Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: A08
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: 123748673
ACGTcount: A:0.31, C:0.17, G:0.17, T:0.31
Warning! 5630000 characters in sequence are not A, C, G, or T
File 88 of 373
Found at i:28002269 original size:49 final size:50
Alignment explanation
Indices: 28002189--28002584 Score: 447
Period size: 49 Copynumber: 7.9 Consensus size: 50
28002179 AGCTATTGTG
*
28002189 AGGTCACGTGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGATAATT
1 AGGTCACATGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGATAATT
* * * **
28002239 -GGTCGCATGTGTAGTACTAAGTGCAGGCTACTATGCGTACCTCATAACTT
1 AGGTCACATGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGATAA-TT
* * * * * **
28002289 CGCTCACGTGTGTAGTACTAAGTGCAGGCTACTACGTGTATCAAATGGTT
1 AGGTCACATGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGATAATT
*
28002339 AGGTCACATGTGTAGTACTAAGTACAGGCTACTACGTGTACCAGATAATT
1 AGGTCACATGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGATAATT
* * * * ** *
28002389 -GGTCGCATGTTTAGTACTAAGTGCAGGTTACTATGCATACCTGATAACTT
1 AGGTCACATGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGATAA-TT
* * * * * * **
28002439 CGATCACGTGTGTAGTACTAAGTGTAGGCTACTACGTGTATCAAATGGTT
1 AGGTCACATGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGATAATT
* *
28002489 AGGTCACGTGTGTAGTACTAAGTGCAGGCTACTACGTGTACCGGATAATT
1 AGGTCACATGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGATAATT
* * *
28002539 -GGTCGCATGTGTAGTACTAAGTGCAGGCTACTATGCGTACCAGATA
1 AGGTCACATGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGATA
28002585 GCTTCGGCTA
Statistics
Matches: 283, Mismatches: 59, Indels: 9
0.81 0.17 0.03
Matches are distributed among these distances:
49 121 0.43
50 92 0.33
51 70 0.25
ACGTcount: A:0.27, C:0.19, G:0.25, T:0.30
Consensus pattern (50 bp):
AGGTCACATGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGATAATT
Found at i:28002460 original size:150 final size:150
Alignment explanation
Indices: 28002189--28002590 Score: 705
Period size: 150 Copynumber: 2.7 Consensus size: 150
28002179 AGCTATTGTG
28002189 AGGTCACGTGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGATAATTGGTCGCATGTGTAGT
1 AGGTCACGTGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGATAATTGGTCGCATGTGTAGT
* *
28002254 ACTAAGTGCAGGCTACTATGCGTACCTCATAACTTCGCTCACGTGTGTAGTACTAAGTGCAGGCT
66 ACTAAGTGCAGGCTACTATGCGTACCTGATAACTTCGATCACGTGTGTAGTACTAAGTGCAGGCT
28002319 ACTACGTGTATCAAATGGTT
131 ACTACGTGTATCAAATGGTT
* * *
28002339 AGGTCACATGTGTAGTACTAAGTACAGGCTACTACGTGTACCAGATAATTGGTCGCATGTTTAGT
1 AGGTCACGTGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGATAATTGGTCGCATGTGTAGT
* * *
28002404 ACTAAGTGCAGGTTACTATGCATACCTGATAACTTCGATCACGTGTGTAGTACTAAGTGTAGGCT
66 ACTAAGTGCAGGCTACTATGCGTACCTGATAACTTCGATCACGTGTGTAGTACTAAGTGCAGGCT
28002469 ACTACGTGTATCAAATGGTT
131 ACTACGTGTATCAAATGGTT
*
28002489 AGGTCACGTGTGTAGTACTAAGTGCAGGCTACTACGTGTACCGGATAATTGGTCGCATGTGTAGT
1 AGGTCACGTGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGATAATTGGTCGCATGTGTAGT
* *
28002554 ACTAAGTGCAGGCTACTATGCGTACCAGATAGCTTCG
66 ACTAAGTGCAGGCTACTATGCGTACCTGATAACTTCG
28002591 GCTACAAGTG
Statistics
Matches: 236, Mismatches: 16, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
150 236 1.00
ACGTcount: A:0.26, C:0.19, G:0.25, T:0.30
Consensus pattern (150 bp):
AGGTCACGTGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGATAATTGGTCGCATGTGTAGT
ACTAAGTGCAGGCTACTATGCGTACCTGATAACTTCGATCACGTGTGTAGTACTAAGTGCAGGCT
ACTACGTGTATCAAATGGTT
Found at i:28013278 original size:15 final size:15
Alignment explanation
Indices: 28013260--28013293 Score: 68
Period size: 15 Copynumber: 2.3 Consensus size: 15
28013250 AAACCCCGAA
28013260 AACCTGAAAACAAAG
1 AACCTGAAAACAAAG
28013275 AACCTGAAAACAAAG
1 AACCTGAAAACAAAG
28013290 AACC
1 AACC
28013294 CTCAAAATGA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.59, C:0.24, G:0.12, T:0.06
Consensus pattern (15 bp):
AACCTGAAAACAAAG
Found at i:28017686 original size:25 final size:25
Alignment explanation
Indices: 28017624--28017672 Score: 98
Period size: 25 Copynumber: 2.0 Consensus size: 25
28017614 AAGGCATGAG
28017624 AACAAATTATATACATAAAGATGTA
1 AACAAATTATATACATAAAGATGTA
28017649 AACAAATTATATACATAAAGATGT
1 AACAAATTATATACATAAAGATGT
28017673 TTTAAATTAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.55, C:0.08, G:0.08, T:0.29
Consensus pattern (25 bp):
AACAAATTATATACATAAAGATGTA
Found at i:28018563 original size:14 final size:14
Alignment explanation
Indices: 28018488--28018569 Score: 51
Period size: 14 Copynumber: 5.9 Consensus size: 14
28018478 ATCTAGGGTT
*
28018488 CAAGGTCCAAGGCC
1 CAAGGTCCAAGGTC
* *
28018502 CATGGTCCAAGGTG
1 CAAGGTCCAAGGTC
* **
28018516 TAAGGTGTAAGGT-
1 CAAGGTCCAAGGTC
* * *
28018529 CTAGGT-CTAGAGTT
1 CAAGGTCCAAG-GTC
*
28018543 CAGGGTCCAAGGTC
1 CAAGGTCCAAGGTC
28018557 CAAGGTCCAAGGT
1 CAAGGTCCAAGGT
28018570 TTAGGGTCCA
Statistics
Matches: 49, Mismatches: 16, Indels: 6
0.69 0.23 0.08
Matches are distributed among these distances:
12 2 0.04
13 6 0.12
14 38 0.78
15 3 0.06
ACGTcount: A:0.26, C:0.21, G:0.33, T:0.21
Consensus pattern (14 bp):
CAAGGTCCAAGGTC
Found at i:28018640 original size:21 final size:21
Alignment explanation
Indices: 28018590--28018640 Score: 57
Period size: 21 Copynumber: 2.4 Consensus size: 21
28018580 TAGTACAAGA
*
28018590 TCAAGGATTCAAGGTCCAGTGT
1 TCAAGG-TTCAAGGTCCAGAGT
* *
28018612 TCAGGGTTCAAGGTCTAGAGT
1 TCAAGGTTCAAGGTCCAGAGT
*
28018633 TGAAGGTT
1 TCAAGGTT
28018641 TAGGGATTAG
Statistics
Matches: 24, Mismatches: 5, Indels: 1
0.80 0.17 0.03
Matches are distributed among these distances:
21 19 0.79
22 5 0.21
ACGTcount: A:0.25, C:0.14, G:0.31, T:0.29
Consensus pattern (21 bp):
TCAAGGTTCAAGGTCCAGAGT
Found at i:28019253 original size:24 final size:25
Alignment explanation
Indices: 28019205--28019261 Score: 73
Period size: 24 Copynumber: 2.3 Consensus size: 25
28019195 TAATATTAAA
28019205 ATATAAAATTAAATATTATATAATT
1 ATATAAAATTAAATATTATATAATT
*
28019230 ATATAATATT-AATATTCATA-AATT
1 ATATAAAATTAAATATT-ATATAATT
*
28019254 ATACAAAA
1 ATATAAAA
28019262 CTTATCATTT
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
24 16 0.57
25 12 0.43
ACGTcount: A:0.56, C:0.04, G:0.00, T:0.40
Consensus pattern (25 bp):
ATATAAAATTAAATATTATATAATT
Found at i:28023358 original size:26 final size:26
Alignment explanation
Indices: 28023329--28023382 Score: 99
Period size: 26 Copynumber: 2.1 Consensus size: 26
28023319 ACGAGAAGGA
*
28023329 AGATGGGCCAACTAATGTGGATCGAC
1 AGATGGGCCAACTAATGTGGACCGAC
28023355 AGATGGGCCAACTAATGTGGACCGAC
1 AGATGGGCCAACTAATGTGGACCGAC
28023381 AG
1 AG
28023383 TTTGTGAAAC
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 27 1.00
ACGTcount: A:0.31, C:0.20, G:0.31, T:0.17
Consensus pattern (26 bp):
AGATGGGCCAACTAATGTGGACCGAC
Found at i:28024394 original size:30 final size:30
Alignment explanation
Indices: 28024360--28024420 Score: 77
Period size: 30 Copynumber: 2.0 Consensus size: 30
28024350 TTCCCGAGCC
28024360 TAGGGGAAAAAGTGTAAATATGCAAAAGTT
1 TAGGGGAAAAAGTGTAAATATGCAAAAGTT
* * * * *
28024390 TAGGGGCAAAATTGTAATTTTGCCAAAGTT
1 TAGGGGAAAAAGTGTAAATATGCAAAAGTT
28024420 T
1 T
28024421 GAGTTAAGGA
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
30 26 1.00
ACGTcount: A:0.39, C:0.07, G:0.25, T:0.30
Consensus pattern (30 bp):
TAGGGGAAAAAGTGTAAATATGCAAAAGTT
Found at i:28031227 original size:15 final size:15
Alignment explanation
Indices: 28031207--28031236 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
28031197 AAAACCGACA
28031207 AGGATGATTTTCAAT
1 AGGATGATTTTCAAT
28031222 AGGATGATTTTCAAT
1 AGGATGATTTTCAAT
28031237 TGCAATCAGG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.33, C:0.07, G:0.20, T:0.40
Consensus pattern (15 bp):
AGGATGATTTTCAAT
Found at i:28033754 original size:50 final size:51
Alignment explanation
Indices: 28033690--28033818 Score: 208
Period size: 50 Copynumber: 2.5 Consensus size: 51
28033680 GATCATAGCA
* *
28033690 ACAAATGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAAGACAAGTG
1 ACAAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAAGACAAATG
*
28033741 A-AAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGGACAAATG
1 ACAAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAAGACAAATG
28033791 ACAAGTGGA-AAGTGATAGCTTCGGCTAC
1 ACAAGT-GATAAGTGATAGCTTCGGCTAC
28033819 CTGATCAGTG
Statistics
Matches: 73, Mismatches: 3, Indels: 4
0.91 0.04 0.05
Matches are distributed among these distances:
50 47 0.64
51 24 0.33
52 2 0.03
ACGTcount: A:0.36, C:0.17, G:0.22, T:0.25
Consensus pattern (51 bp):
ACAAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAAGACAAATG
Found at i:28033841 original size:31 final size:31
Alignment explanation
Indices: 28033794--28033942 Score: 217
Period size: 31 Copynumber: 4.8 Consensus size: 31
28033784 ACAAATGACA
* *
28033794 AGTGGAAAGTGATAGCTTCGGCTACCTGATC
1 AGTGAAAAGTGGTAGCTTCGGCTACCTGATC
* *
28033825 AGTGAAAAGTGGTAGCTTCTGCTACTTGATC
1 AGTGAAAAGTGGTAGCTTCGGCTACCTGATC
* **
28033856 AGTGAAAAGTGGTAGCTCCAACTACCTGATC
1 AGTGAAAAGTGGTAGCTTCGGCTACCTGATC
*
28033887 AGTGAAAAATGGTAGCTTCGGCTACCTGATC
1 AGTGAAAAGTGGTAGCTTCGGCTACCTGATC
*
28033918 AGTGAATAGTGGTAGCTTCGGCTAC
1 AGTGAAAAGTGGTAGCTTCGGCTAC
28033943 AAGTGACAAG
Statistics
Matches: 104, Mismatches: 14, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
31 104 1.00
ACGTcount: A:0.28, C:0.19, G:0.27, T:0.27
Consensus pattern (31 bp):
AGTGAAAAGTGGTAGCTTCGGCTACCTGATC
Found at i:28034028 original size:47 final size:47
Alignment explanation
Indices: 28033959--28034082 Score: 169
Period size: 47 Copynumber: 2.7 Consensus size: 47
28033949 CAAGTGATTT
* *
28033959 CTGTATAAGACCATATCTGGGATATGGCATCAGTGTGATATATGCTA
1 CTGTATAAGACCATATCTGGGATATGGCATCAGTGAGATATATGATA
* *
28034006 CTGTATAAGACCATATCTGGGATATGGCATCAGTGAGATATGTGATT
1 CTGTATAAGACCATATCTGGGATATGGCATCAGTGAGATATATGATA
* * * *
28034053 C-GTGTAAGACCATAGCTGGGCTATGACATC
1 CTGTATAAGACCATATCTGGGATATGGCATC
28034083 GATATATAAA
Statistics
Matches: 69, Mismatches: 8, Indels: 1
0.88 0.10 0.01
Matches are distributed among these distances:
46 25 0.36
47 44 0.64
ACGTcount: A:0.29, C:0.16, G:0.25, T:0.30
Consensus pattern (47 bp):
CTGTATAAGACCATATCTGGGATATGGCATCAGTGAGATATATGATA
Found at i:28034115 original size:42 final size:43
Alignment explanation
Indices: 28034054--28034168 Score: 144
Period size: 42 Copynumber: 2.7 Consensus size: 43
28034044 TATGTGATTC
* * *
28034054 GTGTAAGACCATAGCTGGGCTATGACATCGA-TATATAAATAT
1 GTGTAAGACCATAGTTGGGCTATGGCATCGATTATATAAAGAT
* *
28034096 GTGTAAGACCATAGTTGGGCTATGGCATC-ATTATGTGAAGAT
1 GTGTAAGACCATAGTTGGGCTATGGCATCGATTATATAAAGAT
* **
28034138 GTGTAAGAACATAGTTGAACTATGGCATCGA
1 GTGTAAGACCATAGTTGGGCTATGGCATCGA
28034169 GAAAACGAAG
Statistics
Matches: 63, Mismatches: 8, Indels: 3
0.85 0.11 0.04
Matches are distributed among these distances:
41 1 0.02
42 61 0.97
43 1 0.02
ACGTcount: A:0.33, C:0.13, G:0.25, T:0.29
Consensus pattern (43 bp):
GTGTAAGACCATAGTTGGGCTATGGCATCGATTATATAAAGAT
Found at i:28038506 original size:43 final size:42
Alignment explanation
Indices: 28038459--28038556 Score: 124
Period size: 42 Copynumber: 2.3 Consensus size: 42
28038449 CCTAGACGTG
* * *
28038459 GTCTTACATGTAATCAAATATCTATGCCACTATCCCAGACAGA
1 GTCTTACATGTAATCAAATA-CGATGCCAATATCACAGACAGA
* * *
28038502 GTCTTACATGAAATCAAATACGATGCCAATGTCACAGACATA
1 GTCTTACATGTAATCAAATACGATGCCAATATCACAGACAGA
*
28038544 GTCTTGCATGTAA
1 GTCTTACATGTAA
28038557 ATCTCAAATC
Statistics
Matches: 47, Mismatches: 8, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
42 28 0.60
43 19 0.40
ACGTcount: A:0.36, C:0.22, G:0.14, T:0.28
Consensus pattern (42 bp):
GTCTTACATGTAATCAAATACGATGCCAATATCACAGACAGA
Found at i:28038559 original size:43 final size:42
Alignment explanation
Indices: 28038434--28038559 Score: 130
Period size: 43 Copynumber: 3.0 Consensus size: 42
28038424 CGAAAAGCTC
* *
28038434 ATACAATGCCAATGTCCTAGACGTGGTCTTACATGT-AATCAA
1 ATACAATGCCAATGTCC-AGACATAGTCTTACATGTAAATCAA
* * * *
28038476 ATATCTATGCCACTATCCCAGACAGAGTCTTACATG-AAATCAA
1 ATA-CAATGCCAATGT-CCAGACATAGTCTTACATGTAAATCAA
* *
28038519 ATACGATGCCAATGTCACAGACATAGTCTTGCATGTAAATC
1 ATACAATGCCAATGTC-CAGACATAGTCTTACATGTAAATC
28038560 TCAAATCGAA
Statistics
Matches: 68, Mismatches: 11, Indels: 9
0.77 0.12 0.10
Matches are distributed among these distances:
41 1 0.01
42 28 0.41
43 37 0.54
44 2 0.03
ACGTcount: A:0.35, C:0.23, G:0.15, T:0.27
Consensus pattern (42 bp):
ATACAATGCCAATGTCCAGACATAGTCTTACATGTAAATCAA
Found at i:28038584 original size:44 final size:42
Alignment explanation
Indices: 28038459--28038584 Score: 103
Period size: 42 Copynumber: 2.9 Consensus size: 42
28038449 CCTAGACGTG
* * * * *
28038459 GTCTTACATGTAATCAAATATCTATGCC-ACTATCCCAGACAGA
1 GTCTTACATGAAATCAAATA-CGAAGCCAAC-GTCACAGACAGA
* * *
28038502 GTCTTACATGAAATCAAATACGATGCCAATGTCACAGACATA
1 GTCTTACATGAAATCAAATACGAAGCCAACGTCACAGACAGA
* *
28038544 GTCTTGCATGTAAATCTCAAAT-CGAAGCCAACGTCTCAGAC
1 GTCTTACATG-AAA--TCAAATACGAAGCCAACGTCACAGAC
28038585 GTGGTCTTAC
Statistics
Matches: 69, Mismatches: 10, Indels: 7
0.80 0.12 0.08
Matches are distributed among these distances:
42 24 0.35
43 23 0.33
44 16 0.23
45 6 0.09
ACGTcount: A:0.36, C:0.25, G:0.14, T:0.25
Consensus pattern (42 bp):
GTCTTACATGAAATCAAATACGAAGCCAACGTCACAGACAGA
Found at i:28040317 original size:61 final size:61
Alignment explanation
Indices: 28040174--28040305 Score: 237
Period size: 61 Copynumber: 2.2 Consensus size: 61
28040164 TAGTACAGCA
* *
28040174 TGGTGTGTAGGGATGGGTGGGTCGATTTTATCCCTACATAGTGTGTAGGGTTGGACGGCGT
1 TGGTGTGTAAGGATGGGTGGGTCGATTTTATCCCTACATAGTGTGTAGGGTTGGACGGAGT
*
28040235 TGGTGTGTAAGGATGGGTGGGTCGATTTTATCCCTACATGGTGTGTAGGGTTGGACGGAGT
1 TGGTGTGTAAGGATGGGTGGGTCGATTTTATCCCTACATAGTGTGTAGGGTTGGACGGAGT
28040296 TGGTGTGTAA
1 TGGTGTGTAA
28040306 AGGCTGGTGG
Statistics
Matches: 68, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
61 68 1.00
ACGTcount: A:0.16, C:0.10, G:0.41, T:0.33
Consensus pattern (61 bp):
TGGTGTGTAAGGATGGGTGGGTCGATTTTATCCCTACATAGTGTGTAGGGTTGGACGGAGT
Found at i:28048205 original size:39 final size:40
Alignment explanation
Indices: 28048104--28048366 Score: 326
Period size: 39 Copynumber: 6.7 Consensus size: 40
28048094 TTGAATGATG
*
28048104 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTA-AGTGAC-AAT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGA-T-ACTAAT
*
28048143 ATCCGGACTAAGAT-CCGAAGGCATTTGTGCGAGATACTAAT
1 -TCCGGGCTAAG-TCCCGAAGGCATTTGTGCGAGATACTAAT
*
28048184 TCCGGGCTAAG-CCCGAAGGCATTTGTGCAAGATACTAAT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGATACTAAT
28048223 TCCGGGCTAAG-CCCGAAGGCATTTGTGCGAGATACTAAT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGATACTAAT
* * * *
28048262 TCCGGGCTAAG-CCCGAAGGCATTTGTGCAAGTTATTAAA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGATACTAAT
* *
28048301 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACT-AT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGATACTAAT
* *
28048340 AACCGGGCTATGTCCCGAAGGCATTTG
1 -TCCGGGCTAAGTCCCGAAGGCATTTG
28048367 AACGAGGAGC
Statistics
Matches: 200, Mismatches: 16, Indels: 14
0.87 0.07 0.06
Matches are distributed among these distances:
39 110 0.55
40 76 0.38
41 13 0.06
42 1 0.00
ACGTcount: A:0.26, C:0.22, G:0.27, T:0.25
Consensus pattern (40 bp):
TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGATACTAAT
Found at i:28069101 original size:28 final size:28
Alignment explanation
Indices: 28069061--28069117 Score: 114
Period size: 28 Copynumber: 2.0 Consensus size: 28
28069051 CGATACCGAT
28069061 ATAAGTTCAATTCAATGGAATGGCACTA
1 ATAAGTTCAATTCAATGGAATGGCACTA
28069089 ATAAGTTCAATTCAATGGAATGGCACTA
1 ATAAGTTCAATTCAATGGAATGGCACTA
28069117 A
1 A
28069118 GTGTGCGATA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 29 1.00
ACGTcount: A:0.40, C:0.14, G:0.18, T:0.28
Consensus pattern (28 bp):
ATAAGTTCAATTCAATGGAATGGCACTA
Found at i:28075969 original size:40 final size:40
Alignment explanation
Indices: 28075939--28076123 Score: 171
Period size: 40 Copynumber: 4.7 Consensus size: 40
28075929 GCTCCTCGTT
* *
28075939 CAAATGCCTTCGGGACATAGCCCGGTTATAGTAACTCGCA
1 CAAATGCCTTCGGGACATAACCCGGATATAGTAACTCGCA
* * *
28075979 CAAATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCA
1 CAAATGCCTTCGGGACATAACCCGGATATAGTAACTCGCA
* * *
28076019 CAAATGCCTTCGGG-CTTAGCCCGGA-ATTAGTATCTCGCA
1 CAAATGCCTTCGGGACATAACCCGGATA-TAGTAACTCGCA
* ** * * *
28076058 CAAATGCCTTC-GGATCTTAGTCCGGATATTGTCACTTAGCA
1 CAAATGCCTTCGGGA-CATAACCCGGATATAGTAAC-TCGCA
* *
28076099 CAAA-GCCTTCGGGACTTAGCCCGGA
1 CAAATGCCTTCGGGACATAACCCGGA
28076124 CATCATTCAA
Statistics
Matches: 124, Mismatches: 15, Indels: 12
0.82 0.10 0.08
Matches are distributed among these distances:
38 2 0.02
39 31 0.25
40 79 0.64
41 12 0.10
ACGTcount: A:0.26, C:0.28, G:0.22, T:0.25
Consensus pattern (40 bp):
CAAATGCCTTCGGGACATAACCCGGATATAGTAACTCGCA
Found at i:28076050 original size:79 final size:82
Alignment explanation
Indices: 28075939--28076123 Score: 231
Period size: 79 Copynumber: 2.3 Consensus size: 82
28075929 GCTCCTCGTT
* *
28075939 CAAATGCCTTCGGGACATAGCCCGG-TTATAGTAACTCGCACAAATGCCTTCGGGA-CTTAACCC
1 CAAATGCCTTCGGGACTTAGCCCGGAATATAGTAACTCGCACAAATGCCTTC-GGATCTTAACCC
*
28076002 GGAT-TTAATAAC-TCGCA
65 GGATATT-ATAACTTAGCA
* **
28076019 CAAATGCCTTCGGG-CTTAGCCCGGAAT-TAGTATCTCGCACAAATGCCTTCGGATCTTAGTCCG
1 CAAATGCCTTCGGGACTTAGCCCGGAATATAGTAACTCGCACAAATGCCTTCGGATCTTAACCCG
* *
28076082 GATATTGTCACTTAGCA
66 GATATTATAACTTAGCA
28076099 CAAA-GCCTTCGGGACTTAGCCCGGA
1 CAAATGCCTTCGGGACTTAGCCCGGA
28076124 CATCATTCAA
Statistics
Matches: 92, Mismatches: 8, Indels: 10
0.84 0.07 0.09
Matches are distributed among these distances:
78 3 0.03
79 53 0.58
80 36 0.39
ACGTcount: A:0.26, C:0.28, G:0.22, T:0.25
Consensus pattern (82 bp):
CAAATGCCTTCGGGACTTAGCCCGGAATATAGTAACTCGCACAAATGCCTTCGGATCTTAACCCG
GATATTATAACTTAGCA
Found at i:28079807 original size:39 final size:39
Alignment explanation
Indices: 28079690--28079951 Score: 316
Period size: 39 Copynumber: 6.6 Consensus size: 39
28079680 GCTCCTCGTT
* * * *
28079690 CAAATGCCTTCGGGACATAGCCCGG-TTATAGTAACTCGTA
1 CAAATGCCTTCGGG-CTTAGCCCGGAAT-TAGTATCTCGCA
* * * *
28079730 CAAATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCA
1 CAAATGCCTTCGGG-CTTAGCCCGGAATTAGTATCTCGCA
28079770 CAAATGCCTTCGGGCTTAGCCCGGAATTAGTATCTCGCA
1 CAAATGCCTTCGGGCTTAGCCCGGAATTAGTATCTCGCA
*
28079809 CAAATGCCTTCGGGCTTAGCCCGGAATTAGTATCTTGCA
1 CAAATGCCTTCGGGCTTAGCCCGGAATTAGTATCTCGCA
28079848 CAAATGCCTTCGGGCTTAGCCCGGAATTAGTATCTCGCA
1 CAAATGCCTTCGGGCTTAGCCCGGAATTAGTATCTCGCA
* * *
28079887 CAAATGCCTTCGGATCTTAGTCCGGATATT-GTCA-CTTAGCA
1 CAAATGCCTTCGG-GCTTAGCCCGGA-ATTAGT-ATC-TCGCA
*
28079928 CAAA-GCCTTCGGACTTAGCCCGGA
1 CAAATGCCTTCGGGCTTAGCCCGGA
28079952 CATCATTCAA
Statistics
Matches: 202, Mismatches: 15, Indels: 11
0.89 0.07 0.05
Matches are distributed among these distances:
39 120 0.59
40 68 0.34
41 14 0.07
ACGTcount: A:0.25, C:0.27, G:0.22, T:0.26
Consensus pattern (39 bp):
CAAATGCCTTCGGGCTTAGCCCGGAATTAGTATCTCGCA
Found at i:28087662 original size:40 final size:40
Alignment explanation
Indices: 28087618--28087837 Score: 260
Period size: 40 Copynumber: 5.7 Consensus size: 40
28087608 GCTCCTCGTT
* *
28087618 CAAATGCCTTCGGGACATAGCCCGGTTATAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATATAGTAACTCGCA
* *
28087658 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATATAGTAACTCGCA
28087698 CAAATGCCTTC-GG-CTTA-CCCGGAT-TAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATATAGTAACTCGCA
* *
28087734 CAAATGCCTTTGGG-CTTAGCCCGGA-ATTAGTATCTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATA-TAGTAACTCGCA
* * * *
28087773 CAAATGCCTTC-GGATCTTAGTCCGGATATTGTCACTTAGC-
1 CAAATGCCTTCGGGA-CTTAGCCCGGATATAGTAAC-TCGCA
28087813 CAAA-GCCTTCGGGACTTAGCCCGGA
1 CAAATGCCTTCGGGACTTAGCCCGGA
28087838 CATCATTCAA
Statistics
Matches: 158, Mismatches: 13, Indels: 19
0.83 0.07 0.10
Matches are distributed among these distances:
36 22 0.14
37 13 0.08
38 12 0.08
39 39 0.25
40 68 0.43
41 4 0.03
ACGTcount: A:0.25, C:0.28, G:0.22, T:0.25
Consensus pattern (40 bp):
CAAATGCCTTCGGGACTTAGCCCGGATATAGTAACTCGCA
Found at i:28087776 original size:75 final size:79
Alignment explanation
Indices: 28087618--28087837 Score: 263
Period size: 75 Copynumber: 2.8 Consensus size: 79
28087608 GCTCCTCGTT
*
28087618 CAAATGCCTTCGGGACATAGCCCGGTTATAGTAACTCGCACAAATGCCTTCGGGACTTAACCCGG
1 CAAATGCCTTC-GGACATAGCCCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAACCCGG
*
28087683 ATTTAGTAACTCGCA
65 AATTAGTAACTCGCA
* * *
28087698 CAAATGCCTTCGG-CTTA-CCCGGAT-TAGTAACTCGCACAAATGCCTTTGGG-CTTAGCCCGGA
1 CAAATGCCTTCGGACATAGCCCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAACCCGGA
*
28087759 ATTAGTATCTCGCA
66 ATTAGTAACTCGCA
* * * * * *
28087773 CAAATGCCTTCGGATCTTAGTCCGGATATTGTCACTTAGC-CAAA-GCCTTCGGGACTTAGCCCG
1 CAAATGCCTTCGGA-CATAGCCCGGATATAGTAAC-TCGCACAAATGCCTTCGGGACTTAACCCG
28087836 GA
64 GA
28087838 CATCATTCAA
Statistics
Matches: 123, Mismatches: 11, Indels: 13
0.84 0.07 0.09
Matches are distributed among these distances:
75 35 0.28
76 25 0.20
77 10 0.08
78 17 0.14
79 22 0.18
80 14 0.11
ACGTcount: A:0.25, C:0.28, G:0.22, T:0.25
Consensus pattern (79 bp):
CAAATGCCTTCGGACATAGCCCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAACCCGGA
ATTAGTAACTCGCA
Found at i:28109798 original size:38 final size:38
Alignment explanation
Indices: 28109751--28109911 Score: 170
Period size: 38 Copynumber: 4.2 Consensus size: 38
28109741 GGCTTAAAGA
28109751 CCCGCAGGCTAT-ATGCTGGAATTATATCTGGGTTAAAT
1 CCCGCAGGCT-TCATGCTGGAATTATATCTGGGTTAAAT
* * *
28109789 CCCGTAGGCTTCGTGCTGGTAA-TATATCCGGGTTAAAT
1 CCCGCAGGCTTCATGCTGG-AATTATATCTGGGTTAAAT
*
28109827 CCCGCAGGCTTCATGCTGGTATTATATCCT-GGTTAAAT
1 CCCGCAGGCTTCATGCTGGAATTATAT-CTGGGTTAAAT
* * *
28109865 CCCGC-GGCCT-AGTGCTGGTATTATATCTGAGCTTAAAGT
1 CCCGCAGGCTTCA-TGCTGGAATTATATCTG-GGTTAAA-T
28109904 CCCGCAGG
1 CCCGCAGG
28109912 TTTTTGTGCT
Statistics
Matches: 105, Mismatches: 9, Indels: 16
0.81 0.07 0.12
Matches are distributed among these distances:
36 3 0.03
37 20 0.19
38 71 0.68
39 9 0.09
40 2 0.02
ACGTcount: A:0.22, C:0.23, G:0.25, T:0.30
Consensus pattern (38 bp):
CCCGCAGGCTTCATGCTGGAATTATATCTGGGTTAAAT
Found at i:28109834 original size:76 final size:76
Alignment explanation
Indices: 28109735--28109911 Score: 216
Period size: 76 Copynumber: 2.3 Consensus size: 76
28109725 ATTTGATGTG
*
28109735 TATCCGGGCTTAAAGACCCGCAGGCTAT-ATGCTGGAATTATAT-CTGGGTTAAATCCCGTAGGC
1 TATCCGGG-TTAAAGTCCCGCAGGCT-TCATGCTGGAATTATATCCT-GGTTAAATCCCG-AGGC
* *
28109798 TTCGTGCTGGTAATA
62 CTAGTGCTGGTAATA
* *
28109813 TATCCGGGTTAAA-TCCCGCAGGCTTCATGCTGGTATTATATCCTGGTTAAATCCCGCGGCCTAG
1 TATCCGGGTTAAAGTCCCGCAGGCTTCATGCTGGAATTATATCCTGGTTAAATCCCGAGGCCTAG
*
28109877 TGCTGGTATTA
66 TGCTGGTAATA
* *
28109888 TATCTGAGCTTAAAGTCCCGCAGG
1 TATCCG-GGTTAAAGTCCCGCAGG
28109912 TTTTTGTGCT
Statistics
Matches: 87, Mismatches: 8, Indels: 9
0.84 0.08 0.09
Matches are distributed among these distances:
75 21 0.24
76 42 0.48
77 16 0.18
78 8 0.09
ACGTcount: A:0.23, C:0.23, G:0.25, T:0.30
Consensus pattern (76 bp):
TATCCGGGTTAAAGTCCCGCAGGCTTCATGCTGGAATTATATCCTGGTTAAATCCCGAGGCCTAG
TGCTGGTAATA
Found at i:28118826 original size:40 final size:40
Alignment explanation
Indices: 28118752--28118972 Score: 297
Period size: 40 Copynumber: 5.6 Consensus size: 40
28118742 AACCCAAGTA
* * *
28118752 CCTTCAGGATTTAG-CCGGATATAG-CAACTCGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTC-ACTAGCACAAATG
* *
28118791 CCTTCGGGTCTTAGCCCGGATATAGTCACTAGCACAAAAG
1 CCTTCGGGACTTAGCCCGGATATAGTCACTAGCACAAATG
* *
28118831 CCTTCGGGACTTAGCCTGGATATAG-CAACTCGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTC-ACTAGCACAAATG
* * *
28118871 CCTTCGGGACTTAGCCCGGGTATAGTCAATAGCACAACTG
1 CCTTCGGGACTTAGCCCGGATATAGTCACTAGCACAAATG
*
28118911 CCTTCGGGACTTAGCCCGGATATAGTCACTAGCAC-CATG
1 CCTTCGGGACTTAGCCCGGATATAGTCACTAGCACAAATG
28118950 CCTTCGGGACTTAGCCCGGATAT
1 CCTTCGGGACTTAGCCCGGATAT
28118973 CATCCGAATA
Statistics
Matches: 160, Mismatches: 18, Indels: 8
0.86 0.10 0.04
Matches are distributed among these distances:
39 37 0.23
40 121 0.76
41 2 0.01
ACGTcount: A:0.26, C:0.28, G:0.23, T:0.23
Consensus pattern (40 bp):
CCTTCGGGACTTAGCCCGGATATAGTCACTAGCACAAATG
Found at i:28121439 original size:38 final size:38
Alignment explanation
Indices: 28121397--28121525 Score: 179
Period size: 38 Copynumber: 3.4 Consensus size: 38
28121387 GCAGGCTATA
28121397 TGCTGGAATTATATCCGGGTTAAATCCCGTAGGCTTCG
1 TGCTGGAATTATATCCGGGTTAAATCCCGTAGGCTTCG
*
28121435 TGCTGGTAA-TATATCCGGGTTAAATCCCGCAGGCTTCG
1 TGCTGG-AATTATATCCGGGTTAAATCCCGTAGGCTTCG
* * * *
28121473 TGCTGGTATTATATCCGGGTTAACTCCCGTAGGCCTAG
1 TGCTGGAATTATATCCGGGTTAAATCCCGTAGGCTTCG
* *
28121511 TGCTAGTATTATATC
1 TGCTGGAATTATATC
28121526 TGAGCTTAAA
Statistics
Matches: 82, Mismatches: 7, Indels: 4
0.88 0.08 0.04
Matches are distributed among these distances:
37 1 0.01
38 79 0.96
39 2 0.02
ACGTcount: A:0.21, C:0.22, G:0.25, T:0.33
Consensus pattern (38 bp):
TGCTGGAATTATATCCGGGTTAAATCCCGTAGGCTTCG
Found at i:28121467 original size:76 final size:77
Alignment explanation
Indices: 28121368--28121545 Score: 225
Period size: 76 Copynumber: 2.3 Consensus size: 77
28121358 ATTTGATGTG
* *
28121368 TATCCGGGCTTAAAGACCCGCAGGCTAT-ATGCTGGAATTATATCCGGGTTAAATCCCGTAGGCT
1 TATCCGGG-TTAAAGTCCCGCAGGCT-TCATGCTGGAATTATATCCGGGTTAAATCCCGTAGGCC
* *
28121432 TCGTGCTGGTAATA
64 TAGTGCTAGTAATA
* * *
28121446 TATCCGGGTTAAA-TCCCGCAGGCTTCGTGCTGGTATTATATCCGGGTTAACTCCCGTAGGCCTA
1 TATCCGGGTTAAAGTCCCGCAGGCTTCATGCTGGAATTATATCCGGGTTAAATCCCGTAGGCCTA
*
28121510 GTGCTAGTATTA
66 GTGCTAGTAATA
* *
28121522 TATCTGAGCTTAAAGTCCCGCAGG
1 TATCCG-GGTTAAAGTCCCGCAGG
28121546 TTTTGTGCTG
Statistics
Matches: 87, Mismatches: 10, Indels: 6
0.84 0.10 0.06
Matches are distributed among these distances:
75 1 0.01
76 58 0.67
77 11 0.13
78 17 0.20
ACGTcount: A:0.22, C:0.23, G:0.25, T:0.29
Consensus pattern (77 bp):
TATCCGGGTTAAAGTCCCGCAGGCTTCATGCTGGAATTATATCCGGGTTAAATCCCGTAGGCCTA
GTGCTAGTAATA
Found at i:28123279 original size:47 final size:47
Alignment explanation
Indices: 28123208--28123711 Score: 783
Period size: 47 Copynumber: 10.6 Consensus size: 47
28123198 CCCTTCGGGA
* * ** * *
28123208 CTTATCACATTTATACACTTTCACATCCATCACATTTGCCACTCGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
* * * *
28123255 CCTATCACATATATACACTCTCACATTCATCACATTGGCCATTCGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
28123302 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
28123349 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
*
28123396 CTTATCACATATATACACTTTCACATTCATCACATCGGCTATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
* **
28123443 CTTATCACATATATACACTTTCACATTCATCATATCGGTGATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
28123490 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGG-C
28123538 TTATCTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 ----CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
* *
28123589 CTTATCACATATATACACTTTCACATTCATCACATTGGCCATTCGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
* *
28123636 CTTATCAAATATATATACACTTTCACATTCATCACATTGGCCATTAGGC
1 CTTATC--ACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
28123685 CTTATCACATATATACACTTTCACATT
1 CTTATCACATATATACACTTTCACATT
28123712 TATTCAAATA
Statistics
Matches: 428, Mismatches: 22, Indels: 14
0.92 0.05 0.03
Matches are distributed among these distances:
47 335 0.78
48 1 0.00
49 45 0.11
51 1 0.00
52 46 0.11
ACGTcount: A:0.29, C:0.29, G:0.08, T:0.34
Consensus pattern (47 bp):
CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
Found at i:28123287 original size:25 final size:24
Alignment explanation
Indices: 28123258--28123336 Score: 65
Period size: 25 Copynumber: 3.3 Consensus size: 24
28123248 ACTCGGCCCT
28123258 ATCACATATATACACTCTCACATTC
1 ATCACATATATACACT-TCACATTC
*** * *
28123283 ATCACAT-TGGCCA-TTCGGCCTT-
1 ATCACATATATACACTTC-ACATTC
28123305 ATCACATATATACACTTTCACATTC
1 ATCACATATATACAC-TTCACATTC
28123330 ATCACAT
1 ATCACAT
28123337 CGGCCATTAG
Statistics
Matches: 39, Mismatches: 10, Indels: 10
0.66 0.17 0.17
Matches are distributed among these distances:
22 9 0.23
23 7 0.18
24 6 0.15
25 17 0.44
ACGTcount: A:0.32, C:0.30, G:0.05, T:0.33
Consensus pattern (24 bp):
ATCACATATATACACTTCACATTC
Found at i:28129103 original size:14 final size:14
Alignment explanation
Indices: 28129084--28129122 Score: 55
Period size: 14 Copynumber: 2.9 Consensus size: 14
28129074 CATTAGGTAA
28129084 ATAATATAAATGTT
1 ATAATATAAATGTT
28129098 ATAATATAACAT-TT
1 ATAATATAA-ATGTT
28129112 ATAATA-AAATG
1 ATAATATAAATG
28129123 ATGTTCATAT
Statistics
Matches: 23, Mismatches: 0, Indels: 5
0.82 0.00 0.18
Matches are distributed among these distances:
12 2 0.09
13 2 0.09
14 17 0.74
15 2 0.09
ACGTcount: A:0.54, C:0.03, G:0.05, T:0.38
Consensus pattern (14 bp):
ATAATATAAATGTT
Found at i:28136673 original size:38 final size:39
Alignment explanation
Indices: 28136621--28136701 Score: 101
Period size: 39 Copynumber: 2.1 Consensus size: 39
28136611 GTCTGAACTA
* * * * *
28136621 AAAACATGTGTTAAAGATGT-CTGAACTAAGACATATTT
1 AAAACATATATTAAAGATATCCTAAACTAAGACATAATT
*
28136659 AAAACATATATTAAAGATATCCTAAACTATGACATAATT
1 AAAACATATATTAAAGATATCCTAAACTAAGACATAATT
28136698 AAAA
1 AAAA
28136702 ACCCTTATGT
Statistics
Matches: 36, Mismatches: 6, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
38 17 0.47
39 19 0.53
ACGTcount: A:0.49, C:0.11, G:0.10, T:0.30
Consensus pattern (39 bp):
AAAACATATATTAAAGATATCCTAAACTAAGACATAATT
Found at i:28137084 original size:25 final size:25
Alignment explanation
Indices: 28137030--28137084 Score: 58
Period size: 25 Copynumber: 2.2 Consensus size: 25
28137020 CGCGTCAGTG
28137030 TTGGCCATGTGTTTTGGTTGTTGAA
1 TTGGCCATGTGTTTTGGTTGTTGAA
* * * *
28137055 ATGGCTATTTGTTTTGGCTT-TTGAT
1 TTGGCCATGTGTTTTGG-TTGTTGAA
28137080 TTGGC
1 TTGGC
28137085 ACTTTGATAA
Statistics
Matches: 24, Mismatches: 5, Indels: 2
0.77 0.16 0.06
Matches are distributed among these distances:
25 22 0.92
26 2 0.08
ACGTcount: A:0.11, C:0.09, G:0.29, T:0.51
Consensus pattern (25 bp):
TTGGCCATGTGTTTTGGTTGTTGAA
Found at i:28147410 original size:25 final size:24
Alignment explanation
Indices: 28147347--28147414 Score: 91
Period size: 24 Copynumber: 2.8 Consensus size: 24
28147337 ATTCCAAGCC
*
28147347 ACAGTTCATGAGAGCATACCGATT
1 ACAGCTCATGAGAGCATACCGATT
**
28147371 ACAGCTTGTGAGAGCATACCGATTT
1 ACAGCTCATGAGAGCATACCGA-TT
*
28147396 ACAGCTCATGTGAGCATAC
1 ACAGCTCATGAGAGCATAC
28147415 ATGTACAGGA
Statistics
Matches: 37, Mismatches: 6, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
24 19 0.51
25 18 0.49
ACGTcount: A:0.31, C:0.22, G:0.22, T:0.25
Consensus pattern (24 bp):
ACAGCTCATGAGAGCATACCGATT
Found at i:28148234 original size:30 final size:30
Alignment explanation
Indices: 28148198--28148260 Score: 126
Period size: 30 Copynumber: 2.1 Consensus size: 30
28148188 AAGTTAATTC
28148198 AATAGCTTGAATTTATGCAATCTGGATTGT
1 AATAGCTTGAATTTATGCAATCTGGATTGT
28148228 AATAGCTTGAATTTATGCAATCTGGATTGT
1 AATAGCTTGAATTTATGCAATCTGGATTGT
28148258 AAT
1 AAT
28148261 TTAGTTTATT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 33 1.00
ACGTcount: A:0.32, C:0.10, G:0.19, T:0.40
Consensus pattern (30 bp):
AATAGCTTGAATTTATGCAATCTGGATTGT
Found at i:28159489 original size:40 final size:40
Alignment explanation
Indices: 28159411--28159591 Score: 258
Period size: 40 Copynumber: 4.5 Consensus size: 40
28159401 ACCCAAGTAT
* * *
28159411 CTTCGAGATTTAG-CCGGATATAG-CAACTCGCACAAATGC
1 CTTCGGGACTTAGCCCGGATATAGTC-ACTAGCACAAATGC
* **
28159450 CTTCGGGTCTTAGCCCGGATATAGTCACTAGCATGAATGC
1 CTTCGGGACTTAGCCCGGATATAGTCACTAGCACAAATGC
28159490 CTTCGGGACTTAGCCCGGATATAGTCACTAGCACAAATGC
1 CTTCGGGACTTAGCCCGGATATAGTCACTAGCACAAATGC
* *
28159530 CTTCGGGACTTAGCCCGGATATAGTAACTTGCACAAATGC
1 CTTCGGGACTTAGCCCGGATATAGTCACTAGCACAAATGC
*
28159570 CTTCGGGACTTAGCCTGGATAT
1 CTTCGGGACTTAGCCCGGATAT
28159592 TATCCGAATA
Statistics
Matches: 128, Mismatches: 12, Indels: 3
0.90 0.08 0.02
Matches are distributed among these distances:
39 10 0.08
40 117 0.91
41 1 0.01
ACGTcount: A:0.26, C:0.25, G:0.23, T:0.25
Consensus pattern (40 bp):
CTTCGGGACTTAGCCCGGATATAGTCACTAGCACAAATGC
Found at i:28167668 original size:40 final size:40
Alignment explanation
Indices: 28167595--28167735 Score: 205
Period size: 40 Copynumber: 3.5 Consensus size: 40
28167585 ACCCAAGTAT
* * *
28167595 CTTCGAGATTTAG-CCGGATATAG-CAACTCGCACAAATGC
1 CTTCGGGACTTAGCCCGGATATAGTC-ACTAGCACAAATGC
*
28167634 CTTCGGGTCTTAGCCCGGATATAGTCACTAGCACAAATGC
1 CTTCGGGACTTAGCCCGGATATAGTCACTAGCACAAATGC
* *
28167674 CTTCGGGACTTAGCCCGGATATAGTAACTTGCACAAATGC
1 CTTCGGGACTTAGCCCGGATATAGTCACTAGCACAAATGC
28167714 CTTCGGGACTTAGCCCGGATAT
1 CTTCGGGACTTAGCCCGGATAT
28167736 TATCCGAATA
Statistics
Matches: 93, Mismatches: 7, Indels: 3
0.90 0.07 0.03
Matches are distributed among these distances:
39 10 0.11
40 82 0.88
41 1 0.01
ACGTcount: A:0.26, C:0.26, G:0.23, T:0.25
Consensus pattern (40 bp):
CTTCGGGACTTAGCCCGGATATAGTCACTAGCACAAATGC
Found at i:28174118 original size:22 final size:22
Alignment explanation
Indices: 28174090--28174132 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 22
28174080 GAGAAAAGAG
*
28174090 AGGAGAGGGTAGTAGCTTCCAA
1 AGGAGAGGGTAGCAGCTTCCAA
*
28174112 AGGAGAGGGTAGCAGTTTCCA
1 AGGAGAGGGTAGCAGCTTCCA
28174133 GAGCAAAAAA
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:0.14, G:0.37, T:0.19
Consensus pattern (22 bp):
AGGAGAGGGTAGCAGCTTCCAA
Found at i:28175959 original size:79 final size:79
Alignment explanation
Indices: 28175848--28176064 Score: 278
Period size: 79 Copynumber: 2.7 Consensus size: 79
28175838 GCTACTCGTT
* *
28175848 CAAATGCCTTCGGGACATAGCCCGGTTATAGTAACTCGCACAAATGCCTTCGGGACTTAACCCGG
1 CAAATGCCTTCGGG-CTTAGCCCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAACCCGG
*
28175913 AGTTAGTAACTCGCA
65 AATTAGTAACTCGCA
* *
28175928 CAAATGCCTTCGGGCTTAGCCCGGA-ATTAGTATCTCGCACAAATGCCTTCGGG-CTTAGCCCGG
1 CAAATGCCTTCGGGCTTAGCCCGGATA-TAGTAACTCGCACAAATGCCTTCGGGACTTAACCCGG
*
28175991 AATTAGTATCTCGCA
65 AATTAGTAACTCGCA
* * * * *
28176006 CAAATGCCTTCGGATCTTAGTCCGGATATGGTCACTTAGCACAAA-GCCTTCGGGACTTA
1 CAAATGCCTTCGG-GCTTAGCCCGGATATAGTAAC-TCGCACAAATGCCTTCGGGACTTA
28176065 GCCCAGACAT
Statistics
Matches: 120, Mismatches: 12, Indels: 10
0.85 0.08 0.07
Matches are distributed among these distances:
78 36 0.30
79 57 0.47
80 27 0.22
ACGTcount: A:0.25, C:0.27, G:0.23, T:0.25
Consensus pattern (79 bp):
CAAATGCCTTCGGGCTTAGCCCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAACCCGGA
ATTAGTAACTCGCA
Found at i:28175965 original size:39 final size:40
Alignment explanation
Indices: 28175848--28176068 Score: 274
Period size: 40 Copynumber: 5.6 Consensus size: 40
28175838 GCTACTCGTT
* *
28175848 CAAATGCCTTCGGGACATAGCCCGG-TTATAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGAAT-TAGTAACTCGCA
* *
28175888 CAAATGCCTTCGGGACTTAACCCGGAGTTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGAATTAGTAACTCGCA
*
28175928 CAAATGCCTTCGGG-CTTAGCCCGGAATTAGTATCTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGAATTAGTAACTCGCA
*
28175967 CAAATGCCTTCGGG-CTTAGCCCGGAATTAGTATCTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGAATTAGTAACTCGCA
* * * *
28176006 CAAATGCCTTC-GGATCTTAGTCCGG-ATATGGTCACTTAGCA
1 CAAATGCCTTCGGGA-CTTAGCCCGGAAT-TAGTAAC-TCGCA
28176047 CAAA-GCCTTCGGGACTTAGCCC
1 CAAATGCCTTCGGGACTTAGCCC
28176069 AGACATCATT
Statistics
Matches: 163, Mismatches: 12, Indels: 12
0.87 0.06 0.06
Matches are distributed among these distances:
38 2 0.01
39 74 0.45
40 75 0.46
41 12 0.07
ACGTcount: A:0.25, C:0.28, G:0.23, T:0.24
Consensus pattern (40 bp):
CAAATGCCTTCGGGACTTAGCCCGGAATTAGTAACTCGCA
Found at i:28184039 original size:39 final size:40
Alignment explanation
Indices: 28183918--28184141 Score: 262
Period size: 40 Copynumber: 5.7 Consensus size: 40
28183908 GCTACTCGTT
* *
28183918 CAAATGCCTTCGGGACATAGCCCGG-TTATAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGAAT-TAGTAACTCGCA
* *
28183958 CAAATGCCTTCGGGACTTAACCCGGAGTTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGAATTAGTAACTCGCA
* *
28183998 CAAATGCCTTCGGG-CTTAGCCCAGAATTAGTATCTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGAATTAGTAACTCGCA
* *
28184037 CAAATGCCTTCGGG-CTTAGCTCGGAATTAGTATCTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGAATTAGTAACTCGCA
* * * *
28184076 CAAATGCCTTC-GGATCTTAGTCCGG-ATATGGTCACTTAGCA
1 CAAATGCCTTCGGGA-CTTAGCCCGGAAT-TAGTAAC-TCGCA
28184117 CAAA-GCCTTCGGGACTTAGCCCGGA
1 CAAATGCCTTCGGGACTTAGCCCGGA
28184142 CATCATTCAA
Statistics
Matches: 161, Mismatches: 16, Indels: 13
0.85 0.08 0.07
Matches are distributed among these distances:
38 2 0.01
39 71 0.44
40 76 0.47
41 12 0.07
ACGTcount: A:0.25, C:0.27, G:0.23, T:0.25
Consensus pattern (40 bp):
CAAATGCCTTCGGGACTTAGCCCGGAATTAGTAACTCGCA
Found at i:28184101 original size:118 final size:120
Alignment explanation
Indices: 28183918--28184138 Score: 283
Period size: 118 Copynumber: 1.9 Consensus size: 120
28183908 GCTACTCGTT
*
28183918 CAAATGCCTTCGGGACATAGCCCGGTTATAGTAACTCGCACAAATGCCTTCGGGACTTAACCCGG
1 CAAATGCCTTCGGGACATAGCCCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAACCCGG
*
28183983 AGT-TAGTAAC-TCGCACAAATGCCTTCGGG-CTTAGCCCAGAATTAGTATCTCGCA
66 A-TATAGTAACTTAGCACAAA-GCCTTCGGGACTTAGCCCAGAATTAGTATCTCGCA
* * * **
28184037 CAAATGCCTTCGGG-CTTAGCTCGGA-ATTAGTATCTCGCACAAATGCCTTC-GGATCTTAGTCC
1 CAAATGCCTTCGGGACATAGCCCGGATA-TAGTAACTCGCACAAATGCCTTCGGGA-CTTAACCC
* *
28184099 GGATATGGTCACTTAGCACAAAGCCTTCGGGACTTAGCCC
64 GGATATAGTAACTTAGCACAAAGCCTTCGGGACTTAGCCC
28184139 GGACATCATT
Statistics
Matches: 88, Mismatches: 9, Indels: 10
0.82 0.08 0.09
Matches are distributed among these distances:
117 5 0.06
118 53 0.60
119 30 0.34
ACGTcount: A:0.25, C:0.28, G:0.22, T:0.25
Consensus pattern (120 bp):
CAAATGCCTTCGGGACATAGCCCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAACCCGG
ATATAGTAACTTAGCACAAAGCCTTCGGGACTTAGCCCAGAATTAGTATCTCGCA
Found at i:28189278 original size:29 final size:29
Alignment explanation
Indices: 28189245--28189301 Score: 71
Period size: 29 Copynumber: 2.0 Consensus size: 29
28189235 AAATTGATTT
* *
28189245 TCAA-GCCTAAGGGTAAAATGGTCATTTTG
1 TCAAGGCCT-AGGGCAAAATGGTAATTTTG
*
28189274 TCAAGGTCTAGGGCAAAATGGTAATTTT
1 TCAAGGCCTAGGGCAAAATGGTAATTTT
28189302 ACCAAAGAAG
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
29 21 0.88
30 3 0.12
ACGTcount: A:0.32, C:0.12, G:0.25, T:0.32
Consensus pattern (29 bp):
TCAAGGCCTAGGGCAAAATGGTAATTTTG
Found at i:28189833 original size:47 final size:46
Alignment explanation
Indices: 28189654--28189850 Score: 165
Period size: 46 Copynumber: 4.2 Consensus size: 46
28189644 TGTGAGAGCT
* * *
28189654 AGTGTAAGACCATGTCTGGGACATTGCATT-GGCATTGAGACTAGT--GCT
1 AGTGTAAGACCATGTCTGGGACA-TGC-TTCGAC-TCGAGA-TA-TAAGCC
* **
28189702 AGTGTAAGA-CATGTCTGGGACATGCATCGACCTCGAGACGTAAGCC
1 AGTGTAAGACCATGTCTGGGACATGCTTCGA-CTCGAGATATAAGCC
* * *
28189748 AGTGTAAGA-CATGTCT-GGAGCATGCGTCGGCTACGAGATGAT-AGTC
1 AGTGTAAGACCATGTCTGGGA-CATGCTTCGACT-CGAGAT-ATAAGCC
*
28189794 AGTGTAAGACCATGTCTGGGACATGGCTTCGACTTGAGATATAAGCC
1 AGTGTAAGACCATGTCTGGGACAT-GCTTCGACTCGAGATATAAGCC
28189841 AGTGTAAGAC
1 AGTGTAAGAC
28189851 TGTGTTTGGG
Statistics
Matches: 123, Mismatches: 15, Indels: 23
0.76 0.09 0.14
Matches are distributed among these distances:
44 1 0.01
45 6 0.05
46 54 0.44
47 43 0.35
48 19 0.15
ACGTcount: A:0.27, C:0.19, G:0.29, T:0.24
Consensus pattern (46 bp):
AGTGTAAGACCATGTCTGGGACATGCTTCGACTCGAGATATAAGCC
Found at i:28205719 original size:47 final size:48
Alignment explanation
Indices: 28205646--28205814 Score: 183
Period size: 46 Copynumber: 3.6 Consensus size: 48
28205636 CAATTGTTAG
* * *
28205646 AGCTAGTGTAAGACCATGTCTAGGACATGACATCGGCATTGAGACGAGT
1 AGCTAGTGTAAGACCATGTCTGGGACATG-CGTCGGCATCGAGACGAGT
28205695 A-CTAGTGTAAGA-CATGTCTGGGACATGCGTCGGCCA-CGAGAC--GT
1 AGCTAGTGTAAGACCATGTCTGGGACATGCGTCGG-CATCGAGACGAGT
* * *
28205739 AAGCCAGTGTAAGA-CATGTCTGGGACATGCGTCGAC-TACGAGATGA-T
1 -AGCTAGTGTAAGACCATGTCTGGGACATGCGTCGGCAT-CGAGACGAGT
*
28205786 AGTTAGTGTAAGACCATGTCTGGGACATG
1 AGCTAGTGTAAGACCATGTCTGGGACATG
28205815 GCTTTGACTT
Statistics
Matches: 104, Mismatches: 8, Indels: 18
0.80 0.06 0.14
Matches are distributed among these distances:
44 2 0.02
45 2 0.02
46 56 0.54
47 32 0.31
48 11 0.11
49 1 0.01
ACGTcount: A:0.28, C:0.19, G:0.30, T:0.22
Consensus pattern (48 bp):
AGCTAGTGTAAGACCATGTCTGGGACATGCGTCGGCATCGAGACGAGT
Found at i:28205829 original size:47 final size:47
Alignment explanation
Indices: 28205698--28205857 Score: 184
Period size: 46 Copynumber: 3.4 Consensus size: 47
28205688 GACGAGTACT
* * **
28205698 AGTGTAAGA-CATGTCTGGGACATGCGTCGGCCACGAGACGTAAGCC
1 AGTGTAAGACCATGTCTGGGACATGCGTCGACTACGAGATATAAGCC
**
28205744 AGTGTAAGA-CATGTCTGGGACATGCGTCGACTACGAGATGAT-AGTT
1 AGTGTAAGACCATGTCTGGGACATGCGTCGACTACGAGAT-ATAAGCC
* * *
28205790 AGTGTAAGACCATGTCTGGGACATGGCTTTGACT-TGAGATATAAGCC
1 AGTGTAAGACCATGTCTGGGACAT-GCGTCGACTACGAGATATAAGCC
*
28205837 AGTGTAAGACCGTGTCTGGGA
1 AGTGTAAGACCATGTCTGGGA
28205858 TATGACATCG
Statistics
Matches: 98, Mismatches: 12, Indels: 7
0.84 0.10 0.06
Matches are distributed among these distances:
46 49 0.50
47 42 0.43
48 7 0.07
ACGTcount: A:0.27, C:0.18, G:0.31, T:0.24
Consensus pattern (47 bp):
AGTGTAAGACCATGTCTGGGACATGCGTCGACTACGAGATATAAGCC
Found at i:28209181 original size:2 final size:2
Alignment explanation
Indices: 28209174--28209198 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
28209164 GGGATATGAG
28209174 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
28209199 GACTCATGAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:28209428 original size:14 final size:15
Alignment explanation
Indices: 28209411--28209439 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
28209401 AAGTATGGTA
28209411 AAATA-TTAAAAAAT
1 AAATATTTAAAAAAT
28209425 AAATATTTAAAAAAT
1 AAATATTTAAAAAAT
28209440 CACTAATAGT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 5 0.36
15 9 0.64
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (15 bp):
AAATATTTAAAAAAT
Found at i:28209864 original size:12 final size:12
Alignment explanation
Indices: 28209847--28209871 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
28209837 CATTCATAAT
28209847 ATAAAATTAAAA
1 ATAAAATTAAAA
28209859 ATAAAATTAAAA
1 ATAAAATTAAAA
28209871 A
1 A
28209872 ATTAAAAGTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (12 bp):
ATAAAATTAAAA
Found at i:28211973 original size:18 final size:17
Alignment explanation
Indices: 28211948--28211992 Score: 56
Period size: 17 Copynumber: 2.6 Consensus size: 17
28211938 GGCATGTCAC
*
28211948 ATTAAAAAAATTTTAAA
1 ATTAAAAAAATATTAAA
28211965 ATATAAAAAAA-ATTAAA
1 AT-TAAAAAAATATTAAA
*
28211982 ATTAATAAAAT
1 ATTAAAAAAAT
28211993 CATATATATA
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
16 7 0.29
17 9 0.38
18 8 0.33
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (17 bp):
ATTAAAAAAATATTAAA
Found at i:28211989 original size:19 final size:18
Alignment explanation
Indices: 28211950--28211992 Score: 54
Period size: 18 Copynumber: 2.5 Consensus size: 18
28211940 CATGTCACAT
*
28211950 TAAAAAAATTTTAAAATA
1 TAAAAAAATATTAAAATA
28211968 TAAAAAAA-ATTAAAAT-
1 TAAAAAAATATTAAAATA
*
28211984 TAATAAAAT
1 TAAAAAAAT
28211993 CATATATATA
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
16 7 0.32
17 7 0.32
18 8 0.36
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (18 bp):
TAAAAAAATATTAAAATA
Found at i:28218138 original size:14 final size:15
Alignment explanation
Indices: 28218121--28218149 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
28218111 GCACAAAAAT
28218121 TTCACACAT-ATAAA
1 TTCACACATAATAAA
28218135 TTCACACATAATAAA
1 TTCACACATAATAAA
28218150 CATAGAAAAT
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:0.52, C:0.21, G:0.00, T:0.28
Consensus pattern (15 bp):
TTCACACATAATAAA
Found at i:28221848 original size:63 final size:63
Alignment explanation
Indices: 28221767--28221890 Score: 194
Period size: 63 Copynumber: 2.0 Consensus size: 63
28221757 ACATCCTTAA
* *
28221767 TTGTTTACTTGTTTAGTTAAATATTATTCATATAATCTTTTTCATAATTGCCATTGCATTTAG
1 TTGTTTACTTGTTCAGTTAAATATTATTCATATAATCATTTTCATAATTGCCATTGCATTTAG
* * * *
28221830 TTGTTTACTTGTTCAGTTACATCTTATTCATATACTCATTTTCTTAATTGCCATTGCATTT
1 TTGTTTACTTGTTCAGTTAAATATTATTCATATAATCATTTTCATAATTGCCATTGCATTT
28221891 TTACTCTTGC
Statistics
Matches: 55, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
63 55 1.00
ACGTcount: A:0.24, C:0.15, G:0.09, T:0.52
Consensus pattern (63 bp):
TTGTTTACTTGTTCAGTTAAATATTATTCATATAATCATTTTCATAATTGCCATTGCATTTAG
Found at i:28222370 original size:18 final size:18
Alignment explanation
Indices: 28222344--28222386 Score: 77
Period size: 18 Copynumber: 2.4 Consensus size: 18
28222334 AAAAGCTGTT
*
28222344 TTTACATATATTAATAAA
1 TTTATATATATTAATAAA
28222362 TTTATATATATTAATAAA
1 TTTATATATATTAATAAA
28222380 TTTATAT
1 TTTATAT
28222387 TTTAAATTAT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.47, C:0.02, G:0.00, T:0.51
Consensus pattern (18 bp):
TTTATATATATTAATAAA
Found at i:28222448 original size:14 final size:14
Alignment explanation
Indices: 28222429--28222496 Score: 52
Period size: 14 Copynumber: 4.9 Consensus size: 14
28222419 TATTTATAAA
*
28222429 TAAATAAATCAAAT
1 TAAATATATCAAAT
*
28222443 TAAATATATAATAAT
1 TAAATATATCA-AAT
*
28222458 ACTCAAT-TAT-AAA-
1 --TAAATATATCAAAT
*
28222471 TAAATAAATCAAAT
1 TAAATATATCAAAT
28222485 TAAATATATCAA
1 TAAATATATCAA
28222497 TCAAATGGTT
Statistics
Matches: 42, Mismatches: 6, Indels: 12
0.70 0.10 0.20
Matches are distributed among these distances:
11 4 0.10
12 2 0.05
13 3 0.07
14 22 0.52
15 4 0.10
16 3 0.07
17 4 0.10
ACGTcount: A:0.60, C:0.07, G:0.00, T:0.32
Consensus pattern (14 bp):
TAAATATATCAAAT
Found at i:28222448 original size:18 final size:18
Alignment explanation
Indices: 28222425--28222502 Score: 75
Period size: 18 Copynumber: 4.0 Consensus size: 18
28222415 GATTTATTTA
28222425 TAAATAAATAAATCAAAT
1 TAAATAAATAAATCAAAT
*
28222443 TAAATATATAATAATACTCAATT
1 T-AA-ATA-AATAA-A-TCAAAT
28222466 ATAAATAAATAAATCAAAT
1 -TAAATAAATAAATCAAAT
* *
28222485 TAAATATATCAATCAAAT
1 TAAATAAATAAATCAAAT
28222503 GGTTTAATTG
Statistics
Matches: 50, Mismatches: 4, Indels: 12
0.76 0.06 0.18
Matches are distributed among these distances:
18 17 0.34
19 7 0.14
20 4 0.08
21 10 0.20
22 4 0.08
23 7 0.14
24 1 0.02
ACGTcount: A:0.60, C:0.08, G:0.00, T:0.32
Consensus pattern (18 bp):
TAAATAAATAAATCAAAT
Found at i:28225018 original size:6 final size:6
Alignment explanation
Indices: 28225007--28225054 Score: 87
Period size: 6 Copynumber: 8.0 Consensus size: 6
28224997 AAGGATGGGA
*
28225007 GAAGGG GAAGGG GAAAGG GAAGGG GAAGGG GAAGGG GAAGGG GAAGGG
1 GAAGGG GAAGGG GAAGGG GAAGGG GAAGGG GAAGGG GAAGGG GAAGGG
28225055 AAGATTGGTG
Statistics
Matches: 40, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
6 40 1.00
ACGTcount: A:0.35, C:0.00, G:0.65, T:0.00
Consensus pattern (6 bp):
GAAGGG
Found at i:28225288 original size:15 final size:15
Alignment explanation
Indices: 28225262--28225304 Score: 79
Period size: 15 Copynumber: 2.9 Consensus size: 15
28225252 CTTAATTCCA
28225262 TTAGTT-TATTTAAG
1 TTAGTTATATTTAAG
28225276 TTAGTTATATTTAAG
1 TTAGTTATATTTAAG
28225291 TTAGTTATATTTAA
1 TTAGTTATATTTAA
28225305 TTTCTATAGG
Statistics
Matches: 28, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
14 6 0.21
15 22 0.79
ACGTcount: A:0.33, C:0.00, G:0.12, T:0.56
Consensus pattern (15 bp):
TTAGTTATATTTAAG
Found at i:28238333 original size:35 final size:35
Alignment explanation
Indices: 28238294--28238391 Score: 133
Period size: 35 Copynumber: 2.8 Consensus size: 35
28238284 TATATGATCG
* *
28238294 AATATACAAGCTCAATATAACATCACATGTAGTCA
1 AATATACAAGTTCAATATAACATCACATGTAGCCA
* ** *
28238329 AATATTCAAGTTTGATATAACATCACATGTGGCCA
1 AATATACAAGTTCAATATAACATCACATGTAGCCA
*
28238364 AATATACAAGTTCAATATATCATCACAT
1 AATATACAAGTTCAATATAACATCACAT
28238392 ATGTACATAC
Statistics
Matches: 53, Mismatches: 10, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
35 53 1.00
ACGTcount: A:0.43, C:0.18, G:0.09, T:0.30
Consensus pattern (35 bp):
AATATACAAGTTCAATATAACATCACATGTAGCCA
Found at i:28242950 original size:43 final size:43
Alignment explanation
Indices: 28242902--28242985 Score: 141
Period size: 43 Copynumber: 2.0 Consensus size: 43
28242892 ATCACATGTA
* *
28242902 TCGCATCCATTATCAACTTGGACCACTCAACGAGCTCGGATGC
1 TCGCATCCATAATCAACTCGGACCACTCAACGAGCTCGGATGC
*
28242945 TCGCATCCATAATGAACTCGGACCACTCAACGAGCTCGGAT
1 TCGCATCCATAATCAACTCGGACCACTCAACGAGCTCGGAT
28242986 TCCACATATA
Statistics
Matches: 38, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
43 38 1.00
ACGTcount: A:0.27, C:0.32, G:0.19, T:0.21
Consensus pattern (43 bp):
TCGCATCCATAATCAACTCGGACCACTCAACGAGCTCGGATGC
Found at i:28243600 original size:8 final size:8
Alignment explanation
Indices: 28243587--28243612 Score: 52
Period size: 8 Copynumber: 3.2 Consensus size: 8
28243577 TATTACTACT
28243587 CACTTTTA
1 CACTTTTA
28243595 CACTTTTA
1 CACTTTTA
28243603 CACTTTTA
1 CACTTTTA
28243611 CA
1 CA
28243613 AACAAGTCCC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 18 1.00
ACGTcount: A:0.27, C:0.27, G:0.00, T:0.46
Consensus pattern (8 bp):
CACTTTTA
Found at i:28244368 original size:21 final size:22
Alignment explanation
Indices: 28244323--28244374 Score: 61
Period size: 21 Copynumber: 2.4 Consensus size: 22
28244313 AAGGTATAAG
* *
28244323 TTATGTGGTAGTTTATCTACGA
1 TTATGTGGTAGTTTATCGACAA
*
28244345 TTATGTGGTCG-TTATCGACAA
1 TTATGTGGTAGTTTATCGACAA
*
28244366 TTATTTGGT
1 TTATGTGGT
28244375 GGCTTGTCCA
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
21 16 0.62
22 10 0.38
ACGTcount: A:0.21, C:0.10, G:0.23, T:0.46
Consensus pattern (22 bp):
TTATGTGGTAGTTTATCGACAA
Found at i:28248783 original size:39 final size:39
Alignment explanation
Indices: 28248731--28249011 Score: 445
Period size: 39 Copynumber: 7.2 Consensus size: 39
28248721 CCCGAAATTT
* * *
28248731 TATTACCAGCACAAAGCCTGCGGGACTTTAGCCCGGATT
1 TATTTCCAGCACAAAGCCTGCGGGTCTTTAGCCCGGATA
28248770 TATTTCCAGCACAAAGCCTGCGGGTCTTTAGCCCGGATA
1 TATTTCCAGCACAAAGCCTGCGGGTCTTTAGCCCGGATA
* * * *
28248809 CATTTCCAGCACGAAGCCTGCGAGTCTTTGGCCCGGATA
1 TATTTCCAGCACAAAGCCTGCGGGTCTTTAGCCCGGATA
*
28248848 TATTTCCAGCACAAAGCCTGCGGGACTTTAGCCCGGATA
1 TATTTCCAGCACAAAGCCTGCGGGTCTTTAGCCCGGATA
*
28248887 CATTTCCAGCACAAAGCCTGCGGGTCTTTAGCCCGGATA
1 TATTTCCAGCACAAAGCCTGCGGGTCTTTAGCCCGGATA
* * *
28248926 CATTTCCAGCACGAAGCCTGCGGGTCTTTGGCCCGGATA
1 TATTTCCAGCACAAAGCCTGCGGGTCTTTAGCCCGGATA
*
28248965 TATTTCCAGCACAAAGCTTGCGGGTCTTTAGCCCGGATA
1 TATTTCCAGCACAAAGCCTGCGGGTCTTTAGCCCGGATA
28249004 TATTTCCA
1 TATTTCCA
28249012 TACACATTTC
Statistics
Matches: 222, Mismatches: 20, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
39 222 1.00
ACGTcount: A:0.23, C:0.29, G:0.23, T:0.25
Consensus pattern (39 bp):
TATTTCCAGCACAAAGCCTGCGGGTCTTTAGCCCGGATA
Found at i:28248942 original size:117 final size:117
Alignment explanation
Indices: 28248731--28249011 Score: 508
Period size: 117 Copynumber: 2.4 Consensus size: 117
28248721 CCCGAAATTT
* *
28248731 TATTACCAGCACAAAGCCTGCGGGACTTTAGCCCGGATTTATTTCCAGCACAAAGCCTGCGGGTC
1 TATTTCCAGCACAAAGCCTGCGGGACTTTAGCCCGGATATATTTCCAGCACAAAGCCTGCGGGTC
28248796 TTTAGCCCGGATACATTTCCAGCACGAAGCCTGCGAGTCTTTGGCCCGGATA
66 TTTAGCCCGGATACATTTCCAGCACGAAGCCTGCGAGTCTTTGGCCCGGATA
*
28248848 TATTTCCAGCACAAAGCCTGCGGGACTTTAGCCCGGATACATTTCCAGCACAAAGCCTGCGGGTC
1 TATTTCCAGCACAAAGCCTGCGGGACTTTAGCCCGGATATATTTCCAGCACAAAGCCTGCGGGTC
*
28248913 TTTAGCCCGGATACATTTCCAGCACGAAGCCTGCGGGTCTTTGGCCCGGATA
66 TTTAGCCCGGATACATTTCCAGCACGAAGCCTGCGAGTCTTTGGCCCGGATA
* *
28248965 TATTTCCAGCACAAAGCTTGCGGGTCTTTAGCCCGGATATATTTCCA
1 TATTTCCAGCACAAAGCCTGCGGGACTTTAGCCCGGATATATTTCCA
28249012 TACACATTTC
Statistics
Matches: 157, Mismatches: 7, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
117 157 1.00
ACGTcount: A:0.23, C:0.29, G:0.23, T:0.25
Consensus pattern (117 bp):
TATTTCCAGCACAAAGCCTGCGGGACTTTAGCCCGGATATATTTCCAGCACAAAGCCTGCGGGTC
TTTAGCCCGGATACATTTCCAGCACGAAGCCTGCGAGTCTTTGGCCCGGATA
Found at i:28264883 original size:31 final size:30
Alignment explanation
Indices: 28264848--28264913 Score: 96
Period size: 31 Copynumber: 2.2 Consensus size: 30
28264838 TCCCAGACGT
* *
28264848 GGTCTTACATGTAATCAAATATCGATGCCAA
1 GGTCTTACATGAAATCAAATA-CGACGCCAA
28264879 GGTCTTACATGAAATCAAATACGACGCCAA
1 GGTCTTACATGAAATCAAATACGACGCCAA
*
28264909 CGTCT
1 GGTCT
28264914 CAGACGTGGT
Statistics
Matches: 32, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
30 12 0.38
31 20 0.62
ACGTcount: A:0.35, C:0.23, G:0.17, T:0.26
Consensus pattern (30 bp):
GGTCTTACATGAAATCAAATACGACGCCAA
Found at i:28264962 original size:44 final size:44
Alignment explanation
Indices: 28264879--28265019 Score: 198
Period size: 44 Copynumber: 3.2 Consensus size: 44
28264869 TCGATGCCAA
* * *
28264879 GGTCTTACATG-AAATCA-AA-TACGACGCCAACGTCTCAGACGT
1 GGTCTTACACGTAAATCATAAGT-CGATGCCAACGTCCCAGACGT
*
28264921 GGTCTTACACGTAAATCATAAGTCGATGCCAACATCCCAGACGT
1 GGTCTTACACGTAAATCATAAGTCGATGCCAACGTCCCAGACGT
* *
28264965 GGTCTTACATGTAAATCATAAGTCGATTCCAACGTCCCAGACGT
1 GGTCTTACACGTAAATCATAAGTCGATGCCAACGTCCCAGACGT
28265009 GGTCTTACACG
1 GGTCTTACACG
28265020 ATAACACATA
Statistics
Matches: 88, Mismatches: 8, Indels: 4
0.88 0.08 0.04
Matches are distributed among these distances:
42 10 0.11
43 6 0.07
44 71 0.81
45 1 0.01
ACGTcount: A:0.30, C:0.26, G:0.19, T:0.24
Consensus pattern (44 bp):
GGTCTTACACGTAAATCATAAGTCGATGCCAACGTCCCAGACGT
Found at i:28268412 original size:42 final size:42
Alignment explanation
Indices: 28268361--28268470 Score: 141
Period size: 43 Copynumber: 2.6 Consensus size: 42
28268351 TTTGAGATTA
*
28268361 CATGTAAGACCATATCTGGGATATGACATCGATATGAGA-CTT
1 CATGTAAGACCATATCTGGGATATGACATCGATATGAGATC-C
* * * * *
28268403 CGTGTAAGACCATAGCTAGGCTATTGGCATCGATATGAGATCC
1 CATGTAAGACCATATCTGGGATA-TGACATCGATATGAGATCC
28268446 CATGTAAGACCATATCTGGGATATG
1 CATGTAAGACCATATCTGGGATATG
28268471 GCATTGGTAT
Statistics
Matches: 56, Mismatches: 10, Indels: 4
0.80 0.14 0.06
Matches are distributed among these distances:
42 21 0.38
43 34 0.61
44 1 0.02
ACGTcount: A:0.31, C:0.18, G:0.24, T:0.27
Consensus pattern (42 bp):
CATGTAAGACCATATCTGGGATATGACATCGATATGAGATCC
Found at i:28273155 original size:34 final size:34
Alignment explanation
Indices: 28273084--28273155 Score: 83
Period size: 34 Copynumber: 2.1 Consensus size: 34
28273074 GCATTTCTGT
* * *
28273084 TACTGTTACTGTAATAGGCTAAGGCCTACACTGA
1 TACTATTACTGTAATAGGCTAAGCCCTACACTAA
* *
28273118 TACTATTACTGTAATGGGCTATTGCCCTA-ACTAA
1 TACTATTACTGTAATAGGCTA-AGCCCTACACTAA
28273152 TACT
1 TACT
28273156 GGATTGTCAC
Statistics
Matches: 32, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
34 27 0.84
35 5 0.16
ACGTcount: A:0.29, C:0.21, G:0.17, T:0.33
Consensus pattern (34 bp):
TACTATTACTGTAATAGGCTAAGCCCTACACTAA
Found at i:28278129 original size:100 final size:100
Alignment explanation
Indices: 28278025--28278211 Score: 277
Period size: 100 Copynumber: 1.9 Consensus size: 100
28278015 ATGAAGGTAT
* * * *
28278025 GCACAAATGTGATATTATATTTGAAT-TTGTATATTCAGCCATATAAGTAAATACATATGTAATG
1 GCACAAATGTGATATTAAATTTG-ATCTTGCATATTCAGCCATATAAGTAAACACATATGTAATA
*
28278089 TTAATTTTGATCTTGCATATTCGACAATATAGATAA
65 TTAAATTTGATCTTGCATATTCGACAATATAGATAA
* * *
28278125 GCACATATGTGATATTAAATTTGATCTTGCATATTCAGCCATATAAGTAAGCACATATGTGATAT
1 GCACAAATGTGATATTAAATTTGATCTTGCATATTCAGCCATATAAGTAAACACATATGTAATAT
*
28278190 TAAATTTGATCTTGTATATTCG
66 TAAATTTGATCTTGCATATTCG
28278212 GCCAAATAAG
Statistics
Matches: 77, Mismatches: 9, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
99 2 0.03
100 75 0.97
ACGTcount: A:0.36, C:0.11, G:0.14, T:0.39
Consensus pattern (100 bp):
GCACAAATGTGATATTAAATTTGATCTTGCATATTCAGCCATATAAGTAAACACATATGTAATAT
TAAATTTGATCTTGCATATTCGACAATATAGATAA
Found at i:28278221 original size:50 final size:50
Alignment explanation
Indices: 28277950--28278222 Score: 250
Period size: 50 Copynumber: 5.5 Consensus size: 50
28277940 GCTAAATGAC
* * * * * **
28277950 CTTGTATATTCGGCCACATAGGTATGTACATATGTGATGTTGTATTTGAT
1 CTTGTATATTCGGCCAAATAAGTAAGCACATATGTGATATTAAATTTGAT
* * * * *
28278000 CTTGAATATTAGGCC--ATGAAGGTATGCACAAATGTGATATTATATTTGAAT
1 CTTGTATATTCGGCCAAAT-AA-GTAAGCACATATGTGATATTAAATTTG-AT
* * ** * * *
28278051 -TTGTATATTCAGCCATATAAGTAAATACATATGTAATGTTAATTTTGAT
1 CTTGTATATTCGGCCAAATAAGTAAGCACATATGTGATATTAAATTTGAT
* *
28278100 CTTGCATATTC-GAC-AATATAGATAAGCACATATGTGATATTAAATTTGAT
1 CTTGTATATTCGGCCAAATA-AG-TAAGCACATATGTGATATTAAATTTGAT
* * *
28278150 CTTGCATATTCAGCCATATAAGTAAGCACATATGTGATATTAAATTTGAT
1 CTTGTATATTCGGCCAAATAAGTAAGCACATATGTGATATTAAATTTGAT
28278200 CTTGTATATTCGGCCAAATAAGT
1 CTTGTATATTCGGCCAAATAAGT
28278223 GATGTTGGTA
Statistics
Matches: 182, Mismatches: 31, Indels: 20
0.78 0.13 0.09
Matches are distributed among these distances:
48 5 0.03
49 7 0.04
50 157 0.86
51 8 0.04
52 5 0.03
ACGTcount: A:0.34, C:0.12, G:0.16, T:0.38
Consensus pattern (50 bp):
CTTGTATATTCGGCCAAATAAGTAAGCACATATGTGATATTAAATTTGAT
Found at i:28279272 original size:14 final size:14
Alignment explanation
Indices: 28279253--28279287 Score: 70
Period size: 14 Copynumber: 2.5 Consensus size: 14
28279243 GTATATATAA
28279253 TATGTTTCATAATG
1 TATGTTTCATAATG
28279267 TATGTTTCATAATG
1 TATGTTTCATAATG
28279281 TATGTTT
1 TATGTTT
28279288 AATATTTAAT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.26, C:0.06, G:0.14, T:0.54
Consensus pattern (14 bp):
TATGTTTCATAATG
Found at i:28285697 original size:50 final size:50
Alignment explanation
Indices: 28285559--28285771 Score: 196
Period size: 50 Copynumber: 4.3 Consensus size: 50
28285549 GCTAAATGAC
* * * * * * ** *
28285559 CTTGTATATTCGACCACATAGGTATGTACATATGTGATGTTGTATTGGAT
1 CTTGTATATTCGGCCATATAAGTAAGCACATATGTGATATTAAATTTGAT
** * * * * * *
28285609 CTTAAATATTCAGCCATGA-AGGTATGCACAAATCTGATATTATATTTGAAT
1 CTTGTATATTCGGCCAT-ATAAGTAAGCACATATGTGATATTAAATTTG-AT
*
28285660 -TTGTATATTCGGCCATATAAGTAAGGACATATGTGATATTAAATTTGAT
1 CTTGTATATTCGGCCATATAAGTAAGCACATATGTGATATTAAATTTGAT
* * **
28285709 CTTGCATATTTGGCCATATTGGTAAGCACATATGTGATATTAAATTTGAT
1 CTTGTATATTCGGCCATATAAGTAAGCACATATGTGATATTAAATTTGAT
28285759 CTTGTATATTCGG
1 CTTGTATATTCGG
28285772 TAAAATGAGT
Statistics
Matches: 132, Mismatches: 27, Indels: 8
0.79 0.16 0.05
Matches are distributed among these distances:
49 3 0.02
50 126 0.95
51 3 0.02
ACGTcount: A:0.31, C:0.12, G:0.18, T:0.39
Consensus pattern (50 bp):
CTTGTATATTCGGCCATATAAGTAAGCACATATGTGATATTAAATTTGAT
Found at i:28300477 original size:25 final size:27
Alignment explanation
Indices: 28300420--28300477 Score: 66
Period size: 25 Copynumber: 2.2 Consensus size: 27
28300410 TTTTCTCTTA
*
28300420 AATTTTAATTTTATTCAATTAATTAAT
1 AATTTTAATTTCATTCAATTAATTAAT
** *
28300447 TTTTTTAA-TTCATTGAATT-ATTAAT
1 AATTTTAATTTCATTCAATTAATTAAT
28300472 AATTTT
1 AATTTT
28300478 TATTAAATCT
Statistics
Matches: 25, Mismatches: 6, Indels: 2
0.76 0.18 0.06
Matches are distributed among these distances:
25 10 0.40
26 9 0.36
27 6 0.24
ACGTcount: A:0.36, C:0.03, G:0.02, T:0.59
Consensus pattern (27 bp):
AATTTTAATTTCATTCAATTAATTAAT
Found at i:28300477 original size:26 final size:27
Alignment explanation
Indices: 28300422--28300479 Score: 66
Period size: 26 Copynumber: 2.2 Consensus size: 27
28300412 TTCTCTTAAA
* *
28300422 TTTTAATTTTATTCAATTAATTAATTT
1 TTTTAATTTCATTCAATTAATTAATAT
*
28300449 TTTTAA-TTCATTGAATT-ATTAATAAT
1 TTTTAATTTCATTCAATTAATTAAT-AT
28300475 TTTTA
1 TTTTA
28300480 TTAAATCTTA
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
25 6 0.22
26 15 0.56
27 6 0.22
ACGTcount: A:0.34, C:0.03, G:0.02, T:0.60
Consensus pattern (27 bp):
TTTTAATTTCATTCAATTAATTAATAT
Found at i:28309999 original size:43 final size:43
Alignment explanation
Indices: 28309948--28310117 Score: 200
Period size: 43 Copynumber: 4.0 Consensus size: 43
28309938 TAGAATTCCA
*
28309948 ATATGTGATTTCGTGTAAGACCACGTCTGGGACATTGGCATCG
1 ATATGTGATTTCATGTAAGACCACGTCTGGGACATTGGCATCG
* * * * *
28309991 ATTTGTGATTTACGTGTAAGACCATGTCTGGGACATCGGCGTCG
1 ATATGTGATTT-CATGTAAGACCACGTCTGGGACATTGGCATCG
* * * *
28310035 -TATATGAGTTCATGTAAGACC-CTGTCTAGGACAGTGGCATCG
1 ATATGTGATTTCATGTAAGACCAC-GTCTGGGACATTGGCATCG
* *
28310077 ATATGTGATTACATGTAAGACCACGTCTGGGACGTTGGCAT
1 ATATGTGATTTCATGTAAGACCACGTCTGGGACATTGGCAT
28310118 TGTACGAGCT
Statistics
Matches: 104, Mismatches: 19, Indels: 8
0.79 0.15 0.06
Matches are distributed among these distances:
42 25 0.24
43 49 0.47
44 30 0.29
ACGTcount: A:0.24, C:0.18, G:0.28, T:0.30
Consensus pattern (43 bp):
ATATGTGATTTCATGTAAGACCACGTCTGGGACATTGGCATCG
Found at i:28324816 original size:39 final size:39
Alignment explanation
Indices: 28324762--28324877 Score: 205
Period size: 39 Copynumber: 3.0 Consensus size: 39
28324752 TTCAGTGATG
28324762 TATATCCGGACTTAGGGTCCGCAGGCTATGTGCTGGAAT
1 TATATCCGGACTTAGGGTCCGCAGGCTATGTGCTGGAAT
*
28324801 TATATCCGGACTTAGGATCCGCAGGCTATGTGCTGGAAT
1 TATATCCGGACTTAGGGTCCGCAGGCTATGTGCTGGAAT
* *
28324840 TATATCCGGACTTAAGGTCCGCAGGCTACGTGCTGGAA
1 TATATCCGGACTTAGGGTCCGCAGGCTATGTGCTGGAA
28324878 ATATGTCCTG
Statistics
Matches: 73, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
39 73 1.00
ACGTcount: A:0.22, C:0.22, G:0.29, T:0.27
Consensus pattern (39 bp):
TATATCCGGACTTAGGGTCCGCAGGCTATGTGCTGGAAT
Found at i:28324901 original size:39 final size:38
Alignment explanation
Indices: 28324762--28324925 Score: 179
Period size: 39 Copynumber: 4.2 Consensus size: 38
28324752 TTCAGTGATG
* *
28324762 TATATCCGGACTTAGGGTCCGCAGGCTATGTGCTGGAAT
1 TATATCCGGAC-TAAGGTCCGCAGGCTACGTGCTGGAAT
* *
28324801 TATATCCGGACTTAGGATCCGCAGGCTATGTGCTGGAAT
1 TATATCCGGACTAAGG-TCCGCAGGCTACGTGCTGGAAT
*
28324840 TATATCCGGACTTAAGGTCCGCAGGCTACGTGCTGGAAA
1 TATATCCGGAC-TAAGGTCCGCAGGCTACGTGCTGGAAT
* * * * *
28324879 TATGTCCTGG-CTAAAGTCCCGCAGGCTTCGAGCTGGTAT
1 TATATCC-GGACTAAGGT-CCGCAGGCTACGTGCTGGAAT
28324918 TATA-CCGG
1 TATATCCGG
28324926 GTTTAAATTC
Statistics
Matches: 109, Mismatches: 12, Indels: 10
0.83 0.09 0.08
Matches are distributed among these distances:
37 2 0.02
38 10 0.09
39 91 0.83
40 6 0.06
ACGTcount: A:0.22, C:0.23, G:0.29, T:0.27
Consensus pattern (38 bp):
TATATCCGGACTAAGGTCCGCAGGCTACGTGCTGGAAT
Found at i:28324901 original size:78 final size:78
Alignment explanation
Indices: 28324762--28324905 Score: 202
Period size: 78 Copynumber: 1.8 Consensus size: 78
28324752 TTCAGTGATG
* * * * *
28324762 TATATCCGGACTTAGGGTCCGCAGGCTATGTGCTGGAATTATATCCGGACTTAGGATCCGCAGGC
1 TATATCCGGACTTAAGGTCCGCAGGCTACGTGCTGGAAATATATCCGGACTAAAGATCCGCAGGC
28324827 TATGTGCTGGAAT
66 TATGTGCTGGAAT
*
28324840 TATATCCGGACTTAAGGTCCGCAGGCTACGTGCTGGAAATATGTCCTGG-CTAAAG-TCCCGCAG
1 TATATCCGGACTTAAGGTCCGCAGGCTACGTGCTGGAAATATATCC-GGACTAAAGAT-CCGCAG
28324903 GCT
64 GCT
28324906 TCGAGCTGGT
Statistics
Matches: 58, Mismatches: 6, Indels: 4
0.85 0.09 0.06
Matches are distributed among these distances:
77 1 0.02
78 55 0.95
79 2 0.03
ACGTcount: A:0.22, C:0.23, G:0.28, T:0.26
Consensus pattern (78 bp):
TATATCCGGACTTAAGGTCCGCAGGCTACGTGCTGGAAATATATCCGGACTAAAGATCCGCAGGC
TATGTGCTGGAAT
Found at i:28324914 original size:78 final size:78
Alignment explanation
Indices: 28324762--28324925 Score: 201
Period size: 78 Copynumber: 2.1 Consensus size: 78
28324752 TTCAGTGATG
* * * * *
28324762 TATATCCGGACTTAGGGTCCGCAGGCTATGTGCTGGAATTATATCCGGACTTAGGATCCGCAGGC
1 TATATCCGGACTTAAGGTCCGCAGGCTACGTGCTGGAAATATATCCGGACTAAAGATCCGCAGGC
*
28324827 TATGTGCTGGAAT
66 TATGAGCTGGAAT
*
28324840 TATATCCGGACTTAAGGTCCGCAGGCTACGTGCTGGAAATATGTCCTGG-CTAAAG-TCCCGCAG
1 TATATCCGGACTTAAGGTCCGCAGGCTACGTGCTGGAAATATATCC-GGACTAAAGAT-CCGCAG
*
28324903 GCT-TCGAGCTGGTAT
64 GCTAT-GAGCTGGAAT
28324918 TATA-CCGG
1 TATATCCGG
28324926 GTTTAAATTC
Statistics
Matches: 75, Mismatches: 8, Indels: 7
0.83 0.09 0.08
Matches are distributed among these distances:
77 6 0.08
78 67 0.89
79 2 0.03
ACGTcount: A:0.22, C:0.23, G:0.29, T:0.27
Consensus pattern (78 bp):
TATATCCGGACTTAAGGTCCGCAGGCTACGTGCTGGAAATATATCCGGACTAAAGATCCGCAGGC
TATGAGCTGGAAT
Found at i:28326789 original size:16 final size:17
Alignment explanation
Indices: 28326760--28326791 Score: 57
Period size: 16 Copynumber: 1.9 Consensus size: 17
28326750 AAGGTCACTT
28326760 TCATAATGATCATGAAC
1 TCATAATGATCATGAAC
28326777 TCATAAT-ATCATGAA
1 TCATAATGATCATGAA
28326792 GCCAATGCTT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 8 0.53
17 7 0.47
ACGTcount: A:0.44, C:0.16, G:0.09, T:0.31
Consensus pattern (17 bp):
TCATAATGATCATGAAC
Found at i:28327106 original size:84 final size:84
Alignment explanation
Indices: 28326946--28327107 Score: 193
Period size: 84 Copynumber: 1.9 Consensus size: 84
28326936 CATACCAATA
* ** * * *
28326946 CCATATCCCAGATTTGGTCTTACATGGGATCTCATATCGATGCCAATAGCCCAGCTATGGTTTTA
1 CCATATCCCAGATATGGTCTTACATGAAATCTCATATCGATGCCAATAACCCAGATATGGTCTTA
**
28327011 CACGATTCTCATATCGATG
66 CACGAGACTCATATCGATG
* * *
28327030 CCATGTCCCTGATATGGTCTTACATGAAATCTTATAAT-GATGCC-ATAACCCAGATATGGTCTT
1 CCATATCCCAGATATGGTCTTACATGAAATCTCAT-ATCGATGCCAATAACCCAGATATGGTCTT
28327093 ACACGTAGACTCATA
65 ACACG-AGACTCATA
28327108 ACCCTAATGT
Statistics
Matches: 65, Mismatches: 11, Indels: 4
0.81 0.14 0.05
Matches are distributed among these distances:
83 21 0.32
84 42 0.65
85 2 0.03
ACGTcount: A:0.28, C:0.24, G:0.17, T:0.31
Consensus pattern (84 bp):
CCATATCCCAGATATGGTCTTACATGAAATCTCATATCGATGCCAATAACCCAGATATGGTCTTA
CACGAGACTCATATCGATG
Found at i:28345496 original size:40 final size:39
Alignment explanation
Indices: 28345422--28345646 Score: 299
Period size: 40 Copynumber: 5.6 Consensus size: 39
28345412 AACCCAAGTA
* *
28345422 CCTTCGGGATTTAG-CCGGATATAGCAACTCGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGC-ACTAGCACAAATG
*
28345461 CCTTCGGGTCTTAGCCCGGATATAGTCACTAGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAG-CACTAGCACAAATG
* *
28345501 CCTTCGGGACTTGGCCCGGGTATAGCAACTACTCGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGC-ACTA---GCACAAATG
*
28345544 CCTTCGGGACTTCGCCCGGATATAGTCACTAGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAG-CACTAGCACAAATG
* *
28345584 CCTTCGGGACTTAGCCCGGATATAGGAACTCGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATA-GCACTAGCACAAATG
28345624 CCTTCGGGACTTAGCCCGGATAT
1 CCTTCGGGACTTAGCCCGGATAT
28345647 CGTCCGAATA
Statistics
Matches: 167, Mismatches: 11, Indels: 15
0.87 0.06 0.08
Matches are distributed among these distances:
39 13 0.08
40 115 0.69
41 2 0.01
43 36 0.22
44 1 0.01
ACGTcount: A:0.25, C:0.28, G:0.24, T:0.23
Consensus pattern (39 bp):
CCTTCGGGACTTAGCCCGGATATAGCACTAGCACAAATG
Found at i:28345542 original size:83 final size:80
Alignment explanation
Indices: 28345422--28345646 Score: 353
Period size: 83 Copynumber: 2.8 Consensus size: 80
28345412 AACCCAAGTA
* * *
28345422 CCTTCGGGATTTAG-CCGGATATAGCAACTCGCACAAATGCCTTCGGGTCTTAGCCCGGATATAG
1 CCTTCGGGACTTAGCCCGGATATAGAAACTCGCACAAATGCCTTCGGGACTTAGCCCGGATATAG
28345486 TCACTAGCACAAATG
66 TCACTAGCACAAATG
* * *
28345501 CCTTCGGGACTTGGCCCGGGTATAGCAACTACTCGCACAAATGCCTTCGGGACTTCGCCCGGATA
1 CCTTCGGGACTTAGCCCGGATATAG-AA--ACTCGCACAAATGCCTTCGGGACTTAGCCCGGATA
28345566 TAGTCACTAGCACAAATG
63 TAGTCACTAGCACAAATG
*
28345584 CCTTCGGGACTTAGCCCGGATATAGGAACTCGCACAAATGCCTTCGGGACTTAGCCCGGATAT
1 CCTTCGGGACTTAGCCCGGATATAGAAACTCGCACAAATGCCTTCGGGACTTAGCCCGGATAT
28345647 CGTCCGAATA
Statistics
Matches: 132, Mismatches: 10, Indels: 7
0.89 0.07 0.05
Matches are distributed among these distances:
79 12 0.09
80 44 0.33
81 1 0.01
82 1 0.01
83 74 0.56
ACGTcount: A:0.25, C:0.28, G:0.24, T:0.23
Consensus pattern (80 bp):
CCTTCGGGACTTAGCCCGGATATAGAAACTCGCACAAATGCCTTCGGGACTTAGCCCGGATATAG
TCACTAGCACAAATG
Found at i:28347769 original size:16 final size:16
Alignment explanation
Indices: 28347744--28347774 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
28347734 GCAAATCCCA
*
28347744 AAATGTCGAAAAGTCG
1 AAATGCCGAAAAGTCG
28347760 AAATGCCGAAAAGTC
1 AAATGCCGAAAAGTC
28347775 AAAAGTTTGG
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.45, C:0.16, G:0.23, T:0.16
Consensus pattern (16 bp):
AAATGCCGAAAAGTCG
Found at i:28348037 original size:29 final size:28
Alignment explanation
Indices: 28347995--28348052 Score: 73
Period size: 29 Copynumber: 2.0 Consensus size: 28
28347985 ACATGGCTTG
28347995 GAATTGATTCGGGCC-AGATGGGCCATAT
1 GAATTGATTCGGGCCTAG-TGGGCCATAT
* *
28348023 GAATATGATTTGGGCCTAGTGGGCTATAT
1 GAAT-TGATTCGGGCCTAGTGGGCCATAT
28348052 G
1 G
28348053 CATGTATGTA
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
28 4 0.15
29 20 0.77
30 2 0.08
ACGTcount: A:0.24, C:0.14, G:0.33, T:0.29
Consensus pattern (28 bp):
GAATTGATTCGGGCCTAGTGGGCCATAT
Found at i:28349326 original size:17 final size:18
Alignment explanation
Indices: 28349293--28349326 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
28349283 TTTAAAGAAG
28349293 GGTTTTCAATGAAAACAA
1 GGTTTTCAATGAAAACAA
*
28349311 GGTTTTCGAT-AAAACA
1 GGTTTTCAATGAAAACA
28349327 CTTCAATGTG
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 6 0.40
18 9 0.60
ACGTcount: A:0.41, C:0.12, G:0.18, T:0.29
Consensus pattern (18 bp):
GGTTTTCAATGAAAACAA
Found at i:28354448 original size:47 final size:47
Alignment explanation
Indices: 28354393--28354584 Score: 285
Period size: 47 Copynumber: 4.1 Consensus size: 47
28354383 TTAGGATTTT
* * *
28354393 AATGTGATGAATGTGAACATGCGTATGTGTGACAAGGCCGAATGGCC
1 AATGTGATGAATGTGAACATGCATATATGTGATAAGGCCGAATGGCC
* * * *
28354440 ACTGTGATGAATGTGAACATGCGTATGTGCGATAAGGCCGAATGGCC
1 AATGTGATGAATGTGAACATGCATATATGTGATAAGGCCGAATGGCC
*
28354487 AATGTGATGAATGTGAACATGCATATATGAGATAAGGCCGAATGGCC
1 AATGTGATGAATGTGAACATGCATATATGTGATAAGGCCGAATGGCC
* * *
28354534 AATGTGATGAATGTGAACATGTATATATGTGGTAAGGCCGAATGGCT
1 AATGTGATGAATGTGAACATGCATATATGTGATAAGGCCGAATGGCC
28354581 AATG
1 AATG
28354585 CGAAATGTGT
Statistics
Matches: 134, Mismatches: 11, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
47 134 1.00
ACGTcount: A:0.32, C:0.13, G:0.30, T:0.25
Consensus pattern (47 bp):
AATGTGATGAATGTGAACATGCATATATGTGATAAGGCCGAATGGCC
Found at i:28354694 original size:46 final size:46
Alignment explanation
Indices: 28354558--28354703 Score: 184
Period size: 46 Copynumber: 3.1 Consensus size: 46
28354548 GAACATGTAT
* * *
28354558 ATATGTGGTAAGGCCGAATGGCTAATGCGAAATGTGTATGAGTTAG
1 ATATGTGGTAAAGCCGAATGGCTAATGCGAAATGTGTATGAGATGG
* * *
28354604 ATATGAGATAAAGCCGAATGGCTAATGCGAAACGTGTATGAGATGG
1 ATATGTGGTAAAGCCGAATGGCTAATGCGAAATGTGTATGAGATGG
* * * *
28354650 ATATGTGGTAAAGCCAAATGGCTAATGTGAGATATGTATGAGATGTG
1 ATATGTGGTAAAGCCGAATGGCTAATGCGAAATGTGTATGAGATG-G
28354697 TATATGT
1 -ATATGT
28354704 ATATATATAT
Statistics
Matches: 85, Mismatches: 13, Indels: 2
0.85 0.13 0.02
Matches are distributed among these distances:
46 78 0.92
47 1 0.01
48 6 0.07
ACGTcount: A:0.34, C:0.08, G:0.30, T:0.28
Consensus pattern (46 bp):
ATATGTGGTAAAGCCGAATGGCTAATGCGAAATGTGTATGAGATGG
Found at i:28360032 original size:28 final size:27
Alignment explanation
Indices: 28359975--28360126 Score: 232
Period size: 27 Copynumber: 5.6 Consensus size: 27
28359965 TAAATTGTGC
* *
28359975 AGCACTAAGTGTGCGAATTGAATATGT
1 AGCACTAAGTGTGCGAGTTGACTATGT
28360002 AGCACTAAGTGTGCGAGTTTGACTATGT
1 AGCACTAAGTGTGCGAG-TTGACTATGT
28360030 AGCACTAAGTGTGCGAGTTGACTATGT
1 AGCACTAAGTGTGCGAGTTGACTATGT
*
28360057 AGCACTAAGTGTGCGAGTATGATTATGT
1 AGCACTAAGTGTGCGAGT-TGACTATGT
* *
28360085 AGCACTAAGTGTGCGAGTTGATTATAT
1 AGCACTAAGTGTGCGAGTTGACTATGT
*
28360112 AGCACTGAGTGTGCG
1 AGCACTAAGTGTGCG
28360127 GACTTAATAA
Statistics
Matches: 118, Mismatches: 5, Indels: 4
0.93 0.04 0.03
Matches are distributed among these distances:
27 66 0.56
28 52 0.44
ACGTcount: A:0.28, C:0.13, G:0.29, T:0.30
Consensus pattern (27 bp):
AGCACTAAGTGTGCGAGTTGACTATGT
Found at i:28360039 original size:55 final size:55
Alignment explanation
Indices: 28359975--28360126 Score: 241
Period size: 55 Copynumber: 2.8 Consensus size: 55
28359965 TAAATTGTGC
* *
28359975 AGCACTAAGTGTGCGAATTGAATATGTAGCACTAAGTGTGCGAGTTTGACTATGT
1 AGCACTAAGTGTGCGAGTTGAATATGTAGCACTAAGTGTGCGAGTATGACTATGT
* *
28360030 AGCACTAAGTGTGCGAGTTGACTATGTAGCACTAAGTGTGCGAGTATGATTATGT
1 AGCACTAAGTGTGCGAGTTGAATATGTAGCACTAAGTGTGCGAGTATGACTATGT
* * *
28360085 AGCACTAAGTGTGCGAGTTGATTATATAGCACTGAGTGTGCG
1 AGCACTAAGTGTGCGAGTTGAATATGTAGCACTAAGTGTGCG
28360127 GACTTAATAA
Statistics
Matches: 90, Mismatches: 7, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
55 90 1.00
ACGTcount: A:0.28, C:0.13, G:0.29, T:0.30
Consensus pattern (55 bp):
AGCACTAAGTGTGCGAGTTGAATATGTAGCACTAAGTGTGCGAGTATGACTATGT
Found at i:28376949 original size:40 final size:40
Alignment explanation
Indices: 28376801--28377012 Score: 214
Period size: 40 Copynumber: 5.3 Consensus size: 40
28376791 CATTTGAATG
* * * *
28376801 ATATCCGGGCTAAGTCTCGAAGGCATTTATGCTAGTGATT
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAGTGATT
* * * * *
28376841 TTATCCGGGCTAAGTCCCAAAGGCATTTATGCTAGTGATT
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAGTGATT
* *
28376881 TTATCCGGGCTAAGACCCGAAGGCATTTGTCCGAGTTGA-T
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAG-TGATT
*
28376921 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTG-CT
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAG-TGATT
* * * * ** *
28376961 ATACCCGGGTTAAGACCTGAAGGCAATTGTGCTTGTGGTT
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAGTGATT
28377001 ATATCC-GGCTAA
1 ATATCCGGGCTAA
28377013 ATTCCGAAGA
Statistics
Matches: 150, Mismatches: 19, Indels: 7
0.85 0.11 0.04
Matches are distributed among these distances:
39 7 0.05
40 140 0.93
41 3 0.02
ACGTcount: A:0.24, C:0.20, G:0.26, T:0.29
Consensus pattern (40 bp):
ATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAGTGATT
Found at i:28382547 original size:32 final size:33
Alignment explanation
Indices: 28382499--28382577 Score: 108
Period size: 32 Copynumber: 2.4 Consensus size: 33
28382489 ATTTGCATTT
*
28382499 CTGATACTGAATTGTAATGGGCTAA-GCCCACA
1 CTGATACTGAACTGTAATGGGCTAAGGCCCACA
*
28382531 CTGATACTGTACTGTAATGGGCTAAGGCCCACA
1 CTGATACTGAACTGTAATGGGCTAAGGCCCACA
*
28382564 -TCGATACTGGACTG
1 CT-GATACTGAACTG
28382578 ATACTGAAAT
Statistics
Matches: 42, Mismatches: 3, Indels: 3
0.88 0.06 0.06
Matches are distributed among these distances:
32 24 0.57
33 18 0.43
ACGTcount: A:0.28, C:0.23, G:0.24, T:0.25
Consensus pattern (33 bp):
CTGATACTGAACTGTAATGGGCTAAGGCCCACA
Found at i:28420373 original size:27 final size:27
Alignment explanation
Indices: 28420334--28420394 Score: 72
Period size: 27 Copynumber: 2.3 Consensus size: 27
28420324 TTACTCGTGA
28420334 ATTTTTATAATAT-TAATTTTATTATA-
1 ATTTTTATAATATCTAATTTT-TTATAT
* *
28420360 AGTTTTTATCATATCTGATTTTTTATAT
1 A-TTTTTATAATATCTAATTTTTTATAT
28420388 ATTTTTA
1 ATTTTTA
28420395 AAATTATTTA
Statistics
Matches: 30, Mismatches: 2, Indels: 5
0.81 0.05 0.14
Matches are distributed among these distances:
26 1 0.03
27 22 0.73
28 7 0.23
ACGTcount: A:0.31, C:0.03, G:0.03, T:0.62
Consensus pattern (27 bp):
ATTTTTATAATATCTAATTTTTTATAT
Found at i:28425295 original size:65 final size:65
Alignment explanation
Indices: 28425221--28425351 Score: 262
Period size: 65 Copynumber: 2.0 Consensus size: 65
28425211 AGTCCCATGC
28425221 ATCAGATAATAATAACATGGCATGCAGTAAATAGTAACAGTCAAACATGCATTCAGGTCAACCTT
1 ATCAGATAATAATAACATGGCATGCAGTAAATAGTAACAGTCAAACATGCATTCAGGTCAACCTT
28425286 ATCAGATAATAATAACATGGCATGCAGTAAATAGTAACAGTCAAACATGCATTCAGGTCAACCTT
1 ATCAGATAATAATAACATGGCATGCAGTAAATAGTAACAGTCAAACATGCATTCAGGTCAACCTT
28425351 A
1 A
28425352 ACCCTAGGGG
Statistics
Matches: 66, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
65 66 1.00
ACGTcount: A:0.42, C:0.18, G:0.15, T:0.24
Consensus pattern (65 bp):
ATCAGATAATAATAACATGGCATGCAGTAAATAGTAACAGTCAAACATGCATTCAGGTCAACCTT
Found at i:28427647 original size:68 final size:66
Alignment explanation
Indices: 28427500--28427685 Score: 202
Period size: 68 Copynumber: 2.8 Consensus size: 66
28427490 ATATAGTTCG
* *
28427500 GCTCTCTTGTACACATGGTGAACACTCAGTACCACCCATGTGACCTAGC--CA-ATTTATCTCAT
1 GCTCTCTTGTACACATGGTGTACACTCAGTACCACCCATGTGACCTAGCTACATATATATCTCAT
28427562 A
66 A
* *
28427563 GCTCTCTTGT-CTACATGGTGTACACAT-AGTATCACCCATGTGACCTAGCTACATCATAATGTC
1 GCTCTCTTGTAC-ACATGGTGTACAC-TCAGTACCACCCATGTGACCTAGCTACAT-AT-ATATC
**
28427626 TTGTA
62 TCATA
* * * **
28427631 GCTCTCTTGTACACATGATGTGCACTCAGCACCATACATGTGACCTAGCTACATA
1 GCTCTCTTGTACACATGGTGTACACTCAGTACCACCCATGTGACCTAGCTACATA
28427686 CTATCTGTAT
Statistics
Matches: 102, Mismatches: 12, Indels: 14
0.80 0.09 0.11
Matches are distributed among these distances:
62 1 0.01
63 43 0.42
64 1 0.01
65 2 0.02
67 4 0.04
68 50 0.49
69 1 0.01
ACGTcount: A:0.26, C:0.28, G:0.16, T:0.30
Consensus pattern (66 bp):
GCTCTCTTGTACACATGGTGTACACTCAGTACCACCCATGTGACCTAGCTACATATATATCTCAT
A
Found at i:28443534 original size:21 final size:22
Alignment explanation
Indices: 28443505--28443551 Score: 69
Period size: 21 Copynumber: 2.2 Consensus size: 22
28443495 CAGAAGGAGT
*
28443505 GAGTAGTACTTCACAGCAGGTG
1 GAGTAGTACTCCACAGCAGGTG
*
28443527 GAGT-GTACTCCGCAGCAGGTG
1 GAGTAGTACTCCACAGCAGGTG
28443548 GAGT
1 GAGT
28443552 TTGAGCAGAG
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
21 19 0.83
22 4 0.17
ACGTcount: A:0.23, C:0.19, G:0.36, T:0.21
Consensus pattern (22 bp):
GAGTAGTACTCCACAGCAGGTG
Found at i:28446072 original size:20 final size:20
Alignment explanation
Indices: 28446034--28446072 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
28446024 TTCACCTCGC
* *
28446034 GATTCTGGAAGTAAGTGTAT
1 GATTCTAGAAGCAAGTGTAT
*
28446054 GATTCTAGAAGCAATTGTA
1 GATTCTAGAAGCAAGTGTA
28446073 CGTGTCATTA
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.33, C:0.08, G:0.26, T:0.33
Consensus pattern (20 bp):
GATTCTAGAAGCAAGTGTAT
Found at i:28448034 original size:40 final size:40
Alignment explanation
Indices: 28447949--28448166 Score: 268
Period size: 40 Copynumber: 5.5 Consensus size: 40
28447939 ATGCTGTCCA
* *
28447949 GGCTAAGTCCCGAAGGC--TTGTGCTAAGTGAC-AATATCCG
1 GGCTAAGTCCCGAAGGCATTTGTGC-GAGTTACTAA-ATCCG
* * * *
28447988 GACTAAGAT-CCGAAGGAATTTGTGCGAGATACTAATTCCG
1 GGCTAAG-TCCCGAAGGCATTTGTGCGAGTTACTAAATCCG
28448028 GGCTAAG-CCCGAAGGCATTTGTGCGAGTTACTAAATCCG
1 GGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAATCCG
*
28448067 GGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAATCCG
1 GGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAATCCG
* *
28448107 GGTTAAGTCCCGAAGGCATTTGTGCGAATTACTATAA-CCG
1 GGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTA-AATCCG
*
28448147 GGCTATGTCCCGAAGGCATT
1 GGCTAAGTCCCGAAGGCATT
28448167 CAAACGAGGA
Statistics
Matches: 158, Mismatches: 14, Indels: 13
0.85 0.08 0.07
Matches are distributed among these distances:
39 47 0.30
40 101 0.64
41 10 0.06
ACGTcount: A:0.27, C:0.21, G:0.27, T:0.25
Consensus pattern (40 bp):
GGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAATCCG
Found at i:28448186 original size:80 final size:80
Alignment explanation
Indices: 28448018--28448201 Score: 205
Period size: 80 Copynumber: 2.3 Consensus size: 80
28448008 TGTGCGAGAT
* * * *
28448018 ACTAATTCCGGGCTAAG-CCCGAAGGCATTTGTGCGAGTTACTAAATCCGGGTTAAGTCCCGAAG
1 ACTAAATCCGGGTTAAGTCCCGAAGGCATTTGTGCGAATTACTAAATCCGGGCTAAGTCCCGAAG
**** *
28448082 GCATTTGTGCGAGTT
66 GCATTCAAACGAGTG
*
28448097 ACTAAATCCGGGTTAAGTCCCGAAGGCATTTGTGCGAATTACTATAA-CCGGGCTATGTCCCGAA
1 ACTAAATCCGGGTTAAGTCCCGAAGGCATTTGTGCGAATTACTA-AATCCGGGCTAAGTCCCGAA
28448161 GGCATTCAAACGAG-G
65 GGCATTCAAACGAGTG
* * *
28448176 AGCTATATCC-GGTTAAATTCCGAAGG
1 A-CTAAATCCGGGTTAAGTCCCGAAGG
28448202 TACGTGATTT
Statistics
Matches: 89, Mismatches: 13, Indels: 6
0.82 0.12 0.06
Matches are distributed among these distances:
79 30 0.34
80 57 0.64
81 2 0.02
ACGTcount: A:0.27, C:0.22, G:0.26, T:0.25
Consensus pattern (80 bp):
ACTAAATCCGGGTTAAGTCCCGAAGGCATTTGTGCGAATTACTAAATCCGGGCTAAGTCCCGAAG
GCATTCAAACGAGTG
Found at i:28456002 original size:40 final size:39
Alignment explanation
Indices: 28455913--28456133 Score: 261
Period size: 40 Copynumber: 5.6 Consensus size: 39
28455903 TTGAATGCTG
* * *
28455913 TCCGGGCTAAGTCCCGAAGGC--TTGTGCTAAGTGACAATA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGC-GAGTTACTA-A
* *
28455952 TCCGGACTAAGAT-CCGAAGGCATTTGTGCGAGATACTAA
1 TCCGGGCTAAG-TCCCGAAGGCATTTGTGCGAGTTACTAA
28455991 TTCCGGGCTAAG-CCCGAAGGCATTTGTGCGAGTTACTAA
1 -TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAA
*
28456030 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACT-AA
* *
28456070 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAATTACTATA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTA-A
* * *
28456110 ACTGGGCTATGTCCCGAAGGCATT
1 TCCGGGCTAAGTCCCGAAGGCATT
28456134 CGAACGAGGA
Statistics
Matches: 161, Mismatches: 13, Indels: 15
0.85 0.07 0.08
Matches are distributed among these distances:
38 10 0.06
39 70 0.43
40 75 0.47
41 6 0.04
ACGTcount: A:0.25, C:0.22, G:0.27, T:0.26
Consensus pattern (39 bp):
TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAA
Found at i:28456008 original size:39 final size:40
Alignment explanation
Indices: 28455913--28456133 Score: 235
Period size: 39 Copynumber: 5.6 Consensus size: 40
28455903 TTGAATGCTG
*
28455913 TCCGGGCTAAGTCCCGAAGGC--TTGTGCTA-AGTGAC-AAT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGA-T-ACTAAT
*
28455951 ATCCGGACTAAGAT-CCGAAGGCATTTGTGCGAGATACTAAT
1 -TCCGGGCTAAG-TCCCGAAGGCATTTGTGCGAGATACTAAT
*
28455992 TCCGGGCTAAG-CCCGAAGGCATTTGTGCGAGTTACTAA-
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGATACTAAT
* * *
28456030 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGATACTAAT
*
28456070 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGA-ATTACT-AT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGA-TACTAAT
* * *
28456109 AACTGGGCTATGTCCCGAAGGCATT
1 -TCCGGGCTAAGTCCCGAAGGCATT
28456134 CGAACGAGGA
Statistics
Matches: 161, Mismatches: 11, Indels: 19
0.84 0.06 0.10
Matches are distributed among these distances:
38 10 0.06
39 71 0.44
40 68 0.42
41 11 0.07
42 1 0.01
ACGTcount: A:0.25, C:0.22, G:0.27, T:0.26
Consensus pattern (40 bp):
TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGATACTAAT
Found at i:28456047 original size:78 final size:80
Alignment explanation
Indices: 28455913--28456133 Score: 281
Period size: 78 Copynumber: 2.8 Consensus size: 80
28455903 TTGAATGCTG
* * * *
28455913 TCCGGGCTAAGTCCCGAAGGC--TTGTGCTAAGTGACAATATCCGGACTAAGAT-CCGAAGGCAT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGC-GAGTTACTATATCCGGGCTAAG-TCCCGAAGGCAT
*
28455975 TTGTGCGAGATACTAAT
64 TTGTGCGAGATACTAAA
*
28455992 TCCGGGCTAAG-CCCGAAGGCATTTGTGCGAGTTACTA-ATCCGGGTTAAGTCCCGAAGGCATTT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATATCCGGGCTAAGTCCCGAAGGCATTT
*
28456055 GTGCGAGTTACTAAA
66 GTGCGAGATACTAAA
* * * * *
28456070 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAATTACTATAACTGGGCTATGTCCCGAAGGCATT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATATCCGGGCTAAGTCCCGAAGGCATT
28456134 CGAACGAGGA
Statistics
Matches: 124, Mismatches: 13, Indels: 9
0.85 0.09 0.06
Matches are distributed among these distances:
77 1 0.01
78 54 0.44
79 42 0.34
80 27 0.22
ACGTcount: A:0.25, C:0.22, G:0.27, T:0.26
Consensus pattern (80 bp):
TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATATCCGGGCTAAGTCCCGAAGGCATTT
GTGCGAGATACTAAA
Found at i:28456157 original size:79 final size:79
Alignment explanation
Indices: 28455913--28456168 Score: 204
Period size: 79 Copynumber: 3.3 Consensus size: 79
28455903 TTGAATGCTG
* * * *
28455913 TCCGGGCTAAGTCCCGAAGGC--TTGTGCTAAGTGAC-AATATCCGGACTAAGAT-CCGAAGGCA
1 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAA-TTACTAA-A-CCGGGCTAAG-TCCCGAAGGCA
* ** *
28455974 TTTGTGCGAGAT-ACTAAT
62 TTCGAACGAG-TGACTAAA
* * * * *
28455992 TCCGGGCTAAG-CCCGAAGGCATTTGTGCGAGTTACTAATCCGGGTTAAGTCCCGAAGGCATTTG
1 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAATTACTAAACCGGGCTAAGTCCCGAAGGCATTCG
** *
28456056 TGCGAGTTACTAAA
66 AACGAGTGACTAAA
* *
28456070 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAATTACTATAACTGGGCTATGTCCCGAAGGCATTC
1 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAATTACTA-AACCGGGCTAAGTCCCGAAGGCATTC
*
28456135 GAACGAG-GAGCTATA
65 GAACGAGTGA-CTAAA
* *
28456150 TCC-GGTTAAATTCCGAAGG
1 TCCGGGTTAAGTCCCGAAGG
28456169 TACGTGATTT
Statistics
Matches: 149, Mismatches: 20, Indels: 16
0.81 0.11 0.09
Matches are distributed among these distances:
77 2 0.01
78 51 0.34
79 54 0.36
80 42 0.28
ACGTcount: A:0.26, C:0.21, G:0.27, T:0.25
Consensus pattern (79 bp):
TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAATTACTAAACCGGGCTAAGTCCCGAAGGCATTCG
AACGAGTGACTAAA
Found at i:28457485 original size:10 final size:10
Alignment explanation
Indices: 28457472--28457512 Score: 50
Period size: 10 Copynumber: 4.3 Consensus size: 10
28457462 CGGGTGTTAC
28457472 ATTTTGTTTT
1 ATTTTGTTTT
*
28457482 ATTTTGTTTC
1 ATTTTGTTTT
*
28457492 ATTTTG-ATT
1 ATTTTGTTTT
28457501 -TTTTGTTTT
1 ATTTTGTTTT
28457510 ATT
1 ATT
28457513 GATTAATTTC
Statistics
Matches: 25, Mismatches: 4, Indels: 4
0.76 0.12 0.12
Matches are distributed among these distances:
8 5 0.20
9 3 0.12
10 17 0.68
ACGTcount: A:0.12, C:0.02, G:0.10, T:0.76
Consensus pattern (10 bp):
ATTTTGTTTT
Found at i:28457547 original size:17 final size:18
Alignment explanation
Indices: 28457506--28457547 Score: 52
Period size: 17 Copynumber: 2.4 Consensus size: 18
28457496 TGATTTTTTG
28457506 TTTTATTGATTAATTTCT
1 TTTTATTGATTAATTTCT
*
28457524 TTATATT-ATT-ATTTCAT
1 TTTTATTGATTAATTTC-T
28457541 TTTTATT
1 TTTTATT
28457548 TTTAAATTGA
Statistics
Matches: 21, Mismatches: 2, Indels: 3
0.81 0.08 0.12
Matches are distributed among these distances:
16 5 0.24
17 10 0.48
18 6 0.29
ACGTcount: A:0.24, C:0.05, G:0.02, T:0.69
Consensus pattern (18 bp):
TTTTATTGATTAATTTCT
Found at i:28459244 original size:5 final size:6
Alignment explanation
Indices: 28459222--28459268 Score: 51
Period size: 6 Copynumber: 7.7 Consensus size: 6
28459212 ACTTTTAGAC
* *
28459222 TTTAGT TTTAGT TTTAG- TTTAGT TTTAGAAT TTTATT TTTATT TTTA
1 TTTAGT TTTAGT TTTAGT TTTAGT TTTAG--T TTTAGT TTTAGT TTTA
28459269 TTTATTAACA
Statistics
Matches: 37, Mismatches: 1, Indels: 6
0.84 0.02 0.14
Matches are distributed among these distances:
5 5 0.14
6 27 0.73
8 5 0.14
ACGTcount: A:0.21, C:0.00, G:0.11, T:0.68
Consensus pattern (6 bp):
TTTAGT
Found at i:28459244 original size:11 final size:12
Alignment explanation
Indices: 28459222--28459268 Score: 51
Period size: 11 Copynumber: 3.8 Consensus size: 12
28459212 ACTTTTAGAC
28459222 TTTAGTTTTAGT
1 TTTAGTTTTAGT
28459234 TTTAG-TTTAGT
1 TTTAGTTTTAGT
*
28459245 TTTAGAATTTTATT
1 TTTAG--TTTTAGT
*
28459259 TTTATTTTTA
1 TTTAGTTTTA
28459269 TTTATTAACA
Statistics
Matches: 30, Mismatches: 2, Indels: 6
0.79 0.05 0.16
Matches are distributed among these distances:
11 11 0.37
12 10 0.33
14 9 0.30
ACGTcount: A:0.21, C:0.00, G:0.11, T:0.68
Consensus pattern (12 bp):
TTTAGTTTTAGT
Found at i:28459250 original size:30 final size:30
Alignment explanation
Indices: 28459214--28459272 Score: 75
Period size: 31 Copynumber: 2.0 Consensus size: 30
28459204 TTGTTTAGAC
28459214 TTTTAG-ACTTTAGTTTTAGTTTTAGTTTAG
1 TTTTAGAACTTTAGTTTTAGTTTTA-TTTAG
* * *
28459244 TTTTAGAATTTTATTTTTATTTTTATTTA
1 TTTTAGAACTTTAGTTTTAGTTTTATTTA
28459273 TTAACATTAT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
30 10 0.40
31 15 0.60
ACGTcount: A:0.22, C:0.02, G:0.10, T:0.66
Consensus pattern (30 bp):
TTTTAGAACTTTAGTTTTAGTTTTATTTAG
Found at i:28461134 original size:26 final size:26
Alignment explanation
Indices: 28461098--28461149 Score: 104
Period size: 26 Copynumber: 2.0 Consensus size: 26
28461088 GAATCCAAAG
28461098 TAAGGATCAAGGAAGATTTTGAAGAA
1 TAAGGATCAAGGAAGATTTTGAAGAA
28461124 TAAGGATCAAGGAAGATTTTGAAGAA
1 TAAGGATCAAGGAAGATTTTGAAGAA
28461150 CAATTATGAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.46, C:0.04, G:0.27, T:0.23
Consensus pattern (26 bp):
TAAGGATCAAGGAAGATTTTGAAGAA
Found at i:28462523 original size:27 final size:27
Alignment explanation
Indices: 28462481--28462580 Score: 103
Period size: 27 Copynumber: 3.7 Consensus size: 27
28462471 TTGTTCTTTG
*
28462481 CCACAAAGACAATTCTTTCATAATGCT
1 CCACAAAGACATTTCTTTCATAATGCT
* * ** *
28462508 CCGCAAAGGCATTTCTTTTGTGATG-T
1 CCACAAAGACATTTCTTTCATAATGCT
*
28462534 GCCACAAAGACATTTCTTTCATAATGCA
1 -CCACAAAGACATTTCTTTCATAATGCT
* *
28462562 CCAAAAAGGCATTTCTTTC
1 CCACAAAGACATTTCTTTC
28462581 TTGACATGTT
Statistics
Matches: 57, Mismatches: 14, Indels: 4
0.76 0.19 0.05
Matches are distributed among these distances:
26 1 0.02
27 56 0.98
ACGTcount: A:0.31, C:0.24, G:0.13, T:0.32
Consensus pattern (27 bp):
CCACAAAGACATTTCTTTCATAATGCT
Found at i:28467486 original size:84 final size:84
Alignment explanation
Indices: 28467388--28467565 Score: 284
Period size: 84 Copynumber: 2.1 Consensus size: 84
28467378 ATAGAAATGG
* *
28467388 AAATGAAAATTTGCAATCCTATATGGATTACTTAAAACTGATGGGAAGAATAAGTTTATATTTTT
1 AAATGAAAATTTGCAATCCTATATAGATTACTTAAAACAGATGGGAAGAATAAGTTTATATTTTT
* *
28467453 GGACTATTTTGAAGCTTGA
66 GGACTAATTTGAAGCCTGA
* * *
28467472 AAATGAAAATTTGCAATCTTATATAGATTACTTAAAACAGATTGGAAGAATAAGTTTATGTTTTT
1 AAATGAAAATTTGCAATCCTATATAGATTACTTAAAACAGATGGGAAGAATAAGTTTATATTTTT
*
28467537 GGACTAATTTGAAGCCTGG
66 GGACTAATTTGAAGCCTGA
28467556 AAATGAAAAT
1 AAATGAAAAT
28467566 AAACTATTCG
Statistics
Matches: 86, Mismatches: 8, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
84 86 1.00
ACGTcount: A:0.39, C:0.08, G:0.17, T:0.35
Consensus pattern (84 bp):
AAATGAAAATTTGCAATCCTATATAGATTACTTAAAACAGATGGGAAGAATAAGTTTATATTTTT
GGACTAATTTGAAGCCTGA
Found at i:28470072 original size:50 final size:50
Alignment explanation
Indices: 28469944--28470184 Score: 268
Period size: 50 Copynumber: 4.8 Consensus size: 50
28469934 GATAATAACA
* ** * * * **
28469944 TGCCAAAGCCATGTCCCAGACATGGTCTTACATGGGATGTTTCCTGTATG
1 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGG
* * * * ** * *
28469994 -GCCAATGCCATATTCCAGATATGGTCTTACATGGGAGTTCTCATATTGG
1 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGG
* * * **
28470043 TGCCCATGCCATGTCCCAAACATGGTCTTACGGGGGACCTCTCATCTCGG
1 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGG
* *
28470093 TGCCAACGCCATGTCCCAAACATGGTCTTACATGGGACCTCTTATCTCGG
1 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGG
28470143 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCT
1 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCT
28470185 TTACCCAAAT
Statistics
Matches: 162, Mismatches: 28, Indels: 2
0.84 0.15 0.01
Matches are distributed among these distances:
49 38 0.23
50 124 0.77
ACGTcount: A:0.22, C:0.29, G:0.22, T:0.27
Consensus pattern (50 bp):
TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGG
Found at i:28471291 original size:12 final size:12
Alignment explanation
Indices: 28471276--28471302 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
28471266 GAACGAAATT
28471276 TTCAGGAAATCA
1 TTCAGGAAATCA
28471288 TTCAGGAAATCA
1 TTCAGGAAATCA
28471300 TTC
1 TTC
28471303 TGTGAAATTG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.37, C:0.19, G:0.15, T:0.30
Consensus pattern (12 bp):
TTCAGGAAATCA
Found at i:28488820 original size:38 final size:38
Alignment explanation
Indices: 28488750--28488875 Score: 186
Period size: 37 Copynumber: 3.3 Consensus size: 38
28488740 GGACTAAGAT
*
28488750 CCGAAGGCATTTGTGCGAG-TACTAATTCCGGGTAAGC
1 CCGAAGGCATTTGTGCGAGTTACTAAATCCGGGTAAGC
28488787 CCGAAGGCATTTGTGCGAGTTACTAAATCCGGGTAAGTC
1 CCGAAGGCATTTGTGCGAGTTACTAAATCCGGGTAAG-C
* *
28488826 CCGAAGGCATTTGTGC-AGTTACTAAA-CCGGGCTATGT
1 CCGAAGGCATTTGTGCGAGTTACTAAATCCGGG-TAAGC
28488863 CCGAAGGCATTTG
1 CCGAAGGCATTTG
28488876 AACGAGTAGC
Statistics
Matches: 83, Mismatches: 3, Indels: 6
0.90 0.03 0.07
Matches are distributed among these distances:
37 37 0.45
38 29 0.35
39 17 0.20
ACGTcount: A:0.25, C:0.21, G:0.29, T:0.25
Consensus pattern (38 bp):
CCGAAGGCATTTGTGCGAGTTACTAAATCCGGGTAAGC
Found at i:28488882 original size:76 final size:76
Alignment explanation
Indices: 28488750--28488908 Score: 189
Period size: 76 Copynumber: 2.1 Consensus size: 76
28488740 GGACTAAGAT
* **
28488750 CCGAAGGCATTTGTGCGAGTACTAATTCCGGGTAAGCCCGAAGGCATTTGTGCGAGTTA-CTAAA
1 CCGAAGGCATTTGTGCGAGTACTAATACCGGGTAAGCCCGAAGGCATTTGAACGAG-TAGCTAAA
*
28488814 TCCGGGTAAGTC
65 TCCGGGTAAATC
* * *
28488826 CCGAAGGCATTTGTGC-AGTTACTAA-ACCGGGCTATGTCCGAAGGCATTTGAACGAGTAGCTAT
1 CCGAAGGCATTTGTGCGAG-TACTAATACCGGG-TAAGCCCGAAGGCATTTGAACGAGTAGCTAA
* *
28488889 ATCCGGTTAAATT
64 ATCCGGGTAAATC
28488902 CCGAAGG
1 CCGAAGG
28488909 TACGTGATTT
Statistics
Matches: 71, Mismatches: 9, Indels: 6
0.83 0.10 0.07
Matches are distributed among these distances:
75 9 0.13
76 62 0.87
ACGTcount: A:0.26, C:0.21, G:0.28, T:0.25
Consensus pattern (76 bp):
CCGAAGGCATTTGTGCGAGTACTAATACCGGGTAAGCCCGAAGGCATTTGAACGAGTAGCTAAAT
CCGGGTAAATC
Found at i:28496729 original size:79 final size:80
Alignment explanation
Indices: 28496593--28496777 Score: 209
Period size: 79 Copynumber: 2.3 Consensus size: 80
28496583 TTGAATGATG
* *
28496593 TCCGGGCTAAGTCCCGAAGGCTTTGTGCTAAGTGACCATATCCGGACTAAGATCCGAAGGCATTT
1 TCCGGGCTAAGTCCCGAAGGCTTTGTGCTAAGTGACCAAATCCGGACTAAGATCCGAAGGCAATT
28496658 GTGCGAGATACTA-A
66 GTGCGAGATACTATA
* * * *
28496672 TTCCGGGCTAAG-CCCGAAGGCATTTGTG-TGAGTTACTAAATCCGG-GTCAAG-TCCCGAAGGC
1 -TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACCAAATCCGGACT-AAGAT-CCGAAGGC
*
28496733 AATTGTGCGAGTTACTATA
62 AATTGTGCGAGATACTATA
* *
28496752 ACCGGGCTATGTCCCGAAGGCCTTTG
1 TCCGGGCTAAGTCCCGAAGG-CTTTG
28496778 AACGAGTAGC
Statistics
Matches: 90, Mismatches: 9, Indels: 12
0.81 0.08 0.11
Matches are distributed among these distances:
78 2 0.02
79 57 0.63
80 30 0.33
81 1 0.01
ACGTcount: A:0.24, C:0.23, G:0.28, T:0.25
Consensus pattern (80 bp):
TCCGGGCTAAGTCCCGAAGGCTTTGTGCTAAGTGACCAAATCCGGACTAAGATCCGAAGGCAATT
GTGCGAGATACTATA
Found at i:28496784 original size:40 final size:40
Alignment explanation
Indices: 28496593--28496777 Score: 200
Period size: 40 Copynumber: 4.7 Consensus size: 40
28496583 TTGAATGATG
* * * *
28496593 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACCATA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGC-GAGTTACTAAA
* * *
28496633 TCCGGACTAAGAT-CCGAAGGCATTTGTGCGAGATACTAAT
1 TCCGGGCTAAG-TCCCGAAGGCATTTGTGCGAGTTACTAAA
*
28496673 TCCGGGCTAAG-CCCGAAGGCATTTGTGTGAGTTACTAAA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
*
28496712 TCCGGG-TCAAGTCCCGAAGGCAATTGTGCGAGTTACTATAA
1 TCCGGGCT-AAGTCCCGAAGGCATTTGTGCGAGTTACTA-AA
* *
28496753 -CCGGGCTATGTCCCGAAGGCCTTTG
1 TCCGGGCTAAGTCCCGAAGGCATTTG
28496778 AACGAGTAGC
Statistics
Matches: 122, Mismatches: 16, Indels: 14
0.80 0.11 0.09
Matches are distributed among these distances:
38 1 0.01
39 33 0.27
40 77 0.63
41 11 0.09
ACGTcount: A:0.24, C:0.23, G:0.28, T:0.25
Consensus pattern (40 bp):
TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
Found at i:28496808 original size:79 final size:79
Alignment explanation
Indices: 28496645--28496810 Score: 176
Period size: 79 Copynumber: 2.1 Consensus size: 79
28496635 CGGACTAAGA
* * ***
28496645 TCCGAAGGCATTTGTGCGAGATACTAATTCCGGGCTAAGCCCGAAGGCATTTGTGTGAGTTACTA
1 TCCGAAGGCAATTGTGCGAGATACTAATACCGGGCTAAGCCCGAAGGCATTTGAACGAGTTACTA
*
28496710 AATCCGGGTCAAGT
66 AATCCGGGTCAAAT
* * * *
28496724 CCCGAAGGCAATTGTGCGAGTTACT-ATAACCGGGCTATGTCCCGAAGGCCTTTGAACGAG-TAG
1 TCCGAAGGCAATTGTGCGAGATACTAAT-ACCGGGCTAAG-CCCGAAGGCATTTGAACGAGTTA-
* *
28496787 CTATATCC-GGTTAAAT
63 CTAAATCCGGGTCAAAT
28496803 TCCGAAGG
1 TCCGAAGG
28496811 TACGTGATTT
Statistics
Matches: 71, Mismatches: 13, Indels: 6
0.79 0.14 0.07
Matches are distributed among these distances:
78 2 0.03
79 46 0.65
80 23 0.32
ACGTcount: A:0.26, C:0.22, G:0.27, T:0.25
Consensus pattern (79 bp):
TCCGAAGGCAATTGTGCGAGATACTAATACCGGGCTAAGCCCGAAGGCATTTGAACGAGTTACTA
AATCCGGGTCAAAT
Done.