTGCC
CCTGTTTGTAC
Found at i:829560 original size:40 final size:40
Alignment explanation
Indices: 829509--829685 Score: 327
Period size: 40 Copynumber: 4.4 Consensus size: 40
829499 CTGTTTGTAC
829509 CATACGTGCCCCTGTTTGTACCTCGGTACCCCTGATTGCA
1 CATACGTGCCCCTGTTTGTACCTCGGTACCCCTGATTGCA
*
829549 CATACGTGCCCCTGTTTGTACCTCGATACCCCTGATTGCA
1 CATACGTGCCCCTGTTTGTACCTCGGTACCCCTGATTGCA
*
829589 CATACATGCCCCTGTTTGTACCTCGGTACCCCTGATTGCA
1 CATACGTGCCCCTGTTTGTACCTCGGTACCCCTGATTGCA
*
829629 CATACGTGCCCCTGTTTGTACCTCAGTACCCCTGATTGCA
1 CATACGTGCCCCTGTTTGTACCTCGGTACCCCTGATTGCA
829669 CATACGTGCCCCTGTTT
1 CATACGTGCCCCTGTTT
829686 ACACTTCAAT
Statistics
Matches: 132, Mismatches: 5, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
40 132 1.00
ACGTcount: A:0.16, C:0.35, G:0.18, T:0.31
Consensus pattern (40 bp):
CATACGTGCCCCTGTTTGTACCTCGGTACCCCTGATTGCA
Found at i:829588 original size:101 final size:101
Alignment explanation
Indices: 829408--829610 Score: 352
Period size: 101 Copynumber: 2.0 Consensus size: 101
829398 ATTGATTGCA
* * *
829408 CATATGTGCCCCTGTTTGTACCTCGGTACCCTTGATTGCACATATGTGCCCCTGTTTGTACCTCG
1 CATACGTGCCCCTGTTTGTACCTCGGTACCCCTGATTGCACATACGTGCCCCTGTTTGTACCTCG
* *
829473 GCACCCCTGATTGCACATACGTGCCCCTGTTTGTAC
66 ACACCCCTGATTGCACATACATGCCCCTGTTTGTAC
829509 CATACGTGCCCCTGTTTGTACCTCGGTACCCCTGATTGCACATACGTGCCCCTGTTTGTACCTCG
1 CATACGTGCCCCTGTTTGTACCTCGGTACCCCTGATTGCACATACGTGCCCCTGTTTGTACCTCG
*
829574 ATACCCCTGATTGCACATACATGCCCCTGTTTGTAC
66 ACACCCCTGATTGCACATACATGCCCCTGTTTGTAC
829610 C
1 C
829611 TCGGTACCCC
Statistics
Matches: 96, Mismatches: 6, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
101 96 1.00
ACGTcount: A:0.16, C:0.34, G:0.19, T:0.32
Consensus pattern (101 bp):
CATACGTGCCCCTGTTTGTACCTCGGTACCCCTGATTGCACATACGTGCCCCTGTTTGTACCTCG
ACACCCCTGATTGCACATACATGCCCCTGTTTGTAC
Found at i:829640 original size:181 final size:181
Alignment explanation
Indices: 829331--829685 Score: 593
Period size: 181 Copynumber: 2.0 Consensus size: 181
829321 GATTGCACAA
* * * *
829331 ACGTGCCCCTATTTGTACTTTGGTACCCTTGATTGCACATACGTGCCCCTGTTTGTACCTCGGTA
1 ACGTGCCCCTATTTGTACCTCGGTACCCCTGATTGCACATACGTGCCCCTGTTTGTACCTCGATA
* ** * *
829396 CCATTGATTGCACATATGTGCCCCTGTTTGTACCTCGGTACCCTTGATTGCACATATGTGCCCCT
66 CCACTGATTGCACATACATGCCCCTGTTTGTACCTCGGTACCCCTGATTGCACATACGTGCCCCT
*
829461 GTTTGTACCTCGGCACCCCTGATTGCACATACGTGCCCCTGTTTGTACCAT
131 GTTTGTACCTCAGCACCCCTGATTGCACATACGTGCCCCTGTTTGTACCAT
*
829512 ACGTGCCCCTGTTTGTACCTCGGTACCCCTGATTGCACATACGTGCCCCTGTTTGTACCTCGATA
1 ACGTGCCCCTATTTGTACCTCGGTACCCCTGATTGCACATACGTGCCCCTGTTTGTACCTCGATA
*
829577 CCCCTGATTGCACATACATGCCCCTGTTTGTACCTCGGTACCCCTGATTGCACATACGTGCCCCT
66 CCACTGATTGCACATACATGCCCCTGTTTGTACCTCGGTACCCCTGATTGCACATACGTGCCCCT
*
829642 GTTTGTACCTCAGTACCCCTGATTGCACATACGTGCCCCTGTTT
131 GTTTGTACCTCAGCACCCCTGATTGCACATACGTGCCCCTGTTT
829686 ACACTTCAAT
Statistics
Matches: 161, Mismatches: 13, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
181 161 1.00
ACGTcount: A:0.16, C:0.33, G:0.19, T:0.32
Consensus pattern (181 bp):
ACGTGCCCCTATTTGTACCTCGGTACCCCTGATTGCACATACGTGCCCCTGTTTGTACCTCGATA
CCACTGATTGCACATACATGCCCCTGTTTGTACCTCGGTACCCCTGATTGCACATACGTGCCCCT
GTTTGTACCTCAGCACCCCTGATTGCACATACGTGCCCCTGTTTGTACCAT
Found at i:837691 original size:25 final size:25
Alignment explanation
Indices: 837663--837732 Score: 81
Period size: 25 Copynumber: 2.8 Consensus size: 25
837653 TCCTGTACAT
*
837663 GTATGCTCATACAAGCTGTGAATCG
1 GTATGCTCATACAAGCTGTAAATCG
837688 GTATGCTC-TCACGAA-CTGTAAATCG
1 GTATGCTCAT-AC-AAGCTGTAAATCG
* *
837713 GTAAGCTCATACTAGCTGTA
1 GTATGCTCATACAAGCTGTA
837733 GGGCTGTACA
Statistics
Matches: 38, Mismatches: 3, Indels: 8
0.78 0.06 0.16
Matches are distributed among these distances:
24 2 0.05
25 33 0.87
26 3 0.08
ACGTcount: A:0.29, C:0.21, G:0.21, T:0.29
Consensus pattern (25 bp):
GTATGCTCATACAAGCTGTAAATCG
Found at i:845829 original size:50 final size:50
Alignment explanation
Indices: 845709--845943 Score: 188
Period size: 50 Copynumber: 4.6 Consensus size: 50
845699 AAATCCCATC
* ** * * *
845709 TAAGACCATGTCTGGGACATGGCATTGGCATTATTGAGGTTATGAGAAGTCCTATG
1 TAAGACCATATCTGGGACATGGCATTGGC---ACCGA-G--ATGAGAACTCCCACG
* ** *
845765 TAAGACCATATCTGGGACATGGCGTTGGCACCGAGATGAGAGGTCCCCCG
1 TAAGACCATATCTGGGACATGGCATTGGCACCGAGATGAGAACTCCCACG
* * * *
845815 TAAGACCATGTCTGGGACATGGCATGGGCACCGATATGAGAACTCCCATG
1 TAAGACCATATCTGGGACATGGCATTGGCACCGAGATGAGAACTCCCACG
* * * *
845865 TAAGACCATATCTGGGATATGGCATTGGCA--GTACA-GAAAACATCCCATG
1 TAAGACCATATCTGGGACATGGCATTGGCACCG-AGATGAGAAC-TCCCACG
* * *
845914 TAAAACCATGTCTGGGACATGGCTTTGGCA
1 TAAGACCATATCTGGGACATGGCATTGGCA
845944 TGTTATTATT
Statistics
Matches: 152, Mismatches: 25, Indels: 11
0.81 0.13 0.06
Matches are distributed among these distances:
48 6 0.04
49 35 0.23
50 80 0.53
52 1 0.01
53 3 0.02
56 27 0.18
ACGTcount: A:0.28, C:0.21, G:0.28, T:0.23
Consensus pattern (50 bp):
TAAGACCATATCTGGGACATGGCATTGGCACCGAGATGAGAACTCCCACG
Found at i:859460 original size:29 final size:30
Alignment explanation
Indices: 859301--859638 Score: 169
Period size: 29 Copynumber: 11.8 Consensus size: 30
859291 ATTTCTGTAT
* *
859301 AAGAAAGCCTTTGTGTCTATCTCT-G--AA
1 AAGAATGCCTTTGTGGCTATCTCTAGTTAA
* *
859328 TAG-ACGCCTTTGTGGCTATCTC----TAA
1 AAGAATGCCTTTGTGGCTATCTCTAGTTAA
* * * *
859353 AAGAAAGCATTTGTGGCGATCT-TTGTTATA
1 AAGAATGCCTTTGTGGCTATCTCTAGTTA-A
* * *
859383 AGGAA-GCC-ATATGGCTATCTCT-GTTAA
1 AAGAATGCCTTTGTGGCTATCTCTAGTTAA
* * **
859410 AAGAATGTCTATGTTTCTATCT-TAGTTAA
1 AAGAATGCCTTTGTGGCTATCTCTAGTTAA
* *
859439 AAGAATGCCTTTGTGGCAATCT-TTGTTATA
1 AAGAATGCCTTTGTGGCTATCTCTAGTTA-A
* * * *
859469 AGGAA-GCCTTTGTAGCGA--TCTACGTTAT
1 AAGAATGCCTTTGTGGCTATCTCTA-GTTAA
* * * * *
859497 AAGAAAGCATTTGTCGCGATCTCT-GTTAT
1 AAGAATGCCTTTGTGGCTATCTCTAGTTAA
* *
859526 AAGGATGCCTTTGTGGCTATCTCTA-CTAA
1 AAGAATGCCTTTGTGGCTATCTCTAGTTAA
* * *
859555 ATGAATACCTTTGTGGATATCTCTA-TTAA
1 AAGAATGCCTTTGTGGCTATCTCTAGTTAA
* *
859584 ATGAATGCCTTTATGGCTATCTCT-GTTAA
1 AAGAATGCCTTTGTGGCTATCTCTAGTTAA
* * *
859613 AAGGACGCCTTTGTGGCGAGTCTCTA
1 AAGAATGCCTTTGTGGCTA-TCTCTA
859639 AAAGTAAAGC
Statistics
Matches: 239, Mismatches: 51, Indels: 38
0.73 0.16 0.12
Matches are distributed among these distances:
25 4 0.02
26 32 0.13
27 8 0.03
28 21 0.09
29 156 0.65
30 15 0.06
31 3 0.01
ACGTcount: A:0.27, C:0.17, G:0.20, T:0.36
Consensus pattern (30 bp):
AAGAATGCCTTTGTGGCTATCTCTAGTTAA
Found at i:862480 original size:39 final size:39
Alignment explanation
Indices: 862371--862487 Score: 135
Period size: 39 Copynumber: 3.0 Consensus size: 39
862361 GATATCAAGA
* * **
862371 GTACTGAAGTACACCAGGGGCACGTAAGTGCAATTAGGG
1 GTACTGAAGTACAACAGGGGCACGTAAGTGCGACCAGGG
* * ** *
862410 GTATTGAAGTACAACAGGAGCACACAAGTGCGACCGGGG
1 GTACTGAAGTACAACAGGGGCACGTAAGTGCGACCAGGG
* *
862449 GTACCGAAGTACAACAGGGGCACGTAAGTGCGATCAGGG
1 GTACTGAAGTACAACAGGGGCACGTAAGTGCGACCAGGG
862488 ATATAATTAT
Statistics
Matches: 62, Mismatches: 16, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
39 62 1.00
ACGTcount: A:0.32, C:0.20, G:0.34, T:0.15
Consensus pattern (39 bp):
GTACTGAAGTACAACAGGGGCACGTAAGTGCGACCAGGG
Found at i:870206 original size:10 final size:11
Alignment explanation
Indices: 870188--870220 Score: 50
Period size: 10 Copynumber: 3.1 Consensus size: 11
870178 TCTCCTTCCT
870188 TTCTTTCTTTC
1 TTCTTTCTTTC
870199 TT-TTTCTTTC
1 TTCTTTCTTTC
*
870209 TTCTTTTTTTC
1 TTCTTTCTTTC
870220 T
1 T
870221 ATTAATTTGC
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
10 10 0.50
11 10 0.50
ACGTcount: A:0.00, C:0.21, G:0.00, T:0.79
Consensus pattern (11 bp):
TTCTTTCTTTC
Found at i:870217 original size:14 final size:14
Alignment explanation
Indices: 870187--870216 Score: 53
Period size: 13 Copynumber: 2.2 Consensus size: 14
870177 CTCTCCTTCC
870187 TTTCTTTCTTTCTT
1 TTTCTTTCTTTCTT
870201 TTTCTTTC-TTCTT
1 TTTCTTTCTTTCTT
870214 TTT
1 TTT
870217 TTCTATTAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 8 0.50
14 8 0.50
ACGTcount: A:0.00, C:0.20, G:0.00, T:0.80
Consensus pattern (14 bp):
TTTCTTTCTTTCTT
Found at i:880464 original size:132 final size:132
Alignment explanation
Indices: 880287--881197 Score: 1394
Period size: 132 Copynumber: 6.9 Consensus size: 132
880277 ACAGTGAAGT
* * *
880287 AGATCGAAAATGGCGGATTTTACCTCCTTGTGGTTACAGTGGAGTACATTGAAGCTAGTAATTCT
1 AGATCGAAGATGGCGGATTTTACCTCCCTGTGGTTACAGTGGAGTACATTGAAGCCAGTAATTCT
*
880352 ACTTCCCTGGGCAACAGTGGAATAGATTGAAGATTTCAGATCTTATCTCCCTAAGCAGTAGTGGA
66 ACTTCCCTGGACAACAGTGGAATAGATTGAAGATTTCAGATCTTATCTCCCTAAGCAGTAGTGGA
880417 GC
131 GC
** * * * *
880419 AGATCGAAGATGGCAAATTTGACCTCCCTATGGTTACAGTAGAGTACATTGAAACCAGTAATTCT
1 AGATCGAAGATGGCGGATTTTACCTCCCTGTGGTTACAGTGGAGTACATTGAAGCCAGTAATTCT
880484 ACTTCCCTGGACAACAGTGGAATAGATTGAAGATTTCAGATCTTATCTCCCTAAGCAGTAGTGGA
66 ACTTCCCTGGACAACAGTGGAATAGATTGAAGATTTCAGATCTTATCTCCCTAAGCAGTAGTGGA
880549 GC
131 GC
* *
880551 AGATCGAAGATGGCGGATTTTACCTCCCTGTGGTTACAGTGGAGTACATTAAAGCCAGTAACTCT
1 AGATCGAAGATGGCGGATTTTACCTCCCTGTGGTTACAGTGGAGTACATTGAAGCCAGTAATTCT
* *
880616 ACTTCCCTGGGCAACAATGGAATAGATTGAAGATTTCAGATCTTATCTCCCTAAGCAGTAGTGGA
66 ACTTCCCTGGACAACAGTGGAATAGATTGAAGATTTCAGATCTTATCTCCCTAAGCAGTAGTGGA
880681 GC
131 GC
* * *
880683 AGATCGAAGATGGCGGATTTTACCTCCTTGTGGTTACAATAGAGTACATTGAAGCCAAG-AATTC
1 AGATCGAAGATGGCGGATTTTACCTCCCTGTGGTTACAGTGGAGTACATTGAAGCC-AGTAATTC
* *
880747 TACTTCCCTGGGCAACAGTGGAATAGATTGAAGATTTCAGATCTTATCTCCCTAAGCAGTAATGG
65 TACTTCCCTGGACAACAGTGGAATAGATTGAAGATTTCAGATCTTATCTCCCTAAGCAGTAGTGG
880812 AGC
130 AGC
* * * *
880815 AGATCGAAGATGGCGAATTTTACCTCCCTGTGGTTATAGTGGAGTACATTGAGGCCAGAAATTCT
1 AGATCGAAGATGGCGGATTTTACCTCCCTGTGGTTACAGTGGAGTACATTGAAGCCAGTAATTCT
*
880880 ACTTCCCTGGACAGACAGTGGAATAGATTGAAGATTTCAGATCTTATCTCCCTAAGCGGTAGTGG
66 ACTTCCCTGGACA-ACAGTGGAATAGATTGAAGATTTCAGATCTTATCTCCCTAAGCAGTAGTGG
880945 AGC
130 AGC
* * * * *
880948 AGATCGAATATAGCGGATTTTACCTCCCTGTGGTTATAGTGGAGTACATTGAGGCCAGAAATTCT
1 AGATCGAAGATGGCGGATTTTACCTCCCTGTGGTTACAGTGGAGTACATTGAAGCCAGTAATTCT
*
881013 ACTTCCCTGGACAGACAGTGGAATAGATTGAAGATTTCAGATCTTATCTCCCTAAGCGGTAGTGG
66 ACTTCCCTGGACA-ACAGTGGAATAGATTGAAGATTTCAGATCTTATCTCCCTAAGCAGTAGTGG
881078 AGC
130 AGC
* * * * *
881081 AGATCGAATATAGCGGATTTTACCTCCCTGTGGTTATAGTGGAGTACATTGAAACCAATAATTCT
1 AGATCGAAGATGGCGGATTTTACCTCCCTGTGGTTACAGTGGAGTACATTGAAGCCAGTAATTCT
* * ** * * *
881146 ACTTCCCTAGTCAGTAGTGGAATAGGTTGAAGATTGTAAG-CCTTATCTCCCT
66 ACTTCCCTGGACAACAGTGGAATAGATTGAAGATT-TCAGATCTTATCTCCCT
881198 GAAATTGCAG
Statistics
Matches: 725, Mismatches: 50, Indels: 8
0.93 0.06 0.01
Matches are distributed among these distances:
131 2 0.00
132 464 0.64
133 259 0.36
ACGTcount: A:0.29, C:0.19, G:0.23, T:0.29
Consensus pattern (132 bp):
AGATCGAAGATGGCGGATTTTACCTCCCTGTGGTTACAGTGGAGTACATTGAAGCCAGTAATTCT
ACTTCCCTGGACAACAGTGGAATAGATTGAAGATTTCAGATCTTATCTCCCTAAGCAGTAGTGGA
GC
Found at i:882770 original size:26 final size:27
Alignment explanation
Indices: 882725--882776 Score: 79
Period size: 26 Copynumber: 2.0 Consensus size: 27
882715 CACATGTATA
*
882725 TATATTTTTTTTAAACGAATATTTTCC
1 TATATTTTTTTTAAACGAATACTTTCC
*
882752 TATA-TTTTTTTAAATGAATACTTTC
1 TATATTTTTTTTAAACGAATACTTTC
882777 ATATTTATAT
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
26 19 0.83
27 4 0.17
ACGTcount: A:0.31, C:0.10, G:0.04, T:0.56
Consensus pattern (27 bp):
TATATTTTTTTTAAACGAATACTTTCC
Found at i:883552 original size:98 final size:98
Alignment explanation
Indices: 883433--883627 Score: 336
Period size: 98 Copynumber: 2.0 Consensus size: 98
883423 AGATTTTTTT
*
883433 TAAAGGAAATATTCCGAGTTTGAGATTCTAAAGGAATTGTGCCCTAACATATTGGGTGTGATTTC
1 TAAAGGAAATATTCCGAGTTTGAGATTCTAAAGGAATCGTGCCCTAACATATTGGGTGTGATTTC
* *
883498 TTAAATCTTGGATGAGTGGATGTTCTTTTAAAA
66 TTAAATCTTGGACGAGTGGATGTTCCTTTAAAA
* * *
883531 TAAAGGAAATATTCCGAGTTTGGGATTCTAAAGGGATCGTGCCCTAACGTATTGGGTGTGATTTC
1 TAAAGGAAATATTCCGAGTTTGAGATTCTAAAGGAATCGTGCCCTAACATATTGGGTGTGATTTC
883596 TTAAATCTTGGACGAGTGGATGTTCCTTTAAA
66 TTAAATCTTGGACGAGTGGATGTTCCTTTAAA
883628 GTTTTATTGT
Statistics
Matches: 91, Mismatches: 6, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
98 91 1.00
ACGTcount: A:0.29, C:0.12, G:0.24, T:0.35
Consensus pattern (98 bp):
TAAAGGAAATATTCCGAGTTTGAGATTCTAAAGGAATCGTGCCCTAACATATTGGGTGTGATTTC
TTAAATCTTGGACGAGTGGATGTTCCTTTAAAA
Found at i:884230 original size:26 final size:26
Alignment explanation
Indices: 884196--884248 Score: 72
Period size: 28 Copynumber: 2.0 Consensus size: 26
884186 TGAAAAGTAG
884196 TTTTAAAATT-TTATCTCTTAGAAATA
1 TTTTAAAATTATTATCTCTTA-AAATA
*
884222 TTTTGAAATTAATTATCTCTTAAAATA
1 TTTTAAAATT-ATTATCTCTTAAAATA
884249 AACATTATTT
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
26 9 0.38
27 5 0.21
28 10 0.42
ACGTcount: A:0.40, C:0.08, G:0.04, T:0.49
Consensus pattern (26 bp):
TTTTAAAATTATTATCTCTTAAAATA
Found at i:884601 original size:3 final size:3
Alignment explanation
Indices: 884593--884640 Score: 66
Period size: 3 Copynumber: 17.0 Consensus size: 3
884583 TAGTTTACCC
*
884593 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T-C TAA -AA T-A TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
884638 TAA
1 TAA
884641 ATTCTAATAC
Statistics
Matches: 40, Mismatches: 2, Indels: 6
0.83 0.04 0.12
Matches are distributed among these distances:
2 5 0.12
3 35 0.88
ACGTcount: A:0.65, C:0.02, G:0.00, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:897170 original size:20 final size:20
Alignment explanation
Indices: 897141--897180 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
897131 AATAAACACC
* *
897141 AAAAATTTATTTTTAAAATA
1 AAAAAATTATTTTAAAAATA
897161 AAAAAATTATTTTAAAAATA
1 AAAAAATTATTTTAAAAATA
897181 TTTTAAAATT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (20 bp):
AAAAAATTATTTTAAAAATA
Found at i:901141 original size:23 final size:23
Alignment explanation
Indices: 901115--901194 Score: 74
Period size: 23 Copynumber: 3.5 Consensus size: 23
901105 AGGCATCATT
901115 GAATACGCCACACAGGCCTTACA
1 GAATACGCCACACAGGCCTTACA
* * * *
901138 GAATATGCCACTA-AGACTTTGCA
1 GAATACGCCAC-ACAGGCCTTACA
* *
901161 G-ATCATGCCACACAGGCCTTATA
1 GAAT-ACGCCACACAGGCCTTACA
901184 GAATACGCCAC
1 GAATACGCCAC
901195 CAAGACTTTG
Statistics
Matches: 44, Mismatches: 9, Indels: 8
0.72 0.15 0.13
Matches are distributed among these distances:
22 3 0.07
23 38 0.86
24 3 0.07
ACGTcount: A:0.34, C:0.30, G:0.17, T:0.19
Consensus pattern (23 bp):
GAATACGCCACACAGGCCTTACA
Found at i:901173 original size:46 final size:46
Alignment explanation
Indices: 901119--901229 Score: 168
Period size: 46 Copynumber: 2.4 Consensus size: 46
901109 ATCATTGAAT
* *
901119 ACGCCACACAGGCCTTACAGAATATGCCACTAAGACTTTGCAGATC
1 ACGCCACACAGGCCTTACAGAATACGCCACCAAGACTTTGCAGATC
* *
901165 ATGCCACACAGGCCTTATAGAATACGCCACCAAGACTTTGCAGATC
1 ACGCCACACAGGCCTTACAGAATACGCCACCAAGACTTTGCAGATC
* *
901211 ACGCCACATAGGCATTACA
1 ACGCCACACAGGCCTTACA
901230 AAGAGTTACG
Statistics
Matches: 57, Mismatches: 8, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
46 57 1.00
ACGTcount: A:0.33, C:0.31, G:0.17, T:0.19
Consensus pattern (46 bp):
ACGCCACACAGGCCTTACAGAATACGCCACCAAGACTTTGCAGATC
Found at i:901214 original size:23 final size:23
Alignment explanation
Indices: 901144--901217 Score: 64
Period size: 23 Copynumber: 3.2 Consensus size: 23
901134 TACAGAATAT
* *
901144 GCCACTAAGACTTTGCAGATCAT
1 GCCACCAAGACTTTGCAGATCAC
* *
901167 GCCACACAGGCCTTAT--AGAAT-AC
1 GCCAC-CAAGACTT-TGCAG-ATCAC
901190 GCCACCAAGACTTTGCAGATCAC
1 GCCACCAAGACTTTGCAGATCAC
901213 GCCAC
1 GCCAC
901218 ATAGGCATTA
Statistics
Matches: 39, Mismatches: 6, Indels: 12
0.68 0.11 0.21
Matches are distributed among these distances:
21 1 0.03
22 8 0.21
23 22 0.56
24 7 0.18
25 1 0.03
ACGTcount: A:0.31, C:0.32, G:0.18, T:0.19
Consensus pattern (23 bp):
GCCACCAAGACTTTGCAGATCAC
Found at i:905986 original size:16 final size:17
Alignment explanation
Indices: 905967--905998 Score: 57
Period size: 16 Copynumber: 1.9 Consensus size: 17
905957 TTTTGGGTAC
905967 AATTTTTTT-TAATTTT
1 AATTTTTTTATAATTTT
905983 AATTTTTTTATAATTT
1 AATTTTTTTATAATTT
905999 ATATACTTTT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 9 0.60
17 6 0.40
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (17 bp):
AATTTTTTTATAATTTT
Found at i:906046 original size:9 final size:9
Alignment explanation
Indices: 905987--906053 Score: 55
Period size: 9 Copynumber: 7.2 Consensus size: 9
905977 AATTTTAATT
905987 TTTTTATAA
1 TTTTTATAA
* *
905996 TTTATATAC
1 TTTTTATAA
906005 TTTTTA-AA
1 TTTTTATAA
*
906013 GTTTTTAAGAA
1 -TTTTT-ATAA
* *
906024 TTTTAAATAT
1 TTTT-TATAA
906034 TTTTTATAA
1 TTTTTATAA
906043 TTTTTATAA
1 TTTTTATAA
906052 TT
1 TT
906054 AGGACTAAAA
Statistics
Matches: 45, Mismatches: 9, Indels: 8
0.73 0.15 0.13
Matches are distributed among these distances:
8 1 0.02
9 31 0.69
10 11 0.24
11 2 0.04
ACGTcount: A:0.34, C:0.01, G:0.03, T:0.61
Consensus pattern (9 bp):
TTTTTATAA
Found at i:913602 original size:43 final size:42
Alignment explanation
Indices: 913530--913757 Score: 282
Period size: 42 Copynumber: 5.4 Consensus size: 42
913520 ACGTCTCTAA
*
913530 CTTTTGCGGCGCTTACAGGAAAAAACGCCGCTAAAGATCATGTT
1 CTTTAGCGGCGCTT--AGGAAAAAACGCCGCTAAAGATCATGTT
* *
913574 CTTTAGCGGCGCTAAGGAAATAAACGCCGCTAAAGATCCTGTT
1 CTTTAGCGGCGCTTAGGAAA-AAACGCCGCTAAAGATCATGTT
* * *
913617 CTTTAGCGGCGCTTATGAAAAAACGCCGCTAAAAATCCTGTT
1 CTTTAGCGGCGCTTAGGAAAAAACGCCGCTAAAGATCATGTT
* *
913659 CTTTAGCGGCGCTTAGAAAAAAACGCCGCT-AAGAGTAATGTT
1 CTTTAGCGGCGCTTAGGAAAAAACGCCGCTAAAGA-TCATGTT
* **
913701 CTATAGCGGCGCTTAGTCAAAAACGCCGCTAAA-AGT-AGTGTT
1 CTTTAGCGGCGCTTAGGAAAAAACGCCGCTAAAGA-TCA-TGTT
913743 CTTTAGCGGCGCTTA
1 CTTTAGCGGCGCTTA
913758 TTTCACAAAC
Statistics
Matches: 165, Mismatches: 15, Indels: 10
0.87 0.08 0.05
Matches are distributed among these distances:
41 4 0.02
42 108 0.65
43 41 0.25
44 12 0.07
ACGTcount: A:0.30, C:0.22, G:0.23, T:0.25
Consensus pattern (42 bp):
CTTTAGCGGCGCTTAGGAAAAAACGCCGCTAAAGATCATGTT
Found at i:915058 original size:40 final size:41
Alignment explanation
Indices: 914941--915064 Score: 223
Period size: 41 Copynumber: 3.0 Consensus size: 41
914931 TCTTCAAGGT
* *
914941 CCTGAACATTAGCGGCGCTTATTCAAAAACGCCGCTAAAGA
1 CCTGAGCATTAGCGGCGCTTATTCAGAAACGCCGCTAAAGA
914982 CCTGAGCATTAGCGGCGCTTATTCAGAAACGCCGCTAAAGA
1 CCTGAGCATTAGCGGCGCTTATTCAGAAACGCCGCTAAAGA
915023 CCTGAGCATTAGCGGCGCTT-TTCAGAAACGCCGCTAAAGA
1 CCTGAGCATTAGCGGCGCTTATTCAGAAACGCCGCTAAAGA
915063 CC
1 CC
915065 CCAAAAACTC
Statistics
Matches: 81, Mismatches: 2, Indels: 1
0.96 0.02 0.01
Matches are distributed among these distances:
40 22 0.27
41 59 0.73
ACGTcount: A:0.30, C:0.28, G:0.23, T:0.19
Consensus pattern (41 bp):
CCTGAGCATTAGCGGCGCTTATTCAGAAACGCCGCTAAAGA
Found at i:915147 original size:113 final size:113
Alignment explanation
Indices: 915008--915472 Score: 777
Period size: 113 Copynumber: 4.1 Consensus size: 113
914998 GCTTATTCAG
915008 AAACGCCGCTAAAGACCTGAGCATTAGCGGCGCTTTTCAGAAACGCCGCTAAAGACCCCAAAAAC
1 AAACGCCGCTAAAGACCTGAGCATTAGCGGCGCTTTTCAGAAACGCCGCTAAAGACCCCAAAAAC
915073 TCAGAAAACGGTGCCGTTGGGCTTAGGCTTTTTGCGGCGCTTTTAAAA
66 TCAGAAAACGGTGCCGTTGGGCTTAGGCTTTTTGCGGCGCTTTTAAAA
* * *
915121 AAACGCTGCTAAACACCTGAGCATTAGCGGCGCTTTTCAGAAACGCTGCTAAAGACCCCAAAAAC
1 AAACGCCGCTAAAGACCTGAGCATTAGCGGCGCTTTTCAGAAACGCCGCTAAAGACCCCAAAAAC
* * *
915186 TCAGAAAACGGTGTCGTTTGGCTTAGGCTTTTTGCGGCGCTTTTAACA
66 TCAGAAAACGGTGCCGTTGGGCTTAGGCTTTTTGCGGCGCTTTTAAAA
* * * ** * *
915234 AAACGCCGCTAAAAGACTTGAGAATTAGCGGCGCATAACAGAAATGCCGCGAAAGACCCCAAAAA
1 AAACGCCGCT-AAAGACCTGAGCATTAGCGGCGCTTTTCAGAAACGCCGCTAAAGACCCCAAAAA
*
915299 CTCAGAAAACGGTGCCGTTGGGTTTAGGCTTTTTGCGGCGCTTTTAAAA
65 CTCAGAAAACGGTGCCGTTGGGCTTAGGCTTTTTGCGGCGCTTTTAAAA
915348 AAACGCCGCTAAAGACCTGAGCATTAGCGGCGCTTTTCAGAAACGCCGCTAAAGACCCCAAAAAC
1 AAACGCCGCTAAAGACCTGAGCATTAGCGGCGCTTTTCAGAAACGCCGCTAAAGACCCCAAAAAC
**
915413 TCAGAAAACGGTGCCGTTGGGCTTAGGCTTTTTGCGGCGCTTTCCAAA
66 TCAGAAAACGGTGCCGTTGGGCTTAGGCTTTTTGCGGCGCTTTTAAAA
915461 AAACGCCGCTAA
1 AAACGCCGCTAA
915473 TGCTTATTTT
Statistics
Matches: 321, Mismatches: 30, Indels: 2
0.91 0.08 0.01
Matches are distributed among these distances:
113 221 0.69
114 100 0.31
ACGTcount: A:0.30, C:0.25, G:0.23, T:0.21
Consensus pattern (113 bp):
AAACGCCGCTAAAGACCTGAGCATTAGCGGCGCTTTTCAGAAACGCCGCTAAAGACCCCAAAAAC
TCAGAAAACGGTGCCGTTGGGCTTAGGCTTTTTGCGGCGCTTTTAAAA
Found at i:915425 original size:227 final size:227
Alignment explanation
Indices: 915008--915472 Score: 781
Period size: 227 Copynumber: 2.1 Consensus size: 227
914998 GCTTATTCAG
* * ** *
915008 AAACGCCGCT-AAAGACCTGAGCATTAGCGGCGCTTTTCAGAAACGCCGCTAAAGACCCCAAAAA
1 AAACGCCGCTAAAAGACCTGAGAATTAGCGGCGCATAACAGAAACGCCGCGAAAGACCCCAAAAA
*
915072 CTCAGAAAACGGTGCCGTTGGGCTTAGGCTTTTTGCGGCGCTTTTAAAAAAACGCTGCTAAACAC
66 CTCAGAAAACGGTGCCGTTGGGCTTAGGCTTTTTGCGGCGCTTTTAAAAAAACGCCGCTAAACAC
* *
915137 CTGAGCATTAGCGGCGCTTTTCAGAAACGCTGCTAAAGACCCCAAAAACTCAGAAAACGGTGTCG
131 CTGAGCATTAGCGGCGCTTTTCAGAAACGCCGCTAAAGACCCCAAAAACTCAGAAAACGGTGCCG
* *
915202 TTTGGCTTAGGCTTTTTGCGGCGCTTT-TAACA
196 TTGGGCTTAGGCTTTTTGCGGCGCTTTCCAA-A
* *
915234 AAACGCCGCTAAAAGACTTGAGAATTAGCGGCGCATAACAGAAATGCCGCGAAAGACCCCAAAAA
1 AAACGCCGCTAAAAGACCTGAGAATTAGCGGCGCATAACAGAAACGCCGCGAAAGACCCCAAAAA
* *
915299 CTCAGAAAACGGTGCCGTTGGGTTTAGGCTTTTTGCGGCGCTTTTAAAAAAACGCCGCTAAAGAC
66 CTCAGAAAACGGTGCCGTTGGGCTTAGGCTTTTTGCGGCGCTTTTAAAAAAACGCCGCTAAACAC
915364 CTGAGCATTAGCGGCGCTTTTCAGAAACGCCGCTAAAGACCCCAAAAACTCAGAAAACGGTGCCG
131 CTGAGCATTAGCGGCGCTTTTCAGAAACGCCGCTAAAGACCCCAAAAACTCAGAAAACGGTGCCG
915429 TTGGGCTTAGGCTTTTTGCGGCGCTTTCCAAA
196 TTGGGCTTAGGCTTTTTGCGGCGCTTTCCAAA
915461 AAACGCCGCTAA
1 AAACGCCGCTAA
915473 TGCTTATTTT
Statistics
Matches: 223, Mismatches: 14, Indels: 3
0.93 0.06 0.01
Matches are distributed among these distances:
226 10 0.04
227 211 0.95
228 2 0.01
ACGTcount: A:0.30, C:0.25, G:0.23, T:0.21
Consensus pattern (227 bp):
AAACGCCGCTAAAAGACCTGAGAATTAGCGGCGCATAACAGAAACGCCGCGAAAGACCCCAAAAA
CTCAGAAAACGGTGCCGTTGGGCTTAGGCTTTTTGCGGCGCTTTTAAAAAAACGCCGCTAAACAC
CTGAGCATTAGCGGCGCTTTTCAGAAACGCCGCTAAAGACCCCAAAAACTCAGAAAACGGTGCCG
TTGGGCTTAGGCTTTTTGCGGCGCTTTCCAAA
Found at i:916204 original size:28 final size:27
Alignment explanation
Indices: 916159--916218 Score: 68
Period size: 27 Copynumber: 2.2 Consensus size: 27
916149 TTCTAAAAGG
916159 TAAATATAAAAATATTTTAAAACTTTTT
1 TAAATATAAAAATATTTTAAAA-TTTTT
* *
916187 TAAATAT-AATATATTTTTATAATTTTT
1 TAAATATAAAAATA-TTTTAAAATTTTT
*
916214 AAAAT
1 TAAAT
916219 TAGAGCTAAA
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
27 14 0.50
28 14 0.50
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.50
Consensus pattern (27 bp):
TAAATATAAAAATATTTTAAAATTTTT
Found at i:916551 original size:12 final size:12
Alignment explanation
Indices: 916524--916563 Score: 66
Period size: 12 Copynumber: 3.5 Consensus size: 12
916514 CCTTGCTTGC
916524 AAATT-ATATC-
1 AAATTAATATCA
916534 AAATTAATATCA
1 AAATTAATATCA
916546 AAATTAATATCA
1 AAATTAATATCA
916558 AAATTA
1 AAATTA
916564 TTATTATTCT
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
10 5 0.18
11 5 0.18
12 18 0.64
ACGTcount: A:0.57, C:0.07, G:0.00, T:0.35
Consensus pattern (12 bp):
AAATTAATATCA
Found at i:922444 original size:13 final size:13
Alignment explanation
Indices: 922411--922444 Score: 50
Period size: 13 Copynumber: 2.6 Consensus size: 13
922401 TTTAAAAAAT
*
922411 AAAAAAATTTGTG
1 AAAAAAAATTGTG
*
922424 AGAAAAAATTGTG
1 AAAAAAAATTGTG
922437 AAAAAAAA
1 AAAAAAAA
922445 ACAAAAGATG
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.65, C:0.00, G:0.15, T:0.21
Consensus pattern (13 bp):
AAAAAAAATTGTG
Found at i:923346 original size:12 final size:12
Alignment explanation
Indices: 923331--923374 Score: 54
Period size: 12 Copynumber: 3.7 Consensus size: 12
923321 AATTGAGATT
923331 GAGAAAGAAAAA
1 GAGAAAGAAAAA
*
923343 GAGAAAGAAAAT
1 GAGAAAGAAAAA
*
923355 GAGAGAACAAAAA
1 GAGA-AAGAAAAA
923368 GA-AAAGA
1 GAGAAAGA
923375 GGTTCGAGTA
Statistics
Matches: 27, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
11 3 0.11
12 16 0.59
13 8 0.30
ACGTcount: A:0.70, C:0.02, G:0.25, T:0.02
Consensus pattern (12 bp):
GAGAAAGAAAAA
Found at i:928436 original size:5 final size:5
Alignment explanation
Indices: 928428--928456 Score: 58
Period size: 5 Copynumber: 5.8 Consensus size: 5
928418 CATTCATTAC
928428 ATTTT ATTTT ATTTT ATTTT ATTTT ATTT
1 ATTTT ATTTT ATTTT ATTTT ATTTT ATTT
928457 GCATATTAGT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 24 1.00
ACGTcount: A:0.21, C:0.00, G:0.00, T:0.79
Consensus pattern (5 bp):
ATTTT
Found at i:930709 original size:54 final size:52
Alignment explanation
Indices: 930648--930832 Score: 246
Period size: 54 Copynumber: 3.5 Consensus size: 52
930638 CCATGACAAG
* *
930648 TGAAGACCATATAGTGTAAGGCATAGACGTTTGATATGGCATCATATGGGGAA
1 TGAAGACCATATAGTGTAAGGCCTAG-CGTTTGCTATGGCATCATATGGGGAA
* *
930701 CTGAAGACCATATAGTGTAAGGCCCAGCTATTTGCTATGGCATCATATGGGGAAA
1 -TGAAGACCATATAGTGTAAGGCCTAGC-GTTTGCTATGGCATCATATGGGG-AA
*
930756 TGAAGACCATATAGTGTAAGGCCTACCCGTTTGCTATGGCATCATAT-GGGAA
1 TGAAGACCATATAGTGTAAGGCCTA-GCGTTTGCTATGGCATCATATGGGGAA
* * *
930808 AGAAGACCACATAGTGTAAGACCTA
1 TGAAGACCATATAGTGTAAGGCCTA
930833 TTTTGGGACT
Statistics
Matches: 118, Mismatches: 10, Indels: 8
0.87 0.07 0.06
Matches are distributed among these distances:
52 24 0.20
53 4 0.03
54 87 0.74
55 3 0.03
ACGTcount: A:0.33, C:0.17, G:0.25, T:0.25
Consensus pattern (52 bp):
TGAAGACCATATAGTGTAAGGCCTAGCGTTTGCTATGGCATCATATGGGGAA
Found at i:930845 original size:52 final size:51
Alignment explanation
Indices: 930649--930856 Score: 231
Period size: 54 Copynumber: 3.9 Consensus size: 51
930639 CATGACAAGT
* * * *
930649 GAAGACCATATAGTGTAAGGCATAGACGTTTGATATGGCATCATATGGGGAACT
1 GAAGACCATATAGTGTAAGGCCT--ACTTTTGCTATGGCATCATATGGGGAA-A
*
930703 GAAGACCATATAGTGTAAGGCCCAGCTATTTGCTATGGCATCATATGGGGAAA
1 GAAGACCATATAGTGTAAGGCCTA-CT-TTTGCTATGGCATCATATGGGGAAA
*
930756 TGAAGACCATATAGTGTAAGGCCTACCCGTTTGCTATGGCATCATAT-GGGAAA
1 -GAAGACCATATAGTGTAAGGCCTA--CTTTTGCTATGGCATCATATGGGGAAA
* *
930809 GAAGACCACATAGTGTAAGACCTA-TTTTGGGACTATGGCATCATATGG
1 GAAGACCATATAGTGTAAGGCCTACTTTT--G-CTATGGCATCATATGG
930857 AGAGAAGATG
Statistics
Matches: 135, Mismatches: 11, Indels: 17
0.83 0.07 0.10
Matches are distributed among these distances:
49 3 0.02
51 1 0.01
52 37 0.27
53 8 0.06
54 85 0.63
55 1 0.01
ACGTcount: A:0.32, C:0.16, G:0.26, T:0.26
Consensus pattern (51 bp):
GAAGACCATATAGTGTAAGGCCTACTTTTGCTATGGCATCATATGGGGAAA
Found at i:931063 original size:31 final size:29
Alignment explanation
Indices: 930969--931067 Score: 153
Period size: 29 Copynumber: 3.3 Consensus size: 29
930959 AAAAGTGATA
930969 CCTTTGTGGCTGAATCTGTTATATGTGAG
1 CCTTTGTGGCTGAATCTGTTATATGTGAG
* * *
930998 CCTTTGTGGCTAAATCTATTTTATGTGAG
1 CCTTTGTGGCTGAATCTGTTATATGTGAG
931027 CCTTTGTGGCTGAATCTGTTATATGTGGAAG
1 CCTTTGTGGCTGAATCTGTTATATGT-G-AG
931058 CCTTTGTGGC
1 CCTTTGTGGC
931068 CGTTCTTTGT
Statistics
Matches: 62, Mismatches: 6, Indels: 2
0.89 0.09 0.03
Matches are distributed among these distances:
29 49 0.79
30 1 0.02
31 12 0.19
ACGTcount: A:0.17, C:0.15, G:0.26, T:0.41
Consensus pattern (29 bp):
CCTTTGTGGCTGAATCTGTTATATGTGAG
Found at i:931092 original size:30 final size:29
Alignment explanation
Indices: 930969--931092 Score: 115
Period size: 29 Copynumber: 4.2 Consensus size: 29
930959 AAAAGTGATA
* *
930969 CCTTTGTGGCTGAATCTGTTATATGTGAG
1 CCTTTGTGGCCGAATCTGTTACATGTGAG
** * **
930998 CCTTTGTGGCTAAATCTATTTTATGTGAG
1 CCTTTGTGGCCGAATCTGTTACATGTGAG
* *
931027 CCTTTGTGGCTGAATCTGTTATATGTGGAAG
1 CCTTTGTGGCCGAATCTGTTACATGT-G-AG
*
931058 CCTTTGTGGCCG-TTCTTTGTTACATGTGAG
1 CCTTTGTGGCCGAATC--TGTTACATGTGAG
931088 CCTTT
1 CCTTT
931093 ATGGTGATAT
Statistics
Matches: 82, Mismatches: 9, Indels: 7
0.84 0.09 0.07
Matches are distributed among these distances:
29 49 0.60
30 10 0.12
31 14 0.17
32 9 0.11
ACGTcount: A:0.16, C:0.16, G:0.25, T:0.43
Consensus pattern (29 bp):
CCTTTGTGGCCGAATCTGTTACATGTGAG
Found at i:938642 original size:25 final size:25
Alignment explanation
Indices: 938587--938669 Score: 87
Period size: 25 Copynumber: 3.3 Consensus size: 25
938577 GAGTTATAAA
* *
938587 CGGTAAGCTCATACGAGCTAAATAA
1 CGGTAAGCTCATATGAGCTAAATAT
* *
938612 CAGTAAGCTCATGTGAGCTAAATAT
1 CGGTAAGCTCATATGAGCTAAATAT
* * *
938637 TGGTAAGCTC-TCTCGAGCTGAATAT
1 CGGTAAGCTCATAT-GAGCTAAATAT
938662 CGGTAAGC
1 CGGTAAGC
938670 CCTCTCAAGC
Statistics
Matches: 48, Mismatches: 9, Indels: 2
0.81 0.15 0.03
Matches are distributed among these distances:
24 2 0.04
25 46 0.96
ACGTcount: A:0.33, C:0.19, G:0.23, T:0.25
Consensus pattern (25 bp):
CGGTAAGCTCATATGAGCTAAATAT
Found at i:938674 original size:25 final size:25
Alignment explanation
Indices: 938626--938696 Score: 83
Period size: 25 Copynumber: 2.9 Consensus size: 25
938616 AAGCTCATGT
* * *
938626 GAGCTAAATATTGGTAAGCTCTCTC
1 GAGCTGAATATCGGTAAGCCCTCTC
938651 GAGCTGAATATCGGTAAGCCCTCTC
1 GAGCTGAATATCGGTAAGCCCTCTC
*
938676 AAGCTGAGA-ATCGGTAA-CCCT
1 GAGCTGA-ATATCGGTAAGCCCT
938697 AATGACATGT
Statistics
Matches: 41, Mismatches: 4, Indels: 3
0.85 0.08 0.06
Matches are distributed among these distances:
24 4 0.10
25 36 0.88
26 1 0.02
ACGTcount: A:0.28, C:0.24, G:0.23, T:0.25
Consensus pattern (25 bp):
GAGCTGAATATCGGTAAGCCCTCTC
Found at i:946728 original size:5 final size:5
Alignment explanation
Indices: 946704--946738 Score: 52
Period size: 5 Copynumber: 6.6 Consensus size: 5
946694 ACTTAAACTA
946704 AAAATG AAAAG AAGAAG AAAAG AAAAG AAAAG AAA
1 AAAA-G AAAAG AA-AAG AAAAG AAAAG AAAAG AAA
946739 CCCTAACCAT
Statistics
Matches: 28, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
5 19 0.68
6 9 0.32
ACGTcount: A:0.77, C:0.00, G:0.20, T:0.03
Consensus pattern (5 bp):
AAAAG
Found at i:948581 original size:29 final size:29
Alignment explanation
Indices: 948549--948649 Score: 105
Period size: 29 Copynumber: 3.5 Consensus size: 29
948539 AATTTTCGTA
*
948549 AAAAGGACGCCTTTGTGGCTATCTCTGTT
1 AAAAGGAAGCCTTTGTGGCTATCTCTGTT
* * * *
948578 AAAAGGAAACCTTTGTGG-TGGTTTCTATT
1 AAAAGGAAGCCTTTGTGGCT-ATCTCTGTT
* * *
948607 AAAAGTAAGCCTTTGTGGCGATGTCTGTT
1 AAAAGGAAGCCTTTGTGGCTATCTCTGTT
*
948636 AAAAGAAAGCCTTT
1 AAAAGGAAGCCTTT
948650 ATAGCGAACC
Statistics
Matches: 58, Mismatches: 12, Indels: 4
0.78 0.16 0.05
Matches are distributed among these distances:
28 1 0.02
29 57 0.98
ACGTcount: A:0.28, C:0.15, G:0.24, T:0.34
Consensus pattern (29 bp):
AAAAGGAAGCCTTTGTGGCTATCTCTGTT
Found at i:955346 original size:22 final size:22
Alignment explanation
Indices: 955311--955363 Score: 79
Period size: 22 Copynumber: 2.4 Consensus size: 22
955301 GAACGGTAAT
*
955311 GATACCATCTATGAGAAATATC
1 GATACCATCCATGAGAAATATC
*
955333 GATACTATCCATGAGAAATATC
1 GATACCATCCATGAGAAATATC
*
955355 GATATCATC
1 GATACCATC
955364 GAATGAGTAT
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
22 27 1.00
ACGTcount: A:0.40, C:0.19, G:0.13, T:0.28
Consensus pattern (22 bp):
GATACCATCCATGAGAAATATC
Found at i:959336 original size:20 final size:19
Alignment explanation
Indices: 959299--959337 Score: 51
Period size: 19 Copynumber: 2.0 Consensus size: 19
959289 AATTTTAAAA
*
959299 TATTTTGAAAATACTTTTT
1 TATTTTGAAAATAATTTTT
*
959318 TATTTTTAAAATAAATTTTT
1 TATTTTGAAAAT-AATTTTT
959338 GGTGTTTATT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
19 11 0.65
20 6 0.35
ACGTcount: A:0.36, C:0.03, G:0.03, T:0.59
Consensus pattern (19 bp):
TATTTTGAAAATAATTTTT
Found at i:960795 original size:14 final size:13
Alignment explanation
Indices: 960756--960797 Score: 52
Period size: 11 Copynumber: 3.3 Consensus size: 13
960746 TTATATATAT
*
960756 ATATATTAAAAT-
1 ATATATAAAAATA
960768 -TATATAAAAATA
1 ATATATAAAAATA
960780 ATATATAAAAATTA
1 ATATATAAAAA-TA
960794 ATAT
1 ATAT
960798 GGACAGGCCG
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
11 10 0.38
13 10 0.38
14 6 0.23
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (13 bp):
ATATATAAAAATA
Found at i:962576 original size:18 final size:18
Alignment explanation
Indices: 962561--962596 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
962551 GGTTTGAATT
962561 ATTGGAACTTCATGAAGA
1 ATTGGAACTTCATGAAGA
962579 ATTGGAACTTCATGAAGA
1 ATTGGAACTTCATGAAGA
962597 CTTATTCTTT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.39, C:0.11, G:0.22, T:0.28
Consensus pattern (18 bp):
ATTGGAACTTCATGAAGA
Found at i:962580 original size:21 final size:21
Alignment explanation
Indices: 962556--962602 Score: 64
Period size: 18 Copynumber: 2.4 Consensus size: 21
962546 TTTTAGGTTT
962556 GAATTATTGGAACTTCATGAA
1 GAATTATTGGAACTTCATGAA
962577 G-A--ATTGGAACTTCATGAA
1 GAATTATTGGAACTTCATGAA
*
962595 GACTTATT
1 GAATTATT
962603 CTTTCAACTA
Statistics
Matches: 22, Mismatches: 1, Indels: 6
0.76 0.03 0.21
Matches are distributed among these distances:
18 17 0.77
20 1 0.05
21 4 0.18
ACGTcount: A:0.36, C:0.11, G:0.19, T:0.34
Consensus pattern (21 bp):
GAATTATTGGAACTTCATGAA
Found at i:973879 original size:20 final size:20
Alignment explanation
Indices: 973854--973891 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
973844 ACGAGCTCAA
973854 TGAGCTGAA-TTGAGCTCGTG
1 TGAGCT-AACTTGAGCTCGTG
973874 TGAGCTAACTTGAGCTCG
1 TGAGCTAACTTGAGCTCG
973892 AATGAACTGA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
19 2 0.12
20 15 0.88
ACGTcount: A:0.21, C:0.18, G:0.32, T:0.29
Consensus pattern (20 bp):
TGAGCTAACTTGAGCTCGTG
Found at i:975805 original size:7 final size:6
Alignment explanation
Indices: 975717--975856 Score: 93
Period size: 6 Copynumber: 23.0 Consensus size: 6
975707 TCAATCTCAA
* * * ** **
975717 TTTCTT TTTCAAT TTTCTTT TCTTCGT TTTCTT TTTCTC TCACTT TTTCGA
1 TTTCTT TTTC-TT TTTC-TT T-TTCTT TTTCTT TTTCTT TTTCTT TTTCTT
*** * * *
975768 TTTCTT TTTC-T TTTGAA TTTCTT TTTCTT TTTCGT TTTCTA TTTCTA
1 TTTCTT TTTCTT TTTCTT TTTCTT TTTCTT TTTCTT TTTCTT TTTCTT
** * *
975815 TTTCTT TTTCAC TTTCTA TTTCTT TTTATT TTTCTT TTTCTT
1 TTTCTT TTTCTT TTTCTT TTTCTT TTTCTT TTTCTT TTTCTT
975857 CATTTTTGTT
Statistics
Matches: 100, Mismatches: 31, Indels: 6
0.73 0.23 0.04
Matches are distributed among these distances:
5 4 0.04
6 84 0.84
7 9 0.09
8 3 0.03
ACGTcount: A:0.08, C:0.18, G:0.03, T:0.71
Consensus pattern (6 bp):
TTTCTT
Found at i:979244 original size:26 final size:26
Alignment explanation
Indices: 979164--979246 Score: 68
Period size: 26 Copynumber: 3.2 Consensus size: 26
979154 GATGAACACG
*
979164 TGTGTAGTACTATGTGAAGGCTACTA
1 TGTGTAGTACTAAGTGAAGGCTACTA
* *
979190 CGTGTA-T-CGATAAAT-AATGG-TCAC-A
1 TGTGTAGTAC--TAAGTGAA-GGCT-ACTA
979215 TGTGTAGTACTAAGTGAAGGCTACTA
1 TGTGTAGTACTAAGTGAAGGCTACTA
979241 TGTGTA
1 TGTGTA
979247 CTGAGAAGTT
Statistics
Matches: 43, Mismatches: 5, Indels: 18
0.65 0.08 0.27
Matches are distributed among these distances:
24 1 0.02
25 18 0.42
26 23 0.53
27 1 0.02
ACGTcount: A:0.30, C:0.12, G:0.25, T:0.33
Consensus pattern (26 bp):
TGTGTAGTACTAAGTGAAGGCTACTA
Found at i:979336 original size:102 final size:102
Alignment explanation
Indices: 979160--979501 Score: 412
Period size: 102 Copynumber: 3.4 Consensus size: 102
979150 TATCGATGAA
*
979160 CACGTGTGTAGTACTATGTGAAGGCTACTACGTGTATCGATAAA-TAATGGTCACATGTGTAGTA
1 CACGTGTGTAGTACTATGTGAAGGCTACTACGTGTATCGGTAAACT-ATGGTCACATGTGTAGTA
* *
979224 CTAAGTGAAGGCTACTATGTGTACTGAGAAGTTTTGAG-
65 CTAAGTGAAGGCTACTATGTGTACTGAAAAGCTTTG-GT
* * * * *
979262 CACGTGTGTAGTACTGTGTGAAAGTTACTACGTGTATCGGTAAACTATGGTTACATGTGTGGTAC
1 CACGTGTGTAGTACTATGTGAAGGCTACTACGTGTATCGGTAAACTATGGTCACATGTGTAGTAC
979327 TAAGTGAAGGCTACTATG-GATACTGAAAAGCTTTGGT
66 TAAGTGAAGGCTACTATGTG-TACTGAAAAGCTTTGGT
* * * * *
979364 CACGTATGTAGTACTATGTGAAGGCTACTACGTG-AGCCGTAAAACT-TGATCACGTGTGTAGTA
1 CACGTGTGTAGTACTATGTGAAGGCTACTACGTGTATCGGT-AAACTATGGTCACATGTGTAGTA
* * * *
979427 CTATGTGAAGGCTACTACGTGAACTGTAAAA-C--TGAT
65 CTAAGTGAAGGCTACTATGTGTACTG-AAAAGCTTTGGT
* *
979463 CTCGTGTGTTGTACTATGTGAAGGCTACTACGTGTATCG
1 CACGTGTGTAGTACTATGTGAAGGCTACTACGTGTATCG
979502 AATGATAAAA
Statistics
Matches: 206, Mismatches: 27, Indels: 16
0.83 0.11 0.06
Matches are distributed among these distances:
99 34 0.17
100 2 0.01
101 41 0.20
102 128 0.62
103 1 0.00
ACGTcount: A:0.28, C:0.15, G:0.26, T:0.31
Consensus pattern (102 bp):
CACGTGTGTAGTACTATGTGAAGGCTACTACGTGTATCGGTAAACTATGGTCACATGTGTAGTAC
TAAGTGAAGGCTACTATGTGTACTGAAAAGCTTTGGT
Found at i:979482 original size:49 final size:50
Alignment explanation
Indices: 979160--979496 Score: 292
Period size: 51 Copynumber: 6.7 Consensus size: 50
979150 TATCGATGAA
* * *
979160 CACGTGTGTAGTACTATGTGAAGGCTACTACGTGTA-TCGATAAATA-ATGGT
1 CACGTGTGTAGTACTATGTGAAGGCTACTACGTGAACT-G-TAAA-ACTTGAT
* * * * ** *
979211 CACATGTGTAGTACTAAGTGAAGGCTACTATGTGTACTG-AGAAGTTTTGAG
1 CACGTGTGTAGTACTATGTGAAGGCTACTACGTGAACTGTA-AA-ACTTGAT
* * * * * *
979262 CACGTGTGTAGTACTGTGTGAAAGTTACTACGTGTATCGGT-AAACTATGGT
1 CACGTGTGTAGTACTATGTGAAGGCTACTACGTG-AACTGTAAAACT-TGAT
* * * * * *
979313 TACATGTGTGGTACTAAGTGAAGGCTACTATG-GATACTG-AAAAGCTTTGGT
1 CACGTGTGTAGTACTATGTGAAGGCTACTACGTGA-ACTGTAAAA-C-TTGAT
* * *
979364 CACGTATGTAGTACTATGTGAAGGCTACTACGTGAGCCGTAAAACTTGAT
1 CACGTGTGTAGTACTATGTGAAGGCTACTACGTGAACTGTAAAACTTGAT
979414 CACGTGTGTAGTACTATGTGAAGGCTACTACGTGAACTGTAAAAC-TGAT
1 CACGTGTGTAGTACTATGTGAAGGCTACTACGTGAACTGTAAAACTTGAT
* *
979463 CTCGTGTGTTGTACTATGTGAAGGCTACTACGTG
1 CACGTGTGTAGTACTATGTGAAGGCTACTACGTG
979497 TATCGAATGA
Statistics
Matches: 229, Mismatches: 45, Indels: 26
0.76 0.15 0.09
Matches are distributed among these distances:
49 38 0.17
50 55 0.24
51 126 0.55
52 10 0.04
ACGTcount: A:0.28, C:0.15, G:0.26, T:0.31
Consensus pattern (50 bp):
CACGTGTGTAGTACTATGTGAAGGCTACTACGTGAACTGTAAAACTTGAT
Found at i:986854 original size:51 final size:51
Alignment explanation
Indices: 986793--987131 Score: 309
Period size: 51 Copynumber: 6.7 Consensus size: 51
986783 CGATGAACAA
* *
986793 GTGTGTAGTACTGTGTGAAGGCTACTACGTGTATCGATAAATAATGGTCAC
1 GTGTGTAGTACTATGTGAAGGCTACTACGTGTATCGATAAATATTGGTCAC
* * * * * * *
986844 ATGTGTAGTACTAAGTGAAGGCTACTATGTGTACCGAGAAGTTTTGAG-CAC
1 GTGTGTAGTACTATGTGAAGGCTACTACGTGTATCGATAAATATTG-GTCAC
* * * *
986895 GTGTGTAGTACTGTGTGAAAGCTACTACGTGTATCGGTAAACTATT-GTTAC
1 GTGTGTAGTACTATGTGAAGGCTACTACGTGTATCGATAAA-TATTGGTCAC
* * * * * * **
986946 ATGTGTGGTACTAAGTGAAGGCTGCTATG-GATACCGA-AAAGCTTGGTCAC
1 GTGTGTAGTACTATGTGAAGGCTACTACGTG-TATCGATAAATATTGGTCAC
* * * *
986996 GTATGTAGTACTATGTGAAGGCTACTACGTG-AGCCATAAA-ACTTGATCAC
1 GTGTGTAGTACTATGTGAAGGCTACTACGTGTATCGATAAATA-TTGGTCAC
* * * *
987046 GTGTGTAGTACTATGTGAAGGCTACTACGTG-AACTG-TAAA-ACTGATCTC
1 GTGTGTAGTACTATGTGAAGGCTACTACGTGTATC-GATAAATATTGGTCAC
987095 GTGTGTAGTACTATGTGAAGGCTACTACGTGTATCGA
1 GTGTGTAGTACTATGTGAAGGCTACTACGTGTATCGA
987132 ATGATAAAAA
Statistics
Matches: 229, Mismatches: 48, Indels: 23
0.76 0.16 0.08
Matches are distributed among these distances:
49 43 0.19
50 81 0.35
51 101 0.44
52 4 0.02
ACGTcount: A:0.28, C:0.15, G:0.27, T:0.30
Consensus pattern (51 bp):
GTGTGTAGTACTATGTGAAGGCTACTACGTGTATCGATAAATATTGGTCAC
Found at i:986974 original size:102 final size:101
Alignment explanation
Indices: 986793--987131 Score: 370
Period size: 102 Copynumber: 3.4 Consensus size: 101
986783 CGATGAACAA
986793 GTGTGTAGTACTGTGTGAAGGCTACTACGTGTATCGATAAATAATGGTCACATGTGTAGTACTAA
1 GTGTGTAGTACTGTGTGAAGGCTACTACGTGTATCGATAAATAATGGTCACATGTGTAGTACTAA
* *
986858 GTGAAGGCTACTATGTG-TACCGAGAAGTTTTGAG-CAC
66 GTGAAGGCTACTATG-GATACCGAAAAG-CTTG-GTCAC
* * * * *
986895 GTGTGTAGTACTGTGTGAAAGCTACTACGTGTATCGGTAAACT-ATTGTTACATGTGTGGTACTA
1 GTGTGTAGTACTGTGTGAAGGCTACTACGTGTATCGATAAA-TAATGGTCACATGTGTAGTACTA
*
986959 AGTGAAGGCTGCTATGGATACCGAAAAGCTTGGTCAC
65 AGTGAAGGCTACTATGGATACCGAAAAGCTTGGTCAC
* * * * * * *
986996 GTATGTAGTACTATGTGAAGGCTACTACGTG-AGCCATAAA-ACTTGATCACGTGTGTAGTACTA
1 GTGTGTAGTACTGTGTGAAGGCTACTACGTGTATCGATAAATA-ATGGTCACATGTGTAGTACTA
* * * * *
987059 TGTGAAGGCTACTACGTGA-ACTGTAAAA-C-TGATCTC
65 AGTGAAGGCTACTATG-GATACCG-AAAAGCTTGGTCAC
*
987095 GTGTGTAGTACTATGTGAAGGCTACTACGTGTATCGA
1 GTGTGTAGTACTGTGTGAAGGCTACTACGTGTATCGA
987132 ATGATAAAAA
Statistics
Matches: 200, Mismatches: 29, Indels: 18
0.81 0.12 0.07
Matches are distributed among these distances:
99 35 0.17
100 42 0.21
101 41 0.20
102 81 0.41
103 1 0.00
ACGTcount: A:0.28, C:0.15, G:0.27, T:0.30
Consensus pattern (101 bp):
GTGTGTAGTACTGTGTGAAGGCTACTACGTGTATCGATAAATAATGGTCACATGTGTAGTACTAA
GTGAAGGCTACTATGGATACCGAAAAGCTTGGTCAC
Found at i:989540 original size:28 final size:27
Alignment explanation
Indices: 989504--989556 Score: 70
Period size: 28 Copynumber: 1.9 Consensus size: 27
989494 CGGCATTGAC
989504 TAAGACATAATAAAAACTTGTAATAGT
1 TAAGACATAATAAAAACTTGTAATAGT
* * *
989531 TAAGAACATATTAATAAGTTGTAATA
1 TAAG-ACATAATAAAAACTTGTAATA
989557 ATACTTTCTA
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
27 4 0.18
28 18 0.82
ACGTcount: A:0.51, C:0.06, G:0.11, T:0.32
Consensus pattern (27 bp):
TAAGACATAATAAAAACTTGTAATAGT
Found at i:989682 original size:20 final size:20
Alignment explanation
Indices: 989648--989686 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
989638 ATAAGCTAAA
**
989648 TTGAGCTCGTGTGAGCTGAC
1 TTGAGCTCGAATGAGCTGAC
989668 TTGAGCTCGAATGAGCTGA
1 TTGAGCTCGAATGAGCTGA
989687 ACCACATGGA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.21, C:0.18, G:0.33, T:0.28
Consensus pattern (20 bp):
TTGAGCTCGAATGAGCTGAC
Found at i:993466 original size:50 final size:50
Alignment explanation
Indices: 993341--993531 Score: 150
Period size: 50 Copynumber: 3.8 Consensus size: 50
993331 GATAATAACA
* * * * ** * * * *
993341 TGCCAAAGCTATGTCCCAAACATAGTCTTACATGGGATGTTTCTTGT-AC
1 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATATCAG
* * * ** *
993390 TGCCAATGCCATATCCCAGATATGGTCTTACATGGGAGTTCTCATATCGG
1 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATATCAG
* * * * ** *
993440 TTCCCATGTCATGTCCCAGACATGGTCTTACGGGGGACCTCTCATCTCAG
1 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATATCAG
* *
993490 TGCCAACGCCATGTCTCAGACATGGTCTTACATGGGATCTCT
1 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCT
993532 TTACCCAAAT
Statistics
Matches: 109, Mismatches: 32, Indels: 1
0.77 0.23 0.01
Matches are distributed among these distances:
49 36 0.33
50 73 0.67
ACGTcount: A:0.23, C:0.27, G:0.21, T:0.30
Consensus pattern (50 bp):
TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATATCAG
Found at i:995902 original size:50 final size:50
Alignment explanation
Indices: 995835--996025 Score: 220
Period size: 50 Copynumber: 3.7 Consensus size: 50
995825 TTTCTTGTAC
* * **
995835 TGCCAATGCCATATCCCAGATATGGTCTTACATGGGAGTTCTCATATAGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATATAGG
* *** * *
995885 TGCCCATGCCATGTCCCAGACATGGTCTTATGGGGGACCTCTCATCTCGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATATAGG
* *
995935 TGCCAATGCCATGTCCCAGACATGGTCTTACATGAGACCTCTCATAATCTCAATGA
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCAT-A--T--A-GG
995991 TGCCAATGCCATGTCCCAGACATGGTCTTACATGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGG
996026 NNNNNNNNNN
Statistics
Matches: 116, Mismatches: 19, Indels: 6
0.82 0.13 0.04
Matches are distributed among these distances:
50 80 0.69
53 1 0.01
56 35 0.30
ACGTcount: A:0.24, C:0.28, G:0.21, T:0.27
Consensus pattern (50 bp):
TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATATAGG
Found at i:995944 original size:100 final size:104
Alignment explanation
Indices: 995835--996020 Score: 263
Period size: 100 Copynumber: 1.8 Consensus size: 104
995825 TTTCTTGTAC
* * ** * *
995835 TGCCAATGCCATATCCCAGATATGGTCTTACATGGGAGTTCTCAT-A-T-A-GGTGCCCATGCCA
1 TGCCAATGCCATATCCCAGACATGGTCTTACATGAGACCTCTCATAACTAATGATGCCAATGCCA
995896 TGTCCCAGACATGGTCTTATGGGGGACCTCTCATCTCGG
66 TGTCCCAGACATGGTCTTATGGGGGACCTCTCATCTCGG
*
995935 TGCCAATGCCATGTCCCAGACATGGTCTTACATGAGACCTCTCATAATCTCAATGATGCCAATGC
1 TGCCAATGCCATATCCCAGACATGGTCTTACATGAGACCTCTCATAA-CT-AATGATGCCAATGC
996000 CATGTCCCAGACATGGTCTTA
64 CATGTCCCAGACATGGTCTTA
996021 CATGGNNNNN
Statistics
Matches: 73, Mismatches: 7, Indels: 6
0.85 0.08 0.07
Matches are distributed among these distances:
100 40 0.55
101 1 0.01
103 1 0.01
105 1 0.01
106 30 0.41
ACGTcount: A:0.24, C:0.28, G:0.21, T:0.27
Consensus pattern (104 bp):
TGCCAATGCCATATCCCAGACATGGTCTTACATGAGACCTCTCATAACTAATGATGCCAATGCCA
TGTCCCAGACATGGTCTTATGGGGGACCTCTCATCTCGG
Found at i:1014045 original size:25 final size:24
Alignment explanation
Indices: 1013991--1014058 Score: 66
Period size: 24 Copynumber: 2.8 Consensus size: 24
1013981 GGCTATATAA
1013991 CGGGAAGCTCATAAGAGCCTAAAT
1 CGGGAAGCTCATAAGAGCCTAAAT
* * *
1014015 CAGGAAGTTCATAAGGAGCCTTTAAT
1 CGGGAAGCTCATAA-GAGCC-TAAAT
**
1014041 -GGGAAGCTCCGAAGAGCC
1 CGGGAAGCTCATAAGAGCC
1014059 ATTAATCAGA
Statistics
Matches: 35, Mismatches: 7, Indels: 4
0.76 0.15 0.09
Matches are distributed among these distances:
24 17 0.49
25 14 0.40
26 4 0.11
ACGTcount: A:0.34, C:0.21, G:0.28, T:0.18
Consensus pattern (24 bp):
CGGGAAGCTCATAAGAGCCTAAAT
Found at i:1014096 original size:25 final size:25
Alignment explanation
Indices: 1014053--1014160 Score: 98
Period size: 25 Copynumber: 4.4 Consensus size: 25
1014043 GAAGCTCCGA
*
1014053 AGAGCCAT-TAATC-AGAAGTTCCAG
1 AGAGCCATAT-ATCGAGAAGTTCAAG
*
1014077 ATAGCCATATATCGAGAAGTTCAAG
1 AGAGCCATATATCGAGAAGTTCAAG
* * *
1014102 CGAGCCATATATTGGGAAGTTCAAG
1 AGAGCCATATATCGAGAAGTTCAAG
* * *
1014127 CGAGCCA-A-ATCGAGAAGCTCTAG
1 AGAGCCATATATCGAGAAGTTCAAG
*
1014150 ATAGCCATATA
1 AGAGCCATATA
1014161 ACAGGACGCT
Statistics
Matches: 68, Mismatches: 12, Indels: 7
0.78 0.14 0.08
Matches are distributed among these distances:
23 16 0.24
24 12 0.18
25 40 0.59
ACGTcount: A:0.37, C:0.19, G:0.22, T:0.21
Consensus pattern (25 bp):
AGAGCCATATATCGAGAAGTTCAAG
Found at i:1016782 original size:11 final size:11
Alignment explanation
Indices: 1016766--1016799 Score: 52
Period size: 11 Copynumber: 3.2 Consensus size: 11
1016756 AGGCATAAAG
1016766 ATGTTCACACC
1 ATGTTCACACC
*
1016777 ATGTTCA-GCC
1 ATGTTCACACC
1016787 ATGTTCACACC
1 ATGTTCACACC
1016798 AT
1 AT
1016800 ATGGCTCTTC
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
10 9 0.45
11 11 0.55
ACGTcount: A:0.26, C:0.32, G:0.12, T:0.29
Consensus pattern (11 bp):
ATGTTCACACC
Found at i:1019561 original size:25 final size:24
Alignment explanation
Indices: 1019504--1019579 Score: 66
Period size: 24 Copynumber: 3.1 Consensus size: 24
1019494 CCTGGCTATA
1019504 TAACGGGAAGCT-CATAAGAGCC-T
1 TAACGGGAAGCTCCA-AAGAGCCAT
* * * *
1019527 AAATCAGGAAGTTCACAAAGAGCCTT
1 TAA-CGGGAAGCTC-CAAAGAGCCAT
*
1019553 TAACGGGAAGCTCCGAAGAGCCAT
1 TAACGGGAAGCTCCAAAGAGCCAT
1019577 TAA
1 TAA
1019580 TCAGAAGTTC
Statistics
Matches: 41, Mismatches: 8, Indels: 7
0.73 0.14 0.12
Matches are distributed among these distances:
23 2 0.05
24 19 0.46
25 15 0.37
26 5 0.12
ACGTcount: A:0.38, C:0.21, G:0.24, T:0.17
Consensus pattern (24 bp):
TAACGGGAAGCTCCAAAGAGCCAT
Found at i:1019609 original size:49 final size:50
Alignment explanation
Indices: 1019501--1019611 Score: 129
Period size: 49 Copynumber: 2.3 Consensus size: 50
1019491 TATCCTGGCT
*
1019501 ATATAACGGGAAGCTCATAAGAGCCTAAATCAGGAAGTTCACAAAGAGCC
1 ATATAACGGGAAGCTCAGAAGAGCCTAAATCAGGAAGTTCACAAAGAGCC
* * * * *
1019551 -TTTAACGGGAAGCTCCGAAGAGCCATTAATCA-GAAGTTC-CAGATAGCC
1 ATATAACGGGAAGCTCAGAAGAGCC-TAAATCAGGAAGTTCACAAAGAGCC
*
1019599 ATATATCGGGAAG
1 ATATAACGGGAAG
1019612 TTCAAACGAG
Statistics
Matches: 51, Mismatches: 8, Indels: 5
0.80 0.12 0.08
Matches are distributed among these distances:
48 7 0.14
49 38 0.75
50 6 0.12
ACGTcount: A:0.38, C:0.20, G:0.23, T:0.19
Consensus pattern (50 bp):
ATATAACGGGAAGCTCAGAAGAGCCTAAATCAGGAAGTTCACAAAGAGCC
Found at i:1019613 original size:25 final size:26
Alignment explanation
Indices: 1019533--1019652 Score: 85
Period size: 25 Copynumber: 4.8 Consensus size: 26
1019523 GCCTAAATCA
* *
1019533 GGAAGTTCACAAA-GAGCC-TTTAACG
1 GGAAGTTC-CAAACGAGCCATATATCG
* *
1019558 GGAAGCTCCGAA-GAGCCAT-TAATC-
1 GGAAGTTCCAAACGAGCCATAT-ATCG
* * *
1019582 AGAAGTTCCAGA-TAGCCATATATCG
1 GGAAGTTCCAAACGAGCCATATATCG
*
1019607 GGAAGTT-CAAACGAGCCATATATTG
1 GGAAGTTCCAAACGAGCCATATATCG
*
1019632 GGAAGTT-CAAGCGAGCCATAT
1 GGAAGTTCCAAACGAGCCATAT
1019653 CAAGAAGCTC
Statistics
Matches: 77, Mismatches: 13, Indels: 10
0.77 0.13 0.10
Matches are distributed among these distances:
24 29 0.38
25 48 0.62
ACGTcount: A:0.35, C:0.20, G:0.24, T:0.21
Consensus pattern (26 bp):
GGAAGTTCCAAACGAGCCATATATCG
Found at i:1031175 original size:22 final size:22
Alignment explanation
Indices: 1031147--1031189 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 22
1031137 CATCTTTTCC
**
1031147 TTTTATTTTTCAAGATATTTAA
1 TTTTATTTCCCAAGATATTTAA
1031169 TTTTATTTCCCAAGATATTTA
1 TTTTATTTCCCAAGATATTTA
1031190 GACAAAAGGG
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.30, C:0.09, G:0.05, T:0.56
Consensus pattern (22 bp):
TTTTATTTCCCAAGATATTTAA
Found at i:1032861 original size:34 final size:34
Alignment explanation
Indices: 1032800--1032867 Score: 86
Period size: 34 Copynumber: 2.0 Consensus size: 34
1032790 TCACAGTTGA
*
1032800 ACAGTCTTGGGCCTAAGCCATTTTCAATATCAGTG
1 ACAGTCTTGGGCCTAAGCCATTCTCAATA-CAGTG
*
1032835 ACAGT-TTGGGCCTTAGCCCA-TCTCAATACAGTG
1 ACAGTCTTGGGCCTAAG-CCATTCTCAATACAGTG
1032868 TCAAAAATGC
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
33 5 0.17
34 17 0.57
35 8 0.27
ACGTcount: A:0.25, C:0.25, G:0.21, T:0.29
Consensus pattern (34 bp):
ACAGTCTTGGGCCTAAGCCATTCTCAATACAGTG
Found at i:1036272 original size:21 final size:20
Alignment explanation
Indices: 1036246--1036309 Score: 57
Period size: 21 Copynumber: 3.3 Consensus size: 20
1036236 CATAATTCTA
1036246 TACTTAGCTAAGACAACACTT
1 TACTTAGCT-AGACAACACTT
*
1036267 TACTTA-CT---CATAC-CTA
1 TACTTAGCTAGACA-ACACTT
1036283 TACTTAGCTATGACAACACTT
1 TACTTAGCTA-GACAACACTT
1036304 TACTTA
1 TACTTA
1036310 CTCATATCTA
Statistics
Matches: 34, Mismatches: 2, Indels: 14
0.68 0.04 0.28
Matches are distributed among these distances:
16 10 0.29
17 4 0.12
20 4 0.12
21 16 0.47
ACGTcount: A:0.34, C:0.25, G:0.06, T:0.34
Consensus pattern (20 bp):
TACTTAGCTAGACAACACTT
Found at i:1036298 original size:37 final size:37
Alignment explanation
Indices: 1036243--1036324 Score: 146
Period size: 37 Copynumber: 2.2 Consensus size: 37
1036233 ACACATAATT
1036243 CTATACTTAGCTAAGACAACACTTTACTTACTCATAC
1 CTATACTTAGCTAAGACAACACTTTACTTACTCATAC
* *
1036280 CTATACTTAGCTATGACAACACTTTACTTACTCATAT
1 CTATACTTAGCTAAGACAACACTTTACTTACTCATAC
1036317 CTATACTT
1 CTATACTT
1036325 TGCCAAATGG
Statistics
Matches: 43, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
37 43 1.00
ACGTcount: A:0.33, C:0.26, G:0.05, T:0.37
Consensus pattern (37 bp):
CTATACTTAGCTAAGACAACACTTTACTTACTCATAC
Found at i:1043856 original size:31 final size:31
Alignment explanation
Indices: 1043818--1043889 Score: 90
Period size: 33 Copynumber: 2.3 Consensus size: 31
1043808 AGGCCTTTTG
1043818 GCGGCGCTAAAAAGCGCAGCAAAAAGAATTT
1 GCGGCGCTAAAAAGCGCAGCAAAAAGAATTT
** * *
1043849 GCGGCGCTTTTGAAAGCGCTGCAAAAAGTATTT
1 GCGGCGC--TAAAAAGCGCAGCAAAAAGAATTT
1043882 GCGGCGCT
1 GCGGCGCT
1043890 TTTGAAAGCG
Statistics
Matches: 35, Mismatches: 4, Indels: 4
0.81 0.09 0.09
Matches are distributed among these distances:
31 8 0.23
33 27 0.77
ACGTcount: A:0.31, C:0.21, G:0.29, T:0.19
Consensus pattern (31 bp):
GCGGCGCTAAAAAGCGCAGCAAAAAGAATTT
Found at i:1043873 original size:33 final size:33
Alignment explanation
Indices: 1043828--1043908 Score: 144
Period size: 33 Copynumber: 2.5 Consensus size: 33
1043818 GCGGCGCTAA
*
1043828 AAAGCGCAGCAAAAAGAATTTGCGGCGCTTTTG
1 AAAGCGCTGCAAAAAGAATTTGCGGCGCTTTTG
*
1043861 AAAGCGCTGCAAAAAGTATTTGCGGCGCTTTTG
1 AAAGCGCTGCAAAAAGAATTTGCGGCGCTTTTG
1043894 AAAGCGCTGCAAAAA
1 AAAGCGCTGCAAAAA
1043909 ATGCCGCTGA
Statistics
Matches: 46, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
33 46 1.00
ACGTcount: A:0.35, C:0.19, G:0.26, T:0.21
Consensus pattern (33 bp):
AAAGCGCTGCAAAAAGAATTTGCGGCGCTTTTG
Found at i:1044019 original size:43 final size:43
Alignment explanation
Indices: 1043956--1044135 Score: 306
Period size: 43 Copynumber: 4.2 Consensus size: 43
1043946 TTATAGAAAT
* *
1043956 AAACGCCGCTAAAGGTCATGTTCTTTAGCGGCACTTTTCCCGC
1 AAACGCCGCTAAAGGCCATGTTCTTTAGCGGCGCTTTTCCCGC
*
1043999 AAACGCCGCTAAAGGCCATGTTCTTTAGCGGCGCTTTTTCCGC
1 AAACGCCGCTAAAGGCCATGTTCTTTAGCGGCGCTTTTCCCGC
*
1044042 AAACGCCGCTAAAGGCCATGTTCTTTAGCGGCGCTTTTTCCGC
1 AAACGCCGCTAAAGGCCATGTTCTTTAGCGGCGCTTTTCCCGC
*
1044085 AAACGCCGCTAAAGGCCATGTTCTTTAGCGGCGCTTTTCCCAC
1 AAACGCCGCTAAAGGCCATGTTCTTTAGCGGCGCTTTTCCCGC
*
1044128 AAAAGCCG
1 AAACGCCG
1044136 TTATTGTTTG
Statistics
Matches: 131, Mismatches: 6, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
43 131 1.00
ACGTcount: A:0.21, C:0.31, G:0.22, T:0.26
Consensus pattern (43 bp):
AAACGCCGCTAAAGGCCATGTTCTTTAGCGGCGCTTTTCCCGC
Found at i:1051193 original size:73 final size:72
Alignment explanation
Indices: 1051112--1051251 Score: 217
Period size: 73 Copynumber: 1.9 Consensus size: 72
1051102 GCTTTCTTAT
* *
1051112 AAACGCTGCTAAATCCCCGAAAGCTCAGAAAACGGCGTCATTGGGCTTAGGTTTTTTTGCGGCGC
1 AAACGCTGCTAAATCCCCGAAAGCTCAGAAAACGACGTCATTGGGATTA-GTTTTTTTGCGGCGC
1051177 TTTACGAA
65 TTTACGAA
** * *
1051185 AAACGCTGCTAAATCCCCGAAAGCTTGGGAAACGACGTCGTTGGGATTAGTTTTTTTGCGGCGCT
1 AAACGCTGCTAAATCCCCGAAAGCTCAGAAAACGACGTCATTGGGATTAGTTTTTTTGCGGCGCT
1051250 TT
66 TT
1051252 CTCAAAAACG
Statistics
Matches: 61, Mismatches: 6, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
72 18 0.30
73 43 0.70
ACGTcount: A:0.24, C:0.22, G:0.26, T:0.28
Consensus pattern (72 bp):
AAACGCTGCTAAATCCCCGAAAGCTCAGAAAACGACGTCATTGGGATTAGTTTTTTTGCGGCGCT
TTACGAA
Found at i:1053238 original size:65 final size:65
Alignment explanation
Indices: 1053156--1053277 Score: 217
Period size: 65 Copynumber: 1.9 Consensus size: 65
1053146 ACACGCTCAG
* * *
1053156 GTGCTTAAACCGTGTACAAATCGAAAATAGGGTCACATGGTCGTGTCCCTAGGCCGTTTAATCGT
1 GTGCTGAAACCGTGTACAAATCGAAAATAGGGTCACATAGCCGTGTCCCTAGGCCGTTTAATCGT
1053221 GTGCTGAAACCGTGTACAAATCGAAAATAGGGTCACATAGCCGTGTCCCTAGGCCGT
1 GTGCTGAAACCGTGTACAAATCGAAAATAGGGTCACATAGCCGTGTCCCTAGGCCGT
1053278 GTAACTAACT
Statistics
Matches: 54, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
65 54 1.00
ACGTcount: A:0.27, C:0.23, G:0.25, T:0.25
Consensus pattern (65 bp):
GTGCTGAAACCGTGTACAAATCGAAAATAGGGTCACATAGCCGTGTCCCTAGGCCGTTTAATCGT
Found at i:1054325 original size:13 final size:13
Alignment explanation
Indices: 1054302--1054371 Score: 77
Period size: 13 Copynumber: 5.3 Consensus size: 13
1054292 TCATACATCT
1054302 ATTTCCATATAACC
1 ATTT-CATATAACC
*
1054316 AATTCATATAACC
1 ATTTCATATAACC
** *
1054329 ATTTCATGCAATC
1 ATTTCATATAACC
1054342 ATTTCATATAACC
1 ATTTCATATAACC
**
1054355 ATTTTGTATAACC
1 ATTTCATATAACC
1054368 ATTT
1 ATTT
1054372 GATTTAAATA
Statistics
Matches: 46, Mismatches: 10, Indels: 1
0.81 0.18 0.02
Matches are distributed among these distances:
13 43 0.93
14 3 0.07
ACGTcount: A:0.36, C:0.21, G:0.03, T:0.40
Consensus pattern (13 bp):
ATTTCATATAACC
Found at i:1054385 original size:39 final size:38
Alignment explanation
Indices: 1054301--1054397 Score: 95
Period size: 39 Copynumber: 2.5 Consensus size: 38
1054291 TTCATACATC
*
1054301 TATTTCCATATAACCAATTCATATAACCATTTCATGCAA
1 TATTT-CATATAACCAATTCATATAACCATTTCATGAAA
* ** * *
1054340 TCATTTCATATAACCATTTTGTATAACCATTTGATTTAAA
1 T-ATTTCATATAACCAATTCATATAACCATTTCA-TGAAA
* *
1054380 TATTTCATTTAAACAATT
1 TATTTCATATAACCAATT
1054398 AACACATAAT
Statistics
Matches: 47, Mismatches: 9, Indels: 4
0.78 0.15 0.07
Matches are distributed among these distances:
39 39 0.83
40 8 0.17
ACGTcount: A:0.37, C:0.18, G:0.03, T:0.42
Consensus pattern (38 bp):
TATTTCATATAACCAATTCATATAACCATTTCATGAAA
Found at i:1055209 original size:18 final size:18
Alignment explanation
Indices: 1055186--1055224 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
1055176 GCTTCCTTAA
*
1055186 ATTTTT-AATGTTTTATTC
1 ATTTTTAAAT-TTTAATTC
1055204 ATTTTTAAATTTTAATTC
1 ATTTTTAAATTTTAATTC
1055222 ATT
1 ATT
1055225 AATAATAACA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
18 16 0.84
19 3 0.16
ACGTcount: A:0.28, C:0.05, G:0.03, T:0.64
Consensus pattern (18 bp):
ATTTTTAAATTTTAATTC
Found at i:1055564 original size:14 final size:14
Alignment explanation
Indices: 1055545--1055582 Score: 67
Period size: 14 Copynumber: 2.7 Consensus size: 14
1055535 TTTAGGGACA
1055545 AACCATTTGTACCT
1 AACCATTTGTACCT
1055559 AACCATTTGTACCT
1 AACCATTTGTACCT
*
1055573 AACTATTTGT
1 AACCATTTGT
1055583 TCACTTAGAA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
14 23 1.00
ACGTcount: A:0.29, C:0.24, G:0.08, T:0.39
Consensus pattern (14 bp):
AACCATTTGTACCT
Found at i:1056691 original size:28 final size:28
Alignment explanation
Indices: 1056617--1056693 Score: 100
Period size: 28 Copynumber: 2.8 Consensus size: 28
1056607 TAGTACAGTA
* * * * *
1056617 TGGGCCTTAGACCAAAACAATAACAATG
1 TGGGCCTTAGCCCAATACAGTAATAGTG
1056645 TGGGCCTTAGCCCAATACAGTAATAGTG
1 TGGGCCTTAGCCCAATACAGTAATAGTG
*
1056673 TGGGCCTTAGCCCAGTACAGT
1 TGGGCCTTAGCCCAATACAGT
1056694 CCAATAATGC
Statistics
Matches: 43, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
28 43 1.00
ACGTcount: A:0.31, C:0.23, G:0.23, T:0.22
Consensus pattern (28 bp):
TGGGCCTTAGCCCAATACAGTAATAGTG
Found at i:1057005 original size:27 final size:27
Alignment explanation
Indices: 1056975--1057188 Score: 218
Period size: 27 Copynumber: 7.9 Consensus size: 27
1056965 TCATCTCCTA
** *
1056975 GGGGTATAACAGTCATTTTACCCTATG
1 GGGGTATTTCAGTCATTTTACCCTCTG
* * *
1057002 GGGGTATTTTAGTCATTTTACCTTTTG
1 GGGGTATTTCAGTCATTTTACCCTCTG
** * *
1057029 GGGGTATTTTGGTCATTTTACCCTTTT
1 GGGGTATTTCAGTCATTTTACCCTCTG
* * * *
1057056 AGGGTATTTCGGTCATTTTACCATCCG
1 GGGGTATTTCAGTCATTTTACCCTCTG
*
1057083 GGGGTATTTCAGTTATTTTACCCTAC-G
1 GGGGTATTTCAGTCATTTTACCCT-CTG
* *
1057110 GGGGTATTTCAGTCATTTGACCCTCTA
1 GGGGTATTTCAGTCATTTTACCCTCTG
*
1057137 GGGGTATTTC-GATCATTTTACCCTCTA
1 GGGGTATTTCAG-TCATTTTACCCTCTG
1057164 GGGGTATTTC-GATCATTTTACCCTC
1 GGGGTATTTCAG-TCATTTTACCCTC
1057189 CAGGGTATTT
Statistics
Matches: 162, Mismatches: 22, Indels: 6
0.85 0.12 0.03
Matches are distributed among these distances:
26 2 0.01
27 159 0.98
28 1 0.01
ACGTcount: A:0.18, C:0.19, G:0.21, T:0.42
Consensus pattern (27 bp):
GGGGTATTTCAGTCATTTTACCCTCTG
Found at i:1057914 original size:5 final size:5
Alignment explanation
Indices: 1057897--1057963 Score: 120
Period size: 5 Copynumber: 13.8 Consensus size: 5
1057887 GAATGAAGAG
1057897 GAGAA GA-AA -AGAA GAGAA GAGAA GAGAA GAGAA GAGAA GAGAA GAGAA
1 GAGAA GAGAA GAGAA GAGAA GAGAA GAGAA GAGAA GAGAA GAGAA GAGAA
1057945 GAGAA GAGAA GAGAA GAGA
1 GAGAA GAGAA GAGAA GAGA
1057964 GAGGGTTCAA
Statistics
Matches: 60, Mismatches: 0, Indels: 4
0.94 0.00 0.06
Matches are distributed among these distances:
3 1 0.02
4 4 0.07
5 55 0.92
ACGTcount: A:0.61, C:0.00, G:0.39, T:0.00
Consensus pattern (5 bp):
GAGAA
Found at i:1059710 original size:43 final size:42
Alignment explanation
Indices: 1059664--1059960 Score: 333
Period size: 43 Copynumber: 6.9 Consensus size: 42
1059654 AGCTAAAAGT
* * *
1059664 CATGACCTTTAGCGGTGCTTCTCCCACAAACGCCGCTATAGAT
1 CATGACCTTTAGCGGCGCTT-TCCCACAAACGCCGCTAAAGAA
* * * * *
1059707 CATGACTTTTAGCGACGCTTTTCCCACAAACGCTGCTATAGAT
1 CATGACCTTTAGCGGCGC-TTTCCCACAAACGCCGCTAAAGAA
* * *
1059750 CATGACTTTTAGCGGTGCTTTTCCCACAAACGCCGCTATAGAA
1 CATGACCTTTAGCGGCGC-TTTCCCACAAACGCCGCTAAAGAA
* * *
1059793 CATGAGCTTTAGCGGCACTTTACCACAAACGCCGCTAAAGAA
1 CATGACCTTTAGCGGCGCTTTCCCACAAACGCCGCTAAAGAA
* *
1059835 CATGACCTTTAGCGTCGCTTTACCAACAAACGCCGCTAAAGAA
1 CATGACCTTTAGCGGCGCTTT-CCCACAAACGCCGCTAAAGAA
* * *
1059878 CATGATCTTTAGCGGCACTTTACCCACAAATGCCGCTAAAGAA
1 CATGACCTTTAGCGGCGCTTT-CCCACAAACGCCGCTAAAGAA
* * **
1059921 CATGATCTTTAGCGGCACTTTTATCACAAACGCCGCTAAA
1 CATGACCTTTAGCGGCGC-TTTCCCACAAACGCCGCTAAA
1059961 AGTATGGTTC
Statistics
Matches: 224, Mismatches: 27, Indels: 6
0.87 0.11 0.02
Matches are distributed among these distances:
42 40 0.18
43 179 0.80
44 5 0.02
ACGTcount: A:0.29, C:0.29, G:0.17, T:0.25
Consensus pattern (42 bp):
CATGACCTTTAGCGGCGCTTTCCCACAAACGCCGCTAAAGAA
Found at i:1059839 original size:128 final size:128
Alignment explanation
Indices: 1059664--1059960 Score: 380
Period size: 128 Copynumber: 2.3 Consensus size: 128
1059654 AGCTAAAAGT
** * * * * *
1059664 CATGACCTTTAGCGGTGCTTCTCCCACAAACGCCGCTATAGATCATGACTTTTAGCGACGCTTTT
1 CATGACCTTTAGCGGCACTT-TACCACAAACGCCGCTAAAGAACATGACCTTTAGCGACGCTTTA
* * * * ** * *
1059729 CCCACAAACGCTGCTATAGATCATGA-CTTTTAGCGGTGCTTTTCCCACAAACGCCGCTATAGAA
65 CCAACAAACGCCGCTAAAGAACATGATC-TTTAGCGGCACTTTACCCACAAACGCCGCTAAAGAA
* *
1059793 CATGAGCTTTAGCGGCACTTTACCACAAACGCCGCTAAAGAACATGACCTTTAGCGTCGCTTTAC
1 CATGACCTTTAGCGGCACTTTACCACAAACGCCGCTAAAGAACATGACCTTTAGCGACGCTTTAC
*
1059858 CAACAAACGCCGCTAAAGAACATGATCTTTAGCGGCACTTTACCCACAAATGCCGCTAAAGAA
66 CAACAAACGCCGCTAAAGAACATGATCTTTAGCGGCACTTTACCCACAAACGCCGCTAAAGAA
* *
1059921 CATGATCTTTAGCGGCACTTTTATCACAAACGCCGCTAAA
1 CATGACCTTTAGCGGCAC-TTTACCACAAACGCCGCTAAA
1059961 AGTATGGTTC
Statistics
Matches: 146, Mismatches: 20, Indels: 4
0.86 0.12 0.02
Matches are distributed among these distances:
128 108 0.74
129 38 0.26
ACGTcount: A:0.29, C:0.29, G:0.17, T:0.25
Consensus pattern (128 bp):
CATGACCTTTAGCGGCACTTTACCACAAACGCCGCTAAAGAACATGACCTTTAGCGACGCTTTAC
CAACAAACGCCGCTAAAGAACATGATCTTTAGCGGCACTTTACCCACAAACGCCGCTAAAGAA
Found at i:1062111 original size:86 final size:84
Alignment explanation
Indices: 1061936--1062201 Score: 291
Period size: 86 Copynumber: 3.1 Consensus size: 84
1061926 TTAACACAAA
* * * * * * *
1061936 TCAATCTTACAACAGTTTATGTGAAACAAATTAGCAAAAATCAACT-ATTCATAGTTCATATATT
1 TCAATTTTATAACAATTTATATGCAACAAATTAGCAAAAATCAA-TGGTTCA-AGTTCATGTATT
** * *
1062000 TACTGACAATAGGGCTAAATCT
64 TACCAACAATA-GACTAAATTT
* *
1062022 TCAATTTCTATAACGATTTATATGCAACAAATTAACAAAAATCAATGGTTCAAGTTCATGTATTT
1 TCAATTT-TATAACAATTTATATGCAACAAATTAGCAAAAATCAATGGTTCAAGTTCATGTATTT
* *
1062087 ACCAAAAATTAGACTAATTTT
65 ACCAACAA-TAGACTAAATTT
* * *
1062108 TCAATATTTATAACAACTTATATGCAACAAATTAGCAAAAATAAATGGTTCAAGTTCATGCATTT
1 TCAAT-TTTATAACAATTTATATGCAACAAATTAGCAAAAATCAATGGTTCAAGTTCATGTATTT
*
1062173 ACCAACAACCAGACTAAATTT
65 ACCAACAA-TAGACTAAATTT
1062194 TCAATTTT
1 TCAATTTT
1062202 CAATTTTTAA
Statistics
Matches: 152, Mismatches: 24, Indels: 9
0.82 0.13 0.05
Matches are distributed among these distances:
85 3 0.02
86 110 0.72
87 39 0.26
ACGTcount: A:0.42, C:0.16, G:0.09, T:0.34
Consensus pattern (84 bp):
TCAATTTTATAACAATTTATATGCAACAAATTAGCAAAAATCAATGGTTCAAGTTCATGTATTTA
CCAACAATAGACTAAATTT
Found at i:1062308 original size:30 final size:30
Alignment explanation
Indices: 1062272--1062342 Score: 124
Period size: 30 Copynumber: 2.4 Consensus size: 30
1062262 ATTTAAGGAG
1062272 ATATAAAAAATCATCATTTCAACAATTTAC
1 ATATAAAAAATCATCATTTCAACAATTTAC
1062302 ATATAAAAAATCATCATTTCAACAATTTAC
1 ATATAAAAAATCATCATTTCAACAATTTAC
**
1062332 ATGCAAAAAAT
1 ATATAAAAAAT
1062343 TAGCAAAAAT
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
30 39 1.00
ACGTcount: A:0.52, C:0.15, G:0.01, T:0.31
Consensus pattern (30 bp):
ATATAAAAAATCATCATTTCAACAATTTAC
Found at i:1062707 original size:168 final size:168
Alignment explanation
Indices: 1062429--1062750 Score: 459
Period size: 168 Copynumber: 1.9 Consensus size: 168
1062419 TTTTAAATGC
* ** * * *
1062429 AACAAATTAGCACAAATTAACAATTCAAGTTCATATATTCACCAAAAACCAGACTAAATTTTCAA
1 AACAAATTAGCAAAAACCAACAATTCAAGTGCATATATGCACCAAAAACCAGACTAAATTTCCAA
* ** * *
1062494 TTTTTATAAAATAAGAGGATGGAAGTCTAACAAATTAAAGTTTCCAATGAAATTCAGACTTACAC
66 TTTTTACAAAATAAGAGGATCAAAGTCTAACAAATTAAAGTTTCCAATGAAATTCAAAATTACAC
1062559 CATTAAGTAAATAAGAGTTTTAAACTATTGAAGATCAA
131 CATTAAGTAAATAAGAGTTTTAAACTATTGAAGATCAA
** *
1062597 AACAAATTAGCAAAAACCAACTGTTCAAGTGCATGTATGCACCAAAAA-CAGGA-TCAAATTTCC
1 AACAAATTAGCAAAAACCAACAATTCAAGTGCATATATGCACCAAAAACCA-GACT-AAATTTCC
* * *
1062660 AATTTTTGCAAATTAAGAGGATCAAATTCTAACAAATTAAAGTTTCCAATGAAATTCAAAATTAC
64 AATTTTTACAAAATAAGAGGATCAAAGTCTAACAAATTAAAGTTTCCAATGAAATTCAAAATTAC
1062725 ACCATTAAGTAAATAAGAGTTTTAAA
129 ACCATTAAGTAAATAAGAGTTTTAAA
1062751 TTACCTGAGA
Statistics
Matches: 135, Mismatches: 17, Indels: 4
0.87 0.11 0.03
Matches are distributed among these distances:
167 3 0.02
168 132 0.98
ACGTcount: A:0.46, C:0.15, G:0.11, T:0.28
Consensus pattern (168 bp):
AACAAATTAGCAAAAACCAACAATTCAAGTGCATATATGCACCAAAAACCAGACTAAATTTCCAA
TTTTTACAAAATAAGAGGATCAAAGTCTAACAAATTAAAGTTTCCAATGAAATTCAAAATTACAC
CATTAAGTAAATAAGAGTTTTAAACTATTGAAGATCAA
Found at i:1068962 original size:8 final size:7
Alignment explanation
Indices: 1068944--1069080 Score: 66
Period size: 7 Copynumber: 19.0 Consensus size: 7
1068934 ACTAATTAAT
1068944 CTAAACC
1 CTAAACC
1068951 CTAAACCC
1 CTAAA-CC
1068959 CT-AACC
1 CTAAACC
* *
1068965 CTTATCC
1 CTAAACC
1068972 CTAAACC
1 CTAAACC
*
1068979 CTAAATC
1 CTAAACC
*
1068986 ATAAACCC
1 CTAAA-CC
1068994 CT-AACC
1 CTAAACC
*
1069000 CTTAGGTACAC
1 C-TA--AAC-C
1069011 CT-AACC
1 CTAAACC
1069017 CTAAACC
1 CTAAACC
*
1069024 TTAAACC
1 CTAAACC
*
1069031 C-CAACC
1 CTAAACC
1069037 CTTAAACC
1 C-TAAACC
*
1069045 ATAAACC
1 CTAAACC
* *
1069052 ATAATCC
1 CTAAACC
1069059 CTAAACC
1 CTAAACC
*
1069066 CATAATCC
1 C-TAAACC
*
1069074 ATAAACC
1 CTAAACC
1069081 TTAAGATAGT
Statistics
Matches: 98, Mismatches: 20, Indels: 24
0.69 0.14 0.17
Matches are distributed among these distances:
6 15 0.15
7 63 0.64
8 15 0.15
10 3 0.03
11 2 0.02
ACGTcount: A:0.39, C:0.39, G:0.01, T:0.20
Consensus pattern (7 bp):
CTAAACC
Found at i:1069068 original size:15 final size:15
Alignment explanation
Indices: 1069033--1069080 Score: 62
Period size: 15 Copynumber: 3.3 Consensus size: 15
1069023 CTTAAACCCC
* *
1069033 AACCCTTAAACCATA
1 AACCCATAATCCATA
*
1069048 AA-CCATAATCCCTA
1 AACCCATAATCCATA
1069062 AACCCATAATCCATA
1 AACCCATAATCCATA
1069077 AACC
1 AACC
1069081 TTAAGATAGT
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
14 11 0.39
15 17 0.61
ACGTcount: A:0.46, C:0.35, G:0.00, T:0.19
Consensus pattern (15 bp):
AACCCATAATCCATA
Found at i:1069318 original size:21 final size:20
Alignment explanation
Indices: 1069271--1069320 Score: 55
Period size: 21 Copynumber: 2.4 Consensus size: 20
1069261 ACTCCTAACT
* *
1069271 CCTAAACCTTAAACCCCAAC
1 CCTAAACCATAAACCACAAC
*
1069291 CCTTAAACCATAAACCATAATC
1 CC-TAAACCATAAACCACAA-C
1069313 CCTAAACC
1 CCTAAACC
1069321 CATGATCCAT
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
20 2 0.08
21 20 0.80
22 3 0.12
ACGTcount: A:0.42, C:0.40, G:0.00, T:0.18
Consensus pattern (20 bp):
CCTAAACCATAAACCACAAC
Found at i:1069323 original size:15 final size:15
Alignment explanation
Indices: 1069288--1069335 Score: 53
Period size: 15 Copynumber: 3.3 Consensus size: 15
1069278 CTTAAACCCC
* *
1069288 AACCCTTAAACCATA
1 AACCCATAATCCATA
*
1069303 AA-CCATAATCCCTA
1 AACCCATAATCCATA
*
1069317 AACCCATGATCCATA
1 AACCCATAATCCATA
1069332 AACC
1 AACC
1069336 TTAAGATAGT
Statistics
Matches: 27, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
14 11 0.41
15 16 0.59
ACGTcount: A:0.44, C:0.35, G:0.02, T:0.19
Consensus pattern (15 bp):
AACCCATAATCCATA
Found at i:1069410 original size:255 final size:260
Alignment explanation
Indices: 1068871--1069459 Score: 877
Period size: 255 Copynumber: 2.2 Consensus size: 260
1068861 GTTAATATAA
* * *
1068871 TAAAATTAATATTATCTCTTTTACAATTATATAAGAAATTATTTAACATATAAATTAAAAAACAC
1 TAAAATTAATACTATCTCTTTTACGATTATATAAGAAATTATTTAATATATAAATTAAAAAACAC
* * *
1068936 TAATTAATCTAAACCCTAAACCCCTAACCCTTATCCCTAAACCCTAAATCATAAACCCCTAACCC
66 TAATTAATCTAAACCCTAAACCCCTAACCCCTATCCCTAAACCATAAATCAGAAA--CCT-A-CC
1069001 TTAGGTACACCTAACCCTAAACCTTAAACCCCAACCCTTAAACCATAAACCATAATCCCTAAACC
127 ----GTACACCT-A-CCTAAACCTTAAACCCCAACCCTTAAACCATAAACCATAATCCCTAAACC
1069066 CATAATCCATAAACCTTAAGATAGTAACTCCTAAACCTTAAACCCTAAACTATAATGATAATTAA
186 CATAATCCATAAACCTTAAGATAGTAACTCCTAAACCTTAAACCCTAAACTATAATGATAATTAA
* **
1069131 TTTAATGTTT
251 TTCAACATTT
*
1069141 TAAAATTAATACTATCTCTTTTACGATTATATAAGAAATTATTTAATATATAAATTAAATAACAC
1 TAAAATTAATACTATCTCTTTTACGATTATATAAGAAATTATTTAATATATAAATTAAAAAACAC
* *
1069206 TAATTAATCT-AACCCTTAAACCCTTATCCCCTATCCCCTAAACCATAAATCAGAAA-CT-CC-T
66 TAATTAATCTAAACCC-TAAACCCCTAACCCCTAT-CCCTAAACCATAAATCAGAAACCTACCGT
*
1069267 A-A-CT-CCTAAACCTTAAACCCCAACCCTTAAACCATAAACCATAATCCCTAAACCCATGATCC
129 ACACCTACCTAAACCTTAAACCCCAACCCTTAAACCATAAACCATAATCCCTAAACCCATAATCC
*
1069329 ATAAACCTTAAGATAGTAACTCCTAAACCTTAAACCTTAAACTATAATGATAATTAATTCAACAT
194 ATAAACCTTAAGATAGTAACTCCTAAACCTTAAACCCTAAACTATAATGATAATTAATTCAACAT
1069394 TT
259 TT
* *
1069396 TAAAATTAATACTATCTCTTTTACGATTATATAAGAAATTATTTAATACATAAACTAAAAAACA
1 TAAAATTAATACTATCTCTTTTACGATTATATAAGAAATTATTTAATATATAAATTAAAAAACA
1069460 ATCAATAATG
Statistics
Matches: 300, Mismatches: 17, Indels: 19
0.89 0.05 0.06
Matches are distributed among these distances:
255 181 0.60
258 2 0.01
259 1 0.00
260 2 0.01
265 2 0.01
268 2 0.01
269 5 0.02
270 86 0.29
271 19 0.06
ACGTcount: A:0.43, C:0.24, G:0.03, T:0.30
Consensus pattern (260 bp):
TAAAATTAATACTATCTCTTTTACGATTATATAAGAAATTATTTAATATATAAATTAAAAAACAC
TAATTAATCTAAACCCTAAACCCCTAACCCCTATCCCTAAACCATAAATCAGAAACCTACCGTAC
ACCTACCTAAACCTTAAACCCCAACCCTTAAACCATAAACCATAATCCCTAAACCCATAATCCAT
AAACCTTAAGATAGTAACTCCTAAACCTTAAACCCTAAACTATAATGATAATTAATTCAACATTT
Found at i:1069745 original size:41 final size:41
Alignment explanation
Indices: 1069683--1069958 Score: 250
Period size: 41 Copynumber: 6.7 Consensus size: 41
1069673 TTTTCGCAGA
* ** * * *
1069683 GCTTTTTCAAAAATGCCGCTAAAGCCCCGAGAATTAGCGGC
1 GCTTCTTCAAAAACACCGCTAAAGCACCGAGCATTAGCGAC
* *
1069724 GTTTCTTCAAAAACATCGCTAAAGCACCGAGCATTAGCGAC
1 GCTTCTTCAAAAACACCGCTAAAGCACCGAGCATTAGCGAC
* * *
1069765 GTTTCTTCAAAAACGCCGCTAAAGCACCGAGCATTCGCGAC
1 GCTTCTTCAAAAACACCGCTAAAGCACCGAGCATTAGCGAC
* * **
1069806 GCTTCTTCGAAAACGCCGCTAAAGCACCGAGCATTAGCGGT
1 GCTTCTTCAAAAACACCGCTAAAGCACCGAGCATTAGCGAC
* * * *
1069847 GCTTCTTCGAAAACATCGCTAAAGCATCGAGCATTAG-TAGC
1 GCTTCTTCAAAAACACCGCTAAAGCACCGAGCATTAGCGA-C
** * * **
1069888 GCTT-TTCCAAAAATGCCCCTAAAGTACCGAGCATTAGCGGT
1 GCTTCTT-CAAAAACACCGCTAAAGCACCGAGCATTAGCGAC
* * ** *
1069929 ACTTTTTCAAAAATGCCGCTAAAGCCCCGA
1 GCTTCTTCAAAAACACCGCTAAAGCACCGA
1069959 AAGGTAAGAA
Statistics
Matches: 195, Mismatches: 36, Indels: 8
0.82 0.15 0.03
Matches are distributed among these distances:
40 2 0.01
41 191 0.98
42 2 0.01
ACGTcount: A:0.30, C:0.28, G:0.20, T:0.22
Consensus pattern (41 bp):
GCTTCTTCAAAAACACCGCTAAAGCACCGAGCATTAGCGAC
Found at i:1069826 original size:82 final size:82
Alignment explanation
Indices: 1069688--1069958 Score: 280
Period size: 82 Copynumber: 3.3 Consensus size: 82
1069678 GCAGAGCTTT
* * * * * **
1069688 TTCAAAAATGCCGCTAAAGCCCCGAGAATTAGCGGCGTTTCTTCAAAAACATCGCTAAAGCACCG
1 TTCAAAAACGCCGCTAAAGCACCGAGCATTAGCGACGCTTCTTCAAAAACGCCGCTAAAGCACCG
1069753 AGCATTAGCGACGTTTC
66 AGCATTAGCGACGTTTC
* *
1069770 TTCAAAAACGCCGCTAAAGCACCGAGCATTCGCGACGCTTCTTCGAAAACGCCGCTAAAGCACCG
1 TTCAAAAACGCCGCTAAAGCACCGAGCATTAGCGACGCTTCTTCAAAAACGCCGCTAAAGCACCG
** *
1069835 AGCATTAGCGGTGCTTC
66 AGCATTAGCGACGTTTC
* ** * * * * *
1069852 TTCGAAAACATCGCTAAAGCATCGAGCATTAG-TAGCGCTT-TTCCAAAAATGCCCCTAAAGTAC
1 TTCAAAAACGCCGCTAAAGCACCGAGCATTAGCGA-CGCTTCTT-CAAAAACGCCGCTAAAGCAC
1069915 CGAGCATTAGCGGTAC-TTT-
64 CGAGCATTAGC-G-ACGTTTC
* *
1069934 TTCAAAAATGCCGCTAAAGCCCCGA
1 TTCAAAAACGCCGCTAAAGCACCGA
1069959 AAGGTAAGAA
Statistics
Matches: 154, Mismatches: 31, Indels: 8
0.80 0.16 0.04
Matches are distributed among these distances:
81 3 0.02
82 148 0.96
83 3 0.02
ACGTcount: A:0.31, C:0.28, G:0.20, T:0.21
Consensus pattern (82 bp):
TTCAAAAACGCCGCTAAAGCACCGAGCATTAGCGACGCTTCTTCAAAAACGCCGCTAAAGCACCG
AGCATTAGCGACGTTTC
Found at i:1069899 original size:123 final size:122
Alignment explanation
Indices: 1069675--1069958 Score: 358
Period size: 123 Copynumber: 2.3 Consensus size: 122
1069665 TAAAATGTTT
*
1069675 TTCGCAGAGCTTTTTCAAAAATGCCGCTAAAGCCCCGAGAATTAGCGGCGTTTCTTCAAAAACAT
1 TTCGC-GAGCTTTTTCAAAAATGCCGCTAAAGCCCCGAGAATTAGCGGCGCTTCTTCAAAAACAT
* * *
1069740 CGCTAAAGCACCGAGCATTAGCGACGTTTCTTCAAAAACGCCGCTAAAGCACCGAGCA
65 CGCTAAAGCACCGAGCATTAGAGACGTTTCTCCAAAAACGCCCCTAAAGCACCGAGCA
* * * * * * *
1069798 TTCGCGACGCTTCTTCGAAAACGCCGCTAAAGCACCGAGCATTAGCGGTGCTTCTTCGAAAACAT
1 TTCGCGA-GCTTTTTCAAAAATGCCGCTAAAGCCCCGAGAATTAGCGGCGCTTCTTCAAAAACAT
* * *
1069863 CGCTAAAGCATCGAGCATTAGTAG-CGCTTT-TCCAAAAATGCCCCTAAAGTACCGAGCA
65 CGCTAAAGCACCGAGCATTAG-AGACG-TTTCTCCAAAAACGCCCCTAAAGCACCGAGCA
*
1069921 TTAGCG-GTACTTTTTCAAAAATGCCGCTAAAGCCCCGA
1 TTCGCGAG--CTTTTTCAAAAATGCCGCTAAAGCCCCGA
1069959 AAGGTAAGAA
Statistics
Matches: 137, Mismatches: 19, Indels: 10
0.83 0.11 0.06
Matches are distributed among these distances:
121 1 0.01
122 2 0.01
123 130 0.95
124 4 0.03
ACGTcount: A:0.30, C:0.28, G:0.20, T:0.22
Consensus pattern (122 bp):
TTCGCGAGCTTTTTCAAAAATGCCGCTAAAGCCCCGAGAATTAGCGGCGCTTCTTCAAAAACATC
GCTAAAGCACCGAGCATTAGAGACGTTTCTCCAAAAACGCCCCTAAAGCACCGAGCA
Found at i:1070051 original size:40 final size:40
Alignment explanation
Indices: 1070007--1070119 Score: 117
Period size: 40 Copynumber: 2.8 Consensus size: 40
1069997 GACGATTTTT
* *
1070007 GAAAAAATGCCGCTAATGC-TCATTTTCAGCGGCGTGTTCC
1 GAAAAAGTGCCGCTAATGCTTGATTTT-AGCGGCGTGTTCC
*
1070047 G-AAAAGTGCCG-TAAATGCTTGATCTTTAGCGGCGTTTTCC
1 GAAAAAGTGCCGCT-AATGCTTGAT-TTTAGCGGCGTGTTCC
* *
1070087 -ATAAAGCGCCGCTAATGCTTGATTTTTAGCGGC
1 GAAAAAGTGCCGCTAATGCTTGA-TTTTAGCGGC
1070120 ATTTTTTGTC
Statistics
Matches: 62, Mismatches: 5, Indels: 12
0.78 0.06 0.15
Matches are distributed among these distances:
38 1 0.02
39 14 0.23
40 42 0.68
41 5 0.08
ACGTcount: A:0.24, C:0.22, G:0.24, T:0.30
Consensus pattern (40 bp):
GAAAAAGTGCCGCTAATGCTTGATTTTAGCGGCGTGTTCC
Found at i:1071762 original size:22 final size:20
Alignment explanation
Indices: 1071736--1071776 Score: 55
Period size: 20 Copynumber: 1.9 Consensus size: 20
1071726 GCTATTTCAG
1071736 TTAAATTCATGTCGAAAAATAA
1 TTAAATT-ATGT-GAAAAATAA
*
1071758 TTAAATTATGTTAAAAATA
1 TTAAATTATGTGAAAAATA
1071777 TGAACATGAT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 7 0.39
21 4 0.22
22 7 0.39
ACGTcount: A:0.51, C:0.05, G:0.07, T:0.37
Consensus pattern (20 bp):
TTAAATTATGTGAAAAATAA
Found at i:1080359 original size:27 final size:27
Alignment explanation
Indices: 1080321--1080378 Score: 116
Period size: 27 Copynumber: 2.1 Consensus size: 27
1080311 ATGTCTGTAA
1080321 TACGGTCTTAGATGGTTTCCAATCCAG
1 TACGGTCTTAGATGGTTTCCAATCCAG
1080348 TACGGTCTTAGATGGTTTCCAATCCAG
1 TACGGTCTTAGATGGTTTCCAATCCAG
1080375 TACG
1 TACG
1080379 ACTTCAATTT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 31 1.00
ACGTcount: A:0.22, C:0.22, G:0.22, T:0.33
Consensus pattern (27 bp):
TACGGTCTTAGATGGTTTCCAATCCAG
Found at i:1083841 original size:28 final size:28
Alignment explanation
Indices: 1083797--1083873 Score: 120
Period size: 28 Copynumber: 2.8 Consensus size: 28
1083787 CCTATACAGT
1083797 AACAGT-ACAGTGTGGGCCTTAGCCCAA
1 AACAGTAACAGTGTGGGCCTTAGCCCAA
*
1083824 AACAGTAACAATGTGGGCCTTAGCCCAA
1 AACAGTAACAGTGTGGGCCTTAGCCCAA
* *
1083852 TACAGTAATAGTGTGGGCCTTA
1 AACAGTAACAGTGTGGGCCTTA
1083874 CCCTAGTACA
Statistics
Matches: 45, Mismatches: 4, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
27 6 0.13
28 39 0.87
ACGTcount: A:0.31, C:0.22, G:0.25, T:0.22
Consensus pattern (28 bp):
AACAGTAACAGTGTGGGCCTTAGCCCAA
Found at i:1083883 original size:28 final size:28
Alignment explanation
Indices: 1083798--1083886 Score: 119
Period size: 28 Copynumber: 3.2 Consensus size: 28
1083788 CTATACAGTA
*
1083798 ACAGT-ACAGTGTGGGCCTTAGCCCAAA
1 ACAGTAACAGTGTGGGCCTTAGCCCAAT
*
1083825 ACAGTAACAATGTGGGCCTTAGCCCAAT
1 ACAGTAACAGTGTGGGCCTTAGCCCAAT
* *
1083853 ACAGTAATAGTGTGGGCCTTA-CCCTAGT
1 ACAGTAACAGTGTGGGCCTTAGCCC-AAT
1083881 ACAGTA
1 ACAGTA
1083887 TAATATTGCA
Statistics
Matches: 55, Mismatches: 5, Indels: 3
0.87 0.08 0.05
Matches are distributed among these distances:
27 8 0.15
28 47 0.85
ACGTcount: A:0.30, C:0.24, G:0.24, T:0.22
Consensus pattern (28 bp):
ACAGTAACAGTGTGGGCCTTAGCCCAAT
Found at i:1084249 original size:27 final size:26
Alignment explanation
Indices: 1084230--1084451 Score: 150
Period size: 27 Copynumber: 8.2 Consensus size: 26
1084220 GGTATACCAA
1084230 TCATTTTACCTGATGAGGGTATTTCAG
1 TCATTTTACCT-ATGAGGGTATTTCAG
*
1084257 TCATTTTACCCTTTGAGGGTATTTCAG
1 TCATTTTA-CCTATGAGGGTATTTCAG
*
1084284 TCATTTTACC-ATTCGGGGGTATTTC-G
1 TCATTTTACCTA-T-GAGGGTATTTCAG
* * **
1084310 ATCATTTTACCCATCAGGGGTATTTTGG
1 -TCATTTTACCTATGA-GGGTATTTCAG
* *
1084338 TCATTTTACCCTCTAAGGGTATTTC-G
1 TCATTTTA-CCTATGAGGGTATTTCAG
*
1084364 ATCATTTTACCT-TACAGAGGTATTTCAG
1 -TCATTTTACCTAT-GAG-GGTATTTCAG
* *
1084392 TCATTTTACCT-TGCGGGGATATTT-TG
1 TCATTTTACCTATG-AGGG-TATTTCAG
** *
1084418 ATCATTTTACTCTCCGGGGGTATTTCAG
1 -TCATTTTAC-CTATGAGGGTATTTCAG
1084446 TCATTT
1 TCATTT
1084452 GCCCACGAAT
Statistics
Matches: 161, Mismatches: 16, Indels: 36
0.76 0.08 0.17
Matches are distributed among these distances:
25 1 0.01
26 13 0.08
27 129 0.80
28 17 0.11
29 1 0.01
ACGTcount: A:0.20, C:0.18, G:0.19, T:0.42
Consensus pattern (26 bp):
TCATTTTACCTATGAGGGTATTTCAG
Found at i:1084304 original size:54 final size:53
Alignment explanation
Indices: 1084246--1084451 Score: 204
Period size: 54 Copynumber: 3.8 Consensus size: 53
1084236 TACCTGATGA
*
1084246 GGGTATTTC-AGTCATTTTACCCTTTGAGGGTATTTCAGTCATTTTACCATTCGG
1 GGGTATTTCGA-TCATTTTACCCTTTCAGGGTATTTCAGTCATTTTACC-TTCGG
* ** * **
1084300 GGGTATTTCGATCATTTTACCC-ATCAGGGGTATTTTGGTCATTTTACCCTCTAA
1 GGGTATTTCGATCATTTTACCCTTTCA-GGGTATTTCAGTCATTTTACCTTC-GG
*
1084354 GGGTATTTCGATCATTTTA-CCTTACAGAGGTATTTCAGTCATTTTACCTTGCGG
1 GGGTATTTCGATCATTTTACCCTTTCAG-GGTATTTCAGTCATTTTACCTT-CGG
* * * * *
1084408 GGATATTTTGATCATTTTACTC-TCCGGGGGTATTTCAGTCATTT
1 GGGTATTTCGATCATTTTACCCTTTC-AGGGTATTTCAGTCATTT
1084452 GCCCACGAAT
Statistics
Matches: 125, Mismatches: 19, Indels: 16
0.78 0.12 0.10
Matches are distributed among these distances:
53 7 0.06
54 114 0.91
55 4 0.03
ACGTcount: A:0.19, C:0.18, G:0.20, T:0.42
Consensus pattern (53 bp):
GGGTATTTCGATCATTTTACCCTTTCAGGGTATTTCAGTCATTTTACCTTCGG
Found at i:1084341 original size:81 final size:80
Alignment explanation
Indices: 1084229--1084451 Score: 231
Period size: 81 Copynumber: 2.8 Consensus size: 80
1084219 GGGTATACCA
* * ** *
1084229 ATCATTTTACCTGATGA-GGGTATTTCAGTCATTTTACCCTTTGAGGGTATTTCAGTCATTTTAC
1 ATCATTTTACC-CATCAGGGGTATTTTGGTCATTTTACCCTCTGAGGGTATTTCAGTCATTTTAC
* *
1084293 CATT-CGGGGGTATTTC
65 C-TTACAGAGGTATTTC
*
1084309 GATCATTTTACCCATCAGGGGTATTTTGGTCATTTTACCCTCTAAGGGTATTTC-GATCATTTTA
1 -ATCATTTTACCCATCAGGGGTATTTTGGTCATTTTACCCTCTGAGGGTATTTCAG-TCATTTTA
1084373 CCTTACAGAGGTATTTC
64 CCTTACAGAGGTATTTC
* * * * *
1084390 AGTCATTTTA-CCTTGC-GGGGATATTTTGATCATTTTACTCTCCGGGGGTATTTCAGTCATTT
1 A-TCATTTTACCCAT-CAGGGG-TATTTTGGTCATTTTACCCTCTGAGGGTATTTCAGTCATTT
1084452 GCCCACGAAT
Statistics
Matches: 121, Mismatches: 14, Indels: 14
0.81 0.09 0.09
Matches are distributed among these distances:
80 14 0.12
81 106 0.88
82 1 0.01
ACGTcount: A:0.20, C:0.18, G:0.19, T:0.42
Consensus pattern (80 bp):
ATCATTTTACCCATCAGGGGTATTTTGGTCATTTTACCCTCTGAGGGTATTTCAGTCATTTTACC
TTACAGAGGTATTTC
Found at i:1086007 original size:24 final size:24
Alignment explanation
Indices: 1085948--1086008 Score: 68
Period size: 24 Copynumber: 2.5 Consensus size: 24
1085938 CATTCTATTA
* * *
1085948 GCCTTTATGGCATATTTTTATTTG
1 GCCTTTATGGCATATTCTGATTGG
* *
1085972 ACCTTTAGGGCATATTCTGATTGG
1 GCCTTTATGGCATATTCTGATTGG
*
1085996 GCCTTCATGGCAT
1 GCCTTTATGGCAT
1086009 TTTGTTAGCC
Statistics
Matches: 29, Mismatches: 8, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
24 29 1.00
ACGTcount: A:0.18, C:0.18, G:0.21, T:0.43
Consensus pattern (24 bp):
GCCTTTATGGCATATTCTGATTGG
Found at i:1086066 original size:19 final size:20
Alignment explanation
Indices: 1086003--1086066 Score: 62
Period size: 19 Copynumber: 3.3 Consensus size: 20
1085993 TGGGCCTTCA
*
1086003 TGGCATTTTGTTAGCCTTTG
1 TGGCATTATGTTAGCCTTTG
* * *
1086023 TGGAAATCT-TTAGCCGTTT-
1 TGGCATTATGTTAGCC-TTTG
1086042 TGGCATTATGTT-GCCTTTG
1 TGGCATTATGTTAGCCTTTG
1086061 TGGCAT
1 TGGCAT
1086067 ACTCTGTATA
Statistics
Matches: 35, Mismatches: 6, Indels: 7
0.73 0.12 0.15
Matches are distributed among these distances:
18 3 0.09
19 21 0.60
20 11 0.31
ACGTcount: A:0.14, C:0.16, G:0.25, T:0.45
Consensus pattern (20 bp):
TGGCATTATGTTAGCCTTTG
Found at i:1105092 original size:16 final size:15
Alignment explanation
Indices: 1105051--1105089 Score: 60
Period size: 16 Copynumber: 2.5 Consensus size: 15
1105041 TGATGACTTT
1105051 CTAGGGTTGTCAAGC
1 CTAGGGTTGTCAAGC
*
1105066 CTAAGGATTGTCAAGC
1 CT-AGGGTTGTCAAGC
1105082 CTAGGGTT
1 CTAGGGTT
1105090 TGTTTCACAT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
15 7 0.33
16 14 0.67
ACGTcount: A:0.23, C:0.18, G:0.31, T:0.28
Consensus pattern (15 bp):
CTAGGGTTGTCAAGC
Found at i:1109863 original size:25 final size:25
Alignment explanation
Indices: 1109835--1109884 Score: 82
Period size: 25 Copynumber: 2.0 Consensus size: 25
1109825 TAAAGGGGAC
1109835 TAAGGCATTTCACATGAATTTTTAA
1 TAAGGCATTTCACATGAATTTTTAA
**
1109860 TAAGGCATTTCGTATGAATTTTTAA
1 TAAGGCATTTCACATGAATTTTTAA
1109885 AGTATGTTTC
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
25 23 1.00
ACGTcount: A:0.34, C:0.10, G:0.14, T:0.42
Consensus pattern (25 bp):
TAAGGCATTTCACATGAATTTTTAA
Found at i:1111968 original size:19 final size:22
Alignment explanation
Indices: 1111942--1111991 Score: 70
Period size: 22 Copynumber: 2.4 Consensus size: 22
1111932 GAACTAGATT
1111942 AGGTTAAAA-GGG-TG-TTTTA
1 AGGTTAAAAGGGGATGTTTTTA
*
1111961 ATGTTAAAAGGGGATGTTTTTA
1 AGGTTAAAAGGGGATGTTTTTA
1111983 AGGTTAAAA
1 AGGTTAAAA
1111992 ATCGAGCATA
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
19 8 0.31
20 3 0.12
21 2 0.08
22 13 0.50
ACGTcount: A:0.36, C:0.00, G:0.28, T:0.36
Consensus pattern (22 bp):
AGGTTAAAAGGGGATGTTTTTA
Found at i:1118609 original size:18 final size:18
Alignment explanation
Indices: 1118586--1118620 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
1118576 CCACTTTCCA
1118586 CTTTTAAGTTT-TTTTTAT
1 CTTTTAA-TTTATTTTTAT
1118604 CTTTTAATTTATTTTTA
1 CTTTTAATTTATTTTTA
1118621 CAATTTTATT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 3 0.19
18 13 0.81
ACGTcount: A:0.20, C:0.06, G:0.03, T:0.71
Consensus pattern (18 bp):
CTTTTAATTTATTTTTAT
Found at i:1135989 original size:51 final size:52
Alignment explanation
Indices: 1135821--1135993 Score: 287
Period size: 52 Copynumber: 3.3 Consensus size: 52
1135811 ACTAATGACT
1135821 CAAGTGTGGTACTATGTGAAGGCCACTTTGTGAAGAAAGATAGCTTTGGTCA
1 CAAGTGTGGTACTATGTGAAGGCCACTTTGTGAAGAAAGATAGCTTTGGTCA
* *
1135873 CCAGTGTGGTACTATGTGAAGGCCACTTTGTGAAGAAATATAGCTTTGGTCA
1 CAAGTGTGGTACTATGTGAAGGCCACTTTGTGAAGAAAGATAGCTTTGGTCA
*
1135925 CAAGTGTGGTACTATGTGAAGGCCACTTTGTGAAG-AAGGTAGCTTTGG-CTA
1 CAAGTGTGGTACTATGTGAAGGCCACTTTGTGAAGAAAGATAGCTTTGGTC-A
*
1135976 CAAGGGTGGTACTATGTG
1 CAAGTGTGGTACTATGTG
1135994 CAAGCCATCG
Statistics
Matches: 114, Mismatches: 6, Indels: 3
0.93 0.05 0.02
Matches are distributed among these distances:
50 1 0.01
51 29 0.25
52 84 0.74
ACGTcount: A:0.27, C:0.14, G:0.30, T:0.29
Consensus pattern (52 bp):
CAAGTGTGGTACTATGTGAAGGCCACTTTGTGAAGAAAGATAGCTTTGGTCA
Found at i:1138092 original size:20 final size:20
Alignment explanation
Indices: 1138069--1138110 Score: 57
Period size: 20 Copynumber: 2.1 Consensus size: 20
1138059 ATTGATACCA
1138069 CTTAAAGAAAATATCGATAC
1 CTTAAAGAAAATATCGATAC
* **
1138089 CTTAATGTCAATATCGATAC
1 CTTAAAGAAAATATCGATAC
1138109 CT
1 CT
1138111 GCGGGCATTT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.40, C:0.19, G:0.10, T:0.31
Consensus pattern (20 bp):
CTTAAAGAAAATATCGATAC
Found at i:1158460 original size:20 final size:20
Alignment explanation
Indices: 1158435--1158667 Score: 80
Period size: 20 Copynumber: 11.7 Consensus size: 20
1158425 TCTTGAATAA
1158435 GTGCTCCTGATAGTACTACG
1 GTGCTCCTGATAGTACTACG
* *
1158455 GTGCTCCTGGA-AATACTTTC-
1 GTGCTCCT-GATAGTAC-TACG
* **
1158475 GTACTCCTGATAACACTACG
1 GTGCTCCTGATAGTACTACG
* * ***
1158495 GTGCTCCTGACAATACTTTT
1 GTGCTCCTGATAGTACTACG
* * *
1158515 GTACTCTTGATAGCACTACG
1 GTGCTCCTGATAGTACTACG
* * *
1158535 GTGCTCCTGACAGTAGTTTC-
1 GTGCTCCTGATAGTA-CTACG
* * * *
1158555 ATACTCCTGATAGCACTATG
1 GTGCTCCTGATAGTACTACG
* * * ***
1158575 GTGCTCCTAACAGTTCTTTT
1 GTGCTCCTGATAGTACTACG
* *
1158595 GTACTCCT-ATTAGCACTACG
1 GTGCTCCTGA-TAGTACTACG
* *
1158615 GTGCTCTTGATAGTACTTTC-
1 GTGCTCCTGATAGTAC-TACG
* * *
1158635 GTACTCCTGTTAGCACTACG
1 GTGCTCCTGATAGTACTACG
*
1158655 GTGCTCTTGATAG
1 GTGCTCCTGATAG
1158668 CATATTCAAG
Statistics
Matches: 144, Mismatches: 59, Indels: 20
0.65 0.26 0.09
Matches are distributed among these distances:
19 8 0.06
20 127 0.88
21 9 0.06
ACGTcount: A:0.21, C:0.25, G:0.19, T:0.34
Consensus pattern (20 bp):
GTGCTCCTGATAGTACTACG
Found at i:1158667 original size:40 final size:40
Alignment explanation
Indices: 1158438--1158660 Score: 279
Period size: 40 Copynumber: 5.6 Consensus size: 40
1158428 TGAATAAGTG
* *
1158438 CTCCTGATAGTACTACGGTGCTCCTGGA-AATACTTTCGTA
1 CTCCTGATAGCACTACGGTGCTCCT-GACAGTACTTTCGTA
* * *
1158478 CTCCTGATAACACTACGGTGCTCCTGACAATACTTTTGTA
1 CTCCTGATAGCACTACGGTGCTCCTGACAGTACTTTCGTA
* * *
1158518 CTCTTGATAGCACTACGGTGCTCCTGACAGTAGTTTCATA
1 CTCCTGATAGCACTACGGTGCTCCTGACAGTACTTTCGTA
* * * *
1158558 CTCCTGATAGCACTATGGTGCTCCTAACAGTTCTTTTGTA
1 CTCCTGATAGCACTACGGTGCTCCTGACAGTACTTTCGTA
* *
1158598 CTCCT-ATTAGCACTACGGTGCTCTTGATAGTACTTTCGTA
1 CTCCTGA-TAGCACTACGGTGCTCCTGACAGTACTTTCGTA
*
1158638 CTCCTGTTAGCACTACGGTGCTC
1 CTCCTGATAGCACTACGGTGCTC
1158661 TTGATAGCAT
Statistics
Matches: 157, Mismatches: 23, Indels: 6
0.84 0.12 0.03
Matches are distributed among these distances:
39 3 0.02
40 154 0.98
ACGTcount: A:0.21, C:0.26, G:0.18, T:0.34
Consensus pattern (40 bp):
CTCCTGATAGCACTACGGTGCTCCTGACAGTACTTTCGTA
Found at i:1158682 original size:40 final size:40
Alignment explanation
Indices: 1158438--1158696 Score: 157
Period size: 40 Copynumber: 6.5 Consensus size: 40
1158428 TGAATAAGTG
* * * ** *
1158438 CTCCTGATAGTACTACGGTGCTCCTGGA-AATACTTTCGTA
1 CTCCTGTTAGCACTACGGTGCT-CTTGATAGCACTTTCGAA
* * * * ** * *
1158478 CTCCTGATAACACTACGGTGCTCCTGACAATACTTTTGTA
1 CTCCTGTTAGCACTACGGTGCTCTTGATAGCACTTTCGAA
* * * * * *
1158518 CTCTTGATAGCACTACGGTGCTCCTGACAGTAGTTTC-ATA
1 CTCCTGTTAGCACTACGGTGCTCTTGATAGCACTTTCGA-A
* * * * * ** * *
1158558 CTCCTGATAGCACTATGGTGCTCCTAACAGTTCTTTTGTA
1 CTCCTGTTAGCACTACGGTGCTCTTGATAGCACTTTCGAA
* * *
1158598 CTCCTATTAGCACTACGGTGCTCTTGATAGTACTTTCGTA
1 CTCCTGTTAGCACTACGGTGCTCTTGATAGCACTTTCGAA
1158638 CTCCTGTTAGCACTACGGTGCTCTTGATAGCA-TATTC-AA
1 CTCCTGTTAGCACTACGGTGCTCTTGATAGCACT-TTCGAA
*
1158677 GCTCCTGTTTGCACTACGGT
1 -CTCCTGTTAGCACTACGGT
1158697 ACCCCTAATT
Statistics
Matches: 184, Mismatches: 30, Indels: 10
0.82 0.13 0.04
Matches are distributed among these distances:
39 5 0.03
40 179 0.97
ACGTcount: A:0.21, C:0.26, G:0.19, T:0.34
Consensus pattern (40 bp):
CTCCTGTTAGCACTACGGTGCTCTTGATAGCACTTTCGAA
Found at i:1158682 original size:80 final size:79
Alignment explanation
Indices: 1158449--1158696 Score: 214
Period size: 80 Copynumber: 3.1 Consensus size: 79
1158439 TCCTGATAGT
* * * * * *
1158449 ACTACGGTGCTCCTGGA-AATACTTTCGTACTCCTGATAACACTACGGTGCTCCTGACAATACTT
1 ACTACGGTGCTCCT-GACAGTACTTTCATACTCCTGATAGCACTACGGTGCTCCTAACAGT-CTA
** *
1158513 TTGTACTCTTGA-TAGC
64 TTCAACTCCT-ATTAGC
* * *
1158529 ACTACGGTGCTCCTGACAGTAGTTTCATACTCCTGATAGCACTATGGTGCTCCTAACAGTTCTTT
1 ACTACGGTGCTCCTGACAGTACTTTCATACTCCTGATAGCACTACGGTGCTCCTAACAG-TCTAT
**
1158594 TGTACTCCTATTAGC
65 TCAACTCCTATTAGC
* * * * * * *
1158609 ACTACGGTGCTCTTGATAGTACTTTCGTACTCCTGTTAGCACTACGGTGCTCTTGATAG-CATAT
1 ACTACGGTGCTCCTGACAGTACTTTCATACTCCTGATAGCACTACGGTGCTCCTAACAGTC-TAT
* *
1158673 TCAAGCTCCTGTTTGC
65 TCAA-CTCCTATTAGC
1158689 ACTACGGT
1 ACTACGGT
1158697 ACCCCTAATT
Statistics
Matches: 141, Mismatches: 22, Indels: 10
0.82 0.13 0.06
Matches are distributed among these distances:
78 1 0.01
79 7 0.05
80 132 0.94
81 1 0.01
ACGTcount: A:0.21, C:0.26, G:0.19, T:0.34
Consensus pattern (79 bp):
ACTACGGTGCTCCTGACAGTACTTTCATACTCCTGATAGCACTACGGTGCTCCTAACAGTCTATT
CAACTCCTATTAGC
Found at i:1158682 original size:120 final size:120
Alignment explanation
Indices: 1158437--1158696 Score: 296
Period size: 120 Copynumber: 2.2 Consensus size: 120
1158427 TTGAATAAGT
*
1158437 GCTCCTGATAGTACTACGGTGCTCCTGGAAATACTTTCGTACTCCTGATAACACTACGGTGCTCC
1 GCTCCTGATAGCACTACGGTGCTCCT-GAAATACTTTCGTACTCCTGATAACACTACGGTGCTCC
* * *
1158502 TGACAATACTTTTGTACTCTTGATAGCACTACGGTGCTCCTGACAGTAGTTTCATA
65 TGACAATACTTTCGTACTCCTGATAGCACTACGGTGCTCCTGACAGCAGTTTCATA
* * * *
1158558 -CTCCTGATAGCACTATGGTGCTCCT-AACAGTTCTTTTGTACTCCT-ATTAGCACTACGGTGCT
1 GCTCCTGATAGCACTACGGTGCTCCTGAA-A-TACTTTCGTACTCCTGA-TAACACTACGGTGCT
* * * * * *
1158620 CTTGATAGTACTTTCGTACTCCTGTTAGCACTACGGTGCTCTTGATAGCA-TATTCA-A
63 CCTGACAATACTTTCGTACTCCTGATAGCACTACGGTGCTCCTGACAGCAGT-TTCATA
* *
1158677 GCTCCTGTTTGCACTACGGT
1 GCTCCTGATAGCACTACGGT
1158697 ACCCCTAATT
Statistics
Matches: 117, Mismatches: 17, Indels: 11
0.81 0.12 0.08
Matches are distributed among these distances:
118 2 0.02
119 4 0.03
120 111 0.95
ACGTcount: A:0.21, C:0.26, G:0.19, T:0.34
Consensus pattern (120 bp):
GCTCCTGATAGCACTACGGTGCTCCTGAAATACTTTCGTACTCCTGATAACACTACGGTGCTCCT
GACAATACTTTCGTACTCCTGATAGCACTACGGTGCTCCTGACAGCAGTTTCATA
Found at i:1159566 original size:3 final size:3
Alignment explanation
Indices: 1159558--1159584 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
1159548 TTTGGTCTAT
1159558 TGA TGA TGA TGA TGA TGA TGA TGA TGA
1 TGA TGA TGA TGA TGA TGA TGA TGA TGA
1159585 ATTTGATGTT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.33, C:0.00, G:0.33, T:0.33
Consensus pattern (3 bp):
TGA
Found at i:1168754 original size:29 final size:29
Alignment explanation
Indices: 1168717--1168794 Score: 104
Period size: 29 Copynumber: 2.7 Consensus size: 29
1168707 TTTCAGAGTT
1168717 TCACCACAAAAGCTTCCTTTTAAAAGAGA
1 TCACCACAAAAGCTTCCTTTTAAAAGAGA
* *
1168746 TCACCACAAAGGCTTCCTTTTAATAGAGA
1 TCACCACAAAAGCTTCCTTTTAAAAGAGA
**
1168775 TCGTCAC-AAAGACTTCCTTT
1 TCACCACAAAAG-CTTCCTTT
1168795 CAAAGATAGC
Statistics
Matches: 43, Mismatches: 5, Indels: 2
0.86 0.10 0.04
Matches are distributed among these distances:
28 3 0.07
29 40 0.93
ACGTcount: A:0.35, C:0.26, G:0.12, T:0.28
Consensus pattern (29 bp):
TCACCACAAAAGCTTCCTTTTAAAAGAGA
Found at i:1178808 original size:41 final size:42
Alignment explanation
Indices: 1178762--1178942 Score: 105
Period size: 41 Copynumber: 4.4 Consensus size: 42
1178752 ATTTTTCTTC
1178762 AATAAATTTGAATT-TTGTTAAGTATGCTAAATTTAAGTATG
1 AATAAATTTGAATTATTGTTAAGTATGCTAAATTTAAGTATG
* ** *
1178803 AATAAAGTTTG-ATTATT-TTAATTAT--T-AATTCCACTCA-G
1 AATAAA-TTTGAATTATTGTTAAGTATGCTAAATTTAAGT-ATG
*** * * * ** *
1178841 AATAAAATTTTTCTTTTAATTGTGAA-TATGATATATTTTTGT-TC
1 AAT-AAA--TTTGAATT-ATTGTTAAGTATGCTAAATTTAAGTATG
1178885 AATAAATTTGAATT-TTGTTAAGTATGCTAAATTTAAGTATG
1 AATAAATTTGAATTATTGTTAAGTATGCTAAATTTAAGTATG
1178926 AATAAATTTTG-ATTATT
1 AATAAA-TTTGAATTATT
1178943 TCAATAAATT
Statistics
Matches: 101, Mismatches: 23, Indels: 31
0.65 0.15 0.20
Matches are distributed among these distances:
38 10 0.10
39 11 0.11
40 15 0.15
41 33 0.33
42 18 0.18
43 6 0.06
44 4 0.04
45 4 0.04
ACGTcount: A:0.37, C:0.04, G:0.11, T:0.48
Consensus pattern (42 bp):
AATAAATTTGAATTATTGTTAAGTATGCTAAATTTAAGTATG
Found at i:1178927 original size:123 final size:123
Alignment explanation
Indices: 1178703--1178943 Score: 446
Period size: 123 Copynumber: 2.0 Consensus size: 123
1178693 GAAAATTGAA
*
1178703 ATTATTTCCACTCAGAATAAAATTTTTCTTTTAATTATGAATATGATATATTTTTCTTCAATAAA
1 ATTAATTCCACTCAGAATAAAATTTTTCTTTTAATTATGAATATGATATATTTTTCTTCAATAAA
1178768 TTTGAATTTTGTTAAGTATGCTAAATTTAAGTATGAATAAAGTTTGATTATTTTAATT
66 TTTGAATTTTGTTAAGTATGCTAAATTTAAGTATGAATAAAGTTTGATTATTTTAATT
* *
1178826 ATTAATTCCACTCAGAATAAAATTTTTCTTTTAATTGTGAATATGATATATTTTTGTTCAATAAA
1 ATTAATTCCACTCAGAATAAAATTTTTCTTTTAATTATGAATATGATATATTTTTCTTCAATAAA
*
1178891 TTTGAATTTTGTTAAGTATGCTAAATTTAAGTATGAATAAATTTTGATTATTT
66 TTTGAATTTTGTTAAGTATGCTAAATTTAAGTATGAATAAAGTTTGATTATTT
1178944 CAATAAATTG
Statistics
Matches: 114, Mismatches: 4, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
123 114 1.00
ACGTcount: A:0.36, C:0.06, G:0.10, T:0.49
Consensus pattern (123 bp):
ATTAATTCCACTCAGAATAAAATTTTTCTTTTAATTATGAATATGATATATTTTTCTTCAATAAA
TTTGAATTTTGTTAAGTATGCTAAATTTAAGTATGAATAAAGTTTGATTATTTTAATT
Found at i:1180236 original size:14 final size:15
Alignment explanation
Indices: 1180211--1180239 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
1180201 AAAAAAAGGG
1180211 TCTAGTTGAACCGAA
1 TCTAGTTGAACCGAA
1180226 TCTAG-TGAACCGAA
1 TCTAGTTGAACCGAA
1180240 CCAGCCACCA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 9 0.64
15 5 0.36
ACGTcount: A:0.34, C:0.21, G:0.21, T:0.24
Consensus pattern (15 bp):
TCTAGTTGAACCGAA
Found at i:1185980 original size:14 final size:14
Alignment explanation
Indices: 1185961--1186013 Score: 81
Period size: 14 Copynumber: 3.8 Consensus size: 14
1185951 TCAGAAAAGT
1185961 AAATCATTTTCCAG
1 AAATCATTTTCCAG
1185975 AAATCATTTTCCA-
1 AAATCATTTTCCAG
1185988 AAAGTCATTTTCCAG
1 AAA-TCATTTTCCAG
*
1186003 AAGTCATTTTC
1 AAATCATTTTC
1186014 AGTGAAACAA
Statistics
Matches: 36, Mismatches: 1, Indels: 4
0.88 0.02 0.10
Matches are distributed among these distances:
13 3 0.08
14 31 0.86
15 2 0.06
ACGTcount: A:0.34, C:0.21, G:0.08, T:0.38
Consensus pattern (14 bp):
AAATCATTTTCCAG
Found at i:1186641 original size:65 final size:65
Alignment explanation
Indices: 1186537--1186663 Score: 227
Period size: 65 Copynumber: 2.0 Consensus size: 65
1186527 AAAACATTTT
* *
1186537 AGCCCGTCATTTAATTTTTTATCTTTTTTAGCTCTTAAACCTGCGTTTTTGTCAAATCATCCCAA
1 AGCCCGTCATTTAATTTTTCATCTTTTTTAGCTCTTAAACCTGCGTTTTTATCAAATCATCCCAA
*
1186602 AGCCCGTCATTTAATTTTTCATCTTTTTTAGCTCTTAAACTTGCGTTTTTATCAAATCATCC
1 AGCCCGTCATTTAATTTTTCATCTTTTTTAGCTCTTAAACCTGCGTTTTTATCAAATCATCC
1186664 AAAAATGGAT
Statistics
Matches: 59, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
65 59 1.00
ACGTcount: A:0.23, C:0.23, G:0.09, T:0.46
Consensus pattern (65 bp):
AGCCCGTCATTTAATTTTTCATCTTTTTTAGCTCTTAAACCTGCGTTTTTATCAAATCATCCCAA
Found at i:1189841 original size:34 final size:33
Alignment explanation
Indices: 1189767--1189839 Score: 94
Period size: 34 Copynumber: 2.1 Consensus size: 33
1189757 CAAAATTGCA
*
1189767 TAAATATT-TAAAATTTGAAAAACAAAAAATATT
1 TAAA-ATTGTAAAATTTGAAAAACAAAAAATACT
1189800 TAGAAATTGTAAAATTTGAAAAAACGAAAAAATACT
1 TA-AAATTGTAAAATTTG-AAAAAC-AAAAAATACT
1189836 TAAA
1 TAAA
1189840 TTTTTGTATA
Statistics
Matches: 35, Mismatches: 1, Indels: 6
0.83 0.02 0.14
Matches are distributed among these distances:
33 5 0.14
34 11 0.31
35 8 0.23
36 11 0.31
ACGTcount: A:0.60, C:0.04, G:0.07, T:0.29
Consensus pattern (33 bp):
TAAAATTGTAAAATTTGAAAAACAAAAAATACT
Done.