Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01004583.1 Kokia drynarioides strain JFW-HI SEQ_118072, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 26473
ACGTcount: A:0.32, C:0.19, G:0.18, T:0.32
Found at i:819 original size:429 final size:429
Alignment explanation
Indices: 20--823 Score: 1234
Period size: 429 Copynumber: 1.9 Consensus size: 429
10 GGTGGTGGTG
* * * * ** *
20 GTATGGCTGCTGGGGGTGGTTTTAAGTTTGGGATTAGAGGTGGAATAAGAGGAGGATTTGGTGGA
1 GTATGGCTGCTAGGGGTGGTTTTAAGTTTGGGATTAGAGGCGGAATAAAAGCAGGAGCTAGTGGA
** * *
85 AATAGTGCTAGAAGTGGTGGCACTAATGTTGGTGGTGGGGCAGGAGGCCATGTCGAAGGTGTTGG
66 AATAGTGCTAGAAGTGGTGAAACTAATGTTGGTGGAGGGGCAGGAGGCCATGTCGAAAGTGTTGG
* * *
150 TAGTGGTGCAACTAGTACAAGTAGTAGTCTTAGCGGAGCAAAGAGTAGTGAGGACAAAGCTAGTG
131 TAGTGGTGCAACTAGTACAAGTAGCAGTCTTAGCGGAGCAAAGAGTAGTGAAGACAAAACTAGTG
* *
215 ATACTAGTAAGAGTGAGGCTAAAGCTGGTTTTGAAGGTAAAGTAGGAGGGAAAGGAAAGGTTGGT
196 ATACTAGTAAAAGTGAGGCAAAAGCTGGTTTTGAAGGTAAAGTAGGAGGGAAAGGAAAGGTTGGT
* * * * *
280 GGAAATAGTGGTGGAAGTGGTAGCTCTAGTATTTATGGTAAGGTAGGAGGGCAAGGTGGAGGTGT
261 GGAAATAGTGATGGAAGTGGTAGCACTAGTATTTATAGTAAGGTAGGAGGACAAAGTGGAGGTGT
* * * *
345 TGGTAGTGGTAGTACTGATGCAAGTGGTAGTCATAGCAATGAAAAAGATAGTGGAATTGGAGGTG
326 TGGCAGTGATAGTACTCATGCAAGTGGTACTCATAGCAATGAAAAAGATAGTGGAATTGGAGGTG
410 CAGGTGGCGGTGGTGGTGCAAGTGTAGGTGGTAGTGGCA
391 CAGGTGGCGGTGGTGGTGCAAGTGTAGGTGGTAGTGGCA
* *
449 GTATGGCTGCTAGGGGTGGTTTTAAGTTTGGGTTTAGAGGCGGAATAAAAGCAGGGGCTAGTGGA
1 GTATGGCTGCTAGGGGTGGTTTTAAGTTTGGGATTAGAGGCGGAATAAAAGCAGGAGCTAGTGGA
* * * *
514 AATGGTGGTGGAAGTGGTGAAACTAATGTTGGTGGAGGGGCAGGAGGCCATGTTGAAAGTGTTGG
66 AATAGTGCTAGAAGTGGTGAAACTAATGTTGGTGGAGGGGCAGGAGGCCATGTCGAAAGTGTTGG
* *
579 TAGTGGTGCAACTAGTGCAAGTGGCAGTCTTAGCGGAGCAAAGAGTAGTGATAGA-AAAACTAGT
131 TAGTGGTGCAACTAGTACAAGTAGCAGTCTTAGCGGAGCAAAGAGTAGTGA-AGACAAAACTAGT
* *
643 GATACTAGTAAAAGTGAGGGAAAAGCTGGTTTTGAAGGTAAAGTAGGA-GGACAAGGAGAGGTTG
195 GATACTAGTAAAAGTGAGGCAAAAGCTGGTTTTGAAGGTAAAGTAGGAGGGA-AAGGAAAGGTTG
* *
707 GTGGAAATAGTGATGGAAGTGGTAGCACTAGTGTTTCTAGTAAGGTAGGAGGACAAAGTGGAGGT
259 GTGGAAATAGTGATGGAAGTGGTAGCACTAGTATTTATAGTAAGGTAGGAGGACAAAGTGGAGGT
*
772 GTTGGCAGTGATAGTACTCATGCAAGTGGTACTCATAGCAGTGAAAAAGATA
324 GTTGGCAGTGATAGTACTCATGCAAGTGGTACTCATAGCAATGAAAAAGATA
824 ATGATGGAAA
Statistics
Matches: 335, Mismatches: 38, Indels: 4
0.89 0.10 0.01
Matches are distributed among these distances:
428 3 0.01
429 330 0.99
430 2 0.01
ACGTcount: A:0.29, C:0.08, G:0.39, T:0.25
Consensus pattern (429 bp):
GTATGGCTGCTAGGGGTGGTTTTAAGTTTGGGATTAGAGGCGGAATAAAAGCAGGAGCTAGTGGA
AATAGTGCTAGAAGTGGTGAAACTAATGTTGGTGGAGGGGCAGGAGGCCATGTCGAAAGTGTTGG
TAGTGGTGCAACTAGTACAAGTAGCAGTCTTAGCGGAGCAAAGAGTAGTGAAGACAAAACTAGTG
ATACTAGTAAAAGTGAGGCAAAAGCTGGTTTTGAAGGTAAAGTAGGAGGGAAAGGAAAGGTTGGT
GGAAATAGTGATGGAAGTGGTAGCACTAGTATTTATAGTAAGGTAGGAGGACAAAGTGGAGGTGT
TGGCAGTGATAGTACTCATGCAAGTGGTACTCATAGCAATGAAAAAGATAGTGGAATTGGAGGTG
CAGGTGGCGGTGGTGGTGCAAGTGTAGGTGGTAGTGGCA
Found at i:1340 original size:474 final size:473
Alignment explanation
Indices: 449--2320 Score: 2274
Period size: 486 Copynumber: 4.0 Consensus size: 473
439 GGTAGTGGCA
* * * *
449 GTATGGCTGCTAGGGGTGGTTTTAAGTTTGGGTTTAGAGGCGGAATAAAAGCAGGGGCTAGTGGA
1 GTATGGCTGCTGGGGGTGGTTTTAAGTTTGGGTTTAAAGGCGGAATAAGAGCAGGGGCTGGTGGA
* ** *
514 AATGGTGGTGGAAGTGGTGAAACTAATGTTGGTGGAGGGGCAGGAGGCCATGTTGAAAGTGTTGG
66 AATAGTGGTGGAAGTGGTGAAACTAATGTTGGTGGAGGGGCAGGAGGCCATGCCGAAGGTGTTGG
* * * *
579 TAGTGGTGCAACTAGTGCAAGTGGCAGTCTTAGCGGAGCAAAGAGTAGTGATAGAAAAACTAGTG
131 TAGTGGTGCAACTAGTACAAGTGGTAGTCTTAGCGGAGCAAAGAGTAGTGATGGCAAAACTAGTG
** * * *
644 ATACTAGTAAAAGTGAGGGAAAAGCTGGTTTTGAAGGTAAAGTAGGAGGACAAGGAGAGGTTGGT
196 ATACTAGTAAAAGTGAGGCTAAAGATAGTTTTGAAGGTAAAGTAGGAGGACAAGGAGAAGTTGGT
* * * *
709 GGAAATAGTGATGGAAGTGGTAGCACTAGTGTTTCTAGTAAGGTAGGA-GGACAAAGTGGAGGTG
261 GGAAATAGTGGTGGAAGTGGTAGCACTAGTGTTGCTGGTAAGGTAGGAGGGA-AAGGTGGAGGTG
* * * *
773 TTGGCAGTGATAGTACTCATGCAAGTGGTACTCATAGCAGTGAAAAAGATAATGATGGAAAAACT
325 TTGGCAGTGGTAGTACTGATGCAAGTGGTACTCATAACGGTGAAAAAGATAATGATGGAAAAACT
* * * *
838 AGTGCTACTAGTAAGGGTGAAACTAAAGATGGATTTAAAGGTACAGTAAAAGAGAAAGGAGGTGA
390 AGTGCTACTAGTAAGGGTGAAGCTAAAGATGGATTTAAAGGTAAAGTAGAAGGGAAA-GAGGTGA
*
903 TGGTGGCGGTGGCGGTAGTG
454 TGGTGGAGGTGGCGGTAGTG
* * *
923 GTATGGCTGTTGGGGGTGGTTTTAAGTTTGGGTTTAAAGGTGGAATAAGAGCAGGGGTTGGTGGA
1 GTATGGCTGCTGGGGGTGGTTTTAAGTTTGGGTTTAAAGGCGGAATAAGAGCAGGGGCTGGTGGA
*
988 AATAGTGGTGGAAGTGGTGAAACTAATGTTGGTGGAGGGGTAGGAGGCCATGCCGAAGGTGTTGG
66 AATAGTGGTGGAAGTGGTGAAACTAATGTTGGTGGAGGGGCAGGAGGCCATGCCGAAGGTGTTGG
* *
1053 TAATGGTGCAACTAGTACAAGTGGTAGTCTTAGCGGAGCAAAGAGTAGTGATGGCAAAGCTAGTG
131 TAGTGGTGCAACTAGTACAAGTGGTAGTCTTAGCGGAGCAAAGAGTAGTGATGGCAAAACTAGTG
* ** * * * *
1118 ATACTAGCAAAAGTGATACTAAAGATGGTTTTGATGGTAAAGTAGGAGGGCAAGGACAAGTTGGT
196 ATACTAGTAAAAGTGAGGCTAAAGATAGTTTTGAAGGTAAAGTAGGAGGACAAGGAGAAGTTGGT
* *
1183 GGAAATAGTGGTGGAAGTGGTAGCAGTAGTGTAGCTGGTAAGGTAGGAGGGAAAGGTGGAGGTGT
261 GGAAATAGTGGTGGAAGTGGTAGCACTAGTGTTGCTGGTAAGGTAGGAGGGAAAGGTGGAGGTGT
* * *
1248 TGGCAGTAGTAGTACTGATGCAAGTGGTACTCATAATGGTGAAAAAGATAATTATGGAAAAACTA
326 TGGCAGTGGTAGTACTGATGCAAGTGGTACTCATAACGGTGAAAAAGATAATGATGGAAAAACTA
*
1313 GTGTTACTAGTAAGGGTGAAGCTAAAGATGGATTTAAAGGTAAAGTAGAAGGGCAAAGAGGTGGC
391 GTGCTACTAGTAAGGGTGAAGCTAAAGATGGATTTAAAGGTAAAGTAGAAGGG-AAAGAGGT-G-
*
1378 AGTGGAGGAGGAAAAGGTGGTGGCGGTAGTG
453 A-T---GGTGG---A---GGTGGCGGTAGTG
* * * *
1409 GTATGGCTGCTGAGGGTGGTTTTAAGTTTGGGTTTAAAGGAGGAATAAGAGTAAGGGCTGGTGGA
1 GTATGGCTGCTGGGGGTGGTTTTAAGTTTGGGTTTAAAGGCGGAATAAGAGCAGGGGCTGGTGGA
* *
1474 AATAGTGGTGGAAGTGGTCG-AACTAATGTTGGTGGAGGGGCAGAAGGCCATGTCGAAGGTGTTG
66 AATAGTGGTGGAAGTGGT-GAAACTAATGTTGGTGGAGGGGCAGGAGGCCATGCCGAAGGTGTTG
* * * *
1538 CTAGTGGTGCAACTAGTACAAATGGTAGTCTTAGCGGAGCAAAGAGTAGTGTTGGCAAAGA-TCG
130 GTAGTGGTGCAACTAGTACAAGTGGTAGTCTTAGCGGAGCAAAGAGTAGTGATGGCAAA-ACTAG
* * * * *
1602 TGATACTAGTAAGAGTGATGCTAAAGATAGTTTTGAAGGTCAAGTAAGAGGACAAGGAGAGGTTG
194 TGATACTAGTAAAAGTGAGGCTAAAGATAGTTTTGAAGGTAAAGTAGGAGGACAAGGAGAAGTTG
* *
1667 GTGGAAATAGTGGTGGAAGTGGTAGCACTAGTATTGCTGGTAAGGTCGGAGGGAAAGGTGGAGGT
259 GTGGAAATAGTGGTGGAAGTGGTAGCACTAGTGTTGCTGGTAAGGTAGGAGGGAAAGGTGGAGGT
* * * * * * *
1732 GTTGGAAGTGGTAGTACTGATGCAAGTGCTTCTCATAGCGATGAAAAAGATAGTGACGGAAAAAC
324 GTTGGCAGTGGTAGTACTGATGCAAGTGGTACTCATAACGGTGAAAAAGATAATGATGGAAAAAC
* * * *
1797 TAGTGCTTCTAGTAAGGGTGAAGCTAAAGATGTG-TTTGAAGGTAAAGTAGGAGGGCAA-A---G
389 TAGTGCTACTAGTAAGGGTGAAGCTAAAGATG-GATTTAAAGGTAAAGTAGAAGGGAAAGAGGTG
1857 A-GGTGGAGGT----G--GTG
453 ATGGTGGAGGTGGCGGTAGTG
* * * * * * ***
1871 GTATAGCTGGTGGGGGTGGTTTTAAGTTTGGGTTTAGAGGCGGAATAGGATCTGGCTTTGGTGGA
1 GTATGGCTGCTGGGGGTGGTTTTAAGTTTGGGTTTAAAGGCGGAATAAGAGCAGGGGCTGGTGGA
* * * ** * *
1936 AATAATGGAGGAAGTGTTGGCACTAATGTTGGTGGAGGGGTTA-GAGGCCATACCGAAGGTGTTG
66 AATAGTGGTGGAAGTGGTGAAACTAATGTTGGTGGAGGGG-CAGGAGGCCATGCCGAAGGTGTTG
* * * * * *
2000 GTAGTGGTGCAACTAGTACAAGTGGTAGTCATAACAGAGTAAAGAGCAGTGATGGCAAAACTAAT
130 GTAGTGGTGCAACTAGTACAAGTGGTAGTCTTAGCGGAGCAAAGAGTAGTGATGGCAAAACTAGT
* * * * *
2065 GATATTAGTAAGAGTGAGGCTAAA-ACAAGATTTGAAGGTAAAGTAGGAGGAAAAGGAG-AG--G
195 GATACTAGTAAAAGTGAGGCTAAAGA-TAGTTTTGAAGGTAAAGTAGGAGGACAAGGAGAAGTTG
* * * * *
2126 TTGGAAATAGTGGTGGAAGTGGTAGCATTAATGTTGCAGGTAAGGTAGGAGGGCAAGGTGGAGGT
259 GTGGAAATAGTGGTGGAAGTGGTAGCACTAGTGTTGCTGGTAAGGTAGGAGGGAAAGGTGGAGGT
** * * * * *
2191 GTTGGTGGTGGTAGTACTGATGCTAGTGATAC-CAATAATGGTGAAAAAGATAGTGATGGAAAAG
324 GTTGGCAGTGGTAGTACTGATGCAAGTGGTACTC-ATAACGGTGAAAAAGATAATGATGGAAAAA
* * * * * * * *
2255 CAAGTGCTACTAGTAAGGGTAAAGCTAATGATGGGTTTAAGGGTAAAATAGGAGGGCAAGGAGGT
388 CTAGTGCTACTAGTAAGGGTGAAGCTAAAGATGGATTTAAAGGTAAAGTAGAAGGG-AAAGAGGT
2320 G
452 G
2321 TAGGTGGTGG
Statistics
Matches: 1212, Mismatches: 158, Indels: 66
0.84 0.11 0.05
Matches are distributed among these distances:
458 2 0.00
459 158 0.13
460 1 0.00
461 5 0.00
462 209 0.17
463 1 0.00
464 2 0.00
468 3 0.00
471 1 0.00
474 402 0.33
475 7 0.01
476 1 0.00
477 1 0.00
479 1 0.00
480 5 0.00
484 1 0.00
485 2 0.00
486 408 0.34
487 2 0.00
ACGTcount: A:0.31, C:0.08, G:0.37, T:0.24
Consensus pattern (473 bp):
GTATGGCTGCTGGGGGTGGTTTTAAGTTTGGGTTTAAAGGCGGAATAAGAGCAGGGGCTGGTGGA
AATAGTGGTGGAAGTGGTGAAACTAATGTTGGTGGAGGGGCAGGAGGCCATGCCGAAGGTGTTGG
TAGTGGTGCAACTAGTACAAGTGGTAGTCTTAGCGGAGCAAAGAGTAGTGATGGCAAAACTAGTG
ATACTAGTAAAAGTGAGGCTAAAGATAGTTTTGAAGGTAAAGTAGGAGGACAAGGAGAAGTTGGT
GGAAATAGTGGTGGAAGTGGTAGCACTAGTGTTGCTGGTAAGGTAGGAGGGAAAGGTGGAGGTGT
TGGCAGTGGTAGTACTGATGCAAGTGGTACTCATAACGGTGAAAAAGATAATGATGGAAAAACTA
GTGCTACTAGTAAGGGTGAAGCTAAAGATGGATTTAAAGGTAAAGTAGAAGGGAAAGAGGTGATG
GTGGAGGTGGCGGTAGTG
Found at i:2468 original size:24 final size:24
Alignment explanation
Indices: 2441--2505 Score: 87
Period size: 24 Copynumber: 2.7 Consensus size: 24
2431 AAATTTGAGA
2441 CATCTCAT-AGCAATGAAACTAAAT
1 CATCTCATAAG-AATGAAACTAAAT
*
2465 CATCTCATAAGAGTGAAACTAAAT
1 CATCTCATAAGAATGAAACTAAAT
* *
2489 CATCTCGTAAGAGTGAA
1 CATCTCATAAGAATGAA
2506 CACAAAGCTA
Statistics
Matches: 38, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
24 36 0.95
25 2 0.05
ACGTcount: A:0.43, C:0.18, G:0.14, T:0.25
Consensus pattern (24 bp):
CATCTCATAAGAATGAAACTAAAT
Found at i:2711 original size:6 final size:6
Alignment explanation
Indices: 2702--2836 Score: 101
Period size: 6 Copynumber: 22.5 Consensus size: 6
2692 AGTAAATATG
* * * * *
2702 AAGCTG AAGCTA AAGCTA AGGCTA AAGC-A GAAGATA AAGCTA AGGCTG
1 AAGCTA AAGCTA AAGCTA AAGCTA AAGCTA -AAGCTA AAGCTA AAGCTA
* * ** * **
2750 AAGCTA AAGCTA AAGTTG AAGCCG AAGCTA AAGCTA AAGCGA AAGGAA
1 AAGCTA AAGCTA AAGCTA AAGCTA AAGCTA AAGCTA AAGCTA AAGCTA
* * * * *
2798 AAACTG AAGCTG AAGCTA AAGCTA AAGATG AAGCTA AAG
1 AAGCTA AAGCTA AAGCTA AAGCTA AAGCTA AAGCTA AAG
2837 GAAAAGTTGA
Statistics
Matches: 99, Mismatches: 28, Indels: 4
0.76 0.21 0.03
Matches are distributed among these distances:
5 1 0.01
6 97 0.98
7 1 0.01
ACGTcount: A:0.47, C:0.14, G:0.25, T:0.14
Consensus pattern (6 bp):
AAGCTA
Found at i:2726 original size:36 final size:34
Alignment explanation
Indices: 2677--2824 Score: 117
Period size: 36 Copynumber: 4.3 Consensus size: 34
2667 TAGTGATGGA
**
2677 AAAGCTAGTGCTAATAGTAAATATGAAGCTGAAGCT
1 AAAGCTAAAGCTAA-AG-AAATATGAAGCTGAAGCT
* * *
2713 AAAGCTAAGGCTAAAGCAGAAGATAAAGCT-AAGGCT
1 AAAGCTAAAGCTAAAG-A-AATATGAAGCTGAA-GCT
* *
2749 GAAGCTAAAGCTAAAG---T-TGAAGCCGAAGCT
1 AAAGCTAAAGCTAAAGAAATATGAAGCTGAAGCT
* *
2779 AAAGCTAAAGCGAAAGGAAAAACTGAAGCTGAAGCT
1 AAAGCTAAAGCTAAA-GAAATA-TGAAGCTGAAGCT
2815 AAAGCTAAAG
1 AAAGCTAAAG
2825 ATGAAGCTAA
Statistics
Matches: 89, Mismatches: 14, Indels: 18
0.74 0.12 0.15
Matches are distributed among these distances:
30 21 0.24
31 3 0.03
35 5 0.06
36 60 0.67
ACGTcount: A:0.46, C:0.14, G:0.24, T:0.16
Consensus pattern (34 bp):
AAAGCTAAAGCTAAAGAAATATGAAGCTGAAGCT
Found at i:2729 original size:24 final size:24
Alignment explanation
Indices: 2702--2836 Score: 112
Period size: 24 Copynumber: 5.6 Consensus size: 24
2692 AGTAAATATG
2702 AAGCTGAAGCTAAAGCTAAGGCTA
1 AAGCTGAAGCTAAAGCTAAGGCTA
* * *
2726 AAGCAGAAGATAAAGCTAAGGCTG
1 AAGCTGAAGCTAAAGCTAAGGCTA
* * **
2750 AAGCTAAAGCTAAAGTTGAA-GCCG
1 AAGCTGAAGCTAAAGCT-AAGGCTA
* * *
2774 AAGCTAAAGCTAAAGCGAAAGG-AA
1 AAGCTGAAGCTAAAGC-TAAGGCTA
* * *
2798 AAACTGAAGCTGAAGCTAAAGCTA
1 AAGCTGAAGCTAAAGCTAAGGCTA
*
2822 AAGATGAAGCTAAAG
1 AAGCTGAAGCTAAAG
2837 GAAAAGTTGA
Statistics
Matches: 86, Mismatches: 21, Indels: 8
0.75 0.18 0.07
Matches are distributed among these distances:
23 3 0.03
24 80 0.93
25 3 0.03
ACGTcount: A:0.47, C:0.14, G:0.25, T:0.14
Consensus pattern (24 bp):
AAGCTGAAGCTAAAGCTAAGGCTA
Found at i:2842 original size:18 final size:18
Alignment explanation
Indices: 2808--2848 Score: 55
Period size: 18 Copynumber: 2.3 Consensus size: 18
2798 AAACTGAAGC
*
2808 TGAAGCTAAAGCTAAAGA
1 TGAAGCTAAAGCAAAAGA
* *
2826 TGAAGCTAAAGGAAAAGT
1 TGAAGCTAAAGCAAAAGA
2844 TGAAG
1 TGAAG
2849 ATAGAGCTAA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.49, C:0.07, G:0.27, T:0.17
Consensus pattern (18 bp):
TGAAGCTAAAGCAAAAGA
Found at i:2842 original size:24 final size:24
Alignment explanation
Indices: 2815--2861 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 24
2805 AGCTGAAGCT
2815 AAAGCTAAAGAT-GAAGCTAAAGGA
1 AAAGCTAAAGATAG-AGCTAAAGGA
* *
2839 AAAGTTGAAGATAGAGCTAAAGG
1 AAAGCTAAAGATAGAGCTAAAGG
2862 TGGAATAGAA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
24 19 0.95
25 1 0.05
ACGTcount: A:0.51, C:0.06, G:0.28, T:0.15
Consensus pattern (24 bp):
AAAGCTAAAGATAGAGCTAAAGGA
Found at i:3171 original size:24 final size:24
Alignment explanation
Indices: 2992--3174 Score: 235
Period size: 24 Copynumber: 7.6 Consensus size: 24
2982 ATTTAGCACT
2992 TCTCAT-AGTAGTGAAACTAAATCA
1 TCTCATAAG-AGTGAAACTAAATCA
* *
3016 TTTCATAAGAGTGAAACTAGATCA
1 TCTCATAAGAGTGAAACTAAATCA
* *
3040 TCTCATAAAAGTGAAAGTAAATCA
1 TCTCATAAGAGTGAAACTAAATCA
*
3064 TCTCATATAG-GCGAAACTAAATCA
1 TCTCATA-AGAGTGAAACTAAATCA
* *
3088 TCTCATATGGGTGAAACTAAATCA
1 TCTCATAAGAGTGAAACTAAATCA
* *
3112 TCTCATATGAGTGAAAGTAAATCA
1 TCTCATAAGAGTGAAACTAAATCA
* *
3136 TCTCATATGAGTGAAAGTAAATCA
1 TCTCATAAGAGTGAAACTAAATCA
3160 TCTCATAAGAGTGAA
1 TCTCATAAGAGTGAA
3175 CACAAAGCTA
Statistics
Matches: 142, Mismatches: 14, Indels: 6
0.88 0.09 0.04
Matches are distributed among these distances:
23 1 0.01
24 138 0.97
25 3 0.02
ACGTcount: A:0.42, C:0.15, G:0.15, T:0.28
Consensus pattern (24 bp):
TCTCATAAGAGTGAAACTAAATCA
Found at i:3549 original size:24 final size:24
Alignment explanation
Indices: 3529--3582 Score: 81
Period size: 24 Copynumber: 2.2 Consensus size: 24
3519 TTTTCATAGC
3529 AATGAAACTAAATCATCTCATAAG
1 AATGAAACTAAATCATCTCATAAG
* *
3553 AGTGAAACTAAATCATCTCGTAAG
1 AATGAAACTAAATCATCTCATAAG
*
3577 AGTGAA
1 AATGAA
3583 CACAAAGCTA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.46, C:0.15, G:0.15, T:0.24
Consensus pattern (24 bp):
AATGAAACTAAATCATCTCATAAG
Found at i:3805 original size:18 final size:18
Alignment explanation
Indices: 3778--4030 Score: 159
Period size: 18 Copynumber: 14.7 Consensus size: 18
3768 TAGTAAAGAT
*
3778 GAAGTTAAAGCTGAAGCA
1 GAAGCTAAAGCTGAAGCA
*
3796 GAAGCAAAAGCT--A--A
1 GAAGCTAAAGCTGAAGCA
* *
3810 G--GCTGAAGCAGAAGCTA
1 GAAGCTAAAGCTGAAGC-A
*
3827 -AAGCTAAGGCTGAAGCA
1 GAAGCTAAAGCTGAAGCA
* *
3844 GAAGCTAAAGCTAAAGCT
1 GAAGCTAAAGCTGAAGCA
*
3862 GAAGCTAAAGCCGAAGCTA
1 GAAGCTAAAGCTGAAGC-A
*
3881 -AAGCTAAAGCAGAAGCTA
1 GAAGCTAAAGCTGAAGC-A
*
3899 -AAGCTAAAGATGAAGCTA
1 GAAGCTAAAGCTGAAGC-A
*
3917 -AAGCTAAAGCTGAAGTA
1 GAAGCTAAAGCTGAAGCA
*
3934 GAAGCTAAAGCTAAAG-A
1 GAAGCTAAAGCTGAAGCA
3951 TGAAGCTAAAGCT-----A
1 -GAAGCTAAAGCTGAAGCA
3965 -AAGCTAAAG-TAGAAGCCA
1 GAAGCTAAAGCT-GAAG-CA
*
3983 -AAGCTAAAGATGAAGCTA
1 GAAGCTAAAGCTGAAGC-A
* *
4001 -AAGCTGAAGCTGAAGCT
1 GAAGCTAAAGCTGAAGCA
4018 GAAGCTAAAGCTG
1 GAAGCTAAAGCTG
4031 GAATAGGGGG
Statistics
Matches: 190, Mismatches: 24, Indels: 42
0.74 0.09 0.16
Matches are distributed among these distances:
11 1 0.01
12 15 0.08
14 4 0.02
16 1 0.01
17 5 0.03
18 163 0.86
19 1 0.01
ACGTcount: A:0.45, C:0.15, G:0.25, T:0.14
Consensus pattern (18 bp):
GAAGCTAAAGCTGAAGCA
Found at i:3842 original size:42 final size:42
Alignment explanation
Indices: 3771--4029 Score: 313
Period size: 42 Copynumber: 6.0 Consensus size: 42
3761 GTGCTACTAG
* * * * *
3771 TAAAGATGAAGTTAAAGCTGAAGCAGAAGCAAAAGCTAAGGC
1 TAAAGATGAAGCTAAAGCTAAAGCTGAAGCAGAAGCTAAAGC
* *
3813 TGAAGCA-GAAGCTAAAGCTAAGGCTGAAGCAGAAGCTAAAGC
1 TAAAG-ATGAAGCTAAAGCTAAAGCTGAAGCAGAAGCTAAAGC
* *
3855 TAAAGCTGAAGCTAAAGCCGAAGCTAAAGCTAAAGCAGAAGCTAAAGC
1 TAAAGATGAAGCT--A----AAGCTAAAGCTGAAGCAGAAGCTAAAGC
*
3903 TAAAGATGAAGCTAAAGCTAAAGCTGAAGTAGAAGCTAAAGC
1 TAAAGATGAAGCTAAAGCTAAAGCTGAAGCAGAAGCTAAAGC
* * *
3945 TAAAGATGAAGCTAAAGCTAAAGCTAAAGTAGAAGCCAAAGC
1 TAAAGATGAAGCTAAAGCTAAAGCTGAAGCAGAAGCTAAAGC
* *
3987 TAAAGATGAAGCTAAAGCTGAAGCTGAAGCTGAAGCTAAAGC
1 TAAAGATGAAGCTAAAGCTAAAGCTGAAGCAGAAGCTAAAGC
4029 T
1 T
4030 GGAATAGGGG
Statistics
Matches: 188, Mismatches: 21, Indels: 16
0.84 0.09 0.07
Matches are distributed among these distances:
42 147 0.78
43 1 0.01
44 1 0.01
46 1 0.01
48 38 0.20
ACGTcount: A:0.46, C:0.15, G:0.25, T:0.15
Consensus pattern (42 bp):
TAAAGATGAAGCTAAAGCTAAAGCTGAAGCAGAAGCTAAAGC
Found at i:4029 original size:24 final size:24
Alignment explanation
Indices: 3783--4030 Score: 247
Period size: 24 Copynumber: 10.3 Consensus size: 24
3773 AAGATGAAGT
*
3783 TAAAGCTGAAGC-AGAAGCAAAAGC
1 TAAAGCTGAAGCTA-AAGCTAAAGC
*
3807 TAAGGCTGAAGC-AGAAGCTAAAGC
1 TAAAGCTGAAGCTA-AAGCTAAAGC
*
3831 TAAGGCTGAAGC-AGAAGCTAAAGC
1 TAAAGCTGAAGCTA-AAGCTAAAGC
**
3855 TAAAGCTGAAGCTAAAGCCGAAGC
1 TAAAGCTGAAGCTAAAGCTAAAGC
*
3879 TAAAGCTAAAGC-AGAAGCTAAAGC
1 TAAAGCTGAAGCTA-AAGCTAAAGC
*
3903 TAAAGATGAAGCTAAAGCTAAAGC
1 TAAAGCTGAAGCTAAAGCTAAAGC
* *
3927 TGAAG-TAGAAGCTAAAGCTAAAGA
1 TAAAGCT-GAAGCTAAAGCTAAAGC
* *
3951 TGAAGCTAAAGCTAAAGCTAAAG-
1 TAAAGCTGAAGCTAAAGCTAAAGC
** * *
3974 TAGAAGCCAAAGCTAAAGATGAAGC
1 TA-AAGCTGAAGCTAAAGCTAAAGC
* *
3999 TAAAGCTGAAGCTGAAGCTGAAGC
1 TAAAGCTGAAGCTAAAGCTAAAGC
4023 TAAAGCTG
1 TAAAGCTG
4031 GAATAGGGGG
Statistics
Matches: 196, Mismatches: 21, Indels: 14
0.85 0.09 0.06
Matches are distributed among these distances:
23 3 0.02
24 188 0.96
25 5 0.03
ACGTcount: A:0.46, C:0.15, G:0.25, T:0.14
Consensus pattern (24 bp):
TAAAGCTGAAGCTAAAGCTAAAGC
Found at i:4136 original size:39 final size:33
Alignment explanation
Indices: 4093--4202 Score: 157
Period size: 33 Copynumber: 3.2 Consensus size: 33
4083 TAATGCTGCA
4093 GGTGGTGGTGGTGGTCACATGCATTTTGCTGTTGGCGGT
1 GGTGGTGGTGGTGGTCACATGCATTTTG--G-T---GGT
*
4132 GGTGGTGGTGGTGGTCACATTCATTTTGGTGGT
1 GGTGGTGGTGGTGGTCACATGCATTTTGGTGGT
4165 GGTGGTGGTGGTGGTCACATGCATTTTGGTGGT
1 GGTGGTGGTGGTGGTCACATGCATTTTGGTGGT
4198 GGTGG
1 GGTGG
4203 ATTTAAATTT
Statistics
Matches: 69, Mismatches: 2, Indels: 6
0.90 0.03 0.08
Matches are distributed among these distances:
33 40 0.58
36 1 0.01
37 1 0.01
39 27 0.39
ACGTcount: A:0.08, C:0.10, G:0.45, T:0.36
Consensus pattern (33 bp):
GGTGGTGGTGGTGGTCACATGCATTTTGGTGGT
Found at i:12128 original size:18 final size:18
Alignment explanation
Indices: 12089--12142 Score: 63
Period size: 18 Copynumber: 3.0 Consensus size: 18
12079 TCAACCTCAT
* * *
12089 CTTTTCCTTCAGCTTTAG
1 CTTTACCTTCAGCTTCAC
12107 CTTTACCTTCAGCTTCAC
1 CTTTACCTTCAGCTTCAC
* *
12125 CTTTAGCTCCAGCTTCAC
1 CTTTACCTTCAGCTTCAC
12143 TAAACCCTCC
Statistics
Matches: 31, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 31 1.00
ACGTcount: A:0.15, C:0.35, G:0.09, T:0.41
Consensus pattern (18 bp):
CTTTACCTTCAGCTTCAC
Found at i:12265 original size:6 final size:6
Alignment explanation
Indices: 12256--12307 Score: 50
Period size: 6 Copynumber: 8.7 Consensus size: 6
12246 TCCGGCTTGT
* * * * * *
12256 GCTTCA GCTTCA GCTTTA GCTTTA CCTTCA TCTTTA GTTTTA GCTTTA
1 GCTTTA GCTTTA GCTTTA GCTTTA GCTTTA GCTTTA GCTTTA GCTTTA
12304 GCTT
1 GCTT
12308 CACTAAACCC
Statistics
Matches: 38, Mismatches: 8, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
6 38 1.00
ACGTcount: A:0.15, C:0.23, G:0.13, T:0.48
Consensus pattern (6 bp):
GCTTTA
Found at i:12277 original size:18 final size:18
Alignment explanation
Indices: 12256--12307 Score: 59
Period size: 18 Copynumber: 2.9 Consensus size: 18
12246 TCCGGCTTGT
*
12256 GCTTCAGCTTCAGCTTTA
1 GCTTTAGCTTCAGCTTTA
* *
12274 GCTTTACCTTCATCTTTA
1 GCTTTAGCTTCAGCTTTA
* *
12292 GTTTTAGCTTTAGCTT
1 GCTTTAGCTTCAGCTT
12308 CACTAAACCC
Statistics
Matches: 27, Mismatches: 7, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
18 27 1.00
ACGTcount: A:0.15, C:0.23, G:0.13, T:0.48
Consensus pattern (18 bp):
GCTTTAGCTTCAGCTTTA
Found at i:12284 original size:24 final size:24
Alignment explanation
Indices: 12257--12309 Score: 70
Period size: 24 Copynumber: 2.2 Consensus size: 24
12247 CCGGCTTGTG
12257 CTTCAGCTTCAGCTTTAGCTTTAC
1 CTTCAGCTTCAGCTTTAGCTTTAC
* * * *
12281 CTTCATCTTTAGTTTTAGCTTTAG
1 CTTCAGCTTCAGCTTTAGCTTTAC
12305 CTTCA
1 CTTCA
12310 CTAAACCCTC
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.17, C:0.25, G:0.11, T:0.47
Consensus pattern (24 bp):
CTTCAGCTTCAGCTTTAGCTTTAC
Found at i:12430 original size:6 final size:6
Alignment explanation
Indices: 12421--12612 Score: 159
Period size: 6 Copynumber: 32.0 Consensus size: 6
12411 TTCGACTTTT
** * ** * * * *
12421 GCTTCA GCTTTT GCGTCA GCTTCA GCTTTT CCTTCA TCTTTA GCTTTA
1 GCTTCA GCTTCA GCTTCA GCTTCA GCTTCA GCTTCA GCTTCA GCTTCA
* * * * ** *
12469 GCTTTA CCTTCA GCTTCA GCTTTA CCTTCA GCTTCA GCTTTT GCTTGA
1 GCTTCA GCTTCA GCTTCA GCTTCA GCTTCA GCTTCA GCTTCA GCTTCA
* * * ** *
12517 GCTTCA TCTTCA GCTTTA GCTTCA TCTTCA GCTTTG GCTTCA GCATCA
1 GCTTCA GCTTCA GCTTCA GCTTCA GCTTCA GCTTCA GCTTCA GCTTCA
* * *
12565 GCTTCA GCTTCA GCTTCA GCTTTA GCTTTA GCTTTA GCTTCA GCTTCA
1 GCTTCA GCTTCA GCTTCA GCTTCA GCTTCA GCTTCA GCTTCA GCTTCA
12613 TCTTTACCAC
Statistics
Matches: 146, Mismatches: 40, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
6 146 1.00
ACGTcount: A:0.15, C:0.28, G:0.15, T:0.42
Consensus pattern (6 bp):
GCTTCA
Found at i:12485 original size:42 final size:42
Alignment explanation
Indices: 12421--12620 Score: 229
Period size: 42 Copynumber: 4.8 Consensus size: 42
12411 TTCGACTTTT
* * * * * *
12421 GCTTCAGCTTTTGCGTCAGCTTCAGCTTTTCCTTCATCTTTA
1 GCTTTAGCTTTAGCTTCAGCTTCAGCTTTACCTTCAGCTTCA
*
12463 GCTTTAGCTTTACCTTCAGCTTCAGCTTTACCTTCAGCTTCA
1 GCTTTAGCTTTAGCTTCAGCTTCAGCTTTACCTTCAGCTTCA
* * * * *
12505 GCTTTTGCTTGAGCTTCATCTTCAGCTTTAGCTTCATCTTCA
1 GCTTTAGCTTTAGCTTCAGCTTCAGCTTTACCTTCAGCTTCA
* * * * * *
12547 GCTTTGGCTTCAGCATCAGCTTCAGCTTCAGCTTCAGCTTTA
1 GCTTTAGCTTTAGCTTCAGCTTCAGCTTTACCTTCAGCTTCA
*
12589 GCTTTAGCTTTAGCTTCAGCTTCATCTTTACC
1 GCTTTAGCTTTAGCTTCAGCTTCAGCTTTACC
12621 ACTTGTATCT
Statistics
Matches: 132, Mismatches: 26, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
42 132 1.00
ACGTcount: A:0.15, C:0.28, G:0.14, T:0.42
Consensus pattern (42 bp):
GCTTTAGCTTTAGCTTCAGCTTCAGCTTTACCTTCAGCTTCA
Found at i:12883 original size:198 final size:201
Alignment explanation
Indices: 12613--13068 Score: 564
Period size: 198 Copynumber: 2.3 Consensus size: 201
12603 TTCAGCTTCA
* * * * * * * *
12613 TCTTTACCACTTGTATCTATATTACCACTACTAGCTCTTCCACCTTTTCTTTTTACCCTACCAGA
1 TCTTTACCACTTGCATCTATATTACCACTACCATCTCCTCTACCTTGTCCTTTTACCCCACCAGA
* * *
12678 ATCATTAGAGCTATCACTTTCACC-ATTATTTCCATCAACCTTTCTTTGTCCTCCAAATTTTCC-
66 ATCATTAGAGCTATCACTTCCACCTA-CATTTCCATCAACCTTTCCTTGTCCTCCAAATTTTCCT
* * * * *
12741 TT-C-AGCTTTAGCTTCACCTTTACGA-TTAGCATCTATGTTATCACTGCCATCTCCTCCACCTT
130 TTACTAGCTTTAGATTCACCTTTACCACTT-GCATCTATATTACCACTACCATCTCCTCCACCTT
12803 GTCCTTTT
194 GTCCTTTT
* * *
12811 TCTTTACCACTTGCATCTGTATTACCATTACCATCTCCTCTACCTTGTCCTTTTACCCCACTAGA
1 TCTTTACCACTTGCATCTATATTACCACTACCATCTCCTCTACCTTGTCCTTTTACCCCACCAGA
* *
12876 ATCATTAGAGTTGTCACTTCCACCTACATTTCCATCAACCTTTCCTTGTCCTCCAAATTTTCCTT
66 ATCATTAGAGCTATCACTTCCACCTACATTTCCATCAACCTTTCCTTGTCCTCCAAATTTTCCTT
* * *
12941 TAGCTTTAGCTTTAGATTCCCCTTTACCACTTGCATCTGTATTACCACTATCATCTCCTCCACCT
131 TA-C--TAGCTTTAGATTCACCTTTACCACTTGCATCTATATTACCACTACCATCTCCTCCACCT
13006 TGTCCTTTT
193 TGTCCTTTT
** * *
13015 TCTTTACC-CTTTGCATCTATATTACTGCTATCATCTCCTTTACCTTGTCCTTTT
1 TCTTTACCAC-TTGCATCTATATTACCACTACCATCTCCTCTACCTTGTCCTTTT
13069 TCTTTACCAC
Statistics
Matches: 219, Mismatches: 30, Indels: 12
0.84 0.11 0.05
Matches are distributed among these distances:
198 110 0.50
199 3 0.01
201 1 0.00
203 1 0.00
204 102 0.47
205 2 0.01
ACGTcount: A:0.20, C:0.32, G:0.07, T:0.42
Consensus pattern (201 bp):
TCTTTACCACTTGCATCTATATTACCACTACCATCTCCTCTACCTTGTCCTTTTACCCCACCAGA
ATCATTAGAGCTATCACTTCCACCTACATTTCCATCAACCTTTCCTTGTCCTCCAAATTTTCCTT
TACTAGCTTTAGATTCACCTTTACCACTTGCATCTATATTACCACTACCATCTCCTCCACCTTGT
CCTTTT
Found at i:13046 original size:54 final size:54
Alignment explanation
Indices: 12962--13122 Score: 252
Period size: 54 Copynumber: 3.0 Consensus size: 54
12952 TTAGATTCCC
12962 CTTTACCACTTGCATCTGTATTACCACTATCATCTCCTCCACCTTGTCCTTTTT
1 CTTTACCACTTGCATCTGTATTACCACTATCATCTCCTCCACCTTGTCCTTTTT
* ** **
13016 CTTTACC-CTTTGCATCTATATTACTGCTATCATCTCCTTTACCTTGTCCTTTTT
1 CTTTACCAC-TTGCATCTGTATTACCACTATCATCTCCTCCACCTTGTCCTTTTT
*
13070 CTTTACCACTTGCATCTGTATTACCACTACCATCTCCTCCACCTTGTCCTTTT
1 CTTTACCACTTGCATCTGTATTACCACTATCATCTCCTCCACCTTGTCCTTTT
13123 ACCCCTCCAG
Statistics
Matches: 94, Mismatches: 11, Indels: 4
0.86 0.10 0.04
Matches are distributed among these distances:
53 1 0.01
54 92 0.98
55 1 0.01
ACGTcount: A:0.16, C:0.34, G:0.06, T:0.44
Consensus pattern (54 bp):
CTTTACCACTTGCATCTGTATTACCACTATCATCTCCTCCACCTTGTCCTTTTT
Found at i:13286 original size:252 final size:252
Alignment explanation
Indices: 12769--13506 Score: 1077
Period size: 252 Copynumber: 2.9 Consensus size: 252
12759 TTTACGATTA
* * ** *
12769 GCATCTATGTTATCACTGCCATCTCCTCCACCTTGTCCTTTTTCTTTACCACTTGCATCTGTATT
1 GCATCTATATTACCACCACCATCTCCTCTACCTTGTCCTTTTTCTTTACCACTTGCATCTGTATT
* * * * *
12834 ACCATTACCATCTCCTCTACCTTGTCCTTTTACCCCACTAGAATCATTAGAGTTGTCACTTCCAC
66 ACCACTACCATCTCCTCCACCTTGTCCTTTTACCCCACCAGAATCACTAGAGCTGTCACTTCCAC
* * * *
12899 C-TACATTTCCATCAACCTTTCCTTGTCCTCCAAATTTTCCTTTAGCTTTAGCTTTAGATTCCCC
131 CAT-TATTTCTATCGACCTTTCCTTGTCCTCCAAATTTTCCTTCAGCTTTAGCTTT--A----CC
* * *
12963 TTTACCACTTGCATCTGTATTACCACTATCATCTCCTCCACCTTGTCCTTTTTCTTTACCCTTT
189 TTTACCACTAGCATCTATATTACCACTACCATCTCCTCCACCTTGTCCTTTTTCTTTACCCTTT
** * * *
13027 GCATCTATATTACTGCTATCATCTCCTTTACCTTGTCCTTTTTCTTTACCACTTGCATCTGTATT
1 GCATCTATATTACCACCACCATCTCCTCTACCTTGTCCTTTTTCTTTACCACTTGCATCTGTATT
* * *
13092 ACCACTACCATCTCCTCCACCTTGTCCTTTTACCCCTCCAGAATCACTATAGCTATCACTTCCAC
66 ACCACTACCATCTCCTCCACCTTGTCCTTTTACCCCACCAGAATCACTAGAGCTGTCACTTCCAC
* *
13157 CATTATTTCTATCGACCTTTTCTTGTCTTCCAAATTTTCCTTCAGCTTTAGCTTTACCTTTACCA
131 CATTATTTCTATCGACCTTTCCTTGTCCTCCAAATTTTCCTTCAGCTTTAGCTTTACCTTTACCA
13222 CTAGCATCTATATTACCACTACCATCTCCTCCACCTTGTCCTTTTTCTTTACCAC-TT
196 CTAGCATCTATATTACCACTACCATCTCCTCCACCTTGTCCTTTTTCTTTACC-CTTT
* *
13279 GCATCTATTTTACCACCACCATCTCCTCTACCTTGTCCTTTTCCTTTACCACTTGCATCTGTATT
1 GCATCTATATTACCACCACCATCTCCTCTACCTTGTCCTTTTTCTTTACCACTTGCATCTGTATT
13344 ACCACTACCATCTCCTCCACCTTGTCCTTTTACCCCACCAGAATCACTAGAGCTGTCACTTCCAC
66 ACCACTACCATCTCCTCCACCTTGTCCTTTTACCCCACCAGAATCACTAGAGCTGTCACTTCCAC
* *
13409 CAATATTTCCT-TCGACCTTTCCTTGTCCTCCAAATTTTCCTTCAGCTTTAGCTTCACCTTTACC
131 CATTATTT-CTATCGACCTTTCCTTGTCCTCCAAATTTTCCTTCAGCTTTAGCTTTACCTTTACC
* *
13473 ATTAACATCTATATTACCACTACCATCTCCTCCA
195 ACTAGCATCTATATTACCACTACCATCTCCTCCA
13507 GCTCCTCCAC
Statistics
Matches: 436, Mismatches: 41, Indels: 12
0.89 0.08 0.02
Matches are distributed among these distances:
252 270 0.62
253 3 0.01
256 1 0.00
258 161 0.37
259 1 0.00
ACGTcount: A:0.20, C:0.35, G:0.06, T:0.40
Consensus pattern (252 bp):
GCATCTATATTACCACCACCATCTCCTCTACCTTGTCCTTTTTCTTTACCACTTGCATCTGTATT
ACCACTACCATCTCCTCCACCTTGTCCTTTTACCCCACCAGAATCACTAGAGCTGTCACTTCCAC
CATTATTTCTATCGACCTTTCCTTGTCCTCCAAATTTTCCTTCAGCTTTAGCTTTACCTTTACCA
CTAGCATCTATATTACCACTACCATCTCCTCCACCTTGTCCTTTTTCTTTACCCTTT
Found at i:13300 original size:54 final size:54
Alignment explanation
Indices: 13208--13374 Score: 271
Period size: 54 Copynumber: 3.1 Consensus size: 54
13198 TCAGCTTTAG
* *
13208 CTTTACCTTTACCACTAGCATCTATATTACCACTACCATCTCCTCCACCTTGTC
1 CTTTTCCTTTACCACTTGCATCTATATTACCACTACCATCTCCTCCACCTTGTC
* * * *
13262 CTTTTTCTTTACCACTTGCATCTATTTTACCACCACCATCTCCTCTACCTTGTC
1 CTTTTCCTTTACCACTTGCATCTATATTACCACTACCATCTCCTCCACCTTGTC
*
13316 CTTTTCCTTTACCACTTGCATCTGTATTACCACTACCATCTCCTCCACCTTGTC
1 CTTTTCCTTTACCACTTGCATCTATATTACCACTACCATCTCCTCCACCTTGTC
13370 CTTTT
1 CTTTT
13375 ACCCCACCAG
Statistics
Matches: 102, Mismatches: 11, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
54 102 1.00
ACGTcount: A:0.18, C:0.38, G:0.04, T:0.40
Consensus pattern (54 bp):
CTTTTCCTTTACCACTTGCATCTATATTACCACTACCATCTCCTCCACCTTGTC
Found at i:14032 original size:165 final size:165
Alignment explanation
Indices: 13735--14032 Score: 377
Period size: 165 Copynumber: 1.8 Consensus size: 165
13725 GTTAGTGCTT
* *
13735 CCACTTCCACCACTTTTTCCACCACCATCTCCTTTCCCTCCAACTTTACCTTCAAAACCAACTTT
1 CCACTTCCACCACTATTTCCACCAACATCTCCTTTCCCTCCAACTTTACCTTCAAAACCAACTTT
* * * * * * * * *
13800 AGCTTCACCTTTATTAGTAGCAGTAGCTTTTCCATCACTACCTTTTTCACCATTATGAGTACCAC
66 ACCCTCACCTTTACTAGTAGCACTAGCTTTGCCATCACTACCTTTTGCACCACTAAGACTACCAC
13865 TTGCATCAGTTCTACTACTGCCGACACCTCCACTA
131 TTGCATCAGTTCTACTACTGCCGACACCTCCACTA
* * * *
13900 CCACTTCCACCACTATTTCCACCAACTTCTCCTTGT-CCTCCTAGTTTACCTTCAAAACCAGCTT
1 CCACTTCCACCACTATTTCCACCAACATCTCCTT-TCCCTCCAACTTTACCTTCAAAACCAACTT
* * * *
13964 TACCCTCA-CTCTTACTAGTATCACTAGCTTTGCCATCACTA-CTCTTTGCTCCGCTAAGACTGC
65 TACCCTCACCT-TTACTAGTAGCACTAGCTTTGCCATCACTACCT-TTTGCACCACTAAGACTAC
14027 CACTTG
128 CACTTG
14033 TACTAGTTGC
Statistics
Matches: 111, Mismatches: 19, Indels: 6
0.82 0.14 0.04
Matches are distributed among these distances:
164 4 0.04
165 106 0.95
166 1 0.01
ACGTcount: A:0.22, C:0.37, G:0.07, T:0.33
Consensus pattern (165 bp):
CCACTTCCACCACTATTTCCACCAACATCTCCTTTCCCTCCAACTTTACCTTCAAAACCAACTTT
ACCCTCACCTTTACTAGTAGCACTAGCTTTGCCATCACTACCTTTTGCACCACTAAGACTACCAC
TTGCATCAGTTCTACTACTGCCGACACCTCCACTA
Found at i:15632 original size:11 final size:11
Alignment explanation
Indices: 15616--15641 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
15606 CTTCTTTCCC
15616 TTTTTTTTTGT
1 TTTTTTTTTGT
15627 TTTTTTTTTGT
1 TTTTTTTTTGT
15638 TTTT
1 TTTT
15642 CACGCGGCCT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.00, C:0.00, G:0.08, T:0.92
Consensus pattern (11 bp):
TTTTTTTTTGT
Found at i:19294 original size:66 final size:65
Alignment explanation
Indices: 19204--19407 Score: 255
Period size: 66 Copynumber: 3.1 Consensus size: 65
19194 CATCAGTTGC
* * **
19204 CTCCACCAGCAACATTACCGCTACCACTTCCACCACCTTTTCCTCCAAATCCTCCTTATCCTCCT
1 CTCCACCAGCAACATTA-CGCTACCACTTCCACCACCTTTTCCACCAAACCCTCCTTGCCCTCCT
19269 A
65 A
* * * * * * *
19270 CTCCACGACCAACATTAGCACTACCACTTCCAACACCATTTCCGCCGAACCCTCCTTGCCCTCCT
1 CTCCACCAGCAACATTA-CGCTACCACTTCCACCACCTTTTCCACCAAACCCTCCTTGCCCTCCT
19335 A
65 A
* * *
19336 CTCCACCTGCAACATTACTGCTACCACTTCCACCACCTTTTCCACCAAACCCCCCTTGCCCTCCA
1 CTCCACCAGCAACATTAC-GCTACCACTTCCACCACCTTTTCCACCAAACCCTCCTTGCCCTCCT
19401 A
65 A
19402 CTCCAC
1 CTCCAC
19408 TTTTTCCACC
Statistics
Matches: 116, Mismatches: 21, Indels: 2
0.83 0.15 0.01
Matches are distributed among these distances:
65 1 0.01
66 115 0.99
ACGTcount: A:0.23, C:0.49, G:0.05, T:0.24
Consensus pattern (65 bp):
CTCCACCAGCAACATTACGCTACCACTTCCACCACCTTTTCCACCAAACCCTCCTTGCCCTCCTA
Found at i:19392 original size:18 final size:18
Alignment explanation
Indices: 19368--19428 Score: 52
Period size: 18 Copynumber: 3.4 Consensus size: 18
19358 ACCACTTCCA
19368 CCACCTTTTCCACCAAAC
1 CCACCTTTTCCACCAAAC
* ** *
19386 CCCCCTTGCCCTCC-AAC
1 CCACCTTTTCCACCAAAC
*
19403 TCCACTTTTTCCACCAAAC
1 -CCACCTTTTCCACCAAAC
*
19422 CCTCCTT
1 CCACCTT
19429 GTCCTCCTAC
Statistics
Matches: 30, Mismatches: 11, Indels: 4
0.67 0.24 0.09
Matches are distributed among these distances:
17 3 0.10
18 24 0.80
19 3 0.10
ACGTcount: A:0.20, C:0.52, G:0.02, T:0.26
Consensus pattern (18 bp):
CCACCTTTTCCACCAAAC
Found at i:19419 original size:36 final size:36
Alignment explanation
Indices: 19368--19443 Score: 116
Period size: 36 Copynumber: 2.1 Consensus size: 36
19358 ACCACTTCCA
19368 CCACCTTTTCCACCAAACCCCCCTTGCCCTCCAACT
1 CCACCTTTTCCACCAAACCCCCCTTGCCCTCCAACT
* * * *
19404 CCACTTTTTCCACCAAACCCTCCTTGTCCTCCTACT
1 CCACCTTTTCCACCAAACCCCCCTTGCCCTCCAACT
19440 CCAC
1 CCAC
19444 GAGCAACTTT
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
36 36 1.00
ACGTcount: A:0.18, C:0.53, G:0.03, T:0.26
Consensus pattern (36 bp):
CCACCTTTTCCACCAAACCCCCCTTGCCCTCCAACT
Found at i:19425 original size:102 final size:102
Alignment explanation
Indices: 19308--19509 Score: 262
Period size: 102 Copynumber: 2.0 Consensus size: 102
19298 TCCAACACCA
* * * * * *
19308 TTTCCGCCGAACCCTCCTTGCCCTCCTACTCCACCTGCAACATTA-CTGCTACCACTTCCACCAC
1 TTTCCACCAAACCCTCCTTGCCCTCCTACTCCACCAGCAACATTAGC-ACTACCACTTCCAACAA
*
19372 CTTTTCCACCAAACCCCCCTTGCCCTCCAACTCCACTT
65 CATTTCCACCAAACCCCCCTTGCCCTCCAACTCCACTT
* * *
19410 TTTCCACCAAACCCTCCTTGTCCTCCTACTCCACGAGCAACTTTAGCACTACCACTTCCAACAAC
1 TTTCCACCAAACCCTCCTTGCCCTCCTACTCCACCAGCAACATTAGCACTACCACTTCCAACAAC
** * *
19475 ATTTCCATGAAACCCTCCTTGCCCTCCTACTCCAC
66 ATTTCCACCAAACCCCCCTTGCCCTCCAACTCCAC
19510 CAGCAACATT
Statistics
Matches: 85, Mismatches: 14, Indels: 2
0.84 0.14 0.02
Matches are distributed among these distances:
102 84 0.99
103 1 0.01
ACGTcount: A:0.21, C:0.47, G:0.06, T:0.26
Consensus pattern (102 bp):
TTTCCACCAAACCCTCCTTGCCCTCCTACTCCACCAGCAACATTAGCACTACCACTTCCAACAAC
ATTTCCACCAAACCCCCCTTGCCCTCCAACTCCACTT
Found at i:19491 original size:168 final size:168
Alignment explanation
Indices: 19236--19576 Score: 567
Period size: 168 Copynumber: 2.0 Consensus size: 168
19226 ACCACTTCCA
* *
19236 CCACCTTTTCCTCCAAATCCTCCTTATCCTCCTACTCCACGACCAACATTAGCACTACCACTTCC
1 CCACCTTTTCCACCAAACCCTCCTTATCCTCCTACTCCACGACCAACATTAGCACTACCACTTCC
* * *
19301 AACACCATTTCCGCCGAACCCTCCTTGCCCTCCTACTCCACCTGCAACATTACTGCTACCACTTC
66 AACAACATTTCCGACGAACCCTCCTTGCCCTCCTACTCCACCAGCAACATTACTGCTACCACTTC
19366 CACCACCTTTTCCACCAAACCCCCCTTGCCCTCCAACT
131 CACCACCTTTTCCACCAAACCCCCCTTGCCCTCCAACT
* * * *
19404 CCACTTTTTCCACCAAACCCTCCTTGTCCTCCTACTCCACGAGCAACTTTAGCACTACCACTTCC
1 CCACCTTTTCCACCAAACCCTCCTTATCCTCCTACTCCACGACCAACATTAGCACTACCACTTCC
*
19469 AACAACATTTCC-ATGAAACCCTCCTTGCCCTCCTACTCCACCAGCAACATTACTGCTACCACTT
66 AACAACATTTCCGACG-AACCCTCCTTGCCCTCCTACTCCACCAGCAACATTACTGCTACCACTT
*
19533 CCACCACCTTTTCCACCAAACCCCCCTTGCCCTCCTACT
130 CCACCACCTTTTCCACCAAACCCCCCTTGCCCTCCAACT
19572 CCACC
1 CCACC
19577 AGCAACACTA
Statistics
Matches: 160, Mismatches: 12, Indels: 2
0.92 0.07 0.01
Matches are distributed among these distances:
167 1 0.01
168 159 0.99
ACGTcount: A:0.23, C:0.48, G:0.05, T:0.25
Consensus pattern (168 bp):
CCACCTTTTCCACCAAACCCTCCTTATCCTCCTACTCCACGACCAACATTAGCACTACCACTTCC
AACAACATTTCCGACGAACCCTCCTTGCCCTCCTACTCCACCAGCAACATTACTGCTACCACTTC
CACCACCTTTTCCACCAAACCCCCCTTGCCCTCCAACT
Found at i:19494 original size:66 final size:66
Alignment explanation
Indices: 19410--20220 Score: 667
Period size: 66 Copynumber: 12.3 Consensus size: 66
19400 AACTCCACTT
* * * *
19410 TTTCCACCAAACCCTCCTTGTCCTCCTACTCCACGAGCAACTTTAGCACTACCACTTCCAACAAC
1 TTTCCACCAAACCCTCCTTGCCCTCCTACTCCACCAGCAACATTAGCACTACCACTTCCAACACC
19475 A
66 A
** * *
19476 TTTCCATGAAACCCTCCTTGCCCTCCTACTCCACCAGCAACATTA-CTGCTACCACTTCCACCAC
1 TTTCCACCAAACCCTCCTTGCCCTCCTACTCCACCAGCAACATTAGC-ACTACCACTTCCAACAC
*
19540 CT
65 CA
* * * ** *
19542 TTTCCACCAAACCCCCCTTGCCCTCCTACTCCACCAGCAACACTACCGTTACCACTTCCACCACC
1 TTTCCACCAAACCCTCCTTGCCCTCCTACTCCACCAGCAACATTAGCACTACCACTTCCAACACC
*
19607 T
66 A
* * *
19608 TTTCCACCAAACCCTCCTTGTCCTCCAACT-CACCCAGCAACATTAGCACTACCACTTGCAACAC
1 TTTCCACCAAACCCTCCTTGCCCTCCTACTCCA-CCAGCAACATTAGCACTACCACTTCCAACAC
19672 CA
65 CA
* * * * * * * *
19674 TTCCCACTAGACCCTCCTTGCCCTCGTACTCCACTAGCAGCATTACCGCTACCACTTCCAACACC
1 TTTCCACCAAACCCTCCTTGCCCTCCTACTCCACCAGCAACATTAGCACTACCACTTCCAACACC
*
19739 T
66 A
* *
19740 TTTCCACCAAACCCTCCTTGCCCTCCAACTCCCCCAGCAACA-TAGCACTACCACTTCCAACACC
1 TTTCCACCAAACCCTCCTTGCCCTCCTACTCCACCAGCAACATTAGCACTACCACTTCCAACACC
19804 A
66 A
* ** * * * *** * *
19805 TTTCCAGCAAACCCTCCTTGCCCTCCTACTCCAGCTTGTCCACCA--AACCCTCATTGTCCTCCT
1 TTTCCACCAAACCCTCCTTGCCCTCCTACTCCA-CCAG--CAACATTAGCACT-A-CCACTTCCA
19868 ACACCA
61 ACACCA
**** ** * ** * * * * ** * * *
19874 GCAACATTAGCACTATCACTT-CCAACACC-ATTTCCGCCAAACCCCCCTT-GCCCT-CCAATT-
1 TTTCCACCA-AACCCTC-CTTGCC--CTCCTA-CTCCACC--AGCAACATTAGCACTACCACTTC
*
19934 C--CACCT
59 CAACACCA
* *
19940 TTTCCACCAAACCCTCCCTGTCCTCCTACTCCACCAGCAACATTAGCACTACCACTTCCAACACC
1 TTTCCACCAAACCCTCCTTGCCCTCCTACTCCACCAGCAACATTAGCACTACCACTTCCAACACC
20005 A
66 A
* *** *
20006 TTTCCACCAAACCCTCCTTGCCCTCCTACTCCACCAGTAACATTAATGCTACCACTTCCACCACC
1 TTTCCACCAAACCCTCCTTGCCCTCCTACTCCACCAGCAACATTAGCACTACCACTTCCAACACC
20071 -
66 A
* * * *
20071 TTGTCCACCAAACCCTCCTTGTCCTCCTACTCCACCAGCAACATTAGTACTACGACTTCCAACAT
1 TT-TCCACCAAACCCTCCTTGCCCTCCTACTCCACCAGCAACATTAGCACTACCACTTCCAACAC
20136 CA
65 CA
* * * * * * * *
20138 TTTCCACCAAAACCTCCTTGCCCCCCTACTCCACCAACAACATTACCGCTACCATTTCCACCACT
1 TTTCCACCAAACCCTCCTTGCCCTCCTACTCCACCAGCAACATTAGCACTACCACTTCCAACACC
*
20203 T
66 A
*
20204 TTTCCACTAAACCCTCC
1 TTTCCACCAAACCCTCC
20221 ACTCCCTCCT
Statistics
Matches: 584, Mismatches: 134, Indels: 54
0.76 0.17 0.07
Matches are distributed among these distances:
61 5 0.01
62 4 0.01
63 13 0.02
64 4 0.01
65 60 0.10
66 445 0.76
67 9 0.02
68 6 0.01
69 14 0.02
70 6 0.01
71 8 0.01
72 10 0.02
ACGTcount: A:0.25, C:0.46, G:0.06, T:0.23
Consensus pattern (66 bp):
TTTCCACCAAACCCTCCTTGCCCTCCTACTCCACCAGCAACATTAGCACTACCACTTCCAACACC
A
Found at i:19635 original size:234 final size:234
Alignment explanation
Indices: 19204--19638 Score: 613
Period size: 234 Copynumber: 1.9 Consensus size: 234
19194 CATCAGTTGC
* * * * * *
19204 CTCCACCAGCAACATTACCGCTACCACTTCCACCACCTTTTCCTCCAAATCCTCCTTATCCTCCT
1 CTCCACCAGCAACATTACCACTACCACTTCCAACAACATTTCCTCCAAACCCTCCTTACCCTCCT
* * * *
19269 ACTCCACGACCAACATTAGCACTACCACTTCCAACACCATTTCCGCCGAACCCTCCTTGCCCTCC
66 ACTCCACCACCAACATTAGCACTACCACTTCCAACACCATTTCCACCAAACCCCCCTTGCCCTCC
* * *
19334 TACTCCACCTGCAACATTACTGCTACCACTTCCACCACCTTTTCCACCAAACCCCCCTTGCCCTC
131 TACTCCACCAGCAACACTACCGCTACCACTTCCACCACCTTTTCCACCAAACCCCCCTTGCCCTC
19399 CAACTCCACTTTTTCCACCAAACCCTCCTTGTCCTCCTA
196 CAACTCCACTTTTTCCACCAAACCCTCCTTGTCCTCCTA
* * * * *
19438 CTCCACGAGCAACTTTAGCACTACCACTTCCAACAACATTTCCAT-GAAACCCTCCTTGCCCTCC
1 CTCCACCAGCAACATTACCACTACCACTTCCAACAACATTTCC-TCCAAACCCTCCTTACCCTCC
* * * *
19502 TACTCCACCAGCAACATTA-CTGCTACCACTTCCACCACCTTTTCCACCAAACCCCCCTTGCCCT
65 TACTCCACCACCAACATTAGC-ACTACCACTTCCAACACCATTTCCACCAAACCCCCCTTGCCCT
* * *
19566 CCTACTCCACCAGCAACACTACCGTTACCACTTCCACCACCTTTTCCACCAAACCCTCCTTGTCC
129 CCTACTCCACCAGCAACACTACCGCTACCACTTCCACCACCTTTTCCACCAAACCCCCCTTGCCC
19631 TCCAACTC
194 TCCAACTC
19639 ACCCAGCAAC
Statistics
Matches: 174, Mismatches: 25, Indels: 4
0.86 0.12 0.02
Matches are distributed among these distances:
233 1 0.01
234 172 0.99
235 1 0.01
ACGTcount: A:0.23, C:0.47, G:0.05, T:0.24
Consensus pattern (234 bp):
CTCCACCAGCAACATTACCACTACCACTTCCAACAACATTTCCTCCAAACCCTCCTTACCCTCCT
ACTCCACCACCAACATTAGCACTACCACTTCCAACACCATTTCCACCAAACCCCCCTTGCCCTCC
TACTCCACCAGCAACACTACCGCTACCACTTCCACCACCTTTTCCACCAAACCCCCCTTGCCCTC
CAACTCCACTTTTTCCACCAAACCCTCCTTGTCCTCCTA
Found at i:19866 original size:36 final size:36
Alignment explanation
Indices: 19807--19875 Score: 102
Period size: 36 Copynumber: 1.9 Consensus size: 36
19797 CAACACCATT
* * *
19807 TCCAGCAAACCCTCCTTGCCCTCCTACTCCAGCTTG
1 TCCACCAAACCCTCATTGCCCTCCTACACCAGCTTG
*
19843 TCCACCAAACCCTCATTGTCCTCCTACACCAGC
1 TCCACCAAACCCTCATTGCCCTCCTACACCAGC
19876 AACATTAGCA
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
36 29 1.00
ACGTcount: A:0.20, C:0.48, G:0.09, T:0.23
Consensus pattern (36 bp):
TCCACCAAACCCTCATTGCCCTCCTACACCAGCTTG
Found at i:19965 original size:36 final size:36
Alignment explanation
Indices: 19899--19975 Score: 93
Period size: 36 Copynumber: 2.1 Consensus size: 36
19889 TCACTTCCAA
* *
19899 CACCATTTCCGCCAAACCCCCCTTGCCCTCCAATTC
1 CACCATTTCCACCAAACCCCCCTTGCCCTCCAACTC
* * *
19935 CACCTTTTCCACCAAACCCTCCC-TGTCCTCCTACTC
1 CACCATTTCCACCAAACCC-CCCTTGCCCTCCAACTC
19971 CACCA
1 CACCA
19976 GCAACATTAG
Statistics
Matches: 34, Mismatches: 6, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
36 31 0.91
37 3 0.09
ACGTcount: A:0.19, C:0.53, G:0.04, T:0.23
Consensus pattern (36 bp):
CACCATTTCCACCAAACCCCCCTTGCCCTCCAACTC
Found at i:20016 original size:102 final size:102
Alignment explanation
Indices: 19735--20040 Score: 467
Period size: 99 Copynumber: 3.0 Consensus size: 102
19725 CCACTTCCAA
* * *
19735 CACCTTTTCCACCAAACCCTCCTTGCCCTCCAACTCCCCCAGCAACA-TAGCACTACCACTTCCA
1 CACCTTTTCCACCAAACCCTCCTTGTCCTCCTACTCCACCAGCAACATTAGCACTACCACTTCCA
*
19799 ACACCATTTCCAGCAAACCCTCCTTGCCCTCCTACTC
66 ACACCATTTCCACCAAACCCTCCTTGCCCTCCTACTC
* * * *
19836 CAGCTTGTCCACCAAACCCTCATTGTCCTCCTA---CACCAGCAACATTAGCACTATCACTTCCA
1 CACCTTTTCCACCAAACCCTCCTTGTCCTCCTACTCCACCAGCAACATTAGCACTACCACTTCCA
* * * *
19898 ACACCATTTCCGCCAAACCCCCCTTGCCCTCCAATTC
66 ACACCATTTCCACCAAACCCTCCTTGCCCTCCTACTC
*
19935 CACCTTTTCCACCAAACCCTCCCTGTCCTCCTACTCCACCAGCAACATTAGCACTACCACTTCCA
1 CACCTTTTCCACCAAACCCTCCTTGTCCTCCTACTCCACCAGCAACATTAGCACTACCACTTCCA
20000 ACACCATTTCCACCAAACCCTCCTTGCCCTCCTACTC
66 ACACCATTTCCACCAAACCCTCCTTGCCCTCCTACTC
20037 CACC
1 CACC
20041 AGTAACATTA
Statistics
Matches: 180, Mismatches: 21, Indels: 7
0.87 0.10 0.03
Matches are distributed among these distances:
98 10 0.06
99 77 0.43
101 28 0.16
102 65 0.36
ACGTcount: A:0.24, C:0.48, G:0.05, T:0.23
Consensus pattern (102 bp):
CACCTTTTCCACCAAACCCTCCTTGTCCTCCTACTCCACCAGCAACATTAGCACTACCACTTCCA
ACACCATTTCCACCAAACCCTCCTTGCCCTCCTACTC
Found at i:20285 original size:105 final size:105
Alignment explanation
Indices: 20162--20360 Score: 274
Period size: 105 Copynumber: 1.9 Consensus size: 105
20152 TCCTTGCCCC
* ** *
20162 CCTACTCCACCAACAACATTACCGCTACCATTTCCACCACTTTTTCCACTAAACCCTCCACT-CC
1 CCTACTCCACCAACAACATTACCGCTACCACTTCCACCACCGTTTCCACCAAACCCT-CACTGCC
*
20226 CTCCTATATTACCTCCAATTCCAAAACCTCTACCACCGCCT
65 CTCCTATATTACCTCCAAATCCAAAACCTCTACCACCGCCT
* ** ** *
20267 CCTACTCCACCAGCAACATTAGTGCTACCACTTCCACCACCGTTTCCACCAAACCCTCTTTGTCC
1 CCTACTCCACCAACAACATTACCGCTACCACTTCCACCACCGTTTCCACCAAACCCTCACTGCCC
*
20332 TCCTATATTACCTCCAAATCCAACACCTC
66 TCCTATATTACCTCCAAATCCAAAACCTC
20361 CTGCTCGACG
Statistics
Matches: 81, Mismatches: 12, Indels: 2
0.85 0.13 0.02
Matches are distributed among these distances:
104 2 0.02
105 79 0.98
ACGTcount: A:0.26, C:0.45, G:0.04, T:0.26
Consensus pattern (105 bp):
CCTACTCCACCAACAACATTACCGCTACCACTTCCACCACCGTTTCCACCAAACCCTCACTGCCC
TCCTATATTACCTCCAAATCCAAAACCTCTACCACCGCCT
Found at i:25996 original size:48 final size:48
Alignment explanation
Indices: 25912--26010 Score: 117
Period size: 48 Copynumber: 2.1 Consensus size: 48
25902 CCAAACCCTT
* * * *
25912 CTTGCCCACCTACTCCACCAGCAGCATTAGCGCTACCGCTTCCACCAC
1 CTTGCCCACCTACTCCACCAGCAACATTAGCACTACCACTTACACCAC
* * * * *
25960 CTTGCCCTCCTACTCCATCGGCAACATTAGTACTACCACTTAGACCAC
1 CTTGCCCACCTACTCCACCAGCAACATTAGCACTACCACTTACACCAC
26008 CTT
1 CTT
26011 TTCCATTGAA
Statistics
Matches: 42, Mismatches: 9, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
48 42 1.00
ACGTcount: A:0.22, C:0.43, G:0.11, T:0.23
Consensus pattern (48 bp):
CTTGCCCACCTACTCCACCAGCAACATTAGCACTACCACTTACACCAC
Found at i:26049 original size:36 final size:36
Alignment explanation
Indices: 26004--26080 Score: 100
Period size: 36 Copynumber: 2.1 Consensus size: 36
25994 ACCACTTAGA
*** *
26004 CCACCTTTTCCATTGAATCCTCCTTGACCTCCTCCT
1 CCACCTTTTCCACCAAACCCTCCTTGACCTCCTCCT
* *
26040 CCACTTTTTCCACCAAACCCTCCTTGTCCTCCTCCT
1 CCACCTTTTCCACCAAACCCTCCTTGACCTCCTCCT
26076 CCACC
1 CCACC
26081 AGCAACATTA
Statistics
Matches: 34, Mismatches: 7, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
36 34 1.00
ACGTcount: A:0.14, C:0.49, G:0.04, T:0.32
Consensus pattern (36 bp):
CCACCTTTTCCACCAAACCCTCCTTGACCTCCTCCT
Found at i:26110 original size:54 final size:54
Alignment explanation
Indices: 26047--26402 Score: 291
Period size: 54 Copynumber: 6.1 Consensus size: 54
26037 CCTCCACTTT
* * *
26047 TTCCACCAAACCCTCCTTGTCCTCCTCCTCCACCAGCAACATTACCGCTACCAC
1 TTCCACCAAACCCTCCTTGCCCTCCTACTCCACCACCAACATTACCGCTACCAC
* *
26101 TTCCACCAAACCCTTCTTGCCCTCCTACTCCACCACCAACATTAATGCTGCCACTTCCACCACC
1 TTCCACCAAACCCTCCTTGCCCTCCTACTCCACCACCAACATT-A-----CCGC-T--ACCA-C
* * * * * *
26165 TTTTCCACTAAACCCTCCTTGTCCTCCTCCTCCATCAGCAACATTACCGTTACCAC
1 --TTCCACCAAACCCTCCTTGCCCTCCTACTCCACCACCAACATTACCGCTACCAC
* *
26221 TTCCACCAAATCCTCCTTGCCCTCCTACTCCACCACCAACATTAATGTTGCCACTTCCACCACC
1 TTCCACCAAACCCTCCTTGCCCTCCTACTCCACCACCAACATT-A-----CCGC-T--ACCA-C
* * * * *
26285 TTTTCCACCAAACCCTCCTTGTCCTCCTCCTTCACTAGCAATC-TTACCGCTACCAC
1 --TTCCACCAAACCCTCCTTGCCCTCCTACTCCACCACCAA-CATTACCGCTACCAC
** *
26341 TTCCACCAAACCCTCCTTGCCCTCCTACTCCACCACCAACATTAATGCTGCCAC
1 TTCCACCAAACCCTCCTTGCCCTCCTACTCCACCACCAACATTACCGCTACCAC
26395 TTCCACCA
1 TTCCACCA
26403 CCTTTTCCAC
Statistics
Matches: 240, Mismatches: 36, Indels: 52
0.73 0.11 0.16
Matches are distributed among these distances:
53 1 0.00
54 128 0.53
55 2 0.01
56 2 0.01
57 8 0.03
59 2 0.01
60 10 0.04
61 2 0.01
63 8 0.03
64 2 0.01
65 2 0.01
66 72 0.30
67 1 0.00
ACGTcount: A:0.22, C:0.47, G:0.05, T:0.26
Consensus pattern (54 bp):
TTCCACCAAACCCTCCTTGCCCTCCTACTCCACCACCAACATTACCGCTACCAC
Found at i:26179 original size:66 final size:66
Alignment explanation
Indices: 26101--26465 Score: 354
Period size: 66 Copynumber: 5.9 Consensus size: 66
26091 CCGCTACCAC
*
26101 TTCCACCAAACCCTTCTTGCCCTCCTACTCCACCACCAACATTAATGCTGCCACTTCCACCACCT
1 TTCCACCAAACCCTCCTTGCCCTCCTACTCCACCACCAACATTAATGCTGCCACTTCCACCACCT
26166 T
66 T
* * * * * *
26167 TTCCACTAAACCCTCCTTGTCCTCCTCCTCCATCAGCAACATT-A-----CC-GTT--ACCA-C-
1 TTCCACCAAACCCTCCTTGCCCTCCTACTCCACCACCAACATTAATGCTGCCACTTCCACCACCT
26221 -
66 T
* *
26221 TTCCACCAAATCCTCCTTGCCCTCCTACTCCACCACCAACATTAATGTTGCCACTTCCACCACCT
1 TTCCACCAAACCCTCCTTGCCCTCCTACTCCACCACCAACATTAATGCTGCCACTTCCACCACCT
26286 T
66 T
* * * * * *
26287 TTCCACCAAACCCTCCTTGTCCTCCTCCTTCACTAGCAATC-TT-A-----CCGC-T--ACCA-C
1 TTCCACCAAACCCTCCTTGCCCTCCTACTCCACCACCAA-CATTAATGCTGCCACTTCCACCACC
26341 --
65 TT
26341 TTCCACCAAACCCTCCTTGCCCTCCTACTCCACCACCAACATTAATGCTGCCACTTCCACCACCT
1 TTCCACCAAACCCTCCTTGCCCTCCTACTCCACCACCAACATTAATGCTGCCACTTCCACCACCT
26406 T
66 T
* * * *
26407 TTCCACCAAACCCTCCTTG---TCTTACTCCACCGCCAACATTAGTGCTACCACTTCCACCA
1 TTCCACCAAACCCTCCTTGCCCTCCTACTCCACCACCAACATTAATGCTGCCACTTCCACCA
26466 AACCCTCC
Statistics
Matches: 242, Mismatches: 31, Indels: 55
0.74 0.09 0.17
Matches are distributed among these distances:
53 1 0.00
54 73 0.30
55 2 0.01
56 2 0.01
57 8 0.03
59 3 0.01
60 10 0.04
61 3 0.01
63 44 0.18
64 2 0.01
65 2 0.01
66 91 0.38
67 1 0.00
ACGTcount: A:0.22, C:0.46, G:0.05, T:0.26
Consensus pattern (66 bp):
TTCCACCAAACCCTCCTTGCCCTCCTACTCCACCACCAACATTAATGCTGCCACTTCCACCACCT
T
Found at i:26182 original size:156 final size:150
Alignment explanation
Indices: 25896--26198 Score: 381
Period size: 156 Copynumber: 2.0 Consensus size: 150
25886 TCCACCACCA
* * * *
25896 TTTCCACCAAACCCTTCTTGCCCACCTACTCCACCAGCAGCATTAGCGCTACCGCTTCCACCACC
1 TTTCCACCAAACCCTCCTTGCCCACCTACTCCACCAGCAACATTACCGCTACCACTTCCACCACC
* ** * * * * *
25961 TTGCCCTCCTACTCCATCGGCAACATTAGTACTACCACTTAGACCACCTTTTCCATTGAATCCTC
66 TTGCCCTCCTACTCCACCACCAACATTAATACTACCACTTACACCACCTTTTCCACTAAACCCTC
26026 CTTGACCTCCTCCTCCACTT
131 CTTGACCTCCTCCTCCACTT
* * *
26046 TTTCCACCAAACCCTCCTTGTCCTCCTCCTCCACCAGCAACATTACCGCTACCACTTCCACCAAA
1 TTTCCACCAAACCCTCCTTGCCCACCTACTCCACCAGCAACATTACCGCTACCACTTCCACC--A
* * *
26111 CCCTTCTTGCCCTCCTACTCCACCACCAACATTAATGCTGCCACTTCCACCACCTTTTCCACTAA
64 --C--CTTGCCCTCCTACTCCACCACCAACATTAATACTACCACTTACACCACCTTTTCCACTAA
*
26176 ACCCTCCTTGTCCTCCTCCTCCA
125 ACCCTCCTTGACCTCCTCCTCCA
26199 TCAGCAACAT
Statistics
Matches: 128, Mismatches: 19, Indels: 6
0.84 0.12 0.04
Matches are distributed among these distances:
150 55 0.43
152 1 0.01
154 1 0.01
156 71 0.55
ACGTcount: A:0.21, C:0.46, G:0.07, T:0.27
Consensus pattern (150 bp):
TTTCCACCAAACCCTCCTTGCCCACCTACTCCACCAGCAACATTACCGCTACCACTTCCACCACC
TTGCCCTCCTACTCCACCACCAACATTAATACTACCACTTACACCACCTTTTCCACTAAACCCTC
CTTGACCTCCTCCTCCACTT
Found at i:26190 original size:120 final size:120
Alignment explanation
Indices: 26040--26473 Score: 707
Period size: 120 Copynumber: 3.6 Consensus size: 120
26030 ACCTCCTCCT
*
26040 CCACTTTTTCCACCAAACCCTCCTTGTCCTCCTCCTCCACCAGCAACATTACCGCTACCACTTCC
1 CCACCTTTTCCACCAAACCCTCCTTGTCCTCCTCCTCCACCAGCAACATTACCGCTACCACTTCC
*
26105 ACCAAACCCTTCTTGCCCTCCTACTCCACCACCAACATTAATGCTGCCACTTCCA
66 ACCAAACCCTCCTTGCCCTCCTACTCCACCACCAACATTAATGCTGCCACTTCCA
* * *
26160 CCACCTTTTCCACTAAACCCTCCTTGTCCTCCTCCTCCATCAGCAACATTACCGTTACCACTTCC
1 CCACCTTTTCCACCAAACCCTCCTTGTCCTCCTCCTCCACCAGCAACATTACCGCTACCACTTCC
* *
26225 ACCAAATCCTCCTTGCCCTCCTACTCCACCACCAACATTAATGTTGCCACTTCCA
66 ACCAAACCCTCCTTGCCCTCCTACTCCACCACCAACATTAATGCTGCCACTTCCA
* *
26280 CCACCTTTTCCACCAAACCCTCCTTGTCCTCCTCCTTCACTAGCAATC-TTACCGCTACCACTTC
1 CCACCTTTTCCACCAAACCCTCCTTGTCCTCCTCCTCCACCAGCAA-CATTACCGCTACCACTTC
26344 CACCAAACCCTCCTTGCCCTCCTACTCCACCACCAACATTAATGCTGCCACTTCCA
65 CACCAAACCCTCCTTGCCCTCCTACTCCACCACCAACATTAATGCTGCCACTTCCA
* **
26400 CCACCTTTTCCACCAAACCCTCCTTGT-CT--TACTCCACC-GCCAACATTAGTGCTACCACTTC
1 CCACCTTTTCCACCAAACCCTCCTTGTCCTCCTCCTCCACCAG-CAACATTACCGCTACCACTTC
26461 CACCAAACCCTCC
65 CACCAAACCCTCC
Statistics
Matches: 292, Mismatches: 19, Indels: 9
0.91 0.06 0.03
Matches are distributed among these distances:
116 2 0.01
117 36 0.12
119 2 0.01
120 251 0.86
121 1 0.00
ACGTcount: A:0.22, C:0.47, G:0.05, T:0.26
Consensus pattern (120 bp):
CCACCTTTTCCACCAAACCCTCCTTGTCCTCCTCCTCCACCAGCAACATTACCGCTACCACTTCC
ACCAAACCCTCCTTGCCCTCCTACTCCACCACCAACATTAATGCTGCCACTTCCA
Found at i:26190 original size:150 final size:145
Alignment explanation
Indices: 25896--26191 Score: 324
Period size: 150 Copynumber: 2.0 Consensus size: 145
25886 TCCACCACCA
* * * *
25896 TTTCCACCAAACCCTTCTTGCCCACCTACTCCACCAGCAGCATTAGCGCTACCGCTTCCACCACC
1 TTTCCACCAAACCCTCCTTGCCCACCTACTCCACCAGCAACATTACCGCTACCACTTCCACCACC
* ** * * * * *
25961 TTGCCCTCCTACTCCATCGGCAACATTAGTACTACCACTTAGACCACCTTTTCCATTGAATCCTC
66 TTGCCCTCCTACTCCACCACCAACATTAATACTACCACTTACACCACCTTTTCCACTAAACCCTC
26026 CTTGACCTCCTCCTCCACTT
131 CTTG-----CTCCTCCACTT
* * *
26046 TTTCCACCAAACCCTCCTTGTCCTCCTCCTCCACCAGCAACATTACCGCTACCACTTCCACCAAA
1 TTTCCACCAAACCCTCCTTGCCCACCTACTCCACCAGCAACATTACCGCTACCACTTCCACC--A
* * *
26111 CCCTTCTTGCCCTCCTACTCCACCACCAACATTAATGCTGCCACTTCCACCACCTTTTCCACTAA
64 --C--CTTGCCCTCCTACTCCACCACCAACATTAATACTACCACTTACACCACCTTTTCCACTAA
26176 ACCCTCCTTG-TCCTCC
125 ACCCTCCTTGCTCCTCC
26192 TCCTCCATCA
Statistics
Matches: 122, Mismatches: 18, Indels: 12
0.80 0.12 0.08
Matches are distributed among these distances:
150 61 0.50
152 1 0.01
154 1 0.01
156 59 0.48
ACGTcount: A:0.21, C:0.46, G:0.07, T:0.27
Consensus pattern (145 bp):
TTTCCACCAAACCCTCCTTGCCCACCTACTCCACCAGCAACATTACCGCTACCACTTCCACCACC
TTGCCCTCCTACTCCACCACCAACATTAATACTACCACTTACACCACCTTTTCCACTAAACCCTC
CTTGCTCCTCCACTT
Done.